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| author | Peter Amstutz | 2020-11-09 17:30:16 -0500 |
|---|---|---|
| committer | Peter Amstutz | 2020-11-09 17:30:16 -0500 |
| commit | 98a80bd64d8a495b8fddffdef6e07e5a3fbea1e3 (patch) | |
| tree | 57c7df946e1aa1f2054eb49379439ebee4d4c0e6 | |
| parent | 1082b907d816f5da52aba6233073737632d0242f (diff) | |
| download | bh20-seq-resource-98a80bd64d8a495b8fddffdef6e07e5a3fbea1e3.tar.gz bh20-seq-resource-98a80bd64d8a495b8fddffdef6e07e5a3fbea1e3.tar.lz bh20-seq-resource-98a80bd64d8a495b8fddffdef6e07e5a3fbea1e3.zip | |
Extract PDH from result and construct URIs from that fasta-subset-from-query
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
| -rw-r--r-- | bh20simplewebuploader/main.py | 18 |
1 files changed, 15 insertions, 3 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 405544c..51048a4 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -713,8 +713,9 @@ union 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'] @@ -729,7 +730,18 @@ union 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 |