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Several data library bug fixes:

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- Determiining if an accessible dataset exists somewhere in the data library hierarchy now works all the time ( I believe ).  It used to work most of the time, but under corner conditions, it would break.
- When importing dataset from a history into a data library, the dataset permissions are now correctly applied to the library dataset.  The DATASET_MANAGE_PERMISSIONS permission is a spoecial case in that if it exists on the dataset, the LIBRARY_MANAGE permission must be applied to the library dataset.
- Fix for message display and db flushing when importing library dataset into a history.
- Do not render the folder pop-up menu option for selecting library dataset to import into histories if the folder does not contain any accessible library datasets.
This commit is contained in:
Greg Von Kuster
2011-06-01 15:20:43 -04:00
parent 51aeadf8e5
commit 72dfb35375
3 changed files with 49 additions and 17 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/security/__init__.py
+6 -2
View File
@@ -287,8 +287,12 @@ class GalaxyRBACAgent( RBACAgent ):
if self.can_access_library_item( roles, library_dataset, user ):
return True
if search_downward:
for folder in folder.active_folders:
return self.has_accessible_library_datasets( trans, folder, user, roles, search_downward=search_downward )
return self.__active_folders_have_accessible_library_datasets( trans, folder, user, roles )
return False
def __active_folders_have_accessible_library_datasets( self, trans, folder, user, roles ):
for active_folder in folder.active_folders:
if self.has_accessible_library_datasets( trans, active_folder, user, roles ):
return True
return False
def can_access_library_item( self, roles, item, user ):
if type( item ) == self.model.Library:
lib/galaxy/web/controllers/library_common.py
+38 -12
View File
@@ -11,6 +11,7 @@ from galaxy.util import inflector
from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, TextArea, TextField, WorkflowField, WorkflowMappingField, HistoryField
import logging, tempfile, zipfile, tarfile, os, sys, operator
from galaxy.eggs import require
from galaxy.security import Action
# Whoosh is compatible with Python 2.5+ Try to import Whoosh and set flag to indicate whether tool search is enabled.
try:
require( "Whoosh" )
@@ -829,7 +830,7 @@ class LibraryCommon( BaseController, UsesFormDefinitions ):
**kwd )
if created_outputs_dict:
if cntrller == 'api':
# created_outputs_dict can only ever be a string if cntrller == 'api'
# created_outputs_dict can be a string only if cntrller == 'api'
if type( created_outputs_dict ) == str:
return 400, created_outputs_dict
return 200, created_outputs_dict
@@ -1211,6 +1212,27 @@ class LibraryCommon( BaseController, UsesFormDefinitions ):
# LDDA and LibraryDataset.
trans.app.security_agent.copy_library_permissions( folder, ldda )
trans.app.security_agent.copy_library_permissions( folder, ldda.library_dataset )
# Make sure to apply any defined dataset permissions, allowing the permissions inherited from the folder to
# over-ride the same permissions on the dataset, if they exist.
dataset_permissions_dict = trans.app.security_agent.get_permissions( hda.dataset )
current_library_dataset_actions = [ permission.action for permission in ldda.library_dataset.actions ]
# The DATASET_MANAGE_PERMISSIONS permission on a dataset is a special case because if
# it exists, then we need to apply the LIBRARY_MANAGE permission to the library dataset.
dataset_manage_permissions_action = trans.app.security_agent.get_action( 'DATASET_MANAGE_PERMISSIONS' ).action
flush_needed = False
for action, roles in dataset_permissions_dict.items():
if isinstance( action, Action ):
action = action.action
if action == dataset_manage_permissions_action:
