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


[docs]class ValidationContext:
    """Minimal App object for tool validation."""

[docs]    def __init__(
        self,
        app_name,
        security,
        model,
        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.security = security
        self.model = model
        self.config = Bunch()
        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=app.model,
                tool_data_path=work_dir,
                shed_tool_data_path=work_dir,
                tool_data_tables=tool_data_tables,
                registry=app.datatypes_registry,
                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)