def update_variant_tags_handler(request, variant_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_EDIT)
request_json = json.loads(request.body)
updated_tags = request_json.get('tags', [])
updated_functional_data = request_json.get('functionalData', [])
# Update tags
existing_tag_guids = [tag['tagGuid'] for tag in updated_tags if tag.get('tagGuid')]
new_tags = [tag for tag in updated_tags if not tag.get('tagGuid')]
for tag in saved_variant.varianttag_set.exclude(guid__in=existing_tag_guids):
delete_seqr_model(tag)
for tag in new_tags:
variant_tag_type = VariantTagType.objects.get(
Q(name=tag['name']),
Q(project=saved_variant.project) | Q(project__isnull=True)
)
create_seqr_model(
VariantTag,
saved_variant=saved_variant,
variant_tag_type=variant_tag_type,
search_parameters=request_json.get('searchParameters'),
created_by=request.user,
)
# Update functional data
existing_functional_guids = [tag['tagGuid'] for tag in updated_functional_data if tag.get('tagGuid')]
for tag in saved_variant.variantfunctionaldata_set.exclude(guid__in=existing_functional_guids):
delete_seqr_model(tag)
for tag in updated_functional_data:
if tag.get('tagGuid'):
tag_model = VariantFunctionalData.objects.get(
guid=tag.get('tagGuid'),
functional_data_tag=tag.get('name'),
saved_variant=saved_variant
)
update_model_from_json(tag_model, tag, allow_unknown_keys=True)
else:
create_seqr_model(
VariantFunctionalData,
saved_variant=saved_variant,
functional_data_tag=tag.get('name'),
metadata=tag.get('metadata'),
search_parameters=request_json.get('searchParameters'),
created_by=request.user,
)
return create_json_response({
variant_guid: {
'tags': [get_json_for_variant_tag(tag) for tag in saved_variant.varianttag_set.all()],
'functionalData': [get_json_for_variant_functional_data(tag) for tag in saved_variant.variantfunctionaldata_set.all()]
}
})
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, new_genes, existing_gene_ids, new_intervals, existing_interval_guids, request_json, user):
# Update genes
for locus_list_gene in locus_list.locuslistgene_set.exclude(gene_id__in=existing_gene_ids):
delete_seqr_model(locus_list_gene)
for gene_id in new_genes.keys():
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
locus_list.locuslistinterval_set.exclude(guid__in=existing_interval_guids).delete()
for existing_interval in locus_list.locuslistinterval_set.all():
update_model_from_json(existing_interval, {'genomeVersion': genome_version})
for interval in new_intervals:
LocusListInterval.objects.create(
locus_list=locus_list,
chrom=interval['chrom'].lstrip('chr'),
start=interval['start'],
end=interval['end'],
genome_version=genome_version,
)
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 delete_locus_list_handler(request, locus_list_guid):
locus_list = LocusList.objects.get(guid=locus_list_guid)
check_object_permissions(locus_list,
request.user,
permission_level=CAN_EDIT)
delete_seqr_model(locus_list)
return create_json_response({'locusListsByGuid': {locus_list_guid: None}})
def delete_variant_note_handler(request, variant_guid, note_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_VIEW)
note = VariantNote.objects.get(guid=note_guid, saved_variant=saved_variant)
delete_seqr_model(note)
return create_json_response({'savedVariantsByGuid': {variant_guid: {
'notes': [get_json_for_variant_note(tag) for tag in saved_variant.variantnote_set.all()]
}}})
def delete_variant_note_handler(request, variant_guid, note_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_EDIT)
note = VariantNote.objects.get(guid=note_guid, saved_variant=saved_variant)
delete_seqr_model(note)
return create_json_response({variant_guid: {
'notes': [get_json_for_variant_note(tag) for tag in saved_variant.variantnote_set.all()]
}})
def delete_gene_note_handler(request, gene_id, note_guid):
note = GeneNote.objects.get(guid=note_guid)
if not _can_edit_note(note, request.user):
raise PermissionDenied("User does not have permission to delete this note")
delete_seqr_model(note)
return create_json_response({'genesById': {gene_id: {
'notes': _get_gene_notes(gene_id, request.user)
}}})
def delete_gene_note_handler(request, gene_id, note_guid):
note = GeneNote.objects.get(guid=note_guid)
if not _can_edit_note(note, request.user):
raise PermissionDenied(
"User does not have permission to delete this note")
delete_seqr_model(note)
