Mathscinet search is not working

[TimAlderson]

JabRef version

5.12 (latest release)

Operating system

Windows

Details on version and operating system

No response

Checked with the latest development build (copy version output from About dialog)

• I made a backup of my libraries before testing the latest development version.
• I have tested the latest development version and the problem persists

Steps to reproduce the behaviour

Was #10499 closed because it was fixed, or because work is not planned?

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Perform Web search Mathscinet in Jabref

Appendix

...

Log File

Error:
org.jabref.logic.importer.FetcherException: An internal parser error occurred while fetching from https://mathscinet.ams.org/mathscinet/api/publications/search?query=algebraic+geometric+codes+basic+notions&currentPage=1&pageSize=100
at [email protected]/org.jabref.logic.importer.SearchBasedParserFetcher.getBibEntries(Unknown Source)
at [email protected]/org.jabref.logic.importer.SearchBasedParserFetcher.performSearch(Unknown Source)
at [email protected]/org.jabref.logic.importer.SearchBasedFetcher.performSearch(Unknown Source)
at [email protected]/org.jabref.gui.importer.fetcher.WebSearchPaneViewModel.lambda$search$2(Unknown Source)
at [email protected]/org.jabref.gui.util.BackgroundTask$1.call(Unknown Source)
at [email protected]/org.jabref.gui.util.DefaultTaskExecutor$1.call(Unknown Source)
at [email protected]/javafx.concurrent.Task$TaskCallable.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: org.jabref.logic.importer.ParseException: Error when parsing entry
at [email protected]/org.jabref.logic.importer.fetcher.MathSciNet.lambda$getParser$0(Unknown Source)
... 13 more
Caused by: kong.unirest.json.JSONException: JSONObject["all"] not found.
at [email protected]/kong.unirest.json.JSONObject.getProperty(Unknown Source)
at [email protected]/kong.unirest.json.JSONObject.getJSONObject(Unknown Source)
... 14 more

[TimAlderson]

Sorry..wrong log file. Here is the file from the most recent :

org.jabref.logic.importer.FetcherException: An internal parser error occurred while fetching from https://mathscinet.ams.org/mathscinet/api/publications/search?query=algebraic+geometric+codes+basic+notions&currentPage=1&pageSize=100
at [email protected]/org.jabref.logic.importer.SearchBasedParserFetcher.getBibEntries(Unknown Source)
at [email protected]/org.jabref.logic.importer.SearchBasedParserFetcher.performSearch(Unknown Source)
at [email protected]/org.jabref.logic.importer.SearchBasedFetcher.performSearch(Unknown Source)
at [email protected]/org.jabref.gui.importer.fetcher.WebSearchPaneViewModel.lambda$search$2(Unknown Source)
at [email protected]/org.jabref.gui.util.BackgroundTask$1.call(Unknown Source)
at [email protected]/org.jabref.gui.util.DefaultTaskExecutor$1.call(Unknown Source)
at [email protected]/javafx.concurrent.Task$TaskCallable.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: org.jabref.logic.importer.ParseException: Error when parsing entry
at [email protected]/org.jabref.logic.importer.fetcher.MathSciNet.lambda$getParser$0(Unknown Source)
... 13 more
Caused by: kong.unirest.json.JSONException: JSONObject["all"] not found.
at [email protected]/kong.unirest.json.JSONObject.getProperty(Unknown Source)
at [email protected]/kong.unirest.json.JSONObject.getJSONObject(Unknown Source)
... 14 more

[Siedlerchr]

It would be helpful if you could execute the request in the browser and send/paste us the json file as response so we can look at it. Problem is that we currently don't have a subscription to mathcinet and could not verify this

[TimAlderson]

Thank you for the reply.
I have been searching how to extract a json file using Firefox, but have been unable to figure it out. Any chance of a hint on how to do that?

[Siedlerchr]

It should be possible using the Developer Tools (F12):
(It's German, but basically network analysis tab -> then select the request where it shows json -> Right click -> Save answer should give the json

[TimAlderson]

Thank you.
Here are the results from facets and search respectively:

{"authors":[],"journals":[],"entryTypes":[],"itemTypes":[],"reviewStatuses":[],"publicationTypes":[],"primaryClassifications":[],"publicationYears":[],"institutions":[],"statuses":[]}

{"results":[],"total":0}

I performed another search which had more than 0 results (snip below). Is there a file that is more helpful than those above?

[Siedlerchr]

The json for the search with more than zero results would be nice!

