def _update_locus_list_items(locus_list, genes_by_id, intervals, request_json,
user):
# Update genes
for locus_list_gene in locus_list.locuslistgene_set.exclude(
gene_id__in=genes_by_id.keys()):
delete_seqr_model(locus_list_gene)
for gene_id in genes_by_id.keys():
get_or_create_seqr_model(
LocusListGene,
locus_list=locus_list,
gene_id=gene_id,
created_by=user,
)
# Update intervals
genome_version = request_json.get(
'intervalGenomeVersion') or GENOME_VERSION_GRCh37
interval_guids = set()
for interval in intervals:
interval_model, _ = LocusListInterval.objects.get_or_create(
locus_list=locus_list,
chrom=interval['chrom'],
start=interval['start'],
end=interval['end'],
genome_version=genome_version,
)
interval_guids.add(interval_model.guid)
locus_list.locuslistinterval_set.exclude(guid__in=interval_guids).delete()
def _update_locus_list_items(locus_list, genes_by_id, intervals, request_json, user):
# Update genes
for locus_list_gene in locus_list.locuslistgene_set.exclude(gene_id__in=genes_by_id.keys()):
delete_seqr_model(locus_list_gene)
for gene_id in genes_by_id.keys():
get_or_create_seqr_model(
LocusListGene,
locus_list=locus_list,
gene_id=gene_id,
created_by=user,
)
# Update intervals
genome_version = request_json.get('intervalGenomeVersion') or GENOME_VERSION_GRCh37
interval_guids = set()
for interval in intervals:
interval_model, _ = LocusListInterval.objects.get_or_create(
locus_list=locus_list,
chrom=interval['chrom'],
start=interval['start'],
end=interval['end'],
genome_version=genome_version,
)
interval_guids.add(interval_model.guid)
locus_list.locuslistinterval_set.exclude(guid__in=interval_guids).delete()
def _create_project(name, description=None, genome_version=None, user=None):
"""Creates a new project.
Args:
name (string): Project name
description (string): optional description
user (object): Django user that is creating this project
"""
if not name:
raise ValueError("Name not specified: %s" % (name,))
project_args = {
'name': name,
'description': description,
'created_by': user,
'deprecated_project_id': _slugify(name),
}
if genome_version:
project_args['genome_version'] = genome_version
project, _ = get_or_create_seqr_model(Project, **project_args)
if PHENOTIPS_SERVER:
try:
_enable_phenotips_for_project(project)
except Exception as e:
logger.error("Unable to create patient in PhenoTips. Make sure PhenoTips is running: %s", e)
raise
return project
def edit_families_handler(request, project_guid):
"""Edit or one or more Family records.
Args:
project_guid (string): GUID of project that contains these individuals.
"""
request_json = json.loads(request.body)
if request_json.get('uploadedFileId'):
modified_families = load_uploaded_file(
request_json.get('uploadedFileId'))
else:
modified_families = request_json.get('families')
if modified_families is None:
return create_json_response({},
status=400,
reason="'families' not specified")
project = get_project_and_check_permissions(project_guid, request.user,
CAN_EDIT)
updated_families = []
for fields in modified_families:
if fields.get('familyGuid'):
family = Family.objects.get(project=project,
guid=fields['familyGuid'])
elif fields.get(PREVIOUS_FAMILY_ID_FIELD):
family = Family.objects.get(
project=project, family_id=fields[PREVIOUS_FAMILY_ID_FIELD])
else:
family, _ = get_or_create_seqr_model(
Family, project=project, family_id=fields[FAMILY_ID_FIELD])
update_family_from_json(family,
fields,
user=request.user,
allow_unknown_keys=True)
updated_families.append(family)
updated_families_by_guid = {
'familiesByGuid': {
family.guid: _get_json_for_family(family,
request.user,
add_individual_guids_field=True)
for family in updated_families
}
}
return create_json_response(updated_families_by_guid)
def edit_families_handler(request, project_guid):
"""Edit or one or more Family records.
Args:
project_guid (string): GUID of project that contains these individuals.
