details: http://www.bx.psu.edu/hg/galaxy/rev/861756e85b16 changeset: 3540:861756e85b16 user: Greg Von Kuster greg@bx.psu.edu date: Tue Mar 16 16:03:28 2010 -0400 description: Fix for editing library templates, add a new functional test to cover the scenario, and some code cleanup.
diffstat:
lib/galaxy/web/controllers/library_admin.py | 2 +- lib/galaxy/web/controllers/library_common.py | 1 - templates/library/common/browse_library.mako | 10 +- test/base/test_db_util.py | 9 --- test/base/twilltestcase.py | 20 +++++- test/functional/test_library_features.py | 84 +++++++++++++++++++-------- 6 files changed, 82 insertions(+), 44 deletions(-)
diffs (366 lines):
diff -r 4a670e8f4248 -r 861756e85b16 lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Tue Mar 16 15:32:05 2010 -0400 +++ b/lib/galaxy/web/controllers/library_admin.py Tue Mar 16 16:03:28 2010 -0400 @@ -34,7 +34,7 @@ template='/admin/library/grid.mako' default_sort_key = "name" columns = [ - NameColumn( "Library Name", + NameColumn( "Name", key="name", model_class=model.Library, link=( lambda library: dict( operation="browse", id=library.id ) ), diff -r 4a670e8f4248 -r 861756e85b16 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Tue Mar 16 15:32:05 2010 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Tue Mar 16 16:03:28 2010 -0400 @@ -1616,7 +1616,6 @@ response_redirect=web.url_for( controller='library_common', action='edit_template', cntrller=cntrller, - use_panels=use_panels, item_type=item_type, library_id=library_id, folder_id=folder_id, diff -r 4a670e8f4248 -r 861756e85b16 templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako Tue Mar 16 15:32:05 2010 -0400 +++ b/templates/library/common/browse_library.mako Tue Mar 16 16:03:28 2010 -0400 @@ -445,11 +445,11 @@ %endif %if cntrller == 'library_admin': <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library' )}">Delete this data library</a> - %endif - %if show_deleted: - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=False )}">Hide deleted items</a> - %else: - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=True )}">Show deleted items</a> + %if show_deleted: + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=False )}">Hide deleted items</a> + %else: + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=True )}">Show deleted items</a> + %endif %endif %elif cntrller == 'library_admin' and not library.purged: <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library', use_panels=use_panels )}">Undelete this data library</a> diff -r 4a670e8f4248 -r 861756e85b16 test/base/test_db_util.py --- a/test/base/test_db_util.py Tue Mar 16 15:32:05 2010 -0400 +++ b/test/base/test_db_util.py Tue Mar 16 16:03:28 2010 -0400 @@ -112,12 +112,3 @@ .all() def refresh( obj ): sa_session.refresh( obj ) -def set_library_permissions( in_list ): - permissions_in = [] - permissions_out = [] - for k, v in galaxy.model.Library.permitted_actions.items(): - if k in in_list: - permissions_in.append( k ) - else: - permissions_out.append( k ) - return permissions_in, permissions_out diff -r 4a670e8f4248 -r 861756e85b16 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Tue Mar 16 15:32:05 2010 -0400 +++ b/test/base/twilltestcase.py Tue Mar 16 16:03:28 2010 -0400 @@ -1630,7 +1630,6 @@ pass def create_library( self, name='Library One', description='This is Library One', synopsis='Synopsis for Library One' ): """Create a new library""" - self.home() self.visit_url( "%s/library_admin/create_library" % self.url ) self.check_page_for_string( 'Create a new data library' ) tc.fv( "1", "name", name ) @@ -1640,10 +1639,25 @@ check_str = "The new library named '%s' has been created" % name self.check_page_for_string( check_str ) self.home() + def edit_template( self, cntrller, item_type, library_id, folder_id='', ldda_id='', action='add_field', + field_name='', field_name_value='', field_help='', field_help_value='', + field_type='', field_type_value='' ): + """Edit the form fields defining a library template""" + self.visit_url( "%s/library_common/edit_template?cntrller=%s&item_type=%s&library_id=%s" % \ + ( self.url, cntrller, item_type, library_id ) ) + self.check_page_for_string( "Edit form definition" ) + if action == 'add_field': + tc.submit( 