def get_repository_dependency_as_key(self, repository_dependency):
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple(repository_dependency)
return container_util.generate_repository_dependencies_key_for_repository(tool_shed,
name,
owner,
changeset_revision,
prior_installation_required,
only_if_compiling_contained_td)
def get_repository_dependency_as_key( self, repository_dependency ):
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple( repository_dependency )
return container_util.generate_repository_dependencies_key_for_repository( tool_shed,
name,
owner,
changeset_revision,
prior_installation_required,
only_if_compiling_contained_td )
def is_subfolder_of(self, folder, repository_dependency):
toolshed, repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple( repository_dependency )
key = container_util.generate_repository_dependencies_key_for_repository(
toolshed, repository_name, repository_owner, changeset_revision,
prior_installation_required, only_if_compiling_contained_td)
for sub_folder in folder.folders:
if key == sub_folder.key:
return True
return False
def build_invalid_repository_dependencies_root_folder(
self, folder_id, invalid_repository_dependencies_dict):
"""Return a folder hierarchy containing invalid repository dependencies."""
label = 'Invalid repository dependencies'
if invalid_repository_dependencies_dict:
invalid_repository_dependency_id = 0
folder_id += 1
invalid_repository_dependencies_root_folder = \
utility_container_manager.Folder( id=folder_id,
key='root',
label='root',
parent=None )
folder_id += 1
invalid_repository_dependencies_folder = \
utility_container_manager.Folder( id=folder_id,
key='invalid_repository_dependencies',
label=label,
parent=invalid_repository_dependencies_root_folder )
invalid_repository_dependencies_root_folder.folders.append(
invalid_repository_dependencies_folder)
invalid_repository_dependencies = invalid_repository_dependencies_dict[
'repository_dependencies']
for invalid_repository_dependency in invalid_repository_dependencies:
folder_id += 1
invalid_repository_dependency_id += 1
toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error = \
common_util.parse_repository_dependency_tuple( invalid_repository_dependency, contains_error=True )
key = container_util.generate_repository_dependencies_key_for_repository(
toolshed, name, owner, changeset_revision,
prior_installation_required,
only_if_compiling_contained_td)
label = "Repository <b>%s</b> revision <b>%s</b> owned by <b>%s</b>" % (
name, changeset_revision, owner)
folder = utility_container_manager.Folder(
id=folder_id,
key=key,
label=label,
parent=invalid_repository_dependencies_folder)
ird = InvalidRepositoryDependency(
id=invalid_repository_dependency_id,
toolshed=toolshed,
repository_name=name,
repository_owner=owner,
changeset_revision=changeset_revision,
prior_installation_required=util.asbool(
prior_installation_required),
only_if_compiling_contained_td=util.asbool(
only_if_compiling_contained_td),
error=error)
folder.invalid_repository_dependencies.append(ird)
invalid_repository_dependencies_folder.folders.append(folder)
else:
invalid_repository_dependencies_root_folder = None
return folder_id, invalid_repository_dependencies_root_folder
def get_key_for_repository_changeset_revision(self):
# The received toolshed_base_url must include the port, but doesn't have to include the protocol.
prior_installation_required, only_if_compiling_contained_td = \
self.get_prior_installation_required_and_only_if_compiling_contained_td()
# Create a key with the value of prior_installation_required defaulted to False.
key = container_util.generate_repository_dependencies_key_for_repository(
self.tool_shed_url, self.repository.name,
self.repository.user.username,
self.repository_metadata.changeset_revision,
prior_installation_required, only_if_compiling_contained_td)
return key
def get_key_for_repository_changeset_revision( self ):
# The received toolshed_base_url must include the port, but doesn't have to include the protocol.
prior_installation_required, only_if_compiling_contained_td = \
self.get_prior_installation_required_and_only_if_compiling_contained_td()
# Create a key with the value of prior_installation_required defaulted to False.
key = container_util.generate_repository_dependencies_key_for_repository( self.tool_shed_url,
self.repository.name,
self.repository.user.username,
self.repository_metadata.changeset_revision,
prior_installation_required,
only_if_compiling_contained_td )
return key
def is_subfolder_of( self, folder, repository_dependency ):
toolshed, repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple( repository_dependency )
key = container_util.generate_repository_dependencies_key_for_repository( toolshed,
repository_name,
repository_owner,
changeset_revision,
prior_installation_required,
only_if_compiling_contained_td )
for sub_folder in folder.folders:
if key == sub_folder.key:
return True
return False
def build_invalid_repository_dependencies_root_folder( self, folder_id, invalid_repository_dependencies_dict ):
"""Return a folder hierarchy containing invalid repository dependencies."""
