galaxy-commits January 2013

galaxy-commits@lists.galaxyproject.org

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commit/galaxy-central: carlfeberhard: history panel: fix to edit url in failed_metadata hda smallwarningmessage
by Bitbucket 25 Jan '13

25 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4a60baf34969/ changeset: 4a60baf34969 user: carlfeberhard date: 2013-01-25 21:05:38 summary: history panel: fix to edit url in failed_metadata hda smallwarningmessage affected #: 1 file diff -r 982aa4ecc7b5be0d4a4e84b149e47bfc4ef7cc7f -r 4a60baf34969dea43d30b4f18094dfd30c167b25 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -483,7 +483,9 @@ _render_body_failed_metadata : function( parent ){ //TODO: the css for this box is broken (unlike the others) // add a message box about the failure at the top of the body... - parent.append( $( HDABaseView.templates.failedMetadata( this.model.toJSON() ) ) ); + parent.append( $( HDABaseView.templates.failedMetadata( + _.extend( this.model.toJSON(), { urls: this.urls } ) + ))); //...then render the remaining body as STATES.OK (only diff between these states is the box above) this._render_body_ok( parent ); }, 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.

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commit/galaxy-central: greg: Allow repository owners to reset all repository metadata in the tool shed.
by Bitbucket 25 Jan '13

25 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/982aa4ecc7b5/ changeset: 982aa4ecc7b5 user: greg date: 2013-01-25 19:23:59 summary: Allow repository owners to reset all repository metadata in the tool shed. affected #: 1 file diff -r 3cc16ea80b08e9faa2f721051d89167959aceb2a -r 982aa4ecc7b5be0d4a4e84b149e47bfc4ef7cc7f templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -18,7 +18,7 @@ can_push = not is_deprecated and trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_download = not is_deprecated and not is_new and ( not is_malicious or can_push ) can_rate = not is_new and not is_deprecated and trans.user and repository.user != trans.user - can_reset_all_metadata = not is_deprecated and is_admin and len( repo ) > 0 + can_reset_all_metadata = not is_deprecated and len( repo ) > 0 can_review_repository = has_metadata and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ) can_set_metadata = not is_new and not is_deprecated can_set_malicious = metadata and can_set_metadata and is_admin and changeset_revision == repository.tip( trans.app ) 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.

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commit/galaxy-central: greg: Handle complex repository dependency definitions in the tool shed.
by Bitbucket 25 Jan '13