# Apply the LIBRARY_MANAGE permission to the library dataset.
action = trans.app.security_agent.get_action( 'LIBRARY_MANAGE' ).action
# Allow the permissions inherited from the folder to over-ride the same permissions on the dataset.
if action not in current_library_dataset_actions:
for ldp in [ trans.model.LibraryDatasetPermissions( action, ldda.library_dataset, role ) for role in roles ]:
trans.sa_session.add( ldp )
flush_needed = True
if flush_needed:
trans.sa_session.flush()
# Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset
trans.app.security_agent.copy_library_permissions( ldda.library_dataset, ldda )
if created_ldda_ids:
@@ -1605,7 +1627,7 @@ class LibraryCommon( BaseController, UsesFormDefinitions ):
valid_lddas = []
invalid_lddas = []
for ldda in lddas:
if trans.app.security_agent.can_manage_library_item( current_user_roles, ldda ):
if is_admin or trans.app.security_agent.can_manage_library_item( current_user_roles, ldda ):
valid_lddas.append( ldda )
valid_ldda_ids.append( ldda.id )
else:
@@ -1634,7 +1656,7 @@ class LibraryCommon( BaseController, UsesFormDefinitions ):
valid_lddas = []
invalid_lddas = []
for ldda in lddas:
if trans.app.security_agent.can_modify_library_item( current_user_roles, ldda ):
if is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, ldda ):
valid_lddas.append( ldda )
else:
invalid_lddas.append( ldda )
@@ -1859,6 +1881,7 @@ class LibraryCommon( BaseController, UsesFormDefinitions ):
if len( target_histories ) != len( target_history_ids ):
message += "You do not have permission to add datasets to %i requested histories. " % ( len( target_history_ids ) - len( target_histories ) )
status = 'error'
flush_needed = False
for ldda in map( trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get, ldda_ids ):
if ldda is None:
message += "You tried to import a dataset that does not exist. "
@@ -1875,15 +1898,18 @@ class LibraryCommon( BaseController, UsesFormDefinitions ):
else:
for target_history in target_histories:
hda = ldda.to_history_dataset_association( target_history=target_history, add_to_history=True )
trans.sa_session.flush()
hist_names_str = ", ".join( [ target_history.name for target_history in target_histories ] )
num_source = len( ldda_ids ) - invalid_datasets
num_target = len( target_histories )
message = "%i %s imported into %i %s: %s" % ( num_source,
inflector.cond_plural( num_source, "dataset" ),
num_target,
inflector.cond_plural( num_target, "history" ),
hist_names_str )
if not flush_needed:
flush_needed = True
if flush_needed:
trans.sa_session.flush()
hist_names_str = ", ".join( [ target_history.name for target_history in target_histories ] )
num_source = len( ldda_ids ) - invalid_datasets
num_target = len( target_histories )
message += "%i %s imported into %i %s: %s" % ( num_source,
inflector.cond_plural( num_source, "dataset" ),
num_target,
inflector.cond_plural( num_target, "history" ),
hist_names_str )
trans.sa_session.refresh( current_history )
current_user_roles = trans.get_current_user_roles()
source_lddas = []
templates/library/common/browse_library.mako
+5 -3
View File
@@ -314,6 +314,7 @@
from galaxy.web.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, branch_deleted
is_admin = trans.user_is_admin() and cntrller == 'library_admin'
has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False )
if root_folder:
pad = folder_pad
@@ -380,7 +381,7 @@
<a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add sub-folder</a>
%endif
%if not branch_deleted( folder ):
%if self.has_accessible_datasets:
%if has_accessible_library_datasets:
<a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a>
%endif
%if can_modify:
@@ -488,6 +489,7 @@
form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE
self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles )
root_folder_has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles, search_downward=False )
has_accessible_folders = is_admin or trans.app.security_agent.has_accessible_folders( trans, library.root_folder, trans.user, current_user_roles )
tracked_datasets = {}
@@ -500,7 +502,7 @@
def __str__( self ):
return str( self.count )
%>
<h2>Data Library &ldquo;${library.name}&rdquo;</h2>
<ul class="manage-table-actions">
@@ -534,7 +536,7 @@
%endif
<a class="action-button" href="${h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a>
%endif
%if self.has_accessible_datasets:
%if root_folder_has_accessible_library_datasets:
<a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a>
%endif
%elif can_modify and not library.purged: