def update_individual_igv_sample(request, individual_guid):
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_project_permissions(project, request.user, can_edit=True)
request_json = json.loads(request.body)
try:
file_path = request_json.get('filePath')
if not file_path:
raise ValueError('request must contain fields: filePath')
suffix = '.'.join(file_path.split('.')[1:])
sample_type = SAMPLE_TYPE_MAP.get(suffix)
if not sample_type:
raise Exception(
'Invalid file extension for "{}" - valid extensions are {}'.
format(file_path, ', '.join(SAMPLE_TYPE_MAP.keys())))
validate_alignment_dataset_path(file_path)
sample, created = get_or_create_model_from_json(
IgvSample,
create_json={
'individual': individual,
'sample_type': sample_type
},
update_json={
'file_path': file_path,
'sample_id': request_json.get('sampleId')
},
user=request.user)
response = {
'igvSamplesByGuid': {
sample.guid:
get_json_for_sample(sample,
individual_guid=individual_guid,
project_guid=project.guid)
}
}
if created:
response['individualsByGuid'] = {
individual.guid: {
'igvSampleGuids':
[s.guid for s in individual.igvsample_set.all()]
}
}
return create_json_response(response)
except Exception as e:
error = str(e)
return create_json_response({'error': error}, status=400, reason=error)
def handle(self, *args, **options):
samples = IgvSample.objects.filter(
individual__family__project__name__in=args,
).prefetch_related('individual', 'individual__family')
failed = []
for sample in samples:
try:
validate_alignment_dataset_path(sample.file_path)
except Exception as e:
individual_id = sample.individual.individual_id
failed.append(individual_id)
logger.info('Error at {} (Individual: {}): {} '.format(sample.file_path, individual_id, str(e)))
logger.info('---- DONE ----')
logger.info('Checked {} samples'.format(len(samples)))
logger.info('{} failed samples: {}'.format(len(failed), ', '.join(failed)))
def update_individual_igv_sample(request, individual_guid):
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_permissions(project, request.user, CAN_EDIT)
request_json = json.loads(request.body)
try:
required_fields = ['filePath']
if any(field not in request_json for field in required_fields):
raise ValueError("request must contain fields: {}".format(
', '.join(required_fields)))
file_path = request_json['filePath']
if not (file_path.endswith(".bam") or file_path.endswith(".cram")):
raise Exception(
'BAM / CRAM file "{}" must have a .bam or .cram extension'.
format(file_path))
validate_alignment_dataset_path(file_path)
sample, created = IgvSample.objects.get_or_create(
individual=individual)
sample.file_path = file_path
sample.save()
response = {
'igvSamplesByGuid': {
sample.guid:
get_json_for_sample(sample,
individual_guid=individual_guid,
project_guid=project.guid)
}
}
if created:
response['individualsByGuid'] = {
individual.guid: {
'igvSampleGuids':
[s.guid for s in individual.igvsample_set.all()]
}
}
return create_json_response(response)
except Exception as e:
error = e.message or str(e)
return create_json_response({'error': error}, status=400, reason=error)
def handle(self, *args, **options):
samples = Sample.objects.filter(
dataset_type=Sample.DATASET_TYPE_READ_ALIGNMENTS,
is_active=True,
dataset_file_path__isnull=False,
individual__family__project__name__in=args,
).prefetch_related('individual', 'individual__family')
failed = []
for sample in samples:
try:
validate_alignment_dataset_path(sample.dataset_file_path)
except Exception as e:
individual_id = sample.individual.individual_id
failed.append(individual_id)
print('Error at {} (Individual: {}): {} '.format(
sample.dataset_file_path, individual_id, e.message))
print('---- DONE ----')
print('Checked {} samples'.format(len(samples)))
print('{} failed samples: {}'.format(len(failed), ', '.join(failed)))
