def load_tool_from_config(self, repository_id, full_path):
tool_source = get_tool_source(
full_path,
enable_beta_formats=getattr(self.app.config,
"enable_beta_tool_formats", False),
tool_location_fetcher=ToolLocationFetcher(),
)
try:
tool = create_tool_from_source(config_file=full_path,
app=self.app,
tool_source=tool_source,
repository_id=repository_id,
allow_code_files=False)
valid = True
error_message = None
except KeyError as e:
tool = None
valid = False
error_message = 'This file requires an entry for "%s" in the tool_data_table_conf.xml file. Upload a file ' % str(
e)
error_message += 'named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct '
error_message += 'this error. '
log.exception(error_message)
except Exception as e:
tool = None
valid = False
error_message = str(e)
log.exception('Caught exception loading tool from %s:', full_path)
return tool, valid, error_message
def __setup_tool(self):
tool_source = get_tool_source(self.tool_file)
self.tool = create_tool_from_source(self.app, tool_source, config_file=self.tool_file)
self.tool.assert_finalized()
if getattr(self, "tool_action", None):
self.tool.tool_action = self.tool_action
return self.tool
def __setup_tool(self):
tool_source = get_tool_source(self.tool_file)
try:
self.tool = create_tool_from_source(self.app, tool_source, config_file=self.tool_file)
except Exception:
self.tool = None
if getattr(self, "tool_action", None and self.tool):
self.tool.tool_action = self.tool_action
return self.tool
def __setup_tool(self):
tool_source = get_tool_source(self.tool_file)
try:
self.tool = create_tool_from_source(self.app,
tool_source,
config_file=self.tool_file)
except Exception:
self.tool = None
if getattr(self, "tool_action", None and self.tool):
self.tool.tool_action = self.tool_action
return self.tool
def load_tool_from_config(self, repository_id, full_path):
tool_source = get_tool_source(
full_path,
enable_beta_formats=getattr(self.app.config, "enable_beta_tool_formats", False),
tool_location_fetcher=ToolLocationFetcher(),
)
try:
tool = create_tool_from_source(config_file=full_path, app=self.app, tool_source=tool_source, repository_id=repository_id, allow_code_files=False)
valid = True
error_message = None
except KeyError as e:
tool = None
valid = False
error_message = 'This file requires an entry for "%s" in the tool_data_table_conf.xml file. Upload a file ' % str(e)
error_message += 'named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct '
error_message += 'this error. '
except Exception as e:
tool = None
valid = False
error_message = str(e)
return tool, valid, error_message
def main(TMPDIR, WORKING_DIRECTORY, IMPORT_STORE_DIRECTORY):
metadata_params = get_metadata_params(WORKING_DIRECTORY)
datatypes_config = metadata_params["datatypes_config"]
if not os.path.exists(datatypes_config):
datatypes_config = os.path.join(WORKING_DIRECTORY, 'configs', datatypes_config)
datatypes_registry = validate_and_load_datatypes_config(datatypes_config)
object_store = get_object_store(WORKING_DIRECTORY)
import_store = store.imported_store_for_metadata(IMPORT_STORE_DIRECTORY)
# TODO: clean up random places from which we read files in the working directory
job_io = JobIO.from_json(os.path.join(IMPORT_STORE_DIRECTORY, 'job_io.json'), sa_session=import_store.sa_session)
tool_app_config = ToolAppConfig(
name='tool_app',
tool_data_path=job_io.tool_data_path,
galaxy_data_manager_data_path=job_io.galaxy_data_manager_data_path,
nginx_upload_path=TMPDIR,
len_file_path=job_io.len_file_path,
builds_file_path=job_io.builds_file_path,
root=TMPDIR,
is_admin_user=lambda _: job_io.user_context.is_admin)
with open(os.path.join(IMPORT_STORE_DIRECTORY, 'tool_data_tables.json')) as data_tables_json:
tdtm = ToolDataTableManager.from_dict(json.load(data_tables_json))
app = ToolApp(
sa_session=import_store.sa_session,
tool_app_config=tool_app_config,
datatypes_registry=datatypes_registry,
object_store=object_store,
tool_data_table_manager=tdtm,
file_sources=job_io.file_sources,
)
# TODO: could try to serialize just a minimal tool variant instead of the whole thing ?
tool_source = get_tool_source(tool_source_class=job_io.tool_source_class, raw_tool_source=job_io.tool_source)
tool = create_tool_from_source(app, tool_source=tool_source, tool_dir=job_io.tool_dir)
tool_evaluator = evaluation.RemoteToolEvaluator(app=app, tool=tool, job=job_io.job, local_working_directory=WORKING_DIRECTORY)
tool_evaluator.set_compute_environment(compute_environment=SharedComputeEnvironment(job_io=job_io, job=job_io.job))
with open(os.path.join(WORKING_DIRECTORY, 'tool_script.sh'), 'a') as out:
command_line, version_command_line, extra_filenames, environment_variables = tool_evaluator.build()
out.write(f'{version_command_line or ""}{command_line}')
def _deserialize(app, tool_source_class, raw_tool_source):
tool_source = get_tool_source(tool_source_class=tool_source_class,
raw_tool_source=raw_tool_source)
assert type(tool_source).__name__ == tool_source_class
return create_tool_from_source(app, tool_source=tool_source)