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views.py
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views.py
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import os
import re
import tempfile
from itertools import chain
from collections import defaultdict
import uuid
import contextlib
import decimal
import binning
import numpy as np
import requests
from base64 import b64encode
from variants.helpers import get_engine
from django.conf import settings
from django.contrib import messages
from django.contrib.humanize.templatetags.humanize import naturaltime
from django.contrib.postgres.aggregates import ArrayAgg
from django.core.exceptions import ObjectDoesNotExist, ValidationError
from django.db.models import Q
from django.forms.models import model_to_dict
from django.http import HttpResponse, Http404, JsonResponse
from django.db import transaction
from django.shortcuts import render, redirect, get_object_or_404, reverse
from django.utils import timezone
from django.views.generic import (
DetailView,
FormView,
ListView,
View,
RedirectView,
UpdateView,
TemplateView,
)
from django.views.generic.detail import SingleObjectMixin, SingleObjectTemplateResponseMixin
import xlsxwriter
import simplejson as json
from django.views.generic.edit import FormMixin
from projectroles.constants import SODAR_CONSTANTS
from projectroles.models import RemoteSite
from projectroles.templatetags.projectroles_common_tags import site_version
from bgjobs.models import BackgroundJob
from bgjobs.views import DEFAULT_PAGINATION as BGJOBS_DEFAULT_PAGINATION
from clinvar.models import Clinvar
from cohorts.models import Cohort
from extra_annos.views import ExtraAnnosMixin, ExtraAnnoField
from frequencies.models import MT_DB_INFO
from geneinfo.views import get_gene_infos
from geneinfo.models import (
NcbiGeneInfo,
NcbiGeneRif,
HpoName,
Hpo,
EnsemblToGeneSymbol,
Hgnc,
build_entrez_id_to_symbol,
)
from frequencies.views import FrequencyMixin
from projectroles.app_settings import AppSettingAPI
from projectroles.views import (
LoginRequiredMixin,
LoggedInPermissionMixin,
ProjectContextMixin,
ProjectPermissionMixin,
PluginContextMixin,
)
from projectroles.plugins import get_backend_api, get_active_plugins
from genomicfeatures.models import GeneInterval
from varfish.users.models import User
from .queries import (
CaseLoadPrefetchedQuery,
ProjectLoadPrefetchedQuery,
KnownGeneAAQuery,
DeleteStructuralVariantsQuery,
DeleteSmallVariantsQuery,
SmallVariantUserAnnotationQuery,
)
from .models import (
only_source_name,
Case,
ExportFileBgJob,
ExportProjectCasesFileBgJob,
CaddSubmissionBgJob,
DistillerSubmissionBgJob,
SpanrSubmissionBgJob,
ComputeProjectVariantsStatsBgJob,
FilterBgJob,
Project,
CaseAwareProject,
SmallVariant,
SmallVariantFlags,
SmallVariantComment,
SmallVariantQuery,
ProjectCasesSmallVariantQuery,
ProjectCasesFilterBgJob,
annotate_with_phenotype_scores,
annotate_with_pathogenicity_scores,
annotate_with_joint_scores,
AcmgCriteriaRating,
SyncCaseListBgJob,
SmallVariantSet,
ImportVariantsBgJob,
CaseComments,
CASE_STATUS_CHOICES,
RowWithAffectedCasesPerGene,
SmallVariantSummary,
KioskAnnotateBgJob,
update_variant_counts,
DeleteCaseBgJob,
RefreshSmallVariantSummaryBgJob,
ClearOldKioskCasesBgJob,
ClearInactiveVariantSetsBgJob,
ClearExpiredExportedFilesBgJob,
)
from .forms import (
ExportFileResubmitForm,
ExportProjectCasesFileResubmitForm,
FILTER_FORM_TRANSLATE_CLINVAR_STATUS,
FILTER_FORM_TRANSLATE_EFFECTS,
FILTER_FORM_TRANSLATE_SIGNIFICANCE,
FilterForm,
ProjectCasesFilterForm,
EmptyForm,
ProjectStatsJobForm,
SmallVariantCommentForm,
SmallVariantFlagsForm,
AcmgCriteriaRatingForm,
CaseForm,
SyncProjectJobForm,
CaseNotesStatusForm,
CaseCommentsForm,
KioskUploadForm,
save_file,
CaseTermsForm,
RE_FIND_TERMS,
)
from .sync_upstream import fetch_remote_pedigree
from .tasks import (
export_file_task,
export_project_cases_file_task,
cadd_submission_task,
distiller_submission_task,
compute_project_variants_stats,
sync_project_upstream,
single_case_filter_task,
project_cases_filter_task,
run_kiosk_bg_job,
delete_case_bg_job,
spanr_submission_task,
)
from .file_export import RowWithSampleProxy
from .templatetags.variants_tags import get_term_description, smallvar_description
class UUIDEncoder(json.JSONEncoder):
"""JSON encoder for UUIds"""
def default(self, obj):
if isinstance(obj, uuid.UUID):
# If the obj is uuid, we simply return the value of uuid
return obj.hex
# Default implementation raises not-serializable TypeError exception
return json.JSONEncoder.default(self, obj) # pragma: no cover
# Modes of inheritance in HPO: https://hpo.jax.org/app/browse/term/HP:0000005
HPO_INHERITANCE_MAPPING = {
"HP:0000006": "AD",
"HP:0000007": "AR",
"HP:0001417": "X-linked",
"HP:0001419": "XR",
"HP:0001423": "XD",
}
class AlchemyEngineMixin:
"""Cached alchemy connection for CBVs."""
