[galaxy-commits] 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

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/

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