def get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple ):
"""
Parse the received repository_dependencies dictionary that is associated with a repository being installed into Galaxy for the first time
and attempt to determine repository dependencies that are already installed and those that are not.
"""
missing_repository_dependencies = {}
installed_repository_dependencies = {}
missing_rd_tups = []
installed_rd_tups = []
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td = \
suc.get_repo_info_tuple_contents( repo_info_tuple )
if repository_dependencies:
description = repository_dependencies[ 'description' ]
root_key = repository_dependencies[ 'root_key' ]
# 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.
for key, rd_tups in repository_dependencies.items():
if key in [ 'description', 'root_key' ]:
continue
for rd_tup in rd_tups:
tool_shed, name, owner, changeset_revision, prior_installation_required = suc.parse_repository_dependency_tuple( rd_tup )
# Updates to installed repository revisions may have occurred, so make sure to locate the appropriate repository revision if one exists.
# We need to create a temporary repo_info_tuple that includes the correct repository owner which we get from the current rd_tup. The current
# tuple looks like: ( description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td )
tmp_clone_url = suc.generate_clone_url_from_repo_info_tup( rd_tup )
tmp_repo_info_tuple = ( None, tmp_clone_url, changeset_revision, None, owner, None, None )
repository, current_changeset_revision = suc.repository_was_previously_installed( trans, tool_shed, name, tmp_repo_info_tuple )
if repository:
new_rd_tup = [ tool_shed, name, owner, changeset_revision, str( prior_installation_required ), repository.id, repository.status ]
if repository.status == trans.model.ToolShedRepository.installation_status.INSTALLED:
if new_rd_tup not in installed_rd_tups:
installed_rd_tups.append( new_rd_tup )
else:
if new_rd_tup not in missing_rd_tups:
missing_rd_tups.append( new_rd_tup )
else:
new_rd_tup = [ tool_shed, name, owner, changeset_revision, str( prior_installation_required ), None, 'Never installed' ]
if new_rd_tup not in missing_rd_tups:
missing_rd_tups.append( new_rd_tup )
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_for_new_install( trans, repo_info_tuple ):
"""
Parse the received repository_dependencies dictionary that is associated with a repository being installed into Galaxy for the first time
and attempt to determine repository dependencies that are already installed and those that are not.
"""
missing_repository_dependencies = {}
installed_repository_dependencies = {}
missing_rd_tups = []
installed_rd_tups = []
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
suc.get_repo_info_tuple_contents( repo_info_tuple )
if repository_dependencies:
description = repository_dependencies[ 'description' ]
root_key = repository_dependencies[ 'root_key' ]
# 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.
for key, rd_tups in repository_dependencies.items():
if key in [ 'description', 'root_key' ]:
continue
for rd_tup in rd_tups:
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple( rd_tup )
# Updates to installed repository revisions may have occurred, so make sure to locate the appropriate repository revision if one exists.
# We need to create a temporary repo_info_tuple that includes the correct repository owner which we get from the current rd_tup. The current
# tuple looks like: ( description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td )
tmp_clone_url = suc.generate_clone_url_from_repo_info_tup( rd_tup )
tmp_repo_info_tuple = ( None, tmp_clone_url, changeset_revision, None, owner, None, None )
repository, installed_changeset_revision = suc.repository_was_previously_installed( trans, tool_shed, name, tmp_repo_info_tuple )
if repository:
new_rd_tup = [ tool_shed,
name,
owner,
changeset_revision,
prior_installation_required,
only_if_compiling_contained_td,
repository.id,
repository.status ]
if repository.status == trans.install_model.ToolShedRepository.installation_status.INSTALLED:
if new_rd_tup not in installed_rd_tups:
installed_rd_tups.append( new_rd_tup )
else:
# A repository dependency that is not installed will not be considered missing if it's value for only_if_compiling_contained_td is
# True This is because this type of repository dependency will only be considered at the time that the specified tool dependency
# is being installed, and even then only if the compiled binary of the tool dependency could not be installed due to the unsupported
# installation environment.
if not util.asbool( only_if_compiling_contained_td ):
if new_rd_tup not in missing_rd_tups:
missing_rd_tups.append( new_rd_tup )
else:
new_rd_tup = [ tool_shed,
name,
owner,
changeset_revision,
prior_installation_required,
only_if_compiling_contained_td,
None,
'Never installed' ]
if not util.asbool( only_if_compiling_contained_td ):
# A repository dependency that is not installed will not be considered missing if it's value for only_if_compiling_contained_td is
# True - see above...
if new_rd_tup not in missing_rd_tups:
missing_rd_tups.append( new_rd_tup )
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