def update_individual_alignment_sample(request, individual_guid):
"""Create or update samples for the given dataset
Args:
request: Django request object
individual_guid (string): GUID of the individual that should be updated
HTTP POST
Request body - should contain the following json structure:
{
'sampleType': <"WGS", "WES", or "RNA"> (required)
'datasetType': <"VARIANTS", or "ALIGN"> (required)
'elasticsearchIndex': <String>
'datasetPath': <String>
'datasetName': <String>
'ignoreExtraSamplesInCallset': <Boolean>
'mappingFile': { 'uploadedFileId': <Id for temporary uploaded file> }
}
Response body - will contain the following structure:
"""
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_permissions(project, request.user, CAN_EDIT)
request_json = json.loads(request.body)
try:
required_fields = ['sampleType', 'datasetFilePath']
if any(field not in request_json for field in required_fields):
raise ValueError(
"request must contain fields: {}".format(', '.join(required_fields)))
sample_type = request_json['sampleType']
if sample_type not in {choice[0] for choice in Sample.SAMPLE_TYPE_CHOICES}:
raise Exception("Sample type not supported: {}".format(sample_type))
dataset_path = request_json['datasetFilePath']
if not (dataset_path.endswith(".bam") or dataset_path.endswith(".cram")):
raise Exception('BAM / CRAM file "{}" must have a .bam or .cram extension'.format(dataset_path))
validate_alignment_dataset_path(dataset_path)
sample, created = Sample.objects.get_or_create(
individual=individual,
dataset_type=Sample.DATASET_TYPE_READ_ALIGNMENTS,
is_active=True,
)
sample.dataset_file_path = dataset_path
sample.sample_type = sample_type
sample.sample_id = dataset_path.split('/')[-1].split('.')[0]
if created:
sample.loaded_date = timezone.now()
sample.save()
response = {
'samplesByGuid': {
sample.guid: get_json_for_sample(sample, individual_guid=individual_guid, project_guid=project.guid)}
}
if created:
response['individualsByGuid'] = {
individual.guid: {'sampleGuids': [s.guid for s in individual.sample_set.all()]}
}
return create_json_response(response)
except Exception as e:
return create_json_response({}, status=400, reason=e.message or str(e))
def add_alignment_dataset_handler(request, project_guid):
"""Create or update samples for the given dataset
Args:
request: Django request object
project_guid (string): GUID of the project that should be updated
HTTP POST
Request body - should contain the following json structure:
{
'sampleType': <"WGS", "WES", or "RNA"> (required)
'datasetType': <"VARIANTS", or "ALIGN"> (required)
'elasticsearchIndex': <String>
'datasetPath': <String>
'datasetName': <String>
'ignoreExtraSamplesInCallset': <Boolean>
'mappingFile': { 'uploadedFileId': <Id for temporary uploaded file> }
}
Response body - will contain the following structure:
"""
project = get_project_and_check_permissions(project_guid,
request.user,
permission_level=CAN_EDIT)
request_json = json.loads(request.body)
try:
required_fields = ['sampleType', 'mappingFile']
if any(field not in request_json for field in required_fields):
raise ValueError("request must contain fields: {}".format(
', '.join(required_fields)))
sample_type = request_json['sampleType']
if sample_type not in {
choice[0]
for choice in Sample.SAMPLE_TYPE_CHOICES
}:
raise Exception(
"Sample type not supported: {}".format(sample_type))
mapping_file_id = request_json['mappingFile']['uploadedFileId']
sample_id_to_individual_id_mapping = {}
sample_dataset_path_mapping = {}
for individual_id, dataset_path in load_uploaded_mapping_file(
mapping_file_id).items():
if not (dataset_path.endswith(".bam")
or dataset_path.endswith(".cram")):
raise Exception(
'BAM / CRAM file "{}" must have a .bam or .cram extension'.
