A BrAPI-powered bulk germplasm search API server and website
This project is packaged as a node module that includes a small Express web server that runs the search API server and serves the search web page.
To install the package globally directly from GitHub:
npm install -g git+https://[email protected]/TriticeaeToolbox/BrAPI-germplasm-search.git
This will install the executable brapi-germplasm-search which can be used to start the server.
The default configuration options are read from the config.json file in the root of
the project directory. A config.local.json file can be placed in this same directory
and properties found in this file will override the default values.
Available Configuration Options:
- port: the port the web server will listen on
- databases: an array of objects containting pre-configured BrAPI database options
- name: (required) Database name
- address: (required) Database BrAPI endpoint address
- params: an object of additional query params to provide to the BrAPI
GET/germplamcall - version: Database version string (vx.y) (Defaults to v1 if not provided)
- auth_token: BrAPI auth token, if one is required for the BrAPI
GET/germplasmcall - call_limit: The max number of simultaneous connections
- cache:
persistent-cacheoptions- base: The base directory where persistent-cache will save its caches.
- name: The name of the cache. Determines the name of the created folder where the data is stored, which is just base + name.
- duration: The amount of milliseconds a cache entry should be valid for. If not set, cache entries are not invalidated (stay until deleted).
- memory: The amount of milliseconds a cache entry should be valid for. If not set, cache entries are not invalidated (stay until deleted).
- persist: Whether the cache should be persistent, aka if it should write its data to the disk for later use or not. Set this to false to create a memory-only cache.
- auto_update: A cron-like format for scheduling an auto-update of the cache (default: Sundays at 2AM).
- chunk_size: The (max) number of items to store in each chunk of the cache for a single server (default: 50000).
- search: an object default search options (all of these can be overriden as parameters to individual search queries
- database_terms: the database terms to include in the search
- name: germplasm name (default:
true) - synonyms: germplasm alternate names (default:
true) - accession_numbers: germplasm accession numbers (default:
true)
- name: germplasm name (default:
- search_routines: the search routines to use in the search
- exact: find exact matches between search and database terms (default:
true) - punctuation: find matches that are the same after non-alphanumeric characters are removed (default:
false) - accents: find matches that are the same when special characters, such as accented letters, are replaced with simplified characters (default:
false) - substring: find database terms that contain the search term or are contained within the search term (default:
false) - prefix: find matches that are the same when prefixes have been removed (default:
false) - edit_distance: find matches where the edit distance between terms is within the max edit distance (default:
false)
- exact: find exact matches between search and database terms (default:
- search_routine_options: additional options used for individual search routines
- substring:
- substring_length_min: the minimum length of a term to be included as a substring match (default:
3)
- substring_length_min: the minimum length of a term to be included as a substring match (default:
- prefix:
- prefixes: default prefixes to include (default:
[]) - find_db_prefixes: scan the database terms to find common prefixes (default:
true) - prefix_length_min: when finding db prefixes, the minimum length of a prefix to include (default:
2) - prefix_length_max: when finding db prefixes, the maximum length of a prefix to include (default:
5) - threshold: when finding db prefixes, the minimum number of times a prefix is used before it is included (default:
250)
- prefixes: default prefixes to include (default:
- edit_distance:
- max_edit_distance: the maximum number of changes for the edit distance comparison (default:
2)
- max_edit_distance: the maximum number of changes for the edit distance comparison (default:
- substring:
- return_records: when
truethe search results will include the full germplasm record of each math (default:false) - case_sensitive: when
truethe search will performed with case sensitivity (default:false)
- database_terms: the database terms to include in the search
The website can accept a number of query params that can be used to set the initial search parameters.
