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Fix for deleting a list of library datasets - resolves ticket # 102.

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This commit is contained in:
Greg Von Kuster
2010-03-10 11:24:49 -05:00
parent 54b401d58d
commit 02565373ec
6 changed files with 21 additions and 16 deletions
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lib/galaxy/web/controllers/library_admin.py
+2 -2
View File
@@ -169,8 +169,8 @@ class LibraryAdmin( BaseController ):
# deleted / purged contents will have the same state ). When a library or folder has been deleted for
# the amount of time defined in the cleanup_datasets.py script, the library or folder and all of its
# contents will be purged. The association between this method and the cleanup_datasets.py script
# enables clean maintenance of libraries and library dataset disk files. This is also why the following
# 3 objects, and not any of the associations ( the cleanup_datasets.py scipot handles everything else ).
# enables clean maintenance of libraries and library dataset disk files. This is also why the item_types
# are not any of the associations ( the cleanup_datasets.py script handles everything ).
show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
item_types = { 'library': trans.app.model.Library,
'folder': trans.app.model.LibraryFolder,
lib/galaxy/web/controllers/library_common.py
+8 -6
View File
@@ -1246,8 +1246,7 @@ class LibraryCommon( BaseController ):
messagetype=messagetype )
@web.expose
def act_on_multiple_datasets( self, trans, cntrller, library_id, ldda_ids='', **kwd ):
# This method is used by the select list labeled "Perform action on selected datasets"
# on the analysis library browser
# Perform an action on a list of library datasets.
params = util.Params( kwd )
msg = util.restore_text( params.get( 'msg', '' ) )
messagetype = params.get( 'messagetype', 'done' )
@@ -1262,7 +1261,7 @@ class LibraryCommon( BaseController ):
messagetype = 'error'
else:
ldda_ids = util.listify( ldda_ids )
if action == 'add':
if action == 'import_to_history':
history = trans.get_history()
if history is None:
# Must be a bot sending a request without having a history.
@@ -1306,9 +1305,12 @@ class LibraryCommon( BaseController ):
elif action == 'delete':
for ldda_id in ldda_ids:
ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) )
ldda.deleted = True
trans.sa_session.add( ldda )
trans.sa_session.flush()
# Do not delete the association, just delete the library_dataset. The
# cleanup_datasets.py script handles everything else.
ld = ldda.library_dataset
ld.deleted = True
trans.sa_session.add( ld )
trans.sa_session.flush()
msg = "The selected datasets have been removed from this data library"
else:
error = False
templates/library/common/browse_library.mako
+1 -1
View File
@@ -229,7 +229,7 @@
<a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), replace_id=trans.security.encode_id( library_dataset.id ), show_deleted=show_deleted )}">Upload a new version of this dataset</a>
%endif
%if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ldda.has_data:
<a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='add', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a>
<a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='import_to_history', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a>
<a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels )}">Download this dataset</a>
%endif
%if cntrller in [ 'library_admin', 'requests_admin' ]:
templates/library/common/ldda_info.mako
+1 -1
View File
@@ -57,7 +57,7 @@
<a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), replace_id=trans.security.encode_id( ldda.library_dataset.id ) )}">Upload a new version of this dataset</a>
%endif
%if cntrller=='library' and ldda.has_data:
<a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='add', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a>
<a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='import_to_history', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a>
<a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Download this dataset</a>
%endif
</div>
test/base/twilltestcase.py
+6 -3
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@@ -1595,14 +1595,17 @@ class TwillTestCase( unittest.TestCase ):
self.home()
def add_library_dataset( self, cntrller, filename, library_id, folder_id, folder_name,
file_type='auto', dbkey='hg18', roles=[], message='', root=False,
template_field_name1='', template_field_contents1='' ):
template_field_name1='', template_field_contents1='', show_deleted='False',
upload_option='upload_file' ):
"""Add a dataset to a folder"""
filename = self.get_filename( filename )
self.home()
self.visit_url( "%s/library_common/upload_library_dataset?cntrller=%s&upload_option=upload_file&library_id=%s&folder_id=%s&message=%s" % \
( self.url, cntrller, library_id, folder_id, message ) )
self.visit_url( "%s/library_common/upload_library_dataset?cntrller=%s&library_id=%s&folder_id=%s&upload_option=%s&message=%s" % \
( self.url, cntrller, library_id, folder_id, upload_option, message ) )
self.check_page_for_string( 'Upload files' )
tc.fv( "1", "library_id", library_id )
tc.fv( "1", "folder_id", folder_id )
tc.fv( "1", "show_deleted", show_deleted )
tc.formfile( "1", "files_0|file_data", filename )
tc.fv( "1", "file_type", file_type )
tc.fv( "1", "dbkey", dbkey )
test/functional/test_security_and_libraries.py
+3 -3
View File
@@ -1181,7 +1181,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
# Test importing the restricted dataset into a history, can't use the
# ~/library_admin/libraries form as twill barfs on it so we'll simulate the form submission
# by going directly to the form action
self.visit_url( '%s/library_common/act_on_multiple_datasets?cntrller=library&do_action=add&ldda_ids=%s&library_id=%s' \
self.visit_url( '%s/library_common/act_on_multiple_datasets?cntrller=library&do_action=import_to_history&ldda_ids=%s&library_id=%s' \
% ( self.url, self.security.encode_id( ldda_five.id ), self.security.encode_id( library_one.id ) ) )
self.check_page_for_string( '1 dataset(s) have been imported into your history' )
self.logout()
@@ -1473,7 +1473,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
for ldda in lddas:
# Import each library dataset into our history
self.home()
self.visit_url( '%s/library_common/act_on_multiple_datasets?cntrller=library&do_action=add&ldda_ids=%s&library_id=%s' % \
self.visit_url( '%s/library_common/act_on_multiple_datasets?cntrller=library&do_action=import_to_history&ldda_ids=%s&library_id=%s' % \
( self.url, self.security.encode_id( ldda.id ), self.security.encode_id( library_one.id ) ) )
# Determine the new HistoryDatasetAssociation id created when the library dataset was imported into our history
last_hda_created = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
@@ -1522,7 +1522,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
# be all of the above on any of the 3 datasets that are imported into a history
for ldda in lddas:
self.home()
self.visit_url( '%s/library_common/act_on_multiple_datasets?cntrller=library&library_id=%s&do_action=add&ldda_ids=%s' % \
self.visit_url( '%s/library_common/act_on_multiple_datasets?cntrller=library&library_id=%s&do_action=import_to_history&ldda_ids=%s' % \
( self.url, self.security.encode_id( library_one.id ), self.security.encode_id( ldda.id ) ) )
# Determine the new HistoryDatasetAssociation id created when the library dataset was imported into our history
last_hda_created = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \