def _add_locus_lists(projects, genes, include_all_lists=False):
locus_lists = LocusList.objects.filter(projects__in=projects)
if include_all_lists:
locus_lists_by_guid = {
locus_list.guid: {
'intervals': []
}
for locus_list in locus_lists
}
else:
locus_lists_by_guid = defaultdict(lambda: {'intervals': []})
intervals = LocusListInterval.objects.filter(locus_list__in=locus_lists)
for interval in _get_json_for_models(intervals,
nested_fields=[{
'fields': ('locus_list', 'guid')
}]):
locus_lists_by_guid[interval['locusListGuid']]['intervals'].append(
interval)
for locus_list_gene in LocusListGene.objects.filter(
locus_list__in=locus_lists,
gene_id__in=genes.keys()).prefetch_related('locus_list'):
genes[locus_list_gene.gene_id]['locusListGuids'].append(
locus_list_gene.locus_list.guid)
return locus_lists_by_guid
def saved_variants_page(request, tag):
gene = request.GET.get('gene')
if tag == 'ALL':
saved_variant_models = SavedVariant.objects.exclude(varianttag=None)
else:
tag_type = VariantTagType.objects.get(name=tag, project__isnull=True)
saved_variant_models = SavedVariant.objects.filter(varianttag__variant_tag_type=tag_type)
saved_variant_models = saved_variant_models.filter(family__project__in=get_projects_user_can_view(request.user))
if gene:
saved_variant_models = saved_variant_models.filter(saved_variant_json__transcripts__has_key=gene)
elif saved_variant_models.count() > MAX_SAVED_VARIANTS:
return create_json_response({'error': 'Select a gene to filter variants'}, status=400)
prefetch_related_objects(saved_variant_models, 'family__project')
response_json = get_json_for_saved_variants_with_tags(saved_variant_models, add_details=True, include_missing_variants=True)
project_models_by_guid = {variant.family.project.guid: variant.family.project for variant in saved_variant_models}
families = {variant.family for variant in saved_variant_models}
individuals = Individual.objects.filter(family__in=families)
saved_variants = list(response_json['savedVariantsByGuid'].values())
genes = saved_variant_genes(saved_variants)
locus_lists_by_guid = _add_locus_lists(list(project_models_by_guid.values()), genes, include_all_lists=True)
projects_json = get_json_for_projects(list(project_models_by_guid.values()), user=request.user, add_project_category_guids_field=False)
functional_tag_types = get_json_for_variant_functional_data_tag_types()
variant_tag_types = VariantTagType.objects.filter(Q(project__in=project_models_by_guid.values()) | Q(project__isnull=True))
prefetch_related_objects(variant_tag_types, 'project')
variant_tags_json = _get_json_for_models(variant_tag_types)
tag_projects = {vt.guid: vt.project.guid for vt in variant_tag_types if vt.project}
for project_json in projects_json:
project_guid = project_json['projectGuid']
project_variant_tags = [
vt for vt in variant_tags_json if tag_projects.get(vt['variantTagTypeGuid'], project_guid) == project_guid]
project_json.update({
'locusListGuids': list(locus_lists_by_guid.keys()),
'variantTagTypes': sorted(project_variant_tags, key=lambda variant_tag_type: variant_tag_type['order'] or 0),
'variantFunctionalTagTypes': functional_tag_types,
})
families_json = _get_json_for_families(list(families), user=request.user, add_individual_guids_field=True)
individuals_json = _get_json_for_individuals(individuals, add_hpo_details=True, user=request.user)
for locus_list in get_json_for_locus_lists(LocusList.objects.filter(guid__in=locus_lists_by_guid.keys()), request.user):
locus_lists_by_guid[locus_list['locusListGuid']].update(locus_list)
response_json.update({
'genesById': genes,
'projectsByGuid': {project['projectGuid']: project for project in projects_json},
'familiesByGuid': {family['familyGuid']: family for family in families_json},
'individualsByGuid': {indiv['individualGuid']: indiv for indiv in individuals_json},
'locusListsByGuid': locus_lists_by_guid,
})
return create_json_response(response_json)
def _add_omim(gene):
omim_phenotypes = _get_json_for_models(gene.omim_set.all())
return {
'omimPhenotypes': [
phenotype for phenotype in omim_phenotypes
if phenotype['phenotypeMimNumber']
],
'mimNumber':
omim_phenotypes[0]['mimNumber'] if omim_phenotypes else None,
}
def _get_json_for_variant_tag_types(project):
note_counts_by_family = VariantNote.objects.filter(saved_variants__family__project=project)\
