1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/37a28d5134b3/ changeset: 37a28d5134b3 user: greg date: 2012-05-29 20:46:02 summary: Fixes for loading a tool in a tool shed repository. affected #: 4 files
diff -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b -r 37a28d5134b37b8450d9c266e1a5a6bb261461bf lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -785,14 +785,14 @@ for filename in ctx: ctx_file_name = strip_path( filename ) if ctx_file_name == config_file: - return get_named_tmpfile_from_ctx( ctx, filename, dir=dir ) + return get_named_tmpfile_from_ctx( ctx, filename, dir ) # Finally look in the repository manifest. for changeset in repo.changelog: prev_ctx = repo.changectx( changeset ) for ctx_file in prev_ctx.files(): ctx_file_name = strip_path( ctx_file ) if ctx_file_name == config_file: - return get_named_tmpfile_from_ctx( prev_ctx, filename, dir=dir ) + return get_named_tmpfile_from_ctx( prev_ctx, filename, dir ) return None def get_config_from_disk( config_file, relative_install_dir ): for root, dirs, files in os.walk( relative_install_dir ):
diff -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b -r 37a28d5134b37b8450d9c266e1a5a6bb261461bf lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -547,7 +547,7 @@ .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \ .order_by( trans.model.RepositoryMetadata.table.c.id.desc() ) \ .first() -def get_named_tmpfile_from_ctx( ctx, filename, dir=None ): +def get_named_tmpfile_from_ctx( ctx, filename, dir ): fctx = ctx[ filename ] fh = tempfile.NamedTemporaryFile( 'wb', dir=dir ) tmp_filename = fh.name @@ -574,6 +574,28 @@ if parent_id is None: # The tool did not change through all of the changeset revisions. return old_id +def get_previous_valid_changset_revision( repository, repo, before_changeset_revision ): + changeset_tups = [] + for repository_metadata in repository.downloadable_revisions: + changeset_revision = repository_metadata.changeset_revision + ctx = get_changectx_for_changeset( repo, changeset_revision ) + if ctx: + rev = '%04d' % ctx.rev() + else: + rev = '-1' + changeset_tups.append( ( rev, changeset_revision ) ) + previous_changeset_revision = None + current_changeset_revision = None + for changeset_tup in sorted( changeset_tups ): + current_changeset_revision = changeset_tup[ 1 ] + if current_changeset_revision == before_changeset_revision: + if previous_changeset_revision: + return previous_changeset_revision + else: + # Return the hash value of an empty repository changlog - note that this will not be a valid changset revision. + return '000000000000' + else: + previous_changeset_revision = current_changeset_revision def get_repository( trans, id ): """Get a repository from the database via id""" return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) ) @@ -743,8 +765,42 @@ ToolClass = Tool return ToolClass( config_file, root, trans.app ) return None -def load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ): - tool_config = strip_path( tool_config ) +def load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config_filename ): + """ + Return a loaded tool whose tool config file name (e.g., filtering.xml) is the value of tool_config_filename. The value of changeset_revision + is a valid (downloadable) changset revision. If changeset_revision is the repository tip, then the tool will be loaded from it's file on disk. + Otherwise, the tool config will be located in the repository manifest between the received valid changeset revision and the previous valid + changeset revision (if one exists) or the first changeset revision in the repository (if one doesn't). + """ + def load_from_tmp_config( ctx, ctx_file, work_dir ): + tool = None + message = '' + tmp_tool_config = get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir ) + element_tree = util.parse_xml( tmp_tool_config ) + element_tree_root = element_tree.getroot() + # Look for code files required by the tool config. + tmp_code_files = [] + for code_elem in element_tree_root.findall( 'code' ): + code_file_name = code_elem.get( 'file' ) + tmp_code_file_name = copy_file_from_manifest( repo, ctx, code_file_name, work_dir ) + if tmp_code_file_name: + tmp_code_files.append( tmp_code_file_name ) + try: + tool = load_tool( trans, tmp_tool_config ) + except Exception, e: + tool = None + message = "Error loading tool: %s. Clicking <b>Reset metadata</b> may correct this error." % str( e ) + for tmp_code_file in tmp_code_files: + try: + os.unlink( tmp_code_file ) + except: + pass + try: + os.unlink( tmp_tool_config ) + except: + pass + return tool, message + tool_config_filename = strip_path( tool_config_filename ) repository = get_repository( trans, repository_id ) repo_files_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_files_dir ) @@ -757,48 +813,39 @@ if tool_data_table_config: error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) if changeset_revision == repository.tip: + # Load the tool fron it's config file on disk. try: - copied_tool_config = copy_file_from_disk( tool_config, repo_files_dir, work_dir ) + copied_tool_config = copy_file_from_disk( tool_config_filename, repo_files_dir, work_dir ) tool = load_tool( trans, copied_tool_config ) except Exception, e: tool = None - message = "Error loading tool: %s." % str( e ) + message = "Error loading tool from config '%s': %s." % ( tool_config_filename, str( e ) ) else: - # Get the tool config file name from the