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Source code for galaxy.tools.repositories

"""Provides a subset of app for verifying tools."""

import os
import shutil
import tempfile
from contextlib import contextmanager
from typing import Optional

from galaxy.managers.dbkeys import GenomeBuilds
from galaxy.tools.data import ToolDataTableManager
from galaxy.util.bunch import Bunch

[docs]class ValidationContextConfig: tool_data_path: Optional[str] shed_tool_data_path: Optional[str] tool_data_table_config: str shed_tool_data_table_config: str interactivetools_enable: bool len_file_path: str builds_file_path: Optional[str]
[docs]class ValidationContext: """Minimal App object for tool validation.""" is_webapp = True config: ValidationContextConfig
[docs] def __init__( self, app_name: str, model, security, tool_data_path, shed_tool_data_path, tool_data_tables=None, registry=None, hgweb_config_manager=None, biotools_metadata_source=None, ): self.name = app_name self.model = model self.security = security self.config = ValidationContextConfig() self.config.tool_data_path = tool_data_path self.config.shed_tool_data_path = shed_tool_data_path self.temporary_path = tempfile.mkdtemp(prefix="tool_validation_") self.config.tool_data_table_config = os.path.join(self.temporary_path, "tool_data_table_conf.xml") self.config.shed_tool_data_table_config = os.path.join(self.temporary_path, "shed_tool_data_table_conf.xml") self.config.interactivetools_enable = True self.tool_data_tables = tool_data_tables self.tool_shed_registry = Bunch(tool_sheds={}) self.datatypes_registry = registry self.hgweb_config_manager = hgweb_config_manager self.biotools_metadata_source = biotools_metadata_source self.config.len_file_path = os.path.join(self.temporary_path, "chromlen.txt") # If the builds file path is set to None, tools/__init__.py will load the default. # Otherwise it will attempt to load a nonexistent file and log an error. This does # not appear to be an issue with the len_file_path config option. self.config.builds_file_path = None self.genome_builds = GenomeBuilds(self) self.job_search = None
def __enter__(self): return self def __exit__(self, exc_type, exc_val, exc_tb): shutil.rmtree(self.temporary_path)
[docs] @staticmethod @contextmanager def from_app(app, work_dir=None): cleanup = False if not work_dir: work_dir = tempfile.mkdtemp() cleanup = True tool_data_tables = ToolDataTableManager(work_dir) try: with ValidationContext( app_name=app.name, security=app.security, model=getattr(app, "model", None), tool_data_path=work_dir, shed_tool_data_path=work_dir, tool_data_tables=tool_data_tables, registry=getattr(app, "datatypes_registry", None), hgweb_config_manager=getattr(app, "hgweb_config_manager", None), biotools_metadata_source=getattr(app, "biotools_metadata_source", None), ) as app: yield app finally: if cleanup: shutil.rmtree(work_dir, ignore_errors=True)