From 76be1c0da7593ae61c0935747d21b1ff5a844985 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Tue, 21 Jul 2020 11:26:16 +0100 Subject: Sample date and specimen --- bh20simplewebuploader/api.py | 24 +++++++++++++++--------- 1 file changed, 15 insertions(+), 9 deletions(-) (limited to 'bh20simplewebuploader/api.py') diff --git a/bh20simplewebuploader/api.py b/bh20simplewebuploader/api.py index ff82b72..65435ea 100644 --- a/bh20simplewebuploader/api.py +++ b/bh20simplewebuploader/api.py @@ -15,14 +15,18 @@ def fetch_sample_metadata(id): PREFIX sio: PREFIX edam: PREFIX efo: - select distinct ?id ?seq ?info ?sequencer + PREFIX evs: + PREFIX obo: + select distinct ?id ?seq ?date ?info ?specimen ?sequencer { - ?sample sio:SIO_000115 "%s" . - ?sample sio:SIO_000115 ?id . - ?seq pubseq:technology ?tech . - ?seq pubseq:sample ?sample . - ?sample edam:data_2091 ?info . - ?tech efo:EFO_0002699 ?sequencer . + ?sample sio:SIO_000115 "%s" ; + sio:SIO_000115 ?id ; + evs:C25164 ?date . + ?seq pubseq:technology ?tech ; + pubseq:sample ?sample . + ?tech efo:EFO_0002699 ?sequencer . + optional { ?sample edam:data_2091 ?info } . + optional { ?sample obo:OBI_0001479 ?specimen } . } limit 5 """ % id payload = {'query': query, 'format': 'json'} @@ -39,19 +43,21 @@ def version(): def sample(id): # metadata = file.name(seq)+"/metadata.yaml" meta = fetch_sample_metadata(id) + print(meta) return jsonify([{ 'id': x['id']['value'], 'fasta': x['seq']['value'], 'collection': os.path.dirname(x['seq']['value']), + 'date': x['date']['value'], 'info': x['info']['value'], + 'specimen': x['specimen']['value'], 'sequencer': x['sequencer']['value'], } for x in meta]) @app.route('/api/ebi/sample-.xml', methods=['GET']) def ebi_sample(id): meta = fetch_sample_metadata(id)[0] - print("HERE",meta,file=sys.stderr) - page = render_template('ebi-sample.xml',sampleid=id,sequencer=meta['sequencer']['value']) + page = render_template('ebi-sample.xml',sampleid=id,sequencer=meta['sequencer']['value'],date=meta['date']['value'],specimen=meta['specimen']['value']) return page @app.route('/api/search', methods=['GET']) -- cgit v1.2.3