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-rw-r--r--bh20simplewebuploader/main.py35
-rw-r--r--bh20simplewebuploader/static/main.js3
-rw-r--r--bh20simplewebuploader/templates/footer.html2
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("<","&lt;")
+ prefix=data[0][1]["prefix"].replace(/</g,"&lt;");
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 &middot;
<a href="https://github.com/arvados/bh20-seq-resource">Contribute</a> &middot; Powered by <a href="https://www.commonwl.org/">Common Workflow Language</a> &amp; <a href="https://arvados.org/">Arvados</a> &middot; Made for <a href="https://github.com/virtual-biohackathons/covid-19-bh20">COVID-19-BH20</a>
+ &middot;
+ <a href="/contact">Contact us!</a>
</small>
</center>
</div>