Available Query Params:
The following query params will set the initial database properties:
- db: set the selected database by database index or name
- db_address: the BrAPI database address (will set the selected database to 'Custom')
- db_params: A URL encoded string of new-line separated query params in the form of
key=value.- Encoded:
commonCropName%3DWHEAT%0AcountryOfOriginCode%3DUSA - Original:
- Encoded:
commonCropName=WHEAT
countryOfOriginCode=USA
- db_version: the BrAPI database version (will set the selected database to 'Custom')
- db_auth_token: the BrAPI database auth token (will set the selected database to 'Custom')
- db_call_limit: the BrAPI database call limit (will set the selected database to 'Custom')
- force: when set to
1,trueoronfresh germplasm records will be downloaded from the database (otherwise cached records will be used, if available) - case_sensitive: when set to
0,false, oroffthe case sensitive search will be disabled
The following query params use boolean values to toggle the initial search options
(1, true, on = enabled; 0, false, off = disabled):
- name: toggle the name database term type
- synonyms: toggle the synonyms database term type
- accession_numbers: toggle the accession numbers database term type
- exact: toggle the exact match search routine
- punctuation: toggle the punctuation removal search routine
- accents: toggle the special character replacement search routine
- substring: toggle the substring match search routine
- prefix: toggle the prefix removal search routine
- edit_distance: toggle the edit distance comparison search routine
The following query params set the values for specific search routine options
- substring_length_min: (integer) the minimum length of a term to include it as a substring match
- prefixes: (array) used to set custom prefixes
- find_db_prefixes: (boolean) used to toggle the function to find common prefixes from the database terms
- prefix_length_min: (integer) when finding database prefixes, set the minimum length of a prefix
- prefix_length_max: (integer) when finding database prefixes, set the maximum length of a prefix
- threshold: (integer) when finding database prefixes, set the min number of times a prefix occurs before it counts
- max_edit_distance: (integer) set the max edit distance used by the edit distance comparison search routine
The term query param can be used one or more times to specify the search term(s).
When the auto query param is set to 1/true/on the search will start automatically
with the default and provided search parameters.
The RESTful API is available at {{host}}/api with endpoints that can be used to get the list of pre-configured
databases, get the germplasm cache status, update a germplasm cache, start a search and get pending job status
information or results.
Get a list of the database properties for all of the pre-configured BrAPI databases.
Response:
{
"status": "success",
"response": [
{
"name": "T3/Wheat",
"address": "https://wheat.triticeaetoolbox.org/brapi/v1",
"version": "v1.3",
"call_limit": 10
},
{
"name": "T3/Oat",
"address": "https://oat.triticeaetoolbox.org/brapi/v1",
"version": "v1.3",
"call_limit": 10
}
]
}Get the cache status (when the cache was saved and the number of database terms) for all of the cached databases (or the one specified by its address)
Additional server query parameters can be provided as query parameters to this API call.
Response: /cache
{
"status": "success",
"response": [
{
"address": "http://localhost:8080/brapi/v1",
"saved": "2020-05-25T18:00:55.350Z",
"terms": 28869
},
{
"address": "http://localhost:8081/brapi/v1",
"saved": "2020-05-25T18:03:15.374Z",
"terms": 63320
}
]
}Response: /cache?address=http://localhost:8080/brapi/v1
{
"status": "success",
"response": {
"saved": "2020-05-25T17:49:34.592Z",
"terms": 28869
}
}Response: /cache?address=https://oat.triticeaetoolbox.org/brapi/v1&commonCropName=oat
{
"status": "error",
"error": {
"code": 404,
"message": "Cache not found for address https://oat.triticeaetoolbox.org/brapi/v1"
}
}Update the cache of germplasm records for the database specified in the request body. Since this is
long running-task the request is added to a job queue and the response will include the job id. Use the
/job/:id?results=false endpoint to get the status of the job to determine when the update is complete.
Body:
{
"address": "http://localhost:8080/brapi/v1",
"params": {},
"version": "v1.3",
"auth_token": "",
"call_limit": 10
}Response:
{
"status": "queued",
"job": {
"id": "61d43d31-3dbb-470c-80dd-43372bb796ed"
}
}Get the cached record of the specified germplasm from the specified database.
The germplasm is specified by its germplasmDbId and the database is
specified by its BrAPI address.
NOTE: The format of the record response will depend on the BrAPI version of the specified BrAPI server.