return create_json_response(
{gene_id: {
'notes': _get_gene_notes(gene_id, request.user)
}})
def delete_analysis_group_handler(request, project_guid, analysis_group_guid):
project = get_project_and_check_permissions(project_guid,
request.user,
permission_level=CAN_EDIT)
analysis_group = AnalysisGroup.objects.get(guid=analysis_group_guid,
project=project)
delete_seqr_model(analysis_group)
return create_json_response(
{'analysisGroupsByGuid': {
analysis_group_guid: None
}})
def update_variant_tags_handler(request, variant_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_VIEW)
request_json = json.loads(request.body)
updated_tags = request_json.get('tags', [])
updated_functional_data = request_json.get('functionalData', [])
# Update tags
existing_tag_guids = [tag['tagGuid'] for tag in updated_tags if tag.get('tagGuid')]
for tag in saved_variant.varianttag_set.exclude(guid__in=existing_tag_guids):
delete_seqr_model(tag)
_create_new_tags(saved_variant, request_json, request.user)
# Update functional data
existing_functional_guids = [tag['tagGuid'] for tag in updated_functional_data if tag.get('tagGuid')]
for tag in saved_variant.variantfunctionaldata_set.exclude(guid__in=existing_functional_guids):
delete_seqr_model(tag)
for tag in updated_functional_data:
if tag.get('tagGuid'):
tag_model = VariantFunctionalData.objects.get(
guid=tag.get('tagGuid'),
functional_data_tag=tag.get('name'),
saved_variant=saved_variant
)
update_model_from_json(tag_model, tag, allow_unknown_keys=True)
else:
create_seqr_model(
VariantFunctionalData,
saved_variant=saved_variant,
functional_data_tag=tag.get('name'),
metadata=tag.get('metadata'),
search_hash=request_json.get('searchHash'),
created_by=request.user,
)
return create_json_response({'savedVariantsByGuid': {
variant_guid: {
'tags': [get_json_for_variant_tag(tag) for tag in saved_variant.varianttag_set.all()],
'functionalData': [get_json_for_variant_functional_data(tag) for tag in saved_variant.variantfunctionaldata_set.all()]
}
}})
def delete_families_handler(request, project_guid):
"""Edit or delete one or more Individual records.
Args:
project_guid (string): GUID of project that contains these individuals.
"""
project = get_project_and_check_permissions(project_guid, request.user,
CAN_EDIT)
request_json = json.loads(request.body)
logger.info("delete_families_handler %s", request_json)
families_to_delete = request_json.get('families')
if families_to_delete is None:
return create_json_response({},
status=400,
reason="'recordIdsToDelete' not specified")
family_guids_to_delete = [f['familyGuid'] for f in families_to_delete]
# delete individuals 1st
individual_guids_to_delete = [
i.guid for i in Individual.objects.filter(
family__project=project, family__guid__in=family_guids_to_delete)
]
delete_individuals(project, individual_guids_to_delete)
# delete families
for family in Family.objects.filter(project=project,
guid__in=family_guids_to_delete):
delete_seqr_model(family)
# send response
return create_json_response({
'individualsByGuid': {
individual_guid: None
for individual_guid in individual_guids_to_delete
},
'familiesByGuid':
{family_guid: None
for family_guid in family_guids_to_delete},
})
def delete_individuals(project, individual_guids):
"""Delete one or more individuals
Args:
project (object): Django ORM model for project
individual_guids (list): GUIDs of individuals to delete
Returns:
list: Family objects for families with deleted individuals
"""
individuals_to_delete = Individual.objects.filter(
family__project=project, guid__in=individual_guids)
samples_to_delete = Sample.objects.filter(
individual__family__project=project, individual__guid__in=individual_guids)
for sample in samples_to_delete:
logger.info("Deleting sample: %s" % sample)
sample.delete()
families = {}
for individual in individuals_to_delete:
families[individual.family.family_id] = individual.family
# delete phenotips records
try:
delete_patient(project, individual)
except (PhenotipsException, ValueError) as e:
logger.error("Error: couldn't delete patient from phenotips: %s %s",
individual.phenotips_eid,
individual)
# delete Individual
delete_seqr_model(individual)
update_pedigree_images(families.values())
families_with_deleted_individuals = list(families.values())
return families_with_deleted_individuals
def delete_project(project):
"""Delete project.
