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.
"""
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 )
rd_tup = [ tsr.tool_shed, tsr.name, tsr.owner, tsr.changeset_revision, prior_installation_required, tsr.id, tsr.status ]
if tsr.status == trans.model.ToolShedRepository.installation_status.INSTALLED:
installed_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
# dictionary 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 )
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
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
