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commit/galaxy-central: greg: Fix type in my last commit - thanks John!
by commits-noreply＠bitbucket.org 03 Dec '13

03 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f1729c6dcba8/ Changeset: f1729c6dcba8 User: greg Date: 2013-12-03 03:35:00 Summary: Fix type in my last commit - thanks John! Affected #: 1 file diff -r cac7a527140e097e6e7f1f5d0fdcf588a8183ece -r f1729c6dcba86603a9e471688df633251511a22b lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1533,7 +1533,7 @@ if file_name: if os.path.exists( file_name ): try: - os.remove( dir ) + os.remove( file_name ) except: pass 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: Tweak changeset 5b8c91e4183664c90f4d95699ab971e674ffd67d which created symlinks to a required tool dep endncy env.sh file for dependent tool dependencies being installed. This approach was better than the previous approach which parsed the requried repository's tool_dependencies.xml file to create the env.sh file. This changeset uses a slightly different approach: it creates an env.sh file for the dependent tool dependency whose first line "sources" the required
by commits-noreply＠bitbucket.org 03 Dec '13

03 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cac7a527140e/ Changeset: cac7a527140e User: greg Date: 2013-12-03 02:36:59 Summary: Tweak changeset 5b8c91e4183664c90f4d95699ab971e674ffd67d which created symlinks to a required tool dep endncy env.sh file for dependent tool dependencies being installed. This approach was better than the previous approach which parsed the requried repository's tool_dependencies.xml file to create the env.sh file. This changeset uses a slightly different approach: it creates an env.sh file for the dependent tool dependency whose first line "sources" the required tool dende pendcy's env.sh file. This allows for the dependent env.sh file to be managed by its tool dependency (e.g., its tool dependency may require additional env.sh paths beyond those contained in the requyired tool dependency's env.sh file). This changeset also handles sysncing the database with the file system when tool dependencies are being installed when handling a complex repository dependency definition. This process used to be handled only when not dealing with a complex repository dependency definition. This fix should correct problems encounted by the Tool Shed's install and test framework which were introduced in 5b8c91e4183664c90f4d95699ab971e674ffd67d. Affected #: 5 files diff -r ef33472f0aa296e55fd811357e09366f9cee5467 -r cac7a527140e097e6e7f1f5d0fdcf588a8183ece lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3471,46 +3471,6 @@ def can_reinstall_or_activate( self ): return self.deleted - @property - def installing( self ): - """ - Used to determine if tool dependencies can denote this repository as - installing. - """ - return self.status not in [ self.installation_status.DEACTIVATED, - self.installation_status.UNINSTALLED, - self.installation_status.ERROR, - self.installation_status.INSTALLED, - self.installation_status.NEW, - ] - - @property - def installation_complete( self ): - """ - Used to determine if tool dependency installations can proceed. - Installed artifacts must be available on disk. - """ - return self.status in [ self.installation_status.DEACTIVATED, - self.installation_status.INSTALLED, - ] - - def to_dict( self, view='collection', value_mapper=None ): - if value_mapper is None: - value_mapper = {} - rval = {} - try: - visible_keys = self.__getattribute__( 'dict_' + view + '_visible_keys' ) - except AttributeError: - raise Exception( 'Unknown API view: %s' % view ) - for key in visible_keys: - try: - rval[ key ] = self.__getattribute__( key ) - if key in value_mapper: - rval[ key ] = value_mapper.get( key, rval[ key ] ) - except AttributeError: - rval[ key ] = None - return rval - def get_shed_config_filename( self ): shed_config_filename = None if self.metadata: @@ -3659,7 +3619,8 @@ """Return the repository's tool dependencies that are currently installed.""" installed_dependencies = [] for tool_dependency in self.tool_dependencies: - if tool_dependency.status in [ ToolDependency.installation_status.INSTALLED, ToolDependency.installation_status.ERROR ]: + if tool_dependency.status in [ ToolDependency.installation_status.INSTALLED, + ToolDependency.installation_status.ERROR ]: installed_dependencies.append( tool_dependency ) return installed_dependencies @@ -3670,6 +3631,11 @@ return False @property + def is_installed( self ): + return self.status in [ self.installation_status.DEACTIVATED, + self.installation_status.INSTALLED ] + + @property def is_latest_installable_revision( self ): if self.tool_shed_status: return galaxy.util.asbool( self.tool_shed_status.get( 'latest_installable_revision', False ) ) @@ -3804,6 +3770,23 @@ shed_config_filename = property( get_shed_config_filename, set_shed_config_filename ) + def to_dict( self, view='collection', value_mapper=None ): + if value_mapper is None: + value_mapper = {} + rval = {} + try: + visible_keys = self.__getattribute__( 'dict_' + view + '_visible_keys' ) + except AttributeError: + raise Exception( 'Unknown API view: %s' % view ) + for key in visible_keys: + try: + rval[ key ] = self.__getattribute__( key ) + if key in value_mapper: + rval[ key ] = value_mapper.get( key, rval[ key ] ) + except AttributeError: + rval[ key ] = None + return rval + @property def tool_dependencies_being_installed( self ): dependencies_being_installed = [] diff -r ef33472f0aa296e55fd811357e09366f9cee5467 -r cac7a527140e097e6e7f1f5d0fdcf588a8183ece lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -40,14 +40,22 @@ raise Exception( message ) return None - -def find_complex_dependency_package( app, dependent_install_dir, required_install_dir, tool_shed_repository, required_repository, package_name, package_version, tool_dependencies_config ): +def create_tool_dependency_with_initialized_env_sh_file( app, dependent_install_dir, tool_shed_repository, required_repository, package_name, + package_version, tool_dependencies_config ): """ + Create or get a tool_dependency record that is defined by the received package_name and package_version. An env.sh file will be + created for the tool_dependency in the received dependent_install_dir. """ + #The received required_repository refers to a tool_shed_repository record that is defined as a complex repository dependency for this + # tool_dependency. The required_repository may or may not be currently installed (it doesn't matter). If it is installed, it is + # associated with a tool_dependency that has an env.sh file that this new tool_dependency must be able to locate and "source". If it + # is not installed, we can still determine where that env.sh file will be, so we'll initialize this new tool_dependency's env.sh file + # in either case. If the require repository end up with an installation error, this new tool dependency will still be fine because its + # containing repository will be defined as missing dependencies. tool_dependencies = [] if not os.path.exists( dependent_install_dir ): os.makedirs( dependent_install_dir ) - env_file = None + required_tool_dependency_env_file_path = None if tool_dependencies_config: required_td_tree, error_message = xml_util.parse_xml( tool_dependencies_config ) if required_td_tree: @@ -58,51 +66,52 @@ # <package name="bwa" version="0.5.9"> required_td_package_name = required_td_elem.get( 'name', None ) required_td_package_version = required_td_elem.get( 'version', None ) + # Check the database to see if we have a record for the required tool dependency (we may not which is ok). If we + # find a record, we need to see if it is in an error state and if so handle it appropriately. + required_tool_dependency = \ + tool_dependency_util.get_tool_dependency_by_name_version_type_repository( app, + required_repository, + required_td_package_name, + required_td_package_version, + 'package' ) if required_td_package_name == package_name and required_td_package_version == package_version: - tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, - tool_shed_repository=tool_shed_repository, - name=package_name, - version=package_version, - type='package', - status=app.model.ToolDependency.installation_status.NEVER_INSTALLED, - set_status=True ) - - if required_repository.installing: - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.model.ToolDependency.installation_status.INSTALLING ) - # What happens if dependent repository fails or is - # uninstalled during this process. - env_file = required_repository_package_env( app, package_name, package_version, required_repository ) - if required_repository.installation_complete: - if not os.path.exists( env_file ): - error_message = 'env.sh file %s for package %s in dependendent repository could not be found. Required repository has status %s.' % ( package_name, env_file, required_repository.status ) - tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, + # Get or create a database tool_dependency record with which the installed package on disk will be associated. + tool_dependency = \ + tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_shed_repository=tool_shed_repository, + name=package_name, + version=package_version, + type='package', + status=app.model.ToolDependency.installation_status.NEVER_INSTALLED, + set_status=True ) + # Create an env.sh file for the tool_dependency whose first line will source the env.sh file located in + # the path defined by required_tool_dependency_env_file_path. It doesn't matter if the required env.sh + # file currently exists.. + required_tool_dependency_env_file_path = \ + tool_dependency_util.get_required_repository_package_env_sh_path( app, package_name, package_version, required_repository ) + env_file_builder = fabric_util.EnvFileBuilder( tool_dependency.installation_directory( app ) ) + env_file_builder.append_line( action="source", value=required_tool_dependency_env_file_path ) + return_code = env_file_builder.return_code + if return_code: + error_message = 'Error defining env.sh file for package %s, return_code: %s' % ( str( package_name, str( return_code ) ) ) + tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, tool_dependency, error_message, remove_installation_path=False ) - else: - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.model.ToolDependency.installation_status.INSTALLED ) + elif required_tool_dependency.in_error_state: + error_message = "This tool dependency's required tool dependency %s has status %s." % \ + ( str( required_tool_dependency.name ), str( required_tool_dependency.status ) ) + tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, + tool_dependency, + error_message, + remove_installation_path=False ) else: - # Ekk - handling tool depednencies for a dependent - # repository that is not installed. - # - # Go ahead a return the env.sh file - Galaxy will - # proceed to create an invalid symbolic link. - # This is subtle-ly different than the previous - # behavior which would have recreated an env.sh - # from the the required repository's - # tool_dependencies.xml but since it was not - # installed all of the values inside would be - # invalid path modifications. Either way, this file - # is junk until the required repository is - # installed properly. - pass + tool_dependency = \ + tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=app.model.ToolDependency.installation_status.INSTALLED ) tool_dependencies.append( tool_dependency ) - return tool_dependencies, env_file - + return tool_dependencies def get_absolute_path_to_file_in_repository( repo_files_dir, file_name ): """Return the absolute path to a specified disk file contained in a repository.""" @@ -157,6 +166,12 @@ def handle_complex_repository_dependency_for_package( app, elem, package_name, package_version, tool_shed_repository ): + """ + Inspect the repository defined by a complex repository dependency definition and take certain steps to enable installation + of the received package name and version to proceed. The received elem is the <repository> tag set which defines the complex + repository dependency. The received tool_shed_repository is the installed tool shed repository for which the tool dependency + defined by the received package_name and package_version is being installed. + """ handled_tool_dependencies = [] tool_shed = elem.attrib[ 'toolshed' ] required_repository_name = elem.attrib[ 'name' ] @@ -179,7 +194,7 @@ tool_dependency_type='package', tool_dependency_name=package_name, tool_dependency_version=package_version ) - # Define the this dependent repository's tool dependency installation directory that will contain the env.sh file with a path to the + # Define this dependent repository's tool dependency installation directory that will contain the env.sh file with a path to the # required repository's installed tool dependency package. dependent_install_dir = tool_dependency_util.get_tool_dependency_install_dir( app=app, repository_name=tool_shed_repository.name, @@ -188,58 +203,58 @@ tool_dependency_type='package', tool_dependency_name=package_name, tool_dependency_version=package_version ) - # Set this dependent repository's tool dependency env.sh file with a path to the required repository's installed tool dependency package. - # We can get everything we need from the discovered installed required_repository. - if required_repository.installation_complete: - if not os.path.exists( required_repository_package_install_dir ): - print 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir ) - repo_files_dir = required_repository.repo_files_directory( app ) - tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' ) - if tool_dependencies_config: - config_to_use = tool_dependencies_config + if os.path.exists( dependent_install_dir ): + # Notice that we'll throw away the following tool_dependency if it can be installed. + tool_dependency, can_install_tool_dependency = tool_dependency_util.sync_database_with_file_system( app, + tool_shed_repository, + package_name, + package_version, + dependent_install_dir, + tool_dependency_type='package' ) + else: + can_install_tool_dependency = True + if can_install_tool_dependency: + # Set this dependent repository's tool dependency env.sh file with a path to the required repository's installed tool dependency package. + # We can get everything we need from the discovered installed required_repository. + if required_repository.is_installed: + if not os.path.exists( required_repository_package_install_dir ): + print 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir ) + repo_files_dir = required_repository.repo_files_directory( app ) + tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' ) + if tool_dependencies_config: + config_to_use = tool_dependencies_config + else: + message = "Unable to locate required tool_dependencies.xml file for revision %s of installed repository %s owned by %s." % \ + ( str( required_repository.changeset_revision ), str( required_repository.name ), str( required_repository.owner ) ) + raise Exception( message ) else: - message = "Unable to locate required tool_dependencies.xml file for revision %s of installed repository %s owned by %s." % \ - ( str( required_repository.changeset_revision ), str( required_repository.name ), str( required_repository.owner ) ) - raise Exception( message ) + # Make a call to the tool shed to get the changeset revision to which the current value of required_repository_changeset_revision + # should be updated if it's not current. + text = get_updated_changeset_revisions_from_tool_shed( app=app, + tool_shed_url=tool_shed, + name=required_repository_name, + owner=required_repository_owner, + changeset_revision=required_repository_changeset_revision ) + if text: + updated_changeset_revisions = listify( text ) + # The list of changeset revisions is in reverse order, so the newest will be first. + required_repository_changeset_revision = updated_changeset_revisions[ 0 ] + # Make a call to the tool shed to get the required repository's tool_dependencies.xml file. + tmp_filename = create_temporary_tool_dependencies_config( app, + tool_shed, + required_repository_name, + required_repository_owner, + required_repository_changeset_revision ) + config_to_use = tmp_filename + handled_tool_dependencies = create_tool_dependency_with_initialized_env_sh_file( app=app, + dependent_install_dir=dependent_install_dir, + tool_shed_repository=tool_shed_repository, + required_repository=required_repository, + package_name=package_name, + package_version=package_version, + tool_dependencies_config=config_to_use ) + suc.remove_file( tmp_filename ) else: - # Make a call to the tool shed to get the changeset revision to which the current value of required_repository_changeset_revision - # should be updated if it's not current. - text = get_updated_changeset_revisions_from_tool_shed( app=app, - tool_shed_url=tool_shed, - name=required_repository_name, - owner=required_repository_owner, - changeset_revision=required_repository_changeset_revision ) - if text: - updated_changeset_revisions = listify( text ) - # The list of changeset revisions is in reverse order, so the newest will be first. - required_repository_changeset_revision = updated_changeset_revisions[ 0 ] - # Make a call to the tool shed to get the required repository's tool_dependencies.xml file. - tmp_filename = create_temporary_tool_dependencies_config( app, - tool_shed, - required_repository_name, - required_repository_owner, - required_repository_changeset_revision ) - config_to_use = tmp_filename - - tool_dependencies, package_env_sh_file = find_complex_dependency_package( - app=app, - dependent_install_dir=dependent_install_dir, - required_install_dir=required_repository_package_install_dir, - tool_shed_repository=tool_shed_repository, - required_repository=required_repository, - package_name=package_name, - package_version=package_version, - tool_dependencies_config=config_to_use - ) - if package_env_sh_file: - os.symlink( package_env_sh_file, os.path.join( dependent_install_dir, "env.sh" ) ) - if tmp_filename: - try: - os.remove( tmp_filename ) - except: - pass - for tool_dependency in tool_dependencies: - tool_dependency = __mark_tool_dependency_installed( app, tool_dependency) handled_tool_dependencies.append( tool_dependency ) else: message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \ @@ -247,7 +262,6 @@ raise Exception( message ) return handled_tool_dependencies - def install_and_build_package_via_fabric( app, tool_dependency, actions_dict ): sa_session = app.model.context.current try: @@ -262,10 +276,9 @@ tool_dependency, error_message, remove_installation_path=False ) - tool_dependency = __mark_tool_dependency_installed( app, tool_dependency) + tool_dependency = tool_dependency_util.mark_tool_dependency_installed( app, tool_dependency ) return tool_dependency - def install_package( app, elem, tool_shed_repository, tool_dependencies=None ): # The value of tool_dependencies is a partial or full list of ToolDependency records associated with the tool_shed_repository. sa_session = app.model.context.current @@ -298,57 +311,14 @@ tool_dependency_version=package_version ) can_install_tool_dependency = True if os.path.exists( install_dir ): - # The tool dependency installation directory exists, check for the presence of fabric_util.INSTALLATION_LOG, - # which indicates a successful installation. This currently assumes that the tool dependency record will - # always exist in the database. - tool_dependency = tool_dependency_util.get_tool_dependency_by_name_version_type_repository( app, - tool_shed_repository, - package_name, - package_version, - 'package' ) - if tool_dependency.status == app.model.ToolDependency.installation_status.INSTALLING: - # The tool dependency is in an Installing state, so we don't want to do anything to it. If the tool - # dependency is being installed by someone else, we don't want to interfere with that. This assumes - # the installation by "someone else" is not hung in an Installing state, which is a weakness if that - # "someone else" never repaired it. - log.debug( 'Skipping installation of tool dependency %s version %s because it has a status of %s' % \ - ( str( tool_dependency.name ), str( tool_dependency.version ), str( tool_dependency.status ) ) ) - can_install_tool_dependency = False - else: - tool_dependency_installation_directory_contents = os.listdir( install_dir ) - if fabric_util.INSTALLATION_LOG in tool_dependency_installation_directory_contents: - # Since this tool dependency's installation directory contains an installation log, we consider it to be - # installed. In some cases the record may be missing from the database due to some activity outside of - # the control of the Tool Shed. Since a new record was created for it and we don't know the state of the - # files on disk, we will set it to an error state (unless we are running Tool Shed functional tests - see - # below). - log.debug( 'Skipping installation of tool dependency %s version %s because it is installed in %s' % \ - ( str( tool_dependency.name ), str( tool_dependency.version ), str( install_dir ) ) ) - can_install_tool_dependency = False - if app.config.running_functional_tests: - # If we are running functional tests, the state will be set to Installed because previously compiled - # tool dependencies are not deleted by default, from the "install and test" framework.. - tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED - else: - error_message = 'The installation directory for this tool dependency had contents, but the database had no record. ' - error_message += 'The installation log may show this tool dependency to be correctly installed, but due to the ' - error_message += 'missing database record, it is automatically set to Error.' - tool_dependency.status = app.model.ToolDependency.installation_status.ERROR - tool_dependency.error_message = error_message - else: - error_message = '\nInstallation path %s for tool dependency %s version %s exists, but the expected file %s' % \ - ( str( install_dir ), str( package_name ), str( package_version ), str( fabric_util.INSTALLATION_LOG ) ) - error_message += ' is missing. This indicates an installation error so the tool dependency is being' - error_message += ' prepared for re-installation.' - print error_message - tool_dependency.status = app.model.ToolDependency.installation_status.NEVER_INSTALLED - try: - shutil.rmtree( install_dir ) - except Exception, e: - log.exception( 'Unable to remove installation path %s.', install_dir ) - can_install_tool_dependency = True - sa_session.add( tool_dependency ) - sa_session.flush() + # Notice that we'll throw away the following tool_dependency if it can be installed. + tool_dependency, can_install_tool_dependency = \ + tool_dependency_util.sync_database_with_file_system( app, + tool_shed_repository, + package_name, + package_version, + install_dir, + tool_dependency_type='package' ) else: can_install_tool_dependency = True if can_install_tool_dependency: @@ -775,23 +745,6 @@ tool_dependency = install_and_build_package_via_fabric( app, tool_dependency, actions_dict ) return tool_dependency - -# TODO: Move to tool_dependency_util? -def required_repository_package_env( app, package_name, package_version, required_repository ): - """ - Return path to env.sh file in required repository if the required repository has been installed. - """ - env_sh_file_dir = tool_dependency_util.get_tool_dependency_install_dir( app=app, - repository_name=required_repository.name, - repository_owner=required_repository.owner, - repository_changeset_revision=required_repository.installed_changeset_revision, - tool_dependency_type='package', - tool_dependency_name=package_name, - tool_dependency_version=package_version ) - env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' ) - return env_sh_file_path - - def run_proprietary_fabric_method( app, elem, proprietary_fabfile_path, install_dir, package_name=None, **kwd ): """ TODO: Handle this using the fabric api. @@ -846,10 +799,7 @@ tmp_stderr = open( tmp_name, 'rb' ) message = '%s\n' % str( tmp_stderr.read() ) tmp_stderr.close() - try: - os.remove( tmp_name ) - except: - pass + suc.remove_file( tmp_name ) return returncode, message def set_environment( app, elem, tool_shed_repository, attr_tups_of_dependencies_for_install ): @@ -935,17 +885,3 @@ for arg in args: parts.append( arg.strip( '/' ) ) return '/'.join( parts ) - - -# TODO: Move to tool_dependency_util? -def __mark_tool_dependency_installed( app, tool_dependency ): - if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR, - app.model.ToolDependency.installation_status.INSTALLED ]: - log.debug( 'Changing status for tool dependency %s from %s to %s.' % \ - ( str( tool_dependency.name ), str( tool_dependency.status ), str( app.model.ToolDependency.installation_status.INSTALLED ) ) ) - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.model.ToolDependency.installation_status.INSTALLED, - error_message=None, - remove_from_disk=False ) - return tool_dependency diff -r ef33472f0aa296e55fd811357e09366f9cee5467 -r cac7a527140e097e6e7f1f5d0fdcf588a8183ece lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -458,6 +458,7 @@ if index is not None: tool_dependency = tool_dependencies[ index ] if tool_dependency.can_install: + # The database record is currently in a state that allows us to install the package on the file system. try: dependencies_ignored = app.toolbox.dependency_manager and not app.toolbox.dependency_manager.uses_tool_shed_dependencies() if dependencies_ignored: diff -r ef33472f0aa296e55fd811357e09366f9cee5467 -r cac7a527140e097e6e7f1f5d0fdcf588a8183ece lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1521,11 +1521,21 @@ def remove_dir( dir ): """Attempt to remove a directory from disk.""" - if os.path.exists( dir ): - try: - shutil.rmtree( dir ) - except: - pass + if dir: + if os.path.exists( dir ): + try: + shutil.rmtree( dir ) + except: + pass + +def remove_file( file_name ): + """Attempt to remove a file from disk.""" + if file_name: + if os.path.exists( file_name ): + try: + os.remove( dir ) + except: + pass def repository_was_previously_installed( trans, tool_shed_url, repository_name, repo_info_tuple ): """ diff -r ef33472f0aa296e55fd811357e09366f9cee5467 -r cac7a527140e097e6e7f1f5d0fdcf588a8183ece lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -7,6 +7,7 @@ import tool_shed.util.shed_util_common as suc import tool_shed.repository_types.util as rt_util from tool_shed.util import xml_util +from tool_shed.galaxy_install.tool_dependencies import fabric_util log = logging.getLogger( __name__ ) @@ -276,6 +277,18 @@ platform_dict[ 'architecture' ] = machine.lower() return platform_dict +def get_required_repository_package_env_sh_path( app, package_name, package_version, required_repository ): + """Return path to env.sh file in required repository if the required repository has been installed.""" + env_sh_file_dir = get_tool_dependency_install_dir( app=app, + repository_name=required_repository.name, + repository_owner=required_repository.owner, + repository_changeset_revision=required_repository.installed_changeset_revision, + tool_dependency_type='package', + tool_dependency_name=package_name, + tool_dependency_version=package_version ) + env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' ) + return env_sh_file_path + def get_tool_dependency( trans, id ): """Get a tool_dependency from the database via id""" return trans.sa_session.query( trans.model.ToolDependency ).get( trans.security.decode_id( id ) ) @@ -368,6 +381,18 @@ sa_session.flush() return tool_dependency +def mark_tool_dependency_installed( app, tool_dependency ): + if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR, + app.model.ToolDependency.installation_status.INSTALLED ]: + log.debug( 'Changing status for tool dependency %s from %s to %s.' % \ + ( str( tool_dependency.name ), str( tool_dependency.status ), str( app.model.ToolDependency.installation_status.INSTALLED ) ) ) + tool_dependency = set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=app.model.ToolDependency.installation_status.INSTALLED, + error_message=None, + remove_from_disk=False ) + return tool_dependency + def merge_missing_tool_dependencies_to_installed_container( containers_dict ): """ Merge the list of missing tool dependencies into the list of installed tool dependencies.""" missing_td_container_root = containers_dict.get( 'missing_tool_dependencies', None ) @@ -491,6 +516,72 @@ sa_session.flush() return tool_dependency +def sync_database_with_file_system( app, tool_shed_repository, tool_dependency_name, tool_dependency_version, tool_dependency_install_dir, + tool_dependency_type='package' ): + """ + The installation directory defined by the received tool_dependency_install_dir exists, so check for the presence + of fabric_util.INSTALLATION_LOG. If the files exists, we'll assume the tool dependency is installed, but not + necessarily successfully (it could be in an error state on disk. However, we can justifiably assume here that no + matter the state, an associated database record will exist. + """ + # This method should be reached very rarely. It implies that either the Galaxy environment became corrupted (i.e., + # the database records for installed tool dependencies is not synchronized with tool dependencies on disk) or the Tool + # Shed's install and test framework is running. + sa_session = app.model.context.current + can_install_tool_dependency = False + tool_dependency = get_tool_dependency_by_name_version_type_repository( app, + tool_shed_repository, + tool_dependency_name, + tool_dependency_version, + tool_dependency_type ) + if tool_dependency.status == app.model.ToolDependency.installation_status.INSTALLING: + # The tool dependency is in an Installing state, so we don't want to do anything to it. If the tool + # dependency is being installed by someone else, we don't want to interfere with that. This assumes + # the installation by "someone else" is not hung in an Installing state, which is a weakness if that + # "someone else" never repaired it. + log.debug( 'Skipping installation of tool dependency %s version %s because it has a status of %s' % \ + ( str( tool_dependency.name ), str( tool_dependency.version ), str( tool_dependency.status ) ) ) + else: + # We have a pre-existing installation directory on the file system, but our associated database record is + # in a state that allowed us to arrive here - see the comment in common_install_util.handle_tool_dependencies(). + # At this point, we'll inspect the installation directory to see if we have a "proper installation" and + # if so, synchronize the database record rather than reinstalling the dependency if we're "running_functional_tests". + # If we're not "running_functional_tests, we'll set the tool dependency's installation status to ERROR. + tool_dependency_installation_directory_contents = os.listdir( tool_dependency_install_dir ) + if fabric_util.INSTALLATION_LOG in tool_dependency_installation_directory_contents: + # Since this tool dependency's installation directory contains an installation log, we consider it to be + # installed. In some cases the record may be missing from the database due to some activity outside of + # the control of the Tool Shed. Since a new record was created for it and we don't know the state of the + # files on disk, we will set it to an error state (unless we are running Tool Shed functional tests - see + # below). + log.debug( 'Skipping installation of tool dependency %s version %s because it is installed in %s' % \ + ( str( tool_dependency.name ), str( tool_dependency.version ), str( tool_dependency_install_dir ) ) ) + if app.config.running_functional_tests: + # If we are running functional tests, the state will be set to Installed because previously compiled + # tool dependencies are not deleted by default, from the "install and test" framework.. + tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED + else: + error_message = 'The installation directory for this tool dependency had contents, but the database had no record. ' + error_message += 'The installation log may show this tool dependency to be correctly installed, but due to the ' + error_message += 'missing database record, it is automatically set to Error.' + tool_dependency.status = app.model.ToolDependency.installation_status.ERROR + tool_dependency.error_message = error_message + else: + error_message = '\nInstallation path %s for tool dependency %s version %s exists, but the expected file %s' % \ + ( str( tool_dependency_install_dir ), + str( tool_dependency_name ), + str( tool_dependency_version ), + str( fabric_util.INSTALLATION_LOG ) ) + error_message += ' is missing. This indicates an installation error so the tool dependency is being' + error_message += ' prepared for re-installation.' + print error_message + tool_dependency.status = app.model.ToolDependency.installation_status.NEVER_INSTALLED + suc.remove_dir( tool_dependency_install_dir ) + can_install_tool_dependency = True + sa_session.add( tool_dependency ) + sa_session.flush() + return tool_dependency, can_install_tool_dependency + def tool_dependency_is_orphan( 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 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: 2 new changesets
by commits-noreply＠bitbucket.org 02 Dec '13

02 Dec '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0b2ecfd14689/ Changeset: 0b2ecfd14689 User: jmchilton Date: 2013-12-02 21:57:00 Summary: Tell nose functions in lib/galaxy/tools/test.py are not unit tests. Affected #: 1 file diff -r cf0d0001893cabb08a01a6d8938f3aa24be4cada -r 0b2ecfd1468979ea94b00c12eaafcac6f330b37e lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py +++ b/lib/galaxy/tools/test.py @@ -4,6 +4,10 @@ from parameters import basic from parameters import grouping from galaxy.util import string_as_bool +try: + from nose.tools import nottest +except ImportError: + nottest = lambda x: x import logging log = logging.getLogger( __name__ ) @@ -14,6 +18,7 @@ DEFAULT_MAX_SECS = 120 +@nottest def parse_tests_elem(tool, tests_elem): """ Build ToolTestBuilder objects for each "<test>" elements and @@ -196,6 +201,7 @@ return require_file( name, value, extra, self.required_files ) +@nottest def test_data_iter( required_files ): for fname, extra in required_files: data_dict = dict( https://bitbucket.org/galaxy/galaxy-central/commits/ef33472f0aa2/ Changeset: ef33472f0aa2 User: jmchilton Date: 2013-12-02 21:57:00 Summary: Fix test case in test/unit/test_tool_deps.py which fails if modulecmd is unavailable. Affected #: 1 file diff -r 0b2ecfd1468979ea94b00c12eaafcac6f330b37e -r ef33472f0aa296e55fd811357e09366f9cee5467 test/unit/test_tool_deps.py --- a/test/unit/test_tool_deps.py +++ b/test/unit/test_tool_deps.py @@ -293,7 +293,7 @@ def test_config_module_defaults(): with __parse_resolvers('''<dependency_resolvers> - <modules /> + <modules prefetch="false" /></dependency_resolvers> ''') as dependency_resolvers: module_resolver = dependency_resolvers[0] 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: Fix for missing eggs.require in lib/galaxy/exceptions/__init__.py.
