diff options
Diffstat (limited to 'bh20simplewebuploader')
| -rw-r--r-- | bh20simplewebuploader/main.py | 32 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/resource.html | 4 |
2 files changed, 31 insertions, 5 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 73503b4..51048a4 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -675,13 +675,27 @@ 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 . @@ -699,8 +713,9 @@ 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'] @@ -715,7 +730,18 @@ 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 diff --git a/bh20simplewebuploader/templates/resource.html b/bh20simplewebuploader/templates/resource.html index fc52f13..4c50fb9 100644 --- a/bh20simplewebuploader/templates/resource.html +++ b/bh20simplewebuploader/templates/resource.html @@ -10,8 +10,8 @@ <p><a href="https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-5ct8p1i1wrgyjvp#Data_collections">All sequences project</a></p> <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.fasta">All sequences (FASTA) relabled and deduplicated</a></p> <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/mergedmetadata.ttl">Metadata (RDF) for all sequences</a></p> - <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.g6.gfa">All sequences in Graphical Fragment Assembly (GFA)</a> - <a href="https://github.com/GFA-spec/GFA-spec">More about GFA</a></p> - <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.g6.unchop.sorted.odgi">All sequences in Optimized Dynamic Genome/Graph Implementation (ODGI)</a> - <a href="https://github.com/vgteam/odgi">More about ODGI</a></p> + <!-- <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.g6.gfa">All sequences in Graphical Fragment Assembly (GFA)</a> - <a href="https://github.com/GFA-spec/GFA-spec">More about GFA</a></p> --> + <!-- <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.g6.unchop.sorted.odgi">All sequences in Optimized Dynamic Genome/Graph Implementation (ODGI)</a> - <a href="https://github.com/vgteam/odgi">More about ODGI</a></p> --> <!-- <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup_relabeledSeqs_dedup.ttl.xz">All sequences in RDF using spodgi</a> - <a href="https://github.com/pangenome/spodgi">More about spodgi</a></p> --> |