'add_field_button' ) + tc.fv( '1', field_name, field_name_value ) + tc.fv( '1', field_help, field_help_value ) + tc.fv( '1', field_type, field_type_value ) + tc.submit( 'save_changes_button' ) + self.check_page_for_string( "The template for this data library has been updated with your changes." ) + if action == 'add_field': + self.check_page_for_string( field_name_value ) def library_info( self, cntrller, library_id, library_name, new_name='', new_description='', new_synopsis='', ele_1_field_name='', ele_1_contents='', ele_2_field_name='', ele_2_contents='', check_str1='' ): """Edit information about a library, optionally using an existing template with up to 2 elements""" - self.home() self.visit_url( "%s/library_common/library_info?cntrller=%s&id=%s" % ( self.url, cntrller, library_id ) ) if check_str1: self.check_page_for_string( check_str1 ) @@ -1866,7 +1880,7 @@ self.visit_url( url ) self.check_page_for_string( 'Upload a directory of files' ) if check_str1: - self.check_page_for_strin( check_str1 ) + self.check_page_for_string( check_str1 ) tc.fv( "1", "folder_id", folder_id ) tc.fv( "1", "file_type", file_type ) tc.fv( "1", "dbkey", dbkey ) diff -r 4a670e8f4248 -r 861756e85b16 test/functional/test_library_features.py --- a/test/functional/test_library_features.py Tue Mar 16 15:32:05 2010 -0400 +++ b/test/functional/test_library_features.py Tue Mar 16 16:03:28 2010 -0400 @@ -9,21 +9,29 @@ global regular_user1 regular_user1 = get_user( 'test1@bx.psu.edu' ) assert regular_user1 is not None, 'Problem retrieving user with email "test1@bx.psu.edu" from the database' + global regular_user1_private_role + regular_user1_private_role = get_private_role( regular_user1 ) self.logout() self.login( email='test2@bx.psu.edu' ) global regular_user2 regular_user2 = get_user( 'test2@bx.psu.edu' ) assert regular_user2 is not None, 'Problem retrieving user with email "test2@bx.psu.edu" from the database' + global regular_user2_private_role + regular_user2_private_role = get_private_role( regular_user2 ) self.logout() self.login( email='test3@bx.psu.edu' ) global regular_user3 regular_user3 = get_user( 'test3@bx.psu.edu' ) assert regular_user3 is not None, 'Problem retrieving user with email "test3@bx.psu.edu" from the database' + global regular_user3_private_role + regular_user3_private_role = get_private_role( regular_user3 ) self.logout() self.login( email='test@bx.psu.edu' ) global admin_user admin_user = get_user( 'test@bx.psu.edu' ) assert admin_user is not None, 'Problem retrieving user with email "test@bx.psu.edu" from the database' + global admin_user_private_role + admin_user_private_role = get_private_role( admin_user ) def test_005_create_library( self ): """Testing creating a new library, then renaming it""" # Logged in as admin_user @@ -100,7 +108,6 @@ self.security.encode_id( library_one.id ), library_one.name, check_str1=contents ) - contents = '%s library contents' % form_one_field_label contents_edited = contents + ' edited' # Edit the contents and then save them self.library_info( 'library_admin', @@ -113,7 +120,25 @@ self.security.encode_id( library_one.id ), library_one.name, check_str1=contents_edited ) - def test_020_add_public_dataset_to_root_folder( self ): + def test_020_edit_template_admin_view( self ): + """Test editing the layout of a template from the Admin view""" + # Since there is only 1 field currently in the form definition, we'll add another + field_name = 'field_name_1' + field_name_value = 'Field 1' + field_help = 'field_helptext_1' + field_help_value = 'Field 1 help' + field_type = 'field_type_1' + field_type_value = 'TextArea' + self.edit_template( 'library_admin', + 'library', + self.security.encode_id( library_one.id ), + field_name=field_name, + field_name_value=field_name_value, + field_help=field_help, + field_help_value=field_help_value, + field_type=field_type, + field_type_value=field_type_value ) + def test_025_add_public_dataset_to_root_folder( self ): """Testing adding a public dataset to the root folder, making sure library template is inherited""" # Logged in as admin_user message = 'Testing adding a public dataset to the root folder' @@ -145,7 +170,7 @@ self.security.encode_id( ldda_one.id ), ldda_one.name, check_str1=template_contents ) - def