diff options
Diffstat (limited to 'bh20simplewebuploader/main.py')
| -rw-r--r-- | bh20simplewebuploader/main.py | 43 |
1 files changed, 35 insertions, 8 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 27dcd4b..87ef212 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -1066,7 +1066,7 @@ def getSEQbyLocationAndSpecimenSource(): return str(result) -################## SPARQL PLAYGORUND API function ################ +########################## SPARQL PLAYGORUND API function #################### @app.route('/api/demoGetSEQCountbySpecimenSource', methods=['GET']) def demoGetSEQCountbySpecimenSource(): @@ -1193,7 +1193,7 @@ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>""" @app.route('/api/demoGetSEQCountbytech', methods=['GET']) -def dempGetSEQCountbytech(): +def demoGetSEQCountbytech(): prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>""" @@ -1221,7 +1221,7 @@ def demoGetSequencePerDate(): FILTER ( xsd:date(?date) < xsd:date("2020-03-01") ) } ORDER BY ?date""" - description = "Show all sequences with a submission date before 2020-03-01! To accomplish this a FILTER expression is used. Since date is a string, we cast xsd:date(...)" + description = "Show all sequences with a collection date before 2020-03-01! To accomplish this a FILTER expression is used. Since date is a string, we cast xsd:date(...)" payload = {'query': prefix + query, 'format': 'json'} r = requests.get(sparqlURL, params=payload) result = r.json()['results']['bindings'] @@ -1229,8 +1229,8 @@ def demoGetSequencePerDate(): [{'seq': x['seq']['value'], 'date': x['date']['value']} for x in result]) -@app.route('/api/demoLocationGps', methods=['GET']) -def demoLocationGps(): +@app.route('/api/demoGetLocationGps', methods=['GET']) +def demoGetLocationGps(): prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX wiki: <http://www.wikidata.org/prop/direct/>""" @@ -1247,8 +1247,8 @@ PREFIX wiki: <http://www.wikidata.org/prop/direct/>""" [{'location': x['location']['value'], 'GPS': x['GPS']['value']} for x in result]) -@app.route('/api/getNYsamples', methods=['GET']) -def getNYsamples(): +@app.route('/api/demoGetNYsamples', methods=['GET']) +def demoGetNYsamples(): prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX wikiE: <http://www.wikidata.org/entity/>""" @@ -1270,4 +1270,31 @@ PREFIX wikiE: <http://www.wikidata.org/entity/>""" 'key_label': x['key_label']['value'], 'key': x['key']['value'], 'value_label': x['value_label']['value'], - 'value': x['value']['value']} for x in result])
\ No newline at end of file + 'value': x['value']['value']} for x in result]) + + +@app.route('/api/demoGetSouthAmericaSeq', methods=['GET']) +def demoGetSouthAmericaSeq(): + prefix = """PREFIX obo: <http://purl.obolibrary.org/obo/> +PREFIX wiki: <http://www.wikidata.org/prop/direct/> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +""" + + query = """SELECT DISTINCT ?country_label ?seq WHERE + { + ?seq ?y [ obo:GAZ_00000448 ?location] . + ?location wiki:P17 ?country . + ?country rdfs:label ?country_label . + ?country wiki:P30 <http://www.wikidata.org/entity/Q18> . + } +ORDER BY ?country_label +""" + + description = "Show all sequences that are on the continent (P30) South America (Q18)! List the sequence identifiers and the country they belong too." + payload = {'query': prefix + query, 'format': 'json'} + r = requests.get(sparqlURL, params=payload) + result = r.json()['results']['bindings'] + return jsonify([{'description': description}, {'prefix': prefix}, {'query': query}], + [{'seq': x['seq']['value'], + 'country_label': x['country_label']['value']} for x in result]) + |