25 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3cc16ea80b08/ changeset: 3cc16ea80b08 user: greg date: 2013-01-25 17:48:04 summary: Handle complex repository dependency definitions in the tool shed. affected #: 6 files diff -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec -r 3cc16ea80b08e9faa2f721051d89167959aceb2a lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -181,6 +181,7 @@ % ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) ) metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=self.app, repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, repository_clone_url=repository_clone_url, shed_config_dict = self.shed_config_dict, relative_install_dir=relative_install_dir, diff -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec -r 3cc16ea80b08e9faa2f721051d89167959aceb2a lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1323,9 +1323,8 @@ installed_repository_dependencies, missing_repository_dependencies = get_installed_and_missing_repository_dependencies( trans, repository ) # Handle the current repository's tool dependencies. repository_tool_dependencies = metadata.get( 'tool_dependencies', None ) - repository_installed_tool_dependencies, repository_missing_tool_dependencies = get_installed_and_missing_tool_dependencies( trans, - repository, - repository_tool_dependencies ) + repository_installed_tool_dependencies, repository_missing_tool_dependencies = \ + get_installed_and_missing_tool_dependencies( trans, repository, repository_tool_dependencies ) if reinstalling: installed_tool_dependencies, missing_tool_dependencies = \ populate_tool_dependencies_dicts( trans=trans, diff -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec -r 3cc16ea80b08e9faa2f721051d89167959aceb2a lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -103,26 +103,52 @@ defined tool dependencies. The list of tool dependencies may be associated with more than a single repository. """ for dependency_key, requirements_dict in tool_dependencies.items(): - if dependency_key not in [ 'set_environment' ]: - repository_name = requirements_dict.get( 'repository_name', 'unknown' ) - repository_owner = requirements_dict.get( 'repository_owner', 'unknown' ) - changeset_revision = requirements_dict.get( 'changeset_revision', 'unknown' ) - dependency_name = requirements_dict[ 'name' ] - version = requirements_dict[ 'version' ] - type = requirements_dict[ 'type' ] - if trans.app.config.tool_dependency_dir: - root_dir = trans.app.config.tool_dependency_dir + if dependency_key in [ 'set_environment' ]: + continue + repository_name = requirements_dict.get( 'repository_name', 'unknown' ) + repository_owner = requirements_dict.get( 'repository_owner', 'unknown' ) + changeset_revision = requirements_dict.get( 'changeset_revision', 'unknown' ) + dependency_name = requirements_dict[ 'name' ] + version = requirements_dict[ 'version' ] + type = requirements_dict[ 'type' ] + if trans.app.config.tool_dependency_dir: + root_dir = trans.app.config.tool_dependency_dir + else: + root_dir = '<set your tool_dependency_dir in your Galaxy configuration file>' + install_dir = os.path.join( root_dir, + dependency_name, + version, + repository_owner, + repository_name, + changeset_revision ) + requirements_dict[ 'install_dir' ] = install_dir + tool_dependencies[ dependency_key ] = requirements_dict + return tool_dependencies +def add_tool_shed_orphan_settings_to_tool_dependencies( tool_dependencies, tools ): + """Inspect all received tool dependencies and label those that are orphans within the repository in the tool shed.""" + new_tool_dependencies = {} + if tool_dependencies: + for td_key, requirements_dict in tool_dependencies.items(): + if td_key in [ 'set_environment' ]: + new_set_environment_dict_list = [] + for set_environment_dict in requirements_dict: + type = 'set_environment' + name = set_environment_dict.get( 'name', None ) + version = None + is_orphan_in_tool_shed = tool_dependency_is_orphan_in_tool_shed( type, name, version, tools ) + set_environment_dict[ 'is_orphan_in_tool_shed' ] = is_orphan_in_tool_shed + new_set_environment_dict_list.append( set_environment_dict ) + new_tool_dependencies[ td_key ] = new_set_environment_dict_list + new_tool_dependencies[ td_key ] = new_set_environment_dict_list else: - root_dir = '<set your tool_dependency_dir in your Galaxy configuration file>' - install_dir = os.path.join( root_dir, - dependency_name, - version, - repository_owner, - repository_name, - changeset_revision ) - requirements_dict[ 'install_dir' ] = install_dir - tool_dependencies[ dependency_key ] = requirements_dict - return tool_dependencies + type = requirements_dict.get( 'type', 'package' ) + name = requirements_dict.get( 'name', None ) + version = requirements_dict.get( 'version', None ) + if type and name: + is_orphan_in_tool_shed = tool_dependency_is_orphan_in_tool_shed( type, name, version, tools ) + requirements_dict[ 'is_orphan_in_tool_shed' ] = is_orphan_in_tool_shed + new_tool_dependencies[ td_key ] = requirements_dict + return new_tool_dependencies def add_tool_versions( trans, id, repository_metadata, changeset_revisions ): # Build a dictionary of { 'tool id' : 'parent tool id' } pairs for each tool in repository_metadata. metadata = repository_metadata.metadata @@ -316,6 +342,9 @@ if metadata: if 'tool_dependencies' in metadata: tool_dependencies = metadata[ 'tool_dependencies' ] + if trans.webapp.name == 'community': + tools = metadata.get( 'tools', None ) + tool_dependencies = add_tool_shed_orphan_settings_to_tool_dependencies( tool_dependencies, tools ) folder_id, tool_dependencies_root_folder = container_util.build_tool_dependencies_folder( trans, folder_id, tool_dependencies, @@ -441,55 +470,6 @@ if repository_dependency[ 0:3 ] == partial_rd: return False return True -def can_generate_tool_dependency_metadata( root, metadata_dict ): - """ - Make sure the combination of name, version and type (the type will be the value of elem.tag) of each root element tag in the tool_dependencies.xml - file is defined in the <requirement> tag for at least one tool in the repository. - """ - can_generate_dependency_metadata = False - for elem in root: - tool_dependency_type = elem.tag - tool_dependency_version = elem.get( 'version', None ) - if tool_dependency_type == 'package': - can_generate_dependency_metadata = False - tool_dependency_name = elem.get( 'name', None ) - if tool_dependency_name and tool_dependency_version: - for tool_dict in metadata_dict.get( 'tools', [] ): - requirements = tool_dict.get( 'requirements', [] ) - for requirement_dict in requirements: - req_name = requirement_dict.get( 'name', None ) - req_version = requirement_dict.get( 'version', None ) - req_type = requirement_dict.get( 'type', None ) - if req_name==tool_dependency_name and req_version==tool_dependency_version and req_type==tool_dependency_type: - can_generate_dependency_metadata = True - break - if requirements and not can_generate_dependency_metadata: - # We've discovered at least 1 combination of name, version and type that is not defined in the <requirement> - # tag for any tool in the repository. - break - if not can_generate_dependency_metadata: - break - elif tool_dependency_type == 'set_environment': - # Here elem is something like: <set_environment version="1.0"> - for env_var_elem in elem: - can_generate_dependency_metadata = False - # <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> - env_var_name = env_var_elem.get( 'name', None ) - if env_var_name: - for tool_dict in metadata_dict.get( 'tools', [] ): - requirements = tool_dict.get( 'requirements', [] ) - for requirement_dict in requirements: - # {"name": "R_SCRIPT_PATH", "type": "set_environment", "version": null} - req_name = requirement_dict.get( 'name', None ) - req_type = requirement_dict.get( 'type', None ) - if req_name==env_var_name and req_type==tool_dependency_type: - can_generate_dependency_metadata = True - break - if requirements and not can_generate_dependency_metadata: - # We've discovered at least 1 combination of name, version and type that is not defined in the <requirement> - # tag for any tool in the repository. - break - return can_generate_dependency_metadata def can_use_tool_config_disk_file( trans, repository, repo, file_path, changeset_revision ): """ Determine if repository's tool config file on disk can be used. This method is restricted to tool config files since, with the @@ -573,7 +553,7 @@ sample_found = True break if not sample_found: - correction_msg = "This file refers to a file named %s. " % str( index_file ) + correction_msg = "This file refers to a file named %s. " % str( index_file_name ) correction_msg += "Upload a file named %s.sample to the repository to correct this error." % str( index_file_name ) invalid_files_and_errors_tups.append( ( tool_config_name, correction_msg ) ) return invalid_files_and_errors_tups @@ -1007,8 +987,8 @@ for env_elem in elem: env_name = env_elem.get( 'name', None ) if env_name: - requirements_dict [ 'name' ] = env_name - requirements_dict [ 'type' ] = 'set_environment' + requirements_dict[ 'name' ] = env_name + requirements_dict[ 'type' ] = 'set_environment' if requirements_dict: if 'set_environment' in tool_dependencies_dict: tool_dependencies_dict[ 'set_environment' ].append( requirements_dict ) @@ -1051,8 +1031,9 @@ correction_msg = exception_msg.replace( ' ', new_line ).replace( '', bold_start ).replace( '', bold_end ) message += "%s%s%s - %s%s" % ( bold_start, tool_file, bold_end, correction_msg, new_line ) return message -def generate_metadata_for_changeset_revision( app, repository, repository_clone_url, shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, - resetting_all_metadata_on_repository=False, updating_installed_repository=False, persist=False ): +def generate_metadata_for_changeset_revision( app, repository, changeset_revision, repository_clone_url, shed_config_dict=None, relative_install_dir=None, + repository_files_dir=None, resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False ): """ Generate metadata for a repository using it's files on disk. To generate metadata for changeset revisions older than the repository tip, the repository will have been cloned to a temporary location and updated to a specified changeset revision to access that changeset revision's @@ -1202,37 +1183,48 @@ metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) if readme_files: metadata_dict[ 'readme_files' ] = readme_files - 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', files_dir ) - if tool_dependencies_config: - metadata_dict = generate_tool_dependency_metadata( app, - repository, - tool_dependencies_config, - metadata_dict, - original_repository_metadata=original_repository_metadata ) + # This step must be done after metadata for tools has been defined. + tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', files_dir ) + if tool_dependencies_config: + metadata_dict, error_message = generate_tool_dependency_metadata( app, + repository, + changeset_revision, + repository_clone_url, + tool_dependencies_config, + metadata_dict, + original_repository_metadata=original_repository_metadata ) + if error_message: + invalid_file_tups.append( ( 'tool_dependencies.xml', error_message ) ) if invalid_tool_configs: metadata_dict [ 'invalid_tools' ] = invalid_tool_configs # Reset the value of the app's tool_data_path and tool_data_table_config_path to their respective original values. app.config.tool_data_path = original_tool_data_path app.config.tool_data_table_config_path = original_tool_data_table_config_path return metadata_dict, invalid_file_tups -def generate_package_dependency_metadata( elem, tool_dependencies_dict ): +def generate_package_dependency_metadata( app, elem, tool_dependencies_dict ): """The value of package_name must match the value of the "package" type in the tool config's <requirements> tag set.""" + repository_dependency_tup = [] requirements_dict = {} + error_message = '' package_name = elem.get( 'name', None ) package_version = elem.get( 'version', None ) if package_name and package_version: - dependency_key = '%s/%s' % ( package_name, package_version ) - requirements_dict [ 'name' ] = package_name - requirements_dict [ 'version' ] = package_version - requirements_dict [ 'type' ] = 'package' + requirements_dict[ 'name' ] = package_name + requirements_dict[ 'version' ] = package_version + requirements_dict[ 'type' ] = 'package' for sub_elem in elem: if sub_elem.tag == 'readme': requirements_dict[ 'readme' ] = sub_elem.text + elif sub_elem.tag == 'repository': + # We have a complex repository dependency. + current_rd_tups, error_message = handle_repository_elem_for_tool_shed( app=app, + repository_elem=sub_elem, + repository_dependencies_tups=None ) + repository_dependency_tup = current_rd_tups[ 0 ] if requirements_dict: + dependency_key = '%s/%s' % ( package_name, package_version ) tool_dependencies_dict[ dependency_key ] = requirements_dict - return tool_dependencies_dict + return tool_dependencies_dict, repository_dependency_tup, error_message def generate_repository_dependency_metadata_for_installed_repository( app, repository_dependencies_config, metadata_dict ): """ Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config. This method @@ -1281,63 +1273,27 @@ log.debug( error_message ) is_valid = False if is_valid: - sa_session = app.model.context.current for repository_elem in root.findall( 'repository' ): - toolshed = repository_elem.attrib[ 'toolshed' ] - name = repository_elem.attrib[ 'name' ] - owner = repository_elem.attrib[ 'owner'] - changeset_revision = repository_elem.attrib[ 'changeset_revision' ] - user = None - repository = None - if tool_shed_is_this_tool_shed( toolshed ): - try: - user = sa_session.query( app.model.User ) \ - .filter( app.model.User.table.c.username == owner ) \ - .one() - except Exception, e: - error_message = "Invalid owner %s defined for repository %s. Repository dependencies will be ignored." % ( owner, name ) - log.debug( error_message ) - return metadata_dict, error_message - if user: - try: - repository = sa_session.query( app.model.Repository ) \ - .filter( and_( app.model.Repository.table.c.name == name, - app.model.Repository.table.c.user_id == user.id ) ) \ - .first() - except: - error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner ) - log.debug( error_message ) - return metadata_dict, error_message - if repository: - repository_dependencies_tup = ( toolshed, name, owner, changeset_revision ) - if repository_dependencies_tup not in repository_dependencies_tups: - repository_dependencies_tups.append( repository_dependencies_tup ) - else: - error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner ) - log.debug( error_message ) - return metadata_dict, error_message - else: - error_message = "Invalid owner %s defined for owner of repository %s. Repository dependencies will be ignored." % ( owner, name ) - log.debug( error_message ) - return metadata_dict, error_message - else: - # Repository dependencies are currentlhy supported within a single tool shed. - error_message = "Invalid tool shed %s defined for repository %s. " % ( toolshed, name ) - error_message += "Repository dependencies are currently supported within a single tool shed, so your definition will be ignored." + current_rd_tups, error_message = handle_repository_elem_for_tool_shed( app, repository_elem, repository_dependencies_tups ) + if error_message: log.debug( error_message ) return metadata_dict, error_message + for crdt in current_rd_tups: + repository_dependencies_tups.append( crdt ) if repository_dependencies_tups: repository_dependencies_dict = dict( description=root.get( 'description' ), repository_dependencies=repository_dependencies_tups ) metadata_dict[ 'repository_dependencies' ] = repository_dependencies_dict return metadata_dict, error_message -def generate_tool_dependency_metadata( app, repository, tool_dependencies_config, metadata_dict, original_repository_metadata=None ): +def generate_tool_dependency_metadata( app, repository, changeset_revision, repository_clone_url, tool_dependencies_config, metadata_dict, + original_repository_metadata=None ): """ If the combination of name, version and type of each element is defined in the <requirement> tag for at least one tool in the repository, then update the received metadata_dict with information from the parsed tool_dependencies_config. """ + error_message = '' if original_repository_metadata: - # Keep a copy of the original tool dependencies dictionary in the metadata. + # Keep a copy of the original tool dependencies dictionary and the list of tool dictionaries in the metadata. original_tool_dependencies_dict = original_repository_metadata.get( 'tool_dependencies', None ) else: original_tool_dependencies_dict = None @@ -1349,24 +1305,49 @@ root = tree.getroot() ElementInclude.include( root ) tool_dependencies_dict = {} - if can_generate_tool_dependency_metadata( root, metadata_dict ): - for elem in root: - if elem.tag == 'package': - tool_dependencies_dict = generate_package_dependency_metadata( elem, tool_dependencies_dict ) - elif elem.tag == 'set_environment': - tool_dependencies_dict = generate_environment_dependency_metadata( elem, tool_dependencies_dict ) - # Handle tool dependency installation via other means here (future). - if tool_dependencies_dict: - metadata_dict[ 'tool_dependencies' ] = tool_dependencies_dict - else: - log.debug( "Name, version and type from the <requirement> tag does not match the information in the tool_dependencies.xml file. Tool dependencies will be ignored." ) + repository_dependency_tups = [] + for elem in root: + if elem.tag == 'package': + tool_dependencies_dict, repository_dependency_tup, message = generate_package_dependency_metadata( app, elem, tool_dependencies_dict ) + if repository_dependency_tup and repository_dependency_tup not in repository_dependency_tups: + repository_dependency_tups.append( repository_dependency_tup ) + if message: + log.debug( message ) + error_message = '%s %s' % ( error_message, message ) + elif elem.tag == 'set_environment': + tool_dependencies_dict = generate_environment_dependency_metadata( elem, tool_dependencies_dict ) if tool_dependencies_dict: if original_tool_dependencies_dict: # We're generating metadata on an update pulled to a tool shed repository installed into a Galaxy instance, so handle changes to # tool dependencies appropriately. handle_existing_tool_dependencies_that_changed_in_update( app, repository, original_tool_dependencies_dict, tool_dependencies_dict ) metadata_dict[ 'tool_dependencies' ] = tool_dependencies_dict - return metadata_dict + if repository_dependency_tups: + tool_shed = get_tool_shed_from_clone_url( repository_clone_url ) + if app.name == 'community': + repository_owner = repository.user.username + else: + repository_owner = repository.owner + rd_key = container_util.generate_repository_dependencies_key_for_repository( toolshed_base_url=tool_shed, + repository_name=repository.name, + repository_owner=repository_owner, + changeset_revision=changeset_revision ) + repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', None ) + if repository_dependencies_dict: + if rd_key in repository_dependencies_dict: + repository_dependencies = repository_dependencies_dict[ rd_key ] + for repository_dependency_tup in repository_dependency_tups: + if repository_dependency_tup not in repository_dependencies: + repository_dependencies.append( repository_dependency_tup ) + repository_dependencies_dict[ rd_key ] = repository_dependencies + else: + repository_dependencies_dict[ rd_key ] = repository_dependency_tups + else: + repository_dependencies_dict = dict( root_key=rd_key, + description=root.get( 'description' ), + repository_dependencies=repository_dependency_tups ) + metadata_dict[ 'repository_dependencies' ] = repository_dependencies_dict + return metadata_dict, error_message def generate_tool_elem( tool_shed, repository_name, changeset_revision, owner, tool_file_path, tool, tool_section ): if tool_section is not None: tool_elem = SubElement( tool_section, 'tool' ) @@ -2481,6 +2462,79 @@ message = str( e ) error = True return error, message +def has_orphan_tool_dependencies_in_tool_shed( metadata ): + """Inspect tool dependencies included in the received metadata and determine if any of them are orphans within the repository in the tool shed.""" + if metadata: + tools = metadata.get( 'tools', None ) + tool_dependencies = metadata.get( 'tool_dependencies', None ) + if tool_dependencies: + for td_key, requirements_dict in tool_dependencies.items(): + if td_key in [ 'set_environment' ]: + for set_environment_dict in requirements_dict: + type = 'set_environment' + name = set_environment_dict.get( 'name', None ) + version = None + if name: + is_orphan_in_tool_shed = tool_dependency_is_orphan_in_tool_shed( type, name, version, tools ) + if is_orphan_in_tool_shed: + return True + else: + type = requirements_dict.get( 'type', None ) + name = requirements_dict.get( 'name', None ) + version = requirements_dict.get( 'version', None ) + if type and name: + is_orphan_in_tool_shed = tool_dependency_is_orphan_in_tool_shed( type, name, version, tools ) + if is_orphan_in_tool_shed: + return True + return False +def handle_repository_elem_for_tool_shed( app, repository_elem, repository_dependencies_tups ): + if repository_dependencies_tups is None: + new_rd_tups = [] + else: + new_rd_tups = [ rdt for rdt in repository_dependencies_tups ] + error_message = '' + sa_session = app.model.context.current + toolshed = repository_elem.attrib[ 'toolshed' ] + name = repository_elem.attrib[ 'name' ] + owner = repository_elem.attrib[ 'owner' ] + changeset_revision = repository_elem.attrib[ 'changeset_revision' ] + user = None + repository = None + if tool_shed_is_this_tool_shed( toolshed ): + try: + user = sa_session.query( app.model.User ) \ + .filter( app.model.User.table.c.username == owner ) \ + .one() + except Exception, e: + error_message = "Invalid owner %s defined for repository %s. Repository dependencies will be ignored." % ( owner, name ) + log.debug( error_message ) + return new_rd_tups, error_message + if user: + try: + repository = sa_session.query( app.model.Repository ) \ + .filter( and_( app.model.Repository.table.c.name == name, + app.model.Repository.table.c.user_id == user.id ) ) \ + .first() + except: + error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner ) + log.debug( error_message ) + return new_rd_tups, error_message + if repository: + repository_dependencies_tup = ( toolshed, name, owner, changeset_revision ) + if repository_dependencies_tup not in new_rd_tups: + new_rd_tups.append( repository_dependencies_tup ) + else: + error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner ) + log.debug( error_message ) + else: + error_message = "Invalid owner %s defined for owner of repository %s. Repository dependencies will be ignored." % ( owner, name ) + log.debug( error_message ) + else: + # Repository dependencies are currentlhy supported within a single tool shed. + error_message = "Invalid tool shed %s defined for repository %s. " % ( toolshed, name ) + error_message += "Repository dependencies are currently supported within a single tool shed, so your definition will be ignored." + log.debug( error_message ) + return new_rd_tups, error_message def has_previous_repository_reviews( trans, repository, changeset_revision ): """Determine if a repository has a changeset revision review prior to the received changeset revision.""" repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) @@ -2932,6 +2986,7 @@ original_metadata_dict = repository.metadata metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, repository=repository, + changeset_revision=repository.changeset_revision, repository_clone_url=repository_clone_url, shed_config_dict = repository.get_shed_config_dict( trans.app ), relative_install_dir=relative_install_dir, @@ -3012,6 +3067,7 @@ log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) ) current_metadata_dict, invalid_tups = generate_metadata_for_changeset_revision( app=trans.app, repository=repository, + changeset_revision=current_changeset_revision, repository_clone_url=repository_clone_url, relative_install_dir=repo_dir, repository_files_dir=work_dir, @@ -3148,6 +3204,7 @@ repo = hg.repository( get_configured_ui(), repo_dir ) metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, repository=repository, + changeset_revision=repository.tip( trans.app ), repository_clone_url=repository_clone_url, relative_install_dir=repo_dir, repository_files_dir=None, @@ -3197,7 +3254,7 @@ reset_tool_data_tables( trans.app ) return message, status def set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=None, **kwd ): - # Set metadata on the repository tip. + """Set metadata on the repository tip in the tool shed - this method is not called from Galaxy.""" error_message, status = set_repository_metadata( trans, repository, content_alert_str=content_alert_str, **kwd ) if error_message: # If there is an error, display it. @@ -3214,6 +3271,32 @@ except: file_name = fpath return file_name +def tool_dependency_is_orphan_in_tool_shed( type, name, version, tools ): + """ + Determine if the combination of the received type, name and version is defined in the <requirement> tag for at least one tool in the received list of tools. + If not, the tool dependency defined by the combination is considered an orphan in it's repository in the tool shed. + """ + if tools: + if type == 'package': + if name and version: + for tool_dict in tools: + requirements = tool_dict.get( 'requirements', [] ) + for requirement_dict in requirements: + req_name = requirement_dict.get( 'name', None ) + req_version = requirement_dict.get( 'version', None ) + req_type = requirement_dict.get( 'type', None ) + if req_name == name and req_version == version and req_type == type: + return False + elif type == 'set_environment': + if name: + for tool_dict in tools: + requirements = tool_dict.get( 'requirements', [] ) + for requirement_dict in requirements: + req_name = requirement_dict.get( 'name', None ) + req_type = requirement_dict.get( 'type', None ) + if req_name == name and req_type == type: + return False + return True def to_safe_string( text, to_html=True ): """Translates the characters in text to an html string""" if text: diff -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec -r 3cc16ea80b08e9faa2f721051d89167959aceb2a lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -175,11 +175,10 @@ metadata_dict = repository.metadata_revisions[0].metadata else: metadata_dict = {} - if 'tool_dependencies' not in metadata_dict: + if suc.has_orphan_tool_dependencies_in_tool_shed( metadata_dict ): message += 'Name, version and type from a tool requirement tag does not match the information in the "tool_dependencies.xml file", ' - message += 'so the tool dependency definitions will be ignored.' + message += 'so one or more of the defined tool dependencies are considered orphans within this repository.' status = 'warning' - log.debug( 'Error in tool dependencies for repository with id %s and name %s: %s' % ( str( repository.id ), str( repository.name ), message ) ) # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. suc.reset_tool_data_tables( trans.app ) trans.response.send_redirect( web.url_for( controller='repository', diff -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec -r 3cc16ea80b08e9faa2f721051d89167959aceb2a lib/galaxy/webapps/community/util/container_util.py --- a/lib/galaxy/webapps/community/util/container_util.py +++ b/lib/galaxy/webapps/community/util/container_util.py @@ -102,7 +102,7 @@ class ToolDependency( object ): """Tool dependency object""" def __init__( self, id=None, name=None, version=None, type=None, install_dir=None, readme=None, installation_status=None, repository_id=None, - tool_dependency_id=None ): + tool_dependency_id=None, is_orphan=None ): self.id = id self.name = name self.version = version @@ -112,6 +112,7 @@ self.installation_status = installation_status self.repository_id = repository_id self.tool_dependency_id = tool_dependency_id + self.is_orphan = is_orphan @property def listify( self ): return [ self.name, self.version, self.type ] @@ -322,17 +323,35 @@ version='Version', type='Type', install_dir='Install directory', - installation_status='Installation status' ) + readme=None, + installation_status='Installation status', + repository_id=None, + tool_dependency_id=None, + is_orphan=None ) else: tool_dependency = ToolDependency( id=tool_dependency_id, name='Name', version='Version', - type='Type' ) + type='Type', + install_dir=None, + readme=None, + installation_status=None, + repository_id=None, + tool_dependency_id=None, + is_orphan=None ) folder.tool_dependencies.append( tool_dependency ) + is_orphan_description = "these dependencies may not be required by tools in this repository" for dependency_key, requirements_dict in tool_dependencies.items(): tool_dependency_id += 1 - if dependency_key == 'set_environment': + if dependency_key in [ 'set_environment' ]: for set_environment_dict in requirements_dict: + if trans.webapp.name == 'community': + is_orphan = set_environment_dict.get( 'is_orphan_in_tool_shed', False ) + else: + # TODO: handle this is Galaxy + is_orphan = False + if is_orphan: + folder.description = is_orphan_description name = set_environment_dict.get( 'name', None ) type = set_environment_dict[ 'type' ] repository_id = set_environment_dict.get( 'repository_id', None ) @@ -343,12 +362,23 @@ installation_status = None tool_dependency = ToolDependency( id=tool_dependency_id, name=name, + version=None, type=type, + install_dir=None, + readme=None, installation_status=installation_status, repository_id=repository_id, - tool_dependency_id=td_id ) + tool_dependency_id=td_id, + is_orphan=is_orphan ) folder.tool_dependencies.append( tool_dependency ) else: + if trans.webapp.name == 'community': + is_orphan = requirements_dict.get( 'is_orphan_in_tool_shed', False ) + else: + # TODO: handle this is Galaxy + is_orphan = False + if is_orphan: + folder.description = is_orphan_description name = requirements_dict[ 'name' ] version = requirements_dict[ 'version' ] type = requirements_dict[ 'type' ] @@ -364,9 +394,11 @@ version=version, type=type, install_dir=install_dir, + readme=None, installation_status=installation_status, repository_id=repository_id, - tool_dependency_id=td_id ) + tool_dependency_id=td_id, + is_orphan=is_orphan ) folder.tool_dependencies.append( tool_dependency ) else: tool_dependencies_root_folder = None diff -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec -r 3cc16ea80b08e9faa2f721051d89167959aceb2a 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 @@ -661,6 +661,7 @@ shed_config_dict = trans.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, repository_clone_url=repository_clone_url, shed_config_dict=shed_config_dict, relative_install_dir=relative_install_dir, @@ -1692,6 +1693,7 @@ original_metadata_dict = repository.metadata metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, repository=repository, + changeset_revision=repository.changeset_revision, repository_clone_url=repository_clone_url, shed_config_dict = repository.get_shed_config_dict( trans.app ), relative_install_dir=relative_install_dir, @@ -1887,6 +1889,7 @@ # Update the repository metadata. metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, repository=repository, + changeset_revision=latest_changeset_revision, repository_clone_url=repository_clone_url, shed_config_dict = repository.get_shed_config_dict( trans.app ), relative_install_dir=relative_install_dir, 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.

