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Merge ef1be86 into 573c2ae
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@mboudet
mboudet committed Jun 8, 2021
2 parents 573c2ae + ef1be86 commit c9a1380
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Showing 21 changed files with 2,588 additions and 27 deletions.
4 changes: 4 additions & 0 deletions askomics/api/query.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,24 +32,28 @@ def query():
if "user" not in session and current_app.iniconfig.getboolean("askomics", "protect_public"):
startpoints = []
public_queries = []
public_form_queries = []
else:
tse = TriplestoreExplorer(current_app, session)
results_handler = ResultsHandler(current_app, session)
startpoints = tse.get_startpoints()
public_queries = results_handler.get_public_queries()
public_form_queries = results_handler.get_public_form_queries()

except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'startpoints': [],
"publicQueries": [],
"publicFormQueries": [],
'error': True,
'errorMessage': str(e)
}), 500

return jsonify({
'startpoints': startpoints,
"publicQueries": public_queries,
"publicFormQueries": public_form_queries,
'error': False,
'errorMessage': ''
})
Expand Down
162 changes: 161 additions & 1 deletion askomics/api/results.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,15 @@ def get_preview():
file_id = data["fileId"]
result_info = {"id": file_id}
result = Result(current_app, session, result_info)
if not result:
return jsonify({
'preview': [],
'header': [],
'id': file_id,
'error': True,
'errorMessage': "You do not have access to this query"
}), 401

headers, preview = result.get_file_preview()

except Exception as e:
Expand Down Expand Up @@ -132,6 +141,16 @@ def get_graph_and_sparql_query():
file_id = data["fileId"]
result_info = {"id": file_id}
result = Result(current_app, session, result_info)
if not result:
return jsonify({
'graphState': {},
'sparqlQuery': "",
'graphs': [],
'endpoints': [],
'diskSpace': 0,
'error': True,
'errorMessage': "You do not have access to this query"
}), 401

# Get graph state and sparql query
graph_state = result.get_graph_state(formated=True)
Expand Down Expand Up @@ -195,9 +214,18 @@ def get_graph_state():
}), 400

file_id = data["fileId"]
formated = data.get("formated", True)

result_info = {"id": file_id}
result = Result(current_app, session, result_info)
graph_state = result.get_graph_state(formated=True)
if not result:
return jsonify({
'graphState': {},
'id': file_id,
'error': True,
'errorMessage': "You do not have access to this graph"
}), 401
graph_state = result.get_graph_state(formated=formated)

except Exception as e:
traceback.print_exc(file=sys.stdout)
Expand Down Expand Up @@ -232,6 +260,11 @@ def download_result():
file_id = data["fileId"]
result_info = {"id": file_id}
result = Result(current_app, session, result_info)
if not result:
return jsonify({
'error': True,
'errorMessage': "You do not have access to this result"
}), 401
dir_path = result.get_dir_path()
file_name = result.get_file_name()

Expand Down Expand Up @@ -317,6 +350,15 @@ def get_sparql_query():
result_info = {"id": file_id}

result = Result(current_app, session, result_info)
if not result:
return jsonify({
'query': {},
'graphs': [],
'endpoints': [],
'diskSpace': 0,
'error': True,
'errorMessage': "You do not have access to this result"
}), 401
query = SparqlQuery(current_app, session)

sparql = result.get_sparql_query()
Expand Down Expand Up @@ -383,6 +425,12 @@ def set_description():
new_desc = data["newDesc"]

result = Result(current_app, session, result_info)
if not result:
return jsonify({
'files': [],
'error': True,
'errorMessage': "You do not have access to this result"
}), 500
result.update_description(new_desc)

results_handler = ResultsHandler(current_app, session)
Expand Down Expand Up @@ -427,6 +475,12 @@ def publish_query():
result_info = {"id": data["id"]}

