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improve docs and access checks in datalibs manager/api #4560

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Sep 6, 2017
Merged

improve docs and access checks in datalibs manager/api #4560

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b12d29d
improve docs and access checks
martenson Sep 5, 2017
f78eca8
remove unused import
martenson Sep 5, 2017
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37 changes: 17 additions & 20 deletions lib/galaxy/managers/library_datasets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@
from galaxy import util

from galaxy.exceptions import InternalServerError
from galaxy.exceptions import ItemAccessibilityException
from galaxy.exceptions import InsufficientPermissionsException
from galaxy.exceptions import ObjectNotFound
from galaxy.exceptions import RequestParameterInvalidException
Expand Down Expand Up @@ -43,26 +42,25 @@ def get(self, trans, decoded_library_dataset_id, check_accessible=True):
def update(self, trans, ld, payload):
"""
Update the given library dataset - the latest linked ldda.
Updating older lddas (versions) is not supported.

:param ld: library dataset to change
:type ld: LibraryDataset
:param check_ownership: flag whether to check that user owns the item
:type check_ownership: bool
:param check_accessible: flag whether to check that user can access item
:type check_accessible: bool
Updating older lddas (versions) is not allowed.

:param ld: library dataset to change
:type ld: LibraryDataset
:param payload: dictionary structure containing::
:param name: new ld's name, must be longer than 0
:type name: str
:param misc_info: new ld's misc info
:type misc_info: str
:param file_ext: new ld's extension, must exist in the Galaxy registry
:type file_ext: str
:param genome_build: new ld's genome build
:type genome_build: str
:type payload: dict

:returns: the changed library dataset
:rtype: galaxy.model.LibraryDataset

:raises: ItemAccessibilityException, InsufficientPermissionsException
"""
current_user_roles = trans.get_current_user_roles()
self.check_modifiable(trans, ld)
if ld.deleted is True:
raise ItemAccessibilityException("You cannot update a deleted library dataset. Undelete it first.")
if not (trans.user_is_admin or trans.app.security_agent.can_modify_library_item(current_user_roles, ld)):
raise InsufficientPermissionsException('You do not have proper permission to modify this library dataset.')
# we are going to operate on the actual latest ldda
ldda = ld.library_dataset_dataset_association
payload = self._validate_and_parse_update_payload(payload)
Expand Down Expand Up @@ -169,13 +167,12 @@ def check_modifiable(self, trans, ld):

:raises: ObjectNotFound
"""
if trans.user_is_admin():
# all operations are available to an admin
if ld.deleted:
raise ObjectNotFound('Library dataset with the id provided is deleted.')
elif trans.user_is_admin():
return ld
if not trans.app.security_agent.can_modify_library_item(trans.get_current_user_roles(), ld):
raise InsufficientPermissionsException('You do not have proper permission to modify this library dataset.')
elif ld.deleted:
raise ObjectNotFound('Library dataset with the id provided is deleted.')
else:
return ld

Expand Down
14 changes: 12 additions & 2 deletions lib/galaxy/webapps/galaxy/api/library_datasets.py
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Expand Up @@ -171,8 +171,18 @@ def update(self, trans, encoded_dataset_id, payload=None, **kwd):

* PATCH /api/libraries/datasets/{encoded_dataset_id}

:param encoded_dataset_id: the encoded id of the library dataset to update
:type encoded_dataset_id: an encoded id string
:param encoded_dataset_id: the encoded id of the library dataset to update
:type encoded_dataset_id: an encoded id string
:param payload: dictionary structure containing::
:param name: new ld's name, must be longer than 0
:type name: str
:param misc_info: new ld's misc info
:type misc_info: str
:param file_ext: new ld's extension, must exist in the Galaxy registry
:type file_ext: str
:param genome_build: new ld's genome build
:type genome_build: str
:type payload: dict

:returns: detailed library dataset information
:rtype: dictionary
Expand Down