1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/2c56c1e49f28/ changeset: 2c56c1e49f28 user: greg date: 2013-03-12 15:46:15 summary: Handle tool shed repositories that contain only tools that should not be displayed in the Galaxy tool panel from those that contain tools that should be displayed in the Galaxy tool panel appropriately. Selecting a tool pnale section is no longer allowed for repositories that do not contany any tools that should be displayed there. This behavior exists when installing or resinstalling repositories into Galaxy. affected #: 14 files

diff -r 86411cd12e2f591f6f6f7502a8481d832bcf56c0 -r 2c56c1e49f288ed53234f485c0f19606d013dd1b lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3217,6 +3217,14 @@ return 'tools' in self.metadata return False @property + def includes_tools_for_display_in_tool_panel( self ): + if self.includes_tools: + tool_dicts = self.metadata[ 'tools' ] + for tool_dict in tool_dicts: + if tool_dict.get( 'add_to_tool_panel', True ): + return True + return False + @property def includes_tool_dependencies( self ): if self.metadata: return 'tool_dependencies' in self.metadata

diff -r 86411cd12e2f591f6f6f7502a8481d832bcf56c0 -r 2c56c1e49f288ed53234f485c0f19606d013dd1b lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -89,7 +89,8 @@ if repository.uninstalled: # Since we're reinstalling the repository we need to find the latest changeset revision to which it can be updated so that we # can reset the metadata if necessary. This will ensure that information about repository dependencies and tool dependencies - # will be current. Only allow selecting a different section in the tool panel if the repository was uninstalled. + # will be current. Only allow selecting a different section in the tool panel if the repository was uninstalled and it contained + # tools that should be displayed in the tool panel. changeset_revision_dict = shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, repository ) current_changeset_revision = changeset_revision_dict.get( 'changeset_revision', None ) current_ctx_rev = changeset_revision_dict.get( 'ctx_rev', None ) @@ -213,7 +214,7 @@ repository_install_dir = None errors = '' if params.get( 'deactivate_or_uninstall_repository_button', False ): - if tool_shed_repository.includes_tools: + if tool_shed_repository.includes_tools_for_display_in_tool_panel: # Handle tool panel alterations. shed_util.remove_from_tool_panel( trans, tool_shed_repository, shed_tool_conf, uninstall=remove_from_disk_checked ) if tool_shed_repository.includes_data_managers: @@ -944,6 +945,8 @@ tool_panel_section_keys = [] # One or more repositories may include tools, but not necessarily all of them. includes_tools = util.string_as_bool( kwd.get( 'includes_tools', False ) ) + # Some tools should not be displayed in the tool panel (e.g., DataManager tools and datatype converters). + includes_tools_for_display_in_tool_panel = util.string_as_bool( kwd.get( 'includes_tools_for_display_in_tool_panel', False ) ) includes_tool_dependencies = util.string_as_bool( kwd.get( 'includes_tool_dependencies', False ) ) install_tool_dependencies = kwd.get( 'install_tool_dependencies', '' ) encoded_repo_info_dicts = util.listify( kwd.get( 'encoded_repo_info_dicts', None ) ) @@ -960,12 +963,13 @@ response.close() repo_information_dict = json.from_json_string( raw_text ) includes_tools = util.string_as_bool( repo_information_dict.get( 'includes_tools', False ) ) + includes_tools_for_display_in_tool_panel = util.string_as_bool( repo_information_dict.get( 'includes_tools_for_display_in_tool_panel', False ) ) has_repository_dependencies = util.string_as_bool( repo_information_dict.get( 'has_repository_dependencies', False ) ) includes_tool_dependencies = util.string_as_bool( repo_information_dict.get( 'includes_tool_dependencies', False ) ) encoded_repo_info_dicts = util.listify( repo_information_dict.get( 'repo_info_dicts', [] ) ) repo_info_dicts = [ encoding_util.tool_shed_decode( encoded_repo_info_dict ) for encoded_repo_info_dict in encoded_repo_info_dicts ] - if ( ( not includes_tools and not has_repository_dependencies ) and kwd.get( 'select_shed_tool_panel_config_button', False ) ) or \ - ( ( includes_tools or has_repository_dependencies ) and kwd.get( 'select_tool_panel_section_button', False ) ): + if ( ( not includes_tools_for_display_in_tool_panel and not has_repository_dependencies ) and kwd.get( 'select_shed_tool_panel_config_button', False ) ) or \ + ( ( includes_tools_for_display_in_tool_panel or has_repository_dependencies ) and kwd.get( 'select_tool_panel_section_button', False ) ): install_repository_dependencies = CheckboxField.is_checked( install_repository_dependencies ) if includes_tool_dependencies: install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies ) @@ -992,7 +996,7 @@ status='error' ) ) if created_or_updated_tool_shed_repositories: # Handle contained