.values('saved_variants__family__guid').annotate(count=Count('*'))
num_tags = sum(count['count'] for count in note_counts_by_family)
note_tag_type = {
'variantTagTypeGuid': 'notes',
'name': 'Has Notes',
'category': 'Notes',
'description': '',
'color': 'grey',
'order': 100,
'numTags': num_tags,
'numTagsPerFamily': {count['saved_variants__family__guid']: count['count'] for count in note_counts_by_family},
}
tag_counts_by_type_and_family = VariantTag.objects.filter(saved_variants__family__project=project)\
.values('saved_variants__family__guid', 'variant_tag_type__name').annotate(count=Count('*'))
project_variant_tags = _get_json_for_models(VariantTagType.objects.filter(Q(project=project) | Q(project__isnull=True)))
for tag_type in project_variant_tags:
current_tag_type_counts = [counts for counts in tag_counts_by_type_and_family if
counts['variant_tag_type__name'] == tag_type['name']]
num_tags = sum(count['count'] for count in current_tag_type_counts)
tag_type.update({
'numTags': num_tags,
'numTagsPerFamily': {count['saved_variants__family__guid']: count['count'] for count in
current_tag_type_counts},
})
project_variant_tags.append(note_tag_type)
project_variant_tags = sorted(project_variant_tags, key=lambda variant_tag_type: variant_tag_type['order'])
discovery_tag_type_guids = [tag_type['variantTagTypeGuid'] for tag_type in project_variant_tags
if tag_type['category'] == 'CMG Discovery Tags' and tag_type['numTags'] > 0]
discovery_tags = get_json_for_saved_variants(SavedVariant.objects.filter(
family__project=project, varianttag__variant_tag_type__guid__in=discovery_tag_type_guids,
), add_details=True)
project_functional_tags = []
for category, tags in VariantFunctionalData.FUNCTIONAL_DATA_CHOICES:
project_functional_tags += [{
'category': category,
'name': name,
'metadataTitle': json.loads(tag_json).get('metadata_title'),
'color': json.loads(tag_json)['color'],
'description': json.loads(tag_json).get('description'),
} for name, tag_json in tags]
return {
'variantTagTypes': sorted(project_variant_tags, key=lambda variant_tag_type: variant_tag_type['order']),
'variantFunctionalTagTypes': get_json_for_variant_functional_data_tag_types(),
'discoveryTags': discovery_tags,
}
def get_project_variant_tag_types(project,
tag_counts_by_type_and_family=None,
note_counts_by_family=None):
note_tag_type = {
'variantTagTypeGuid': 'notes',
'name': 'Has Notes',
'category': 'Notes',
'description': '',
'color': 'grey',
'order': 100,
'is_built_in': True,
}
if note_counts_by_family is not None:
num_tags = sum(count['count'] for count in note_counts_by_family)
note_tag_type.update({
'numTags': num_tags,
'numTagsPerFamily': {
count['saved_variant__family__guid']: count['count']
for count in note_counts_by_family
},
})
project_variant_tags = _get_json_for_models(
VariantTagType.objects.filter(
Q(project=project) | Q(project__isnull=True)))
if tag_counts_by_type_and_family is not None:
for tag_type in project_variant_tags:
current_tag_type_counts = [
counts for counts in tag_counts_by_type_and_family
if counts['variant_tag_type__name'] == tag_type['name']
]
num_tags = sum(count['count'] for count in current_tag_type_counts)
tag_type.update({
'numTags': num_tags,
'numTagsPerFamily': {
count['saved_variant__family__guid']: count['count']
for count in current_tag_type_counts
},
})
project_variant_tags.append(note_tag_type)
return sorted(project_variant_tags,
key=lambda variant_tag_type: variant_tag_type['order'])
def _get_json_for_genes(genes, user=None, gene_fields=None):
if not gene_fields:
gene_fields = {}
total_gene_constraints = None
if CONSTRAINT in gene_fields:
total_gene_constraints = GeneConstraint.objects.count()
if NOTES in gene_fields:
gene_notes_json = get_json_for_gene_notes_by_gene_id(
[gene.gene_id for gene in genes], user)
def _add_total_constraint_count(result, *args):
result['totalGenes'] = total_gene_constraints
def _process_result(result, gene):
for field, (_, result_func) in gene_fields.items():
if field == NOTES:
updates = {'notes': gene_notes_json.get(result['geneId'], [])}
elif field == CONSTRAINT:
constraint = _get_gene_model(gene, 'geneconstraint')
updates = {
'constraints': _get_json_for_model(
constraint, process_result=_add_total_constraint_count)
if constraint else {}
}
else:
updates = result_func(gene)
result.update(updates)
for model, _ in gene_fields.values():
if model:
prefetch_related_objects(
