def get_graph_of_user(self, username):
"""get all graph of a user
Parameters
----------
username : string
Username
Returns
-------
list
List of graphs
"""
query_launcher = SparqlQueryLauncher(self.app, self.session)
query_builder = SparqlQuery(self.app, self.session)
query = """
SELECT DISTINCT ?graph
WHERE {{
?graph dc:creator <{}> .
}}
""".format(username)
header, data = query_launcher.process_query(query_builder.prefix_query(query))
graphs = []
for result in data:
graphs.append(result["graph"])
return graphs
def get_all_graphs(self):
"""get all graph of a user
Returns
-------
list
List of graphs
"""
query_launcher = SparqlQueryLauncher(self.app, self.session)
query_builder = SparqlQuery(self.app, self.session)
query = """
SELECT DISTINCT ?graph
WHERE {{
?graph dc:creator ?user .
}}
"""
header, data = query_launcher.process_query(
query_builder.prefix_query(query))
graphs = []
for result in data:
graphs.append(result["graph"])
return graphs
def query(self, session, info):
"""Save the query results in filesystem and db
Parameters
----------
session : dict
AskOmics session
graph_state : dict
JSON graph state
Returns
-------
dict
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
try:
info["celery_id"] = self.request.id
result = Result(app, session, info, force_no_db=True)
# Save job in database database
result.set_celery_id(self.request.id)
result.update_db_status("started",
update_celery=True,
update_date=True)
# launch query
query = SparqlQuery(app, session, info["graph_state"])
query.build_query_from_json(for_editor=False)
headers = query.selects
results = []
if query.graphs:
query_launcher = SparqlQueryLauncher(app,
session,
get_result_query=True,
federated=query.federated,
endpoints=query.endpoints)
headers, results = query_launcher.process_query(query.sparql,
isql_api=True)
# write result to a file
file_size = result.save_result_in_file(headers, results)
# Update database status
result.update_db_status("success", size=file_size)
except Exception as e:
traceback.print_exc(file=sys.stdout)
trace = traceback.format_exc()
result.update_db_status("error",
error=True,
error_message=str(e),
traceback=trace)
result.rollback()
raise e
return {'error': True, 'errorMessage': str(e)}
return {'error': False, 'errorMessage': ''}
def set_graphs_and_endpoints(self,
entities=None,
graphs=None,
endpoints=None):
"""Get all public and private graphs containing the given entities
Parameters
----------
entities : list, optional
list of entity uri
"""
substrlst = []
filter_entity_string = ''
if entities:
for entity in entities:
substrlst.append("?entity_uri = <{}>".format(entity))
filter_entity_string = 'FILTER (' + ' || '.join(substrlst) + ')'
filter_public_string = 'FILTER (?public = <true>)'
if 'user' in self.session:
filter_public_string = 'FILTER (?public = <true> || ?creator = <{}>)'.format(
self.session["user"]["username"])
query = '''
SELECT DISTINCT ?graph ?endpoint
WHERE {{
?graph :public ?public .
?graph dc:creator ?creator .
GRAPH ?graph {{
?graph prov:atLocation ?endpoint .
?entity_uri a :entity .
