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author | Pjotr Prins | 2020-05-16 10:18:36 -0500 |
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committer | Pjotr Prins | 2020-05-16 10:18:36 -0500 |
commit | fe56e0ddd8bf91b7cfb4be7562e6aa1ee4c9a285 (patch) | |
tree | 4960e738b88f0ea2b7497afd6dabe0646e764ef2 /bh20simplewebuploader | |
parent | 0e09fafd9e0cbc762a89302ccf4a3567d45297b4 (diff) | |
parent | 6dc16e60eb16cddb3ca1528561734e44507bf1cc (diff) | |
download | bh20-seq-resource-fe56e0ddd8bf91b7cfb4be7562e6aa1ee4c9a285.tar.gz bh20-seq-resource-fe56e0ddd8bf91b7cfb4be7562e6aa1ee4c9a285.tar.lz bh20-seq-resource-fe56e0ddd8bf91b7cfb4be7562e6aa1ee4c9a285.zip |
Merge branch 'master' of github.com:pjotrp/bh20-seq-resource
Diffstat (limited to 'bh20simplewebuploader')
-rw-r--r-- | bh20simplewebuploader/main.py | 19 | ||||
-rw-r--r-- | bh20simplewebuploader/templates/form.html | 2 |
2 files changed, 6 insertions, 15 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 865af97..1dff207 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -439,12 +439,15 @@ def getAllaccessions(): @app.route('/api/getDetailsForSeq', methods=['GET']) def getDetailsForSeq(): seq_id = request.args.get('seq') - query="""SELECT DISTINCT ?key ?value WHERE {<placeholder> ?x [?key ?value]}""" + query="""SELECT DISTINCT ?key ?key_label ?value WHERE { + <http://arvados.org/keep:00a6af865453564f6a59b3d2c81cc7c1+123/sequence.fasta> ?x [?key ?value] . + OPTIONAL {?key <http://www.w3.org/2000/01/rdf-schema#label> ?key_tmp_label } . + BIND(IF(BOUND(?key_tmp_label),?key_tmp_label, ?key) as ?key_label)}""" query=query.replace("placeholder", seq_id) payload = {'query': query, 'format': 'json'} r = requests.get(baseURL, params=payload) result = r.json()['results']['bindings'] - return jsonify([{'uri': x['key']['value'], + return jsonify([{'uri': x['key']['value'], 'key_label': x['key_label']['value'], 'value': x['value']['value']} for x in result]) @@ -463,18 +466,6 @@ def getSEQCountbytech(): 'tech': x['tech']['value'], 'Label': x['tech_label']['value']} for x in result]) -## Is this one really necessary or should we just use getSEQCountbytech instead? -@app.route('/api/getAvailableTech', methods=['GET']) -def getAvailableTech(): - query="""SELECT distinct ?tech ?tech_label WHERE - {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0600047> ?tech] - BIND (concat(?tech,"_label") as ?tech_label) - } """ - payload = {'query': query, 'format': 'json'} - r = requests.get(baseURL, params=payload) - result = r.json()['results']['bindings'] - return str(result) - ## List all Sequences/submissions by a given tech, as example e.g. http://purl.obolibrary.org/obo/OBI_0000759 ## Has to be encoded again so should be --> http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0000759 @app.route('/api/getSEQbytech', methods=['GET']) diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html index 37a7b72..7d7cef8 100644 --- a/bh20simplewebuploader/templates/form.html +++ b/bh20simplewebuploader/templates/form.html @@ -146,7 +146,7 @@ {{ 'placeholder=http://www.wikidata.org/entity/Q30' if record['id']=='metadata.sample.collection_location'}} {{ 'placeholder=MyUniqueSampleId.1' if record['id']=='metadata.sample.sample_id'}} {{ 'value=http://purl.obolibrary.org/obo/NCBITaxon_2697049' if record['id']=='metadata.virus.virus_species'}} - {{ 'readonly=1 value=http://identifiers.org/insdc/MT334571.1#sequence' if record['id']=='metadata.id'}} + {{ 'readonly=1 value=http://genenetwork.org/submission' if record['id']=='metadata.id'}} name="{{ record['id'] }}{{ '[0]' if record['list'] else ''}}" {{ "required" if record['required'] else "" }} {{ ("step=" + record['step']) if 'step' in record else ""}}> {% endif %} |