"""
request_json = json.loads(request.body)
if request_json.get('uploadedFileId'):
modified_families = load_uploaded_file(request_json.get('uploadedFileId'))
else:
modified_families = request_json.get('families')
if modified_families is None:
return create_json_response(
{}, status=400, reason="'families' not specified")
project = get_project_and_check_permissions(project_guid, request.user, CAN_EDIT)
updated_families = []
for fields in modified_families:
if fields.get('familyGuid'):
family = Family.objects.get(project=project, guid=fields['familyGuid'])
elif fields.get(PREVIOUS_FAMILY_ID_FIELD):
family = Family.objects.get(project=project, family_id=fields[PREVIOUS_FAMILY_ID_FIELD])
else:
family, _ = get_or_create_seqr_model(Family, project=project, family_id=fields[FAMILY_ID_FIELD])
update_family_from_json(family, fields, user=request.user, allow_unknown_keys=True)
updated_families.append(family)
updated_families_by_guid = {
'familiesByGuid': {
family.guid: _get_json_for_family(family, request.user, add_individual_guids_field=True) for family in updated_families
}
}
return create_json_response(updated_families_by_guid)
def handle(self, *args, **options):
from_project = Project.objects.get(guid=options['from_project'])
to_project = Project.objects.get(guid=options['to_project'])
family_ids = options['family_ids']
families = Family.objects.filter(project=from_project,
family_id__in=family_ids)
print('Found {} out of {} families. No match for: {}.'.format(
len(families), len(set(family_ids)),
set(family_ids) - set([f.family_id for f in families])))
for f in families:
print("==> Moving phenotips for {}".format(f))
for seqr_individual in f.individual_set.all():
if phenotips_patient_exists(seqr_individual):
# make sure phenotips_patient_id is up to date
data_json = _get_patient_data(
from_project,
seqr_individual,
)
seqr_individual.phenotips_patient_id = data_json["id"]
seqr_individual.save()
# update permissions
phenotips_readonly_username, _ = get_phenotips_uname_and_pwd_for_project(
to_project.phenotips_user_id, read_only=True)
_add_user_to_patient(phenotips_readonly_username,
seqr_individual.phenotips_patient_id,
allow_edit=False)
phenotips_readwrite_username, _ = get_phenotips_uname_and_pwd_for_project(
to_project.phenotips_user_id, read_only=False)
_add_user_to_patient(phenotips_readwrite_username,
seqr_individual.phenotips_patient_id,
allow_edit=True)
for variant_tag_type in VariantTagType.objects.filter(
project=from_project):
variant_tags = VariantTag.objects.filter(
saved_variant__family__in=families,
variant_tag_type=variant_tag_type)
if variant_tags:
print('Updating "{}" tags'.format(variant_tag_type.name))
to_tag_type, created = get_or_create_seqr_model(
VariantTagType,
project=to_project,
name=variant_tag_type.name)
if created:
update_seqr_model(
to_tag_type,
category=variant_tag_type.category,
description=variant_tag_type.description,
color=variant_tag_type.color,
order=variant_tag_type.order,
)
variant_tags.update(variant_tag_type=to_tag_type)
print("Updating families")
families.update(project=to_project)
print("Done.")
def add_or_update_individuals_and_families(project, individual_records, user=None):
"""Add or update individual and family records in the given project.
Args:
project (object): Django ORM model for the project to add families to
individual_records (list): A list of JSON records representing individuals. See
the return value of pedigree_info_utils#convert_fam_file_rows_to_json(..)
