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| author | Pjotr Prins | 2020-07-21 11:26:16 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2020-07-21 11:26:16 +0100 |
| commit | 76be1c0da7593ae61c0935747d21b1ff5a844985 (patch) | |
| tree | 511406dbffd2645935f566ffa428fb5969dce026 | |
| parent | dceac420dffa3aa74ef49a50d9be01e450e9d339 (diff) | |
| download | bh20-seq-resource-76be1c0da7593ae61c0935747d21b1ff5a844985.tar.gz bh20-seq-resource-76be1c0da7593ae61c0935747d21b1ff5a844985.tar.lz bh20-seq-resource-76be1c0da7593ae61c0935747d21b1ff5a844985.zip | |
Sample date and specimen
| -rw-r--r-- | bh20simplewebuploader/api.py | 24 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/ebi-sample.xml | 4 |
2 files changed, 17 insertions, 11 deletions
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: <http://semanticscience.org/resource/> PREFIX edam: <http://edamontology.org/> PREFIX efo: <http://www.ebi.ac.uk/efo/> - select distinct ?id ?seq ?info ?sequencer + PREFIX evs: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#> + PREFIX obo: <http://purl.obolibrary.org/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-<id>.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']) diff --git a/bh20simplewebuploader/templates/ebi-sample.xml b/bh20simplewebuploader/templates/ebi-sample.xml index 0b6b39e..7ede833 100644 --- a/bh20simplewebuploader/templates/ebi-sample.xml +++ b/bh20simplewebuploader/templates/ebi-sample.xml @@ -18,7 +18,7 @@ </SAMPLE_ATTRIBUTE> <SAMPLE_ATTRIBUTE> <TAG>collection date</TAG> - <VALUE>{{ time }}</VALUE> + <VALUE>{{ date }}</VALUE> </SAMPLE_ATTRIBUTE> <SAMPLE_ATTRIBUTE> <TAG>geographic location (latitude)</TAG> @@ -40,7 +40,7 @@ </SAMPLE_ATTRIBUTE> <SAMPLE_ATTRIBUTE> <TAG>environment (material)</TAG> - <VALUE>{{ material }}</VALUE> + <VALUE>{{ specimen }}</VALUE> </SAMPLE_ATTRIBUTE> <SAMPLE_ATTRIBUTE> <TAG>ENA-CHECKLIST</TAG> |