tools. - if includes_tools and ( new_tool_panel_section or tool_panel_section ): + if includes_tools_for_display_in_tool_panel and ( new_tool_panel_section or tool_panel_section ): if new_tool_panel_section: section_id = new_tool_panel_section.lower().replace( ' ', '_' ) tool_panel_section_key = 'section_%s' % str( section_id ) @@ -1021,6 +1025,7 @@ for tsr in created_or_updated_tool_shed_repositories: tool_panel_section_keys.append( tool_panel_section_key ) new_kwd = dict( includes_tools=includes_tools, + includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, has_repository_dependencies=has_repository_dependencies, install_repository_dependencies=install_repository_dependencies, includes_tool_dependencies=includes_tool_dependencies, @@ -1108,10 +1113,11 @@ install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked ) # Handle repository dependencies check box. install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) - if includes_tools or has_repository_dependencies: + if includes_tools_for_display_in_tool_panel or has_repository_dependencies: return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako', encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, + includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, includes_tool_dependencies=includes_tool_dependencies, install_tool_dependencies_check_box=install_tool_dependencies_check_box, has_repository_dependencies=has_repository_dependencies, @@ -1130,6 +1136,7 @@ return trans.fill_template( '/admin/tool_shed_repository/select_shed_tool_panel_config.mako', encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, + includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, includes_tool_dependencies=includes_tool_dependencies, install_tool_dependencies_check_box=install_tool_dependencies_check_box, has_repository_dependencies=has_repository_dependencies, @@ -1169,7 +1176,7 @@ metadata = tool_shed_repository.metadata # Keep track of tool dependencies defined for the current repository or those defined for any of it's repository dependencies. includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies - if tool_shed_repository.includes_tools: + if tool_shed_repository.includes_tools_for_display_in_tool_panel: # Handle the selected tool panel location for loading tools included in the tool shed repository. tool_section, new_tool_panel_section, tool_panel_section_key = \ shed_util.handle_tool_panel_selection( trans=trans, @@ -1239,6 +1246,7 @@ encoded_repository_ids = [ trans.security.encode_id( r.id ) for r in created_or_updated_tool_shed_repositories ] new_kwd = dict( includes_tool_dependencies=includes_tool_dependencies, includes_tools=tool_shed_repository.includes_tools, + includes_tools_for_display_in_tool_panel=tool_shed_repository.includes_tools_for_display_in_tool_panel, install_tool_dependencies=install_tool_dependencies, repo_info_dicts=filtered_repo_info_dicts, message=message, @@ -1316,6 +1324,7 @@ includes_data_managers = updated_repo_info_dict.get( 'includes_data_managers', False ) includes_datatypes = updated_repo_info_dict.get( 'includes_datatypes', False ) includes_tools = updated_repo_info_dict.get( 'includes_tools', False ) + includes_tools_for_display_in_tool_panel = updated_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False ) includes_workflows = updated_repo_info_dict.get( 'includes_workflows', False ) has_repository_dependencies = updated_repo_info_dict.get( 'has_repository_dependencies', False ) includes_tool_dependencies = updated_repo_info_dict.get( 'includes_tool_dependencies', False ) @@ -1327,6 +1336,7 @@ includes_datatypes = False includes_tool_dependencies = False includes_tools = False + includes_tools_for_display_in_tool_panel = False includes_workflows = False readme_files_dict = None tool_dependencies = None @@ -1337,6 +1347,12 @@ includes_datatypes = True if 'tools' in metadata: includes_tools = True + # Handle includes_tools_for_display_in_tool_panel. + tool_dicts = metadata[ 'tools' ] + for tool_dict in tool_dicts: + if tool_dict.get( 'add_to_tool_panel', True ): + includes_tools_for_display_in_tool_panel = True + break if 'tool_dependencies' in metadata: includes_tool_dependencies = True if 'workflows' in metadata: @@ -1365,7 +1381,7 @@ has_repository_dependencies = True else: has_repository_dependencies = False - if includes_tools: + if includes_tools_for_display_in_tool_panel: # Get the location in the tool panel in which the tools were originally loaded. if 'tool_panel_section' in metadata: tool_panel_dict = metadata[ 'tool_panel_section' ] @@ -1428,6 +1444,7 @@ includes_data_managers=includes_data_managers, includes_datatypes=includes_datatypes, includes_tools=includes_tools, + includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, includes_tool_dependencies=includes_tool_dependencies, includes_workflows=includes_workflows, has_repository_dependencies=has_repository_dependencies,

