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| author | Munyoki Kilyungi | 2023-10-25 13:06:01 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2023-10-27 13:45:32 +0300 |
| commit | 278d23ccd27c6ef7f009369d60bdb60ed81b2ecd (patch) | |
| tree | 73f55d154f5c797a0c035b3c39b13f2dc27d009d | |
| parent | 3ccf76ec9d65bc5aaa0850416b0b7117d701478f (diff) | |
| download | genenetwork3-278d23ccd27c6ef7f009369d60bdb60ed81b2ecd.tar.gz | |
Implement "GET /metadata/probesets/:name".
* gn3/api/metadata.py (fetch_group_by_species): New end-point.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| -rw-r--r-- | gn3/api/metadata.py | 67 |
1 files changed, 67 insertions, 0 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py index dfedd27..8355c60 100644 --- a/gn3/api/metadata.py +++ b/gn3/api/metadata.py @@ -1033,3 +1033,70 @@ CONSTRUCT { }) except (RemoteDisconnected, URLError): return jsonify({}) + +@metadata.route("/probesets/<name>", methods=["GET"]) +def probesets(name): + """Fetch a probesets's metadata given it's name""" + try: + sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) + sparql.setQuery(Template(""" +$prefix + +CONSTRUCT { + ?probeset ?predicate ?object ; + gnt:hasChip ?chipName . +} WHERE { + ?probeset rdf:type gnc:Probeset ; + rdfs:label "$name" ; + ?predicate ?object . + FILTER (?predicate != gnt:hasChip) . + OPTIONAL{ + ?probeset gnt:hasChip ?chip . + ?chip rdfs:label ?chipName . + } . +} +""").substitute(prefix=RDF_PREFIXES, name=name)) + results = json.loads(sparql.queryAndConvert().serialize(format="json-ld")) + if not results: + return jsonify({}) + frame = { + "@context": { + "data": "@graph", + "type": "@type", + "id": "@id", + "gnt": "http://genenetwork.org/term/", + "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "skos": "http://www.w3.org/2004/02/skos/core#", + "dct": "http://purl.org/dc/terms/", + "name": "rdfs:label", + "alias": "skos:altLabel", + "chip": "gnt:hasChip", + "targetId": "gnt:hasTargetId", + "symbol": "gnt:symbol", + "description": "dct:description", + "targetsRegion": "gnt:targetsRegion", + "chr": "gnt:chr", + "mb": "gnt:mb", + "mbMm8": "gnt:mbMm8", + "mb2016": "gnt:mb2016", + "specificity": "gnt:hasSpecificity", + "blatScore": "gnt:hasBlatScore", + "blatMbStart": "gnt:hasBlatMbStart", + "blatMbStart2016": "gnt:hasBlatMbStart2016", + "blatMbEnd": "gnt:hasBlatMbEnd", + "blatMbEnd2016": "gnt:hasBlatMbEnd2016", + "blatSeq": "gnt:hasBlatSeq", + "targetSeq": "gnt:hasTargetSeq", + "homologene": "gnt:hasHomologeneId", + "uniprot": "gnt:hasUniprotId", + "pubchem": "gnt:hasPubChemId", + "kegg": "gnt:hasKeggId", + "omim": "gnt:hasOmimId", + "chebi": "gnt:hasChebiId", + }, + } + return jsonld.compact(results, frame) + # return jsonld.compact(jsonld.frame(results, frame), frame) + except (RemoteDisconnected, URLError): + return jsonify({}) |