opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-25 00:12:08 +08:00
Code Issues Packages Projects Releases Wiki Activity

refactor show method to use new manager

Browse Source
This commit is contained in:
Martin Cech
2017-08-17 15:23:32 -04:00
parent dc834a52c1
commit e17ab411e3
2 changed files with 107 additions and 21 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/managers/library_datasets.py
+90
View File
@@ -0,0 +1,90 @@
"""Manager and Serializer for library datasets."""
import logging
from sqlalchemy import and_, false, not_, or_, true
from galaxy import exceptions
log = logging.getLogger( __name__ )
class LibraryDatasetsManager( object ):
"""Interface/service object for interacting with library datasets."""
def __init__( self, app ):
self.app = app
def get( self, trans, decoded_library_dataset_id, check_accessible=True ):
"""
Get the library dataset from the DB.
:param decoded_library_dataset_id: decoded library dataset id
:type decoded_library_dataset_id: int
:param check_accessible: flag whether to check that user can access item
:type check_accessible: bool
:returns: the requested library dataset
:rtype: galaxy.model.LibraryDataset
"""
try:
ld = trans.sa_session.query( trans.app.model.LibraryDataset ).filter( trans.app.model.LibraryDataset.table.c.id == decoded_library_dataset_id ).one()
except Exception as e:
raise exceptions.InternalServerError( 'Error loading from the database.' + str( e ) )
ld = self.secure( trans, ld, check_accessible)
return ld
def update( self, trans, ld, check_ownership=True, check_accessible=True ):
"""
Update the given library dataset.
: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
:returns: the changed library dataset
:rtype: galaxy.model.LibraryDataset
:raises:
"""
def secure( self, trans, ld, check_accessible=True, check_ownership=False ):
"""
Check if library dataset is accessible to user.
:param ld: library dataset
:type ld: galaxy.model.LibraryDataset
:param check_accessible: flag whether to check that user can access library dataset
:type check_accessible: bool
:returns: the original library dataset
:rtype: galaxy.model.LibraryDataset
"""
if trans.user_is_admin():
# all operations are available to an admin
return ld
if check_accessible:
ld = self._check_accessible( trans, ld )
return ld
def check_accessible( self, trans, ld ):
"""
Check whether the library dataset is accessible to current user.
:param ld: library dataset
:type ld: galaxy.model.LibraryDataset
:returns: the original library dataset
:rtype: galaxy.model.LibraryDataset
:raises: ObjectNotFound
"""
if not trans.app.security_agent.can_access_library_item( trans.get_current_user_roles(), ld ):
raise exceptions.ObjectNotFound( 'Library dataset with the id provided was not found.' )
elif ld.deleted:
raise exceptions.ObjectNotFound( 'Library dataset with the id provided is deleted.' )
else:
return ld
lib/galaxy/webapps/galaxy/api/lda_datasets.py
+17 -21
View File
@@ -14,8 +14,8 @@ from galaxy import exceptions
from galaxy import util
from galaxy import web
from galaxy.exceptions import ObjectNotFound
from galaxy.managers import folders, roles, tags
from galaxy.managers import base as managers_base
from galaxy.managers import folders, roles, tags, library_datasets
from galaxy.tools.actions import upload_common
from galaxy.tools.parameters import populate_state
from galaxy.util.streamball import StreamBall
@@ -33,57 +33,53 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin):
self.app = app
self.folder_manager = folders.FolderManager()
self.role_manager = roles.RoleManager(app)
self.ld_manager = library_datasets.LibraryDatasetsManager(app)
@expose_api_anonymous
def show(self, trans, id, **kwd):
"""
show( self, trans, id, **kwd )
Show the details of a library dataset.
* GET /api/libraries/datasets/{encoded_dataset_id}
Displays information about the dataset identified by the encoded ID.
:param id: the encoded id of the dataset to query
:type id: an encoded id string
:returns: detailed dataset information from base controller
:rtype: dictionary
.. seealso:: :attr:`galaxy.web.base.controller.UsesLibraryMixinItems.get_library_dataset`
"""
try:
library_dataset = self.get_library_dataset(trans, id=id, check_ownership=False, check_accessible=True)
except Exception:
raise exceptions.ObjectNotFound('Requested library_dataset was not found.')
current_user_roles = trans.get_current_user_roles()
ld = self.ld_manager.get( trans, managers_base.decode_id( self.app, id ) )
tag_manager = tags.GalaxyTagManager(trans.sa_session)
# Build the full path for breadcrumb purposes.
full_path = self._build_path(trans, library_dataset.folder)
dataset_item = (trans.security.encode_id(library_dataset.id), library_dataset.name)
full_path = self._build_path(trans, ld.folder)
dataset_item = (id, ld.name)
full_path.insert(0, dataset_item)
full_path = full_path[::-1]
# Find expired versions of the library dataset
expired_ldda_versions = []
for expired_ldda in library_dataset.expired_datasets:
for expired_ldda in ld.expired_datasets:
expired_ldda_versions.append((trans.security.encode_id(expired_ldda.id), expired_ldda.name))
rval = trans.security.encode_all_ids(library_dataset.to_dict())
rval = trans.security.encode_all_ids(ld.to_dict())
if len(expired_ldda_versions) > 0:
rval['has_versions'] = True
rval['expired_versions'] = expired_ldda_versions
rval['deleted'] = library_dataset.deleted
rval['deleted'] = ld.deleted
rval['folder_id'] = 'F' + rval['folder_id']
rval['full_path'] = full_path
rval['file_size'] = util.nice_size(int(library_dataset.library_dataset_dataset_association.get_size()))
rval['date_uploaded'] = library_dataset.library_dataset_dataset_association.create_time.strftime("%Y-%m-%d %I:%M %p")
rval['can_user_modify'] = trans.app.security_agent.can_modify_library_item(current_user_roles, library_dataset) or trans.user_is_admin()
rval['is_unrestricted'] = trans.app.security_agent.dataset_is_public(library_dataset.library_dataset_dataset_association.dataset)
rval['tags'] = tag_manager.get_tags_str(library_dataset.library_dataset_dataset_association.tags)
rval['file_size'] = util.nice_size(int(ld.library_dataset_dataset_association.get_size()))
rval['date_uploaded'] = ld.library_dataset_dataset_association.create_time.strftime("%Y-%m-%d %I:%M %p")
rval['can_user_modify'] = trans.app.security_agent.can_modify_library_item(current_user_roles, ld) or trans.user_is_admin()
rval['is_unrestricted'] = trans.app.security_agent.dataset_is_public(ld.library_dataset_dataset_association.dataset)
rval['tags'] = tag_manager.get_tags_str(ld.library_dataset_dataset_association.tags)
# Manage dataset permission is always attached to the dataset itself, not the the ld or ldda to maintain consistency
rval['can_user_manage'] = trans.app.security_agent.can_manage_dataset(current_user_roles, library_dataset.library_dataset_dataset_association.dataset) or trans.user_is_admin()
rval['can_user_manage'] = trans.app.security_agent.can_manage_dataset(current_user_roles, ld.library_dataset_dataset_association.dataset) or trans.user_is_admin()
return rval
@expose_api_anonymous