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._alchemy_engine = None
def get_alchemy_engine(self):
if not self._alchemy_engine:
self._alchemy_engine = get_engine()
return self._alchemy_engine
class CaseListView(
LoginRequiredMixin,
LoggedInPermissionMixin,
ProjectPermissionMixin,
ProjectContextMixin,
ListView,
):
"""Display list of all cases"""
template_name = "variants/case_list.html"
permission_required = "variants.view_data"
model = Case
ordering = ("-date_modified",)
def get_queryset(self):
return (
super()
.get_queryset()
.filter(project__sodar_uuid=self.kwargs["project"])
.prefetch_related("project", "case_comments",)
)
def get_context_data(self, *args, **kwargs):
result = super().get_context_data(*args, **kwargs)
result["project"] = CaseAwareProject.objects.prefetch_related("variant_stats").get(
pk=result["project"].pk
)
result["progress"] = self._compute_progress(result["project"])
return result
def _compute_progress(self, project):
counts = {key: 0 for key, _ in CASE_STATUS_CHOICES}
for case in project.case_set.all():
counts[case.status] = counts.get(case.status, 0) + 1
total_count = sum(counts.values())
result = []
statuses = [k for k, _ in CASE_STATUS_CHOICES if counts.get(k)] # statuses with counts >0
width_sum = 0
if total_count:
for i, key in enumerate(statuses):
if i + 1 < len(statuses):
width = int(100 * (counts.get(key, 0) / total_count))
result.append((width, counts.get(key, 0), total_count, key))
width_sum += width
else:
width = 100 - width_sum
result.append((width, counts.get(key, 0), total_count, key))
else:
result.append((100, total_count, total_count, "initial"))
return result
class CaseListGetAnnotationsView(
LoginRequiredMixin, LoggedInPermissionMixin, ProjectPermissionMixin, ProjectContextMixin, View,
):
template_name = "variants/case_list/annotation.html"
permission_required = "variants.view_data"
model = Case
ordering = ("-date_modified",)
def get(self, *args, **kwargs):
result = dict()
result["project"] = CaseAwareProject.objects.prefetch_related(
"case_set__small_variant_comments",
"case_set__small_variant_flags",
"case_set__acmg_ratings",
"case_set__structural_variant_comments",
"case_set__structural_variant_flags",
"case_set__acmg_ratings",
).get(sodar_uuid=kwargs["project"])
result["limit"] = 100
result["annotation_count"] = result["project"].get_annotation_count()
result["commentsflags"] = self.join_small_var_comments_and_flags(
result["project"], result["limit"]
)
result["sv_commentsflags"] = self.join_sv_comments_and_flags(result["project"])
return render(self.request, self.template_name, self.get_context_data(**result),)
def join_small_var_comments_and_flags(self, project, limit):
def get_gene_symbol(release, chromosome, start, end):
bins = binning.containing_bins(start - 1, end)
gene_intervals = list(
GeneInterval.objects.filter(
database="ensembl",
release=release,
chromosome=chromosome,
bin__in=bins,
start__lte=end,
end__gte=start,
)
)
gene_ids = [itv.gene_id for itv in gene_intervals]
symbols1 = {
o.gene_symbol
for o in EnsemblToGeneSymbol.objects.filter(ensembl_gene_id__in=gene_ids)
}
symbols2 = {o.symbol for o in Hgnc.objects.filter(ensembl_gene_id__in=gene_ids)}
return symbols1 | symbols2
result = defaultdict(
lambda: defaultdict(
lambda: dict(flags=None, comments=[], genes=set(), acmg_rating=None)
)
)
gene_symbol_cache = dict()
for case in project.case_set.all():
