diff --git a/.dockerignore b/.dockerignore index c7613894..a6e04d85 100644 --- a/.dockerignore +++ b/.dockerignore @@ -1,2 +1,3 @@ -/.git -/data +.git +data +logs/* diff --git a/.gitignore b/.gitignore index 97086fc4..510fcea4 100644 --- a/.gitignore +++ b/.gitignore @@ -19,11 +19,12 @@ data/db scripts/dump.json scripts/dump.json.gz scripts/node_modules -lookup/build +build .gradle *.mdb **/node_modules/** **/out **/package-lock.json -lookup/data/db/* -pubmed-glutton/build/* +data/db/* +pubmed-glutton/* +indexing/* diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index 46d390a5..00000000 --- a/Dockerfile +++ /dev/null @@ -1,49 +0,0 @@ - -# ------------------- -# build builder image -# ------------------- -# FROM openjdk:8-jdk-stretch -FROM openjdk:8-jdk as builder - -USER root - -RUN apt-get update -#&& \ -# apt-get -y --no-install-recommends install - -WORKDIR /app/glutton-source - -RUN mkdir -p .gradle -VOLUME /app/glutton-source/.gradle - -# source -COPY lookup/ ./lookup/ -COPY indexing/ ./indexing/ - -RUN cd /app/glutton-source/lookup && ./gradlew clean assemble --no-daemon - -# ------------------- -# build runtime image -# ------------------- -FROM openjdk:8-jre-slim -RUN apt-get update -qq && apt-get -qy install curl build-essential unzip - -RUN mkdir -p /app -WORKDIR /app - -RUN apt-get update -qq && apt-get -y install nodejs npm -COPY --from=builder /app/glutton-source/indexing /app/indexing -RUN cd indexing; npm install - -COPY --from=builder /app/glutton-source/lookup/build/distributions/lookup-service-shadow-*.zip ./lookup-service.zip - -RUN unzip -o ./lookup-service.zip -d ./lookup && \ - mv ./lookup/lookup-service-* ./lookup/lookup-service - -RUN rm *.zip - -WORKDIR /app/lookup/lookup-service - -ENV JAVA_OPTS=-Xmx4g - -CMD java -jar lib/lookup-service-0.2-SNAPSHOT-onejar.jar server data/config/config.yml diff --git a/Readme.md b/Readme.md index 8e1a5c21..8498c63b 100644 --- a/Readme.md +++ b/Readme.md @@ -4,7 +4,7 @@ [![Demo cloud.science-miner.com/glutton](https://img.shields.io/website-up-down-green-red/https/cloud.science-miner.com/glutton/service/data.svg)](http://cloud.science-miner.com/glutton/service/data) [![SWH](https://archive.softwareheritage.org/badge/origin/https://github.com/kermitt2/biblio-glutton/)](https://archive.softwareheritage.org/browse/origin/?origin_url=https://github.com/kermitt2/biblio-glutton) -Framework dedicated to bibliographic information. It includes: +A framework dedicated to scientific bibliographic information. It includes: - a bibliographical reference matching service: from an input such as a raw bibliographical reference and/or a combination of key metadata, the service will return the disambiguated bibliographical object with in particular its DOI and a set of metadata aggregated from Crossref and other sources, - a fast metadata look-up service: from a "strong" identifier such as DOI, PMID, etc. the service will return a set of metadata aggregated from Crossref and other sources, @@ -13,641 +13,39 @@ Framework dedicated to bibliographic information. It includes: - Gap and daily update for Crossref resources (via the Crossref REST API), so that your glutton data service stays always in sync with Crossref, - MeSH classes mapping for PubMed articles. +biblio-glutton should be very handy if you need to run and scale a local full "Crossref" database and API, to aggregate Crossref, Pubmed and other common bibliographical records and to match a large amount of bibliographical records or raw bibliographical reference strings. + The framework is designed both for speed (with several thousands request per second for look-up) and matching accuracy. It can be [scaled](https://github.com/kermitt2/biblio-glutton#architecture) horizontally as needed and can provide high availability. Benchmarking against the Crossref REST API is presented [below](https://github.com/kermitt2/biblio-glutton#matching-accuracy). In the Glutton family, the following complementary tools are available for taking advantage of Open Access resources: -* [biblio-glutton-harvester](https://github.com/kermitt2/biblio-glutton-harvester): A robust, fault tolerant, Python utility for harvesting efficiently (multi-threaded) a large Open Access collection of PDF (Unpaywall, PubMed Central), with the possibility to upload content on Amazon S3, - * [biblio-glutton-extension](https://github.com/kermitt2/biblio-glutton-extension): A browser extension (Firefox & Chrome) for providing bibliographical services, like identifying dynamically Open Access resources on web pages and providing contextual citation services. -Current stable version of biblio-glutton is `0.2`. Working version is `0.3-SNAPSHOT`. - -## The bibliographical look-up and matching REST API - -Once the databases and index are built, the bibliographical REST API can be started. For building the databases and index, see the next sections below. - -### Build the service lookup - -You need Java JDK 1.8 installed for building and running the tool. - -```sh -cd lookup -./gradlew clean build -``` - -### Start the server - -```sh -cd lookup/ -./gradlew clean build -java -jar build/libs/lookup-service-0.2-onejar.jar server -``` +* [biblio-glutton-harvester](https://github.com/kermitt2/biblio-glutton-harvester): A robust, fault tolerant, Python utility for harvesting efficiently (multi-threaded) a large Open Access collection of PDF (Unpaywall, PubMed Central), with the possibility to upload content on Amazon S3, -The service will use the default project configuration located under `biblio-glutton/config/glutton.yml`. If you want to use a configuration file in another location, you can can specify it as additional parameter: +Current stable version of biblio-glutton is `0.3`. Working version is `0.4-SNAPSHOT`. +## Documentation -```sh -cd lookup/ -./gradlew clean build -java -jar build/libs/lookup-service-0.2-onejar.jar server /some/where/glutton.yml -``` +The full documentation is available [here](https://biblio-glutton.readthedocs.io/en/latest/), including an evaluation of the bibliographical reference matching and some expected runtime information. -To check if it works, you can view a report of the data used by the service at `host:port/service/data`. For instance: +## How to cite -> curl localhost:8080/service/data +If you want to cite this work, please refer to the present GitHub project, together with the [Software Heritage](https://www.softwareheritage.org/) project-level permanent identifier and do please indicate any author name. For example, with BibTeX: -```json -{ - "Metadata Lookup Crossref size":"{crossref_Jsondoc=127887559}", - "ISTEX size":"{istex_doi2ids=21325261, istex_istex2ids=21401494, istex_pii2ids=6954799}", - "Metadata Matching Crossref size":"127970581", - "PMID lookup size":"{pmid_doi2ids=25661624, pmid_pmc2ids=7561377, pmid_pmid2ids=33761382}", - "DOI OA size":"{unpayWall_doiOAUrl=30635446}" +```bibtex +@misc{biblio-glutton, + title = {biblio-glutton}, + url = {https://github.com/kermitt2/biblio-glutton}, + publisher = {GitHub}, + year = {2018--2024}, + archivePrefix = {swh}, + eprint = {1:dir:a5a4585625424d7c7428654dbe863837aeda8fa7} } ``` -### Start optional additional GROBID service - -biblio-glutton takes advantage of GROBID for parsing raw bibliographical references. This permits faster and more accurate bibliographical record matching. To use GROBID service: - -* first download and install GROBID as indicated in the [documentation](https://grobid.readthedocs.io/en/latest/Install-Grobid/) - -* start the service as documented [here](https://grobid.readthedocs.io/en/latest/Grobid-service/). You can change the `port` used by GROBID by updating the service config file under `grobid/grobid-home/config/grobid.yaml` - -* update if necessary the host and port information of GROBID in the biblio-glutton config file under `biblio-glutton/config/glutton.yml` (parameter `grobidPath`). - -While GROBID is not required for running biblio-glutton, in particular if it is used only for bibliographical look-up, it is recommended for performing bibliographical record matching. - - - -### REST API - -The service can be queried based on a strong identifier, likeDOI, PMID, etc. as follow: - -- match record by DOI - - `GET host:port/service/lookup?doi=DOI` - - `GET host:port/service/lookup/doi/{DOI}` - -- match record by PMID - - `GET host:port/service/lookup?pmid=PMID` - - `GET host:port/service/lookup/pmid/{PMID}` - -- match record by PMC ID - - `GET host:port/service/lookup?pmc=PMC` - - `GET host:port/service/lookup/pmc/{PMC}` - -- match record by ISTEX ID - - `GET host:port/service/lookup?istexid=ISTEXID` - - `GET host:port/service/lookup/istexid/{ISTEXID}` - -- match record by PII ID - - `GET host:port/service/lookup?pii=PII` - - `GET host:port/service/lookup/pii/{PII}` - -The service can be queried with various metadata like article title (`atitle`), first author last name (`firstAuthor`), journal title (`jtitle`), volume (`volume`), first page (`firstPage`) and publication year (`year`) - -- match record by article title and first author lastname - - `GET host:port/service/lookup?atitle=ARTICLE_TITLE&firstAuthor=FIRST_AUTHOR_SURNAME` - -- match record by journal title or abbreviated title, volume and first page - - `GET host:port/service/lookup?jtitle=JOURNAL_TITLE&volume=VOLUME&firstPage=FIRST_PAGE` - -- match record by journal title or abbreviated title, volume, first page, and first author lastname - - `GET host:port/service/lookup?jtitle=JOURNAL_TITLE&volume=VOLUME&firstPage=FIRST_PAGE&firstAuthor=FIRST_AUTHOR_SURNAME` - -It's possible to query the service based on a raw citation string (`biblio`): - -- match record by raw citation string - - `GET host:port/service/lookup?biblio=BIBLIO_STRING&` - - `POST host:port/service/lookup/biblio` with `ContentType=text/plain` - -Any combinations of these metadata and full raw citation string is possible, for instance: - - - `GET host:port/service/lookup?biblio=BIBLIO_STRING&atitle=ARTICLE_TITLE&firstAuthor=FIRST_AUTHOR_SURNAME` - -or: - - - `GET host:port/service/lookup?jtitle=JOURNAL_TITLE&volume=VOLUME&firstPage=FIRST_PAGE&firstAuthor=FIRST_AUTHOR_SURNAME&atitle=ARTICLE_TITLE` - -or: - - - `GET host:port/service/lookup?biblio=BIBLIO_STRING&atitle=ARTICLE_TITLE&firstAuthor=FIRST_AUTHOR_SURNAME&year=YYYY` - -It is also possible to combine a strong identifier with validation metadata. In this case, if the DOI appears conflicting with the provided metadata, no results will be returned, as a way to detect invalid DOI with post-validation: - - - `GET host:port/service/lookup?doi=DOI&atitle=ARTICLE_TITLE&firstAuthor=FIRST_AUTHOR_SURNAME` - -biblio-glutton will make the best use of all the parameters sent to retrieve in the fastest way a record and apply matching threshold to avoid false positive. It is advised to send __as much metadata as possible__ to try to optimize the DOI matching in term of speed and accuracy, and when possible a full raw bibliographical string. - -The more metadata are available in the query, the better. The original raw bibliographical string is also be exploited when available to control the bibliographical record matching. - -For convenience, in case you are only interested by the Open Access URL for a bibliographical object, the open Access resolver API returns the OA PDF link (URL) only via an identifier: - -- return the best Open Access URL if available - - `GET host:port/service/oa?doi=DOI` return the best Open Accss PDF url for a given DOI - - `GET host:port/service/oa?pmid=PMID` return the best Open Accss PDF url for a given PMID - - `GET host:port/service/oa?pmc=PMC` return the best Open Accss PDF url for a given PMC ID - - `GET host:port/service/oa?pii=PII` return the best Open Accss PDF url for a given PII ID - -- return the best Open Access URL and ISTEX PDF URL if available - - `GET host:port/service/oa_istex?doi=DOI` return the best Open Accss PDF url and ISTEX PDF url for a given DOI - - `GET host:port/service/oa_istex?pmid=PMID` return the best Open Accss PDF url and ISTEX PDF url for a given PMID - - `GET host:port/service/oa_istex?pmc=PMC` return the best Open Accss PDF url and ISTEX PDF url for a given PMC ID - - `GET host:port/service/oa_istex?pii=PII` return the best Open Accss PDF url and ISTEX PDF url for a given PII ID - -### cURL examples - -To illustrate the usage of the API, we provide some cURL example queries: - -Bibliographical metadata lookup by DOI: - -```sh -curl http://localhost:8080/service/lookup?doi=10.1484/J.QUAESTIO.1.103624 -``` - -Matching with title and first author lastname: - -```sh -curl "http://localhost:8080/service/lookup?atitle=Naturalizing+Intentionality+between+Philosophy+and+Brain+Science.+A+Survey+of+Methodological+and+Metaphysical+Issues&firstAuthor=Pecere" - -curl "http://localhost:8080/service/lookup?atitle=Naturalizing+Intentionality+between+Philosophy+and+Brain+Science&firstAuthor=Pecere" -``` - -Matching with raw bibliographical reference string: - -```sh -curl "http://localhost:8080/service/lookup?biblio=Baltz,+R.,+Domon,+C.,+Pillay,+D.T.N.+and+Steinmetz,+A.+(1992)+Characterization+of+a+pollen-specific+cDNA+from+sunflower+encoding+a+zinc+finger+protein.+Plant+J.+2:+713-721" -``` - -Bibliographical metadata lookup by PMID (note that only the number is expected): - -```sh -curl http://localhost:8080/service/lookup?pmid=1605817 -``` - -Bibliographical metadata lookup by PMC ID (note that the `PMC` prefix in the identifier is expected): - -```sh -curl http://localhost:8080/service/lookup?pmc=PMC1017419 -``` - -Bibliographical metadata lookup by PII ID: - -```sh -curl http://localhost:8080/service/lookup?pii= -``` - -Bibliographical metadata lookup by ISTEX ID: - -```sh -curl http://localhost:8080/service/lookup?istexid=E6CF7ECC9B002E3EA3EC590E7CC8DDBF38655723 -``` - -Open Access resolver by DOI: - -```sh -curl "http://localhost:8080/service/oa?doi=10.1038/nature12373" -``` - -Combination of Open Access resolver and ISTEX identifier by DOI: - -```sh -curl "http://localhost:8080/service/oa_istex?doi=10.1038/nature12373" -``` - -## Building the bibliographical data look-up and matching databases - -### Architecture - -Below is an overview of the biblio-glutton architecture. The biblio-glutton server manages locally high performance LMDB databases for all metadata look-up tasks (several thousand requests per second with multiple threads). For the costly metadata matching tasks, an Elasticsearch cluster is used. For scaling this sort of queries, simply add more nodes in this Elasticsearch cluster, keeping a single biblio-glutton server instance. - -![Glutton architecture](doc/glutton-architecture.png) - -#### Scaling evaluation - -1) *Metadata Lookup* - -One glutton instance: 19,792,280 DOI lookup in 3156 seconds, ~ 6270 queries per second. - -2) *Bibliographical reference matching* - -*(to be completed with more nodes!)* - -Processing time for matching 17,015 raw bibliographical reference strings to DOI: - -| number of ES cluster nodes | comment | total runtime (second) | runtime per bib. ref. (second) | queries per second | -|----|---|---|---|---| -| 1 | glutton and Elasticsearch node share the same machine | 2625 | 0.154 | 6.5 | -| 1 | glutton and Elasticsearch node on two separate machines | 1990 | 0.117 | 8.5 | -| 2 | glutton and one of the Elasticsearch node sharing the same machine | 1347 | 0.079 | 12.6 | - -Machines have the same configuration Intel i7 4-cores, 8 threads, 16GB memory, SSD, on Ubuntu 16.04. - -### Loading resources - -To set-up a functional biblio-glutton server, resources need to be loaded following these steps: - -1) Loading of a Crossref full metadata dump as embedded LMDB - -2) Loading the coverage gap between the Crossref dump and the current day (updates are then realized automatically daily as the service is up and running) in the embedded LMDB - -3) Loading the DOI to PMID and PMC ID mapping as embedded LMDB - -4) (Optional) Loading the Open Access information from an Unpaywall datset snapshot as embedded LMDB - -5) (Very optional) Loading the ISTEX ID mapping as embedded LMDB - -6) Creating the Elasticsearch index - -### Resources - -For building the database and index used by service, you will need these resources: - -* Crossref metadata dump, available: - - strongly recommended: via the [Crossref Metadata APIs Plus](https://www.crossref.org/services/metadata-delivery/plus-service/) service for a current snapshot, or - - [public Crossref dump](https://www.crossref.org/blog/new-public-data-file-120-million-metadata-records/) available with Academic Torrents (2021-01-07 for the latest version, no update in 2022 as far as we known), - - Internet Archive, see https://github.com/greenelab/crossref and for instance the latest Internet Archive Crossref [dump](https://archive.org/download/crossref_doi_dump_201909) (2019-09). - -We recommend to use a Crossref Metadata Plus snapshot in order to have a version of the Crossref metadata without large coverage gap. With the `Crossref-Plus-API-Token`, the following command for instance will download the full snapshot for the indicated year/month: - -```console -wget -c --header='Crossref-Plus-API-Token: Bearer __Crossref-Plus-API-Token-Here_' https://api.crossref.org/snapshots/monthly/YYYY/MM/all.json.tar.gz -``` - -Without Metadata Plus subscription, it's possible to use the Academic Torrents Crossref dumps. For instance, with the Linux command line `aria2` and a high speed internet connection (e.g. 500Mb/s), the dump can be downloaded in a few minutes. However, the coverage gap will be important and updating these older snapshot via the normal Crossref Web API will take an enormous amount of time. - -* DOI to PMID and PMC mapping: available at Europe PMC and regularly updated at ftp://ftp.ebi.ac.uk/pub/databases/pmc/DOI/PMID_PMCID_DOI.csv.gz, - -* optionally, but recommended, the Unpaywall dataset to get Open Access links aggregated with the bibliographical metadata, see [here](http://unpaywall.org/products/snapshot) to get the latest database snapshot. - -* optionally, usually not required, for getting ISTEX identifier information, you need to build the ISTEX ID mapping, see below. - -The bibliographical matching service uses a combination of high-performance embedded databases (LMDB), for fast look-up and cache, and Elasticsearch for blocking via text-based search. As Elasticsearch is much slower than embedded databases, it is used only when absolutely required. - -The databases and Elasticsearch index must first be built from the resource files. The full service needs around 300 GB of space for building this index and it is highly recommended to use SSD for best performance. - -### Build the embedded LMDB databases - -Resource dumps will be compiled in high performance LMDB databases. The system can read compressed (`gzip` or `.xz`) or plain text files (`json`), so in practice you do not need to uncompress anything. - -#### Build the data loader - -```sh -cd lookup -./gradlew clean build -``` - -All the following commands need to be launched under the subdirectory `lookup/`. The loading of the following database can be done in parallel. The default configuration file under `biblio-glutton/config/glutton.yml` will be used if not indicated. To use a configuration file in another location, just add the full path as additional parameter like for running the sevice. - -#### Crossref metadata - -General command line pattern: - -```sh -java -jar build/libs/lookup-service-0.2-onejar.jar crossref --input /path/to/crossref/json/file path/to/config/file/glutton.yml -``` - -Example with Crossref Metadata Plus snapshot (path to a `.tar.gz` file which archives many json files): - -```sh -java -jar build/libs/lookup-service-0.2-onejar.jar crossref --input ~/tmp/crossref_metadata_plus.tar.gz ../config/glutton.yml -``` - -The last parameter is the project config file normally under `biblio-glutton/config/glutton.yml`: - -```sh -java -jar build/libs/lookup-service-0.2-onejar.jar crossref --input /path/to/crossref/json/file ../config/glutton.yml -``` - -Example with Crossref dump Academic Torrent file (path to a repository of `*.json.gz` files): - - -```sh -java -jar build/libs/lookup-service-0.2-onejar.jar crossref --input ~/tmp/crossref_public_data_file_2021_01 ../config/glutton.yml -``` - -Example with xz-compressed file (e.g. GreeneLab dump): - -```sh -java -jar build/libs/lookup-service-0.2-onejar.jar crossref --input crossref-works.2019-09-09.json.xz ../config/glutton.yml -``` - -**Note:** By default the `abstract`, the `reference` and the original `indexed` fields included in Crossref records are ignored to save some disk space. The `reference` field is particularly large as it lists all the citations for almost half of the DOI records. You can change the list of fields to be filtered out in the config file under `biblio-glutton/config/glutton.yml`, by editing the lines: - -``` -ignoreCrossRefFields: - - reference - - abstract - - indexed -``` - -Example loading the Crossref Metadata Plus snapshot of March 2022, loading time around 4 hours (dump files on slow hard drive). - -``` --- Counters -------------------------------------------------------------------- -crossrefLookup_rejectedRecords - count = 5472493 - --- Meters ---------------------------------------------------------------------- -crossrefLookup - count = 126812507 - mean rate = 11368.21 events/second - 1-minute rate = 6520.71 events/second - 5-minute rate = 6403.19 events/second - 15-minute rate = 7240.26 events/second -``` - -The 5,472,493 rejected records correspond to all the DOI "components" (given to figures, tables, etc. part of document) which are filtered out. -As a March 2022, we thus have 121,340,014 crossref article records. - - -#### Crossref metadata gap coverage - -Once the main Crossref metadata snapshot has been loaded, the metadata and index will be updated daily automatically via the Crossref web API. However, there is always a gap of coverage between the last day covered by the used large snapshot image and the start of the daily update. - -Currently new Crossref Metadata Plus snapshot are available on the 5th of every month, covering all the metadata updates for until the previous month. It means that in the best case, there will be a coverage gap of 5 days to be recovered. More generally, users of Crossref Metadata Plus snapshot can load first a snapshot of the last month, then an additional snapshot mid-month update is available with the registered content that has changed in the first half of the month. This permits to minimize the coverage gap usually to a few days. - -Using the Crossref web API to cover the remaining gap (from the latest update day in the full snapshot to the current day) is done with the following command (still under `biblio-glutton/lookup/`): - -```sh -java -jar build/libs/lookup-service-0.2-onejar.jar gap_crossref path/to/config/file/glutton.yml -``` - -For instance: - -```sh -java -jar build/libs/lookup-service-0.2-onejar.jar gap_crossref ../config/glutton.yml -``` - -Be sure to indicate in the configution file `glutton.yml` your polite usage email and/or crossref matadata plus token for using the Crossref web API. - -This command should thus be launched only one time after the loading of a full Crossref snapshot, it will resync the current metadata and index to the current day, and the daily update will then ensure everything remain in sync with the reference Crossref metadata as long the service is up and running. - -__Warning:__ If an older snapshot is used, like the Crossref dump Academic Torrent file, the coverage gap is not a few days, but usually several months or more than one year (since Crossref has not updated the Academic Torrent dump in 2022). Using the Crossweb API to cover such a long gap will unfortunately take an enormous amount of time (more than a week) due to API usage rate limitations and is likely not a acceptable solution. In addition, the Crossref web API is not always reliable, which might cause further delays. - -#### PMID and PMC ID - -```sh -java -jar build/libs/lookup-service-0.2-onejar.jar pmid --input /path/to/pmid/csv/file path/to/config/file/glutton.yml -``` - -Example: - -```sh -java -jar build/libs/lookup-service-0.2-onejar.jar pmid --input PMID_PMCID_DOI.csv.gz ../config/glutton.yml -``` - -As of March 2022, the latest mapping covers 34,310,000 PMID, with 25,661,624 having a DOI (which means 8,648,376 PMID are not represented in Crossref). - -#### OA via Unpaywall - -```sh -java -jar build/libs/lookup-service-0.2-onejar.jar unpaywall --input /path/to/unpaywall/json/file path/to/config/file/glutton.yml -``` - -Example: - -```sh -java -jar build/libs/lookup-service-0.2-onejar.jar unpaywall --input unpaywall_snapshot_2022-03-09T083001.jsonl.gz ../config/glutton.yml -``` - -As of March 2022, the Unpaywall snapshot should provide at least one Open Access link to 30,618,764 Crossref entries. - -#### ISTEX - -Note that ISTEX mapping is only relevant for ISTEX full text resource users, so only public research institutions in France. So you can generally skip this step. - -```sh -java -jar build/libs/lookup-service-0.2-onejar.jar istex --input /path/to/istex/json/file path/to/config/file/glutton.yml -``` - -Example: - -```sh -java -jar build/libs/lookup-service-0.2-onejar.jar istex --input istexIds.all.gz ../config/glutton.yml -``` - -Note: see bellow how to create this mapping file `istexIds.all.gz`. - -### Build the Elasticsearch index - -Elasticsearch `7.*` is required. `node.js` version 10 or more should work fine. - -A node.js utility under the subdirectory `indexing/` is used to build the Elasticsearch index. Indexing will take a few hours. For 116M crossref entries, the indexing takes around 6 hours (with SSD, 16GB RAM) and around 22GB of index space (per ES node if you plan to use several ES nodes). - -#### Install and configure - -You need first to install and start ElasticSearch, version `7.*`. Edit the project configuration file `biblio-glutton/config/glutton.yml` to indicate the host name and port of the Elasticsearch server. In this configuration file, it is possible to specify the name of the index ('default `crossref`) and the batch size of the bulk indexing. - -Install the node.js module: - -```sh -cd indexing/ -npm install -``` - -#### Build the index - -Usage information for indexing: - -```sh -cd biblio-glutton/indexing/ -node main -dump *PATH_TO_THE_CROSSREF_DUMP* index -``` - -Example with Crossref dump Academic Torrent file (path to a repository of `*.json.gz` files): - -```sh -node main -dump ~/tmp/crossref_public_data_file_2021_01 index -``` - -Example with Crossref Metadata Plus snapshot (path to a file `.tar.gz` which archives many json files): - -```sh -node main -dump ~/tmp/crossref_sample.tar.gz index -``` - -Example with GreeneLab/Internet Archive dump file: - -```sh -node main -dump ~/tmp/crossref-works.2019-09-09.json.xz index -``` - -Note that launching the above command will fully re-index the data, deleting existing index. The default name of the index is `crossref`, but this can be changed via the global config file `biblio-glutton/config/glutton.yml`. - -For getting health check information about the selected ElasticSearch cluster: - -```sh -node main health -``` - -Example loading the [public Crossref dump](https://www.crossref.org/blog/new-public-data-file-120-million-metadata-records/) available with Academic Torrents (2021-01-07), index on SSD, dump files on hard drive, Ubuntu 18.04, 4 cores, 16MB RAM 6 years old machine: - -- 115,972,356 indexed records (perfect match with metadata db) -- around 6:30 for indexing (working on the same time on the computer), 4797 records/s -- 25.94GB index size - -Like for the metadata database, the Crossref objects of type `component` are skipped. - -## Matching accuracy - -Here is some evaluation on the bibliographical reference matching. - -### Dataset - -We created a dataset of [17,015 bibliographical reference/DOI pairs](doc/references-doi-matching.json.gz) with GROBID and the PMC 1943 sample (a set of 1943 PubMed Central articles from 1943 different journals with both PDF and XML NLM files available, see below). For the bibliographical references present in the NLM file with a DOI, we try to align the raw reference string extracted from the PDF by GROBID and the parsed XML present in the NLM file. Raw reference string are thus coming from the PDF, and we included additional metadata as extracted by GROBID from the PDF. - -Example of the two first of the 17.015 entries: - -```json -{"reference": "Classen M, Demling L. Endoskopishe shinkterotomie der papilla \nVateri und Stein extraction aus dem Duktus Choledochus [Ger-\nman]. Dtsch Med Wochenschr. 1974;99:496-7.", "doi": "10.1055/s-0028-1107790", "pmid": "4835515", "atitle": "Endoskopishe shinkterotomie der papilla Vateri und Stein extraction aus dem Duktus Choledochus [German]", "firstAuthor": "Classen", "jtitle": "Dtsch Med Wochenschr", "volume": "99", "firstPage": "496"}, -{"reference": "Kawai K, Akasaka Y, Murakami K. Endoscopic sphincterotomy \nof the ampulla of Vater. Gastrointest Endosc. 1974;20:148-51.", "doi": "10.1016/S0016-5107(74)73914-1", "pmid": "4825160", "atitle": "Endoscopic sphincterotomy of the ampulla of Vater", "firstAuthor": "Kawai", "jtitle": "Gastrointest Endosc", "volume": "20", "firstPage": "148"}, -``` - -The goal of Glutton matching is to identify the right DOI from raw metadata. We compare the results with the Crossref REST API, using the `query.bibliographic` field for raw reference string matching, and author/title field queries for first author lastname (`query.author`) plus title matching (`query.title`). - -Limits: - -- The DOI present in the NLM files are not always reliable (e.g. DOI not valid anymore following some updates in Crossref). A large amount of the matching errors are actually not due to the matching service, but to NLM reference DOI data quality. However, errors will be the same for all matching services, so it's still valid for comparing them, although for this reason the resulting accuracy is clearly lower than what it should be. - -- GROBID extraction is not always reliable, as well the alignment mechanism with NLM (based on soft match), and some raw reference string might not be complete or include unexpected extra material from the PDF. However, this can be view as part of the matching challenge in real world conditions! - -- the NLM references with DOI are usually simpler reference than in general: there are much fewer abbreviated references (without title nor authors) and references without titles as compared to general publications from non-medicine publishers. - - - -### How to run the evaluation - -You can use the DOI matching evaluation set (with 17,015 bibliographical reference/DOI pairs) from the indicated above address ([here](doc/references-doi-matching.json.gz)) or recreate this dataset with GROBID as follow: - -- [Install GROBID](https://grobid.readthedocs.io/en/latest/Install-Grobid/). - -- Download the [PMC 1943 sample](https://grobid.s3.amazonaws.com/PMC_sample_1943.zip) (around 1.5GB in size). - -- Create the evaluation dataset: - -> ./gradlew PrepareDOIMatching -Pp2t=ABS_PATH_TO_PMC/PMC_sample_1943 - -The evaluation dataset will be saved under `ABS_PATH_TO_PMC/PMC_sample_1943` with the name `references-doi-matching.json` - -- For launching an evaluation: - -1) Select the matching method (`crossref` or `glutton`) in the `grobid-home/config/grobid.yaml` file: - -```yaml -consolidation: - # define the bibliographical data consolidation service to be used, either "crossref" for Crossref REST API or - # "glutton" for https://github.com/kermitt2/biblio-glutton - #service: "crossref" - service: "glutton" -``` - -2) If Glutton is setected, start the Glutton server as indicated above (we assume that it is running at `localhost:8080`). - -3) Launch from GROBID the evaluation, indicating the path where the evaluation dataset has been created - here we suppose that the file `references-doi-matching.json` has been saved under `ABS_PATH_TO_PMC/PMC_sample_1943`: - -> ./gradlew EvaluateDOIMatching -Pp2t=ABS_PATH_TO_PMC/PMC_sample_1943 - - -### Full raw bibliographical reference matching - -Runtime corresponds to a processing on a single machine running Glutton REST API server, Elasticsearch and GROBID evaluation with CRF for the citation model, with Crossref index dated Sept. 2021. - -``` -======= GLUTTON API ======= -17015 bibliographical references processed in 1145.593 seconds, 0.06732841610343815 seconds per bibliographical reference. -Found 16699 DOI - -precision: 97.33 -recall: 95.52 -F1-score: 96.42 -``` - -With `BiLSTM-CRF` model instead of CRF for parsing the raw references prior to matching: - -``` -======= GLUTTON API ======= - -precision: 97.34 -recall: 95.83 -f-score: 96.58 -``` - -In the case of Crossref API, we use as much as possible the concurrent queries (usually 50) allowed by the service with the GROBID Crossref multithreaded client. - -``` -======= CROSSREF API ======= - -17015 bibliographical references processed in 3057.464 seconds, 0.1797 seconds per bibliographical reference. -Found 16502 DOI - -======= CROSSREF API ======= - -precision: 97.19 -recall: 94.26 -F1-score: 95.69 -``` - -## ISTEX mapping - -If you don't know what ISTEX is, you can safely skip this section. - -### ISTEX identifier mapping - -For creating a dump of all ISTEX identifiers associated with existing identifiers (DOI, ark, PII), use the node.js script as follow: - -* install: - -```sh -cd scripts -npm install requestretry -``` - -* Generate the json dump: - -```sh -node dump-istexid-and-other-ids.js > istexIds.all -``` - -Be sure to have a good internet bandwidth for ensuring a high rate usage of the ISTEX REST API. - -You can then move the json dump (e.g. `istexIds.all`) to the Istex data path indicated in the file `config/glutton.yaml` (by default `data/istex/`). - -### ISTEX to PubMed mapping - -The mapping adds PudMed information (in particular MeSH classes) to ISTEX entries. -See the instructions [here](pubmed-glutton/Readme.md) - - ## Main authors and contact - Patrice Lopez ([@kermitt2](https://github.com/kermitt2), patrice.lopez@science-miner.com) @@ -657,3 +55,5 @@ See the instructions [here](pubmed-glutton/Readme.md) ## License Distributed under [Apache 2.0 license](http://www.apache.org/licenses/LICENSE-2.0). + +If you contribute to this project, you agree to share your contribution following this license. diff --git a/build.gradle b/build.gradle new file mode 100644 index 00000000..34a733e6 --- /dev/null +++ b/build.gradle @@ -0,0 +1,252 @@ +buildscript { + repositories { + mavenLocal() + mavenCentral() + maven { + url 'https://plugins.gradle.org/m2/' + } + } + + dependencies { + classpath 'gradle.plugin.org.kt3k.gradle.plugin:coveralls-gradle-plugin:2.12.0' + classpath "gradle.plugin.com.github.jengelman.gradle.plugins:shadow:7.0.0" + } +} + +apply plugin: 'application' +apply plugin: 'java' +apply plugin: 'java-library' +//apply plugin: 'maven' +apply plugin: 'maven-publish' +apply plugin: 'com.github.johnrengelman.shadow' + +group 'com.scienceminer.glutton' +version '0.3-SNAPSHOT' + +//sourceCompatibility = 1.8 +sourceCompatibility = 1.11 +targetCompatibility = 1.11 + +// The main class of the application +mainClassName = 'com.scienceminer.glutton.web.LookupServiceApplication' +tasks.run.workingDir = rootProject.rootDir + +repositories { + mavenLocal() + mavenCentral() +} + +sourceSets.main.resources { + srcDirs = ["src/main/resources"]; +} + +configurations { + all*.exclude group: 'org.slf4j', module: "slf4j-log4j12" + all*.exclude group: 'log4j', module: "log4j" + all*.exclude group: 'log4j2', module: "log4j2" + implementation.setCanBeResolved(true) +} + +processResources { + filesMatching('config/glutton.yml') { + filter { + it.replace('project.version', project.property('version_placeholder')) + } + } +} + +task install(dependsOn: installShadowDist) + +dependencies { + testImplementation group: 'junit', name: 'junit', version: '4.12' + testImplementation "org.hamcrest:hamcrest-all:1.3" + testImplementation "org.easymock:easymock:3.5" + + implementation "com.google.code.gson:gson:2.8.1" + + //Dropwizard + implementation 'ru.vyarus:dropwizard-guicey:7.0.0' + + implementation 'io.dropwizard:dropwizard-bom:4.0.0' + implementation 'io.dropwizard:dropwizard-core:4.0.0' + implementation 'io.dropwizard:dropwizard-assets:4.0.0' + implementation 'io.dropwizard:dropwizard-testing:4.0.0' + implementation 'io.dropwizard.modules:dropwizard-testing-junit4:4.0.0' + implementation 'io.dropwizard:dropwizard-forms:4.0.0' + implementation 'io.dropwizard:dropwizard-client:4.0.0' + implementation 'io.dropwizard:dropwizard-auth:4.0.0' + implementation 'io.dropwizard.metrics:metrics-core:4.2.22' + implementation 'io.dropwizard.metrics:metrics-servlets:4.2.22' + + implementation 'jakarta.validation:jakarta.validation-api:2.0.2' + + implementation 'org.slf4j:slf4j-api:1.7.30' + implementation 'ch.qos.logback:logback-classic:1.2.3' + implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.8.2' + + implementation "com.rockymadden.stringmetric:stringmetric-core_2.10:0.27.3" + + //Parsing XML/Json + implementation group: 'org.codehaus.woodstox', name: 'stax2-api', version: '4.0.0' + implementation group: 'org.codehaus.woodstox', name: 'woodstox-core-asl', version: '4.4.1' + + implementation 'org.lmdbjava:lmdbjava:0.9.0' + implementation 'de.ruedigermoeller:fst:2.56' + implementation 'org.xerial.snappy:snappy-java:1.1.7.2' + + implementation 'org.elasticsearch.client:elasticsearch-rest-high-level-client:7.17.2' + implementation 'co.elastic.clients:elasticsearch-java:8.12.1' + implementation ('org.apache.solr:solr-solrj:9.5.0') { + exclude group: 'org.eclipse.jetty', module: 'jetty-http2' + exclude group: 'org.eclipse.jetty.http2', module: 'http2-client' + } + + implementation 'org.apache.commons:commons-collections4:4.1' + implementation 'commons-beanutils:commons-beanutils:1.9.4' + implementation 'commons-io:commons-io:2.6' + implementation group: 'org.apache.commons', name: 'commons-compress', version: '1.20' + + implementation group: 'org.tukaani', name: 'xz', version: '1.8' + + implementation "com.fasterxml.jackson.core:jackson-core:2.14.3" + implementation "com.fasterxml.jackson.core:jackson-databind:2.14.3" + implementation "com.fasterxml.jackson.module:jackson-module-afterburner:2.14.3" + implementation "com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.14.3" + + implementation group: 'com.opencsv', name: 'opencsv', version: '5.0' +} + +distributions { + shadow { + /*contents { + from(new File(rootProject.rootDir, "data/config")) { + into "data/config" + } + }*/ + } +} + +shadowJar { + classifier = 'onejar' + mergeServiceFiles() + zip64 true + manifest { + attributes 'Main-Class': mainClassName + } + exclude("logback.xml") + duplicatesStrategy = DuplicatesStrategy.EXCLUDE +} + +distTar.enabled = false +distZip.enabled = false +shadowDistTar.enabled = false + +artifacts { + archives shadowJar +} + +// arguments for exec tasks +ext.getArg = { propName, defaultVal -> + return project.hasProperty(propName) ? project.getProperty(propName) : defaultVal; +} + +task server(dependsOn: 'classes', type: JavaExec, group: 'service') { + main = 'com.scienceminer.glutton.web.LookupServiceApplication' + classpath = sourceSets.main.runtimeClasspath + args 'server', 'config/glutton.yml' + if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) { + jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED" + } else { + jvmArgs '-Xmx3072m' + } +} + +task crossref(dependsOn: 'classes', type: JavaExec, group: 'data') { + main = 'com.scienceminer.glutton.web.LookupServiceApplication' + classpath = sourceSets.main.runtimeClasspath + args 'crossref', '--input', getArg('input', ''), getArg('config', 'config/glutton.yml') + if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) { + jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED" + } else { + jvmArgs '-Xmx3072m' + } +} + +task gap_crossref(dependsOn: 'classes', type: JavaExec, group: 'data') { + main = 'com.scienceminer.glutton.web.LookupServiceApplication' + classpath = sourceSets.main.runtimeClasspath + args 'gap_crossref', getArg('config', 'config/glutton.yml') + if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) { + jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED" + } else { + jvmArgs '-Xmx3072m' + } +} + +task hal(dependsOn: 'classes', type: JavaExec, group: 'data') { + main = 'com.scienceminer.glutton.web.LookupServiceApplication' + classpath = sourceSets.main.runtimeClasspath + args 'hal', getArg('config', 'config/glutton.yml') + if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) { + jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED" + } else { + jvmArgs '-Xmx3072m' + } +} + +task pmid(dependsOn: 'classes', type: JavaExec, group: 'service') { + main = 'com.scienceminer.glutton.web.LookupServiceApplication' + classpath = sourceSets.main.runtimeClasspath + args 'pmid', getArg('config', 'config/glutton.yml') + if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) { + jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED" + } else { + jvmArgs '-Xmx3072m' + } +} + +task unpaywall(dependsOn: 'classes', type: JavaExec, group: 'data') { + main = 'com.scienceminer.glutton.web.LookupServiceApplication' + classpath = sourceSets.main.runtimeClasspath + args 'unpaywall', '--input', getArg('input', ''), getArg('config', 'config/glutton.yml') + if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) { + jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED" + } else { + jvmArgs '-Xmx3072m' + } +} + +task istex(dependsOn: 'classes', type: JavaExec, group: 'data') { + main = 'com.scienceminer.glutton.web.LookupServiceApplication' + classpath = sourceSets.main.runtimeClasspath + args 'istex', '--input', getArg('input', ''), getArg('config', 'config/glutton.yml') + if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) { + jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED" + } else { + jvmArgs '-Xmx3072m' + } +} + +// only used it to re-create the search index from scratch, keeping the LMDB unchanged +task index(dependsOn: 'classes', type: JavaExec, group: 'search') { + main = 'com.scienceminer.glutton.web.LookupServiceApplication' + classpath = sourceSets.main.runtimeClasspath + args 'index', getArg('config', 'config/glutton.yml') + if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) { + jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED" + } else { + jvmArgs '-Xmx3072m' + } +} + +// experimental +task hal_audit(dependsOn: 'classes', type: JavaExec, group: 'search') { + main = 'com.scienceminer.glutton.web.LookupServiceApplication' + classpath = sourceSets.main.runtimeClasspath + args 'hal_audit', getArg('config', 'config/glutton.yml') + if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) { + jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED" + } else { + jvmArgs '-Xmx3072m' + } +} \ No newline at end of file diff --git a/config/elastic-settings.json b/config/elastic-settings.json new file mode 100644 index 00000000..33f7586f --- /dev/null +++ b/config/elastic-settings.json @@ -0,0 +1,110 @@ +{ + "settings": { + "index": { + "number_of_replicas": 0, + "refresh_interval": -1, + "codec": "best_compression" + }, + "analysis": { + "filter": { + "my_stop": { + "type": "stop", + "stopwords": "_english_" + + } + }, + "analyzer": { + "case_insensitive_keyword": { + "type": "custom", + "tokenizer": "keyword", + "filter": "lowercase" + }, + "case_insensitive_folding_keyword": { + "type": "custom", + "tokenizer": "keyword", + "filter": [ + "lowercase", + "asciifolding" + ] + }, + "case_insensitive_folding_text": { + "type": "custom", + "tokenizer": "standard", + "filter": [ + "lowercase", + "asciifolding" + ] + }, + "case_insensitive_folding_text_stopwords": { + "type": "custom", + "tokenizer": "standard", + "filter": [ + "lowercase", + "asciifolding", + "my_stop" + ] + } + } + } + }, + "mappings": { + "properties": { + "DOI": { + "type": "text", + "analyzer": "case_insensitive_keyword" + }, + "halId": { + "type": "text", + "analyzer": "case_insensitive_keyword" + }, + "title": { + "type": "text", + "analyzer": "case_insensitive_folding_text_stopwords" + }, + "first_author": { + "type": "text", + "analyzer": "case_insensitive_folding_keyword" + }, + "author": { + "type": "text", + "analyzer": "case_insensitive_folding_text" + }, + "first_page": { + "type": "text", + "analyzer": "case_insensitive_folding_keyword" + }, + "journal": { + "type": "text", + "analyzer": "case_insensitive_folding_text_stopwords" + }, + "abbreviated_journal": { + "type": "text", + "analyzer": "case_insensitive_folding_keyword" + }, + "volume": { + "type": "text", + "analyzer": "case_insensitive_folding_keyword" + }, + "issue": { + "type": "text", + "analyzer": "case_insensitive_folding_keyword" + }, + "year": { + "type": "text", + "analyzer": "case_insensitive_folding_keyword" + }, + "query": { + "type": "text", + "analyzer": "case_insensitive_folding_text" + }, + "bibliographic": { + "type": "text", + "analyzer": "case_insensitive_folding_text_stopwords" + }, + "type": { + "type": "text", + "analyzer": "case_insensitive_folding_text" + } + } + } +} \ No newline at end of file diff --git a/config/glutton.yml b/config/glutton.yml index 60a25381..e6d1e84b 100644 --- a/config/glutton.yml +++ b/config/glutton.yml @@ -1,18 +1,14 @@ -version: 0.2 +version: 0.3 -# where the metadata are stored, it takes more than 200GB for all Crossref, Unpaywall, PubMed and ISTEX mappings -storage: data/db -#storage: /media/lopez/T5/data/db - -# Crossref fields to be ignored when storing metadata, reference field in particular take a lot of space -ignoreCrossRefFields: - - reference - - abstract - - indexed +# where the compiled metadata are stored, it takes more than 200GB for all Crossref, Unpaywall, PubMed and ISTEX mappings, +# this is a single location for all compiled resources +#storage: data/db +#storage: /media/lopez/data2/glutton-data/data/db +storage: /media/lopez/Samsung_T515/glutton/data/db/ # batch size for preparing the data -loadingBatchSize: 10000 -indexBatchSize: 500 +storingBatchSize: 10000 +indexingBatchSize: 10000 # max blocking size (number of candidates considered for pairwise matching) blockSize: 4 @@ -24,19 +20,35 @@ timeZone: UTC # the day hour for lauching the automatic daily incremental update, format is HH:MM dailyUpdateTime: 03:00 -# a node of the elasticsearch cluster to be used and a name for the index +# define the search infrastructure to be used, possible values are "elasticSearch" or "solr" +searchEngine: elasticSearch +#searchEngine: solr + +# a node of the ElasticSearch cluster to be used and a name for the main index elastic: #host: localhost:9200 host: 0.0.0.0:9200 - index: crossref + #host: 192.168.1.30:9200 + index: glutton maxConnections: 20 +# solr settings +solr: + host: 0.0.0.0:8983 + core: glutton + proxy: # proxy to be used when doing external call to crossref or unpaywall host: port: crossref: + # Crossref fields to be ignored when storing metadata, reference field in particular takes a lot of space + ignoreCrossrefFields: + - reference + - abstract + - indexed + # a directory where the crossref incremental update files (gap or daily update) will be located # to be changed according to your storage dumpPath: /media/lopez/data2/crossref @@ -54,6 +66,25 @@ crossref: #token: "yourmysteriouscrossrefmetadataplusauthorizationtokentobeputhere" token: +# the following is used only for pubmed related enrichments and extractions +#pubmed: + # path to the medline downloaded resources, to be changed according to your storage + #pubmedDirectory: /media/lopez/data2/medline_2023 + # path to PMC mapping data + #pmcDirectory: data/pmc + # elasticsearch index for pubmed, used to create extraction based on MeSH terms + #index: pubmed + # path to the working pubmed databases, to be changed according to your storage + #dbDirectory: /media/lopez/T51/data2/db + +hal: + # OAI PMH endpoint for harvesting HAL metadata + api: "http://api.archives-ouvertes.fr/oai/hal" + +dblp: + # URL of the DBLP metadata dump + dump: "https://dblp.uni-trier.de/xml/dblp.xml.gz" + unpaywall: dumpPath: # a directory where the unpaywall update data feed change files will be located @@ -80,29 +111,44 @@ server: registerDefaultExceptionMappers: false maxThreads: 2048 maxQueuedRequests: 2048 - acceptQueueSize: 2048 - + # change the following for having all http requests logged + requestLog: + appenders: [] + +# logging: +# level: INFO +# appenders: +# - type: console +# threshold: WARN +# timeZone: UTC +# - type: file +# currentLogFilename: logs/lookup-service.log +# threshold: INFO +# archive: true +# archivedLogFilenamePattern: logs/lookup-service-%d.log +# archivedFileCount: 5 +# timeZone: UTC + +# these logging settings apply to the service usage mode logging: level: INFO + loggers: + org.glassfish.jersey.internal: "OFF" + com.squarespace.jersey2.guice.JerseyGuiceUtils: "OFF" appenders: - - type: console - threshold: INFO - timeZone: UTC - - type: file - currentLogFilename: logs/lookup-service.log - threshold: INFO - archive: true - archivedLogFilenamePattern: logs/lookup-service-%d.log - archivedFileCount: 5 - timeZone: UTC - -# the following is used only for pubmed related enrichments and extractions -pubmed: - # path to the medline resources, to be changed according to your storage - pubmedDirectory: /media/lopez/data/biblio/medline2021/ - # path to PMC mapping data - pmcDirectory: data/pmc - # elasticsearch index for pubmed, used to create extraction based on MeSH terms - index: pubmed - # path to the working pubmed databases, to be changed according to your storage - dbDirectory: /media/lopez/T5/data2/db + - type: console + threshold: INFO + timeZone: UTC + # uncomment to have the logs in json format + #layout: + # type: json + - type: file + currentLogFilename: logs/biblio-glutton.log + threshold: INFO + archive: true + archivedLogFilenamePattern: logs/biblio-glutton-%d.log + archivedFileCount: 5 + timeZone: UTC + # uncomment to have the logs in json format + #layout: + # type: json diff --git a/doc/API.md b/doc/API.md new file mode 100644 index 00000000..75684391 --- /dev/null +++ b/doc/API.md @@ -0,0 +1,134 @@ +## REST API + +The service can be queried based on a strong identifier, likeDOI, PMID, etc. as follow: + +- match record by DOI + - `GET host:port/service/lookup?doi=DOI` + - `GET host:port/service/lookup/doi/{DOI}` + +- match record by PMID + - `GET host:port/service/lookup?pmid=PMID` + - `GET host:port/service/lookup/pmid/{PMID}` + +- match record by PMC ID + - `GET host:port/service/lookup?pmc=PMC` + - `GET host:port/service/lookup/pmc/{PMC}` + +- match record by ISTEX ID + - `GET host:port/service/lookup?istexid=ISTEXID` + - `GET host:port/service/lookup/istexid/{ISTEXID}` + +- match record by PII ID + - `GET host:port/service/lookup?pii=PII` + - `GET host:port/service/lookup/pii/{PII}` + +The service can be queried with various metadata like article title (`atitle`), first author last name (`firstAuthor`), journal title (`jtitle`), volume (`volume`), first page (`firstPage`) and publication year (`year`) + +- match record by article title and first author lastname + - `GET host:port/service/lookup?atitle=ARTICLE_TITLE&firstAuthor=FIRST_AUTHOR_SURNAME` + +- match record by journal title or abbreviated title, volume and first page + - `GET host:port/service/lookup?jtitle=JOURNAL_TITLE&volume=VOLUME&firstPage=FIRST_PAGE` + +- match record by journal title or abbreviated title, volume, first page, and first author lastname + - `GET host:port/service/lookup?jtitle=JOURNAL_TITLE&volume=VOLUME&firstPage=FIRST_PAGE&firstAuthor=FIRST_AUTHOR_SURNAME` + +It's possible to query the service based on a raw citation string (`biblio`): + +- match record by raw citation string + - `GET host:port/service/lookup?biblio=BIBLIO_STRING&` + - `POST host:port/service/lookup/biblio` with `ContentType=text/plain` + +Any combinations of these metadata and full raw citation string is possible, for instance: + + - `GET host:port/service/lookup?biblio=BIBLIO_STRING&atitle=ARTICLE_TITLE&firstAuthor=FIRST_AUTHOR_SURNAME` + +or: + + - `GET host:port/service/lookup?jtitle=JOURNAL_TITLE&volume=VOLUME&firstPage=FIRST_PAGE&firstAuthor=FIRST_AUTHOR_SURNAME&atitle=ARTICLE_TITLE` + +or: + + - `GET host:port/service/lookup?biblio=BIBLIO_STRING&atitle=ARTICLE_TITLE&firstAuthor=FIRST_AUTHOR_SURNAME&year=YYYY` + +It is also possible to combine a strong identifier with validation metadata. In this case, if the DOI appears conflicting with the provided metadata, no results will be returned, as a way to detect invalid DOI with post-validation: + + - `GET host:port/service/lookup?doi=DOI&atitle=ARTICLE_TITLE&firstAuthor=FIRST_AUTHOR_SURNAME` + +biblio-glutton will make the best use of all the parameters sent to retrieve in the fastest way a record and apply matching threashold to avoid false positive. It is advised to send __as much metadata as possible__ to try to optimize the DOI matching in term of speed and accuracy, and when possible a full raw bibliographical string. + +The more metadata are available in the query, the better. The original raw bibliographical string is also be exploited when availableto control the bibliographical record matching. + +For convenience, in case you are only interested by the Open Access URL for a bibliographical object, the open Access resolver API returns the OA PDF link (URL) only via an identifier: + +- return the best Open Access URL if available + - `GET host:port/service/oa?doi=DOI` return the best Open Accss PDF url for a given DOI + - `GET host:port/service/oa?pmid=PMID` return the best Open Accss PDF url for a given PMID + - `GET host:port/service/oa?pmc=PMC` return the best Open Accss PDF url for a given PMC ID + - `GET host:port/service/oa?pii=PII` return the best Open Accss PDF url for a given PII ID + +- return the best Open Access URL and ISTEX PDF URL if available + - `GET host:port/service/oa_istex?doi=DOI` return the best Open Accss PDF url and ISTEX PDF url for a given DOI + - `GET host:port/service/oa_istex?pmid=PMID` return the best Open Accss PDF url and ISTEX PDF url for a given PMID + - `GET host:port/service/oa_istex?pmc=PMC` return the best Open Accss PDF url and ISTEX PDF url for a given PMC ID + - `GET host:port/service/oa_istex?pii=PII` return the best Open Accss PDF url and ISTEX PDF url for a given PII ID + +## cURL examples + +To illustrate the usage of the API, we provide some cURL example queries: + +Bibliographical metadata lookup by DOI: + +```sh +curl http://localhost:8080/service/lookup?doi=10.1484/J.QUAESTIO.1.103624 +``` + +Matching with title and first authort lastname: + +```sh +curl "http://localhost:8080/service/lookup?atitle=Naturalizing+Intentionality+between+Philosophy+and+Brain+Science.+A+Survey+of+Methodological+and+Metaphysical+Issues&firstAuthor=Pecere" + +curl "http://localhost:8080/service/lookup?atitle=Naturalizing+Intentionality+between+Philosophy+and+Brain+Science&firstAuthor=Pecere" +``` + +Matching with raw bibliographical reference string: + +```sh +curl "http://localhost:8080/service/lookup?biblio=Baltz,+R.,+Domon,+C.,+Pillay,+D.T.N.+and+Steinmetz,+A.+(1992)+Characterization+of+a+pollen-specific+cDNA+from+sunflower+encoding+a+zinc+finger+protein.+Plant+J.+2:+713-721" +``` + +Bibliographical metadata lookup by PMID (note that only the number is expected): + +```sh +curl http://localhost:8080/service/lookup?pmid=1605817 +``` + +Bibliographical metadata lookup by PMC ID (note that the `PMC` prefix in the identifier is expected): + +```sh +curl http://localhost:8080/service/lookup?pmc=PMC1017419 +``` + +Bibliographical metadata lookup by PII ID: + +```sh +curl http://localhost:8080/service/lookup?pii= +``` + +Bibliographical metadata lookup by ISTEX ID: + +```sh +curl http://localhost:8080/service/lookup?istexid=E6CF7ECC9B002E3EA3EC590E7CC8DDBF38655723 +``` + +Open Access resolver by DOI: + +```sh +curl "http://localhost:8080/service/oa?doi=10.1038/nature12373" +``` + +Combination of Open Access resolver and ISTEX identifier by DOI: + +```sh +curl "http://localhost:8080/service/oa_istex?doi=10.1038/nature12373" +``` diff --git a/doc/Benchmarking.md b/doc/Benchmarking.md new file mode 100644 index 00000000..9f2daf50 --- /dev/null +++ b/doc/Benchmarking.md @@ -0,0 +1,98 @@ +## Matching accuracy + +Here is an evaluation of the bibliographical reference matching accuracy against CrossRef DOI, based on 17,015 bibliographical references. It includes a comparison with the CrossRef REST API used for the same task. + +### Dataset + +We created a dataset of [17,015 bibliographical reference/DOI pairs](doc/references-doi-matching.json.gz) with GROBID and the PMC 1943 sample (a set of 1943 PubMed Central articles from 1943 different journals with both PDF and XML NLM files available, see below). For the bibliographical references present in the NLM file with a DOI, we try to align the raw reference string extracted from the PDF by GROBID and the parsed XML present in the NLM file. Raw reference string are thus coming from the PDF, and we included additional metadata as extracted by GROBID from the PDF. + +Example of the two first of the 17.015 entries: + +```json +{"reference": "Classen M, Demling L. Endoskopishe shinkterotomie der papilla \nVateri und Stein extraction aus dem Duktus Choledochus [Ger-\nman]. Dtsch Med Wochenschr. 1974;99:496-7.", "doi": "10.1055/s-0028-1107790", "pmid": "4835515", "atitle": "Endoskopishe shinkterotomie der papilla Vateri und Stein extraction aus dem Duktus Choledochus [German]", "firstAuthor": "Classen", "jtitle": "Dtsch Med Wochenschr", "volume": "99", "firstPage": "496"}, +{"reference": "Kawai K, Akasaka Y, Murakami K. Endoscopic sphincterotomy \nof the ampulla of Vater. Gastrointest Endosc. 1974;20:148-51.", "doi": "10.1016/S0016-5107(74)73914-1", "pmid": "4825160", "atitle": "Endoscopic sphincterotomy of the ampulla of Vater", "firstAuthor": "Kawai", "jtitle": "Gastrointest Endosc", "volume": "20", "firstPage": "148"}, +``` + +The goal of Glutton matching is to identify the right DOI from raw metadata. We compare the results with the CrossRef REST API, using the `query.bibliographic` field for raw reference string matching, and author/title field queries for first author lastname (`query.author`) plus title matching (`query.title`). + +Limits: + +- The DOI present in the NLM files are not always reliable (e.g. DOI not valid anymore following some updates in CrossRef). A large amount of the matching errors are actually not due to the matching service, but to NLM reference DOI data quality. However, errors will be the same for all matching services, so it's still valid for comparing them, although for this reason the resulting accuracy is clearly lower than what it should be. + +- GROBID extraction is not always reliable, as well the alignment mechanism with NLM (based on soft match), and some raw reference string might not be complete or include unexpected extra material from the PDF. However, this can be view as part of the matching challenge in real world conditions! + +- the NLM references with DOI are usually simpler reference than in general: there are much fewer abbreviated references (without title nor authors) and references without titles as compared to general publications from non-medicine publishers. + + + +### How to run the evaluation + +You can use the DOI matching evaluation set (with 17,015 bibliographical reference/DOI pairs) from the indicated above address ([here](doc/references-doi-matching.json.gz)) or recreate this dataset with GROBID as follow: + +- [Install GROBID](https://grobid.readthedocs.io/en/latest/Install-Grobid/). + +- Download the [PMC 1943 sample](https://grobid.s3.amazonaws.com/PMC_sample_1943.zip) (around 1.5GB in size). + +- Create the evaluation dataset: + +> ./gradlew PrepareDOIMatching -Pp2t=ABS_PATH_TO_PMC/PMC_sample_1943 + +The evaluation dataset will be saved under `ABS_PATH_TO_PMC/PMC_sample_1943` with the name `references-doi-matching.json` + +- For launching an evaluation: + +1) Select the matching method (`crossref` or `glutton`) in the `grobid-home/config/grobid.yaml` file: + +```yaml +consolidation: + # define the bibliographical data consolidation service to be used, either "crossref" for CrossRef REST API or + # "glutton" for https://github.com/kermitt2/biblio-glutton + #service: "crossref" + service: "glutton" +``` + +2) If Glutton is setected, start the Glutton server as indicated above (we assume that it is running at `localhost:8080`). + +3) Launch from GROBID the evaluation, indicating the path where the evaluation dataset has been created - here we suppose that the file `references-doi-matching.json` has been saved under `ABS_PATH_TO_PMC/PMC_sample_1943`: + +> ./gradlew EvaluateDOIMatching -Pp2t=ABS_PATH_TO_PMC/PMC_sample_1943 + + +### Full raw bibliographical reference matching + +Runtime corresponds to a processing on a single machine running Glutton REST API server, ElasticSearch and GROBID evaluation with CRF for the citation model, with CrossRef index dated Sept. 2021. + +``` +======= GLUTTON API ======= +17015 bibliographical references processed in 1145.593 seconds, 0.06732841610343815 seconds per bibliographical reference. +Found 16699 DOI + +precision: 97.33 +recall: 95.52 +F1-score: 96.42 +``` + +With `BiLSTM-CRF` model instead of CRF for parsing the raw references prior to matching: + +``` +======= GLUTTON API ======= + +precision: 97.34 +recall: 95.83 +f-score: 96.58 +``` + +In the case of CrossRef API, we use as much as possible the concurrent queries (usually 50) allowed by the service with the GROBID CrossRef multithreaded client. + +``` +======= CROSSREF API ======= + +17015 bibliographical references processed in 3057.464 seconds, 0.1797 seconds per bibliographical reference. +Found 16502 DOI + +======= CROSSREF API ======= + +precision: 97.19 +recall: 94.26 +F1-score: 95.69 +``` diff --git a/doc/Build-Databases.md b/doc/Build-Databases.md new file mode 100644 index 00000000..342ca151 --- /dev/null +++ b/doc/Build-Databases.md @@ -0,0 +1,194 @@ +## Building the bibliographical data look-up and matching databases + +The loading of bibliographical metadata records and their indexing in the search cluster is done in one step. + +### Loading resources + +To set-up a functional biblio-glutton server, resources need to be loaded following these steps: + +1) Loading and indexing of a Crossref full metadata dump as embedded LMDB + +2) Loading and indexing got the coverage gap between the Crossref dump and the current day (updates are then realized automatically daily as the service is up and running) in the embedded LMDB + +3) (Optional) Loading and indexing of HAL archive metadata + +4) (Optional) Loading the DOI to PMID and PMC ID mapping (as embedded LMDB) + +5) (Optional) Loading the Open Access information from an Unpaywall datset snapshot as embedded LMDB + +6) (Very optional) Loading the ISTEX ID mapping as embedded LMDB + +It is possible to only load HAL archive metadata, skipping entirely CrossRef, but the service will be much more limited - so we suggest to always start with CrossRef. It is also possible to skip HAL archive resources. Step 4) is fast and we suggest to also always include it. + +### Resources + +For building the database and index used by service, you will need these resources: + +* CrossRef metadata dump, available at different places: + - strongly recommended: via the [Crossref Metadata APIs Plus](https://www.crossref.org/services/metadata-delivery/plus-service/) service for a current snapshot, or + - [public CrossRef dump](https://www.crossref.org/blog/2023-public-data-file-now-available-with-new-and-improved-retrieval-options/) available with Academic Torrents (2023-05-02 for the latest version), + - not recommended: Internet Archive, see https://github.com/greenelab/crossref and for instance the latest Internet Archive CrossRef [dump](https://archive.org/download/crossref_doi_dump_201909) (2019-09). + +We recommend to use a Crossref Metadata Plus snapshot in order to have a version of the Crossref metadata without large coverage gap. With the `Crossref-Plus-API-Token`, the following command for instance will download the full snapshot for the indicated year/month: + +```console +wget -c --header='Crossref-Plus-API-Token: Bearer __Crossref-Plus-API-Token-Here_' https://api.crossref.org/snapshots/monthly/YYYY/MM/all.json.tar.gz +``` + +Without Metadata Plus subscription, it's possible to use the Academic Torrents CrossRef dumps. For instance, with the Linux command line `aria2` and a high speed internet connection (e.g. 500Mb/s), the dump can be downloaded in a few minutes. However, the coverage gap will be more important. If the difference between the release date of the public dump and the current date is important (e.g. several months), updating the older snapshot via the normal CrossRef Web API will take an enormous amount of time. + +* DOI to PMID and PMC mapping: available at Europe PMC and regularly updated at ftp://ftp.ebi.ac.uk/pub/databases/pmc/DOI/PMID_PMCID_DOI.csv.gz, + +* optionally, but recommended, the Unpaywall dataset to get Open Access links aggregated with the bibliographical metadata, see [here](http://unpaywall.org/products/snapshot) to get the latest database snapshot. + +* optionally, usually not required, for getting ISTEX identifier informations, you need to build the ISTEX ID mapping, see below. + +The bibliographical matching service uses a combination of high performance embedded databases (LMDB), for fast look-up and cache, and Elasticsearch for blocking via text-based search. As Elasticsearch is much slower than embedded databases, it is used only when absolutely required. + +The databases and elasticsearch index must first be built from the resource files. The full service needs around 300 GB of space for building these index and it is necessary to use SSD for best performance. + +### Build the embedded LMDB databases + +Resource dumps will be compiled in high performance LMDB databases. The system can read compressed (`gzip` or `.xz`) or plain text files (`json`), so in practice you do not need to uncompress anything. + +#### Build the data loader + +```sh +./gradlew clean build +``` + +All the following commands need to be launched under the project root `biblio-glutton/`. The loading of the following database can be done in parallel. The default configuration file under `biblio-glutton/config/glutton.yml` will be used. For specifying a configuration file in another location add the following argument to a task: `-Pconfig="other/config/path/glutton.yml`, for example: + +```sh +./gradlew hal -Pconfig=new_config/glutton.yml +``` + +#### CrossRef metadata + +General command line pattern: + +```sh +./gradlew crossref -Pinput=/path/to/crossref/json/file -Pconfig=path/to/config/file/glutton.yml +``` + +Example with Crossref Metadata Plus snapshot (path to a `.tar.gz` file which archives many json files, usually called `all.json.tar.gz`): + +```sh +./gradlew crossref -Pinput=../tmp/crossref_metadata_plus.tar.gz +``` + +Example with CrossRef dump Academic Torrent file (path to a repository of `*.json.gz` files): + + +```sh +./gradlew crossref -Pinput=../tmp/crossref_public_data_file_2021_01 +``` + +Example with xz-compressed file (e.g. GreeneLab dump): + +```sh +./gradlew crossref -Pinput=crossref-works.2019-09-09.json.xz +``` + +**Note:** By default the `abstract`, the `reference` and the original `indexed` fields included in CrossRef records are ignored to save some disk space. The `reference` field is particularly large as it lists all the citations for almost half of the DOI records. You can change the list of fields to be filtered out in the config file under `biblio-glutton/config/glutton.yml`, by editing the lines: + +**Note:** Crossref records of type `component` are filtered out, because they do not correspond to a document, but to a part of document (figures, tables, etc.). + +``` +ignoreCrossRefFields: + - reference + - abstract + - indexed +``` + +Example loading the Crossref Metadata Plus snapshot of March 2022, loading time around 4 hours (dump files on SSD). + +``` +-- Counters -------------------------------------------------------------------- +crossrefLookup_rejectedRecords + count = 5472493 + +-- Meters ---------------------------------------------------------------------- +crossrefLookup + count = 126812507 + mean rate = 11368.21 events/second + 1-minute rate = 6520.71 events/second + 5-minute rate = 6403.19 events/second + 15-minute rate = 7240.26 events/second +``` + +On the above example, the 5,472,493 rejected records correspond to all the DOI entries of type "components" (part of document), which are filtered out. + +As a February 2024, we have for example 146,808,255 accepted crossref records and 8,015,190 rejected component records (last indexed date in dump file is 2024-02-02). + +#### CrossRef metadata gap coverage + +Once the main Crossref metadata snapshot has been loaded, the metadata and index will be updated daily automatically via the Crossref web API. However, there is always a gap of coverage between the last day covered by the used large snapshot image and the start of the daily update. + +Currently new Crossref Metadata Plus snapshot are available on the 5th of every month, covering all the metadata updates for until the previous month. It means that in the best case, there will be a coverage gap of 5 days to be recovered. More generally, users of Crossref Metadata Plus snapshot can load first a snapshot of the last month, then an additional snapshot mid-month update is available with the registered content that has changed in the first half of the month. This permits to minimize the coverage gap usually to a few days. + +Using the Crossref web API to cover the remaining gap (from the latest update day in the full snapshot to the current day) is done with the following command (still under root project `biblio-glutton/`): + +```sh +./gradlew crossref gap_crossref +``` + +Be sure to indicate in the configution file `glutton.yml` your polite usage email and/or crossref metadata plus token for using the Crossref web API. + +This command should thus be launched only one time after the loading of a full Crossref snapshot, it will resync the current metadata and index to the current day, and the daily update will then ensure everything remain in sync with the reference Crossref metadata as long the service is up and running. + +__Warning:__ If an older snapshot is used, like the CrossRef dump Academic Torrent file, the coverage gap is not a few days, but usually several months or more than one year (since Crossref has not updated the Academic Torrent dump in 2022). Using the Crossweb API to cover such a long gap will unfortunately take an enormous amount of time (more than a week) due to API usage rate limitations and is likely not a acceptable solution. In addition, the Crossref web API is not always reliable, which might cause further delays. + +#### PMID and PMC ID + +Launch the following command and go grab a coffee: + +```sh +./gradlew pmid +``` + +As of March 2022, the latest mapping covers 34,310,000 PMID, with 25,661,624 having a DOI (which means 8,648,376 PMID are not represented in Crossref and do not have a DOI). + +#### HAL archive + +Launch the following command and go grab a lunch: + +```sh +./gradlew hal +``` + +HAL archive contains around 3.5M records, with curated metadadata. + +#### OA via Unpaywall + +Pre-requisite is to download an Unpaywall snapshot. Public snapshots were available and updated from time to time, and it might still be possile to download a fresh up-to-date snapshot when subscribing to OpenAlex Premium. Supporting OpenAlex would be of course a clear future requirement for biblio-glutton. + +The following command will load the Open Access information to biblio-glutton to enrich the response metadata records: + +```sh +./gradlew unpaywall -Pinput=/path/to/unpaywall/json/file -Pconfig=path/to/config/file/glutton.yml +``` + +Example: + +```sh +./gradlew unpaywall --input unpaywall_snapshot_2022-03-09T083001.jsonl.gz +``` + +As of March 2022, the Unpaywall snapshot should provide at least one Open Access information to 30,618,764 Crossref entries. + +#### ISTEX + +Note that ISTEX mapping is only relevant for ISTEX full text resource users, so only public research institutions in France. So you can generally skip this step. + +```sh +./gradlew istex -Pinput=/path/to/istex/json/file -Pconfig=path/to/config/file/glutton.yml +``` + +Example: + +```sh +./gradlew istex -Pinput=istexIds.all.gz +``` + +**Note:** see the [FAQ](Frequently-asked-questions.md) on how to create this mapping file `istexIds.all.gz`. diff --git a/doc/Create-Index.md b/doc/Create-Index.md new file mode 100644 index 00000000..cdc78ee2 --- /dev/null +++ b/doc/Create-Index.md @@ -0,0 +1,67 @@ +## Build the Elasticsearch index + +### Architecture + +Below is an overview of the biblio-glutton architecture. The biblio-glutton server manages locally high performance LMDB databases for all metadata look-up tasks (several thousand requests per second with multiple threads). For the costly metadata matching tasks, an Elasticsearch cluster is used. For scaling this sort of queries, simply add more nodes in this elasticsearch cluster, keepping a single biblio-glutton server instance. + +![Glutton architecture](doc/glutton-architecture.png) + +### Create the index + +Elasticsearch `7.*` is required. `node.js` version 10 or more should work fine. + +A node.js utility under the subdirectory `indexing/` is used to build the Elasticsearch index. Indexing will take a few hours. For 116M crossref entries, the indexing takes around 6 hours (with SSD, 16GB RAM) and around 22GB of index space (per ES node if you plan to use several ES nodes). + +#### Install and configure + +You need first to install and start ElasticSearch, version `7.*`. Edit the project configuration file `biblio-glutton/config/glutton.yml` to indicate the host name and port of the Elasticsearch server. In this configuration file, it is possible to specify the name of the index ('default `crossref`) and the batch size of the bulk indexing. + +Install the node.js module: + +```sh +cd indexing/ +npm install +``` + +#### Build the index + +Usage information for indexing: + +```sh +cd biblio-glutton/indexing/ +node main -dump *PATH_TO_THE_CROSSREF_DUMP* index +``` + +Example with CrossRef dump Academic Torrent file (path to a repository of `*.json.gz` files): + +```sh +node main -dump ~/tmp/crossref_public_data_file_2021_01 index +``` + +Example with CrossRef Metadata Plus snapshot (path to a file `.tar.gz` which archives many json files): + +```sh +node main -dump ~/tmp/crossref_sample.tar.gz index +``` + +Example with GreeneLab/Internet Archive dump file: + +```sh +node main -dump ~/tmp/crossref-works.2019-09-09.json.xz index +``` + +Note that launching the above command will fully re-index the data, deleting existing index. The default name of the index is `crossref`, but this can be changed via the global config file `biblio-glutton/config/glutton.yml`. + +For getting health check information about the selected ElasticSearch cluster: + +```sh +node main health +``` + +Example loading the [public CrossRef dump](https://www.crossref.org/blog/new-public-data-file-120-million-metadata-records/) available with Academic Torrents (2021-01-07), index on SSD, dump files on hard drive, Ubuntu 18.04, 4 cores, 16MB RAM 6 years old machine: + +- 115,972,356 indexed records (perfect match with metadata db) +- around 6:30 for indexing (working on the same time on the computer), 4797 records/s +- 25.94GB index size + +Like for the metadata database, the Crossref objects of type `component` are skipped. diff --git a/doc/Frequently-asked-questions.md b/doc/Frequently-asked-questions.md new file mode 100644 index 00000000..34d0042f --- /dev/null +++ b/doc/Frequently-asked-questions.md @@ -0,0 +1,48 @@ +## Frequently asked questions + +### How to cite this work? + +If you want to cite this work, please refer to the present GitHub project, together with the [Software Heritage](https://www.softwareheritage.org/) project-level permanent identifier and do please indicate any author name. For example, with BibTeX: + +```bibtex +@misc{biblio-glutton, + title = {biblio-glutton}, + url = {https://github.com/kermitt2/biblio-glutton}, + publisher = {GitHub}, + year = {2018--2024}, + archivePrefix = {swh}, + eprint = {1:dir:a5a4585625424d7c7428654dbe863837aeda8fa7} +} +``` + +Note: `biblio-glutton` is spelled all lower case. + +### How can I add ISTEX identifier mapping? + +If you don't know what ISTEX is, you can safely skip this section. +For creating a dump of all ISTEX identifiers associated with existing identifiers (DOI, ark, PII), use the node.js script as follow: + +* install: + +```sh +cd scripts +npm install requestretry +``` + +* Generate the json dump: + +```sh +node dump-istexid-and-other-ids.js > istexIds.all +``` + +Be sure to have a good internet bandwidth for ensuring a high rate usage of the ISTEX REST API. + +You can then move the json dump (e.g. `istexIds.all`) to the Istex data path indicated in the file `config/glutton.yaml` (by default `data/istex/`). + +### ISTEX to PubMed mapping + +The mapping adds PudMed information (in particular MeSH classes) to ISTEX entries. +See the instructions [here](pubmed-glutton/Readme.md) + + + diff --git a/doc/Install.md b/doc/Install.md new file mode 100644 index 00000000..b4754489 --- /dev/null +++ b/doc/Install.md @@ -0,0 +1,80 @@ +## The bibliographical look-up and matching REST API + + +### Architecture + +Below is an overview of the biblio-glutton architecture. The biblio-glutton server manages locally high performance LMDB databases for all metadata look-up tasks (several thousand requests per second with multiple threads). For the costly metadata matching tasks, an Elasticsearch cluster is used. For scaling this sort of matching queries, simply add more nodes to this elasticsearch cluster, keepping a single biblio-glutton server instance. + +![Glutton architecture](doc/glutton-architecture.png) + +#### Runtime evaluation + +1) *Metadata Lookup* + +One glutton instance: 19,792,280 DOI lookup in 3156 seconds, ~ 6270 queries per second. + +2) *Bibliographical reference matching* + +*(to be completed with more nodes!)* + +Processing time for matching 17,015 raw bibliographical reference strings to DOI: + +| number of ES cluster nodes | comment | total runtime (second) | runtime per bib. ref. (second) | queries per second | +|----|---|---|---|---| +| 1 | glutton and Elasticsearch node share the same machine | 2625 | 0.154 | 6.5 | +| 1 | glutton and Elasticsearch node on two separate machines | 1990 | 0.117 | 8.5 | +| 2 | glutton and one of the Elasticsearch node sharing the same machine | 1347 | 0.079 | 12.6 | + +Machines have the same configuration Intel i7 4-cores, 8 threads, 16GB memory, SSD, on Ubuntu 16.04. + +The first step to deploy a biblio-glutton instance is to to create the bibliographical databases and search index, see the page [Build-Databases](Build-Databases.md) for detailed explanation. + +After installing all or a selection of bibliographical databases, the bibliographical REST API can be started. + +The following describes how to build and start the bibliographical service. + +### Build the service + +You need Java JDK 1.11 or more installed for building and running the tool. + +```sh +./gradlew clean build +``` + +### Start the server + +```sh +./gradlew server +``` + +The service will use the default project configuration located under `biblio-glutton/config/glutton.yml`. To select a configuration file in another location use the additional parameter `-Pconfig=/other/path/glutton.yml` as follow: + +```sh +./gradlew server -Pconfig=/other/path/glutton.yml +``` + +To check if it works, you can view a report of the data used by the service at `host:port/service/data`. For instance: + +> curl localhost:8080/service/data + +```json +{ + "Metadata Lookup Crossref size":"{crossref_Jsondoc=127887559}", + "ISTEX size":"{istex_doi2ids=21325261, istex_istex2ids=21401494, istex_pii2ids=6954799}", + "Metadata Matching Crossref size":"127970581", + "PMID lookup size":"{pmid_doi2ids=25661624, pmid_pmc2ids=7561377, pmid_pmid2ids=33761382}", + "DOI OA size":"{unpayWall_doiOAUrl=30635446}" +} +``` + +### Start optional additional GROBID service + +biblio-glutton takes advantage of GROBID for parsing raw bibliographical references. This permits faster and more accurate bibliographical record matching. To use GROBID service: + +* First download and install GROBID as indicated in the [documentation](https://grobid.readthedocs.io/en/latest/Install-Grobid/), normally as a docker image to take advantage of Deep Learning models for more accurate parsing of bibliographical references. + +* Start the service as documented [here](https://grobid.readthedocs.io/en/latest/Grobid-service/). You can change the `port` used by GROBID when strating the docker container, or by updating the service config file under `grobid/grobid-home/config/grobid.yaml`. + +* Update if necessary the host and port information of GROBID in the biblio-glutton config file under `biblio-glutton/config/glutton.yml` (parameter `grobidPath`). + +While GROBID is not required for running biblio-glutton, in particular if it is used only for bibliographical look-up, it is strongly recommended for performing bibliographical record matching. And vice-vera, configuration the biblio-glutton service for Grobid will provide high quality consolidation services to resolve the bibliographical references automatically extracted by Grobid. diff --git a/doc/Introduction.md b/doc/Introduction.md new file mode 100644 index 00000000..f1e0bd32 --- /dev/null +++ b/doc/Introduction.md @@ -0,0 +1,42 @@ +# biblio-glutton + +[![License](http://img.shields.io/:license-apache-blue.svg)](http://www.apache.org/licenses/LICENSE-2.0.html) +[![Demo cloud.science-miner.com/glutton](https://img.shields.io/website-up-down-green-red/https/cloud.science-miner.com/glutton/service/data.svg)](http://cloud.science-miner.com/glutton/service/data) +[![SWH](https://archive.softwareheritage.org/badge/origin/https://github.com/kermitt2/biblio-glutton/)](https://archive.softwareheritage.org/browse/origin/?origin_url=https://github.com/kermitt2/biblio-glutton) + +A framework dedicated to scientific and technical bibliographic information. It includes: + +- a bibliographical reference matching service: from an input such as a raw bibliographical reference and/or a combination of key metadata, the service will return the disambiguated bibliographical object with in particular its DOI and a set of metadata aggregated from CrossRef and other sources, +- a fast metadata look-up service: from a "strong" identifier such as DOI, PMID, etc. the service will return a set of metadata aggregated from CrossRef and other sources, +- various mapping between DOI, PMID, PMC, HAL ID, ISTEX ID and ark, integrated in the bibliographical service, +- Open Access resolver: Integration of Open Access links via the Unpaywall dataset from Impactstory, +- Gap and daily update for CrossRef resources (via the CrossRef REST API), so that your glutton data service stays always in sync with CrossRef, +- MeSH classes mapping for PubMed articles. + +biblio-glutton should be very handy if you need to run and scale a local full "Crossref" database and API, to aggregate Crossref, Pubmed, HAL and other common bibliographical records and to match a large amount of bibliographical records or raw bibliographical reference strings. + +The framework is designed both for speed (with several thousands request per second for look-up) and matching accuracy. It can be [scaled](https://github.com/kermitt2/biblio-glutton#architecture) horizontally as needed and can provide high availability. + +Benchmarking against the CrossRef REST API is presented [below](https://github.com/kermitt2/biblio-glutton#matching-accuracy). + +In the Glutton family, the following complementary tools are available for taking advantage of Open Access resources: + +* [biblio-glutton-extension](https://github.com/kermitt2/biblio-glutton-extension): A browser extension (Firefox & Chrome) for providing bibliographical services, like identifying dynamically Open Access resources on web pages and providing contextual citation services. + +* [biblio-glutton-harvester](https://github.com/kermitt2/biblio-glutton-harvester): A robust, fault tolerant, Python utility for harvesting efficiently (multi-threaded) a large Open Access collection of PDF (Unpaywall, PubMed Central), with the possibility to upload content on Amazon S3, + +Current stable version of biblio-glutton is `0.3`. Working version is `0.4-SNAPSHOT`. + +## Evaluation of bibliographical reference matching + +See [here](Benchmarking.md) on benchmarking the bibliographical reference matching. + +## Requirements + +biblio-glutton is a Java software requiring JDK 1.11 or more. + +You will need an ElasticSearch cluster to make possible bibliographical reference matching and resolution. The current version has been tested with Elasticsearch `8.*`. + +Optionally a Grobid service can be added to perform combined raw bibliographical reference string and reference resolution. Use the latest Grobid version. + +For storing the compiled metadata records, you will need a large amount of SSD space, at least 350 GB. SSD ensures fast and predictible runtime lookup based on memory paging. diff --git a/doc/License.md b/doc/License.md new file mode 100644 index 00000000..724b5d64 --- /dev/null +++ b/doc/License.md @@ -0,0 +1,11 @@ +## Main authors and contact + +- Patrice Lopez ([@kermitt2](https://github.com/kermitt2), patrice.lopez@science-miner.com) + +- Luca Foppiano ([@lfoppiano](https://github.com/lfoppiano)) + +## License + +Distributed under [Apache 2.0 license](http://www.apache.org/licenses/LICENSE-2.0). + +If you contribute to this project, you agree to share your contribution following this license. diff --git a/doc/hal-doi-missing.tsv b/doc/hal-doi-missing.tsv new file mode 100644 index 00000000..84fa5a80 --- /dev/null +++ b/doc/hal-doi-missing.tsv @@ -0,0 +1,9778 @@ +halId doi score +hal-282114 10.3934/dcdsb.2007.8.61 0.7134092064094498 +cea-00273504 10.1063/1.2814260 0.8 +cea-00273848 10.1002/pssa.200778869 0.700212262149029 +cea-00273568 10.1063/1.2837027 1.0 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a/doc/index.md b/doc/index.md new file mode 100644 index 00000000..02321e56 --- /dev/null +++ b/doc/index.md @@ -0,0 +1,22 @@ +

biblio-glutton Documentation

+ +

About

+ +* [Introduction](Introduction.md) + +* [License](License.md) + +

User manual

+ +* [Install](Install.md) + +* [Bibliographical Databases](Build-Databases.md) + +* [REST API](API.md) + +* [Frequently asked Questions)](Frequently-asked-questions.md) + +

Benchmarking

+ +* [Reference resolutions](Benchmarking.md) + diff --git a/docker-compose.yml b/docker-compose.yml deleted file mode 100644 index 8252c57f..00000000 --- a/docker-compose.yml +++ /dev/null @@ -1,24 +0,0 @@ -version: "2" -services: - biblio: - build: . - restart: always - ports: - - 8080:8080 - volumes: - - ./data:/app/data - grobid: - image: lfoppiano/grobid:0.5.5 - restart: always - ports: - - 8070:8070 - elasticsearch: - image: elasticsearch:6.7.1 - environment: - - "discovery.type=single-node" - volumes: - - elasticsearch-data:/usr/share/elasticsearch/data - restart: always -volumes: - elasticsearch-data: - driver: local diff --git a/lookup/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar similarity index 100% rename from lookup/gradle/wrapper/gradle-wrapper.jar rename to gradle/wrapper/gradle-wrapper.jar diff --git a/lookup/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties similarity index 93% rename from lookup/gradle/wrapper/gradle-wrapper.properties rename to gradle/wrapper/gradle-wrapper.properties index 242590d1..b0f68021 100644 --- a/lookup/gradle/wrapper/gradle-wrapper.properties +++ b/gradle/wrapper/gradle-wrapper.properties @@ -3,4 +3,4 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-7.1.1-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-7.2-bin.zip diff --git a/lookup/gradlew b/gradlew similarity index 100% rename from lookup/gradlew rename to gradlew diff --git a/lookup/gradlew.bat b/gradlew.bat similarity index 100% rename from lookup/gradlew.bat rename to gradlew.bat diff --git a/indexing/package.json b/indexing/package.json index 79843e41..90ccecb6 100644 --- a/indexing/package.json +++ b/indexing/package.json @@ -1,6 +1,6 @@ { "name": "indexing", - "version": "0.2", + "version": "0.3", "description": "indexing CrossRef DOI metadata", "main": "main.js", "scripts": { @@ -19,6 +19,7 @@ "lzma-native": "^6.0.1", "async": "^2.6.1", "js-yaml": "^4.1.0", - "tar-stream": "^2.2.0" + "tar-stream": "^2.2.0", + "requestretry": "^7.0.2" } } diff --git a/lookup/.circleci/config.yml b/lookup/.circleci/config.yml deleted file mode 100644 index d45b35fe..00000000 --- a/lookup/.circleci/config.yml +++ /dev/null @@ -1,42 +0,0 @@ -# Java Gradle CircleCI 2.0 configuration file -# -# Check https://circleci.com/docs/2.0/language-java/ for more details -# -version: 2 -jobs: - build: - docker: - # specify the version you desire here - - image: circleci/openjdk:8-jdk - - # Specify service dependencies here if necessary - # CircleCI maintains a library of pre-built images - # documented at https://circleci.com/docs/2.0/circleci-images/ - # - image: circleci/postgres:9.4 - - working_directory: ~/repo - - environment: - # Customize the JVM maximum heap limit - JVM_OPTS: -Xmx3200m - TERM: dumb - - steps: - - checkout - - # Download and cache dependencies - - restore_cache: - keys: - - v1-dependencies-{{ checksum "build.gradle" }} - # fallback to using the latest cache if no exact match is found - - v1-dependencies- - - - run: gradle dependencies - - - save_cache: - paths: - - ~/.gradle - key: v1-dependencies-{{ checksum "build.gradle" }} - - # run tests! - - run: gradle test \ No newline at end of file diff --git a/lookup/build.gradle b/lookup/build.gradle deleted file mode 100644 index 36638beb..00000000 --- a/lookup/build.gradle +++ /dev/null @@ -1,124 +0,0 @@ -buildscript { - repositories { - mavenLocal() - mavenCentral() - maven { - url 'https://plugins.gradle.org/m2/' - } - //jcenter() - } - - dependencies { - classpath 'gradle.plugin.org.kt3k.gradle.plugin:coveralls-gradle-plugin:2.12.0' - classpath "gradle.plugin.com.github.jengelman.gradle.plugins:shadow:7.0.0" - //classpath 'com.github.jengelman.gradle.plugins:shadow:6.1.0' - } -} - -apply plugin: 'application' -apply plugin: 'java' -apply plugin: 'java-library' -//apply plugin: 'maven' -apply plugin: 'maven-publish' -apply plugin: 'com.github.johnrengelman.shadow' - -group 'com.scienceminer.glutton' -version '0.2' - -sourceCompatibility = 1.8 - -// The main class of the application -mainClassName = 'com.scienceminer.lookup.web.LookupServiceApplication' -tasks.run.workingDir = rootProject.rootDir - -repositories { - mavenLocal() - mavenCentral() -} - -sourceSets.main.resources { - srcDirs = ["src/main/resources"]; -} - -processResources { - filesMatching('../config/glutton.yml') { - filter { - it.replace('project.version', project.property('version_placeholder')) - } - } -} - -task install(dependsOn: installShadowDist) - -dependencies { - testImplementation group: 'junit', name: 'junit', version: '4.12' - testImplementation "org.hamcrest:hamcrest-all:1.3" - testImplementation "org.easymock:easymock:3.5" - - implementation "com.google.code.gson:gson:2.8.1" - - implementation "io.dropwizard:dropwizard-core:1.3.29" - implementation "io.dropwizard:dropwizard-assets:1.3.29" - implementation "com.hubspot.dropwizard:dropwizard-guicier:1.3.5.2" - implementation "io.dropwizard:dropwizard-testing:1.3.29" - implementation "io.dropwizard:dropwizard-forms:1.3.29" - implementation "io.dropwizard:dropwizard-client:1.3.29" - implementation "io.dropwizard:dropwizard-auth:1.3.29" - implementation "io.dropwizard.metrics:metrics-core:4.0.5" - implementation "io.dropwizard.metrics:metrics-servlets:4.0.5" - implementation group: 'org.apache.logging.log4j', name: 'log4j-to-slf4j', version: '2.16.0' - - implementation "com.rockymadden.stringmetric:stringmetric-core_2.10:0.27.3" - - //Parsing XML/Json - implementation group: 'org.codehaus.woodstox', name: 'stax2-api', version: '4.0.0' - implementation group: 'org.codehaus.woodstox', name: 'woodstox-core-asl', version: '4.4.1' - - implementation 'org.lmdbjava:lmdbjava:0.8.1' - implementation 'de.ruedigermoeller:fst:2.56' - implementation 'org.xerial.snappy:snappy-java:1.1.7.2' - - implementation 'org.elasticsearch.client:elasticsearch-rest-high-level-client:7.14.1' - -// compile group: 'org.apache.httpcomponents', name: 'httpmime', version: '4.5.3' - implementation 'org.apache.commons:commons-collections4:4.1' - implementation 'commons-io:commons-io:2.6' - implementation group: 'org.apache.commons', name: 'commons-compress', version: '1.20' - - implementation group: 'org.tukaani', name: 'xz', version: '1.8' - - implementation "com.fasterxml.jackson.core:jackson-core:2.9.10" - implementation "com.fasterxml.jackson.core:jackson-databind:2.9.10" - implementation "com.fasterxml.jackson.module:jackson-module-afterburner:2.9.10" -} - -distributions { - shadow { - /*contents { - from(new File(rootProject.rootDir, "data/config")) { - into "data/config" - } - }*/ - } -} - -shadowJar { -// archiveClassifier = 'onejar' - classifier = 'onejar' - mergeServiceFiles() - zip64 true - manifest { - attributes 'Main-Class': mainClassName - } - duplicatesStrategy = DuplicatesStrategy.EXCLUDE -} - -distTar.enabled = false -distZip.enabled = false -shadowDistTar.enabled = false - -artifacts { - archives shadowJar -// archives shadowDistZip -// archives shadowDistTar -} \ No newline at end of file diff --git a/lookup/src/main/java/com/scienceminer/lookup/command/LoadPMIDCommand.java b/lookup/src/main/java/com/scienceminer/lookup/command/LoadPMIDCommand.java deleted file mode 100644 index 70b09c69..00000000 --- a/lookup/src/main/java/com/scienceminer/lookup/command/LoadPMIDCommand.java +++ /dev/null @@ -1,75 +0,0 @@ -package com.scienceminer.lookup.command; - -import com.codahale.metrics.ConsoleReporter; -import com.codahale.metrics.MetricRegistry; -import com.scienceminer.lookup.configuration.LookupConfiguration; -import com.scienceminer.lookup.reader.PmidReader; -import com.scienceminer.lookup.storage.StorageEnvFactory; -import com.scienceminer.lookup.storage.lookup.PMIdsLookup; -import io.dropwizard.cli.ConfiguredCommand; -import io.dropwizard.setup.Bootstrap; -import net.sourceforge.argparse4j.inf.Namespace; -import net.sourceforge.argparse4j.inf.Subparser; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.io.InputStream; -import java.nio.file.Files; -import java.nio.file.Paths; -import java.util.concurrent.TimeUnit; -import java.util.zip.GZIPInputStream; - -/** - * Command for loading data for the PMID/PMCID/DOI mappings - */ -public class LoadPMIDCommand extends ConfiguredCommand { - private static final Logger LOGGER = LoggerFactory.getLogger(LoadPMIDCommand.class); - - public static final String PMID_SOURCE = "pmidSource"; - - public LoadPMIDCommand() { - super("pmid", "Prepare the pmid database lookup"); - } - - @Override - public void configure(Subparser subparser) { - super.configure(subparser); - - subparser.addArgument("--input") - .dest(PMID_SOURCE) - .type(String.class) - .required(true) - .help("The path to the source file for pmid mapping"); - } - - @Override - protected void run(Bootstrap bootstrap, Namespace namespace, LookupConfiguration configuration) throws Exception { - - final MetricRegistry metrics = new MetricRegistry(); - - ConsoleReporter reporter = ConsoleReporter.forRegistry(metrics) - .convertRatesTo(TimeUnit.SECONDS) - .convertDurationsTo(TimeUnit.MILLISECONDS) - .build(); - - reporter.start(15, TimeUnit.SECONDS); - - final String pmidMappingPath = namespace.get(PMID_SOURCE); - LOGGER.info("Preparing the system. Loading data for PMID from " + pmidMappingPath); - - StorageEnvFactory storageEnvFactory = new StorageEnvFactory(configuration); - - long start = System.nanoTime(); - - PMIdsLookup pmidLookup = new PMIdsLookup(storageEnvFactory); - InputStream inputStreampmidMapping = Files.newInputStream(Paths.get(pmidMappingPath)); - if (pmidMappingPath.endsWith(".gz")) { - inputStreampmidMapping = new GZIPInputStream(inputStreampmidMapping); - } - pmidLookup.loadFromFile(inputStreampmidMapping, new PmidReader(), metrics.meter("pmidLookup")); - LOGGER.info("Istex lookup loaded " + pmidLookup.getSize() + " records. "); - - LOGGER.info("Finished in " + - TimeUnit.SECONDS.convert(System.nanoTime() - start, TimeUnit.NANOSECONDS) + " s"); - } -} diff --git a/lookup/src/main/java/com/scienceminer/lookup/web/module/LookupServiceModule.java b/lookup/src/main/java/com/scienceminer/lookup/web/module/LookupServiceModule.java deleted file mode 100644 index 89cd1c07..00000000 --- a/lookup/src/main/java/com/scienceminer/lookup/web/module/LookupServiceModule.java +++ /dev/null @@ -1,53 +0,0 @@ -package com.scienceminer.lookup.web.module; - -import com.codahale.metrics.MetricRegistry; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.inject.Binder; -import com.google.inject.Provides; -import com.hubspot.dropwizard.guicier.DropwizardAwareModule; -import com.scienceminer.lookup.configuration.LookupConfiguration; -import com.scienceminer.lookup.storage.StorageEnvFactory; -import com.scienceminer.lookup.web.resource.DataController; -import com.scienceminer.lookup.web.resource.LookupController; -import com.scienceminer.lookup.web.resource.OAController; -import com.scienceminer.lookup.web.resource.OaIstexController; - -import javax.ws.rs.client.Client; -import javax.ws.rs.client.ClientBuilder; - -public class LookupServiceModule extends DropwizardAwareModule { - - - @Override - public void configure(Binder binder) { - //REST - binder.bind(LookupController.class); - binder.bind(DataController.class); - binder.bind(OAController.class); - binder.bind(OaIstexController.class); - - //LMDB - binder.bind(StorageEnvFactory.class); - } - - @Provides - protected ObjectMapper getObjectMapper() { - return getEnvironment().getObjectMapper(); - } - - @Provides - protected MetricRegistry provideMetricRegistry() { - return getMetricRegistry(); - } - - //for unit tests - protected MetricRegistry getMetricRegistry() { - return getEnvironment().metrics(); - } - - @Provides - Client provideClient() { - return ClientBuilder.newClient(); - } - -} diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 00000000..4f7a6851 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,22 @@ +site_name: biblio-glutton Documentation +repo_url: https://github.com/kermitt2/biblio-glutton/ +repo_name: GitHub +theme: readthedocs +site_description: Documentation for biblio-glutton +docs_dir: doc +plugins: + - search +theme: + name: readthedocs +nav: + - Home: 'index.md' + - About: + - 'Introduction': 'Introduction.md' + - 'Licence': 'License.md' + - User manual: + - 'Install': 'Install.md' + - 'Databases': 'Build-Databases' + - 'REST API': 'API.md' + - 'Frequently asked Questions': 'Frequently-asked-questions.md' + - Benchmarking: + - 'Matching': 'Benchmarking.md' diff --git a/lookup/notes.md b/notes.md similarity index 100% rename from lookup/notes.md rename to notes.md diff --git a/pubmed-glutton/Readme.md b/pubmed-glutton/Readme.md index e14e19c4..544e1644 100644 --- a/pubmed-glutton/Readme.md +++ b/pubmed-glutton/Readme.md @@ -30,6 +30,12 @@ Convert the downloaded MEDLINE/PubMed metadata XML files into a dump in the Cros > java -Xmx1024m -jar build/libs/com.scienceminer.glutton-0.2-SNAPSHOT-onejar.jar -exe pubmedDump -tdata /path/to/medline/ -out /path/to/new/dump/ ``` +After a while (Medline/PubMed 2023): + +``` +total PMID entries parsed, converted and written: 38808476 +``` + ### MEDLINE/PubMed indexing Be sure to have the full Medline data downloaded (see https://www.nlm.nih.gov/databases/download/pubmed_medline.html), and indicate in the config file `biblio-glutton/config/glutton.yml` the path to the repository containing the Medline bulk download, e.g. diff --git a/pubmed-glutton/build.gradle b/pubmed-glutton/build.gradle index 96931090..eb4ac2c9 100644 --- a/pubmed-glutton/build.gradle +++ b/pubmed-glutton/build.gradle @@ -23,7 +23,7 @@ apply plugin: 'maven-publish' apply plugin: 'com.github.johnrengelman.shadow' group 'com.scienceminer.glutton' -version '0.2' +version '0.3-SNAPSHOT' sourceCompatibility = 1.8 @@ -38,7 +38,7 @@ repositories { } wrapper { - gradleVersion "7.1.1" + gradleVersion "7.2" } // The main class of the application diff --git a/pubmed-glutton/gradle/wrapper/gradle-wrapper.properties b/pubmed-glutton/gradle/wrapper/gradle-wrapper.properties index 54165851..8ad73a75 100644 --- a/pubmed-glutton/gradle/wrapper/gradle-wrapper.properties +++ b/pubmed-glutton/gradle/wrapper/gradle-wrapper.properties @@ -2,4 +2,4 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-7.1.1-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-7.2-bin.zip diff --git a/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/Biblio.java b/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/Biblio.java index b6e76039..003e8548 100644 --- a/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/Biblio.java +++ b/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/Biblio.java @@ -185,6 +185,9 @@ public String getDoi() { } public void setDoi(String doi) { + doi = doi.replace("https://doi.org/", ""); + doi = doi.replace("http://doi.org/", ""); + doi = doi.replace("doi.org/", ""); setPublisherAttribute("doi", StringUtils.trim(doi)); } @@ -249,6 +252,56 @@ public String getPubmedId() { } public void setPubmedId(String pubmedId) { + // string might be empty + if (pubmedId != null && pubmedId.trim().length() == 0) + return; + + // case ID given as "PMID: 34189422" + if (pubmedId != null && (pubmedId.startsWith("PMID:") || pubmedId.startsWith("pmid:"))) { + pubmedId = pubmedId.replace("PMID:", ""); + pubmedId = pubmedId.replace("pmid:", ""); + } + + // case "pubmed.ncbi.nlm.nih.gov/34133859/" or "https://pubmed.ncbi.nlm.nih.gov/25886103/" + // or "http://www.ncbi.nlm.nih.gov/pmc/articles/pmc7813351/" or "www.ncbi.nlm.nih.gov/pubmed/" + if (pubmedId != null && (pubmedId.startsWith("pubmed.ncbi.nlm.nih.gov/") || + pubmedId.startsWith("https://pubmed.ncbi.nlm.nih.gov/"))) { + pubmedId = pubmedId.replace("https://pubmed.ncbi.nlm.nih.gov/", ""); + pubmedId = pubmedId.replace("pubmed.ncbi.nlm.nih.gov/", ""); + pubmedId = pubmedId.replace("www.ncbi.nlm.nih.gov/pubmed/", ""); + } + if (pubmedId != null && (pubmedId.startsWith("http://www.ncbi.nlm.nih.gov/pmc/articles/pmc") || + pubmedId.startsWith("https://www.ncbi.nlm.nih.gov/pmc/articles/pmc"))) { + pubmedId = pubmedId.replace("http://www.ncbi.nlm.nih.gov/pmc/articles/", ""); + pubmedId = pubmedId.replace("https://www.ncbi.nlm.nih.gov/pmc/articles/", ""); + } + + //case ID ends with "/", which is quite common + if (pubmedId != null && pubmedId.endsWith("/")) { + pubmedId = pubmedId.replace("/", ""); + } + + // sometimes it's a DOI + if (pubmedId != null && (pubmedId.startsWith("10.") || pubmedId.startsWith("doi.org/10.")) && pubmedId.indexOf("/") != -1) { + if (getDoi() == null) { + setDoi(pubmedId); + return; + } + } + + // sometimes it's a PMC ID "PMC2655142" + if (pubmedId != null && (pubmedId.startsWith("PMC") || pubmedId.startsWith("pmc"))) { + if (getPmc() == null) { + setPmc(pubmedId); + return; + } + } + + // other weird quite common case "22642955DOI" + if (pubmedId != null && pubmedId.endsWith("DOI")) { + pubmedId = pubmedId.replace("DOI", ""); + } + setPublisherAttribute("pubmedid", StringUtils.trim(pubmedId)); } diff --git a/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/Repository.java b/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/Repository.java deleted file mode 100644 index fcff7f7e..00000000 --- a/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/Repository.java +++ /dev/null @@ -1,108 +0,0 @@ -package com.scienceminer.glutton.data; - -import java.io.Serializable; - -public class Repository implements Serializable { - private int id = -1; - private String name = null; - private int openDoarId = -1; - private int coreId = -1; - private String uri = null; - private String countryCode = null; - private Double latitude = null; - private Double longitude = null; - - public int getId() { - return id; - } - - public void setId(int id) { - this.id = id; - } - - public String getName() { - return name; - } - - public void setName(String name) { - this.name = name; - } - - public int getOpenDoarId() { - return openDoarId; - } - - public void setOpenDoarId(int id) { - this.openDoarId = id; - } - - public int getCoreId() { - return coreId; - } - - public void setCoreId(int id) { - this.coreId = id; - } - - public String getUri() { - return uri; - } - - public void setUri(String uri) { - this.uri = uri; - } - - public String getCountryCode() { - return countryCode; - } - - public void setCountryCode(String code) { - this.countryCode = code; - } - - public Double getLatitude() { - return latitude; - } - - public void setLatitude(Double latitude) { - this.latitude = latitude; - } - - public Double getLongitude() { - return longitude; - } - - public void setLongitude(Double longitude) { - this.longitude = longitude; - } - - public String toJson() { - StringBuilder json = new StringBuilder(); - json.append("{"); - json.append("\"id\":"+id); - - if (coreId != -1) { - json.append(", \"coreId\":"+coreId); - } - if (openDoarId != -1) { - json.append(", \"openDoarId\":"+openDoarId); - } - if (name != null) { - json.append(", \"name\":\""+name+"\""); - } - if (uri != null) { - json.append(", \"uri\":\""+uri+"\""); - } - if (countryCode != null) { - json.append(", \"countryCode\":\""+countryCode+"\""); - } - if (latitude != null) { - json.append(", \"latitude\":"+latitude); - } - if (longitude != null) { - json.append(", \"longitude\":"+longitude); - } - json.append("}"); - return json.toString(); - } -} \ No newline at end of file diff --git a/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/db/KBDatabase.java b/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/db/KBDatabase.java deleted file mode 100644 index 518d192c..00000000 --- a/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/db/KBDatabase.java +++ /dev/null @@ -1,253 +0,0 @@ -package com.scienceminer.glutton.data.db; - -import com.scienceminer.glutton.data.db.KBEnvironment.EnvironmentType; - -import java.io.BufferedReader; -import java.io.ByteArrayInputStream; -import java.io.File; -import java.io.FileInputStream; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.io.InputStreamReader; -import java.io.UnsupportedEncodingException; -import java.util.concurrent.*; - -import javax.xml.stream.XMLStreamException; - -import org.apache.log4j.Logger; - -import java.util.concurrent.*; - -import org.fusesource.lmdbjni.*; -import static org.fusesource.lmdbjni.Constants.*; - -/** - * - * @param the key type - * @param the value type - */ -public abstract class KBDatabase { - - /** - * Database types - */ - public enum DatabaseType { - /** - * Associates a strong identifier (DOI, PMID, PII, PMC, ISTEX) with a biblio id or another id. - */ - identifier, - - /** - * Associates a biblio ID to a bibliographical record - */ - biblio, - - /** - * Associates a repository ID to a repository record - */ - repository, - - /** - * Associates a strong identifier (DOI, PMID, PII) to a resource URL - */ - resource, - - /** - * Associates integer {@link KBEnvironment.StatisticName#ordinal()} with the value relevant to this statistic. - */ - statistics - } - - protected Env environment = null; - protected Database db = null; - protected String envFilePath = null; - protected boolean isLoaded = false; - - protected String name = null; - protected DatabaseType type = null; - protected KBEnvironment env = null; - - protected boolean isCached = false; - protected ConcurrentMap cache = null; - - /** - * Creates or connects to a database, whose name will match the given {@link KBDatabase.DatabaseType} - * - * @param env the KBEnvironment surrounding this database - * @param type the type of database - */ - public KBDatabase(KBEnvironment env, DatabaseType type) { - this.env = env; - this.type = type; - this.name = type.name(); - - /*if (env.getType() == KBEnvironment.EnvironmentType.staging) - this.envFilePath = env.getConfiguration().pubmed.getDbDirectory() + "/staging/" + type.toString(); - else if (env.getType() == KBEnvironment.EnvironmentType.service) - this.envFilePath = env.getConfiguration().pubmed.getDbDirectory() + "/service/" + type.toString(); - else */ - this.envFilePath = env.getConfiguration().pubmed.getDbDirectory() + "/" + type.toString(); - //System.out.println("db path: " + this.envFilePath); - - this.environment = new Env(); - this.environment.setMapSize(100 * 1024 * 1024, ByteUnit.KIBIBYTES); - File thePath = new File(this.envFilePath); - if (!thePath.exists()) { - thePath.mkdirs(); - isLoaded = false; - } else { - // we assume that if the DB files exist, it has been already loaded - isLoaded = true; - } - System.out.println(type.toString() + " / isLoaded: " + isLoaded); - this.environment.open(envFilePath, Constants.NOTLS); - db = this.environment.openDatabase(); - } - - /** - * Creates or connects to a database with the given name. - * - * @param env the KBEnvironment surrounding this database - * @param type the type of database - * @param name the name of the database - */ - public KBDatabase(KBEnvironment env, DatabaseType type, String name) { - this.env = env; - this.type = type; - this.name = name; - - /*if (env.getType() == KBEnvironment.EnvironmentType.staging) - this.envFilePath = env.getConfiguration().pubmed.getDbDirectory() + "/staging/" + name; - else if (env.getType() == KBEnvironment.EnvironmentType.service) - this.envFilePath = env.getConfiguration().pubmed.getDbDirectory() + "/service/" + name; - else */ - this.envFilePath = env.getConfiguration().pubmed.getDbDirectory() + "/" + name; - - this.environment = new Env(); - this.environment.setMapSize(200 * 1024 * 1024, ByteUnit.KIBIBYTES); - File thePath = new File(this.envFilePath); - if (!thePath.exists()) { - thePath.mkdirs(); - isLoaded = false; - } else { - // we assume that if the DB files exist, it has been already loaded - isLoaded = true; - } - System.out.println(name + " / isLoaded: " + isLoaded); - this.environment.open(envFilePath); - db = this.environment.openDatabase(); - } - - public Database getDatabase() { - return db; - } - - public Env getEnvironment() { - return environment; - } - - /** - * Returns the type of this database - * - * @return the type of this database - */ - public DatabaseType getType() { - return type; - } - - /** - * Returns the name of this database - * - * @return the name of this database - */ - public String getName() { - return name; - } - - /** - * Returns the number of entries in the database - * - * @return the number of entries in the database - */ - public long getDatabaseSize() { - Stat statistics = db.stat(); - return statistics.ms_entries; - } - - /** - * Retrieves the value associated with the given key, either from the persistent database, or from memory if - * the database has been cached. This will return null if the key is not found, or has been excluded from the cache. - * - * @param key the key to search for - * @return the value associated with the given key, or null if none exists. - */ - //public abstract V retrieve(K key); - public V retrieve(K key) { - byte[] cachedData = null; - V record = null; - try (Transaction tx = environment.createReadTransaction()) { - //cachedData = db.get(tx, BigInteger.valueOf(key).toByteArray()); - cachedData = db.get(tx, KBEnvironment.serialize(key)); - if (cachedData != null) { - record = (V)KBEnvironment.deserialize(cachedData); - } - } catch(Exception e) { - e.printStackTrace(); - } - return record; - } - - /** - * Decides whether an entry should be indexed or not. - * - * @param e the key,value pair to be filtered - * @param conf a configuration containing options for controling the indexing - * @return the value that should be cached along with the given key, or null if it should be excluded - */ - public V filterEntry(KBEntry e) { - // default, no filter - return e.getValue(); - } - - /** - * Add a single entry in the database. - */ - /*protected void add(KBEntry entry) { - try (Transaction tx = environment.createWriteTransaction()) { - db.put(tx, KBEnvironment.serialize(entry.getKey()), KBEnvironment.serialize(entry.getValue())); - tx.commit(); - } catch(Exception e) { - e.printStackTrace(); - } - }*/ - - /** - * Builds the persistent database from a file. - * - * @param dataFile the file (a JSON or CSV file) containing data to be loaded - * @param overwrite true if the existing database should be overwritten, otherwise false - * @throws IOException if there is a problem reading or deserialising the given data file. - */ - public abstract void loadFromFile(File dataFile, boolean overwrite) throws IOException; - - /** - * @return an iterator for the entries in this database, in ascending key order. - */ - public KBIterator getIterator() { - return new KBIterator(this); - } - - /** - * Closes the underlying database - */ - public void close() { - if (db != null) - db.close(); - if (environment != null) - environment.close(); - } - - public boolean isLoaded() { - return isLoaded; - } -} diff --git a/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/db/KBEntry.java b/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/db/KBEntry.java deleted file mode 100644 index e09b6f64..00000000 --- a/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/db/KBEntry.java +++ /dev/null @@ -1,25 +0,0 @@ -package com.scienceminer.glutton.data.db; - -/** - * An entry (key,value pair) to be used for an LMDB database implementation - * - * @param the key type - * @param the value type - */ -public class KBEntry { - private K key = null; - private V value = null; - - public KBEntry(K k, V v) { - this.key = k; - this.value = v; - } - - public K getKey() { - return key; - } - - public V getValue() { - return value; - } -} \ No newline at end of file diff --git a/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/db/KBEnvironment.java b/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/db/KBEnvironment.java deleted file mode 100644 index 95aaa05e..00000000 --- a/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/db/KBEnvironment.java +++ /dev/null @@ -1,124 +0,0 @@ -package com.scienceminer.glutton.data.db; - -import com.scienceminer.glutton.utilities.*; - -import java.io.*; -import java.util.Map; -import java.util.List; -import java.util.HashMap; -import java.util.concurrent.*; -import java.math.BigInteger; - -import org.nustaq.serialization.*; -import javax.xml.stream.XMLStreamException; - -import org.apache.log4j.Logger; - -import com.scienceminer.glutton.data.db.KBDatabase.DatabaseType; - -import org.fusesource.lmdbjni.*; -import static org.fusesource.lmdbjni.Constants.*; - -/** - * An abstract KB for storing aggregated bibliographical data which is concretely - * stored as a set of LMDB databases. - * - */ -public abstract class KBEnvironment { - - // this is the singleton FST configuration for all serialization operations with the KB - protected static FSTConfiguration singletonConf = FSTConfiguration.createDefaultConfiguration(); - //protected static FSTConfiguration singletonConf = FSTConfiguration.createUnsafeBinaryConfiguration(); - - // Glutton configuration for the KB instance - protected GluttonConfig conf = null; - - // database registry for the environment - protected Map> databasesByType = null; - - protected EnvironmentType type = null; - - public enum EnvironmentType { - /* working environment for data aggregation */ - staging, - - /* finalized environment for service */ - service - } - - public EnvironmentType getType() { - return type; - } - - public static FSTConfiguration getFSTConfigurationInstance() { - return singletonConf; - } - - /** - * Serialization in the KBEnvironment with FST - */ - public static byte[] serialize(Object obj) throws IOException { - byte data[] = getFSTConfigurationInstance().asByteArray(obj); - return data; - } - - /** - * Deserialization in the KBEnvironment with FST. The returned Object needs to be casted - * in the expected actual object. - */ - public static Object deserialize(byte[] data) throws IOException, ClassNotFoundException { - return getFSTConfigurationInstance().asObject(data); - } - - /** - * Constructor - */ - public KBEnvironment(GluttonConfig conf) { - this.conf = conf; - // register classes to be serialized - //singletonConf.registerClass(DbPage.class, DbIntList.class, DbTranslations.class); - //initDatabases(); - } - - /** - * Returns the configuration of this environment - */ - public GluttonConfig getConfiguration() { - return conf; - } - - protected abstract void initDatabases(); - - protected List getDatabase(DatabaseType dbType) { - return databasesByType.get(dbType); - } - - public void close() { - for (List dbs : this.databasesByType.values()) { - for(KBDatabase db : dbs) - db.close(); - } - } - - /** - * Builds a KBEnvironment, by loading all of the data files stored in the given directory into persistent databases. - * - * It will not create the environment or any databases unless all of the required files are found in the given directory. - * - * It will not delete any existing databases, and will only overwrite them if explicitly specified (even if they are incomplete). - * - * @param conf a configuration specifying where the databases are to be stored, etc. - * @param overwrite true if existing databases should be overwritten, otherwise false - * @throws IOException if any of the required files cannot be read - */ - public abstract void buildEnvironment(boolean overwrite) throws IOException; - - protected static File getDataFile(File dataDirectory, String fileName) throws IOException { - File file = new File(dataDirectory + File.separator + fileName); - if (!file.canRead()) { - Logger.getLogger(KBEnvironment.class).info(file + " is not readable"); - return null; - } else - return file; - } -} diff --git a/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/db/KBIterator.java b/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/db/KBIterator.java deleted file mode 100644 index a93ae62b..00000000 --- a/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/db/KBIterator.java +++ /dev/null @@ -1,50 +0,0 @@ -package com.scienceminer.glutton.data.db; - -import java.util.Iterator; -import java.util.NoSuchElementException; -import java.io.Serializable; - -import org.apache.log4j.Logger; - -import org.fusesource.lmdbjni.*; -import static org.fusesource.lmdbjni.Constants.*; - -/** - * Iterator for entries of an LMDB database. - * - */ -public class KBIterator { - - private KBDatabase database; - private Database db = null; - private EntryIterator iterator = null; - private Env environment = null; - private Transaction tx = null; - - public KBIterator(KBDatabase database) { - this.database = database; - environment = database.getEnvironment(); - db = database.getDatabase(); - tx = environment.createReadTransaction(); - iterator = db.iterate(tx); - } - - public boolean hasNext() { - return iterator.hasNext(); - } - - public void remove() { - throw new UnsupportedOperationException(); - } - - public void close() { - if (iterator != null) - iterator.close(); - if (tx != null) - tx.close(); - } - - public Entry next() { - return iterator.next(); - } -} diff --git a/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/db/KBStagingEnvironment.java b/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/db/KBStagingEnvironment.java deleted file mode 100644 index 38fbc355..00000000 --- a/pubmed-glutton/src/main/java/com/scienceminer/glutton/data/db/KBStagingEnvironment.java +++ /dev/null @@ -1,1403 +0,0 @@ -package com.scienceminer.glutton.data.db; - -import com.scienceminer.glutton.utilities.*; - -import java.io.*; -import java.util.zip.GZIPInputStream; -import java.util.Map; -import java.util.List; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.concurrent.*; -import java.math.BigInteger; - -import org.nustaq.serialization.*; - -import org.apache.log4j.Logger; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.io.IOUtils; - -import com.scienceminer.glutton.data.db.KBDatabase.DatabaseType; -import com.scienceminer.glutton.data.db.KBEnvironment.EnvironmentType; -import com.scienceminer.glutton.data.*; -import com.scienceminer.glutton.utilities.sax.MedlineSaxHandler; -import com.scienceminer.glutton.utilities.sax.DumbEntityResolver; - -import com.fasterxml.jackson.core.*; -import com.fasterxml.jackson.databind.*; -import com.fasterxml.jackson.databind.node.*; -import com.fasterxml.jackson.annotation.*; -import com.fasterxml.jackson.core.io.*; - -import javax.xml.parsers.SAXParser; -import javax.xml.parsers.SAXParserFactory; - -import org.fusesource.lmdbjni.*; -import static org.fusesource.lmdbjni.Constants.*; - -/** - * The working KB instance corresponding to the staging area, which is concretely stored - * as a set of LMDB databases. - * - */ -public class KBStagingEnvironment extends KBEnvironment { - - // the different databases of the KB - - // map DOI to PMID - private KBDatabase dbDOI2PMID = null; - - // map DOI to PMC - private KBDatabase dbDOI2PMC = null; - - // map PMID to DOI - private KBDatabase dbPMID2DOI = null; - - // map PMID to PMC - private KBDatabase dbPMID2PMC = null; - - // map PMC to DOI - private KBDatabase dbPMC2DOI = null; - - // map PMC to PMID - private KBDatabase dbPMC2PMID = null; - - // map PMC to open access information - private KBDatabase dbPMC2OABiblio = null; - - // map PMID to Open Access biblio info - private KBDatabase dbPMID2Biblio = null; - - // map ISTEX ids to all the available external ids encoded in JSON - private KBDatabase dbISTEX2IDs = null; - - // map CORE identifiers to JSON CORE objects - //private KBDatabase dbCore2JSON = null; - - // map CORE identifiers to Biblio objects - //private KBDatabase dbCore2Biblio = null; - - // map repository identifiers to repository objects - //private KBDatabase dbRepository = null; - - /** - * Constructor - */ - public KBStagingEnvironment(GluttonConfig conf) { - super(conf); - type = KBEnvironment.EnvironmentType.staging; - // register classes to be serialized - //singletonConf.registerClass(Repository.class, Biblio.class, ClassificationClass.class, - // Person.class, Identifier.class, Affiliation.class, MeSHClass.class); - initDatabases(); - } - - /** - * Returns the {@link DatabaseType#biblio} database - */ - /*public KBDatabase getDbBiblio() { - return dbBiblio; - }*/ - - /** - * Returns the {@link DatabaseType#identifier} database - */ - public KBDatabase getDbDOI2PMID() { - return dbDOI2PMID; - } - - /** - * Returns the {@link DatabaseType#identifier} database - */ - public KBDatabase getDbDOI2PMC() { - return dbDOI2PMC; - } - - /** - * Returns the {@link DatabaseType#identifier} database - */ - public KBDatabase getDbPMID2DOI() { - return dbPMID2DOI; - } - - /** - * Returns the {@link DatabaseType#identifier} database - */ - public KBDatabase getDbPMID2PMC() { - return dbPMID2PMC; - } - - /** - * Returns the {@link DatabaseType#identifier} database - */ - public KBDatabase getDbPMC2DOI() { - return dbPMC2DOI; - } - - /** - * Returns the {@link DatabaseType#identifier} database - */ - public KBDatabase getDbPMC2PMID() { - return dbPMC2PMID; - } - - /** - * Returns the {@link DatabaseType#identifier} database - */ - public KBDatabase getDbPMC2OABiblio() { - return dbPMC2OABiblio; - } - - /** - * Returns the {@link DatabaseType#identifier} database - */ - public KBDatabase getDbISTEX2IDs() { - return dbISTEX2IDs; - } - - /** - * Returns the {@link DatabaseType#biblio} database - */ - /*public KBDatabase getDbCore2JSON() { - return dbCore2JSON; - }*/ - - /** - * Returns the {@link DatabaseType#biblio} database - */ - /*public KBDatabase getDbCore2Biblio() { - return dbCore2Biblio; - }*/ - - /** - * Returns the {@link DatabaseType#repository} database - */ - /*public KBDatabase getDbRepository() { - return dbRepository; - }*/ - - /** - * Returns the {@link DatabaseType#biblio} database - */ - public KBDatabase getDbPMID2Biblio() { - return dbPMID2Biblio; - } - - @Override - protected void initDatabases() { - System.out.println("\ninit staging environment"); - - File dbDirectory = new File(conf.pubmed.getDbDirectory()); - if (!dbDirectory.exists()) - dbDirectory.mkdirs(); - File dbStagingDirectory = dbDirectory; - - /*File dbStagingDirectory = new File(conf.pubmed.getDbDirectory()+"/staging/"); - if (!dbStagingDirectory.exists()) - dbStagingDirectory.mkdirs();*/ - - databasesByType = new HashMap>(); - List theBases = databasesByType.get(DatabaseType.biblio); - - /*dbBiblio = buildBiblioDatabase(); - if (theBases == null) { - theBases = new ArrayList(); - } - theBases.add(dbBiblio); - databasesByType.put(DatabaseType.biblio, theBases);*/ - - dbDOI2PMID = buildDbDOI2PMIDDatabase(); - theBases = databasesByType.get(DatabaseType.identifier); - if (theBases == null) { - theBases = new ArrayList(); - } - theBases.add(dbDOI2PMID); - databasesByType.put(DatabaseType.identifier, theBases); - - dbDOI2PMC = buildDbDOI2PMCDatabase(); - theBases = databasesByType.get(DatabaseType.identifier); - if (theBases == null) { - theBases = new ArrayList(); - } - theBases.add(dbDOI2PMC); - databasesByType.put(DatabaseType.identifier, theBases); - - dbPMID2DOI = buildDbPMID2DOIDatabase(); - theBases = databasesByType.get(DatabaseType.identifier); - if (theBases == null) { - theBases = new ArrayList(); - } - theBases.add(dbPMID2DOI); - databasesByType.put(DatabaseType.identifier, theBases); - - dbPMID2PMC = buildDbPMID2PMCDatabase(); - theBases = databasesByType.get(DatabaseType.identifier); - if (theBases == null) { - theBases = new ArrayList(); - } - theBases.add(dbPMID2PMC); - databasesByType.put(DatabaseType.identifier, theBases); - - dbPMC2DOI = buildDbPMC2DOIDatabase(); - theBases = databasesByType.get(DatabaseType.identifier); - if (theBases == null) { - theBases = new ArrayList(); - } - theBases.add(dbPMC2DOI); - databasesByType.put(DatabaseType.identifier, theBases); - - dbPMC2PMID = buildDbPMC2PMIDDatabase(); - theBases = databasesByType.get(DatabaseType.identifier); - if (theBases == null) { - theBases = new ArrayList(); - } - theBases.add(dbPMC2PMID); - databasesByType.put(DatabaseType.identifier, theBases); - - dbPMC2OABiblio = buildPMC2OABiblioDatabase(); - theBases = databasesByType.get(DatabaseType.identifier); - if (theBases == null) { - theBases = new ArrayList(); - } - theBases.add(dbPMC2OABiblio); - databasesByType.put(DatabaseType.identifier, theBases); - - /*dbISTEX2IDs = buildDbISTEX2IDsDatabase(); - theBases = databasesByType.get(DatabaseType.identifier); - if (theBases == null) { - theBases = new ArrayList(); - } - theBases.add(dbISTEX2IDs); - databasesByType.put(DatabaseType.identifier, theBases);*/ - - /*dbCore2JSON = buildCore2JsonDatabase(); - theBases = databasesByType.get(DatabaseType.biblio); - if (theBases == null) { - theBases = new ArrayList(); - } - theBases.add(dbCore2JSON); - databasesByType.put(DatabaseType.biblio, theBases); */ - - /*dbCore2Biblio= buildCore2BiblioDatabase(); - theBases = databasesByType.get(DatabaseType.biblio); - if (theBases == null) { - theBases = new ArrayList(); - } - theBases.add(dbCore2Biblio); - databasesByType.put(DatabaseType.biblio, theBases); */ - - /*dbRepository = buildRepositoryDatabase(); - theBases = databasesByType.get(DatabaseType.repository); - if (theBases == null) { - theBases = new ArrayList(); - } - theBases.add(dbRepository); - databasesByType.put(DatabaseType.repository, theBases);*/ - - /*dbPMID2Biblio = buildPMID2BiblioDatabase(); - theBases = databasesByType.get(DatabaseType.biblio); - if (theBases == null) { - theBases = new ArrayList(); - } - theBases.add(dbPMID2Biblio); - databasesByType.put(DatabaseType.biblio, theBases);*/ - } - - /** - * Builds a KBEnvironment, by loading all of the data files stored in the given directory into persistent databases. - * - * It will not create the environment or any databases unless all of the required files are found in the given directory. - * - * It will not delete any existing databases, and will only overwrite them if explicitly specified (even if they are incomplete). - * - * @param conf a configuration specifying where the databases are to be stored, etc. - * @param overwrite true if existing databases should be overwritten, otherwise false - * @throws IOException if any of the required files cannot be read - */ - @Override - public void buildEnvironment(boolean overwrite) throws IOException { - System.out.println("building Environment for staging area"); - - //check all files exist and are readable before doing anything - File pmcDirectory = new File(conf.pubmed.getPmcDirectory()); - File pmcDOIData = getDataFile(pmcDirectory, "PMID_PMCID_DOI.csv.gz"); - File oaData = getDataFile(pmcDirectory, "oa_file_list.txt"); - - //File istexDirectory = new File(conf.getIstexDirectory()); - //File istexIdData = getDataFile(istexDirectory, "istexIds.all.gz"); - - //File coreDirectory = new File(conf.getCoreDirectory()); - //File coreData = getDataFile(coreDirectory, "repository_metadata_2016-10-05.tar.gz"); - - //now load databases - - //System.out.println("Building dbDOI2PMID"); - dbDOI2PMID.loadFromFile(pmcDOIData, overwrite); - System.out.println(dbDOI2PMID.getDatabaseSize() + " DOI/PMID mappings."); - - //System.out.println("Building dbDOI2PMC"); - dbDOI2PMC.loadFromFile(pmcDOIData, overwrite); - System.out.println(dbDOI2PMC.getDatabaseSize() + " DOI/PMC mappings."); - - //System.out.println("Building dbPMID2DOI"); - dbPMID2DOI.loadFromFile(pmcDOIData, overwrite); - - //System.out.println("Building dbPMID2PMC"); - dbPMID2PMC.loadFromFile(pmcDOIData, overwrite); - System.out.println(dbPMID2PMC.getDatabaseSize() + " PMID/PMC mappings."); - - //System.out.println("Building dbPMID2DOI"); - dbPMC2DOI.loadFromFile(pmcDOIData, overwrite); - - //System.out.println("Building dbPMID2PMC"); - dbPMC2PMID.loadFromFile(pmcDOIData, overwrite); - - //System.out.println("Building dbISTEX2IDs"); - //dbISTEX2IDs.loadFromFile(istexIdData, overwrite); - - /*System.out.println("Building dbCore2JSON"); - dbCore2JSON.loadFromFile(coreData, overwrite);*/ - - /*System.out.println("Building dbCore2Biblio"); - dbCore2Biblio.loadFromFile(coreData, overwrite); - System.out.println(dbCore2Biblio.getDatabaseSize() + " CORE Biblio objects."); - */ - - /*System.out.println("Building dbRepository"); - dbRepository.loadFromFile(coreData, overwrite); - System.out.println(dbRepository.getDatabaseSize() + " repository objects.");*/ - - System.out.println("Building dbPMID2Biblio"); - dbPMC2OABiblio.loadFromFile(oaData, overwrite); - System.out.println(dbPMC2OABiblio.getDatabaseSize() + " Open Access biblio information."); - - System.out.println("Environment built"); - } - - /** - * Create a database associating integer id of a bibliographical item to its Biblio object - */ - private KBDatabase buildBiblioDatabase() { - return new KBDatabase(this, DatabaseType.biblio, "biblio") { - - /** - * Builds the persistent database from a file. - * - * @param dataFile the file (here a text file with fields separated by a tabulation) containing data to be loaded - * @param overwrite true if the existing database should be overwritten, otherwise false - * @throws IOException if there is a problem reading or deserialising the given data file. - */ - public void loadFromFile(File dataFile, boolean overwrite) throws IOException { - System.out.println("input file: " + dataFile.getPath()); - if (isLoaded && !overwrite) - return; - System.out.println("Loading " + name + " database"); - } - }; - } - - /** - * Create a database associating a DOI to a PMID - */ - private KBDatabase buildDbDOI2PMIDDatabase() { - return new KBDatabase(this, DatabaseType.identifier, "DOI2PMID") { - - /** - * Builds the persistent database from a file. - * - * @param dataFile the file (here a text file with fields separated by a tabulation) containing data to be loaded - * @param overwrite true if the existing database should be overwritten, otherwise false - * @throws IOException if there is a problem reading or deserialising the given data file. - */ - public void loadFromFile(File dataFile, boolean overwrite) throws IOException { -//System.out.println("input file: " + dataFile.getPath()); -System.out.println("isLoaded: " + isLoaded); - if (isLoaded && !overwrite) - return; - System.out.println("Building " + name + " database"); - - InputStream fileStream = new FileInputStream(dataFile); - InputStream gzipStream = new GZIPInputStream(fileStream); - BufferedReader input = new BufferedReader(new InputStreamReader(gzipStream, "UTF-8")); - String line = null; - int nbToAdd = 0; - Transaction tx = environment.createWriteTransaction(); - boolean first = true; - while ((line=input.readLine()) != null) { - // first line to ignore - if (first) { - first = false; - continue; - } - - // format is PMID,PMCID,"DOI" - // PMID is a number, PMCID is a number with PMC as prefix, - // DOI is a doi (will be lowercased) with the "https://doi.org/" prefix to be removed - if (nbToAdd == 10000) { - tx.commit(); - tx.close(); - nbToAdd = 0; - tx = environment.createWriteTransaction(); - } - - String[] pieces = line.split(","); - if (pieces.length != 3) - continue; - // only PMID interests us here - if (pieces[0].trim().length() == 0) - continue; - Integer keyVal = null; - try { - keyVal = Integer.parseInt(pieces[0]); - } catch(Exception e) { - e.printStackTrace(); - } - if (keyVal == null) - continue; - String doi = pieces[2].substring(1,pieces[2].length()-1); - doi = doi.replace("https://doi.org/", "").toLowerCase(); - if (doi.trim().length() == 0) - continue; - KBEntry entry = new KBEntry(doi, keyVal); - if (entry != null) { - try { - db.put(tx, KBEnvironment.serialize(entry.getKey()), KBEnvironment.serialize(entry.getValue())); - nbToAdd++; - } catch(Exception e) { - e.printStackTrace(); - } - } - } - tx.commit(); - tx.close(); - input.close(); - isLoaded = true; - } - }; - } - - /** - * Create a database associating a PMID to a DOI - */ - private KBDatabase buildDbPMID2DOIDatabase() { - return new KBDatabase(this, DatabaseType.identifier, "PMID2DOI") { - - /** - * Builds the persistent database from a file. - * - * @param dataFile the file (here a text file with fields separated by a tabulation) containing data to be loaded - * @param overwrite true if the existing database should be overwritten, otherwise false - * @throws IOException if there is a problem reading or deserialising the given data file. - */ - public void loadFromFile(File dataFile, boolean overwrite) throws IOException { -//System.out.println("input file: " + dataFile.getPath()); -System.out.println("isLoaded: " + isLoaded); - if (isLoaded && !overwrite) - return; - System.out.println("Building " + name + " database"); - - InputStream fileStream = new FileInputStream(dataFile); - InputStream gzipStream = new GZIPInputStream(fileStream); - BufferedReader input = new BufferedReader(new InputStreamReader(gzipStream, "UTF-8")); - String line = null; - int nbToAdd = 0; - Transaction tx = environment.createWriteTransaction(); - boolean first = true; - while ((line=input.readLine()) != null) { - // first line to ignore - if (first) { - first = false; - continue; - } - - // format is PMID,PMCID,"DOI" - // PMID is a number, PMCID is a number with PMC as prefix, - // DOI is a doi (will be lowercased) with the "https://doi.org/" prefix to be removed - if (nbToAdd == 10000) { - tx.commit(); - tx.close(); - nbToAdd = 0; - tx = environment.createWriteTransaction(); - } - - String[] pieces = line.split(","); - if (pieces.length != 3) - continue; - // only PMID interests us here - if (pieces[0].trim().length() == 0) - continue; - Integer keyVal = null; - try { - keyVal = Integer.parseInt(pieces[0]); - } catch(Exception e) { - e.printStackTrace(); - } - if (keyVal == null) - continue; - String doi = pieces[2].substring(1,pieces[2].length()-1); - doi = doi.replace("https://doi.org/", "").toLowerCase(); - if (doi.trim().length() == 0) - continue; - KBEntry entry = new KBEntry(keyVal, doi); - if (entry != null) { - try { - db.put(tx, KBEnvironment.serialize(entry.getKey()), KBEnvironment.serialize(entry.getValue())); - nbToAdd++; - } catch(Exception e) { - e.printStackTrace(); - } - } - } - tx.commit(); - tx.close(); - input.close(); - isLoaded = true; - } - }; - } - - - /** - * Create a database associating a DOI to a PMC - */ - private KBDatabase buildDbDOI2PMCDatabase() { - return new KBDatabase(this, DatabaseType.identifier, "DOI2PMC") { - - /** - * Builds the persistent database from a file. - * - * @param dataFile the file (here a text file with fields separated by a tabulation) containing data to be loaded - * @param overwrite true if the existing database should be overwritten, otherwise false - * @throws IOException if there is a problem reading or deserialising the given data file. - */ - public void loadFromFile(File dataFile, boolean overwrite) throws IOException { -//System.out.println("input file: " + dataFile.getPath()); -System.out.println("isLoaded: " + isLoaded); - if (isLoaded && !overwrite) - return; - System.out.println("Building " + name + " database"); - - InputStream fileStream = new FileInputStream(dataFile); - InputStream gzipStream = new GZIPInputStream(fileStream); - BufferedReader input = new BufferedReader(new InputStreamReader(gzipStream, "UTF-8")); - String line = null; - int nbToAdd = 0; - Transaction tx = environment.createWriteTransaction(); - boolean first = true; - while ((line=input.readLine()) != null) { - // first line to ignore - if (first) { - first = false; - continue; - } - - // format is PMID,PMCID,"DOI" - // PMID is a number, PMCID is a number with PMC as prefix, - // DOI is a doi (will be lowercased) with the "https://doi.org/" prefix to be removed - if (nbToAdd == 10000) { - tx.commit(); - tx.close(); - nbToAdd = 0; - tx = environment.createWriteTransaction(); - } - - String[] pieces = line.split(","); - if (pieces.length != 3) - continue; - // only PMCID interests us here - if (pieces[1].trim().length() == 0) - continue; - String pmc = pieces[1]; - - if (pmc == null || pmc.trim().length() == 0) - continue; - - String doi = pieces[2].substring(1,pieces[2].length()-1); - doi = doi.replace("https://doi.org/", "").toLowerCase(); - if (doi.trim().length() == 0) - continue; - KBEntry entry = new KBEntry(doi, pmc); - if (entry != null) { - try { - db.put(tx, KBEnvironment.serialize(entry.getKey()), KBEnvironment.serialize(entry.getValue())); - nbToAdd++; - } catch(Exception e) { - e.printStackTrace(); - } - } - } - tx.commit(); - tx.close(); - input.close(); - isLoaded = true; - } - }; - } - - /** - * Create a database associating a PMID to a PMC - */ - private KBDatabase buildDbPMID2PMCDatabase() { - return new KBDatabase(this, DatabaseType.identifier, "PMID2PMC") { - - /** - * Builds the persistent database from a file. - * - * @param dataFile the file (here a text file with fields separated by a tabulation) containing data to be loaded - * @param overwrite true if the existing database should be overwritten, otherwise false - * @throws IOException if there is a problem reading or deserialising the given data file. - */ - public void loadFromFile(File dataFile, boolean overwrite) throws IOException { -//System.out.println("input file: " + dataFile.getPath()); -System.out.println("isLoaded: " + isLoaded); - if (isLoaded && !overwrite) - return; - System.out.println("Building " + name + " database"); - - InputStream fileStream = new FileInputStream(dataFile); - InputStream gzipStream = new GZIPInputStream(fileStream); - BufferedReader input = new BufferedReader(new InputStreamReader(gzipStream, "UTF-8")); - String line = null; - int nbToAdd = 0; - Transaction tx = environment.createWriteTransaction(); - boolean first = true; - while ((line=input.readLine()) != null) { - // first line to ignore - if (first) { - first = false; - continue; - } - - // format is PMID,PMCID,"DOI" - // PMID is a number, PMCID is a number with PMC as