by commits-noreply＠bitbucket.org 02 Dec '13

02 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cf0d0001893c/ Changeset: cf0d0001893c User: dan Date: 2013-12-02 20:48:30 Summary: Fix for missing eggs.require in lib/galaxy/exceptions/__init__.py. Affected #: 1 file diff -r cd94f9721265741d448a225df511141190049f34 -r cf0d0001893cabb08a01a6d8938f3aa24be4cada lib/galaxy/exceptions/__init__.py --- a/lib/galaxy/exceptions/__init__.py +++ b/lib/galaxy/exceptions/__init__.py @@ -1,6 +1,10 @@ """ Custom exceptions for Galaxy """ + +from galaxy import eggs +eggs.require( "Paste" ) + from paste import httpexceptions class MessageException( Exception ): 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: 2 new changesets
by commits-noreply＠bitbucket.org 02 Dec '13

02 Dec '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/44acfec11d87/ Changeset: 44acfec11d87 User: jmchilton Date: 2013-11-27 17:12:48 Summary: Patch from Peter Cock. Allow overriding composite type main file in archives. Affected #: 1 file diff -r 372ff609235643994e50f1502fb9c73d37a3f97f -r 44acfec11d87f2efc38bccb2b3333e86b9d96667 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -199,6 +199,29 @@ out = "Can't create peek %s" % str( exc ) return out + def _archive_main_file(self, archive, outfname, data_filename): + """Called from _archive_composite_dataset to add central file to archive. + + Unless subclassed, this will add the main dataset file (argument data_filename) + to the archive, as an HTML file with its filename derived from the dataset name + (argument outfname). + + Returns a tuple of boolean, string, string: (error, msg, messagetype) + """ + error, msg, messagetype = False, "", "" + htmlname = os.path.splitext(outfname)[0] + if not htmlname.endswith(ext): + htmlname = '%s_%s' % (htmlname, ext) + archname = '%s.html' % htmlname # fake the real nature of the html file + try: + archive.add(data_filename, archname) + except IOError: + error = True + log.exception("Unable to add composite parent %s to temporary library download archive" % data_filename) + msg = "Unable to create archive for download, please report this error" + messagetype = "error" + return error, msg, messagetype + def _archive_composite_dataset( self, trans, data=None, **kwd ): # save a composite object into a compressed archive for downloading params = util.Params( kwd ) @@ -233,33 +256,25 @@ messagetype = 'error' if not error: current_user_roles = trans.get_current_user_roles() - ext = data.extension path = data.file_name fname = os.path.split(path)[-1] efp = data.extra_files_path - htmlname = os.path.splitext(outfname)[0] - if not htmlname.endswith(ext): - htmlname = '%s_%s' % (htmlname,ext) - archname = '%s.html' % htmlname # fake the real nature of the html file - try: - archive.add(data.file_name,archname) - except IOError: - error = True - log.exception( "Unable to add composite parent %s to temporary library download archive" % data.file_name) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' - for root, dirs, files in os.walk(efp): - for fname in files: - fpath = os.path.join(root,fname) - rpath = os.path.relpath(fpath,efp) - try: - archive.add( fpath,rpath ) - except IOError: - error = True - log.exception( "Unable to add %s to temporary library download archive" % rpath) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' - continue + #Add any central file to the archive, + error, msg, messagetype = self._archive_main_file(archive, outfname, path) + if not error: + #Add any child files to the archive, + for root, dirs, files in os.walk(efp): + for fname in files: + fpath = os.path.join(root,fname) + rpath = os.path.relpath(fpath,efp) + try: + archive.add( fpath,rpath ) + except IOError: + error = True + log.exception( "Unable to add %s to temporary library download archive" % rpath) + msg = "Unable to create archive for download, please report this error" + messagetype = 'error' + continue if not error: if params.do_action == 'zip': archive.close() https://bitbucket.org/galaxy/galaxy-central/commits/cd94f9721265/ Changeset: cd94f9721265 User: jmchilton Date: 2013-12-02 19:40:43 Summary: Fix default behavior of composite archival broken with previous changeset. Other small tweaks this implementation. Affected #: 1 file diff -r 44acfec11d87f2efc38bccb2b3333e86b9d96667 -r cd94f9721265741d448a225df511141190049f34 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -199,7 +199,7 @@ out = "Can't create peek %s" % str( exc ) return out - def _archive_main_file(self, archive, outfname, data_filename): + def _archive_main_file(self, archive, display_name, data_filename): """Called from _archive_composite_dataset to add central file to archive. Unless subclassed, this will add the main dataset file (argument data_filename) @@ -209,10 +209,7 @@ Returns a tuple of boolean, string, string: (error, msg, messagetype) """ error, msg, messagetype = False, "", "" - htmlname = os.path.splitext(outfname)[0] - if not htmlname.endswith(ext): - htmlname = '%s_%s' % (htmlname, ext) - archname = '%s.html' % htmlname # fake the real nature of the html file + archname = '%s.html' % display_name # fake the real nature of the html file try: archive.add(data_filename, archname) except IOError: @@ -256,11 +253,17 @@ messagetype = 'error' if not error: current_user_roles = trans.get_current_user_roles() + ext = data.extension path = data.file_name fname = os.path.split(path)[-1] efp = data.extra_files_path #Add any central file to the archive, - error, msg, messagetype = self._archive_main_file(archive, outfname, path) + + display_name = os.path.splitext(outfname)[0] + if not display_name.endswith(ext): + display_name = '%s_%s' % (display_name, ext) + + error, msg, messagetype = self._archive_main_file(archive, display_name, path) if not error: #Add any child files to the archive, for root, dirs, files in os.walk(efp): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Grids: Fix unescaping strings
by commits-noreply＠bitbucket.org 02 Dec '13

02 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/372ff6092356/ Changeset: 372ff6092356 User: guerler Date: 2013-12-02 19:07:17 Summary: Grids: Fix unescaping strings Affected #: 1 file diff -r 752929cea6d37423c14f46f317ef3815cfc3c3d0 -r 372ff609235643994e50f1502fb9c73d37a3f97f templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -403,9 +403,10 @@ value = column_settings['value'] inbound = column_settings['inbound'] - # check if formatting is defined - value = str(value).replace('//', '/') - + # unescape value + if isinstance(value, unicode): + value = value.replace('//', '/') + # Attach popup menu? id = "" cls = "" 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: jmchilton: Update LWR client through LWR revision acecc74f7016.
by commits-noreply＠bitbucket.org 01 Dec '13

01 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/752929cea6d3/ Changeset: 752929cea6d3 User: jmchilton Date: 2013-12-01 13:14:32 Summary: Update LWR client through LWR revision acecc74f7016. Mostly small modifications related Python 3 compat. (no iteritems, diff. StringIO, exception syntax, urllib diffs,) and improved handling of unicode data. Affected #: 6 files diff -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 -r 752929cea6d37423c14f46f317ef3815cfc3c3d0 lib/galaxy/jobs/runners/lwr_client/action_mapper.py --- a/lib/galaxy/jobs/runners/lwr_client/action_mapper.py +++ b/lib/galaxy/jobs/runners/lwr_client/action_mapper.py @@ -21,7 +21,7 @@ >>> from tempfile import NamedTemporaryFile >>> from os import unlink >>> f = NamedTemporaryFile(delete=False) - >>> f.write(json_string) + >>> write_result = f.write(json_string.encode('UTF-8')) >>> f.close() >>> class MockClient(): ... default_file_action = 'none' @@ -30,23 +30,23 @@ >>> mapper = FileActionMapper(MockClient()) >>> unlink(f.name) >>> # Test first config line above, implicit path prefix mapper - >>> mapper.action('/opt/galaxy/tools/filters/catWrapper.py', 'input') - ('none',) + >>> mapper.action('/opt/galaxy/tools/filters/catWrapper.py', 'input')[0] == u'none' + True >>> # Test another (2nd) mapper, this one with a different action - >>> mapper.action('/galaxy/data/files/000/dataset_1.dat', 'input') - ('transfer',) + >>> mapper.action('/galaxy/data/files/000/dataset_1.dat', 'input')[0] == u'transfer' + True >>> # Always at least copy work_dir outputs. - >>> mapper.action('/opt/galaxy/database/working_directory/45.sh', 'work_dir') - ('copy',) + >>> mapper.action('/opt/galaxy/database/working_directory/45.sh', 'work_dir')[0] == u'copy' + True >>> # Test glob mapper (matching test) - >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam', 'input') - ('copy',) + >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam', 'input')[0] == u'copy' + True >>> # Test glob mapper (non-matching test) - >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam.bai', 'input') - ('none',) + >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam.bai', 'input')[0] == u'none' + True >>> # Regex mapper test. - >>> mapper.action('/old/galaxy/data/dataset_10245.dat', 'input') - ('copy',) + >>> mapper.action('/old/galaxy/data/dataset_10245.dat', 'input')[0] == u'copy' + True """ def __init__(self, client): diff -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 -r 752929cea6d37423c14f46f317ef3815cfc3c3d0 lib/galaxy/jobs/runners/lwr_client/destination.py --- a/lib/galaxy/jobs/runners/lwr_client/destination.py +++ b/lib/galaxy/jobs/runners/lwr_client/destination.py @@ -51,9 +51,10 @@ >>> destination_params = {"private_token": "12345", "submit_native_specification": "-q batch"} >>> result = submit_params(destination_params) - >>> result.items() - [('native_specification', '-q batch')] + >>> result + {'native_specification': '-q batch'} """ - return dict([(key[len(SUBMIT_PREFIX):], value) - for key, value in (destination_params or {}).iteritems() + destination_params = destination_params or {} + return dict([(key[len(SUBMIT_PREFIX):], destination_params[key]) + for key in destination_params if key.startswith(SUBMIT_PREFIX)]) diff -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 -r 752929cea6d37423c14f46f317ef3815cfc3c3d0 lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -5,8 +5,18 @@ from queue import Queue from threading import Thread from os import getenv -from urllib import urlencode -from StringIO import StringIO +try: + from urllib import urlencode +except ImportError: + from urllib.parse import urlencode +try: + from StringIO import StringIO as BytesIO +except ImportError: + from io import BytesIO +try: + from six import text_type +except ImportError: + from galaxy.util import unicodify as text_type from .client import Client, InputCachingClient from .transport import get_transport @@ -27,10 +37,10 @@ """ def __init__(self, **kwds): if 'job_manager' in kwds: - self.job_manager_interface_class = LocalJobManagerInterface + self.job_manager_interface_class = LocalLwrInterface self.job_manager_interface_args = dict(job_manager=kwds['job_manager'], file_cache=kwds['file_cache']) else: - self.job_manager_interface_class = HttpJobManagerInterface + self.job_manager_interface_class = HttpLwrInterface transport_type = kwds.get('transport_type', None) transport = get_transport(transport_type) self.job_manager_interface_args = dict(transport=transport) @@ -55,7 +65,11 @@ return self.client_class(destination_params, job_id, job_manager_interface, **self.extra_client_kwds) def __parse_destination_params(self, destination_params): - if isinstance(destination_params, str) or isinstance(destination_params, unicode): + try: + unicode_type = unicode + except NameError: + unicode_type = str + if isinstance(destination_params, str) or isinstance(destination_params, unicode_type): destination_params = url_to_destination_params(destination_params) return destination_params @@ -76,7 +90,7 @@ """ -class HttpJobManagerInterface(object): +class HttpLwrInterface(object): def __init__(self, destination_params, transport): self.transport = transport @@ -92,12 +106,13 @@ def __build_url(self, command, args): if self.private_key: args["private_key"] = self.private_key - data = urlencode(args) + arg_bytes = dict([(k, text_type(args[k]).encode('utf-8')) for k in args]) + data = urlencode(arg_bytes) url = self.remote_host + command + "?" + data return url -class LocalJobManagerInterface(object): +class LocalLwrInterface(object): def __init__(self, destination_params, job_manager, file_cache): self.job_manager = job_manager @@ -113,6 +128,7 @@ } def execute(self, command, args={}, data=None, input_path=None, output_path=None): + # If data set, should be unicode (on Python 2) or str (on Python 3). from lwr import routes from lwr.framework import build_func_args controller = getattr(routes, command) @@ -129,9 +145,9 @@ def __build_body(self, data, input_path): if data is not None: - return StringIO(data) + return BytesIO(data.encode('utf-8')) elif input_path is not None: - return open(input_path, 'r') + return open(input_path, 'rb') else: return None @@ -188,4 +204,4 @@ int_val = int(val) return int_val -__all__ = [ClientManager, HttpJobManagerInterface] +__all__ = [ClientManager, HttpLwrInterface] diff -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 -r 752929cea6d37423c14f46f317ef3815cfc3c3d0 lib/galaxy/jobs/runners/lwr_client/stager.py --- a/lib/galaxy/jobs/runners/lwr_client/stager.py +++ b/lib/galaxy/jobs/runners/lwr_client/stager.py @@ -1,6 +1,7 @@ from os.path import abspath, basename, join, exists from os import listdir, sep from re import findall +from io import open from .action_mapper import FileActionMapper @@ -24,22 +25,24 @@ >>> import tempfile >>> tf = tempfile.NamedTemporaryFile() >>> def setup_inputs(tf): - ... open(tf.name, "w").write("world /path/to/input the rest") - ... inputs = JobInputs("hello /path/to/input", [tf.name]) + ... open(tf.name, "w").write(u"world /path/to/input the rest") + ... inputs = JobInputs(u"hello /path/to/input", [tf.name]) ... return inputs >>> inputs = setup_inputs(tf) - >>> inputs.rewrite_paths("/path/to/input", 'C:\\input') - >>> inputs.rewritten_command_line - 'hello C:\\\\input' - >>> inputs.rewritten_config_files[tf.name] - 'world C:\\\\input the rest' + >>> inputs.rewrite_paths(u"/path/to/input", u'C:\\input') + >>> inputs.rewritten_command_line == u'hello C:\\\\input' + True + >>> inputs.rewritten_config_files[tf.name] == u'world C:\\\\input the rest' + True >>> tf.close() >>> tf = tempfile.NamedTemporaryFile() >>> inputs = setup_inputs(tf) - >>> inputs.find_referenced_subfiles('/path/to') - ['/path/to/input'] + >>> inputs.find_referenced_subfiles('/path/to') == [u'/path/to/input'] + True >>> inputs.path_referenced('/path/to') True + >>> inputs.path_referenced(u'/path/to') + True >>> inputs.path_referenced('/path/to/input') True >>> inputs.path_referenced('/path/to/notinput') @@ -92,7 +95,7 @@ self.rewritten_command_line = self.rewritten_command_line.replace(local_path, remote_path) def __rewrite_config_files(self, local_path, remote_path): - for config_file, rewritten_contents in self.rewritten_config_files.iteritems(): + for config_file, rewritten_contents in self.rewritten_config_files.items(): self.rewritten_config_files[config_file] = rewritten_contents.replace(local_path, remote_path) def __items(self): @@ -140,7 +143,7 @@ For each file that has been transferred and renamed, updated command_line and configfiles to reflect that rewrite. """ - for local_path, remote_path in self.file_renames.iteritems(): + for local_path, remote_path in self.file_renames.items(): self.job_inputs.rewrite_paths(local_path, remote_path) def __action(self, path, type): @@ -283,7 +286,7 @@ self.transfer_tracker.rewrite_input_paths() def __upload_rewritten_config_files(self): - for config_file, new_config_contents in self.job_inputs.rewritten_config_files.iteritems(): + for config_file, new_config_contents in self.job_inputs.rewritten_config_files.items(): self.client.put_file(config_file, input_type='config', contents=new_config_contents) def get_rewritten_command_line(self): @@ -304,7 +307,7 @@ try: action = action_mapper.action(output_file, 'output') client.fetch_work_dir_output(source_file, working_directory, output_file, action[0]) - except Exception, e: + except Exception as e: download_failure_exceptions.append(e) # Remove from full output_files list so don't try to download directly. output_files.remove(output_file) @@ -312,7 +315,7 @@ try: action = action_mapper.action(output_file, 'output') client.fetch_output(output_file, working_directory=working_directory, action=action[0]) - except Exception, e: + except Exception as e: download_failure_exceptions.append(e) return __clean(download_failure_exceptions, cleanup_job, client) @@ -340,9 +343,9 @@ def _read(path): """ Utility method to quickly read small files (config files and tool - wrappers) into memory as strings. + wrappers) into memory as bytes. """ - input = open(path, "r") + input = open(path, "r", encoding="utf-8") try: return input.read() finally: diff -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 -r 752929cea6d37423c14f46f317ef3815cfc3c3d0 lib/galaxy/jobs/runners/lwr_client/transport/curl.py --- a/lib/galaxy/jobs/runners/lwr_client/transport/curl.py +++ b/lib/galaxy/jobs/runners/lwr_client/transport/curl.py @@ -1,4 +1,7 @@ -from cStringIO import StringIO +try: + from cStringIO import StringIO +except ImportError: + from io import StringIO try: from pycurl import Curl except: @@ -25,6 +28,8 @@ c.setopt(c.INFILESIZE, filesize) if data: c.setopt(c.POST, 1) + if type(data).__name__ == 'unicode': + data = data.encode('UTF-8') c.setopt(c.POSTFIELDS, data) c.perform() if not output_path: diff -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 -r 752929cea6d37423c14f46f317ef3815cfc3c3d0 lib/galaxy/jobs/runners/lwr_client/transport/standard.py --- a/lib/galaxy/jobs/runners/lwr_client/transport/standard.py +++ b/lib/galaxy/jobs/runners/lwr_client/transport/standard.py @@ -3,16 +3,23 @@ """ from __future__ import with_statement import mmap -import urllib2 +try: + from urllib2 import urlopen +except ImportError: + from urllib.request import urlopen +try: + from urllib2 import Request +except ImportError: + from urllib.request import Request class Urllib2Transport(object): def _url_open(self, request, data): - return urllib2.urlopen(request, data) + return urlopen(request, data) def execute(self, url, data=None, input_path=None, output_path=None): - request = urllib2.Request(url=url, data=data) + request = Request(url=url, data=data) input = None try: if input_path: @@ -26,7 +33,7 @@ with open(output_path, 'wb') as output: while True: buffer = response.read(1024) - if buffer == "": + if not buffer: break output.write(buffer) return response Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 30 Nov '13

