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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 Optional

import galaxy.datatypes.registry
import galaxy.model
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 = MockApp() self.app.config.new_file_path = os.path.join(self.test_directory, "new_files") self.app.config.admin_users = "mary@example.com" self.app.job_search = None
[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 self.app.job_config["get_job_tool_configurations"] = lambda ids, tool_classes: [Bunch(handler=Bunch())] 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) self.tool.assert_finalized() 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', )