def __init__(self, smtp_conf=None, **kwargs):
super(SubmissionTransaction, self).__init__(role="submit", **kwargs)
self.app_config = capp.config
if utils.should_send_email(self.app_config):
self.smtp_conf = smtp_conf
try:
program, project = self.transaction.project_id.split("-", 1)
authorize(program, project, [ROLE_SUBMIT])
except AuthZError:
return self.record_error(
"You do not have submit permission for project {}".format(
self.project_id),
type=EntityErrors.INVALID_PERMISSIONS,
)
self.project_node = utils.lookup_project(self.db_driver, self.program,
self.project)
def __init__(self, transaction, node):
super(DeletionEntity, self).__init__(transaction, node)
self.action = "delete"
self.dependents = {
# entity.node.node_id: entity
}
if isinstance(node, MissingNode):
self.neighbors = ()
return
self.neighbors = (edge.src for edge in node.edges_in)
# Check user permissions for deleting nodes
try:
program, project = self.transaction.project_id.split("-", 1)
authorize(program, project, ["delete"])
except AuthZError:
return self.record_error(
"You do not have delete permission for project {}".format(
self.transaction.project_id))
def get_node_merge(self):
"""
This is called for a PATCH operation and supports upsert. It will
lookup an existing node or create one if it doesn't exist.
Return:
Optional[psqlgraph.Node]
"""
# Expect one existing node matching the secondary keys.
try:
node = lookup_node(
self.transaction.db_driver,
self.entity_type,
self.entity_id,
self.secondary_keys,
).one()
except sqlalchemy.orm.exc.NoResultFound:
return self.get_node_create()
except sqlalchemy.orm.exc.MultipleResultsFound:
self.record_error(
"Entity is not unique, multiple entities found with {}".format(
self.secondary_keys
),
type=EntityErrors.NOT_UNIQUE,
)
return None
# Check user permissions for updating nodes
try:
program, project = self.transaction.project_id.split("-", 1)
authorize(program, project, ["update"])
except AuthZError:
return self.record_error(
"You do not have update permission for project {}".format(
self.transaction.project_id
),
type=EntityErrors.INVALID_PERMISSIONS,
)
self.old_props = {k: v for k, v in node.props.items()}
if node.label != self.entity_type:
self.record_error(
"Existing {} entity found with type different from {}".format(
node.label, self.entity_type
),
type=EntityErrors.NOT_UNIQUE,
)
return None
# Verify that the node is in the correct project
if not self._verify_node_project_id(node):
self.record_error(
"Entity is owned by project {}, not {}".format(
node.project_id, self.transaction.project_id
),
type=EntityErrors.INVALID_PERMISSIONS,
)
self._merge_doc_links(node)
if self.entity_id and node.node_id != self.entity_id:
self.record_error(
"Existing {} entity found with id different from {}".format(
node, self.entity_id
),
type=EntityErrors.NOT_UNIQUE,
)
return None
# Since we are updating the node, we have to set its state to
# ``validated``. This means that this version of the node has
# not been submitted and will not be displayed on the portal.
# The node is now essential a draft.
if node.state is None:
node.state = "validated"
# Fill in default system property values
for key in self.get_system_property_defaults():
self.logger.debug(
"{}: setting system prop self.doc['{}'] to '{}'".format(
node, key, node._props.get(key)
)
)
if self.doc.get(key) and self.doc.get(key) != node._props.get(key):
msg = (
"Property '{}' ({}) is a system property and will be" " ignored."
).format(key, self.doc.get(key))
self.record_warning(msg, keys=[key], type=EntityErrors.INVALID_PROPERTY)
self.doc[key] = node._props.get(key)
self.action = "update"
self.entity_id = node.node_id
return node
def get_node_create(self, skip_node_lookup=False):
"""
This is called for a POST operation.
Check that:
#. The user isn't supplying an id
#. If not `skip_node_lookup`, the node does not already exist
Return:
psqlgraph.Node
"""
# Check user permissions for updating nodes
try:
program, project = self.transaction.project_id.split("-", 1)
authorize(program, project, ["create"])
except AuthZError:
return self.record_error(
"You do not have create permission for project {}".format(
self.transaction.project_id
),
type=EntityErrors.INVALID_PERMISSIONS,
)
# Check to see if it's registered in dbGaP is is an exception
# to the rule
if self.entity_type == "case":
submitter_id = self.doc.get("submitter_id")
allowed = True
try:
if self._config.get("USE_DBGAP", False):
allowed = self.is_case_creation_allowed(submitter_id)
except InternalError as e:
return self.record_error(
"Unable to validate case against dbGaP. {}".format(str(e)),
keys=["submitter_id"],
type=EntityErrors.NOT_FOUND,
)
else:
if not allowed:
return self.record_error(
"Case submitter_id '{}' not found in dbGaP.".format(
submitter_id
),
keys=["submitter_id"],
type=EntityErrors.NOT_FOUND,
)
if not self.entity_id:
self.entity_id = str(uuid.uuid4())
# Assert that the node doesn't already exist
if not skip_node_lookup:
nodes = lookup_node(
self.transaction.db_driver,
self.entity_type,
self.entity_id,
self.secondary_keys,
)
if nodes.count():
return self.record_error(
"Cannot create entity that already exists. "
"Try updating entity (PUT instead of POST)",
keys=["id"],
type=EntityErrors.NOT_UNIQUE,
)
# Fill in default system property values
for key, val in self.get_system_property_defaults().items():
if self.doc.get(key, None) is None:
self.doc[key] = val
# Create the node and populate its properties
cls = psqlgraph.Node.get_subclass(self.entity_type)
self.logger.debug("Creating new {}".format(cls.__name__))
node = cls(self.entity_id)
self.action = "create"
return node