def _covert_to_cwl_format(val):
file_obj = copy.deepcopy(val)
location = file_obj.pop('location', None)
if location:
try:
file_db_object = FileProcessor.get_file_obj(location)
except FileHelperException as e:
raise PortProcessorException('File %s not found' % location)
path = file_db_object.path
path_obj = Path(path)
checksum = FileProcessor.get_file_checksum(file_db_object)
if checksum:
file_obj['checksum'] = checksum
size = FileProcessor.get_file_size(file_db_object)
if size:
file_obj['size'] = size
file_obj['basename'] = path_obj.name
file_obj['nameext'] = path_obj.suffix
file_obj['nameroot'] = path_obj.stem
file_obj['path'] = path
secondary_files = file_obj.pop('secondaryFiles', [])
secondary_files_value = PortProcessor.process_files(
secondary_files, PortAction.CONVERT_TO_CWL_FORMAT)
if secondary_files_value:
file_obj['secondaryFiles'] = secondary_files_value
return file_obj
def _register_file(val, size, group_id, metadata, file_list):
file_obj = copy.deepcopy(val)
file_obj.pop("basename", None)
file_obj.pop("nameroot", None)
file_obj.pop("nameext", None)
uri = file_obj.pop('location', None)
checksum = file_obj.pop("checksum", None)
try:
file_obj_db = FileProcessor.create_file_obj(uri, size, checksum, group_id, metadata)
except FileConflictException as e:
logger.warning(str(e))
file_obj_db = FileProcessor.get_file_obj(uri)
# TODO: Check what to do in case file already exist in DB. Note: This should never happen
# raise PortProcessorException(e)
secondary_files = file_obj.pop('secondaryFiles', [])
secondary_file_list = []
secondary_files_obj = PortProcessor.process_files(secondary_files,
PortAction.REGISTER_OUTPUT_FILES,
group_id=group_id,
metadata=metadata,
file_list=secondary_file_list)
if secondary_files_obj:
file_obj['secondaryFiles'] = secondary_files_obj
file_obj['location'] = FileProcessor.get_bid_from_file(file_obj_db)
if file_list is not None:
file_list.append('bid://%s' % FileProcessor.get_bid_from_file(file_obj_db))
file_list.extend([f['location'] for f in secondary_files_obj])
return file_obj
def to_db(self):
if self.port_object:
self.port_object.name = self.name
self.port_object.port_type = self.port_type
self.port_object.schema = self.schema
self.port_object.secondary_files = self.secondary_files
self.port_object.db_value = self.db_value
self.port_object.value = self.value
self.port_object.save()
self.port_object.files.set(
[FileProcessor.get_file_obj(v) for v in self.files])
self.port_object.notify = self.notify
self.port_object.save()
else:
try:
run_object = Run.objects.get(id=self.run_id)
except Run.DoesNotExist:
raise PortObjectConstructException(
"Port save failed. Run with id: %s doesn't exist.")
new_port = Port(
run=run_object,
name=self.name,
port_type=self.port_type,
schema=self.schema,
secondary_files=self.secondary_files,
db_value=self.db_value,
value=self.value,
notify=self.name in run_object.notify_for_outputs,
)
new_port.save()
new_port.files.set(
[FileProcessor.get_file_obj(v) for v in self.files])
new_port.save()
self.port_object = new_port
def get_files_from_run(r):
files = list()
inp_port = Port.objects.filter(run_id=r.id, name='pair').first()
for p in inp_port.db_value[0]['R1']:
files.append(FileProcessor.get_file_path(p['location']))
for p in inp_port.db_value[0]['R2']:
files.append(FileProcessor.get_file_path(p['location']))
for p in inp_port.db_value[0]['zR1']:
files.append(FileProcessor.get_file_path(p['location']))
for p in inp_port.db_value[0]['zR2']:
files.append(FileProcessor.get_file_path(p['location']))
return files
def get_files_from_run(r):
files = list()
inp_port = Port.objects.filter(run_id=r.id, name="pair").first()
for p in inp_port.db_value[0]["R1"]:
files.append(FileProcessor.get_file_path(p["location"]))
for p in inp_port.db_value[0]["R2"]:
files.append(FileProcessor.get_file_path(p["location"]))
for p in inp_port.db_value[0]["zR1"]:
files.append(FileProcessor.get_file_path(p["location"]))
for p in inp_port.db_value[0]["zR2"]:
files.append(FileProcessor.get_file_path(p["location"]))
return files
def _fix_locations_in_db(val, file_list):
"""
Temporary method for fixing Values in DB
:param val:
:param file_list:
:return:
"""
file_obj = copy.deepcopy(val)
location = val.get('location')
if not location:
location = val.get('path')
if not location:
print("Couldn't fix value: %s. File doesn't exist" % file_obj)
return file_obj
if location.startswith('/'):
location = 'juno://%s' % location
elif PortProcessor.is_uuid(location):
location = 'bid://%s' % location
elif not location.startswith('juno://') and not location.startswith(
'bid:/'):
print("Couldn't fix value: %s" % file_obj)
return file_obj
try:
bid = FileProcessor.get_file_id(location)
except FileHelperException as e:
print("Couldn't fix value: %s. File doesn't exist" % file_obj)
return file_obj
file_obj['location'] = 'bid://%s' % bid
if file_obj.get('path'):
file_obj.pop('path')
if file_list is not None:
file_list.append('bid://%s' % bid)
return file_obj
def test_create_file_obj_bad_file_group(self):
file_group_id = str(uuid.uuid4())
with self.assertRaises(Exception) as context:
file_obj = FileProcessor.create_file_obj(
"file:///path/to/file.unknown_data_type", 123345, "sha1$calculated checksum", file_group_id, {}
)
self.assertTrue("Invalid FileGroup id: %s" % file_group_id in context.exception)
def _send_as_notification(val, job_group):
uri = val.get('location')
path = FileProcessor.parse_path_from_uri(uri)
file_name = os.path.basename(path)
if job_group:
event = UploadAttachmentEvent(str(job_group.id), file_name, path, download=True)
send_notification.delay(event.to_dict())
logger.info("Can't upload file:%s. JobGroup not specified", path)
return val
def ready(self):
[CWLPortObject.ready(p) for p in self.inputs]
samples = set()
for p in self.inputs:
for f in p.files:
file_obj = FileProcessor.get_file_obj(f)
if file_obj.sample:
samples.add(file_obj.sample)
self.samples = list(samples)
[CWLPortObject.ready(p) for p in self.outputs]
self.status = RunStatus.READY
def _register_file(val, size, group_id, metadata, file_list):
file_obj = copy.deepcopy(val)
file_obj.pop("basename", None)
file_obj.pop("nameroot", None)
file_obj.pop("nameext", None)
uri = file_obj.pop("location", None)
checksum = file_obj.pop("checksum", None)
try:
file_obj_db = FileProcessor.create_file_obj(uri, size, checksum, group_id, metadata)
except FileConflictException as e:
logger.warning(str(e))
# TODO: Check what to do in case file already exist in DB.
file_obj_db = FileProcessor.get_file_obj(uri)
FileProcessor.update_file(file_obj_db, file_obj_db.path, metadata)
secondary_files = file_obj.pop("secondaryFiles", [])
secondary_file_list = []
secondary_files_obj = PortProcessor.process_files(
secondary_files,
PortAction.REGISTER_OUTPUT_FILES,
group_id=group_id,
metadata=metadata,
file_list=secondary_file_list,
)
if secondary_files_obj:
file_obj["secondaryFiles"] = secondary_files_obj
file_obj["location"] = FileProcessor.get_bid_from_file(file_obj_db)
if file_list is not None:
file_list.append("bid://%s" % FileProcessor.get_bid_from_file(file_obj_db))
file_list.extend([f["location"] for f in secondary_files_obj])
return file_obj
def populate_run_samples(apps, _):
Run = apps.get_model('runner', 'Run')
for run in Run.objects.all():
samples = set()
try:
run_obj = RunObject.from_db(run.id)
except Exception as e:
print("Run %s can't be migrated" % str(run.id))
for p in run_obj.inputs:
for f in p.files:
file_obj = FileProcessor.get_file_obj(f)
if file_obj.sample:
samples.add(file_obj.sample)
run_obj.samples = list(samples)
run_obj.to_db()
def from_db(cls, port_id):
try:
port = Port.objects.get(id=port_id)
except Port.DoesNotExist:
raise PortObjectConstructException('Port with id:')
return cls(str(port.run.id),
port.name,
port.port_type,
port.schema,
port.secondary_files,
port.db_value,
port.value,
[FileProcessor.get_bid_from_file(f) for f in port.files.all()],
port_id=port_id,
notify=port.notify)
def _convert_to_path(val):
file_obj = copy.deepcopy(val)