}}
{}
{}
}}
'''.format(filter_public_string, filter_entity_string)
query_launcher = SparqlQueryLauncher(self.app, self.session)
header, results = query_launcher.process_query(
self.prefix_query(query))
self.graphs = []
self.endpoints = []
for res in results:
if not graphs or res["graph"] in graphs:
self.graphs.append(res["graph"])
# If local triplestore url is not accessible by federetad query engine
if res["endpoint"] == self.settings.get(
'triplestore',
'endpoint') and self.local_endpoint_f is not None:
endpoint = self.local_endpoint_f
else:
endpoint = res["endpoint"]
if not endpoints or endpoint in endpoints:
self.endpoints.append(endpoint)
self.endpoints = Utils.unique(self.endpoints)
self.federated = len(self.endpoints) > 1
def create_result(self, has_form=False):
"""Create a result entry in db
Returns
-------
dict
Result info
"""
# Query: transcript concerned by DE and included in QTL
if has_form:
with open("tests/data/graphState_simple_query_form.json", "r") as file:
file_content = file.read()
else:
with open("tests/data/graphState_simple_query.json", "r") as file:
file_content = file.read()
json_query = json.loads(file_content)
# Get query and endpoints and graphs of the query
query = SparqlQuery(self.app, self.session, json_query)
query_launcher = SparqlQueryLauncher(self.app, self.session)
query.build_query_from_json(preview=False, for_editor=False)
info = {
"graph_state": json_query,
"query": query.sparql,
"celery_id": '00000000-0000-0000-0000-000000000000',
"graphs": query.graphs,
"endpoints": query.endpoints
}
# Save job in database database
result = Result(self.app, self.session, info)
result.save_in_db()
# Execute query and write result to file
headers, results = query_launcher.process_query(query.sparql)
file_size = result.save_result_in_file(headers, results)
# Update database status
result.update_db_status("success", size=file_size)
return {
"id": result.id,
"path": result.file_path,
"start": result.start,
"end": result.end,
"size": file_size
}
def get_preview():
"""Get a preview of query
Returns
-------
json
resultsPreview: Preview of the query results
headerPreview: Header of the results table
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
try:
# If public datasets and queries are protected, dont return anything to unlogged users
if "user" not in session and current_app.iniconfig.getboolean("askomics", "protect_public"):
preview = []
header = []
else:
data = request.get_json()
if not (data and data.get("graphState")):
return jsonify({
'resultsPreview': [],
'headerPreview': [],
'error': True,
'errorMessage': "Missing graphState parameter"
}), 400
query = SparqlQuery(current_app, session, data["graphState"], get_graphs=False)
query.build_query_from_json(preview=True, for_editor=False)
endpoints = query.endpoints
federated = query.federated
header = query.selects
preview = []
if query.graphs:
query_launcher = SparqlQueryLauncher(current_app, session, get_result_query=True, federated=federated, endpoints=endpoints)
header, preview = query_launcher.process_query(query.sparql)
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'resultsPreview': [],
'headerPreview': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'resultsPreview': preview,
'headerPreview': header,
'error': False,
'errorMessage': ''
})
def set_triples_number(self):
"""Set graph triples number by requesting the triplestore"""
query = """
SELECT count(*) AS ?count
FROM <{}>
WHERE {{
?s ?p ?o .
}}
""".format(self.file_graph)
sparql = SparqlQueryLauncher(self.app, self.session)
result = sparql.process_query(query)
self.ntriples = result[1][0]["count"]
def sparql_query(self, session, info):
"""Save the sparql query results in filesystem and db
Parameters
----------
session : dict
AskOmics session
info : dict
sparql query
Returns
-------
dict
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
try:
info["celery"] = self.request.id
result = Result(app, session, info, force_no_db=True)
# Save job in db
result.set_celery_id(self.request.id)
result.update_db_status("started", update_celery=True)
query_launcher = SparqlQueryLauncher(app,
session,
get_result_query=True,
federated=info["federated"],
endpoints=info["endpoints"])
header, data = query_launcher.process_query(info["sparql_query"],
isql_api=True)
# Write results in file
file_size = result.save_result_in_file(header, data)
# Update database status
result.update_db_status("success", size=file_size)
except Exception as e:
traceback.print_exc(file=sys.stdout)
trace = traceback.format_exc()
result.update_db_status("error",