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commit/galaxy-central: jgoecks: Cuffcompare wrapper fixes + update test files for v2.0.2
by Bitbucket 25 Jan '13

25 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b99d93d0f137/ changeset: b99d93d0f137 user: jgoecks date: 2013-01-25 00:02:22 summary: Cuffcompare wrapper fixes + update test files for v2.0.2 affected #: 2 files diff -r 5fda62776e3d09702d18ba7a1e4a106425949f15 -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec test-data/cuffcompare_out7.txt --- a/test-data/cuffcompare_out7.txt +++ b/test-data/cuffcompare_out7.txt @@ -1,5 +1,5 @@ -# Cuffcompare v1.3.0 | Command line was: -#cuffcompare -o cc_output -r /Users/jeremy/projects/galaxy-central/database/files/010/dataset_10703.dat -R ./input1 ./input2 +# Cuffcompare v2.0.2 | Command line was: +#cuffcompare -o cc_output -r /Users/jeremy/projects/galaxy-central/database/files/002/dataset_2770.dat -R ./input1 ./input2 # #= Summary for dataset: ./input1 : diff -r 5fda62776e3d09702d18ba7a1e4a106425949f15 -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml +++ b/tools/ngs_rna/cuffcompare_wrapper.xml @@ -78,7 +78,7 @@ <outputs><data format="txt" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy" from_work_dir="cc_output.stats" /> - <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: ${first_input.hid} data tmap file" + <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: data ${first_input.hid} tmap file" from_work_dir="cc_output.input1.tmap" /><data format="tabular" name="input1_refmap" label="${tool.name} on ${on_string}: data ${first_input.hid} refmap file" @@ -86,12 +86,12 @@ <filter>annotation['use_ref_annotation'] == 'Yes'</filter></data><data format="tabular" name="input2_tmap" label="${tool.name} on ${on_string}: data ${input_files[0]['additional_input'].hid} tmap file" from_work_dir="cc_output.input2.tmap"> - <filter>len( input_files ) > 1</filter> + <filter>len( input_files ) >= 1</filter></data><data format="tabular" name="input2_refmap" label="${tool.name} on ${on_string}: data ${input_files[0]['additional_input'].hid} refmap file" from_work_dir="cc_output.input2.refmap"> - <filter>annotation['use_ref_annotation'] == 'Yes' and len( input_files ) > 1</filter> + <filter>annotation['use_ref_annotation'] == 'Yes' and len( input_files ) >= 1</filter></data><data format="tabular" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking" from_work_dir="cc_output.tracking"><filter>len( input_files ) > 0</filter> 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.

