1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/69f446023855/ changeset: 69f446023855 user: greg date: 2012-09-25 19:36:43 summary: Fixes for handling sample files in tool shed repositories. affected #: 4 files diff -r 5f739cf9187bde20a0b9d368bf83ffcac19eedc0 -r 69f446023855cd7ed585ca6dde5ee581043e61f0 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1469,7 +1469,7 @@ error, message = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) tool, valid, message2 = load_tool_from_config( trans.app, tool_config_filepath ) message = concat_messages( message, message2 ) - return tool, valid, message + return tool, valid, message, sample_files def handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ): tool = None message = '' @@ -1490,7 +1490,7 @@ if manifest_ctx and ctx_file: tool, message2 = load_tool_from_tmp_config( trans, repo, manifest_ctx, ctx_file, work_dir ) message = concat_messages( message, message2 ) - return tool, message + return tool, message, sample_files def handle_sample_tool_data_table_conf_file( app, filename, persist=False ): """ Parse the incoming filename and add new entries to the in-memory app.tool_data_tables dictionary. If persist is True (should only occur) diff -r 5f739cf9187bde20a0b9d368bf83ffcac19eedc0 -r 69f446023855cd7ed585ca6dde5ee581043e61f0 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -1010,9 +1010,8 @@ message += '<b><toolbox></b> tag that includes a <b>tool_path</b> attribute value which is a directory relative to the Galaxy installation ' message += 'directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name <b>shed_tool_conf.xml</b> whose ' message += '<b><toolbox></b> tag is <b><toolbox tool_path="../shed_tools"></b>).<p/>See the ' - message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_..." ' - message += 'target="_blank">Automatic installation of Galaxy tool shed repository tools into a local Galaxy instance</a> section of the ' - message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed" target="_blank">Galaxy tool shed wiki</a> for all of the details.' + message += '<a href="http://wiki.g2.bx.psu.edu/InstallingRepositoriesToGalaxy" target="_blank">Installation of Galaxy tool shed repository tools ' + message += 'into a local Galaxy instance</a> section of the Galaxy tool shed wiki for all of the details.' return trans.show_error_message( message ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) diff -r 5f739cf9187bde20a0b9d368bf83ffcac19eedc0 -r 69f446023855cd7ed585ca6dde5ee581043e61f0 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -620,7 +620,7 @@ can_use_disk_file = can_use_tool_config_disk_file( trans, repository, repo, tool_config_filepath, changeset_revision ) if can_use_disk_file: trans.app.config.tool_data_path = work_dir - tool, valid, message = handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, tool_config_filepath, work_dir ) + tool, valid, message, sample_files = handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, tool_config_filepath, work_dir ) if tool is not None: invalid_files_and_errors_tups = check_tool_input_params( trans.app, repo_files_dir, @@ -637,7 +637,7 @@ message = concat_messages( message, message2 ) status = 'error' else: - tool, message = handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ) + tool, message, sample_files = handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ) try: shutil.rmtree( work_dir ) except: diff -r 5f739cf9187bde20a0b9d368bf83ffcac19eedc0 -r 69f446023855cd7ed585ca6dde5ee581043e61f0 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -2301,11 +2301,18 @@ can_use_disk_file = can_use_tool_config_disk_file( trans, repository, repo, full_path_to_tool_config, changeset_revision ) if can_use_disk_file: trans.app.config.tool_data_path = work_dir - tool, valid, message = handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, full_path_to_tool_config, work_dir ) + tool, valid, message, sample_files = handle_sample_files_and_load_tool_from_disk( trans, + repo_files_dir, + full_path_to_tool_config, + work_dir ) if message: status = 'error' else: - tool, message = handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ) + tool, message, sample_files = handle_sample_files_and_load_tool_from_tmp_config( trans, + repo, + changeset_revision, + tool_config_filename, + work_dir ) if message: status = 'error' break Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.