30 Nov '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/842d13d7925c/ Changeset: 842d13d7925c User: jgoecks Date: 2013-11-29 17:41:26 Summary: Trackster: move static CSS settings out of JavaScript and into CSS file. Affected #: 3 files diff -r 8b613225f1def637af4774b860578a77a7fb0fe4 -r 842d13d7925c67764a0099a445b133392a0b0e13 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -32,8 +32,7 @@ var moveable = function(element, handle_class, container_selector, element_js_obj) { // HACK: set default value for container selector. container_selector = ".group"; - var css_border_props = {}; - + // Register element with its object. html_elt_js_obj_dict[element.attr("id")] = element_js_obj; @@ -130,14 +129,9 @@ html_elt_js_obj_dict[parent.attr("id")].move_drawable(this_obj, (d.deltaY > 0 ? i-1 : i) ); } }).bind("dragstart", function() { - css_border_props["border-top"] = element.css("border-top"); - css_border_props["border-bottom"] = element.css("border-bottom"); - $(this).css({ - "border-top": "1px solid blue", - "border-bottom": "1px solid blue" - }); + $(this).addClass('dragging'); }).bind("dragend", function() { - $(this).css(css_border_props); + $(this).removeClass('dragging'); }); }; @@ -236,7 +230,7 @@ this.container_div.append(this.header_div); // Icons container. - this.icons_div = $("<div/>").css("float", "left").hide().appendTo(this.header_div); + this.icons_div = $("<div/>").addClass('track-icons').hide().appendTo(this.header_div); this.build_action_icons(this.action_icons_def); this.header_div.append( $("<div style='clear: both'/>") ); @@ -930,7 +924,7 @@ // Top container for things that are fixed at the top this.top_container = $("<div/>").addClass("top-container").appendTo(parent_element); // Browser content, primary tracks are contained in here - this.browser_content_div = $("<div/>").addClass("content").css("position", "relative").appendTo(parent_element); + this.browser_content_div = $("<div/>").addClass("content").appendTo(parent_element); // Bottom container for things that are fixed at the bottom this.bottom_container = $("<div/>").addClass("bottom-container").appendTo(parent_element); // Label track fixed at top @@ -967,7 +961,7 @@ this.default_overview_height = this.overview_box.height(); this.nav_controls = $("<div/>").addClass("nav-controls").appendTo(this.nav); - this.chrom_select = $("<select/>").attr({ "name": "chrom"}).css("width", "15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls); + this.chrom_select = $("<select/>").attr({ "name": "chrom"}).addClass('chrom-nav').append("<option value=''>Loading</option>").appendTo(this.nav_controls); var submit_nav = function(e) { if (e.type === "focusout" || (e.keyCode || e.which) === 13 || (e.keyCode || e.which) === 27 ) { if ((e.keyCode || e.which) !== 27) { // Not escape key @@ -1708,7 +1702,7 @@ // Add buttons for running on dataset, region. var run_tool_row = $("<div>").addClass("param-row").appendTo(parent_div); var run_on_dataset_button = $("<input type='submit'>").attr("value", "Run on complete dataset").appendTo(run_tool_row); - var run_on_region_button = $("<input type='submit'>").attr("value", "Run on visible region").css("margin-left", "3em").appendTo(run_tool_row); + var run_on_region_button = $("<input type='submit'>").attr("value", "Run on visible region").appendTo(run_tool_row); run_on_region_button.click( function() { // Run tool to create new track. self.run_on_region(); @@ -2027,7 +2021,10 @@ else if ( param.type === 'color' ) { var container_div = $("<div/>").appendTo(row), - input = $('<input />').attr("id", id ).attr("name", id ).val( value ).css("float", "left") + input = $('<input/>').attr({ + id: id, + name: id + }).val( value ).addClass('color-input') .appendTo(container_div).click(function(e) { // Hide other pickers. $(".tooltip").removeClass( "in" ); @@ -2517,7 +2514,7 @@ }, build_container_div: function () { - return $("<div/>").addClass('track').attr("id", "track_" + this.id).css("position", "relative"); + return $("<div/>").addClass('track').attr("id", "track_" + this.id); }, build_header_div: function() { @@ -3532,7 +3529,6 @@ while ( position < view.high ) { var screenPosition = ( position - view.low ) / range * width; new_div.append( $("<div/>").addClass('label').text(commatize( position )).css( { - // Reduce by one to account for border left: screenPosition })); position += tickDistance; diff -r 8b613225f1def637af4774b860578a77a7fb0fe4 -r 842d13d7925c67764a0099a445b133392a0b0e13 static/style/blue/trackster.css --- a/static/style/blue/trackster.css +++ b/static/style/blue/trackster.css @@ -1,14 +1,14 @@ .viewport-container{overflow-x:hidden;overflow-y:auto;background:white} .trackster-nav-container{width:100%;height:0;text-align:center} .trackster-nav{padding:0 0;color:#333;font-weight:bold;background:#cccccc;position:relative;display:inline-block;top:-2em;background:transparent;border:none} -.content{font:10px verdana} +.chrom-nav{width:15em} +.content{font:10px verdana;position:relative} .nav-controls{text-align:center;padding:1px 0}.nav-controls input{margin:0 5px} #zoom-in,#zoom-out{display:inline-block;height:16px;width:16px;margin-bottom:-3px;cursor:pointer} #zoom-out{background:transparent url(../images/fugue/magnifier-zoom-out.png) center center no-repeat} #zoom-in{margin-left:10px;background:transparent url(../images/fugue/magnifier-zoom.png) center center no-repeat} .nav-input{font-size:12px;width:30em;z-index:2} .location{display:inline-block;width:15em;margin:0 10px} -.draghandle{margin-top:2px;cursor:move;float:left;background:transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;width:10px;height:12px} .intro{z-index:2;margin-left:auto;margin-right:auto;color:#555;text-align:center;font-size:16px}.intro .action-button{background-color:#CCC;margin-top:10px;padding:1em;text-decoration:underline} .overview{width:100%;margin:0px;color:white} .overview-viewport{position:relative;height:14px;background:white;margin:0} @@ -28,7 +28,7 @@ .overlay{position:absolute;left:0;top:0} .track-tile{position:absolute;background:white}.track-tile canvas{position:relative;z-index:1} .tile-message{border-bottom:solid 1px red;text-align:center;color:red;background-color:white} -.track{border-bottom:1px solid #bbb}.track.error{background-color:#ECB4AF;background-image:none} +.track{position:relative;border-bottom:1px solid #bbb}.track.error{background-color:#ECB4AF;background-image:none} .track.nodata .track-content{background-color:white;background-image:none} .track.pending .track-content{background-color:white;background-image:none} .track-content{text-align:center;position:relative;min-height:20px;padding:0px 0px 1px 0px} @@ -40,7 +40,8 @@ .right-float{float:right;margin-left:5px} .top-labeltrack{position:relative;border-bottom:solid #999 1px} .nav-labeltrack{border-top:solid #999 1px;border-bottom:solid #333 1px} -input{font:10px verdana}input[type="submit"]{padding:0px;font-size:inherit} +input{font:10px verdana}input[type="submit"]{padding:0px;margin-right:20px;font-size:inherit} +input.color-input{float:left} .dynamic-tool,.filters{padding-top:18px;padding-bottom:0.5em;margin-left:0.25em} .dynamic-tool{width:410px} .filters{float:left;margin:1em;width:60%;position:relative} @@ -53,6 +54,7 @@ .param-label{float:left;font-weight:bold;padding-top:0.2em;width:50%} .menu-button{margin:0px 4px 0px 4px} .exclamation{background:transparent url(../images/fugue/exclamation.png) no-repeat;margin-left:5em} +.track-icons{float:left} .icon-button.bookmarks{background:transparent url('../images/fugue/bookmarks-bw.png') no-repeat}.icon-button.bookmarks:hover{background:transparent url('../images/fugue/bookmarks.png') no-repeat} .icon-button.layers-stack{background:transparent url('../images/fugue/layers-stack-bw.png') no-repeat}.icon-button.layers-stack:hover{background:transparent url('../images/fugue/layers-stack.png') no-repeat} .icon-button.hammer{background:transparent url('../images/fugue/hammer-bw.png') no-repeat}.icon-button.hammer:hover{background:transparent url('../images/fugue/hammer.png') no-repeat} @@ -77,3 +79,5 @@ .feature-popup{position:absolute;z-index:2;padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);background-position:top center} .feature-popup-inner{padding:5px 8px 4px 8px;background-color:black;color:white} .zoom-area{position:absolute;top:0px;background-color:#ccf;opacity:0.5;z-index:2} +.draghandle{margin-top:2px;cursor:move;float:left;background:transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;width:10px;height:12px} +.dragging{border:1px solid blue} diff -r 8b613225f1def637af4774b860578a77a7fb0fe4 -r 842d13d7925c67764a0099a445b133392a0b0e13 static/style/src/less/trackster.less --- a/static/style/src/less/trackster.less +++ b/static/style/src/less/trackster.less @@ -31,8 +31,13 @@ border: none; } +.chrom-nav { + width: 15em; +} + .content { font: 10px verdana; + position: relative; } .nav-controls { @@ -72,15 +77,6 @@ margin: 0 10px; } -.draghandle { - margin-top: 2px; - cursor: move; - float: left; - background: transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat; - width: 10px; - height: 12px; -} - .intro { z-index: @overlay-index; /* margin-top: 200px;*/ @@ -244,6 +240,8 @@ } .track { + position: relative; + // Separates tracks. border-bottom: 1px solid @separator-color; @@ -340,8 +338,13 @@ // Override Galaxy defaults to make a smaller button. &[type="submit"] { padding: 0px; + margin-right: 20px; font-size: inherit; } + + &.color-input { + float: left; + } } .dynamic-tool, .filters { @@ -415,6 +418,10 @@ margin-left: 5em; } +.track-icons { + float: left +} + // Defines icons that change from black/white to normal on hover. Note that the images // are required to exist in the location specified. // TODO: make images into spritemap. @@ -523,4 +530,19 @@ background-color: #ccf; opacity: 0.5; z-index: @overlay-index; +} + +.draghandle { + margin-top: 2px; + cursor: move; + float: left; + background: transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat; + width: 10px; + height: 12px; +} + +// Highlight for element(s) being dragged. This definition must be after definition of draggable +// elements (e.g. track, group) in order to take precedence. +.dragging { + border: 1px solid blue; } \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/c2d705f7b50a/ Changeset: c2d705f7b50a User: jgoecks Date: 2013-11-30 23:00:01 Summary: Trackster: (a) use colors to denote track state and (b) add and use function to show messages. Affected #: 3 files diff -r 842d13d7925c67764a0099a445b133392a0b0e13 -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -2667,23 +2667,35 @@ }, /** + * Remove visualization content and display message. + */ + show_message: function(msg_html) { + this.tiles_div.remove(); + return $('<span/>').addClass('message').html(msg_html).appendTo(this.content_div); + }, + + /** * Initialize and draw the track. */ init: function(retry) { + // FIXME: track should have a 'state' attribute that is checked on load; this state attribute should be + // used in this function to determine what action(s) to take. + var track = this; track.enabled = false; track.tile_cache.clear(); track.data_manager.clear(); - track.tiles_div.css("height", "auto"); /* if (!track.content_div.text()) { track.content_div.text(DATA_LOADING); } */ // Remove old track content (e.g. tiles, messages). - track.tiles_div.text('').children().remove(); + track.content_div.children().remove(); track.container_div.removeClass("nodata error pending"); - + + track.tiles_div = $("<div/>").addClass("tiles").appendTo(track.content_div); + // // Tracks with no dataset id are handled differently. // FIXME: is this really necessary? @@ -2705,16 +2717,16 @@ if (!result || result === "error" || result.kind === "error") { // Dataset is in error state. track.container_div.addClass("error"); - track.content_div.text(DATA_ERROR); + var msg_elt = track.show_message(DATA_ERROR); if (result.message) { // Add links to (a) show error and (b) try again. - track.content_div.append( + msg_elt.append( $("<a href='javascript:void(0);'></a>").text("View error").click(function() { Galaxy.modal.show({title: "Trackster Error", body: "<pre>" + result.message + "</pre>", buttons : {'Close' : function() { Galaxy.modal.hide(); } } }); }) ); - track.content_div.append( $('<span/>').text(' ') ); - track.content_div.append( + msg_elt.append( $('<span/>').text(' ') ); + msg_elt.append( $("<a href='javascript:void(0);'></a>").text("Try again").click(function() { track.init(true); }) @@ -2723,15 +2735,15 @@ } else if (result === "no converter") { track.container_div.addClass("error"); - track.tiles_div.text(DATA_NOCONVERTER); + track.show_message(DATA_NOCONVERTER); } else if (result === "no data" || (result.data !== undefined && (result.data === null || result.data.length === 0))) { track.container_div.addClass("nodata"); - track.tiles_div.text(DATA_NONE); + track.show_message(DATA_NONE); } else if (result === "pending") { track.container_div.addClass("pending"); - track.tiles_div.html(DATA_PENDING); + track.show_message(DATA_PENDING); //$("<img/>").attr("src", image_path + "/yui/rel_interstitial_loading.gif").appendTo(track.tiles_div); setTimeout(function() { track.init(); }, track.data_query_wait); } diff -r 842d13d7925c67764a0099a445b133392a0b0e13 -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 static/style/blue/trackster.css --- a/static/style/blue/trackster.css +++ b/static/style/blue/trackster.css @@ -20,7 +20,7 @@ .yaxislabel{z-index:2;position:absolute;right:20px} .yaxislabel.bottom{bottom:2px} .group-handle{cursor:move;float:left;background:#eee url('../images/tracks/block.png');width:12px;height:12px} -.group{min-height:20px;border-top:1px solid #bbb;border-bottom:1px solid #bbb}.group>.track-header{position:relative;float:left} +.group{min-height:20px;border-top:1px solid #888;border-bottom:1px solid #888}.group>.track-header{position:relative;float:left} .track-header{height:16px;position:absolute;z-index:2;background-color:rgba(1,1,1,0.1);border-radius:5px;padding:0px 2px;text-align:left;margin:2px;}.track-header:hover{background-color:#DDDDDD} .track-header .menubutton{margin-left:0px} .track-name{float:left;margin-top:2px} @@ -28,10 +28,10 @@ .overlay{position:absolute;left:0;top:0} .track-tile{position:absolute;background:white}.track-tile canvas{position:relative;z-index:1} .tile-message{border-bottom:solid 1px red;text-align:center;color:red;background-color:white} -.track{position:relative;border-bottom:1px solid #bbb}.track.error{background-color:#ECB4AF;background-image:none} -.track.nodata .track-content{background-color:white;background-image:none} -.track.pending .track-content{background-color:white;background-image:none} -.track-content{text-align:center;position:relative;min-height:20px;padding:0px 0px 1px 0px} +.track{position:relative;border-bottom:1px solid #888}.track.error{background:#ECB4AF} +.track.nodata{background:#EEEEEE} +.track.pending{background:#FFFFCC} +.track-content{text-align:center;position:relative;min-height:20px;padding:0px 0px 1px 0px}.track-content .message{position:relative;top:4px} .loading{min-height:100px} .label-track{font-size:10px;border:none;padding:0;margin:0;height:1.5em;overflow:hidden}.label-track .label-container{position:relative;height:1.3em} .label-track .label{position:absolute;border-left:solid #999 1px;padding:1px;padding-bottom:2px;display:inline-block} diff -r 842d13d7925c67764a0099a445b133392a0b0e13 -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 static/style/src/less/trackster.less --- a/static/style/src/less/trackster.less +++ b/static/style/src/less/trackster.less @@ -3,7 +3,7 @@ @overlay-index: @base-index + 1; @track-header-height: 16px; @min-track-height: (@track-header-height + 4); -@separator-color: #BBB; +@separator-color: #888; .viewport-container { overflow-x: hidden; @@ -246,22 +246,15 @@ border-bottom: 1px solid @separator-color; &.error { - background-color: #ECB4AF; - background-image: none; + background: #ECB4AF; } &.nodata { - .track-content { - background-color: white; - background-image: none; - } + background: #EEEEEE; } &.pending { - .track-content { - background-color: white; - background-image: none; - } + background: #FFFFCC; } } @@ -270,6 +263,12 @@ position: relative; min-height: @min-track-height; padding: 0px 0px 1px 0px; + + .message { + position: relative; + // To vertically center message in track: + top: 4px; + } } .loading { https://bitbucket.org/galaxy/galaxy-central/commits/9a5a8d18cd16/ Changeset: 9a5a8d18cd16 User: jgoecks Date: 2013-11-30 23:00:44 Summary: Automated merge of local changesets with default branch. Affected #: 14 files diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3471,6 +3471,29 @@ def can_reinstall_or_activate( self ): return self.deleted + @property + def installing( self ): + """ + Used to determine if tool dependencies can denote this repository as + installing. + """ + return self.status not in [ self.installation_status.DEACTIVATED, + self.installation_status.UNINSTALLED, + self.installation_status.ERROR, + self.installation_status.INSTALLED, + self.installation_status.NEW, + ] + + @property + def installation_complete( self ): + """ + Used to determine if tool dependency installations can proceed. + Installed artifacts must be available on disk. + """ + return self.status in [ self.installation_status.DEACTIVATED, + self.installation_status.INSTALLED, + ] + def to_dict( self, view='collection', value_mapper=None ): if value_mapper is None: value_mapper = {} diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/galaxy/webapps/galaxy/api/provenance.py --- a/lib/galaxy/webapps/galaxy/api/provenance.py +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -58,6 +58,8 @@ for p in job.parameters: out[p.name] = p.value for in_d in job.input_datasets: + if not in_d.dataset: + continue if follow: out[in_d.name] = self._get_record(trans, in_d.dataset, follow) else: diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -107,10 +107,9 @@ skip_tool_test = kwd.get( 'skip_tool_test', None ) if skip_tool_test is not None: skip_tool_test = util.string_as_bool( skip_tool_test ) + if skip_tool_test: skipped_metadata_ids_subquery = select( [ trans.app.model.SkipToolTest.table.c.repository_metadata_id ] ) - if skip_tool_test: - clause_list.append( trans.model.RepositoryMetadata.id.in_( skipped_metadata_ids_subquery ) ) - else: + if skipped_metadata_ids_subquery: clause_list.append( not_( trans.model.RepositoryMetadata.id.in_( skipped_metadata_ids_subquery ) ) ) # Generate and execute the query. try: diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -390,7 +390,7 @@ with lcd( current_dir ): with settings( warn_only=True ): for tarball_name in tarball_names: - cmd = '''export PATH=$PATH:$R_HOME/bin && export R_LIBS=$INSTALL_DIR && + cmd = '''PATH=$PATH:$R_HOME/bin; export PATH; R_LIBS=$INSTALL_DIR; export R_LIBS; && Rscript -e "install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE)"''' % ( str( tarball_name ) ) cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) ) return_code = handle_command( app, tool_dependency, install_dir, cmd ) @@ -432,24 +432,24 @@ gem, gem_version = ruby_package_tup if os.path.isfile( gem ): # we assume a local shipped gem file - cmd = '''export PATH=$PATH:$RUBY_HOME/bin && export GEM_HOME=$INSTALL_DIR && + cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; gem install --local %s''' % ( gem ) elif gem.find( '://' ) != -1: # We assume a URL to a gem file. url = gem gem_name = url.split( '/' )[ -1 ] td_common_util.url_download( work_dir, gem_name, url, extract=False ) - cmd = '''export PATH=$PATH:$RUBY_HOME/bin && export GEM_HOME=$INSTALL_DIR && + cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; gem install --local %s ''' % ( gem_name ) else: # gem file from rubygems.org with or without version number if gem_version: # version number was specified - cmd = '''export PATH=$PATH:$RUBY_HOME/bin && export GEM_HOME=$INSTALL_DIR && + cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; gem install %s --version "=%s"''' % ( gem, gem_version) else: # no version number given - cmd = '''export PATH=$PATH:$RUBY_HOME/bin && export GEM_HOME=$INSTALL_DIR && + cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; gem install %s''' % ( gem ) cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) ) return_code = handle_command( app, tool_dependency, install_dir, cmd ) @@ -490,7 +490,7 @@ for perl_package in perl_packages: # If set to a true value then MakeMaker's prompt function will always # return the default without waiting for user input. - cmd = '''export PERL_MM_USE_DEFAULT=1 && ''' + cmd = '''PERL_MM_USE_DEFAULT=1; export PERL_MM_USE_DEFAULT; ''' if perl_package.find( '://' ) != -1: # We assume a URL to a gem file. url = perl_package diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -40,6 +40,70 @@ raise Exception( message ) return None + +def find_complex_dependency_package( app, dependent_install_dir, required_install_dir, tool_shed_repository, required_repository, package_name, package_version, tool_dependencies_config ): + """ + """ + tool_dependencies = [] + if not os.path.exists( dependent_install_dir ): + os.makedirs( dependent_install_dir ) + env_file = None + if tool_dependencies_config: + required_td_tree, error_message = xml_util.parse_xml( tool_dependencies_config ) + if required_td_tree: + required_td_root = required_td_tree.getroot() + for required_td_elem in required_td_root: + # Find the appropriate package name and version. + if required_td_elem.tag == 'package': + # <package name="bwa" version="0.5.9"> + required_td_package_name = required_td_elem.get( 'name', None ) + required_td_package_version = required_td_elem.get( 'version', None ) + if required_td_package_name == package_name and required_td_package_version == package_version: + tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_shed_repository=tool_shed_repository, + name=package_name, + version=package_version, + type='package', + status=app.model.ToolDependency.installation_status.NEVER_INSTALLED, + set_status=True ) + + if required_repository.installing: + tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=app.model.ToolDependency.installation_status.INSTALLING ) + # What happens if dependent repository fails or is + # uninstalled during this process. + env_file = required_repository_package_env( app, package_name, package_version, required_repository ) + if required_repository.installation_complete: + if not os.path.exists( env_file ): + error_message = 'env.sh file %s for package %s in dependendent repository could not be found. Required repository has status %s.' % ( package_name, env_file, required_repository.status ) + tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, + tool_dependency, + error_message, + remove_installation_path=False ) + else: + tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=app.model.ToolDependency.installation_status.INSTALLED ) + else: + # Ekk - handling tool depednencies for a dependent + # repository that is not installed. + # + # Go ahead a return the env.sh file - Galaxy will + # proceed to create an invalid symbolic link. + # This is subtle-ly different than the previous + # behavior which would have recreated an env.sh + # from the the required repository's + # tool_dependencies.xml but since it was not + # installed all of the values inside would be + # invalid path modifications. Either way, this file + # is junk until the required repository is + # installed properly. + pass + tool_dependencies.append( tool_dependency ) + return tool_dependencies, env_file + + def get_absolute_path_to_file_in_repository( repo_files_dir, file_name ): """Return the absolute path to a specified disk file contained in a repository.""" stripped_file_name = strip_path( file_name ) @@ -91,6 +155,7 @@ text = common_util.tool_shed_get( app, tool_shed_url, url ) return text + def handle_complex_repository_dependency_for_package( app, elem, package_name, package_version, tool_shed_repository ): handled_tool_dependencies = [] tool_shed = elem.attrib[ 'toolshed' ] @@ -125,8 +190,7 @@ tool_dependency_version=package_version ) # Set this dependent repository's tool dependency env.sh file with a path to the required repository's installed tool dependency package. # We can get everything we need from the discovered installed required_repository. - if required_repository.status in [ app.model.ToolShedRepository.installation_status.DEACTIVATED, - app.model.ToolShedRepository.installation_status.INSTALLED ]: + if required_repository.installation_complete: if not os.path.exists( required_repository_package_install_dir ): print 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir ) repo_files_dir = required_repository.repo_files_directory( app ) @@ -156,22 +220,26 @@ required_repository_owner, required_repository_changeset_revision ) config_to_use = tmp_filename - tool_dependencies, actions_dict = populate_actions_dict( app=app, - dependent_install_dir=dependent_install_dir, - required_install_dir=required_repository_package_install_dir, - tool_shed_repository=tool_shed_repository, - required_repository=required_repository, - package_name=package_name, - package_version=package_version, - tool_dependencies_config=config_to_use ) + + tool_dependencies, package_env_sh_file = find_complex_dependency_package( + app=app, + dependent_install_dir=dependent_install_dir, + required_install_dir=required_repository_package_install_dir, + tool_shed_repository=tool_shed_repository, + required_repository=required_repository, + package_name=package_name, + package_version=package_version, + tool_dependencies_config=config_to_use + ) + if package_env_sh_file: + os.symlink( package_env_sh_file, os.path.join( dependent_install_dir, "env.sh" ) ) if tmp_filename: try: os.remove( tmp_filename ) except: pass for tool_dependency in tool_dependencies: - # Install and build the package via fabric and update the tool_dependency record accordingly.. - tool_dependency = install_and_build_package_via_fabric( app, tool_dependency, actions_dict ) + tool_dependency = __mark_tool_dependency_installed( app, tool_dependency) handled_tool_dependencies.append( tool_dependency ) else: message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \ @@ -179,113 +247,6 @@ raise Exception( message ) return handled_tool_dependencies -def handle_set_environment_entry_for_package( app, install_dir, tool_shed_repository, package_name, package_version, elem, required_repository ): - """ - Populate a list of actions for creating an env.sh file for a dependent repository. The received elem is the <package> tag set associated - with the tool-dependencies.xml file for one of the received tool_shed_repository's repository dependency. - """ - action_dict = {} - actions = [] - tool_dependencies = [] - for package_elem in elem: - if package_elem.tag == 'install': - # Create the new tool_dependency record in the database. - tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, - tool_shed_repository=tool_shed_repository, - name=package_name, - version=package_version, - type='package', - status=app.model.ToolDependency.installation_status.NEVER_INSTALLED, - set_status=True ) - # Get the installation method version from a tag like: <install version="1.0"> - package_install_version = package_elem.get( 'version', '1.0' ) - if package_install_version == '1.0': - # Update the tool dependency's status. - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.model.ToolDependency.installation_status.INSTALLING ) - # Since the required tool dependency is installed for a repository dependency, we first need to inspect the <actions> tag set to find - # the <action type="set_environment"> tag. - env_var_dicts = [] - for actions_elem in package_elem: - for action_elem in actions_elem: - action_type = action_elem.get( 'type', 'shell_command' ) - if action_type == 'set_environment': - # <action type="set_environment"> - # <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> - # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - # </action> - for env_elem in action_elem: - if env_elem.tag == 'environment_variable': - env_var_dict = td_common_util.create_env_var_dict( env_elem, tool_dependency_install_dir=install_dir ) - if env_var_dict: - if env_var_dict not in env_var_dicts: - env_var_dicts.append( env_var_dict ) - elif action_type == 'setup_virtualenv': - # Add the virtualenv's site-packages to PYTHONPATH and bin to PATH. This is a bit hackish. - site_packages_command = "%s -c 'import os, sys; print os.path.join(sys.prefix, \"lib\", \"python\" + sys.version[:3], \"site-packages\")'" % os.path.join( install_dir, "venv", "bin", "python" ) - output = fabric_util.handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True ) - if output.return_code: - log.error( 'Tool dependency %s includes a setup_virtualenv action but venv python is broken: ' % \ - ( str( tool_dependency.name ), str( output.stderr ) ) ) - elif not os.path.exists( output.stdout ): - log.error( "virtualenv's site-packages directory '%s' does not exist", str( output.stdout ) ) - else: - env_var_dicts.append( dict( name="PYTHONPATH", action="prepend_to", value=output.stdout ) ) - env_var_dicts.append( dict( name="PATH", action="prepend_to", value=os.path.join( install_dir, 'venv', 'bin' ) ) ) - if env_var_dicts: - if required_repository.status in [ app.model.ToolShedRepository.installation_status.INSTALLED, - app.model.ToolShedRepository.installation_status.DEACTIVATED ]: - # Handle the case where we have an installed required repository due to the prior_installation_required = True - # setting in the received tool_shed_repository's tool_dependencies.xml file and the required repository's - # tool_dependencies.xml file may include the use of the $ENV[] variable inheritance feature. To handle this, - # we will replace the current "value" entries in each env_var_dict with the actual path taken from the env.sh - # file generated for the installed required repository. Each env_var_dict currently looks something like this: - # {'action': 'append_to', 'name': 'LD_LIBRARY_PATH', 'value': '$BOOST_ROOT_DIR/lib/'} - # We'll read the contents of the received required_repository's env.sh file and replace the 'value' entry of - # each env_var_dict with the associated value in the env.sh file. - new_env_var_dicts = [] - env_sh_file_dir = tool_dependency_util.get_tool_dependency_install_dir( app=app, - repository_name=required_repository.name, - repository_owner=required_repository.owner, - repository_changeset_revision=required_repository.installed_changeset_revision, - tool_dependency_type='package', - tool_dependency_name=package_name, - tool_dependency_version=package_version ) - env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' ) - if os.path.exists( env_sh_file_path ): - for i, line in enumerate( open( env_sh_file_path, 'r' ) ): - env_var_dict = env_var_dicts[ i ] - action = env_var_dict.get( 'action', None ) - name = env_var_dict.get( 'name', None ) - value = env_var_dict.get( 'value', None ) - if action and name and value: - new_value = parse_env_shell_entry( action, name, value, line ) - env_var_dict[ 'value' ] = new_value - new_env_var_dicts.append( env_var_dict ) - else: - error_message = 'Invalid file %s specified, ignoring set_environment_for_install action.' % str( env_sh_file_path ) - tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, - tool_dependency, - error_message, - remove_installation_path=False ) - action_dict[ 'environment_variable' ] = new_env_var_dicts - else: - action_dict[ 'environment_variable' ] = env_var_dicts - actions.append( ( 'set_environment', action_dict ) ) - if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR, - app.model.ToolDependency.installation_status.INSTALLED ]: - # Update the tool dependency's status. - tool_dependency = \ - tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.model.ToolDependency.installation_status.INSTALLED ) - # Accumulate processed tool dependencies to return to the caller. - tool_dependencies.append( tool_dependency ) - else: - raise NotImplementedError( 'Only install version 1.0 is currently supported (i.e., change your tag to be <install version="1.0">).' ) - return tool_dependencies, actions - return tool_dependencies, actions def install_and_build_package_via_fabric( app, tool_dependency, actions_dict ): sa_session = app.model.context.current @@ -301,17 +262,10 @@ tool_dependency, error_message, remove_installation_path=False ) - if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR, - app.model.ToolDependency.installation_status.INSTALLED ]: - log.debug( 'Changing status for tool dependency %s from %s to %s.' % \ - ( str( tool_dependency.name ), str( tool_dependency.status ), str( app.model.ToolDependency.installation_status.INSTALLED ) ) ) - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.model.ToolDependency.installation_status.INSTALLED, - error_message=None, - remove_from_disk=False ) + tool_dependency = __mark_tool_dependency_installed( app, tool_dependency) return tool_dependency + def install_package( app, elem, tool_shed_repository, tool_dependencies=None ): # The value of tool_dependencies is a partial or full list of ToolDependency records associated with the tool_shed_repository. sa_session = app.model.context.current @@ -821,60 +775,22 @@ tool_dependency = install_and_build_package_via_fabric( app, tool_dependency, actions_dict ) return tool_dependency -def parse_env_shell_entry( action, name, value, line ): - new_value = value - var_name = '$%s' % name - tmp_value = line.split( '=' )[ 1 ] - if action == 'prepend_to': - # PATH=/test/package_rdkit_2012_12/62ebd7bb637a/rdkit/bin:$PATH; export PATH - new_value = tmp_value.split( ':%s' % var_name )[ 0 ] - elif action == 'set_to': - # RDBASE=test/package_rdkit_2012_12/62ebd7bb637a/rdkit; export RDBASE - new_value = tmp_value.split( ';' )[ 0 ] - elif action == 'append_to': - # LD_LIBRARY_PATH=$LD_LIBRARY_PATH:test/package_rdkit_2012_12/62ebd7bb637a/rdkit/lib/; export LD_LIBRARY_PATH - new_value = tmp_value.split( ':' )[ 1 ] - new_value = new_value.split( ';' )[ 0 ] - return new_value -def populate_actions_dict( app, dependent_install_dir, required_install_dir, tool_shed_repository, required_repository, package_name, package_version, tool_dependencies_config ): +# TODO: Move to tool_dependency_util? +def required_repository_package_env( app, package_name, package_version, required_repository ): """ - Populate an actions dictionary that can be sent to fabric_util.install_and_build_package. This method handles the scenario where a tool_dependencies.xml - file defines a complex repository dependency. In this case, the tool dependency package will be installed in a separate repository and the tool dependency - defined for the dependent repository will use an environment_variable setting defined in it's env.sh file to locate the required package. This method - basically does what the install_via_fabric method does, but restricts it's activity to the <action type="set_environment"> tag set within the required - repository's tool_dependencies.xml file. + Return path to env.sh file in required