def update_variant_main_transcript(request, variant_guid, transcript_id):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_project_permissions(saved_variant.family.project, request.user, can_edit=True)
update_model_from_json(saved_variant, {'selected_main_transcript_id': transcript_id}, request.user)
return create_json_response({'savedVariantsByGuid': {variant_guid: {'selectedMainTranscriptId': transcript_id}}})
def update_variant_tags_handler(request, variant_guids):
request_json = json.loads(request.body)
family_guid = request_json.pop('familyGuid')
family = Family.objects.get(guid=family_guid)
check_project_permissions(family.project, request.user)
all_variant_guids = set(variant_guids.split(','))
saved_variants = SavedVariant.objects.filter(guid__in=all_variant_guids)
if len(saved_variants) != len(all_variant_guids):
error = 'Unable to find the following variant(s): {}'.format(
', '.join([guid for guid in all_variant_guids if guid not in {sv.guid for sv in saved_variants}]))
return create_json_response({'error': error}, status=400, reason=error)
deleted_tag_guids = _delete_removed_tags(saved_variants, all_variant_guids, request_json.get('tags', []), request.user)
created_tags = _create_new_tags(saved_variants, request_json, request.user)
tag_updates = {tag['tagGuid']: tag for tag in get_json_for_variant_tags(created_tags)}
tag_updates.update({guid: None for guid in deleted_tag_guids})
saved_variants_by_guid = {}
for saved_variant in saved_variants:
tags = saved_variant.varianttag_set.all()
saved_variants_by_guid[saved_variant.guid] = {'tagGuids': [t.guid for t in tags]}
if not tags:
if not saved_variant.variantnote_set.count() > 0:
saved_variant.delete_model(request.user, user_can_delete=True)
saved_variants_by_guid[saved_variant.guid] = None
return create_json_response({
'savedVariantsByGuid': saved_variants_by_guid,
'variantTagsByGuid': tag_updates,
})
def delete_variant_note_handler(request, variant_guids, note_guid):
variant_guids = variant_guids.split(',')
note = VariantNote.objects.get(guid=note_guid)
projects = {
saved_variant.family.project
for saved_variant in note.saved_variants.all()
}
for project in projects:
check_project_permissions(project, request.user)
note.delete()
saved_variants_by_guid = {}
for saved_variant in SavedVariant.objects.filter(guid__in=variant_guids):
notes = saved_variant.variantnote_set.all()
saved_variants_by_guid[saved_variant.guid] = {
'noteGuids': [n.guid for n in notes]
}
if not notes:
if not saved_variant.varianttag_set.count() > 0:
saved_variant.delete()
saved_variants_by_guid[saved_variant.guid] = None
return create_json_response({
'savedVariantsByGuid': saved_variants_by_guid,
'variantNotesByGuid': {
note_guid: None
},
})
def create_saved_variant_handler(request):
variant_json = json.loads(request.body)
family_guid = variant_json['familyGuid']
family = Family.objects.get(guid=family_guid)
check_project_permissions(family.project, request.user)
variants_json = variant_json['variant']
if not isinstance(variant_json['variant'], list):
variants_json = [variants_json]
saved_variants = []
for single_variant_json in variants_json:
try:
parsed_variant_json = _get_parsed_variant_args(single_variant_json, family)
except ValueError as e:
return create_json_response({'error': str(e)}, status=400)
saved_variant, _ = get_or_create_model_from_json(
SavedVariant, create_json=parsed_variant_json,
update_json={'saved_variant_json': single_variant_json}, user=request.user)
saved_variants.append(saved_variant)
if variant_json.get('note'):
_create_variant_note(saved_variants, variant_json, request.user)
elif variant_json.get('tags'):
_create_new_tags(saved_variants, variant_json, request.user)
return create_json_response(get_json_for_saved_variants_with_tags(saved_variants, add_details=True))
def update_individual_hpo_terms(request, individual_guid):
"""Updates features fields for the given Individual
"""
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)
for feature_key in [
'features', 'absentFeatures', 'nonstandardFeatures',
'absentNonstandardFeatures'
]:
orm_key = _to_snake_case(feature_key)
value = [get_parsed_feature(feature) for feature in request_json[feature_key]] \
if request_json.get(feature_key) else None
setattr(individual, orm_key, value)
individual.save()
return create_json_response({
individual.guid:
_get_json_for_individual(individual,
request.user,
add_hpo_details=True)
})
def update_individual_hpo_terms(request, individual_guid):
"""Updates features fields for the given Individual
"""
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)
update_json = {
key:
[get_parsed_feature(feature)
for feature in request_json[key]] if request_json.get(key) else None
for key in [
'features', 'absentFeatures', 'nonstandardFeatures',
'absentNonstandardFeatures'
]
}
update_model_from_json(individual, update_json, user=request.user)
return create_json_response({
individual.guid:
_get_json_for_individual(individual,
request.user,
add_hpo_details=True)
})
def update_individual_handler(request, individual_guid):
"""Updates a single field in an Individual record.
