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-rw-r--r--bh20simplewebuploader/main.py69
1 files changed, 53 insertions, 16 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index d3542c3..37f4590 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -663,11 +663,48 @@ def contact_page():
buf = get_html_body('doc/web/contact.html','https://github.com/arvados/bh20-seq-resource/blob/master/doc/web/contact.org')
return render_template('about.html',menu='CONTACT',embed=buf)
+##
+## Linked data permanent links/resources
+##
+sparqlURL='http://sparql.genenetwork.org/sparql/'
+
+##
+# Example http://host/resource/MT326090.1
+@app.route('/resource/<id>')
+def resource(id):
+ """Get a COVID19 resource using identifier"""
+ query="""
+PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
+PREFIX sio: <http://semanticscience.org/resource/>
+select distinct ?sample ?geoname ?date ?source ?geo ?sampletype
+{
+ ?sample sio:SIO_000115 "MT326090.1" .
+ ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> ?geo .
+ ?geo rdfs:label ?geoname .
+ ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date .
+ OPTIONAL {?sample <http://edamontology.org/data_2091> ?source }
+ OPTIONAL {?sample <http://purl.obolibrary.org/obo/OBI_0001479> ?sampletype }
+}
+ """
+ payload = {'query': query, 'format': 'json'}
+ r = requests.get(sparqlURL, params=payload)
+ result = r.json()['results']['bindings']
+ # for now we just take the first one
+ sample = result[0]
+ logging.info(sample)
+ logging.info("^^^^^^^^^^^^^^^^^^^^^^^^^^^^")
+ # return jsonify({'sequences': int(result[0]["num"]["value"])})
+ locationuri=sample['geo']['value']
+ location=sample['geoname']['value']
+ date=sample['date']['value']
+ source=sample['source']['value']
+ sampletype=sample['sampletype']['value']
+ return render_template('permalink.html',id=id,menu='',uri=f"http://covid19.genenetwork.org/resource/{id}",locationuri=locationuri,location=location,date=date,source=source,sampletype=sampletype)
+
## Dynamic API functions starting here
## This is quick and dirty for now, just to get something out and demonstrate the queries
## Feel free to rename the functions/endpoints, feel free to process result so we get nicer JSON
## but most likely you don't want to touch the queries, Cheers.
-baseURL='http://sparql.genenetwork.org/sparql/'
@app.route('/api/getCount', methods=['GET'])
def getCount():
@@ -693,7 +730,7 @@ def getCountDB():
}
"""
payload = {'query': query, 'format': 'json'}
- r = requests.get(baseURL, params=payload)
+ r = requests.get(sparqlURL, params=payload)
result = r.json()['results']['bindings']
# [{'num': {'type': 'typed-literal', 'datatype': 'http://www.w3.org/2001/XMLSchema#integer', 'value': '1352'}}]
# print(result, file=sys.stderr)
@@ -703,7 +740,7 @@ def getCountDB():
def getAllaccessions():
query="""SELECT DISTINCT ?fasta ?value WHERE {?fasta ?x[ <http://edamontology.org/data_2091> ?value ]}"""
payload = {'query': query, 'format': 'json'}
- r = requests.get(baseURL, params=payload)
+ r = requests.get(sparqlURL, params=payload)
result = r.json()['results']['bindings']
return jsonify([{'uri': x['fasta']['value'],
'value': x['value']['value']} for x in result])
@@ -720,7 +757,7 @@ def getDetailsForSeq():
BIND(IF(BOUND(?key_tmp_label),?key_tmp_label, ?key) as ?key_label)}"""
query=query.replace("placeholder", seq_id)
payload = {'query': query, 'format': 'json'}
- r = requests.get(baseURL, params=payload)
+ r = requests.get(sparqlURL, params=payload)
result = r.json()['results']['bindings']
return jsonify([{'uri': x['key']['value'], 'key_label': x['key_label']['value'],
'value': x['value']['value']} for x in result])
@@ -737,7 +774,7 @@ def getCountByGPS():
GROUP BY ?location ?location_label ?GPS
"""
payload = {'query': query, 'format': 'json'}
- r = requests.get(baseURL, params=payload)
+ r = requests.get(sparqlURL, params=payload)