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commit/galaxy-central: jgoecks: Enable BedGraph to be used as input to wig-to-bigwig tool.
by Bitbucket 24 Jan '13

24 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5fda62776e3d/ changeset: 5fda62776e3d user: jgoecks date: 2013-01-24 23:06:51 summary: Enable BedGraph to be used as input to wig-to-bigwig tool. affected #: 3 files diff -r 3c243143d68b4fa7fb5b3c4c502f21a8926c775e -r 5fda62776e3d09702d18ba7a1e4a106425949f15 test-data/1.bedgraph --- /dev/null +++ b/test-data/1.bedgraph @@ -0,0 +1,30 @@ +chr1 0 14361 0 +chr1 14361 14829 1 +chr1 14829 14969 0 +chr1 14969 15038 1 +chr1 15038 15795 0 +chr1 15795 15947 1 +chr1 15947 16606 0 +chr1 16606 16765 1 +chr1 16765 16857 0 +chr1 16857 17055 1 +chr1 17055 17232 0 +chr1 17232 17368 1 +chr1 17368 17605 0 +chr1 17605 17742 1 +chr1 17742 17914 0 +chr1 17914 18061 1 +chr1 18061 18267 0 +chr1 18267 18366 1 +chr1 18366 24737 0 +chr1 24737 24891 1 +chr1 24891 29320 0 +chr1 29320 29370 1 +chr1 29370 34610 0 +chr1 34610 35174 2 +chr1 35174 35276 0 +chr1 35276 35481 2 +chr1 35481 35720 0 +chr1 35720 36081 2 +chr1 36081 69090 0 +chr1 69090 69093 3 diff -r 3c243143d68b4fa7fb5b3c4c502f21a8926c775e -r 5fda62776e3d09702d18ba7a1e4a106425949f15 test-data/3.bigwig Binary file test-data/3.bigwig has changed diff -r 3c243143d68b4fa7fb5b3c4c502f21a8926c775e -r 5fda62776e3d09702d18ba7a1e4a106425949f15 tools/filters/wig_to_bigwig.xml --- a/tools/filters/wig_to_bigwig.xml +++ b/tools/filters/wig_to_bigwig.xml @@ -1,4 +1,4 @@ -<tool id="wig_to_bigWig" name="Wig-to-bigWig" version="1.1.0"> +<tool id="wig_to_bigWig" name="Wig/BedGraph-to-bigWig" version="1.1.0"><description>converter</description><command>grep -v "^track" $input1 | wigToBigWig stdin $chromInfo $out_file1 #if $settings.settingsType == "full": @@ -11,7 +11,7 @@ <requirement type="package">ucsc_tools</requirement></requirements><inputs> - <param format="wig" name="input1" type="data" label="Convert"> + <param format="wig,bedgraph" name="input1" type="data" label="Convert"><validator type="unspecified_build" /></param><conditional name="settings"> @@ -46,11 +46,16 @@ <param name="settingsType" value="preset" /><output name="out_file1" file="2.bigwig"/></test> + <test> + <param name="input1" value="1.bedgraph" dbkey="hg19" ftype="bedgraph"/> + <param name="settingsType" value="preset" /> + <output name="out_file1" file="3.bigwig"/> + </test></tests><help> **Syntax** -This tool converts wiggle data into bigWig type. +This tool converts bedgraph or wiggle data into bigWig type. - **Wiggle format**: The .wig format is line-oriented. Wiggle data is preceded by a UCSC track definition line. Following the track definition line is the track data, which can be entered in three different formats described below. @@ -71,5 +76,9 @@ dataValue1 dataValue2 +- The **BedGraph format** is described in detail at the `UCSC Bioinformatics website`_ + +.. _UCSC Bioinformatics website: http://genome.ucsc.edu/goldenPath/help/bedgraph.html + </help></tool> 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.

