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-rw-r--r--bh20simplewebuploader/main.py32
1 files changed, 29 insertions, 3 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 510df1c..fc145e6 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -687,13 +687,27 @@ sparqlURL='http://sparql.genenetwork.org/sparql/'
@app.route('/resource/<id>')
def resource(id):
"""Get a COVID19 resource using identifier"""
+
query=f"""
PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
PREFIX sio: <http://semanticscience.org/resource/>
select distinct ?sample ?geoname ?date ?source ?geo ?sampletype ?institute ?sequenceuri
+where {{
{{
?sample sio:SIO_000115 "{id}" .
?sequenceuri pubseq:sample ?sample .
+}}
+union
+{{
+ <http://collections.lugli.arvadosapi.com/c={id}/sequence.fasta> pubseq:sample ?sample .
+ ?sequenceuri pubseq:sample ?sample .
+}}
+union
+{{
+ <http://covid19.genenetwork.org/resource/{id}> pubseq:sample ?sample .
+ ?sequenceuri pubseq:sample ?sample .
+}}
+
?sample <http://purl.obolibrary.org/obo/GAZ_00000448> ?geo .
?geo rdfs:label ?geoname .
?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date .
@@ -711,8 +725,9 @@ select distinct ?sample ?geoname ?date ?source ?geo ?sampletype ?institute ?sequ
logging.info("^^^^^^^^^^^^^^^^^^^^^^^^^^^^")
# return jsonify({'sequences': int(result[0]["num"]["value"])})
sequenceuri=sample['sequenceuri']['value']
- collectionuri=sequenceuri.split('sequence.fasta')[0]
- metauri=collectionuri+'metadata.yaml'
+ m = re.match(r"http://collections.lugli.arvadosapi.com/c=([^/]*)/sequence.fasta|http://covid19.genenetwork.org/resource/(.*)", sequenceuri)
+ fastauri = "http://collections.lugli.arvadosapi.com/c=%s/sequence.fasta" % m.group(1)
+ metauri = "http://collections.lugli.arvadosapi.com/c=%s/metadata.yaml" % m.group(1)
locationuri=sample['geo']['value']
location=sample['geoname']['value']
date=sample['date']['value']
@@ -727,7 +742,18 @@ select distinct ?sample ?geoname ?date ?source ?geo ?sampletype ?institute ?sequ
institute=''
if 'institute' in sample:
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)
+ return render_template('permalink.html',
+ id=id,
+ menu='',
+ uri=f"http://covid19.genenetwork.org/resource/{id}",
+ sequenceuri=fastauri,
+ locationuri=locationuri,
+ location=location,
+ date=date,
+ source=source,
+ sampletype=sampletype,
+ institute=institute,
+ 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