result = r.json()['results']['bindings']
return jsonify([{'count': x['fastaCount']['value'],
'Location': x['location']['value'],
@@ -754,7 +791,7 @@ def getSEQCountbytech():
GROUP BY ?tech ?tech_label ORDER BY DESC (?fastaCount)
"""
payload = {'query': query, 'format': 'json'}
- r = requests.get(baseURL, params=payload)
+ r = requests.get(sparqlURL, params=payload)
result = r.json()['results']['bindings']
return jsonify([{'count': x['fastaCount']['value'],
'key': x['tech']['value'],
@@ -770,7 +807,7 @@ def getSEQbytech():
tech = request.args.get('tech')
query=query.replace("placeholder", tech)
payload = {'query': query, 'format': 'json'}
- r = requests.get(baseURL, params=payload)
+ r = requests.get(sparqlURL, params=payload)
result = r.json()['results']['bindings']
return str(result)
@@ -783,7 +820,7 @@ def getSEQbyLocation():
query=query.replace("placeholder", location)
print(query)
payload = {'query': query, 'format': 'json'}
- r = requests.get(baseURL, params=payload)
+ r = requests.get(sparqlURL, params=payload)
result = r.json()['results']['bindings']
return str(result)
@@ -797,7 +834,7 @@ def getSEQCountbyLocation():
GROUP BY ?geoLocation ?geoLocation_label ORDER BY DESC (?fastaCount)
"""
payload = {'query': query, 'format': 'json'}
- r = requests.get(baseURL, params=payload)
+ r = requests.get(sparqlURL, params=payload)
result = r.json()['results']['bindings']
return jsonify([{'count': x['fastaCount']['value'],
'key': x['geoLocation']['value'],
@@ -816,7 +853,7 @@ def getSEQCountbyContinent():
GROUP BY ?continent ?continent_label
"""
payload = {'query': query, 'format': 'json'}
- r = requests.get(baseURL, params=payload)
+ r = requests.get(sparqlURL, params=payload)
result = r.json()['results']['bindings']
return jsonify([{'count': x['fastaCount']['value'],
'key': x['continent']['value'],
@@ -837,7 +874,7 @@ def getSEQCountbyCountryContinent():
continent = request.args.get('continent')
query = query.replace("placeholder", continent)
payload = {'query': query, 'format': 'json'}
- r = requests.get(baseURL, params=payload)
+ r = requests.get(sparqlURL, params=payload)
result = r.json()['results']['bindings']
return jsonify([{'count': x['fastaCount']['value'],
'key': x['location']['value'],
@@ -855,7 +892,7 @@ def getSEQCountbySpecimenSource():
ORDER BY DESC (?fastaCount)
"""
payload = {'query': query, 'format': 'json'}
- r = requests.get(baseURL, params=payload)
+ r = requests.get(sparqlURL, params=payload)
result = r.json()['results']['bindings']
return jsonify([{'count': x['fastaCount']['value'],
'key': x['specimen_source']['value'],
@@ -871,7 +908,7 @@ def getSEQBySpecimenSource():
specimen=request.args.get('specimen')
query = query.replace("placeholder", specimen)
payload = {'query': query, 'format': 'json'}
- r = requests.get(baseURL, params=payload)
+ r = requests.get(sparqlURL, params=payload)
result = r.json()['results']['bindings']
return str(result)
@@ -885,7 +922,7 @@ def getSEQCountbyHostHealthStatus():
ORDER BY DESC (?fastaCount)
"""
payload = {'query': query, 'format': 'json'}
- r = requests.get(baseURL, params=payload)
+ r = requests.get(sparqlURL, params=payload)
result = r.json()['results']['bindings']
return str(result)
@@ -899,7 +936,7 @@ def getSEQbyLocationAndTech():
query = query.replace("placeholderTech", tech)
print(query)
payload = {'query': query, 'format': 'json'}
- r = requests.get(baseURL, params=payload)
+ r = requests.get(sparqlURL, params=payload)
result = r.json()['results']['bindings']
return str(result)
@@ -917,6 +954,6 @@ def getSEQbyLocationAndSpecimenSource():
query = query.replace("placeholderSpecimen", specimen)
print(query)
payload = {'query': query, 'format': 'json'}
- r = requests.get(baseURL, params=payload)
+ r = requests.get(sparqlURL, params=payload)
result = r.json()['results']['bindings']
return str(result)
generated by cgit v1.2.3 (git 2.44.0) at 2024-05-18 20:10:33 +0000