def setUp(self): Step.autoGeneratePrereqs=tStep.dummy_autoGeneratePrereqs.im_func self.obj=Step(self.workspace, self.vital_parameters)
class tStep(unittest.TestCase):
workspace=Mock(input_file="input_file", work_dir="work_dir")
vital_parameters=Mock(pval=1e-5, fp=1.5, fn=.150, min_molecule_len=100, min_molecule_sites=6)
native_autoGeneratePrereqs=Step.autoGeneratePrereqs
def dummy_autoGeneratePrereqs(self):
self.autoGeneratePrereqsCalled=True
def dummy_getStepDir(self):
return "tmp"
def dummy_isComplete_true(self):
return True
def dummy_isComplete_false(self):
return False
def dummy_getQualityFileName(self):
return "Quality.json"
def dummy_createQualityObject(self):
self.quality=Quality()
def dummy_createQualityObject_wSave(self):
self.quality=Quality(key="value")
native_getQualityFileName=Step.getQualityFileName
Step.getQualityFileName=tStep.dummy_getQualityFileName.im_func
self.saveQualityObjectToFile()
Step.getQualityFileName=native_getQualityFileName
def dummy_loadQualityReportItems(self):
return {"1": 1, "2": 2, "1.0": 1, "4": 4, "3": 3}
def setUp(self):
Step.autoGeneratePrereqs=tStep.dummy_autoGeneratePrereqs.im_func
self.obj=Step(self.workspace, self.vital_parameters)
def tearDown(self):
Step.autoGeneratePrereqs=self.native_autoGeneratePrereqs
def test_constructor(self):
self.assertEqual([self.workspace, self.vital_parameters, None, True], [self.obj.workspace, self.obj.vital_parameters, self.obj.quality, self.obj.autoGeneratePrereqsCalled])
def test_hash(self):
class_name="Step"
expected=hash((self.workspace.input_file, self.workspace.work_dir, self.vital_parameters.pval, self.vital_parameters.fp, self.vital_parameters.fn, self.vital_parameters.min_molecule_len, self.vital_parameters.min_molecule_sites, class_name))
self.assertEqual(expected, self.obj.__hash__())
def test_eq(self):
obj_copy=copy.deepcopy(self.obj)
before_change=obj_copy==self.obj
self.obj.dummy_var="dummy"
after_change_one=obj_copy==self.obj
obj_copy.dummy_var="dummy"
after_change_two=obj_copy==self.obj
self.assertEqual([True, False, True], [before_change, after_change_one, after_change_two])
def test_ne(self):
obj_copy=copy.deepcopy(self.obj)
before_change=obj_copy!=self.obj
self.obj.dummy_var="dummy"
after_change_one=obj_copy!=self.obj
obj_copy.dummy_var="dummy"
after_change_two=obj_copy!=self.obj
self.assertEqual([False, True, False], [before_change, after_change_one, after_change_two])
def test_str(self):
expected="{'min_molecule_sites': " + str(self.vital_parameters.min_molecule_sites) + ", 'fp': " + str(self.vital_parameters.fp) + ", 'min_molecule_len': " + str(self.vital_parameters.min_molecule_len) + ", 'fn': " + str(self.vital_parameters.fn) + ", 'pval': " + str(self.vital_parameters.pval) + "}"
self.assertEqual(expected,str(self.obj))
def test_write_code(self):
with self.assertRaises(Exception):
self.obj.writeCode()
def test_get_step_dir(self):
with self.assertRaises(Exception):
self.obj.getStepDir()
def test_get_output_file_extension(self):
with self.assertRaises(Exception):
self.obj.getOutputFileExtension()
def test_auto_generate_prereqs(self):
Step.autoGeneratePrereqs=self.native_autoGeneratePrereqs
with self.assertRaises(Exception):
self.obj.autoGeneratePrereqs()
def test_get_prereq(self):
with self.assertRaises(Exception):
self.obj.getPrereq()
def test_is_complete_while_is(self):
native_getStepDir=Step.getStepDir
Step.getStepDir=tStep.dummy_getStepDir.im_func
actual=-1
os.mkdir("tmp")
with open("tmp/Complete.status", "w"):
actual=self.obj.isComplete()
os.remove("tmp/Complete.status")
os.rmdir("tmp")
Step.getStepDir=native_getStepDir
self.assertEqual(True, actual)
def test_is_complete_while_is_not(self):
native_getStepDir=Step.getStepDir
Step.getStepDir=tStep.dummy_getStepDir.im_func
actual=self.obj.isComplete()
Step.getStepDir=native_getStepDir
self.assertEqual(False, actual)
def test_getQualityFileName(self):
native_getStepDir=Step.getStepDir
Step.getStepDir=tStep.dummy_getStepDir.im_func
expected=self.dummy_getStepDir() + "/Quality.json"
actual=self.obj.getQualityFileName()
Step.getStepDir=native_getStepDir
self.assertEqual(expected, actual)
def dummy_loadQualityObjectFromFile(self):
self.quality=Mock(dummy=True)
def test_loadQualityReport_noQuality_cutoff1(self):
native_loadQualityObjectFromFile=Step.loadQualityObjectFromFile
Step.loadQualityObjectFromFile=tStep.dummy_loadQualityObjectFromFile.im_func
native_loadQualityReportItems=Step.loadQualityReportItems
