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Source code for galaxy.tools.remote_tool_eval

import json
import os
import shutil
import tempfile
import traceback
from typing import (
    Callable,
    NamedTuple,
)

from galaxy.datatypes.registry import Registry
from galaxy.files import ConfiguredFileSources
from galaxy.job_execution.compute_environment import SharedComputeEnvironment
from galaxy.job_execution.setup import JobIO
from galaxy.metadata.set_metadata import (
    get_metadata_params,
    get_object_store,
    validate_and_load_datatypes_config,
)
from galaxy.model import store
from galaxy.model.store import SessionlessContext
from galaxy.objectstore import ObjectStore
from galaxy.structured_app import MinimalToolApp
from galaxy.tools import (
    create_tool_from_representation,
    evaluation,
)
from galaxy.tools.data import ToolDataTableManager
from galaxy.util.bunch import Bunch
from galaxy.util.dbkeys import GenomeBuilds


[docs]class ToolAppConfig(NamedTuple): name: str tool_data_path: str galaxy_data_manager_data_path: str nginx_upload_path: str len_file_path: str builds_file_path: str root: str is_admin_user: Callable admin_users: list = []
[docs]class ToolApp(MinimalToolApp): """Dummy App that allows loading tools""" name = "tool_app"
[docs] def __init__( self, sa_session: SessionlessContext, tool_app_config: ToolAppConfig, datatypes_registry: Registry, object_store: ObjectStore, tool_data_table_manager: ToolDataTableManager, file_sources: ConfiguredFileSources, ): self.model = Bunch(context=sa_session) self.config = tool_app_config self.datatypes_registry = datatypes_registry self.object_store = object_store self.genome_builds = GenomeBuilds(self) self.tool_data_tables = tool_data_table_manager self.file_sources = file_sources self.biotools_metadata_source = None
[docs]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 = create_tool_from_representation( app=app, raw_tool_source=job_io.tool_source, tool_dir=job_io.tool_dir, tool_source_class=job_io.tool_source_class, ) 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}')
if __name__ == "__main__": TMPDIR = tempfile.mkdtemp() WORKING_DIRECTORY = os.getcwd() WORKING_PARENT = os.path.join(WORKING_DIRECTORY, os.path.pardir) if not os.path.isdir("working") and os.path.isdir(os.path.join(WORKING_PARENT, "working")): # We're probably in pulsar WORKING_DIRECTORY = WORKING_PARENT METADATA_DIRECTORY = os.path.join(WORKING_DIRECTORY, "metadata") IMPORT_STORE_DIRECTORY = os.path.join(METADATA_DIRECTORY, "outputs_new") EXPORT_STORE_DIRECTORY = os.path.join(METADATA_DIRECTORY, "outputs_populated") try: main(TMPDIR, WORKING_DIRECTORY, IMPORT_STORE_DIRECTORY) except Exception: os.makedirs(EXPORT_STORE_DIRECTORY, exist_ok=True) with open(os.path.join(EXPORT_STORE_DIRECTORY, "traceback.txt"), "w") as out: out.write(traceback.format_exc()) raise finally: shutil.rmtree(TMPDIR, ignore_errors=True)