1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/676546e7038a/ changeset: 676546e7038a user: greg date: 2012-05-24 22:36:32 summary: Enhance setting metadata on tool shed repositories tha tinclude tools that require entries in the tool_data_table_conf.xml file. affected #: 5 files

diff -r 95c05fcbbceb69e9100d8689694c22cc13d16b23 -r 676546e7038ae833e524bbc4b4b26c81c71954bd lib/galaxy/tool_shed/tool_dependencies/fabric_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py @@ -8,6 +8,7 @@ from galaxy import eggs import pkg_resources

+pkg_resources.require('ssh' ) pkg_resources.require( 'Fabric' )

from fabric.api import env, lcd, local

diff -r 95c05fcbbceb69e9100d8689694c22cc13d16b23 -r 676546e7038ae833e524bbc4b4b26c81c71954bd lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1,4 +1,5 @@ import sys, os, tempfile, shutil, logging, string, urllib2 +import galaxy.tools.data from datetime import date, datetime, timedelta from time import strftime, gmtime from galaxy import util @@ -528,10 +529,11 @@ exported_workflow_dict = from_json_string( workflow_text ) if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) - # This step must be done after metadata for tools has been defined. - tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', relative_install_dir ) - if tool_dependencies_config: - metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) + if 'tools' in metadata_dict: + # This step must be done after metadata for tools has been defined. + tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', relative_install_dir ) + if tool_dependencies_config: + metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) return metadata_dict def generate_tool_guid( repository_clone_url, tool ): """ @@ -1026,6 +1028,8 @@ # Reload the tool into the local list of repository_tools_tups. repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ), guid=guid ) repository_tools_tups[ index ] = ( tup_path, guid, repository_tool ) + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( app ) return repository_tools_tups def handle_missing_index_file( app, tool_path, sample_files, repository_tools_tups ): """ @@ -1398,6 +1402,9 @@ if uninstall: # 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 reset_tool_data_tables( app ): + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + app.tool_data_tables = galaxy.tools.data.ToolDataTableManager( app.config.tool_data_table_config_path ) def strip_path( fpath ): file_path, file_name = os.path.split( fpath ) return file_name

