diff options
Diffstat (limited to 'bh20simplewebuploader/main.py')
| -rw-r--r-- | bh20simplewebuploader/main.py | 211 |
1 files changed, 209 insertions, 2 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 0495613..27dcd4b 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -949,8 +949,8 @@ def getSEQCountbyLocation(): @app.route('/api/getSEQCountbyContinent', methods=['GET']) def getSEQCountbyContinent(): query="""SELECT DISTINCT ?continent ?continent_label (count(?fasta) as ?fastaCount) WHERE { - ?fasta ?x[ <http://purl.obolibrary.org/obo/GAZ_00000448> ?location] . - ?location <http://www.wikidata.org/prop/direct/P17> ?country . + ?fasta ?x [ <http://purl.obolibrary.org/obo/GAZ_00000448> ?location] . + ?location <http://www.wikidata.org/prop/direct/P17> ?country . ?country <http://www.wikidata.org/prop/direct/P30> ?continent . OPTIONAL { ?continent rdfs:label ?key_tmp_label } BIND(IF(BOUND(?key_tmp_label),?key_tmp_label, ?location) as ?continent_label) @@ -1064,3 +1064,210 @@ def getSEQbyLocationAndSpecimenSource(): r = requests.get(sparqlURL, params=payload) result = r.json()['results']['bindings'] return str(result) + + +################## SPARQL PLAYGORUND API function ################ + +@app.route('/api/demoGetSEQCountbySpecimenSource', methods=['GET']) +def demoGetSEQCountbySpecimenSource(): + prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>""" + + query="""SELECT ?specimen_source ?specimen_source_label (count(?seq) as ?seqCount) WHERE + { + ?seq ?x [obo:OBI_0001479 ?specimen_source] . + ?specimen_source rdfs:label ?specimen_source_label + } + GROUP BY ?specimen_source ?specimen_source_label + ORDER BY DESC (?seqCount) + """ + + description="Get the count of all sequences, grouped by specimen source and specimen label (This is a 1-to-1 relationship). In addition we want to order by the sequence count descending." + 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}],[{'count': x['seqCount']['value'], + 'key': x['specimen_source']['value'], + 'label': x['specimen_source_label']['value']} for x in result]) + + +@app.route('/api/demoGetSEQCountbyLocation', methods=['GET']) +def demoGetSEQCountbyLocation(): + prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>""" + + query=""" + SELECT ?geoLocation ?geoLocation_label (count(?seq) as ?seqCount) WHERE + { + ?seq ?x [obo:GAZ_00000448 ?geoLocation] . + ?geoLocation rdfs:label ?geoLocation_label + } + GROUP BY ?geoLocation ?geoLocation_label + """ + description = "Get count of all sequences grouped by geoLocation and geoLocation_label (1-to-1 relationship)" + 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}],[{'count': x['seqCount']['value'], + 'key': x['geoLocation']['value'], + 'label': x['geoLocation_label']['value']} for x in result]) + + + +@app.route('/api/demoGetAuthors', methods=['GET']) +def demoGetAuthors(): + prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX wiki: <http://www.wikidata.org/prop/direct/>""" + + query = """SELECT DISTINCT ?author ?country_label ?continent_label WHERE { + ?fasta ?x [ obo:GAZ_00000448 ?location] . + ?fasta ?y [ obo:NCIT_C42781 ?author] . + + ?location wiki:P17 ?country . + ?country wiki:P30 ?continent . + ?country rdfs:label ?country_label . + ?continent rdfs:label ?continent_label + } + ORDER BY ?author + LIMIT 500 + """ + + description = "Get all autors (obo:NCIT_C42781) that are in the DB and the country/continent where their samples were taken. The result is limited to 500." + 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}],[{'author': x['author']['value'], + 'country_label': x['country_label']['value'], + 'continent_label': x['continent_label']['value']} for x in result]) + + +@app.route('/api/demoInstitutesPublications', methods=['GET']) +def demoInstitutesPublications(): + prefix="PREFIX obo: <http://purl.obolibrary.org/obo/>" + query=""" + SELECT DISTINCT ?originating_lab ?publication WHERE { + ?seq ?x [ obo:NCIT_C37984 ?originating_lab] . + ?seq ?y [ obo:NCIT_C19026 ?publication] . + } + """ + + description = "List institutes (originating_lab, obo:NCIT_C37984) associated their publications in the DB" + 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}],[{'originating_lab': x['originating_lab']['value'], + 'publication': x['publication']['value']} for x in result]) + + + +@app.route('/api/demoGetSEQCountbytechContinent', methods=['GET']) +def demoGetSEQCountbytechContinent(): + 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 ?continent_label ?tech_label (count(?seq) as ?seqCount) WHERE + { + ?seq ?x [ obo:OBI_0600047 ?tech] . + ?seq ?y [ obo:GAZ_00000448 ?location] . + + ?tech rdfs:label ?tech_label . + + ?location wiki:P17 ?country . + ?country wiki:P30 ?continent . + ?continent rdfs:label ?continent_label + } + + GROUP BY ?tech_label ?continent_label + ORDER BY ?continent_label ?seqCount + """ + + description = "List institutes (originating_lab, obo:NCIT_C37984) and their associated publications in the DB" + 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}],[{'continent_label': x['continent_label']['value'], + 'tech_label': x['tech_label']['value'], 'seqCount': x['seqCount']['value']} for x in result]) + + +@app.route('/api/demoGetSEQCountbytech', methods=['GET']) +def dempGetSEQCountbytech(): + prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>""" + + query="""SELECT ?tech ?tech_label (count(?seq) as ?seqCount) WHERE + { + ?seq ?x [obo:OBI_0600047 ?tech] . + ?tech rdfs:label ?tech_label + } + GROUP BY ?tech ?tech_label ORDER BY DESC (?seqCount) + """ + description = "Show count per sequence technology" + 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}], + [{'tech_label': x['tech_label']['value'], + 'tech': x['tech']['value'], 'seqCount': x['seqCount']['value']} for x in result]) + + +@app.route('/api/demoGetSequencePerDate', methods=['GET']) +def demoGetSequencePerDate(): + prefix="" + query="""SELECT ?seq ?date WHERE { + ?seq ?a [<http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date] + 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(...)" + 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'], + 'date': x['date']['value']} for x in result]) + +@app.route('/api/demoLocationGps', methods=['GET']) +def demoLocationGps(): + prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/> +PREFIX wiki: <http://www.wikidata.org/prop/direct/>""" + + query="""SELECT distinct ?location ?GPS WHERE { + ?seq ?a [ obo:GAZ_00000448 ?location] . + ?location wiki:P625 ?GPS + } + """ + description = "Show all locations with their GPS coordinates that we have in the database. GPS coordinates are encoded as Point tuple." + 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}], + [{'location': x['location']['value'], + 'GPS': x['GPS']['value']} for x in result]) + +@app.route('/api/getNYsamples', methods=['GET']) +def getNYsamples(): + prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/> +PREFIX wikiE: <http://www.wikidata.org/entity/>""" + + query="""SELECT DISTINCT ?seq ?key_label ?key ?value_label ?value WHERE { + ?seq ?x [ obo:GAZ_00000448 wikiE:Q1384] . + ?seq ?y [?key ?value] . + + ?key rdfs:label ?key_label . + ?value rdfs:label ?value_label + } + ORDER BY ?seq""" + + description = "Get all samples and their information (key, values) that were taken in New York (Q1384)!" + 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'], + 'key_label': x['key_label']['value'], + 'key': x['key']['value'], + 'value_label': x['value_label']['value'], + 'value': x['value']['value']} for x in result])
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