repository if the required repository has been installed. """ - sa_session = app.model.context.current - if not os.path.exists( dependent_install_dir ): - os.makedirs( dependent_install_dir ) - actions_dict = dict( install_dir=dependent_install_dir ) - if package_name: - actions_dict[ 'package_name' ] = package_name - tool_dependencies = [] - action_dict = {} - if tool_dependencies_config: - required_td_tree, error_message = xml_util.parse_xml( tool_dependencies_config ) - if required_td_tree: - required_td_root = required_td_tree.getroot() - for required_td_elem in required_td_root: - # Find the appropriate package name and version. - if required_td_elem.tag == 'package': - # <package name="bwa" version="0.5.9"> - required_td_package_name = required_td_elem.get( 'name', None ) - required_td_package_version = required_td_elem.get( 'version', None ) - if required_td_package_name==package_name and required_td_package_version==package_version: - tool_dependencies, actions = handle_set_environment_entry_for_package( app=app, - install_dir=required_install_dir, - tool_shed_repository=tool_shed_repository, - package_name=package_name, - package_version=package_version, - elem=required_td_elem, - required_repository=required_repository ) - if actions: - actions_dict[ 'actions' ] = actions - break - return tool_dependencies, actions_dict + env_sh_file_dir = tool_dependency_util.get_tool_dependency_install_dir( app=app, + repository_name=required_repository.name, + repository_owner=required_repository.owner, + repository_changeset_revision=required_repository.installed_changeset_revision, + tool_dependency_type='package', + tool_dependency_name=package_name, + tool_dependency_version=package_version ) + env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' ) + return env_sh_file_path + def run_proprietary_fabric_method( app, elem, proprietary_fabfile_path, install_dir, package_name=None, **kwd ): """ @@ -1019,3 +935,17 @@ for arg in args: parts.append( arg.strip( '/' ) ) return '/'.join( parts ) + + +# TODO: Move to tool_dependency_util? +def __mark_tool_dependency_installed( app, tool_dependency ): + if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR, + app.model.ToolDependency.installation_status.INSTALLED ]: + log.debug( 'Changing status for tool dependency %s from %s to %s.' % \ + ( str( tool_dependency.name ), str( tool_dependency.status ), str( app.model.ToolDependency.installation_status.INSTALLED ) ) ) + tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=app.model.ToolDependency.installation_status.INSTALLED, + error_message=None, + remove_from_disk=False ) + return tool_dependency diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -95,18 +95,25 @@ invalid_revisions = 0 records_checked = 0 # Do not check metadata records that have an entry in the skip_tool_tests table, since they won't be tested anyway. - skip_metadata_ids = select( [ app.model.SkipToolTest.table.c.repository_metadata_id ] ) + print '# -------------------------------------------------------------------------------------------' + print '# The skip_tool_test setting has been set for the following repository revision, so they will not be tested.' + skip_metadata_ids = [] + for skip_tool_test in app.sa_session.query( app.model.SkipToolTest ): + print '# repository_metadata_id: %s, changeset_revision: %s' % \ + ( str( skip_tool_test.repository_metadata_id ), str( skip_tool_test.initial_changeset_revision ) ) + print 'reason: %s' % str( skip_tool_test.comment ) + skip_metadata_ids.append( skip_tool_test.repository_metadata_id ) # Get the list of metadata records to check for functional tests and test data. Limit this to records that have not been flagged do_not_test, # since there's no need to check them again if they won't be tested anyway. Also filter out changeset revisions that are not downloadable, # because it's redundant to test a revision that a user can't install. for repository_metadata in app.sa_session.query( app.model.RepositoryMetadata ) \ .filter( and_( app.model.RepositoryMetadata.table.c.downloadable == True, app.model.RepositoryMetadata.table.c.includes_tools == True, - app.model.RepositoryMetadata.table.c.do_not_test == False, - not_( app.model.RepositoryMetadata.table.c.id.in_( skip_metadata_ids ) ) ) ): - # Clear any old invalid tests for this metadata revision, since this could lead to duplication of invalid test rows, - # or tests incorrectly labeled as invalid. + app.model.RepositoryMetadata.table.c.do_not_test == False ) ): + # Initialize some items. missing_test_components = [] + revision_has_test_data = False + testable_revision = False repository = repository_metadata.repository records_checked += 1 # Check the next repository revision. @@ -117,15 +124,14 @@ repository = repository_metadata.repository if repository.id not in checked_repository_ids: checked_repository_ids.append( repository.id ) - if verbosity >= 1: - print '# -------------------------------------------------------------------------------------------' - print '# Now checking revision %s of %s, owned by %s.' % ( changeset_revision, name, owner ) + print '# -------------------------------------------------------------------------------------------' + print '# Checking revision %s of %s owned by %s.' % ( changeset_revision, name, owner ) + if repository_metadata.id in skip_metadata_ids: + print'# Skipping revision %s of %s owned by %s because the skip_tool_test setting has been set.' % ( changeset_revision, name, owner ) # If this changeset revision has no tools, we don't need to do anything here, the install and test script has a filter for returning # only repositories that contain tools. tool_dicts = metadata.get( 'tools', None ) if tool_dicts is not None: - has_test_data = False - testable_revision = False # Clone the repository up to the changeset revision we're checking. repo_dir = repository.repo_path( app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) @@ -139,29 +145,30 @@ if '.hg' in dirs: dirs.remove( '.hg' ) if 'test-data' in dirs: - has_test_data = True + revision_has_test_data = True test_data_path = os.path.join( root, dirs[ dirs.index( 'test-data' ) ] ) break - if verbosity >= 1: - if has_test_data: - print '# Test data directory found in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) - else: - print '# Test data directory missing in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) - print '# Checking for functional tests in changeset revision %s of %s, owned by %s.' % \ - ( changeset_revision, name, owner ) - # Inspect each tool_dict for defined functional tests. + if revision_has_test_data: + print '# Test data directory found in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + else: + print '# Test data directory missing in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + print '# Checking for functional tests in changeset revision %s of %s, owned by %s.' % \ + ( changeset_revision, name, owner ) + # Inspect each tool_dict for defined functional tests. If there are no tests, this tool should not be tested, since the + # tool functional tests only report failure if the test itself fails, not if it's missing or undefined. Filtering out those + # repositories at this step will reduce the number of "false negatives" the automated functional test framework produces. for tool_dict in tool_dicts: + failure_reason = '' + problem_found = False + tool_has_defined_tests = False + tool_has_test_files = False + missing_test_files = [] tool_count += 1 tool_id = tool_dict[ 'id' ] tool_version = tool_dict[ 'version' ] tool_guid = tool_dict[ 'guid' ] - if verbosity >= 2: - print "# Checking tool ID '%s' in changeset revision %s of %s." % \ - ( tool_id, changeset_revision, name ) - # If there are no tests, this tool should not be tested, since the tool functional tests only report failure if the test itself fails, - # not if it's missing or undefined. Filtering out those repositories at this step will reduce the number of "false negatives" the - # automated functional test framework produces. - tool_has_tests = False + if verbosity >= 1: + print "# Checking tool ID '%s' in changeset revision %s of %s." % ( tool_id, changeset_revision, name ) defined_test_dicts = tool_dict.get( 'tests', None ) if defined_test_dicts is not None: # We need to inspect the <test> tags because the following tags... @@ -182,33 +189,26 @@ outputs = defined_test_dict.get( 'outputs', [] ) if inputs and outputs: # At least one tool within the repository has a valid <test> tag. - tool_has_tests = True + tool_has_defined_tests = True break - if tool_has_tests: - if verbosity >= 2: - print "# Tool ID '%s' in changeset revision %s of %s has one or more valid functional tests defined." % \ - ( tool_id, changeset_revision, name ) + if tool_has_defined_tests: + print "# Tool ID '%s' in changeset revision %s of %s has one or more valid functional tests defined." % \ + ( tool_id, changeset_revision, name ) has_tests += 1 else: - if verbosity >= 2: - print '# No functional tests defined for %s.' % tool_id + print '# No functional tests defined for %s.' % tool_id no_tests += 1 - failure_reason = '' - problem_found = False - missing_test_files = [] - has_test_files = False - if tool_has_tests and has_test_data: + if tool_has_defined_tests and revision_has_test_data: missing_test_files = check_for_missing_test_files( defined_test_dicts, test_data_path ) if missing_test_files: - if verbosity >= 2: - print "# Tool ID '%s' in changeset revision %s of %s is missing one or more required test files: %s" % \ - ( tool_id, changeset_revision, name, ', '.join( missing_test_files ) ) + print "# Tool id '%s' in changeset revision %s of %s is missing one or more required test files: %s" % \ + ( tool_id, changeset_revision, name, ', '.join( missing_test_files ) ) else: - has_test_files = True - if not has_test_data: + tool_has_test_files = True + if not revision_has_test_data: failure_reason += 'Repository does not have a test-data directory. ' problem_found = True - if not tool_has_tests: + if not tool_has_defined_tests: failure_reason += 'Functional test definitions missing for %s. ' % tool_id problem_found = True if missing_test_files: @@ -219,23 +219,22 @@ if problem_found: if test_errors not in missing_test_components: missing_test_components.append( test_errors ) - if tool_has_tests and has_test_files: + if tool_has_defined_tests and tool_has_test_files: + print '# Revision %s of %s owned by %s is a testable revision.' % ( changeset_revision, name, owner ) testable_revision = True # Remove the cloned repository path. This has to be done after the check for required test files, for obvious reasons. if os.path.exists( work_dir ): shutil.rmtree( work_dir ) if not missing_test_components: valid_revisions += 1 - if verbosity >= 1: - print '# All tools have functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + print '# All tools have functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) else: invalid_revisions += 1 + print '# Some tools have problematic functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) if verbosity >= 1: - print '# Some tools have problematic functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) - if verbosity >= 2: - for invalid_test in missing_test_components: - if 'missing_components' in invalid_test: - print '# %s' % invalid_test[ 'missing_components' ] + for missing_test_component in missing_test_components: + if 'missing_components' in missing_test_component: + print '# %s' % missing_test_component[ 'missing_components' ] if not info_only: # Get or create the list of tool_test_results dictionaries. if repository_metadata.tool_test_results is not None: @@ -249,8 +248,9 @@ # install_and_test_tool_sed_repositories.sh script which will further populate the tool_test_results_dict. tool_test_results_dict = tool_test_results_dicts[ 0 ] if len( tool_test_results_dict ) <= 1: - # We can re-use the mostly empty tool_test_results_dict for this run, but we need to eliminate it from - # the list of tool_test_results_dicts since it will be re-inserted later. + # We can re-use the mostly empty tool_test_results_dict for this run because it is either empty or it contains only + # a test_environment entry. If we use it we need to temporarily eliminate it from the list of tool_test_results_dicts + # since it will be re-inserted later. tool_test_results_dict = tool_test_results_dicts.pop( 0 ) else: # The latest tool_test_results_dict has been populated with the results of a test run, so it cannot be used. @@ -259,6 +259,11 @@ # Create a new dictionary for the most recent test run. tool_test_results_dict = {} test_environment_dict = tool_test_results_dict.get( 'test_environment', {} ) + # Add the current time as the approximate time that this test run occurs. A similar value will also be + # set to the repository_metadata.time_last_tested column, but we also store it here because the Tool Shed + # may be configured to store multiple test run results, so each must be associated with a time stamp. + now = time.strftime( "%Y-%m-%d %H:%M:%S" ) + test_environment_dict[ 'time_tested' ] = now test_environment_dict[ 'tool_shed_database_version' ] = get_database_version( app ) test_environment_dict[ 'tool_shed_mercurial_version' ] = __version__.version test_environment_dict[ 'tool_shed_revision' ] = get_repository_current_revision( os.getcwd() ) @@ -281,7 +286,13 @@ print "# and it is not the latest downloadable revision." repository_metadata.do_not_test = True repository_metadata.tools_functionally_correct = False - repository_metadata.missing_test_components = True + if not testable_revision: + # Even though some tools may be missing test components, it may be possible to test other tools. Since the + # install and test framework filters out repositories marked as missing test components, we'll set it only if + # no tools can be tested. + print '# Setting missing_test_components to True for revision %s of %s owned by %s because all tools are missing test components.' % \ + ( changeset_revision, name, owner ) + repository_metadata.missing_test_components = True tool_test_results_dict[ 'missing_test_components' ] = missing_test_components # Store only the configured number of test runs. num_tool_test_results_saved = int( app.config.num_tool_test_results_saved ) diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -1052,45 +1052,51 @@ """Return a folder hierarchy containing tool dependencies.""" # This container is displayed only in the tool shed. if tool_test_results_dicts: - multiple_tool_test_results_dicts = len( tool_test_results_dicts ) > 1 test_results_dict_id = 0 folder_id += 1 tool_test_results_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) + multiple_tool_test_results_dicts = len( tool_test_results_dicts ) > 1 + if multiple_tool_test_results_dicts: + folder_id += 1 + test_runs_folder = Folder( id=folder_id, key='test_runs', label='Test runs', parent=tool_test_results_root_folder ) + tool_test_results_root_folder.folders.append( test_runs_folder ) for index, tool_test_results_dict in enumerate( tool_test_results_dicts ): test_environment_dict = tool_test_results_dict.get( 'test_environment', None ) - if test_environment_dict is not None: - time_tested = test_environment_dict.get( 'time_tested', 'unknown_%d' % index ) - if multiple_tool_test_results_dicts: - folder_id += 1 - containing_folder = Folder( id=folder_id, key='test_results', label=time_tested, parent=tool_test_results_root_folder ) - else: - containing_folder = tool_test_results_root_folder - test_results_dict_id += 1 - #folder_id += 1 - #test_results_folder = Folder( id=folder_id, key='test_results', label='Automated test environment', parent=containing_folder ) - #containing_folder.folders.append( test_results_folder ) + if test_environment_dict is None: + # the test environment entry will exist only if the preparation script check_re;ositories_for_functional_tests.py + # was executed prior to the ~/install_and_test_repositories/functional_tests.py script. If that did not occur, + # we'll display test result, but the test_environment entries will not be complete. + test_environment_dict = {} + time_tested = test_environment_dict.get( 'time_tested', 'unknown_%d' % index ) + if multiple_tool_test_results_dicts: folder_id += 1 - folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=containing_folder ) - containing_folder.folders.append( folder ) - architecture = test_environment_dict.get( 'architecture', '' ) - galaxy_database_version = test_environment_dict.get( 'galaxy_database_version', '' ) - galaxy_revision = test_environment_dict.get( 'galaxy_revision', '' ) - python_version = test_environment_dict.get( 'python_version', '' ) - system = test_environment_dict.get( 'system', '' ) - tool_shed_database_version = test_environment_dict.get( 'tool_shed_database_version', '' ) - tool_shed_mercurial_version = test_environment_dict.get( 'tool_shed_mercurial_version', '' ) - tool_shed_revision = test_environment_dict.get( 'tool_shed_revision', '' ) - test_environment = TestEnvironment( id=1, - architecture=architecture, - galaxy_database_version=galaxy_database_version, - galaxy_revision=galaxy_revision, - python_version=python_version, - system=system, - time_tested=time_tested, - tool_shed_database_version=tool_shed_database_version, - tool_shed_mercurial_version=tool_shed_mercurial_version, - tool_shed_revision=tool_shed_revision ) - folder.test_environments.append( test_environment ) + containing_folder = Folder( id=folder_id, key='test_results', label=time_tested, parent=test_runs_folder ) + test_runs_folder.folders.append( containing_folder ) + else: + containing_folder = tool_test_results_root_folder + test_results_dict_id += 1 + folder_id += 1 + folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=containing_folder ) + containing_folder.folders.append( folder ) + architecture = test_environment_dict.get( 'architecture', '' ) + galaxy_database_version = test_environment_dict.get( 