flags = case.small_variant_flags.all()
comments = case.small_variant_comments.all()
acmg_ratings = case.acmg_ratings.all()
for record in flags:
position_key = (record.release, record.chromosome, record.start, record.end)
if not position_key in gene_symbol_cache:
gene_symbol_cache[position_key] = get_gene_symbol(*position_key)
result[(record.chromosome, record.start, record.reference, record.alternative)][
case
]["flags"] = model_to_dict(record)
result[(record.chromosome, record.start, record.reference, record.alternative)][
case
]["genes"] |= gene_symbol_cache[position_key]
for record in comments:
position_key = (record.release, record.chromosome, record.start, record.end)
if not position_key in gene_symbol_cache:
gene_symbol_cache[position_key] = get_gene_symbol(*position_key)
result[(record.chromosome, record.start, record.reference, record.alternative)][
case
]["comments"].append(
{
**model_to_dict(record),
"date_created": record.date_created,
"user": record.user,
"username": record.user.username,
}
)
result[(record.chromosome, record.start, record.reference, record.alternative)][
case
]["genes"] |= gene_symbol_cache[position_key]
for record in acmg_ratings:
position_key = (record.release, record.chromosome, record.start, record.end)
if not position_key in gene_symbol_cache:
gene_symbol_cache[position_key] = get_gene_symbol(*position_key)
result[(record.chromosome, record.start, record.reference, record.alternative)][
case
]["acmg_rating"] = {"data": record, "class": record.acmg_class}
result[(record.chromosome, record.start, record.reference, record.alternative)][
case
]["genes"] |= gene_symbol_cache[position_key]
if limit and len(result) > limit:
break
for variant, data in result.items():
result[variant] = dict(data)
for case in data:
result[variant][case]["genes"] = sorted(result[variant][case]["genes"])
return dict(result)
def join_sv_comments_and_flags(self, project):
result = defaultdict(lambda: defaultdict(lambda: dict(flags=None, comments=[])))
for case in project.case_set.all():
flags = case.structural_variant_flags.all()
comments = case.structural_variant_comments.all()
for record in flags:
result[(record.chromosome, record.start, record.end, record.sv_type)][case][
"flags"
] = model_to_dict(record)
for record in comments:
result[(record.chromosome, record.start, record.end, record.sv_type)][case][
"comments"
].append(
{
**model_to_dict(record),
"date_created": record.date_created,
"user": record.user,
"username": record.user.username,
}
)
for variant, data in result.items():
result[variant] = dict(data)
return dict(result)
class CaseListGetQCView(
LoginRequiredMixin, LoggedInPermissionMixin, ProjectPermissionMixin, ProjectContextMixin, View,
):
template_name = "variants/case_list/qc.html"
permission_required = "variants.view_data"
model = Case
ordering = ("-date_modified",)
def get(self, *args, **kwargs):
result = dict()
result["project"] = CaseAwareProject.objects.prefetch_related("variant_stats").get(
sodar_uuid=kwargs["project"]
)
result["samples"] = result["project"].get_members()
result["effects"] = list(FILTER_FORM_TRANSLATE_EFFECTS.values())
result["dps_keys"] = list(chain(range(0, 20), range(20, 50, 2), range(50, 200, 5), (200,)))
result["ontarget_effect_counts"] = {sample: {} for sample in result["samples"]}
result["indel_sizes"] = {sample: {} for sample in result["samples"]}
result["indel_sizes_keys"] = []
