def project_page_data(request, project_guid):
"""Returns a JSON object containing information used by the project page:
::
json_response = {
'project': {..},
'familiesByGuid': {..},
'individualsByGuid': {..},
'samplesByGuid': {..},
}
Args:
project_guid (string): GUID of the Project to retrieve data for.
"""
project = get_project_and_check_permissions(project_guid, request.user)
update_project_from_json(project, {'last_accessed_date': timezone.now()})
response = _get_project_child_entities(project, request.user)
project_json = _get_json_for_project(project, request.user)
project_json['collaborators'] = get_json_for_project_collaborator_list(project)
project_json['locusListGuids'] = response['locusListsByGuid'].keys()
project_json['detailsLoaded'] = True
project_json.update(_get_json_for_variant_tag_types(project))
gene_ids = set()
for tag in project_json['discoveryTags']:
gene_ids.update(tag.get('transcripts', {}).keys())
response.update({
'projectsByGuid': {project_guid: project_json},
'genesById': get_genes(gene_ids),
})
return create_json_response(response)
def project_page_data(request, project_guid):
"""Returns a JSON object containing information used by the project page:
::
json_response = {
'project': {..},
'familiesByGuid': {..},
'individualsByGuid': {..},
'samplesByGuid': {..},
}
Args:
project_guid (string): GUID of the Project to retrieve data for.
"""
project = get_project_and_check_permissions(project_guid, request.user)
update_project_from_json(project, {'last_accessed_date': timezone.now()})
families_by_guid, individuals_by_guid, samples_by_guid, analysis_groups_by_guid, locus_lists_by_guid = _get_project_child_entities(
project, request.user)
project_json = _get_json_for_project(project, request.user)
project_json['collaborators'] = get_json_for_project_collaborator_list(
project)
project_json.update(
_get_json_for_variant_tag_types(project, request.user,
individuals_by_guid))
project_json['locusListGuids'] = locus_lists_by_guid.keys()
project_json['detailsLoaded'] = True
return create_json_response({
'projectsByGuid': {
project_guid: project_json
},
'familiesByGuid':
families_by_guid,
'individualsByGuid':
individuals_by_guid,
'samplesByGuid':
samples_by_guid,
'locusListsByGuid':
locus_lists_by_guid,
'analysisGroupsByGuid':
analysis_groups_by_guid,
})
def update_project_handler(request, project_guid):
"""Update project metadata - including one or more of these fields: name, description
Args:
project_guid (string): GUID of the project that should be updated
HTTP POST
Request body - should contain the following json structure:
{
'form' : {
'name': <project name>,
'description': <project description>,
}
}
Response body - will contain the following structure, representing the updated project:
{
'projectsByGuid': {
<projectGuid1> : { ... <project key-value pairs> ... }
}
}
"""
project = Project.objects.get(guid=project_guid)
check_project_permissions(project, request.user, can_edit=True)
request_json = json.loads(request.body)
update_project_from_json(project,
request_json,
request.user,
allow_unknown_keys=True)
return create_json_response({
'projectsByGuid': {
project.guid: _get_json_for_project(project, request.user)
},
})
def update_project_handler(request, project_guid):
"""Update project metadata - including one or more of these fields: name, description
Args:
project_guid (string): GUID of the project that should be updated
HTTP POST
Request body - should contain the following json structure:
{
'form' : {
'name': <project name>,
'description': <project description>,
}
}
Response body - will contain the following structure, representing the updated project:
{
'projectsByGuid': {
<projectGuid1> : { ... <project key-value pairs> ... }
}
}
"""
project = Project.objects.get(guid=project_guid)
check_permissions(project, request.user, CAN_EDIT)
request_json = json.loads(request.body)
update_project_from_json(project, request_json, allow_unknown_keys=True)
return create_json_response({
'projectsByGuid': {
project.guid: _get_json_for_project(project, request.user)
},
})
def add_variants_dataset_handler(request, project_guid):
"""Create or update samples for the given variant 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:
{
'elasticsearchIndex': <String> (required)
'ignoreExtraSamplesInCallset': <Boolean>
'mappingFilePath': <String>
}
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:
if 'elasticsearchIndex' not in request_json:
raise ValueError('"elasticsearchIndex" is required')
elasticsearch_index = request_json['elasticsearchIndex'].strip()
sample_ids, index_metadata = get_elasticsearch_index_samples(elasticsearch_index)
validate_index_metadata(index_metadata, project, elasticsearch_index)
sample_type = index_metadata['sampleType']
dataset_path = index_metadata['sourceFilePath']
sample_id_to_individual_id_mapping = load_mapping_file(
request_json['mappingFilePath']) if request_json.get('mappingFilePath') else {}
matched_sample_id_to_sample_record = match_sample_ids_to_sample_records(
project=project,
sample_ids=sample_ids,
sample_type=sample_type,
dataset_type=Sample.DATASET_TYPE_VARIANT_CALLS,
elasticsearch_index=elasticsearch_index,
sample_id_to_individual_id_mapping=sample_id_to_individual_id_mapping,
)
unmatched_samples = set(sample_ids) - set(matched_sample_id_to_sample_record.keys())
if request_json.get('ignoreExtraSamplesInCallset'):
if len(matched_sample_id_to_sample_record) == 0:
raise Exception(
"None of the individuals or samples in the project matched the {} expected sample id(s)".format(