'galaxy_database_version', '' ) + galaxy_revision = test_environment_dict.get( 'galaxy_revision', '' ) + python_version = test_environment_dict.get( 'python_version', '' ) + system = test_environment_dict.get( 'system', '' ) + tool_shed_database_version = test_environment_dict.get( 'tool_shed_database_version', '' ) + tool_shed_mercurial_version = test_environment_dict.get( 'tool_shed_mercurial_version', '' ) + tool_shed_revision = test_environment_dict.get( 'tool_shed_revision', '' ) + test_environment = TestEnvironment( id=1, + architecture=architecture, + galaxy_database_version=galaxy_database_version, + galaxy_revision=galaxy_revision, + python_version=python_version, + system=system, + time_tested=time_tested, + tool_shed_database_version=tool_shed_database_version, + tool_shed_mercurial_version=tool_shed_mercurial_version, + tool_shed_revision=tool_shed_revision ) + folder.test_environments.append( test_environment ) not_tested_dict = tool_test_results_dict.get( 'not_tested', {} ) if not_tested_dict: folder_id += 1 @@ -1120,6 +1126,9 @@ containing_folder.folders.append( folder ) failed_test_id = 0 for failed_tests_dict in failed_tests_dicts: + # TODO: Remove this when invalid test data is eliminated. + if isinstance( failed_tests_dict, list ): + failed_tests_dict = failed_tests_dict[ 0 ] failed_test_id += 1 failed_test = FailedTest( id=failed_test_id, stderr=failed_tests_dict.get( 'stderr', '' ), @@ -1153,6 +1162,7 @@ key='installation_errors', label='Installation errors', parent=containing_folder ) + containing_folder.installation_errors.append( installation_error_base_folder ) if current_repository_errors: folder_id += 1 subfolder = Folder( id=folder_id, @@ -1203,10 +1213,6 @@ error_message=tool_dependency_error_dict.get( 'error_message', '' ) ) subfolder.tool_dependency_installation_errors.append( tool_dependency_installation_error ) installation_error_base_folder.folders.append( subfolder ) - containing_folder.installation_errors.append( installation_error_base_folder ) - #containing_folder.folders.append( containing_folder ) - if multiple_tool_test_results_dicts: - tool_test_results_root_folder.folders.append( containing_folder ) else: tool_test_results_root_folder = None return folder_id, tool_test_results_root_folder diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -363,6 +363,8 @@ """ error_message = '' latest_revision_only = '-check_all_revisions' not in sys.argv + if latest_revision_only: + log.debug( 'Testing is restricted to the latest downloadable revision in this test run.' ) repository_dicts = [] params = urllib.urlencode( dict( do_not_test='false', downloadable='true', @@ -374,13 +376,12 @@ baseline_repository_dicts, error_message = json_from_url( api_url ) if error_message: return None, error_message - log.debug( 'The Tool Shed API returned %d metadata revisions for installation and testing.' % len( baseline_repository_dicts ) ) for baseline_repository_dict in baseline_repository_dicts: # We need to get some details from the tool shed API, such as repository name and owner, to pass on to the # module that will generate the install methods. repository_dict, error_message = get_repository_dict( galaxy_tool_shed_url, baseline_repository_dict ) if error_message: - log.debug( 'Error getting additional details about repository %s from the API: %s' % ( str( name ), error_message ) ) + log.debug( 'Error getting additional details from the API: %s' % str( error_message ) ) else: # Don't test empty repositories. changeset_revision = baseline_repository_dict[ 'changeset_revision' ] @@ -393,10 +394,6 @@ repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) else: repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) - if latest_revision_only: - skipped_previous = ' and metadata revisions that are not the most recent' - else: - skipped_previous = '' if testing_single_repository: tsr_name = testing_single_repository[ 'name' ] tsr_owner = testing_single_repository[ 'owner' ] @@ -414,14 +411,15 @@ return repository_dicts, error_message return repository_dicts, error_message # Get a list of repositories to test from the tool shed specified in the GALAXY_INSTALL_TEST_TOOL_SHED_URL environment variable. - log.debug( "Retrieved %d repositories from the API url: %s." % ( len( repository_dicts ), str( galaxy_tool_shed_url ) ) ) - if '-list_repositories' in sys.argv: - log.debug( "Repositories for testing:" ) - for repository_dict in repository_dicts: - log.debug( "Revision %s of repository %s owned by %s" % \ - ( str( repository_dict.get( 'changeset_revision', None ) ), \ - str( repository_dict.get( 'name', None ) ), \ - str( repository_dict.get( 'owner', None ) ) ) ) + log.debug( "The Tool Shed's API url...\n%s" % str( api_url ) ) + log.debug( "...retrieved %d repository revisions for testing." % len( repository_dicts ) ) + #if '-list_repositories' in sys.argv: + log.debug( "Repository revisions for testing:" ) + for repository_dict in repository_dicts: + log.debug( "Revision %s of repository %s owned by %s" % \ + ( str( repository_dict.get( 'changeset_revision', None ) ), \ + str( repository_dict.get( 'name', None ) ), \ + str( repository_dict.get( 'owner', None ) ) ) ) return repository_dicts, error_message def get_static_settings(): @@ -503,7 +501,7 @@ params = dict( tools_functionally_correct=False, do_not_test=False, test_install_error=True ) - # TODO: do something usefule with response_dict + # TODO: do something useful with response_dict response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) # Since this repository is missing components, we do not want to test it, so deactivate it or uninstall it. # The deactivate flag is set to True if the environment variable GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES @@ -618,33 +616,39 @@ name = str( repository_dict[ 'name' ] ) owner = str( repository_dict[ 'owner' ] ) changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + log.debug( "Processing revision %s of repository %s owned by %s..." % ( changeset_revision, name, owner ) ) # Populate the tool_test_results_dict. tool_test_results_dicts, error_message = get_tool_test_results_dicts( galaxy_tool_shed_url, encoded_repository_metadata_id ) - # The preparation script ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered - # information in the 'test_environment' and possibly the 'missing_test_components' entries of the first - # tool_test_results_dict in the list of tool_test_results_dicts. We need to be careful to not lose this - # information. - tool_test_results_dict = tool_test_results_dicts.pop( 0 ) - # See if this repository should be skipped for any reason. - skip_this_repository = False - skip_reason = None - for exclude_dict in exclude_list: - reason = exclude_dict[ 'reason' ] - exclude_repositories = exclude_dict[ 'repositories' ] - if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: - skip_this_repository = True - skip_reason = reason - break - if skip_this_repository: - tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason ) - params = dict( tools_functionally_correct=False, - do_not_test=False ) - # TODO: do something usefule with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) - log.debug( "Not testing revision %s of repository %s owned by %s." % ( changeset_revision, name, owner ) ) + if error_message: + log.debug( error_message ) else: - if error_message: - log.debug( error_message ) + # The preparation script ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered + # information in the 'test_environment' and possibly the 'missing_test_components' entries of the first + # tool_test_results_dict in the list of tool_test_results_dicts. We need to be careful to not lose this + # information. + try: + tool_test_results_dict = tool_test_results_dicts.pop( 0 ) + except Exception, e: + log.exception( "Invalid list of tool_test_results_dicts %s: %s" % ( str( tool_test_results_dicts ), str( e ) ) ) + continue + # See if this repository should be skipped for any reason. + this_repository_is_in_the_exclude_lost = False + skip_reason = None + for exclude_dict in exclude_list: + reason = exclude_dict[ 'reason' ] + exclude_repositories = exclude_dict[ 'repositories' ] + if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: + this_repository_is_in_the_exclude_lost = True + skip_reason = reason + break + if this_repository_is_in_the_exclude_lost: + tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason ) + params = dict( tools_functionally_correct=False, + do_not_test=False ) + # TODO: do something useful with response_dict + response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) + log.debug( "Not testing revision %s of repository %s owned by %s because it is in the exclude list for this test run." % \ + ( changeset_revision, name, owner ) ) else: test_environment_dict = tool_test_results_dict.get( 'test_environment', None ) test_environment_dict = get_test_environment( test_environment_dict ) @@ -678,7 +682,7 @@ params = dict( tools_functionally_correct=False, test_install_error=True, do_not_test=False ) - # TODO: do something usefule with response_dict + # TODO: do something useful with response_dict response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) try: if deactivate: @@ -736,7 +740,7 @@ params = dict( tools_functionally_correct=False, do_not_test=False, test_install_error=False ) - # TODO: do something usefule with response_dict + # TODO: do something useful with response_dict response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, @@ -1066,13 +1070,14 @@ exclude_count += 1 exclude_dict[ 'repositories' ].append( repository_tuple ) exclude_list.append( exclude_dict ) - log.debug( '%s repositories will be excluded from testing...' % str( exclude_count ) ) - if '-list_repositories' in sys.argv: - for name, owner, changeset_revision in exclude_verbose: - if changeset_revision: - log.debug( 'Repository %s owned by %s, changeset revision %s.' % ( str( name ), str( owner ), str( changeset_revision ) ) ) - else: - log.debug( 'Repository %s owned by %s, all revisions.' % ( str( name ), str( owner ) ) ) + log.debug( 'The xml document %s containing the exclude list defines the following %s repositories to be excluded from testing...' % \ + ( str( xml_filename ), str( exclude_count ) ) ) + #if '-list_repositories' in sys.argv: + for name, owner, changeset_revision in exclude_verbose: + if changeset_revision: + log.debug( 'Repository %s owned by %s, changeset revision %s.' % ( str( name ), str( owner ), str( changeset_revision ) ) ) + else: + log.debug( 'Repository %s owned by %s, all revisions.' % ( str( name ), str( owner ) ) ) return exclude_list def register_test_result( url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ): @@ -1202,17 +1207,18 @@ params = dict( tools_functionally_correct=True, do_not_test=False, test_install_error=False ) - # TODO: do something usefule with response_dict + # TODO: do something useful with response_dict response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) log.debug( 'Revision %s of repository %s installed and passed functional tests.' % ( str( changeset_revision ), str( name ) ) ) else: - tool_test_results_dict[ 'failed_tests' ].append( extract_log_data( result, from_tool_test=True ) ) + # The extract_log_data() netod returns a list. + tool_test_results_dict[ 'failed_tests' ] = extract_log_data( result, from_tool_test=True ) results_dict[ 'repositories_failed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) set_do_not_test = not is_latest_downloadable_revision( galaxy_tool_shed_url, repository_dict ) params = dict( tools_functionally_correct=False, test_install_error=False, do_not_test=str( set_do_not_test ) ) - # TODO: do something usefule with response_dict + # TODO: do something useful with response_dict response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) log.debug( 'Revision %s of repository %s installed successfully but did not pass functional tests.' % \ ( str( changeset_revision ), str( name ) ) ) diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -280,8 +280,6 @@ <section id="peak_calling" name="NGS: Peak Calling"><tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /> - <tool file="genetrack/genetrack_indexer.xml" /> - <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section id="ngs-rna-tools" name="NGS: RNA Analysis"><label id="rna_seq" text="RNA-seq" /> diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -340,8 +340,6 @@ <tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /><tool file="peak_calling/ccat_wrapper.xml" /> - <tool file="genetrack/genetrack_indexer.xml" /> - <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section id="ngs-simulation" name="NGS: Simulation"><tool file="ngs_simulation/ngs_simulation.xml" /> diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 tools/genetrack/genetrack_indexer.py --- a/tools/genetrack/genetrack_indexer.py +++ /dev/null @@ -1,42 +0,0 @@ -#!/usr/bin/env python - -""" -Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy. - -usage: %prog input output shift -""" - -import sys, shutil, os -from galaxy import eggs -import pkg_resources -pkg_resources.require( "GeneTrack" ) - -from genetrack.scripts import tabs2genetrack -from genetrack import logger - -if __name__ == "__main__": - import os - os.environ[ 'LC_ALL' ] = 'C' - #os.system( 'export' ) - - parser = tabs2genetrack.option_parser() - - options, args = parser.parse_args() - - # uppercase the format - options.format = options.format.upper() - - if options.format not in ('BED', 'GFF'): - sys.stdout = sys.stderr - parser.print_help() - sys.exit(-1) - - logger.disable(options.verbosity) - - # missing file names - if not (options.inpname and options.outname and options.format): - parser.print_help() - sys.exit(-1) - else: - tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\ - format=options.format, shift=options.shift, index=options.index, options=options) diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 tools/genetrack/genetrack_indexer.xml --- a/tools/genetrack/genetrack_indexer.xml +++ /dev/null @@ -1,64 +0,0 @@ -<tool id="bed2genetrack" name="GeneTrack indexer" version="1.0.1"> - - <description>on a BED file</description> - - <command interpreter="python"> - genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x - </command> - - <inputs> - - <param format="bed6" name="input" type="data" help="Input data"> - <label>Select input bed file</label> - </param> - - <param name="shift" size="4" type="integer" value="0" help="distance in basepairs"> - <label>Shift at 5' end</label> - </param> - -  - - </inputs> - - <outputs> - <data format="genetrack" name="output" /> - </outputs> - -<help> -**Help** - -This tool will create a visualization of the bed file that is selected. - -**Parameters** - -- **Shift at 5' end** should be used when the location of interest is at a fixed distance from - the 5' end for **all sequenced fragments**! - - For example if the sequenced sample consists - mono-nucleosomal DNA (146bp) we should expect that - each nucleosome midpoint is located at 73 bp from the 5' end of the fragment. - Therefore we would enter 73 as the shift parameter. Once corrected the reads - on each strand will coincide and indicate the actual midpoints - of the nucleosomes. - - When shifting the averaging process in GeneTrack is able correct for longer or shorter - than expected fragment sizes as long as the errors are reasonably random. - -See http://genetrack.bx.psu.edu/ for more information on GeneTrack. - ------- - -**Citation** - -For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_ - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - -</help> - -</tool> diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 tools/genetrack/genetrack_peak_prediction.py --- a/tools/genetrack/genetrack_peak_prediction.py +++ /dev/null @@ -1,40 +0,0 @@ -#!/usr/bin/env python - -""" -Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy. - -usage: %prog input output level sigma mode exclusion strand -""" - -import sys -from galaxy import eggs -import pkg_resources -pkg_resources.require( "GeneTrack" ) - -from genetrack.scripts import peakpred -from genetrack import logger - -if __name__ == "__main__": - - parser = peakpred.option_parser() - - options, args = parser.parse_args() - - logger.disable(options.verbosity) - - from genetrack import conf - - # trigger test mode - if options.test: - options.inpname = conf.testdata('test-hdflib-input.gtrack') - options.outname = conf.testdata('predictions.bed') - - # missing input file name - if not options.inpname and not options.outname: - parser.print_help() - else: - print 'Sigma = %s' % options.sigma - print 'Minimum peak = %s' % options.level - print 'Peak-to-peak = %s' % options.exclude - - peakpred.predict(options.inpname, options.outname, options) diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 tools/genetrack/genetrack_peak_prediction.xml --- a/tools/genetrack/genetrack_peak_prediction.xml +++ /dev/null @@ -1,69 +0,0 @@ -<tool id="predict2genetrack" name="Peak predictor"> - - <description>on GeneTrack index</description> - - <command interpreter="python"> - genetrack_peak_prediction.py -i $input -o $output --level=$level --sigma=$sigma --mode=$mode --exclusion=$exclusion --strand=$strand -v 0 -x - </command> - - <inputs> - - <param format="genetrack" name="input" type="data" help="Input data" label="Select input data"/> - - <param name="method" type="select" label="Smoothing method" help="The function used to average nearby read values"> - <option value="gauss">Gaussian kernel</option> -  - </param> - - <param name="sigma" size="4" type="integer" value="10" label="Smoothing factor" help="The interval over which each read is averaged" /> - - - <param name="mode" type="select" label="Peak prediction" help="Peak prediction method"> - <option value="nolap">Maximal non-overlapping</option> -  - <option value="all">All peaks</option> - </param> - - <param name="exclusion" type="integer" size="4" value="0" help="The minimal distance between peaks" label="Peak-to-peak distance"> - </param> - - <param name="level" size="4" type="float" value="1" label="Threshold" help="Return only peaks above this value" /> - - <param name="strand" type="select" label="Strands" help="Combine strand data or predict on each strand separately"> - <option value="all">Merge strands</option> -  - <option value="two">Separate strands</option> - </param> - - </inputs> - - <outputs> - <data format="bed" name="output" /> - </outputs> - -<help> -**Help** - -This tool will generate genome wide peak prediction from an index file. - -**Parameters** - -- **Smoothing method** the function used to average nearby values - -- **Smoothing value** the factor used in the method - -- **Prediction method** the function used to average nearby values - -See http://genetrack.bx.psu.edu/ for more information on GeneTrack. - ------- - -**Citation** - -For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_ - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - -</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.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 30 Nov '13