Step.loadQualityReportItems=tStep.dummy_loadQualityReportItems.im_func
expecteds=[["1", "1.0"], Mock(dummy=True)]
actuals=[
self.obj.loadQualityReport(1),
self.obj.quality
]
Step.loadQualityObjectFromFile=native_loadQualityObjectFromFile
Step.loadQualityReportItems=native_loadQualityReportItems
self.assertEqual(expecteds, actuals)
def test_loadQualityReport_quality_cutoff2(self):
self.obj.quality=Mock(dummy=False)
native_loadQualityReportItems=Step.loadQualityReportItems
Step.loadQualityReportItems=tStep.dummy_loadQualityReportItems.im_func
expecteds=[["1", "2", "1.0"], Mock(dummy=False)]
actuals=[
self.obj.loadQualityReport(2),
self.obj.quality
]
Step.loadQualityReportItems=native_loadQualityReportItems
self.assertEqual(expecteds, actuals)
def test_loadQualityReport_quality_cutoff1(self):
self.obj.quality=Mock(dummy=False)
native_loadQualityReportItems=Step.loadQualityReportItems
Step.loadQualityReportItems=tStep.dummy_loadQualityReportItems.im_func
expecteds=[["1", "1.0"], Mock(dummy=False)]
actuals=[
self.obj.loadQualityReport(1),
self.obj.quality
]
Step.loadQualityReportItems=native_loadQualityReportItems
self.assertEqual(expecteds, actuals)
def test_loadQualityReport_quality_cutoff0(self):
self.obj.quality=Mock(dummy=False)
native_loadQualityReportItems=Step.loadQualityReportItems
Step.loadQualityReportItems=tStep.dummy_loadQualityReportItems.im_func
expecteds=[[], Mock(dummy=False)]
actuals=[
self.obj.loadQualityReport(0),
self.obj.quality
]
Step.loadQualityReportItems=native_loadQualityReportItems
self.assertEqual(expecteds, actuals)
def test_create_quality_object(self):
with self.assertRaises(Exception):
self.obj.createQualityObject()
def test_load_quality_report_items(self):
with self.assertRaises(Exception):
self.obj.loadQualityReportItems()
def test_saveQualityObjectToFile_objectDoesNotExist(self):
native_createQualityObject=Step.createQualityObject
Step.createQualityObject=tStep.dummy_createQualityObject.im_func
native_getQualityFileName=Step.getQualityFileName
Step.getQualityFileName=tStep.dummy_getQualityFileName.im_func
self.obj.saveQualityObjectToFile()
Step.createQualityObject=native_createQualityObject
Step.getQualityFileName=native_getQualityFileName
expected="{}"
actual=""
with open(self.dummy_getQualityFileName()) as qual_file:
actual=qual_file.read()
os.remove(self.dummy_getQualityFileName())
self.assertEqual(expected, actual)
def test_saveQualityObjectToFile_objectDoesExist(self):
native_getQualityFileName=Step.getQualityFileName
Step.getQualityFileName=tStep.dummy_getQualityFileName.im_func
self.obj.quality=Quality(key="value")
self.obj.saveQualityObjectToFile()
Step.getQualityFileName=native_getQualityFileName
expected="{\n \"key\": \"value\"\n}"
actual=""
with open(self.dummy_getQualityFileName()) as qual_file:
actual=qual_file.read()
os.remove(self.dummy_getQualityFileName())
self.assertEqual(expected, actual)
def test_loadQualityObjectFromFile_fileDoesExist(self):
native_getQualityFileName=Step.getQualityFileName
Step.getQualityFileName=tStep.dummy_getQualityFileName.im_func
with open(self.dummy_getQualityFileName(), "w") as quality_file:
quality_file.write("{\n \"key\": \"value\"\n}")
self.obj.loadQualityObjectFromFile()
Step.getQualityFileName=native_getQualityFileName
os.remove(self.dummy_getQualityFileName())
self.assertEqual(Quality(key="value"), self.obj.quality)
def test_loadQualityObjectFromFile_fileDoesNotExist(self):
native_getQualityFileName=Step.getQualityFileName
Step.getQualityFileName=tStep.dummy_getQualityFileName.im_func
native_createQualityObject=Step.createQualityObject
Step.createQualityObject=tStep.dummy_createQualityObject_wSave.im_func
self.obj.loadQualityObjectFromFile()
Step.getQualityFileName=native_getQualityFileName
Step.createQualityObject=native_createQualityObject
os.remove(self.dummy_getQualityFileName())
self.assertEqual(Quality(key="value"), self.obj.quality)
def test_get_mem(self):
with self.assertRaises(Exception):
self.obj.getMem()
def test_get_time(self):
with self.assertRaises(Exception):
self.obj.getTime()
def test_get_threads(self):
with self.assertRaises(Exception):
self.obj.getThreads()
def test_get_error_notification_email(self):
self.obj.workspace.errorNotificationEmail=None
actual1=self.obj.getErrorNotificationEmail()
email="*****@*****.**"
self.obj.workspace.errorNotificationEmail=email
actual2=self.obj.getErrorNotificationEmail()
self.assertEqual([None, email], [actual1, actual2])
