1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/b5090cb80444/ changeset: b5090cb80444 user: greg date: 2012-05-10 02:19:01 summary: Fixes for handling errors when uploading a tarball to a tool shed repository that contains problematic contents. A bit of code cleanup is included as well. affected #: 1 file
diff -r a722c37dee3fb167c47c6f4b93e74518237f7d28 -r b5090cb8044469b7f5d3136cedbe80f009745f0b lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -123,15 +123,8 @@ content_alert_str = '' commands.add( repo.ui, repo, full_path ) # Convert from unicode to prevent "TypeError: array item must be char" - full_path = full_path.encode('ascii', 'replace') - try: - commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) - except Exception, e: - # I never have a problem with commands.commit on a Mac, but in the test/production - # tool shed environment, it occasionally throws a "TypeError: array item must be char" - # exception. If this happens, we'll try the following. - repo.dirstate.write() - repo.commit( user=trans.user.username, text=commit_message ) + full_path = full_path.encode( 'ascii', 'replace' ) + commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) if full_path.endswith( 'tool_data_table_conf.xml.sample' ): # Handle the special case where a tool_data_table_conf.xml.sample # file is being uploaded by parsing the file and adding new entries @@ -205,18 +198,18 @@ repo = hg.repository( get_configured_ui(), repo_dir ) files_to_remove = [] content_alert_str = '' + undesirable_dirs_removed = 0 + undesirable_files_removed = 0 ok, message = self.__check_archive( tar ) if not ok: tar.close() uploaded_file.close() - return ok, message, files_to_remove, content_alert_str + return ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed else: if upload_point is not None: full_path = os.path.abspath( os.path.join( repo_dir, upload_point ) ) else: full_path = os.path.abspath( repo_dir ) - undesirable_dirs_removed = 0 - undesirable_files_removed = 0 filenames_in_archive = [] for tarinfo_obj in tar.getmembers(): ok = os.path.basename( tarinfo_obj.name ) not in undesirable_files @@ -253,14 +246,11 @@ if full_name not in filenames_in_archive: files_to_remove.append( full_name ) for repo_file in files_to_remove: - # Remove files in the repository (relative to the upload point) - # that are not in the uploaded archive. + # Remove files in the repository (relative to the upload point) that are not in the uploaded archive. try: commands.remove( repo.ui, repo, repo_file, force=True ) except Exception, e: - # I never have a problem with commands.remove on a Mac, but in the test/production - # tool shed environment, it throws an exception whenever I delete all files from a - # repository. If this happens, we'll try the following. + log.debug( "Error removing files using the mercurial API, so trying a different approach, the error was: %s" % str( e )) relative_selected_file = selected_file.split( 'repo_%d' % repository.id )[1].lstrip( '/' ) repo.dirstate.remove( relative_selected_file ) repo.dirstate.write() @@ -294,18 +284,11 @@ # appending them to the shed's tool_data_table_conf.xml file on disk. error, message = handle_sample_tool_data_table_conf_file( trans.app, filename_in_archive ) if error: - return False, message, files_to_remove, content_alert_str + return False, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed if filename_in_archive.endswith( '.loc.sample' ): # Handle the special case where a xxx.loc.sample file is being uploaded by copying it to ~/tool-data/xxx.loc. copy_sample_file( trans.app, filename_in_archive ) - try: - commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) - except Exception, e: - # I never have a problem with commands.commit on a Mac, but in the test/production - # tool shed environment, it occasionally throws a "TypeError: array item must be char" - # exception. If this happens, we'll try the following. - repo.dirstate.write() - repo.commit( user=trans.user.username, text=commit_message ) + commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) # See if the content of the change set was valid. admin_only = len( repository.downloadable_revisions ) != 1 handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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