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commit/galaxy-central: inithello: Update test data for kCCA to allow for a wider range of possible output values.
by Bitbucket 24 Jan '13

24 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3c243143d68b/ changeset: 3c243143d68b user: inithello date: 2013-01-24 17:09:43 summary: Update test data for kCCA to allow for a wider range of possible output values. affected #: 1 file diff -r c901bbb4eca8142b442fa348b8136d4ff3bcfaf8 -r 3c243143d68b4fa7fb5b3c4c502f21a8926c775e test-data/kcca_out1.tabular --- a/test-data/kcca_out1.tabular +++ b/test-data/kcca_out1.tabular @@ -256,7 +256,7 @@ 1\d*\ \-?0\.001\d*\ \-?0\.001\d*\ \-?0\.013\d*\ \-?0\.013\d* 1\d*\ \-?0\.0017\d*\ \-?0\.0017\d*\ \-?0\.011\d*\ \-?0\.011\d* 1\d*\ \-?0\.0024\d*\ \-?0\.0024\d*\ \-?0\.008\d*\ \-?0\.008\d* -1\d*\ \-?8\.7\d*e\-?\d*\ \-?8\.7\d*e\-?\d*\ \-?0\.00049\d*\ \-?0\.00049\d* +1\d*\ \-?8\.[6-8]\d*e\-?\d*\ \-?8\.[6-8]\d*e\-?\d*\ \-?0\.00049\d*\ \-?0\.00049\d* 1\d*\ \-?0\.0007\d*\ \-?0\.0007\d*\ \-?7\.8\d*e\-?\d*\ \-?7\.8\d*e\-?\d* 1\d*\ \-?0\.00075\d*\ \-?0\.00075\d*\ \-?0\.056\d*\ \-?0\.056\d* 1\d*\ \-?0\.004\d*\ \-?0\.004\d*\ \-?0\.04\d*\ \-?0\.04\d* @@ -291,7 +291,7 @@ 1\d*\ \-?0\.0053\d*\ \-?0\.0053\d*\ \-?0\.0019\d*\ \-?0\.0019\d* 1\d*\ \-?0\.0021\d*\ \-?0\.0021\d*\ \-?0\.0096\d*\ \-?0\.0096\d* 1\d*\ \-?0\.0010\d*\ \-?0\.0010\d*\ \-?0\.038\d*\ \-?0\.038\d* -1\d*\ \-?3\.5\d*e-\d*\ \-?3\.5\d*e-\d*\ \-?0\.0081\d*\ \-?0\.0081\d* +1\d*\ \-?3\.[4-6]\d*e-\d*\ \-?3\.[4-6]\d*e-\d*\ \-?0\.0081\d*\ \-?0\.0081\d* 1\d*\ \-?0\.0053\d*\ \-?0\.0053\d*\ \-?0\.0019\d*\ \-?0\.0019\d* 1\d*\ \-?0\.0038\d*\ \-?0\.0038\d*\ \-?0\.0085\d*\ \-?0\.0085\d* 1\d*\ \-?0\.001\d*\ \-?0\.001\d*\ \-?0\.013\d*\ \-?0\.013\d* 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.

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commit/galaxy-central: dannon: Tasks: Adjust the id_tag to use the format "<jobid>_<taskid>", instead of "<jobid>:<taskid>". This resolves issues with particular cluster runners being able to submit.
by Bitbucket 24 Jan '13

24 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c901bbb4eca8/ changeset: c901bbb4eca8 user: dannon date: 2013-01-24 17:03:49 summary: Tasks: Adjust the id_tag to use the format "<jobid>_<taskid>", instead of "<jobid>:<taskid>". This resolves issues with particular cluster runners being able to submit. affected #: 1 file diff -r 6189b2690b4688c4e35066bf09aaf95e1c272d5e -r c901bbb4eca8142b442fa348b8136d4ff3bcfaf8 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -346,7 +346,7 @@ Return an id tag suitable for identifying the task. This combines the task's job id and the task's own id. """ - return "%s:%s" % ( self.job.get_id(), self.get_id() ) + return "%s_%s" % ( self.job.get_id(), self.get_id() ) def get_command_line( self ): return self.command_line def get_parameters( self ): 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.

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commit/galaxy-central: inithello: Functional test to verify correct display of tool migration stages.
by Bitbucket 24 Jan '13