hgweb url, something like: /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml - old_tool_config_file_name = tool_config.split( '/' )[ -1 ] - in_ctx = False + found = False + tool = None + # Get the tool config from ctx if present. for ctx_file in ctx.files(): ctx_file_name = strip_path( ctx_file ) - if ctx_file_name == old_tool_config_file_name: - in_ctx = True + if ctx_file_name == tool_config_filename: + found = True break - if in_ctx: - tmp_tool_config = get_named_tmpfile_from_ctx( ctx, ctx_file, dir=work_dir ) - element_tree = util.parse_xml( tmp_tool_config ) - element_tree_root = element_tree.getroot() - # Look for code files required by the tool config. - tmp_code_files = [] - for code_elem in element_tree_root.findall( 'code' ): - code_file_name = code_elem.get( 'file' ) - tmp_code_file_name = copy_file_from_manifest( repo, ctx, code_file_name, work_dir ) - if tmp_code_file_name: - tmp_code_files.append( tmp_code_file_name ) - try: - tool = load_tool( trans, tmp_tool_config ) - except Exception, e: - tool = None - message = "Error loading tool: %s. Clicking <b>Reset metadata</b> may correct this error." % str( e ) - for tmp_code_file in tmp_code_files: - try: - os.unlink( tmp_code_file ) - except: - pass - try: - os.unlink( tmp_tool_config ) - except: - pass + if found: + if found: + tool, message = load_from_tmp_config( ctx, ctx_file, work_dir ) else: - tool = None + # Get the tool config from the repository manifest between valid changeset revisions. + previous_valid_changset_revision = get_previous_valid_changset_revision( repository, repo, changeset_revision ) + for changeset in reversed_filtered_changelog( repo, previous_valid_changset_revision, changeset_revision ): + manifest_changeset_revision = str( repo.changectx( changeset ) ) + manifest_ctx = repo.changectx( changeset ) + for ctx_file in manifest_ctx.files(): + ctx_file_name = strip_path( ctx_file ) + if ctx_file_name == tool_config_filename: + found = True + break + if found: + tool, message = load_from_tmp_config( manifest_ctx, ctx_file, work_dir ) + break # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. reset_tool_data_tables( trans.app ) try: @@ -811,7 +858,7 @@ tool = None valid = False error_message = '' - tmp_config = get_named_tmpfile_from_ctx( ctx, filename, dir=dir ) + tmp_config = get_named_tmpfile_from_ctx( ctx, filename, dir ) if not ( check_binary( tmp_config ) or check_image( tmp_config ) or check_gzip( tmp_config )[ 0 ] or check_bz2( tmp_config )[ 0 ] or check_zip( tmp_config ) ): try: @@ -979,6 +1026,26 @@ clean_repository_metadata( trans, id, changeset_revisions ) add_repository_metadata_tool_versions( trans, id, changeset_revisions ) return '', 'ok' +def reversed_filtered_changelog( repo, excluded_lower_bounds_changeset_revision, included_upper_bounds_changeset_revision ): + """ + Return a reversed list of changesets in the repository changelog after the excluded_lower_bounds_changeset_revision, but up to and + including the included_upper_bounds_changeset_revision. The value of excluded_lower_bounds_changeset_revision will be '000000000000' + if no valid changesets exist before included_upper_bounds_changeset_revision. + """ + if excluded_lower_bounds_changeset_revision == '000000000000': + appending_started = True + else: + appending_started = False + reversed_changelog = [] + for changeset in repo.changelog: + changeset_hash = str( repo.changectx( changeset ) ) + if appending_started: + reversed_changelog.insert( 0, changeset ) + if changeset_hash == excluded_lower_bounds_changeset_revision and not appending_started: + appending_started = True + if changeset_hash == included_upper_bounds_changeset_revision: + break + return reversed_changelog def set_repository_metadata( trans, id, changeset_revision, content_alert_str='', **kwd ): """ Set repository metadata on the repository tip, returning specific error messages (if any) to alert the repository owner that the changeset
diff -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b -r 37a28d5134b37b8450d9c266e1a5a6bb261461bf lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -402,7 +402,6 @@ url_args=url_args, allow_multiple=False, async_compatible=False ) ] - # Render the list view return self.valid_repository_list_grid( trans, **kwd ) @web.expose def browse_invalid_tools( self, trans, **kwd ): @@ -1891,7 +1890,7 @@ for filename in ctx: ctx_file_name = strip_path( filename ) if ctx_file_name == tool_config: - tool_config_path = get_named_tmpfile_from_ctx( ctx, filename, dir=work_dir ) + tool_config_path = get_named_tmpfile_from_ctx( ctx, filename, work_dir ) break metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, repo,
diff -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b -r 37a28d5134b37b8450d9c266e1a5a6bb261461bf lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -43,7 +43,6 @@ # See the handle_email_alerts() method for the definition of the scenarios. new_repo_alert = repository.is_new if params.get( 'upload_button', False ): - current_working_dir = os.getcwd() if file_data == '' and url == '': message = 'No files were entered on the upload form.' status = 'error' @@ -270,9 +269,6 @@ 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, 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 ) 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
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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