Return:
2-tuple: updated_families, updated_individuals containing Django ORM models
"""
families = {}
updated_individuals = set()
parent_updates = []
for i, record in enumerate(individual_records):
# family id will be in different places in the json depending on whether it comes from a flat uploaded file or from the nested individual object
family_id = record.get(JsonConstants.FAMILY_ID_COLUMN) or record.get('family', {}).get('familyId')
if not family_id:
raise ValueError("record #%s doesn't contain a 'familyId' key: %s" % (i, record))
if JsonConstants.INDIVIDUAL_ID_COLUMN not in record and 'individualGuid' not in record:
raise ValueError("record #%s doesn't contain an 'individualId' key: %s" % (i, record))
family = families.get(family_id)
if family:
created = False
else:
family, created = get_or_create_seqr_model(Family, project=project, family_id=family_id)
if created:
logger.info("Created family: %s", family)
# uploaded files do not have unique guid's so fall back to a combination of family and individualId
if record.get('individualGuid'):
individual_filters = {'guid': record['individualGuid']}
else:
individual_id = record.get(JsonConstants.PREVIOUS_INDIVIDUAL_ID_COLUMN) or record[JsonConstants.INDIVIDUAL_ID_COLUMN]
individual_filters = {'family': family, 'individual_id': individual_id}
individual, created = get_or_create_seqr_model(Individual, **individual_filters)
if created:
record.update({
'caseReviewStatus': 'I',
})
record['family'] = family
record.pop('familyId', None)
if individual.family != family:
families[individual.family.family_id] = individual.family
if record.get(JsonConstants.PREVIOUS_INDIVIDUAL_ID_COLUMN):
updated_individuals.update(individual.maternal_children.all())
updated_individuals.update(individual.paternal_children.all())
record['displayName'] = ''
# Update the parent ids last, so if they are referencing updated individuals they will check for the correct ID
if record.get('maternalId') or record.get('paternalId'):
parent_updates.append({
'individual': individual,
'maternalId': record.pop('maternalId', None),
'paternalId': record.pop('paternalId', None),
})
update_individual_from_json(individual, record, allow_unknown_keys=True, user=user)
updated_individuals.add(individual)
families[family.family_id] = family
for update in parent_updates:
individual = update.pop('individual')
update_individual_from_json(individual, update, user=user)
updated_families = list(families.values())
# update pedigree images
update_pedigree_images(updated_families, project_guid=project.guid)
return updated_families, list(updated_individuals)
def add_or_update_individuals_and_families(project,
individual_records,
user=None):
"""Add or update individual and family records in the given project.
Args:
project (object): Django ORM model for the project to add families to
individual_records (list): A list of JSON records representing individuals. See
the return value of pedigree_info_utils#convert_fam_file_rows_to_json(..)
Return:
2-tuple: updated_families, updated_individuals containing Django ORM models
"""
families = {}
updated_individuals = []
for i, record in enumerate(individual_records):
# family id will be in different places in the json depending on whether it comes from a flat uploaded file or from the nested individual object
family_id = record.get('familyId') or record.get('family',
{}).get('familyId')
if not family_id:
raise ValueError(
"record #%s doesn't contain a 'familyId' key: %s" %
(i, record))
if 'individualId' not in record and 'individualGuid' not in record:
raise ValueError(
"record #%s doesn't contain an 'individualId' key: %s" %
(i, record))
family, created = get_or_create_seqr_model(Family,
project=project,
family_id=family_id)
if created:
logger.info("Created family: %s", family)
if not family.display_name:
update_seqr_model(family, display_name=family.family_id)
# uploaded files do not have unique guid's so fall back to a combination of family and individualId
if record.get('individualGuid'):
individual_filters = {'guid': record['individualGuid']}
else:
individual_filters = {
'family': family,
'individual_id': record['individualId']
}
individual, created = get_or_create_seqr_model(Individual,
**individual_filters)
record['family'] = family
record.pop('familyId', None)
update_individual_from_json(individual,
record,
allow_unknown_keys=True,
user=user)
updated_individuals.append(individual)
# apply additional json fields which don't directly map to Individual model fields
individual.phenotips_eid = individual.guid # use guid instead of indiv_id to avoid collisions