prefix, - // DOI is a doi (will be lowercased) with the "https://doi.org/" prefix to be removed - if (nbToAdd == 10000) { - tx.commit(); - tx.close(); - nbToAdd = 0; - tx = environment.createWriteTransaction(); - } - - String[] pieces = line.split(","); - if (pieces.length != 3) - continue; - // only PMID interests us here - if (pieces[0].trim().length() == 0) - continue; - Integer keyVal = null; - try { - keyVal = Integer.parseInt(pieces[0]); - } catch(Exception e) { - e.printStackTrace(); - } - if (keyVal == null) - continue; - - String pmc = pieces[1]; - if (pmc == null || pmc.trim().length() == 0) - continue; - - KBEntry entry = new KBEntry(keyVal, pmc); - if (entry != null) { - try { - db.put(tx, KBEnvironment.serialize(entry.getKey()), KBEnvironment.serialize(entry.getValue())); - nbToAdd++; - } catch(Exception e) { - e.printStackTrace(); - } - } - } - tx.commit(); - tx.close(); - input.close(); - isLoaded = true; - } - }; - } - - /** - * Create a database associating a PMC to a DOI - */ - private KBDatabase buildDbPMC2DOIDatabase() { - return new KBDatabase(this, DatabaseType.identifier, "PMC2DOI") { - - /** - * Builds the persistent database from a file. - * - * @param dataFile the file (here a text file with fields separated by a tabulation) containing data to be loaded - * @param overwrite true if the existing database should be overwritten, otherwise false - * @throws IOException if there is a problem reading or deserialising the given data file. - */ - public void loadFromFile(File dataFile, boolean overwrite) throws IOException { -//System.out.println("input file: " + dataFile.getPath()); -System.out.println("isLoaded: " + isLoaded); - if (isLoaded && !overwrite) - return; - System.out.println("Building " + name + " database"); - - InputStream fileStream = new FileInputStream(dataFile); - InputStream gzipStream = new GZIPInputStream(fileStream); - BufferedReader input = new BufferedReader(new InputStreamReader(gzipStream, "UTF-8")); - String line = null; - int nbToAdd = 0; - Transaction tx = environment.createWriteTransaction(); - boolean first = true; - while ((line=input.readLine()) != null) { - // first line to ignore - if (first) { - first = false; - continue; - } - - // format is PMID,PMCID,"DOI" - // PMID is a number, PMCID is a number with PMC as prefix, - // DOI is a doi (will be lowercased) with the "https://doi.org/" prefix to be removed - if (nbToAdd == 10000) { - tx.commit(); - tx.close(); - nbToAdd = 0; - tx = environment.createWriteTransaction(); - } - - String[] pieces = line.split(","); - if (pieces.length != 3) - continue; - // only PMCID interests us here - if (pieces[1].trim().length() == 0) - continue; - String pmc = pieces[1]; - if (pmc == null || pmc.trim().length() == 0) - continue; - - String doi = pieces[2].substring(1,pieces[2].length()-1); - doi = doi.replace("https://doi.org/", "").toLowerCase(); - if (doi.trim().length() == 0) - continue; - KBEntry entry = new KBEntry(pmc, doi); - if (entry != null) { - try { - db.put(tx, KBEnvironment.serialize(entry.getKey()), KBEnvironment.serialize(entry.getValue())); - nbToAdd++; - } catch(Exception e) { - e.printStackTrace(); - } - } - } - tx.commit(); - tx.close(); - input.close(); - isLoaded = true; - } - }; - } - - - /** - * Create a database associating a PMC to a PMID - */ - private KBDatabase buildDbPMC2PMIDDatabase() { - return new KBDatabase(this, DatabaseType.identifier, "PMC2PMID") { - - /** - * Builds the persistent database from a file. - * - * @param dataFile the file (here a text file with fields separated by a tabulation) containing data to be loaded - * @param overwrite true if the existing database should be overwritten, otherwise false - * @throws IOException if there is a problem reading or deserialising the given data file. - */ - public void loadFromFile(File dataFile, boolean overwrite) throws IOException { -//System.out.println("input file: " + dataFile.getPath()); -System.out.println("isLoaded: " + isLoaded); - if (isLoaded && !overwrite) - return; - System.out.println("Building " + name + " database"); - - InputStream fileStream = new FileInputStream(dataFile); - InputStream gzipStream = new GZIPInputStream(fileStream); - BufferedReader input = new BufferedReader(new InputStreamReader(gzipStream, "UTF-8")); - String line = null; - int nbToAdd = 0; - Transaction tx = environment.createWriteTransaction(); - boolean first = true; - while ((line=input.readLine()) != null) { - // first line to ignore - if (first) { - first = false; - continue; - } - - // format is PMID,PMCID,"DOI" - // PMID is a number, PMCID is a number with PMC as prefix, - // DOI is a doi (will be lowercased) with the "https://doi.org/" prefix to be removed - if (nbToAdd == 10000) { - tx.commit(); - tx.close(); - nbToAdd = 0; - tx = environment.createWriteTransaction(); - } - - String[] pieces = line.split(","); - if (pieces.length != 3) - continue; - // only PMID interests us here - if (pieces[0].trim().length() == 0) - continue; - Integer keyVal = null; - try { - keyVal = Integer.parseInt(pieces[0]); - } catch(Exception e) { - e.printStackTrace(); - } - if (keyVal == null) - continue; - - String pmc = pieces[1]; - if (pmc == null || pmc.trim().length() == 0) - continue; - - KBEntry entry = new KBEntry(pmc, keyVal); - if (entry != null) { - try { - db.put(tx, KBEnvironment.serialize(entry.getKey()), KBEnvironment.serialize(entry.getValue())); - nbToAdd++; - } catch(Exception e) { - e.printStackTrace(); - } - } - } - tx.commit(); - tx.close(); - input.close(); - isLoaded = true; - } - }; - } - - /** - * Create a database associating a PMC to Open Access information (as json string) - */ - private KBDatabase buildPMC2OABiblioDatabase() { - return new KBDatabase(this, DatabaseType.identifier, "PMC2OABiblio") { - - /** - * Builds the persistent database from a file. - * - * @param dataFile the file (here a text file with fields separated by a tabulation) containing data to be loaded - * @param overwrite true if the existing database should be overwritten, otherwise false - * @throws IOException if there is a problem reading or deserialising the given data file. - */ - public void loadFromFile(File dataFile, boolean overwrite) throws IOException { -//System.out.println("input file: " + dataFile.getPath()); -System.out.println("isLoaded: " + isLoaded); - if (isLoaded && !overwrite) - return; - System.out.println("Building " + name + " database"); - - InputStream fileStream = new FileInputStream(dataFile); - InputStream fullStream = null; - if (dataFile.getName().endsWith(".gz")) - fullStream = new GZIPInputStream(fileStream); - else - fullStream = fileStream; - - BufferedReader input = new BufferedReader(new InputStreamReader(fullStream, "UTF-8")); - String line = null; - int nbToAdd = 0; - Transaction tx = environment.createWriteTransaction(); - boolean first = true; - while ((line=input.readLine()) != null) { - // first line to ignore - if (first) { - first = false; - continue; - } - - // format is CSV: - // tar path (to be completed by ftp access prefix), some useless biblio, PMCID, PMID, CC or NO-CC (boolean), CC license code - // oa_package/08/e0/PMC13900.tar.gz Breast Cancer Res. 2001 Nov 2; 3(1):55-60 PMC13900 PMID:11250746 NO-CC CODE - - // PMID given as "PMID:11151091" - // PMC ID as normal - - if (nbToAdd == 10000) { - tx.commit(); - tx.close(); - nbToAdd = 0; - tx = environment.createWriteTransaction(); - } - - String[] pieces = line.split("\t"); - - if (pieces.length != 5) - continue; - - // PMC is the key - if (pieces[2].trim().length() == 0) - continue; - String pmc = pieces[2]; - if (pmc == null || pmc.trim().length() == 0) - continue; - - StringBuilder json = new StringBuilder(); - - String url = pieces[0]; - if (url != null && url.trim().length() > 0) - url = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/" + url.trim(); - else - url = null; - - String pmidStr = pieces[3]; - Integer pmid = null; - if (pmidStr != null && pmidStr.trim().length() > 0) { - pmidStr = pmidStr.trim(); - pmidStr = pmidStr.replace("PMID:", ""); - try { - pmid = Integer.parseInt(pmidStr); - } catch(Exception e) { - e.printStackTrace(); - } - } - - String license = pieces[4]; - if (license == null || license.trim().length() == 0) { - license = null; - } else { - license = license.trim(); - } - - json.append("{ \"localInfo\": { \"pmc\": \"" + pmc + "\""); - - if (url != null) { - json.append(", \"url\": \"" + url + "\""); - } - if (pmid != null) { - json.append(", \"pmid\": " + pmid); - } - if (license != null) { - json.append(", \"license\": \"" + license + "\""); - } - json.append("}}"); - - KBEntry entry = new KBEntry(pmc, json.toString()); - if (entry != null) { - try { - db.put(tx, KBEnvironment.serialize(entry.getKey()), KBEnvironment.serialize(entry.getValue())); - nbToAdd++; - } catch(Exception e) { - e.printStackTrace(); - } - } - } - tx.commit(); - tx.close(); - input.close(); - isLoaded = true; - } - }; - } - - /** - * Create a database associating an ISTEX id to all known external IDs - */ -/* private KBDatabase buildDbISTEX2IDsDatabase() { - return new KBDatabase(this, DatabaseType.identifier, "ISTEX2IDs") { - - public void loadFromFile(File dataFile, boolean overwrite) throws IOException { -System.out.println("input file: " + dataFile.getPath()); -System.out.println("isLoaded: " + isLoaded); - if (isLoaded && !overwrite) - return; - System.out.println("Loading " + name + " database"); - - InputStream fileStream = new FileInputStream(dataFile); - InputStream gzipStream = new GZIPInputStream(fileStream); - BufferedReader input = new BufferedReader(new InputStreamReader(gzipStream, "UTF-8")); - String line = null; - int nbToAdd = 0; - int nbTotal = 0; - Transaction tx = environment.createWriteTransaction(); - ObjectMapper mapper = new ObjectMapper(); - while ((line=input.readLine()) != null) { - if (nbToAdd == 10000) { - tx.commit(); - tx.close(); - nbToAdd = 0; - tx = environment.createWriteTransaction(); - } - // each line is a JSON - if (line.trim().length() == 0) - continue; - - JsonNode rootNode = mapper.readTree(line); - JsonNode istexNode = rootNode.findPath("istexId"); - String keyVal = null; - if ((istexNode != null) && (!istexNode.isMissingNode())) { - keyVal = istexNode.textValue(); - } - - if ( (keyVal == null) || (keyVal.trim().length() == 0) ) - continue; - try { - db.put(tx, KBEnvironment.serialize(keyVal), KBEnvironment.serialize(line)); - nbToAdd++; - } catch(Exception e) { - e.printStackTrace(); - } - nbTotal++; - } - tx.commit(); - tx.close(); - input.close(); - isLoaded = true; - - System.out.println("Total of IstexID loaded: " + nbTotal); - } - }; - }*/ - - /** - * Create a database associating an identifier to a JSON CORE object - */ -/* private KBDatabase buildCore2JsonDatabase() { - return new KBDatabase(this, DatabaseType.biblio, "Core2Json") { - - public void loadFromFile(File dataFile, boolean overwrite) throws IOException { - if (isLoaded && !overwrite) - return; - System.out.println("Loading " + name + " database"); - - InputStream fileStream = new FileInputStream(dataFile); - InputStream gzipStream = new GZIPInputStream(fileStream); - BufferedReader input = new BufferedReader(new InputStreamReader(gzipStream, "UTF-8")); - String line = null; - int nbToAdd = 0; - - Transaction tx = environment.createWriteTransaction(); - ObjectMapper mapper = new ObjectMapper(); - int index = 0; - while ((line=input.readLine()) != null) { - if (line.trim().length() == 0) - continue; - - if (!line.startsWith("{")) { - // when data for a new repo starts, we have some junk data before the start - // of the json - int ind = line.indexOf("{"); - line = line.substring(ind, line.length()); - } - - if (nbToAdd == 10000) { - tx.commit(); - tx.close(); - nbToAdd = 0; - tx = environment.createWriteTransaction(); - } - - line = line.replace("\"identifier\"", "\"id\": "+ index +",\"coreId\""); - - // at this stage each line is a JSON - JsonNode rootNode = mapper.readTree(line); - JsonNode coreIdNode = rootNode.findPath("coreId"); - Integer keyVal = new Integer(index); - Integer coreId = null; - if ((coreIdNode != null) && (!coreIdNode.isMissingNode())) { - coreId = coreIdNode.intValue(); - } - - if (coreId == null) - continue; - - try { - db.put(tx, - KBEnvironment.serialize(keyVal), - KBEnvironment.serialize(line) ); - nbToAdd++; - index++; - } catch(Exception e) { - e.printStackTrace(); - } - - } - tx.commit(); - tx.close(); - input.close(); - isLoaded = true; - } - }; - }*/ - - /** - * Create a database associating a biblio identifiers to a Biblio object built from CORE service - */ - /*private KBDatabase buildCore2BiblioDatabase() { - return new KBDatabase(this, DatabaseType.biblio, "Core2Biblio") { - - public void loadFromFile(File dataFile, boolean overwrite) throws IOException { - if (isLoaded && !overwrite) - return; - System.out.println("Loading " + name + " database"); - - InputStream fileStream = new FileInputStream(dataFile); - InputStream gzipStream = new GZIPInputStream(fileStream); - BufferedReader input = new BufferedReader(new InputStreamReader(gzipStream, "UTF-8")); - String line = null; - int nbToAdd = 0; - - Transaction tx = environment.createWriteTransaction(); - ObjectMapper mapper = new ObjectMapper(); - int index = 0; - while ((line=input.readLine()) != null) { - if (line.trim().length() == 0) - continue; - - if (!line.startsWith("{")) { - // when data for a new repo starts, we have some junk data before the start - // of the json - int ind = line.indexOf("{"); - line = line.substring(ind, line.length()); - } - - if (nbToAdd == 10000) { - tx.commit(); - tx.close(); - nbToAdd = 0; - tx = environment.createWriteTransaction(); - } - - line = line.replace("\"identifier\"", "\"id\": "+ index +",\"coreId\""); - - // at this stage each line is a JSON - JsonNode rootNode = mapper.readTree(line); - JsonNode coreIdNode = rootNode.findPath("coreId"); - Integer coreId = null; - if ((coreIdNode != null) && (!coreIdNode.isMissingNode())) { - coreId = coreIdNode.intValue(); - } - - if (coreId == null) - continue; - - // metadata available in the CORE dump file (not a lot!) - Biblio bib = new Biblio(); - bib.setCoreId(coreId); - - Integer keyVal = new Integer(bib.getId()); - - // item title (we assume article title) - JsonNode titleNode = rootNode.findPath("bibo:shortTitle"); - if ((titleNode != null) && (!titleNode.isMissingNode())) { - String title = titleNode.textValue(); - if (!StringUtils.isEmpty(title)) - bib.setArticleTitle(title); - } - - // repo as core repo id - JsonNode repoNode = rootNode.findPath("ep:Repository"); - if ((repoNode != null) && (!repoNode.isMissingNode())) { - int coreRepoId = repoNode.asInt(); - bib.setRepoId(coreRepoId); - } - - // abstract - JsonNode abstractNode = rootNode.findPath("bibo:abstract"); - if ((abstractNode != null) && (!abstractNode.isMissingNode())) { - String abstractText = abstractNode.textValue(); - if (!StringUtils.isEmpty(abstractText)) - bib.setAbstract(abstractText); - } - - // DOI sometime is present - JsonNode doiNode = rootNode.findPath("doi"); - if ((doiNode != null) && (!doiNode.isMissingNode())) { - String doi = doiNode.textValue(); - if (!StringUtils.isEmpty(doi)) - bib.setDoi(doi); - } - - // date indicated as dc:date, we suppose the publication date, but it could be the upload - // date on the repository? - //bib.setPublicationDate(); - - - // .. - - - //bib.setPublisherAttribute("authors", authors); - - try { - db.put(tx, - KBEnvironment.serialize(keyVal), - KBEnvironment.serialize(line) ); - nbToAdd++; - index++; - } catch(Exception e) { - e.printStackTrace(); - } - - } - tx.commit(); - tx.close(); - input.close(); - isLoaded = true; - } - }; - }*/ - - - /** - * Create a database associating a repository identifier to a repository object - */ -/* private KBDatabase buildRepositoryDatabase() { - return new KBDatabase(this, DatabaseType.repository) { - - public void loadFromFile(File dataFile, boolean overwrite) throws IOException { - - if (isLoaded && !overwrite) - return; - System.out.println("Loading " + name + " database"); - - InputStream fileStream = new FileInputStream(dataFile); - InputStream gzipStream = new GZIPInputStream(fileStream); - BufferedReader input = new BufferedReader(new InputStreamReader(gzipStream, "UTF-8")); - - List repos = null; - ObjectMapper mapper = new ObjectMapper(); - String line = null; - int index = 0; - while ((line=input.readLine()) != null) { - if (line.trim().length() == 0) - continue; - - if (!line.startsWith("{")) { - // when data for a new repo starts, we have some junk data before the start - // of the json - int ind = line.indexOf("{"); - line = line.substring(ind, line.length()); - } - - // at this stage each line is a JSON - JsonNode rootNode = mapper.readTree(line); - Integer repoId = null; - JsonNode repoNode = rootNode.findPath("ep:Repository"); - if ((repoNode != null) && (!repoNode.isMissingNode())) { - repoId = repoNode.asInt(); - } - if (repoId != null) { - if (repos == null) - repos = new ArrayList(); - if (!repos.contains(repoId)) - repos.add(repoId); - } - } - input.close(); - - Transaction tx = environment.createWriteTransaction(); - for(Integer repoIdentifier : repos) { - try { - Repository repository = new Repository(); - repository.setId(index); - repository.setCoreId(repoIdentifier); - db.put(tx, - KBEnvironment.serialize(new Integer(index)), - KBEnvironment.serialize(repository)); - index++; - } catch(Exception e) { - e.printStackTrace(); - } - } - tx.commit(); - tx.close(); - isLoaded = true; - } - }; - }*/ - - - /** - * Create a database associating a pubmed identifier to its pubmed metadata, including MeSH classes - */ -/* private KBDatabase buildPMID2BiblioDatabase() { - return new KBDatabase(this, DatabaseType.biblio, "PMID2Biblio") { - - public void loadFromFile(File dataDirectory, boolean overwrite) throws IOException { - if (isLoaded && !overwrite) - return; - System.out.println("Loading " + name + " database"); - - if (!dataDirectory.exists()) { - System.out.println("The data directory for pubmed data is not valid"); - return; - } - - - // read directory - File[] files = dataDirectory.listFiles(new FilenameFilter() { - public boolean accept(File dir, String name) { - return name.toLowerCase().endsWith(".gz"); - } - }); - - if ( (files == null) || (files.length == 0) ) - return; - - Transaction tx = environment.createWriteTransaction(); - int nbToAdd = 0; - int totalAdded = 0; - for(int i=0; i= 10000) { - tx.commit(); - tx.close(); - nbToAdd = 0; - tx = environment.createWriteTransaction(); - } - - File file = files[i]; - InputStream gzipStream = null; - try { - InputStream fileStream = new FileInputStream(file); - gzipStream = new GZIPInputStream(fileStream); - - MedlineSaxHandler handler = new MedlineSaxHandler(); - SAXParserFactory spf = SAXParserFactory.newInstance(); - spf.setValidating(false); - spf.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false); - - // get a new instance of parser - SAXParser saxParser = spf.newSAXParser(); - saxParser.getXMLReader().setEntityResolver(new DumbEntityResolver()); - saxParser.parse(gzipStream, handler); - - List biblios = handler.getBiblios(); - if ((biblios != null) && (biblios.size() > 0)) { - totalAdded += biblios.size(); - System.out.println(totalAdded + " parsed MedLine entries"); - for(Biblio biblio : biblios) { - Integer pmid = biblio.getPmid(); - try { - db.put(tx, - KBEnvironment.serialize(pmid), - KBEnvironment.serialize(biblio)); - nbToAdd++; - } catch(Exception e) { - e.printStackTrace(); - } - } - } - - //gzipStream.close(); - } catch (Exception e) { - System.out.println("Cannot parse file: " + file.getPath()); - e.printStackTrace(); - } finally { - IOUtils.closeQuietly(gzipStream); - } - } - tx.commit(); - tx.close(); - - System.out.println("total PMID biblio added: " + totalAdded); - } - }; - }*/ - -} diff --git a/pubmed-glutton/src/main/java/com/scienceminer/glutton/export/PubMedSerializer.java b/pubmed-glutton/src/main/java/com/scienceminer/glutton/export/PubMedSerializer.java index 34fb7535..ad5846db 100644 --- a/pubmed-glutton/src/main/java/com/scienceminer/glutton/export/PubMedSerializer.java +++ b/pubmed-glutton/src/main/java/com/scienceminer/glutton/export/PubMedSerializer.java @@ -34,11 +34,13 @@ import static org.apache.commons.lang3.StringUtils.isNotEmpty; /** - * Class for serializing PubMed biblio objects in different formats. + * Class for serializing PubMed biblio objects to the Crossref JSON schema without information loss. */ public class PubMedSerializer { + static String INVALID_MSG = "NOT_FOUND;INVALID_JOURNAL"; + /** * The export follows the same JSON schema as Crossref JSON (derived from Crossref Unixref) */ @@ -77,14 +79,14 @@ public static String serializeJson(Biblio biblio, KBStagingEnvironment env) thro if (biblio.getDoi() == null) { // try to get a DOI via PMID and/or PMC - if (biblio.getPubmedId() != null) { + if (biblio.getPubmedId() != null && env != null) { String doi = env.getDbPMID2DOI().retrieve(new Integer(biblio.getPubmedId())); if (doi != null) { biblio.setDoi(doi); } } - if (biblio.getDoi() == null && biblio.getPmc() != null) { + if (biblio.getDoi() == null && biblio.getPmc() != null && env != null) { String doi = env.getDbPMC2DOI().retrieve(biblio.getPmc()); if (doi != null) { biblio.setDoi(doi); @@ -264,14 +266,14 @@ public static String serializeJson(Biblio biblio, KBStagingEnvironment env) thro if (biblio.getPubmedId() == null) { // try to get a PMID via DOI and/or PMC - if (biblio.getDoi() != null) { + if (biblio.getDoi() != null && env != null) { Integer pmid = env.getDbDOI2PMID().retrieve(biblio.getDoi()); if (pmid != null) { biblio.setPubmedId(""+pmid); } } - if (biblio.getPubmedId() == null && biblio.getPmc() != null) { + if (biblio.getPubmedId() == null && biblio.getPmc() != null && env != null) { Integer pmid = env.getDbPMC2PMID().retrieve(biblio.getPmc()); if (pmid != null) { biblio.setPubmedId(""+pmid); @@ -286,14 +288,14 @@ public static String serializeJson(Biblio biblio, KBStagingEnvironment env) thro if (biblio.getPmc() == null) { // try to get a PMC via PMID and/or DOI - if (biblio.getPubmedId() != null) { + if (biblio.getPubmedId() != null && env != null) { String pmc = env.getDbPMID2PMC().retrieve(new Integer(biblio.getPubmedId())); if (pmc != null) { biblio.setPmc(pmc); } } - if (biblio.getPmc() == null && biblio.getDoi() != null) { + if (biblio.getPmc() == null && biblio.getDoi() != null && env != null) { String pmc = env.getDbDOI2PMC().retrieve(biblio.getDoi()); if (pmc != null) { biblio.setPmc(pmc); @@ -349,45 +351,47 @@ public static String serializeJson(Biblio biblio, KBStagingEnvironment env) thro } // license information injected for PMC - String jsonLicense = env.getDbPMC2OABiblio().retrieve(biblio.getPmc()); - String urlValue = null; - if (jsonLicense != null) { - - JsonNode treeNode = mapper.readTree(jsonLicense); - JsonNode infoNode = treeNode.get("localInfo"); - if (infoNode != null && infoNode.isObject()) { -//System.out.println(jsonLicense); - JsonNode licenseNode = infoNode.get("license"); - if (licenseNode != null && licenseNode.isObject()) { - builder.append(", \"license\": ["); - builder.append("{\"code\": " + mapper.writeValueAsString(licenseNode.textValue())); - builder.append("}]"); - } - JsonNode urlNode = infoNode.get("url"); - if (urlNode != null) { - urlValue = urlNode.textValue(); + if (env != null) { + String jsonLicense = env.getDbPMC2OABiblio().retrieve(biblio.getPmc()); + String urlValue = null; + if (jsonLicense != null) { + + JsonNode treeNode = mapper.readTree(jsonLicense); + JsonNode infoNode = treeNode.get("localInfo"); + if (infoNode != null && infoNode.isObject()) { + //System.out.println(jsonLicense); + JsonNode licenseNode = infoNode.get("license"); + if (licenseNode != null && licenseNode.isObject()) { + builder.append(", \"license\": ["); + builder.append("{\"code\": " + mapper.writeValueAsString(licenseNode.textValue())); + builder.append("}]"); + } + JsonNode urlNode = infoNode.get("url"); + if (urlNode != null) { + urlValue = urlNode.textValue(); + } } } - } + + if (urlValue != null || biblio.getPmc() != null) { + builder.append(", \"link\": ["); - if (urlValue != null || biblio.getPmc() != null) { - builder.append(", \"link\": ["); + if (urlValue != null) { + builder.append("{\"URL\": " + mapper.writeValueAsString(urlValue)); + builder.append(", \"content-type\": \"application/tar+gzip\"}"); + } + + if (biblio.getPmc() != null) { + if (urlValue != null) + builder.append(", "); - if (urlValue != null) { - builder.append("{\"URL\": " + mapper.writeValueAsString(urlValue)); - builder.append(", \"content-type\": \"application/tar+gzip\"}"); - } - - if (biblio.getPmc() != null) { - if (urlValue != null) - builder.append(", "); + String pmcPdf = "https://www.ncbi.nlm.nih.gov/pmc/articles/" + biblio.getPmc() + "/pdf/"; + builder.append("{\"URL\": " + mapper.writeValueAsString(pmcPdf)); + builder.append(", \"content-type\": \"application/pdf\"}"); + } - String pmcPdf = "https://www.ncbi.nlm.nih.gov/pmc/articles/" + biblio.getPmc() + "/pdf/"; - builder.append("{\"URL\": " + mapper.writeValueAsString(pmcPdf)); - builder.append(", \"content-type\": \"application/pdf\"}"); + builder.append("]"); } - - builder.append("]"); } if (biblio.getReferenceCount() != null) { @@ -411,7 +415,7 @@ public static String serializeJson(Biblio biblio, KBStagingEnvironment env) thro if (reference.getDoi() == null) { // try to get a DOI via PMID and/or PMC - if (reference.getPubmedId() != null) { + if (reference.getPubmedId() != null && !INVALID_MSG.equals(reference.getPubmedId()) && env != null) { try { String doi = env.getDbPMID2DOI().retrieve(Integer.parseInt(reference.getPubmedId())); if (doi != null) { @@ -422,7 +426,7 @@ public static String serializeJson(Biblio biblio, KBStagingEnvironment env) thro } } - if (reference.getDoi() == null && reference.getPmc() != null) { + if (reference.getDoi() == null && reference.getPmc() != null && env != null) { String doi = env.getDbPMC2DOI().retrieve(reference.getPmc()); if (doi != null) { reference.setDoi(doi); @@ -435,7 +439,7 @@ public static String serializeJson(Biblio biblio, KBStagingEnvironment env) thro if (reference.getPmc() == null) { // try to get the PMC via the PMID - if (reference.getPubmedId() != null) { + if (reference.getPubmedId() != null && !INVALID_MSG.equals(reference.getPubmedId()) && env != null) { try { String pmc = env.getDbPMID2PMC().retrieve(Integer.parseInt(reference.getPubmedId())); if (pmc != null) { @@ -446,7 +450,7 @@ public static String serializeJson(Biblio biblio, KBStagingEnvironment env) thro } } - if (reference.getPmc() == null && reference.getDoi() != null) { + if (reference.getPmc() == null && reference.getDoi() != null && env != null) { String pmc = env.getDbDOI2PMC().retrieve(reference.getDoi()); if (pmc != null) { reference.setPmc(pmc); @@ -457,8 +461,6 @@ public static String serializeJson(Biblio biblio, KBStagingEnvironment env) thro builder.append(", \"pmcid\": " + mapper.writeValueAsString(reference.getPmc())); } - - if (reference.getPii() != null) { builder.append(", \"pii\": " + mapper.writeValueAsString(reference.getPii())); } diff --git a/pubmed-glutton/src/test/java/com/scienceminer/glutton/export/TestCrossrefExport.java b/pubmed-glutton/src/test/java/com/scienceminer/glutton/export/TestCrossrefExport.java index 4003439d..5ea17462 100644 --- a/pubmed-glutton/src/test/java/com/scienceminer/glutton/export/TestCrossrefExport.java +++ b/pubmed-glutton/src/test/java/com/scienceminer/glutton/export/TestCrossrefExport.java @@ -58,7 +58,7 @@ public void testMedlineEntry() { assertThat(biblios.size(), is(1)); - String json = PubMedSerializer.serializeJson(biblios.get(0)); + String json = PubMedSerializer.serializeJson(biblios.get(0), null); assertTrue(json.length() > 0); diff --git a/readthedocs.yml b/readthedocs.yml new file mode 100644 index 00000000..a03262ec --- /dev/null +++ b/readthedocs.yml @@ -0,0 +1,20 @@ +# .readthedocs.yaml +# Read the Docs configuration file +# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + +# Required +version: 2 + +# Set the version of Python and other tools you might need +build: + os: ubuntu-22.04 + tools: + python: "3.11" + +python: + install: + - requirements: doc/requirements.txt + +mkdocs: + configuration: mkdocs.yml + fail_on_warning: false diff --git a/lookup/settings.gradle b/settings.gradle similarity index 100% rename from lookup/settings.gradle rename to settings.gradle diff --git a/lookup/src/main/java/com/scienceminer/lookup/command/GapUpdateCrossrefCommand.java b/src/main/java/com/scienceminer/glutton/command/GapUpdateCrossrefCommand.java similarity index 75% rename from lookup/src/main/java/com/scienceminer/lookup/command/GapUpdateCrossrefCommand.java rename to src/main/java/com/scienceminer/glutton/command/GapUpdateCrossrefCommand.java index 44fac328..84d3d30d 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/command/GapUpdateCrossrefCommand.java +++ b/src/main/java/com/scienceminer/glutton/command/GapUpdateCrossrefCommand.java @@ -1,15 +1,15 @@ -package com.scienceminer.lookup.command; +package com.scienceminer.glutton.command; import com.codahale.metrics.ConsoleReporter; import com.codahale.metrics.Counter; import com.codahale.metrics.Meter; import com.codahale.metrics.MetricRegistry; -import com.scienceminer.lookup.configuration.LookupConfiguration; -import com.scienceminer.lookup.storage.StorageEnvFactory; -import com.scienceminer.lookup.storage.lookup.MetadataLookup; -import com.scienceminer.lookup.utils.crossrefclient.IncrementalLoaderTask; -import io.dropwizard.cli.ConfiguredCommand; -import io.dropwizard.setup.Bootstrap; +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.storage.StorageEnvFactory; +import com.scienceminer.glutton.storage.lookup.CrossrefMetadataLookup; +import com.scienceminer.glutton.utils.crossrefclient.IncrementalLoaderTask; +import io.dropwizard.core.cli.ConfiguredCommand; +import io.dropwizard.core.setup.Bootstrap; import net.sourceforge.argparse4j.inf.Namespace; import net.sourceforge.argparse4j.inf.Subparser; import org.apache.commons.lang3.StringUtils; @@ -55,14 +55,16 @@ protected void run(Bootstrap bootstrap, Namespace namespace, LookupConfiguration reporter.start(15, TimeUnit.SECONDS); StorageEnvFactory storageEnvFactory = new StorageEnvFactory(configuration); - MetadataLookup metadataLookup = MetadataLookup.getInstance(storageEnvFactory); + CrossrefMetadataLookup metadataLookup = CrossrefMetadataLookup.getInstance(storageEnvFactory); final String crossrefFilePathString = configuration.getCrossref().getDumpPath(); Path crossrefFilePath = Paths.get(crossrefFilePathString); LOGGER.info("Preparing the system. Loading data from Crossref REST API, saving them into " + crossrefFilePathString); - final Meter meter = metrics.meter("crossrefGapUpdate"); - final Counter counterInvalidRecords = metrics.counter("crossrefGapUpdate_rejectedRecords"); + final Meter meter = metrics.meter("crossref_gap_update_load"); + final Counter counterInvalidRecords = metrics.counter("crossref_gap_update_loading_rejected_records"); + final Counter counterIndexedRecords = metrics.counter("crossref_gap_update_indexed_records"); + final Counter counterFailedIndexedRecords = metrics.counter("crossref_gap_update_failed_indexed_records"); System.out.println("Run gap update..."); @@ -72,7 +74,9 @@ protected void run(Bootstrap bootstrap, Namespace namespace, LookupConfiguration configuration, meter, counterInvalidRecords, - false, // no ES indexing + counterIndexedRecords, + counterFailedIndexedRecords, + true, // with indexing false); // not daily incremental update Future future = executor.submit(task); // wait until done (in ms) diff --git a/src/main/java/com/scienceminer/glutton/command/HALAuditCommand.java b/src/main/java/com/scienceminer/glutton/command/HALAuditCommand.java new file mode 100644 index 00000000..4c4eb022 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/command/HALAuditCommand.java @@ -0,0 +1,94 @@ +package com.scienceminer.glutton.command; + +import com.codahale.metrics.ConsoleReporter; +import com.codahale.metrics.Counter; +import com.codahale.metrics.Meter; +import com.codahale.metrics.MetricRegistry; + +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.storage.StorageEnvFactory; +import com.scienceminer.glutton.storage.lookup.HALLookup; +import com.scienceminer.glutton.storage.LookupEngine; +import com.scienceminer.glutton.indexing.ElasticSearchIndexer; +import io.dropwizard.core.cli.ConfiguredCommand; +import io.dropwizard.core.setup.Bootstrap; +import java.io.*; +import java.nio.file.*; +import net.sourceforge.argparse4j.inf.Namespace; +import net.sourceforge.argparse4j.inf.Subparser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.concurrent.TimeUnit; +import java.net.URL; + +/** + * Command for producing an audit of HAL records: estimate of duplicated records and of missing DOI. + */ +public class HALAuditCommand extends ConfiguredCommand { + private static final Logger LOGGER = LoggerFactory.getLogger(HALAuditCommand.class); + + public HALAuditCommand() { + super("hal_audit", "Analyze the HAL metadata database"); + } + + @Override + public void configure(Subparser subparser) { + super.configure(subparser); + } + + @Override + protected void run(Bootstrap bootstrap, Namespace namespace, LookupConfiguration configuration) throws Exception { + + final MetricRegistry metrics = new MetricRegistry(); + + ConsoleReporter reporter = ConsoleReporter.forRegistry(metrics) + .convertRatesTo(TimeUnit.SECONDS) + .convertDurationsTo(TimeUnit.MILLISECONDS) + .build(); + + reporter.start(30, TimeUnit.SECONDS); + + LOGGER.info("Preparing the system. Analyze the HAL metadata database..."); + + StorageEnvFactory storageEnvFactory = new StorageEnvFactory(configuration); + + long start = System.nanoTime(); + + LookupEngine lookupEngine = new LookupEngine(storageEnvFactory); + HALLookup halLookup = HALLookup.getInstance(storageEnvFactory); + + final Meter meter = metrics.meter("HAL_visited_records"); + final Counter counterDuplicatedRecords = metrics.counter("HAL_duplicated_records"); + final Counter counterHasDOIRecords = metrics.counter("HAL_has_DOI_records"); + final Counter counterMissingDOILookup = metrics.counter("HAL_missing_DOI_lookup"); + final Counter counterMissingDOIRecords = metrics.counter("HAL_missing_DOI_records"); + + // file for reporting duplicated records + String duplicatedRecordsReport = "duplicatedRecordsReport.txt"; + + // file for reporting missing DOI + String missingDOIReport = "missingDOIReport.txt"; + + halLookup.analyzeHALRecords(lookupEngine, + meter, + counterDuplicatedRecords, + counterHasDOIRecords, + counterMissingDOILookup, + counterMissingDOIRecords, + duplicatedRecordsReport, + missingDOIReport); + + LOGGER.info("HAL analyzed with " + halLookup.getSize() + " records. "); + + LOGGER.info("Finished in " + + TimeUnit.SECONDS.convert(System.nanoTime() - start, TimeUnit.NANOSECONDS) + " s"); + + reporter.report(); + + LOGGER.info("Audit file produced: " + duplicatedRecordsReport.toString()); + LOGGER.info("Audit file produced: " + missingDOIReport.toString()); + + System.exit(0); + } +} diff --git a/src/main/java/com/scienceminer/glutton/command/IndexCommand.java b/src/main/java/com/scienceminer/glutton/command/IndexCommand.java new file mode 100644 index 00000000..d3e0bc14 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/command/IndexCommand.java @@ -0,0 +1,74 @@ +package com.scienceminer.glutton.command; + +import com.codahale.metrics.ConsoleReporter; +import com.codahale.metrics.Counter; +import com.codahale.metrics.Meter; +import com.codahale.metrics.MetricRegistry; +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.indexing.ElasticSearchIndexer; +import com.scienceminer.glutton.storage.StorageEnvFactory; +import com.scienceminer.glutton.storage.lookup.HALLookup; +import com.scienceminer.glutton.storage.lookup.CrossrefMetadataLookup; +import io.dropwizard.core.cli.ConfiguredCommand; +import io.dropwizard.core.setup.Bootstrap; +import net.sourceforge.argparse4j.inf.Namespace; +import net.sourceforge.argparse4j.inf.Subparser; +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.io.InputStream; +import java.io.FileInputStream; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.concurrent.TimeUnit; +import java.util.concurrent.*; + +/** + * Command for launching an indexing of all the JSON metadata documents stored in the LMDB. + **/ +public class IndexCommand extends ConfiguredCommand { + private static final Logger LOGGER = LoggerFactory.getLogger(IndexCommand.class); + + public IndexCommand() { + super("index", "Index in the selected search engine all the JSON metadata documents currently stored in the LMDB"); + } + + @Override + protected void run(Bootstrap bootstrap, Namespace namespace, LookupConfiguration configuration) throws Exception { + + final MetricRegistry metrics = new MetricRegistry(); + + ConsoleReporter reporter = ConsoleReporter.forRegistry(metrics) + .convertRatesTo(TimeUnit.SECONDS) + .convertDurationsTo(TimeUnit.MILLISECONDS) + .build(); + + reporter.start(15, TimeUnit.SECONDS); + + StorageEnvFactory storageEnvFactory = new StorageEnvFactory(configuration); + + ElasticSearchIndexer indexer = ElasticSearchIndexer.getInstance(configuration); + final Meter meter = metrics.meter("metadataIndexing"); + final Counter counterIndexedRecords = metrics.counter("indexedRecords"); + + indexer.setupIndex(false); + long start = System.nanoTime(); + + HALLookup halLookup = HALLookup.getInstance(storageEnvFactory); + halLookup.indexMetadata(indexer, meter, counterIndexedRecords); + + CrossrefMetadataLookup crossrefMetadataLookup = CrossrefMetadataLookup.getInstance(storageEnvFactory); + crossrefMetadataLookup.indexMetadata(indexer, meter, counterIndexedRecords); + + LOGGER.info("Number of metadata records processed: " + meter.getCount()); + LOGGER.info("Finished in " + + TimeUnit.SECONDS.convert(System.nanoTime() - start, TimeUnit.NANOSECONDS) + " s"); + LOGGER.info("Metadata record indexing task completed"); + + System.exit(0); + } + +} \ No newline at end of file diff --git a/lookup/src/main/java/com/scienceminer/lookup/command/LoadCrossrefCommand.java b/src/main/java/com/scienceminer/glutton/command/LoadCrossrefCommand.java similarity index 81% rename from lookup/src/main/java/com/scienceminer/lookup/command/LoadCrossrefCommand.java rename to src/main/java/com/scienceminer/glutton/command/LoadCrossrefCommand.java index a9ff1f52..ed545167 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/command/LoadCrossrefCommand.java +++ b/src/main/java/com/scienceminer/glutton/command/LoadCrossrefCommand.java @@ -1,18 +1,19 @@ -package com.scienceminer.lookup.command; +package com.scienceminer.glutton.command; import com.codahale.metrics.ConsoleReporter; import com.codahale.metrics.Counter; import com.codahale.metrics.Meter; import com.codahale.metrics.MetricRegistry; -import com.scienceminer.lookup.configuration.LookupConfiguration; -import com.scienceminer.lookup.reader.CrossrefJsonReader; -import com.scienceminer.lookup.reader.CrossrefJsonlReader; -import com.scienceminer.lookup.reader.CrossrefJsonArrayReader; -import com.scienceminer.lookup.storage.StorageEnvFactory; -import com.scienceminer.lookup.storage.lookup.MetadataLookup; -import io.dropwizard.cli.ConfiguredCommand; -import io.dropwizard.setup.Bootstrap; +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.reader.CrossrefJsonReader; +import com.scienceminer.glutton.reader.CrossrefJsonlReader; +import com.scienceminer.glutton.reader.CrossrefJsonArrayReader; +import com.scienceminer.glutton.storage.StorageEnvFactory; +import com.scienceminer.glutton.storage.lookup.CrossrefMetadataLookup; +import com.scienceminer.glutton.indexing.ElasticSearchIndexer; +import io.dropwizard.core.cli.ConfiguredCommand; +import io.dropwizard.core.setup.Bootstrap; import net.sourceforge.argparse4j.inf.Namespace; import net.sourceforge.argparse4j.inf.Subparser; @@ -79,14 +80,19 @@ protected void run(Bootstrap bootstrap, Namespace namespace, LookupConfiguration reporter.start(15, TimeUnit.SECONDS); StorageEnvFactory storageEnvFactory = new StorageEnvFactory(configuration); - MetadataLookup metadataLookup = MetadataLookup.getInstance(storageEnvFactory); + CrossrefMetadataLookup metadataLookup = CrossrefMetadataLookup.getInstance(storageEnvFactory); final String crossrefFilePathString = namespace.get(CROSSREF_SOURCE); Path crossrefFilePath = Paths.get(crossrefFilePathString); LOGGER.info("Preparing the system. Loading data from Crossref dump from " + crossrefFilePathString); - final Meter meter = metrics.meter("crossrefLookup"); - final Counter counterInvalidRecords = metrics.counter("crossrefLookup_rejectedRecords"); + final Meter meter = metrics.meter("crossref_storing"); + final Counter counterInvalidRecords = metrics.counter("crossref_storing_rejected_records"); + final Counter counterIndexedRecords = metrics.counter("crossref_indexed_records"); + final Counter counterFailedIndexedRecords = metrics.counter("crossref_failed_indexed_records"); + + ElasticSearchIndexer.getInstance(configuration).setupIndex(true); + if (Files.isDirectory(crossrefFilePath)) { try (Stream stream = Files.walk(crossrefFilePath, 1)) { CrossrefJsonArrayReader readerJsonArray = new CrossrefJsonArrayReader(configuration); @@ -109,7 +115,12 @@ protected void run(Bootstrap bootstrap, Namespace namespace, LookupConfiguration if (reader != null) { try (InputStream inputStreamCrossref = selectStream(dumpFile)) { - metadataLookup.loadFromFile(inputStreamCrossref, reader, meter, counterInvalidRecords); + metadataLookup.loadFromFile(inputStreamCrossref, + reader, + meter, + counterInvalidRecords, + counterIndexedRecords, + counterFailedIndexedRecords); // possibly update with the lastest indexed date obtained from this file if (metadataLookup.getLastIndexed() == null || metadataLookup.getLastIndexed().isBefore(reader.getLastIndexed())) @@ -132,7 +143,12 @@ protected void run(Bootstrap bootstrap, Namespace namespace, LookupConfiguration //System.out.println("processing file " + currentEntry.getName()); try { CrossrefJsonArrayReader reader = new CrossrefJsonArrayReader(configuration); - metadataLookup.loadFromFile(tarInput, reader, meter, counterInvalidRecords); + metadataLookup.loadFromFile(tarInput, + reader, + meter, + counterInvalidRecords, + counterIndexedRecords, + counterFailedIndexedRecords); // possibly update with the lastest indexed date obtained from this file if (metadataLookup.getLastIndexed() == null || metadataLookup.getLastIndexed().isBefore(reader.getLastIndexed())) @@ -159,7 +175,12 @@ protected void run(Bootstrap bootstrap, Namespace namespace, LookupConfiguration if (reader != null) { try (InputStream inputStreamCrossref = selectStream(crossrefFilePath)) { - metadataLookup.loadFromFile(inputStreamCrossref, reader, meter, counterInvalidRecords); + metadataLookup.loadFromFile(inputStreamCrossref, + reader, + meter, + counterInvalidRecords, + counterIndexedRecords, + counterFailedIndexedRecords); metadataLookup.setLastIndexed(reader.getLastIndexed()); } catch (Exception e) { LOGGER.error("Error while processing " + crossrefFilePath, e); @@ -173,6 +194,8 @@ protected void run(Bootstrap bootstrap, Namespace namespace, LookupConfiguration } else LOGGER.info("Crossref latest indexed date is not set."); + + System.exit(0); } private InputStream selectStream(Path crossrefFilePath) throws IOException { diff --git a/src/main/java/com/scienceminer/glutton/command/LoadHALCommand.java b/src/main/java/com/scienceminer/glutton/command/LoadHALCommand.java new file mode 100644 index 00000000..983a9623 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/command/LoadHALCommand.java @@ -0,0 +1,75 @@ +package com.scienceminer.glutton.command; + +import com.codahale.metrics.ConsoleReporter; +import com.codahale.metrics.Counter; +import com.codahale.metrics.Meter; +import com.codahale.metrics.MetricRegistry; + +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.storage.StorageEnvFactory; +import com.scienceminer.glutton.storage.lookup.HALLookup; +import com.scienceminer.glutton.indexing.ElasticSearchIndexer; +import io.dropwizard.core.cli.ConfiguredCommand; +import io.dropwizard.core.setup.Bootstrap; +import net.sourceforge.argparse4j.inf.Namespace; +import net.sourceforge.argparse4j.inf.Subparser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.concurrent.TimeUnit; +import java.net.URL; + +/** + * Command for loading record from HAL via OAI-PMH + */ +public class LoadHALCommand extends ConfiguredCommand { + private static final Logger LOGGER = LoggerFactory.getLogger(LoadHALCommand.class); + + public static final String HAL_SOURCE = "halSource"; + + public LoadHALCommand() { + super("hal", "Prepare the HAL database"); + } + + @Override + public void configure(Subparser subparser) { + super.configure(subparser); + } + + @Override + protected void run(Bootstrap bootstrap, Namespace namespace, LookupConfiguration configuration) throws Exception { + + final MetricRegistry metrics = new MetricRegistry(); + + ConsoleReporter reporter = ConsoleReporter.forRegistry(metrics) + .convertRatesTo(TimeUnit.SECONDS) + .convertDurationsTo(TimeUnit.MILLISECONDS) + .build(); + + reporter.start(30, TimeUnit.SECONDS); + + LOGGER.info("Preparing the system. Loading metadadata for HAL via HAL web API..."); + + StorageEnvFactory storageEnvFactory = new StorageEnvFactory(configuration); + + long start = System.nanoTime(); + + HALLookup halLookup = HALLookup.getInstance(storageEnvFactory); + + final Meter meter = metrics.meter("HAL_storing_records"); + final Counter counterInvalidRecords = metrics.counter("HAL_rejected_records"); + final Counter counterIndexedRecords = metrics.counter("HAL_indexed_records"); + final Counter counterFailedIndexedRecords = metrics.counter("HAL_failed_indexed_records"); + + ElasticSearchIndexer.getInstance(configuration).setupIndex(true); + + halLookup.loadFromHALAPI(meter, counterInvalidRecords, counterIndexedRecords, counterFailedIndexedRecords); + + LOGGER.info("HAL loaded " + halLookup.getSize() + " records. "); + + LOGGER.info("Finished in " + + TimeUnit.SECONDS.convert(System.nanoTime() - start, TimeUnit.NANOSECONDS) + " s"); + + System.exit(0); + } +} diff --git a/lookup/src/main/java/com/scienceminer/lookup/command/LoadIstexIdsCommand.java b/src/main/java/com/scienceminer/glutton/command/LoadIstexIdsCommand.java similarity index 90% rename from lookup/src/main/java/com/scienceminer/lookup/command/LoadIstexIdsCommand.java rename to src/main/java/com/scienceminer/glutton/command/LoadIstexIdsCommand.java index 39bd963e..d79868f9 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/command/LoadIstexIdsCommand.java +++ b/src/main/java/com/scienceminer/glutton/command/LoadIstexIdsCommand.java @@ -1,13 +1,13 @@ -package com.scienceminer.lookup.command; +package com.scienceminer.glutton.command; import com.codahale.metrics.ConsoleReporter; import com.codahale.metrics.MetricRegistry; -import com.scienceminer.lookup.configuration.LookupConfiguration; -import com.scienceminer.lookup.reader.IstexIdsReader; -import com.scienceminer.lookup.storage.StorageEnvFactory; -import com.scienceminer.lookup.storage.lookup.IstexIdsLookup; -import io.dropwizard.cli.ConfiguredCommand; -import io.dropwizard.setup.Bootstrap; +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.reader.IstexIdsReader; +import com.scienceminer.glutton.storage.StorageEnvFactory; +import com.scienceminer.glutton.storage.lookup.IstexIdsLookup; +import io.dropwizard.core.cli.ConfiguredCommand; +import io.dropwizard.core.setup.Bootstrap; import net.sourceforge.argparse4j.inf.Namespace; import net.sourceforge.argparse4j.inf.Subparser; import org.slf4j.Logger; diff --git a/src/main/java/com/scienceminer/glutton/command/LoadPMIDCommand.java b/src/main/java/com/scienceminer/glutton/command/LoadPMIDCommand.java new file mode 100644 index 00000000..d3be21a3 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/command/LoadPMIDCommand.java @@ -0,0 +1,116 @@ +package com.scienceminer.glutton.command; + +import com.codahale.metrics.ConsoleReporter; +import com.codahale.metrics.MetricRegistry; +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.reader.PmidReader; +import com.scienceminer.glutton.storage.StorageEnvFactory; +import com.scienceminer.glutton.storage.lookup.PMIdsLookup; +import io.dropwizard.core.cli.ConfiguredCommand; +import io.dropwizard.core.setup.Bootstrap; +import net.sourceforge.argparse4j.inf.Namespace; +import net.sourceforge.argparse4j.inf.Subparser; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.InputStream; +import java.io.File; +import java.nio.file.Files; +import java.nio.file.Paths; +import java.util.concurrent.TimeUnit; +import java.util.zip.GZIPInputStream; + +import org.apache.commons.io.FileUtils; +import java.net.URL; + +/** + * Command for loading data for the PMID/PMCID/DOI mappings + */ +public class LoadPMIDCommand extends ConfiguredCommand { + private static final Logger LOGGER = LoggerFactory.getLogger(LoadPMIDCommand.class); + + public static final String PMID_SOURCE = "pmidSource"; + + public LoadPMIDCommand() { + super("pmid", "Prepare the pmid database lookup"); + } + + @Override + public void configure(Subparser subparser) { + super.configure(subparser); + + /*subparser.addArgument("--input") + .dest(PMID_SOURCE) + .type(String.class) + .required(true) + .help("The path to the source file for pmid mapping");*/ + } + + @Override + protected void run(Bootstrap bootstrap, Namespace namespace, LookupConfiguration configuration) throws Exception { + + // Download needed resources + String url1 = "https://ftp.ebi.ac.uk/pub/databases/pmc/DOI/PMID_PMCID_DOI.csv.gz"; + String file1Path = "data" + File.separator + "pmc" + File.separator + "PMID_PMCID_DOI.csv.gz"; + String url2 = "https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_file_list.txt"; + String file2Path = "data" + File.separator + "pmc" + File.separator + "oa_file_list.txt"; + try { + System.out.println("Downloading "+ url1 + " ..."); + FileUtils.copyURLToFile(new URL(url1), new File(file1Path)); + + System.out.println("Downloading "+ url2 + " ..."); + FileUtils.copyURLToFile(new URL(url2), new File(file2Path)); + } catch (Exception e) { + throw new RuntimeException(e); + } + + final MetricRegistry metrics = new MetricRegistry(); + + ConsoleReporter reporter = ConsoleReporter.forRegistry(metrics) + .convertRatesTo(TimeUnit.SECONDS) + .convertDurationsTo(TimeUnit.MILLISECONDS) + .build(); + + reporter.start(15, TimeUnit.SECONDS); + + //final String pmidMappingPath = namespace.get(PMID_SOURCE); + final String pmidMappingPath = file1Path; + LOGGER.info("Preparing the system. Loading data for PMID from " + pmidMappingPath); + + StorageEnvFactory storageEnvFactory = new StorageEnvFactory(configuration); + + long start = System.nanoTime(); + + PMIdsLookup pmidLookup = PMIdsLookup.getInstance(storageEnvFactory); + InputStream inputStreampmidMapping = Files.newInputStream(Paths.get(pmidMappingPath)); + if (pmidMappingPath.endsWith(".gz")) { + inputStreampmidMapping = new GZIPInputStream(inputStreampmidMapping); + } + pmidLookup.loadFromFile(inputStreampmidMapping, new PmidReader(), metrics.meter("pmidLookup")); + LOGGER.info("PubMed lookup loaded " + pmidLookup.getSize() + " records. "); + + // adding license and subpath information + inputStreampmidMapping = Files.newInputStream(Paths.get(file2Path)); + if (file1Path.endsWith(".gz")) { + inputStreampmidMapping = new GZIPInputStream(inputStreampmidMapping); + } + pmidLookup.loadFromFileExtra(inputStreampmidMapping, metrics.meter("pmidLookupExtra")); + LOGGER.info("PubMed lookup extra infos loaded in " + pmidLookup.getSize() + " records. "); + + LOGGER.info("Cleaning downloaded resource files"); + + // cleaning resource files + File fileToDelete = FileUtils.getFile(file1Path); + boolean success = FileUtils.deleteQuietly(fileToDelete); + if (!success) + LOGGER.warn("Downloaded resource file not deleted: " + file1Path); + + fileToDelete = FileUtils.getFile(file2Path); + success = FileUtils.deleteQuietly(fileToDelete); + if (!success) + LOGGER.warn("Downloaded resource file not deleted: " + file2Path); + + LOGGER.info("Finished in " + + TimeUnit.SECONDS.convert(System.nanoTime() - start, TimeUnit.NANOSECONDS) + " s"); + } +} diff --git a/lookup/src/main/java/com/scienceminer/lookup/command/LoadUnpayWallCommand.java b/src/main/java/com/scienceminer/glutton/command/LoadUnpayWallCommand.java similarity index 87% rename from lookup/src/main/java/com/scienceminer/lookup/command/LoadUnpayWallCommand.java rename to src/main/java/com/scienceminer/glutton/command/LoadUnpayWallCommand.java index 72165995..00c4e410 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/command/LoadUnpayWallCommand.java +++ b/src/main/java/com/scienceminer/glutton/command/LoadUnpayWallCommand.java @@ -1,13 +1,13 @@ -package com.scienceminer.lookup.command; +package com.scienceminer.glutton.command; import com.codahale.metrics.ConsoleReporter; import com.codahale.metrics.MetricRegistry; -import com.scienceminer.lookup.configuration.LookupConfiguration; -import com.scienceminer.lookup.reader.UnpayWallReader; -import com.scienceminer.lookup.storage.StorageEnvFactory; -import com.scienceminer.lookup.storage.lookup.OALookup; -import io.dropwizard.cli.ConfiguredCommand; -import io.dropwizard.setup.Bootstrap; +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.reader.UnpayWallReader; +import com.scienceminer.glutton.storage.StorageEnvFactory; +import com.scienceminer.glutton.storage.lookup.OALookup; +import io.dropwizard.core.cli.ConfiguredCommand; +import io.dropwizard.core.setup.Bootstrap; import net.sourceforge.argparse4j.inf.Namespace; import net.sourceforge.argparse4j.inf.Subparser; import org.slf4j.Logger; diff --git a/lookup/src/main/java/com/scienceminer/lookup/configuration/LookupConfiguration.java b/src/main/java/com/scienceminer/glutton/configuration/LookupConfiguration.java similarity index 77% rename from lookup/src/main/java/com/scienceminer/lookup/configuration/LookupConfiguration.java rename to src/main/java/com/scienceminer/glutton/configuration/LookupConfiguration.java index 99be9778..7d1aa9ab 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/configuration/LookupConfiguration.java +++ b/src/main/java/com/scienceminer/glutton/configuration/LookupConfiguration.java @@ -1,17 +1,20 @@ -package com.scienceminer.lookup.configuration; +package com.scienceminer.glutton.configuration; import com.fasterxml.jackson.annotation.JsonProperty; -import io.dropwizard.Configuration; +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import io.dropwizard.client.HttpClientConfiguration; +import io.dropwizard.core.Configuration; -import javax.validation.Valid; -import javax.validation.constraints.NotNull; +import jakarta.validation.Valid; +import jakarta.validation.constraints.NotNull; import java.util.List; import java.io.File; +@JsonIgnoreProperties(ignoreUnknown = true) public class LookupConfiguration extends Configuration { - private int loadingBatchSize = 10000; + private int storingBatchSize = 10000; + private int indexingBatchSize = 500; private int blockSize = 0; @@ -21,8 +24,12 @@ public class LookupConfiguration extends Configuration { private Source source; + private String searchEngine; + private Elastic elastic; + private Solr solr; + private Crossref crossref; private String grobidHost; @@ -57,8 +64,6 @@ public void setHttpClientConfiguration(HttpClientConfiguration httpClient) { @JsonProperty private String corsAllowedHeaders = "X-Requested-With,Content-Type,Accept,Origin"; - private List ignoreCrossRefFields; - private int maxAcceptedRequests; public String getStorage() { @@ -79,6 +84,14 @@ public void setVersion(String version) { this.version = version; } + public String getSearchEngine() { + return searchEngine; + } + + public void setSearchEngine(String searchEnginesearchEngine) { + this.searchEngine = searchEngine; + } + public Source getSource() { return source; } @@ -87,32 +100,36 @@ public Elastic getElastic() { return elastic; } + public Solr getSolr() { + return solr; + } + public Crossref getCrossref() { return crossref; } - public int getLoadingBatchSize() { - return loadingBatchSize; + public int getStoringBatchSize() { + return storingBatchSize; } - public void setLoadingBatchSize(int loadingBatchSize) { - this.loadingBatchSize = loadingBatchSize; + public void setStoringBatchSize(int storingBatchSize) { + this.storingBatchSize = storingBatchSize; } - public int getBlockSize() { - return blockSize; + public int getIndexingBatchSize() { + return indexingBatchSize; } - public void setBlockSize(int blockSize) { - this.blockSize = blockSize; + public void setIndexingBatchSize(int indexingBatchSize) { + this.indexingBatchSize = indexingBatchSize; } - public List getIgnoreCrossRefFields() { - return this.ignoreCrossRefFields; + public int getBlockSize() { + return blockSize; } - public void setIgnoreCrossRefFields(List ignoreCrossRefFields) { - this.ignoreCrossRefFields = ignoreCrossRefFields; + public void setBlockSize(int blockSize) { + this.blockSize = blockSize; } public int getMaxAcceptedRequests() { @@ -192,7 +209,7 @@ public String getIndex() { public void setIndex(String index) { this.index = index; } - + public int getMaxConnections() { return maxConnections; } @@ -202,11 +219,42 @@ public void setMaxConnections(int maxConnections) { } } + public class Solr { + + private String host; + private String core; + + public String getHost() { + return host; + } + + public void setHost(String host) { + this.host = host; + } + + public String getCore() { + return core; + } + + public void setCore(String core) { + this.core = core; + } + } + public class Crossref { private String dumpPath; private boolean cleanProcessFiles; private String mailto; private String token; + private List ignoreCrossrefFields; + + public List getIgnoreCrossrefFields() { + return this.ignoreCrossrefFields; + } + + public void setIgnoreCrossrefFields(List ignoreCrossrefFields) { + this.ignoreCrossrefFields = ignoreCrossrefFields; + } public String getDumpPath() { return dumpPath; @@ -294,7 +342,7 @@ private static String checkPath(String path) { if (path != null) { File file = new File(path); if (!file.isAbsolute()) { - path = ".." + File.separator + path; + path = "." + File.separator + path; } } return path; diff --git a/src/main/java/com/scienceminer/glutton/data/Affiliation.java b/src/main/java/com/scienceminer/glutton/data/Affiliation.java new file mode 100644 index 00000000..7522b3c9 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/data/Affiliation.java @@ -0,0 +1,411 @@ +package com.scienceminer.glutton.data; + +import java.io.Serializable; + +import java.util.ArrayList; +import java.util.List; + +/** + * Class for representing and exchanging affiliation information. + * + * @author Patrice Lopez + */ +public class Affiliation implements Serializable { + + private String acronym = null; + private String name = null; + private String url = null; + private List institutions = null; // for additional institutions + private List departments = null; // for additional departments + private List laboratories = null; // for additional laboratories + + private String country = null; + private String postCode = null; + private String postBox = null; + private String region = null; + private String settlement = null; + private String addrLine = null; + private String marker = null; + + private String addressString = null; // unspecified address field + private String affiliationString = null; // unspecified affiliation field + + private boolean failAffiliation = true; // tag for unresolved affiliation attachment + + // an identifier for the affiliation independent from the marker, present in the TEI result + private String key = null; + + // list of identifiers, e.g. orcid, etc. + private List identifiers = null; + + public Affiliation() { + } + + public Affiliation(String raw) { + this.affiliationString = raw; + } + + public Affiliation(com.scienceminer.glutton.data.Affiliation aff) { + acronym = aff.getAcronym(); + name = aff.getName(); + url = aff.getURL(); + addressString = aff.getAddressString(); + country = aff.getCountry(); + marker = aff.getMarker(); + departments = aff.getDepartments(); + institutions = aff.getInstitutions(); + laboratories = aff.getLaboratories(); + postCode = aff.getPostCode(); + postBox = aff.getPostBox(); + region = aff.getRegion(); + settlement = aff.getSettlement(); + addrLine = aff.getAddrLine(); + affiliationString = aff.getAffiliationString(); + identifiers = aff.getIdentifiers(); + } + + public String getAcronym() { + return acronym; + } + + public String getName() { + return name; + } + + public String getURL() { + return url; + } + + public String getAddressString() { + return addressString; + } + + public String getCountry() { + return country; + } + + public String getMarker() { + return marker; + } + + public String getPostCode() { + return postCode; + } + + public String getPostBox() { + return postBox; + } + + public String getRegion() { + return region; + } + + public String getSettlement() { + return settlement; + } + + public String getAddrLine() { + return addrLine; + } + + public String getAffiliationString() { + return affiliationString; + } + + public List getInstitutions() { + return institutions; + } + + public List getLaboratories() { + return laboratories; + } + + public List getDepartments() { + return departments; + } + + public String getKey() { + return key; + } + + public List getIdentifiers() { + return this.identifiers; + } + + public void setAcronym(String s) { + acronym = s; + } + + public void setName(String s) { + name = s; + } + + public void setURL(String s) { + url = s; + } + + public void setAddressString(String s) { + addressString = s; + } + + public void setCountry(String s) { + country = s; + } + + public void setMarker(String s) { + marker = s; + } + + public void setPostCode(String s) { + postCode = s; + } + + public void setPostBox(String s) { + postBox = s; + } + + public void setRegion(String s) { + region = s; + } + + public void setSettlement(String s) { + settlement = s; + } + + public void setAddrLine(String s) { + addrLine = s; + } + + public void setAffiliationString(String s) { + affiliationString = s; + } + + public void setInstitutions(List affs) { + institutions = affs; + } + + public void addInstitution(String aff) { + if (institutions == null) + institutions = new ArrayList(); + institutions.add(aff); + } + + public void setDepartments(List affs) { + departments = affs; + } + + public void addDepartment(String aff) { + if (departments == null) + departments = new ArrayList(); + departments.add(aff); + } + + public void setIdentifiers(List identifiers) { + this.identifiers = identifiers; + } + + public void addIdentifier(Identifier identifier) { + if (identifiers == null) { + identifiers = new ArrayList(); + } + identifiers.add(identifier); + } + + public void setLaboratories(List affs) { + laboratories = affs; + } + + public void addLaboratory(String aff) { + if (laboratories == null) + laboratories = new ArrayList(); + laboratories.add(aff); + } + + public void extendFirstInstitution(String theExtend) { + if (institutions == null) { + institutions = new ArrayList(); + institutions.add(theExtend); + } else { + String first = institutions.get(0); + first = first + theExtend; + institutions.set(0, first); + } + } + + public void extendLastInstitution(String theExtend) { + if (institutions == null) { + institutions = new ArrayList(); + institutions.add(theExtend); + } else { + String first = institutions.get(institutions.size() - 1); + first = first + theExtend; + institutions.set(institutions.size() - 1, first); + } + } + + public void extendFirstDepartment(String theExtend) { + if (departments == null) { + departments = new ArrayList(); + departments.add(theExtend); + } else { + String first = departments.get(0); + first = first + theExtend; + departments.set(0, first); + } + } + + public void extendLastDepartment(String theExtend) { + if (departments == null) { + departments = new ArrayList(); + departments.add(theExtend); + } else { + String first = departments.get(departments.size() - 1); + first = first + theExtend; + departments.set(departments.size() - 1, first); + } + } + + public void extendFirstLaboratory(String theExtend) { + if (laboratories == null) { + laboratories = new ArrayList(); + laboratories.add(theExtend); + } else { + String first = laboratories.get(0); + first = first + theExtend; + laboratories.set(0, first); + } + } + + public void extendLastLaboratory(String theExtend) { + if (laboratories == null) { + laboratories = new ArrayList(); + laboratories.add(theExtend); + } else { + String first = laboratories.get(laboratories.size() - 1); + first = first + theExtend; + laboratories.set(laboratories.size() - 1, first); + } + } + + public boolean notNull() { + return !((departments == null) & + (institutions == null) & + (laboratories == null) & + (country == null) & + (postCode == null) & + (postBox == null) & + (region == null) & + (settlement == null) & + (addrLine == null) & + (affiliationString == null) & + (addressString == null)); + } + + public void setFailAffiliation(boolean b) { + failAffiliation = b; + } + + public boolean getFailAffiliation() { + return failAffiliation; + } + + public void setKey(String key) { + this.key = key; + } + + public void clean() { + if (departments != null) { + List newDepartments = new ArrayList(); + for (String department : departments) { + if (department.length() > 2) { + newDepartments.add(department); + } + } + departments = newDepartments; + } + + if (institutions != null) { + List newInstitutions = new ArrayList(); + for (String institution : institutions) { + if (institution.length() > 1) { + newInstitutions.add(institution); + } + } + institutions = newInstitutions; + } + + if (laboratories != null) { + List newLaboratories = new ArrayList(); + for (String laboratorie : laboratories) { + if (laboratorie.length() > 2) { + newLaboratories.add(laboratorie); + } + } + laboratories = newLaboratories; + } + + if (country != null) { + if (country.endsWith(")")) { + // for some reason the ) at the end of this field is not removed + country = country.substring(0,country.length()-1); + } + if (country.length() < 2) + country = null; + } + if (postCode != null) { + if (postCode.length() < 2) + postCode = null; + } + if (postBox != null) { + if (postBox.length() < 2) + postBox = null; + } + if (region != null) { + if (region.length() < 2) + region = null; + } + if (settlement != null) { + if (settlement.length() < 2) + settlement = null; + } + if (addrLine != null) { + if (addrLine.length() < 2) + addrLine = null; + } + if (addressString != null) { + if (addressString.length() < 2) + addressString = null; + } + if (affiliationString != null) { + if (affiliationString.length() < 2) + affiliationString = null; + } + if (marker != null) { + marker = marker.replace(" ", ""); + } + } + + @Override + public String toString() { + return "Affiliation{" + + "name='" + name + '\'' + + ", url='" + url + '\'' + + ", key='" + key + '\'' + + ", institutions=" + institutions + + ", departments=" + departments + + ", laboratories=" + laboratories + + ", country='" + country + '\'' + + ", postCode='" + postCode + '\'' + + ", postBox='" + postBox + '\'' + + ", region='" + region + '\'' + + ", settlement='" + settlement + '\'' + + ", addrLine='" + addrLine + '\'' + + ", marker='" + marker + '\'' + + ", addressString='" + addressString + '\'' + + ", affiliationString='" + affiliationString + '\'' + + ", failAffiliation=" + failAffiliation + + '}'; + } + + +} \ No newline at end of file diff --git a/src/main/java/com/scienceminer/glutton/data/Biblio.java b/src/main/java/com/scienceminer/glutton/data/Biblio.java new file mode 100644 index 00000000..c21e9bf1 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/data/Biblio.java @@ -0,0 +1,1052 @@ +package com.scienceminer.glutton.data; + +import java.io.Serializable; +import java.lang.reflect.InvocationTargetException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.List; +import java.util.Map; +import java.util.TreeMap; +import java.util.concurrent.atomic.AtomicInteger; + +import org.apache.commons.beanutils.PropertyUtils; +import org.apache.commons.collections.CollectionUtils; +import org.apache.commons.collections.Predicate; +import org.apache.commons.collections.Transformer; +import org.apache.commons.lang3.StringUtils; + +import org.joda.time.Partial; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * A generic loosy data model for bibliographical data. + */ +public class Biblio implements Serializable { + private static final Logger LOGGER = LoggerFactory.getLogger(Biblio.class); + + // to ensure unique ID for multi-threaded object creation + static AtomicInteger nextId = new AtomicInteger(); + private final int id; // int is OK for 2 billion values + + // document type is givne by the type of the target object and the type of its host + private int documentType = BiblioDefinitions.UNKNOWN; + private int hostType = BiblioDefinitions.UNKNOWN; + + // bibliographical attributes + private final Map attributes = new TreeMap(); + + // classification information + private final List classifications = new ArrayList(); + + // targets information - only the first target (as ranked by the link resolver) is kept + private String publisherWebSite; + private List fullTextUrls; + + // the URL given by the primary publisher in the official DOI record at CrossRef + private String doiPublisherUrl; + + // list of grants + private List grants; + + // list of structured keyword objects (in contrast to a raw list of keywords as attribute field) + private List keywords; + + private List references = null; + + // TBD + // erroneous biblio item + private boolean error = false; + + public static String dateInDisplayFormat(Partial date) { + String result = DateUtils.formatDayMonthYear(date); + return result == null ? "" : result; + } + + public static String dateISODisplayFormat(Partial date) { + String result = DateUtils.formatYearMonthDay(date); + return result == null ? "" : result; + } + + public static String duplicateDateInDisplayFormat(String date) { + String result = DateUtils.formatDuplicateOrdinalDate(date); + return result == null ? "" : result; + } + + public static String issnInDisplayFormat(String issn) { + String result = BiblioUtils.formatIssn(issn); + return result == null ? "" : result; + } + + public static String isbnInDisplayFormat(String isbn) { + String result = BiblioUtils.formatIsbn(isbn); + return result == null ? "" : result; + } + + public Biblio() { + this.id = nextId.incrementAndGet(); + } + + public Biblio(int documentType, int hostType) { + this.id = nextId.incrementAndGet(); + this.documentType = documentType; + this.hostType = hostType; + } + + /** + * Return the unique immutable identifier of the biblio object + */ + public int getId() { + return this.id; + } + + protected void setPublisherAttribute(String key, Object value) { + BiblioAttribute att = attributes.get(key); + if (att != null) { + att.setAttributeValue(value); + attributes.put(key, att); + } + else { + BiblioAttribute att2 = BiblioAttribute.createPublisherAttribute(key, value); + attributes.put(key, att2); + } + } + + public Object getAttributeValue(String attributeName) { + BiblioAttribute att = attributes.get(attributeName); + return att != null ? att.getAttributeValue() : null; + } + + public BiblioAttribute getAttribute(String attributeName) { + return attributes.get(attributeName); + } + + public String getPublisherWebSite() { + return publisherWebSite; + } + + public void setPublisherWebSite(String publisherWebSite) { + this.publisherWebSite = publisherWebSite; + } + + public List getFullTextUrls() { + return fullTextUrls; + } + + public void setFullTextUrls(List targetUrls) { + this.fullTextUrls = targetUrls; + } + + public void addFullTextUrl(String targetUrl) { + if (this.fullTextUrls == null) + this.fullTextUrls = new ArrayList(); + this.fullTextUrls.add(targetUrl); + } + + public String getBestFullTextUrl() { + if ( (this.fullTextUrls == null) || (this.fullTextUrls.size() == 0) ) + return null; + else + return fullTextUrls.get(0); + } + + public String getDOIPublisherUrl() { + return doiPublisherUrl; + } + + public void setDOIPublisherUrl(String doiPublisherUrl) { + this.doiPublisherUrl = doiPublisherUrl; + } + + public String getArticleTitle() { + return (String) getAttributeValue("articleTitle"); + } + + public void setArticleTitle(String value) { + setPublisherAttribute("articleTitle", value); + } + + public String getLanguage() { + return (String) getAttributeValue("language"); + } + + public void setLanguage(String language) { + setPublisherAttribute("language", language); + } + + public String getRawLanguage() { + return (String) getAttributeValue("rawLanguage"); + } + + public void setRawLanguage(String language) { + setPublisherAttribute("rawLanguage", language); + } + + public String getDoi() { + return (String) getAttributeValue("doi"); + } + + public void setDoi(String doi) { + doi = doi.replace("https://doi.org/", ""); + doi = doi.replace("http://doi.org/", ""); + doi = doi.replace("doi.org/", ""); + setPublisherAttribute("doi", StringUtils.trim(doi)); + } + + public String getHalId() { + return (String) getAttributeValue("halid"); + } + + public void setHalId(String halid) { + setPublisherAttribute("halid", StringUtils.trim(halid)); + } + + public String getHalUri() { + return (String) getAttributeValue("haluri"); + } + + public void setHalUri(String haluri) { + setPublisherAttribute("haluri", StringUtils.trim(haluri)); + } + + public String getRawPublicationType() { + return (String) getAttributeValue("rawPublicationType"); + } + + public void setRawPublicationType(String rawPublicationType) { + setPublisherAttribute("rawPublicationType", StringUtils.trim(rawPublicationType)); + } + + public String getPublicationTypeUI() { + return (String) getAttributeValue("publicationTypeUI"); + } + + public void setPublicationTypeUI(String publicationTypeUI) { + setPublisherAttribute("publicationTypeUI", StringUtils.trim(publicationTypeUI)); + } + + public void setCoreId(Integer coreId) { + setPublisherAttribute("coreId", coreId); + } + + public Integer getCoreId() { + return (Integer) getAttributeValue("coreId"); + } + + public void setPmid(Integer pmid) { + setPublisherAttribute("pmid", pmid); + } + + public Integer getPmid() { + return (Integer) getAttributeValue("pmid"); + } + + public void setPmc(String pmc) { + setPublisherAttribute("pmc", pmc); + } + + public String getPmc() { + return (String) getAttributeValue("pmc"); + } + + public void setPii(String pii) { + setPublisherAttribute("pii", pii); + } + + public String getPii() { + return (String) getAttributeValue("pii"); + } + + public void setRepoId(Integer repoId) { + setPublisherAttribute("repoId", repoId); + } + + public Integer getRepoId() { + return (Integer) getAttributeValue("repoId"); + } + + public String getPubmedId() { + return (String) getAttributeValue("pubmedid"); + } + + public void setPubmedId(String pubmedId) { + // string might be empty + if (pubmedId != null && pubmedId.trim().length() == 0) + return; + + // case ID given as "PMID: 34189422" + if (pubmedId != null && (pubmedId.startsWith("PMID:") || pubmedId.startsWith("pmid:"))) { + pubmedId = pubmedId.replace("PMID:", ""); + pubmedId = pubmedId.replace("pmid:", ""); + } + + // case "pubmed.ncbi.nlm.nih.gov/34133859/" or "https://pubmed.ncbi.nlm.nih.gov/25886103/" + // or "http://www.ncbi.nlm.nih.gov/pmc/articles/pmc7813351/" or "www.ncbi.nlm.nih.gov/pubmed/" + if (pubmedId != null && (pubmedId.startsWith("pubmed.ncbi.nlm.nih.gov/") || + pubmedId.startsWith("https://pubmed.ncbi.nlm.nih.gov/"))) { + pubmedId = pubmedId.replace("https://pubmed.ncbi.nlm.nih.gov/", ""); + pubmedId = pubmedId.replace("pubmed.ncbi.nlm.nih.gov/", ""); + pubmedId = pubmedId.replace("www.ncbi.nlm.nih.gov/pubmed/", ""); + } + if (pubmedId != null && (pubmedId.startsWith("http://www.ncbi.nlm.nih.gov/pmc/articles/pmc") || + pubmedId.startsWith("https://www.ncbi.nlm.nih.gov/pmc/articles/pmc"))) { + pubmedId = pubmedId.replace("http://www.ncbi.nlm.nih.gov/pmc/articles/", ""); + pubmedId = pubmedId.replace("https://www.ncbi.nlm.nih.gov/pmc/articles/", ""); + } + + //case ID ends with "/", which is quite common + if (pubmedId != null && pubmedId.endsWith("/")) { + pubmedId = pubmedId.replace("/", ""); + } + + // sometimes it's a DOI + if (pubmedId != null && (pubmedId.startsWith("10.") || pubmedId.startsWith("doi.org/10.")) && pubmedId.indexOf("/") != -1) { + if (getDoi() == null) { + setDoi(pubmedId); + return; + } + } + + // sometimes it's a PMC ID "PMC2655142" + if (pubmedId != null && (pubmedId.startsWith("PMC") || pubmedId.startsWith("pmc"))) { + if (getPmc() == null) { + setPmc(pubmedId); + return; + } + } + + // other weird quite common case "22642955DOI" + if (pubmedId != null && pubmedId.endsWith("DOI")) { + pubmedId = pubmedId.replace("DOI", ""); + } + + setPublisherAttribute("pubmedid", StringUtils.trim(pubmedId)); + } + + public String getPublisher() { + return (String) getAttributeValue("publisher"); + } + + public void setPublisher(String publisher) { + setPublisherAttribute("publisher", publisher); + } + + public int getDocumentType() { + return documentType; + } + + public void setDocumentType(int documentType) { + this.documentType = documentType; + } + + public Partial getPublicationDate() { + return (Partial) getAttributeValue("publicationDate"); + } + + /** + * Returns the earliest of the printed and the electronic publication dates. + * If the two dates have the same root, but one is more specific, then the more specific + * one is returned (i.e. 2001-02-01 will be returned in favour of 2001-02) + */ + public Partial getOldestPublicationDate() { + Partial printed = getPublicationDate(); + Partial electronic = getEPublicationDate(); + + if (printed == null) { + return electronic; + } + if (electronic == null) { + return printed; + } + + int[] fieldsPrinted = printed.getValues(); + int[] fieldsElectronic = electronic.getValues(); + + // the fields are returned largest to smallest. + for (int i = 0; i < Math.min(fieldsPrinted.length, fieldsElectronic.length); i++) { + if (fieldsPrinted[i] != fieldsElectronic[i]) { + return fieldsPrinted[i] < fieldsElectronic[i] ? printed : electronic; + } + } + + // if we got this far, either they are an exact match (in which case it doesn't matter which we return), + // or one is more specific than the other, in which case we return the most detailed. + return fieldsPrinted.length > fieldsElectronic.length ? printed : electronic; + } + + public void setPublicationDate(Partial date) { + setPublisherAttribute("publicationDate", date); + } + + public Partial getEPublicationDate() { + return (Partial) getAttributeValue("ePublicationDate"); + } + + public void setEPublicationDate(Partial date) { + setPublisherAttribute("ePublicationDate", date); + } + + public Partial getLastUpdateDate() { + return (Partial) getAttributeValue("lastUpdateDate"); + } + + public void setLastUpdateDate(Partial date) { + setPublisherAttribute("lastUpdateDate", date); + } + + public String getTitle() { + return (String) getAttributeValue("title"); + } + + public void setTitle(String title) { + setPublisherAttribute("title", title); + } + + public String getJournalAbbrev() { + return (String) getAttributeValue("journal_abbrev"); + } + + public void setJournalAbbrev(String abbrev) { + setPublisherAttribute("journal_abbrev", abbrev); + } + + public String getVolume() { + return (String) getAttributeValue("volume"); + } + + public void setVolume(String volume) { + setPublisherAttribute("volume", volume); + } + + public String getStartPage() { + return (String) getAttributeValue("start_page"); + } + + public void setStartPage(String page) { + setPublisherAttribute("start_page", page); + } + + public String getEndPage() { + return (String) getAttributeValue("end_page"); + } + + public void setEndPage(String page) { + setPublisherAttribute("end_page", page); + } + + public Integer getStartPageInt() { + return (Integer) getAttributeValue("start_page_int"); + } + + public void setStartPageInt(Integer page) { + setPublisherAttribute("start_page_int", page); + } + + public Integer getEndPageInt() { + return (Integer) getAttributeValue("end_page_int"); + } + + public void setEndPageInt(Integer page) { + setPublisherAttribute("end_page_int", page); + } + + public Integer getReferenceCount() { + if (references != null) + return references.size(); + else + return null; + } + + public void addReference(Reference reference) { + if (this.references == null) { + this.references = new ArrayList<>(); + } + this.references.add(reference); + } + + public void setReference(List theReferences) { + this.references = theReferences; + } + + public List getReferences() { + return this.references; + } + + public String getPagination() { + return (String) getAttributeValue("pagination"); + } + + public void setPagination(String page) { + setPublisherAttribute("pagination", page); + } + + + public int getHostType() { + return hostType; + } + + public void setHostType(int hostType) { + this.hostType = hostType; + } + + public String getIssn() { + return (String) getAttributeValue("issn"); + } + + public void setIssn(String issn) { + setPublisherAttribute("issn", StringUtils.replace(issn, "-", "")); + } + + public String getEIssn() { + return (String) getAttributeValue("eissn"); + } + + public void setEIssn(String eissn) { + setPublisherAttribute("eissn", StringUtils.replace(eissn, "-", "")); + } + + public String getNumber() { + return (String) getAttributeValue("number"); + } + + public void setNumber(String number) { + setPublisherAttribute("number", number); + } + + public String getOriginalDocumentype() { + return (String) getAttributeValue("originalDocumentype"); + } + + public void setOriginalDocumentype(String theType) { + setPublisherAttribute("originalDocumentype", theType); + } + + public String getIsbn() { + return (String) getAttributeValue("isbn13"); + } + + public void setIsbn(String isbn13) { + String isbn = StringUtils.replace(isbn13, "-", ""); + + if (isbn.length() == 10) { + try { + isbn = BiblioUtils.isbn10to13(isbn); + } catch(Exception e) { + // log this invalid isbn + LOGGER.error("Invalid ISBN format: " + isbn13); + return; + } + } + + setPublisherAttribute("isbn13", isbn); + } + + public void setAuthors(List authors) { + if ( (authors == null) || (authors.size() == 0) ) + return; + else { + setFirstAuthor(authors.get(0)); + for (int i=1; i authors = getCoAuthors(); + + boolean present = isPresent(newAuthor, authors); + + if (!present) { + authors.add(newAuthor); + } + + if (!newAuthor.isEmptyPerson()) { + stripEmptyAuthors(); + } + } + + private void stripEmptyAuthors() { + CollectionUtils.filter(getCoAuthors(), new Predicate() { + + public boolean evaluate(Object arg0) { + Person person = (Person) arg0; + return !person.isEmptyPerson(); + } + }); + } + + @SuppressWarnings("unchecked") + public List getCoAuthors() { + List authors = (List) getAttributeValue("authors"); + + if (authors == null) { + authors = new ArrayList(); + setPublisherAttribute("authors", authors); + } + + return authors; + } + + @SuppressWarnings("unchecked") + public List getAuthors() { + List allAuthors = new ArrayList<>(); + + Person firstAuthor = getFirstAuthor(false); + if (firstAuthor != null) + allAuthors.add(firstAuthor); + + List authors = (List) getAttributeValue("authors"); + if (authors != null) { + allAuthors.addAll(authors); + } + + return allAuthors; + } + + public Person getFirstAuthor() { + return getFirstAuthor(false); + } + + /** Returns the first author, creating an entry if it isn't already present. */ + protected Person getFirstAuthor(boolean createIfNotPresent) { + Person person = (Person) getAttributeValue("firstAuthor"); + if (person == null && createIfNotPresent) { + person = new Person(); + setFirstAuthor(person); + } + return person; + } + + public void setFirstAuthor(Person person) { + setPublisherAttribute("firstAuthor", person); + } + + public void setCoAuthors(List authors) { + setPublisherAttribute("authors", authors); + } + + public String getCoAuthorsAsString() { + return (String) getAttributeValue("coAuthors"); + } + + /** + * Returns a string containing the formatted list of authors (not including the first). + * @param generate is this is set, generate the string if it was not already present. + * @return + */ + public String getCoAuthorsAsString(boolean generate) { + String result = getCoAuthorsAsString(); + if (StringUtils.isBlank(result) && generate) { + result = generateAdditionalAuthorsOrEditorsString(getCoAuthors()); + } + return result; + } + + public void setCoAuthorsAsString(String authors) { + setPublisherAttribute("coAuthors", Person.normalizeName(authors)); + } + + public String getEditorsAsString() { + return (String) getAttributeValue("editorsAsString"); + } + + public String getEditorsAsString(boolean generate) { + String result = (String) getAttributeValue("editorsAsString"); + if (StringUtils.isEmpty(result) && generate) { + result = printEditorList(); + } + return result; + } + + public void setEditorsAsString(String editors) { + setPublisherAttribute("editorsAsString", editors); + } + + public void addEditor(Person editor) { + List editors = getEditors(); + boolean present = isPresent(editor, editors); + + if (!present) { + editors.add(editor); + } + + setPublisherAttribute("editors", editors); + } + + protected boolean isPresent(Person testPerson, List persons) { + for (Person person : persons) { + if (isSame(person, testPerson)) { + return true; + } + } + return false; + } + + private static boolean isSame(Person person, Person testPerson) { + if (person == null || person.getLastName() == null || testPerson == null) { + return false; + } + + if (person.getLastName().equals(testPerson.getLastName())) { + if (person.getFirstName() != null) { + return person.getFirstName().equals(testPerson.getFirstName()); + } + else if (person.getInits() != null) { + return person.getInits().equals(testPerson.getInits()); + } + return true; + } + return false; + + } + + @SuppressWarnings("unchecked") + public List getEditors() { + List editors = (List) getAttributeValue("editors"); + if (editors == null) { + editors = new ArrayList(); + setEditors(editors); + } + return editors; + } + + public void setEditors(List editors) { + setPublisherAttribute("editors", editors); + } + + public String getAbstract() { + return (String) getAttributeValue("abstractBlock"); + } + + public void setAbstract(String abstractBlock) { + setPublisherAttribute("abstractBlock", abstractBlock); + } + + public String getKeywords() { + return (String) getAttributeValue("keywords"); + } + + public void setKeywords(String keywords) { + setPublisherAttribute("keywords", keywords); + } + + public List getKeywordItems() { + return keywords; + } + + public void setKeywordItems(List keywords) { + this.keywords = keywords; + } + + public void addKeywordItems(Keyword keyword) { + if (this.keywords == null) + this.keywords = new ArrayList<>(); + this.keywords.add(keyword); + } + + public String getCollectionTitle() { + return (String) getAttributeValue("collection_title"); + } + + public void setCollectionTitle(String collectionTitle) { + setPublisherAttribute("collection_title", collectionTitle); + } + + public String getEventName() { + return (String) getAttributeValue("event_name"); + } + + public void setEventName(String name) { + setPublisherAttribute("event_name", name); + } + + public String getEventLocation() { + return (String) getAttributeValue("event_location"); + } + + public void setEventLocation(String location) { + setPublisherAttribute("event_location", location); + } + + public Partial getEventStartDate() { + return (Partial) getAttributeValue("event_start_date"); + } + + public void setEventStartDate(Partial startDate) { + setPublisherAttribute("event_start_date", startDate); + } + + public Partial getEventEndDate() { + return (Partial) getAttributeValue("event_end_date"); + } + + public void setEventEndDate(Partial date) { + setPublisherAttribute("event_end_date", date); + } + + public Partial getServerOnlineDate() { + return (Partial) getAttributeValue("server_online_date"); + } + + public void setServerOnlineDate(Partial date) { + setPublisherAttribute("server_online_date", date); + } + + public Partial getRetrievalDate() { + return (Partial) getAttributeValue("retrieval_date"); + } + + public void setRetrievalDate(Partial date) { + setPublisherAttribute("retrieval_date", date); + } + + public String getPublicationPlace() { + return (String) getAttributeValue("publication_place"); + } + + public void setPublicationPlace(String place) { + setPublisherAttribute("publication_place", place); + } + + public String getUrl() { + return (String) getAttributeValue("url"); + } + + public void setUrl(String url) { + setPublisherAttribute("url", url); + } + + public boolean getIsSinglePage() { + return StringUtils.isBlank(getStartPage()) || StringUtils.isBlank(getEndPage()) + || StringUtils.equals(getStartPage(), getEndPage()); + } + + public String getPageRange() { + /*if (StringUtils.isNotBlank(getStartPage()) && StringUtils.isNotBlank(getEndPage()) + && getStartPage().equals(getEndPage())) { + return getStartPage(); + }*/ + if (StringUtils.isNotBlank(getStartPage()) && StringUtils.isNotBlank(getEndPage())) { + if (getStartPage().equals(getEndPage())) + return getStartPage(); + else + return getStartPage() + "-" + getEndPage(); + } + if (StringUtils.isNotBlank(getStartPage())) { + return getStartPage(); + } + if (StringUtils.isNotBlank(getEndPage())) { + return getEndPage(); + } + return ""; + } + + public void setFirstAuthorSurname(String name) { + getFirstAuthor(true).setLastName(Person.normalizeName(name)); + } + + public void setFirstAuthorMiddleName(String name) { + getFirstAuthor(true).setMiddleName(Person.normalizeName(name)); + } + + public void setFirstAuthorFirstName(String name) { + getFirstAuthor(true).setFirstName(Person.normalizeName(name)); + } + + public List getGrants() { + return grants; + } + + public void setGrants(List grants) { + this.grants = grants; + } + + public void addGrant(Grant grant) { + if (this.grants == null) { + this.grants = new ArrayList<>(); + } + this.grants.add(grant); + } + + /** Returns the page range. */ + public String printPages() { + if (StringUtils.isNotBlank(getPageRange())) { + String prefix = getIsSinglePage() ? "Page" : "Pages"; + return prefix + " " + getPageRange(); + } + return ""; + } + + /** Prints the conference dates for display. */ + public String printConferenceDates() { + String result = null; + if (getEventStartDate() != null) { + result = dateInDisplayFormat(getEventStartDate()); + } + + if (getEventEndDate() != null) { + if (StringUtils.isNotEmpty(result)) { + result += " - "; + } + result += dateInDisplayFormat(getEventEndDate()); + } + return result; + } + + /** Returns the article title, or 'No Title' if not set. */ + public String printArticleTitle() { + return StringUtils.isNotBlank(getArticleTitle()) ? getArticleTitle() : "No Title"; + } + + /** Returns the name of the first author. */ + public String printFirstAuthor() { + Person firstAuthor = getFirstAuthor(); + return firstAuthor == null ? "" : StringUtils.trimToEmpty(firstAuthor.getLastName()); + } + + /** Returns a comma separated String of the author names. */ + public String printAuthorList() { + return printAuthorOrEditors(getFirstAuthor(), getCoAuthors(), getCoAuthorsAsString()); + } + + /** Returns a comma separated String of the editor names. */ + public String printEditorList() { + return printAuthorOrEditors(null, getEditors(), getEditorsAsString()); + } + + private String printAuthorOrEditors(Person first, List list, String flatList) { + String result = first != null ? first.printFullName() : ""; + + if (StringUtils.isNotBlank(flatList)) { + if (StringUtils.isNotBlank(result)) { + result += ", "; + } + result += flatList; + } + else if (!list.isEmpty()) { + if (StringUtils.isNotBlank(result)) { + result += ", "; + } + result += generateAdditionalAuthorsOrEditorsString(list); + } + + return result; + } + + public List getClassifications() { + return this.classifications; + } + + public void addClassifications(List newClasses) { + for(ClassificationClass classification : newClasses) + addClass(classification); + } + + /** Add a classification class */ + public void addClass(ClassificationClass theClass) { + classifications.add(theClass); + } + + /** Generates a comma separated string from all entries except the first. */ + @SuppressWarnings("rawtypes") + private String generateAdditionalAuthorsOrEditorsString(List people) { + Collection formatted = CollectionUtils.collect(people, new Transformer() { + public Object transform(Object input) { + return ((Person) input).printFullName(); + } + }); + return StringUtils.join(formatted, ", "); + } + + /** Correct fields of the first Biblio item based on the second one. */ + public void correct(Biblio source) { + if (source == null) { + return; + } + + defaultPropertyIfNull(this, source, "hostType"); + defaultPropertyIfNull(this, source, "documentType"); + defaultPropertyIfNull(this, source, "doi"); + defaultPropertyIfNull(this, source, "pii"); + defaultPropertyIfNull(this, source, "pmc"); + defaultPropertyIfNull(this, source, "pubmedid"); + defaultPropertyIfNull(this, source, "title"); + defaultPropertyIfNull(this, source, "firstAuthor"); + defaultPropertyIfNull(this, source, "volume"); + defaultPropertyIfNull(this, source, "number"); + defaultPropertyIfNull(this, source, "startPage"); + defaultPropertyIfNull(this, source, "endPage"); + defaultPropertyIfNull(this, source, "publicationPlace"); + defaultPropertyIfNull(this, source, "publisher"); + defaultPropertyIfNull(this, source, "articleTitle"); + defaultPropertyIfNull(this, source, "collectionTitle"); + defaultPropertyIfNull(this, source, "journalAbbrev"); + defaultPropertyIfNull(this, source, "issn"); + defaultPropertyIfNull(this, source, "EIssn"); + defaultPropertyIfNull(this, source, "isbn"); + defaultPropertyIfNull(this, source, "abstract"); + defaultPropertyIfNull(this, source, "keywords"); + defaultPropertyIfNull(this, source, "eventName"); + defaultPropertyIfNull(this, source, "eventLocation"); + defaultPropertyIfNull(this, source, "fullTextUrl"); + defaultPropertyIfNull(this, source, "publisherWebSite"); + + if (source.getCoAuthors().size() >= getCoAuthors().size()) { + setCoAuthors(source.getCoAuthors()); + } + + if (source.getEditors().size() >= getEditors().size()) { + setEditors(source.getEditors()); + } + + // DOI linking is not represented as bibliographical attribute but as a special variable + if (source.getDOIPublisherUrl() != null) { + setDOIPublisherUrl(source.getDOIPublisherUrl()); + } + + if (getPublicationDate() == null) { + setPublicationDate(source.getPublicationDate()); + } + else if (source.getPublicationDate() != null + && source.getPublicationDate().size() >= getPublicationDate().size()) { + setPublicationDate(source.getPublicationDate()); + } + + if (getEventStartDate() == null && source.getEventStartDate() != null) { + setEventStartDate(source.getEventStartDate()); + } + + if (getEventEndDate() == null && source.getEventEndDate() != null) { + setEventEndDate(source.getEventEndDate()); + } + } + + /** Given that nearly everything here is using a hash map, would be far cleaner to use that instead of reflection. */ + private static void defaultPropertyIfNull(Biblio target, Biblio source, String propertyName) { + try { + Object srcValue = PropertyUtils.getProperty(source, propertyName); + + if (srcValue != null) { + PropertyUtils.setProperty(target, propertyName, srcValue); + } + } + catch (IllegalAccessException e) { + throw new RuntimeException("Unable to access property " + propertyName); + } + catch (InvocationTargetException e) { + throw new RuntimeException("Unable to access property " + propertyName); + } + catch (NoSuchMethodException e) { + throw new RuntimeException("No getter/setter for property " + propertyName); + } + } + +} \ No newline at end of file diff --git a/src/main/java/com/scienceminer/glutton/data/BiblioAttribute.java b/src/main/java/com/scienceminer/glutton/data/BiblioAttribute.java new file mode 100644 index 00000000..b77ac29f --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/data/BiblioAttribute.java @@ -0,0 +1,89 @@ +package com.scienceminer.glutton.data; + +import java.io.Serializable; + +/** + * Encapsulates a property of the Biblio attribute. + */ +@SuppressWarnings("serial") +public class BiblioAttribute implements Serializable { + + // source + public static final int PUBLISHER = 0; + public static final int EXTRACTION = 1; + public static final int USER = 2; + + // user status + public static final int NOT_VALIDATED = 0; + public static final int VALIDATED = 1; + + private String attributeName = null; + private Object attributeValue = null; + private int attributeSource = -1; + private int userStatus = -1; + private double confidence = 0.0; + + public static BiblioAttribute createPublisherAttribute(String name, Object value) { + BiblioAttribute att = new BiblioAttribute(); + att.attributeName = name; + att.attributeValue = value; + att.attributeSource = PUBLISHER; + att.userStatus = NOT_VALIDATED; + att.confidence = 1.0; + return att; + } + + public static BiblioAttribute createExtractedAttribute(String name, Object value, double conf) { + BiblioAttribute att = new BiblioAttribute(); + att.attributeName = name; + att.attributeValue = value; + att.attributeSource = EXTRACTION; + att.userStatus = NOT_VALIDATED; + att.confidence = conf; + return att; + } + + public void setAttributeName(String attributeName) { + this.attributeName = attributeName; + } + + public String getAttributeName() { + return attributeName; + } + + public void setAttributeValue(Object attributeValue) { + this.attributeValue = attributeValue; + } + + public Object getAttributeValue() { + return attributeValue; + } + + public void setAttributeSource(int attributeSource) { + this.attributeSource = attributeSource; + } + + public int getAttributeSource() { + return attributeSource; + } + + public void setUserStatus(int userStatus) { + this.userStatus = userStatus; + } + + public int getUserStatus() { + return userStatus; + } + + public void setConfidence(double confidence) { + this.confidence = confidence; + } + + public double getConfidence() { + return confidence; + } + + public String toString() { + return attributeName + ":" + attributeValue; + } +} diff --git a/src/main/java/com/scienceminer/glutton/data/BiblioDefinitions.java b/src/main/java/com/scienceminer/glutton/data/BiblioDefinitions.java new file mode 100644 index 00000000..f107d33d --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/data/BiblioDefinitions.java @@ -0,0 +1,156 @@ +package com.scienceminer.glutton.data; + +import java.io.Serializable; +import java.lang.reflect.InvocationTargetException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.List; +import java.util.Map; +import java.util.TreeMap; +import java.util.concurrent.atomic.AtomicInteger; + +import org.apache.commons.beanutils.PropertyUtils; +import org.apache.commons.collections.CollectionUtils; +import org.apache.commons.collections.Predicate; +import org.apache.commons.collections.Transformer; +import org.apache.commons.lang3.StringUtils; + +import org.joda.time.Partial; + +/** + * Static metadata characterization of publication types. + */ +public class BiblioDefinitions { + static final char[] NAME_DELIMITERS = new char[]{'.', ',', ';', ':', '-', ' '}; + + // document type + public static final int ARTICLE = 0; + public static final int JOURNAL = 1; + public static final int PROCEEDINGS = 2; + public static final int COLLECTION = 3; + public static final int BOOK = 4; + public static final int ONLINE = 5; + public static final int REPORT = 6; + public static final int UNKNOWN = -1; + + // data management attributes + private static final List DATA_MANAGEMENT = Arrays.asList("coreDate", "crossrefDate", + "coreJson", "crossrefString", + "istexDate", "istexJson", + "dc:type", "repoId", "coreId", + "pmid", "pmc", "pii", + "language", "rawLanguage"); + + // bibliographical item profile per bibliographical type + // article published in a journal + private static final List ARTICLE_IN_JOURNAL = Arrays.asList("articleTitle", + "authors", "year", "month", + "day", "eyear", "emonth", + "eday", "title", "volume", + "number", "start_page", + "end_page", "pagination", + "start_page_int", "end_page_int", + "editors", + "issn", "eissn", "doi", + "publisher"); + private static final List ARTICLE_IN_JOURNAL_COMPACT = Arrays.asList("articleTitle", + "firstAuthorSurname", + "journal_abbrev", "volume", + "number", "start_page", + "pagination", + "start_page_int", "end_page_int", + "end_page", "day", "month", + "year"); + // article published in conference proceedings + private static final List ARTICLE_IN_PROCEEDINGS = Arrays.asList("articleTitle", + "authors", "year", "month", + "day", "eyear", "emonth", + "eday", "title", "volume", + "start_page", "end_page", + "pagination", + "start_page_int", "end_page_int", + "editors", "event_name", + "event_location", + "event_start_date", + "event_end_date", "doi", + "isbn", "publisher", + "publication_place"); + private static final List ARTICLE_IN_PROCEEDINGS_COMPACT = Arrays.asList("articleTitle", + "firstAuthorSurname", + "title", + "event_start_date", + "event_end_date", "volume", + "start_page", "end_page", + "pagination", + "start_page_int", "end_page_int", + "day", "month", "year"); + // article published in a book + private static final List ARTICLE_IN_BOOK = Arrays.asList("articleTitle", + "authors", "year", "month", + "day", "eyear", "emonth", + "eday", "title", + "start_page", "end_page", + "start_page_int", "end_page_int", + "pagination", + "editors", "doi", "isbn", + "publisher", + "publication_place"); + private static final List ARTICLE_IN_BOOK_COMPACT = Arrays.asList("articleTitle", + "firstAuthorSurname", + "title", "start_page", + "pagination", + "start_page_int", "end_page_int", + "end_page", "day", "month", + "year"); + // article published in a collection (e.g. Lecture Notes in computer Sciences) + private static final List ARTICLE_IN_COLLECTION = Arrays.asList("articleTitle", + "authors", "year", "month", + "day", "eyear", "emonth", + "eday", "title", + "start_page", "end_page", + "pagination", + "start_page_int", "end_page_int", + "collection_title", + "editors", "isbn", "issn", + "eissn", "volume", "doi", + "publisher", + "publication_place"); + private static final List ARTICLE_IN_COLLECTION_COMPACT = Arrays.asList("articleTitle", + "firstAuthorSurname", + "title", + "collection_title", + "start_page", "end_page", + "pagination", + "start_page_int", "end_page_int", + "day", "month", "year"); + + // document published online (e.g. on a research archive or on the author's home page) + // this format have to encompass what ever we find online, i.e. + // to handle all types of PDF documents submitted without bibliographic data. + // note that the URL is here important and it is different from getTargetUrl + private static final List DOCUMENT_ONLINE = Arrays.asList("articleTitle", + "authors", "year", "month", + "day", "eyear", "emonth", + "eday", "title", + "start_page", "end_page", + "pagination", + "start_page_int", "end_page_int", + "editors", "doi", + "publisher", "isbn", + "server_online_date", + "publication_place", + "retrieval_date", + "publisher", "url"); + private static final List DOCUMENT_ONLINE_COMPACT = Arrays.asList("articleTitle", + "firstAuthorSurname", + "year", "month", "day", + "eday", "emonth", "title", + "start_page", "end_page", + "pagination", + "start_page_int", "end_page_int", + "eyear"); + + + +} \ No newline at end of file diff --git a/src/main/java/com/scienceminer/glutton/data/BiblioUtils.java b/src/main/java/com/scienceminer/glutton/data/BiblioUtils.java new file mode 100644 index 00000000..d3fe0f9e --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/data/BiblioUtils.java @@ -0,0 +1,90 @@ +package com.scienceminer.glutton.data; + +/** + * Utility class, to easily handle Biblio related tasks. + */ +public final class BiblioUtils { + + private BiblioUtils() { + } + + /** + * Convert ISBN10 to ISBN13, as documented on http://www.isbn-13.info/ + * + * @param isbn the isbn10 to convert, assuming there are only numbers in the string + * @return the converted isbn13 string + */ + public static String isbn10to13(String isbn) { + if (isbn.length() != 10) { + throw new IllegalArgumentException("Can only convert ISBN10. Incorrect length (" + isbn.length() + + ") for: " + isbn); + } + + String isbn13 = "978" + isbn.substring(0, 9); + + int checksum = 0; + for (int i = 1; i <= isbn13.length(); i++) { + + try { + int a = Integer.parseInt(String.valueOf(isbn13.charAt(i - 1))); + + if (i % 2 == 1) { + checksum += a; + } + else { + checksum += 3 * a; + } + } catch(Exception e) { + // nothing to be done then + throw new IllegalArgumentException("Invalid ISBN10, it must be only digits: " + isbn); + } + } + + checksum = 10 - (checksum % 10); + + return isbn13 + String.valueOf(checksum); + } + + /** + * Formats an issn String to ####-####. + * + * @param issn the issn, assuming the string contains 8 numbers + * @return + */ + public static String formatIssn(String issn) { + if (issn == null) { + return null; + } + + StringBuilder builder = new StringBuilder(issn); + + if (builder.length() == 8) { + builder.insert(4, '-'); + } + + return builder.toString(); + } + + /** + * Formats an ISBN String to ###-#-##-######-#. + * + * @param isbn the isbn, assuming the string contains 13 numbers + * @return + */ + public static String formatIsbn(String isbn) { + if (isbn == null) { + return null; + } + + StringBuilder builder = new StringBuilder(isbn); + + if (builder.length() == 13) { + builder.insert(12, '-'); + builder.insert(6, '-'); + builder.insert(4, '-'); + builder.insert(3, '-'); + } + + return builder.toString(); + } +} diff --git a/src/main/java/com/scienceminer/glutton/data/ClassificationClass.java b/src/main/java/com/scienceminer/glutton/data/ClassificationClass.java new file mode 100644 index 00000000..3126d2f0 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/data/ClassificationClass.java @@ -0,0 +1,36 @@ +package com.scienceminer.glutton.data; + +import java.io.Serializable; +import java.lang.reflect.InvocationTargetException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.List; +import java.util.Map; +import java.util.TreeMap; +import java.util.concurrent.atomic.AtomicInteger; + +import org.apache.commons.beanutils.PropertyUtils; +import org.apache.commons.collections.CollectionUtils; +import org.apache.commons.collections.Predicate; +import org.apache.commons.collections.Transformer; +import org.apache.commons.lang3.StringUtils; + +import org.joda.time.Partial; + +/** + * A class for classification classes + */ +public class ClassificationClass implements Serializable { + + private String scheme; + + public ClassificationClass(String scheme) { + this.scheme = scheme; + } + + public String getScheme() { + return this.scheme; + } + +} \ No newline at end of file diff --git a/src/main/java/com/scienceminer/glutton/data/DateUtils.java b/src/main/java/com/scienceminer/glutton/data/DateUtils.java new file mode 100644 index 00000000..4a5e5302 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/data/DateUtils.java @@ -0,0 +1,200 @@ +package com.scienceminer.glutton.data; + +import java.util.Date; + +import org.apache.commons.lang3.StringUtils; +import org.joda.time.DateTimeFieldType; +import org.joda.time.DateTimeZone; +import org.joda.time.LocalDate; +import org.joda.time.Partial; +import org.joda.time.format.*; + +/** + * Utility class to handle all {@link Partial} date related tasks regarding the Biblio class. + * + * @see Partial + */ +public final class DateUtils { + + /** The standard three fields used for constructing a date - YEAR, MONTH, DAY. */ + public static final DateTimeFieldType[] YEAR_MONTH_DAY = {DateTimeFieldType.year(), + DateTimeFieldType.monthOfYear(), DateTimeFieldType.dayOfMonth()}; + + private DateUtils() { + } + + /** Prints a partial date in dd-MM-yyyy format, where dd and MM are optional. */ + public static String formatDayMonthYear(Partial date) { + if (date == null) { + return null; + } + + StringBuilder builder = new StringBuilder(12); + + if (date.isSupported(DateTimeFieldType.year())) { + builder.append(date.get(DateTimeFieldType.year())); + + if (date.isSupported(DateTimeFieldType.monthOfYear())) { + builder.insert(0, '-'); + builder.insert(0, + StringUtils.leftPad(String.valueOf(date.get(DateTimeFieldType.monthOfYear())), 2, '0')); + + if (date.isSupported(DateTimeFieldType.dayOfMonth())) { + builder.insert(0, '-'); + builder.insert(0, + StringUtils.leftPad(String.valueOf(date.get(DateTimeFieldType.dayOfMonth())), 2, '0')); + } + } + } + return builder.toString(); + } + + /** Prints a partial date in yyyy-MM-dd format, where dd and MM are optional. */ + public static String formatYearMonthDay(Partial date) { + if (date == null) { + return null; + } + + StringBuilder builder = new StringBuilder(12); + + if (date.isSupported(DateTimeFieldType.year())) { + builder.append(date.get(DateTimeFieldType.year())); + + if (date.isSupported(DateTimeFieldType.monthOfYear())) { + builder.append('-'); + String theMonth = String.valueOf(date.get(DateTimeFieldType.monthOfYear())); + if (theMonth.length() == 1) + theMonth = "0" + theMonth; + builder.append(theMonth); + + if (date.isSupported(DateTimeFieldType.dayOfMonth())) { + builder.append('-'); + String theDay = String.valueOf(date.get(DateTimeFieldType.dayOfMonth())); + if (theDay.length() == 1) + theDay = "0" + theDay; + builder.append(theDay); + } + } + } + return builder.toString(); + } + + /** To convert a partial date to a full java.util.Date, we need to fill in any missing fields. */ + public static Date asDate(Partial partialDate) { + if (partialDate == null || !partialDate.isSupported(DateTimeFieldType.year())) { + return null; + } + int year = partialDate.get(DateTimeFieldType.year()); + int month = partialDate.isSupported(DateTimeFieldType.monthOfYear()) ? partialDate.get(DateTimeFieldType + .monthOfYear()) : 1; + int day = partialDate.isSupported(DateTimeFieldType.dayOfMonth()) ? partialDate.get(DateTimeFieldType + .dayOfMonth()) : 1; + + LocalDate dateTime = new LocalDate(year, month, day); + return dateTime.toDateTimeAtStartOfDay().toDate(); + } + + /** Builds a date from DMY format, where day and month are optional. */ + public static Partial buildDate(String day, String month, String year) { + if (StringUtils.isNotBlank(year)) { + Partial date = new Partial(); + date = date.with(DateTimeFieldType.year(), Integer.valueOf(year)); + + if (StringUtils.isNotBlank(month)) { + date = date.with(DateTimeFieldType.monthOfYear(), Integer.valueOf(month)); + + if (StringUtils.isNotBlank(day)) { + date = date.with(DateTimeFieldType.dayOfMonth(), Integer.valueOf(day)); + } + } + return date; + } + + return null; + } + + /** Builds a date from dd-MM-yyyy format, where day and month are optional. */ + public static Partial partialFromDMYDateString(String date) { + if (StringUtils.isBlank(date)) { + return null; + } + + try { + switch (date.length()) { + case 4 : + // yyyy + return buildDate(null, null, date); + case 7 : + // MM-yyyy + return buildDate(null, date.substring(0, 2), date.substring(3)); + case 10 : + // dd-MM-yyyy + return buildDate(date.substring(0, 2), date.substring(3, 5), date.substring(6)); + default : + break; + } + + return null; + } + catch (NumberFormatException e) { + // we can not handle this exception to anything better + return null; + } + } + + /** Builds a date from yyyy-MM-dd format, where day and month are optional. */ + public static Partial partialFromYMDDateString(String date) { + if (StringUtils.isBlank(date)) { + return null; + } + + try { + switch (date.length()) { + case 4 : + // yyyy + return buildDate(null, null, date); + case 7 : + // yyyy-MM + return buildDate(null, date.substring(5), date.substring(0, 4)); + case 10 : + // yyyy-MM-dd + return buildDate(date.substring(8), date.substring(5, 7), date.substring(0, 4)); + default : + return null; + } + } + catch (NumberFormatException e) { + // we can not handle this exception to anything better + return null; + } + } + + /** + * Formats the date with extra invalid day/month + */ + public static String formatDuplicateOrdinalDate(String date) { + if (date == null) { + return null; + } + else if (date.matches("\\d{4}-00(-00)?")) { + return date.substring(0, 4); + } + else if (date.matches("\\d{4}-(0[1-9]|1[012])-(0[1-9]|[12][0-9]|3[01])")) { + return date.substring(8, 10) + "-" + date.substring(5, 7) + "-" + date.substring(0, 4); + } + else { + return date; + } + } + + /** + * Serialize partial date into ISO format + */ + public static String dateISO(Partial date) { + if (date == null) { + return null; + } + DateTimeFormatter fmt = ISODateTimeFormat.dateTime().withZone(DateTimeZone.getDefault()); + return date.toString(fmt); + } +} diff --git a/src/main/java/com/scienceminer/glutton/data/Grant.java b/src/main/java/com/scienceminer/glutton/data/Grant.java new file mode 100644 index 00000000..59694e3c --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/data/Grant.java @@ -0,0 +1,72 @@ +package com.scienceminer.glutton.data; + +import java.io.Serializable; +import java.util.*; + +import org.apache.commons.lang3.NotImplementedException; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.lang3.text.WordUtils; + +/** + * Encapsulates information about a Grant attached to a bibliographical work. + */ +@SuppressWarnings("serial") +public class Grant implements Serializable { + + private String grantID; + private String acronym; + private String agency; + private String country; + + public Grant() { + } + + public Grant(String grantID, String acronym, String agency, String country) { + setGrantID(grantID); + setAcronym(acronym); + setAgency(agency); + setCountry(country); + } + + public String getGrantID() { + return grantID; + } + + public void setGrantID(String grantID) { + this.grantID = grantID; + } + + public String getAcronym() { + return acronym; + } + + public void setAcronym(String acronym) { + this.acronym = acronym; + } + + public String getAgency() { + return agency; + } + + public void setAgency(String agency) { + this.agency = agency; + } + + public String getCountry() { + return country; + } + + public void setCountry(String country) { + this.country = country; + } + + @Override + public String toString() { + return "Grant{" + + "grantID='" + grantID + '\'' + + ", acronym='" + acronym + '\'' + + ", agency='" + agency + '\'' + + ", country=" + country + + '}'; + } +} \ No newline at end of file diff --git a/src/main/java/com/scienceminer/glutton/data/Identifier.java b/src/main/java/com/scienceminer/glutton/data/Identifier.java new file mode 100644 index 00000000..339a0746 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/data/Identifier.java @@ -0,0 +1,49 @@ +package com.scienceminer.glutton.data; + +import java.io.Serializable; +import com.fasterxml.jackson.core.io.JsonStringEncoder; + +/** + * A generic representation for an identifier, because there are so many identifiers around now + */ +public class Identifier implements Serializable { + private String identifierName; + private String identifierValue; + + public Identifier(String idType, String value) { + this.identifierName = idType; + this.identifierValue = value; + } + + public String getIdentifierName() { + return this.identifierName; + } + + public void setIdentifierName(String idType) { + this.identifierName = idType; + } + + public String getIdentifierValue() { + return this.identifierValue; + } + + public void setIdentifierValue(String value) { + this.identifierValue = value; + } + + public String toJson() { + JsonStringEncoder encoder = JsonStringEncoder.getInstance(); + StringBuilder json = new StringBuilder(); + json.append("{"); + if (identifierValue != null) { + byte[] encoded = encoder.quoteAsUTF8(identifierValue); + String output = new String(encoded); + json.append("\"id\":\""+output+"\""); + } + if (identifierName != null) { + json.append(", \"type\":\""+identifierName+"\""); + } + json.append("}"); + return json.toString(); + } +} \ No newline at end of file diff --git a/lookup/src/main/java/com/scienceminer/lookup/data/IstexData.java b/src/main/java/com/scienceminer/glutton/data/IstexData.java similarity index 97% rename from lookup/src/main/java/com/scienceminer/lookup/data/IstexData.java rename to src/main/java/com/scienceminer/glutton/data/IstexData.java index b9cfc14d..f1b662a2 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/data/IstexData.java +++ b/src/main/java/com/scienceminer/glutton/data/IstexData.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.data; +package com.scienceminer.glutton.data; import java.io.Serializable; import java.util.List; diff --git a/src/main/java/com/scienceminer/glutton/data/Keyword.java b/src/main/java/com/scienceminer/glutton/data/Keyword.java new file mode 100644 index 00000000..1e372ad8 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/data/Keyword.java @@ -0,0 +1,75 @@ + package com.scienceminer.glutton.data; + +import java.io.Serializable; +import java.lang.reflect.InvocationTargetException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.List; +import java.util.Map; +import java.util.TreeMap; +import java.util.concurrent.atomic.AtomicInteger; + +import org.apache.commons.beanutils.PropertyUtils; +import org.apache.commons.collections.CollectionUtils; +import org.apache.commons.collections.Predicate; +import org.apache.commons.collections.Transformer; +import org.apache.commons.lang3.StringUtils; + +import com.fasterxml.jackson.core.io.*; + +import org.joda.time.Partial; + +/** + * A class for representing keywords. A keyword can be assocated to a source (origin) + * and a boolean value indicating if it is a major topic or not. + */ +public class Keyword implements Serializable { + + private String value; + private String origin; + private Boolean isMajorTopic; + + public Keyword() { + } + + public Keyword(String value, String origin, Boolean isMajorTopic) { + setValue(value); + setOrigin(origin); + setIsMajorTopic(isMajorTopic); + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } + + public String getOrigin() { + return origin; + } + + public void setOrigin(String origin) { + this.origin = origin; + } + + public Boolean getIsMajorTopic() { + return isMajorTopic; + } + + public void setIsMajorTopic(Boolean isMajorTopic) { + this.isMajorTopic = isMajorTopic; + } + + @Override + public String toString() { + return "Keyword{" + + "value='" + value + '\'' + + ", origin='" + origin + '\'' + + ", isMajorTopic='" + isMajorTopic + '\'' + + '}'; + } + +} \ No newline at end of file diff --git a/lookup/src/main/java/com/scienceminer/lookup/data/MatchingDocument.java b/src/main/java/com/scienceminer/glutton/data/MatchingDocument.java similarity index 74% rename from lookup/src/main/java/com/scienceminer/lookup/data/MatchingDocument.java rename to src/main/java/com/scienceminer/glutton/data/MatchingDocument.java index 2a25741d..1b2bbf8a 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/data/MatchingDocument.java +++ b/src/main/java/com/scienceminer/glutton/data/MatchingDocument.java @@ -1,10 +1,15 @@ -package com.scienceminer.lookup.data; +package com.scienceminer.glutton.data; import java.util.List; import java.util.ArrayList; public class MatchingDocument { + private String id; + private String DOI; + private String halId; + private String pmid; + private String firstAuthor; private String atitle; @@ -25,6 +30,8 @@ public class MatchingDocument { private boolean isException = false; private Throwable exception; + + // TBD: rename, it's a JSON string, not a JSON object private String finalJsonObject; public MatchingDocument(Throwable throwable) { @@ -32,12 +39,28 @@ public MatchingDocument(Throwable throwable) { this.exception = throwable; } - public MatchingDocument(String DOI) { - this.DOI = DOI; - } - - public MatchingDocument(String DOI, String jsonObject) { - this.DOI = DOI; + public MatchingDocument(String identifier) { + this.id = identifier; + if (identifier.startsWith("crossref")) + this.DOI = identifier; + else if (identifier.startsWith("hal")) + this.halId = identifier; + else if (identifier.startsWith("pubmed")) + this.pmid = identifier; + else + this.DOI = DOI; + } + + public MatchingDocument(String identifier, String jsonObject) { + this.id = identifier; + if (identifier.startsWith("crossref")) + this.DOI = identifier; + else if (identifier.startsWith("hal")) + this.halId = identifier; + else if (identifier.startsWith("pubmed")) + this.pmid = identifier; + else + this.DOI = DOI; this.jsonObject = jsonObject; } @@ -50,7 +73,10 @@ public MatchingDocument(MatchingDocument other) { } public void fillFromMatchindDocument(MatchingDocument otherMatchingDocument) { + this.setId(otherMatchingDocument.getId()); this.setDOI(otherMatchingDocument.getDOI()); + this.setHalId(otherMatchingDocument.getHalId()); + this.setPmid(otherMatchingDocument.getPmid()); this.setFirstAuthor(otherMatchingDocument.getFirstAuthor()); this.setJsonObject(otherMatchingDocument.getJsonObject()); this.setATitle(otherMatchingDocument.getATitle()); @@ -64,6 +90,14 @@ public void setJsonObject(String jsonObject) { this.jsonObject = jsonObject; } + public String getId() { + return this.id; + } + + public void setId(String id) { + this.id = id; + } + public String getDOI() { return DOI; } @@ -72,6 +106,22 @@ public void setDOI(String DOI) { this.DOI = DOI; } + public String getHalId() { + return halId; + } + + public void setHalId(String halId) { + this.halId = halId; + } + + public String getPmid() { + return pmid; + } + + public void setPmid(String pmid) { + this.pmid = pmid; + } + public String getFirstAuthor() { return firstAuthor; } @@ -109,10 +159,12 @@ public void setException(Throwable exception) { this.isException = true; } + // TBD: rename, it's a JSON string, not a JSON object public void setFinalJsonObject(String finalJsonObject) { this.finalJsonObject = finalJsonObject; } + // TBD: rename, it's a JSON string, not a JSON object public String getFinalJsonObject() { if (finalJsonObject != null) finalJsonObject = finalJsonObject.replace("\n", ""); diff --git a/src/main/java/com/scienceminer/glutton/data/MeSHClass.java b/src/main/java/com/scienceminer/glutton/data/MeSHClass.java new file mode 100644 index 00000000..5dfbd68e --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/data/MeSHClass.java @@ -0,0 +1,188 @@ +package com.scienceminer.glutton.data; + +import java.io.Serializable; +import java.lang.reflect.InvocationTargetException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.List; +import java.util.Map; +import java.util.TreeMap; +import java.util.concurrent.atomic.AtomicInteger; + +import org.apache.commons.beanutils.PropertyUtils; +import org.apache.commons.collections.CollectionUtils; +import org.apache.commons.collections.Predicate; +import org.apache.commons.collections.Transformer; +import org.apache.commons.lang3.StringUtils; + +import com.fasterxml.jackson.core.io.*; + +import org.joda.time.Partial; + +/** + * A class for MeSH classification classes + */ +public class MeSHClass extends ClassificationClass implements Serializable { + private String descriptorUI = null; + private String descriptorName = null; + private List qualifierUIs = null; + private List qualifierNames = null; + private boolean majorTopicDescriptor = false; + private List majorTopicQualifiers = null; + + private String chemicalNameOfSubstance = null; + private String chemicalRegistryNumber = null; + private String chemicalUI = null; + + public MeSHClass() { + super("MeSH"); + } + + public String getDescriptorUI() { + return this.descriptorUI; + } + + public void setDescriptorUI(String ui) { + this.descriptorUI = ui; + } + + public String getDescriptorName() { + return this.descriptorName; + } + + public void setDescriptorName(String name) { + this.descriptorName = name; + } + + public List getQualifierUIs() { + return this.qualifierUIs; + } + + public void setQualifierUIs(List uis) { + this.qualifierUIs = uis; + } + + public void addQualifierUIs(String ui) { + if (this.qualifierUIs == null) + this.qualifierUIs = new ArrayList(); + this.qualifierUIs.add(ui); + } + + public List getQualifierNames() { + return this.qualifierNames; + } + + public void setQualifierNames(List names) { + this.qualifierNames = names; + } + + public void addQualifierName(String name) { + if (this.qualifierNames == null) + this.qualifierNames = new ArrayList(); + this.qualifierNames.add(name); + } + + public boolean getMajorTopicDescriptor() { + return majorTopicDescriptor; + } + + public void setMajorTopicDescriptor(boolean major) { + this.majorTopicDescriptor = major; + } + + public List getMajorTopicQualifiers() { + return majorTopicQualifiers; + } + + public void setMajorTopicQualifiers(List major) { + this.majorTopicQualifiers = major; + } + + public void addMajorTopicQualifiers(Boolean major) { + if (this.majorTopicQualifiers == null) + this.majorTopicQualifiers = new ArrayList(); + this.majorTopicQualifiers.add(major); + } + + public String getChemicalNameOfSubstance() { + return this.chemicalNameOfSubstance; + } + + public void setChemicalNameOfSubstance(String name) { + this.chemicalNameOfSubstance = name; + } + + public String getChemicalRegistryNumber() { + return this.chemicalRegistryNumber; + } + + public void setChemicalRegistryNumber(String number) { + this.chemicalRegistryNumber = number; + } + + public String getChemicalUI() { + return this.chemicalUI; + } + + public void setChemicalUI(String ui) { + this.chemicalUI = ui; + } + + public String toJson() { + StringBuilder json = new StringBuilder(); + JsonStringEncoder encoder = JsonStringEncoder.getInstance(); + json.append("{"); + if ( (descriptorName != null) && (descriptorName.length() > 0) ) { + json.append("\"descriptor\":{"); + + byte[] encodedDescriptorName = encoder.quoteAsUTF8(descriptorName); + String outputDescriptorName = new String(encodedDescriptorName); + + json.append("\"term\":\"").append(outputDescriptorName).append("\""); + if ( (descriptorUI != null) && (descriptorUI.length() > 0) ) { + json.append(",\"meshId\":\"").append(descriptorUI).append("\""); + } + json.append(", \"majorTopic\":\"").append(majorTopicDescriptor).append("\""); + json.append("}"); + if ( (qualifierNames != null) && (qualifierNames.size() > 0) ) { + json.append(",\"qualifiers\":["); + for(int i=0; i < qualifierNames.size(); i++) { + if (i !=0 ) + json.append(","); + json.append("{\"qualifier\":{"); + + byte[] encodedQualifierName = encoder.quoteAsUTF8(qualifierNames.get(i)); + String outputQualifierName = new String(encodedQualifierName); + + json.append("\"term\":\"").append(outputQualifierName).append("\""); + if ( (qualifierUIs != null) && (qualifierUIs.size() > i) ) { + json.append(", \"meshId\":\"").append(qualifierUIs.get(i)).append("\""); + } + if ( (majorTopicQualifiers != null) && (majorTopicQualifiers.size() > i) ) { + json.append(",\"majorTopic\":\"").append(majorTopicQualifiers.get(i)).append("\""); + } + json.append("}}"); + } + json.append("]"); + } + } else if ( (chemicalNameOfSubstance != null) && (chemicalNameOfSubstance.length() > 0) ) { + json.append("\"chemical\":{"); + + byte[] encodedChemicalNameOfSubstance = encoder.quoteAsUTF8(chemicalNameOfSubstance); + String outputChemicalNameOfSubstance = new String(encodedChemicalNameOfSubstance); + + json.append("\"term\":\"").append(outputChemicalNameOfSubstance).append("\""); + if ( (chemicalUI != null) && (chemicalUI.length() > 0) ) { + json.append(", \"meshId\":\"").append(chemicalUI).append("\""); + } + if ( (chemicalRegistryNumber != null) && (chemicalRegistryNumber.length() > 0)) { + json.append(",\"chemicalRegistryNumber\":\"").append(chemicalRegistryNumber).append("\""); + } + json.append("}"); + } + json.append("}"); + + return json.toString(); + } +} \ No newline at end of file diff --git a/lookup/src/main/java/com/scienceminer/lookup/data/OALocation.java b/src/main/java/com/scienceminer/glutton/data/OALocation.java similarity index 98% rename from lookup/src/main/java/com/scienceminer/lookup/data/OALocation.java rename to src/main/java/com/scienceminer/glutton/data/OALocation.java index 944c7db1..74a22a36 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/data/OALocation.java +++ b/src/main/java/com/scienceminer/glutton/data/OALocation.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.data; +package com.scienceminer.glutton.data; import com.fasterxml.jackson.annotation.JsonProperty; import com.fasterxml.jackson.annotation.JsonIgnore; diff --git a/lookup/src/main/java/com/scienceminer/lookup/data/OAResource.java b/src/main/java/com/scienceminer/glutton/data/OAResource.java similarity index 90% rename from lookup/src/main/java/com/scienceminer/lookup/data/OAResource.java rename to src/main/java/com/scienceminer/glutton/data/OAResource.java index d833f35c..014a3e84 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/data/OAResource.java +++ b/src/main/java/com/scienceminer/glutton/data/OAResource.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.data; +package com.scienceminer.glutton.data; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; diff --git a/lookup/src/main/java/com/scienceminer/lookup/data/OaIstexResource.java b/src/main/java/com/scienceminer/glutton/data/OaIstexResource.java similarity index 95% rename from lookup/src/main/java/com/scienceminer/lookup/data/OaIstexResource.java rename to src/main/java/com/scienceminer/glutton/data/OaIstexResource.java index 76f8c885..9e9bdad6 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/data/OaIstexResource.java +++ b/src/main/java/com/scienceminer/glutton/data/OaIstexResource.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.data; +package com.scienceminer.glutton.data; import org.apache.commons.lang3.tuple.Pair; import com.fasterxml.jackson.annotation.JsonInclude; diff --git a/src/main/java/com/scienceminer/glutton/data/Person.java b/src/main/java/com/scienceminer/glutton/data/Person.java new file mode 100644 index 00000000..1ce92535 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/data/Person.java @@ -0,0 +1,152 @@ +package com.scienceminer.glutton.data; + +import java.io.Serializable; +import java.util.*; + +import org.apache.commons.lang3.NotImplementedException; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.lang3.text.WordUtils; + +/** + * Encapsulates information about an author or editor. + * All name parts are normalized on setting (ie. MASON would be converted to Mason). + */ +@SuppressWarnings("serial") +public class Person implements Serializable { + + private String firstName; + private String middleName; + private String lastName; + private String title; + private String suffix; + private String inits; + + // the author identifiers, e.g. ORCID, VIAF, ... + private List identifiers = null; + + // the affiliations of the person + private List affiliations = null; + + public Person() { + } + + public Person(String lastName) { + setLastName(lastName); + } + + public Person(String lastName, String middle, String firstName) { + setLastName(lastName); + setMiddleName(middle); + setFirstName(firstName); + } + + public static Person parse(String text) { + throw new NotImplementedException("Can not parse a java.lang.String to org.epo.spp.citenpl.beans.Person object"); + } + + public String getFirstName() { + return firstName; + } + + public void setFirstName(String firstName) { + this.firstName = normalizeName(firstName); + } + + public String getMiddleName() { + return middleName; + } + + public void setMiddleName(String middleName) { + this.middleName = normalizeName(middleName); + } + + public String getLastName() { + return lastName; + } + + public void setLastName(String lastName) { + this.lastName = normalizeName(lastName); + } + + public String getTitle() { + return title; + } + + public void setTitle(String title) { + this.title = title; + } + + public String getSuffix() { + return suffix; + } + + public void setSuffix(String suffix) { + this.suffix = suffix; + } + + public String getInits() { + return inits; + } + + public void setInits(String inits) { + this.inits = normalizeName(inits); + } + + public boolean isEmptyPerson() { + return StringUtils.isBlank(lastName) && StringUtils.isBlank(firstName) && StringUtils.isBlank(middleName); + } + + public List getIdentifiers() { + return identifiers; + } + + public void setIdentifiers(List ids) { + this.identifiers = ids; + } + + public void addIdentifier(Identifier id) { + if (identifiers == null) + identifiers = new ArrayList(); + identifiers.add(id); + } + + public List getAffiliations() { + return this.affiliations; + } + + public void setAffiliations(List affiliations) { + this.affiliations = affiliations; + } + + public void addAffiliation(Affiliation affiliation) { + if (affiliations == null) + affiliations = new ArrayList(); + affiliations.add(affiliation); + } + + @Override + public String toString() { + return printFullName(); + } + + public String printFullName() { + StringBuilder builder = new StringBuilder(); + + if (StringUtils.isNotBlank(lastName)) { + builder.append(lastName); + } + if (StringUtils.isNotBlank(firstName)) { + builder.append(" " + firstName); + } + if (StringUtils.isNotBlank(middleName)) { + builder.append(" " + middleName); + } + + return builder.toString(); + } + + /** All Author and Editor names should be normalized so that only the first letter is capitalized. */ + public static String normalizeName(String inputName) { + return WordUtils.capitalizeFully(inputName, BiblioDefinitions.NAME_DELIMITERS); + } +} diff --git a/lookup/src/main/java/com/scienceminer/lookup/data/PmidData.java b/src/main/java/com/scienceminer/glutton/data/PmidData.java similarity index 58% rename from lookup/src/main/java/com/scienceminer/lookup/data/PmidData.java rename to src/main/java/com/scienceminer/glutton/data/PmidData.java index bf2b99a5..48377332 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/data/PmidData.java +++ b/src/main/java/com/scienceminer/glutton/data/PmidData.java @@ -1,18 +1,27 @@ -package com.scienceminer.lookup.data; +package com.scienceminer.glutton.data; import java.io.Serializable; import static org.apache.commons.lang3.StringUtils.startsWith; +/** + * Resources needed for creating these objects: + * - mapping identifiers: + * https://ftp.ebi.ac.uk/pub/databases/pmc/DOI/PMID_PMCID_DOI.csv.gz + * - mapping path and licences for PMC ID: + * https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_file_list.txt + **/ + public class PmidData implements Serializable { public static final String DOI_PREFIX_HTTPS = "https://doi.org/"; public static final String DOI_PREFIX_HTTP = "http://doi.org/"; + private String pmid; - private String doi; - private String pmcid; + private String license; + private String subpath; public PmidData(String pmid, String pmcid, String doi) { setPmid(pmid); @@ -21,7 +30,7 @@ public PmidData(String pmid, String pmcid, String doi) { } public String getPmid() { - return pmid; + return this.pmid; } public void setPmid(String pmid) { @@ -29,7 +38,7 @@ public void setPmid(String pmid) { } public String getDoi() { - return doi; + return this.doi; } public void setDoi(String doi) { @@ -43,10 +52,26 @@ public void setDoi(String doi) { } public String getPmcid() { - return pmcid; + return this.pmcid; } public void setPmcid(String pmcid) { this.pmcid = pmcid; } + + public String getLicense() { + return this.license; + } + + public void setLicense(String license) { + this.license = license; + } + + public String getSubpath() { + return this.subpath; + } + + public void setSubpath(String subpath) { + this.subpath = subpath; + } } diff --git a/src/main/java/com/scienceminer/glutton/data/Reference.java b/src/main/java/com/scienceminer/glutton/data/Reference.java new file mode 100644 index 00000000..bab4fc18 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/data/Reference.java @@ -0,0 +1,108 @@ +package com.scienceminer.glutton.data; + +import java.io.Serializable; +import java.util.*; + +import org.apache.commons.lang3.NotImplementedException; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.lang3.text.WordUtils; + +/** + * Encapsulates information for a reference present in a bibliographical record. + */ +@SuppressWarnings("serial") +public class Reference implements Serializable { + + private String referenceString; + private Biblio biblioObject; + + public Reference() { + } + + public Reference(String theReferenceString) { + setReferenceString(theReferenceString); + } + + public Reference(String theReferenceString, Biblio biblio) { + setReferenceString(theReferenceString); + setBiblioObject(biblio); + } + + public String getReferenceString() { + return this.referenceString; + } + + public void setReferenceString(String rawRef) { + this.referenceString = cleanReference(rawRef); + } + + public Biblio getBiblioObject() { + return this.biblioObject; + } + + public void setBiblioObject(Biblio biblio) { + this.biblioObject = biblio; + } + + public String getDoi() { + if (biblioObject == null) + return null; + else + return biblioObject.getDoi(); + } + + public void setDoi(String doi) { + if (biblioObject == null) + biblioObject = new Biblio(); + biblioObject.setDoi(doi); + } + + public String getPubmedId() { + if (biblioObject == null) + return null; + else + return biblioObject.getPubmedId(); + } + + public void setPubmedId(String pmid) { + if (biblioObject == null) + biblioObject = new Biblio(); + biblioObject.setPubmedId(pmid); + } + + public String getPii() { + if (biblioObject == null) + return null; + else + return biblioObject.getPii(); + } + + public void setPii(String pii) { + if (biblioObject == null) + biblioObject = new Biblio(); + biblioObject.setPii(pii); + } + + public String getPmc() { + if (biblioObject == null) + return null; + else + return biblioObject.getPmc(); + } + + public void setPmc(String pmc) { + if (biblioObject == null) + biblioObject = new Biblio(); + biblioObject.setPmc(pmc); + } + + /** + * Basic sanity check and normalization for the reference string + */ + public static String cleanReference(String reference) { + reference = reference.replace("\n", " "); + reference = reference.replace("\t", " "); + reference = reference.replaceAll("( )+", " "); + return reference.trim(); + } +} diff --git a/lookup/src/main/java/com/scienceminer/lookup/data/UnpayWallMetadata.java b/src/main/java/com/scienceminer/glutton/data/UnpayWallMetadata.java similarity index 99% rename from lookup/src/main/java/com/scienceminer/lookup/data/UnpayWallMetadata.java rename to src/main/java/com/scienceminer/glutton/data/UnpayWallMetadata.java index 0e31cae6..4ccb9017 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/data/UnpayWallMetadata.java +++ b/src/main/java/com/scienceminer/glutton/data/UnpayWallMetadata.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.data; +package com.scienceminer.glutton.data; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; diff --git a/src/main/java/com/scienceminer/glutton/exception/DataException.java b/src/main/java/com/scienceminer/glutton/exception/DataException.java new file mode 100644 index 00000000..fef5d1c3 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/exception/DataException.java @@ -0,0 +1,25 @@ +package com.scienceminer.glutton.exception; + +/** + * This class represent an exception when the data content causes some problems. + * Parsing, extraction, null values. + */ +public class DataException extends RuntimeException { + + public DataException() { + super(); + } + + public DataException(String message) { + super(message); + } + + public DataException(Throwable cause) { + super(cause); + } + + public DataException(String message, Throwable cause) { + super(message, cause); + } + +} diff --git a/lookup/src/main/java/com/scienceminer/lookup/exception/NotFoundException.java b/src/main/java/com/scienceminer/glutton/exception/NotFoundException.java similarity index 86% rename from lookup/src/main/java/com/scienceminer/lookup/exception/NotFoundException.java rename to src/main/java/com/scienceminer/glutton/exception/NotFoundException.java index bc48582d..7e0fb556 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/exception/NotFoundException.java +++ b/src/main/java/com/scienceminer/glutton/exception/NotFoundException.