Args:
request (object): Django HTTP Request object.
individual_guid (string): GUID of the Individual.
Request:
body should be a json dictionary like: { 'value': xxx }
Response:
json dictionary representing the updated individual like:
{
<individualGuid> : {
individualId: xxx,
sex: xxx,
affected: xxx,
...
}
}
"""
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)
update_individual_from_json(individual, request_json, user=request.user, allow_unknown_keys=True)
return create_json_response({
individual.guid: _get_json_for_individual(individual, request.user)
})
def create_saved_variant_handler(request):
variant_json = json.loads(request.body)
family_guid = variant_json['familyGuid']
family = Family.objects.get(guid=family_guid)
check_project_permissions(family.project, request.user)
if isinstance(variant_json['variant'], list):
# are compound hets
saved_variants = []
for single_variant_json in variant_json['variant']:
saved_variant, created = SavedVariant.objects.get_or_create(
**_get_parsed_variant_args(single_variant_json, family))
if created:
saved_variant.saved_variant_json = single_variant_json
saved_variant.save()
saved_variants.append(saved_variant)
else:
saved_variant = SavedVariant.objects.create(
saved_variant_json=variant_json['variant'],
**_get_parsed_variant_args(variant_json['variant'], family))
saved_variants = [saved_variant]
if variant_json.get('note'):
_create_variant_note(saved_variants, variant_json, request.user)
elif variant_json.get('tags'):
_create_new_tags(saved_variants, variant_json, request.user)
return create_json_response(
get_json_for_saved_variants_with_tags(saved_variants,
add_details=True))
def update_family_pedigree_image(request, family_guid):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
"""
family = Family.objects.get(guid=family_guid)
# check permission
check_project_permissions(family.project, request.user, can_edit=True)
if len(request.FILES) == 0:
pedigree_image = None
elif len(request.FILES) > 1:
return create_json_response({},
status=400,
reason='Received {} files'.format(
len(request.FILES)))
else:
pedigree_image = next(iter((request.FILES.values())))
family.pedigree_image = pedigree_image
family.save()
return create_json_response(
{family.guid: _get_json_for_family(family, request.user)})
def update_family_assigned_analyst(request, family_guid):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
"""
family = Family.objects.get(guid=family_guid)
# assigned_analyst can be edited by anyone with access to the project
check_project_permissions(family.project, request.user, can_edit=False)
request_json = json.loads(request.body)
assigned_analyst_username = request_json.get('assigned_analyst_username')
if assigned_analyst_username:
try:
assigned_analyst = User.objects.get(
username=assigned_analyst_username)
except Exception:
return create_json_response({},
status=400,
reason="specified user does not exist")
else:
assigned_analyst = None
family.assigned_analyst = assigned_analyst
family.save()
return create_json_response(
{family.guid: _get_json_for_family(family, request.user)})
def create_variant_note_handler(request, variant_guids):
request_json = json.loads(request.body)
save_as_gene_note = request_json.get('saveAsGeneNote')
family_guid = request_json.pop('familyGuid')
family = Family.objects.get(guid=family_guid)
check_project_permissions(family.project, request.user)
all_variant_guids = variant_guids.split(',')
saved_variants = SavedVariant.objects.filter(guid__in=all_variant_guids)
if len(saved_variants) != len(all_variant_guids):
error = 'Unable to find the following variant(s): {}'.format(', '.join(
[
guid for guid in all_variant_guids
if guid not in {sv.guid
for sv in saved_variants}
]))
return create_json_response({'error': error}, status=400, reason=error)
# update saved_variants
note = _create_variant_note(saved_variants, request_json, request.user)
note_json = get_json_for_variant_note(note, add_variant_guids=False)
note_json['variantGuids'] = all_variant_guids
response = {
'savedVariantsByGuid': {
saved_variant.guid: {
'noteGuids':
[n.guid for n in saved_variant.variantnote_set.all()]
}
for saved_variant in saved_variants
},
'variantNotesByGuid': {
note.guid: note_json
},
}
if save_as_gene_note:
main_transcript_id = saved_variants[
0].selected_main_transcript_id or saved_variants[
0].saved_variant_json['mainTranscriptId']
gene_id = next(
(gene_id for gene_id, transcripts in saved_variants[0].
