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authorlltommy2020-04-26 22:05:53 +0200
committerlltommy2020-04-26 22:05:53 +0200
commit163c84b48a70b5a351f48a49339dbdb28da96469 (patch)
treec2367841207157bde7da08f050e538e70b5609ce /bh20simplewebuploader
parentfd29a73ae0ea231e91377776dd5b8fa18b5ba5e2 (diff)
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Pushing some new functions, rename some old ones
Diffstat (limited to 'bh20simplewebuploader')
-rw-r--r--bh20simplewebuploader/main.py86
1 files changed, 78 insertions, 8 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 75adc74..6ca9a78 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -376,8 +376,8 @@ def getDetailsForSeq():
'value': x['value']['value']} for x in result])
-@app.route('/api/getSEQbytech', methods=['GET'])
-def getSEQbytech():
+@app.route('/api/getSEQCountbytech', methods=['GET'])
+def getSEQCountbytech():
query="""SELECT ?tech ?tech_label (count(?fasta) as ?fastaCount) WHERE
{?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0600047> ?tech]
BIND (concat(?tech,"_label") as ?tech_label)}
@@ -390,11 +390,22 @@ def getSEQbytech():
'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/getSEQbySelectedtech', methods=['GET'])
-def getSEQbySelectedtech():
+@app.route('/api/getSEQbytech', methods=['GET'])
+def getSEQbytech():
query="""SELECT ?fasta WHERE
{?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0600047> <placeholder>] }
"""
@@ -406,8 +417,21 @@ def getSEQbySelectedtech():
return str(result)
+## Example location, encoded http%3A%2F%2Fwww.wikidata.org%2Fentity%2FQ1223
@app.route('/api/getSEQbyLocation', methods=['GET'])
def getSEQbyLocation():
+ query="""SELECT ?fasta WHERE {?fasta ?x[ <http://purl.obolibrary.org/obo/GAZ_00000448> <placeholder>]}"""
+ location=request.args.get('location')
+ query=query.replace("placeholder", location)
+ print(query)
+ payload = {'query': query, 'format': 'json'}
+ r = requests.get(baseURL, params=payload)
+ result = r.json()['results']['bindings']
+ return str(result)
+
+
+@app.route('/api/getSEQCountbyLocation', methods=['GET'])
+def getSEQCountbyLocation():
query="""SELECT ?geoLocation ?geoLocation_label (count(?fasta) as ?fastaCount) WHERE
{?fasta ?x [<http://purl.obolibrary.org/obo/GAZ_00000448> ?geoLocation]
BIND (concat(?geoLocation,"_label") as ?geoLocation_label)}
@@ -421,8 +445,8 @@ def getSEQbyLocation():
'GeoLocation Label': x['geoLocation_label']['value']} for x in result])
-@app.route('/api/getSEQbySpecimenSource', methods=['GET'])
-def getSEQbySpecimenSource():
+@app.route('/api/getSEQCountbySpecimenSource', methods=['GET'])
+def getSEQCountbySpecimenSource():
query="""SELECT ?specimen_source ?specimen_source_label (count(?fasta) as ?fastaCount) WHERE
{?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0001479> ?specimen_source]
BIND (concat(?specimen_source,"_label") as ?specimen_source_label)}
@@ -436,9 +460,23 @@ def getSEQbySpecimenSource():
'Specimen Source': x['specimen_source']['value'],
'Label': x['specimen_source_label']['value']} for x in result])
+# Example specimen http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C155831
+@app.route('/api/getSEQbySpecimenSource', methods=['GET'])
+def getSEQBySpecimenSource():
+ query="""SELECT ?fasta ?specimen_source ?specimen_source_label WHERE
+ {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0001479> <placeholder>]
+ BIND (concat(?specimen_source,"_label") as ?specimen_source_label)}
+ """
+ specimen=request.args.get('specimen')
+ query = query.replace("placeholder", specimen)
+ payload = {'query': query, 'format': 'json'}
+ r = requests.get(baseURL, params=payload)
+ result = r.json()['results']['bindings']
+ return str(result)
+
#No data for this atm
-@app.route('/api/getSEQbyHostHealthStatus', methods=['GET'])
-def getSEQbyHostHealthStatus():
+@app.route('/api/getSEQCountbyHostHealthStatus', methods=['GET'])
+def getSEQCountbyHostHealthStatus():
query="""SELECT ?health_status ?health_status_label (count(?fasta) as ?fastaCount) WHERE
{?fasta ?x [<http://purl.obolibrary.org/obo/NCIT_C25688> ?health_status]
BIND (concat(?health_status,"_label") as ?health_status_label)}
@@ -449,3 +487,35 @@ def getSEQbyHostHealthStatus():
r = requests.get(baseURL, params=payload)
result = r.json()['results']['bindings']
return str(result)
+
+@app.route('/api/getSEQbyLocationAndTech', methods=['GET'])
+def getSEQbyLocationAndTech():
+ query="""SELECT ?fasta WHERE { ?fasta ?x [
+ <http://purl.obolibrary.org/obo/GAZ_00000448> <placeholderLoc>; <http://purl.obolibrary.org/obo/OBI_0600047> <placeholderTech> ]}"""
+ location=request.args.get('location')
+ tech=request.args.get('tech')
+ query=query.replace("placeholderLoc", location)
+ query = query.replace("placeholderTech", tech)
+ print(query)
+ payload = {'query': query, 'format': 'json'}
+ r = requests.get(baseURL, params=payload)
+ result = r.json()['results']['bindings']
+ return str(result)
+
+
+# Example Location http%3A%2F%2Fwww.wikidata.org%2Fentity%2FQ1223
+# Example specimen http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C155831
+@app.route('/api/getSEQbyLocationAndSpecimenSource', methods=['GET'])
+def getSEQbyLocationAndSpecimenSource():
+ query="""SELECT ?fasta WHERE { ?fasta ?x [
+ <http://purl.obolibrary.org/obo/GAZ_00000448> <placeholderLoc>; <http://purl.obolibrary.org/obo/OBI_0001479> <placeholderSpecimen> ]}
+ """
+ location = request.args.get('location')
+ specimen = request.args.get('specimen')
+ query = query.replace("placeholderLoc", location)
+ query = query.replace("placeholderSpecimen", specimen)
+ print(query)
+ payload = {'query': query, 'format': 'json'}
+ r = requests.get(baseURL, params=payload)
+ result = r.json()['results']['bindings']
+ return str(result) \ No newline at end of file