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.exception; +package com.scienceminer.glutton.exception; public class NotFoundException extends RuntimeException { public NotFoundException() { diff --git a/lookup/src/main/java/com/scienceminer/lookup/exception/ServiceException.java b/src/main/java/com/scienceminer/glutton/exception/ServiceException.java similarity index 93% rename from lookup/src/main/java/com/scienceminer/lookup/exception/ServiceException.java rename to src/main/java/com/scienceminer/glutton/exception/ServiceException.java index b178b75d..0091078c 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/exception/ServiceException.java +++ b/src/main/java/com/scienceminer/glutton/exception/ServiceException.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.exception; +package com.scienceminer.glutton.exception; /** * Exception thrown when an external service is not responding correctly diff --git a/lookup/src/main/java/com/scienceminer/lookup/exception/ServiceOverloadedException.java b/src/main/java/com/scienceminer/glutton/exception/ServiceOverloadedException.java similarity index 91% rename from lookup/src/main/java/com/scienceminer/lookup/exception/ServiceOverloadedException.java rename to src/main/java/com/scienceminer/glutton/exception/ServiceOverloadedException.java index bb521436..ce77c70a 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/exception/ServiceOverloadedException.java +++ b/src/main/java/com/scienceminer/glutton/exception/ServiceOverloadedException.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.exception; +package com.scienceminer.glutton.exception; /** * This exception represent a state where the service is not able to respond all the requests and diff --git a/src/main/java/com/scienceminer/glutton/harvester/HALAPIHarvester.java b/src/main/java/com/scienceminer/glutton/harvester/HALAPIHarvester.java new file mode 100644 index 00000000..b3f8476e --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/harvester/HALAPIHarvester.java @@ -0,0 +1,140 @@ +package com.scienceminer.glutton.harvester; + +import com.scienceminer.glutton.utils.Utilities; +import com.scienceminer.glutton.data.Biblio; +import com.scienceminer.glutton.configuration.LookupConfiguration; + +import java.io.*; +import java.net.MalformedURLException; +import java.net.URL; +import java.text.ParseException; +import java.util.ArrayList; +import java.util.List; +import javax.xml.parsers.DocumentBuilder; +import javax.xml.parsers.DocumentBuilderFactory; +import javax.xml.parsers.ParserConfigurationException; +import org.apache.commons.io.IOUtils; +import org.w3c.dom.Document; +import org.w3c.dom.Element; +import org.xml.sax.SAXException; + +import com.scienceminer.glutton.storage.lookup.TransactionWrapper; +import com.scienceminer.glutton.storage.lookup.HALLookup; + +import com.codahale.metrics.Counter; +import com.codahale.metrics.Meter; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * HAL harvester via the HAL web API, which should be faster than OAI-PMH + **/ +public class HALAPIHarvester extends Harvester { + private static final Logger LOGGER = LoggerFactory.getLogger(HALAPIHarvester.class); + + private static String OAI_FORMAT = "xml-tei"; + + // the api url + protected String api_url = "https://api.archives-ouvertes.fr/search"; + + private TransactionWrapper transactionWrapper; + + private HALAPIResponseParser apiResponseParser = null; + + private HALLookup halLookup; + + public HALAPIHarvester(TransactionWrapper transactionWrapper) { + super(); + this.apiResponseParser = new HALAPIResponseParser(); + this.transactionWrapper = transactionWrapper; + } + + public void fetchAllDocuments(HALLookup halLookup, + Meter meterValidRecord, + Counter counterInvalidRecords, + Counter counterIndexedRecords, + Counter counterFailedIndexedRecords) { + this.halLookup = halLookup; + boolean stop = false; + String nextCursorMark = null; + String previousCursorMark = "*"; + int toStore = 0; + int toIndex = 0; + List documents = null; + while (!stop) { + try { + String request = String.format("%s/?q=*:*&rows=2000&sort=%s&fl=dateLastIndexed_tdate,label_xml&wt=json&cursorMark=%s", + this.api_url, "docid%20asc", previousCursorMark); + + logger.info("Sending: " + request); + //System.out.println(request); + + InputStream in = null; + try { + in = Utilities.request(request); + List grabbedObjects = this.apiResponseParser.getGrabbedObjects(in, counterInvalidRecords); + + for (Biblio biblioObj : grabbedObjects) { + if (toStore >= halLookup.getStoringBatchSize()) { + halLookup.commitTransactions(transactionWrapper); + meterValidRecord.mark(toStore); + toStore = 0; + } + + if (toIndex >= halLookup.getIndexingBatchSize()) { + halLookup.indexDocuments(documents, true, counterIndexedRecords, counterFailedIndexedRecords); + //counterIndexedRecords.inc(toIndex); + toIndex = 0; + documents = null; + } + + if (biblioObj != null && biblioObj.getHalId() != null) { + // storing those things + halLookup.storeObject(biblioObj, transactionWrapper.tx); + if (documents == null) + documents = new ArrayList<>(); + documents.add(biblioObj); + toStore++; + toIndex++; + } + } + + // token if any + nextCursorMark = this.apiResponseParser.getNextCursorMark(); + if (nextCursorMark == null || nextCursorMark.equals(previousCursorMark) || grabbedObjects.size() == 0) { + stop = true; + } else + previousCursorMark = nextCursorMark; + } finally { + try { + if (in != null) + in.close(); + } catch (IOException ioex) { + LOGGER.error("Couldn't close opened harvesting stream source.", ioex); + } + } + } catch (MalformedURLException mue) { + logger.error(mue.getMessage(), mue); + } + } + // last batch + if (toStore > 0) { + halLookup.commitTransactions(transactionWrapper); + meterValidRecord.mark(toStore); + } + if (toIndex > 0) { + halLookup.indexDocuments(documents, true, counterIndexedRecords, counterFailedIndexedRecords); + } + } + + @Override + public void fetchAllDocuments() { + throw new UnsupportedOperationException("Use halLookup argument"); + } + + @Override + public void sample() throws IOException, SAXException, ParserConfigurationException, ParseException { + throw new UnsupportedOperationException("Not supported yet."); + } +} diff --git a/src/main/java/com/scienceminer/glutton/harvester/HALAPIResponseParser.java b/src/main/java/com/scienceminer/glutton/harvester/HALAPIResponseParser.java new file mode 100644 index 00000000..0eaa09c8 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/harvester/HALAPIResponseParser.java @@ -0,0 +1,125 @@ +package com.scienceminer.glutton.harvester; + +import java.io.*; +import java.util.Iterator; +import java.util.ArrayList; +import java.util.List; + +import com.scienceminer.glutton.data.Biblio; +import com.scienceminer.glutton.exception.*; +import com.scienceminer.glutton.utils.Utilities; +import com.scienceminer.glutton.utils.xml.HALTEISaxHandler; +import com.scienceminer.glutton.utils.xml.DumbEntityResolver; + +import org.xml.sax.SAXException; +import org.xml.sax.InputSource; +import javax.xml.parsers.SAXParser; +import javax.xml.parsers.SAXParserFactory; + +import com.fasterxml.jackson.core.*; +import com.fasterxml.jackson.databind.node.*; +import com.fasterxml.jackson.databind.*; + +import com.codahale.metrics.Counter; +import com.codahale.metrics.Meter; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * Extract and parse records from OAI-PMH response. + * + * @author Achraf, Patrice + */ +public class HALAPIResponseParser { + + protected static final Logger logger = LoggerFactory.getLogger(HALAPIResponseParser.class); + + private final static String source = Harvester.Source.HAL.getName(); + + private SAXParserFactory spf; + private String currentCursor; + private ObjectMapper objectMapper; + + public HALAPIResponseParser() { + spf = SAXParserFactory.newInstance(); + try { + spf.setValidating(false); + spf.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false); + } catch (Exception e) { + logger.warn("SAXParserFactory is not happy", e); + } + objectMapper = new ObjectMapper(); + } + + /* + ** Collectes Biblio objects from the inputStream, and saves the metadata. + */ + public List getGrabbedObjects(InputStream in, Counter counterInvalidRecords) { + List biblioobjs = new ArrayList(); + try { + JsonNode rootNode = objectMapper.readTree(in); + JsonNode jsonNode = rootNode.get("response"); + if (jsonNode != null && (!jsonNode.isMissingNode())) { + JsonNode docsNode = jsonNode.get("docs"); + if (docsNode != null && (!docsNode.isMissingNode()) && docsNode.isArray() && ((ArrayNode)docsNode).size() > 0) { + Iterator docIter = ((ArrayNode)docsNode).elements(); + while (docIter.hasNext()) { + JsonNode docNode = docIter.next(); + JsonNode teiNode = docNode.get("label_xml"); + if (teiNode != null && (!teiNode.isMissingNode())) { + String tei = teiNode.asText(); + Biblio biblio = processRecord(tei); + if (biblio != null) { + biblioobjs.add(biblio); + } else { + counterInvalidRecords.inc(); + } + } + } + } + } else { + logger.warn("Response without any documents, continuing harvesting..."); + } + + JsonNode cursorNode = rootNode.get("nextCursorMark"); + if (cursorNode != null && (!cursorNode.isMissingNode())) + this.currentCursor = cursorNode.asText(); + else + this.currentCursor = null; + } catch(JsonProcessingException e) { + logger.error("failed to parse JSON response from HAL web API", e); + } catch(IOException e) { + logger.error("failed to read JSON response from HAL web API", e); + } + + return biblioobjs; + } + + public Biblio processRecord(String tei) { + Biblio biblioObj = null; + try { + InputSource is = new InputSource(new StringReader(tei)); + + // SAX parser for the TEI metadata of the record + HALTEISaxHandler handler = new HALTEISaxHandler(); + + // get a new instance of parser + SAXParser saxParser = spf.newSAXParser(); + saxParser.getXMLReader().setEntityResolver(new DumbEntityResolver()); + saxParser.parse(is, handler); + + biblioObj = handler.getBiblio(); + } catch (Exception e) { + logger.warn("Failed to parse HAL TEI XML", e); + logger.error(tei); + } + + return biblioObj; + } + + public String getNextCursorMark() { + return this.currentCursor; + } + +} \ No newline at end of file diff --git a/src/main/java/com/scienceminer/glutton/harvester/HALOAIPMHDomParser.java b/src/main/java/com/scienceminer/glutton/harvester/HALOAIPMHDomParser.java new file mode 100644 index 00000000..d961d96b --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/harvester/HALOAIPMHDomParser.java @@ -0,0 +1,384 @@ +package com.scienceminer.glutton.harvester; + +import java.io.*; +import java.net.URLEncoder; +import java.nio.charset.StandardCharsets; +import java.util.ArrayList; +import java.util.List; +import javax.xml.parsers.DocumentBuilder; +import javax.xml.parsers.DocumentBuilderFactory; +import javax.xml.parsers.ParserConfigurationException; +import javax.xml.xpath.XPath; +import javax.xml.xpath.XPathConstants; +import javax.xml.xpath.XPathExpressionException; +import javax.xml.xpath.XPathFactory; + +import org.w3c.dom.DOMException; +import org.w3c.dom.Document; +import org.w3c.dom.Element; +import org.w3c.dom.Node; +import org.w3c.dom.NodeList; +import org.w3c.dom.ls.DOMImplementationLS; +import org.w3c.dom.ls.LSSerializer; + +import org.xml.sax.SAXException; +import org.xml.sax.InputSource; +import javax.xml.parsers.SAXParser; +import javax.xml.parsers.SAXParserFactory; +import com.scienceminer.glutton.utils.xml.DumbEntityResolver; + +import javax.xml.parsers.DocumentBuilderFactory; +import javax.xml.parsers.ParserConfigurationException; +import javax.xml.transform.OutputKeys; +import javax.xml.transform.Transformer; +import javax.xml.transform.TransformerException; +import javax.xml.transform.TransformerFactory; +import javax.xml.transform.dom.DOMSource; +import javax.xml.transform.stream.StreamResult; + +import com.scienceminer.glutton.data.Biblio; +import com.scienceminer.glutton.exception.*; +import com.scienceminer.glutton.utils.Utilities; +import com.scienceminer.glutton.utils.xml.HALTEISaxHandler; + +import com.codahale.metrics.Counter; +import com.codahale.metrics.Meter; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * Extract and parse records from OAI-PMH response. + * + * @author Achraf, Patrice + */ +public class HALOAIPMHDomParser { + + protected static final Logger logger = LoggerFactory.getLogger(HALOAIPMHDomParser.class); + + private final static String source = Harvester.Source.HAL.getName(); + + private Document doc; + private String token; + private XPath xPath; + private SAXParserFactory spf; + + public HALOAIPMHDomParser() { + xPath = XPathFactory.newInstance().newXPath(); + spf = SAXParserFactory.newInstance(); + try { + spf.setValidating(false); + spf.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false); + } catch (Exception e) { + logger.warn("SAXParserFactory is not happy", e); + } + } + + /* + ** Collectes Biblio objects from the inputStream, and saves the metadata. + */ + public List getGrabbedObjects(InputStream in, Counter counterInvalidRecords) { + List biblioobjs = new ArrayList(); + setDoc(parse(in)); + if (doc != null) { + Element rootElement = doc.getDocumentElement(); + NodeList listRecords = getRecords(rootElement); + + //XPath xPath = XPathFactory.newInstance().newXPath();//play with it + //NodeList nodes = (NodeList)xPath.evaluate("/OAI-PMH/ListRecords/record/metadata", rootElement, XPathConstants.NODESET); + setToken(rootElement); + logger.info(listRecords.getLength() + " records found"); + + if (listRecords.getLength() >= 1) { + for (int i = listRecords.getLength() - 1; i >= 0; i--) { + if ((listRecords.item(i) instanceof Element)) { + Element record = (Element) listRecords.item(i); + + Element metadata = (Element) record.getElementsByTagName(OAIPMHPathsItf.TeiElement).item(0); + NodeList metadataNodes = metadata.getChildNodes(); + for (int o = metadataNodes.getLength() - 1; o >= 0; o--) { + if ((metadataNodes.item(o) instanceof Element)) { + Element element = (Element) metadataNodes.item(o); + element.setAttribute("xmlns:tei", "http://www.tei-c.org/ns/1.0"); + //HAL OAI PMH adds a tei namespace before each tag + renameNode(element); + + Biblio biblio = processRecord(element); + if (biblio != null) { + biblioobjs.add(biblio); + } else { + counterInvalidRecords.inc(); + } + } + } + } + } + + } + } + return biblioobjs; + } + + public Biblio processRecord(Element theRecord) { + Biblio biblioObj = null; + + String type = getPublicationType(theRecord); + //if (isConsideredType(type.split("_")[0])) + { + String repositoryDocId = getRepositoryDocId(theRecord); + String currentVersion = getCurrentVersion(theRecord); +// String docVersion = Utilities.getVersionFromURI(completeRepositoryDocId); + //if not the current version normally we don't need the update. +// if (docVersion.equals(currentVersion)) { + String tei = getTei(theRecord); +//System.out.println(tei); + try { + InputSource is = new InputSource(new StringReader(tei)); + + // SAX parser for the TEI metadata of the record + HALTEISaxHandler handler = new HALTEISaxHandler(); + + // get a new instance of parser + SAXParser saxParser = spf.newSAXParser(); + saxParser.getXMLReader().setEntityResolver(new DumbEntityResolver()); + saxParser.parse(is, handler); + + biblioObj = handler.getBiblio(); + } catch (Exception e) { + logger.warn("Failed to parse HAL TEI XML", e); + } + + /*biblioObj = new Biblio(null, source, repositoryDocId, tei); + biblioObj.setRepositoryDocId(repositoryDocId); + biblioObj.setRepositoryDocVersion(currentVersion); + biblioObj.setDoi(getDoi(record)); + + biblioObj.setPublicationType(type); + biblioObj.setDomains(getDomains(record)); + + //biblioObj.setPdf(getFile(record, repositoryDocId, currentVersion, biblioObj.getDoi(), type)); + + biblioObj.setMetadataURL("https://hal.archives-ouvertes.fr/" + repositoryDocId + "/tei");*/ + + //logger.info("TEI of " + repositoryDocId + " extracted."); + } + return biblioObj; + } + + public String getCurrentVersion(Node record) { + String currentVersion = null; + try { + Element node = (Element) xPath.compile(OAIPMHPathsItf.EditionElement).evaluate(record, XPathConstants.NODE); + currentVersion = node.getAttribute("n"); + } catch (DataException | XPathExpressionException ex) { + logger.info("No current version found ."); + } + return currentVersion; + } + + public String getRef(Node ref) { + String reference = null; + Node node = null; + try { + node = (Node) xPath.compile(OAIPMHPathsItf.RefPATH).evaluate(ref, XPathConstants.NODE); + if (node != null) { + reference = node.getTextContent(); + } else { + throw new DataException(); + } + } catch (DataException | XPathExpressionException | DOMException ex) { + logger.info("hal ref not found"); + } + return reference; + } + + public String getDoi(Node ref) { + String doi = null; + try { + Node node = (Node) xPath.compile(OAIPMHPathsItf.DoiPATH).evaluate(ref, XPathConstants.NODE); + if (node != null) { + doi = node.getTextContent(); + } else { + throw new DataException(); + } + } catch (DataException | XPathExpressionException | DOMException ex) { + logger.info("DOI not found"); + } + return doi; + } + + public List getDomains(Node ref) { + List domains = new ArrayList(); + try { + NodeList nodes = (NodeList) xPath.compile(OAIPMHPathsItf.DomainsPATH).evaluate(ref, XPathConstants.NODESET); + if (nodes != null) { + if (nodes.getLength() >= 1) { + for (int i = nodes.getLength() - 1; i >= 0; i--) { + if ((nodes.item(i) instanceof Element)) { + domains.add(((Element) nodes.item(i)).getAttribute("n") + "_" + ((Element) nodes.item(i)).getTextContent()); + } + } + } + } else { + throw new DataException(); + } + } catch (DataException | XPathExpressionException | DOMException ex) { + logger.info("no publication type found"); + } + return domains; + } + + public String getPublicationType(Node ref) { + String type = null; + try { + Element node = (Element) xPath.compile(OAIPMHPathsItf.PublicationTypePATH).evaluate(ref, XPathConstants.NODE); + if (node != null) { + type = node.getAttribute("n") + "_" + node.getTextContent(); + } else { + throw new DataException(); + } + } catch (DataException | XPathExpressionException | DOMException ex) { + logger.info("no publication type found"); + } + return type; + } + + public String getToken() { + return this.token; + } + + private void setToken(Element rootElement) { + try { + this.token = URLEncoder.encode( + rootElement.getElementsByTagName(OAIPMHPathsItf.ResumptionToken).item(0).getTextContent(), + StandardCharsets.UTF_8.toString()); + } catch (Exception ex) { + this.token = null; + } + } + + private void setDoc(Document doc) { + this.doc = doc; + } + + private Document parse(InputStream in) { + try { + DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); + DocumentBuilder db = dbf.newDocumentBuilder(); + return db.parse(in); + } catch (DataException | IOException | ParserConfigurationException | SAXException e) {// + logger.error("Could not parse document because " + + e.getMessage()); + } + return null; + } + + public String getTei(Node tei) { + StringBuilder sb = new StringBuilder(); + sb.append(""); + + String teiString = sb.append(innerXmlToString(tei)).toString(); + DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance(); + docFactory.setValidating(false); + Document teiDoc = null; + try { + DocumentBuilder docBuilder = docFactory.newDocumentBuilder(); + teiDoc = docBuilder.parse(new ByteArrayInputStream(teiString.getBytes())); + } catch (SAXException | ParserConfigurationException | IOException e) { + e.printStackTrace(); + } + +// teiDoc = createTEICorpus(teiDoc); +// +// Utilities.generateIDs(teiDoc); + try { + teiString = toString(teiDoc); + } catch (DataException de) { + de.printStackTrace(); + } + return teiString; + } + + private void renameNode(Element teiElement) { + if (teiElement.getTagName().contains(":")) { + doc.renameNode(teiElement, null, teiElement.getTagName().split(":")[1]); + NodeList nodes = teiElement.getChildNodes(); + for (int i = nodes.getLength() - 1; i >= 0; i--) { + if (nodes.item(i) instanceof Element) { + Element element = (Element) nodes.item(i); + renameNode(element); + } + } + } + } + + public String getRepositoryDocId(Node record) { + String repositoryDocId = null; + try { + Element node = (Element) xPath.compile(OAIPMHPathsItf.IdElementPath).evaluate(record, XPathConstants.NODE); + if (node != null) { + repositoryDocId = node.getTextContent(); + } else { + throw new DataException(); + } + } catch (DataException | XPathExpressionException | DOMException ex) { + logger.info("no publication repository id found"); + } + return repositoryDocId; + } + + public String getDocumentType(NodeList sets) { + String type = null; + for (int i = sets.getLength() - 1; i >= 0; i--) { + String content = sets.item(i).getTextContent(); + if (content.contains("type")) { + String[] n = content.split(":"); + type = n.length > 1 ? n[1] : null; + break; + } + } + return type; + } + + private NodeList getRecords(Element rootElement) { + return rootElement.getElementsByTagName(OAIPMHPathsItf.RecordElement); + } + + private boolean isConsideredType(String setSpec) { + try { + OAIPMHPathsItf.ConsideredTypes.valueOf(setSpec); + return true; + } catch (NullPointerException | IllegalArgumentException ex) { + return false; + } + } + + private static String toString(Document doc) { + try { + StringWriter sw = new StringWriter(); + TransformerFactory tf = TransformerFactory.newInstance(); + Transformer transformer = tf.newTransformer(); + transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "no"); + transformer.setOutputProperty(OutputKeys.METHOD, "xml"); + transformer.setOutputProperty(OutputKeys.INDENT, "yes"); + transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8"); + transformer.transform(new DOMSource(doc), new StreamResult(sw)); + return sw.toString(); + } catch (IllegalArgumentException | TransformerException ex) { + throw new DataException("Error converting to String", ex); + } + } + + private static String innerXmlToString(Node node) { + DOMImplementationLS lsImpl + = (DOMImplementationLS) node.getOwnerDocument().getImplementation().getFeature("LS", "3.0"); + LSSerializer lsSerializer = lsImpl.createLSSerializer(); + lsSerializer.getDomConfig().setParameter("xml-declaration", false); + NodeList childNodes = node.getChildNodes(); + StringBuilder sb = new StringBuilder(); + //for (int i = 0; i < childNodes.getLength(); i++) { + sb.append(lsSerializer.writeToString(node)); + //} + return sb.toString(); + } +} diff --git a/src/main/java/com/scienceminer/glutton/harvester/HALOAIPMHHarvester.java b/src/main/java/com/scienceminer/glutton/harvester/HALOAIPMHHarvester.java new file mode 100644 index 00000000..315fea65 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/harvester/HALOAIPMHHarvester.java @@ -0,0 +1,131 @@ +package com.scienceminer.glutton.harvester; + +import com.scienceminer.glutton.utils.Utilities; +import com.scienceminer.glutton.data.Biblio; + +import java.io.BufferedReader; +import java.io.ByteArrayInputStream; +import java.io.FileReader; + +import java.io.IOException; +import java.io.InputStream; +import java.net.MalformedURLException; +import java.net.URL; +import java.text.ParseException; +import java.util.ArrayList; +import java.util.List; +import javax.xml.parsers.DocumentBuilder; +import javax.xml.parsers.DocumentBuilderFactory; +import javax.xml.parsers.ParserConfigurationException; +import org.apache.commons.io.IOUtils; +import org.w3c.dom.Document; +import org.w3c.dom.Element; +import org.xml.sax.SAXException; + +import com.scienceminer.glutton.storage.lookup.TransactionWrapper; +import com.scienceminer.glutton.storage.lookup.HALLookup; + +import com.codahale.metrics.Counter; +import com.codahale.metrics.Meter; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * HAL OAI-PMH harvester implementation + * + * @author Achraf, Patrice + */ +public class HALOAIPMHHarvester extends Harvester { + private static final Logger LOGGER = LoggerFactory.getLogger(HALOAIPMHHarvester.class); + + private static String OAI_FORMAT = "xml-tei"; + + // the api url + protected String oai_url = "https://api.archives-ouvertes.fr/oai/hal"; + + // hal url for harvesting from a file list + //private static String halUrl = "https://hal.archives-ouvertes.fr/"; + + private HALOAIPMHDomParser oaiDom; + + private TransactionWrapper transactionWrapper; + + private HALLookup halLookup; + + public HALOAIPMHHarvester(TransactionWrapper transactionWrapper) { + super(); + this.oaiDom = new HALOAIPMHDomParser(); + this.transactionWrapper = transactionWrapper; + } + + /** + * Gets results given a date as suggested by OAI-PMH. + */ + protected void fetchDocumentsByDate(String date, Meter meterValidRecord, Counter counterInvalidRecords) throws MalformedURLException { + boolean stop = false; + String tokenn = null; + while (!stop) { + String request = String.format("%s/?verb=ListRecords&metadataPrefix=%s&from=%s&until=%s", + this.oai_url, OAI_FORMAT, date, date); + + if (tokenn != null && tokenn.length()>0) { + request = String.format("%s/?verb=ListRecords&resumptionToken=%s", this.oai_url, tokenn); + } + logger.info("Sending: " + request); + System.out.println(request); + + InputStream in = Utilities.request(request); + List grabbedObjects = this.oaiDom.getGrabbedObjects(in, counterInvalidRecords); + + for (Biblio biblioObj : grabbedObjects) { + if (biblioObj != null && biblioObj.getHalId() != null) { + // storing those things + halLookup.storeObject(biblioObj, transactionWrapper.tx); + meterValidRecord.mark(); + } + } + + if (grabbedObjects.size()>0) + halLookup.commitTransactions(transactionWrapper); + + // token if any + tokenn = oaiDom.getToken(); + if (tokenn == null) { + stop = true; + } + try { + in.close(); + } catch (IOException ioex) { + LOGGER.error("Couldn't close opened harvesting stream source.", ioex); + } + } + } + + @Override + public void fetchAllDocuments() { + throw new UnsupportedOperationException("Use halLookup argument"); + } + + public void fetchAllDocuments(HALLookup halLookup, Meter meterValidRecord, Counter counterInvalidRecords) { + this.halLookup = halLookup; + String currentDate = ""; + try { + for (String date : Utilities.getDates()) { + logger.info("Extracting publications TEIs for : " + date); + currentDate = date; + fetchDocumentsByDate(date, meterValidRecord, counterInvalidRecords); + } + } catch (MalformedURLException mue) { + logger.error(mue.getMessage(), mue); + } catch (Exception e) { + logger.error(e.getMessage(), e); + } + } + + @Override + public void sample() throws IOException, SAXException, ParserConfigurationException, ParseException { + throw new UnsupportedOperationException("Not supported yet."); + } + +} diff --git a/src/main/java/com/scienceminer/glutton/harvester/Harvester.java b/src/main/java/com/scienceminer/glutton/harvester/Harvester.java new file mode 100644 index 00000000..b40cd83e --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/harvester/Harvester.java @@ -0,0 +1,159 @@ +package com.scienceminer.glutton.harvester; + +import com.scienceminer.glutton.data.Biblio; + +import java.io.IOException; +import java.util.List; +import java.util.Date; +import java.text.ParseException; +import javax.xml.parsers.ParserConfigurationException; +import org.xml.sax.SAXException; +import java.net.MalformedURLException; +import java.util.ArrayList; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * Abstract class for all harvester of the system. A particular harvester will + * implement a specific harvesting and/or loading protocol for the acquisition + * of bibliographical objects (e.g. an article with all its associated resources + * such as PDF, TEI, metadata header, annexes, suppplementary information), + * possibly among several versions (because we are also addressing prepring + * archives). + * + */ +public abstract class Harvester { + + protected static final Logger logger = LoggerFactory.getLogger(Harvester.class); + + protected List grabbedObjects = new ArrayList(); + + // Source of the harvesting + public enum Source { + HAL("hal"), + ISTEX("istex"), + ARXIV("arxiv"); + + private String name; + + private Source(String name) { + this.name = name; + } + + public String getName() { + return name; + } + + public static boolean contains(String test) { + for (Source c : Source.values()) { + if (c.name().toLowerCase().equals(test)) { + return true; + } + } + return false; + } + }; + + protected Source source = null; + + public Harvester() { + } + + abstract public void fetchAllDocuments() throws IOException, SAXException, ParserConfigurationException, ParseException; + + abstract public void sample() throws IOException, SAXException, ParserConfigurationException, ParseException; + + public Source getSource() { + return source; + } + + public void setSource(Source source) { + this.source = source; + } + + /** + * Stores the given teis and downloads attachements(main file(s), annexes + * ..) . + */ + /*protected void saveObjects() { + if ((grabbedObjects == null) || (grabbedObjects.size() == 0)) { + return; + } + for (BiblioObject object : grabbedObjects) { + String metadataString = object.getMetadata(); + String pdfUrl = ""; + if (object.getPdf() != null) { + pdfUrl = object.getPdf().getUrl(); + } + String repositoryDocId = object.getRepositoryDocId(); + logger.info("\t\t Processing metadata from " + object.getSource() + " document :" + repositoryDocId); + if (metadataString.length() > 0) { + if (!HarvestProperties.isReset() && mm.isSavedObject(repositoryDocId, object.getRepositoryDocVersion())) { + logger.info("\t\t Already grabbed, Skipping..."); + continue; + } + try { + if (object.getPdf() != null) { + logger.info("\t\t\t\t downloading PDF file."); + requestFile(object.getPdf()); + if(object.getPdf().getStream() == null) + object.setIsWithFulltext(Boolean.FALSE); + } else { + object.setIsWithFulltext(Boolean.FALSE); + mm.save(object.getRepositoryDocId(), "harvestProcess", "no URL for binary"); + logger.info("\t\t\t\t PDF not found !"); + } + if (object.getAnnexes() != null) { + for (BinaryFile file : object.getAnnexes()) { + requestFile(file); + } + } + } catch (BinaryNotAvailableException bna) { + logger.error(bna.getMessage()); + mm.save(object.getRepositoryDocId(), "harvestProcess", "file not downloaded"); + } catch (ParseException | IOException e) { + logger.error("\t\t Error occured while processing TEI for " + object.getRepositoryDocId(), e); + mm.save(object.getRepositoryDocId(), "harvestProcess", "harvest error"); + } + + logger.info("\t\t\t\t Storing object " + repositoryDocId); + mm.insertBiblioObject(object); + } else { + logger.info("\t\t\t No TEI metadata !!!"); + } + } + }*/ + + /** + * Requests the given file if is not under embargo and register it either as + * main file or as an annex. + */ + /*protected void requestFile(BinaryFile bf) throws ParseException, IOException { + Date embDate = Utilities.parseStringDate(bf.getEmbargoDate()); + Date today = new Date(); + if (embDate == null || embDate.before(today) || embDate.equals(today)) { + logger.info("\t\t\t Downloading: " + bf.getUrl()); + try { + bf.setStream(Utilities.request(bf.getUrl())); + } catch (MalformedURLException | ServiceException se) { + logger.error(se.getMessage()); + throw new BinaryNotAvailableException(); + } + + if (bf.getStream() == null) { + mm.log(bf.getRepositoryDocId(), bf.getAnhalyticsId(), bf.getUrl(), bf.getDocumentType(), bf.isIsAnnexFile(), "nostream", ""); + } else { + if (bf.isIsAnnexFile()) { + int n = bf.getUrl().lastIndexOf("/"); + String filename = bf.getUrl().substring(n + 1); + bf.setFileName(filename); + logger.info("\t\t\t\t Getting annex file " + filename + " for pub ID :" + bf.getRepositoryDocId()); + } + } + } else { + mm.log(bf.getRepositoryDocId(), bf.getAnhalyticsId(), bf.getUrl(), bf.getDocumentType(), bf.isIsAnnexFile(), "embargo", bf.getEmbargoDate()); + logger.info("\t\t\t file under embargo !"); + } + }*/ +} diff --git a/src/main/java/com/scienceminer/glutton/harvester/OAIPMHPathsItf.java b/src/main/java/com/scienceminer/glutton/harvester/OAIPMHPathsItf.java new file mode 100644 index 00000000..d15bf628 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/harvester/OAIPMHPathsItf.java @@ -0,0 +1,31 @@ +package com.scienceminer.glutton.harvester; + +import org.w3c.dom.Node; +import org.w3c.dom.NodeList; + +/** + * + * @author Achraf + */ + +/* to be reviewed */ + +public interface OAIPMHPathsItf { + public final static String ListRecordsElement = "ListRecords"; + public final static String RecordElement = "record"; + public final static String TeiElement = "metadata"; + public final static String IdElementPath = "text/body/listBibl/biblFull/publicationStmt/idno[@type='halId']"; + public final static String ResumptionToken = "resumptionToken"; + public final static String AnnexesUrlsElement = "text/body/listBibl/biblFull/editionStmt/edition[@type='current']/ref[@type='annex']"; + public final static String FileElement = "text/body/listBibl/biblFull/editionStmt/edition[@type='current']/ref[@type='file'][1]"; + public final static String EditionElement = "text/body/listBibl/biblFull/editionStmt/edition[@type='current']"; + public final static String RefPATH = "text/body/listBibl/biblFull/publicationStmt/idno[@type='halRef']"; + public final static String DoiPATH = "text/body/listBibl/biblFull/sourceDesc/biblStruct/idno[@type='doi']"; + public final static String PublicationTypePATH = "text/body/listBibl/biblFull/profileDesc/textClass/classCode[@scheme='halTypology']"; + public final static String DomainsPATH = "text/body/listBibl/biblFull/profileDesc/textClass/classCode[@scheme='halDomain']"; + + /* note: these are HAL specific types */ + enum ConsideredTypes { + ART, COMM, OUV, POSTER, DOUV, PATENT, REPORT, THESE, HDR, LECTURE, COUV, OTHER, UNDEFINED //IMG, VIDEO, AUDIOS, SON, MAP + }; +} diff --git a/src/main/java/com/scienceminer/glutton/indexing/ElasticSearchAsyncIndexer.java b/src/main/java/com/scienceminer/glutton/indexing/ElasticSearchAsyncIndexer.java new file mode 100644 index 00000000..b0b11589 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/indexing/ElasticSearchAsyncIndexer.java @@ -0,0 +1,204 @@ +package com.scienceminer.glutton.indexing; + +import java.io.*; +import java.util.*; + +import com.scienceminer.glutton.configuration.LookupConfiguration; + +import co.elastic.clients.elasticsearch.*; +import co.elastic.clients.elasticsearch.cluster.*; +import co.elastic.clients.elasticsearch.core.*; +import co.elastic.clients.transport.*; +import org.elasticsearch.client.RestClient; +import co.elastic.clients.elasticsearch.indices.*; +import co.elastic.clients.json.jackson.JacksonJsonpMapper; +import co.elastic.clients.transport.rest_client.RestClientTransport; +import co.elastic.clients.elasticsearch.ElasticsearchAsyncClient; +import co.elastic.clients.transport.ElasticsearchTransport; +import co.elastic.clients.transport.endpoints.*; +import co.elastic.clients.elasticsearch.cat.IndicesResponse; +import co.elastic.clients.elasticsearch.indices.ExistsRequest; +import co.elastic.clients.elasticsearch.indices.RefreshRequest; +import co.elastic.clients.elasticsearch.core.bulk.*; + +import com.fasterxml.jackson.databind.node.*; +import com.fasterxml.jackson.core.*; +import com.fasterxml.jackson.databind.*; + +import com.scienceminer.glutton.exception.ServiceException; +import com.scienceminer.glutton.exception.ServiceOverloadedException; +import com.scienceminer.glutton.utils.BinarySerialiser; + +import org.apache.http.HttpHost; +import org.apache.commons.io.FileUtils; + +import com.codahale.metrics.Meter; +import com.codahale.metrics.Counter; + +import org.lmdbjava.*; +import java.nio.ByteBuffer; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +public class ElasticSearchAsyncIndexer { + protected static final Logger logger = LoggerFactory.getLogger(ElasticSearchAsyncIndexer.class); + + private static volatile ElasticSearchAsyncIndexer instance; + + private LookupConfiguration configuration; + private RestClient restClient; + private ElasticsearchTransport transport; + private ElasticsearchAsyncClient elasticsearchAsyncClient; + + private String settingsPath = "config/elastic-settings.json"; + + public static ElasticSearchAsyncIndexer getInstance(LookupConfiguration configuration) { + if (instance == null) { + synchronized (ElasticSearchAsyncIndexer.class) { + if (instance == null) { + getNewInstance(configuration); + } + } + } + return instance; + } + + /** + * Creates a new instance. + */ + private static synchronized void getNewInstance(LookupConfiguration configuration) { + instance = new ElasticSearchAsyncIndexer(configuration); + } + + private ElasticSearchAsyncIndexer(LookupConfiguration configuration) { + this.configuration = configuration; + + // Create the low-level client + restClient = RestClient + .builder(HttpHost.create(configuration.getElastic().getHost())) + //.setDefaultHeaders(new Header[]{ + // new BasicHeader("Authorization", "ApiKey " + apiKey) + //}) + .build(); + + // Create the transport with a Jackson mapper + transport = new RestClientTransport( + restClient, new JacksonJsonpMapper()); + + // And create the API client + elasticsearchAsyncClient = new ElasticsearchAsyncClient(transport); + } + + /** + * Extend an existing index with a set of documents. The expected values are JSON + * documents in the CrossRef format. + * + * Asynchronous version useful when combining processes of storing and indexing. + * + * Document identifier is the source prefixed by the main identifier of the this source: + * e.g. crossref:DOI, hal:HalID, pubmed:pmid + * + * Already existing keys are skipt if update is false. + * + **/ + public void asyncIndexDocuments(List documents, + boolean update, + Counter counterIndexedRecords, + Counter counterFailedIndexedRecords) { + BulkRequest.Builder br = new BulkRequest.Builder(); + for(String document : documents) { + MetadataObj objToIndex = MetadataObjBuilder.createMetadataObj(document); + if (objToIndex != null && !MetadataObjBuilder.isFilteredType(objToIndex)) { + objToIndex.type = null; + String localIdentifier = objToIndex._id; + objToIndex._id = null; + br.operations(op -> op + .index(idx -> idx + .index(configuration.getElastic().getIndex()) + .id(localIdentifier) + .document(objToIndex) + ) + ); + } + + if (objToIndex == null) { + // counter here for records that failed to index + counterFailedIndexedRecords.inc(); + } + } + + try { + this.elasticsearchAsyncClient.bulk( + br.build() + ).whenComplete((response, exception) -> { + if (exception != null) { + logger.error("Batch indexing failed", exception); + } else { + counterIndexedRecords.inc(documents.size()); + } + + if (response.errors()) { + logger.error("Bulk had errors"); + for (BulkResponseItem item: response.items()) { + if (item.error() != null) { + logger.error(item.error().reason()); + } + } + } + }); + + } catch (Exception e) { + logger.error("Batch indexing failed", e); + } + } + + public void asyncIndexJsonObjects(List documents, boolean update, Counter counterIndexedRecords, Counter counterFailedIndexedRecords) { + BulkRequest.Builder br = new BulkRequest.Builder(); + for(JsonNode document : documents) { + MetadataObj objToIndex = MetadataObjBuilder.createMetadataObjFromJsonNode(document); + if (objToIndex != null && !MetadataObjBuilder.isFilteredType(objToIndex)) { + objToIndex.type = null; + String localIdentifier = objToIndex._id; + objToIndex._id = null; + br.operations(op -> op + .index(idx -> idx + .index(configuration.getElastic().getIndex()) + .id(localIdentifier) + .document(objToIndex) + ) + ); + } + + if (objToIndex == null) { + // counter here for records that failed to index + counterFailedIndexedRecords.inc(); + } + } + + try { + this.elasticsearchAsyncClient.bulk( + br.build() + ).whenComplete((response, exception) -> { + if (exception != null) { + logger.error("Batch indexing failed", exception); + } else { + counterIndexedRecords.inc(documents.size()); + } + + if (response.errors()) { + logger.error("Bulk had errors"); + for (BulkResponseItem item: response.items()) { + if (item.error() != null) { + logger.error(item.error().reason()); + } + } + } + }); + + } catch (Exception e) { + logger.error("Batch indexing failed", e); + } + } + +} diff --git a/src/main/java/com/scienceminer/glutton/indexing/ElasticSearchIndexer.java b/src/main/java/com/scienceminer/glutton/indexing/ElasticSearchIndexer.java new file mode 100644 index 00000000..aee2e162 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/indexing/ElasticSearchIndexer.java @@ -0,0 +1,351 @@ +package com.scienceminer.glutton.indexing; + +import java.io.*; +import java.util.*; + +import com.scienceminer.glutton.configuration.LookupConfiguration; + +import co.elastic.clients.elasticsearch.*; +import co.elastic.clients.elasticsearch.cluster.*; +import co.elastic.clients.elasticsearch.core.*; +import co.elastic.clients.transport.*; +import org.elasticsearch.client.RestClient; +import co.elastic.clients.elasticsearch.indices.*; +import co.elastic.clients.json.jackson.JacksonJsonpMapper; +import co.elastic.clients.transport.rest_client.RestClientTransport; +import co.elastic.clients.elasticsearch.ElasticsearchClient; +import co.elastic.clients.transport.ElasticsearchTransport; +import co.elastic.clients.transport.endpoints.*; +import co.elastic.clients.elasticsearch.cat.IndicesResponse; +import co.elastic.clients.elasticsearch.indices.ExistsRequest; +import co.elastic.clients.elasticsearch.indices.RefreshRequest; +import co.elastic.clients.elasticsearch.core.bulk.*; + +import com.scienceminer.glutton.exception.ServiceException; +import com.scienceminer.glutton.exception.ServiceOverloadedException; +import com.scienceminer.glutton.utils.BinarySerialiser; + +import org.apache.http.HttpHost; +import org.apache.commons.io.FileUtils; + +import com.codahale.metrics.Meter; +import com.codahale.metrics.Counter; + +import org.lmdbjava.*; +import java.nio.ByteBuffer; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +public class ElasticSearchIndexer { + protected static final Logger logger = LoggerFactory.getLogger(ElasticSearchIndexer.class); + + private static volatile ElasticSearchIndexer instance; + + private LookupConfiguration configuration; + private RestClient restClient; + private ElasticsearchTransport transport; + private ElasticsearchClient elasticsearchClient; + + private String settingsPath = "config/elastic-settings.json"; + + public static ElasticSearchIndexer getInstance(LookupConfiguration configuration) { + if (instance == null) { + synchronized (ElasticSearchIndexer.class) { + if (instance == null) { + getNewInstance(configuration); + } + } + } + return instance; + } + + /** + * Creates a new instance. + */ + private static synchronized void getNewInstance(LookupConfiguration configuration) { + instance = new ElasticSearchIndexer(configuration); + } + + private ElasticSearchIndexer(LookupConfiguration configuration) { + this.configuration = configuration; + + // Create the low-level client + restClient = RestClient + .builder(HttpHost.create(configuration.getElastic().getHost())) + //.setDefaultHeaders(new Header[]{ + // new BasicHeader("Authorization", "ApiKey " + apiKey) + //}) + .build(); + + // Create the transport with a Jackson mapper + transport = new RestClientTransport( + restClient, new JacksonJsonpMapper()); + + // And create the API client + elasticsearchClient = new ElasticsearchClient(transport); + } + + public void healthCheck() { + // view information about relevant indexes + // The information includes the health status, running status, index names, index IDs, number of primary shards, and number of replica shards. + try{ + IndicesResponse indicesResponse = elasticsearchClient.cat().indices(); + indicesResponse.valueBody().forEach(info -> System.out.println(info.index() + "\t" + info.health() + + "\t"+ info.status() + "\tid: " + info.uuid() +"\tprimary: " + info.pri() + "\treplica: " + info.rep())); + } catch (IOException ioException) { + logger.error("Health check status failed", ioException); + } + } + + public void deleteIndex(String indexName) { + try { + // Delete the index. + DeleteIndexResponse deleteResponse = elasticsearchClient.indices().delete(createIndexBuilder -> createIndexBuilder + .index(indexName) + ); + logger.info("Delete index successfully - " + deleteResponse.toString()); + } catch (IOException ioException) { + logger.error("Delete index failed", ioException); + } + } + + /** + * Create the biblio-glutton search index and load the index settings and mapping + **/ + public void createIndex(String indexName) { + try { + // settings and mappings + String mappingJsonString = FileUtils.readFileToString(new File(settingsPath), "UTF-8"); + + try (InputStream input = new FileInputStream(settingsPath)) { + CreateIndexResponse createResponse = this.elasticsearchClient + .indices().create(new CreateIndexRequest.Builder() + .withJson(input) + .index(indexName) + .build()); + logger.info("Create index successfully - \n" + createResponse.toString()); + } catch (IOException ioException) { + logger.error("Create index failed", ioException); + } + } catch (IOException ioException) { + logger.error("Reading ElasticSearch settings/mapping failed", ioException); + } + } + + /** + * Index all the values of a LMDB storage. The expected values are JSON documents + * in the CrossRef format. + * Document identifier is the source prefixed by the main identifier of the this source: + * e.g. crossref:DOI, hal:HalID, pubmed:pmid + * + * Already existing keys are skipt if update is false. + **/ + public void indexCollection(Env environment, Dbi jsonMetadataDb, boolean update, Meter meter, Counter counterIndexedRecords) { + int counter = 0; + long total = 0; + + try (final Txn txn = environment.txnRead()) { + total = jsonMetadataDb.stat(txn).entries; + } catch (Env.ReadersFullException e) { + throw new ServiceOverloadedException("Not enough readers for LMDB access, increase them or reduce the parallel request rate. ", e); + } +//System.out.println("total: " + total); + BulkRequest.Builder br = new BulkRequest.Builder(); + int bulkSize = 0; + try (Txn txn = environment.txnRead()) { + try (CursorIterable it = jsonMetadataDb.iterate(txn, KeyRange.all())) { + for (final CursorIterable.KeyVal kv : it) { + String key = null; + String value = null; + try { + key = (String) BinarySerialiser.deserialize(kv.key()); + value = (String) BinarySerialiser.deserializeAndDecompress(kv.val()); + + MetadataObj objToIndex = MetadataObjBuilder.createMetadataObj(value); + if (objToIndex != null && !MetadataObjBuilder.isFilteredType(objToIndex)) { + objToIndex.type = null; + String localIdentifier = objToIndex._id; + objToIndex._id = null; + + if (br == null) + br = new BulkRequest.Builder(); + + br.operations(op -> op + .index(idx -> idx + .index(configuration.getElastic().getIndex()) + .id(localIdentifier) + .document(objToIndex) + ) + ); + bulkSize++; + } + + if (bulkSize >= configuration.getIndexingBatchSize()) { + try { + BulkResponse result = this.elasticsearchClient.bulk(br.build()); + if (result.errors()) { + logger.error("Bulk had errors"); + for (BulkResponseItem item: result.items()) { + if (item.error() != null) { + logger.error(item.error().reason()); + } + } + } + meter.mark(configuration.getIndexingBatchSize()); + counterIndexedRecords.inc(configuration.getIndexingBatchSize()); + } catch (IOException e) { + logger.error("Batch indexing failed", e); + } + + br = new BulkRequest.Builder(); + bulkSize = 0; + } + } catch (IOException e) { + logger.error("Cannot decompress document with key: " + key, e); + } + if (counter >= total) { + txn.close(); + break; + } + counter++; + } + } + } catch (Env.ReadersFullException e) { + throw new ServiceOverloadedException("Not enough readers for LMDB access, increase them or reduce the parallel request rate. ", e); + } + + // last bulk, if not empty + if (bulkSize > 0) { + try { + BulkResponse result = this.elasticsearchClient.bulk(br.build()); + if (result.errors()) { + logger.error("Bulk had errors"); + for (BulkResponseItem item: result.items()) { + if (item.error() != null) { + logger.error(item.error().reason()); + } + } + } + meter.mark(bulkSize); + counterIndexedRecords.inc(bulkSize); + } catch (IOException e) { + logger.error("Batch indexing failed", e); + } + } + + // as final step we refresh the index, something we have prevented before for speed reasons + refreshIndex(configuration.getElastic().getIndex()); + } + + /** + * Extend an existing index with a set of documents. The expected values are JSON + * documents in the CrossRef format. + * Document identifier is the source prefixed by the main identifier of the this source: + * e.g. crossref:DOI, hal:HalID, pubmed:pmid + * + * Already existing keys are skipt if update is false. + * + **/ + public void indexDocuments(List documents, boolean update, Counter counterIndexedRecords) { + BulkRequest.Builder br = new BulkRequest.Builder(); + for(String document : documents) { + MetadataObj objToIndex = MetadataObjBuilder.createMetadataObj(document); + if (objToIndex != null && !MetadataObjBuilder.isFilteredType(objToIndex)) { + objToIndex.type = null; + String localIdentifier = objToIndex._id; + objToIndex._id = null; + br.operations(op -> op + .index(idx -> idx + .index(configuration.getElastic().getIndex()) + .id(localIdentifier) + .document(objToIndex) + ) + ); + } + } + + try { + BulkResponse result = this.elasticsearchClient.bulk(br.build()); + if (result.errors()) { + logger.error("Bulk had errors"); + for (BulkResponseItem item: result.items()) { + if (item.error() != null) { + logger.error(item.error().reason()); + } + } + } + counterIndexedRecords.inc(documents.size()); + } catch (IOException e) { + logger.error("Batch indexing failed", e); + } + } + + public void asyncIndexDocuments(List documents, boolean update, Counter counterIndexedRecords) { + BulkRequest.Builder br = new BulkRequest.Builder(); + for(String document : documents) { + MetadataObj objToIndex = MetadataObjBuilder.createMetadataObj(document); + if (objToIndex != null && !MetadataObjBuilder.isFilteredType(objToIndex)) { + objToIndex.type = null; + String localIdentifier = objToIndex._id; + objToIndex._id = null; + br.operations(op -> op + .index(idx -> idx + .index(configuration.getElastic().getIndex()) + .id(localIdentifier) + .document(objToIndex) + ) + ); + } + } + + try { + BulkResponse result = this.elasticsearchClient.bulk(br.build()); + if (result.errors()) { + logger.error("Bulk had errors"); + for (BulkResponseItem item: result.items()) { + if (item.error() != null) { + logger.error(item.error().reason()); + } + } + } + counterIndexedRecords.inc(documents.size()); + } catch (IOException e) { + logger.error("Batch indexing failed", e); + } + } + + public boolean indexExists(String indexName) { + boolean result = false; + try { + BooleanResponse resultResponse = elasticsearchClient.indices().exists(ExistsRequest.of(e -> e.index(indexName))); + result = resultResponse.value(); + } catch (IOException ioException) { + logger.error("Exists index failed", ioException); + } + return result; + } + + public void setupIndex(boolean extend) { + healthCheck(); + if (!extend && indexExists(configuration.getElastic().getIndex())) { + logger.warn("Deleting existing ElasicSearch index..."); + deleteIndex(configuration.getElastic().getIndex()); + } + + if (!indexExists(configuration.getElastic().getIndex())) { + logger.warn("Creating new fresh ElasicSearch index..."); + createIndex(configuration.getElastic().getIndex()); + } + } + + public void refreshIndex(String indexName) { + try { + RefreshResponse resultResponse = elasticsearchClient.indices().refresh(RefreshRequest.of(e -> e.index(indexName))); + //logger.info("Refresh existing ElasicSearch index..."); + } catch (IOException ioException) { + logger.error("Refresh index failed", ioException); + } + } + +} diff --git a/src/main/java/com/scienceminer/glutton/indexing/MetadataObj.java b/src/main/java/com/scienceminer/glutton/indexing/MetadataObj.java new file mode 100644 index 00000000..c1ea9910 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/indexing/MetadataObj.java @@ -0,0 +1,44 @@ +package com.scienceminer.glutton.indexing; + +import java.util.*; + +/** + * Object to be indexed for search + **/ +public class MetadataObj { + public String _id; + public List title; + public String DOI; + public String halId; + public String first_author; + public String author; + public String first_page; + public List journal; + public List abbreviated_journal; + public String volume; + public String issue; + public String year; + public String bibliographic; + public String query; + public String type; + + public String toString() { + StringBuilder builder = new StringBuilder(); + builder.append("_id: ").append(_id).append(", "); + builder.append("title: ").append(title.toString()).append(", "); + builder.append("DOI: ").append(DOI).append(", "); + builder.append("halId: ").append(halId).append(", "); + builder.append("first_author: ").append(first_author).append(", "); + builder.append("author: ").append(author).append(", "); + builder.append("first_page: ").append(first_page).append(", "); + builder.append("journal: ").append(journal.toString()).append(", "); + builder.append("abbreviated_journal: ").append(abbreviated_journal.toString()).append(", "); + builder.append("volume: ").append(volume).append(", "); + builder.append("issue: ").append(issue).append(", "); + builder.append("year: ").append(year).append(", "); + builder.append("bibliographic: ").append(bibliographic).append(", "); + builder.append("type: ").append(type); + + return builder.toString(); + } +} diff --git a/src/main/java/com/scienceminer/glutton/indexing/MetadataObjBuilder.java b/src/main/java/com/scienceminer/glutton/indexing/MetadataObjBuilder.java new file mode 100644 index 00000000..85f8267a --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/indexing/MetadataObjBuilder.java @@ -0,0 +1,396 @@ +package com.scienceminer.glutton.indexing; + +import java.io.*; +import java.util.*; + +import org.apache.commons.lang3.StringUtils; +import com.scienceminer.glutton.utils.Utilities; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.dataformat.yaml.YAMLFactory; +import com.fasterxml.jackson.core.*; +import com.fasterxml.jackson.databind.*; +import com.fasterxml.jackson.databind.node.*; +import com.fasterxml.jackson.annotation.*; +import com.fasterxml.jackson.core.io.*; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import static org.apache.commons.lang3.StringUtils.isNotEmpty; +import static org.apache.commons.lang3.StringUtils.isNotBlank; + +/** + * Class for creating object to be indexed from a bibliographical record in crossref JSON format. + */ + +public class MetadataObjBuilder { + protected static final Logger logger = LoggerFactory.getLogger(MetadataObjBuilder.class); + + private static ObjectMapper objectMapper = new ObjectMapper(); + + public static MetadataObj createMetadataObj(String recordJson) { + try { + JsonNode rootNode = objectMapper.readTree(recordJson); + return createMetadataObjFromJsonNode(rootNode); + } catch(Exception e) { + logger.error("fail to parse the JSON document prior to indexing", e); + logger.error(recordJson); + } + + return null; + } + + public static MetadataObj createMetadataObjFromJsonNode(JsonNode rootNode) { + MetadataObj metadataObj = new MetadataObj(); + + String source = null; + JsonNode sourceNode = rootNode.get("source"); + if (sourceNode != null && (!sourceNode.isMissingNode())) { + source = sourceNode.asText(); + } + + if (source == null) { + logger.error("The source of the metadata record is not specified! The record will be ignored"); + return null; + } else + source = source.toLowerCase(); + + // set strong identifier, and canonical record identifier (prefix is the source, then the source identifier) + JsonNode doiNode = rootNode.get("DOI"); + if (doiNode != null && (!doiNode.isMissingNode())) { + metadataObj.DOI = doiNode.asText(); + } + + JsonNode halIdNode = rootNode.get("halId"); + if (halIdNode != null && (!halIdNode.isMissingNode())) { + metadataObj.halId = halIdNode.asText(); + } + + if ("hal".equals(source)) { + if (metadataObj._id == null) + metadataObj._id = source+":"+metadataObj.halId; + } else if ("crossref".equals(source)) { + if (metadataObj._id == null) + metadataObj._id = source+":"+metadataObj.DOI; + } else { + logger.error("The source of the metadata record is not supported: " + source); + } + + // we go through the fields we want to index + + JsonNode titleNode = rootNode.get("title"); + if (titleNode != null && (!titleNode.isMissingNode())) { + if (titleNode.isArray() && ((ArrayNode)titleNode).size() > 0) { + Iterator oneTitleIter = ((ArrayNode)titleNode).elements(); + while (oneTitleIter.hasNext()) { + JsonNode oneDocNode = oneTitleIter.next(); + String localTitle = oneDocNode.asText(); + localTitle = localTitle.replace("\n", " "); + localTitle = localTitle.replaceAll("( )+", " "); + if (metadataObj.title == null) + metadataObj.title = new ArrayList<>(); + if (isNotBlank(localTitle)) + metadataObj.title.add(localTitle); + } + } else { + String localTitle = titleNode.asText(); + localTitle = localTitle.replace("\n", " "); + localTitle = localTitle.replaceAll("( )+", " "); + if (isNotBlank(localTitle)) + metadataObj.title = Arrays.asList(localTitle); + } + } + + JsonNode authorNode = rootNode.get("author"); + if (authorNode != null && (!authorNode.isMissingNode())) { + if (authorNode.isArray() && ((ArrayNode)authorNode).size() > 0) { + Iterator oneAuthorIter = ((ArrayNode)authorNode).elements(); + boolean firstAuthorSet = false; + int rank = 0; + String first_author_family_name = null; + while (oneAuthorIter.hasNext()) { + JsonNode oneAuthorNode = oneAuthorIter.next(); + + JsonNode sequenceNode = oneAuthorNode.get("sequence"); + String sequenceValue = ""; + if (sequenceNode != null && (!sequenceNode.isMissingNode())) { + sequenceValue = sequenceNode.asText(); + } + + if ("first".equals(sequenceValue)) { + JsonNode familyNode = oneAuthorNode.get("family"); + if (familyNode != null && (!familyNode.isMissingNode())) { + metadataObj.first_author = familyNode.asText(); + firstAuthorSet = true; + } + } + + JsonNode familyNode = oneAuthorNode.get("family"); + if (familyNode != null && (!familyNode.isMissingNode())) { + if (metadataObj.author == null) + metadataObj.author = ""; + metadataObj.author += familyNode.asText() + " "; + if (rank == 0) + first_author_family_name = familyNode.asText(); + } + + rank++; + } + + if (!firstAuthorSet) { + // no sequence information apparently, so as fallback we use the first + // author in the author list + if (first_author_family_name != null) { + metadataObj.first_author = first_author_family_name; + } + } + } + } + + + // parse page metadata to get the first page only + JsonNode pageNode = rootNode.get("page"); + if (pageNode != null && (!pageNode.isMissingNode())) { + String pageChunk = pageNode.asText(); + pageChunk = pageChunk.trim(); + String[] pagePieces = pageChunk.split(",|-| "); + if (pagePieces.length > 0) { + metadataObj.first_page = pagePieces[0]; + } + } + + /*if (data.page) { + var pagePieces = data.page.split(/,|-| /g); + if (pagePieces && pagePieces.length > 0) { + obj.first_page = pagePieces[0]; + //console.log(data.page, obj.first_page); + } + }*/ + + JsonNode containerTitleNode = rootNode.get("container-title"); + if (containerTitleNode != null && (!containerTitleNode.isMissingNode())) { + if (containerTitleNode.isArray() && ((ArrayNode)containerTitleNode).size() > 0) { + Iterator oneTitleIter = ((ArrayNode)containerTitleNode).elements(); + while (oneTitleIter.hasNext()) { + JsonNode oneTitleNode = oneTitleIter.next(); + String localTitle = oneTitleNode.asText(); + localTitle = localTitle.replace("\n", " "); + localTitle = localTitle.replaceAll("( )+", " "); + if (isNotBlank(localTitle)) { + if (metadataObj.journal == null) + metadataObj.journal = new ArrayList<>(); + metadataObj.journal.add(localTitle); + } + } + } + } + + JsonNode containerShortTitleNode = rootNode.get("short-container-title"); + if (containerShortTitleNode != null && (!containerShortTitleNode.isMissingNode())) { + if (containerShortTitleNode.isArray() && ((ArrayNode)containerShortTitleNode).size() > 0) { + + Iterator containerShortTitleIter = ((ArrayNode)containerShortTitleNode).elements(); + while (containerShortTitleIter.hasNext()) { + JsonNode oneContainerShortTitleNode = containerShortTitleIter.next(); + String localTitle = oneContainerShortTitleNode.asText(); + localTitle = localTitle.replace("\n", " "); + localTitle = localTitle.replaceAll("( )+", " "); + if (isNotBlank(localTitle)) { + if (metadataObj.abbreviated_journal == null) + metadataObj.abbreviated_journal = new ArrayList<>(); + metadataObj.abbreviated_journal.add(localTitle); + } + } + } + } + + JsonNode volumeNode = rootNode.get("volume"); + if (volumeNode != null && (!volumeNode.isMissingNode())) { + String volumeString = volumeNode.asText(); + if (isNotBlank(volumeString)) + metadataObj.volume = volumeString; + } + + // year is a date part (first one) in issued or created or published-online or published-print (we follow this order) + JsonNode yearNode = rootNode.get("issued"); + if (yearNode != null && (!yearNode.isMissingNode())) { + JsonNode datePartsNode = yearNode.get("date-parts"); + if (datePartsNode != null && (!datePartsNode.isMissingNode())) { + if (datePartsNode.isArray() && ((ArrayNode)datePartsNode).size() > 0) { + Iterator datePartsNodeIter = ((ArrayNode)datePartsNode).elements(); + while (datePartsNodeIter.hasNext()) { + JsonNode yearPartsNodeIterNode = datePartsNodeIter.next(); + String year = yearPartsNodeIterNode.asText(); + if (isNotBlank(year)) + metadataObj.year = year; + break; + } + } + } + } + + if (metadataObj.year == null) { + yearNode = rootNode.get("published"); + if (yearNode != null && (!yearNode.isMissingNode())) { + JsonNode datePartsNode = yearNode.get("date-parts"); + if (datePartsNode != null && (!datePartsNode.isMissingNode())) { + if (datePartsNode.isArray() && ((ArrayNode)datePartsNode).size() > 0) { + Iterator datePartsNodeIter = ((ArrayNode)datePartsNode).elements(); + while (datePartsNodeIter.hasNext()) { + JsonNode yearPartsNodeIterNode = datePartsNodeIter.next(); + String year = yearPartsNodeIterNode.asText(); + if (isNotBlank(year)) + metadataObj.year = year; + break; + } + } + } + } + } + + if (metadataObj.year == null) { + yearNode = rootNode.get("published-online"); + if (yearNode != null && (!yearNode.isMissingNode())) { + JsonNode datePartsNode = yearNode.get("date-parts"); + if (datePartsNode != null && (!datePartsNode.isMissingNode())) { + if (datePartsNode.isArray() && ((ArrayNode)datePartsNode).size() > 0) { + Iterator datePartsNodeIter = ((ArrayNode)datePartsNode).elements(); + while (datePartsNodeIter.hasNext()) { + JsonNode yearPartsNodeIterNode = datePartsNodeIter.next(); + String year = yearPartsNodeIterNode.asText(); + if (isNotBlank(year)) + metadataObj.year = year; + break; + } + } + } + } + } + + if (metadataObj.year == null) { + yearNode = rootNode.get("published-print"); + if (yearNode != null && (!yearNode.isMissingNode())) { + JsonNode datePartsNode = yearNode.get("date-parts"); + if (datePartsNode != null && (!datePartsNode.isMissingNode())) { + if (datePartsNode.isArray() && ((ArrayNode)datePartsNode).size() > 0) { + Iterator datePartsNodeIter = ((ArrayNode)datePartsNode).elements(); + while (datePartsNodeIter.hasNext()) { + JsonNode yearPartsNodeIterNode = datePartsNodeIter.next(); + String year = yearPartsNodeIterNode.asText(); + if (isNotBlank(year)) + metadataObj.year = year; + break; + } + } + } + } + } + + // this is deposit date, normally we will never use it, but it will ensure + // that we always have a date as conservative fallback + if (metadataObj.year == null) { + yearNode = rootNode.get("created"); + if (yearNode != null && (!yearNode.isMissingNode())) { + JsonNode datePartsNode = yearNode.get("date-parts"); + if (datePartsNode != null && (!datePartsNode.isMissingNode())) { + if (datePartsNode.isArray() && ((ArrayNode)datePartsNode).size() > 0) { + Iterator datePartsNodeIter = ((ArrayNode)datePartsNode).elements(); + while (datePartsNodeIter.hasNext()) { + JsonNode yearPartsNodeIterNode = datePartsNodeIter.next(); + String year = yearPartsNodeIterNode.asText(); + if (isNotBlank(year)) + metadataObj.year = year; + break; + } + } + } + } + } + + + /*if (data.issued) { + if (data.issued["date-parts"]) { + obj.year = data.issued["date-parts"][0][0] + } + } + if (!obj.year && data["published-online"]) { + if (data["published-online"]["date-parts"]) { + obj.year = data["published-online"]["date-parts"][0][0] + } + } + if (!obj.year && data["published-print"]) { + if (data["published-print"]["date-parts"]) { + obj.year = data["published-print"]["date-parts"][0][0] + } + } + // this is deposit date, normally we will never use it, but it will ensure + // that we always have a date as conservative fallback + if (!obj.year && data.created) { + if (data.created["date-parts"]) { + obj.year = data.created["date-parts"][0][0] + } + }*/ + //console.log(obj.year); + + // bibliographic field is the concatenation of usual bibliographic metadata + String biblio = buildBibliographicField(metadataObj); + if (isNotBlank(biblio)) { + metadataObj.bibliographic = biblio; + } + + JsonNode typeNode = rootNode.get("type"); + if (typeNode != null && (!typeNode.isMissingNode())) { + String localType = typeNode.asText(); + if (isNotBlank(localType)) + metadataObj.type = localType; + } + + return metadataObj; + } + + public static String buildBibliographicField(MetadataObj obj) { + StringBuilder res = new StringBuilder(); + + if (isNotBlank(obj.author)) + res.append(obj.author); + else if (isNotBlank(obj.first_author)) + res.append(obj.first_author); + + if (obj.title != null && obj.title.size()>0) + res.append(" ").append(obj.title.get(0)); + + if (obj.journal != null && obj.journal.size()>0) + res.append(" ").append(obj.journal); + + if (obj.abbreviated_journal != null && obj.abbreviated_journal.size()>0) + res.append(" ").append(obj.abbreviated_journal); + + if (isNotBlank(obj.volume)) + res.append(" ").append(obj.volume); + + if (isNotBlank(obj.issue)) + res.append(" ").append(obj.issue); + + if (isNotBlank(obj.first_page)) + res.append(" ").append(obj.first_page); + + if (isNotBlank(obj.year)) + res.append(" ").append(obj.year); + + return res.toString(); + } + + public static boolean isFilteredType(MetadataObj obj) { + // if document type is component, we ignore it (it means that the DOI is + // for a sub-part of a publication, like 10.1371/journal.pone.0104614.t002) + if ("component".equals(obj.type)) { + return true; + } + // add other DOI type to be ignored here + return false; + } + + public static Map createMapFieldSolr(String recordJson) { + return null; + } +} \ No newline at end of file diff --git a/src/main/java/com/scienceminer/glutton/indexing/SolrIndexer.java b/src/main/java/com/scienceminer/glutton/indexing/SolrIndexer.java new file mode 100644 index 00000000..480f9d02 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/indexing/SolrIndexer.java @@ -0,0 +1,27 @@ +package com.scienceminer.glutton.indexing; + +import java.io.IOException; +import java.util.*; + +import com.scienceminer.glutton.configuration.LookupConfiguration; + +import org.apache.solr.client.solrj.SolrClient; +import org.apache.solr.client.solrj.SolrServerException; +import org.apache.solr.client.solrj.impl.HttpSolrClient; +import org.apache.solr.common.SolrInputDocument; + +import org.lmdbjava.*; +import java.nio.ByteBuffer; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +public class SolrIndexer { + protected static final Logger logger = LoggerFactory.getLogger(SolrIndexer.class); + + private static volatile SolrIndexer instance; + + private LookupConfiguration configuration; + + +} diff --git a/lookup/src/main/java/com/scienceminer/lookup/reader/CrossrefJsonArrayReader.java b/src/main/java/com/scienceminer/glutton/reader/CrossrefJsonArrayReader.java similarity index 95% rename from lookup/src/main/java/com/scienceminer/lookup/reader/CrossrefJsonArrayReader.java rename to src/main/java/com/scienceminer/glutton/reader/CrossrefJsonArrayReader.java index df3ab5f3..8d095280 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/reader/CrossrefJsonArrayReader.java +++ b/src/main/java/com/scienceminer/glutton/reader/CrossrefJsonArrayReader.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.reader; +package com.scienceminer.glutton.reader; import com.codahale.metrics.Counter; import com.codahale.metrics.Meter; @@ -8,7 +8,7 @@ import com.fasterxml.jackson.databind.JsonMappingException; import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.ObjectMapper; -import com.scienceminer.lookup.configuration.LookupConfiguration; +import com.scienceminer.glutton.configuration.LookupConfiguration; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.NotImplementedException; import org.slf4j.Logger; diff --git a/lookup/src/main/java/com/scienceminer/lookup/reader/CrossrefJsonReader.java b/src/main/java/com/scienceminer/glutton/reader/CrossrefJsonReader.java similarity index 84% rename from lookup/src/main/java/com/scienceminer/lookup/reader/CrossrefJsonReader.java rename to src/main/java/com/scienceminer/glutton/reader/CrossrefJsonReader.java index bf5d4db7..bc620aaa 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/reader/CrossrefJsonReader.java +++ b/src/main/java/com/scienceminer/glutton/reader/CrossrefJsonReader.java @@ -1,10 +1,10 @@ -package com.scienceminer.lookup.reader; +package com.scienceminer.glutton.reader; import com.codahale.metrics.Counter; import com.codahale.metrics.Meter; import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.node.ObjectNode; -import com.scienceminer.lookup.configuration.LookupConfiguration; +import com.scienceminer.glutton.configuration.LookupConfiguration; import org.apache.commons.lang3.StringUtils; import java.io.InputStream; @@ -87,8 +87,10 @@ public JsonNode postProcessRecord(JsonNode crossrefData) { } } - if (configuration != null && configuration.getIgnoreCrossRefFields() != null) { - for(String field : configuration.getIgnoreCrossRefFields()) { + if (configuration != null && + configuration.getCrossref() != null && + configuration.getCrossref().getIgnoreCrossrefFields() != null) { + for(String field : configuration.getCrossref().getIgnoreCrossrefFields()) { object.remove(field); } } @@ -117,6 +119,13 @@ public static boolean isJsonArray(InputStream inputStreamCrossref) { String firstLine = r.readLine(); if (firstLine.startsWith("{\"items\":[")) result = true; + else { + String secondLine = r.readLine(); + // from https://github.com/karatekaneen, NOTE: The 2023 dump has a space before ":" + if (StringUtils.strip(secondLine).startsWith("\"items\": [") || + StringUtils.strip(secondLine).startsWith("\"items\" : [")) + result = true; + } } catch(IOException e) { LOGGER.error("cannot read input stream when trying to detect json format type", e); } diff --git a/lookup/src/main/java/com/scienceminer/lookup/reader/CrossrefJsonlReader.java b/src/main/java/com/scienceminer/glutton/reader/CrossrefJsonlReader.java similarity index 95% rename from lookup/src/main/java/com/scienceminer/lookup/reader/CrossrefJsonlReader.java rename to src/main/java/com/scienceminer/glutton/reader/CrossrefJsonlReader.java index 5d8d4752..a4b78c0f 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/reader/CrossrefJsonlReader.java +++ b/src/main/java/com/scienceminer/glutton/reader/CrossrefJsonlReader.