saved_variant_json['transcripts'].items() if any(
t['transcriptId'] == main_transcript_id
for t in transcripts)), None) if main_transcript_id else None
GeneNote.objects.create(
note=request_json.get('note'),
gene_id=gene_id,
created_by=request.user,
)
response['genesById'] = {
gene_id: {
'notes':
get_json_for_gene_notes_by_gene_id([gene_id],
request.user)[gene_id],
}
}
return create_json_response(response)
def update_mme_submission(request, submission_guid=None):
"""
Create or update the submission for the given individual.
"""
submission_json = json.loads(request.body)
phenotypes = submission_json.pop('phenotypes', [])
gene_variants = submission_json.pop('geneVariants', [])
if not phenotypes and not gene_variants:
return create_json_response({}, status=400, reason='Genotypes or phentoypes are required')
genomic_features = []
for gene_variant in gene_variants:
if not gene_variant.get('geneId'):
return create_json_response({}, status=400, reason='Gene id is required for genomic features')
feature = {'gene': {'id': gene_variant['geneId']}}
if 'numAlt' in gene_variant and gene_variant['numAlt'] > 0:
feature['zygosity'] = gene_variant['numAlt']
if gene_variant.get('pos'):
genome_version = gene_variant['genomeVersion']
feature['variant'] = {
'referenceName': gene_variant['chrom'],
'start': gene_variant['pos'],
'assembly': GENOME_VERSION_LOOKUP.get(genome_version, genome_version),
}
if gene_variant.get('alt'):
feature['variant'].update({
'alternateBases': gene_variant['alt'],
'referenceBases': gene_variant['ref'],
})
elif gene_variant.get('end'):
feature['variant']['end'] = gene_variant['end']
genomic_features.append(feature)
submission_json.update({
'features': phenotypes,
'genomicFeatures': genomic_features,
'deletedDate': None,
'deletedBy': None,
})
if submission_guid:
submission = MatchmakerSubmission.objects.get(guid=submission_guid)
check_mme_permissions(submission, request.user)
else:
individual_guid = submission_json.get('individualGuid')
if not individual_guid:
return create_json_response({}, status=400, reason='Individual is required for a new submission')
individual = Individual.objects.get(guid=individual_guid)
check_project_permissions(individual.family.project, request.user)
submission = MatchmakerSubmission.objects.create(
individual=individual,
submission_id=individual.guid,
label=individual.individual_id,
)
update_model_from_json(submission, submission_json, allow_unknown_keys=True)
# search for new matches
return _search_matches(submission, request.user)
def _update_variant_tag_models(request,
variant_guids,
tag_key,
model_cls,
get_tag_create_data,
get_tags_json,
response_guid_key=None,
delete_variants_if_empty=False):
request_json = json.loads(request.body)
family_guid = request_json.pop('familyGuid')
family = Family.objects.get(guid=family_guid)
check_project_permissions(family.project, request.user)
all_variant_guids = set(variant_guids.split(','))
saved_variants = SavedVariant.objects.filter(guid__in=all_variant_guids)
if len(saved_variants) != len(all_variant_guids):
error = 'Unable to find the following variant(s): {}'.format(', '.join(
[
guid for guid in all_variant_guids
if guid not in {sv.guid
for sv in saved_variants}
]))
return create_json_response({'error': error}, status=400, reason=error)
tag_type = tag_key.lower().rstrip('s')
updated_data = request_json.get(tag_key, [])
deleted_guids = _delete_removed_tags(saved_variants, all_variant_guids,
updated_data, request.user, tag_type)
updated_models = _update_tags(saved_variants, request_json, request.user,