diff -r 86411cd12e2f591f6f6f7502a8481d832bcf56c0 -r 2c56c1e49f288ed53234f485c0f19606d013dd1b lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -928,10 +928,12 @@ includes_data_managers = False includes_datatypes = False includes_tools = False + includes_tools_for_display_in_tool_panel = False has_repository_dependencies = False includes_tool_dependencies = False includes_workflows = False if repository_metadata: + includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel metadata = repository_metadata.metadata if metadata: if 'data_manager' in metadata: @@ -946,7 +948,7 @@ has_repository_dependencies = True if 'workflows' in metadata: includes_workflows = True - return includes_data_managers, includes_datatypes, includes_tools, includes_tool_dependencies, has_repository_dependencies, includes_workflows + return includes_data_managers, includes_datatypes, includes_tools, includes_tools_for_display_in_tool_panel, includes_tool_dependencies, has_repository_dependencies, includes_workflows params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -958,7 +960,7 @@ repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) - includes_data_managers, includes_datatypes, includes_tools, includes_tool_dependencies, has_repository_dependencies, includes_workflows = \ + includes_data_managers, includes_datatypes, includes_tools, includes_tools_for_display_in_tool_panel, includes_tool_dependencies, has_repository_dependencies, includes_workflows = \ has_galaxy_utilities( repository_metadata ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) @@ -971,6 +973,7 @@ includes_data_managers=includes_data_managers, includes_datatypes=includes_datatypes, includes_tools=includes_tools, + includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, includes_tool_dependencies=includes_tool_dependencies, has_repository_dependencies=has_repository_dependencies, includes_workflows=includes_workflows ) @@ -995,7 +998,7 @@ trans.security.encode_id( repository.id ), changeset_hash ) if update_to_repository_metadata: - includes_data_managers, includes_datatypes, includes_tools, includes_tool_dependencies, has_repository_dependencies, includes_workflows = \ + includes_data_managers, includes_datatypes, includes_tools, includes_tools_for_display_in_tool_panel, includes_tool_dependencies, has_repository_dependencies, includes_workflows = \ has_galaxy_utilities( update_to_repository_metadata ) # We found a RepositoryMetadata record. if changeset_hash == repository.tip( trans.app ): @@ -1012,6 +1015,7 @@ update_dict[ 'includes_data_managers' ] = includes_data_managers update_dict[ 'includes_datatypes' ] = includes_datatypes update_dict[ 'includes_tools' ] = includes_tools + update_dict[ 'includes_tools_for_display_in_tool_panel' ] = includes_tools_for_display_in_tool_panel update_dict[ 'includes_tool_dependencies' ] = includes_tool_dependencies update_dict[ 'includes_workflows' ] = includes_workflows update_dict[ 'has_repository_dependencies' ] = has_repository_dependencies @@ -1115,6 +1119,7 @@ a local Galaxy instance. """ includes_tools = False + includes_tools_for_display_in_tool_panel = False has_repository_dependencies = False includes_tool_dependencies = False repo_info_dicts = [] @@ -1127,6 +1132,8 @@ if not includes_tools: if 'tools' in metadata: includes_tools = True + if not includes_tools_for_display_in_tool_panel: + includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel if not has_repository_dependencies: if 'repository_dependencies' in metadata: has_repository_dependencies = True @@ -1148,6 +1155,7 @@ repository_dependencies=None ) repo_info_dicts.append( encoding_util.tool_shed_encode( repo_info_dict ) ) return dict( includes_tools=includes_tools, + includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, has_repository_dependencies=has_repository_dependencies, includes_tool_dependencies=includes_tool_dependencies, repo_info_dicts=repo_info_dicts ) @@ -1261,6 +1269,7 @@ includes_data_managers = False includes_datatypes = False includes_tools = False + includes_tools_for_display_in_tool_panel = False includes_workflows = False readme_files_dict = None metadata = repository_metadata.metadata @@ -1271,6 +1280,12 @@ includes_datatypes = True if 'tools' in metadata: includes_tools = True + # Handle includes_tools_for_display_in_tool_panel. + tool_dicts = metadata[ 'tools' ] + for tool_dict in tool_dicts: + if tool_dict.get( 'includes_tools_for_display_in_tool_panel', False ): + includes_tools_for_display_in_tool_panel = True + break if 'workflows' in metadata: includes_workflows = True readme_files_dict = suc.build_readme_files_dict( metadata ) @@ -1289,6 +1304,7 @@ return dict( includes_data_managers=includes_data_managers, includes_datatypes=includes_datatypes, includes_tools=includes_tools, + includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, has_repository_dependencies=has_repository_dependencies, includes_tool_dependencies=includes_tool_dependencies, includes_workflows=includes_workflows,