result["dps"] = {sample: {} for sample in result["samples"]}
# Build list of properly sorted coverage keys.
result["sample_variant_stats"] = result["project"].sample_variant_stats()
try:
coverages = set()
for stats in result["sample_variant_stats"]:
if stats.sample_name not in result["samples"]:
continue
result["ontarget_effect_counts"][stats.sample_name] = stats.ontarget_effect_counts
for key, value in stats.ontarget_indel_sizes.items():
result["indel_sizes"][stats.sample_name][int(key)] = value
for key, value in stats.ontarget_dps.items():
result["dps"][stats.sample_name][int(key)] = value
result["indel_sizes_keys"] = list(
sorted(
set(
chain(
*list(
map(int, indel_sizes.keys())
for indel_sizes in result["indel_sizes"].values()
)
)
)
)
)
for case in (
result["project"]
.case_set.prefetch_related("latest_variant_set__casealignmentstats")
.all()
):
variant_set = case.latest_variant_set
if variant_set:
if hasattr(variant_set, "casealignmentstats"):
for min_covs in variant_set.casealignmentstats.bam_stats.values():
if "min_cov_target" in min_covs:
coverages |= set(map(int, min_covs["min_cov_target"]))
if coverages:
filtered = filter(lambda x: x > 0, coverages)
result["coverages"] = list(map(str, sorted(filtered)))[:5]
result["qcdata_relatedness"] = self.get_relatedness_content(result["project"])
result["qcdata_sample_variant_stats"] = self.get_sample_variant_stats_content(
result["project"], result["sample_variant_stats"]
)
except (SmallVariantSet.variant_stats.RelatedObjectDoesNotExist, AttributeError) as e:
pass # swallow, defaults set above
# Prepare effect counts data for QC download
qcdata_effect_content = ["\t".join(["Effect"] + result["samples"])]
for effect in result["effects"]:
record = [effect]
for sample in result["samples"]:
record.append(str(result["ontarget_effect_counts"][sample].get(effect, 0)))
qcdata_effect_content.append("\t".join(record))
result["qcdata_effects"] = b64encode("\n".join(qcdata_effect_content).encode("utf-8"))
# Prepare InDel size data for QC download
qcdata_indel_size_content = ["\t".join(["InDel Size"] + result["samples"])]
for indel_size in result["indel_sizes_keys"]:
record = [
">= %d" % indel_size
if indel_size == 10
else "<= %d" % indel_size
if indel_size == -10
else str(indel_size)
]
for sample in result["samples"]:
record.append(str(result["indel_sizes"][sample].get(indel_size, 0)))
qcdata_indel_size_content.append("\t".join(record))
result["qcdata_indel_sizes"] = b64encode(
"\n".join(qcdata_indel_size_content).encode("utf-8")
)
# Prepare depth data for QC download
qcdata_site_depth_content = ["\t".join(["Depth"] + result["samples"])]
for site_depth in result["dps_keys"]:
record = [">= %d" % site_depth if site_depth == 200 else str(site_depth)]
for sample in result["samples"]:
record.append(str(result["dps"][sample].get(site_depth, 0)))
qcdata_site_depth_content.append("\t".join(record))
result["qcdata_site_depths"] = b64encode(
"\n".join(qcdata_site_depth_content).encode("utf-8")
)
return render(self.request, self.template_name, self.get_context_data(**result),)
def get_relatedness_content(self, project):
result = [
"\t".join(
[
"Sample 1",
"Sample 2",
"Het_1,2",
"Het_1",
"Het_2",
"n_IBS0",
"n_IBS1",
"n_IBS2",
"relatedness",
]
)
]
for rel in project.variant_stats.relatedness.all():
result.append(
"\t".join(
[
rel.sample1,
rel.sample2,
str(rel.het_1_2),
str(rel.het_1),
str(rel.het_2),
str(rel.n_ibs0),
str(rel.n_ibs1),
str(rel.n_ibs2),
str(rel.relatedness()),
]
)
)
return b64encode("\n".join(result).encode("utf-8"))
def get_sample_variant_stats_content(self, project, sample_variant_stats):
result = [
"\t".join(["Sample", "Ts", "Tv", "Ts/Tv", "SNVs", "InDels", "MNVs", "X hom./het.",])
]
for item in sample_variant_stats:
result.append(
"\t".join(
[
item.sample_name,
str(item.ontarget_transitions),
str(item.ontarget_transversions),
str(item.ontarget_ts_tv_ratio()),
str(item.ontarget_snvs),
str(item.ontarget_indels),
str(item.ontarget_mnvs),
str(item.chrx_het_hom),
]
)
)
return b64encode("\n".join(result).encode("utf-8"))
class CaseListSyncRemoteView(
LoginRequiredMixin,
LoggedInPermissionMixin,
ProjectPermissionMixin,
ProjectContextMixin,
FormView,
):
"""Confirm creating a new upstream synchronization job."""