location = file_obj.pop("location", None)
if not location and val.get("contents"):
logger.debug("Processing file literal %s", str(val))
return val
try:
path = FileProcessor.get_file_path(location)
except FileHelperException as e:
raise PortProcessorException("File %s not found" % location)
secondary_files = file_obj.pop("secondaryFiles", [])
secondary_files_value = PortProcessor.process_files(secondary_files, PortAction.CONVERT_TO_PATH)
if secondary_files_value:
file_obj["secondaryFiles"] = secondary_files_value
file_obj["path"] = path
return file_obj
def _update_location_to_bid(val, file_list):
file_obj = copy.deepcopy(val)
location = val.get('location')
if not location and val.get('contents'):
logger.debug("Processing file literal %s", str(val))
return val
bid = FileProcessor.get_file_id(location)
file_obj['location'] = 'bid://%s' % bid
secondary_files = file_obj.pop('secondaryFiles', [])
secondary_file_list = []
secondary_files_obj = PortProcessor.process_files(secondary_files,
PortAction.CONVERT_TO_BID,
file_list=secondary_file_list)
if secondary_files_obj:
file_obj['secondaryFiles'] = secondary_files_obj
if file_obj.get('path'):
file_obj.pop('path')
if file_list is not None:
file_list.append('bid://%s' % bid)
file_list.extend([f['location'] for f in secondary_files_obj])
return file_obj
def test_run_complete_job(
self, mock_populate_job_group_notifier, mock_get_pipeline, memcache_task_lock, send_notification
):
with open("runner/tests/run/pair-workflow.cwl", "r") as f:
app = json.load(f)
with open("runner/tests/run/inputs.json", "r") as f:
inputs = json.load(f)
mock_populate_job_group_notifier.return_value = None
mock_get_pipeline.return_value = app
memcache_task_lock.return_value = True
send_notification.return_value = False
run = RunObjectFactory.from_definition(str(self.run.id), inputs)
run.to_db()
operator_run = OperatorRun.objects.first()
operator_run.runs.add(run.run_obj)
num_completed_runs = operator_run.num_completed_runs
complete_job(run.run_id, self.outputs)
operator_run.refresh_from_db()
self.assertEqual(operator_run.num_completed_runs, num_completed_runs + 1)
run_obj = RunObjectFactory.from_db(run.run_id)
file_obj = File.objects.filter(path=self.outputs["maf"]["location"].replace("file://", "")).first()
run_obj.to_db()
for out in run_obj.outputs:
if out.name == "maf":
self.assertEqual(out.value["location"], self.outputs["maf"]["location"])
self.assertEqual(FileProcessor.get_bid_from_file(file_obj), out.db_value["location"])
port = Port.objects.filter(run_id=run_obj.run_id, name="bams").first()
self.assertEqual(len(port.files.all()), 4)
expected_result = (
"/output/argos_pair_workflow/425194f6-a974-4c2f-995f-f27d7ba54ddc/outputs/test_1.rg.md.abra.printreads.bam",
"/output/argos_pair_workflow/425194f6-a974-4c2f-995f-f27d7ba54ddc/outputs/test_1.rg.md.abra.printreads.bai",
"/output/argos_pair_workflow/425194f6-a974-4c2f-995f-f27d7ba54ddc/outputs/test_2.rg.md.abra.printreads.bam",
"/output/argos_pair_workflow/425194f6-a974-4c2f-995f-f27d7ba54ddc/outputs/test_2.rg.md.abra.printreads.bai",
)
self.assertTrue(port.files.all()[0].path in expected_result)
self.assertTrue(port.files.all()[1].path in expected_result)
self.assertTrue(port.files.all()[2].path in expected_result)
self.assertTrue(port.files.all()[3].path in expected_result)
def test_run_complete_job(self, mock_get_pipeline):
with open('runner/tests/run/pair-workflow.cwl', 'r') as f:
app = json.load(f)
with open('runner/tests/run/inputs.json', 'r') as f:
inputs = json.load(f)
mock_get_pipeline.return_value = app
run = RunObject.from_cwl_definition(str(self.run.id), inputs)
run.to_db()
operator_run = OperatorRun.objects.first()
operator_run.runs.add(run.run_obj)
num_completed_runs = operator_run.num_completed_runs
complete_job(run.run_id, self.outputs)
operator_run.refresh_from_db()
self.assertEqual(operator_run.num_completed_runs,
num_completed_runs + 1)
run_obj = RunObject.from_db(run.run_id)
file_obj = File.objects.filter(path=self.outputs['maf']['location'].
