def test_mixed_hcv_skipped():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession(skipped_types={PipelineType.MIXED_HCV_MAIN,
PipelineType.MIXED_HCV_MIDI})
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(SampleGroup(
'2130A',
('2130A-HCV_S15_L001_R1_001.fastq.gz',
'2130AMIDI-MidHCV_S16_L001_R1_001.fastq.gz')))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # start main and midi
assert {102: dict(id=102,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.MAIN),
103: dict(id=103,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.MIDI)
} == session.active_runs
expected_active_samples = {'2130A-HCV_S15_L001_R1_001.fastq.gz',
'2130AMIDI-MidHCV_S16_L001_R1_001.fastq.gz'}
assert expected_active_samples == folder_watcher.active_samples
assert 2 == len(folder_watcher.active_runs)
def test_hcv_mixed_hcv_running_on_singleton():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession()
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(SampleGroup(
'NEG1',
('NEG1-HCV_S15_L001_R1_001.fastq.gz', None)))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # start main, midi, and mixed HCV
folder_watcher.poll_runs() # main, midi, and mixed HCV still running
assert {102: dict(id=102,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.MIXED_HCV_MAIN),
103: dict(id=103,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.MAIN)
} == session.active_runs
expected_active_samples = {'NEG1-HCV_S15_L001_R1_001.fastq.gz'}
assert expected_active_samples == folder_watcher.active_samples
assert 2 == len(folder_watcher.active_runs)
def test_mixed_hcv_skipped_and_complete():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession(
skipped_types={
PipelineType.MIXED_HCV_MAIN, PipelineType.MIXED_HCV_MIDI,
PipelineType.DENOVO_MAIN, PipelineType.DENOVO_MIDI,
PipelineType.DENOVO_RESISTANCE
})
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(
SampleGroup('2130A', ('2130A-HCV_S15_L001_R1_001.fastq.gz',
'2130AMIDI-MidHCV_S16_L001_R1_001.fastq.gz'),
('HCV', 'MidHCV')))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # start main and midi
session.finish_all_runs() # Finish main and midi
folder_watcher.poll_runs() # start resistance
session.finish_all_runs() # Finish resistance
folder_watcher.poll_runs() # done
assert not session.active_runs
assert not folder_watcher.active_runs
assert not folder_watcher.active_samples
assert folder_watcher.is_complete
def test_main_failed():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession()
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(
SampleGroup('1234A', ('1234A-V3LOOP_R1_001.fastq.gz', None),
('V3LOOP', None)))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # Start main
denovo_main, mapping_main = session.active_runs.values()
session.fail_run(mapping_main)
folder_watcher.poll_runs() # Notice run failed
is_complete_after_failure = folder_watcher.is_complete
session.finish_all_runs()
folder_watcher.poll_runs()
is_complete_at_end = folder_watcher.is_complete
assert not is_complete_after_failure
assert is_complete_at_end
def test_hcv_mixed_hcv_not_finished():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession()
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(SampleGroup(
'2130A',
('2130A-HCV_S15_L001_R1_001.fastq.gz',
'2130AMIDI-MidHCV_S16_L001_R1_001.fastq.gz')))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # start main, midi, and mixed HCV
session.finish_run(dict(id=104)) # Finish main
session.finish_run(dict(id=105)) # Finish midi
folder_watcher.poll_runs() # mixed HCV still running, resistance started
session.finish_run(dict(id=106)) # Finish res
folder_watcher.poll_runs() # mixed HCV still running, resistance finished
assert {102: dict(id=102,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.MIXED_HCV_MAIN),
103: dict(id=103,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.MIXED_HCV_MIDI)
} == session.active_runs
expected_active_samples = {'2130A-HCV_S15_L001_R1_001.fastq.gz',
'2130AMIDI-MidHCV_S16_L001_R1_001.fastq.gz'}
assert expected_active_samples == folder_watcher.active_samples
assert 2 == len(folder_watcher.active_runs)
assert not folder_watcher.is_complete
def test_denovo_main_finished():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession()
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(
SampleGroup('1234A', ('1234A-V3LOOP_R1_001.fastq.gz', None),
('V3LOOP', None)))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # Start main
session.finish_all_runs() # Finish main
folder_watcher.poll_runs() # Start resistance
assert {
104:
dict(id=104,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.DENOVO_RESISTANCE),
105:
dict(id=105,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.RESISTANCE)
} == session.active_runs
assert 2 == len(folder_watcher.active_runs)
def test_resistance_running():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession(
skipped_types={
PipelineType.DENOVO_MAIN, PipelineType.DENOVO_MIDI,
PipelineType.DENOVO_RESISTANCE
})
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(
SampleGroup('1234A', ('1234A-V3LOOP_R1_001.fastq.gz', None),
('V3LOOP', None)))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # Start main
