diff options
| -rw-r--r-- | gn3/api/metadata.py | 75 |
1 files changed, 38 insertions, 37 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py index dcb06f4..e4099ba 100644 --- a/gn3/api/metadata.py +++ b/gn3/api/metadata.py @@ -2,11 +2,14 @@ from string import Template from http.client import RemoteDisconnected from urllib.error import URLError +from pathlib import Path + from flask import Blueprint from flask import jsonify from flask import request from flask import current_app +from gn3.db.datasets import retrieve_dataset_metadata from gn3.db.rdf import RDF_PREFIXES from gn3.db.rdf import (query_frame_and_compact, query_and_compact, @@ -148,62 +151,60 @@ CONSTRUCT { ?dataset ?predicate ?term ; gnt:usesNormalization ?normalization . ?inbredSet rdfs:label ?inbredSetName . - ?platform ?platformPred ?platformObject ; - gnt:hasPlatformInfo ?platformInfo . + ?platform ?platformPred ?platformObject . ?normalization rdfs:label ?normalizationName . - ?tissue ?tissuePred ?tissueObj ; - gnt:hasTissueInfo ?tissueInfo . + ?tissue ?tissuePred ?tissueObj . ?investigator foaf:name ?investigatorName ; - foaf:homepage ?homepage . + foaf:homepage ?homepage . ?type skos:prefLabel ?altName . } WHERE { ?dataset rdf:type dcat:Dataset ; ?predicate ?term ; (rdfs:label|dct:identifier|skos:prefLabel) "$name" . - FILTER (!regex(str(?predicate), '(hasTissueInfo)', 'i')) . FILTER (!regex(str(?predicate), '(usesNormalization)', 'i')) . - FILTER (!regex(str(?predicate), '(platformInfo)', 'i')) . - OPTIONAL { ?dataset gnt:hasPlatformInfo ?platformInfo . } . - OPTIONAL { + OPTIONAL { ?inbredSet ^skos:member gnc:Set ; ^gnt:belongsToGroup ?dataset ; rdfs:label ?inbredSetName . - } . - OPTIONAL { - ?type ^xkos:classifiedUnder ?dataset ; - ^skos:member gnc:DatasetType ; - skos:prefLabel ?altName . - } . - OPTIONAL { - ?investigator foaf:name ?investigatorName ; - foaf:homepage ?homepage ; - ^dcat:contactPoint ?dataset . - } . - OPTIONAL { - ?platform ^gnt:usesPlatform ?dataset ; - ?platformPred ?platformObject . - } . - OPTIONAL { - ?dataset gnt:usesNormalization ?normalization . - ?normalization rdf:type gnc:avgMethod ; - rdfs:label ?normalizationName . - } . - OPTIONAL { ?dataset gnt:hasPlatformInfo ?platformInfo . } . - OPTIONAL { ?dataset gnt:hasTissueInfo ?tissueInfo . } . - OPTIONAL { - ?dataset gnt:hasTissue ?tissue . - ?tissue rdfs:label ?tissueName ; - ?tissuePred ?tissueObj . - } . + } . + OPTIONAL { + ?type ^xkos:classifiedUnder ?dataset ; + ^skos:member gnc:DatasetType ; + skos:prefLabel ?altName . + } . + OPTIONAL { + ?investigator foaf:name ?investigatorName ; + foaf:homepage ?homepage ; + ^dcat:contactPoint ?dataset . + } . + OPTIONAL { + ?platform ^gnt:usesPlatform ?dataset ; + ?platformPred ?platformObject . + } . + OPTIONAL { + ?dataset gnt:usesNormalization ?normalization . + ?normalization rdf:type gnc:avgMethod ; + rdfs:label ?normalizationName . + } . + OPTIONAL { + ?dataset gnt:hasTissue ?tissue . + ?tissue rdfs:label ?tissueName ; + ?tissuePred ?tissueObj . + } . }""").substitute(prefix=RDF_PREFIXES, name=name) _context = { "@context": BASE_CONTEXT | DATASET_CONTEXT, "type": "dcat:Dataset", } - return query_frame_and_compact( + __result = query_frame_and_compact( _query, _context, current_app.config.get("SPARQL_ENDPOINT") ) + return __result | retrieve_dataset_metadata( + Path( + current_app.config.get("DATA_DIR") + ).joinpath(__result.get("id", "")).as_posix() + ) except (RemoteDisconnected, URLError): return jsonify({}) |