len(sample_ids)
))
elif len(unmatched_samples) > 0:
raise Exception(
'Matches not found for ES sample ids: {}. Uploading a mapping file for these samples, or select the "Ignore extra samples in callset" checkbox to ignore.'.format(
", ".join(unmatched_samples)))
prefetch_related_objects(matched_sample_id_to_sample_record.values(), 'individual__family')
included_families = {sample.individual.family for sample in matched_sample_id_to_sample_record.values()}
missing_individuals = Individual.objects.filter(
family__in=included_families,
sample__is_active=True,
sample__dataset_type=Sample.DATASET_TYPE_VARIANT_CALLS,
).exclude(sample__in=matched_sample_id_to_sample_record.values()).select_related('family')
missing_family_individuals = defaultdict(list)
for individual in missing_individuals:
missing_family_individuals[individual.family].append(individual)
if missing_family_individuals:
raise Exception(
'The following families are included in the callset but are missing some family members: {}.'.format(
', '.join(
['{} ({})'.format(family.family_id, ', '.join([i.individual_id for i in missing_indivs]))
for family, missing_indivs in missing_family_individuals.items()]
)))
inactivate_sample_guids = _update_variant_samples(
matched_sample_id_to_sample_record, elasticsearch_index=elasticsearch_index, dataset_path=dataset_path
)
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': {}})
update_project_from_json(project, {'has_new_search': True})
reset_cached_search_results(project)
update_xbrowse_vcfffiles(
project, sample_type, elasticsearch_index, dataset_path, matched_sample_id_to_sample_record
)
families_to_update = [
family for family in included_families if family.analysis_status == Family.ANALYSIS_STATUS_WAITING_FOR_DATA]
for family in families_to_update:
update_model_from_json(family, {'analysis_status': Family.ANALYSIS_STATUS_ANALYSIS_IN_PROGRESS})
response_json = _get_samples_json(matched_sample_id_to_sample_record, inactivate_sample_guids, project_guid)
response_json['familiesByGuid'] = {family.guid: {'analysisStatus': Family.ANALYSIS_STATUS_ANALYSIS_IN_PROGRESS}
for family in families_to_update}
return create_json_response(response_json)
def add_variants_dataset_handler(request, project_guid):
"""Create or update samples for the given variant 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:
{
'elasticsearchIndex': <String> (required)
'ignoreExtraSamplesInCallset': <Boolean>
'ignoreMissingFamilyMembers': <Boolean>
'mappingFilePath': <String>
}
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:
if 'elasticsearchIndex' not in request_json:
raise ValueError('"elasticsearchIndex" is required')
elasticsearch_index = request_json['elasticsearchIndex'].strip()
sample_ids, index_metadata = get_elasticsearch_index_samples(elasticsearch_index)
validate_index_metadata(index_metadata, project, elasticsearch_index)
sample_type = index_metadata['sampleType']
dataset_path = index_metadata['sourceFilePath']
sample_id_to_individual_id_mapping = load_mapping_file(
request_json['mappingFilePath']) if request_json.get('mappingFilePath') else {}
matched_sample_id_to_sample_record = match_sample_ids_to_sample_records(
project=project,
sample_ids=sample_ids,
sample_type=sample_type,
dataset_type=Sample.DATASET_TYPE_VARIANT_CALLS,
elasticsearch_index=elasticsearch_index,
sample_id_to_individual_id_mapping=sample_id_to_individual_id_mapping,
)
unmatched_samples = set(sample_ids) - set(matched_sample_id_to_sample_record.keys())
if request_json.get('ignoreExtraSamplesInCallset'):
if len(matched_sample_id_to_sample_record) == 0:
raise Exception(
"None of the individuals or samples in the project matched the {} expected sample id(s)".format(
len(sample_ids)
))
elif len(unmatched_samples) > 0:
raise Exception(
'Matches not found for ES sample ids: {}. Uploading a mapping file for these samples, or select the "Ignore extra samples in callset" checkbox to ignore.'.format(
", ".join(unmatched_samples)))
if not request_json.get('ignoreMissingFamilyMembers'):
included_family_individuals = defaultdict(set)
for sample in matched_sample_id_to_sample_record.values():
included_family_individuals[sample.individual.family].add(sample.individual.individual_id)
missing_family_individuals = []
for family, individual_ids in included_family_individuals.items():
missing_indivs = family.individual_set.filter(
sample__sample_status=Sample.SAMPLE_STATUS_LOADED,
sample__dataset_type=Sample.DATASET_TYPE_VARIANT_CALLS
).exclude(individual_id__in=individual_ids)
if missing_indivs:
missing_family_individuals.append(
'{} ({})'.format(family.family_id, ', '.join([i.individual_id for i in missing_indivs]))
)
if missing_family_individuals:
raise Exception(
'The following families are included in the callset but are missing some family members: {}. This can lead to errors in variant search. If you still want to upload this callset, select the "Ignore missing family members" checkbox.'.format(
', '.join(missing_family_individuals)
))
_update_samples(
matched_sample_id_to_sample_record, elasticsearch_index=elasticsearch_index, dataset_path=dataset_path
)
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': {}})
update_project_from_json(project, {'has_new_search': True})
reset_cached_search_results(project)
_deprecated_update_vcfffiles(
project, sample_type, elasticsearch_index, dataset_path, matched_sample_id_to_sample_record
)
return create_json_response(_get_samples_json(matched_sample_id_to_sample_record, project_guid))