24 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6189b2690b46/ changeset: 6189b2690b46 user: inithello date: 2013-01-24 15:29:29 summary: Functional test to verify correct display of tool migration stages. affected #: 2 files diff -r aa8298344ed5b5f7c209a4341999815d25a2e305 -r 6189b2690b4688c4e35066bf09aaf95e1c272d5e test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -667,6 +667,10 @@ ( self.security.encode_id( repository.id ), tool_xml_path, changeset_revision ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def load_galaxy_tool_migrations_page( self, strings_displayed=[], strings_not_displayed=[] ): + url = '/admin/review_tool_migration_stages' + self.visit_galaxy_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) def load_workflow_image_in_tool_shed( self, repository, workflow_name, changeset_revision=None, strings_displayed=[], strings_not_displayed=[] ): if not changeset_revision: changeset_revision = self.get_repository_tip( repository ) diff -r aa8298344ed5b5f7c209a4341999815d25a2e305 -r 6189b2690b4688c4e35066bf09aaf95e1c272d5e test/tool_shed/functional/test_1400_review_migration_stages.py --- /dev/null +++ b/test/tool_shed/functional/test_1400_review_migration_stages.py @@ -0,0 +1,30 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +class TestToolMigrationStages( ShedTwillTestCase ): + '''Verify that the migration stages display correctly.''' + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin user.""" + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_load_migration_stages_page( self ): + '''Load the migration page and check for the appropriate migration stages.''' + stages = [ + 'emboss_5', 'emboss_datatypes', 'emboss', '5.0.0', '0002_tools.sh', + 'freebayes', '0.9.4_a46483351fd0196637614121868fb5c386612b55', 'samtools', '0.1.18', 'FreeBayes requires g++', + 'ncurses', 'zlib', '0003_tools.sh', + 'ncbi_blast_plus', 'blast_datatypes', 'blast+', '2.2.26+', 'blast.ncbi.nlm.nih.gov', 'NCBI BLAST+ tools', '0004_tools.sh', + 'bwa_wrappers', '0.5.9', 'zlib and libpthread', 'Map with BWA for Illumina', '0005_tools.sh', + 'picard', '1.56.0', 'FASTQ to BAM', '0006_tools.sh', + 'lastz', '1.02.00', 'bowtie', '0.12.7', 'Map with Bowtie for Illumina', 'Bowtie requires libpthread', '0007_tools.sh' + ] + self.load_galaxy_tool_migrations_page( strings_displayed=stages ) + 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.

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commit/galaxy-central: inithello: Make wrapper compatible with python 2.5.
by Bitbucket 23 Jan '13

23 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/aa8298344ed5/ changeset: aa8298344ed5 user: inithello date: 2013-01-23 18:32:05 summary: Make wrapper compatible with python 2.5. affected #: 1 file diff -r da970ef6075702286d47b9ccf83942092eaac27d -r aa8298344ed5b5f7c209a4341999815d25a2e305 tools/evolution/add_scores.py --- a/tools/evolution/add_scores.py +++ b/tools/evolution/add_scores.py @@ -17,11 +17,11 @@ def open_or_die( filename, mode='r', message=None ): if message is None: - message = 'Error opening {0}'.format( filename ) + message = 'Error opening %s' % filename try: fh = open( filename, mode ) except IOError, err: - die( '{0}: {1}'.format( message, err.strerror ) ) + die( '%s: %s' % ( message, err.strerror ) ) return fh ################################################################################ @@ -48,16 +48,16 @@ if not line.startswith( self.comment_chars ): elems = line.split( self.delimiter ) if len( elems ) <= self.key_column: - die( 'Location file {0} line {1}: less than {2} columns'.format( self.filename, line_number, self.key_column + 1 ) ) + die( 'Location file %s line %d: less than %d columns' % ( self.filename, line_number, self.key_column + 1 ) ) else: key = elems.pop( self.key_column ) if key in self._map: if self._map[key] != elems: - die( 'Location file {0} line {1}: duplicate key "{2}"'.format( self.filename, line_number, key ) ) + die( 'Location file %s line %d: duplicate key "%s"' % ( self.filename, line_number, key ) ) else: self._map[key] = elems except IOError, err: - die( 'Error opening location file {0}: {1}'.format( self.filename, err.strerror ) ) + die( 'Error opening location file %s: %s' % ( self.filename, err.strerror ) ) def get_values( self, key ): if key in self._map: @@ -67,7 +67,7 @@ else: return rval else: - die( 'key "{0}" not found in location file {1}'.format( key, self.filename ) ) + die( 'key "%s" not found in location file %s' % ( key, self.filename ) ) ################################################################################ @@ -77,10 +77,10 @@ # open input, output, and bigwig files location_file = LocationFile( loc_filename ) bigwig_filename = location_file.get_values( loc_key ) - bwfh = open_or_die( bigwig_filename, message='Error opening BigWig file {0}'.format( bigwig_filename ) ) + bwfh = open_or_die( bigwig_filename, message='Error opening BigWig file %s' % bigwig_filename ) bw = BigWigFile( file=bwfh ) - ifh = open_or_die( input_filename, message='Error opening input file {0}'.format( input_filename ) ) - ofh = open_or_die( output_filename, mode='w', message='Error opening output file {0}'.format( output_filename ) ) + ifh = open_or_die( input_filename, message='Error opening input file %s' % input_filename ) + ofh = open_or_die( output_filename, mode='w', message='Error opening output file %s' % output_filename ) # make column numbers 0-based chrom_col = int( chrom_col ) - 1 @@ -101,11 +101,11 @@ score_list_len = len( score_list ) if score_list_len == 1: beg, end, score = score_list[0] - score_val = '{0:1.3f}'.format( score ) + score_val = '%1.3f' % score elif score_list_len == 0: score_val = 'NA' else: - die( '{0} line {1}: chrom={2}, start={3}, score_list_len = {4}'.format( input_filename, line_number, chrom, start, score_list_len ) ) + die( '%s line %d: chrom=%s, start=%d, score_list_len = %d' % ( input_filename, line_number, chrom, start, score_list_len ) ) print >> ofh, '\t'.join( [line, score_val] ) else: print >> ofh, line 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.

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commit/galaxy-central: dan: Add missing import in galaxy.util. Fixes bug in .mkstemp_ln().
by Bitbucket 23 Jan '13

23 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/da970ef60757/ changeset: da970ef60757 user: dan date: 2013-01-23 18:27:12 summary: Add missing import in galaxy.util. Fixes bug in .mkstemp_ln(). affected #: 1 file diff -r 3c752f2d4d958f34f085f2cc707c503693b4680d -r da970ef6075702286d47b9ccf83942092eaac27d lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -2,7 +2,7 @@ Utility functions used systemwide. """ -import logging, threading, random, string, re, binascii, pickle, time, datetime, math, re, os, sys, tempfile, stat, grp, smtplib +import logging, threading, random, string, re, binascii, pickle, time, datetime, math, re, os, sys, tempfile, stat, grp, smtplib, errno from email.MIMEText import MIMEText # Older py compatibility 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.

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galaxy-commits January 2013