def tvm(self):
return tool_version_manager.ToolVersionManager(self.app)
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 = hg_util.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)
metadata_dict = tool_shed_repository.metadata
if 'tools' in metadata_dict:
# Initialize the ToolVersionManager.
tvm = tool_version_manager.ToolVersionManager(self.app)
irm.update_tool_shed_repository_status(
tool_shed_repository,
self.app.install_model.ToolShedRepository.
installation_status.SETTING_TOOL_VERSIONS)
# Get the tool_versions from the tool shed for each tool in the installed change set.
params = dict(name=tool_shed_repository.name,
owner=self.repository_owner,
changeset_revision=tool_shed_repository.
installed_changeset_revision)
pathspec = ['repository', 'get_tool_versions']
text = util.url_get(
self.tool_shed_url,
password_mgr=self.app.tool_shed_registry.url_auth(
self.tool_shed_url),
pathspec=pathspec,
params=params)
if text:
tool_version_dicts = json.loads(text)
tvm.handle_tool_versions(tool_version_dicts,
tool_shed_repository)
else:
# Set the tool versions since they seem to be missing
# for this repository in the tool shed. CRITICAL NOTE:
# These default settings may not properly handle all
# parent/child associations.
for tool_dict in metadata_dict['tools']:
tool_id = tool_dict['guid']
old_tool_id = tool_dict['id']
tool_version_using_old_id = tvm.get_tool_version(
old_tool_id)
tool_version_using_guid = tvm.get_tool_version(
tool_id)
if not tool_version_using_old_id:
tool_version_using_old_id = self.app.install_model.ToolVersion(
tool_id=old_tool_id,
tool_shed_repository=tool_shed_repository)
self.app.install_model.context.add(
tool_version_using_old_id)
self.app.install_model.context.flush()
if not tool_version_using_guid:
tool_version_using_guid = self.app.install_model.ToolVersion(
tool_id=tool_id,
tool_shed_repository=tool_shed_repository)
self.app.install_model.context.add(
tool_version_using_guid)
self.app.install_model.context.flush()
# Associate the two versions as parent / child.
tool_version_association = tvm.get_tool_version_association(
tool_version_using_old_id,
tool_version_using_guid)
if not tool_version_association:
tool_version_association = \
self.app.install_model.ToolVersionAssociation( tool_id=tool_version_using_guid.id,
parent_id=tool_version_using_old_id.id )
self.app.install_model.context.add(
tool_version_association)
self.app.install_model.context.flush()
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',
str(tool_shed_repository.name), str(error_message))
irm.update_tool_shed_repository_status(
tool_shed_repository,
self.app.install_model.ToolShedRepository.
installation_status.ERROR,
error_message=error_message)
