def get_projects():
"""
Get all projects high level information, if a deployment is configured
to set PUBLIC_DATASETS to True, this endpoint will be open to
anonymous users
"""
if os.environ.get("PUBLIC_DATASETS", "false").lower() == "true":
set_read_access_projects_for_public_endpoint()
else:
set_read_access_projects()
projects = flask.g.read_access_projects
if not projects:
return flask.jsonify({"projects": []})
# construct a query that get counts for all projects
# because graphql can't add structure to group by projects,
# we labeled the count by project index and later parse it
# with regex to add structure to response
query = "{project (first: 0) { name code dbgap_accession_number "
for field in ["description", "image_url"]:
if dictionary.schema["project"]["properties"].get(field):
query += field + " "
query += "}}"
data, errors = graphql.execute_query(query, variables={})
if errors:
return flask.jsonify({"data": data, "errors": errors}), 400
return flask.jsonify({"projects": data["project"]})
def get_datasets():
"""
Get dataset level summary counts, if a deployment is configured
to set PUBLIC_DATASETS to True, this endpoint will be open to
anonymous users
"""
nodes = flask.request.args.get("nodes", "")
nodes = nodes.split(",")
if not nodes:
raise UserError("Need to provide target nodes in query param")
if os.environ.get("PUBLIC_DATASETS", "false").lower() == "true":
set_read_access_projects_for_public_endpoint()
else:
set_read_access_projects()
projects = flask.g.read_access_projects
if not projects:
return flask.jsonify({})
# construct a query that get counts for all projects
# because graphql can't add structure to group by projects,
# we labeled the count by project index and later parse it
# with regex to add structure to response
query = "{"
for i, project_id in enumerate(projects):
query += (
" ".join(
map(
lambda x: """i{i}_{node}: _{node}_count(project_id: "{p}")""".format(
i=i, node=x, p=project_id
),
nodes,
)
)
+ " "
)
query += "}"
data, errors = graphql.execute_query(query, variables={})
if errors:
return flask.jsonify({"data": data, "errors": errors}), 400
result = {project_id: {} for project_id in projects}
for name, value in data.iteritems():
match = re.search("^i(\d+)_(.*)", name)
index = int(match.group(1))
node = match.group(2)
result[projects[index]][node] = value
return flask.jsonify(result)
def root_graphql_query():
"""
Run a graphql query.
"""
# Short circuit if user is not recognized. Make sure that the list of
# projects that the user has read access to is set.
try:
set_read_access_projects()
except AuthZError:
data = flask.jsonify({"data": {}, "errors": ["Unauthorized query."]})
return data, 403
payload = peregrine.utils.parse_request_json()
query = payload.get("query")
variables, errors = peregrine.utils.get_variables(payload)
if errors:
return flask.jsonify({"data": None, "errors": errors}), 400
return peregrine.utils.jsonify_check_errors(
graphql.execute_query(query, variables))