test_025_add_new_folder_to_root_folder( self ): + def test_030_add_new_folder_to_root_folder( self ): """Testing adding a folder to a library root folder""" # logged in as admin_user root_folder = library_one.root_folder @@ -177,7 +202,7 @@ self.security.encode_id( library_one.id ), field_name=form_one_field_name, contents=template_contents ) - def test_030_add_subfolder_to_folder( self ): + def test_035_add_subfolder_to_folder( self ): """Testing adding a folder to a library folder""" # logged in as admin_user name = "Folder One's Subfolder" @@ -208,7 +233,7 @@ self.security.encode_id( library_one.id ), field_name=form_one_field_name, contents=template_contents ) - def test_035_add_2nd_new_folder_to_root_folder( self ): + def test_040_add_2nd_new_folder_to_root_folder( self ): """Testing adding a 2nd folder to a library root folder""" # logged in as admin_user root_folder = library_one.root_folder @@ -226,7 +251,7 @@ self.security.encode_id( library_one.id ), check_str1=name, check_str2=description ) - def test_040_add_public_dataset_to_root_folders_2nd_subfolder( self ): + def test_045_add_public_dataset_to_root_folders_2nd_subfolder( self ): """Testing adding a public dataset to the root folder's 2nd sub-folder""" # Logged in as admin_user message = "Testing adding a public dataset to the folder named %s" % folder_two.name @@ -258,7 +283,7 @@ self.security.encode_id( ldda_two.id ), ldda_two.name, check_str1=template_contents ) - def test_045_add_2nd_public_dataset_to_root_folders_2nd_subfolder( self ): + def test_050_add_2nd_public_dataset_to_root_folders_2nd_subfolder( self ): """Testing adding a 2nd public dataset to the root folder's 2nd sub-folder""" # Logged in as admin_user message = "Testing adding a 2nd public dataset to the folder named %s" % folder_two.name @@ -290,7 +315,7 @@ self.security.encode_id( ldda_three.id ), ldda_three.name, check_str1=template_contents ) - def test_050_copy_dataset_from_history_to_subfolder( self ): + def test_055_copy_dataset_from_history_to_subfolder( self ): """Testing copying a dataset from the current history to a subfolder""" # logged in as admin_user self.new_history() @@ -314,7 +339,7 @@ ldda_four.name, check_str1=form_one_field_name, not_displayed=contents ) - def test_055_editing_dataset_attribute_info( self ): + def test_060_editing_dataset_attribute_info( self ): """Testing editing a library dataset's attribute information""" # logged in as admin_user new_ldda_name = '4.bed ( version 1 )' @@ -335,7 +360,7 @@ ldda_four.name, check_str1=form_one_field_name, not_displayed=contents ) - def test_060_uploading_new_dataset_version( self ): + def test_065_uploading_new_dataset_version( self ): """Testing uploading a new version of a library dataset""" # logged in as admin_user message = 'Testing uploading a new version of a dataset' @@ -384,22 +409,32 @@ self.browse_library( 'library_admin', self.security.encode_id( library_one.id ), not_displayed=ldda_four.name ) - def test_065_upload_directory_of_files_from_libraries_view( self ): + def test_070_upload_directory_of_files_from_libraries_view( self ): """Testing uploading a directory of files to a root folder from the Data Libraries view""" # logged in as admin_user # admin_user will not have the option to upload a directory of files from the # Libraries view since a sub-directory named the same as their email is not contained - # in the configured user_library_import_dir. However, since members of role_one have - # the LIBRARY_ADD permission, we can test this feature as regular_user1 or regular_user3 + # in the configured user_library_import_dir ( in the test_data directory, only regular_user1 + # and regular_user3 have directories ). We'll need to give these 2 user LIBRARY_ADD permission + # on library_one to test this feature. + permissions_in = [ 'LIBRARY_ADD' ] + permissions_out = [ 'LIBRARY_ACCESS', 'LIBRARY_MODIFY', 'LIBRARY_MANAGE' ] + role_ids = '%s,%s' % ( str( regular_user1_private_role.id ), str( regular_user3_private_role.id ) ) + # Role one members are: admin_user, regular_user1, regular_user3. Each of these users will be permitted for + # LIBRARY_ACCESS, LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE on this library and it's