replace('file://', '')).first()
run_obj.to_db()
for out in run_obj.outputs:
if out.name == 'maf':
self.assertEqual(out.value['location'],
self.outputs['maf']['location'])
self.assertEqual(FileProcessor.get_bid_from_file(file_obj),
out.db_value['location'])
port = Port.objects.filter(run_id=run_obj.run_id, name='bams').first()
self.assertEqual(len(port.files.all()), 4)
expected_result = (
'/output/argos_pair_workflow/425194f6-a974-4c2f-995f-f27d7ba54ddc/outputs/test_1.rg.md.abra.printreads.bam',
'/output/argos_pair_workflow/425194f6-a974-4c2f-995f-f27d7ba54ddc/outputs/test_1.rg.md.abra.printreads.bai',
'/output/argos_pair_workflow/425194f6-a974-4c2f-995f-f27d7ba54ddc/outputs/test_2.rg.md.abra.printreads.bam',
'/output/argos_pair_workflow/425194f6-a974-4c2f-995f-f27d7ba54ddc/outputs/test_2.rg.md.abra.printreads.bai'
)
self.assertTrue(port.files.all()[0].path in expected_result)
self.assertTrue(port.files.all()[1].path in expected_result)
self.assertTrue(port.files.all()[2].path in expected_result)
self.assertTrue(port.files.all()[3].path in expected_result)
def get_jobs(self):
files = FileRepository.filter(queryset=self.files,
metadata={
"requestId": self.request_id,
"igocomplete": True
})
argos_jobs = list()
cnt_tumors = FileRepository.filter(queryset=self.files,
metadata={
"requestId": self.request_id,
"tumorOrNormal": "Tumor",
"igocomplete": True
}).count()
if cnt_tumors == 0:
cant_do = CantDoEvent(self.job_group_notifier_id).to_dict()
send_notification.delay(cant_do)
all_normals_event = SetLabelEvent(self.job_group_notifier_id,
"all_normals").to_dict()
send_notification.delay(all_normals_event)
return argos_jobs
data = list()
for f in files:
sample = dict()
sample["id"] = f.file.id
sample["path"] = f.file.path
sample["file_name"] = f.file.file_name
sample["metadata"] = f.metadata
data.append(sample)
files = list()
samples = list()
# group by igoId
igo_id_group = dict()
for sample in data:
igo_id = sample["metadata"]["sampleId"]
if igo_id not in igo_id_group:
igo_id_group[igo_id] = list()
igo_id_group[igo_id].append(sample)
for igo_id in igo_id_group:
samples.append(build_sample(igo_id_group[igo_id]))
argos_inputs, error_samples = construct_argos_jobs(samples)
number_of_inputs = len(argos_inputs)
sample_pairing = ""
sample_mapping = ""
pipeline = self.get_pipeline_id()
try:
pipeline_obj = Pipeline.objects.get(id=pipeline)
except Pipeline.DoesNotExist:
pass
for i, job in enumerate(argos_inputs):
tumor_sample_name = job["pair"][0]["ID"]
for p in job["pair"][0]["R1"]:
filepath = FileProcessor.parse_path_from_uri(p["location"])
if filepath not in files:
sample_mapping += "\t".join([tumor_sample_name, filepath
]) + "\n"
files.append(filepath)
for p in job["pair"][0]["R2"]:
filepath = FileProcessor.parse_path_from_uri(p["location"])
if filepath not in files:
sample_mapping += "\t".join([tumor_sample_name, filepath
]) + "\n"
files.append(filepath)
for p in job["pair"][0]["zR1"]:
filepath = FileProcessor.parse_path_from_uri(p["location"])
if filepath not in files:
sample_mapping += "\t".join([tumor_sample_name, filepath
]) + "\n"
files.append(filepath)
for p in job["pair"][0]["zR2"]:
filepath = FileProcessor.parse_path_from_uri(p["location"])
if filepath not in files:
sample_mapping += "\t".join([tumor_sample_name, filepath
]) + "\n"
files.append(filepath)
normal_sample_name = job["pair"][1]["ID"]
for p in job["pair"][1]["R1"]:
filepath = FileProcessor.parse_path_from_uri(p["location"])
if filepath not in files:
sample_mapping += "\t".join([normal_sample_name, filepath
]) + "\n"
files.append(filepath)
for p in job["pair"][1]["R2"]:
filepath = FileProcessor.parse_path_from_uri(p["location"])
if filepath not in files:
sample_mapping += "\t".join([normal_sample_name, filepath
]) + "\n"
files.append(filepath)
for p in job["pair"][1]["zR1"]:
filepath = FileProcessor.parse_path_from_uri(p["location"])
if filepath not in files:
sample_mapping += "\t".join([normal_sample_name, filepath
]) + "\n"
files.append(filepath)
for p in job["pair"][1]["zR2"]:
filepath = FileProcessor.parse_path_from_uri(p["location"])
if filepath not in files:
sample_mapping += "\t".join([normal_sample_name, filepath
]) + "\n"
files.append(filepath)
for p in job["pair"][1]["bam"]:
filepath = FileProcessor.parse_path_from_uri(p["location"])
if filepath not in files:
sample_mapping += "\t".join([normal_sample_name, filepath
]) + "\n"
files.append(filepath)
name = "ARGOS %s, %i of %i" % (self.request_id, i + 1,
number_of_inputs)
assay = job["assay"]
pi = job["pi"]
pi_email = job["pi_email"]
sample_pairing += "\t".join(
[normal_sample_name, tumor_sample_name]) + "\n"
tags = {
"requestId": self.request_id,
"sampleNameTumor": tumor_sample_name,
"sampleNameNormal": normal_sample_name,
"labHeadName": pi,
"labHeadEmail": pi_email,
}
argos_jobs.append(
RunCreator(app=pipeline, inputs=job, name=name, tags=tags))
operator_run_summary = UploadAttachmentEvent(
self.job_group_notifier_id, "sample_pairing.txt",
sample_pairing).to_dict()
send_notification.delay(operator_run_summary)
mapping_file_event = UploadAttachmentEvent(self.job_group_notifier_id,
"sample_mapping.txt",
sample_mapping).to_dict()
send_notification.delay(mapping_file_event)
data_clinical = generate_sample_data_content(
files,
pipeline_name=pipeline_obj.name,
pipeline_github=pipeline_obj.github,
pipeline_version=pipeline_obj.version,
)
sample_data_clinical_event = UploadAttachmentEvent(
self.job_group_notifier_id, "sample_data_clinical.txt",
data_clinical).to_dict()
send_notification.delay(sample_data_clinical_event)
self.evaluate_sample_errors(error_samples)
self.summarize_pairing_info(argos_inputs)
return argos_jobs
def get_jobs(self):
argos_jobs = list()
if self.request_id:
files = FileRepository.filter(queryset=self.files,
metadata={
'requestId': self.request_id,
'igocomplete': True
},
filter_redact=True)
cnt_tumors = FileRepository.filter(queryset=self.files,
metadata={
'requestId':
self.request_id,
'tumorOrNormal': 'Tumor',
'igocomplete': True
},
filter_redact=True).count()
elif self.pairing:
files, cnt_tumors = self.get_files_for_pairs()
if cnt_tumors == 0:
cant_do = CantDoEvent(self.job_group_notifier_id).to_dict()
send_notification.delay(cant_do)
all_normals_event = SetLabelEvent(self.job_group_notifier_id,
'all_normals').to_dict()
send_notification.delay(all_normals_event)
return argos_jobs
data = list()
for f in files:
sample = dict()
sample['id'] = f.file.id
sample['path'] = f.file.path
sample['file_name'] = f.file.file_name
sample['metadata'] = f.metadata
data.append(sample)
files = list()
samples = list()
# group by igoId
igo_id_group = dict()
for sample in data:
igo_id = sample['metadata']['sampleId']
if igo_id not in igo_id_group:
igo_id_group[igo_id] = list()
igo_id_group[igo_id].append(sample)
for igo_id in igo_id_group:
samples.append(build_sample(igo_id_group[igo_id]))
argos_inputs, error_samples = construct_argos_jobs(
samples, self.pairing)
number_of_inputs = len(argos_inputs)
sample_pairing = ""
sample_mapping = ""
pipeline = self.get_pipeline_id()
try:
pipeline_obj = Pipeline.objects.get(id=pipeline)
except Pipeline.DoesNotExist:
pass
check_for_duplicates = list()
for i, job in enumerate(argos_inputs):
