diff options
| -rw-r--r-- | bh20simplewebuploader/main.py | 35 | ||||
| -rw-r--r-- | bh20simplewebuploader/static/main.js | 3 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/footer.html | 2 |
3 files changed, 21 insertions, 19 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index ea4ec10..9e817fb 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -653,7 +653,7 @@ def export_page(): @app.route('/demo') def demo_page(): - return render_template('demo.html',menu='DEMO',load_map=True) + return render_template('demo.html',menu='DEMO',load_map=False) @app.route('/apidoc') def apidoc_page(): @@ -1070,7 +1070,7 @@ def getSEQbyLocationAndSpecimenSource(): @app.route('/api/demoGetSEQCountbySpecimenSource', methods=['GET']) def demoGetSEQCountbySpecimenSource(): - prefix="""PREFIX obo: <http://purl.obolibrary.org/obo/> + 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 @@ -1103,7 +1103,7 @@ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>""" ?seq ?x [obo:GAZ_00000448 ?geoLocation] . ?geoLocation rdfs:label ?geoLocation_label } - GROUP BY ?geoLocation ?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'} @@ -1124,7 +1124,7 @@ 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 . @@ -1146,7 +1146,7 @@ PREFIX wiki: <http://www.wikidata.org/prop/direct/>""" @app.route('/api/demoInstitutesPublications', methods=['GET']) def demoInstitutesPublications(): prefix="PREFIX obo: <http://purl.obolibrary.org/obo/>" - query=""" + query=""" SELECT DISTINCT ?originating_lab ?publication WHERE { ?seq ?x [ obo:NCIT_C37984 ?originating_lab] . ?seq ?y [ obo:NCIT_C19026 ?publication] . @@ -1165,7 +1165,7 @@ def demoInstitutesPublications(): @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 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 @@ -1174,11 +1174,11 @@ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>""" ?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 @@ -1200,7 +1200,7 @@ 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 + ?tech rdfs:label ?tech_label } GROUP BY ?tech ?tech_label ORDER BY DESC (?seqCount) """ @@ -1237,7 +1237,7 @@ 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'} @@ -1255,7 +1255,7 @@ 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 } @@ -1276,7 +1276,7 @@ PREFIX wikiE: <http://www.wikidata.org/entity/>""" @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 wiki: <http://www.wikidata.org/prop/direct/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> """ @@ -1286,7 +1286,7 @@ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> ?location wiki:P17 ?country . ?country rdfs:label ?country_label . ?country wiki:P30 <http://www.wikidata.org/entity/Q18> . - } + } ORDER BY ?country_label """ @@ -1309,7 +1309,7 @@ def demoGetSeqByAgeGender(): ?seq ?hostSchema [ obo:PATO_0000011 ?age ] . ?sex rdfs:label ?gender . } -Order by ?age +Order by ?age """ description = "List all sequences that have an entry in the field 'host_sex' and 'host_age'. Instead of the IRI we want to show the human readable label and order results by age" @@ -1346,7 +1346,7 @@ PREFIX efo: <http://www.ebi.ac.uk/efo/>""" def demoGetSeqWithStrain(): prefix = """PREFIX SIO: <http://semanticscience.org/resource/>""" query="""SELECT DISTINCT ?strain ?seq WHERE { -?seq ?virusSchema [SIO:SIO_010055 ?strain] +?seq ?virusSchema [SIO:SIO_010055 ?strain] }""" description = "List all sequences with data in 'virus_strain'. Show the strain and the relevant identifer!" @@ -1361,14 +1361,14 @@ def demoGetSeqWithStrain(): @app.route('/api/demoGetContinentSpecimentSeqCount', methods=['GET']) def demoGetContinentSpecimentSeqCount(): - prefix = """PREFIX obo: <http://purl.obolibrary.org/obo/> + 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 ?continent_label ?specimen_source_label (count(?seq) as ?seqCount) WHERE { ?seq ?x [obo:OBI_0001479 ?specimen_source] . ?seq ?y [ obo:GAZ_00000448 ?location] . - + ?location wiki:P17 ?country . ?location wiki:P30 ?continent . @@ -1387,4 +1387,3 @@ PREFIX wiki: <http://www.wikidata.org/prop/direct/>""" [{'continent_label': x['continent_label']['value'], 'specimen_source_label': x['specimen_source_label']['value'], 'seqCount': x['seqCount']['value']} for x in result]) - diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js index aa1f06f..efbf615 100644 --- a/bh20simplewebuploader/static/main.js +++ b/bh20simplewebuploader/static/main.js @@ -92,8 +92,9 @@ function demofetchHTMLTable(apiEndPoint) { return response.json(); }) .then(data => { + console.log(data); htmlString="<h3>Description</h3><p>"+data[0][0]["description"]+"</p>" - prefix=data[0][1]["prefix"].replaceAll("<","<") + prefix=data[0][1]["prefix"].replace(/</g,"<"); htmlString+="<h4>Namespace</h4><pre>"+prefix+"</pre>"//prefix to construct correct query @data[0][1]["prefix"] htmlString+="<h3>SPARQL query</h3><pre>"+data[0][2]["query"]+"</pre>" htmlString+="<h3>SPARQL results table</h3><table>" diff --git a/bh20simplewebuploader/templates/footer.html b/bh20simplewebuploader/templates/footer.html index efa1817..dcdd692 100644 --- a/bh20simplewebuploader/templates/footer.html +++ b/bh20simplewebuploader/templates/footer.html @@ -50,6 +50,8 @@ <small> COVID-19 PubSeq · <a href="https://github.com/arvados/bh20-seq-resource">Contribute</a> · Powered by <a href="https://www.commonwl.org/">Common Workflow Language</a> & <a href="https://arvados.org/">Arvados</a> · Made for <a href="https://github.com/virtual-biohackathons/covid-19-bh20">COVID-19-BH20</a> + · + <a href="/contact">Contact us!</a> </small> </center> </div> |