session.finish_all_runs() # Finish main
folder_watcher.poll_runs() # Start resistance
folder_watcher.poll_runs() # resistance still running
assert {
103:
dict(id=103,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.RESISTANCE)
} == session.active_runs
assert {'1234A-V3LOOP_R1_001.fastq.gz'} == folder_watcher.active_samples
assert not folder_watcher.is_complete
def test_mid_hcv_complete():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession(skipped_types={
PipelineType.MIXED_HCV_MAIN, PipelineType.MIXED_HCV_MIDI
})
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(
SampleGroup('2130A', ('2130A-HCV_S15_L001_R1_001.fastq.gz',
'2130AMIDI-MidHCV_S16_L001_R1_001.fastq.gz')))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # start main and midi
session.finish_run(dict(id=103)) # Finish midi
folder_watcher.poll_runs()
assert {
102:
dict(id=102,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.MAIN)
} == session.active_runs
assert 1 == len(folder_watcher.active_runs)
expected_active_samples = {'2130A-HCV_S15_L001_R1_001.fastq.gz'}
assert expected_active_samples == folder_watcher.active_samples
def test_filter_quality_failed():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession()
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(SampleGroup('1234A', ('1234A-V3LOOP_R1_001.fastq.gz', None)))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
filter_quality, = session.active_runs.values()
session.fail_run(filter_quality)
folder_watcher.poll_runs() # start main
assert {} == session.active_runs
assert folder_watcher.is_complete
def test_filter_quality_running():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession()
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(SampleGroup('1234A', ('1234A-V3LOOP_R1_001.fastq.gz', None)))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
folder_watcher.poll_runs() # filter_quality still running
assert {101: dict(id=101,
folder_watcher=folder_watcher,
sample_watcher=None,
pipeline_type=PipelineType.FILTER_QUALITY)
} == session.active_runs
def test_folder_watcher_run_details():
base_calls_folder = '/path/140101_M01234_JUNK/Data/Intensities/BaseCalls'
expected_run_folder = Path('/path/140101_M01234_JUNK')
expected_run_name = '140101_M01234'
watcher = FolderWatcher(base_calls_folder)
assert expected_run_folder == watcher.run_folder
assert expected_run_name == watcher.run_name
def test_filter_quality_finished():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession()
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(SampleGroup('1234A', ('1234A-V3LOOP_R1_001.fastq.gz', None)))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # start main
assert {102: dict(id=102,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.MAIN)
} == session.active_runs
def test_filter_quality_running():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession()
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(
SampleGroup('1234A', ('1234A-V3LOOP_R1_001.fastq.gz', None)))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
folder_watcher.poll_runs() # filter_quality still running
assert {
101:
dict(id=101,
folder_watcher=folder_watcher,
sample_watcher=None,
pipeline_type=PipelineType.FILTER_QUALITY)
} == session.active_runs
def test_hcv_mixed_hcv_not_finished():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession(
skipped_types={
PipelineType.DENOVO_MAIN, PipelineType.DENOVO_MIDI,
PipelineType.DENOVO_RESISTANCE
})
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(
SampleGroup('2130A', ('2130A-HCV_S15_L001_R1_001.fastq.gz',
'2130AMIDI-MidHCV_S16_L001_R1_001.fastq.gz'),
('HCV', 'MidHCV')))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # start main, midi, and mixed HCV
session.finish_run(dict(id=104)) # Finish main
session.finish_run(dict(id=105)) # Finish midi
folder_watcher.poll_runs() # mixed HCV still running, resistance started
session.finish_run(dict(id=106)) # Finish res
folder_watcher.poll_runs() # mixed HCV still running, resistance finished
assert {
102:
dict(id=102,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.MIXED_HCV_MAIN),
103:
dict(id=103,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.MIXED_HCV_MIDI)
} == session.active_runs
expected_active_samples = {
'2130A-HCV_S15_L001_R1_001.fastq.gz',
'2130AMIDI-MidHCV_S16_L001_R1_001.fastq.gz'
}
assert expected_active_samples == folder_watcher.active_samples
assert 2 == len(folder_watcher.active_runs)
assert not folder_watcher.is_complete
def test_resistance_finished():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession()
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(
SampleGroup('1234A', ('1234A-V3LOOP_R1_001.fastq.gz', None)))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # Start main
session.finish_all_runs() # Finish main
folder_watcher.poll_runs() # Start resistance
session.finish_all_runs() # Finish resistance
folder_watcher.poll_runs() # Finish sample
assert not session.active_runs
assert not folder_watcher.active_samples
assert not folder_watcher.active_runs
assert folder_watcher.is_complete
def add_sample_group(self, base_calls, sample_group):
""" Add a sample group (main and optional midi sample) to process.
