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Refactor dataset fetching in get/set dataset method in web controller.

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This commit is contained in:
John Chilton
2019-02-22 13:10:12 -05:00
parent 6feef2a280
commit 656b3c2f87
1 changed files with 31 additions and 25 deletions
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lib/galaxy/webapps/galaxy/controllers/dataset.py
+31 -25
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@@ -251,27 +251,11 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
@web.expose_api_anonymous
def get_edit(self, trans, dataset_id=None, **kwd):
"""Produces the input definitions available to modify dataset attributes"""
message = None
status = None
if dataset_id is not None:
id = self.decode_id(dataset_id)
data = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id)
else:
trans.log_event("dataset_id is None, cannot load a dataset to edit.")
return self.message_exception(trans, 'You must provide a dataset id to edit attributes.')
if data is None:
trans.log_event("Problem retrieving dataset id (%s)." % dataset_id)
return self.message_exception(trans, 'The dataset id is invalid.')
if dataset_id is not None and data.history.user is not None and data.history.user != trans.user:
trans.log_event("User attempted to edit a dataset they do not own (encoded: %s, decoded: %s)." % (dataset_id, id))
return self.message_exception(trans, 'The dataset id is invalid.')
if data.history.user and not data.dataset.has_manage_permissions_roles(trans):
# Permission setting related to DATASET_MANAGE_PERMISSIONS was broken for a period of time,
# so it is possible that some Datasets have no roles associated with the DATASET_MANAGE_PERMISSIONS
# permission. In this case, we'll reset this permission to the hda user's private role.
manage_permissions_action = trans.app.security_agent.get_action(trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action)
permissions = {manage_permissions_action : [trans.app.security_agent.get_private_user_role(data.history.user)]}
trans.app.security_agent.set_dataset_permission(data.dataset, permissions)
data, message = self._get_dataset_for_edit(trans, dataset_id)
if message:
return message
if self._can_access_dataset(trans, data):
if data.state == trans.model.Dataset.states.UPLOAD:
return self.message_exception(trans, 'Please wait until this dataset finishes uploading before attempting to edit its metadata.')
@@ -416,13 +400,13 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
return False
return True
message = None
status = 'success'
dataset_id = payload.get('dataset_id')
operation = payload.get('operation')
if dataset_id is not None:
id = self.decode_id(dataset_id)
data = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id)
dataset_id = payload.get('dataset_id')
data, message = self._get_dataset_for_edit(trans, dataset_id)
if message:
return message
if operation == 'attributes':
# The user clicked the Save button on the 'Edit Attributes' form
data.name = payload.get('name')
@@ -510,6 +494,28 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
return self.message_exception(trans, 'Invalid operation identifier (%s).' % operation)
return {'status': status, 'message': sanitize_text(message)}
def _get_dataset_for_edit(self, trans, dataset_id):
if dataset_id is not None:
id = self.decode_id(dataset_id)
data = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id)
else:
trans.log_event("dataset_id is None, cannot load a dataset to edit.")
return None, self.message_exception(trans, 'You must provide a dataset id to edit attributes.')
if data is None:
trans.log_event("Problem retrieving dataset id (%s)." % dataset_id)
return None, self.message_exception(trans, 'The dataset id is invalid.')
if dataset_id is not None and data.history.user is not None and data.history.user != trans.user:
trans.log_event("User attempted to edit a dataset they do not own (encoded: %s, decoded: %s)." % (dataset_id, id))
return None, self.message_exception(trans, 'The dataset id is invalid.')
if data.history.user and not data.dataset.has_manage_permissions_roles(trans):
# Permission setting related to DATASET_MANAGE_PERMISSIONS was broken for a period of time,
# so it is possible that some Datasets have no roles associated with the DATASET_MANAGE_PERMISSIONS
# permission. In this case, we'll reset this permission to the hda user's private role.
manage_permissions_action = trans.app.security_agent.get_action(trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action)
permissions = {manage_permissions_action : [trans.app.security_agent.get_private_user_role(data.history.user)]}
trans.app.security_agent.set_dataset_permission(data.dataset, permissions)
return data, None
@web.expose
@web.json
@web.require_login("see all available datasets")