diff options
Diffstat (limited to 'bh20simplewebuploader/main.py')
| -rw-r--r-- | bh20simplewebuploader/main.py | 44 |
1 files changed, 38 insertions, 6 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 92cea2e..0be9d9f 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -668,6 +668,7 @@ def contact_page(): ## sparqlURL='http://sparql.genenetwork.org/sparql/' + ## # Example http://covid19.genenetwork.org/resource/MT326090.1 # Example http://host/resource/SRR11621868 @@ -716,6 +717,30 @@ select distinct ?sample ?geoname ?date ?source ?geo ?sampletype ?institute ?sequ institute=sample['institute']['value'] return render_template('permalink.html',id=id,menu='',uri=f"http://covid19.genenetwork.org/resource/{id}",sequenceuri=sequenceuri,locationuri=locationuri,location=location,date=date,source=source,sampletype=sampletype,institute=institute,collectionuri=collectionuri,metauri=metauri) +# http://covid19.genenetwork.org/location?label=http://www.wikidata.org/entity/Q114 +# http://localhost:5067/location?label=http://www.wikidata.org/entity/Q114 +@app.route('/location', methods=['GET']) +def location(): + """Show country resource""" + loc = request.args.get('label') + logging.info(loc) + logging.info("^^^^^^^^^^^^^^^^^^^^^^^^^^^^") + query = f""" + PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> + PREFIX sio: <http://semanticscience.org/resource/> + select distinct ?name ?date where + {{ + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <{loc}> . + ?sample <http://semanticscience.org/resource/SIO_000115> ?name . + ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date . + }} order by ?name + """ + payload = {'query': query, 'format': 'json'} + r = requests.get(sparqlURL, params=payload) + result = r.json()['results']['bindings'] + logging.info(result) + return render_template('list.html',id=loc,menu='',h=['name','date'],l=result) + ## Dynamic API functions starting here ## This is quick and dirty for now, just to get something out and demonstrate the queries ## Feel free to rename the functions/endpoints, feel free to process result so we get nicer JSON @@ -753,7 +778,12 @@ def getCountDB(): @app.route('/api/getAllaccessions', methods=['GET']) def getAllaccessions(): - query="""SELECT DISTINCT ?fasta ?value WHERE {?fasta ?x[ <http://edamontology.org/data_2091> ?value ]}""" + query=""" + SELECT DISTINCT ?fasta ?value WHERE + { + ?fasta ?x[ <http://edamontology.org/data_2091> ?value ] + } + """ payload = {'query': query, 'format': 'json'} r = requests.get(sparqlURL, params=payload) result = r.json()['results']['bindings'] @@ -780,11 +810,13 @@ def getDetailsForSeq(): # Endpoint should provide all necessary information to draw a map (!) @app.route('/api/getCountByGPS', methods=['GET']) def getCountByGPS(): - query="""SELECT DISTINCT ?location ?location_label ?GPS (count(?fasta) as ?fastaCount) WHERE { - ?fasta ?x[ <http://purl.obolibrary.org/obo/GAZ_00000448> ?location] . - ?location <http://www.wikidata.org/prop/direct/P625> ?GPS . - OPTIONAL { ?location rdfs:label ?key_tmp_label } - BIND(IF(BOUND(?key_tmp_label),?key_tmp_label, ?location) as ?location_label) + query=""" + SELECT DISTINCT ?location ?location_label ?GPS (count(?fasta) as ?fastaCount) WHERE + { + ?fasta ?x[ <http://purl.obolibrary.org/obo/GAZ_00000448> ?location] . + ?location <http://www.wikidata.org/prop/direct/P625> ?GPS . + OPTIONAL { ?location rdfs:label ?key_tmp_label } + BIND(IF(BOUND(?key_tmp_label),?key_tmp_label, ?location) as ?location_label) } GROUP BY ?location ?location_label ?GPS """ |