diff -r 86411cd12e2f591f6f6f7502a8481d832bcf56c0 -r 2c56c1e49f288ed53234f485c0f19606d013dd1b lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -215,6 +215,14 @@ self.includes_tools = includes_tools self.includes_tool_dependencies = includes_tool_dependencies self.includes_workflows = includes_workflows + @property + def includes_tools_for_display_in_tool_panel( self ): + if self.metadata: + tool_dicts = self.metadata.get( 'tools', [] ) + for tool_dict in tool_dicts: + if tool_dict.get( 'add_to_tool_panel', True ): + return True + return False def as_dict( self, value_mapper=None ): return self.get_api_value( view='element', value_mapper=value_mapper ) def get_api_value( self, view='collection', value_mapper=None ):

diff -r 86411cd12e2f591f6f6f7502a8481d832bcf56c0 -r 2c56c1e49f288ed53234f485c0f19606d013dd1b lib/tool_shed/util/shed_util.py --- a/lib/tool_shed/util/shed_util.py +++ b/lib/tool_shed/util/shed_util.py @@ -28,7 +28,7 @@ shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) repository.deleted = False repository.status = trans.model.ToolShedRepository.installation_status.INSTALLED - if repository.includes_tools: + if repository.includes_tools_for_display_in_tool_panel: metadata = repository.metadata repository_tools_tups = suc.get_repository_tools_tups( trans.app, metadata ) # Reload tools into the appropriate tool panel section. @@ -963,6 +963,7 @@ includes_data_managers = update_dict.get( 'includes_data_managers', False ) includes_datatypes = update_dict.get( 'includes_datatypes', False ) includes_tools = update_dict.get( 'includes_tools', False ) + includes_tools_for_display_in_tool_panel = update_dict.get( 'includes_tools_for_display_in_tool_panel', False ) includes_tool_dependencies = update_dict.get( 'includes_tool_dependencies', False ) includes_workflows = update_dict.get( 'includes_workflows', False ) has_repository_dependencies = update_dict.get( 'has_repository_dependencies', False ) @@ -972,6 +973,7 @@ changeset_revision_dict[ 'includes_data_managers' ] = includes_data_managers changeset_revision_dict[ 'includes_datatypes' ] = includes_datatypes changeset_revision_dict[ 'includes_tools' ] = includes_tools + changeset_revision_dict[ 'includes_tools_for_display_in_tool_panel' ] = includes_tools_for_display_in_tool_panel changeset_revision_dict[ 'includes_tool_dependencies' ] = includes_tool_dependencies changeset_revision_dict[ 'includes_workflows' ] = includes_workflows changeset_revision_dict[ 'has_repository_dependencies' ] = has_repository_dependencies @@ -982,6 +984,7 @@ changeset_revision_dict[ 'includes_data_managers' ] = False changeset_revision_dict[ 'includes_datatypes' ] = False changeset_revision_dict[ 'includes_tools' ] = False + changeset_revision_dict[ 'includes_tools_for_display_in_tool_panel' ] = False changeset_revision_dict[ 'includes_tool_dependencies' ] = False changeset_revision_dict[ 'includes_workflows' ] = False changeset_revision_dict[ 'has_repository_dependencies' ] = False