Args:
project (object): Django ORM model for the project to delete
"""
Sample.objects.filter(individual__family__project=project).delete()
for individual in Individual.objects.filter(family__project=project):
delete_seqr_model(individual)
for family in Family.objects.filter(project=project):
delete_seqr_model(family)
delete_seqr_model(project)
def _delete_project(project):
"""Delete project.
Args:
project (object): Django ORM model for the project to delete
"""
Sample.objects.filter(individual__family__project=project).delete()
for individual in Individual.objects.filter(family__project=project):
delete_seqr_model(individual)
for family in Family.objects.filter(project=project):
delete_seqr_model(family)
delete_seqr_model(project)
def delete_analysis_group_handler(request, project_guid, analysis_group_guid):
project = get_project_and_check_permissions(project_guid, request.user, permission_level=CAN_EDIT)
analysis_group = AnalysisGroup.objects.get(guid=analysis_group_guid, project=project)
delete_seqr_model(analysis_group)
return create_json_response({'analysisGroupsByGuid': {analysis_group_guid: None}})
def update_variant_tags_handler(request, variant_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.family.project, request.user, CAN_VIEW)
request_json = json.loads(request.body)
updated_tags = request_json.get('tags', [])
updated_functional_data = request_json.get('functionalData', [])
# Update tags
existing_tag_guids = [
tag['tagGuid'] for tag in updated_tags if tag.get('tagGuid')
]
for tag in saved_variant.varianttag_set.exclude(
guid__in=existing_tag_guids):
delete_seqr_model(tag)
_create_new_tags(saved_variant, request_json, request.user)
# Update functional data
existing_functional_guids = [
tag['tagGuid'] for tag in updated_functional_data if tag.get('tagGuid')
]
for tag in saved_variant.variantfunctionaldata_set.exclude(
guid__in=existing_functional_guids):
delete_seqr_model(tag)
for tag in updated_functional_data:
if tag.get('tagGuid'):
tag_model = VariantFunctionalData.objects.get(
guid=tag.get('tagGuid'),
functional_data_tag=tag.get('name'),
saved_variant=saved_variant)
update_model_from_json(tag_model, tag, allow_unknown_keys=True)
else:
create_seqr_model(
VariantFunctionalData,
saved_variant=saved_variant,
functional_data_tag=tag.get('name'),
metadata=tag.get('metadata'),
search_hash=request_json.get('searchHash'),
created_by=request.user,
)
return create_json_response({
'savedVariantsByGuid': {
variant_guid: {
'tags': [
get_json_for_variant_tag(tag)
for tag in saved_variant.varianttag_set.all()
],
'functionalData': [
get_json_for_variant_functional_data(tag)
for tag in saved_variant.variantfunctionaldata_set.all()
]
}
}
})
def delete_locus_list_handler(request, locus_list_guid):
locus_list = LocusList.objects.get(guid=locus_list_guid)
check_object_permissions(locus_list, request.user, permission_level=CAN_EDIT)
delete_seqr_model(locus_list)
return create_json_response({'locusListsByGuid': {locus_list_guid: None}})