diff -r 95c05fcbbceb69e9100d8689694c22cc13d16b23 -r 676546e7038ae833e524bbc4b4b26c81c71954bd lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -7,7 +7,7 @@ from galaxy.util.hash_util import * from galaxy.util.shed_util import copy_sample_file, generate_datatypes_metadata, generate_tool_dependency_metadata, generate_tool_metadata from galaxy.util.shed_util import generate_workflow_metadata, get_changectx_for_changeset, get_config, get_configured_ui, handle_sample_tool_data_table_conf_file -from galaxy.util.shed_util import make_tmp_directory, NOT_TOOL_CONFIGS, strip_path, to_html_escaped, to_html_str, update_repository +from galaxy.util.shed_util import make_tmp_directory, NOT_TOOL_CONFIGS, reset_tool_data_tables, strip_path, to_html_escaped, to_html_str, update_repository from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * @@ -245,6 +245,8 @@ correction_msg = "This file refers to a file named <b>%s</b>. " % str( index_file ) correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( index_file_name ) invalid_files.append( ( xml_file_in_ctx, correction_msg ) ) + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) return sample_files_copied, can_set_metadata, invalid_files def clean_repository_metadata( trans, id, changeset_revisions ): # Delete all repository_metadata reecords associated with the repository that have a changeset_revision that is not in changeset_revisions. @@ -437,16 +439,20 @@ work_dir = make_tmp_directory() datatypes_config = get_config( 'datatypes_conf.xml', repo, repo_dir, ctx, work_dir ) if datatypes_config: - metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) + metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) sample_files = get_sample_files( repo, repo_dir, dir=work_dir ) + # Handle the tool_data_table_conf.xml.sample file if it is included in the repository. + if 'tool_data_table_conf.xml.sample' in sample_files: + tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', work_dir ) + error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) if sample_files: trans.app.config.tool_data_path = work_dir for filename in ctx: # Find all tool configs. ctx_file_name = strip_path( filename ) if ctx_file_name not in NOT_TOOL_CONFIGS and filename.endswith( '.xml' ): - valid, tool = load_tool_from_tmp_directory( trans, repo, repo_dir, ctx, filename, work_dir ) - if valid and tool is not None: + is_tool_config, valid, tool, error_message = load_tool_from_tmp_directory( trans, repo, repo_dir, ctx, filename, work_dir ) + if is_tool_config and valid and tool is not None: sample_files_copied, can_set_metadata, invalid_files = check_tool_input_params( trans, repo, repo_dir, @@ -484,9 +490,11 @@ os.unlink( os.path.join( original_tool_data_path, copied_file ) ) except: pass - elif tool is not None: - # We have a tool config but it is invalid. - invalid_files.append( ( ctx_file_name, 'Problems loading tool.' ) ) + elif is_tool_config: + if not error_message: + error_message = 'Unknown problems loading tool.' + # We have a tool config but it is invalid or the tool does not properly load. + invalid_files.append( ( ctx_file_name, error_message ) ) invalid_tool_configs.append( ctx_file_name ) # Find all exported workflows. elif filename.endswith( '.ga' ): @@ -498,15 +506,18 @@ metadata_dict = generate_workflow_metadata( '', exported_workflow_dict, metadata_dict ) except Exception, e: invalid_files.append( ( ctx_file_name, str( e ) ) ) - # Find tool_dependencies.xml if it exists. This step must be done after metadata for tools has been defined. - tool_dependencies_config = get_config( 'tool_dependencies.xml', repo, repo_dir, ctx, work_dir ) - if tool_dependencies_config: - metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) + if 'tools' in metadata_dict: + # Find tool_dependencies.xml if it exists. This step must be done after metadata for tools has been defined. + tool_dependencies_config = get_config( 'tool_dependencies.xml', repo, repo_dir, ctx, work_dir ) + if tool_dependencies_config: + metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) if invalid_tool_configs: metadata_dict [ 'invalid_tools' ] = invalid_tool_configs if sample_files: # Don't forget to reset the value of trans.app.config.tool_data_path! trans.app.config.tool_data_path = original_tool_data_path + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) try: shutil.rmtree( work_dir ) except: @@ -737,9 +748,14 @@ repository = get_repository( trans, repository_id ) repo_files_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_files_dir ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) tool = None message = '' work_dir = make_tmp_directory() + # Load entries into the tool_data_tables if the tool requires them. + tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', work_dir ) + 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: try: copied_tool_config = copy_file_from_disk( tool_config, repo_files_dir, work_dir ) @@ -750,7 +766,6 @@ 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 ] - ctx = get_changectx_for_changeset( repo, changeset_revision ) in_ctx = False for ctx_file in ctx.files(): ctx_file_name = strip_path( ctx_file ) @@ -784,14 +799,18 @@ pass else: tool = None + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) try: shutil.rmtree( work_dir ) except: pass return tool, message def load_tool_from_tmp_directory( trans, repo, repo_dir, ctx, filename, dir ): + is_tool_config = False tool = None valid = False + error_message = '' tmp_config = get_named_tmpfile_from_ctx( ctx, filename, dir=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 ) ): @@ -799,11 +818,15 @@ # Make sure we're looking at a tool config and not a display application config or something else. element_tree = util.parse_xml( tmp_config ) element_tree_root = element_tree.getroot() - is_tool = element_tree_root.tag == 'tool' + is_tool_config = element_tree_root.tag == 'tool' except Exception, e: log.debug( "Error parsing %s, exception: %s" % ( tmp_config, str( e ) ) ) - is_tool = False - if is_tool: + is_tool_config = False + if is_tool_config: + # Load entries into the tool_data_tables if the tool requires them. + tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', dir ) + if tool_data_table_config: + error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) # Look for code files required by the tool config. The directory to which dir refers should be removed by the caller. for code_elem in element_tree_root.findall( 'code' ): code_file_name = code_elem.get( 'file' ) @@ -814,9 +837,17 @@ try: tool = load_tool( trans, tmp_config ) valid = True - except: + except KeyError, e: valid = False - return valid, tool + error_message = 'This file requires an entry for "%s" in the tool_data_table_conf.xml file. Upload a file ' % str( e ) + error_message += 'named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct ' + error_message += 'this error. ' + except Exception, e: + valid = False + error_message = str( e ) + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) + return is_tool_config, valid, tool, error_message def new_tool_metadata_required( trans, id, metadata_dict ): """ Compare the last saved metadata for each tool in the repository with the new metadata @@ -1049,13 +1080,11 @@ error_message, status = reset_all_metadata_on_repository( trans, id, **kwd ) if error_message: # If there is an error, display it. - message += '%s<br/>%s ' % ( message, error_message ) - status = 'error' return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', id=id, - message=message, - status=status ) ) + message=error_message, + status='error' ) ) def update_for_browsing( trans, repository, current_working_dir, commit_message='' ): # This method id deprecated, but we'll keep it around for a while in case we need it. The problem is that hg purge # is not supported by the mercurial API.

diff -r 95c05fcbbceb69e9100d8689694c22cc13d16b23 -r 676546e7038ae833e524bbc4b4b26c81c71954bd lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -950,7 +950,12 @@ for filename in ctx: # Find all tool configs in this repository changeset_revision. if filename not in NOT_TOOL_CONFIGS and filename.endswith( '.xml' ): - valid, tool = load_tool_from_tmp_directory( trans, repo, repo_dir, ctx, filename, work_dir ) + is_tool_config, valid, tool, error_message = load_tool_from_tmp_directory( trans, + repo, + repo_dir, + ctx, + filename, + work_dir ) if valid and tool is not None: tool_guids.append( generate_tool_guid( trans, repository, tool ) ) tool_guids.sort()

diff -r 95c05fcbbceb69e9100d8689694c22cc13d16b23 -r 676546e7038ae833e524bbc4b4b26c81c71954bd lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -3,7 +3,7 @@ from galaxy.model.orm import * from galaxy.datatypes.checkers import * from common import * -from galaxy.util.shed_util import get_configured_ui, handle_sample_tool_data_table_conf_file +from galaxy.util.shed_util import get_configured_ui, reset_tool_data_tables, handle_sample_tool_data_table_conf_file

from galaxy import eggs eggs.require('mercurial') @@ -168,6 +168,8 @@ status=status ) ) else: status = 'error' + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] return trans.fill_template( '/webapps/community/repository/upload.mako', repository=repository,

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

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