Also checks to see whether the folder finished processing since the
last folder scan.
:param base_calls: path to the BaseCalls folder with FASTQ files in it
:param SampleGroup sample_group: the sample(s) to add
:return: SampleWatcher for the sample group, or None if that folder has
already finished processing
"""
for attempt_count in count(1):
# noinspection PyBroadException
try:
self.check_session()
folder_watcher = self.folder_watchers.get(base_calls)
if folder_watcher is None:
folder_watcher = FolderWatcher(base_calls, self)
# Check if folder has finished since it was scanned.
results_path = self.get_results_path(folder_watcher)
done_path = results_path / "doneprocessing"
if done_path.exists():
return None
error_path = folder_watcher.run_folder / "errorprocessing"
if error_path.exists():
return None
self.create_batch(folder_watcher)
self.upload_filter_quality(folder_watcher)
shutil.rmtree(results_path, ignore_errors=True)
self.folder_watchers[base_calls] = folder_watcher
for sample_watcher in folder_watcher.sample_watchers:
if sample_watcher.sample_group == sample_group:
return sample_watcher
sample_watcher = SampleWatcher(sample_group)
for fastq1 in filter(None, sample_group.names):
fastq2 = fastq1.replace('_R1_', '_R2_')
for fastq_name, direction in ((fastq1, 'forward'), (fastq2, 'reverse')):
with (base_calls / fastq_name).open('rb') as fastq_file:
fastq_dataset = self.find_or_upload_dataset(
fastq_file,
fastq_name,
direction + ' read from MiSeq run ' +
folder_watcher.run_name)
sample_watcher.fastq_datasets.append(fastq_dataset)
folder_watcher.sample_watchers.append(sample_watcher)
return sample_watcher
except Exception:
if not self.retry:
raise
wait_for_retry(attempt_count)
def test_hcv_mixed_hcv_running_on_singleton():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession()
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(
SampleGroup('NEG1', ('NEG1-HCV_S15_L001_R1_001.fastq.gz', None)))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # start main, midi, and mixed HCV
folder_watcher.poll_runs() # main, midi, and mixed HCV still running
assert {
102:
dict(id=102,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.MIXED_HCV_MAIN),
103:
dict(id=103,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.MAIN)
} == session.active_runs
expected_active_samples = {'NEG1-HCV_S15_L001_R1_001.fastq.gz'}
assert expected_active_samples == folder_watcher.active_samples
assert 2 == len(folder_watcher.active_runs)
def test_filter_quality_finished():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession(
skipped_types={
PipelineType.DENOVO_MAIN, PipelineType.DENOVO_MIDI,
PipelineType.DENOVO_RESISTANCE
})
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(
SampleGroup('1234A', ('1234A-V3LOOP_R1_001.fastq.gz', None),
('V3LOOP', None)))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # start main
assert {
102:
dict(id=102,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.MAIN)
} == session.active_runs
def test_resistance_finished():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession()
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(SampleGroup('1234A', ('1234A-V3LOOP_R1_001.fastq.gz', None)))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # Start main
session.finish_all_runs() # Finish main
folder_watcher.poll_runs() # Start resistance
session.finish_all_runs() # Finish resistance
folder_watcher.poll_runs() # Finish sample
assert not session.active_runs
assert not folder_watcher.active_samples
assert not folder_watcher.active_runs
assert folder_watcher.is_complete
def test_denovo_resistance_complete():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession()
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(
