|
- chr{{ variant.0 }}:{{ variant.1|intcomma }}-{{ variant.2 }}-{{ variant.3 }}
+ {{ data.variants.0.human_readable }}
|
- {{ data|keyvalue:"genes"|join:", "|default:"-" }}
+ {% for variant in data.variants %}
+ {{ gene_id_to_symbol|keyvalue:variant.refseq_gene_id }}:{{ variant.refseq_hgvs_p|default:variant.refseq_hgvs_c|default:"-" }}{% if not forloop.last %},{% endif %}
+ {% endfor %}
|
- {% if data|keyvalue:"acmg_rating" %}
-
- {{ data|keyvalue:"acmg_rating"|keyvalue:"class" }}
+ {% if data.acmg_rating %}
+
+ {{ data.acmg_rating|acmg_classification2 }}
{% else %}
No ACMG rating.
{% endif %}
|
- {% if data|keyvalue:"flags" %}
+ {% if data.flags %}
-
-
-
-
-
-
-
+
+
+
+
+
+
+
|
-
+
|
-
+
|
-
+
|
-
+
|
-
+
|
{% else %}
No flags. |
{% endif %}
|
IGV
diff --git a/variants/templates/variants/case_list/annotation.html b/variants/templates/variants/case_list/annotation.html
index 4f56d6dfb..c0e808014 100644
--- a/variants/templates/variants/case_list/annotation.html
+++ b/variants/templates/variants/case_list/annotation.html
@@ -11,6 +11,25 @@
Annotated Variants
+
+
diff --git a/variants/tests/test_views.py b/variants/tests/test_views.py
index d6e9deccf..cf04c3ede 100644
--- a/variants/tests/test_views.py
+++ b/variants/tests/test_views.py
@@ -225,6 +225,74 @@ def test_render_with_variant_stats(self):
self.assertEqual(response.context["object"].name, self.case.name)
+class CaseDownloadAnnotationsView(ViewTestBase):
+ """Smoke test for downloading all user annotations for one case."""
+
+ def setUp(self):
+ super().setUp()
+ self.case, self.variant_set, _ = CaseWithVariantSetFactory.get("small")
+
+ def test_render_empty_tsv(self):
+ with self.login(self.user):
+ response = self.client.get(
+ reverse(
+ "variants:case-download-annotations",
+ kwargs={"project": self.case.project.sodar_uuid, "case": self.case.sodar_uuid},
+ )
+ )
+ self.assertEqual(response.status_code, 200)
+ self.assertEqual(response["content-type"], "text/tsv")
+
+ def test_render_empty_xlsx(self):
+ with self.login(self.user):
+ response = self.client.get(
+ reverse(
+ "variants:case-download-annotations",
+ kwargs={"project": self.case.project.sodar_uuid, "case": self.case.sodar_uuid},
+ )
+ + "?format=xlsx"
+ )
+ self.assertEqual(response.status_code, 200)
+ self.assertEqual(
+ response["content-type"],
+ "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
+ )
+
+
+class ProjectDownloadAnnotationsView(ViewTestBase):
+ """Smoke test for downloading all user annotations for one project."""
+
+ def setUp(self):
+ super().setUp()
+ self.case, self.variant_set, _ = CaseWithVariantSetFactory.get("small")
+
+ def test_render_empty_tsv(self):
+ with self.login(self.user):
+ response = self.client.get(
+ reverse(
+ "variants:project-download-annotations",
+ kwargs={"project": self.case.project.sodar_uuid,},
+ )
+ )
+ self.assertEqual(response.status_code, 200)
+ self.assertEqual(response["content-type"], "text/tsv")
+
+ def test_render_empty_xlsx(self):
+ with self.login(self.user):
+ response = self.client.get(
+ reverse(
+ "variants:project-download-annotations",
+ kwargs={"project": self.case.project.sodar_uuid},
+ )
+ + "?format=xlsx"
+ )
+ self.assertEqual(response.status_code, 200)
+ self.assertEqual(
+ response["content-type"],
+ "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
+ )
+
+
class TestCaseUpdateView(ViewTestBase):
def setUp(self):
super().setUp()
diff --git a/variants/urls.py b/variants/urls.py
index d11fa3e0a..cff28f746 100644
--- a/variants/urls.py
+++ b/variants/urls.py
@@ -51,6 +51,16 @@
view=views.CaseDeleteView.as_view(),
name="case-delete",
),
+ url(
+ regex=r"^(?P[0-9a-f-]+)/case/download-annotations/(?P[0-9a-f-]+)/$",
+ view=views.CaseDownloadAnnotationsView.as_view(),
+ name="case-download-annotations",
+ ),
+ url(
+ regex=r"^(?P[0-9a-f-]+)/case/download-annotations/$",
+ view=views.ProjectDownloadAnnotationsView.as_view(),
+ name="project-download-annotations",
+ ),
url(
regex=r"^(?P[0-9a-f-]+)/case-delete-job/detail/(?P[0-9a-f-]+)/$",
view=views.CaseDeleteJobDetailView.as_view(),
diff --git a/variants/views.py b/variants/views.py
index 512651286..e16ed915b 100644
--- a/variants/views.py
+++ b/variants/views.py
@@ -26,6 +26,7 @@
from django.utils import timezone
from django.views.generic import DetailView, FormView, ListView, View, RedirectView, UpdateView
