diff options
| -rw-r--r-- | bh20simplewebuploader/main.py | 19 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/form.html | 2 | ||||
| -rw-r--r-- | paper/paper.md | 5 |
3 files changed, 11 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 %} diff --git a/paper/paper.md b/paper/paper.md index 4df267f..cf9ba92 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -47,6 +47,9 @@ authors: - name: Andrea Guarracino orcid: https://orcid.org/0000-0001-9744-131X affiliation: 14 + - name: Danielle Welter + orcid: https://orcid.org/0000-0003-1058-2668 + affiliation: 15 affiliations: - name: Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, USA. index: 1 @@ -62,6 +65,8 @@ affiliations: index: 8 - name: Centre for Molecular Bioinformatics, Department of Biology, University Of Rome Tor Vergata, Rome, Italy index: 14 + - name: Luxembourg Centre for Systems Biomedecine, University of Luxembourg, Luxembourg + index: 15 date: 11 April 2020 event: COVID2020 group: Public Sequence Uploader |