result = Result(current_app, session, result_info)
if not result:
return jsonify({
'files': [],
'error': True,
'errorMessage': 'Failed to publish query: \n{}'.format("You do not have access to this query")
}), 401
result.publish_query(data.get("public", False))

results_handler = ResultsHandler(current_app, session)
Expand Down Expand Up @@ -471,6 +525,12 @@ def template_query():
result_info = {"id": data["id"]}

result = Result(current_app, session, result_info)
if not result:
return jsonify({
'files': [],
'error': True,
'errorMessage': 'Failed to publish query: \n{}'.format("You do not have access to this query")
}), 401
result.template_query(data.get("template", False))

results_handler = ResultsHandler(current_app, session)
Expand All @@ -491,6 +551,56 @@ def template_query():
})


@results_bp.route('/api/results/form', methods=['POST'])
@api_auth
@login_required
def form_query():
"""Create a form from a result
Returns
-------
json
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
try:
data = request.get_json()
if not (data and data.get("id")):
return jsonify({
'files': [],
'error': True,
'errorMessage': "Missing id parameter"
}), 400

result_info = {"id": data["id"]}

result = Result(current_app, session, result_info)
if not result:
return jsonify({
'files': [],
'error': True,
'errorMessage': 'Failed to publish query: \n{}'.format("You do not have access to this query")
}), 401
result.form_query(data.get("template", False))

results_handler = ResultsHandler(current_app, session)
files = results_handler.get_files_info()

except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'files': [],
'error': True,
'errorMessage': 'Failed to create form template query: \n{}'.format(str(e))
}), 500

return jsonify({
'files': files,
'error': False,
'errorMessage': ''
})


@results_bp.route('/api/results/send2galaxy', methods=['POST'])
@api_auth
@login_required
Expand All @@ -513,6 +623,11 @@ def send2galaxy():

result_info = {"id": data["fileId"]}
result = Result(current_app, session, result_info)
if not result:
return jsonify({
'error': True,
'errorMessage': 'Failed to publish query: \n{}'.format("You do not have access to this query")
}), 401
result.send2galaxy(data["fileToSend"])
except Exception as e:
traceback.print_exc(file=sys.stdout)
Expand All @@ -525,3 +640,48 @@ def send2galaxy():
'error': False,
'errorMessage': ''
})


@results_bp.route('/api/results/save_form', methods=['POST'])
@api_auth
@login_required
def save_form():
"""Update a form
Returns
-------
json
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
try:
# Get query and endpoints and graphs of the query
data = request.get_json()
if not (data and data.get("graphState") and data.get("formId")):
return jsonify({
'error': True,
'errorMessage': "Missing graphState or formId parameter"
}), 400

result_info = {"id": data["formId"]}

result = Result(current_app, session, result_info)
if not result:
return jsonify({
'error': True,
'errorMessage': 'Failed to edit form: \n{}'.format("You do not have access to this form")
}), 401

result.update_graph(data.get("graphState"))

except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'error': True,
'errorMessage': str(e),
}), 500

return jsonify({
'error': False,
'errorMessage': ''
})
24 changes: 24 additions & 0 deletions askomics/libaskomics/Database.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -233,6 +233,8 @@ def create_results_table(self):
traceback text,
graphs_and_endpoints text,
template boolean,
has_form_attr boolean,
form boolean,
FOREIGN KEY(user_id) REFERENCES users(user_id)
)
'''
Expand Down Expand Up @@ -296,6 +298,28 @@ def update_results_table(self):
except Exception:
pass

query = '''
ALTER TABLE results
ADD has_form_attr boolean NULL
DEFAULT(0)
'''

try:
self.execute_sql_query(query)
except Exception:
pass

query = '''
ALTER TABLE results
ADD form boolean NULL
DEFAULT(0)
'''

try:
self.execute_sql_query(query)
except Exception:
pass

def create_endpoints_table(self):
"""Create the endpoints table"""
query = '''
Expand Down

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