from django.views.generic.detail import SingleObjectMixin, SingleObjectTemplateResponseMixin
+import xlsxwriter
import simplejson as json
from django.views.generic.edit import FormMixin
@@ -41,7 +42,15 @@
from extra_annos.views import ExtraAnnosMixin
from frequencies.models import MT_DB_INFO
from geneinfo.views import get_gene_infos
-from geneinfo.models import NcbiGeneInfo, NcbiGeneRif, HpoName, Hpo, EnsemblToGeneSymbol, Hgnc
+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 (
@@ -61,6 +70,7 @@
KnownGeneAAQuery,
DeleteStructuralVariantsQuery,
DeleteSmallVariantsQuery,
+ SmallVariantUserAnnotationQuery,
)
from .models import (
only_source_name,
@@ -847,6 +857,47 @@ 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(SQLALCHEMY_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, {})
+
+ for small_var in annotated_small_vars.small_variants:
+ case_uuid = case_id_to_uuid[small_var.case_id]
+ result.setdefault(case_uuid, {})
+ result[case_uuid].setdefault(
+ small_var.get_description(),
+ {"variants": [], "flags": None, "comments": [], "acmg_rating": None,},
+ )
+ 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]
+ result[case_uuid][flags.get_variant_description()]["flags"] = flags
+ for comments in annotated_small_vars.small_variant_comments:
+ case_uuid = case_id_to_uuid[flags.case_id]
+ 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[flags.case_id]
+ result[case_uuid][rating.get_variant_description()]["acmg_rating"] = rating
+ return result
+
+
class CaseDetailView(
LoginRequiredMixin,
LoggedInPermissionMixin,
@@ -877,6 +928,13 @@ def get_context_data(self, *args, **kwargs):
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(),
@@ -1088,65 +1146,7 @@ def get_effect_content(self):
def join_small_var_comments_and_flags(self):
case = self.get_object()
- flags = case.small_variant_flags.all()
- comments = case.small_variant_comments.all()
- acmg_ratings = case.acmg_ratings.all()
- result = defaultdict(lambda: dict(flags=None, comments=[], genes=set(), acmg_rating=None))
-
- 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
-
- for record in flags:
- result[(record.chromosome, record.start, record.reference, record.alternative)][
- "flags"
- ] = model_to_dict(record)
- result[(record.chromosome, record.start, record.reference, record.alternative)][
- "genes"
- ] |= get_gene_symbol(record.release, record.chromosome, record.start, record.end)
-
- for record in comments:
- result[(record.chromosome, record.start, record.reference, record.alternative)][
- "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)][
- "genes"
- ] |= get_gene_symbol(record.release, record.chromosome, record.start, record.end)
-
- for record in acmg_ratings:
- result[(record.chromosome, record.start, record.reference, record.alternative)][
- "acmg_rating"
- ] = {"data": record, "class": record.acmg_class}
- result[(record.chromosome, record.start, record.reference, record.alternative)][
- "genes"
- ] |= get_gene_symbol(record.release, record.chromosome, record.start, record.end)
-
- for var in result:
- result[var]["genes"] = sorted(result[var]["genes"])
- return dict(result)
+ return get_annotations_by_variant(case=case)[case.sodar_uuid]
def join_sv_comments_and_flags(self):
case = self.get_object()
@@ -1446,6 +1446,188 @@ def get(self, *args, **kwargs):
return redirect(delete_job.get_absolute_url())
+#: Header for for table when downloading annotation data.
+ANNOTATION_DOWNLOAD_HEADER = [
+ "case",
+ "genome_release",
+ "chromosome",
+ "position",
+ "reference",
+ "alternative",
+ "refseq_genes",
+ "refseq_transcripts",
+ "refseq_hgvs",
+ "refseq_effects",
+ "acmg_rating",
+ "flag_bookmarked",
+ "flag_candidate",
+ "flag_final_causative",
+ "flag_for_validation",
+ "flag_no_disease_association",
+ "flag_segregates",
+ "flag_doesnt_segregate",
+ "flag_visual",
+ "flag_molecular",
+ "flag_validation",
+ "flag_phenotype_match",
+ "flag_summary",
+ "comments",
+]
+
+
+class BaseDownloadAnnotationsView(
+ LoginRequiredMixin,
+ LoggedInPermissionMixin,
+ ProjectPermissionMixin,
+ ProjectContextMixin,
+ DetailView,
+):
+ """Download case user annotations as Excel file."""
+
+ permission_required = "variants.view_data"
+ slug_field = "sodar_uuid"
+
+ def get_impl(self, case=None, cases=None, project=None):
+ with tempfile.NamedTemporaryFile("w+b") as f:
+ # Write output to temporary file.
