def create_or_update_tool_shed_repository_record(self,
name,
owner,
changeset_revision,
description=None):
# Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision>
relative_clone_dir = os.path.join(self.tool_shed, 'repos', owner, name,
changeset_revision)
clone_dir = os.path.join(self.tool_path, relative_clone_dir)
if not self.__iscloned(clone_dir):
repository_clone_url = os.path.join(self.tool_shed_url, 'repos',
owner, name)
ctx_rev = suc.get_ctx_rev(self.app, self.tool_shed_url, name,
owner, changeset_revision)
tool_shed_repository = create_or_update_tool_shed_repository(
app=self.app,
name=name,
description=description,
installed_changeset_revision=changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
status=self.app.install_model.ToolShedRepository.
installation_status.NEW,
metadata_dict={},
current_changeset_revision=None,
owner=self.repository_owner,
dist_to_shed=True)
return tool_shed_repository
return None
def get_or_create_tool_shed_repository(self, tool_shed, name, owner,
changeset_revision):
"""
Return a tool shed repository database record defined by the combination of
tool shed, repository name, repository owner and changeset_revision or
installed_changeset_revision. A new tool shed repository record will be
created if one is not located.
"""
install_model = self.app.install_model
# We store the port in the database.
tool_shed = common_util.remove_protocol_from_tool_shed_url(tool_shed)
# This method is used only in Galaxy, not the tool shed.
repository = repository_util.get_repository_for_dependency_relationship(
self.app, tool_shed, name, owner, changeset_revision)
if not repository:
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(
self.app, tool_shed)
repository_clone_url = os.path.join(tool_shed_url, 'repos', owner,
name)
ctx_rev = get_ctx_rev(self.app, tool_shed_url, name, owner,
changeset_revision)
repository = repository_util.create_or_update_tool_shed_repository(
app=self.app,
name=name,
description=None,
installed_changeset_revision=changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
status=install_model.ToolShedRepository.installation_status.
NEW,
metadata_dict={},
current_changeset_revision=None,
owner=owner,
dist_to_shed=False)
return repository
def install_repository(self, repository_elem, tool_shed_repository, install_dependencies, is_repository_dependency=False):
"""Install a single repository, loading contained tools into the tool panel."""
# Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision>
relative_clone_dir = os.path.join(tool_shed_repository.tool_shed,
'repos',
tool_shed_repository.owner,
tool_shed_repository.name,
tool_shed_repository.installed_changeset_revision)
clone_dir = os.path.join(self.tool_path, relative_clone_dir)
cloned_ok = self.__iscloned(clone_dir)
is_installed = False
# Any of the following states should count as installed in this context.
if tool_shed_repository.status in [self.app.install_model.ToolShedRepository.installation_status.INSTALLED,
self.app.install_model.ToolShedRepository.installation_status.ERROR,
self.app.install_model.ToolShedRepository.installation_status.UNINSTALLED,
self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED]:
is_installed = True
if cloned_ok and is_installed:
log.info("Skipping automatic install of repository '%s' because it has already been installed in location %s",
tool_shed_repository.name, clone_dir)
else:
irm = install_manager.InstallRepositoryManager(self.app, self.tpm)
repository_clone_url = os.path.join(self.tool_shed_url, 'repos', tool_shed_repository.owner, tool_shed_repository.name)
relative_install_dir = os.path.join(relative_clone_dir, tool_shed_repository.name)
install_dir = os.path.join(clone_dir, tool_shed_repository.name)
ctx_rev = suc.get_ctx_rev(self.app,
self.tool_shed_url,
tool_shed_repository.name,
tool_shed_repository.owner,
tool_shed_repository.installed_changeset_revision)
if not cloned_ok:
irm.update_tool_shed_repository_status(tool_shed_repository,
self.app.install_model.ToolShedRepository.installation_status.CLONING)
cloned_ok, error_message = clone_repository(repository_clone_url, os.path.abspath(install_dir), ctx_rev)
if cloned_ok and not is_installed:
self.handle_repository_contents(tool_shed_repository=tool_shed_repository,
repository_clone_url=repository_clone_url,
relative_install_dir=relative_install_dir,
repository_elem=repository_elem,
install_dependencies=install_dependencies,
is_repository_dependency=is_repository_dependency)
self.app.install_model.context.refresh(tool_shed_repository)
irm.update_tool_shed_repository_status(tool_shed_repository,
self.app.install_model.ToolShedRepository.installation_status.INSTALLED)
else:
log.error('Error attempting to clone repository %s: %s', tool_shed_repository.name, error_message)
irm.update_tool_shed_repository_status(tool_shed_repository,
self.app.install_model.ToolShedRepository.installation_status.ERROR,
error_message=error_message)