permission_required = "variants.view_data"
template_name = "variants/sync_job_create.html"
form_class = SyncProjectJobForm
def form_valid(self, form):
with transaction.atomic():
# Construct background job objects
bg_job = BackgroundJob.objects.create(
name="Sync VarFish project with upstream SODAR",
project=self.get_project(self.request, self.kwargs),
job_type=SyncCaseListBgJob.spec_name,
user=self.request.user,
)
sync_job = SyncCaseListBgJob.objects.create(
project=self.get_project(self.request, self.kwargs), bg_job=bg_job
)
sync_project_upstream.delay(sync_job_pk=sync_job.pk)
messages.info(self.request, "Created background job to sync with upstream SODAR.")
return redirect(sync_job.get_absolute_url())
class CaseListQcStatsApiView(
LoginRequiredMixin,
LoggedInPermissionMixin,
ProjectPermissionMixin,
ProjectContextMixin,
ListView,
):
"""Render JSON with project-wide case statistics"""
template_name = "variants/case_list.html"
permission_required = "variants.view_data"
model = Case
ordering = ("-date_modified",)
def get_queryset(self):
return (
super()
.get_queryset()
.filter(project__sodar_uuid=self.kwargs["project"])
.prefetch_related(
"smallvariantset_set__variant_stats",
"smallvariantset_set__variant_stats__sample_variant_stats",
"project",
)
)
def get(self, *args, **kwargs):
self.object_list = self.get_queryset()
context_data = self.get_context_data()
project = CaseAwareProject.objects.prefetch_related("variant_stats").get(
pk=context_data["project"].pk
)
try:
rel_data = list(
build_rel_data(
list(chain(*[case.pedigree for case in self.get_queryset()])),
project.variant_stats.relatedness.all(),
)
)
except Project.variant_stats.RelatedObjectDoesNotExist:
rel_data = []
result = {
"pedigree": [
{**line, "patient": only_source_name(line["patient"])}
for case in self.get_queryset()
for line in case.pedigree
],
"relData": rel_data,
**build_sex_data(project),
**build_cov_data(
list(
project.case_set.prefetch_related(
"smallvariantset_set__variant_stats__sample_variant_stats"
).all()
)
),
}
return JsonResponse(result)
def _undecimal(the_dict):
"""Helper to replace Decimal values in a dict."""
result = {}
for key, value in the_dict.items():
if isinstance(value, decimal.Decimal):
result[key] = float(value)
else:
result[key] = value
return result
class CaseNotesStatusApiView(
LoginRequiredMixin,
LoggedInPermissionMixin,
ProjectPermissionMixin,
ProjectContextMixin,
SingleObjectMixin,
SingleObjectTemplateResponseMixin,
FormMixin,
View,
):
"""API view to save case notes and status."""
permission_required = "variants.view_data"
model = Case
form_class = CaseNotesStatusForm
slug_url_kwarg = "case"
slug_field = "sodar_uuid"
def post(self, *args, **kwargs):
case = self.get_object()
form = self.get_form()
timeline = get_backend_api("timeline_backend")
if form.is_valid():
case.notes = form.cleaned_data["notes"]
case.status = form.cleaned_data["status"]
case.tags = form.cleaned_data["tags"]
case.save()
if timeline:
tl_event = timeline.add_event(
project=self.get_project(self.request, self.kwargs),
app_name="variants",
user=self.request.user,
event_name="case_status_notes_submit",
description="submit status and note for case {{case}}: {status}, {text}".format(
status=case.status, text=case.shortened_notes_text()
),
status_type="OK",
)
tl_event.add_object(obj=case, label="case", name=case.name)
return JsonResponse(
{
"notes": form.cleaned_data["notes"],
"status": form.cleaned_data["status"],
"tags": form.cleaned_data["tags"],
}
)
if timeline:
tl_event = timeline.add_event(
project=self.get_project(self.request, self.kwargs),
app_name="variants",
user=self.request.user,
event_name="case_status_notes_submit",
description="failed submit status and note for case {{case}}: {status}, {text}".format(
status=case.status, text=case.shortened_notes_text()
),
status_type="FAILED",
)
tl_event.add_object(obj=case, label="case", name=case.name)
return JsonResponse(dict(form.errors.items()), status=500)
def get_form_kwargs(self):
kwargs = super().get_form_kwargs()
case = self.get_object()
kwargs.update({"project": case.project})
return kwargs
class CaseCommentsSubmitApiView(
LoginRequiredMixin,
LoggedInPermissionMixin,
ProjectPermissionMixin,
ProjectContextMixin,
SingleObjectMixin,
SingleObjectTemplateResponseMixin,
FormMixin,
View,
):
"""API view to save case comments."""
