mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Nicola Soranzo
2cd95c48f6
- Add flake8-import-order to flake8 Pipfile and remove py27-lint-imports and py27-lint-imports-include-list tox envs - Fix most E201 and E202 errors reported by flake8-import-order v0.15, but pin flake8-import-order to v0.14.3 until https://github.com/PyCQA/flake8-import-order/issues/123 is fixed This let us drop 2 jobs on Travis per each job.
143 lines
4.4 KiB
Python
143 lines
4.4 KiB
Python
""" Module contains test fixtures meant to aide in the testing of jobs and
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tool evaluation. Such extensive "fixtures" are something of an anti-pattern
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so use of this should be limitted to tests of very 'extensive' classes.
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"""
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import os.path
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import shutil
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import string
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import tempfile
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from collections import defaultdict
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import galaxy.datatypes.registry
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import galaxy.model
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from galaxy.tools import create_tool_from_source
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from galaxy.tools.parser import get_tool_source
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from galaxy.util.bunch import Bunch
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from .unittest_utils import galaxy_mock
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datatypes_registry = galaxy.datatypes.registry.Registry()
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datatypes_registry.load_datatypes()
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galaxy.model.set_datatypes_registry(datatypes_registry)
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class UsesApp(object):
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def setup_app(self):
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self.test_directory = tempfile.mkdtemp()
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self.app = galaxy_mock.MockApp()
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self.app.config.new_file_path = os.path.join(self.test_directory, "new_files")
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self.app.config.admin_users = "mary@example.com"
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def tear_down_app(self):
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shutil.rmtree(self.test_directory)
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# Simple tool with just one text parameter and output.
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SIMPLE_TOOL_CONTENTS = '''<tool id="${tool_id}" name="Test Tool" version="$version" profile="$profile">
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<command>echo "$param1" < $out1</command>
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<inputs>
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<param type="text" name="param1" value="" />
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</inputs>
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<outputs>
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<data name="out1" format="data" label="Output ($param1)" />
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</outputs>
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</tool>
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'''
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# A tool with data parameters (kind of like cat1) my favorite test tool :)
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SIMPLE_CAT_TOOL_CONTENTS = '''<tool id="${tool_id}" name="Test Tool" version="$version" profile="$profile">
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<command>cat "$param1" #for $r in $repeat# "$r.param2" #end for# < $out1</command>
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<inputs>
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<param type="data" format="tabular" name="param1" value="" />
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<repeat name="repeat1" label="Repeat 1">
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<param type="data" format="tabular" name="param2" value="" />
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</repeat>
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</inputs>
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<outputs>
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<data name="out1" format="data" />
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</outputs>
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</tool>
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'''
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class UsesTools(object):
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def _init_tool(
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self,
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tool_contents=SIMPLE_TOOL_CONTENTS,
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filename="tool.xml",
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version="1.0",
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profile="16.01",
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tool_id="test_tool",
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extra_file_contents=None,
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extra_file_path=None,
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):
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self._init_app_for_tools()
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self.tool_file = os.path.join(self.test_directory, filename)
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contents_template = string.Template(tool_contents)
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tool_contents = contents_template.safe_substitute(dict(version=version, profile=profile, tool_id=tool_id))
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self.__write_tool(tool_contents)
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if extra_file_contents and extra_file_path:
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self.__write_tool(extra_file_contents, path=os.path.join(self.test_directory, extra_file_path))
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return self.__setup_tool()
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def _init_app_for_tools(self):
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self.app.config.drmaa_external_runjob_script = ""
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self.app.config.tool_secret = "testsecret"
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self.app.config.track_jobs_in_database = False
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self.app.job_config["get_job_tool_configurations"] = lambda ids: [Bunch(handler=Bunch())]
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def __setup_tool(self):
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tool_source = get_tool_source(self.tool_file)
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try:
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self.tool = create_tool_from_source(self.app, tool_source, config_file=self.tool_file)
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except Exception:
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self.tool = None
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if getattr(self, "tool_action", None and self.tool):
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self.tool.tool_action = self.tool_action
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return self.tool
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def __write_tool(self, contents, path=None):
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path = path or self.tool_file
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open(path, "w").write(contents)
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class MockContext(object):
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def __init__(self, model_objects=None):
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self.expunged_all = False
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self.flushed = False
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self.model_objects = model_objects or defaultdict(lambda: {})
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self.created_objects = []
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self.current = self
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def expunge_all(self):
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self.expunged_all = True
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def query(self, clazz):
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return MockQuery(self.model_objects.get(clazz))
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def flush(self):
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self.flushed = True
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def add(self, object):
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self.created_objects.append(object)
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class MockQuery(object):
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def __init__(self, class_objects):
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self.class_objects = class_objects
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def filter_by(self, **kwds):
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return Bunch(first=lambda: None)
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def get(self, id):
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return self.class_objects.get(id, None)
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__all__ = ('UsesApp', )
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