def test_pre_task_list_pangea(self):
psample = PangeaSample(
PANGEA_SAMPLE.uuid,
None,
None,
None,
None,
None,
knex=PANGEA_SAMPLE.knex,
sample=PANGEA_SAMPLE,
)
set_config(PANGEA_ENDPOINT,
PANGEA_USER,
PANGEA_PASS,
name_is_uuid=True)
tasks = get_task_list_for_sample(psample, 'all', '')
self.assertEqual(len(tasks), 4)
fast_detect, covid_genome_coverage, _, _ = tasks
self.assertTrue(isinstance(fast_detect.reads, PangeaCapTask))
self.assertTrue(
isinstance(covid_genome_coverage.bam.reads, PangeaCapTask))
nonhuman_reads = covid_genome_coverage.bam.reads
self.assertFalse(
isinstance(nonhuman_reads.mouse_removed_reads, PangeaCapTask))
self.assertFalse(
isinstance(
nonhuman_reads.mouse_removed_reads.adapter_removed_reads,
PangeaCapTask))
self.assertTrue(
isinstance(
nonhuman_reads.mouse_removed_reads.adapter_removed_reads.reads,
PangeaCapTask))
self.assertIs(
fast_detect.reads,
nonhuman_reads.mouse_removed_reads.adapter_removed_reads.reads)
def test_run_pangea_on_sample_with_work_order(self):
psample = PangeaSample(
PANGEA_SAMPLE_2.uuid,
None,
None,
None,
None,
None,
knex=PANGEA_SAMPLE_2.knex,
sample=PANGEA_SAMPLE_2,
)
wop = WorkOrderProto.from_name(PANGEA_SAMPLE_2.knex, WOP_NAME)
wo = wop.create_work_order_for_sample(PANGEA_SAMPLE_2)
set_config(PANGEA_ENDPOINT,
PANGEA_USER,
PANGEA_PASS,
name_is_uuid=True,
work_order_name=WOP_NAME)
tasks = get_task_list_for_sample(psample, 'fast')
tasks = [tasks[1]] # just basic stats class
tasks[0].taxa = DummyFastKraken2()
luigi.build(tasks, local_scheduler=True)
self.assertTrue(
PANGEA_SAMPLE_2.analysis_result(
'cap2::basic_sample_stats').exists())
jo = wo.get_job_order_by_name('cap2::basic_sample_stats')
jo.invalidate_cache()
jo = JobOrder.from_uuid(wo, jo.uuid)
self.assertTrue(jo.exists())
self.assertEqual(jo.status, 'success')
def test_pre_task_list_pangea(self):
psample = PangeaSample(
PANGEA_SAMPLE.uuid,
None,
None,
None,
None,
None,
knex=PANGEA_SAMPLE.knex,
sample=PANGEA_SAMPLE,
)
set_config(PANGEA_ENDPOINT,
PANGEA_USER,
PANGEA_PASS,
name_is_uuid=True)
tasks = get_task_list_for_sample(psample, 'pre')
self.assertEqual(len(tasks), 1)
self.assertTrue(isinstance(tasks[0], PangeaCapTask))
self.assertFalse(isinstance(tasks[0].ec_reads, PangeaCapTask))
self.assertTrue(
isinstance(tasks[0].ec_reads.nonhuman_reads, PangeaCapTask))
self.assertFalse(
isinstance(tasks[0].ec_reads.nonhuman_reads.mouse_removed_reads,
PangeaCapTask))
self.assertFalse(
isinstance(
tasks[0].ec_reads.nonhuman_reads.mouse_removed_reads.
adapter_removed_reads, PangeaCapTask))
self.assertTrue(
isinstance(
tasks[0].ec_reads.nonhuman_reads.mouse_removed_reads.
adapter_removed_reads.reads, PangeaCapTask))
def test_pangea_cap_task_instance(self):
psample = PangeaSample(
PANGEA_SAMPLE.uuid,
None,
None,
None,
None,
None,
knex=PANGEA_SAMPLE.knex,
sample=PANGEA_SAMPLE,
)
set_config(PANGEA_ENDPOINT, '', '', name_is_uuid=True)
pct_type = PangeaCapTask.new_task_type(FastQC)
pct_instance = pct_type(
pe1=psample.r1,
pe2=psample.r2,
sample_name=psample.name,
config_filename='',
)
self.assertTrue(pct_instance.wrapped_instance)
def test_run_pangea_on_sample(self):
psample = PangeaSample(
PANGEA_SAMPLE.uuid,
None,
None,
None,
None,
None,
knex=PANGEA_SAMPLE.knex,
sample=PANGEA_SAMPLE,
)
set_config(PANGEA_ENDPOINT,
PANGEA_USER,
PANGEA_PASS,
name_is_uuid=True)
tasks = get_task_list_for_sample(psample, 'fast')
tasks = [tasks[1]] # just basic stats class
tasks[0].taxa = DummyFastKraken2()
luigi.build(tasks, local_scheduler=True)
self.assertTrue(
PANGEA_SAMPLE.analysis_result('cap2::basic_sample_stats').exists())
def test_pangea_versions(self):
psample = PangeaSample(
PANGEA_SAMPLE.uuid,
None,
None,
None,
None,
None,
knex=PANGEA_SAMPLE.knex,
sample=PANGEA_SAMPLE,
)
set_config(PANGEA_ENDPOINT,
PANGEA_USER,
PANGEA_PASS,
name_is_uuid=True)
wrapped_flag_b = wrap_task(psample,
FlagTaskVersionB,
config_path=TEST_CONFIG,
check_versions=False)
luigi.build([wrapped_flag_b], local_scheduler=True)
remove(wrapped_flag_b.flag_filepath)
self.assertTrue(
PANGEA_SAMPLE.analysis_result(
'cap2::test_flag',
replicate='B df7ebee60a5c',
).exists())
wrapped_downstream = recursively_wrap_task(psample,
TaskThatReliesOnFlagTask,
config_path=TEST_CONFIG)
self.assertIn('B', [
x[0]
for x in wrapped_downstream.config.allowed_versions(wrapped_flag_b)
])
luigi.build([wrapped_downstream], local_scheduler=True)
self.assertEqual(wrapped_downstream.flag.version(), 'B')
self.assertTrue(
PANGEA_SAMPLE.analysis_result(
'cap2::test_task_that_relies_on_flag', ).exists())
def test_pct_instance_is_pct_and_luigi_task(self):
psample = PangeaSample(
PANGEA_SAMPLE.uuid,
None,
None,
None,
None,
None,
knex=PANGEA_SAMPLE.knex,
sample=PANGEA_SAMPLE,
)
set_config(PANGEA_ENDPOINT, '', '', name_is_uuid=True)
pct_type = PangeaCapTask.new_task_type(FastQC)
pct_instance = pct_type(
pe1=psample.r1,
pe2=psample.r2,
sample_name=psample.name,
config_filename='',
)
self.assertTrue(isinstance(pct_instance, PangeaCapTask))
self.assertTrue(isinstance(pct_instance, luigi.Task))
self.assertTrue(isinstance(pct_instance, pct_type))
def test_load_task_versions(self):
psample = PangeaSample(
PANGEA_SAMPLE.uuid,
None,
None,
None,
None,
None,
knex=PANGEA_SAMPLE.knex,
sample=PANGEA_SAMPLE,
)
set_config(PANGEA_ENDPOINT,
PANGEA_USER,
PANGEA_PASS,
name_is_uuid=True)
wrapped_flag_b = wrap_task(psample,
FlagTaskVersionB,
config_path=TEST_CONFIG,
check_versions=False)
luigi.build([wrapped_flag_b], local_scheduler=True)
remove(wrapped_flag_b.flag_filepath)
self.assertTrue(
PANGEA_SAMPLE.analysis_result(
'cap2::test_flag',
replicate='B df7ebee60a5c',
).exists())
instance = recursively_wrap_task(psample,
TaskThatReliesOnFlagTask,
config_path=TEST_CONFIG)
self.assertEqual(instance.flag.version(), 'B')
ivt = instance.version_tree()
cvt = TaskThatReliesOnFlagTask.version_tree()
self.assertNotEqual(ivt, cvt)
self.assertEqual(instance.version_tree().replace('==B', '==A'),
TaskThatReliesOnFlagTask.version_tree())
self.assertNotEqual(instance.version_hash(),
TaskThatReliesOnFlagTask.version_hash())