genes,
Prefetch('{}_set'.format(model.__name__.lower()),
queryset=model.objects.only(
'gene__gene_id', *model._meta.json_fields)))
return _get_json_for_models(genes, process_result=_process_result)
def _get_projects_details(projects, user, project_category_guid=None):
for project in projects:
check_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 = set()
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(
variant_tag_types_by_guid.values())
for project_json in projects_json:
project = project_models_by_guid[project_json['projectGuid']]
project_locus_lists = get_project_locus_list_models(project)
locus_lists.update(project_locus_lists)
project_json.update({
'locusListGuids':
[locus_list.guid for locus_list in project_locus_lists],
'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,
})
families = _get_json_for_families(
Family.objects.filter(project__in=projects), user)
individuals = _get_json_for_individuals(
Individual.objects.filter(family__project__in=projects), user=user)
samples = get_json_for_samples(
Sample.objects.filter(individual__family__project__in=projects))
analysis_groups = get_json_for_analysis_groups(
AnalysisGroup.objects.filter(project__in=projects))
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'])
for individual in individuals:
individual['sampleGuids'] = 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},
'locusListsByGuid': {
ll['locusListGuid']: ll
for ll in get_json_for_locus_lists(list(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 saved_variants_page(request, tag):
gene = request.GET.get('gene')
tag_type = VariantTagType.objects.get(name=tag, project__isnull=True)
saved_variant_models = SavedVariant.objects.filter(
varianttag__variant_tag_type=tag_type)
if gene:
saved_variant_models = saved_variant_models.filter(
saved_variant_json__transcripts__has_key=gene)
if saved_variant_models.count() > 10000 and not gene:
return create_json_response(
{'message': 'Select a gene to filter variants'}, status=400)
prefetch_related_objects(saved_variant_models, 'family__project')
saved_variants = get_json_for_saved_variants(saved_variant_models,
add_tags=True,
add_details=True)
project_models_by_guid = {
variant.family.project.guid: variant.family.project
for variant in saved_variant_models
}
families = {variant.family for variant in saved_variant_models}
individuals = Individual.objects.filter(family__in=families)
genes = _saved_variant_genes(saved_variants)
locus_list_guids = _add_locus_lists(project_models_by_guid.values(),
saved_variants, genes)
projects_json = get_json_for_projects(
project_models_by_guid.values(),
user=request.user,
add_project_category_guids_field=False)
functional_tag_types = get_json_for_variant_functional_data_tag_types()
variant_tag_types = VariantTagType.objects.filter(
Q(project__in=project_models_by_guid.values())
| Q(project__isnull=True))
prefetch_related_objects(variant_tag_types, 'project')
variant_tags_json = _get_json_for_models(variant_tag_types)
tag_projects = {
vt.guid: vt.project.guid
for vt in variant_tag_types if vt.project
}
for project_json in projects_json:
project_guid = project_json['projectGuid']
project_variant_tags = [
vt for vt in variant_tags_json if tag_projects.get(
vt['variantTagTypeGuid'], project_guid) == project_guid
]
project_json.update({
'locusListGuids':
locus_list_guids,
'variantTagTypes':
sorted(project_variant_tags,
key=lambda variant_tag_type: variant_tag_type['order']),
'variantFunctionalTagTypes':
functional_tag_types,
})
families_json = _get_json_for_families(list(families),
user=request.user,
add_individual_guids_field=True)
individuals_json = _get_json_for_individuals(individuals,
user=request.user)
locus_lists_by_guid = {
locus_list['locusListGuid']: locus_list
for locus_list in get_json_for_locus_lists(
LocusList.objects.filter(guid__in=locus_list_guids), request.user)
}
return create_json_response({
'savedVariantsByGuid':
{variant['variantGuid']: variant
for variant in saved_variants},
'genesById': genes,
'projectsByGuid':
{project['projectGuid']: project
for project in projects_json},
'familiesByGuid':
{family['familyGuid']: family
for family in families_json},
'individualsByGuid':
{indiv['individualGuid']: indiv
for indiv in individuals_json},
'locusListsByGuid': locus_lists_by_guid,
})
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
