"""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)