error=True,
error_message=str(e),
traceback=trace)
raise e
return {'error': True, 'errorMessage': str(e)}
return {'error': False, 'errorMessage': ''}
def clean_triplestore(self):
"""remove all test graph in the triplestore"""
query = '''
SELECT ?graph
WHERE {{
GRAPH ?graph {{ ?s ?p ?o . }}
FILTER (strStarts(str(?graph), "{}"))
}}
'''.format(self.get_config("triplestore", "default_graph"))
query_launcher = SparqlQueryLauncher(self.app, {})
header, data = query_launcher.process_query(query)
for result in data:
query_launcher.drop_dataset(result["graph"])
def get_preview():
"""Get a preview of query
Returns
-------
json
resultsPreview: Preview of the query results
headerPreview: Header of the results table
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
try:
data = request.get_json()
query_builder = SparqlQueryBuilder(current_app, session)
query = query_builder.build_query_from_json(data["graphState"],
preview=True,
for_editor=False)
endpoints = query_builder.endpoints
federated = query_builder.federated
header = query_builder.selects
preview = []
if query_builder.graphs:
query_launcher = SparqlQueryLauncher(current_app,
session,
get_result_query=True,
federated=federated,
endpoints=endpoints)
header, preview = query_launcher.process_query(query)
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'resultsPreview': [],
'headerPreview': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'resultsPreview': preview,
'headerPreview': header,
'error': False,
'errorMessage': ''
})
def update_base_url(self, graph, old_url, new_url):
"""Update base url for a graph
Parameters
----------
graph : string
Graph to update
old_url : string
Old base_url
new_url : string
New base_url
Returns
-------
list
List of graphs
"""
query_launcher = SparqlQueryLauncher(self.app, self.session)
query_builder = SparqlQuery(self.app, self.session)
query = """
WITH <{0}>
DELETE{{
?s ?p ?o
}}
INSERT{{
?s2 ?p2 ?o2
}}
WHERE {{
?s ?p ?o
FILTER(REGEX(?s, '{1}', 'i') || REGEX(?p, '{1}', 'i') || REGEX(?o, '{1}', 'i')) .
BIND(IF (isURI(?o), URI(REPLACE(STR(?o), '{1}', '{2}')), ?o) AS ?o2) .
BIND(IF (isURI(?s), URI(REPLACE(STR(?s), '{1}', '{2}')), ?s) AS ?s2) .
BIND(IF (isURI(?p), URI(REPLACE(STR(?p), '{1}', '{2}')), ?p) AS ?p2) .
}}
""".format(graph, old_url, new_url)
header, data = query_launcher.process_query(
query_builder.prefix_query(query))
def get_abstraction_relations(self):
"""Get user abstraction relations from the triplestore
Returns
-------
list
Relations
"""
filter_user = ""
if self.logged_user():
filter_user = "******".format(
self.session["user"]["username"])
query_launcher = SparqlQueryLauncher(self.app, self.session)
query_builder = SparqlQueryBuilder(self.app, self.session)
query = '''
SELECT DISTINCT ?graph ?entity_uri ?entity_faldo ?entity_label ?node_type ?attribute_uri ?attribute_faldo ?attribute_label ?attribute_range ?property_uri ?property_faldo ?property_label ?range_uri ?category_value_uri ?category_value_label
WHERE {{
# Graphs
?graph :public ?public .
?graph dc:creator ?creator .
GRAPH ?graph {{
# Property (relations and categories)
?property_uri a owl:ObjectProperty .
?property_uri a :AskomicsRelation .
?property_uri rdfs:label ?property_label .
?property_uri rdfs:domain ?entity_uri .
?property_uri rdfs:range ?range_uri .
}}
FILTER (
?public = <true>{}
)
}}
'''.format(filter_user)
header, data = query_launcher.process_query(
query_builder.prefix_query(query))
relations_list = []
relations = []
for result in data:
# Relation
if "property_uri" in result:
rel_tpl = (result["property_uri"], result["entity_uri"],
result["range_uri"])
if rel_tpl not in relations_list:
relations_list.append(rel_tpl)
relation = {
"uri": result["property_uri"],
"label": result["property_label"],
"graphs": [
result["graph"],
],
"source": result["entity_uri"],
"target": result["range_uri"]
}
relations.append(relation)
else:
# if graph is diff, append it
index_relation = relations_list.index(rel_tpl)
if result["graph"] not in relations[index_relation][
"graphs"]:
relations[index_relation]["graphs"].append(
result["graph"])
return relations
def get_startpoints(self):
"""Get public and user startpoints
Returns
-------
list
Startpoints
"""
filter_user = ""
if self.logged_user():
filter_user = "******".format(
self.session["user"]["username"])
query_launcher = SparqlQueryLauncher(self.app, self.session)
query_builder = SparqlQueryBuilder(self.app, self.session)
query = '''
SELECT DISTINCT ?endpoint ?graph ?entity ?entity_label ?creator ?public
WHERE {{
?graph :public ?public .
