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Source code for galaxy.app_unittest_utils.tools_support

""" Module contains test fixtures meant to aide in the testing of jobs and
tool evaluation. Such extensive "fixtures" are something of an anti-pattern
so use of this should be limitted to tests of very 'extensive' classes.

import os.path
import shutil
import string
import tempfile
from collections import defaultdict
from typing import (

import galaxy.datatypes.registry
import galaxy.model
from galaxy.app import UniverseApplication
from galaxy.app_unittest_utils.galaxy_mock import MockApp
from galaxy.tool_util.parser import get_tool_source
from galaxy.tools import create_tool_from_source
from galaxy.util.bunch import Bunch

datatypes_registry = galaxy.datatypes.registry.Registry()

[docs]class UsesApp:
[docs] def setup_app(self): self.test_directory = tempfile.mkdtemp() self.app = cast(UniverseApplication, MockApp()) self.app.config.new_file_path = os.path.join(self.test_directory, "new_files") self.app.config.admin_users = "mary@example.com"
[docs] def tear_down_app(self): shutil.rmtree(self.test_directory)
# Simple tool with just one text parameter and output. SIMPLE_TOOL_CONTENTS = """<tool id="${tool_id}" name="Test Tool" version="$version" profile="$profile"> <command>echo "$param1" &lt; $out1</command> <inputs> <param type="text" name="param1" value="" /> </inputs> <outputs> <data name="out1" format="data" label="Output ($param1)" /> </outputs> </tool> """ # A tool with data parameters (kind of like cat1) my favorite test tool :) SIMPLE_CAT_TOOL_CONTENTS = """<tool id="${tool_id}" name="Test Tool" version="$version" profile="$profile"> <command>cat "$param1" #for $r in $repeat# "$r.param2" #end for# &lt; $out1</command> <inputs> <param type="data" format="tabular" name="param1" value="" /> <repeat name="repeat1" label="Repeat 1"> <param type="data" format="tabular" name="param2" value="" /> </repeat> </inputs> <outputs> <data name="out1" format="data" /> </outputs> </tool> """ class MockActionI: def execute(self, tool, trans, **kwds): pass class UsesTools(UsesApp): tool_action: Optional[MockActionI] = None def _init_tool( self, tool_contents=SIMPLE_TOOL_CONTENTS, filename="tool.xml", version="1.0", profile="16.01", tool_id="test_tool", extra_file_contents=None, extra_file_path=None, tool_path=None, ): if tool_path is None: self.tool_file = os.path.join(self.test_directory, filename) contents_template = string.Template(tool_contents) tool_contents = contents_template.safe_substitute(dict(version=version, profile=profile, tool_id=tool_id)) self.__write_tool(tool_contents) if extra_file_contents and extra_file_path: self.__write_tool(extra_file_contents, path=os.path.join(self.test_directory, extra_file_path)) else: self.tool_file = tool_path return self.__setup_tool() def _init_tool_for_path(self, tool_file): self.tool_file = tool_file return self.__setup_tool() def setup_app(self): super().setup_app() self.app.config.drmaa_external_runjob_script = "" self.app.config.tool_secret = "testsecret" self.app.config.track_jobs_in_database = False def __setup_tool(self): tool_source = get_tool_source(self.tool_file) self.tool = create_tool_from_source(self.app, tool_source, config_file=self.tool_file) if getattr(self, "tool_action", None): self.tool.tool_action = self.tool_action return self.tool def __write_tool(self, contents, path=None): path = path or self.tool_file with open(path, "w") as out: out.write(contents) class MockContext: def __init__(self, model_objects=None): self.expunged_all = False self.flushed = False self.model_objects = model_objects or defaultdict(lambda: {}) self.created_objects = [] self.current = self def expunge_all(self): self.expunged_all = True def query(self, clazz): return MockQuery(self.model_objects.get(clazz)) def flush(self): self.flushed = True def add(self, object): self.created_objects.append(object) class MockQuery: def __init__(self, class_objects): self.class_objects = class_objects def filter_by(self, **kwds): return Bunch(first=lambda: None) def get(self, id): return self.class_objects.get(id, None) __all__ = ("UsesApp",)