def handle_key_rd_dicts_for_repository(self, current_repository_key, repository_key_rd_dicts):
key_rd_dict = repository_key_rd_dicts.pop(0)
repository_dependency = key_rd_dict[current_repository_key]
toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple(repository_dependency)
if suc.tool_shed_is_this_tool_shed(toolshed):
required_repository = tool_shed.util.repository_util.get_repository_by_name_and_owner(self.app, name, owner)
self.repository = required_repository
repository_id = self.app.security.encode_id(required_repository.id)
required_repository_metadata = \
metadata_util.get_repository_metadata_by_repository_id_changeset_revision(self.app,
repository_id,
changeset_revision)
self.repository_metadata = required_repository_metadata
if required_repository_metadata:
# The required_repository_metadata changeset_revision is installable.
required_metadata = required_repository_metadata.metadata
if required_metadata:
for current_repository_key_rd_dict in repository_key_rd_dicts:
if not self.in_key_rd_dicts(current_repository_key_rd_dict, self.key_rd_dicts_to_be_processed):
# Add the current repository_dependency into self.key_rd_dicts_to_be_processed.
self.key_rd_dicts_to_be_processed.append(current_repository_key_rd_dict)
if not self.in_key_rd_dicts(key_rd_dict, self.handled_key_rd_dicts):
# Add the current repository_dependency into self.handled_key_rd_dicts.
self.handled_key_rd_dicts.append(key_rd_dict)
if self.in_key_rd_dicts(key_rd_dict, self.key_rd_dicts_to_be_processed):
# Remove the current repository from self.key_rd_dicts_to_be_processed.
self.key_rd_dicts_to_be_processed = self.remove_from_key_rd_dicts(key_rd_dict, self.key_rd_dicts_to_be_processed)
else:
# The repository is in a different tool shed, so build an url and send a request.
error_message = "Repository dependencies are currently supported only within the same Tool Shed. "
error_message += "Ignoring repository dependency definition for tool shed "
error_message += "{}, name {}, owner {}, changeset revision {}".format(toolshed, name, owner, changeset_revision)
log.debug(error_message)
def handle_key_rd_dicts_for_repository( self, current_repository_key, repository_key_rd_dicts ):
key_rd_dict = repository_key_rd_dicts.pop( 0 )
repository_dependency = key_rd_dict[ current_repository_key ]
toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple( repository_dependency )
if suc.tool_shed_is_this_tool_shed( toolshed ):
required_repository = tool_shed.util.repository_util.get_repository_by_name_and_owner( self.app, name, owner )
self.repository = required_repository
repository_id = self.app.security.encode_id( required_repository.id )
required_repository_metadata = \
metadata_util.get_repository_metadata_by_repository_id_changeset_revision( self.app,
repository_id,
changeset_revision )
self.repository_metadata = required_repository_metadata
if required_repository_metadata:
# The required_repository_metadata changeset_revision is installable.
required_metadata = required_repository_metadata.metadata
if required_metadata:
for current_repository_key_rd_dict in repository_key_rd_dicts:
if not self.in_key_rd_dicts( current_repository_key_rd_dict, self.key_rd_dicts_to_be_processed ):
# Add the current repository_dependency into self.key_rd_dicts_to_be_processed.
self.key_rd_dicts_to_be_processed.append( current_repository_key_rd_dict )
if not self.in_key_rd_dicts( key_rd_dict, self.handled_key_rd_dicts ):
# Add the current repository_dependency into self.handled_key_rd_dicts.
self.handled_key_rd_dicts.append( key_rd_dict )
if self.in_key_rd_dicts( key_rd_dict, self.key_rd_dicts_to_be_processed ):
# Remove the current repository from self.key_rd_dicts_to_be_processed.
self.key_rd_dicts_to_be_processed = self.remove_from_key_rd_dicts( key_rd_dict, self.key_rd_dicts_to_be_processed )
else:
# The repository is in a different tool shed, so build an url and send a request.
error_message = "Repository dependencies are currently supported only within the same Tool Shed. "
error_message += "Ignoring repository dependency definition for tool shed "
error_message += "%s, name %s, owner %s, changeset revision %s" % ( toolshed, name, owner, changeset_revision )
log.debug( error_message )
def get_updated_changeset_revisions_for_repository_dependencies(self, key_rd_dicts):
updated_key_rd_dicts = []
for key_rd_dict in key_rd_dicts:
key = next(iter(key_rd_dict))
repository_dependency = key_rd_dict[key]
rd_toolshed, rd_name, rd_owner, rd_changeset_revision, \
rd_prior_installation_required, \
rd_only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple(repository_dependency)
if suc.tool_shed_is_this_tool_shed(rd_toolshed):
repository = tool_shed.util.repository_util.get_repository_by_name_and_owner(self.app, rd_name, rd_owner)
if repository:
repository_id = self.app.security.encode_id(repository.id)
repository_metadata = \
metadata_util.get_repository_metadata_by_repository_id_changeset_revision(self.app,
repository_id,
rd_changeset_revision)
if repository_metadata:
# The repository changeset_revision is installable, so no updates are available.
new_key_rd_dict = {}
new_key_rd_dict[key] = repository_dependency
updated_key_rd_dicts.append(key_rd_dict)
else:
# The repository changeset_revision is no longer installable, so see if there's been an update.
changeset_revision = metadata_util.get_next_downloadable_changeset_revision(self.app, repository, rd_changeset_revision)
if changeset_revision != rd_changeset_revision:
repository_metadata = \
metadata_util.get_repository_metadata_by_repository_id_changeset_revision(self.app,
repository_id,
changeset_revision)
if repository_metadata:
new_key_rd_dict = {}
new_key_rd_dict[key] = \
[rd_toolshed,
rd_name,
rd_owner,
repository_metadata.changeset_revision,
rd_prior_installation_required,
rd_only_if_compiling_contained_td]
# We have the updated changeset revision.
updated_key_rd_dicts.append(new_key_rd_dict)
else:
repository_components_tuple = container_util.get_components_from_key(key)
components_list = tool_shed.util.repository_util.extract_components_from_tuple(repository_components_tuple)
toolshed, repository_name, repository_owner, repository_changeset_revision = components_list[0:4]
# For backward compatibility to the 12/20/12 Galaxy release.
if len(components_list) in (4, 5):
rd_only_if_compiling_contained_td = 'False'
message = "The revision %s defined for repository %s owned by %s is invalid, so repository " % \
(str(rd_changeset_revision), str(rd_name), str(rd_owner))
message += "dependencies defined for repository %s will be ignored." % str(repository_name)
log.debug(message)
else:
repository_components_tuple = container_util.get_components_from_key(key)
components_list = tool_shed.util.repository_util.extract_components_from_tuple(repository_components_tuple)
toolshed, repository_name, repository_owner, repository_changeset_revision = components_list[0:4]
message = "The revision %s defined for repository %s owned by %s is invalid, so repository " % \
(str(rd_changeset_revision), str(rd_name), str(rd_owner))
message += "dependencies defined for repository %s will be ignored." % str(repository_name)
log.debug(message)
return updated_key_rd_dicts
def get_updated_changeset_revisions_for_repository_dependencies( self, key_rd_dicts ):
updated_key_rd_dicts = []
for key_rd_dict in key_rd_dicts:
key = next(iter(key_rd_dict))
repository_dependency = key_rd_dict[ key ]
rd_toolshed, rd_name, rd_owner, rd_changeset_revision, \
rd_prior_installation_required, \
rd_only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple( repository_dependency )
if suc.tool_shed_is_this_tool_shed( rd_toolshed ):
repository = tool_shed.util.repository_util.get_repository_by_name_and_owner( self.app, rd_name, rd_owner )
if repository:
repository_id = self.app.security.encode_id( repository.id )
repository_metadata = \
metadata_util.get_repository_metadata_by_repository_id_changeset_revision( self.app,
repository_id,
rd_changeset_revision )
if repository_metadata:
# The repository changeset_revision is installable, so no updates are available.
new_key_rd_dict = {}
new_key_rd_dict[ key ] = repository_dependency
updated_key_rd_dicts.append( key_rd_dict )
else:
# The repository changeset_revision is no longer installable, so see if there's been an update.
repo = hg_util.get_repo_for_repository( self.app, repository=repository, repo_path=None, create=False )
changeset_revision = metadata_util.get_next_downloadable_changeset_revision( repository, repo, rd_changeset_revision )
if changeset_revision != rd_changeset_revision:
repository_metadata = \
metadata_util.get_repository_metadata_by_repository_id_changeset_revision( self.app,
repository_id,
changeset_revision )
if repository_metadata:
new_key_rd_dict = {}
new_key_rd_dict[ key ] = \
[ rd_toolshed,
rd_name,
rd_owner,
repository_metadata.changeset_revision,
rd_prior_installation_required,
rd_only_if_compiling_contained_td ]
# We have the updated changeset revision.
updated_key_rd_dicts.append( new_key_rd_dict )
else:
repository_components_tuple = container_util.get_components_from_key( key )
components_list = tool_shed.util.repository_util.extract_components_from_tuple( repository_components_tuple )
toolshed, repository_name, repository_owner, repository_changeset_revision = components_list[ 0:4 ]
# For backward compatibility to the 12/20/12 Galaxy release.
if len( components_list ) in (4, 5):
rd_only_if_compiling_contained_td = 'False'
message = "The revision %s defined for repository %s owned by %s is invalid, so repository " % \
( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ) )
message += "dependencies defined for repository %s will be ignored." % str( repository_name )
log.debug( message )
else:
repository_components_tuple = container_util.get_components_from_key( key )
components_list = tool_shed.util.repository_util.extract_components_from_tuple( repository_components_tuple )
toolshed, repository_name, repository_owner, repository_changeset_revision = components_list[ 0:4 ]
message = "The revision %s defined for repository %s owned by %s is invalid, so repository " % \
( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ) )
message += "dependencies defined for repository %s will be ignored." % str( repository_name )
log.debug( message )
return updated_key_rd_dicts