permission_required = "variants.view_data"
model = Case
form_class = CaseCommentsForm
slug_url_kwarg = "case"
slug_field = "sodar_uuid"
def post(self, *args, **kwargs):
case = self.get_object()
form = self.get_form()
timeline = get_backend_api("timeline_backend")
if form.is_valid():
if self.request.POST.get("sodar_uuid"):
kwargs = {"sodar_uuid": self.request.POST.get("sodar_uuid")}
if not self.request.user.is_superuser:
kwargs["user"] = self.request.user
try:
record = CaseComments.objects.get(**kwargs)
except ObjectDoesNotExist as e:
return HttpResponse(
json.dumps(
{"result": "Not authorized to update comment or no comment found."}
),
content_type="application/json",
status=500,
)
record.comment = form.cleaned_data["comment"]
record.save()
if timeline:
tl_event = timeline.add_event(
project=self.get_project(self.request, self.kwargs),
app_name="variants",
user=self.request.user,
event_name="case_comment_edit",
description="edit comment for case {case}: {text}",
status_type="OK",
)
tl_event.add_object(obj=case, label="case", name=case.name)
tl_event.add_object(obj=record, label="text", name=record.shortened_text())
else:
record = CaseComments(
case=case, user=self.request.user, comment=form.cleaned_data["comment"]
)
record.save()
if timeline:
tl_event = timeline.add_event(
project=self.get_project(self.request, self.kwargs),
app_name="variants",
user=self.request.user,
event_name="case_comment_add",
description="add comment for case {case}: {text}",
status_type="OK",
)
tl_event.add_object(obj=case, label="case", name=case.name)
tl_event.add_object(obj=record, label="text", name=record.shortened_text())
return HttpResponse(
json.dumps(
{
"comment": record.comment,
"date_created": record.date_created.strftime("%Y/%m/%d %H:%M"),
"user": str(record.user),
"sodar_uuid": str(record.sodar_uuid),
}
),
content_type="application/json",
)
class CaseCommentsDeleteApiView(
LoginRequiredMixin,
LoggedInPermissionMixin,
ProjectPermissionMixin,
ProjectContextMixin,
SingleObjectMixin,
SingleObjectTemplateResponseMixin,
View,
):
"""API view to save case comments."""
permission_required = "variants.view_data"
model = Case
slug_url_kwarg = "case"
slug_field = "sodar_uuid"
def post(self, *args, **kwargs):
kwargs = {"sodar_uuid": self.request.POST.get("sodar_uuid")}
if not self.request.user.is_superuser:
kwargs["user"] = self.request.user
try:
comment = CaseComments.objects.get(**kwargs)
except ObjectDoesNotExist as e:
return HttpResponse(
json.dumps({"result": "Not authorized to delete comment or no comment found."}),
content_type="application/json",
status=500,
)
comment.delete()
timeline = get_backend_api("timeline_backend")
if timeline:
tl_event = timeline.add_event(
project=self.get_project(self.request, self.kwargs),
app_name="variants",
user=self.request.user,
event_name="case_comment_delete",
description="delete comment for case {case}",
status_type="OK",
)
tl_event.add_object(obj=self.get_object(), label="case", name=self.get_object().name)
return HttpResponse(json.dumps({"result": "OK"}), content_type="application/json")
class CaseCommentsCountApiView(
LoginRequiredMixin,
LoggedInPermissionMixin,
ProjectPermissionMixin,
ProjectContextMixin,
SingleObjectMixin,
SingleObjectTemplateResponseMixin,
View,
):
"""API view to save case comments."""
permission_required = "variants.view_data"
model = Case
slug_url_kwarg = "case"
slug_field = "sodar_uuid"
def get(self, *args, **kwargs):
return JsonResponse({"count": self.get_object().case_comments.count()})
def get_annotations_by_variant(case=None, cases=None, project=None):
"""Helper function to get all annotations by case and variant.
The result is a dict. First level of keys is case SODAR UUID, second is variant description, then
"variants", "flags", "comments", "acmg_rating".