?graph dc:creator ?creator .
GRAPH ?graph {{
?graph prov:atLocation ?endpoint .
?entity a :entity .
?entity a :startPoint .
?entity rdfs:label ?entity_label .
}}
FILTER (
?public = <true>{}
)
}}
'''.format(filter_user)
header, data = query_launcher.process_query(
query_builder.prefix_query(query))
startpoints = []
entities = []
for result in data:
if result["endpoint"] == self.settings.get("triplestore",
"endpoint"):
endpoint_name = "local"
else:
try:
endpoint_name = tld.get_fld(
result["endpoint"]).split('.')[0]
except Exception:
endpoint_name = urlparse(result["endpoint"]).netloc
if result["entity"] not in entities:
# new entity
entities.append(result['entity'])
startpoint = {
"entity":
result["entity"],
"entity_label":
result["entity_label"],
"graphs": [{
"uri": result["graph"],
"public": result["public"],
"creator": result["creator"]
}],
"endpoints": [{
"url": result["endpoint"],
"name": endpoint_name
}],
"public":
self.str_to_bool(result["public"]),
"private":
not self.str_to_bool(result["public"])
}
startpoints.append(startpoint)
else:
# update existing entity
index = entities.index(result['entity'])
graph = {
"uri": result["graph"],
"public": result["public"],
"creator": result["creator"]
}
startpoints[index]["graphs"].append(graph)
startpoints[index]["endpoints"].append({
"url":
result["endpoint"],
"name":
endpoint_name
})
if self.str_to_bool(result["public"]):
startpoints[index]["public"] = True
else:
startpoints[index]["private"] = True
return startpoints
def get_abstraction_attributes(self):
"""Get user abstraction attributes from the triplestore
Returns
-------
list
AskOmics attributes
"""
filter_user = ""
if self.logged_user():
filter_user = "******".format(
self.session["user"]["username"])
litterals = ("http://www.w3.org/2001/XMLSchema#string",
"http://www.w3.org/2001/XMLSchema#decimal")
query_launcher = SparqlQueryLauncher(self.app, self.session)
query_builder = SparqlQueryBuilder(self.app, self.session)
query = '''
SELECT DISTINCT ?graph ?entity_uri ?attribute_uri ?attribute_type ?attribute_faldo ?attribute_label ?attribute_range ?category_value_uri ?category_value_label
WHERE {{
# Graphs
?graph :public ?public .
?graph dc:creator ?creator .
GRAPH ?graph {{
?attribute_uri a ?attribute_type .
VALUES ?attribute_type {{ owl:DatatypeProperty :AskomicsCategory }}
?attribute_uri rdfs:label ?attribute_label .
?attribute_uri rdfs:domain ?entity_uri .
?attribute_uri rdfs:range ?attribute_range .
# Faldo
OPTIONAL {{
?attribute_uri a ?attribute_faldo .
VALUES ?attribute_faldo {{ askomics:faldoStart askomics:faldoEnd askomics:faldoStrand askomics:faldoReference }}
}}
# Categories (DK)
OPTIONAL {{
?attribute_range askomics:category ?category_value_uri .
?category_value_uri rdfs:label ?category_value_label .
