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(object):
    """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):
        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.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.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)

    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)
        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)
                               ) as app:
            yield app
        if cleanup:
            shutil.rmtree(work_dir, ignore_errors=True)