30 Nov '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/63006e23bf7d/ Changeset: 63006e23bf7d Branch: stable User: natefoo Date: 2013-11-30 18:46:53 Summary: Remove broken GeneTrack tools. Affected #: 6 files diff -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 -r 63006e23bf7d32e18033e0e59c0c194259935f6d tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -284,8 +284,6 @@ <section id="peak_calling" name="NGS: Peak Calling"><tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /> - <tool file="genetrack/genetrack_indexer.xml" /> - <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section id="ngs-rna-tools" name="NGS: RNA Analysis"><label id="rna_seq" text="RNA-seq" /> diff -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 -r 63006e23bf7d32e18033e0e59c0c194259935f6d tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -345,8 +345,6 @@ <tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /><tool file="peak_calling/ccat_wrapper.xml" /> - <tool file="genetrack/genetrack_indexer.xml" /> - <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section id="ngs-simulation" name="NGS: Simulation"><tool file="ngs_simulation/ngs_simulation.xml" /> diff -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 -r 63006e23bf7d32e18033e0e59c0c194259935f6d tools/genetrack/genetrack_indexer.py --- a/tools/genetrack/genetrack_indexer.py +++ /dev/null @@ -1,42 +0,0 @@ -#!/usr/bin/env python - -""" -Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy. - -usage: %prog input output shift -""" - -import sys, shutil, os -from galaxy import eggs -import pkg_resources -pkg_resources.require( "GeneTrack" ) - -from genetrack.scripts import tabs2genetrack -from genetrack import logger - -if __name__ == "__main__": - import os - os.environ[ 'LC_ALL' ] = 'C' - #os.system( 'export' ) - - parser = tabs2genetrack.option_parser() - - options, args = parser.parse_args() - - # uppercase the format - options.format = options.format.upper() - - if options.format not in ('BED', 'GFF'): - sys.stdout = sys.stderr - parser.print_help() - sys.exit(-1) - - logger.disable(options.verbosity) - - # missing file names - if not (options.inpname and options.outname and options.format): - parser.print_help() - sys.exit(-1) - else: - tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\ - format=options.format, shift=options.shift, index=options.index, options=options) diff -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 -r 63006e23bf7d32e18033e0e59c0c194259935f6d tools/genetrack/genetrack_indexer.xml --- a/tools/genetrack/genetrack_indexer.xml +++ /dev/null @@ -1,64 +0,0 @@ -<tool id="bed2genetrack" name="GeneTrack indexer" version="1.0.1"> - - <description>on a BED file</description> - - <command interpreter="python"> - genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x - </command> - - <inputs> - - <param format="bed6" name="input" type="data" help="Input data"> - <label>Select input bed file</label> - </param> - - <param name="shift" size="4" type="integer" value="0" help="distance in basepairs"> - <label>Shift at 5' end</label> - </param> - -  - - </inputs> - - <outputs> - <data format="genetrack" name="output" /> - </outputs> - -<help> -**Help** - -This tool will create a visualization of the bed file that is selected. - -**Parameters** - -- **Shift at 5' end** should be used when the location of interest is at a fixed distance from - the 5' end for **all sequenced fragments**! - - For example if the sequenced sample consists - mono-nucleosomal DNA (146bp) we should expect that - each nucleosome midpoint is located at 73 bp from the 5' end of the fragment. - Therefore we would enter 73 as the shift parameter. Once corrected the reads - on each strand will coincide and indicate the actual midpoints - of the nucleosomes. - - When shifting the averaging process in GeneTrack is able correct for longer or shorter - than expected fragment sizes as long as the errors are reasonably random. - -See http://genetrack.bx.psu.edu/ for more information on GeneTrack. - ------- - -**Citation** - -For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_ - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - -</help> - -</tool> diff -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 -r 63006e23bf7d32e18033e0e59c0c194259935f6d tools/genetrack/genetrack_peak_prediction.py --- a/tools/genetrack/genetrack_peak_prediction.py +++ /dev/null @@ -1,40 +0,0 @@ -#!/usr/bin/env python - -""" -Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy. - -usage: %prog input output level sigma mode exclusion strand -""" - -import sys -from galaxy import eggs -import pkg_resources -pkg_resources.require( "GeneTrack" ) - -from genetrack.scripts import peakpred -from genetrack import logger - -if __name__ == "__main__": - - parser = peakpred.option_parser() - - options, args = parser.parse_args() - - logger.disable(options.verbosity) - - from genetrack import conf - - # trigger test mode - if options.test: - options.inpname = conf.testdata('test-hdflib-input.gtrack') - options.outname = conf.testdata('predictions.bed') - - # missing input file name - if not options.inpname and not options.outname: - parser.print_help() - else: - print 'Sigma = %s' % options.sigma - print 'Minimum peak = %s' % options.level - print 'Peak-to-peak = %s' % options.exclude - - peakpred.predict(options.inpname, options.outname, options) diff -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 -r 63006e23bf7d32e18033e0e59c0c194259935f6d tools/genetrack/genetrack_peak_prediction.xml --- a/tools/genetrack/genetrack_peak_prediction.xml +++ /dev/null @@ -1,69 +0,0 @@ -<tool id="predict2genetrack" name="Peak predictor"> - - <description>on GeneTrack index</description> - - <command interpreter="python"> - genetrack_peak_prediction.py -i $input -o $output --level=$level --sigma=$sigma --mode=$mode --exclusion=$exclusion --strand=$strand -v 0 -x - </command> - - <inputs> - - <param format="genetrack" name="input" type="data" help="Input data" label="Select input data"/> - - <param name="method" type="select" label="Smoothing method" help="The function used to average nearby read values"> - <option value="gauss">Gaussian kernel</option> -  - </param> - - <param name="sigma" size="4" type="integer" value="10" label="Smoothing factor" help="The interval over which each read is averaged" /> - - - <param name="mode" type="select" label="Peak prediction" help="Peak prediction method"> - <option value="nolap">Maximal non-overlapping</option> -  - <option value="all">All peaks</option> - </param> - - <param name="exclusion" type="integer" size="4" value="0" help="The minimal distance between peaks" label="Peak-to-peak distance"> - </param> - - <param name="level" size="4" type="float" value="1" label="Threshold" help="Return only peaks above this value" /> - - <param name="strand" type="select" label="Strands" help="Combine strand data or predict on each strand separately"> - <option value="all">Merge strands</option> -  - <option value="two">Separate strands</option> - </param> - - </inputs> - - <outputs> - <data format="bed" name="output" /> - </outputs> - -<help> -**Help** - -This tool will generate genome wide peak prediction from an index file. - -**Parameters** - -- **Smoothing method** the function used to average nearby values - -- **Smoothing value** the factor used in the method - -- **Prediction method** the function used to average nearby values - -See http://genetrack.bx.psu.edu/ for more information on GeneTrack. - ------- - -**Citation** - -For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_ - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - -</help> - -</tool> https://bitbucket.org/galaxy/galaxy-central/commits/a508799de645/ Changeset: a508799de645 User: natefoo Date: 2013-11-30 18:47:19 Summary: merge stable. Affected #: 6 files diff -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 -r a508799de64595113ad4d26b8f2f9df7b64f1f69 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -280,8 +280,6 @@ <section id="peak_calling" name="NGS: Peak Calling"><tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /> - <tool file="genetrack/genetrack_indexer.xml" /> - <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section id="ngs-rna-tools" name="NGS: RNA Analysis"><label id="rna_seq" text="RNA-seq" /> diff -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 -r a508799de64595113ad4d26b8f2f9df7b64f1f69 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -340,8 +340,6 @@ <tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /><tool file="peak_calling/ccat_wrapper.xml" /> - <tool file="genetrack/genetrack_indexer.xml" /> - <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section id="ngs-simulation" name="NGS: Simulation"><tool file="ngs_simulation/ngs_simulation.xml" /> diff -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 -r a508799de64595113ad4d26b8f2f9df7b64f1f69 tools/genetrack/genetrack_indexer.py --- a/tools/genetrack/genetrack_indexer.py +++ /dev/null @@ -1,42 +0,0 @@ -#!/usr/bin/env python - -""" -Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy. - -usage: %prog input output shift -""" - -import sys, shutil, os -from galaxy import eggs -import pkg_resources -pkg_resources.require( "GeneTrack" ) - -from genetrack.scripts import tabs2genetrack -from genetrack import logger - -if __name__ == "__main__": - import os - os.environ[ 'LC_ALL' ] = 'C' - #os.system( 'export' ) - - parser = tabs2genetrack.option_parser() - - options, args = parser.parse_args() - - # uppercase the format - options.format = options.format.upper() - - if options.format not in ('BED', 'GFF'): - sys.stdout = sys.stderr - parser.print_help() - sys.exit(-1) - - logger.disable(options.verbosity) - - # missing file names - if not (options.inpname and options.outname and options.format): - parser.print_help() - sys.exit(-1) - else: - tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\ - format=options.format, shift=options.shift, index=options.index, options=options) diff -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 -r a508799de64595113ad4d26b8f2f9df7b64f1f69 tools/genetrack/genetrack_indexer.xml --- a/tools/genetrack/genetrack_indexer.xml +++ /dev/null @@ -1,64 +0,0 @@ -<tool id="bed2genetrack" name="GeneTrack indexer" version="1.0.1"> - - <description>on a BED file</description> - - <command interpreter="python"> - genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x - </command> - - <inputs> - - <param format="bed6" name="input" type="data" help="Input data"> - <label>Select input bed file</label> - </param> - - <param name="shift" size="4" type="integer" value="0" help="distance in basepairs"> - <label>Shift at 5' end</label> - </param> - -  - - </inputs> - - <outputs> - <data format="genetrack" name="output" /> - </outputs> - -<help> -**Help** - -This tool will create a visualization of the bed file that is selected. - -**Parameters** - -- **Shift at 5' end** should be used when the location of interest is at a fixed distance from - the 5' end for **all sequenced fragments**! - - For example if the sequenced sample consists - mono-nucleosomal DNA (146bp) we should expect that - each nucleosome midpoint is located at 73 bp from the 5' end of the fragment. - Therefore we would enter 73 as the shift parameter. Once corrected the reads - on each strand will coincide and indicate the actual midpoints - of the nucleosomes. - - When shifting the averaging process in GeneTrack is able correct for longer or shorter - than expected fragment sizes as long as the errors are reasonably random. - -See http://genetrack.bx.psu.edu/ for more information on GeneTrack. - ------- - -**Citation** - -For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_ - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - -</help> - -</tool> diff -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 -r a508799de64595113ad4d26b8f2f9df7b64f1f69 tools/genetrack/genetrack_peak_prediction.py --- a/tools/genetrack/genetrack_peak_prediction.py +++ /dev/null @@ -1,40 +0,0 @@ -#!/usr/bin/env python - -""" -Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy. - -usage: %prog input output level sigma mode exclusion strand -""" - -import sys -from galaxy import eggs -import pkg_resources -pkg_resources.require( "GeneTrack" ) - -from genetrack.scripts import peakpred -from genetrack import logger - -if __name__ == "__main__": - - parser = peakpred.option_parser() - - options, args = parser.parse_args() - - logger.disable(options.verbosity) - - from genetrack import conf - - # trigger test mode - if options.test: - options.inpname = conf.testdata('test-hdflib-input.gtrack') - options.outname = conf.testdata('predictions.bed') - - # missing input file name - if not options.inpname and not options.outname: - parser.print_help() - else: - print 'Sigma = %s' % options.sigma - print 'Minimum peak = %s' % options.level - print 'Peak-to-peak = %s' % options.exclude - - peakpred.predict(options.inpname, options.outname, options) diff -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 -r a508799de64595113ad4d26b8f2f9df7b64f1f69 tools/genetrack/genetrack_peak_prediction.xml --- a/tools/genetrack/genetrack_peak_prediction.xml +++ /dev/null @@ -1,69 +0,0 @@ -<tool id="predict2genetrack" name="Peak predictor"> - - <description>on GeneTrack index</description> - - <command interpreter="python"> - genetrack_peak_prediction.py -i $input -o $output --level=$level --sigma=$sigma --mode=$mode --exclusion=$exclusion --strand=$strand -v 0 -x - </command> - - <inputs> - - <param format="genetrack" name="input" type="data" help="Input data" label="Select input data"/> - - <param name="method" type="select" label="Smoothing method" help="The function used to average nearby read values"> - <option value="gauss">Gaussian kernel</option> -  - </param> - - <param name="sigma" size="4" type="integer" value="10" label="Smoothing factor" help="The interval over which each read is averaged" /> - - - <param name="mode" type="select" label="Peak prediction" help="Peak prediction method"> - <option value="nolap">Maximal non-overlapping</option> -  - <option value="all">All peaks</option> - </param> - - <param name="exclusion" type="integer" size="4" value="0" help="The minimal distance between peaks" label="Peak-to-peak distance"> - </param> - - <param name="level" size="4" type="float" value="1" label="Threshold" help="Return only peaks above this value" /> - - <param name="strand" type="select" label="Strands" help="Combine strand data or predict on each strand separately"> - <option value="all">Merge strands</option> -  - <option value="two">Separate strands</option> - </param> - - </inputs> - - <outputs> - <data format="bed" name="output" /> - </outputs> - -<help> -**Help** - -This tool will generate genome wide peak prediction from an index file. - -**Parameters** - -- **Smoothing method** the function used to average nearby values - -- **Smoothing value** the factor used in the method - -- **Prediction method** the function used to average nearby values - -See http://genetrack.bx.psu.edu/ for more information on GeneTrack. - ------- - -**Citation** - -For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_ - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - -</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: 2 new changesets
by commits-noreply＠bitbucket.org 30 Nov '13

30 Nov '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3b6cdcd97595/ Changeset: 3b6cdcd97595 Branch: stable User: jmchilton Date: 2013-11-30 15:28:38 Summary: Fix from Jim Johnson for optional input handling in provenance API. Affected #: 1 file diff -r 51b4282dce3a411d02b982d1cca137884d5f6c2b -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 lib/galaxy/webapps/galaxy/api/provenance.py --- a/lib/galaxy/webapps/galaxy/api/provenance.py +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -54,6 +54,8 @@ for p in job.parameters: out[p.name] = p.value for in_d in job.input_datasets: + if not in_d.dataset: + continue if follow: out[in_d.name] = self._get_record(trans, in_d.dataset, follow) else: https://bitbucket.org/galaxy/galaxy-central/commits/2b5329b6fba3/ Changeset: 2b5329b6fba3 User: jmchilton Date: 2013-11-30 15:29:06 Summary: Merge latest stable. Affected #: 1 file diff -r 228156daa575892f92d81c30a7e0f0ec4fa6b960 -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 lib/galaxy/webapps/galaxy/api/provenance.py --- a/lib/galaxy/webapps/galaxy/api/provenance.py +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -58,6 +58,8 @@ for p in job.parameters: out[p.name] = p.value for in_d in job.input_datasets: + if not in_d.dataset: + continue if follow: out[in_d.name] = self._get_record(trans, in_d.dataset, follow) else: 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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