"""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)