galaxy/test/unit/tools_support.py

""" 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

import galaxy.datatypes.registry
import galaxy.model
from galaxy.tool_util.parser import get_tool_source
from galaxy.tools import create_tool_from_source
from galaxy.util.bunch import Bunch
from .unittest_utils import galaxy_mock


datatypes_registry = galaxy.datatypes.registry.Registry()
datatypes_registry.load_datatypes()
galaxy.model.set_datatypes_registry(datatypes_registry)


class UsesApp(object):

    def setup_app(self):
        self.test_directory = tempfile.mkdtemp()
        self.app = galaxy_mock.MockApp()
        self.app.config.new_file_path = os.path.join(self.test_directory, "new_files")
        self.app.config.admin_users = "mary@example.com"

    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 UsesTools(object):

    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,
    ):
        self._init_app_for_tools()
        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))
        return self.__setup_tool()

    def _init_tool_for_path(self, tool_file):
        self._init_app_for_tools()
        self.tool_file = tool_file
        return self.__setup_tool()

    def _init_app_for_tools(self):
        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: [Bunch(handler=Bunch())]

    def __setup_tool(self):
        tool_source = get_tool_source(self.tool_file)
        try:
            self.tool = create_tool_from_source(self.app, tool_source, config_file=self.tool_file)
        except Exception:
            self.tool = None
        if getattr(self, "tool_action", None and self.tool):
            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(object):

    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(object):

    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', )