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Merge 1bccb24 into c86c690
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@mboudet
mboudet committed Feb 10, 2023
2 parents c86c690 + 1bccb24 commit b9f551e
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Showing 6 changed files with 27 additions and 26 deletions.
2 changes: 1 addition & 1 deletion askomics/libaskomics/SparqlQuery.py
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Original file line number Diff line number Diff line change
Expand Up @@ -273,7 +273,7 @@ def toggle_public(self, graph, public):
'''.format(graph=graph, public=public)

query_launcher = SparqlQueryLauncher(self.app, self.session)
query_launcher.execute_query(self.prefix_query(query))
query_launcher.execute_query(self.prefix_query(query), is_update=True)

def get_default_query_with_prefix(self):
"""Get default query with the prefixes
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27 changes: 14 additions & 13 deletions askomics/libaskomics/SparqlQueryLauncher.py
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Original file line number Diff line number Diff line change
Expand Up @@ -163,7 +163,7 @@ def load_data_virtuoso(self, file_name, graph, host_url):
)

query = "LOAD <{}> INTO GRAPH <{}>".format(file_url, graph)
return self.execute_query(query)
return self.execute_query(query, is_update=True)

def get_triples_from_graph(self, graph):
"""Get triples from a rdflib graph
Expand Down Expand Up @@ -206,7 +206,7 @@ def insert_ttl_string(self, ttl_string, graph):
}}
'''.format(graph, ttl_string)

return self.execute_query(query)
return self.execute_query(query, is_update=True)

def insert_data(self, ttl, graph, metadata=False):
"""Insert data into the triplesotre using INSERT
Expand Down Expand Up @@ -235,7 +235,7 @@ def insert_data(self, ttl, graph, metadata=False):
}}
'''.format(graph, triples)

return self.execute_query(query)
return self.execute_query(query, is_update=True)

def drop_dataset(self, graph):
"""Drop the datasets of the triplestore and its metadata
Expand All @@ -248,9 +248,9 @@ def drop_dataset(self, graph):
query = '''
DROP SILENT GRAPH <{}>
'''.format(graph)
self.execute_query(query, disable_log=True, isql_api=True)
self.execute_query(query, disable_log=True, isql_api=True, is_update=True)

def process_query(self, query, isql_api=False):
def process_query(self, query, isql_api=False, is_update=False):
"""Execute a query and return parsed results
Parameters
Expand All @@ -263,9 +263,9 @@ def process_query(self, query, isql_api=False):
list
Parsed results
"""
return self.parse_results(self.execute_query(query, isql_api=isql_api))
return self.parse_results(self.execute_query(query, isql_api=isql_api, is_update=is_update))

def execute_query(self, query, disable_log=False, isql_api=False):
def execute_query(self, query, disable_log=False, isql_api=False, is_update=False):
"""Execute a sparql query
Parameters
Expand Down Expand Up @@ -299,24 +299,25 @@ def execute_query(self, query, disable_log=False, isql_api=False):

if use_isql:
formatted_query = "SPARQL {}".format(query)
json = {"command": formatted_query, "disable_log": disable_log, "sparql_select": not self.endpoint.isSparqlUpdateRequest()}
json = {"command": formatted_query, "disable_log": disable_log, "sparql_select": not is_update}
response = requests.post(url=isql_api_url, json=json)
results = response.json()
if results["status"] == 500:
raise HTTPError("isqlapi: {}".format(results["message"]))

else:
# Update
if self.endpoint.isSparqlUpdateRequest():
if is_update:
self.endpoint.setMethod('POST')
# Virtuoso hack
# if self.triplestore == 'virtuoso':
# self.endpoint.queryType = "SELECT"

# Force sending to secure endpoint
self.endpoint.queryType = "INSERT"
results = self.endpoint.query()

# Select
else:
self.endpoint.setReturnFormat(JSON)
# Force sending to public endpoint
self.endpoint.queryType = "SELECT"
results = self.endpoint.query().convert()

self.query_time = time.time() - start_time
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2 changes: 1 addition & 1 deletion config/askomics.test.ini
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Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,7 @@ autocomplete_max_results = 20
# name of the triplestore, can be virtuoso or fuseki
triplestore = virtuoso
# Sparql endpoint
endpoint = http://localhost:8891/sparql-auth
endpoint = http://localhost:8891/sparql
# Sparql updatepoint
updatepoint = http://localhost:8891/sparql-auth
# Isql API
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2 changes: 1 addition & 1 deletion tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -489,7 +489,7 @@ def upload_and_integrate_ontology(self):
# integrate
int_ontology = self.integrate_file({
"id": 1,
}, set_graph=True, endpoint="http://localhost:8891/sparql-auth")
}, set_graph=True, endpoint="http://localhost:8891/sparql")

return {
"upload": up_ontology,
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8 changes: 4 additions & 4 deletions tests/results/abstraction.json
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Original file line number Diff line number Diff line change
Expand Up @@ -525,7 +525,7 @@
"entities": [
{
"endpoints": [
"http://localhost:8891/sparql-auth"
"http://localhost:8891/sparql"
],
"faldo": true,
"graphs": [
Expand All @@ -540,7 +540,7 @@
},
{
"endpoints": [
"http://localhost:8891/sparql-auth"
"http://localhost:8891/sparql"
],
"faldo": true,
"graphs": [
Expand All @@ -555,7 +555,7 @@
},
{
"endpoints": [
"http://localhost:8891/sparql-auth"
"http://localhost:8891/sparql"
],
"faldo": true,
"graphs": [
Expand All @@ -569,7 +569,7 @@
},
{
"endpoints": [
"http://localhost:8891/sparql-auth"
"http://localhost:8891/sparql"
],
"faldo": false,
"graphs": [
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12 changes: 6 additions & 6 deletions tests/results/startpoints.json
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Original file line number Diff line number Diff line change
Expand Up @@ -8,10 +8,10 @@
[{
"endpoints": [{
"name": "local",
"url": "http://localhost:8891/sparql-auth"
"url": "http://localhost:8891/sparql"
}, {
"name": "local",
"url": "http://localhost:8891/sparql-auth"
"url": "http://localhost:8891/sparql"
}],
"entity":
"http://askomics.org/test/data/transcript",
Expand All @@ -37,10 +37,10 @@
{
"endpoints": [{
"name": "local",
"url": "http://localhost:8891/sparql-auth"
"url": "http://localhost:8891/sparql"
}, {
"name": "local",
"url": "http://localhost:8891/sparql-auth"
"url": "http://localhost:8891/sparql"
}],
"entity":
"http://askomics.org/test/data/gene",
Expand Down Expand Up @@ -70,7 +70,7 @@
{
"endpoints": [{
"name": "local",
"url": "http://localhost:8891/sparql-auth"
"url": "http://localhost:8891/sparql"
}],
"entity":
"http://askomics.org/test/data/DifferentialExpression",
Expand All @@ -89,7 +89,7 @@
{
"endpoints": [{
"name": "local",
"url": "http://localhost:8891/sparql-auth"
"url": "http://localhost:8891/sparql"
}],
"entity":
"http://askomics.org/test/data/QTL",
Expand Down

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