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| author | Munyoki Kilyungi | 2023-10-25 12:07:08 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2023-10-27 13:45:32 +0300 |
| commit | ee6510523d68f82f2fd387618d8e21d56ccc6732 (patch) | |
| tree | 7f9b80c66a777f44d2f3e36c2e4dda1f987d9b0f /gn3/api | |
| parent | a228d4a9b08ed0903a3ca36be8fa6fe8766782a3 (diff) | |
| download | genenetwork3-ee6510523d68f82f2fd387618d8e21d56ccc6732.tar.gz | |
Implement "GET /metadata/species".
* gn3/api/metadata.py (list_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'gn3/api')
| -rw-r--r-- | gn3/api/metadata.py | 44 |
1 files changed, 44 insertions, 0 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py index 3731cc1..bbf6a74 100644 --- a/gn3/api/metadata.py +++ b/gn3/api/metadata.py @@ -1283,3 +1283,47 @@ CONSTRUCT { except (RemoteDisconnected, URLError): return jsonify({}) + +@metadata.route("/species", methods=["GET"]) +def list_species(): + """List all species""" + try: + sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")) + sparql.setQuery(Template(""" +$prefix + +CONSTRUCT { + ?species ?predicate ?object . +} WHERE { + ?species ^skos:member gnc:Species ; + ?predicate ?object . + VALUES ?predicate { + rdfs:label skos:prefLabel + skos:altLabel gnt:shortName + gnt:family skos:notation + } + +} +""").substitute(prefix=RDF_PREFIXES)) + results = sparql.queryAndConvert() + results = json.loads( + results.serialize(format="json-ld") + ) + return jsonld.compact(results, { + "@context": { + "data": "@graph", + "type": "@type", + "id": "@id", + "skos": "http://www.w3.org/2004/02/skos/core#", + "gnt": "http://genenetwork.org/term/", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "name": "rdfs:label", + "family": "gnt:family", + "shortName": "gnt:shortName", + "alternateName": "skos:altLabel", + "taxonomicId": "skos:notation", + "fullName": "skos:prefLabel", + }, + }) + except (RemoteDisconnected, URLError): + return jsonify({}) |