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.reader; +package com.scienceminer.glutton.reader; import com.codahale.metrics.Counter; import com.codahale.metrics.Meter; @@ -8,7 +8,7 @@ import com.fasterxml.jackson.databind.JsonMappingException; import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.ObjectMapper; -import com.scienceminer.lookup.configuration.LookupConfiguration; +import com.scienceminer.glutton.configuration.LookupConfiguration; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/lookup/src/main/java/com/scienceminer/lookup/reader/IstexIdsReader.java b/src/main/java/com/scienceminer/glutton/reader/IstexIdsReader.java similarity index 96% rename from lookup/src/main/java/com/scienceminer/lookup/reader/IstexIdsReader.java rename to src/main/java/com/scienceminer/glutton/reader/IstexIdsReader.java index ecd436e9..dd1e95fd 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/reader/IstexIdsReader.java +++ b/src/main/java/com/scienceminer/glutton/reader/IstexIdsReader.java @@ -1,11 +1,11 @@ -package com.scienceminer.lookup.reader; +package com.scienceminer.glutton.reader; import com.fasterxml.jackson.core.JsonGenerationException; import com.fasterxml.jackson.core.JsonParser; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.JsonMappingException; import com.fasterxml.jackson.databind.ObjectMapper; -import com.scienceminer.lookup.data.IstexData; +import com.scienceminer.glutton.data.IstexData; import org.apache.commons.collections4.CollectionUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/lookup/src/main/java/com/scienceminer/lookup/reader/PmidReader.java b/src/main/java/com/scienceminer/glutton/reader/PmidReader.java similarity index 87% rename from lookup/src/main/java/com/scienceminer/lookup/reader/PmidReader.java rename to src/main/java/com/scienceminer/glutton/reader/PmidReader.java index 11d43e17..1f7a7fba 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/reader/PmidReader.java +++ b/src/main/java/com/scienceminer/glutton/reader/PmidReader.java @@ -1,6 +1,6 @@ -package com.scienceminer.lookup.reader; +package com.scienceminer.glutton.reader; -import com.scienceminer.lookup.data.PmidData; +import com.scienceminer.glutton.data.PmidData; import org.apache.commons.lang3.StringUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -17,7 +17,7 @@ import static org.apache.commons.lang3.StringUtils.replaceAll; /** - * Class responsible for reading the istex ids json file + * Class responsible for reading the PMID/PMC/DOI mapping ids csv file **/ public class PmidReader { @@ -28,7 +28,7 @@ public void load(String input, Consumer closure) { stream.forEach(line -> closure.accept(fromCSV(line))); } catch (IOException e) { - LOGGER.error("Some serious error when processing the input Istex ID file.", e); + LOGGER.error("Some serious error when processing the input PMID/PMC/DOI mapping file.", e); } } @@ -45,7 +45,7 @@ public void load(InputStream input, Consumer closure) { }); } catch (IOException e) { - LOGGER.error("Some serious error when processing the input Istex ID file.", e); + LOGGER.error("Some serious error when processing the input PMID/PMC/DOI mapping file.", e); } } diff --git a/lookup/src/main/java/com/scienceminer/lookup/reader/UnpayWallReader.java b/src/main/java/com/scienceminer/glutton/reader/UnpayWallReader.java similarity index 95% rename from lookup/src/main/java/com/scienceminer/lookup/reader/UnpayWallReader.java rename to src/main/java/com/scienceminer/glutton/reader/UnpayWallReader.java index 736ea4e5..1ad00bfd 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/reader/UnpayWallReader.java +++ b/src/main/java/com/scienceminer/glutton/reader/UnpayWallReader.java @@ -1,11 +1,11 @@ -package com.scienceminer.lookup.reader; +package com.scienceminer.glutton.reader; import com.fasterxml.jackson.core.JsonGenerationException; import com.fasterxml.jackson.core.JsonParser; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.JsonMappingException; import com.fasterxml.jackson.databind.ObjectMapper; -import com.scienceminer.lookup.data.UnpayWallMetadata; +import com.scienceminer.glutton.data.UnpayWallMetadata; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/src/main/java/com/scienceminer/glutton/serialization/BiblioSerializer.java b/src/main/java/com/scienceminer/glutton/serialization/BiblioSerializer.java new file mode 100644 index 00000000..bf971d7f --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/serialization/BiblioSerializer.java @@ -0,0 +1,602 @@ +package com.scienceminer.glutton.serialization; + +import java.io.*; +import java.util.*; + +import com.opencsv.*; +import org.apache.commons.lang3.StringUtils; + +import com.scienceminer.glutton.data.*; +//import com.scienceminer.glutton.data.db.KBStagingEnvironment; +import com.scienceminer.glutton.utils.Utilities; +import com.scienceminer.glutton.storage.lookup.*; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.dataformat.yaml.YAMLFactory; +import com.fasterxml.jackson.core.*; +import com.fasterxml.jackson.databind.*; +import com.fasterxml.jackson.databind.node.*; +import com.fasterxml.jackson.annotation.*; +import com.fasterxml.jackson.core.io.*; + +import org.joda.time.DateTimeFieldType; +import org.joda.time.Partial; + +import static org.apache.commons.lang3.StringUtils.isNotEmpty; +import static org.apache.commons.lang3.StringUtils.isNotBlank; + +/** + * Class for serializing biblio objects to the Crossref JSON schema without information loss from PubMed metadata + * and HAL metadata. + */ + +public class BiblioSerializer { + + static String INVALID_MSG = "NOT_FOUND;INVALID_JOURNAL"; + + /** + * The export follows the same JSON schema as Crossref JSON (derived from Crossref Unixref). + * For a Biblio object coming from PubMed medaline metadata, pmidLookup should not be null. + * For a Biblio object coming from HAL metadata, halLookup should not be null. + */ + public static String serializeJson(Biblio biblio, PMIdsLookup pmidLookup, HALLookup halLookup) throws JsonProcessingException { + ObjectMapper mapper = new ObjectMapper(); + StringBuilder builder = new StringBuilder(); + builder.append("{"); + if (pmidLookup != null) + builder.append("\"source\": \"pubmed\""); + else if (halLookup != null) + builder.append("\"source\": \"hal\""); + else + builder.append("\"source\": \"unknown\""); + + // last update + if (biblio.getLastUpdateDate() != null) { + Partial update = biblio.getLastUpdateDate(); + builder.append(", \"indexed\": "); + + builder.append("{\"date-parts\": ["); + + if (update.isSupported(DateTimeFieldType.year())) { + builder.append(update.get(DateTimeFieldType.year())); + + if (update.isSupported(DateTimeFieldType.monthOfYear())) { + int theMonth = update.get(DateTimeFieldType.monthOfYear()); + builder.append(", " + theMonth); + + if (update.isSupported(DateTimeFieldType.dayOfMonth())) { + int theDay = update.get(DateTimeFieldType.dayOfMonth()); + builder.append(", " + theDay); + } + } + } + builder.append("], "); + builder.append("\"date-time\": \""+ Biblio.dateISODisplayFormat(update) + "\"}"); + + // timestamp seems crossref specific + } + + if (biblio.getDoi() == null) { + // try to get a DOI via PMID and/or PMC + + if (pmidLookup != null && biblio.getPubmedId() != null) { + String doi = null; + final PmidData pmidData = pmidLookup.retrieveIdsByPmid(biblio.getPubmedId()); + if (pmidData != null && isNotBlank(pmidData.getDoi())) { + doi = pmidData.getDoi(); + } + + if (doi != null) { + biblio.setDoi(doi); + } + } + + if (pmidLookup != null && biblio.getDoi() == null && biblio.getPmc() != null) { + String doi = null; + final PmidData pmidData = pmidLookup.retrieveIdsByPmc(biblio.getPmc()); + if (pmidData != null && isNotBlank(pmidData.getDoi())) { + doi = pmidData.getDoi(); + } + + if (doi != null) { + biblio.setDoi(doi); + } + } + } + + if (biblio.getDoi() != null) { + builder.append(", \"DOI\": " + mapper.writeValueAsString(biblio.getDoi())); + int ind = biblio.getDoi().indexOf("/"); + if (ind != -1) { + String prefix = biblio.getDoi().substring(0, ind); + builder.append(", \"prefix\": " + mapper.writeValueAsString(prefix)); + } + builder.append(", \"URL\": " + mapper.writeValueAsString("http://dx.doi.org/" + biblio.getDoi())); + } + + if (biblio.getRawPublicationType() != null) { + builder.append(", \"type\": " + mapper.writeValueAsString(biblio.getRawPublicationType())); + } + + if (biblio.getPublisher() != null) { + String localPublisher = Utilities.simpleCleanField(biblio.getPublisher()); + builder.append(", \"publisher\": " + mapper.writeValueAsString(biblio.getPublisher())); + } + + if (biblio.getVolume() != null) { + String localVolume = Utilities.simpleCleanField(biblio.getVolume()); + builder.append(", \"volume\": " + mapper.writeValueAsString(biblio.getVolume())); + } + + if (StringUtils.isNotEmpty(biblio.getNumber())) { + String localNumber = Utilities.simpleCleanField(biblio.getNumber()); + builder.append(", \"journal-issue\": { \"issue\": " + mapper.writeValueAsString(localNumber) + "}"); + builder.append(", \"issue\": " + mapper.writeValueAsString(localNumber)); + } + + // pages + String pageRange = biblio.getPageRange(); + if (pageRange != null && pageRange.length()>0) { + builder.append(", \"page\": " + mapper.writeValueAsString(pageRange)); + } + + // titles + if (StringUtils.isNotEmpty(biblio.getArticleTitle())) { + String localTitle = Utilities.simpleCleanField(biblio.getArticleTitle()); + builder.append(", \"title\": [" + mapper.writeValueAsString(localTitle) + "]"); + } + + if (StringUtils.isNotEmpty(biblio.getTitle())) { + String localTitle = Utilities.simpleCleanField(biblio.getTitle()); + builder.append(", \"container-title\": [" + mapper.writeValueAsString(localTitle)); + + // in case of series (e.g. LNCS), the name of the collection is added after the title of the volume + if (StringUtils.isNotEmpty(biblio.getCollectionTitle())) { + String collectionTitle = Utilities.simpleCleanField(biblio.getCollectionTitle()); + builder.append(", " + mapper.writeValueAsString(localTitle) + "]"); + } else + builder.append("]"); + } + + if (StringUtils.isNotEmpty(biblio.getJournalAbbrev())) { + String localTitle = Utilities.simpleCleanField(biblio.getJournalAbbrev()); + builder.append(", \"short-container-title\": [" + mapper.writeValueAsString(localTitle) + "]"); + } + + if (biblio.getAuthors() != null && biblio.getAuthors().size() > 0) { + builder.append(", \"author\": ["); + + boolean first = true; + for(Person author : biblio.getAuthors()) { + if (!first) + builder.append(", "); + builder.append("{"); + + if (author.getFirstName() != null) { + if (author.getMiddleName() != null) { + builder.append("\"given\": " + + mapper.writeValueAsString(author.getFirstName() + " " + author.getMiddleName())); + } else { + builder.append("\"given\": " + + mapper.writeValueAsString(author.getFirstName())); + } + } + if (author.getLastName() != null) { + if (author.getFirstName() != null) + builder.append(", "); + builder.append("\"family\": " + mapper.writeValueAsString(author.getLastName())); + } + if (first) + builder.append(", \"sequence\": \"first\""); + else + builder.append(", \"sequence\": \"additional\""); + + List identifiers = author.getIdentifiers(); + if (identifiers != null && identifiers.size()>0) { + for(Identifier identifier : identifiers) { + if (identifier.getIdentifierName().toLowerCase().equals("orcid")) { + builder.append(", \"ORCID\": " + + mapper.writeValueAsString(identifier.getIdentifierValue())); + } + } + } + + List affiliations = author.getAffiliations(); + if (affiliations != null && affiliations.size()>0) { + builder.append(", \"affiliation\": ["); + boolean firstAff = true; + for(Affiliation affiliation : affiliations) { + if (firstAff) + firstAff = false; + else + builder.append(", "); + builder.append("{\"name\": "+ + mapper.writeValueAsString(affiliation.getAffiliationString()) + "}"); + } + builder.append("]"); + } + + if (first) + first = false; + + builder.append("}"); + } + builder.append("]"); + } + + // publication date + if (biblio.getPublicationDate() != null) { + Partial publicationDate = biblio.getPublicationDate(); + builder.append(", \"published\": "); + + builder.append("{\"date-parts\": ["); + + if (publicationDate.isSupported(DateTimeFieldType.year())) { + builder.append(publicationDate.get(DateTimeFieldType.year())); + + if (publicationDate.isSupported(DateTimeFieldType.monthOfYear())) { + int theMonth = publicationDate.get(DateTimeFieldType.monthOfYear()); + builder.append(", " + theMonth); + + if (publicationDate.isSupported(DateTimeFieldType.dayOfMonth())) { + int theDay = publicationDate.get(DateTimeFieldType.dayOfMonth()); + builder.append(", " + theDay); + } + } + } + builder.append("], "); + builder.append("\"date-time\": \""+ Biblio.dateISODisplayFormat(publicationDate) + "\"}"); + + // timestamp seems crossref specific + } + + // identifiers + if (biblio.getIssn() != null || biblio.getEIssn() != null) { + builder.append(", \"ISSN\": ["); + + if (biblio.getIssn() != null) + builder.append(mapper.writeValueAsString(Biblio.issnInDisplayFormat(biblio.getIssn()))); + if (biblio.getEIssn() != null) { + if (biblio.getIssn() != null) + builder.append(", "); + builder.append(mapper.writeValueAsString(Biblio.issnInDisplayFormat(biblio.getEIssn()))); + } + builder.append("]"); + + builder.append(", \"issn-type\": ["); + if (biblio.getIssn() != null) { + builder.append("{\"value\": " + mapper.writeValueAsString(Biblio.issnInDisplayFormat(biblio.getIssn())) + ", \"type\": \"print\"}"); + } + if (biblio.getEIssn() != null) { + if (biblio.getIssn() != null) + builder.append(", "); + builder.append("{\"value\": " + mapper.writeValueAsString(Biblio.issnInDisplayFormat(biblio.getEIssn())) + ", \"type\": \"electronic\"}"); + } + builder.append("]"); + } + + if (biblio.getAbstract() != null && biblio.getAbstract().length()>0) { + // note: consider removing mark-ups (Crossref does not remove them, but it has a rather negative value) + builder.append(", \"abstract\": " + mapper.writeValueAsString(biblio.getAbstract())); + } + + if (biblio.getLanguage() != null) { + builder.append(", \"language\": " + mapper.writeValueAsString(biblio.getLanguage())); + } + + if (biblio.getPubmedId() == null) { + // try to get a PMID via DOI and/or PMC + if (pmidLookup != null && biblio.getDoi() != null) { + String pmid = null; + final PmidData pmidData = pmidLookup.retrieveIdsByDoi(biblio.getDoi()); + if (pmidData != null && isNotBlank(pmidData.getPmid())) { + pmid = pmidData.getPmid(); + } + + if (pmid != null) { + biblio.setPubmedId(""+pmid); + } + } + + if (pmidLookup != null && biblio.getPubmedId() == null && biblio.getPmc() != null) { + String pmid = null; + final PmidData pmidData = pmidLookup.retrieveIdsByPmc(biblio.getPmc()); + if (pmidData != null && isNotBlank(pmidData.getPmid())) { + pmid = pmidData.getPmid(); + } + + if (pmid != null) { + biblio.setPubmedId(""+pmid); + } + } + } + + if (biblio.getPubmedId() != null) { + builder.append(", \"pmid\": " + mapper.writeValueAsString(biblio.getPmid())); + } + + if (biblio.getPmc() == null) { + // try to get a PMC via PMID and/or DOI + if (pmidLookup != null && biblio.getPubmedId() != null) { + String pmc = null; + final PmidData pmidData = pmidLookup.retrieveIdsByPmid(biblio.getPubmedId()); + if (pmidData != null && isNotBlank(pmidData.getPmcid())) { + pmc = pmidData.getPmcid(); + } + + if (pmc != null) { + biblio.setPmc(pmc); + } + } + + if (pmidLookup != null && biblio.getPmc() == null && biblio.getDoi() != null) { + String pmc = null; + final PmidData pmidData = pmidLookup.retrieveIdsByDoi(biblio.getDoi()); + if (pmidData != null && isNotBlank(pmidData.getPmcid())) { + pmc = pmidData.getPmcid(); + } + + if (pmc != null) { + biblio.setPmc(pmc); + } + } + } + + if (biblio.getPmc() != null) { + builder.append(", \"pmcid\": " + mapper.writeValueAsString(biblio.getPmc())); + } + + if (biblio.getPii() != null) { + builder.append(", \"pii\": " + mapper.writeValueAsString(biblio.getPii())); + } + + if (biblio.getHalId() != null) { + builder.append(", \"halId\": " + mapper.writeValueAsString(biblio.getHalId())); + } + + if (biblio.getHalUri() != null) { + builder.append(", \"halUri\": " + mapper.writeValueAsString(biblio.getHalUri())); + } + + if (biblio.getGrants() != null && biblio.getGrants().size() > 0) { + builder.append(", \"funder\": ["); + boolean first = true; + for(Grant grant : biblio.getGrants()) { + if (first) + first = false; + else + builder.append(", "); + + if (grant.getAgency() == null || grant.getAgency().length() == 0) + builder.append("{\"name\": \"unknown\""); + else + builder.append("{\"name\": " + mapper.writeValueAsString(grant.getAgency())); + builder.append(", \"country\": " + mapper.writeValueAsString(grant.getCountry())); + builder.append(", \"award\": [" + mapper.writeValueAsString(grant.getGrantID()) + "]}"); + + // not sure what to do with acronym, which is related to award, not considered in crossref funder schema/award + //mapper.writeValueAsString(grant.getAcronym()) + } + builder.append("]"); + } + + // MeSH stuff + List meshClasses = biblio.getClassifications(); + if (meshClasses != null && meshClasses.size() > 0) { + builder.append(", \"mesh\": ["); + boolean first = true; + for(ClassificationClass theClass : meshClasses) { + if (theClass.getScheme().equals("MeSH")) { + if (first) + first = false; + else + builder.append(", "); + builder.append(((MeSHClass)theClass).toJson()); + } + } + builder.append("]"); + } + + // license information injected for PMC + if (pmidLookup != null) { + String license = null; + String subpath = null; + final PmidData pmidData = pmidLookup.retrieveIdsByPmc(biblio.getPmc()); + if (pmidData != null && isNotBlank(pmidData.getLicense())) { + license = pmidData.getLicense(); + } + if (pmidData != null && isNotBlank(pmidData.getSubpath())) { + subpath = pmidData.getSubpath(); + } + + String urlValue = null; + if (license != null) { + builder.append(", \"license\": ["); + builder.append("{\"code\": " + mapper.writeValueAsString(license)); + builder.append("}]"); + } + + if (subpath != null || biblio.getPmc() != null) { + builder.append(", \"link\": ["); + + if (subpath != null) { + builder.append("{\"URL\": " + mapper.writeValueAsString(subpath)); + builder.append(", \"content-type\": \"application/tar+gzip\"}"); + } + + if (biblio.getPmc() != null) { + if (urlValue != null) + builder.append(", "); + + String pmcPdf = "https://www.ncbi.nlm.nih.gov/pmc/articles/" + biblio.getPmc() + "/pdf/"; + builder.append("{\"URL\": " + mapper.writeValueAsString(pmcPdf)); + builder.append(", \"content-type\": \"application/pdf\"}"); + } + + builder.append("]"); + } + } + + + if (biblio.getReferenceCount() != null) { + builder.append(", \"reference-count\": " + biblio.getReferenceCount()); + } + + if (biblio.getReferences() != null && biblio.getReferenceCount() > 0) { + builder.append(", \"reference\": ["); + + boolean first = true; + for(Reference reference : biblio.getReferences()) { + if (first) + first = false; + else + builder.append(", "); + + builder.append("{\"unstructured\": " + mapper.writeValueAsString(reference.getReferenceString())); + if (reference.getPubmedId() != null) { + builder.append(", \"pmid\": " + mapper.writeValueAsString(reference.getPubmedId())); + } + + if (reference.getDoi() == null) { + // try to get a DOI via PMID and/or PMC + if (pmidLookup != null && reference.getPubmedId() != null && !INVALID_MSG.equals(reference.getPubmedId())) { + try { + String doi = null; + final PmidData pmidData = pmidLookup.retrieveIdsByPmid(reference.getPubmedId()); + if (pmidData != null && isNotBlank(pmidData.getDoi())) { + doi = pmidData.getDoi(); + } + + if (doi != null) { + reference.setDoi(doi); + } + } catch(Exception e) { + e.printStackTrace(); + } + } + + if (pmidLookup != null && reference.getDoi() == null && reference.getPmc() != null) { + String doi = null; + final PmidData pmidData = pmidLookup.retrieveIdsByPmc(reference.getPmc()); + if (pmidData != null && isNotBlank(pmidData.getDoi())) { + doi = pmidData.getDoi(); + } + + if (doi != null) { + reference.setDoi(doi); + } + } + } + if (reference.getDoi() != null) { + builder.append(", \"DOI\": " + mapper.writeValueAsString(reference.getDoi())); + } + + if (reference.getPmc() == null) { + // try to get the PMC via the PMID + if (pmidLookup != null && reference.getPubmedId() != null && !INVALID_MSG.equals(reference.getPubmedId())) { + try { + String pmc = null; + final PmidData pmidData = pmidLookup.retrieveIdsByPmid(reference.getPubmedId()); + if (pmidData != null && isNotBlank(pmidData.getPmcid())) { + pmc = pmidData.getPmcid(); + } + + if (pmc != null) { + reference.setPmc(pmc); + } + } catch(Exception e) { + e.printStackTrace(); + } + } + + if (pmidLookup != null && reference.getPmc() == null && reference.getDoi() != null) { + String pmc = null; + final PmidData pmidData = pmidLookup.retrieveIdsByPmid(reference.getDoi()); + if (pmidData != null && isNotBlank(pmidData.getPmcid())) { + pmc = pmidData.getPmcid(); + } + + if (pmc != null) { + reference.setPmc(pmc); + } + } + } + if (reference.getPmc() != null) { + builder.append(", \"pmcid\": " + mapper.writeValueAsString(reference.getPmc())); + } + + if (reference.getPii() != null) { + builder.append(", \"pii\": " + mapper.writeValueAsString(reference.getPii())); + } + builder.append("}"); + } + builder.append("]"); + } + + builder.append("}"); + return builder.toString(); + } + + // csv + public static String[] CSV_HEADERS = { "pmid", "doi", "pmc", "title", "abstract", "MeSH Terms", "publication year", + "authors", "keywords", "publisher", "host", "affiliation", "author countries", "grid", "funding_organization", + "funding country" }; + + public static void serializeCsv(CSVWriter writer, Biblio biblio) throws IOException { + StringBuilder meshTerms = new StringBuilder(); + if (biblio.getClassifications() != null) { + boolean first = true; + for (ClassificationClass theClass : biblio.getClassifications()) { + if (theClass.getScheme().equals("MeSH")) { + if (first) + first = false; + else + meshTerms.append(", "); + meshTerms.append(((MeSHClass)theClass).getDescriptorName()); + } + } + } + + String host = null; + + if (biblio.getHostType() == BiblioDefinitions.JOURNAL) + host = biblio.getTitle(); + else if (biblio.getHostType() == BiblioDefinitions.PROCEEDINGS) + host = biblio.getTitle(); + else if (biblio.getHostType() == BiblioDefinitions.COLLECTION) + host = biblio.getCollectionTitle(); + else if (biblio.getTitle() != null) + host = biblio.getTitle(); + else if (biblio.getHostType() == BiblioDefinitions.UNKNOWN) + host = ""; + else + host = ""; + + // cleaning a bit some text noise from pubmed + String articleTitle = biblio.getArticleTitle(); + if (articleTitle != null) { + if (articleTitle.endsWith(".")) { + articleTitle = articleTitle.substring(0,articleTitle.length()-1); + } + if (articleTitle.startsWith("[")) { + articleTitle = articleTitle.substring(1,articleTitle.length()); + } + if (articleTitle.endsWith("]")) { + articleTitle = articleTitle.substring(0,articleTitle.length()-1); + } + } + + String[] data1 = { ""+biblio.getPmid(), biblio.getDoi(), biblio.getPmc(), articleTitle, biblio.getAbstract(), + meshTerms.toString(), Biblio.dateISODisplayFormat(biblio.getPublicationDate()), biblio.printAuthorList(), biblio.getKeywords(), + biblio.getPublisher(), host, "", "", "", "", "" }; + writer.writeNext(data1); + } + + /** + * Not implemented, because no usage so far... + */ + public static void serializeTei(Writer writer, Biblio biblio) { + + } + +} \ No newline at end of file diff --git a/lookup/src/main/java/com/scienceminer/lookup/storage/DataEngine.java b/src/main/java/com/scienceminer/glutton/storage/DataEngine.java similarity index 63% rename from lookup/src/main/java/com/scienceminer/lookup/storage/DataEngine.java rename to src/main/java/com/scienceminer/glutton/storage/DataEngine.java index 0a1a0fa6..2bbb34f9 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/storage/DataEngine.java +++ b/src/main/java/com/scienceminer/glutton/storage/DataEngine.java @@ -1,8 +1,8 @@ -package com.scienceminer.lookup.storage; +package com.scienceminer.glutton.storage; -import com.scienceminer.lookup.data.IstexData; -import com.scienceminer.lookup.data.PmidData; -import com.scienceminer.lookup.storage.lookup.*; +import com.scienceminer.glutton.data.IstexData; +import com.scienceminer.glutton.data.PmidData; +import com.scienceminer.glutton.storage.lookup.*; import org.apache.commons.lang3.tuple.Pair; import java.util.HashMap; @@ -14,9 +14,10 @@ public class DataEngine { private OALookup oaDoiLookup = null; private IstexIdsLookup istexLookup = null; - private MetadataLookup metadataLookup = null; + private CrossrefMetadataLookup crossrefMetadataLookup = null; private MetadataMatching metadataMatching = null; private PMIdsLookup pmidLookup = null; + private HALLookup halLookup = null; public static Pattern DOIPattern = Pattern.compile("\"DOI\":\"(10\\.\\d{4,5}\\/[^\"\\s]+[^;,.\\s])\""); @@ -26,20 +27,23 @@ public DataEngine() { public DataEngine(StorageEnvFactory storageFactory) { this.oaDoiLookup = new OALookup(storageFactory); this.istexLookup = new IstexIdsLookup(storageFactory); - this.metadataLookup = MetadataLookup.getInstance(storageFactory); - this.metadataMatching = MetadataMatching.getInstance(storageFactory.getConfiguration(), metadataLookup); - this.pmidLookup = new PMIdsLookup(storageFactory); + this.crossrefMetadataLookup = CrossrefMetadataLookup.getInstance(storageFactory); + this.pmidLookup = PMIdsLookup.getInstance(storageFactory); + this.halLookup = HALLookup.getInstance(storageFactory); + this.metadataMatching = + MetadataMatching.getInstance(storageFactory.getConfiguration(), crossrefMetadataLookup, halLookup); } public Map getDataInformation() { Map returnMap = new HashMap<>(); - returnMap.put("DOI OA size", String.valueOf(oaDoiLookup.getSize())); - returnMap.put("Metadata Lookup Crossref size", String.valueOf(metadataLookup.getSize())); - returnMap.put("Metadata Matching Crossref size", String.valueOf(metadataMatching.getSize())); - returnMap.put("PMID lookup size", String.valueOf(pmidLookup.getSize())); + returnMap.put("Crossref Metadata stored size", String.valueOf(crossrefMetadataLookup.getSize())); + returnMap.put("HAL Metadata stored size", String.valueOf(halLookup.getSize())); + returnMap.put("Total metadata indexed size", String.valueOf(crossrefMetadataLookup.getSize())); + returnMap.put("PMID size", String.valueOf(pmidLookup.getSize())); returnMap.put("ISTEX size", String.valueOf(istexLookup.getSize())); + returnMap.put("DOI OA size", String.valueOf(oaDoiLookup.getSize())); return returnMap; } @@ -65,7 +69,7 @@ public List> retrieveIstexRecords_istexToIds(Integer tot } public List> retrieveCrossrefRecords(Integer total) { - return metadataLookup.retrieveList(total); + return crossrefMetadataLookup.retrieveList(total); } public List> retrieveIstexRecords_piiToIds(Integer total) { @@ -82,8 +86,12 @@ protected void setIstexLookup(IstexIdsLookup istexLookup) { this.istexLookup = istexLookup; } - protected void setMetadataLookup(MetadataLookup metadataLookup) { - this.metadataLookup = metadataLookup; + protected void setCrossrefMetadataLookup(CrossrefMetadataLookup crossrefMetadataLookup) { + this.crossrefMetadataLookup = crossrefMetadataLookup; + } + + protected void setHalLookup(HALLookup halLookup) { + this.halLookup = halLookup; } protected void setPmidLookup(PMIdsLookup pmidLookup) { diff --git a/lookup/src/main/java/com/scienceminer/lookup/storage/LookupEngine.java b/src/main/java/com/scienceminer/glutton/storage/LookupEngine.java similarity index 79% rename from lookup/src/main/java/com/scienceminer/lookup/storage/LookupEngine.java rename to src/main/java/com/scienceminer/glutton/storage/LookupEngine.java index 2ca6bbe7..fc541061 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/storage/LookupEngine.java +++ b/src/main/java/com/scienceminer/glutton/storage/LookupEngine.java @@ -1,17 +1,17 @@ -package com.scienceminer.lookup.storage; +package com.scienceminer.glutton.storage; import com.google.gson.JsonArray; import com.google.gson.JsonElement; import com.google.gson.JsonObject; import com.google.gson.JsonParser; import com.rockymadden.stringmetric.similarity.RatcliffObershelpMetric; -import com.scienceminer.lookup.data.IstexData; -import com.scienceminer.lookup.data.MatchingDocument; -import com.scienceminer.lookup.data.PmidData; -import com.scienceminer.lookup.exception.NotFoundException; -import com.scienceminer.lookup.storage.lookup.*; -import com.scienceminer.lookup.utils.grobid.GrobidClient; -import com.scienceminer.lookup.utils.grobid.GrobidResponseStaxHandler.GrobidResponse; +import com.scienceminer.glutton.data.IstexData; +import com.scienceminer.glutton.data.MatchingDocument; +import com.scienceminer.glutton.data.PmidData; +import com.scienceminer.glutton.exception.NotFoundException; +import com.scienceminer.glutton.storage.lookup.*; +import com.scienceminer.glutton.utils.grobid.GrobidClient; +import com.scienceminer.glutton.utils.grobid.GrobidResponseStaxHandler.GrobidResponse; import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.tuple.Pair; @@ -37,9 +37,10 @@ public class LookupEngine { private IstexIdsLookup istexLookup = null; - private MetadataLookup metadataLookup = null; + private CrossrefMetadataLookup crossrefMetadataLookup = null; private MetadataMatching metadataMatching = null; private PMIdsLookup pmidLookup = null; + private HALLookup halLookup = null; // DOI matching regex from GROBID public static Pattern DOIPattern = Pattern.compile("\"DOI\"\\s?:\\s?\"(10\\.\\d{4,5}\\/[^\"\\s]+[^;,.\\s])\""); @@ -56,9 +57,11 @@ public LookupEngine() { public LookupEngine(StorageEnvFactory storageFactory) { this.oaDoiLookup = new OALookup(storageFactory); this.istexLookup = new IstexIdsLookup(storageFactory); - this.metadataLookup = MetadataLookup.getInstance(storageFactory); - this.metadataMatching = MetadataMatching.getInstance(storageFactory.getConfiguration(), metadataLookup); - this.pmidLookup = new PMIdsLookup(storageFactory); + this.crossrefMetadataLookup = CrossrefMetadataLookup.getInstance(storageFactory); + this.halLookup = HALLookup.getInstance(storageFactory); + this.pmidLookup = PMIdsLookup.getInstance(storageFactory); + this.metadataMatching = + MetadataMatching.getInstance(storageFactory.getConfiguration(), crossrefMetadataLookup, halLookup); } /** @@ -142,6 +145,7 @@ public void retrieveByJournalMetadataAsync(String jtitle, /** * Async blocking by full bibliographical reference string, with Grobid parsing for pairwise matching + * */ public void retrieveByBiblioAsync(String biblio, final String firstAuthor, @@ -162,6 +166,7 @@ public void retrieveByBiblioAsync(String biblio, if (parseReference) { try { grobidClient.ping(); + // no consolidation when calling Grobid !! GrobidResponse response = grobidClient.processCitation(biblio, "0"); // TBD: extract more metadata from Grobid result to improve the pairwise ranking @@ -190,8 +195,7 @@ public void retrieveByBiblioAsync(String biblio, jtitle1 = response.getJtitle(); //System.out.println(biblio + " -> " + firstAuthor1 + " | " + atitle1 + " | " + year1 + " | " + jtitle1); - List rankedMatchingDocuments = //pairwiseRanking(atitle1, firstAuthor1, year1, matchingDocuments); - pairwiseRanking(atitle1, firstAuthor1, jtitle1, + List rankedMatchingDocuments = pairwiseRanking(atitle1, firstAuthor1, jtitle1, null, year1, null, null, null, null, matchingDocuments); final MatchingDocument localResultDocument = rankedMatchingDocuments.get(0); @@ -243,6 +247,119 @@ public void retrieveByBiblioAsync(String biblio, }); } + /** + * Experimental: + * Async blocking by full bibliographical reference string, with Grobid parsing for pairwise matching and some additional + * conditions. + * + * toIgnore: one identifier to ignore where returning results (useful for deduplication) or null if nothing to ignore + * + * TBD: add "sources" parameter the sources where to look for bibliographical match, if null we search all the sources + * + */ + public void retrieveByBiblioAsyncConditional(String biblio, + final String firstAuthor, + final String atitle, + final String jtitle, + final String year, + Boolean parseReference, + final List sources, + final String toIgnore, + Consumer callback) { + metadataMatching.retrieveByBiblioAsyncConditional(biblio, sources, toIgnore, matchingDocuments -> { + if (matchingDocuments == null || matchingDocuments.size() == 0) { + callback.accept(new MatchingDocument(new NotFoundException("No matching document found"))); + return; + } + + MatchingDocument resultDocument = matchingDocuments.get(0); + if (!resultDocument.isException()) { + //if (isBlank(firstAuthor) && parseReference) { + if (parseReference) { + try { + grobidClient.ping(); + // no consolidation when calling Grobid !! + GrobidResponse response = grobidClient.processCitation(biblio, "0"); + + // TBD: extract more metadata from Grobid result to improve the pairwise ranking + String firstAuthor1 = null; + if (!isBlank(firstAuthor)) + firstAuthor1 = firstAuthor; + else + firstAuthor1 = isNotBlank(response.getFirstAuthor()) ? response.getFirstAuthor() : response.getFirstAuthorMonograph(); + + String atitle1 = null; + if (!isBlank(atitle)) + atitle1 = atitle; + else + atitle1 = response.getAtitle(); + + String year1 = null; + if (!isBlank(year)) + year1 = year; + else + year1 = response.getYear(); + + String jtitle1 = null; + if (!isBlank(year)) + jtitle1 = jtitle; + else + jtitle1 = response.getJtitle(); + +//System.out.println(biblio + " -> " + firstAuthor1 + " | " + atitle1 + " | " + year1 + " | " + jtitle1); + List rankedMatchingDocuments = pairwiseRanking(atitle1, firstAuthor1, jtitle1, + null, year1, null, null, null, null, matchingDocuments); + + final MatchingDocument localResultDocument = rankedMatchingDocuments.get(0); + + //no title and author, extract with grobid. if grobid unavailable... it will fail. + if (!isBlank(firstAuthor1)) { + if (!areMetadataMatching(localResultDocument)) { + callback.accept(new MatchingDocument(new NotFoundException("Best bibliographical record did not passed the post-validation"))); + return; + } + + final String s = injectIdsByDoi(localResultDocument.getJsonObject(), localResultDocument.getDOI()); + localResultDocument.setFinalJsonObject(s); + callback.accept(localResultDocument); + return; + } + + } catch (Exception e) { + //LOGGER.error("grobid place failure", e); + LOGGER.warn("GROBID not available, no extra metadata available for pairwise ranking"); + } + } + + // pairwise ranking with whatever is available + List rankedMatchingDocuments = //pairwiseRanking(atitle, firstAuthor, year, matchingDocuments); + pairwiseRanking(atitle, firstAuthor, jtitle, + null, year, null, null, null, null, matchingDocuments); + final MatchingDocument localResultDocument = rankedMatchingDocuments.get(0); + if (!isBlank(firstAuthor)) { + + if (!areMetadataMatching(localResultDocument)) { + callback.accept(new MatchingDocument(new NotFoundException("Best bibliographical record did not passed the post-validation"))); + return; + } + + final String s = injectIdsByDoi(localResultDocument.getJsonObject(), localResultDocument.getDOI()); + localResultDocument.setFinalJsonObject(s); + callback.accept(localResultDocument); + return; + } else { + // we cannot post validate + callback.accept(new MatchingDocument(new NotFoundException("No metadata available for post-validation"))); + return; + } + + //resultDocument = localResultDocument; + } + callback.accept(resultDocument); + }); + } + + /** * Async blocking by full bibliographical reference string, without Grobid for pairwise matching, without validation * Without GROBID for extracting metadata, mmm this is not usable. @@ -268,7 +385,17 @@ public String retrieveByDoi(String doi, String firstAuthor, String atitle, String year) throws NotFoundException { - MatchingDocument outputData = metadataLookup.retrieveByMetadata(doi); + MatchingDocument outputData = crossrefMetadataLookup.retrieveByDoi(doi); + // TBD: also use year for post validation of strong identifier + outputData = validateJsonBody(firstAuthor, atitle, outputData); + return injectIdsByDoi(outputData.getJsonObject(), outputData.getDOI()); + } + + public String retrieveByHalId(String halid, + String firstAuthor, + String atitle, + String year) throws NotFoundException { + MatchingDocument outputData = halLookup.retrieveByHalId(halid); // TBD: also use year for post validation of strong identifier outputData = validateJsonBody(firstAuthor, atitle, outputData); return injectIdsByDoi(outputData.getJsonObject(), outputData.getDOI()); @@ -350,12 +477,12 @@ public String retrieveByIstexid(String istexid, String firstAuthor, String atitl if (istexData != null && CollectionUtils.isNotEmpty(istexData.getDoi()) && isNotBlank(istexData.getDoi().get(0))) { final String doi = istexData.getDoi().get(0); - MatchingDocument outputData = metadataLookup.retrieveByMetadata(doi); + MatchingDocument outputData = crossrefMetadataLookup.retrieveByDoi(doi); outputData = validateJsonBody(firstAuthor, atitle, outputData); final String oaLink = oaDoiLookup.retrieveOaLinkByDoi(doi); - return injectIdsAndOALink(outputData.getJsonObject(), doi, istexData, oaLink); + return injectIdsAndOALink(outputData.getJsonObject(), doi, istexData, oaLink, null); } throw new NotFoundException("Cannot find bibliographical record with ISTEX ID " + istexid); @@ -366,12 +493,12 @@ public String retrieveByPii(String pii, String firstAuthor, String atitle, Strin if (istexData != null && CollectionUtils.isNotEmpty(istexData.getDoi()) && isNotBlank(istexData.getDoi().get(0))) { final String doi = istexData.getDoi().get(0); - MatchingDocument outputData = metadataLookup.retrieveByMetadata(doi); + MatchingDocument outputData = crossrefMetadataLookup.retrieveByDoi(doi); outputData = validateJsonBody(firstAuthor, atitle, outputData); final String oaLink = oaDoiLookup.retrieveOaLinkByDoi(doi); - return injectIdsAndOALink(outputData.getJsonObject(), doi, istexData, oaLink); + return injectIdsAndOALink(outputData.getJsonObject(), doi, istexData, oaLink, null); } throw new NotFoundException("Cannot find bibliographical record by PII " + pii); @@ -620,6 +747,7 @@ private double recordDistance(MatchingDocument matchingDocument, MatchingDocumen atitleScore = ratcliffObershelpDistance(referenceDocument.getATitle(), matchingDocument.getATitle(), false); } accumulatedScore += atitleScore; +//System.out.println("atitleScore: " + atitleScore); } // first author component @@ -630,14 +758,17 @@ private double recordDistance(MatchingDocument matchingDocument, MatchingDocumen firstAuthorScore = ratcliffObershelpDistance(referenceDocument.getFirstAuthor(), matchingDocument.getFirstAuthor(), false); } accumulatedScore += firstAuthorScore; +//System.out.println("firstAuthorScore: " + firstAuthorScore); } double blockingScore = matchingDocument.getBlockingScore(); +//System.out.println("blocking score: " + blockingScore); nbCriteria++; accumulatedScore += blockingScore; // journal name component - if (isNotBlank(referenceDocument.getJTitle())) { + // note if we have a pure HAL metadata record, journal name is less reliable because of preprints + if (isNotBlank(referenceDocument.getJTitle()) && (matchingDocument.getDOI() != null || matchingDocument.getPmid() != null)) { nbCriteria++; Double jtitleScore = 0.0; if (isNotBlank(matchingDocument.getJTitle()) || isNotBlank(matchingDocument.getAbbreviatedTitle())) { @@ -651,6 +782,7 @@ private double recordDistance(MatchingDocument matchingDocument, MatchingDocumen } } } +//System.out.println("jtitleScore score: " + jtitleScore); accumulatedScore += jtitleScore; } @@ -663,6 +795,7 @@ private double recordDistance(MatchingDocument matchingDocument, MatchingDocumen yearScore = 1.0; } accumulatedScore += yearScore; +//System.out.println("yearScore score: " + yearScore); } // btitle: currently in the search index jtitle contains all container titles (journal names and book title names) @@ -741,7 +874,6 @@ private boolean areMetadataMatchingTitleAuthor(String atitle, String firstAuthor * Introduce a minimum matching threshold based on the pairwise ranking */ private boolean areMetadataMatching(MatchingDocument result) { -//System.out.println(result.getMatchingScore()); return (result.getMatchingScore() < THRESHOLD_MATCHING) ? false : true; } @@ -768,20 +900,28 @@ private double ratcliffObershelpDistance(String string1, String string2, boolean } protected String injectIdsByDoi(String jsonobj, String doi) { - final IstexData istexData = istexLookup.retrieveByDoi(doi); + if (doi == null) + return jsonobj; - final String oaLink = oaDoiLookup.retrieveOaLinkByDoi(doi); + if (doi.startsWith("crossref:")) + doi = doi.replace("crossref:", ""); - return injectIdsAndOALink(jsonobj, doi, istexData, oaLink); + final IstexData istexData = istexLookup.retrieveByDoi(doi); + final String oaLink = oaDoiLookup.retrieveOaLinkByDoi(doi); + String halId = halLookup.retrieveHalIdByDoi(doi); + if (halId != null && halId.startsWith("hal:")) + halId = halId.replace("hal:", ""); + return injectIdsAndOALink(jsonobj, doi, istexData, oaLink, halId); } - protected String injectIdsAndOALink(String jsonobj, String doi, IstexData istexData, String oaLink) { + protected String injectIdsAndOALink(String jsonobj, String doi, IstexData istexData, String oaLink, String halId) { boolean pmid = false; boolean pmc = false; boolean foundIstexData = false; boolean foundPmidData = false; boolean first = false; boolean foundOaLink = false; + boolean foundHalId = false; StringBuilder sb = new StringBuilder(); if (isBlank(jsonobj)) { @@ -873,6 +1013,16 @@ protected String injectIdsAndOALink(String jsonobj, String doi, IstexData istexD } } + if (isNotBlank(halId)) { + if (!first) { + sb.append(", "); + } else { + first = false; + } + sb.append("\"halId\":\"" + halId + "\""); + foundHalId = true; + } + if (isNotBlank(oaLink)) { if (!first) { sb.append(", "); @@ -883,7 +1033,7 @@ protected String injectIdsAndOALink(String jsonobj, String doi, IstexData istexD foundOaLink = true; } - if (foundIstexData || foundPmidData || foundOaLink) { + if (foundIstexData || foundPmidData || foundOaLink || foundHalId) { sb.append("}"); return sb.toString(); } else { @@ -903,8 +1053,12 @@ public void setIstexLookup(IstexIdsLookup istexLookup) { this.istexLookup = istexLookup; } - public void setMetadataLookup(MetadataLookup metadataLookup) { - this.metadataLookup = metadataLookup; + public void setHALLookup(HALLookup halLookup) { + this.halLookup = halLookup; + } + + public void setCrossrefMetadataLookup(CrossrefMetadataLookup crossrefMetadataLookup) { + this.crossrefMetadataLookup = crossrefMetadataLookup; } public void setPmidLookup(PMIdsLookup pmidLookup) { diff --git a/lookup/src/main/java/com/scienceminer/lookup/storage/StorageEnvFactory.java b/src/main/java/com/scienceminer/glutton/storage/StorageEnvFactory.java similarity index 85% rename from lookup/src/main/java/com/scienceminer/lookup/storage/StorageEnvFactory.java rename to src/main/java/com/scienceminer/glutton/storage/StorageEnvFactory.java index 7f650ffe..0861b01b 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/storage/StorageEnvFactory.java +++ b/src/main/java/com/scienceminer/glutton/storage/StorageEnvFactory.java @@ -1,11 +1,11 @@ -package com.scienceminer.lookup.storage; +package com.scienceminer.glutton.storage; -import com.scienceminer.lookup.configuration.LookupConfiguration; +import com.scienceminer.glutton.configuration.LookupConfiguration; import org.lmdbjava.Env; import org.lmdbjava.EnvFlags; -import javax.inject.Inject; -import javax.inject.Singleton; +import jakarta.inject.Inject; +import jakarta.inject.Singleton; import java.io.File; import java.nio.ByteBuffer; diff --git a/lookup/src/main/java/com/scienceminer/lookup/storage/lookup/MetadataLookup.java b/src/main/java/com/scienceminer/glutton/storage/lookup/CrossrefMetadataLookup.java similarity index 69% rename from lookup/src/main/java/com/scienceminer/lookup/storage/lookup/MetadataLookup.java rename to src/main/java/com/scienceminer/glutton/storage/lookup/CrossrefMetadataLookup.java index 0e3f09d7..71beadcf 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/storage/lookup/MetadataLookup.java +++ b/src/main/java/com/scienceminer/glutton/storage/lookup/CrossrefMetadataLookup.java @@ -1,14 +1,16 @@ -package com.scienceminer.lookup.storage.lookup; +package com.scienceminer.glutton.storage.lookup; import com.codahale.metrics.Counter; import com.codahale.metrics.Meter; -import com.scienceminer.lookup.configuration.LookupConfiguration; -import com.scienceminer.lookup.data.MatchingDocument; -import com.scienceminer.lookup.exception.ServiceException; -import com.scienceminer.lookup.exception.ServiceOverloadedException; -import com.scienceminer.lookup.reader.CrossrefJsonReader; -import com.scienceminer.lookup.storage.StorageEnvFactory; -import com.scienceminer.lookup.utils.BinarySerialiser; +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.data.MatchingDocument; +import com.scienceminer.glutton.exception.ServiceException; +import com.scienceminer.glutton.exception.ServiceOverloadedException; +import com.scienceminer.glutton.reader.CrossrefJsonReader; +import com.scienceminer.glutton.indexing.ElasticSearchIndexer; +import com.scienceminer.glutton.indexing.ElasticSearchAsyncIndexer; +import com.scienceminer.glutton.storage.StorageEnvFactory; +import com.scienceminer.glutton.utils.BinarySerialiser; import org.apache.commons.lang3.tuple.ImmutablePair; import org.apache.commons.lang3.tuple.Pair; import org.lmdbjava.*; @@ -25,19 +27,24 @@ import java.util.concurrent.atomic.AtomicInteger; import java.time.LocalDateTime; -import static com.scienceminer.lookup.web.resource.DataController.DEFAULT_MAX_SIZE_LIST; +import com.fasterxml.jackson.databind.node.*; +import com.fasterxml.jackson.core.*; +import com.fasterxml.jackson.databind.*; + +import static com.scienceminer.glutton.web.resource.DataController.DEFAULT_MAX_SIZE_LIST; import static java.nio.ByteBuffer.allocateDirect; import static org.apache.commons.lang3.StringUtils.isBlank; import static org.apache.commons.lang3.StringUtils.lowerCase; /** + * Warning: this is CrossRef metadata * Singleton class - * Lookup metadata -> doi + * Lookup doi -> metadata */ -public class MetadataLookup { - private static final Logger LOGGER = LoggerFactory.getLogger(MetadataLookup.class); +public class CrossrefMetadataLookup { + private static final Logger LOGGER = LoggerFactory.getLogger(CrossrefMetadataLookup.class); - private static volatile MetadataLookup instance; + private static volatile CrossrefMetadataLookup instance; private Env environment; private Dbi dbCrossrefJson; @@ -45,16 +52,18 @@ public class MetadataLookup { public static final String ENV_NAME = "crossref"; public static final String NAME_CROSSREF_JSON = ENV_NAME + "_Jsondoc"; - private final int batchSize; + + private final int batchStoringSize; + private final int batchIndexingSize; private LookupConfiguration configuration; // this date keeps track of the latest indexed date of the metadata database private LocalDateTime lastIndexed = null; - public static MetadataLookup getInstance(StorageEnvFactory storageEnvFactory) { + public static CrossrefMetadataLookup getInstance(StorageEnvFactory storageEnvFactory) { if (instance == null) { - synchronized (MetadataLookup.class) { + synchronized (CrossrefMetadataLookup.class) { if (instance == null) { getNewInstance(storageEnvFactory); } @@ -67,37 +76,59 @@ public static MetadataLookup getInstance(StorageEnvFactory storageEnvFactory) { * Creates a new instance. */ private static synchronized void getNewInstance(StorageEnvFactory storageEnvFactory) { - instance = new MetadataLookup(storageEnvFactory); + instance = new CrossrefMetadataLookup(storageEnvFactory); } - - private MetadataLookup(StorageEnvFactory storageEnvFactory) { + private CrossrefMetadataLookup(StorageEnvFactory storageEnvFactory) { this.environment = storageEnvFactory.getEnv(ENV_NAME); configuration = storageEnvFactory.getConfiguration(); - batchSize = configuration.getLoadingBatchSize(); + batchStoringSize = configuration.getStoringBatchSize(); + batchIndexingSize = configuration.getIndexingBatchSize(); dbCrossrefJson = this.environment.openDbi(NAME_CROSSREF_JSON, DbiFlags.MDB_CREATE); } - public void loadFromFile(InputStream is, CrossrefJsonReader reader, Meter meterValidRecord, Counter counterInvalidRecords) { + public void loadFromFile(InputStream is, + CrossrefJsonReader reader, + Meter meterValidRecord, + Counter counterInvalidRecords, + Counter counterIndexedRecords, + Counter counterFailedIndexedRecords) { final TransactionWrapper transactionWrapper = new TransactionWrapper(environment.txnWrite()); - final AtomicInteger counter = new AtomicInteger(0); + final AtomicInteger counterStoring = new AtomicInteger(0); + final AtomicInteger counterIndexing = new AtomicInteger(0); + final List documents = new ArrayList<>(); reader.load(is, counterInvalidRecords, crossrefData -> { - if (counter.get() == batchSize) { + if (counterStoring.get() == batchStoringSize) { transactionWrapper.tx.commit(); transactionWrapper.tx.close(); transactionWrapper.tx = environment.txnWrite(); - counter.set(0); + counterStoring.set(0); + } + if (counterIndexing.get() == batchIndexingSize) { + indexDocuments(documents, true, counterIndexedRecords, counterFailedIndexedRecords); + counterIndexing.set(0); + documents.clear(); } - String key = lowerCase(crossrefData.get("DOI").asText()); - store(key, crossrefData.toString(), dbCrossrefJson, transactionWrapper.tx); + String key = lowerCase(crossrefData.get("DOI").asText()); + String crossrefDataJsonString = crossrefData.toString(); + store(key, crossrefDataJsonString, dbCrossrefJson, transactionWrapper.tx); meterValidRecord.mark(); - counter.incrementAndGet(); + documents.add(crossrefData); + counterStoring.incrementAndGet(); + counterIndexing.incrementAndGet(); }); + + // last batch transactionWrapper.tx.commit(); transactionWrapper.tx.close(); + + indexDocuments(documents, true, counterIndexedRecords, counterFailedIndexedRecords); + + // finally refresh the index + ElasticSearchIndexer.getInstance(configuration).refreshIndex(configuration.getElastic().getIndex()); } private void store(String key, String value, Dbi db, Txn tx) { @@ -109,7 +140,7 @@ private void store(String key, String value, Dbi db, Txn valBuffer.put(serializedValue).flip(); db.put(tx, keyBuffer, valBuffer); } catch (Exception e) { - LOGGER.error("Cannot store the entry " + key + ", " + value, e); + LOGGER.error("Cannot store the entry " + key, e); } } @@ -156,13 +187,13 @@ record = (String) BinarySerialiser.deserializeAndDecompress(cachedData); /** * Lookup by DOI **/ - public MatchingDocument retrieveByMetadata(String doi) { + public MatchingDocument retrieveByDoi(String doi) { if (isBlank(doi)) { throw new ServiceException(400, "The supplied DOI is null."); } final String jsonDocument = retrieveJsonDocument(lowerCase(doi)); - return new MatchingDocument(doi, jsonDocument); + return new MatchingDocument("crossref:"+doi, jsonDocument); } public List> retrieveList(Integer total) { @@ -243,6 +274,15 @@ public synchronized void setLastIndexed(LocalDateTime lastIndexed) { } } + public void indexDocuments(List documents, boolean update, Counter counterIndexedRecords, Counter counterFailedIndexedRecords) { + ElasticSearchAsyncIndexer.getInstance(configuration) + .asyncIndexJsonObjects(documents, update, counterIndexedRecords, counterFailedIndexedRecords); + } + + public void indexMetadata(ElasticSearchIndexer indexer, Meter meter, Counter counterIndexedRecords) { + indexer.indexCollection(environment, dbCrossrefJson, false, meter, counterIndexedRecords); + } + public void close() { this.environment.close(); } diff --git a/src/main/java/com/scienceminer/glutton/storage/lookup/HALLookup.java b/src/main/java/com/scienceminer/glutton/storage/lookup/HALLookup.java new file mode 100644 index 00000000..96ab7b03 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/storage/lookup/HALLookup.java @@ -0,0 +1,546 @@ +package com.scienceminer.glutton.storage.lookup; + +import com.codahale.metrics.Counter; +import com.codahale.metrics.Meter; + +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.data.MatchingDocument; +import com.scienceminer.glutton.data.Biblio; +import com.scienceminer.glutton.harvester.HALOAIPMHHarvester; +import com.scienceminer.glutton.harvester.HALAPIHarvester; +import com.scienceminer.glutton.exception.ServiceException; +import com.scienceminer.glutton.exception.ServiceOverloadedException; +import com.scienceminer.glutton.serialization.BiblioSerializer; +import com.scienceminer.glutton.storage.StorageEnvFactory; +import com.scienceminer.glutton.indexing.*; +import com.scienceminer.glutton.utils.BinarySerialiser; +import com.scienceminer.glutton.storage.LookupEngine; + +import org.apache.commons.lang3.tuple.ImmutablePair; +import org.apache.commons.lang3.tuple.Pair; +import org.lmdbjava.*; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.dataformat.yaml.YAMLFactory; +import com.fasterxml.jackson.core.*; +import com.fasterxml.jackson.databind.*; +import com.fasterxml.jackson.databind.node.*; +import com.fasterxml.jackson.annotation.*; +import com.fasterxml.jackson.core.io.*; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.*; +import java.nio.*; +import java.nio.file.*; +import java.nio.ByteBuffer; +import java.util.*; +import java.util.concurrent.atomic.AtomicInteger; +import java.time.LocalDateTime; +import java.nio.channels.AsynchronousFileChannel; +import java.nio.file.StandardOpenOption; + +import static com.scienceminer.glutton.web.resource.DataController.DEFAULT_MAX_SIZE_LIST; +import static java.nio.ByteBuffer.allocateDirect; +import static org.apache.commons.lang3.StringUtils.isBlank; +import static org.apache.commons.lang3.StringUtils.isNotBlank; +import static org.apache.commons.lang3.StringUtils.lowerCase; + +/** + * Warning: this is HAL metadata + * Singleton class + * Lookup hal id -> metadata + * Lookup doi -> hal id + */ +public class HALLookup { + private static final Logger LOGGER = LoggerFactory.getLogger(HALLookup.class); + + private static volatile HALLookup instance; + + private Env environment; + private Dbi dbHALJson; + private Dbi dbDoiToHal; + + public static final String ENV_NAME = "hal"; + + public static final String NAME_HAL_JSON = ENV_NAME + "_Jsondoc"; + public static final String NAME_DOI2HAL = ENV_NAME + "_doi2hal"; + + private final int batchStoringSize; + private final int batchIndexingSize; + + private LookupConfiguration configuration; + + // this date keeps track of the latest indexed date of the metadata database + private LocalDateTime lastIndexed = null; + + public static HALLookup getInstance(StorageEnvFactory storageEnvFactory) { + if (instance == null) { + synchronized (HALLookup.class) { + if (instance == null) { + getNewInstance(storageEnvFactory); + } + } + } + return instance; + } + + /** + * Creates a new instance. + */ + private static synchronized void getNewInstance(StorageEnvFactory storageEnvFactory) { + instance = new HALLookup(storageEnvFactory); + } + + private HALLookup(StorageEnvFactory storageEnvFactory) { + this.environment = storageEnvFactory.getEnv(ENV_NAME); + + configuration = storageEnvFactory.getConfiguration(); + batchStoringSize = configuration.getStoringBatchSize(); + batchIndexingSize = configuration.getIndexingBatchSize(); + + dbHALJson = this.environment.openDbi(NAME_HAL_JSON, DbiFlags.MDB_CREATE); + dbDoiToHal = this.environment.openDbi(NAME_DOI2HAL, DbiFlags.MDB_CREATE); + } + + public void loadFromHALAPI(Meter meterValidRecord, + Counter counterInvalidRecords, + Counter counterIndexedRecords, + Counter counterFailedIndexedRecords) { + final TransactionWrapper transactionWrapper = new TransactionWrapper(environment.txnWrite()); + final AtomicInteger counter = new AtomicInteger(0); + + HALAPIHarvester harvester = new HALAPIHarvester(transactionWrapper); + harvester.fetchAllDocuments(this, meterValidRecord, counterInvalidRecords, + counterIndexedRecords, counterFailedIndexedRecords); + ElasticSearchIndexer.getInstance(configuration).refreshIndex(configuration.getElastic().getIndex()); + } + + @Deprecated + public void loadFromOAIPMH(Meter meterValidRecord, Counter counterInvalidRecords) { + final TransactionWrapper transactionWrapper = new TransactionWrapper(environment.txnWrite()); + final AtomicInteger counter = new AtomicInteger(0); + + HALOAIPMHHarvester harvester = new HALOAIPMHHarvester(transactionWrapper); + harvester.fetchAllDocuments(this, meterValidRecord, counterInvalidRecords); + } + + public void storeObject(Biblio biblio, Txn tx) { + try { + String dbBiblioJson = BiblioSerializer.serializeJson(biblio, null, this); +//System.out.println(dbBiblioJson); + store(lowerCase(biblio.getHalId()), dbBiblioJson, dbHALJson, tx); + if (!isBlank(biblio.getDoi())) + storeNoCompression(lowerCase(biblio.getDoi()), lowerCase(biblio.getHalId()), dbDoiToHal, tx); + } catch (Exception e) { + LOGGER.error("Cannot serialize the metadata", e); + } + } + + private void store(String key, String value, Dbi db, Txn tx) { + try { + final ByteBuffer keyBuffer = allocateDirect(environment.getMaxKeySize()); + keyBuffer.put(BinarySerialiser.serialize(key)).flip(); + final byte[] serializedValue = BinarySerialiser.serializeAndCompress(value); + final ByteBuffer valBuffer = allocateDirect(serializedValue.length); + valBuffer.put(serializedValue).flip(); + db.put(tx, keyBuffer, valBuffer); + } catch (Exception e) { + LOGGER.error("Cannot store the entry " + key, e); + } + } + + private void storeNoCompression(String key, String value, Dbi db, Txn tx) { + try { + final ByteBuffer keyBuffer = allocateDirect(environment.getMaxKeySize()); + keyBuffer.put(BinarySerialiser.serialize(key)).flip(); + final byte[] serializedValue = BinarySerialiser.serialize(value); + final ByteBuffer valBuffer = allocateDirect(serializedValue.length); + valBuffer.put(serializedValue).flip(); + db.put(tx, keyBuffer, valBuffer); + } catch (Exception e) { + LOGGER.error("Cannot store the entry " + key, e); + } + } + + public void commitTransactions(TransactionWrapper transactionWrapper) { + transactionWrapper.tx.commit(); + transactionWrapper.tx.close(); + transactionWrapper.tx = environment.txnWrite(); + } + + public Map getSize() { + + Map sizes = new HashMap<>(); + try (final Txn txn = this.environment.txnRead()) { + sizes.put(NAME_HAL_JSON, dbHALJson.stat(txn).entries); + } catch (Env.ReadersFullException e) { + throw new ServiceOverloadedException("Not enough readers for LMDB access, increase them or reduce the parallel request rate. ", e); + } + + return sizes; + } + + public Long getFullSize() { + long fullsize = 0; + Map sizes = getSize(); + for (Map.Entry entry : sizes.entrySet()) { + fullsize += entry.getValue(); + } + return fullsize; + } + + public String retrieveJsonDocument(String halID) { + final ByteBuffer keyBuffer = allocateDirect(environment.getMaxKeySize()); + ByteBuffer cachedData = null; + String theRecord = null; + try (Txn tx = environment.txnRead()) { + keyBuffer.put(BinarySerialiser.serialize(lowerCase(halID))).flip(); + cachedData = dbHALJson.get(tx, keyBuffer); + if (cachedData != null) { + theRecord = (String) BinarySerialiser.deserializeAndDecompress(cachedData); + } + } catch (Env.ReadersFullException e) { + throw new ServiceOverloadedException("Not enough readers for LMDB access, increase them or reduce the parallel request rate. ", e); + } catch (Exception e) { + LOGGER.error("Cannot retrieve HAL metadata by HAL ID: " + halID, e); + } + + return theRecord; + } + + /** + * Lookup by HAL ID + **/ + public MatchingDocument retrieveByHalId(String halID) { + if (isBlank(halID)) { + throw new ServiceException(400, "The supplied HAL ID is null."); + } + final String jsonDocument = retrieveJsonDocument(lowerCase(halID)); + + return new MatchingDocument("hal:"+halID, jsonDocument); + } + + public String retrieveHalIdByDoi(String doi) { + final ByteBuffer keyBuffer = allocateDirect(environment.getMaxKeySize()); + ByteBuffer cachedData = null; + String halId = null; + try (Txn tx = environment.txnRead()) { + keyBuffer.put(BinarySerialiser.serialize(lowerCase(doi))).flip(); + cachedData = dbDoiToHal.get(tx, keyBuffer); + if (cachedData != null) { + halId = (String) BinarySerialiser.deserialize(cachedData); + } + } catch (Env.ReadersFullException e) { + throw new ServiceOverloadedException("Not enough readers for LMDB access, increase them or reduce the parallel request rate. ", e); + } catch (Exception e) { + LOGGER.error("Cannot retrieve HAL ID by DOI: " + doi, e); + } + + return halId; + } + + public List> retrieveList(Integer total) { + return retrieveList(total, dbHALJson); + } + + public List> retrieveList(Integer total, Dbi db) { + if (total == null || total == 0) { + total = DEFAULT_MAX_SIZE_LIST; + } + + List> values = new ArrayList<>(); + int counter = 0; + + try (Txn txn = environment.txnRead()) { + try (CursorIterable it = db.iterate(txn, KeyRange.all())) { + for (final CursorIterable.KeyVal kv : it) { + String key = null; + try { + key = (String) BinarySerialiser.deserialize(kv.key()); + values.add(new ImmutablePair<>(key, (String) BinarySerialiser.deserializeAndDecompress(kv.val()))); + } catch (IOException e) { + LOGGER.error("Cannot decompress document with key: " + key, e); + } + if (counter == total) { + txn.close(); + break; + } + counter++; + } + } + } catch (Env.ReadersFullException e) { + throw new ServiceOverloadedException("Not enough readers for LMDB access, increase them or reduce the parallel request rate. ", e); + } + + return values; + } + + public synchronized LocalDateTime getLastIndexed() { + if (lastIndexed != null) + return lastIndexed; + else { + // get a possible value made persistent in the db + final ByteBuffer keyBuffer = allocateDirect(environment.getMaxKeySize()); + ByteBuffer cachedData = null; + try (Txn tx = environment.txnRead()) { + keyBuffer.put(BinarySerialiser.serialize("last-indexed-date")).flip(); + cachedData = dbHALJson.get(tx, keyBuffer); + if (cachedData != null) { + lastIndexed = (LocalDateTime) BinarySerialiser.deserializeAndDecompress(cachedData); + } + } catch (Env.ReadersFullException e) { + throw new ServiceOverloadedException("Not enough readers for LMDB access, increase them or reduce the parallel request rate. ", e); + } catch (Exception e) { + LOGGER.error("Cannot retrieve the persistent last indexed date object", e); + } + return lastIndexed; + } + } + + public synchronized void setLastIndexed(LocalDateTime lastIndexed) { + this.lastIndexed = lastIndexed; + + // persistent store of this date + final TransactionWrapper transactionWrapper = new TransactionWrapper(environment.txnWrite()); + try { + final ByteBuffer keyBuffer = allocateDirect(environment.getMaxKeySize()); + keyBuffer.put(BinarySerialiser.serialize("last-indexed-date")).flip(); + final byte[] serializedValue = BinarySerialiser.serializeAndCompress(this.lastIndexed); + final ByteBuffer valBuffer = allocateDirect(serializedValue.length); + valBuffer.put(serializedValue).flip(); + dbHALJson.put(transactionWrapper.tx, keyBuffer, valBuffer); + } catch (Exception e) { + LOGGER.error("Cannot store the last-indexed-date"); + } finally { + transactionWrapper.tx.commit(); + transactionWrapper.tx.close(); + } + } + + public void indexMetadata(ElasticSearchIndexer indexer, Meter meter, Counter counterIndexedRecords) { + ElasticSearchIndexer.getInstance(configuration) + .indexCollection(environment, dbHALJson, true, meter, counterIndexedRecords); + } + + public void indexDocuments(List documents, boolean update, Counter counterIndexedRecords, Counter counterFailedIndexedRecords) { + List jsonRecords = new ArrayList<>(); + for(Biblio document : documents) { + // convert Biblio object into crossref json format + try{ + jsonRecords.add(BiblioSerializer.serializeJson(document, null, this)); + } catch (Exception e) { + LOGGER.error("Cannot serialize the metadata", e); + } + } + ElasticSearchAsyncIndexer.getInstance(configuration) + .asyncIndexDocuments(jsonRecords, update, counterIndexedRecords, counterFailedIndexedRecords); + } + + public int getStoringBatchSize() { + return this.batchStoringSize; + } + + public int getIndexingBatchSize() { + return this.batchIndexingSize; + } + + public void analyzeHALRecords(LookupEngine lookupEngine, + Meter meter, + Counter counterDuplicatedRecords, + Counter counterHasDOIRecords, + Counter counterMissingDOILookup, + Counter counterMissingDOIRecords, + String duplicatedRecordsReport, + String missingDOIReport) { + // go throught every HAL records + // 1) check DOI matching if DOI is missing + // 2) check HAL matching with normal blocking/pairwise comparison, ignoring CrossRef records + long total = getFullSize(); + long counter = 0; + + final List missingDOIReportRows = new ArrayList<>(); + final List duplicateReportRows = new ArrayList<>(); + + try (Txn txn = environment.txnRead()) { + try (CursorIterable it = dbHALJson.iterate(txn, KeyRange.all())) { + for (final CursorIterable.KeyVal kv : it) { + String key = null; + try { + key = (String) BinarySerialiser.deserialize(kv.key()); + String recordJson = (String) BinarySerialiser.deserializeAndDecompress(kv.val()); + + try { + MetadataObj metadataObj = MetadataObjBuilder.createMetadataObj(recordJson); + + // check DOI + checkMissingDOI(lookupEngine, + metadataObj, + counterHasDOIRecords, + counterMissingDOILookup, + counterMissingDOIRecords, + missingDOIReportRows); + + // check duplicate + checkDuplicate(lookupEngine, + metadataObj, + counterDuplicatedRecords, + duplicateReportRows); + + } catch(Exception e) { + LOGGER.error("fail to parse the JSON document prior to indexing", e); + LOGGER.error(recordJson); + } + + meter.mark(); + } catch (IOException e) { + LOGGER.error("Cannot decompress document with key: " + key, e); + } + if (counter == total) { + txn.close(); + break; + } + counter++; + } + } + } catch (Env.ReadersFullException e) { + throw new ServiceOverloadedException("Not enough readers for LMDB access, increase them or reduce the parallel request rate. ", e); + } + + try{ + File missingDOIReportFile = new File(missingDOIReport); + File duplicatedRecordsReportFile = new File(duplicatedRecordsReport); + + // write results + FileWriter fileWriter = new FileWriter(missingDOIReportFile); + PrintWriter printWriter = new PrintWriter(fileWriter); + synchronized(missingDOIReportRows) { + for(String rowReport : missingDOIReportRows) { + printWriter.print(rowReport); + } + } + printWriter.close(); + + try { + // wait a bit to be sure that last matches are completed + Thread.sleep(60000); + } catch(Exception e) { + LOGGER.warn("Problem with sleep()"); + } + + fileWriter = new FileWriter(duplicatedRecordsReport); + printWriter = new PrintWriter(fileWriter); + synchronized(missingDOIReportRows) { + for(String rowReport : duplicateReportRows) { + printWriter.print(rowReport); + } + } + printWriter.close(); + } catch (IOException e) { + e.printStackTrace(); + } + } + + public void checkMissingDOI(LookupEngine lookupEngine, + MetadataObj metadataObj, + Counter counterHasDOIRecords, + Counter counterMissingDOILookup, + Counter counterMissingDOIRecords, + List missingDOIReportRows) { + final String DOI = metadataObj.DOI; + if (isNotBlank(DOI)) { + counterHasDOIRecords.inc(); + return; + } + + final String biblio = metadataObj.bibliographic; + if (isBlank(biblio)) { + // not enough metadata + return; + } + + // create a query for the record + final String halId = metadataObj.halId; + + final String firstAuthor = metadataObj.first_author; + String theTitle = null; + if (metadataObj.title != null && metadataObj.title.size()>0) + theTitle = metadataObj.title.get(0); + final String atitle = theTitle; + String theJtitle = null; + if (metadataObj.journal != null && metadataObj.journal.size()>0) + theJtitle = metadataObj.journal.get(0); + final String jtitle= theJtitle; + final String year = metadataObj.year; + + List sources = Arrays.asList("crossref"); + + counterMissingDOILookup.inc(); + lookupEngine.retrieveByBiblioAsyncConditional(biblio, firstAuthor, atitle, jtitle, year, false, sources, null, matchingDocumentBiblio -> { + if (!matchingDocumentBiblio.isException()) { + if (isNotBlank(matchingDocumentBiblio.getDOI())) { + final String reportLine = halId+"\t"+matchingDocumentBiblio.getDOI()+"\t"+matchingDocumentBiblio.getMatchingScore()+"\n"; + counterMissingDOIRecords.inc(); + //System.out.println(reportLine); + //missingDOIReport.write(ByteBuffer.wrap(reportLine.getBytes()), 0); + synchronized(missingDOIReportRows) { + missingDOIReportRows.add(reportLine); + } + } + } + }); + } + + public void checkDuplicate(LookupEngine lookupEngine, + MetadataObj metadataObj, + Counter counterDuplicatedRecords, + List duplicateReportRows) { + // create a query for the record + final String halId = metadataObj.halId; + if (isBlank(halId)) { + // it should never be the case! + return; + } + + final String biblio = metadataObj.bibliographic; + if (isBlank(biblio)) { + // not enough metadata + return; + } + + final String firstAuthor = metadataObj.first_author; + String theTitle = null; + if (metadataObj.title != null && metadataObj.title.size()>0) + theTitle = metadataObj.title.get(0); + final String atitle = theTitle; + String theJtitle = null; + if (metadataObj.journal != null && metadataObj.journal.size()>0) + theJtitle = metadataObj.journal.get(0); + final String jtitle= theJtitle; + final String year = metadataObj.year; + + List sources = Arrays.asList("hal"); + String toIgnore = "hal:"+halId; + + //System.out.println("Deduplication lookup for " + halId); + + lookupEngine.retrieveByBiblioAsyncConditional(biblio, firstAuthor, atitle, jtitle, year, false, sources, toIgnore, matchingDocumentBiblio -> { + if (!matchingDocumentBiblio.isException()) { + if (isNotBlank(matchingDocumentBiblio.getHalId()) && !halId.equals(matchingDocumentBiblio.getHalId())) { + String reportLine = halId+"\t"+matchingDocumentBiblio.getHalId()+"\t"+matchingDocumentBiblio.getMatchingScore()+"\n"; + counterDuplicatedRecords.inc(); + //System.out.println(reportLine); + //duplicatedRecordsReport.write(ByteBuffer.wrap(reportLine.getBytes()), 0); + synchronized(duplicateReportRows) { + duplicateReportRows.add(reportLine); + } + } + } + }); + } + + public void close() { + this.environment.close(); + } +} diff --git a/lookup/src/main/java/com/scienceminer/lookup/storage/lookup/IstexIdsLookup.java b/src/main/java/com/scienceminer/glutton/storage/lookup/IstexIdsLookup.java similarity index 95% rename from lookup/src/main/java/com/scienceminer/lookup/storage/lookup/IstexIdsLookup.java rename to src/main/java/com/scienceminer/glutton/storage/lookup/IstexIdsLookup.java index dd7e1ccb..77a90c06 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/storage/lookup/IstexIdsLookup.java +++ b/src/main/java/com/scienceminer/glutton/storage/lookup/IstexIdsLookup.java @@ -1,12 +1,12 @@ -package com.scienceminer.lookup.storage.lookup; +package com.scienceminer.glutton.storage.lookup; import com.codahale.metrics.Meter; import com.google.inject.servlet.ServletScopes; -import com.scienceminer.lookup.data.IstexData; -import com.scienceminer.lookup.exception.ServiceOverloadedException; -import com.scienceminer.lookup.reader.IstexIdsReader; -import com.scienceminer.lookup.storage.StorageEnvFactory; -import com.scienceminer.lookup.utils.BinarySerialiser; +import com.scienceminer.glutton.data.IstexData; +import com.scienceminer.glutton.exception.ServiceOverloadedException; +import com.scienceminer.glutton.reader.IstexIdsReader; +import com.scienceminer.glutton.storage.StorageEnvFactory; +import com.scienceminer.glutton.utils.BinarySerialiser; import org.apache.commons.lang3.tuple.ImmutablePair; import org.apache.commons.lang3.tuple.Pair; import org.lmdbjava.