Response: /germplasm/218808?address=https://wheat.triticeaetoolbox.org/brapi/v1
{
"status": "success",
"response": {
"instituteName": "National Small Grains Collection",
"breedingMethodDbId": null,
"subtaxaAuthority": null,
"germplasmPUI": "PI 367088,http://triticumbase.sgn.cornell.edu/stock/218808/view",
"germplasmGenus": "Triticum",
"typeOfGermplasmStorageCode": [],
"germplasmName": "1755",
"biologicalStatusOfAccessionCode": 0,
"countryOfOriginCode": "",
"defaultDisplayName": "1755",
"instituteCode": "NSGC",
"germplasmSeedSource": "",
"seedSource": "",
"genus": "Triticum",
"acquisitionDate": "",
"donors": [],
"pedigree": "NA/NA",
"speciesAuthority": null,
"subtaxa": null,
"species": "Triticum aestivum",
"synonyms": [],
"germplasmSpecies": "Triticum aestivum",
"accessionNumber": "",
"documentationURL": null,
"germplasmDbId": 218808,
"taxonIds": [],
"commonCropName": "Canadian hard winter wheat,bread wheat,common wheat,wheat"
}
}Start a germplasm search on the database, terms and search options provided in the request body. Since this is
long running-task the request is added to a job queue and the response will include the job id. Use the
/job/:id?results=true endpoint to get the status of the job and its results when the job is complete.
Body:
{
"database": {
"address": "http://localhost:8081/brapi/v1",
"params": {},
"version": "v1.3",
"auth_token": "",
"call_limit": 10
},
"terms": ["JERRY", "syn_a", "ogle"],
"config": {
"database_terms": {
"name": true,
"synonyms": true,
"accession_numbers": true
},
"search_routines": {
"name": true,
"punctuation": true,
"accents": true,
"substring": true,
"prefix": false,
"edit_distance": false
},
"search_routine_options": {
"substring": {
"substring_length_min": 3
},
"prefix": {
"prefixes": [],
"find_db_prefixes": true,
"prefix_length_min": 2,
"prefix_length_max": 5,
"threshold": 250
}
"edit_distance": {
"max_edit_distance": 2
}
},
"return_records": false
}
}Response:
{
"status": "queued",
"job": {
"id": "c6a62106-a741-4ddc-a968-b09762908cec"
}
}Get the status of the specified job (status, message, progress) and the results of a completed job. The results can be optionally disabled in the response, which is recommended for jobs that are updating the germplasm cache if you don't actually need the generated database terms (the response with the results is fairly large).
A job can have one of the following statuses:
- pending: the job has been added but not yet started
- running: the job is running (a running job will have the message and progress properties set)
- complete: the job has finished and will include the results if
results=true - removed: the job no longer exists
Running Response:
{
"status": "running",
"job": {
"id": "d2395274-1cbe-414c-b7b5-f6fbeda06547",
"message": {
"title": "Getting germplasm entries from the database",
"subtitle": "This will take a few moments..."
},
"progress": 25.94899169632266
}
}Update Cache Response: ?results=false
{
"status": "complete",
"job": {
"id": "de5b5f37-8229-4cb8-b360-2f2552200aa5"
}
}Search Response: ?results=true
{
"status": "complete",
"job": {
"id": "de5b5f37-8229-4cb8-b360-2f2552200aa5",
"results": {
"JERRY": {
"search_term": "JERRY",
"exact_match": "JERRY",
"search_routines": [
"edit_distance",
"exact",
"substring"
],
"matches": {
"AC_PERCY": {
"germplasmName": "AC_PERCY",
"germplasmDbId": 94029,
"matched_db_terms": [
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "Percy",
"type": "synonym"
}
}
]
},
"GARRY|CIAV6662": {
"germplasmName": "GARRY|CIAV6662",
"germplasmDbId": 90462,
"matched_db_terms": [
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "Garry",
"type": "synonym"
}
}
]
},
"DERBY": {
"germplasmName": "DERBY",
"germplasmDbId": 87209,
"matched_db_terms": [
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "DERBY",
"type": "name"
}
},
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "Derby",
"type": "synonym"
}
}
]
},
"JURY": {
"germplasmName": "JURY",
"germplasmDbId": 100529,
"matched_db_terms": [
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "JURY",
"type": "name"
}
}
]
},
"JERRY": {
"germplasmName": "JERRY",
"germplasmDbId": 102642,
"matched_db_terms": [
{
"search_routine": {
"key": "exact",
"name": "Exact Match",
"weight": 100
},
"db_term": {
"term": "JERRY",
"type": "name"
}
},
{
"search_routine": {
"key": "exact",
"name": "Exact Match",