tumor_sample_name = job['pair'][0]['ID']
for p in job['pair'][0]['R1']:
filepath = FileProcessor.parse_path_from_uri(p['location'])
file_str = "\t".join([tumor_sample_name, filepath]) + "\n"
if file_str not in check_for_duplicates:
check_for_duplicates.append(file_str)
sample_mapping += file_str
if filepath not in files:
files.append(filepath)
for p in job['pair'][0]['R2']:
filepath = FileProcessor.parse_path_from_uri(p['location'])
file_str = "\t".join([tumor_sample_name, filepath]) + "\n"
if file_str not in check_for_duplicates:
check_for_duplicates.append(file_str)
sample_mapping += file_str
if filepath not in files:
files.append(filepath)
for p in job['pair'][0]['zR1']:
filepath = FileProcessor.parse_path_from_uri(p['location'])
file_str = "\t".join([tumor_sample_name, filepath]) + "\n"
if file_str not in check_for_duplicates:
check_for_duplicates.append(file_str)
sample_mapping += file_str
if filepath not in files:
files.append(filepath)
for p in job['pair'][0]['zR2']:
filepath = FileProcessor.parse_path_from_uri(p['location'])
file_str = "\t".join([tumor_sample_name, filepath]) + "\n"
if file_str not in check_for_duplicates:
check_for_duplicates.append(file_str)
sample_mapping += file_str
if filepath not in files:
files.append(filepath)
normal_sample_name = job['pair'][1]['ID']
for p in job['pair'][1]['R1']:
filepath = FileProcessor.parse_path_from_uri(p['location'])
file_str = "\t".join([normal_sample_name, filepath]) + "\n"
if file_str not in check_for_duplicates:
check_for_duplicates.append(file_str)
sample_mapping += file_str
if filepath not in files:
files.append(filepath)
for p in job['pair'][1]['R2']:
filepath = FileProcessor.parse_path_from_uri(p['location'])
file_str = "\t".join([normal_sample_name, filepath]) + "\n"
if file_str not in check_for_duplicates:
check_for_duplicates.append(file_str)
sample_mapping += file_str
if filepath not in files:
sample_mapping += "\t".join([normal_sample_name, filepath
]) + "\n"
files.append(filepath)
for p in job['pair'][1]['zR1']:
filepath = FileProcessor.parse_path_from_uri(p['location'])
file_str = "\t".join([normal_sample_name, filepath]) + "\n"
if file_str not in check_for_duplicates:
check_for_duplicates.append(file_str)
sample_mapping += file_str
if filepath not in files:
files.append(filepath)
for p in job['pair'][1]['zR2']:
filepath = FileProcessor.parse_path_from_uri(p['location'])
file_str = "\t".join([normal_sample_name, filepath]) + "\n"
if file_str not in check_for_duplicates:
check_for_duplicates.append(file_str)
sample_mapping += file_str
if filepath not in files:
files.append(filepath)
for p in job['pair'][1]['bam']:
filepath = FileProcessor.parse_path_from_uri(p['location'])
file_str = "\t".join([normal_sample_name, filepath]) + "\n"
if file_str not in check_for_duplicates:
check_for_duplicates.append(file_str)
sample_mapping += file_str
if filepath not in files:
files.append(filepath)
name = "ARGOS %s, %i of %i" % (self.request_id, i + 1,
number_of_inputs)
assay = job['assay']
pi = job['pi']
pi_email = job['pi_email']
sample_pairing += "\t".join(
[normal_sample_name, tumor_sample_name]) + "\n"
argos_jobs.append((APIRunCreateSerializer(
data={
'app': pipeline,
'inputs': argos_inputs,
'name': name,
'tags': {
'requestId': self.request_id,
'sampleNameTumor': tumor_sample_name,
'sampleNameNormal': normal_sample_name,
'labHeadName': pi,
'labHeadEmail': pi_email
}
}), job))
operator_run_summary = UploadAttachmentEvent(
self.job_group_notifier_id, 'sample_pairing.txt',
sample_pairing).to_dict()
send_notification.delay(operator_run_summary)