tag_key, model_cls, get_tag_create_data)
updates = {tag['tagGuid']: tag for tag in get_tags_json(updated_models)}
updates.update({guid: None for guid in deleted_guids})
if not response_guid_key:
response_guid_key = '{}Guids'.format(tag_key)
saved_variants_by_guid = {}
for saved_variant in saved_variants:
tags = _get_tag_set(saved_variant, tag_type).all()
saved_variants_by_guid[saved_variant.guid] = {
response_guid_key: [t.guid for t in tags]
}
if delete_variants_if_empty and not tags:
if not saved_variant.variantnote_set.count() > 0:
saved_variant.delete_model(request.user, user_can_delete=True)
saved_variants_by_guid[saved_variant.guid] = None
return create_json_response({
'savedVariantsByGuid':
saved_variants_by_guid,
'variant{}{}ByGuid'.format(tag_key[0].upper(), tag_key[1:]):
updates,
})
def discovery_sheet(request, project_guid):
project = Project.objects.filter(guid=project_guid).prefetch_related(
Prefetch('family_set', to_attr='families', queryset=Family.objects.prefetch_related('individual_set'))
).distinct().first()
if not project:
message = 'Invalid project {}'.format(project_guid)
return create_json_response({'error': message}, status = 400, reason = message)
check_project_permissions(project, request.user)
rows = []
errors = []
loaded_samples_by_family = _get_loaded_samples_by_family(project)
saved_variants_by_family = _get_project_saved_discovery_variants_by_family(project)
mme_submission_families = _get_has_mme_submission_families(project)
if not loaded_samples_by_family:
errors.append("No data loaded for project: {}".format(project))
return create_json_response({
'rows': [],
'errors': errors,
})
if "external" in project.name.lower() or "reprocessed" in project.name.lower():
sequencing_approach = "REAN"
else:
sequencing_approach = next(iter(loaded_samples_by_family.values()))[-1].sample_type
initial_row = {
"project_guid": project.guid,
"collaborator": project.name,
"sequencing_approach": sequencing_approach,
}
initial_row.update(DEFAULT_ROW)
now = timezone.now()
for family in project.families:
samples = loaded_samples_by_family.get(family.guid)
if not samples:
errors.append("No data loaded for family: %s. Skipping..." % family)
continue
saved_variants = saved_variants_by_family.get(family.guid)
submitted_to_mme = family in mme_submission_families
rows += _generate_rows(initial_row, family, samples, saved_variants, submitted_to_mme, errors, now=now)
_update_gene_symbols(rows)
_update_hpo_categories(rows, errors)
_update_initial_omim_numbers(rows)
return create_json_response({
'rows': rows,
'errors': errors,
})
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())))
if not does_file_exist(file_path):
raise Exception('Error accessing "{}"'.format(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 update_variant_note_handler(request, variant_guids, note_guid):
note = VariantNote.objects.get(guid=note_guid)
projects = {saved_variant.family.project for saved_variant in note.saved_variants.all()}
for project in projects:
check_project_permissions(project, request.user)
request_json = json.loads(request.body)
update_model_from_json(note, request_json, user=request.user, allow_unknown_keys=True)
note_json = get_json_for_variant_note(note, add_variant_guids=False)
note_json['variantGuids'] = variant_guids.split(',')
return create_json_response({
'variantNotesByGuid': {note.guid: note_json},
})
def update_project_categories_handler(request, project_guid):
"""Update ProjectCategories for the given project.