}}
}}
FILTER (
?public = <true>{}
)
}}
'''.format(filter_user)
header, data = query_launcher.process_query(
query_builder.prefix_query(query))
attributes_list = []
attributes = []
for result in data:
# Attributes
if "attribute_uri" in result and "attribute_label" in result and result[
"attribute_type"] != "{}AskomicsCategory".format(
self.settings.get("triplestore", "prefix")
) and result["attribute_range"] in litterals:
attr_tpl = (result["attribute_uri"], result["entity_uri"])
if attr_tpl not in attributes_list:
attributes_list.append(attr_tpl)
attribute = {
"uri":
result["attribute_uri"],
"label":
result["attribute_label"],
"graphs": [
result["graph"],
],
"entityUri":
result["entity_uri"],
"type":
result["attribute_range"],
"faldo":
result["attribute_faldo"]
if "attribute_faldo" in result else None,
"categories": []
}
attributes.append(attribute)
else:
# if graph is different, store it
index_attribute = attributes_list.index(attr_tpl)
if result["graph"] not in attributes[index_attribute][
"graphs"]:
attributes[index_attribute]["graphs"].append(
result["graph"])
index_attribute = attributes_list.index(attr_tpl)
# Categories
if "attribute_uri" in result and result[
"attribute_type"] == "{}AskomicsCategory".format(
self.settings.get("triplestore", "prefix")):
attr_tpl = (result["attribute_uri"], result["entity_uri"])
if attr_tpl not in attributes_list:
attributes_list.append(attr_tpl)
attribute = {
"uri":
result["attribute_uri"],
"label":
result["attribute_label"],
"graphs": [
result["graph"],
],
"entityUri":
result["entity_uri"],
"type":
result["attribute_type"],
"faldo":
result["attribute_faldo"]
if "attribute_faldo" in result else None,
"categories": [{
"uri": result["category_value_uri"],
"label": result["category_value_label"]
}]
}
attributes.append(attribute)
else:
# if graph diff, store it
index_attribute = attributes_list.index(attr_tpl)
if result["graph"] not in attributes[index_attribute][
"graphs"]:
attributes[index_attribute]["graphs"].append(
result["graph"])
# Store value if new
value = {
"uri": result["category_value_uri"],
"label": result["category_value_label"]
}
if value not in attributes[index_attribute]["categories"]:
attributes[index_attribute]["categories"].append(value)
return attributes
def get_abstraction_entities(self):
"""Get abstraction entities
Returns
-------
list
List of entities available
"""
filter_user = ""
if self.logged_user():
filter_user = "******".format(
self.session["user"]["username"])
query_launcher = SparqlQueryLauncher(self.app, self.session)
query_builder = SparqlQueryBuilder(self.app, self.session)
query = '''
SELECT DISTINCT ?endpoint ?graph ?entity_uri ?entity_type ?entity_faldo ?entity_label ?have_no_label
WHERE {{
?graph :public ?public .
?graph dc:creator ?creator .
GRAPH ?graph {{
?graph prov:atLocation ?endpoint .
?entity_uri a ?entity_type .
VALUES ?entity_type {{ :entity :bnode }} .
# Faldo
OPTIONAL {{
?entity_uri a ?entity_faldo .
VALUES ?entity_faldo {{ :faldo }} .