mapping_file_event = UploadAttachmentEvent(self.job_group_notifier_id,
'sample_mapping.txt',
sample_mapping).to_dict()
send_notification.delay(mapping_file_event)
data_clinical = generate_sample_data_content(
files,
pipeline_name=pipeline_obj.name,
pipeline_github=pipeline_obj.github,
pipeline_version=pipeline_obj.version)
sample_data_clinical_event = UploadAttachmentEvent(
self.job_group_notifier_id, 'sample_data_clinical.txt',
data_clinical).to_dict()
send_notification.delay(sample_data_clinical_event)
self.evaluate_sample_errors(error_samples)
self.summarize_pairing_info(argos_inputs)
return argos_jobs
def generate_sample_pairing_and_mapping_files(run_ids):
sample_pairing = ""
sample_mapping = ""
runs = Run.objects.filter(id__in=run_ids)
request_id_set = set()
files = list()
if runs:
pipeline = runs[0].app
for r in runs:
request_id_set.add(r.tags['requestId'])
inp_port = Port.objects.filter(run_id=r.id, name='pair').first()
tumor_sample_name = inp_port.db_value[0]['ID']
for p in inp_port.db_value[0]['R1']:
sample_mapping += "\t".join([
tumor_sample_name,
FileProcessor.get_file_path(p['location'])
]) + "\n"
files.append(FileProcessor.get_file_path(p['location']))
for p in inp_port.db_value[0]['R2']:
sample_mapping += "\t".join([
tumor_sample_name,
FileProcessor.get_file_path(p['location'])
]) + "\n"
files.append(FileProcessor.get_file_path(p['location']))
for p in inp_port.db_value[0]['zR1']:
sample_mapping += "\t".join([
tumor_sample_name,
FileProcessor.get_file_path(p['location'])
]) + "\n"
files.append(FileProcessor.get_file_path(p['location']))
for p in inp_port.db_value[0]['zR2']:
sample_mapping += "\t".join([
tumor_sample_name,
FileProcessor.get_file_path(p['location'])
]) + "\n"
files.append(FileProcessor.get_file_path(p['location']))
normal_sample_name = inp_port.db_value[1]['ID']
for p in inp_port.db_value[1]['R1']:
sample_mapping += "\t".join([
normal_sample_name,
FileProcessor.get_file_path(p['location'])
]) + "\n"
files.append(FileProcessor.get_file_path(p['location']))
for p in inp_port.db_value[1]['R2']:
sample_mapping += "\t".join([
normal_sample_name,
FileProcessor.get_file_path(p['location'])
]) + "\n"
files.append(FileProcessor.get_file_path(p['location']))
for p in inp_port.db_value[1]['zR1']:
sample_mapping += "\t".join([
normal_sample_name,
FileProcessor.get_file_path(p['location'])
]) + "\n"
files.append(FileProcessor.get_file_path(p['location']))
for p in inp_port.db_value[1]['zR2']:
sample_mapping += "\t".join([
normal_sample_name,
FileProcessor.get_file_path(p['location'])
]) + "\n"
files.append(FileProcessor.get_file_path(p['location']))
for p in inp_port.db_value[1]['bam']:
sample_mapping += "\t".join([
normal_sample_name,
FileProcessor.get_file_path(p['location'])
]) + "\n"
files.append(FileProcessor.get_file_path(p['location']))
sample_pairing += "\t".join([normal_sample_name, tumor_sample_name
]) + "\n"
if runs:
data_clinical = generate_sample_data_content(
files,
pipeline_name=pipeline.name,
pipeline_github=pipeline.github,
pipeline_version=pipeline.version)
return sample_mapping, sample_pairing, data_clinical
def test_create_file_type_unknown(self):
file_obj = FileProcessor.create_file_obj(
'file:///path/to/file.unknown_data_type', 123345,
'sha1$calculated checksum', str(self.file_group.id), {})
self.assertEqual(file_obj.file_type, self.file_type_unknown)
def test_create_file_setting_proper_file_type_based_on_extension(self):
file_obj = FileProcessor.create_file_obj(
'file:///path/to/file.fastq.gz', 123345,
'sha1$calculated checksum', str(self.file_group.id), {})
self.assertEqual(file_obj.file_type, self.file_type_fastq)
