def handle_complex_repository_dependency_for_package(
self,
elem,
package_name,
package_version,
tool_shed_repository,
from_tool_migration_manager=False):
"""
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_url = elem.attrib['toolshed']
required_repository_name = elem.attrib['name']
required_repository_owner = elem.attrib['owner']
default_required_repository_changeset_revision = elem.attrib[
'changeset_revision']
required_repository = suc.get_repository_for_dependency_relationship(
self.app, tool_shed_url, required_repository_name,
required_repository_owner,
default_required_repository_changeset_revision)
tool_shed = common_util.remove_protocol_from_tool_shed_url(
tool_shed_url)
tmp_filename = None
if required_repository:
required_repository_changeset_revision = required_repository.installed_changeset_revision
# Define the installation directory for the required tool dependency package in the required repository.
required_repository_package_install_dir = \
tool_dependency_util.get_tool_dependency_install_dir( app=self.app,
repository_name=required_repository_name,
repository_owner=required_repository_owner,
repository_changeset_revision=required_repository_changeset_revision,
tool_dependency_type='package',
tool_dependency_name=package_name,
tool_dependency_version=package_version )
# 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=self.app,
repository_name=tool_shed_repository.name,
repository_owner=tool_shed_repository.owner,
repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
tool_dependency_type='package',
tool_dependency_name=package_name,
tool_dependency_version=package_version )
if os.path.exists(dependent_install_dir):
# The install manager handles tool migration stages and the sync_database_with_file_system()
# method handles two scenarios: (1) where a Galaxy file system environment related to installed
# Tool Shed repositories and tool dependencies has somehow gotten out of sync with the Galaxy
# database tables associated with these installed items, and (2) the Tool Shed's install and test
# framework which installs repositories in 2 stages, those of type tool_dependency_definition
# followed by those containing valid tools and tool functional test components. Neither of these
# scenarios apply when the install manager is running.
if from_tool_migration_manager:
can_install_tool_dependency = True
else:
# Notice that we'll throw away the following tool_dependency if it can be installed.
tool_dependency, can_install_tool_dependency = self.sync_database_with_file_system(
self.app,
tool_shed_repository,
package_name,
package_version,
dependent_install_dir,
tool_dependency_type='package')
if not can_install_tool_dependency:
log.debug(
"Tool dependency %s version %s cannot be installed (it was probably previously installed), "
"so appending it to the list of handled tool dependencies.",
str(tool_dependency.name),
str(tool_dependency.version))
handled_tool_dependencies.append(tool_dependency)
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_deactivated_or_installed:
if not os.path.exists(
required_repository_package_install_dir):
log.error(
'Missing required tool dependency directory %s' %
str(required_repository_package_install_dir))
repo_files_dir = required_repository.repo_files_directory(
self.app)
if not repo_files_dir:
message = "Unable to locate the repository directory 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)
tool_dependencies_config = suc.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:
# 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 = suc.get_updated_changeset_revisions_from_tool_shed(
app=self.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 = self.create_temporary_tool_dependencies_config(
tool_shed, required_repository_name,
required_repository_owner,
required_repository_changeset_revision)
config_to_use = tmp_filename
handled_tool_dependencies = \
self.create_tool_dependency_with_initialized_env_sh_file( 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 )
self.remove_file(tmp_filename)
else:
message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \
( str( required_repository_name ), str( required_repository_owner ), str( default_required_repository_changeset_revision ) )
raise Exception(message)
return handled_tool_dependencies
def handle_complex_repository_dependency_for_package( self, elem, package_name, package_version, tool_shed_repository,
from_tool_migration_manager=False ):
"""
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_url = elem.attrib[ 'toolshed' ]
required_repository_name = elem.attrib[ 'name' ]
required_repository_owner = elem.attrib[ 'owner' ]
default_required_repository_changeset_revision = elem.attrib[ 'changeset_revision' ]
required_repository = suc.get_repository_for_dependency_relationship( self.app, tool_shed_url,
required_repository_name,
required_repository_owner,
default_required_repository_changeset_revision )
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url )
tmp_filename = None
if required_repository:
required_repository_changeset_revision = required_repository.installed_changeset_revision
# Define the installation directory for the required tool dependency package in the required repository.
required_repository_package_install_dir = \
tool_dependency_util.get_tool_dependency_install_dir( app=self.app,
repository_name=required_repository_name,
repository_owner=required_repository_owner,
repository_changeset_revision=required_repository_changeset_revision,
tool_dependency_type='package',
tool_dependency_name=package_name,
tool_dependency_version=package_version )
# 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=self.app,
repository_name=tool_shed_repository.name,
repository_owner=tool_shed_repository.owner,
repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
tool_dependency_type='package',
tool_dependency_name=package_name,
tool_dependency_version=package_version )
if os.path.exists( dependent_install_dir ):
# The install manager handles tool migration stages and the sync_database_with_file_system()
# method handles two scenarios: (1) where a Galaxy file system environment related to installed
# Tool Shed repositories and tool dependencies has somehow gotten out of sync with the Galaxy
# database tables associated with these installed items, and (2) the Tool Shed's install and test
# framework which installs repositories in 2 stages, those of type tool_dependency_definition
# followed by those containing valid tools and tool functional test components. Neither of these
# scenarios apply when the install manager is running.
if from_tool_migration_manager:
can_install_tool_dependency = True
else:
# Notice that we'll throw away the following tool_dependency if it can be installed.
tool_dependency, can_install_tool_dependency = self.sync_database_with_file_system( self.app,
tool_shed_repository,
package_name,
package_version,
dependent_install_dir,
tool_dependency_type='package' )
if not can_install_tool_dependency:
log.debug( "Tool dependency %s version %s cannot be installed (it was probably previously installed), " %
( str( tool_dependency.name, str( tool_dependency.version ) ) ) )
log.debug( "so appending it to the list of handled tool dependencies." )
handled_tool_dependencies.append( tool_dependency )
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_deactivated_or_installed:
if not os.path.exists( required_repository_package_install_dir ):
log.error( 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir ) )
repo_files_dir = required_repository.repo_files_directory( self.app )
if not repo_files_dir:
message = "Unable to locate the repository directory 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 )
tool_dependencies_config = suc.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:
# 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 = suc.get_updated_changeset_revisions_from_tool_shed( app=self.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 = self.create_temporary_tool_dependencies_config( tool_shed,
required_repository_name,
required_repository_owner,
required_repository_changeset_revision )
config_to_use = tmp_filename
handled_tool_dependencies = \
self.create_tool_dependency_with_initialized_env_sh_file( 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 )
self.remove_file( tmp_filename )
else:
message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \
( str( required_repository_name ), str( required_repository_owner ), str( default_required_repository_changeset_revision ) )
raise Exception( message )
return handled_tool_dependencies