}}
# Label
OPTIONAL {{ ?entity_uri rdfs:label ?entity_label . }}
OPTIONAL {{ ?entity_uri :instancesHaveNoLabels ?have_no_label . }}
}}
FILTER (
?public = <true>{}
)
}}
'''.format(filter_user)
header, data = query_launcher.process_query(
query_builder.prefix_query(query))
entities_list = [] # list of entity uri
entities = [] # list of entity dict
for result in data:
if result["entity_uri"] not in entities_list:
# New entity
entities_list.append(result["entity_uri"])
# Uri, graph and label
label = "" if "entity_label" not in result else result[
"entity_label"]
entity_type = "bnode" if result[
"entity_type"] == "{}bnode".format(
self.settings.get("triplestore", "prefix")) else "node"
entity = {
"uri":
result["entity_uri"],
"type":
entity_type,
"label":
label,
"instancesHaveLabels":
True if "have_no_label" not in result else
False if result["have_no_label"] == "1" else True,
"faldo":
True if "entity_faldo" in result else False,
"endpoints": [result["endpoint"]],
"graphs": [result["graph"]],
}
entities.append(entity)
else:
# if graph is different, store it
index_entity = entities_list.index(result['entity_uri'])
if result["graph"] not in entities[index_entity]["graphs"]:
entities[index_entity]["graphs"].append(result["graph"])
# If endpoint is different, store it
if result["endpoint"] not in entities[index_entity][
"endpoints"]:
entities[index_entity]["endpoints"].append(
result["endpoint"])
return entities
def query():
"""Perform a sparql query
Returns
-------
json
query results
"""
if not can_access(session['user']):
return jsonify({"error": True, "errorMessage": "Admin required"}), 401
data = request.get_json()
if not (data and data.get("query")):
return jsonify({
'error': True,
'errorMessage': "Missing query parameter",
'header': [],
'data': []
}), 400
q = data['query']
graphs = data.get('graphs', [])
endpoints = data.get('endpoints', [])
local_endpoint_f = current_app.iniconfig.get('triplestore', 'endpoint')
try:
local_endpoint_f = current_app.iniconfig.get('federation',
'local_endpoint')
except Exception:
pass
# No graph selected in local TS
if not graphs and local_endpoint_f in endpoints:
return jsonify({
'error': True,
'errorMessage': "No graph selected in local triplestore",
'header': [],
'data': []
}), 400
# No endpoint selected
if not endpoints:
return jsonify({
'error': True,
'errorMessage': "No endpoint selected",
'header': [],
'data': []
}), 400
try:
query = SparqlQuery(current_app, session, get_graphs=False)
query.set_graphs_and_endpoints(graphs=graphs, endpoints=endpoints)
federated = query.is_federated()
replace_froms = query.replace_froms()
sparql = query.format_query(q,
replace_froms=replace_froms,
federated=federated)
# header, data = query_launcher.process_query(query)
header = query.selects
data = []
if query.graphs or query.endpoints:
query_launcher = SparqlQueryLauncher(current_app,
session,
get_result_query=True,
federated=federated,
endpoints=endpoints)
header, data = query_launcher.process_query(sparql)
except Exception as e:
current_app.logger.error(str(e).replace('\\n', '\n'))
traceback.print_exc(file=sys.stdout)
return jsonify({
'error': True,
'errorMessage': str(e).replace('\\n', '\n'),
'header': [],
'data': []
}), 500
return jsonify({'header': header, 'data': data})
def query():
"""Perform a sparql query
Returns
-------
json
query results
"""
q = request.get_json()['query']
graphs = request.get_json()['graphs']
endpoints = request.get_json()['endpoints']
local_endpoint_f = current_app.iniconfig.get('triplestore', 'endpoint')
try:
local_endpoint_f = current_app.iniconfig.get('federation',
'local_endpoint')
except Exception:
pass
# No graph selected in local TS
if not graphs and local_endpoint_f in endpoints:
return jsonify({
'error': True,
'errorMessage': "No graph selected in local triplestore",
'header': [],
'data': []
}), 500
# No endpoint selected
if not endpoints:
return jsonify({
'error': True,
'errorMessage': "No endpoint selected",
'header': [],
'data': []
}), 500
try:
query_builder = SparqlQueryBuilder(current_app, session)
query_builder.set_graphs_and_endpoints(graphs=graphs,
endpoints=endpoints)
federated = query_builder.is_federated()
replace_froms = query_builder.replace_froms()
query = query_builder.format_query(q,
replace_froms=replace_froms,
federated=federated)
# header, data = query_launcher.process_query(query)
header = query_builder.selects
data = []
if query_builder.graphs or query_builder.endpoints:
query_launcher = SparqlQueryLauncher(current_app,
session,
get_result_query=True,
federated=federated,
endpoints=endpoints)
header, data = query_launcher.process_query(query)
except Exception as e:
current_app.logger.error(str(e).replace('\\n', '\n'))
traceback.print_exc(file=sys.stdout)
return jsonify({
'error': True,
'errorMessage': str(e).replace('\\n', '\n'),
'header': [],
'data': []
}), 500
return jsonify({'header': header, 'data': data})