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)
def handle_repository_contents(self,
tool_shed_repository,
repository_clone_url,
relative_install_dir,
repository_elem,
install_dependencies,
is_repository_dependency=False):
"""
Generate the metadata for the installed tool shed repository, among other things. If the installed tool_shed_repository
contains tools that are loaded into the Galaxy tool panel, this method will automatically eliminate all entries for each
of the tools defined in the received repository_elem from all non-shed-related tool panel configuration files since the
entries are automatically added to the reserved migrated_tools_conf.xml file as part of the migration process.
"""
tool_configs_to_filter = []
tool_panel_dict_for_display = {}
if self.tool_path:
repo_install_dir = os.path.join(self.tool_path,
relative_install_dir)
else:
repo_install_dir = relative_install_dir
if not is_repository_dependency:
for tool_elem in repository_elem:
# The tool_elem looks something like this:
# <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" />
tool_config = tool_elem.get('file')
guid = self.get_guid(repository_clone_url,
relative_install_dir, tool_config)
# See if tool_config is defined inside of a section in self.proprietary_tool_panel_elems.
is_displayed, tool_sections = self.get_containing_tool_sections(
tool_config)
if is_displayed:
tool_panel_dict_for_tool_config = \
self.tpm.generate_tool_panel_dict_for_tool_config(guid,
tool_config,
tool_sections=tool_sections)
# The tool-panel_dict has the following structure.
# {<Tool guid> : [{ tool_config : <tool_config_file>,
# id: <ToolSection id>,
# version : <ToolSection version>,
# name : <TooSection name>}]}
# TODO: this code need to be revised
for k, v in tool_panel_dict_for_tool_config.items():
tool_panel_dict_for_display[k] = v
for _tool_panel_dict in v:
# Keep track of tool config file names associated with entries that have been made to the
# migrated_tools_conf.xml file so they can be eliminated from all non-shed-related tool panel configs.
if tool_config not in tool_configs_to_filter:
tool_configs_to_filter.append(tool_config)
else:
log.error(
'The tool "%s" (%s) has not been enabled because it is not defined in a proprietary tool config (%s).'
% (guid, tool_config, ", ".join(
self.proprietary_tool_confs or [])))
if tool_configs_to_filter:
lock = threading.Lock()
lock.acquire(True)
try:
self.filter_and_persist_proprietary_tool_panel_configs(
tool_configs_to_filter)
except Exception:
log.exception(
"Exception attempting to filter and persist non-shed-related tool panel configs"
)
finally:
lock.release()
irmm = InstalledRepositoryMetadataManager(
app=self.app,
tpm=self.tpm,
repository=tool_shed_repository,
changeset_revision=tool_shed_repository.changeset_revision,
repository_clone_url=repository_clone_url,
shed_config_dict=self.shed_config_dict,
relative_install_dir=relative_install_dir,
repository_files_dir=None,
resetting_all_metadata_on_repository=False,
updating_installed_repository=False,
persist=True)
irmm.generate_metadata_for_changeset_revision()
irmm_metadata_dict = irmm.get_metadata_dict()
tool_shed_repository.metadata = irmm_metadata_dict
self.app.install_model.context.add(tool_shed_repository)
self.app.install_model.context.flush()
has_tool_dependencies = self.__has_tool_dependencies(
irmm_metadata_dict)
if has_tool_dependencies:
# All tool_dependency objects must be created before the tools are processed even if no
# tool dependencies will be installed.
tool_dependencies = create_tool_dependency_objects(
self.app,
tool_shed_repository,
relative_install_dir,
set_status=True)
else:
tool_dependencies = None
if 'tools' in irmm_metadata_dict:
tdtm = data_table_manager.ToolDataTableManager(self.app)
sample_files = irmm_metadata_dict.get('sample_files', [])
sample_files = [str(s) for s in sample_files]
tool_index_sample_files = tdtm.get_tool_index_sample_files(
sample_files)
tool_util.copy_sample_files(self.app,
tool_index_sample_files,
tool_path=self.tool_path)
sample_files_copied = [s for s in tool_index_sample_files]
repository_tools_tups = irmm.get_repository_tools_tups()
if repository_tools_tups:
# Handle missing data table entries for tool parameters that are dynamically
# generated select lists.
repository_tools_tups = tdtm.handle_missing_data_table_entry(
relative_install_dir, self.tool_path,
repository_tools_tups)
# Handle missing index files for tool parameters that are dynamically generated select lists.
repository_tools_tups, sample_files_copied = tool_util.handle_missing_index_file(
self.app, self.tool_path, sample_files,
repository_tools_tups, sample_files_copied)
# Copy remaining sample files included in the repository to the ~/tool-data
# directory of the local Galaxy instance.
tool_util.copy_sample_files(
self.app,
sample_files,
tool_path=self.tool_path,
sample_files_copied=sample_files_copied)
if not is_repository_dependency:
self.tpm.add_to_tool_panel(
tool_shed_repository.name,
repository_clone_url,
tool_shed_repository.installed_changeset_revision,
repository_tools_tups,
self.repository_owner,
self.migrated_tools_config,
tool_panel_dict=tool_panel_dict_for_display,
new_install=True)
if install_dependencies and tool_dependencies and has_tool_dependencies:
# Install tool dependencies.
irm = install_manager.InstallRepositoryManager(self.app, self.tpm)
itdm = install_manager.InstallToolDependencyManager(self.app)
irm.update_tool_shed_repository_status(
tool_shed_repository,
self.app.install_model.ToolShedRepository.installation_status.
INSTALLING_TOOL_DEPENDENCIES)
# Get the tool_dependencies.xml file from disk.
tool_dependencies_config = get_config_from_disk(
'tool_dependencies.xml', repo_install_dir)
installed_tool_dependencies = itdm.install_specified_tool_dependencies(
tool_shed_repository=tool_shed_repository,
tool_dependencies_config=tool_dependencies_config,
tool_dependencies=tool_dependencies,
from_tool_migration_manager=True)
for installed_tool_dependency in installed_tool_dependencies:
if installed_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR:
log.error(
'The ToolMigrationManager returned the following error while installing tool dependency %s: %s',
installed_tool_dependency.name,
installed_tool_dependency.error_message)
if 'datatypes' in irmm_metadata_dict:
cdl = custom_datatype_manager.CustomDatatypeLoader(self.app)
tool_shed_repository.status = self.app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES
if not tool_shed_repository.includes_datatypes:
tool_shed_repository.includes_datatypes = True
self.app.install_model.context.add(tool_shed_repository)
self.app.install_model.context.flush()
work_dir = tempfile.mkdtemp(prefix="tmp-toolshed-hrc")
datatypes_config = get_config_from_disk(
suc.DATATYPES_CONFIG_FILENAME, repo_install_dir)
# Load proprietary data types required by tools. The value of override is not
# important here since the Galaxy server will be started after this installation
# completes.
converter_path, display_path = \
cdl.alter_config_and_load_prorietary_datatypes(datatypes_config,
repo_install_dir,
override=False)
if converter_path or display_path:
# Create a dictionary of tool shed repository related information.
repository_dict = \
cdl.create_repository_dict_for_proprietary_datatypes(tool_shed=self.tool_shed_url,
name=tool_shed_repository.name,
owner=self.repository_owner,
installed_changeset_revision=tool_shed_repository.installed_changeset_revision,
tool_dicts=irmm_metadata_dict.get('tools', []),
converter_path=converter_path,
display_path=display_path)
if converter_path:
# Load proprietary datatype converters
self.app.datatypes_registry.load_datatype_converters(
self.toolbox, installed_repository_dict=repository_dict)
if display_path:
# Load proprietary datatype display applications
self.app.datatypes_registry.load_display_applications(
self.app, installed_repository_dict=repository_dict)
remove_dir(work_dir)