[TimAlderson]

Facets:

{"authors":[{"id":"758603","value":"Alderson, Tim L.","total":27},{"id":"692091","value":"Mellinger, Keith E.","total":9},{"id":"42380","value":"Bruen, Aiden A.","total":4},{"id":"50285","value":"Cohen, Gérard D.","total":1},{"id":"615685","value":"Gács, András","total":1},{"id":"1068150","value":"Huntemann, Svenja","total":1},{"id":"1251963","value":"Neri, Alessandro<sup>1</sup>","total":1},{"id":"149440","value":"Rodier, François","total":1},{"id":"863999","value":"Shi, Minjia","total":1},{"id":"191601","value":"Silverman, Robert","total":1},{"id":"225546","value":"Solé, Patrick","total":1},{"id":"1276838","value":"Zhu, Hongwei<sup>1</sup>","total":1}],"journals":[{"id":"6036","value":"Des. Codes Cryptogr.","total":5},{"id":"2292","value":"IEEE Trans. Inform. Theory","total":3},{"id":"6241","value":"Adv. Math. Commun.","total":2},{"id":"4449","value":"Appl. Algebra Engrg. Comm. Comput.","total":2},{"id":"643","value":"Discrete Math.","total":2},{"id":"5510","value":"Ann. Comb.","total":1},{"id":"6137","value":"Antarct. J. Math.","total":1},{"id":"7425","value":"Atl. Electron. J. Math.","total":1},{"id":"4117","value":"Bull. Inst. Combin. Appl.","total":1},{"id":"615","value":"Discrete Appl. Math.","total":1},{"id":"4633","value":"Electron. J. Combin.","total":1},{"id":"4801","value":"Finite Fields Appl.","total":1},{"id":"6154","value":"Innov. Incidence Geom.","total":1},{"id":"7248","value":"Int. J. Inf. Coding Theory","total":1},{"id":"1833","value":"J. Combin. Theory Ser. A","total":1},{"id":"5169","value":"SIAM J. Discrete Math.","total":1},{"id":"8218","value":"Trans. Comb.","total":1}],"entryTypes":[],"itemTypes":[],"reviewStatuses":[{"id":"Reviewed","value":"Reviewed","total":20},{"id":"Summary","value":"Summary","total":10},{"id":"Indexed","value":"Indexed","total":1}],"publicationTypes":[{"id":"Journal Article","value":"Journal Article","total":26},{"id":"Book Collection","value":"Book Collection","total":2},{"id":"Book Collection Article","value":"Book Collection Article","total":2},{"id":"Thesis","value":"Thesis","total":1}],"primaryClassifications":[{"id":"94","value":"Information and communication theory, circuits","total":26},{"id":"51","value":"Geometry ","total":3},{"id":"11","value":"Number theory","total":1}],"publicationYears":[{"id":"2020","value":"2020","total":1},{"id":"2019","value":"2019","total":4},{"id":"2018","value":"2018","total":1},{"id":"2014","value":"2014","total":1},{"id":"2011","value":"2011","total":1},{"id":"2010","value":"2010","total":3},{"id":"2009","value":"2009","total":2},{"id":"2008","value":"2008","total":8},{"id":"2007","value":"2007","total":5},{"id":"2006","value":"2006","total":2},{"id":"2005","value":"2005","total":2},{"id":"2002","value":"2002","total":1}],"institutions":[{"id":"Department of Mathematics, University of New Brunswick","value":"Department of Mathematics, University of New Brunswick","total":21},{"id":"Department of Mathematics, University of Mary Washington","value":"Department of Mathematics, University of Mary Washington","total":9},{"id":"Department of Electrical and Computer Engineering, University of Calgary","value":"Department of Electrical and Computer Engineering, University of Calgary","total":4},{"id":"Department of Mathematics and Statistics, University of New Brunswick","value":"Department of Mathematics and Statistics, University of New Brunswick","total":4},{"id":"Department of Computer Science, Eötvös Loránd University (ELTE)","value":"Department of Computer Science, Eötvös Loránd University (ELTE)","total":1},{"id":"Department of Mathematics and Statistics, Wright State University","value":"Department of Mathematics and Statistics, Wright State University","total":1},{"id":"Institut de Mathématiques de Luminy, Centre National de la Recherche Scientifique (CNRS)","value":"Institut de Mathématiques de Luminy, Centre National de la Recherche Scientifique (CNRS)","total":1},{"id":"Laboratoire d'Analyse, Géométrie et Applications (LAGA), Université de Paris VIII (Université Paris 8 Vincennes-Saint-Denis)","value":"Laboratoire d'Analyse, Géométrie et Applications (LAGA), Université de Paris VIII (Université Paris 8 Vincennes-Saint-Denis)","total":1},{"id":"Laboratory of Intelligent Computing and Signal Processing, Anhui University","value":"Laboratory of Intelligent Computing and Signal Processing, Anhui University","total":1},{"id":"Mathematisches Institut (I-Math), Universität Zürich","value":"Mathematisches Institut (I-Math), Universität Zürich","total":1},{"id":"School of Mathematics, Anhui University","value":"School of Mathematics, Anhui University","total":1},{"id":"University of New Brunswick","value":"University of New Brunswick","total":1},{"id":"École Nationale Supérieure de Télécommunications (Telecom ParisTech)","value":"École Nationale Supérieure de Télécommunications (Telecom ParisTech)","total":1}],"statuses":[]}

Search:

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Theory"},"volSlash":"N","isbn":null,"elementOrd":null},"translatedIssue":null},"book":null,"reviewer":{"public":true,"reviewers":[{"authId":889610,"rvrCode":85231,"name":"Jitman, Somphong"}]},"paging":{"paging":{"text":"5414--5418"},"translatedPaging":null},"counts":{"cited":2},"itemType":"Reviewed","articleUrl":"https://doi.org/10.1109/TIT.2020.2977319","openURL":{"imageLink":"http://www.lib.unb.ca/img/asin/res20x150.gif","targetLink":"https://unb.on.worldcat.org/atoztitles/link?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&rfr_id=info:sid/ams.org:MathSciNet&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft_id=info:doi/10.1109%2FTIT.2020.2977319&rft.aufirst=Tim&rft.auinit=TL&rft.auinit1=T&rft.auinitm=L&rft.aulast=Alderson&rft.genre=article&rft.issn=00189448&rft.title=Institute of Electrical and Electronics Engineers  Transactions on Information Theory&rft.atitle=On the weights of general MDS codes&rft.stitle=IEEE Trans  Inform  Theory&rft.volume=66&rft.date=2020&rft.spage=5414&rft.epage=5418&rft.pages=5414-5418&rft.issue=9&rft.jtitle=Institute of Electrical and Electronics Engineers  Transactions on Information Theory","textLink":""},"prePubl":null,"public":true},{"mrnumber":4019905,"titles":{"title":"$n$-dimensional optical orthogonal codes, bounds and optimal constructions","translatedTitle":null},"entryType":"J","primaryClass":{"code":"94B65","description":"Bounds on codes"},"authors":[{"id":758603,"name":"Alderson, T. 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[Siedlerchr]

Thanks a lot, this is really helpful!
Judging from the json, we need to add a new parser for the search results
Steps for implementation

1. Add a check if we have key all in response .

   jabref/src/main/java/org/jabref/logic/importer/fetcher/MathSciNet.java

   Lines 118 to 119 in 2a7fc1a

   	var element = node.getObject();
   	JSONArray entriesArray = element.getJSONObject("all").getJSONArray("results");

2. Add a new else if for the search result case
3. Create a new MathSciNetParser + Test using the provided json
4. Parse the json and return bib entries

[koppor]

Older issue: #10499

[subhramit]

Hi, I'd like to work on this. Would be great if I could be assigned!

[github-actions]

As a general advice for newcomers: check out Contributing for a start. Also, guidelines for setting up a local workspace is worth having a look at.

Feel free to ask here at GitHub, if you have any issue related questions. If you have questions about how to setup your workspace use JabRef's Gitter chat. Try to open a (draft) pull-request early on, so that people can see you are working on the issue and so that they can see the direction the pull request is heading towards. This way, you will likely receive valuable feedback.

[subhramit]

Hi, so I was writing the new parser. This might be a dumb question (I am new to this), but could you clarify to me the difference between facets and results, and whether both are a part of the results? I wasn't able to understand which json format out of the two should be parsed finally.

[Siedlerchr]

Hi, the search json as we use the search endpoint

Facets seem to be filter data, e.g. a list of all authors or journals in the search results you can then refine your search results by (at least on the website).

[subhramit]

@Siedlerchr got it, tysm!

[subhramit]

Another question. In the existing MathSciNet.java lines 121-122 (linked below), the following is present:
jabref/src/main/java/org/jabref/logic/importer/fetcher/MathSciNet.java

String bibTexFormat = entriesArray.getJSONObject(i).getString("bibTexFormat");
entries.addAll(bibtexParser.parseEntries(bibTexFormat));

This assumes that there is a "bibTexFormat" field in the JSON object that contains a string representing the complete BibTeX entry. The value of that field is retrieved and parsed using the BibtexParser. However, if the JSON format doesn't include the bibTexFormat field or if the field doesn't contain a valid BibTeX string, these lines would fail to parse the entries correctly. And that is the case with the json for "search" as posted above by @TimAlderson . So correct me if I'm wrong, is a conversion mechanism needed for both the "all" case and the "results" case? Or is there a simpler way?

[subhramit]

(With reference to my last comment)
This is one way I've thought of it (an example for "titles" in the json):

else if (element.has("results")) {
    JSONArray entriesArray = element.getJSONArray("results");
    for (int i = 0; i <entriesArray.length(); i++) {
        JsonNode entryNode = entriesArray.getJSONObject(i);
        if (entryNode.has("titles")) {
            String title = entryNode.getObject("titles").getString("title");
            BibEntry bibEntry = new BibEntry();
            bibEntry.setField(StandardField.TITLE, title);
            entries.add(bibEntry);
        }
    }
}

and similarly for the other keys(fields).

[Siedlerchr]

Yes, exactly.
You need to write a new Parser/Convert for all fields present I suggest you create it as new Standalone Parser class. you can take some inspiration from CrossRef/BiodiversityLibrary/Lobid They all work with json

jabref/src/main/java/org/jabref/logic/importer/fetcher/CrossRef.java

Line 121 in 403b8de

private BibEntry jsonItemToBibEntry(JSONObject item) throws ParseException {

[subhramit]

I have been able to fix it :)
I'll create a pull request soon after reading the formality guidelines.
This will be my first one, thank you @Siedlerchr @koppor for the opportunity and help! I'm new into open source and already loving the community.

[Siedlerchr]

@subhramit Yeah! That sounds great! You're welcome! If something is unclear in the guides, just tell us or if you have any questions feel free to ask!