contents. + self.library_permissions( self.security.encode_id( library_one.id ), + library_one.name, + role_ids, + permissions_in, + permissions_out ) self.logout() + # Now that we have permissions set on the library, we can proceed to test uploading files self.login( email=regular_user1.email ) message = 'Uploaded all files in test-data/users/test1...' # Since regular_user1 does not have any sub-directories contained within her configured # user_library_import_dir, the only option in her server_dir select list will be the # directory named the same as her email check_str_after_submit = "Added 1 datasets to the library '%s' (each is selected)." % library_one.root_folder.name - # TODO: gvk( 3/12/10 )this is broken, so commenting until I have time to discover why... - """ self.upload_directory_of_files( 'library', self.security.encode_id( library_one.id ), self.security.encode_id( library_one.root_folder.id ), @@ -426,8 +461,7 @@ self.security.encode_id( library_one.id ), check_str1=regular_user3.email, check_str2=message ) - """ - def test_070_download_archive_of_library_files( self ): + def test_075_download_archive_of_library_files( self ): """Testing downloading an archive of files from the library""" # logged in as regular_user3 self.logout() @@ -439,7 +473,7 @@ format=format ) self.check_archive_contents( archive, ( ldda_one, ldda_two ) ) os.remove( archive ) - def test_075_mark_dataset_deleted( self ): + def test_080_mark_dataset_deleted( self ): """Testing marking a library dataset as deleted""" # Logged in as admin_user self.delete_library_item( self.security.encode_id( library_one.id ), @@ -449,7 +483,7 @@ self.browse_library( 'library_admin', self.security.encode_id( library_one.id ), not_displayed=ldda_two.name ) - def test_080_display_and_hide_deleted_dataset( self ): + def test_085_display_and_hide_deleted_dataset( self ): """Testing displaying and hiding a deleted library dataset""" # Logged in as admin_user self.browse_library( 'library_admin', @@ -459,7 +493,7 @@ self.browse_library( 'library_admin', self.security.encode_id( library_one.id ), not_displayed=ldda_two.name ) - def test_085_mark_folder_deleted( self ): + def test_090_mark_folder_deleted( self ): """Testing marking a library folder as deleted""" # Logged in as admin_user self.delete_library_item( self.security.encode_id( library_one.id ), @@ -469,7 +503,7 @@ self.browse_library( 'library_admin', self.security.encode_id( library_one.id ), not_displayed=folder_two.name ) - def test_090_mark_folder_undeleted( self ): + def test_095_mark_folder_undeleted( self ): """Testing marking a library folder as undeleted""" # Logged in as admin_user self.undelete_library_item( self.security.encode_id( library_one.id ), @@ -482,7 +516,7 @@ self.security.encode_id( library_one.id ), check_str1=folder_two.name, not_displayed=ldda_two.name ) - def test_095_mark_library_deleted( self ): + def test_100_mark_library_deleted( self ): """Testing marking a library as deleted""" # Logged in as admin_user # First mark folder_two as deleted to further test state saving when we undelete the library @@ -496,7 +530,7 @@ item_type='library' ) self.browse_libraries_admin( not_displayed1=library_one.name ) self.browse_libraries_admin( deleted=True, check_str1=library_one.name ) - def test_100_mark_library_undeleted( self ): + def test_105_mark_library_undeleted( self ): """Testing marking a library as undeleted""" # Logged in as admin_user self.undelete_library_item( self.security.encode_id( library_one.id ), @@ -508,7 +542,7 @@ self.security.encode_id( library_one.id ), check_str1=library_one.name, not_displayed=folder_two.name ) - def test_105_purge_library( self ): + def test_110_purge_library( self ): """Testing purging a library""" # Logged in as admin_user self.delete_library_item( self.security.encode_id( library_one.id ), @@ -547,7 +581,7 @@ raise AssertionError( 'The library_dataset id %s named "%s" has not been marked as deleted.' % \ ( str( library_dataset.id ), library_dataset.name ) ) check_folder( library_one.root_folder ) - def test_110_no_library_template( self ): + def test_115_no_library_template( self ): """Test library features when library has no template""" # Logged in as admin_user name = "library features Library Two"