diff -r 86411cd12e2f591f6f6f7502a8481d832bcf56c0 -r 2c56c1e49f288ed53234f485c0f19606d013dd1b templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako --- a/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako +++ b/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako @@ -59,7 +59,7 @@ <div class="toolParamHelp" style="clear: both;"> * The repository and all of it's contents will remain on disk. </div> - %if repository.includes_tools: + %if repository.includes_tools_for_display_in_tool_panel: <div class="toolParamHelp" style="clear: both;"> * The repository's tools will not be loaded into the tool panel. </div> @@ -87,7 +87,7 @@ <div class="toolParamHelp" style="clear: both;"> * The repository and all of it's contents will be removed from disk. </div> - %if repository.includes_tools: + %if repository.includes_tools_for_display_in_tool_panel: <div class="toolParamHelp" style="clear: both;"> * The repository's tool tag sets will be removed from the tool config file in which they are defined. </div>

diff -r 86411cd12e2f591f6f6f7502a8481d832bcf56c0 -r 2c56c1e49f288ed53234f485c0f19606d013dd1b templates/admin/tool_shed_repository/reselect_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako @@ -66,7 +66,7 @@ %else: <input type="hidden" name="shed_tool_conf" value="${shed_tool_conf}"/> %endif - %if includes_tools: + %if includes_tools_for_display_in_tool_panel: <div style="clear: both"></div><div class="form-row"> ${no_changes_check_box.get_html()}

diff -r 86411cd12e2f591f6f6f7502a8481d832bcf56c0 -r 2c56c1e49f288ed53234f485c0f19606d013dd1b templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako --- a/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako +++ b/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako @@ -60,7 +60,7 @@ </div><div class="toolForm"><div class="toolFormBody"> - <form name="select_shed_tool_panel_config" id="select_shed_tool_panel_config" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install', tool_shed_url=tool_shed_url, encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, includes_tool_dependencies=includes_tool_dependencies )}" method="post" > + <form name="select_shed_tool_panel_config" id="select_shed_tool_panel_config" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install', tool_shed_url=tool_shed_url, encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, includes_tool_dependencies=includes_tool_dependencies )}" method="post" ><div style="clear: both"></div><% readme_files_dict = containers_dict.get( 'readme_files', None ) %> %if readme_files_dict:

diff -r 86411cd12e2f591f6f6f7502a8481d832bcf56c0 -r 2c56c1e49f288ed53234f485c0f19606d013dd1b templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -60,7 +60,7 @@ </div><div class="toolForm"><div class="toolFormBody"> - <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install', tool_shed_url=tool_shed_url, encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, includes_tool_dependencies=includes_tool_dependencies )}" method="post" > + <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install', tool_shed_url=tool_shed_url, encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, includes_tool_dependencies=includes_tool_dependencies )}" method="post" ><div style="clear: both"></div><% readme_files_dict = containers_dict.get( 'readme_files', None ) %> %if readme_files_dict:

diff -r 86411cd12e2f591f6f6f7502a8481d832bcf56c0 -r 2c56c1e49f288ed53234f485c0f19606d013dd1b test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -661,7 +661,7 @@ def install_repository( self, name, owner, category_name, install_tool_dependencies=False, install_repository_dependencies=True, changeset_revision=None, strings_displayed=[], strings_not_displayed=[], preview_strings_displayed=[], - post_submit_strings_displayed=[], new_tool_panel_section=None, includes_tools=True, + post_submit_strings_displayed=[], new_tool_panel_section=None, includes_tools_for_display_in_tool_panel=True, **kwd ): self.browse_tool_shed( url=self.url ) self.browse_category( test_db_util.get_category_by_name( category_name ) ) @@ -692,7 +692,7 @@ kwd[ 'shed_tool_conf' ] = self.shed_tool_conf if new_tool_panel_section: kwd[ 'new_tool_panel_section' ] = new_tool_panel_section - if includes_tools: + if includes_tools_for_display_in_tool_panel: self.submit_form( 1, 'select_tool_panel_section_button', **kwd ) self.check_for_strings( post_submit_strings_displayed, strings_not_displayed ) else:

diff -r 86411cd12e2f591f6f6f7502a8481d832bcf56c0 -r 2c56c1e49f288ed53234f485c0f19606d013dd1b test/tool_shed/functional/test_1060_install_repository_with_workflow.py --- a/test/tool_shed/functional/test_1060_install_repository_with_workflow.py +++ b/test/tool_shed/functional/test_1060_install_repository_with_workflow.py @@ -137,7 +137,7 @@ common.test_user_1_name, 'Test 0060 Workflow Features', install_tool_dependencies=False, - includes_tools=False ) + includes_tools_for_display_in_tool_panel=False ) def test_0030_import_workflow_from_installed_repository( self ): '''Import the workflow from the installed repository and verify that it appears in the list of all workflows.''' installed_repository = test_db_util.get_installed_repository_by_name_owner( workflow_repository_name, common.test_user_1_name )

diff -r 86411cd12e2f591f6f6f7502a8481d832bcf56c0 -r 2c56c1e49f288ed53234f485c0f19606d013dd1b test/tool_shed/functional/test_1090_install_tool_from_tool_search.py --- a/test/tool_shed/functional/test_1090_install_tool_from_tool_search.py +++ b/test/tool_shed/functional/test_1090_install_tool_from_tool_search.py @@ -252,7 +252,7 @@ self.install_repository( emboss_datatypes_repository_name, common.test_user_1_name, category_name, - includes_tools=False ) + includes_tools_for_display_in_tool_panel=False ) installed_repositories = [ ( emboss_datatypes_repository_name, common.test_user_1_name ), ( freebayes_repository_name, common.test_user_1_name ) ] uninstalled_repositories = [ ( emboss_repository_name, common.test_user_1_name ),

diff -r 86411cd12e2f591f6f6f7502a8481d832bcf56c0 -r 2c56c1e49f288ed53234f485c0f19606d013dd1b test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py --- a/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py +++ b/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py @@ -233,7 +233,7 @@ install_tool_dependencies=True, preview_strings_displayed=preview_strings_displayed, post_submit_strings_displayed=[ base_repository.name, tool_repository.name, 'new' ], - includes_tools=True ) + includes_tools_for_display_in_tool_panel=True ) def test_0050_verify_installed_repositories( self ): '''Verify that the installed repositories are displayed properly.''' base_repository = test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name )

diff -r 86411cd12e2f591f6f6f7502a8481d832bcf56c0 -r 2c56c1e49f288ed53234f485c0f19606d013dd1b test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py --- a/test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py +++ b/test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py @@ -182,6 +182,6 @@ install_repository_dependencies=True, preview_strings_displayed=preview_strings_displayed, post_submit_strings_displayed=[ repository.name, repository.name, 'new' ], - includes_tools=True ) + includes_tools_for_display_in_tool_panel=True ) repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) self.display_installed_repository_manage_page( repository, strings_not_displayed=[ 'Repository dependencies' ] )

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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