Args:
project_guid (string): GUID of the project that should be updated
HTTP POST
Request body - should contain the following json structure:
{
'form' : {
'categories': a list of category GUIDs for the categories assigned to the given project
}
}
Response body - will contain the following structure, representing the updated project,
as well all categories in seqr:
{
'projectsByGuid': {
<projectGuid1> : { ... <project key-value pairs> ... }
}
'projectCategoriesByGuid': {
<projectCategoryGuid1> : { ... <category key-value pairs> ... }
<projectCategoryGuid2> : { ... <category key-value pairs> ... }
}
}
"""
project = Project.objects.get(guid=project_guid)
# check permissions
check_project_permissions(project, request.user, can_edit=True)
request_json = json.loads(request.body)
# project categories according to the UI
current_category_guids = set(request_json['categories'])
project_categories_by_guid = _update_project_categories(
project, request.user, current_category_guids)
projects_by_guid = {
project.guid: _get_json_for_project(project, request.user)
}
return create_json_response({
'projectsByGuid':
projects_by_guid,
'projectCategoriesByGuid':
project_categories_by_guid,
})
def update_family_analysed_by(request, family_guid):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
field_name (string): Family model field name to update
"""
family = Family.objects.get(guid=family_guid)
# analysed_by can be edited by anyone with access to the project
check_project_permissions(family.project, request.user, can_edit=False)
FamilyAnalysedBy.objects.create(family=family, created_by=request.user)
return create_json_response(
{family.guid: _get_json_for_family(family, request.user)})
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:
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 = str(e)
return create_json_response({'error': error}, status=400, reason=error)
def update_family_fields_handler(request, family_guid):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
"""
family = Family.objects.get(guid=family_guid)
# check permission - can be edited by anyone with access to the project
check_project_permissions(family.project, request.user)
request_json = json.loads(request.body)
update_family_from_json(family, request_json, user=request.user, allow_unknown_keys=True, immutable_keys=[
'family_id', 'display_name',
])
return create_json_response({
family.guid: _get_json_for_family(family, request.user)
})
def update_family_fields_handler(request, family_guid):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
"""
family = Family.objects.get(guid=family_guid)
# check permission
project = family.project
check_project_permissions(project, request.user, can_edit=True)
request_json = json.loads(request.body)
update_family_from_json(family, request_json, user=request.user, allow_unknown_keys=True)
return create_json_response({
family.guid: _get_json_for_family(family, request.user)
})
def update_variant_functional_data_handler(request, variant_guids):
request_json = json.loads(request.body)
family_guid = request_json.pop('familyGuid')
family = Family.objects.get(guid=family_guid)
check_project_permissions(family.project, request.user)
all_variant_guids = set(variant_guids.split(','))
saved_variants = SavedVariant.objects.filter(guid__in=all_variant_guids)
if len(saved_variants) != len(all_variant_guids):
error = 'Unable to find the following variant(s): {}'.format(
', '.join([guid for guid in all_variant_guids if guid not in {sv.guid for sv in saved_variants}]))
return create_json_response({'error': error}, status=400, reason=error)
updated_functional_data = request_json.get('functionalData', [])
deleted_functional_guids = _delete_removed_tags(
saved_variants, all_variant_guids, updated_functional_data, request.user, tag_type='functionaldata')
updated_functional_models = []
for tag in updated_functional_data:
if tag.get('tagGuid'):
functional_data = VariantFunctionalData.objects.get(guid=tag.get('tagGuid'))
update_model_from_json(functional_data, tag, user=request.user, allow_unknown_keys=True)
else:
functional_data = create_model_from_json(VariantFunctionalData, {
'functional_data_tag': tag.get('name'),
'metadata': tag.get('metadata'),
'search_hash': request_json.get('searchHash'),
}, request.user)
functional_data.saved_variants.set(saved_variants)
updated_functional_models.append(functional_data)
functional_updates = {tag['tagGuid']: tag for tag in get_json_for_variant_functional_data_tags(updated_functional_models)}
functional_updates.update({guid: None for guid in deleted_functional_guids})
return create_json_response({
'savedVariantsByGuid': {saved_variant.guid: {
'functionalDataGuids': [t.guid for t in saved_variant.variantfunctionaldata_set.all()],
} for saved_variant in saved_variants},
'variantFunctionalDataByGuid': functional_updates,
})
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 _get_projects_details(projects, user, project_category_guid=None):
for project in projects:
check_project_permissions(project, user)
prefetch_related_objects(projects, 'can_view_group')
