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| author | Peter Amstutz | 2020-11-09 17:20:27 -0500 |
|---|---|---|
| committer | Peter Amstutz | 2020-11-09 17:20:27 -0500 |
| commit | 1082b907d816f5da52aba6233073737632d0242f (patch) | |
| tree | 8ad59d268234bbea42b3d6b42bd2d352eb56df28 | |
| parent | b5143c79de268b844f3a6a63d92c6389b047f35e (diff) | |
| download | bh20-seq-resource-1082b907d816f5da52aba6233073737632d0242f.tar.gz bh20-seq-resource-1082b907d816f5da52aba6233073737632d0242f.tar.lz bh20-seq-resource-1082b907d816f5da52aba6233073737632d0242f.zip | |
Make resource link work for both portable data hashes and sample id
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
| -rw-r--r-- | bh20simplewebuploader/main.py | 14 | ||||
| -rw-r--r-- | workflows/pangenome-generate/collect-seqs.py | 2 |
2 files changed, 15 insertions, 1 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 73503b4..405544c 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 . diff --git a/workflows/pangenome-generate/collect-seqs.py b/workflows/pangenome-generate/collect-seqs.py index af4a0dc..1a0807c 100644 --- a/workflows/pangenome-generate/collect-seqs.py +++ b/workflows/pangenome-generate/collect-seqs.py @@ -38,7 +38,7 @@ for item in validated: pdh = item["portable_data_hash"] with arvados.collection.CollectionReader(pdh, api_client=api, keep_client=keepclient) as col: with col.open("sequence.fasta", "rt") as fa: - subject = "http://collections.lugli.arvadosapi.com/c=%s/sequence.fasta" % pdh + subject = "http://covid19.genenetwork.org/resource/%s" % pdh label = fa.readline().strip() merged_metadata.write("<%s> <http://biohackathon.org/bh20-seq-schema/original_fasta_label> \"%s\" .\n" % (subject, label[1:].replace('"', '\\"'))) skip = (subject in blacklist or label[1:] in blacklist) |