if created:
# create new PhenoTips patient record
patient_record = create_patient(project, individual)
update_seqr_model(individual,
phenotips_patient_id=patient_record['id'],
case_review_status='I')
logger.info(
"Created PhenoTips record with patient id %s and external id %s"
% (str(individual.phenotips_patient_id),
str(individual.phenotips_eid)))
if record.get(JsonConstants.HPO_TERMS_PRESENT_COLUMN) or record.get(
JsonConstants.FINAL_DIAGNOSIS_OMIM_COLUMN):
# update phenotips hpo ids
logger.info("Setting PhenoTips HPO Terms to: %s" %
(record.get(JsonConstants.HPO_TERMS_PRESENT_COLUMN), ))
set_patient_hpo_terms(
project,
individual,
hpo_terms_present=record.get(
JsonConstants.HPO_TERMS_PRESENT_COLUMN, []),
hpo_terms_absent=record.get(
JsonConstants.HPO_TERMS_ABSENT_COLUMN, []),
final_diagnosis_mim_ids=record.get(
JsonConstants.FINAL_DIAGNOSIS_OMIM_COLUMN, []))
if not individual.display_name:
update_seqr_model(individual,
display_name=individual.individual_id)
families[family.family_id] = family
updated_families = list(families.values())
# update pedigree images
update_pedigree_images(updated_families)
return updated_families, updated_individuals
def handle(self, *args, **options):
from_project = Project.objects.get(guid=options['from_project'])
to_project = Project.objects.get(guid=options['to_project'])
to_base_project = find_matching_xbrowse_model(to_project)
family_ids = options['family_ids']
families = Family.objects.filter(project=from_project,
family_id__in=family_ids)
print('Found {} out of {} families. No match for: {}.'.format(
len(families), len(set(family_ids)),
set(family_ids) - set([f.family_id for f in families])))
for f in families:
print("==> Moving {}".format(f))
for seqr_individual in f.individual_set.all():
base_individual = find_matching_xbrowse_model(seqr_individual)
base_individual.project = to_base_project
base_individual.save()
# Update individuals in phenotips
if _phenotips_patient_exists(seqr_individual):
# make sure phenotips_patient_id is up to date
data_json = _get_patient_data(
from_project,
seqr_individual,
)
seqr_individual.phenotips_patient_id = data_json["id"]
seqr_individual.save()
# update permissions
phenotips_readonly_username, _ = _get_phenotips_uname_and_pwd_for_project(
to_project.phenotips_user_id, read_only=True)
_add_user_to_patient(phenotips_readonly_username,
seqr_individual.phenotips_patient_id,
allow_edit=False)
phenotips_readwrite_username, _ = _get_phenotips_uname_and_pwd_for_project(
to_project.phenotips_user_id, read_only=False)
_add_user_to_patient(phenotips_readwrite_username,
seqr_individual.phenotips_patient_id,
allow_edit=True)
# Update individuals samples/ VCFs
for from_vcf_file in base_individual.vcf_files.all():
to_vcf_file, _ = VCFFile.objects.get_or_create(
project=to_base_project,
elasticsearch_index=from_vcf_file.elasticsearch_index,
file_path=from_vcf_file.file_path,
dataset_type=from_vcf_file.dataset_type,
sample_type=from_vcf_file.sample_type,
loaded_date=from_vcf_file.loaded_date,
)
base_individual.vcf_files.add(to_vcf_file)
base_individual.vcf_files.remove(from_vcf_file)
# Update variant tags/ notes
saved_variants = SavedVariant.objects.filter(family=f)
for variant_tag in VariantTag.objects.filter(
saved_variant__in=saved_variants).select_related(
'variant_tag_type'):
if variant_tag.variant_tag_type.project:
to_tag_type, created = get_or_create_seqr_model(
VariantTagType,
project=to_project,
name=variant_tag.variant_tag_type.name)
if created:
update_seqr_model(
to_tag_type,
category=variant_tag.variant_tag_type.category,
description=variant_tag.variant_tag_type.
description,
color=variant_tag.variant_tag_type.color,
order=variant_tag.variant_tag_type.order,
)
update_seqr_model(variant_tag,
variant_tag_type=to_tag_type)
else:
to_project_tag, created = ProjectTag.objects.get_or_create(
project=to_base_project,
tag=variant_tag.variant_tag_type.name)
if created:
to_project_tag.category = variant_tag.variant_tag_type.category
to_project_tag.title = variant_tag.variant_tag_type.description
to_project_tag.color = variant_tag.variant_tag_type.color
to_project_tag.order = variant_tag.variant_tag_type.order
to_project_tag.save()
variant_tag.project_tag = to_project_tag
variant_tag.save()
base_family = find_matching_xbrowse_model(f)
for note in BaseVariantNote.objects.filter(family=base_family):
note.project = to_base_project
note.save()
# Update families
update_seqr_model(f, project=to_project)
print("Done.")