label = 'Invalid repository dependencies'
if invalid_repository_dependencies_dict:
invalid_repository_dependency_id = 0
folder_id += 1
invalid_repository_dependencies_root_folder = \
utility_container_manager.Folder( id=folder_id,
key='root',
label='root',
parent=None )
folder_id += 1
invalid_repository_dependencies_folder = \
utility_container_manager.Folder( id=folder_id,
key='invalid_repository_dependencies',
label=label,
parent=invalid_repository_dependencies_root_folder )
invalid_repository_dependencies_root_folder.folders.append( invalid_repository_dependencies_folder )
invalid_repository_dependencies = invalid_repository_dependencies_dict[ 'repository_dependencies' ]
for invalid_repository_dependency in invalid_repository_dependencies:
folder_id += 1
invalid_repository_dependency_id += 1
toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error = \
common_util.parse_repository_dependency_tuple( invalid_repository_dependency, contains_error=True )
key = container_util.generate_repository_dependencies_key_for_repository( toolshed,
name,
owner,
changeset_revision,
prior_installation_required,
only_if_compiling_contained_td )
label = "Repository <b>%s</b> revision <b>%s</b> owned by <b>%s</b>" % ( name, changeset_revision, owner )
folder = utility_container_manager.Folder( id=folder_id,
key=key,
label=label,
parent=invalid_repository_dependencies_folder )
ird = InvalidRepositoryDependency( id=invalid_repository_dependency_id,
toolshed=toolshed,
repository_name=name,
repository_owner=owner,
changeset_revision=changeset_revision,
prior_installation_required=util.asbool( prior_installation_required ),
only_if_compiling_contained_td=util.asbool( only_if_compiling_contained_td ),
error=error )
folder.invalid_repository_dependencies.append( ird )
invalid_repository_dependencies_folder.folders.append( folder )
else:
invalid_repository_dependencies_root_folder = None
return folder_id, invalid_repository_dependencies_root_folder
def get_installed_and_missing_repository_dependencies( trans, repository ):
"""
Return the installed and missing repository dependencies for a tool shed repository that has a record in the Galaxy database, but
may or may not be installed. In this case, the repository dependencies are associated with the repository in the database. Do not
include a repository dependency if it is required only to compile a tool dependency defined for the dependent repository since these
special kinds of repository dependencies are really a dependency of the dependent repository's contained tool dependency, and only if
that tool dependency requires compilation.
"""
missing_repository_dependencies = {}
installed_repository_dependencies = {}
has_repository_dependencies = repository.has_repository_dependencies
if has_repository_dependencies:
# The repository dependencies container will include only the immediate repository dependencies of this repository, so the container
# will be only a single level in depth.
metadata = repository.metadata
installed_rd_tups = []
missing_rd_tups = []
for tsr in repository.repository_dependencies:
prior_installation_required = suc.set_prior_installation_required( repository, tsr )
only_if_compiling_contained_td = suc.set_only_if_compiling_contained_td( repository, tsr )
rd_tup = [ tsr.tool_shed,
tsr.name,
tsr.owner,
tsr.changeset_revision,
prior_installation_required,
only_if_compiling_contained_td,
tsr.id,
tsr.status ]
if tsr.status == trans.install_model.ToolShedRepository.installation_status.INSTALLED:
installed_rd_tups.append( rd_tup )
else:
# We'll only add the rd_tup to the missing_rd_tups list if the received repository has tool dependencies that are not
# correctly installed. This may prove to be a weak check since the repository in question may not have anything to do
# with compiling the missing tool dependencies. If we discover that this is a problem, more granular checking will be
# necessary here.
if repository.missing_tool_dependencies:
if not repository_dependency_needed_only_for_compiling_tool_dependency( repository, tsr ):
missing_rd_tups.append( rd_tup )
else:
missing_rd_tups.append( rd_tup )
if installed_rd_tups or missing_rd_tups:
# Get the description from the metadata in case it has a value.
repository_dependencies = metadata.get( 'repository_dependencies', {} )
description = repository_dependencies.get( 'description', None )
# We need to add a root_key entry to one or both of installed_repository_dependencies dictionary and the
# missing_repository_dependencies dictionaries for proper display parsing.
root_key = container_util.generate_repository_dependencies_key_for_repository( repository.tool_shed,
repository.name,
repository.owner,
repository.installed_changeset_revision,
prior_installation_required,
only_if_compiling_contained_td )
if installed_rd_tups:
installed_repository_dependencies[ 'root_key' ] = root_key
installed_repository_dependencies[ root_key ] = installed_rd_tups
installed_repository_dependencies[ 'description' ] = description
if missing_rd_tups:
missing_repository_dependencies[ 'root_key' ] = root_key
missing_repository_dependencies[ root_key ] = missing_rd_tups
missing_repository_dependencies[ 'description' ] = description
return installed_repository_dependencies, missing_repository_dependencies
