2 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/8990b28bb0e7/ changeset: 8990b28bb0e7 user: inithello date: 2012-12-21 16:32:45 summary: Fix handling of repository tools and tool dependencies. Fix issue with functional tests altering the integrated tool panel. affected #: 2 files

diff -r 5c9971aba1b4f4062e27dcbdd9262e3e81c88ddf -r 8990b28bb0e77dbf06a83e47e0f76045c28968f3 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -75,8 +75,9 @@ # Replace the old list of in-memory config_elems with the new list for this shed_tool_conf_dict. shed_tool_conf_dict[ 'config_elems' ] = config_elems app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict - # Write the current in-memory version of the integrated_tool_panel.xml file to disk. - app.toolbox.write_integrated_tool_panel_config_file() + if app.config.update_integrated_tool_panel: + # Write the current in-memory version of the integrated_tool_panel.xml file to disk. + app.toolbox.write_integrated_tool_panel_config_file() app.toolbox_search = ToolBoxSearch( app.toolbox ) def alter_config_and_load_prorietary_datatypes( app, datatypes_config, relative_install_dir, deactivate=False, override=True ): """ @@ -1055,7 +1056,7 @@ shed_tool_conf_dict[ 'config_elems' ] = config_elems trans.app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox ) - if uninstall: + if uninstall and trans.app.config.update_integrated_tool_panel: # Write the current in-memory version of the integrated_tool_panel.xml file to disk. trans.app.toolbox.write_integrated_tool_panel_config_file() def remove_tool_dependency( trans, tool_dependency ):

diff -r 5c9971aba1b4f4062e27dcbdd9262e3e81c88ddf -r 8990b28bb0e77dbf06a83e47e0f76045c28968f3 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 @@ -1088,14 +1088,16 @@ if ( not includes_tools and not includes_repository_dependencies ) or \ ( ( includes_tools or includes_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 ) + if includes_tools: shed_tool_conf = kwd[ 'shed_tool_conf' ] else: - install_tool_dependencies = False # If installing a repository that includes no tools, get the relative tool_path from the file to which the migrated_tools_config # setting points. shed_tool_conf = trans.app.config.migrated_tools_config + if includes_tool_dependencies: + install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies ) + else: + install_tool_dependencies = False tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ) created_or_updated_tool_shed_repositories, repo_info_dicts, filtered_repo_info_dicts, message = \ shed_util.create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False )

https://bitbucket.org/galaxy/galaxy-central/changeset/5e60f799a868/ changeset: 5e60f799a868 user: inithello date: 2012-12-21 16:33:18 summary: Make functional tests explicitly specify which shed tool config to use. affected #: 2 files

diff -r 8990b28bb0e77dbf06a83e47e0f76045c28968f3 -r 5e60f799a8687d92fb41dd8a764d434623837772 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -28,6 +28,7 @@ self.file_dir = os.environ.get( 'TOOL_SHED_TEST_FILE_DIR', None ) self.tool_shed_test_file = None self.tool_data_path = os.environ.get( 'GALAXY_TEST_TOOL_DATA_PATH' ) + self.shed_tool_conf = os.environ.get( 'GALAXY_TEST_SHED_TOOL_CONF' ) # TODO: Figure out a way to alter these attributes during tests. self.galaxy_tool_dependency_dir = None # os.environ.get( 'GALAXY_TEST_TOOL_DEPENDENCY_DIR' ) self.shed_tools_dict = {} @@ -431,6 +432,8 @@ checkbox.selected = True else: checkbox.selected = False + if 'shed_tool_conf' not in kwd: + kwd[ 'shed_tool_conf' ] = self.shed_tool_conf self.submit_form( 1, 'select_tool_panel_section_button', **kwd ) self.initiate_installation_process() self.wait_for_repository_installation( repository, changeset_revision )

diff -r 8990b28bb0e77dbf06a83e47e0f76045c28968f3 -r 5e60f799a8687d92fb41dd8a764d434623837772 test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -256,6 +256,7 @@ shed_tool_conf_template_parser = string.Template( shed_tool_conf_xml_template ) shed_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_shed_tool_path ) file( galaxy_shed_tool_conf_file, 'w' ).write( shed_tool_conf_xml ) + os.environ[ 'GALAXY_TEST_SHED_TOOL_CONF' ] = galaxy_shed_tool_conf_file

# ---- Build Galaxy Application -------------------------------------------------- galaxy_global_conf = { '__file__' : 'universe_wsgi.ini.sample' }

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

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