+ if self.request.GET.get("format", "tsv") == "xlsx":
+ content_type = "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"
+ file_ext = "xlsx"
+ self.write_xlsx(case=case, cases=cases, project=project, output_f=f)
+ else:
+ content_type = "text/tsv"
+ file_ext = "tsv"
+ self.write_tsv(case=case, cases=cases, project=project, output_f=f)
+ # Build HTTP response.
+ f.flush()
+ f.seek(0)
+ if case:
+ identifier = case.name
+ elif cases:
+ identifier = "-".join(cases[:5].name)
+ else:
+ identifier = project.title.replace(" ", "-")
+ response = HttpResponse(f.read(), content_type=content_type,)
+ response["Content-Disposition"] = "attachment; filename=case-annotations-%s.%s" % (
+ identifier,
+ file_ext,
+ )
+ return response
+
+ def write_xlsx(self, *, case, cases, project, output_f):
+ """Write output XLSX file."""
+ workbook = xlsxwriter.Workbook(output_f.name, {"remove_timezone": True})
+ header_format = workbook.add_format({"bold": True})
+ sheet = workbook.add_worksheet("Small Variants")
+ for rowno, row in enumerate(self.yield_rows(case=case, cases=cases, project=project)):
+ if rowno == 0:
+ sheet.write_row(0, 0, row, header_format)
+ else:
+ sheet.write_row(rowno, 0, row)
+ workbook.close()
+
+ def write_tsv(self, *, case, cases, project, output_f):
+ """Write output TSV file."""
+ for row in self.yield_rows(case=case, cases=cases, project=project):
+ output_f.write(("\t".join(map(str, row)) + "\n").encode())
+
+ def yield_rows(self, *, case, cases, project):
+ yield ANNOTATION_DOWNLOAD_HEADER
+
+ res = get_annotations_by_variant(case=case, cases=cases, project=project)
+ case_uuid_to_name = {
+ c.sodar_uuid: c.name for c in Case.objects.filter(sodar_uuid__in=res.keys())
+ }
+
+ # import pdb; pdb.set_trace()
+ for case_uuid, annos in res.items():
+ for anno in annos.values():
+ comments = [
+ "%s @%s: %s"
+ % (
+ comment.user.username,
+ comment.date_modified.strftime("%Y-%m-%d %H:%M"),
+ comment.text.replace("\t", " ").replace("\n", " "),
+ )
+ for comment in anno["comments"]
+ ]
+
+ gene_id_to_symbol = build_entrez_id_to_symbol(
+ [x.refseq_gene_id for x in anno["variants"]]
+ )
+ genes = ", ".join(
+ gene_id_to_symbol[x.refseq_gene_id]
+ for x in anno["variants"]
+ if x.refseq_gene_id
+ )
+ transcripts = ", ".join(
+ x.refseq_transcript_id for x in anno["variants"] if x.refseq_gene_id
+ )
+ hgvs = ", ".join(
+ x.refseq_hgvs_p or x.refseq_hgvs_c for x in anno["variants"] if x.refseq_gene_id
+ )
+ effects = ", ".join(
+ "&".join(x.refseq_effect) for x in anno["variants"] if x.refseq_gene_id
+ )
+
+ variant = anno["variants"][0]
+ if not anno["flags"]:
+ row_flags = ["N/A"] * 12
+ else:
+ row_flags = [
+ anno["flags"].flag_bookmarked,
+ anno["flags"].flag_candidate,
+ anno["flags"].flag_final_causative,
+ anno["flags"].flag_for_validation,
+ anno["flags"].flag_no_disease_association,
+ anno["flags"].flag_segregates,
+ anno["flags"].flag_doesnt_segregate,
+ anno["flags"].flag_visual,
+ anno["flags"].flag_molecular,
+ anno["flags"].flag_validation,
+ anno["flags"].flag_phenotype_match,
+ anno["flags"].flag_summary,
+ ]
+ row = (
+ [
+ case_uuid_to_name[case_uuid],
+ variant.release,
+ variant.chromosome,
+ variant.start,
+ variant.reference,
+ variant.alternative,
+ genes,
+ transcripts,
+ hgvs,
+ effects,
+ anno["acmg_rating"].acmg_class if anno["acmg_rating"] else "N/A",
+ ]
+ + row_flags
+ + ["|".join(comments),]
+ )
+ yield row
+
+
+class CaseDownloadAnnotationsView(BaseDownloadAnnotationsView):
+ """Download case user annotations as Excel file."""
+
+ model = Case
+ slug_url_kwarg = "case"
+
+ def get(self, *args, **kwargs):
+ return self.get_impl(case=self.get_object())
+
+
+class ProjectDownloadAnnotationsView(BaseDownloadAnnotationsView):
+ """Download project user annotations as Excel file."""
+
+ model = Project
+ slug_url_kwarg = "project"
+
+ def get(self, *args, **kwargs):
+ return self.get_impl(project=self.get_object())
+
+
class SmallVariantsDeleteView(
LoginRequiredMixin,
LoggedInPermissionMixin,
|