def _get_tool_source(self, source_file_name=None, source_contents=None):
if source_file_name is None:
source_file_name = self.source_file_name
if source_contents is None:
source_contents = self.source_contents
if not os.path.isabs(source_file_name):
path = os.path.join(self.temp_directory, source_file_name)
open(path, "w").write(source_contents)
else:
path = source_file_name
tool_source = get_tool_source(path)
return tool_source
def _get_tool_source(self, source_file_name=None, source_contents=None, macro_contents=None):
macro_path = None
if source_file_name is None:
source_file_name = self.source_file_name
if source_contents is None:
source_contents = self.source_contents
if not os.path.isabs(source_file_name):
path = os.path.join(self.temp_directory, source_file_name)
with open(path, "w") as out:
out.write(source_contents)
if macro_contents:
macro_path = os.path.join(self.temp_directory, 'macros.xml')
with open(macro_path, "w") as out:
out.write(macro_contents)
else:
path = source_file_name
tool_source = get_tool_source(path, macro_paths=[macro_path])
return tool_source
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}')