SampleGroup('1234A', ('1234A-V3LOOP_R1_001.fastq.gz', None),
('V3LOOP', None)))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # Start main
session.finish_all_runs() # Finish main
folder_watcher.poll_runs() # Start resistance
denovo_resistance = sample_watcher.runs[PipelineType.DENOVO_RESISTANCE]
session.finish_run(denovo_resistance)
folder_watcher.poll_runs() # denovo resistance finished
folder_watcher.poll_runs() # main resistance still running
assert not folder_watcher.is_complete
def test_hcv_filter_quality_finished():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession()
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(
SampleGroup('2130A', ('2130A-HCV_S15_L001_R1_001.fastq.gz',
'2130AMIDI-MidHCV_S16_L001_R1_001.fastq.gz'),
('HCV', 'MidHCV')))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # start main, midi, and mixed HCV
assert {
102:
dict(id=102,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.MIXED_HCV_MAIN),
103:
dict(id=103,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.MIXED_HCV_MIDI),
104:
dict(id=104,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.DENOVO_MAIN),
105:
dict(id=105,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.DENOVO_MIDI),
106:
dict(id=106,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.MAIN),
107:
dict(id=107,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.MIDI)
} == session.active_runs
expected_active_samples = {
'2130A-HCV_S15_L001_R1_001.fastq.gz',
'2130AMIDI-MidHCV_S16_L001_R1_001.fastq.gz'
}
assert expected_active_samples == folder_watcher.active_samples
assert 6 == len(folder_watcher.active_runs)
def test_mixed_hcv_skipped_and_complete():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession(skipped_types={PipelineType.MIXED_HCV_MAIN,
PipelineType.MIXED_HCV_MIDI})
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(SampleGroup(
'2130A',
('2130A-HCV_S15_L001_R1_001.fastq.gz',
'2130AMIDI-MidHCV_S16_L001_R1_001.fastq.gz')))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # start main and midi
session.finish_all_runs() # Finish main and midi
folder_watcher.poll_runs() # start resistance
session.finish_all_runs() # Finish resistance
folder_watcher.poll_runs() # done
assert not session.active_runs
assert not folder_watcher.active_runs
assert not folder_watcher.active_samples
assert folder_watcher.is_complete
def test_filter_quality_failed():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession()
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(
SampleGroup('1234A', ('1234A-V3LOOP_R1_001.fastq.gz', None)))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
filter_quality, = session.active_runs.values()
session.fail_run(filter_quality)
folder_watcher.poll_runs() # start main
assert {} == session.active_runs
assert folder_watcher.is_complete
def test_resistance_running():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession()
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(SampleGroup('1234A', ('1234A-V3LOOP_R1_001.fastq.gz', None)))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # Start main
session.finish_all_runs() # Finish main
folder_watcher.poll_runs() # Start resistance
folder_watcher.poll_runs() # resistance still running
assert {103: dict(id=103,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.RESISTANCE)
} == session.active_runs
assert {'1234A-V3LOOP_R1_001.fastq.gz'} == folder_watcher.active_samples
assert not folder_watcher.is_complete
def test_main_running():
base_calls_folder = '/path/Data/Intensities/BaseCalls'
session = DummySession()
folder_watcher = FolderWatcher(base_calls_folder, runner=session)
sample_watcher = SampleWatcher(
SampleGroup('1234A', ('1234A-V3LOOP_R1_001.fastq.gz', None)))
folder_watcher.sample_watchers.append(sample_watcher)