"""
annotated_small_vars = SmallVariantUserAnnotationQuery(get_engine()).run(
case=case, cases=cases, project=project
)
case_ids = list(sorted({x.case_id for x in annotated_small_vars.small_variants}))
case_id_to_uuid = {}
for case in Case.objects.filter(id__in=case_ids).order_by("name"):
case_id_to_uuid[case.id] = case.sodar_uuid
result = {}
# Ensure that at least one entry is there if exactly one case is to be queried for.
if case:
result.setdefault(case.sodar_uuid, {})
def init_var(description):
result[case_uuid].setdefault(
description, {"variants": [], "flags": None, "comments": [], "acmg_rating": None,},
)
for small_var in annotated_small_vars.small_variants:
case_uuid = case_id_to_uuid[small_var.case_id]
result.setdefault(case_uuid, {})
init_var(small_var.get_description())
result[case_uuid][small_var.get_description()]["variants"].append(small_var)
for flags in annotated_small_vars.small_variant_flags:
case_uuid = case_id_to_uuid[flags.case_id]
init_var(flags.get_variant_description())
result[case_uuid][flags.get_variant_description()]["flags"] = flags
for comments in annotated_small_vars.small_variant_comments:
case_uuid = case_id_to_uuid[comments.case_id]
init_var(comments.get_variant_description())
result[case_uuid][comments.get_variant_description()]["comments"].append(comments)
for rating in annotated_small_vars.acmg_criteria_rating:
case_uuid = case_id_to_uuid[rating.case_id]
init_var(rating.get_variant_description())
result[case_uuid][rating.get_variant_description()]["acmg_rating"] = rating
return result
class CaseDetailView(
LoginRequiredMixin,
LoggedInPermissionMixin,
ProjectPermissionMixin,
ProjectContextMixin,
AlchemyEngineMixin, # XXX
FormMixin,
DetailView,
):
"""Display a case in detail."""
template_name = "variants/case_detail.html"
permission_required = "variants.view_data"
model = Case
slug_url_kwarg = "case"
slug_field = "sodar_uuid"
form_class = CaseNotesStatusForm
def get_context_data(self, *args, **kwargs):
result = super().get_context_data(*args, **kwargs)
case = result["object"]
result["samples"] = case.get_members_with_samples()
result["effects"] = list(FILTER_FORM_TRANSLATE_EFFECTS.values())
result["dps_keys"] = list(chain(range(0, 20), range(20, 50, 2), range(50, 200, 5), (200,)))
result["ontarget_effect_counts"] = {sample: {} for sample in result["samples"]}
result["indel_sizes"] = {sample: {} for sample in result["samples"]}
result["indel_sizes_keys"] = []
result["dps"] = {sample: {} for sample in result["samples"]}
result["casecommentsform"] = CaseCommentsForm()
result["commentsflags"] = self.join_small_var_comments_and_flags()
result["gene_id_to_symbol"] = build_entrez_id_to_symbol(
[
v.refseq_gene_id
for entry in result["commentsflags"].values()
for v in entry["variants"]
]
)
result["sv_commentsflags"] = self.join_sv_comments_and_flags()
result["acmg_summary"] = {
"count": case.acmg_ratings.count(),
**{
str(i): len(
[rating for rating in case.acmg_ratings.all() if rating.acmg_class == i]
)
for i in range(1, 6)
},
}
result["flag_summary"] = {
"count": case.small_variant_flags.count(),
**{
key: len(
[
flag
for flag in case.small_variant_flags.all()
if getattr(flag, "flag_%s" % key, None)
]
)
for key in ("final_causative", "candidate")
},
}
result["user"] = self.request.user
try:
variant_set = case.latest_variant_set
import_job = ImportVariantsBgJob.objects.filter(case_name=case.name).order_by(
"-date_created"
)
if import_job and not import_job[0].bg_job.status == "done":
return result
if variant_set:
result["ontarget_effect_counts"] = {
stats.sample_name: stats.ontarget_effect_counts
for stats in variant_set.variant_stats.sample_variant_stats.all()
}
result["indel_sizes"] = {
stats.sample_name: {
int(key): value for key, value in stats.ontarget_indel_sizes.items()
}
for stats in variant_set.variant_stats.sample_variant_stats.all()
}
result["indel_sizes_keys"] = list(
sorted(
set(
chain(
*list(
map(int, indel_sizes.keys())
for indel_sizes in result["indel_sizes"].values()
)
)
)
)
)
result["dps"] = {
stats.sample_name: {