*; @@ -21,7 +21,7 @@ import java.util.Map; import java.util.concurrent.atomic.AtomicInteger; -import static com.scienceminer.lookup.web.resource.DataController.DEFAULT_MAX_SIZE_LIST; +import static com.scienceminer.glutton.web.resource.DataController.DEFAULT_MAX_SIZE_LIST; import static java.nio.ByteBuffer.allocateDirect; import static org.apache.commons.lang3.StringUtils.isNotBlank; import static org.apache.commons.lang3.StringUtils.lowerCase; @@ -51,7 +51,7 @@ public class IstexIdsLookup { public IstexIdsLookup(StorageEnvFactory storageEnvFactory) { this.environment = storageEnvFactory.getEnv(ENV_NAME); - batchSize = storageEnvFactory.getConfiguration().getLoadingBatchSize(); + batchSize = storageEnvFactory.getConfiguration().getStoringBatchSize(); dbDoiToIds = this.environment.openDbi(NAME_DOI2IDS, DbiFlags.MDB_CREATE); dbIstexToIds = this.environment.openDbi(NAME_ISTEX2IDS, DbiFlags.MDB_CREATE); diff --git a/lookup/src/main/java/com/scienceminer/lookup/storage/lookup/MetadataMatching.java b/src/main/java/com/scienceminer/glutton/storage/lookup/MetadataMatching.java similarity index 82% rename from lookup/src/main/java/com/scienceminer/lookup/storage/lookup/MetadataMatching.java rename to src/main/java/com/scienceminer/glutton/storage/lookup/MetadataMatching.java index ba8fb285..35b9931e 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/storage/lookup/MetadataMatching.java +++ b/src/main/java/com/scienceminer/glutton/storage/lookup/MetadataMatching.java @@ -1,10 +1,10 @@ -package com.scienceminer.lookup.storage.lookup; +package com.scienceminer.glutton.storage.lookup; -import com.scienceminer.lookup.configuration.LookupConfiguration; -import com.scienceminer.lookup.data.MatchingDocument; -import com.scienceminer.lookup.exception.NotFoundException; -import com.scienceminer.lookup.exception.ServiceException; -import com.scienceminer.lookup.storage.lookup.async.ESClientWrapper; +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.data.MatchingDocument; +import com.scienceminer.glutton.exception.NotFoundException; +import com.scienceminer.glutton.exception.ServiceException; +import com.scienceminer.glutton.storage.lookup.async.ESClientWrapper; import org.apache.commons.collections4.CollectionUtils; import org.apache.http.HttpHost; import org.elasticsearch.action.search.SearchRequest; @@ -41,6 +41,7 @@ import com.fasterxml.jackson.core.io.*; import static org.apache.commons.lang3.StringUtils.isBlank; +import static org.apache.commons.lang3.StringUtils.isNotBlank; public class MetadataMatching { private static final Logger LOGGER = LoggerFactory.getLogger(MetadataMatching.class); @@ -49,13 +50,16 @@ public class MetadataMatching { private LookupConfiguration configuration; private ESClientWrapper esClient; - private MetadataLookup metadataLookup; + private CrossrefMetadataLookup crossrefMetadataLookup; + private HALLookup halLookup; public static final String INDEX_FIELD_NAME_ID = "id"; public static final String INDEX_FIELD_NAME_ATITLE = "title"; public static final String INDEX_FIELD_NAME_FIRST_PAGE = "first_page"; public static final String INDEX_FIELD_NAME_FIRST_AUTHOR = "first_author"; public static final String INDEX_FIELD_NAME_DOI = "DOI"; + public static final String INDEX_FIELD_NAME_HALID = "halId"; + public static final String INDEX_FIELD_NAME_PMID = "pmid"; public static final String INDEX_FIELD_NAME_VOLUME = "volume"; public static final String INDEX_FIELD_NAME_ISSN = "issn"; public static final String INDEX_FIELD_NAME_BIBLIOGRAPHIC = "bibliographic"; @@ -63,16 +67,17 @@ public class MetadataMatching { public static final String INDEX_FIELD_ABBREVIATED_JOURNAL_TITLE = "abbreviated_journal"; public static final String INDEX_FIELD_NAME_YEAR = "year"; public static final String INDEX_FIELD_NAME_ABBREV_TITLE = "abbreviated_journal"; + public static final String INDEX_FIELD_NAME_SOURCE = "source"; private final String INDEX_FIELD_NAME_JSONDOC = "jsondoc"; - public static MetadataMatching getInstance(LookupConfiguration configuration, - MetadataLookup metadataLookup) { + CrossrefMetadataLookup crossrefMetadataLookup, + HALLookup halLookup) { if (instance == null) { synchronized (MetadataMatching.class) { if (instance == null) { - getNewInstance(configuration, metadataLookup); + getNewInstance(configuration, crossrefMetadataLookup, halLookup); } } } @@ -83,11 +88,14 @@ public static MetadataMatching getInstance(LookupConfiguration configuration, * Creates a new instance. */ private static synchronized void getNewInstance(LookupConfiguration configuration, - MetadataLookup metadataLookup) { - instance = new MetadataMatching(configuration, metadataLookup); + CrossrefMetadataLookup crossrefMetadataLookup, + HALLookup halLookup) { + instance = new MetadataMatching(configuration, crossrefMetadataLookup, halLookup); } - private MetadataMatching(LookupConfiguration configuration, MetadataLookup metadataLookup) { + private MetadataMatching(LookupConfiguration configuration, + CrossrefMetadataLookup crossrefMetadataLookup, + HALLookup halLookup) { this.configuration = configuration; RestHighLevelClient esClient = new RestHighLevelClient( RestClient.builder( @@ -107,7 +115,8 @@ private MetadataMatching(LookupConfiguration configuration, MetadataLookup metad this.esClient = new ESClientWrapper(esClient, configuration.getMaxAcceptedRequests()); - this.metadataLookup = metadataLookup; + this.crossrefMetadataLookup = crossrefMetadataLookup; + this.halLookup = halLookup; } public long getSize() { @@ -236,7 +245,8 @@ public List retrieveByBiblio(String biblio) { /** * Async search by raw bibliographical reference string **/ - public void retrieveByBiblioAsync(String biblio, Consumer> callback) { + public void retrieveByBiblioAsync(String biblio, + Consumer> callback) { if (isBlank(biblio)) { throw new ServiceException(400, "Supplied bibliographical string is empty."); } @@ -245,6 +255,34 @@ public void retrieveByBiblioAsync(String biblio, Consumer executeQueryAsync(query, callback); } + /** + * Async search by raw bibliographical reference string + **/ + public void retrieveByBiblioAsyncConditional(String biblio, + List sources, + String toIgnore, + Consumer> callback) { + if (isBlank(biblio)) { + throw new ServiceException(400, "Supplied bibliographical string is empty."); + } + //MatchQueryBuilder query = null; + BoolQueryBuilder query = null; + if (toIgnore == null) { + // usual case + //query = QueryBuilders.matchQuery(INDEX_FIELD_NAME_BIBLIOGRAPHIC, biblio); + query = QueryBuilders.boolQuery() + .must(QueryBuilders.existsQuery("DOI")) + .should(QueryBuilders.matchQuery(INDEX_FIELD_NAME_BIBLIOGRAPHIC, biblio)); + } else { + //query = QueryBuilders.matchQuery(INDEX_FIELD_NAME_BIBLIOGRAPHIC, biblio); + query = QueryBuilders.boolQuery() + .should(QueryBuilders.matchQuery(INDEX_FIELD_NAME_BIBLIOGRAPHIC, biblio)) + .mustNot(QueryBuilders.termQuery("_id", toIgnore)); + } + + executeQueryAsync(query, callback); + } + private List executeQuery(QueryBuilder query) { SearchRequest request = prepareQueryExecution(query); final List matchingDocuments; @@ -306,6 +344,7 @@ private SearchRequest prepareQueryExecution(QueryBuilder query) { { INDEX_FIELD_NAME_ID, INDEX_FIELD_NAME_DOI, + INDEX_FIELD_NAME_HALID, INDEX_FIELD_NAME_FIRST_AUTHOR, INDEX_FIELD_NAME_ATITLE, INDEX_FIELD_NAME_JTITLE, @@ -333,7 +372,10 @@ private List processResponse(SearchResponse response) { SearchHit hit = it.next(); + String id = (String) hit.getSourceAsMap().get(INDEX_FIELD_NAME_ID); String DOI = (String) hit.getSourceAsMap().get(INDEX_FIELD_NAME_DOI); + String halId = (String) hit.getSourceAsMap().get(INDEX_FIELD_NAME_HALID); + //String pmid = (String) hit.getSourceAsMap().get(INDEX_FIELD_NAME_PMID); String firstAuthor = (String) hit.getSourceAsMap().get(INDEX_FIELD_NAME_FIRST_AUTHOR); final List atitles = (List) hit.getSourceAsMap().get(INDEX_FIELD_NAME_ATITLE); @@ -354,22 +396,34 @@ private List processResponse(SearchResponse response) { abbreviatedTitle = abbrevTtitles.get(0); } - final Integer year = (Integer) hit.getSourceAsMap().get(INDEX_FIELD_NAME_YEAR); + final String year = (String) hit.getSourceAsMap().get(INDEX_FIELD_NAME_YEAR); String yearStr = null; if (year != null) { yearStr = ""+year; } + matchingDocument.setId(id); matchingDocument.setDOI(DOI); + matchingDocument.setHalId(halId); + //matchingDocument.setPmid(pmid); matchingDocument.setFirstAuthor(firstAuthor); matchingDocument.setATitle(atitle); matchingDocument.setJTitle(jtitle); matchingDocument.setAbbreviatedTitle(abbreviatedTitle); matchingDocument.setYear(yearStr); - final String jsonObject = metadataLookup.retrieveJsonDocument(DOI); + String jsonObject = null; + if (isNotBlank(DOI)) { + jsonObject = crossrefMetadataLookup.retrieveJsonDocument(DOI); + } + + if (jsonObject == null && isNotBlank(halId)) { + jsonObject = halLookup.retrieveJsonDocument(halId); + } + if (jsonObject == null) { - LOGGER.warn("The search index returned a result but the corresponding entry cannot be fetched in the metadata db, DOI: " + DOI); + LOGGER.warn("The search index returned a result but the corresponding entry cannot be fetched in the metadata db, DOI: " + + DOI + ", Hal ID: " + halId);// + ", PMID: " + pmid); continue; } @@ -424,6 +478,6 @@ private List processResponse(SearchResponse response) { } public void close() { - this.metadataLookup.close(); + this.crossrefMetadataLookup.close(); } } diff --git a/lookup/src/main/java/com/scienceminer/lookup/storage/lookup/OALookup.java b/src/main/java/com/scienceminer/glutton/storage/lookup/OALookup.java similarity index 91% rename from lookup/src/main/java/com/scienceminer/lookup/storage/lookup/OALookup.java rename to src/main/java/com/scienceminer/glutton/storage/lookup/OALookup.java index 1271275a..336058e0 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/storage/lookup/OALookup.java +++ b/src/main/java/com/scienceminer/glutton/storage/lookup/OALookup.java @@ -1,10 +1,10 @@ -package com.scienceminer.lookup.storage.lookup; +package com.scienceminer.glutton.storage.lookup; import com.codahale.metrics.Meter; -import com.scienceminer.lookup.exception.ServiceOverloadedException; -import com.scienceminer.lookup.reader.UnpayWallReader; -import com.scienceminer.lookup.storage.StorageEnvFactory; -import com.scienceminer.lookup.utils.BinarySerialiser; +import com.scienceminer.glutton.exception.ServiceOverloadedException; +import com.scienceminer.glutton.reader.UnpayWallReader; +import com.scienceminer.glutton.storage.StorageEnvFactory; +import com.scienceminer.glutton.utils.BinarySerialiser; import org.apache.commons.lang3.tuple.ImmutablePair; import org.apache.commons.lang3.tuple.Pair; import org.lmdbjava.*; @@ -19,13 +19,13 @@ import java.util.Map; import java.util.concurrent.atomic.AtomicInteger; -import static com.scienceminer.lookup.web.resource.DataController.DEFAULT_MAX_SIZE_LIST; +import static com.scienceminer.glutton.web.resource.DataController.DEFAULT_MAX_SIZE_LIST; import static java.nio.ByteBuffer.allocateDirect; import static org.apache.commons.lang3.StringUtils.isNotBlank; import static org.apache.commons.lang3.StringUtils.lowerCase; /** - * Lookup doi -> best OA Location + * Lookup doi -> best OA Location via Unpaywall */ public class OALookup { private static final Logger LOGGER = LoggerFactory.getLogger(OALookup.class); @@ -41,7 +41,7 @@ public class OALookup { public OALookup(StorageEnvFactory storageEnvFactory) { this.environment = storageEnvFactory.getEnv(ENV_NAME); - batchSize = storageEnvFactory.getConfiguration().getLoadingBatchSize(); + batchSize = storageEnvFactory.getConfiguration().getStoringBatchSize(); dbDoiOAUrl = this.environment.openDbi(NAME_DOI_OA_URL, DbiFlags.MDB_CREATE); } diff --git a/lookup/src/main/java/com/scienceminer/lookup/storage/lookup/PMIdsLookup.java b/src/main/java/com/scienceminer/glutton/storage/lookup/PMIdsLookup.java similarity index 63% rename from lookup/src/main/java/com/scienceminer/lookup/storage/lookup/PMIdsLookup.java rename to src/main/java/com/scienceminer/glutton/storage/lookup/PMIdsLookup.java index 7307652b..359146a0 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/storage/lookup/PMIdsLookup.java +++ b/src/main/java/com/scienceminer/glutton/storage/lookup/PMIdsLookup.java @@ -1,18 +1,21 @@ -package com.scienceminer.lookup.storage.lookup; +package com.scienceminer.glutton.storage.lookup; import com.codahale.metrics.Meter; -import com.scienceminer.lookup.data.PmidData; -import com.scienceminer.lookup.exception.ServiceOverloadedException; -import com.scienceminer.lookup.reader.PmidReader; -import com.scienceminer.lookup.storage.StorageEnvFactory; -import com.scienceminer.lookup.utils.BinarySerialiser; +import com.scienceminer.glutton.data.PmidData; +import com.scienceminer.glutton.exception.ServiceOverloadedException; +import com.scienceminer.glutton.reader.PmidReader; +import com.scienceminer.glutton.storage.StorageEnvFactory; +import com.scienceminer.glutton.utils.BinarySerialiser; import org.apache.commons.lang3.tuple.ImmutablePair; import org.apache.commons.lang3.tuple.Pair; import org.lmdbjava.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import java.io.BufferedReader; +import java.io.IOException; import java.io.InputStream; +import java.io.InputStreamReader; import java.nio.ByteBuffer; import java.util.ArrayList; import java.util.HashMap; @@ -20,14 +23,17 @@ import java.util.Map; import java.util.concurrent.atomic.AtomicInteger; -import static com.scienceminer.lookup.web.resource.DataController.DEFAULT_MAX_SIZE_LIST; +import static com.scienceminer.glutton.web.resource.DataController.DEFAULT_MAX_SIZE_LIST; import static java.nio.ByteBuffer.allocateDirect; import static org.apache.commons.lang3.StringUtils.isNotBlank; import static org.apache.commons.lang3.StringUtils.lowerCase; +import org.apache.commons.lang3.StringUtils; public class PMIdsLookup { private static final Logger LOGGER = LoggerFactory.getLogger(PMIdsLookup.class); + private static volatile PMIdsLookup instance; + public static final String ENV_NAME = "pmid"; public static final String NAME_DOI2IDS = ENV_NAME + "_doi2ids"; @@ -41,9 +47,27 @@ public class PMIdsLookup { private final int batchSize; - public PMIdsLookup(StorageEnvFactory storageEnvFactory) { + public static PMIdsLookup getInstance(StorageEnvFactory storageEnvFactory) { + if (instance == null) { + synchronized (PMIdsLookup.class) { + if (instance == null) { + getNewInstance(storageEnvFactory); + } + } + } + return instance; + } + + /** + * Creates a new instance. + */ + private static synchronized void getNewInstance(StorageEnvFactory storageEnvFactory) { + instance = new PMIdsLookup(storageEnvFactory); + } + + private PMIdsLookup(StorageEnvFactory storageEnvFactory) { this.environment = storageEnvFactory.getEnv(ENV_NAME); - batchSize = storageEnvFactory.getConfiguration().getLoadingBatchSize(); + batchSize = storageEnvFactory.getConfiguration().getStoringBatchSize(); dbDoiToIds = this.environment.openDbi(NAME_DOI2IDS, DbiFlags.MDB_CREATE); dbPmidToIds = this.environment.openDbi(NAME_PMID2IDS, DbiFlags.MDB_CREATE); @@ -55,27 +79,28 @@ public void loadFromFile(InputStream is, PmidReader reader, Meter metric) { final AtomicInteger counter = new AtomicInteger(0); reader.load(is, pmidData -> { - if (counter.get() == batchSize) { - transactionWrapper.tx.commit(); - transactionWrapper.tx.close(); - transactionWrapper.tx = environment.txnWrite(); - counter.set(0); - } + if (counter.get() == batchSize) { + transactionWrapper.tx.commit(); + transactionWrapper.tx.close(); + transactionWrapper.tx = environment.txnWrite(); + counter.set(0); + } - if (isNotBlank(pmidData.getDoi())) { - store(dbDoiToIds, lowerCase(pmidData.getDoi()), pmidData, transactionWrapper.tx); - } + if (isNotBlank(pmidData.getDoi())) { + store(dbDoiToIds, lowerCase(pmidData.getDoi()), pmidData, transactionWrapper.tx); + } - if (isNotBlank(pmidData.getPmid())) { - store(dbPmidToIds, pmidData.getPmid(), pmidData, transactionWrapper.tx); - } + if (isNotBlank(pmidData.getPmid())) { + store(dbPmidToIds, pmidData.getPmid(), pmidData, transactionWrapper.tx); + } - if (isNotBlank(pmidData.getPmcid())) { - store(dbPmcToIds, pmidData.getPmcid(), pmidData, transactionWrapper.tx); - } - metric.mark(); - counter.incrementAndGet(); + if (isNotBlank(pmidData.getPmcid())) { + store(dbPmcToIds, pmidData.getPmcid(), pmidData, transactionWrapper.tx); } + + metric.mark(); + counter.incrementAndGet(); + } ); transactionWrapper.tx.commit(); transactionWrapper.tx.close(); @@ -83,6 +108,58 @@ public void loadFromFile(InputStream is, PmidReader reader, Meter metric) { LOGGER.info("Cross checking number of records processed:: " + metric.getCount()); } + public void loadFromFileExtra(InputStream is, Meter metric) { + final TransactionWrapper transactionWrapper = new TransactionWrapper(environment.txnWrite()); + final AtomicInteger counter = new AtomicInteger(0); + + BufferedReader reader = new BufferedReader(new InputStreamReader(is)); + try { + while(reader.ready()) { + if (counter.get() == batchSize) { + transactionWrapper.tx.commit(); + transactionWrapper.tx.close(); + transactionWrapper.tx = environment.txnWrite(); + counter.set(0); + } + + String line = reader.readLine(); + final String[] split = StringUtils.splitPreserveAllTokens(line, ","); + + // retrieve pmidData by PMC ID (position 2) + PmidData pmidData = retrieveIdsByPmc(split[2]); + if (split[0].length()>0) + pmidData.setLicense(split[0]); + if (split[4].length()>0) + pmidData.setSubpath(split[4]); + + // update pmidData + if (isNotBlank(pmidData.getDoi())) { + store(dbDoiToIds, lowerCase(pmidData.getDoi()), pmidData, transactionWrapper.tx); + } + + if (isNotBlank(pmidData.getPmid())) { + store(dbPmidToIds, pmidData.getPmid(), pmidData, transactionWrapper.tx); + } + + if (isNotBlank(pmidData.getPmcid())) { + store(dbPmcToIds, pmidData.getPmcid(), pmidData, transactionWrapper.tx); + } + + metric.mark(); + counter.incrementAndGet(); + + } + + transactionWrapper.tx.commit(); + transactionWrapper.tx.close(); + } catch (IOException e) { + LOGGER.error("Some serious error when processing the PMC oa list file.", e); + } + + LOGGER.info("Cross checking number of records processed:: " + metric.getCount()); + } + + public PmidData retrieveIdsByDoi(String doi) { final ByteBuffer keyBuffer = allocateDirect(environment.getMaxKeySize()); ByteBuffer cachedData = null; diff --git a/lookup/src/main/java/com/scienceminer/lookup/storage/lookup/TransactionWrapper.java b/src/main/java/com/scienceminer/glutton/storage/lookup/TransactionWrapper.java similarity index 80% rename from lookup/src/main/java/com/scienceminer/lookup/storage/lookup/TransactionWrapper.java rename to src/main/java/com/scienceminer/glutton/storage/lookup/TransactionWrapper.java index 5e8d516c..997ecd02 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/storage/lookup/TransactionWrapper.java +++ b/src/main/java/com/scienceminer/glutton/storage/lookup/TransactionWrapper.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.storage.lookup; +package com.scienceminer.glutton.storage.lookup; import org.lmdbjava.Txn; diff --git a/lookup/src/main/java/com/scienceminer/lookup/storage/lookup/async/AsyncResponseWrapper.java b/src/main/java/com/scienceminer/glutton/storage/lookup/async/AsyncResponseWrapper.java similarity index 81% rename from lookup/src/main/java/com/scienceminer/lookup/storage/lookup/async/AsyncResponseWrapper.java rename to src/main/java/com/scienceminer/glutton/storage/lookup/async/AsyncResponseWrapper.java index b5ef8041..e39cfbb8 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/storage/lookup/async/AsyncResponseWrapper.java +++ b/src/main/java/com/scienceminer/glutton/storage/lookup/async/AsyncResponseWrapper.java @@ -1,6 +1,6 @@ -package com.scienceminer.lookup.storage.lookup.async; +package com.scienceminer.glutton.storage.lookup.async; -import javax.ws.rs.container.AsyncResponse; +import jakarta.ws.rs.container.AsyncResponse; public class AsyncResponseWrapper { diff --git a/lookup/src/main/java/com/scienceminer/lookup/storage/lookup/async/ESClientWrapper.java b/src/main/java/com/scienceminer/glutton/storage/lookup/async/ESClientWrapper.java similarity index 95% rename from lookup/src/main/java/com/scienceminer/lookup/storage/lookup/async/ESClientWrapper.java rename to src/main/java/com/scienceminer/glutton/storage/lookup/async/ESClientWrapper.java index 0e216358..33be918a 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/storage/lookup/async/ESClientWrapper.java +++ b/src/main/java/com/scienceminer/glutton/storage/lookup/async/ESClientWrapper.java @@ -1,6 +1,6 @@ -package com.scienceminer.lookup.storage.lookup.async; +package com.scienceminer.glutton.storage.lookup.async; -import com.scienceminer.lookup.exception.ServiceException; +import com.scienceminer.glutton.exception.ServiceException; import org.elasticsearch.action.ActionListener; import org.elasticsearch.action.search.SearchRequest; import org.elasticsearch.action.search.SearchResponse; @@ -65,7 +65,7 @@ public void onFailure(Exception e) { Exception returnException = e; if (e instanceof IOException) { -LOGGER.error("es query processing failure", e); + LOGGER.error("es query processing failure", e); returnException = new ServiceException(500, "Cannot connect to Elasticsearch", e); } callback.accept(null, returnException); diff --git a/lookup/src/main/java/com/scienceminer/lookup/utils/BinarySerialiser.java b/src/main/java/com/scienceminer/glutton/utils/BinarySerialiser.java similarity index 97% rename from lookup/src/main/java/com/scienceminer/lookup/utils/BinarySerialiser.java rename to src/main/java/com/scienceminer/glutton/utils/BinarySerialiser.java index b3562ff3..a37092a6 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/utils/BinarySerialiser.java +++ b/src/main/java/com/scienceminer/glutton/utils/BinarySerialiser.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.utils; +package com.scienceminer.glutton.utils; import org.nustaq.serialization.FSTConfiguration; diff --git a/lookup/src/main/java/com/scienceminer/lookup/utils/Compressors.java b/src/main/java/com/scienceminer/glutton/utils/Compressors.java similarity index 96% rename from lookup/src/main/java/com/scienceminer/lookup/utils/Compressors.java rename to src/main/java/com/scienceminer/glutton/utils/Compressors.java index a9e6d233..bfce1694 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/utils/Compressors.java +++ b/src/main/java/com/scienceminer/glutton/utils/Compressors.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.utils; +package com.scienceminer.glutton.utils; import org.xerial.snappy.Snappy; diff --git a/src/main/java/com/scienceminer/glutton/utils/LangUtil.java b/src/main/java/com/scienceminer/glutton/utils/LangUtil.java new file mode 100644 index 00000000..ecc3aab9 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/utils/LangUtil.java @@ -0,0 +1,60 @@ +package com.scienceminer.glutton.utils; + +import java.util.*; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * This class contains some various utility methods related to language. + * + */ +public class LangUtil { + + public static final Logger LOGGER = LoggerFactory + .getLogger(LangUtil.class); + + private static LangUtil instance = null; + + private Map localeMap = null; + + public static/* synchronized */LangUtil getInstance() { + if (instance == null) { + getNewInstance(); + } + return instance; + } + + /** + * Return a new instance. + */ + protected static synchronized void getNewInstance() { + // GrobidProperties.getInstance(); + LOGGER.debug("synchronized getNewInstance"); + instance = new LangUtil(); + } + + /** + * Hidden constructor + */ + private LangUtil() { + String[] languages = Locale.getISOLanguages(); + localeMap = new HashMap(languages.length); + for (String language : languages) { + Locale locale = new Locale(language); + localeMap.put(locale.getISO3Language(), locale); + } + } + + /** + * Convert three letter code language into two letter code language, or in + * other terms convert ISO 639-2 entry into ISO 639-1 entry + */ + public String convertISOLang32ISOLang2(String isoLang) { + Locale theLocale = localeMap.get(isoLang); + if (theLocale != null) + return theLocale.getLanguage(); + else + return null; + } +} diff --git a/src/main/java/com/scienceminer/glutton/utils/Utilities.java b/src/main/java/com/scienceminer/glutton/utils/Utilities.java new file mode 100644 index 00000000..f0bbfaec --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/utils/Utilities.java @@ -0,0 +1,367 @@ +package com.scienceminer.glutton.utils; + +import com.scienceminer.glutton.exception.*; + +import java.util.*; +import java.io.*; +import org.joda.time.DateTime; +import org.joda.time.format.DateTimeFormat; +import org.joda.time.format.DateTimeFormatter; + +import java.net.HttpURLConnection; +import java.net.MalformedURLException; +import java.net.URL; + +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * This class contains some various utility static methods. + * + */ +public class Utilities { + + private static final Logger logger = LoggerFactory.getLogger(Utilities.class); + + private static Set dates = new LinkedHashSet(); + + /** + * Medline month are usually expressed with 3-letter, e.g. Jan, Sep, this method + * convert it into an integer, e.g. 1 for Jan, 9 for Sep. + */ + public static int convertMedlineMonth(String crap) { + if (crap == null) + return -1; + DateTimeFormatter format = DateTimeFormat.forPattern("MMM"); + DateTime instance = null; + try { + instance = format.withLocale(Locale.ENGLISH).parseDateTime(crap); + } catch (Exception e) { + // logger here maybe (it would log a lot of useless failures) + //System.out.println("Failed to parse medline month: " + crap); + } + if (instance == null) + return -1; + else + return instance.getMonthOfYear(); + } + + /** + * Some medline dates are wrong because the day is not valid given the + * month: 2016 Sep 31 + * We check here the month and day, and make it valid, e.g. we change 31 + * to 30 for the day if the month is September. + * We consider Feb has 28 days, and do not take into account the year + * (actually there is no date invalid for February in the whole medline + * as of 2017 August) + * @return valid day according to provided month + */ + public static int correctDay(int day, int month) { + if ( (month == 4) || (month == 6) || (month == 9) || (month == 11) ) { + if (day >= 31) + return 30; + } else if (month == 2) { + if (day >= 29) + return 28; + } + return day; + } + + public final static String simpleCleanField(String input) { + String newInput = input.replace("\n", " "); + newInput = newInput.replaceAll("( )+", " ").trim(); + while (newInput.startsWith("\"")) { + newInput = newInput.substring(1); + } + + while (newInput.endsWith("\"")) { + newInput = newInput.substring(0,newInput.length()-1); + } + + return newInput.trim(); + } + + /** + * Remove useless punctuation at the end and beginning of a metadata field. + *

+ * Use with care ! + */ + public final static String cleanField(String input0) { + if (input0 == null) { + return null; + } + if (input0.length() == 0) { + return null; + } + + String input = input0.replace(",,", ","); + input = input.replace(", ,", ","); + int n = input.length(); + + // characters at the end + for (int i = input.length() - 1; i > 0; i--) { + char c = input.charAt(i); + if ((c == ',') || + (c == ' ') || + (c == '.') || + (c == '-') || + (c == '_') || + (c == '/') || + //(c == ')') || + //(c == '(') || + (c == ':')) { + n = i; + } else if (c == ';') { + // we have to check if we have an html entity finishing + if (i - 3 >= 0) { + char c0 = input.charAt(i - 3); + if (c0 == '&') { + break; + } + } + if (i - 4 >= 0) { + char c0 = input.charAt(i - 4); + if (c0 == '&') { + break; + } + } + if (i - 5 >= 0) { + char c0 = input.charAt(i - 5); + if (c0 == '&') { + break; + } + } + if (i - 6 >= 0) { + char c0 = input.charAt(i - 6); + if (c0 == '&') { + break; + } + } + n = i; + } else + break; + } + + input = input.substring(0, n); + + // characters at the begining + n = 0; + for (int i = 0; i < input.length(); i++) { + char c = input.charAt(i); + if ((c == ',') || + (c == ' ') || + (c == '.') || + (c == ';') || + (c == '-') || + (c == '_') || + //(c == ')') || + //(c == '(') || + (c == ':')) { + n = i; + } else break; + } + + input = input.substring(n, input.length()).trim(); + + if ((input.endsWith(")")) && (input.startsWith("("))) { + input = input.substring(1, input.length() - 1).trim(); + } + + if ((input.length() > 12) && + (input.endsWith(""")) && + (input.startsWith("""))) { + input = input.substring(6, input.length() - 6).trim(); + } + + return input.trim(); + } + + public static InputStream request(String request) throws MalformedURLException { + InputStream in = null; + long startTime = 0; + long endTime = 0; + startTime = System.currentTimeMillis(); + URL url = new URL(request); + HttpURLConnection conn = getConnection(url); + try { + in = conn.getInputStream(); + } catch (IOException e) { + logger.error("Can't get data stream.", e); + } + endTime = System.currentTimeMillis(); + logger.info("spend:" + (endTime - startTime) + " ms"); + return in; + } + + private static final HttpURLConnection getConnection(URL url) { + int retry = 0, retries = 4; + boolean delay = false; + HttpURLConnection connection = null; + do { + try { + if (delay) { + try { + Thread.sleep(2000); + } catch (InterruptedException ex) { + Thread.currentThread().interrupt(); + } + } + connection = (HttpURLConnection) url.openConnection(); + connection.setRequestMethod("GET"); + connection.setRequestProperty("accept-charset", "UTF-8"); + switch (connection.getResponseCode()) { + case HttpURLConnection.HTTP_OK: + logger.info(url + " **OK**"); + return connection; // **EXIT POINT** fine, go on + case HttpURLConnection.HTTP_GATEWAY_TIMEOUT: + logger.info(url + ":" + connection.getResponseCode()); + break;// retry + case HttpURLConnection.HTTP_UNAVAILABLE: + logger.info(url + "**unavailable**" + " :" + connection.getResponseCode()); + break;// retry, server is unstable + default: + //stop + logger.info(url + ":" + connection.getResponseCode()); + } + // we did not succeed with connection (or we would have returned the connection). + connection.disconnect(); + // retry + retry++; + logger.warn("Failed retry " + retry + "/" + retries); + delay = true; + if (retry == retries) { + logger.debug(url + ":" + connection.getResponseCode()); + } + } catch (IOException e) { + logger.error(url + ": The URL does not appear reachable.", e); + } + } while (retry < retries); + return connection; + } + + // managing a list of dates for OAI-PMH + static Calendar toDay = Calendar.getInstance(); + + static int todayYear = toDay.get(Calendar.YEAR); + + static int minYear = 1900; + + static { + int todayMonth = toDay.get(Calendar.MONTH) + 1; + int todayDay = toDay.get(Calendar.DAY_OF_MONTH) + 1; + //for (int year = 1960; year <= todayYear; year++) { + for (int year = 2020; year <= todayYear; year++) { + int monthYear = (year == todayYear) ? todayMonth : 12; + for (int month = 1; month <= monthYear; month++) { + for (int day = 1; day <= daysInMonth(year, month); day++) { + if ((year == todayYear) && (todayMonth == todayMonth) && (todayDay == day)) { + break; + } + StringBuilder date = new StringBuilder(); + date.append(String.format("%04d", year)); + date.append("-"); + date.append(String.format("%02d", month)); + date.append("-"); + date.append(String.format("%02d", day)); + getDates().add(date.toString()); + } + } + } + } + + protected static int daysInMonth(int year, int month) { + int daysInMonth; + switch (month) { + case 1: + case 3: + case 5: + case 7: + case 8: + case 10: + case 12: + daysInMonth = 31; + break; + case 2: + if (((year % 4 == 0) && (year % 100 != 0)) || (year % 400 == 0)) { + daysInMonth = 29; + } else { + daysInMonth = 28; + } + break; + default: + // returns 30 even for nonexistant months + daysInMonth = 30; + } + return daysInMonth; + } + + public static boolean isValidDate(String dateString) { + //consider other options (YY, YY-MM)? + return dates.contains(dateString); + } + + public static String completeDate(String date) { + if (date.endsWith("-")) { + date = date.substring(0, date.length()-1); + } + + String val = ""; + if (date.length() < 4) { + return val; + } else if (date.length() == 4) { + val = date + "-12-31"; + } else if ((date.length() == 7) || (date.length() == 6)) { + int ind = date.indexOf("-"); + String monthStr = date.substring(ind + 1, date.length()); + if (monthStr.length() == 1) { + monthStr = "0" + monthStr; + } + if (monthStr.equals("02")) { + val = date.substring(0, 4) + "-" + monthStr + "-28"; + } else if ((monthStr.equals("04")) || (monthStr.equals("06")) || (monthStr.equals("09")) + || (monthStr.equals("11"))) { + val = date.substring(0, 4) + "-" + monthStr + "-30"; + } else { + int month = Integer.parseInt(monthStr); + if (month > 12 || month < 1) { + monthStr = "12"; + } + val = date.substring(0, 4) + "-" + monthStr + "-31"; + } + } else { + int ind = date.indexOf("-"); + int ind2 = date.lastIndexOf("-"); + String monthStr = date.substring(ind + 1, ind + 3); + try { + int month = Integer.parseInt(monthStr); + if (month > 12 || month < 1) { + val = date.substring(0, 4) + "-12" + date.substring(ind + 3, date.length()); + } + String dayStr = date.substring(ind2 + 1, ind2 + 3); + int day = Integer.parseInt(dayStr); + if (day > 31 || day < 1) { + val = date.substring(0, 8) + "28";// so naif i know + } + } catch (Exception e) { + } + val = date.trim(); + // we have the "lazy programmer" case where the month is 00, e.g. 2012-00-31 + // which means the month is unknown + + ///val = val.replace("-00-", "-12-"); + } + val = val.replace(" ", "T"); // this is for the dateOptionalTime elasticSearch format + + if (!val.matches("\\d{4}-\\d{2}-\\d{2}") || (Integer.parseInt(val.substring(0, 4)) < minYear || todayYear < Integer.parseInt(val.substring(0, 4)))) { + val = ""; + } + return val; + } + + public static Set getDates() { + return dates; + } + +} diff --git a/lookup/src/main/java/com/scienceminer/lookup/utils/crossrefclient/CrossrefClient.java b/src/main/java/com/scienceminer/glutton/utils/crossrefclient/CrossrefClient.java similarity index 94% rename from lookup/src/main/java/com/scienceminer/lookup/utils/crossrefclient/CrossrefClient.java rename to src/main/java/com/scienceminer/glutton/utils/crossrefclient/CrossrefClient.java index c57863fd..7f09aa7d 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/utils/crossrefclient/CrossrefClient.java +++ b/src/main/java/com/scienceminer/glutton/utils/crossrefclient/CrossrefClient.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.utils.crossrefclient; +package com.scienceminer.glutton.utils.crossrefclient; import java.io.Closeable; import java.io.IOException; @@ -11,7 +11,7 @@ import org.apache.commons.lang3.concurrent.TimedSemaphore; import org.apache.http.client.ClientProtocolException; -import com.scienceminer.lookup.configuration.LookupConfiguration; +import com.scienceminer.glutton.configuration.LookupConfiguration; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/lookup/src/main/java/com/scienceminer/lookup/utils/crossrefclient/CrossrefRequest.java b/src/main/java/com/scienceminer/glutton/utils/crossrefclient/CrossrefRequest.java similarity index 98% rename from lookup/src/main/java/com/scienceminer/lookup/utils/crossrefclient/CrossrefRequest.java rename to src/main/java/com/scienceminer/glutton/utils/crossrefclient/CrossrefRequest.java index 5821ba8e..751d94f0 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/utils/crossrefclient/CrossrefRequest.java +++ b/src/main/java/com/scienceminer/glutton/utils/crossrefclient/CrossrefRequest.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.utils.crossrefclient; +package com.scienceminer.glutton.utils.crossrefclient; import org.apache.http.Header; import org.apache.http.HttpEntity; @@ -15,7 +15,7 @@ import org.apache.http.client.config.CookieSpecs; import org.apache.http.client.config.RequestConfig; -import com.scienceminer.lookup.configuration.LookupConfiguration; +import com.scienceminer.glutton.configuration.LookupConfiguration; import java.io.IOException; import java.util.List; diff --git a/lookup/src/main/java/com/scienceminer/lookup/utils/crossrefclient/CrossrefResponse.java b/src/main/java/com/scienceminer/glutton/utils/crossrefclient/CrossrefResponse.java similarity index 95% rename from lookup/src/main/java/com/scienceminer/lookup/utils/crossrefclient/CrossrefResponse.java rename to src/main/java/com/scienceminer/glutton/utils/crossrefclient/CrossrefResponse.java index ae64c8da..657480af 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/utils/crossrefclient/CrossrefResponse.java +++ b/src/main/java/com/scienceminer/glutton/utils/crossrefclient/CrossrefResponse.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.utils.crossrefclient; +package com.scienceminer.glutton.utils.crossrefclient; import java.util.List; diff --git a/lookup/src/main/java/com/scienceminer/lookup/utils/crossrefclient/IncrementalLoaderTask.java b/src/main/java/com/scienceminer/glutton/utils/crossrefclient/IncrementalLoaderTask.java similarity index 86% rename from lookup/src/main/java/com/scienceminer/lookup/utils/crossrefclient/IncrementalLoaderTask.java rename to src/main/java/com/scienceminer/glutton/utils/crossrefclient/IncrementalLoaderTask.java index baa6beab..406a7e7c 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/utils/crossrefclient/IncrementalLoaderTask.java +++ b/src/main/java/com/scienceminer/glutton/utils/crossrefclient/IncrementalLoaderTask.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.utils.crossrefclient; +package com.scienceminer.glutton.utils.crossrefclient; import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.lang3.StringUtils; @@ -8,10 +8,10 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import com.scienceminer.lookup.storage.lookup.MetadataLookup; -import com.scienceminer.lookup.storage.lookup.MetadataMatching; -import com.scienceminer.lookup.configuration.LookupConfiguration; -import com.scienceminer.lookup.reader.CrossrefJsonlReader; +import com.scienceminer.glutton.storage.lookup.CrossrefMetadataLookup; +import com.scienceminer.glutton.storage.lookup.MetadataMatching; +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.reader.CrossrefJsonlReader; import java.util.*; import java.io.*; @@ -42,13 +42,15 @@ public class IncrementalLoaderTask implements Runnable { private static final Logger LOGGER = LoggerFactory.getLogger(IncrementalLoaderTask.class); - private MetadataLookup metadataLookup; + private CrossrefMetadataLookup metadataLookup; private LocalDateTime lastIndexed; private LookupConfiguration configuration; private CrossrefClient client; private Meter meter; private Counter counterInvalidRecords; + private Counter counterIndexedRecords; + private Counter counterFailedIndexedRecords; // if true, we will also index the incremental dump files in elasticsearch during the task via // the external indexing module @@ -58,13 +60,15 @@ public class IncrementalLoaderTask implements Runnable { private DateTimeFormatter formatter = DateTimeFormatter.ofPattern("YYYY-MM-dd"); private LocalDate today; - public IncrementalLoaderTask(MetadataLookup metadataLookup, - LocalDateTime lastIndexed, - LookupConfiguration configuration, - Meter meter, - Counter counterInvalidRecords, - boolean indexing, - boolean daily) { + public IncrementalLoaderTask(CrossrefMetadataLookup metadataLookup, + LocalDateTime lastIndexed, + LookupConfiguration configuration, + Meter meter, + Counter counterInvalidRecords, + Counter counterIndexedRecords, + Counter counterFailedIndexedRecords, + boolean indexing, + boolean daily) { this.metadataLookup = metadataLookup; this.lastIndexed = lastIndexed; this.configuration = configuration; @@ -74,6 +78,8 @@ public IncrementalLoaderTask(MetadataLookup metadataLookup, this.meter = meter; this.counterInvalidRecords = counterInvalidRecords; + this.counterIndexedRecords = counterIndexedRecords; + this.counterFailedIndexedRecords = counterFailedIndexedRecords; this.indexing = indexing; this.daily = daily; @@ -179,7 +185,8 @@ public void run() { // load in another thread ExecutorService executorLoading = Executors.newSingleThreadExecutor(); - Runnable taskLoading = new LoadCrossrefFile(crossrefFile, jsonObjectsStr, this.configuration, meter, counterInvalidRecords); + Runnable taskLoading = new LoadCrossrefFile(crossrefFile, + jsonObjectsStr, this.configuration, meter, counterInvalidRecords, counterIndexedRecords, counterFailedIndexedRecords); executorLoading.submit(taskLoading); nbFiles++; @@ -203,7 +210,7 @@ public void run() { // note: rather than managing termination of threads, we look at storage/index size // for convenience MetadataMatching metadataMatching = - MetadataMatching.getInstance(this.configuration, this.metadataLookup); + MetadataMatching.getInstance(this.configuration, this.metadataLookup, null); if (configuration.getCrossref().getCleanProcessFiles()) { @@ -247,17 +254,23 @@ class LoadCrossrefFile implements Runnable { private LookupConfiguration configuration; private Meter meter; private Counter counterInvalidRecords; + private Counter counterIndexedRecords; + private Counter counterFailedIndexedRecords; public LoadCrossrefFile(File crossrefFile, List results, LookupConfiguration configuration, Meter meter, - Counter counterInvalidRecords) { + Counter counterInvalidRecords, + Counter counterIndexedRecords, + Counter counterFailedIndexedRecords) { this.crossrefFile = crossrefFile; this.results = results; this.configuration = configuration; this.meter = meter; this.counterInvalidRecords = counterInvalidRecords; + this.counterIndexedRecords = counterIndexedRecords; + this.counterFailedIndexedRecords = counterFailedIndexedRecords; } @Override @@ -265,7 +278,8 @@ public void run() { CrossrefJsonlReader reader = new CrossrefJsonlReader(configuration); if (StringUtils.endsWithIgnoreCase(crossrefFile.getName().toString(), ".json.gz")) { try (InputStream inputStreamCrossref = new GZIPInputStream(new FileInputStream(crossrefFile))) { - metadataLookup.loadFromFile(inputStreamCrossref, reader, meter, counterInvalidRecords); + metadataLookup.loadFromFile(inputStreamCrossref, + reader, meter, counterInvalidRecords, counterIndexedRecords, counterFailedIndexedRecords); } catch (Exception e) { LOGGER.error("Error while processing " + crossrefFile.getPath(), e); } diff --git a/lookup/src/main/java/com/scienceminer/lookup/utils/grobid/GrobidClient.java b/src/main/java/com/scienceminer/glutton/utils/grobid/GrobidClient.java similarity index 94% rename from lookup/src/main/java/com/scienceminer/lookup/utils/grobid/GrobidClient.java rename to src/main/java/com/scienceminer/glutton/utils/grobid/GrobidClient.java index 610d4866..c3738eff 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/utils/grobid/GrobidClient.java +++ b/src/main/java/com/scienceminer/glutton/utils/grobid/GrobidClient.java @@ -1,9 +1,9 @@ -package com.scienceminer.lookup.utils.grobid; +package com.scienceminer.glutton.utils.grobid; import com.ctc.wstx.stax.WstxInputFactory; -import com.scienceminer.lookup.exception.ServiceException; -import com.scienceminer.lookup.utils.xml.StaxUtils; -import com.scienceminer.lookup.utils.grobid.GrobidResponseStaxHandler.GrobidResponse; +import com.scienceminer.glutton.exception.ServiceException; +import com.scienceminer.glutton.utils.xml.StaxUtils; +import com.scienceminer.glutton.utils.grobid.GrobidResponseStaxHandler.GrobidResponse; import org.apache.http.client.ClientProtocolException; import org.apache.http.Consts; import org.apache.http.HttpResponse; diff --git a/lookup/src/main/java/com/scienceminer/lookup/utils/grobid/GrobidClientAsync.java b/src/main/java/com/scienceminer/glutton/utils/grobid/GrobidClientAsync.java similarity index 94% rename from lookup/src/main/java/com/scienceminer/lookup/utils/grobid/GrobidClientAsync.java rename to src/main/java/com/scienceminer/glutton/utils/grobid/GrobidClientAsync.java index 127d98a5..7e26e61b 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/utils/grobid/GrobidClientAsync.java +++ b/src/main/java/com/scienceminer/glutton/utils/grobid/GrobidClientAsync.java @@ -1,9 +1,9 @@ -package com.scienceminer.lookup.utils.grobid; +package com.scienceminer.glutton.utils.grobid; import com.ctc.wstx.stax.WstxInputFactory; -import com.scienceminer.lookup.exception.ServiceException; -import com.scienceminer.lookup.utils.xml.StaxUtils; -import com.scienceminer.lookup.utils.grobid.GrobidResponseStaxHandler.GrobidResponse; +import com.scienceminer.glutton.exception.ServiceException; +import com.scienceminer.glutton.utils.xml.StaxUtils; +import com.scienceminer.glutton.utils.grobid.GrobidResponseStaxHandler.GrobidResponse; import org.apache.http.client.ClientProtocolException; import org.apache.http.Consts; import org.apache.http.HttpResponse; diff --git a/lookup/src/main/java/com/scienceminer/lookup/utils/grobid/GrobidResponseStaxHandler.java b/src/main/java/com/scienceminer/glutton/utils/grobid/GrobidResponseStaxHandler.java similarity index 98% rename from lookup/src/main/java/com/scienceminer/lookup/utils/grobid/GrobidResponseStaxHandler.java rename to src/main/java/com/scienceminer/glutton/utils/grobid/GrobidResponseStaxHandler.java index a1790ef6..30e317a5 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/utils/grobid/GrobidResponseStaxHandler.java +++ b/src/main/java/com/scienceminer/glutton/utils/grobid/GrobidResponseStaxHandler.java @@ -1,6 +1,6 @@ -package com.scienceminer.lookup.utils.grobid; +package com.scienceminer.glutton.utils.grobid; -import com.scienceminer.lookup.utils.xml.StaxParserContentHandler; +import com.scienceminer.glutton.utils.xml.StaxParserContentHandler; import org.apache.commons.lang3.StringUtils; import org.codehaus.stax2.XMLStreamReader2; import org.slf4j.Logger; diff --git a/src/main/java/com/scienceminer/glutton/utils/xml/DumbEntityResolver.java b/src/main/java/com/scienceminer/glutton/utils/xml/DumbEntityResolver.java new file mode 100644 index 00000000..c0af0b2e --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/utils/xml/DumbEntityResolver.java @@ -0,0 +1,16 @@ +package com.scienceminer.glutton.utils.xml; + +import org.xml.sax.*; +import java.io.StringReader; + +/** + * A dumb class to neutralise the dumb XML spec/libraries. + * Avoid the SAX parser to download the externally define DTD for each document. + */ +public class DumbEntityResolver implements EntityResolver { + public InputSource resolveEntity(String publicID, String systemID) + throws SAXException { + + return new InputSource(new StringReader("")); + } +} diff --git a/src/main/java/com/scienceminer/glutton/utils/xml/HALTEISaxHandler.java b/src/main/java/com/scienceminer/glutton/utils/xml/HALTEISaxHandler.java new file mode 100644 index 00000000..d356732b --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/utils/xml/HALTEISaxHandler.java @@ -0,0 +1,706 @@ +package com.scienceminer.glutton.utils.xml; + +import com.scienceminer.glutton.data.*; +import com.scienceminer.glutton.utils.*; +import org.apache.commons.lang3.StringUtils; + +import org.xml.sax.*; +import org.xml.sax.helpers.*; + +import org.joda.time.DateTimeFieldType; +import org.joda.time.Partial; + +import java.util.*; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +/** + * SAX parser for HAL TEI metadata + * + * @author Patrice Lopez + */ +public class HALTEISaxHandler extends DefaultHandler { + + private Biblio biblio = null; + private StringBuilder accumulator = new StringBuilder(); // Accumulate parsed text + + // current fields + private String idnoType = null; + private String biblScopeType = null; + private String level = null; + private String dateType = null; + private String foreNameType = null; + private String authorRole = null; + private String currentScheme = null; + private String documentCodeType = null; + + private List authors; + private List affiliations = null; + private String lastName = null; + private String foreName = null; + private String middleName = null; + private String suffix = null; + private String initials = null; + private String identifier = null; + private String identifierSource = null; + private Identifier identifierObject = null; + private Identifier authorIdentifierObject = null; + private String affiliationString = null; + + private String langCode = null; + + // grant + private List grants = null; + private Grant currentGrant = null; + + // position tags + private boolean sourceDesc = false; + private boolean analytic = false; + private boolean monogr = false; + private boolean abbrev = false; + private boolean profileDesc = false; + private boolean publicationStmt = false; + + private DateTimeFieldType[] fieldYMD = new DateTimeFieldType[] { + DateTimeFieldType.year(), + DateTimeFieldType.monthOfYear(), + DateTimeFieldType.dayOfMonth(), + }; + + private DateTimeFieldType[] fieldYM = new DateTimeFieldType[] { + DateTimeFieldType.year(), + DateTimeFieldType.monthOfYear() + }; + + private DateTimeFieldType[] fieldY = new DateTimeFieldType[] { + DateTimeFieldType.year() + }; + + private static volatile Pattern page = Pattern.compile("(\\d+)"); + + public HALTEISaxHandler() { + } + + public HALTEISaxHandler(Biblio b) { + this.biblio = b; + } + + public Biblio getBiblio() { + return this.biblio; + } + + public void characters(char[] ch, int start, int length) { + accumulator.append(ch, start, length); + } + + public String getText() { + return accumulator.toString().trim(); + } + + public void endElement(java.lang.String uri, java.lang.String localName, java.lang.String qName) throws SAXException { + if (qName.equals("sourceDesc")) { + sourceDesc = false; + } else if (qName.equals("analytic")) { + analytic = false; + if ( (authors != null) && (authors.size() >0) ) { + biblio.setAuthors(authors); + authors = null; + } + } else if (qName.equals("monogr")) { + monogr = false; + } else if (qName.equals("profileDesc")) { + profileDesc = false; + } else if (qName.equals("publicationStmt")) { + publicationStmt = false; + } else if (qName.equals("idno") && idnoType != null) { + if (idnoType.equals("issn")) { + String issn = getText(); + if (issn != null && issn.length()>0) + biblio.setIssn(issn); + } else if (idnoType.equals("isbn")) { + String isbn = getText(); + if (isbn != null && isbn.length()>0) + biblio.setIsbn(isbn); + } else if (idnoType.equals("doi")) { + String doi = getText(); + if (doi != null && doi.length()>0) + biblio.setDoi(doi); + } else if (idnoType.equals("halId")) { + String halId = getText(); + if (halId != null && halId.length()>0) + biblio.setHalId(halId); + } else if (idnoType.equals("halUri")) { + String halUri = getText(); + if (halUri != null && halUri.length()>0) + biblio.setHalUri(halUri); + } else if (idnoType.equals("pubmed")) { + String stringPmid = getText(); + if (stringPmid != null & stringPmid.length()>0) { + biblio.setPubmedId(stringPmid); + // we can try to get the numeric representation too + try { + Integer intPmid = Integer.parseInt(stringPmid); + if (intPmid != null) + biblio.setPmid(intPmid); + } catch(Exception e) { + // do nothing ! + } + } + } + idnoType = null; + } else if (qName.equals("biblScope") && sourceDesc) { + if (biblScopeType.equals("volume")) { + String volume = getText(); + if ( (volume != null) && (volume.length() > 0) && !volume.equals("n/a")) + biblio.setVolume(volume); + } else if (biblScopeType.equals("issue")) { + String issue = getText(); + if ( (issue != null) && (issue.length() > 0) && !issue.equals("n/a") ) + biblio.setNumber(issue); + } else if (biblScopeType.equals("serie") || biblScopeType.equals("series")) { + // this is a bit weird, but the collection name is given here, despite being the host for the volume + // that normally contains the paper + String collection = getText(); + if ( (collection != null) && (collection.length() > 0) && !collection.equals("n/a") ) + biblio.setCollectionTitle(collection); + } else if (biblScopeType.equals("pp") || biblScopeType.equals("page")) { + String pagination = getText(); + if ( (pagination != null) && (pagination.length() > 0) && !pagination.equals("n/a") && !pagination.equals("n/a-n/a")) { + //biblio.setPagination(pagination); + // we want to detect start/end page when we have a pagination block + if ( (pagination != null) && (pagination.length() > 0) ) { + // first we might have a "suppl.:"" prefix + pagination = pagination.replace("Suppl:", "").replace("suppl:", "").replace("Suppl", "").replace("suppl", "").trim(); + // TBD: where to capture that we are in some supplementary stuff at the level of pages? + + String firstPage = null; + String lastPage = null; + + // other weirdos + pagination = pagination.replace("passim", "").trim(); + pagination = pagination.replace("CR", "").trim(); + pagination = pagination.replace("concl", "").trim(); + pagination = pagination.replace("cntd", "").trim(); + pagination = pagination.replace("discussion", "").trim(); + pagination = pagination.replace("author reply", "").trim(); + + // format is 117-26 / 121-6 / 1173-9 + // OR + // 5911-5924 + // !!! + int ind = pagination.indexOf("-"); + if (ind != -1) { + firstPage = pagination.substring(0, ind); + lastPage = pagination.substring(ind+1, pagination.length()); + // we must concatenate prefix to last page + int size = lastPage.length(); + if (size < firstPage.length()) { + lastPage = firstPage.substring(0, firstPage.length() - size) + lastPage; + } + } else { + // sometimes we have a comma... + int ind2 = pagination.indexOf(","); + if (ind2 != -1) { + firstPage = pagination.substring(0, ind2); + lastPage = pagination.substring(ind2+1, pagination.length()); + // we must concatenate prefix to last page + int size = lastPage.length(); + if (size < firstPage.length()) { + lastPage = firstPage.substring(0, firstPage.length() - size) + lastPage; + } + } else { + // we assume one page article + firstPage = pagination; + lastPage = pagination; + } + } + //System.out.println(pagination + " -> " + firstPage + " / " + lastPage); + + if ( (firstPage != null) && (firstPage.length() > 0) ) { + biblio.setStartPage(firstPage); + int firstPageVal = -1; + try { + firstPageVal = Integer.parseInt(firstPage); + } catch (Exception e) { + // logger here + //System.out.println("parsing of first page failed: " + firstPage); + } + if (firstPageVal != -1) + biblio.setStartPageInt(firstPageVal); + else { + // set the raw pagination + biblio.setPagination(pagination); + + // try also a more shallow extraction + Matcher matcher = page.matcher(pagination); + if (matcher.find()) { + if (matcher.groupCount() > 0) { + firstPage = matcher.group(0); + if ( (firstPage != null) && (firstPage.length() > 0) && !firstPage.equals("n/a")) { + biblio.setStartPage(firstPage); + try { + firstPageVal = Integer.parseInt(firstPage); + } catch (Exception e) { + // logger here + //System.out.println("parsing of first page failed: " + firstPage); + } + if (firstPageVal != -1) + biblio.setStartPageInt(firstPageVal); + } + } + } + } + } + + if ( (lastPage != null) && (lastPage.length() > 0) ) { + biblio.setEndPage(lastPage); + int lastPageVal = -1; + try { + lastPageVal = Integer.parseInt(lastPage); + } catch (Exception e) { + // logger here + //System.out.println("parsing of last page failed: " + lastPage); + } + if (lastPageVal != -1) + biblio.setEndPageInt(lastPageVal); + else { + // set the raw pagination + biblio.setPagination(pagination); + + // try also a more shallow extraction + Matcher matcher = page.matcher(pagination); + if (matcher.find()) { + if (matcher.groupCount() > 1) { + lastPage = matcher.group(1); + if ( (lastPage != null) && (lastPage.length() > 0) && !lastPage.equals("n/a")) { + biblio.setEndPage(lastPage); + try { + lastPageVal = Integer.parseInt(lastPage); + } catch (Exception e) { + // logger here + //System.out.println("parsing of last page failed: " + firstPage); + } + if (lastPageVal != -1) + biblio.setEndPageInt(lastPageVal); + } + } + } + } + } + } + } + } + + biblScopeType = null; + } else if (qName.equals("title") && sourceDesc) { + if ("j".equals(level) && monogr) { + // full journal title + String title = getText(); + if ( (title != null) && (title.length() > 0) ) + biblio.setTitle(title); + } else if ("j".equals(level) && monogr && abbrev) { + // abbreviated journal title + String journalTitleAbbrev = getText(); + if ( (journalTitleAbbrev != null) && (journalTitleAbbrev.length() > 0) ) + biblio.setJournalAbbrev(journalTitleAbbrev); + } else if ("m".equals(level) && monogr) { + // proceedings, report or book title + String title = getText(); + if ( (title != null) && (title.length() > 0) ) + biblio.setTitle(title); + } else if ("a".equals(level) || analytic) { + // article title + String articleTitle = getText(); + if ( (articleTitle != null) && (articleTitle.length() > 0) ) + biblio.setArticleTitle(articleTitle); + } + + level = null; + abbrev = false; + } else if (qName.equals("publisher") && sourceDesc) { + String publisher = getText(); + if ( (publisher != null) && (publisher.length() > 0) ) + biblio.setPublisher(publisher); + } else if (qName.equals("language")) { + // full language name + String rawLang = getText(); + if ( (rawLang != null) && (rawLang.length() > 0) ) { + biblio.setRawLanguage(rawLang); + } + // the usual ISO 639-1 should be around as attribute + if (langCode != null) + biblio.setLanguage(langCode); + langCode = null; + } else if (qName.equals("date")) { + String dateString = getText(); + if ((dateString != null) && (dateString.length() > 0)) { + if ("datePub".equals(dateType)) { + this.dateProcessing(biblio, "publication", dateString); + } else if ("dateDefended".equals(dateType)) { + // for thesis, this can be considered as publication date too + this.dateProcessing(biblio, "publication", dateString); + } + } + } else if (qName.equals("abstract") && profileDesc) { + String abstractString = getText(); + if ( (abstractString != null) && (abstractString.length() > 0) ) { + // to be reviewed + //biblio.setAbstract(abstractString); + } + } else if (qName.equals("forename")) { + if ("middle".equals(foreNameType)) + middleName = getText(); + else + foreName = getText(); + foreNameType = null; + } else if (qName.equals("surname")) { + lastName = getText(); + } else if (qName.equals("author")) { + Person author = new Person(); + if ( (lastName != null) && (lastName.length() > 0) ) + author.setLastName(lastName); + if ( (foreName != null) && (foreName.length() > 0) ) + author.setFirstName(foreName); + if ( (suffix != null) && (suffix.length() > 0) ) + author.setSuffix(suffix); + if ( (initials != null) && (initials.length() > 0) ) + author.setInits(initials); + if ( (middleName != null) && (middleName.length() > 0) ) + author.setMiddleName(middleName); + + if ( (authorIdentifierObject != null) && + (authorIdentifierObject.getIdentifierName() != null) && + (authorIdentifierObject.getIdentifierValue() != null) ) { + author.addIdentifier(authorIdentifierObject); + } + + if ( (affiliations != null) && (affiliations.size() > 0) ) + author.setAffiliations(affiliations); + + if (author.getLastName() != null && (authorRole == null || authorRole.equals("aut"))) { + if (authors == null) + authors = new ArrayList<>(); + authors.add(author); + } + author = null; + lastName = null; + foreName = null; + middleName = null; + suffix = null; + initials = null; + authorIdentifierObject = null; + affiliations = null; + + authorRole = null; + } + /*else if (qName.equals("AffiliationInfo")) { + // create an affiliation to be attached to the current author + // affiliation is raw affiliation string, consider GROBID to add more usable affiliation/address descriptions + if ( (affiliationString != null) && (affiliationString.length() >0) ) { + Affiliation affiliation = new Affiliation(affiliationString); + if ( (identifierObject != null) && + (identifierObject.getIdentifierName() != null) && + (identifierObject.getIdentifierValue() != null) ) { + affiliation.addIdentifier(identifierObject); + } + if (affiliations == null) + affiliations = new ArrayList(); + affiliations.add(affiliation); + } + inAffiliationInfo = false; + affiliationString = null; + identifierObject = null; + } else if (qName.equals("Affiliation")) { + affiliationString = getText(); + } */ + else if (qName.equals("classCode") && profileDesc) { + // article type: n="ART" scheme="halTypology" + if ("halTypology".equals(currentScheme)) { + String rawPublicationType = getText(); + if ( (rawPublicationType != null) && (rawPublicationType.length() > 0) ) { + biblio.setRawPublicationType(rawPublicationType); + } + mapDocumentType(biblio, documentCodeType); + documentCodeType = null; + } + } + + accumulator.setLength(0); + } + + + public void startElement(String namespaceURI, + String localName, + String qName, + Attributes atts) + throws SAXException { + if (qName.equals("TEI")) { + if (biblio == null) + biblio = new Biblio(); + } else if (qName.equals("idno") && (sourceDesc || publicationStmt)) { + int length = atts.getLength(); + + // Process each attribute + for (int i = 0; i < length; i++) { + // Get names and values for each attribute + String name = atts.getQName(i); + String value = atts.getValue(i); + if ((name != null) && (value != null)) { + if (name.equals("type")) + idnoType = value; + } + } + } else if (qName.equals("biblScope") && sourceDesc) { + int length = atts.getLength(); + + // Process each attribute + for (int i = 0; i < length; i++) { + // Get names and values for each attribute + String name = atts.getQName(i); + String value = atts.getValue(i); + if ((name != null) && (value != null)) { + if (name.equals("unit")) + biblScopeType = value; + } + } + } else if (qName.equals("sourceDesc")) { + sourceDesc = true; + authors = new ArrayList<>(); + affiliations = new ArrayList<>(); + } else if (qName.equals("analytic")) { + analytic = true; + } else if (qName.equals("monogr")) { + monogr = true; + } else if (qName.equals("profileDesc")) { + profileDesc = true; + } else if (qName.equals("publicationStmt")) { + publicationStmt = true; + } else if (qName.equals("title") && sourceDesc) { + int length = atts.getLength(); + + // Process each attribute + for (int i = 0; i < length; i++) { + // Get names and values for each attribute + String name = atts.getQName(i); + String value = atts.getValue(i); + + if ((name != null) && (value != null)) { + if (name.equals("level")) + level = value; + else if (name.equals("type") && value.equals("abbrev")) + abbrev = true; + //else if (name.equals("xml:lang")) + // langCode = value; + } + } + } else if (qName.equals("language") && profileDesc) { + int length = atts.getLength(); + + // Process each attribute + for (int i = 0; i < length; i++) { + // Get names and values for each attribute + String name = atts.getQName(i); + String value = atts.getValue(i); + + if ((name != null) && (value != null)) { + if (name.equals("ident")) { + langCode = value; + if (langCode.length() == 3) { + // if it is a 3 character code + langCode = LangUtil.getInstance().convertISOLang32ISOLang2(langCode); + } + } + } + } + } else if (qName.equals("forename") && sourceDesc) { + int length = atts.getLength(); + + // Process each attribute + for (int i = 0; i < length; i++) { + // Get names and values for each attribute + String name = atts.getQName(i); + String value = atts.getValue(i); + + if ((name != null) && (value != null)) { + if (name.equals("type")) { + foreNameType = value; + } + } + } + } else if (qName.equals("author") && sourceDesc) { + int length = atts.getLength(); + + // Process each attribute + for (int i = 0; i < length; i++) { + // Get names and values for each attribute + String name = atts.getQName(i); + String value = atts.getValue(i); + + if ((name != null) && (value != null)) { + if (name.equals("role")) { + authorRole = value; + } + } + } + } else if (qName.equals("classCode") && profileDesc) { + // scheme="mesh" + // article type: n="ART" scheme="halTypology" + int length = atts.getLength(); + + // Process each attribute + for (int i = 0; i < length; i++) { + // Get names and values for each attribute + String name = atts.getQName(i); + String value = atts.getValue(i); + + if ((name != null) && (value != null)) { + if (name.equals("scheme")) { + currentScheme = value; + } else if (name.equals("n")) { + documentCodeType = value; + } + } + } + } else if (qName.equals("date")) { + int length = atts.getLength(); + + // Process each attribute + for (int i = 0; i < length; i++) { + // Get names and values for each attribute + String name = atts.getQName(i); + String value = atts.getValue(i); + + if ((name != null) && (value != null)) { + if (name.equals("type")) { + dateType = value; + } + } + } + } + } + + private void dateProcessing(Biblio biblio, String type, String rawDate) { + // try to get the best of the date information + String year = null; + String month = null; + String day = null; + + // for HAL dates are YYYY-MM-DD, publication dates are usually only YYYY + if (rawDate == null) + return; + if (rawDate.length() >= 4) { + year = rawDate; + if (rawDate.length() > 4) { + int ind = rawDate.indexOf("-"); + if (ind != -1) { + year = rawDate.substring(0, ind); + if (rawDate.length() >= 7) { + month = rawDate.substring(ind+1, ind+3); + if (rawDate.length() > 7) { + int ind2 = rawDate.indexOf("-", ind+1); + if (ind2 != -1) { + day = rawDate.substring(ind2+1, rawDate.length()); + } + } + } + } + } + } + + int yearVal = -1; + int monthVal = -1; + int dayVal = -1; + + /*if (month != null) { + monthVal = Utilities.convertMedlineMonth(month); + }*/ + + if (year != null) { + try { + yearVal = Integer.parseInt(year); + } catch(Exception e) { + System.err.println("Failure to parse year: " + year); + } + } + + if ((monthVal == -1) && (month != null)) { + try { + monthVal = Integer.parseInt(month); + } catch(Exception e) { + System.err.println("Failure to parse month: " + month); + } + } + + if (day != null) { + try { + dayVal = Integer.parseInt(day); + } catch(Exception e) { + System.err.println("Failure to parse day: " + day); + } + } + + Partial date = null; + try { + if (yearVal != -1) { + if (monthVal != -1) { + if (dayVal != -1) { + dayVal = Utilities.correctDay(dayVal, monthVal); + int[] values = new int[] {yearVal, monthVal, dayVal}; + List types = new ArrayList(Arrays.asList(fieldYMD)); + date = new Partial(fieldYMD, values); + } else { + int[] values = new int[] {yearVal, monthVal}; + List types = new ArrayList(Arrays.asList(fieldYM)); + date = new Partial(fieldYM, values); + } + } else { + int[] values = new int[] {yearVal}; + List types = new ArrayList(Arrays.asList(fieldY)); + date = new Partial(fieldY, values); + } + } + } catch(Exception e) { + // to log... + System.out.println(year + " / " + month + " / " + day); + e.printStackTrace(); + } + if (date != null) { + if (type.equals("publication")) + biblio.setPublicationDate(date); + else if (type.equals("update")) + biblio.setLastUpdateDate(date); + } + } + + public void mapDocumentType(Biblio biblio, String codeType) { + if (codeType == null) + return; + biblio.setOriginalDocumentype(codeType); + if (codeType.equals("ART")) { + biblio.setDocumentType(BiblioDefinitions.ARTICLE); + biblio.setHostType(BiblioDefinitions.JOURNAL); + } else if (codeType.equals("COMM")) { + biblio.setDocumentType(BiblioDefinitions.ARTICLE); + biblio.setHostType(BiblioDefinitions.PROCEEDINGS); + } else if (codeType.equals("POSTER")) { + biblio.setDocumentType(BiblioDefinitions.ARTICLE); + biblio.setHostType(BiblioDefinitions.PROCEEDINGS); + } else if (codeType.equals("COUV")) { + biblio.setDocumentType(BiblioDefinitions.ARTICLE); + biblio.setHostType(BiblioDefinitions.BOOK); + } else if (codeType.equals("REPORT") || codeType.equals("OTHERREPORT")) { + biblio.setDocumentType(BiblioDefinitions.REPORT); + } else if (codeType.equals("CREPORT")) { + biblio.setDocumentType(BiblioDefinitions.ARTICLE); + biblio.setHostType(BiblioDefinitions.REPORT); + } else if (codeType.equals("OUV")) { + biblio.setDocumentType(BiblioDefinitions.BOOK); + } else if (codeType.equals("PROCEEDINGS")) { + biblio.setDocumentType(BiblioDefinitions.PROCEEDINGS); + } else if (codeType.equals("ISSUE")) { + biblio.setDocumentType(BiblioDefinitions.JOURNAL); + } else if (codeType.equals("THESE") || codeType.equals("HDR") || codeType.equals("MEM") || codeType.equals("ETABTHESE")) { + biblio.setDocumentType(BiblioDefinitions.REPORT); + } + } +} \ No newline at end of file diff --git a/src/main/java/com/scienceminer/glutton/utils/xml/MedlineSaxHandler.java b/src/main/java/com/scienceminer/glutton/utils/xml/MedlineSaxHandler.java new file mode 100644 index 00000000..bdfac94d --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/utils/xml/MedlineSaxHandler.java @@ -0,0 +1,846 @@ +package com.scienceminer.glutton.utils.xml; + +import com.scienceminer.glutton.data.