"weight": 100
},
"db_term": {
"term": "Jerry",
"type": "synonym"
}
},
{
"search_routine": {
"key": "substring",
"name": "Substring Match",
"weight": 60
},
"db_term": {
"term": "GG Jerry (oat)",
"type": "accession_number"
}
}
]
},
"LEROY": {
"germplasmName": "LEROY",
"germplasmDbId": 91474,
"matched_db_terms": [
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "LEROY",
"type": "name"
}
},
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "LEROY",
"type": "synonym"
}
},
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "Leroy",
"type": "synonym"
}
}
]
},
"LARRY": {
"germplasmName": "LARRY",
"germplasmDbId": 92923,
"matched_db_terms": [
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "LARRY",
"type": "name"
}
},
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "Larry",
"type": "synonym"
}
}
]
},
"TERRA": {
"germplasmName": "TERRA",
"germplasmDbId": 91600,
"matched_db_terms": [
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "TERRA",
"type": "name"
}
},
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "Terra",
"type": "synonym"
}
}
]
},
"TERRY": {
"germplasmName": "TERRY",
"germplasmDbId": 96502,
"matched_db_terms": [
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 1
}
},
"db_term": {
"term": "TERRY",
"type": "name"
}
},
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 1
}
},
"db_term": {
"term": "Terry",
"type": "synonym"
}
}
]
}
}
},
"syn_a": {
"search_term": "syn_a",
"exact_match": false,
"search_routines": [
"edit_distance"
],
"matches": {
"SANNA": {
"germplasmName": "SANNA",
"germplasmDbId": 97512,
"matched_db_terms": [
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "SANNA",
"type": "name"
}
},
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "Sanna",
"type": "synonym"
}
}
]
},
"SYLVA": {
"germplasmName": "SYLVA",
"germplasmDbId": 90414,
"matched_db_terms": [
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "SYLVA",
"type": "name"
}
},
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "Sylva",
"type": "synonym"
}
}
]
},
"SONJA": {
"germplasmName": "SONJA",
"germplasmDbId": 94470,
"matched_db_terms": [
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "SONJA",
"type": "name"
}
}
]
}
}
},
"ogle": {
"search_term": "ogle",
"exact_match": "OGLE",
"search_routines": [
"edit_distance",
"substring",
"exact"
],
"matches": {
"ADELAAR|PI180946": {
"germplasmName": "ADELAAR|PI180946",
"germplasmDbId": 87607,
"matched_db_terms": [
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "Eagle",
"type": "synonym"
}
}
]
},
"GLEN": {
"germplasmName": "GLEN",
"germplasmDbId": 96127,
"matched_db_terms": [
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "GLEN",
"type": "name"
}
},
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "GLEN",
"type": "synonym"
}
},
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "Glen",
"type": "synonym"
}
}
]
},
"DALE|PI265444": {
"germplasmName": "DALE|PI265444",
"germplasmDbId": 88266,
"matched_db_terms": [
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "Dale",
"type": "synonym"
}
}
]
},
"COLE": {
"germplasmName": "COLE",
"germplasmDbId": 91920,
"matched_db_terms": [
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "COLE",
"type": "name"
}
},
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "COLE",
"type": "synonym"
}
},
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "Cole",
"type": "synonym"
}
}
]
},
"EAGLE|PI264257": {
"germplasmName": "EAGLE|PI264257",
"germplasmDbId": 85246,
"matched_db_terms": [
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "EAGLE",
"type": "synonym"
}
},
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "Eagle",
"type": "synonym"
}
}
]
},
"Opale": {
"germplasmName": "Opale",
"germplasmDbId": 436643,
"matched_db_terms": [
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
"properties": {
"edit_distance": 2
}
},
"db_term": {
"term": "Opale",
"type": "name"
}
}
]
},
"Ogle_1040": {
"germplasmName": "Ogle_1040",
"germplasmDbId": 438859,
"matched_db_terms": [
{
"search_routine": {
"key": "substring",
"name": "Substring Match",
"weight": 60
},
"db_term": {
"term": "Ogle_1040",
"type": "name"
}
}
]
},
"Ogle-C": {
"germplasmName": "Ogle-C",
"germplasmDbId": 438943,
"matched_db_terms": [
{
"search_routine": {
"key": "edit_distance",
"name": "Edit Distance",
"weight": 10,
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