project_models_by_guid = {project.guid: project for project in projects}
projects_json = get_json_for_projects(projects, user)
locus_lists = LocusList.objects.filter(
projects__in=projects).prefetch_related('projects')
project_guid = projects[0].guid if len(projects) == 1 else None
functional_data_tag_types = get_json_for_variant_functional_data_tag_types(
)
variant_tag_types_by_guid = {
vtt.guid: vtt
for vtt in VariantTagType.objects.filter(
Q(project__in=projects)
| Q(project__isnull=True)).prefetch_related('project')
}
variant_tag_types = _get_json_for_models(
list(variant_tag_types_by_guid.values()))
for project_json in projects_json:
project = project_models_by_guid[project_json['projectGuid']]
project_json.update({
'locusListGuids': [
locus_list.guid for locus_list in locus_lists
if project in locus_list.projects.all()
],
'variantTagTypes': [
vtt for vtt in variant_tag_types
if variant_tag_types_by_guid[vtt['variantTagTypeGuid']].project
is None or variant_tag_types_by_guid[vtt['variantTagTypeGuid']]
.project.guid == project_json['projectGuid']
],
'variantFunctionalTagTypes':
functional_data_tag_types,
})
family_models = Family.objects.filter(project__in=projects)
families = _get_json_for_families(family_models,
user,
project_guid=project_guid,
skip_nested=True)
individual_models = Individual.objects.filter(family__in=family_models)
individuals = _get_json_for_individuals(individual_models,
user=user,
project_guid=project_guid,
add_hpo_details=True,
skip_nested=True)
sample_models = Sample.objects.filter(individual__in=individual_models)
samples = get_json_for_samples(sample_models,
project_guid=project_guid,
skip_nested=True)
igv_sample_models = IgvSample.objects.filter(
individual__in=individual_models)
igv_samples = get_json_for_samples(igv_sample_models,
project_guid=project_guid,
skip_nested=True)
analysis_group_models = AnalysisGroup.objects.filter(project__in=projects)
analysis_groups = get_json_for_analysis_groups(analysis_group_models,
project_guid=project_guid,
skip_nested=True)
if not project_guid:
project_id_to_guid = {project.id: project.guid for project in projects}
family_id_to_guid = {
family.id: family.guid
for family in family_models
}
individual_id_to_guid = {
individual.id: individual.guid
for individual in individual_models
}
family_guid_to_project_guid = {}
individual_guid_to_project_guid = {}
for family in families:
project_guid = project_id_to_guid[family.pop('projectId')]
family['projectGuid'] = project_guid
family_guid_to_project_guid[family['familyGuid']] = project_guid
for individual in individuals:
family_guid = family_id_to_guid[individual.pop('familyId')]
project_guid = family_guid_to_project_guid[family_guid]
individual['familyGuid'] = family_guid
individual['projectGuid'] = project_guid
individual_guid_to_project_guid[
individual['individualGuid']] = project_guid
for sample in samples:
individual_guid = individual_id_to_guid[sample.pop('individualId')]
sample['individualGuid'] = individual_guid
sample['projectGuid'] = individual_guid_to_project_guid[
individual_guid]
for sample in igv_samples:
individual_guid = individual_id_to_guid[sample.pop('individualId')]
sample['individualGuid'] = individual_guid
sample['projectGuid'] = individual_guid_to_project_guid[
individual_guid]
for group in analysis_groups:
group['projectGuid'] = project_id_to_guid[group.pop('projectId')]
individual_guids_by_family = defaultdict(list)
for individual in individuals:
individual_guids_by_family[individual['familyGuid']].append(
individual['individualGuid'])
for family in families:
family['individualGuids'] = individual_guids_by_family[
family['familyGuid']]
sample_guids_by_individual = defaultdict(list)
for sample in samples:
sample_guids_by_individual[sample['individualGuid']].append(
sample['sampleGuid'])
igv_sample_guids_by_individual = defaultdict(list)
for sample in igv_samples:
igv_sample_guids_by_individual[sample['individualGuid']].append(
sample['sampleGuid'])
for individual in individuals:
individual['sampleGuids'] = sample_guids_by_individual[
individual['individualGuid']]
individual['igvSampleGuids'] = igv_sample_guids_by_individual[
individual['individualGuid']]
response = {
'projectsByGuid': {p['projectGuid']: p
for p in projects_json},
'familiesByGuid': {f['familyGuid']: f
for f in families},
'individualsByGuid': {i['individualGuid']: i
for i in individuals},
'samplesByGuid': {s['sampleGuid']: s
for s in samples},
'igvSamplesByGuid': {s['sampleGuid']: s
for s in igv_samples},
'locusListsByGuid': {
ll['locusListGuid']: ll
for ll in get_json_for_locus_lists(locus_lists, user)
},
'analysisGroupsByGuid':
{ag['analysisGroupGuid']: ag
for ag in analysis_groups},
}
if project_category_guid:
response['projectCategoriesByGuid'] = {
project_category_guid:
ProjectCategory.objects.get(guid=project_category_guid).json()
}
return response
def _check_results_permission(results_model, user):
families = results_model.families.prefetch_related('project').all()
projects = {family.project for family in families}
for project in projects:
check_project_permissions(project, user)