*; +import com.scienceminer.glutton.utils.*; +import org.apache.commons.lang3.StringUtils; + +import org.xml.sax.*; +import org.xml.sax.helpers.*; + +import org.joda.time.DateTimeFieldType; +import org.joda.time.Partial; + +import java.util.*; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +/** + * SAX parser for XML MedlineSax files. + * + * @author Patrice Lopez + */ +public class MedlineSaxHandler extends DefaultHandler { + + private Biblio biblio = null; + private List biblios = null; + private StringBuilder accumulator = new StringBuilder(); // Accumulate parsed text + + // current fields + + // mesh + private String chemicalUI = null; + private String chemicalNameOfSubstance = null; + private String chemicalRegistryNumber = null; + + private String descriptorUI = null; + private List qualifierUIs = null; + private String descriptorName = null; + private List qualifierNames = null; + private boolean majorTopicDescriptor = false; + private List majorTopicQualifiers = null; + + // biblio + private Integer pmid = null; + private String issne = null; + private String issnp = null; + private String volume = null; + private String issue = null; + private String title = null; + private String journalTitleAbbrev = null; + private String year = null; + private String month = null; + private String day = null; + private String firstPage = null; + private String lastPage = null; + private String articleTitle = null; + + private List authors; + private List affiliations = null; + private String lastName = null; + private String foreName = null; + private String suffix = null; + private String initials = null; + private String identifier = null; + private String identifierSource = null; + private Identifier identifierObject = null; + private Identifier authorIdentifierObject = null; + private String affiliationString = null; + private String abstractString = null; + private String publicationTypeUI = null; + private Reference currentReference = null; + private Keyword currentKeyword = null; + private String currentKeywordOrigin = null; + + private String language = null; + + // grant + private List grants = null; + private Grant currentGrant = null; + + // position tags + private boolean electronic = false; + private boolean print = false; + private boolean inAffiliationInfo = false; + private boolean validElocationTypeDOI = false; + private boolean isArticleIdList = false; + private boolean inReferenceList = false; + + private boolean doiType = false; + private boolean pubmedType = false; + private boolean piiType = false; + private boolean pmcType = false; + + private DateTimeFieldType[] fieldYMD = new DateTimeFieldType[] { + DateTimeFieldType.year(), + DateTimeFieldType.monthOfYear(), + DateTimeFieldType.dayOfMonth(), + }; + + private DateTimeFieldType[] fieldYM = new DateTimeFieldType[] { + DateTimeFieldType.year(), + DateTimeFieldType.monthOfYear() + }; + + private DateTimeFieldType[] fieldY = new DateTimeFieldType[] { + DateTimeFieldType.year() + }; + + private static volatile Pattern page = Pattern.compile("(\\d+)"); + + public MedlineSaxHandler() { + } + + public MedlineSaxHandler(List b) { + biblios = b; + } + + public List getBiblios() { + return biblios; + } + + public void characters(char[] ch, int start, int length) { + accumulator.append(ch, start, length); + } + + public String getText() { + return accumulator.toString().trim(); + } + + public void endElement(java.lang.String uri, java.lang.String localName, java.lang.String qName) throws SAXException { + if (qName.equals("PMID")) { + Integer pmid = null; + String rawPmid = getText(); + try { + pmid = Integer.parseInt(rawPmid); + } catch(Exception e) { + System.out.println("Error parsing this PMID: " + rawPmid); + e.printStackTrace(); + } + biblio.setPmid(pmid); + } else if (qName.equals("PubmedArticle")) { + // new article + if (biblios == null) { + biblios = new ArrayList(); + } + biblios.add(biblio); + } else if (qName.equals("ISSN")) { + if (electronic) + issne = getText(); + else if (print) + issnp = getText(); + electronic = false; + print = false; + + if ( (issne != null) && (issne.length() > 0) ) { + biblio.setEIssn(issne); + } else if ( (issnp != null) && (issnp.length() > 0) ) { + biblio.setIssn(issnp); + } + + issne = null; + issnp = null; + } else if (qName.equals("Volume")) { + volume = getText(); + if ( (volume != null) && (volume.length() > 0) ) + biblio.setVolume(volume); + volume = null; + } else if (qName.equals("Issue")) { + issue = getText(); + if ( (issue != null) && (issue.length() > 0) ) + biblio.setNumber(issue); + issue = null; + } else if (qName.equals("Title")) { + // full journal title + title = getText(); + if ( (title != null) && (title.length() > 0) ) + biblio.setTitle(title); + title = null; + } else if (qName.equals("ISOAbbreviation")) { + // abbreviated journal title + journalTitleAbbrev = getText(); + if ( (journalTitleAbbrev != null) && (journalTitleAbbrev.length() > 0) ) + biblio.setJournalAbbrev(journalTitleAbbrev); + journalTitleAbbrev = null; + } else if (qName.equals("ArticleTitle")) { + // article title + articleTitle = getText(); + if ( (articleTitle != null) && (articleTitle.length() > 0) ) + biblio.setArticleTitle(articleTitle); + articleTitle = null; + } else if (qName.equals("Year")) { + year = getText(); + } else if (qName.equals("Month")) { + month = getText(); + } else if (qName.equals("Day")) { + day = getText(); + } else if (qName.equals("Chemical")) { + // store the chemical + MeSHClass mesh = new MeSHClass(); + if ( (chemicalNameOfSubstance != null) && (chemicalNameOfSubstance.length() > 0) ) + mesh.setChemicalNameOfSubstance(chemicalNameOfSubstance); + if ( (chemicalRegistryNumber != null) && (chemicalRegistryNumber.length() > 0) ) + mesh.setChemicalRegistryNumber(chemicalRegistryNumber); + if ( (chemicalUI != null) && (chemicalUI.length() > 0) ) + mesh.setChemicalUI(chemicalUI); + + if ( (chemicalUI != null) && (chemicalUI.length() > 0) ) + biblio.addClass(mesh); + + chemicalUI = null; + chemicalNameOfSubstance = null; + chemicalRegistryNumber = null; + } else if (qName.equals("MeshHeading")) { + MeSHClass mesh = new MeSHClass(); + if ( (descriptorUI != null) && (descriptorUI.length() > 0) ) + mesh.setDescriptorUI(descriptorUI); + if ( (descriptorName != null) && (descriptorName.length() > 0) ) + mesh.setDescriptorName(descriptorName); + if ( (qualifierUIs != null) && (qualifierUIs.size() > 0) ) + mesh.setQualifierUIs(qualifierUIs); + if ( (qualifierNames != null) && (qualifierNames.size() > 0) ) + mesh.setQualifierNames(qualifierNames); + mesh.setMajorTopicQualifiers(majorTopicQualifiers); + mesh.setMajorTopicDescriptor(majorTopicDescriptor); + + if ( (descriptorUI != null) && (descriptorUI.length() > 0) ) + biblio.addClass(mesh); + + descriptorUI = null; + qualifierUIs = null; + descriptorName = null; + qualifierNames = null; + majorTopicDescriptor = false; + majorTopicQualifiers = null; + } else if (qName.equals("RegistryNumber")) { + chemicalRegistryNumber = getText(); + } else if (qName.equals("NameOfSubstance")) { + chemicalNameOfSubstance = getText(); + } else if (qName.equals("DescriptorName")) { + descriptorName = getText(); + } else if (qName.equals("QualifierName")) { + if (qualifierNames == null) + qualifierNames = new ArrayList(); + qualifierNames.add(getText()); + } else if (qName.equals("MedlinePgn")) { + // pain: this is the pagination type used experimentally given that this is very messy + String pagination = getText(); + if ( (pagination != null) && (pagination.length() > 0) ) { + // first we might have a "suppl.:"" prefix + pagination = pagination.replace("Suppl:", "").replace("suppl:", "").replace("Suppl", "").replace("suppl", "").trim(); + // TBD: where to capture that we are in some supplenmentary stuff at the level of pages? + + // other weirdos + pagination = pagination.replace("passim", "").trim(); + pagination = pagination.replace("CR", "").trim(); + pagination = pagination.replace("concl", "").trim(); + pagination = pagination.replace("cntd", "").trim(); + pagination = pagination.replace("discussion", "").trim(); + pagination = pagination.replace("author reply", "").trim(); + + // format is 117-26 / 121-6 / 1173-9 + // OR + // 5911-5924 + // !!! + int ind = pagination.indexOf("-"); + if (ind != -1) { + firstPage = pagination.substring(0, ind); + lastPage = pagination.substring(ind+1, pagination.length()); + // we must concatenate prefix to last page + int size = lastPage.length(); + if (size < firstPage.length()) { + lastPage = firstPage.substring(0, firstPage.length() - size) + lastPage; + } + } else { + // sometimes we have a comma... + int ind2 = pagination.indexOf(","); + if (ind2 != -1) { + firstPage = pagination.substring(0, ind2); + lastPage = pagination.substring(ind2+1, pagination.length()); + // we must concatenate prefix to last page + int size = lastPage.length(); + if (size < firstPage.length()) { + lastPage = firstPage.substring(0, firstPage.length() - size) + lastPage; + } + } else { + // we assume one page article + firstPage = pagination; + lastPage = pagination; + } + } + //System.out.println(pagination + " -> " + firstPage + " / " + lastPage); + + if ( (firstPage != null) && (firstPage.length() > 0) ) { + biblio.setStartPage(firstPage); + int firstPageVal = -1; + try { + firstPageVal = Integer.parseInt(firstPage); + } catch (Exception e) { + // logger here + //System.out.println("parsing of first page failed: " + firstPage); + } + if (firstPageVal != -1) + biblio.setStartPageInt(firstPageVal); + else { + // set the raw pagination + biblio.setPagination(pagination); + + // try also a more shallow extraction + Matcher matcher = page.matcher(pagination); + if (matcher.find()) { + if (matcher.groupCount() > 0) { + firstPage = matcher.group(0); + if ( (firstPage != null) && (firstPage.length() > 0) ) { + biblio.setStartPage(firstPage); + try { + firstPageVal = Integer.parseInt(firstPage); + } catch (Exception e) { + // logger here + //System.out.println("parsing of first page failed: " + firstPage); + } + if (firstPageVal != -1) + biblio.setStartPageInt(firstPageVal); + } + } + } + } + } + + if ( (lastPage != null) && (lastPage.length() > 0) ) { + biblio.setEndPage(lastPage); + int lastPageVal = -1; + try { + lastPageVal = Integer.parseInt(lastPage); + } catch (Exception e) { + // logger here + //System.out.println("parsing of last page failed: " + lastPage); + } + if (lastPageVal != -1) + biblio.setEndPageInt(lastPageVal); + else { + // set the raw pagination + biblio.setPagination(pagination); + + // try also a more shallow extraction + Matcher matcher = page.matcher(pagination); + if (matcher.find()) { + if (matcher.groupCount() > 1) { + lastPage = matcher.group(1); + if ( (lastPage != null) && (lastPage.length() > 0) ) { + biblio.setEndPage(lastPage); + try { + lastPageVal = Integer.parseInt(lastPage); + } catch (Exception e) { + // logger here + //System.out.println("parsing of last page failed: " + firstPage); + } + if (lastPageVal != -1) + biblio.setEndPageInt(lastPageVal); + } + } + } + } + } + } + pagination = null; + } else if (qName.equals("StartPage")) { + // this clean pagination is not used now but it is supposed to be used in the future :) + firstPage = getText(); + int firstPageVal = -1; + try { + firstPageVal = Integer.parseInt(firstPage); + } catch (Exception e) { + // logger here + //System.out.println("parsing of first page failed: " + firstPage); + } + if ( (firstPage != null) && (firstPage.length() > 0) ) + biblio.setStartPage(firstPage); + if (firstPageVal != -1) + biblio.setStartPageInt(firstPageVal); + firstPage = null; + } else if (qName.equals("EndPage")) { + // this clean pagination is not used now but it is supposed to be used in the future + lastPage = getText(); + int lastPageVal = -1; + try { + lastPageVal = Integer.parseInt(lastPage); + } catch (Exception e) { + // logger here + //System.out.println("parsing of last page failed: " + lastPage); + } + if ( (lastPage != null) && (lastPage.length() > 0) ) + biblio.setEndPage(lastPage); + if (lastPageVal != -1) + biblio.setEndPageInt(lastPageVal); + lastPage = null; + } else if (qName.equals("Language")) { + // that's a three letter code - so possibly ISO 639-2 ? + String rawLang = getText(); + if ( (rawLang != null) && (rawLang.length() > 0) ) { + // "und" is used for undetermined + if (!rawLang.equals("und")) { + // convert into usual ISO 639-1 + String langCode = LangUtil.getInstance().convertISOLang32ISOLang2(rawLang); + if (langCode != null) + biblio.setLanguage(langCode); + else + biblio.setRawLanguage(rawLang); + } + } + } else if (qName.equals("ArticleDate")) { + // best publication date, overwrite possible existing one + this.dateProcessing(biblio, "publication"); + } else if (qName.equals("PubDate")) { + // we keep it only if ArticleDate is not present + if (biblio.getPublicationDate() == null) + this.dateProcessing(biblio, "publication"); + } else if (qName.equals("DateRevised")) { + // this is the last update date for the entry normally + this.dateProcessing(biblio, "update"); + } + else if (qName.equals("LastName")) { + lastName = getText(); + } else if (qName.equals("ForeName")) { + foreName = getText(); + } else if (qName.equals("Suffix")) { + suffix = getText(); + } else if (qName.equals("Initials")) { + initials = getText(); + } else if (qName.equals("Identifier")) { + identifier = getText(); + if (inAffiliationInfo) + identifierObject = new Identifier(identifierSource, identifier); + else + authorIdentifierObject = new Identifier(identifierSource, identifier); + identifier = null; + identifierSource = null; + } else if (qName.equals("Author")) { + Person author = new Person(); + if ( (lastName != null) && (lastName.length() > 0) ) + author.setLastName(lastName); + if ( (foreName != null) && (foreName.length() > 0) ) + author.setFirstName(foreName); + if ( (suffix != null) && (suffix.length() > 0) ) + author.setSuffix(suffix); + if ( (initials != null) && (initials.length() > 0) ) + author.setInits(initials); + + if ( (authorIdentifierObject != null) && + (authorIdentifierObject.getIdentifierName() != null) && + (authorIdentifierObject.getIdentifierValue() != null) ) { + author.addIdentifier(authorIdentifierObject); + } + + if ( (affiliations != null) && (affiliations.size() > 0) ) + author.setAffiliations(affiliations); + + if (author.getLastName() != null) { + authors.add(author); + } + author = null; + lastName = null; + foreName = null; + suffix = null; + initials = null; + authorIdentifierObject = null; + affiliations = null; + } else if (qName.equals("AuthorList")) { + if ( (authors != null) && (authors.size() >0) ) + biblio.setAuthors(authors); + authors = null; + } else if (qName.equals("AffiliationInfo")) { + // create an affiliation to be attached to the current author + // affiliation is raw affiliation string, consider GROBID to add more usable affiliation/address descriptions + if ( (affiliationString != null) && (affiliationString.length() >0) ) { + Affiliation affiliation = new Affiliation(affiliationString); + if ( (identifierObject != null) && + (identifierObject.getIdentifierName() != null) && + (identifierObject.getIdentifierValue() != null) ) { + affiliation.addIdentifier(identifierObject); + } + if (affiliations == null) + affiliations = new ArrayList(); + affiliations.add(affiliation); + } + inAffiliationInfo = false; + affiliationString = null; + identifierObject = null; + } else if (qName.equals("Affiliation")) { + affiliationString = getText(); + } else if (qName.equals("AbstractText")) { + abstractString = getText(); + biblio.setAbstract(abstractString); + abstractString = null; + } else if (qName.equals("ELocationID") && validElocationTypeDOI) { + biblio.setDoi(getText()); + validElocationTypeDOI = false; + } else if (qName.equals("PublicationType")) { + biblio.setRawPublicationType(getText()); + if (publicationTypeUI != null) { + biblio.setPublicationTypeUI(publicationTypeUI); + publicationTypeUI = null; + } + } else if (qName.equals("GrantList")) { + biblio.setGrants(this.grants); + } else if (qName.equals("Grant")) { + if (currentGrant != null && this.grants != null) + grants.add(currentGrant); + currentGrant = null; + } else if (qName.equals("GrantID")) { + if (currentGrant == null) + currentGrant = new Grant(); + currentGrant.setGrantID(getText()); + } else if (qName.equals("Acronym")) { + if (currentGrant != null) + currentGrant.setAcronym(getText()); + } else if (qName.equals("Agency")) { + if (currentGrant != null) + currentGrant.setAgency(getText()); + } else if (qName.equals("Country")) { + if (currentGrant != null) + currentGrant.setCountry(getText()); + } else if (qName.equals("ArticleId")) { + if (isArticleIdList && !inReferenceList) { + if (doiType && biblio.getDoi() == null) { + biblio.setDoi(getText()); + } else if (pubmedType && biblio.getPubmedId() == null) { + biblio.setPubmedId(getText()); + } else if (piiType && biblio.getPii() == null) { + biblio.setPii(getText()); + } else if (pmcType && biblio.getPmc() == null) { + biblio.setPmc(getText()); + } + } else if (inReferenceList && currentReference != null) { + if (doiType) { + currentReference.setDoi(getText()); + } else if (pubmedType) { + currentReference.setPubmedId(getText()); + } else if (piiType) { + currentReference.setPii(getText()); + } else if (pmcType) { + currentReference.setPmc(getText()); + } + } + + doiType = false; + pubmedType = false; + piiType = false; + pmcType = false; + } else if (qName.equals("ArticleIdList")) { + isArticleIdList = false; + } else if (qName.equals("Citation")) { + String referenceString = getText(); + if (currentReference != null) + currentReference.setReferenceString(referenceString); + } else if (qName.equals("Reference") && inReferenceList) { + if (currentReference != null) { + biblio.addReference(currentReference); + } + currentReference = null; + } else if (qName.equals("ReferenceList")) { + inReferenceList = false; + } else if (qName.equals("Keyword")) { + if (currentKeyword == null) { + currentKeyword = new Keyword(); + } + currentKeyword.setValue(getText()); + biblio.addKeywordItems(currentKeyword); + currentKeyword = null; + } else if (qName.equals("KeywordList")) { + currentKeywordOrigin = null; + } + + accumulator.setLength(0); + } + + + public void startElement(String namespaceURI, + String localName, + String qName, + Attributes atts) + throws SAXException { + if (qName.equals("PubmedArticle")) { + biblio = new Biblio(); + this.grants = null; + } else if (qName.equals("NameOfSubstance")) { + int length = atts.getLength(); + + // Process each attribute + for (int i = 0; i < length; i++) { + // Get names and values for each attribute + String name = atts.getQName(i); + String value = atts.getValue(i); + + if ((name != null) & (value != null)) { + if (name.equals("UI")) { + chemicalUI = value; + } + } + } + } else if (qName.equals("DescriptorName")) { + int length = atts.getLength(); + + // Process each attribute + for (int i = 0; i < length; i++) { + // Get names and values for each attribute + String name = atts.getQName(i); + String value = atts.getValue(i); + + if ((name != null) & (value != null)) { + if (name.equals("UI")) { + descriptorUI = value; + } else if (name.equals("MajorTopicYN")) { + if (value.equals("Y")) + majorTopicDescriptor = true; + } + } + } + } else if (qName.equals("QualifierName")) { + int length = atts.getLength(); + + // Process each attribute + for (int i = 0; i < length; i++) { + // Get names and values for each attribute + String name = atts.getQName(i); + String value = atts.getValue(i); + + if ((name != null) & (value != null)) { + if (name.equals("UI")) { + if (qualifierUIs == null) + qualifierUIs = new ArrayList(); + qualifierUIs.add(value); + } else if (name.equals("MajorTopicYN")) { + if (value.equals("Y")) { + if (majorTopicQualifiers == null) + majorTopicQualifiers = new ArrayList(); + majorTopicQualifiers.add(Boolean.valueOf(true)); + } else { + if (majorTopicQualifiers == null) + majorTopicQualifiers = new ArrayList(); + majorTopicQualifiers.add(Boolean.valueOf(false)); + } + } + } + } + } else if (qName.equals("ISSN")) { + int length = atts.getLength(); + + // Process each attribute + for (int i = 0; i < length; i++) { + // Get names and values for each attribute + String name = atts.getQName(i); + String value = atts.getValue(i); + + if ((name != null) & (value != null)) { + if (name.equals("IssnType")) { + if (value.equals("Print")) + print = true; + else if (value.equals("Electronic")) + electronic = true; + } + } + } + } else if (qName.equals("AuthorList")) { + authors = new ArrayList(); + } else if (qName.equals("Author")) { + affiliations = new ArrayList(); + } else if (qName.equals("Identifier")) { + int length = atts.getLength(); + + // Process each attribute + for (int i = 0; i < length; i++) { + // Get names and values for each attribute + String name = atts.getQName(i); + String value = atts.getValue(i); + + if ((name != null) & (value != null)) { + if (name.equals("Source")) { + identifierSource = value; + } + } + } + } else if (qName.equals("AffiliationInfo")) { + inAffiliationInfo = true; + } else if (qName.equals("GrantList")) { + this.grants = new ArrayList<>(); + } else if (qName.equals("Grant")) { + currentGrant = new Grant(); + } else if (qName.equals("ELocationID")) { + // DOI, if any and valid, is here: 10.2147/CMAR.S186042 + int length = atts.getLength(); + boolean isDoi = false; + boolean isValid = false; + + // Process each attribute + for (int i = 0; i < length; i++) { + // Get names and values for each attribute + String name = atts.getQName(i); + String value = atts.getValue(i); + + if ((name != null) & (value != null)) { + if (name.equals("EIdType") && value.equals("doi")) { + isDoi = true; + } else if (name.equals("ValidYN") && value.equals("Y")) { + isValid = true; + } + } + } + + if (isDoi && isValid) + validElocationTypeDOI = true; + } else if (qName.equals("ArticleId") && (isArticleIdList || inReferenceList)) { + int length = atts.getLength(); + + // Process each attribute + for (int i = 0; i < length; i++) { + // Get names and values for each attribute + String name = atts.getQName(i); + String value = atts.getValue(i); + + if ((name != null) & (value != null)) { + if (name.equals("IdType") && value.equals("doi")) { + doiType = true; + } else if (name.equals("IdType") && value.equals("pubmed")) { + pubmedType = true; + } else if (name.equals("IdType") && value.equals("pii")) { + piiType = true; + } else if (name.equals("IdType") && value.equals("pmc")) { + pmcType = true; + } + } + } + } else if (qName.equals("ArticleIdList")) { + isArticleIdList = true; + } else if (qName.equals("ReferenceList")) { + inReferenceList = true; + } else if (qName.equals("Reference") && inReferenceList) { + currentReference = new Reference(); + } else if (qName.equals("KeywordList")) { + int length = atts.getLength(); + + // Process each attribute + for (int i = 0; i < length; i++) { + // Get names and values for each attribute + String name = atts.getQName(i); + String value = atts.getValue(i); + + if ((name != null) & (value != null)) { + if (name.equals("Owner") && value != null) { + currentKeywordOrigin = value; + } + } + } + } else if (qName.equals("Keyword")) { + currentKeyword = new Keyword(); + + int length = atts.getLength(); + + // Process each attribute + for (int i = 0; i < length; i++) { + // Get names and values for each attribute + String name = atts.getQName(i); + String value = atts.getValue(i); + + if ((name != null) & (value != null)) { + if (name.equals("MajorTopicYN") && value.equals("Y")) { + currentKeyword.setIsMajorTopic(true); + } + } + } + + if (currentKeywordOrigin != null) { + currentKeyword.setOrigin(currentKeywordOrigin); + } + } + } + + private void dateProcessing(Biblio biblio, String type) { + // try to get the best of the date information + int yearVal = -1; + int monthVal = -1; + int dayVal = -1; + + if (month != null) { + monthVal = Utilities.convertMedlineMonth(month); + } + + if (year != null) { + try { + yearVal = Integer.parseInt(year); + } catch(Exception e) { + System.err.println("Failure to parse year: " + year); + } + } + + if ((monthVal == -1) && (month != null)) { + try { + monthVal = Integer.parseInt(month); + } catch(Exception e) { + System.err.println("Failure to parse month: " + month); + } + } + + if (day != null) { + try { + dayVal = Integer.parseInt(day); + } catch(Exception e) { + System.err.println("Failure to parse day: " + day); + } + } + + Partial date = null; + try { + if (yearVal != -1) { + if (monthVal != -1) { + if (dayVal != -1) { + dayVal = Utilities.correctDay(dayVal, monthVal); + int[] values = new int[] {yearVal, monthVal, dayVal}; + List types = new ArrayList(Arrays.asList(fieldYMD)); + date = new Partial(fieldYMD, values); + } else { + int[] values = new int[] {yearVal, monthVal}; + List types = new ArrayList(Arrays.asList(fieldYM)); + date = new Partial(fieldYM, values); + } + } else { + int[] values = new int[] {yearVal}; + List types = new ArrayList(Arrays.asList(fieldY)); + date = new Partial(fieldY, values); + } + } + } catch(Exception e) { + // to log... + System.out.println(year + " / " + month + " / " + day); + e.printStackTrace(); + } + if (date != null) { + if (type.equals("publication")) + biblio.setPublicationDate(date); + else if (type.equals("update")) + biblio.setLastUpdateDate(date); + } + + year = null; + month = null; + day = null; + } +} \ No newline at end of file diff --git a/lookup/src/main/java/com/scienceminer/lookup/utils/xml/StaxParserContentHandler.java b/src/main/java/com/scienceminer/glutton/utils/xml/StaxParserContentHandler.java similarity index 88% rename from lookup/src/main/java/com/scienceminer/lookup/utils/xml/StaxParserContentHandler.java rename to src/main/java/com/scienceminer/glutton/utils/xml/StaxParserContentHandler.java index cc78807e..2b68e0b9 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/utils/xml/StaxParserContentHandler.java +++ b/src/main/java/com/scienceminer/glutton/utils/xml/StaxParserContentHandler.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.utils.xml; +package com.scienceminer.glutton.utils.xml; import org.codehaus.stax2.XMLStreamReader2; diff --git a/lookup/src/main/java/com/scienceminer/lookup/utils/xml/StaxUtils.java b/src/main/java/com/scienceminer/glutton/utils/xml/StaxUtils.java similarity index 99% rename from lookup/src/main/java/com/scienceminer/lookup/utils/xml/StaxUtils.java rename to src/main/java/com/scienceminer/glutton/utils/xml/StaxUtils.java index 0c79e123..e8728e20 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/utils/xml/StaxUtils.java +++ b/src/main/java/com/scienceminer/glutton/utils/xml/StaxUtils.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.utils.xml; +package com.scienceminer.glutton.utils.xml; import org.codehaus.stax2.XMLStreamReader2; diff --git a/lookup/src/main/java/com/scienceminer/lookup/web/LookupServiceApplication.java b/src/main/java/com/scienceminer/glutton/web/LookupServiceApplication.java similarity index 74% rename from lookup/src/main/java/com/scienceminer/lookup/web/LookupServiceApplication.java rename to src/main/java/com/scienceminer/glutton/web/LookupServiceApplication.java index ad72cfc9..9311b443 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/web/LookupServiceApplication.java +++ b/src/main/java/com/scienceminer/glutton/web/LookupServiceApplication.java @@ -1,28 +1,27 @@ -package com.scienceminer.lookup.web; +package com.scienceminer.glutton.web; import com.google.common.collect.Lists; import com.google.inject.Module; -import com.scienceminer.lookup.command.LoadCrossrefCommand; -import com.scienceminer.lookup.command.GapUpdateCrossrefCommand; -import com.scienceminer.lookup.command.LoadIstexIdsCommand; -import com.scienceminer.lookup.command.LoadPMIDCommand; -import com.scienceminer.lookup.command.LoadUnpayWallCommand; -import com.scienceminer.lookup.configuration.LookupConfiguration; -import com.scienceminer.lookup.web.healthcheck.LookupHealthCheck; -import com.scienceminer.lookup.web.module.LookupServiceModule; -import com.scienceminer.lookup.web.module.NotFoundExceptionMapper; -import com.scienceminer.lookup.web.module.ServiceExceptionMapper; -import com.scienceminer.lookup.web.module.ServiceOverloadedExceptionMapper; -import com.scienceminer.lookup.utils.crossrefclient.IncrementalLoaderTask; -import com.scienceminer.lookup.storage.lookup.MetadataLookup; -import com.scienceminer.lookup.storage.StorageEnvFactory; - -import io.dropwizard.Application; +import com.scienceminer.glutton.command.*; +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.web.healthcheck.LookupHealthCheck; +import com.scienceminer.glutton.web.module.LookupServiceModule; +import com.scienceminer.glutton.web.module.NotFoundExceptionMapper; +import com.scienceminer.glutton.web.module.ServiceExceptionMapper; +import com.scienceminer.glutton.web.module.ServiceOverloadedExceptionMapper; +import com.scienceminer.glutton.utils.crossrefclient.IncrementalLoaderTask; +import com.scienceminer.glutton.storage.lookup.CrossrefMetadataLookup; +import com.scienceminer.glutton.storage.StorageEnvFactory; + import io.dropwizard.forms.MultiPartBundle; -import io.dropwizard.setup.Bootstrap; -import io.dropwizard.setup.Environment; -import com.hubspot.dropwizard.guicier.GuiceBundle; +import io.dropwizard.core.Application; +import io.dropwizard.core.setup.Bootstrap; +import io.dropwizard.core.setup.Environment; + +//import com.hubspot.dropwizard.guicier.GuiceBundle; +import ru.vyarus.dropwizard.guice.GuiceBundle; +import com.google.inject.AbstractModule; import org.eclipse.jetty.servlets.CrossOriginFilter; import org.eclipse.jetty.servlets.QoSFilter; @@ -34,8 +33,8 @@ import com.codahale.metrics.Meter; import com.codahale.metrics.MetricRegistry; -import javax.servlet.DispatcherType; -import javax.servlet.FilterRegistration; +import jakarta.servlet.DispatcherType; +import jakarta.servlet.FilterRegistration; import java.util.Arrays; import java.util.EnumSet; import java.util.List; @@ -54,7 +53,7 @@ public final class LookupServiceApplication extends Application { private static final Logger LOGGER = LoggerFactory.getLogger(LookupConfiguration.class); private static final String RESOURCES = "/service"; - private static final String[] DEFAULT_CONF_LOCATIONS = {"../config/glutton.yml"}; + private static final String[] DEFAULT_CONF_LOCATIONS = {"config/glutton.yml"}; // ========== Application ========== @Override @@ -90,11 +89,13 @@ private void scheduleDailyUpdate(LookupConfiguration configuration, StorageEnvFa long initalDelay = duration.getSeconds(); //StorageEnvFactory storageEnvFactory = new StorageEnvFactory(configuration); - MetadataLookup metadataLookup = MetadataLookup.getInstance(storageEnvFactory); + CrossrefMetadataLookup metadataLookup = CrossrefMetadataLookup.getInstance(storageEnvFactory); final MetricRegistry metrics = new MetricRegistry(); - final Meter meter = metrics.meter("crossrefDailyUpdate"); - final Counter counterInvalidRecords = metrics.counter("crossrefDailyUpdate_rejectedRecords"); + final Meter meter = metrics.meter("crossref_daily_update_loading"); + final Counter counterInvalidRecords = metrics.counter("crossref_daily_update_rejected_records"); + final Counter counterIndexedRecords = metrics.counter("crossref_gap_update_indexed_records"); + final Counter counterFailedIndexedRecords = metrics.counter("crossref_gap_update_failed_indexed_records"); ScheduledExecutorService executor = Executors.newScheduledThreadPool(1); Runnable task = new IncrementalLoaderTask(metadataLookup, @@ -102,7 +103,9 @@ private void scheduleDailyUpdate(LookupConfiguration configuration, StorageEnvFa configuration, meter, counterInvalidRecords, - true, // with ES indexing + counterIndexedRecords, + counterFailedIndexedRecords, + true, // with indexing true); // this is daily incremental update ScheduledFuture scheduledFuture = executor.scheduleAtFixedRate(task, initalDelay, TimeUnit.DAYS.toSeconds(1), TimeUnit.SECONDS); @@ -143,15 +146,24 @@ public void run(LookupConfiguration configuration, Environment environment) thro scheduleDailyUpdate(configuration, storageEnvFactory); } - private List getGuiceModules() { + /*private List getGuiceModules() { return Lists.newArrayList(new LookupServiceModule()); + }*/ + + private AbstractModule getGuiceModules() { + return new LookupServiceModule(); } @Override public void initialize(Bootstrap bootstrap) { - GuiceBundle guiceBundle = GuiceBundle.defaultBuilder(LookupConfiguration.class) + /*GuiceBundle guiceBundle = GuiceBundle.defaultBuilder(LookupConfiguration.class) .modules(getGuiceModules()) - .build(); + .build();*/ + + GuiceBundle guiceBundle = GuiceBundle.builder() + .modules(getGuiceModules()) + .build(); + bootstrap.addBundle(guiceBundle); bootstrap.addBundle(new MultiPartBundle()); bootstrap.addCommand(new LoadUnpayWallCommand()); @@ -159,6 +171,9 @@ public void initialize(Bootstrap bootstrap) { bootstrap.addCommand(new LoadPMIDCommand()); bootstrap.addCommand(new LoadCrossrefCommand()); bootstrap.addCommand(new GapUpdateCrossrefCommand()); + bootstrap.addCommand(new LoadHALCommand()); + bootstrap.addCommand(new IndexCommand()); + bootstrap.addCommand(new HALAuditCommand()); } public static void main(String... args) throws Exception { diff --git a/lookup/src/main/java/com/scienceminer/lookup/web/healthcheck/LookupHealthCheck.java b/src/main/java/com/scienceminer/glutton/web/healthcheck/LookupHealthCheck.java similarity index 71% rename from lookup/src/main/java/com/scienceminer/lookup/web/healthcheck/LookupHealthCheck.java rename to src/main/java/com/scienceminer/glutton/web/healthcheck/LookupHealthCheck.java index 12365b5d..6a8db784 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/web/healthcheck/LookupHealthCheck.java +++ b/src/main/java/com/scienceminer/glutton/web/healthcheck/LookupHealthCheck.java @@ -1,15 +1,15 @@ -package com.scienceminer.lookup.web.healthcheck; +package com.scienceminer.glutton.web.healthcheck; import com.google.inject.Inject; import com.google.inject.Singleton; -import com.scienceminer.lookup.configuration.LookupConfiguration; -import com.scienceminer.lookup.storage.DataEngine; -import com.scienceminer.lookup.storage.StorageEnvFactory; - -import javax.ws.rs.GET; -import javax.ws.rs.Path; -import javax.ws.rs.Produces; -import javax.ws.rs.core.Response; +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.storage.DataEngine; +import com.scienceminer.glutton.storage.StorageEnvFactory; + +import jakarta.ws.rs.GET; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.Produces; +import jakarta.ws.rs.core.Response; @Path("health") diff --git a/src/main/java/com/scienceminer/glutton/web/module/LookupServiceModule.java b/src/main/java/com/scienceminer/glutton/web/module/LookupServiceModule.java new file mode 100644 index 00000000..cae38627 --- /dev/null +++ b/src/main/java/com/scienceminer/glutton/web/module/LookupServiceModule.java @@ -0,0 +1,53 @@ +package com.scienceminer.glutton.web.module; + +import com.codahale.metrics.MetricRegistry; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.inject.Binder; +import com.google.inject.Provides; +//import com.hubspot.dropwizard.guicier.DropwizardAwareModule; +import ru.vyarus.dropwizard.guice.module.support.DropwizardAwareModule; +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.storage.StorageEnvFactory; +import com.scienceminer.glutton.web.resource.DataController; +import com.scienceminer.glutton.web.resource.LookupController; +import com.scienceminer.glutton.web.resource.OAController; +import com.scienceminer.glutton.web.resource.OaIstexController; + +import jakarta.ws.rs.client.Client; +import jakarta.ws.rs.client.ClientBuilder; + +public class LookupServiceModule extends DropwizardAwareModule { + + @Override + public void configure() { + //REST + bind(LookupController.class); + bind(DataController.class); + bind(OAController.class); + bind(OaIstexController.class); + + //LMDB + bind(StorageEnvFactory.class); + } + + @Provides + protected ObjectMapper getObjectMapper() { + return environment().getObjectMapper(); + } + + @Provides + protected MetricRegistry provideMetricRegistry() { + return getMetricRegistry(); + } + + //for unit tests + protected MetricRegistry getMetricRegistry() { + return environment().metrics(); + } + + @Provides + Client provideClient() { + return ClientBuilder.newClient(); + } + +} diff --git a/lookup/src/main/java/com/scienceminer/lookup/web/module/NotFoundExceptionMapper.java b/src/main/java/com/scienceminer/glutton/web/module/NotFoundExceptionMapper.java similarity index 77% rename from lookup/src/main/java/com/scienceminer/lookup/web/module/NotFoundExceptionMapper.java rename to src/main/java/com/scienceminer/glutton/web/module/NotFoundExceptionMapper.java index f3a82eb0..8d46a7f6 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/web/module/NotFoundExceptionMapper.java +++ b/src/main/java/com/scienceminer/glutton/web/module/NotFoundExceptionMapper.java @@ -1,11 +1,11 @@ -package com.scienceminer.lookup.web.module; +package com.scienceminer.glutton.web.module; -import com.scienceminer.lookup.exception.NotFoundException; +import com.scienceminer.glutton.exception.NotFoundException; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; -import javax.ws.rs.ext.ExceptionMapper; -import javax.ws.rs.ext.Provider; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; +import jakarta.ws.rs.ext.ExceptionMapper; +import jakarta.ws.rs.ext.Provider; import java.util.HashMap; import static org.apache.commons.lang3.StringUtils.isNotBlank; diff --git a/lookup/src/main/java/com/scienceminer/lookup/web/module/ServiceExceptionMapper.java b/src/main/java/com/scienceminer/glutton/web/module/ServiceExceptionMapper.java similarity index 69% rename from lookup/src/main/java/com/scienceminer/lookup/web/module/ServiceExceptionMapper.java rename to src/main/java/com/scienceminer/glutton/web/module/ServiceExceptionMapper.java index c644b987..9094e30d 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/web/module/ServiceExceptionMapper.java +++ b/src/main/java/com/scienceminer/glutton/web/module/ServiceExceptionMapper.java @@ -1,11 +1,11 @@ -package com.scienceminer.lookup.web.module; +package com.scienceminer.glutton.web.module; -import com.scienceminer.lookup.exception.ServiceException; +import com.scienceminer.glutton.exception.ServiceException; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; -import javax.ws.rs.ext.ExceptionMapper; -import javax.ws.rs.ext.Provider; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; +import jakarta.ws.rs.ext.ExceptionMapper; +import jakarta.ws.rs.ext.Provider; import java.util.HashMap; @Provider diff --git a/lookup/src/main/java/com/scienceminer/lookup/web/module/ServiceOverloadedExceptionMapper.java b/src/main/java/com/scienceminer/glutton/web/module/ServiceOverloadedExceptionMapper.java similarity index 76% rename from lookup/src/main/java/com/scienceminer/lookup/web/module/ServiceOverloadedExceptionMapper.java rename to src/main/java/com/scienceminer/glutton/web/module/ServiceOverloadedExceptionMapper.java index 71dea5d5..cb683c55 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/web/module/ServiceOverloadedExceptionMapper.java +++ b/src/main/java/com/scienceminer/glutton/web/module/ServiceOverloadedExceptionMapper.java @@ -1,11 +1,11 @@ -package com.scienceminer.lookup.web.module; +package com.scienceminer.glutton.web.module; -import com.scienceminer.lookup.exception.ServiceOverloadedException; +import com.scienceminer.glutton.exception.ServiceOverloadedException; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; -import javax.ws.rs.ext.ExceptionMapper; -import javax.ws.rs.ext.Provider; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; +import jakarta.ws.rs.ext.ExceptionMapper; +import jakarta.ws.rs.ext.Provider; import java.util.HashMap; import static org.apache.commons.lang3.StringUtils.isNotBlank; diff --git a/lookup/src/main/java/com/scienceminer/lookup/web/resource/DataController.java b/src/main/java/com/scienceminer/glutton/web/resource/DataController.java similarity index 83% rename from lookup/src/main/java/com/scienceminer/lookup/web/resource/DataController.java rename to src/main/java/com/scienceminer/glutton/web/resource/DataController.java index 435ec87b..ce47a37c 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/web/resource/DataController.java +++ b/src/main/java/com/scienceminer/glutton/web/resource/DataController.java @@ -1,20 +1,20 @@ -package com.scienceminer.lookup.web.resource; +package com.scienceminer.glutton.web.resource; import com.codahale.metrics.annotation.Timed; import com.google.inject.Inject; import com.google.inject.Singleton; -import com.scienceminer.lookup.configuration.LookupConfiguration; -import com.scienceminer.lookup.data.IstexData; -import com.scienceminer.lookup.data.PmidData; -import com.scienceminer.lookup.storage.DataEngine; -import com.scienceminer.lookup.storage.StorageEnvFactory; +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.data.IstexData; +import com.scienceminer.glutton.data.PmidData; +import com.scienceminer.glutton.storage.DataEngine; +import com.scienceminer.glutton.storage.StorageEnvFactory; import org.apache.commons.lang3.tuple.Pair; -import javax.ws.rs.GET; -import javax.ws.rs.Path; -import javax.ws.rs.Produces; -import javax.ws.rs.QueryParam; -import javax.ws.rs.core.MediaType; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.Produces; +import jakarta.ws.rs.QueryParam; +import jakarta.ws.rs.core.MediaType; import java.util.List; import java.util.Map; diff --git a/lookup/src/main/java/com/scienceminer/lookup/web/resource/LookupController.java b/src/main/java/com/scienceminer/glutton/web/resource/LookupController.java similarity index 92% rename from lookup/src/main/java/com/scienceminer/lookup/web/resource/LookupController.java rename to src/main/java/com/scienceminer/glutton/web/resource/LookupController.java index 1dcc2ef4..2a050443 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/web/resource/LookupController.java +++ b/src/main/java/com/scienceminer/glutton/web/resource/LookupController.java @@ -1,26 +1,27 @@ -package com.scienceminer.lookup.web.resource; +package com.scienceminer.glutton.web.resource; import com.codahale.metrics.annotation.Timed; import com.google.inject.Inject; import com.google.inject.Singleton; -import com.scienceminer.lookup.configuration.LookupConfiguration; -import com.scienceminer.lookup.data.MatchingDocument; -import com.scienceminer.lookup.exception.NotFoundException; -import com.scienceminer.lookup.exception.ServiceException; -import com.scienceminer.lookup.storage.LookupEngine; -import com.scienceminer.lookup.storage.StorageEnvFactory; -import com.scienceminer.lookup.utils.grobid.GrobidClient; +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.data.MatchingDocument; +import com.scienceminer.glutton.exception.NotFoundException; +import com.scienceminer.glutton.exception.ServiceException; +import com.scienceminer.glutton.storage.LookupEngine; +import com.scienceminer.glutton.storage.StorageEnvFactory; +import com.scienceminer.glutton.utils.grobid.GrobidClient; import io.dropwizard.client.HttpClientBuilder; -import io.dropwizard.setup.Environment; +import io.dropwizard.core.setup.Environment; + import org.apache.http.client.HttpClient; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import javax.ws.rs.*; -import javax.ws.rs.container.AsyncResponse; -import javax.ws.rs.container.Suspended; -import javax.ws.rs.core.MediaType; -import javax.ws.rs.core.Response; +import jakarta.ws.rs.*; +import jakarta.ws.rs.container.AsyncResponse; +import jakarta.ws.rs.container.Suspended; +import jakarta.ws.rs.core.MediaType; +import jakarta.ws.rs.core.Response; import java.util.concurrent.TimeUnit; import static org.apache.commons.lang3.StringUtils.isBlank; @@ -59,6 +60,7 @@ public LookupController(LookupConfiguration configuration, StorageEnvFactory sto @Path("/") public void getByQueryAsync( @QueryParam("doi") String doi, + @QueryParam("halid") String halid, @QueryParam("pmid") String pmid, @QueryParam("pmc") String pmc, @QueryParam("pii") String pii, @@ -83,7 +85,7 @@ public void getByQueryAsync( if (parseReference == null) parseReference = Boolean.TRUE; - processByQuery(doi, pmid, pmc, pii, istexid, firstAuthor, atitle, + processByQuery(doi, halid, pmid, pmc, pii, istexid, firstAuthor, atitle, jtitle, volume, firstPage, year, biblio, parseReference, asyncResponse); } @@ -93,6 +95,7 @@ public void getByQueryAsync( @Path("/") public void postByQueryAsync( @FormParam("doi") String doi, + @FormParam("halid") String halid, @FormParam("pmid") String pmid, @FormParam("pmc") String pmc, @FormParam("pii") String pii, @@ -117,12 +120,12 @@ public void postByQueryAsync( if (parseReference == null) parseReference = Boolean.TRUE; - processByQuery(doi, pmid, pmc, pii, istexid, firstAuthor, atitle, + processByQuery(doi, halid, pmid, pmc, pii, istexid, firstAuthor, atitle, jtitle, volume, firstPage, year, biblio, parseReference, asyncResponse); } @Deprecated - protected void processByQueryMixedMode( + /*protected void processByQueryMixedMode( String doi, String pmid, String pmc, @@ -320,10 +323,11 @@ protected void processByQueryMixedMode( } else { throw new ServiceException(400, "The supplied parameters were not sufficient to select the query"); } - } + }*/ protected void processByQuery( String doi, + String halid, String pmid, String pmc, String pii, @@ -355,6 +359,23 @@ protected void processByQuery( } catch (NotFoundException e) { messagesSb.append(e.getMessage()); LOGGER.warn("DOI did not matched or did not pass post validation"); + //if (isBlank(halid) && isBlank(pmid)) + throw new ServiceException(404, messagesSb.toString()); + } + } + + if (isNotBlank(halid)) { + areParametersEnoughToLookup = true; + try { + final String response = lookupEngine.retrieveByHalId(halid, firstAuthor, atitle, year); + + if (isNotBlank(response)) { + asyncResponse.resume(response); + return; + } + } catch (NotFoundException e) { + messagesSb.append(e.getMessage()); + LOGGER.warn("HAL ID did not matched or did not pass post validation"); throw new ServiceException(404, messagesSb.toString()); } } @@ -526,6 +547,13 @@ public String getByDoi(@PathParam("doi") String doi) { return lookupEngine.retrieveByDoi(doi, null, null, null); } + @GET + @Produces(MediaType.APPLICATION_JSON) + @Path("/halid/{halid}") + public String getByHalId(@PathParam("halid") String halid) { + return lookupEngine.retrieveByHalId(halid, null, null, null); + } + @GET @Produces(MediaType.APPLICATION_JSON) @Path("/pmid/{pmid}") diff --git a/lookup/src/main/java/com/scienceminer/lookup/web/resource/OAController.java b/src/main/java/com/scienceminer/glutton/web/resource/OAController.java similarity index 85% rename from lookup/src/main/java/com/scienceminer/lookup/web/resource/OAController.java rename to src/main/java/com/scienceminer/glutton/web/resource/OAController.java index 24b61da6..1c957b20 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/web/resource/OAController.java +++ b/src/main/java/com/scienceminer/glutton/web/resource/OAController.java @@ -1,16 +1,16 @@ -package com.scienceminer.lookup.web.resource; +package com.scienceminer.glutton.web.resource; import com.codahale.metrics.annotation.Timed; import com.google.inject.Inject; import com.google.inject.Singleton; -import com.scienceminer.lookup.configuration.LookupConfiguration; -import com.scienceminer.lookup.data.OAResource; -import com.scienceminer.lookup.exception.ServiceException; -import com.scienceminer.lookup.storage.LookupEngine; -import com.scienceminer.lookup.storage.StorageEnvFactory; - -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.data.OAResource; +import com.scienceminer.glutton.exception.ServiceException; +import com.scienceminer.glutton.storage.LookupEngine; +import com.scienceminer.glutton.storage.StorageEnvFactory; + +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; import static org.apache.commons.lang3.StringUtils.isNotBlank; diff --git a/lookup/src/main/java/com/scienceminer/lookup/web/resource/OaIstexController.java b/src/main/java/com/scienceminer/glutton/web/resource/OaIstexController.java similarity index 86% rename from lookup/src/main/java/com/scienceminer/lookup/web/resource/OaIstexController.java rename to src/main/java/com/scienceminer/glutton/web/resource/OaIstexController.java index 363b5462..cd14cbb3 100644 --- a/lookup/src/main/java/com/scienceminer/lookup/web/resource/OaIstexController.java +++ b/src/main/java/com/scienceminer/glutton/web/resource/OaIstexController.java @@ -1,16 +1,16 @@ -package com.scienceminer.lookup.web.resource; +package com.scienceminer.glutton.web.resource; import com.codahale.metrics.annotation.Timed; import com.google.inject.Inject; import com.google.inject.Singleton; -import com.scienceminer.lookup.configuration.LookupConfiguration; -import com.scienceminer.lookup.data.OaIstexResource; -import com.scienceminer.lookup.exception.ServiceException; -import com.scienceminer.lookup.storage.LookupEngine; -import com.scienceminer.lookup.storage.StorageEnvFactory; - -import javax.ws.rs.*; -import javax.ws.rs.core.MediaType; +import com.scienceminer.glutton.configuration.LookupConfiguration; +import com.scienceminer.glutton.data.OaIstexResource; +import com.scienceminer.glutton.exception.ServiceException; +import com.scienceminer.glutton.storage.LookupEngine; +import com.scienceminer.glutton.storage.StorageEnvFactory; + +import jakarta.ws.rs.*; +import jakarta.ws.rs.core.MediaType; import static org.apache.commons.lang3.StringUtils.isNotBlank; diff --git a/src/main/resources/elasticSearch/crossref_mapping.json b/src/main/resources/elasticSearch/crossref_mapping.json new file mode 100644 index 00000000..64385eb5 --- /dev/null +++ b/src/main/resources/elasticSearch/crossref_mapping.json @@ -0,0 +1,52 @@ +{ + "properties": { + "DOI": { + "type": "text", + "analyzer": "case_insensitive_keyword" + }, + "title": { + "type": "text", + "analyzer": "case_insensitive_folding_text_stopwords" + }, + "first_author": { + "type": "text", + "analyzer": "case_insensitive_folding_keyword" + }, + "author": { + "type": "text", + "analyzer": "case_insensitive_folding_text" + }, + "first_page": { + "type": "text", + "analyzer": "case_insensitive_folding_keyword" + }, + "journal": { + "type": "text", + "analyzer": "case_insensitive_folding_text_stopwords" + }, + "abbreviated_journal": { + "type": "text", + "analyzer": "case_insensitive_folding_keyword" + }, + "volume": { + "type": "text", + "analyzer": "case_insensitive_folding_keyword" + }, + "issue": { + "type": "text", + "analyzer": "case_insensitive_folding_keyword" + }, + "year": { + "type": "text", + "analyzer": "case_insensitive_folding_keyword" + }, + "query": { + "type": "text", + "analyzer": "case_insensitive_folding_text" + }, + "bibliographic": { + "type": "text", + "analyzer": "case_insensitive_folding_text_stopwords" + } + } +} diff --git a/src/main/resources/elasticSearch/settings.json b/src/main/resources/elasticSearch/settings.json new file mode 100644 index 00000000..dc6ffd98 --- /dev/null +++ b/src/main/resources/elasticSearch/settings.json @@ -0,0 +1,48 @@ +{ + "index": { + "number_of_replicas": 0, + "refresh_interval": -1, + "codec": "best_compression" + }, + "analysis": { + "filter": { + "my_stop": { + "type": "stop", + "stopwords": "_english_" + + } + }, + "analyzer": { + "case_insensitive_keyword": { + "type": "custom", + "tokenizer": "keyword", + "filter": "lowercase" + }, + "case_insensitive_folding_keyword": { + "type": "custom", + "tokenizer": "keyword", + "filter": [ + "lowercase", + "asciifolding" + ] + }, + "case_insensitive_folding_text": { + "type": "custom", + "tokenizer": "standard", + "filter": [ + "lowercase", + "asciifolding" + ] + }, + "case_insensitive_folding_text_stopwords": { + "type": "custom", + "tokenizer": "standard", + "filter": [ + "lowercase", + "asciifolding", + "my_stop" + ] + } + } + } +} \ No newline at end of file diff --git a/src/main/resources/logback.xml b/src/main/resources/logback.xml new file mode 100644 index 00000000..476442ea --- /dev/null +++ b/src/main/resources/logback.xml @@ -0,0 +1,30 @@ + + + + + + %d{HH:mm:ss.SSS} [%thread] %-5level %logger{50} - %msg%n + + + + + + ./logs/biblio-glutton.log + + ./logs/biblio-glutton-%d{yyyy-MM-dd}.log + 5 + 100MB + + + 10MB + + + %d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n + + + + + + + + diff --git a/lookup/src/test/java/com/scienceminer/lookup/reader/IstexIdsReaderTest.java b/src/test/java/com/scienceminer/glutton/reader/IstexIdsReaderTest.java similarity index 95% rename from lookup/src/test/java/com/scienceminer/lookup/reader/IstexIdsReaderTest.java rename to src/test/java/com/scienceminer/glutton/reader/IstexIdsReaderTest.java index 6a1f33a8..dde1a5a0 100644 --- a/lookup/src/test/java/com/scienceminer/lookup/reader/IstexIdsReaderTest.java +++ b/src/test/java/com/scienceminer/glutton/reader/IstexIdsReaderTest.java @@ -1,6 +1,6 @@ -package com.scienceminer.lookup.reader; +package com.scienceminer.glutton.reader; -import com.scienceminer.lookup.data.IstexData; +import com.scienceminer.glutton.data.IstexData; import org.junit.Before; import org.junit.Test; diff --git a/lookup/src/test/java/com/scienceminer/lookup/reader/PmidReaderTest.java b/src/test/java/com/scienceminer/glutton/reader/PmidReaderTest.java similarity index 92% rename from lookup/src/test/java/com/scienceminer/lookup/reader/PmidReaderTest.java rename to src/test/java/com/scienceminer/glutton/reader/PmidReaderTest.java index dc6c4e03..8ef3d257 100644 --- a/lookup/src/test/java/com/scienceminer/lookup/reader/PmidReaderTest.java +++ b/src/test/java/com/scienceminer/glutton/reader/PmidReaderTest.java @@ -1,6 +1,6 @@ -package com.scienceminer.lookup.reader; +package com.scienceminer.glutton.reader; -import com.scienceminer.lookup.data.PmidData; +import com.scienceminer.glutton.data.PmidData; import org.junit.Before; import org.junit.Test; diff --git a/lookup/src/test/java/com/scienceminer/lookup/reader/UnpaidWallReaderTest.java b/src/test/java/com/scienceminer/glutton/reader/UnpaidWallReaderTest.java similarity index 98% rename from lookup/src/test/java/com/scienceminer/lookup/reader/UnpaidWallReaderTest.java rename to src/test/java/com/scienceminer/glutton/reader/UnpaidWallReaderTest.java index 9c4623e7..400d03d9 100644 --- a/lookup/src/test/java/com/scienceminer/lookup/reader/UnpaidWallReaderTest.java +++ b/src/test/java/com/scienceminer/glutton/reader/UnpaidWallReaderTest.java @@ -1,6 +1,6 @@ -package com.scienceminer.lookup.reader; +package com.scienceminer.glutton.reader; -import com.scienceminer.lookup.data.UnpayWallMetadata; +import com.scienceminer.glutton.data.UnpayWallMetadata; import org.junit.Before; import org.junit.Test; diff --git a/lookup/src/test/java/com/scienceminer/lookup/storage/LookupEngineTest.java b/src/test/java/com/scienceminer/glutton/storage/LookupEngineTest.java similarity index 96% rename from lookup/src/test/java/com/scienceminer/lookup/storage/LookupEngineTest.java rename to src/test/java/com/scienceminer/glutton/storage/LookupEngineTest.java index 7a1ffdee..6a459b4a 100644 --- a/lookup/src/test/java/com/scienceminer/lookup/storage/LookupEngineTest.java +++ b/src/test/java/com/scienceminer/glutton/storage/LookupEngineTest.java @@ -1,16 +1,17 @@ -package com.scienceminer.lookup.storage; +package com.scienceminer.glutton.storage; import com.google.gson.JsonElement; import com.google.gson.JsonObject; import com.google.gson.JsonParser; -import com.scienceminer.lookup.data.IstexData; -import com.scienceminer.lookup.data.PmidData; -import com.scienceminer.lookup.storage.lookup.OALookup; +import com.scienceminer.glutton.data.IstexData; +import com.scienceminer.glutton.data.PmidData; +import com.scienceminer.glutton.storage.lookup.OALookup; +import com.scienceminer.glutton.storage.lookup.HALLookup; import org.junit.Before; import org.junit.Ignore; import org.junit.Test; -import com.scienceminer.lookup.storage.lookup.IstexIdsLookup; -import com.scienceminer.lookup.storage.lookup.PMIdsLookup; +import com.scienceminer.glutton.storage.lookup.IstexIdsLookup; +import com.scienceminer.glutton.storage.lookup.PMIdsLookup; import java.util.Collections; @@ -25,6 +26,7 @@ public class LookupEngineTest { private PMIdsLookup mockPmidLookup; private IstexIdsLookup mockIstexLookup; private OALookup mockOALookup; + private HALLookup mockHALLookup; @Before public void setUp() throws Exception { @@ -33,10 +35,12 @@ public void setUp() throws Exception { mockPmidLookup = createMock(PMIdsLookup.class); mockIstexLookup = createMock(IstexIdsLookup.class); mockOALookup = createMock(OALookup.class); + mockHALLookup = createMock(HALLookup.class); target.setIstexLookup(mockIstexLookup); target.setPmidLookup(mockPmidLookup); target.setOaDoiLookup(mockOALookup); + target.setHALLookup(mockHALLookup); } @Test diff --git a/lookup/src/test/java/com/scienceminer/lookup/storage/lookup/DoiLookupTest.java b/src/test/java/com/scienceminer/glutton/storage/lookup/DoiLookupTest.java similarity index 94% rename from lookup/src/test/java/com/scienceminer/lookup/storage/lookup/DoiLookupTest.java rename to src/test/java/com/scienceminer/glutton/storage/lookup/DoiLookupTest.java index 0a43a5fb..fde5cfaa 100644 --- a/lookup/src/test/java/com/scienceminer/lookup/storage/lookup/DoiLookupTest.java +++ b/src/test/java/com/scienceminer/glutton/storage/lookup/DoiLookupTest.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.storage.lookup; +package com.scienceminer.glutton.storage.lookup; import org.junit.After; import org.junit.Before; diff --git a/lookup/src/test/java/com/scienceminer/lookup/storage/lookup/IstexLookupTest.java b/src/test/java/com/scienceminer/glutton/storage/lookup/IstexLookupTest.java similarity index 94% rename from lookup/src/test/java/com/scienceminer/lookup/storage/lookup/IstexLookupTest.java rename to src/test/java/com/scienceminer/glutton/storage/lookup/IstexLookupTest.java index 8cb7b214..21178908 100644 --- a/lookup/src/test/java/com/scienceminer/lookup/storage/lookup/IstexLookupTest.java +++ b/src/test/java/com/scienceminer/glutton/storage/lookup/IstexLookupTest.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.storage.lookup; +package com.scienceminer.glutton.storage.lookup; import org.junit.After; import org.junit.Before; diff --git a/lookup/src/test/java/com/scienceminer/lookup/utils/BinarySerialiserTest.java b/src/test/java/com/scienceminer/glutton/utils/BinarySerialiserTest.java similarity index 97% rename from lookup/src/test/java/com/scienceminer/lookup/utils/BinarySerialiserTest.java rename to src/test/java/com/scienceminer/glutton/utils/BinarySerialiserTest.java index a59e7a97..f51bf04b 100644 --- a/lookup/src/test/java/com/scienceminer/lookup/utils/BinarySerialiserTest.java +++ b/src/test/java/com/scienceminer/glutton/utils/BinarySerialiserTest.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.utils; +package com.scienceminer.glutton.utils; import org.junit.Test; diff --git a/lookup/src/test/java/com/scienceminer/lookup/utils/CompressorsTest.java b/src/test/java/com/scienceminer/glutton/utils/CompressorsTest.java similarity index 98% rename from lookup/src/test/java/com/scienceminer/lookup/utils/CompressorsTest.java rename to src/test/java/com/scienceminer/glutton/utils/CompressorsTest.java index 06ddd298..e10c5833 100644 --- a/lookup/src/test/java/com/scienceminer/lookup/utils/CompressorsTest.java +++ b/src/test/java/com/scienceminer/glutton/utils/CompressorsTest.java @@ -1,4 +1,4 @@ -package com.scienceminer.lookup.utils; +package com.scienceminer.glutton.utils; import org.junit.Test; diff --git a/lookup/src/test/java/com/scienceminer/lookup/utils/grobid/GrobidResponseStaxHandlerTest.java b/src/test/java/com/scienceminer/glutton/utils/grobid/GrobidResponseStaxHandlerTest.java similarity index 95% rename from lookup/src/test/java/com/scienceminer/lookup/utils/grobid/GrobidResponseStaxHandlerTest.java rename to src/test/java/com/scienceminer/glutton/utils/grobid/GrobidResponseStaxHandlerTest.java index d2f173e4..0a45b0dc 100644 --- a/lookup/src/test/java/com/scienceminer/lookup/utils/grobid/GrobidResponseStaxHandlerTest.java +++ b/src/test/java/com/scienceminer/glutton/utils/grobid/GrobidResponseStaxHandlerTest.java @@ -1,7 +1,7 @@ -package com.scienceminer.lookup.utils.grobid; +package com.scienceminer.glutton.utils.grobid; import com.ctc.wstx.stax.WstxInputFactory; -import com.scienceminer.lookup.utils.xml.StaxUtils; +import com.scienceminer.glutton.utils.xml.StaxUtils; import org.codehaus.stax2.XMLStreamReader2; import org.junit.Before; import org.junit.Test; diff --git a/lookup/src/test/java/com/scienceminer/lookup/web/resource/LookupControllerTest.java.bak b/src/test/java/com/scienceminer/glutton/web/resource/LookupControllerTest.java.bak similarity index 100% rename from lookup/src/test/java/com/scienceminer/lookup/web/resource/LookupControllerTest.java.bak rename to src/test/java/com/scienceminer/glutton/web/resource/LookupControllerTest.java.bak diff --git a/lookup/src/test/resources/com/scienceminer/lookup/reader/sample-istex-ids.json.gz b/src/test/resources/com/scienceminer/glutton/reader/sample-istex-ids.json.gz similarity index 100% rename from lookup/src/test/resources/com/scienceminer/lookup/reader/sample-istex-ids.json.gz rename to src/test/resources/com/scienceminer/glutton/reader/sample-istex-ids.json.gz diff --git a/src/test/resources/hal1.tei.xml b/src/test/resources/hal1.tei.xml new file mode 100644 index 00000000..d253d984 --- /dev/null +++ b/src/test/resources/hal1.tei.xml @@ -0,0 +1,682 @@ + + + + + + + + + + HAL TEI export of inserm-00444410 + + + + + + CCSD + + + + Distributed under a Creative Commons Attribution 4.0 International License + + + + + + + + + +

HAL API platform

+ + + + + + + + + + + + + + + + + + Studies on the mechanism of RNAi-dependent heterochromatin assembly. + + + + + + Danesh + + Moazed + + + + 360195-0 + + + + + + + + + + Marc + + Bühler + + + + 360211-0 + + + + + + + + + + S. M. + + Buker + + + + 435145-0 + + + + + + + + + + Serafin + + U. + + Colmenares + + + + 435146-0 + + + + + + + + + + E. L. + + Gerace + + + + 435147-0 + + + + + + + + + + S. A. + + Gerber + + + + 435148-0 + + + + + + + + + + E.-J. E. + + Hong + + + + 435149-0 + + + + + + + + + + Mohammad + + R. + + Motamedi + + + + 435150-0 + + + + + + + + + + André + + Verdel + + + + e1d9764e9b28b89ea3b7178aad37e8db + + univ-grenoble-alpes.fr + + 760474 + + 360191-760474 + + https://orcid.org/0000-0001-6048-3794 + + https://www.idref.fr/065126343 + + + + + + + + + + J. + + Villén + + + + 435151-0 + + + + + + + + + + Serge + + P. + + Gygi + + + + 435152-0 + + + + + + + + + + Andre + + Verdel + + + + 7199d1be51e9bb88fbbd73645c4e9890 + + ujf-grenoble.fr.invalid + + + + + + + + + + 2010-01-06 15:30:32 + + 2010-01-07 14:46:18 + + 2010-01-07 14:46:18 + + 2006 + + + + + + + + contributor + + + + + + Andre + + Verdel + + + + 7199d1be51e9bb88fbbd73645c4e9890 + + ujf-grenoble.fr.invalid + + + + + + + + + + CCSD + + inserm-00444410 + + https://inserm.hal.science/inserm-00444410 + + moazed:inserm-00444410 + + <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, 2006, 71, pp.461-71. <a target="_blank" href="https://dx.doi.org/10.1101/sqb.2006.71.044">&#x27E8;10.1101/sqb.2006.71.044&#x27E9;</a> + + Cold Spring Harbor Symposia on Quantitative Biology, 2006, 71, pp.461-71. &#x27E8;10.1101/sqb.2006.71.044&#x27E9; + + + + + + INSERM - Institut national de la santé et de la recherche médicale + + + + + + International + + No + + Yes + + + + + + + + + + Studies on the mechanism of RNAi-dependent heterochromatin assembly. + + + + + + Danesh + + Moazed + + + + 360195-0 + + + + + + + + + + Marc + + Bühler + + + + 360211-0 + + + + + + + + + + S. M. + + Buker + + + + 435145-0 + + + + + + + + + + Serafin + + U. + + Colmenares + + + + 435146-0 + + + + + + + + + + E. L. + + Gerace + + + + 435147-0 + + + + + + + + + + S. A. + + Gerber + + + + 435148-0 + + + + + + + + + + E.-J. E. + + Hong + + + + 435149-0 + + + + + + + + + + Mohammad + + R. + + Motamedi + + + + 435150-0 + + + + + + + + + + André + + Verdel + + + + e1d9764e9b28b89ea3b7178aad37e8db + + univ-grenoble-alpes.fr + + 760474 + + 360191-760474 + + https://orcid.org/0000-0001-6048-3794 + + https://www.idref.fr/065126343 + + + + + + + + + + J. + + Villén + + + + 435151-0 + + + + + + + + + + Serge + + P. + + Gygi + + + + 435152-0 + + + + + + + + + + 3991 + + 0091-7451 + + Cold Spring Harbor Symposia on Quantitative Biology + + + + Cold Spring Harbor Laboratory; 1999 + + 71 + + 461-71 + + 2006 + + + + + + 10.1101/sqb.2006.71.044 + + 17381328 + + + + + + + + + + English + + + + + + Centromere + + Chromatin Assembly and Disassembly + + RNA, Small Interfering + + Schizosaccharomyces + + Schizosaccharomyces pombe Proteins + + Chromosomes, Fungal + + Genes, Fungal + + Heterochromatin + + Models, Biological + + Models, Genetic + + Multiprotein Complexes + + RNA Interference + + RNA, Fungal + + Life Sciences [q-bio]/Genetics + + Journal articles + + Journal articles + + Journal articles + + + + + +

Assembly of heterochromatin at centromeric DNA regions in the fission yeast Schizosaccharomyces pombe involves an intimate interplay between chromatin modifying complexes and components of the RNAi pathway. The RNA-induced transcriptional silencing (RITS) complex, containing Chp1, Ago1, Tas3, and centromeric siRNAs, localizes to centromeric DNA repeats and is required for the assembly and maintenance of heterochromatin. RITS brings together two types of molecular recognition modules: a chromodomain protein, which binds to lysine 9 methylated histone H3 (H3K9), and Argonaute, which binds to specific sequences by siRNA-directed base-pairing interactions. The RNA-directed RNA polymerase complex (RDRC), composed of Rdp1, the Hrr1 helicase, and the Cid12 Poly(A) polymerase family member, synthesizes double-stranded RNA and creates the substrate for Dicer to generate siRNAs. RDRC physically associates with RITS, and both complexes localize to noncoding centromeric RNAs and centromeric DNA repeats, suggesting that recognition of nascent RNA transcripts may be involved in localization of these complexes to specific chromosome regions. In support of this possibility, tethering of the RITS complex to the transcript of the normally euchromatic ura4 (+) gene results in siRNA generation and RNAi- and heterochromatin-dependent silencing of the ura4 (+) gene. Finally, silencing of a subset of endogenous and transgene promoters within heterochromatic DNA domains occurs by RNAi-dependent degradation of nascent transcripts by a mechanism that we have termed co-transcriptional gene silencing (CTGS).

+ + + + + + + + + + + + + + + + + + Department of cell biology + + + +
+ + Boston, MA 02115 + + + +
+ + + + + + + + + + + + + + https://ror.org/03wevmz92 + + Harvard Medical School [Boston] + + HMS + + + +
+ + 25 Shattuck Street Boston, MA 02115 + + + +
+ + http://www.hms.harvard.edu + + + + + + + + + + + + diff --git a/lookup/src/test/resources/sample.grobid-2.xml b/src/test/resources/sample.grobid-2.xml similarity index 100% rename from lookup/src/test/resources/sample.grobid-2.xml rename to src/test/resources/sample.grobid-2.xml diff --git a/lookup/src/test/resources/sample.grobid-3.xml b/src/test/resources/sample.grobid-3.xml similarity index 100% rename from lookup/src/test/resources/sample.grobid-3.xml rename to src/test/resources/sample.grobid-3.xml diff --git a/lookup/src/test/resources/sample.grobid.xml b/src/test/resources/sample.grobid.xml similarity index 100% rename from lookup/src/test/resources/sample.grobid.xml rename to src/test/resources/sample.grobid.xml diff --git a/lookup/src/test/resources/unpaywall_sample.json.gz b/src/test/resources/unpaywall_sample.json.gz similarity index 100% rename from lookup/src/test/resources/unpaywall_sample.json.gz rename to src/test/resources/unpaywall_sample.json.gz diff --git a/lookup/data/test/Readme.md b/test/Readme.md similarity index 100% rename from lookup/data/test/Readme.md rename to test/Readme.md diff --git a/lookup/data/test/biblio.data.article.test.csv b/test/biblio.data.article.test.csv similarity index 100% rename from lookup/data/test/biblio.data.article.test.csv rename to test/biblio.data.article.test.csv diff --git a/lookup/data/test/biblio.data.journals.test.csv b/test/biblio.data.journals.test.csv similarity index 100% rename from lookup/data/test/biblio.data.journals.test.csv rename to test/biblio.data.journals.test.csv diff --git a/lookup/data/test/biblioList.shuf.csv b/test/biblioList.shuf.csv similarity index 100% rename from lookup/data/test/biblioList.shuf.csv rename to test/biblioList.shuf.csv diff --git a/lookup/data/test/biblioList.shuf.txt b/test/biblioList.shuf.txt similarity index 100% rename from lookup/data/test/biblioList.shuf.txt rename to test/biblioList.shuf.txt