folder_watcher.poll_runs() # Start filter_quality
session.finish_all_runs() # Finish filter_quality
folder_watcher.poll_runs() # start main
folder_watcher.poll_runs() # main still running
assert {
102:
dict(id=102,
folder_watcher=folder_watcher,
sample_watcher=sample_watcher,
pipeline_type=PipelineType.MAIN)
} == session.active_runs
def add_folder(self, base_calls):
folder_watcher = FolderWatcher(base_calls, self)
self.folder_watchers[base_calls] = folder_watcher
return folder_watcher
def test_folder_watcher_repr_with_pathlib():
base_calls_folder = Path('/path/Data/Intensities/BaseCalls')
expected_repr = "FolderWatcher('/path/Data/Intensities/BaseCalls')"
watcher = FolderWatcher(base_calls_folder)
assert expected_repr == repr(watcher)
def run_pipeline(self, folder_watcher: FolderWatcher,
pipeline_type: PipelineType,
sample_watcher: SampleWatcher):
if pipeline_type == PipelineType.FILTER_QUALITY:
return self.find_or_launch_run(
self.config.micall_filter_quality_pipeline_id,
dict(quality_csv=folder_watcher.quality_dataset),
'MiCall filter quality on ' + folder_watcher.run_name,
folder_watcher.batch)
if pipeline_type == PipelineType.RESISTANCE:
run = self.run_resistance_pipeline(
sample_watcher, folder_watcher,
(PipelineType.MAIN, PipelineType.MIDI), 'MiCall resistance')
return run
if pipeline_type == PipelineType.DENOVO_RESISTANCE:
run = self.run_resistance_pipeline(
sample_watcher, folder_watcher,
(PipelineType.DENOVO_MAIN, PipelineType.DENOVO_MIDI),
'MiCall denovo resistance')
return run
if pipeline_type in (PipelineType.MIXED_HCV_MAIN,
PipelineType.MIXED_HCV_MIDI):
if self.config.mixed_hcv_pipeline_id is None:
return None
if pipeline_type == PipelineType.MIXED_HCV_MAIN:
input_datasets = dict(fastq1=sample_watcher.fastq_datasets[0],
fastq2=sample_watcher.fastq_datasets[1])
sample_name = sample_watcher.sample_group.names[0]
else:
input_datasets = dict(fastq1=sample_watcher.fastq_datasets[2],
fastq2=sample_watcher.fastq_datasets[3])
sample_name = sample_watcher.sample_group.names[1]
return self.find_or_launch_run(
self.config.mixed_hcv_pipeline_id, input_datasets,
'Mixed HCV on ' + trim_name(sample_name), folder_watcher.batch)
if pipeline_type == PipelineType.MAIN:
group_position = 0
run_name = 'MiCall main'
pipeline_id = self.config.micall_main_pipeline_id
elif pipeline_type == PipelineType.MIDI:
group_position = 1
run_name = 'MiCall main'
pipeline_id = self.config.micall_main_pipeline_id
elif pipeline_type == PipelineType.DENOVO_MAIN:
group_position = 0
run_name = 'MiCall denovo main'
pipeline_id = self.config.denovo_main_pipeline_id
else:
assert pipeline_type == PipelineType.DENOVO_MIDI
group_position = 1
run_name = 'MiCall denovo main'
pipeline_id = self.config.denovo_main_pipeline_id
if pipeline_id is None:
return None
fastq1, fastq2 = sample_watcher.fastq_datasets[group_position *
2:(group_position + 1) *
2]
sample_name = sample_watcher.sample_group.names[group_position]
run_name += ' on ' + trim_name(sample_name)
sample_info = self.get_sample_info(pipeline_id, sample_watcher,
group_position)
if folder_watcher.bad_cycles_dataset is None:
filter_run_id = folder_watcher.filter_quality_run['id']
run_datasets = self.kive_retry(
lambda: self.session.endpoints.containerruns.get(
f'{filter_run_id}/dataset_list/'))
bad_cycles_run_dataset, = [
run_dataset for run_dataset in run_datasets
if run_dataset['argument_name'] == 'bad_cycles_csv'
]
folder_watcher.bad_cycles_dataset = self.kive_retry(
lambda: self.session.get(bad_cycles_run_dataset['dataset']
).json())
inputs = dict(fastq1=fastq1,
fastq2=fastq2,
bad_cycles_csv=folder_watcher.bad_cycles_dataset)
if sample_info is not None:
inputs['sample_info_csv'] = sample_info
return self.find_or_launch_run(pipeline_id, inputs, run_name,
folder_watcher.batch)