format(dataset_path))
validate_alignment_dataset_path(dataset_path)
sample_id = dataset_path.split('/')[-1].split('.')[0]
sample_id_to_individual_id_mapping[sample_id] = individual_id
sample_dataset_path_mapping[sample_id] = dataset_path
matched_sample_id_to_sample_record = match_sample_ids_to_sample_records(
project=project,
sample_ids=sample_id_to_individual_id_mapping.keys(),
sample_type=sample_type,
dataset_type=Sample.DATASET_TYPE_READ_ALIGNMENTS,
sample_id_to_individual_id_mapping=
sample_id_to_individual_id_mapping,
)
unmatched_samples = set(
sample_id_to_individual_id_mapping.keys()) - set(
matched_sample_id_to_sample_record.keys())
if len(unmatched_samples) > 0:
raise Exception(
'The following Individual IDs do not exist: {}'.format(
", ".join(unmatched_samples)))
_update_samples(
matched_sample_id_to_sample_record,
sample_dataset_path_mapping=sample_dataset_path_mapping)
except Exception as e:
traceback.print_exc()
return create_json_response({'errors': [e.message or str(e)]},
status=400)
if not matched_sample_id_to_sample_record:
return create_json_response({'samplesByGuid': {}})
# Deprecated update VCFFile records
for sample in matched_sample_id_to_sample_record.values():
base_indiv = find_matching_xbrowse_model(sample.individual)
if base_indiv:
base_indiv.bam_file_path = sample.dataset_file_path
base_indiv.save()
return create_json_response(
_get_samples_json(matched_sample_id_to_sample_record, project_guid))
def add_alignment_dataset_handler(request, project_guid):
"""Create or update samples for the given dataset
Args:
request: Django request object
project_guid (string): GUID of the project that should be updated
HTTP POST
Request body - should contain the following json structure:
{
'sampleType': <"WGS", "WES", or "RNA"> (required)
'datasetType': <"VARIANTS", or "ALIGN"> (required)
'elasticsearchIndex': <String>
'datasetPath': <String>
'datasetName': <String>
'ignoreExtraSamplesInCallset': <Boolean>
'mappingFile': { 'uploadedFileId': <Id for temporary uploaded file> }
}
Response body - will contain the following structure:
"""
project = get_project_and_check_permissions(project_guid, request.user, permission_level=CAN_EDIT)
request_json = json.loads(request.body)
try:
required_fields = ['sampleType', 'mappingFile']
if any(field not in request_json for field in required_fields):
raise ValueError(
"request must contain fields: {}".format(', '.join(required_fields)))
sample_type = request_json['sampleType']
if sample_type not in {choice[0] for choice in Sample.SAMPLE_TYPE_CHOICES}:
raise Exception("Sample type not supported: {}".format(sample_type))
mapping_file_id = request_json['mappingFile']['uploadedFileId']
sample_id_to_individual_id_mapping = {}
sample_dataset_path_mapping = {}
for individual_id, dataset_path in load_uploaded_mapping_file(mapping_file_id).items():
if not (dataset_path.endswith(".bam") or dataset_path.endswith(".cram")):
raise Exception('BAM / CRAM file "{}" must have a .bam or .cram extension'.format(dataset_path))
validate_alignment_dataset_path(dataset_path)
sample_id = dataset_path.split('/')[-1].split('.')[0]
sample_id_to_individual_id_mapping[sample_id] = individual_id
sample_dataset_path_mapping[sample_id] = dataset_path
matched_sample_id_to_sample_record = match_sample_ids_to_sample_records(
project=project,
sample_ids=sample_id_to_individual_id_mapping.keys(),
sample_type=sample_type,
dataset_type=Sample.DATASET_TYPE_READ_ALIGNMENTS,
sample_id_to_individual_id_mapping=sample_id_to_individual_id_mapping,
)
unmatched_samples = set(sample_id_to_individual_id_mapping.keys()) - set(matched_sample_id_to_sample_record.keys())
if len(unmatched_samples) > 0:
raise Exception('The following Individual IDs do not exist: {}'.format(", ".join(unmatched_samples)))
_update_samples(matched_sample_id_to_sample_record, sample_dataset_path_mapping=sample_dataset_path_mapping)
except Exception as e:
traceback.print_exc()
return create_json_response({'errors': [e.message or str(e)]}, status=400)
if not matched_sample_id_to_sample_record:
return create_json_response({'samplesByGuid': {}})
# Deprecated update VCFFile records
for sample in matched_sample_id_to_sample_record.values():
for base_indiv in BaseIndividual.objects.filter(seqr_individual=sample.individual).only('id'):
base_indiv.bam_file_path = sample.dataset_file_path
base_indiv.save()
return create_json_response(_get_samples_json(matched_sample_id_to_sample_record, project_guid))