Fixed smallvariant flags filter query. (#544)

Added flags `segregates`, `doesnt_segregate` and `no_disease_association` to file export.

Closes: #502
Related-Issue: #502
Projected-Results-Impact: none

HISTORY.rst

@@ -24,9 +24,11 @@ End-User Summary
 - Adjusting default frequency filters for "clinvar pathogenic" filter: remove all threshold (#464).
 - Adding note about difference with upstream Clinvar (#464).
 - Switching scoring to MutationTaster 85 interface, added back MT 85 link-out alongside MT 2021 link-out (#509).
-- Made flag filter and flag form nomenclature consistent (#297)
+- Made flag filter and flag form nomenclature consistent (#297).
 - Improved developer setup documentation and added Windows installation instructions (#533).
-- Fixed broken VariantValidator query (#523)
+- Fixed broken VariantValidator query (#523).
+- Fixed smallvariant flags filter query (#502).
+- Added flags `segregates`, `doesnt_segregate` and `no_disease_association` to file export (#502).
 
 Full Change List
 ================
@@ -47,12 +49,14 @@ Full Change List
 - Adding note about difference with upstream Clinvar (#464).
 - Switching scoring to MutationTaster 85 interface, added back MT 85 link-out alongside MT 2021 link-out (#509).
 - CADD setup fix for documentation (#520)
-- Made flag filter and flag form nomenclature consistent (#297)
+- Made flag filter and flag form nomenclature consistent (#297).
 - Updating ``utility/*.sh`` scripts from "upstream" sodar-server (#531).
 - Improved developer setup documentation and added Windows installation instructions (#533).
 - Skip commit trailer checks for dependabot (#537).
-- Fixed broken VariantValidator query (#523)
+- Fixed broken VariantValidator query (#523).
 - Converted not cooperative tooltip to standard title on Filter & Display button (#508).
+- Fixed smallvariant flags filter query (#502).
+- Added flags `segregates`, `doesnt_segregate` and `no_disease_association` to file export (#502).
 
 ------
 v1.2.0

svs/tests/factories.py

@@ -165,6 +165,9 @@ class Meta:
     flag_candidate = False
     flag_final_causative = False
     flag_for_validation = False
+    flag_no_disease_association = False
+    flag_segregates = False
+    flag_doesnt_segregate = False
 
     flag_molecular = "empty"
     flag_visual = "empty"

varfish/static/js/flags_comments.js

@@ -96,7 +96,7 @@ function clickVariantBookmark() {
         dataType: "json",
       }).done(function(data) {
         // successfully updated flags, update bookmark display
-        if (data["flag_bookmarked"] || data["flag_for_validation"] || data["flag_candidate"] || data["flag_final_causative"]) {
+        if (data["flag_bookmarked"] || data["flag_for_validation"] || data["flag_candidate"] || data["flag_final_causative"] || data["flag_no_disease_association"] || data["flag_segregates"] || data["flag_doesnt_segregate"]) {
           icon_bookmark.attr("src", "/icons/fa-solid/bookmark.svg");
         } else {
           icon_bookmark.attr("src", "/icons/fa-regular/bookmark.svg");
@@ -635,6 +635,9 @@ function clickVariantAcmgRatingModal(event) {
         flag_for_validation: false,
         flag_candidate: false,
         flag_final_causative: false,
+        flag_no_disease_association: false,
+        flag_segregates: false,
+        flag_doesnt_segregate: false,
         flag_visual: "empty",
         flag_validation: "empty",
         flag_phenotype_match: "empty",
@@ -776,6 +779,9 @@ function clickVariantAcmgRating() {
         flag_for_validation: false,
         flag_candidate: false,
         flag_final_causative: false,
+        flag_no_disease_association: false,
+        flag_segregates: false,
+        flag_doesnt_segregate: false,
         flag_visual: "empty",
         flag_validation: "empty",
         flag_phenotype_match: "empty",

variants/file_export.py

@@ -130,6 +130,9 @@ def to_str(val):
     ("flag_candidate", "Flag: selected as candidate disease-causing", str),
     ("flag_final_causative", "Flag: selected as final causative variant", str),
     ("flag_for_validation", "Flag: selected for validation", str),
+    ("flag_no_disease_association", "Flag: selected for no known disease association", str),
+    ("flag_segregates", "Flag: selected as segregating variant", str),
+    ("flag_doesnt_segregate", "Flag: selected as not segregating variant", str),
     ("flag_molecular", "Rating: variant is molecular", str),
     ("flag_visual", "Rating: visual inspection of alignment", str),
     ("flag_validation", "Rating: validation result", str),

variants/queries.py

@@ -1219,14 +1219,25 @@ class ExtendQueryPartsFlagsJoinAndFilter(ExtendQueryPartsFlagsJoin):
     def extend_conditions(self, _query_parts):
         """Build WHERE clause for the query based on the ``SmallVariantFlags`` and ``SmallVariantComment``."""
         terms = []
+        not_terms = [true()]
+        none_terms = [true()]
         # Add terms for the simple, boolean-valued flags.
-        flag_names = ("bookmarked", "candidate", "final_causative", "for_validation")
+        flag_names = (
+            "bookmarked",
+            "candidate",
+            "final_causative",
+            "for_validation",
+            "segregates",
+            "doesnt_segregate",
+            "no_disease_association",
+        )
         for flag in flag_names:
             flag_name = "flag_%s" % flag
             if self.kwargs.get(flag_name):
                 terms.append(column(flag_name))
-        if self.kwargs.get("flag_simple_empty"):
-            terms.append(and_(not_(column("flag_%s" % flag))))
+            if self.kwargs.get("flag_simple_empty"):
+                not_terms.append(not_(column(flag_name)))
+                none_terms.append(column(flag_name).is_(None))
         # Add terms for the valued flags.
         flag_names = ("visual", "validation", "molecular", "phenotype_match", "summary")
         for flag in flag_names:
@@ -1237,7 +1248,7 @@ def extend_conditions(self, _query_parts):
                     terms.append(column(flag_name) == value)
                     if value == "empty":
                         terms.append(column(flag_name).is_(None))
-        return [or_(*terms)]
+        return [or_(*terms, and_(*not_terms), and_(*none_terms))]
 
 
 class ExtendQueryPartsAcmgCriteriaJoin(ExtendQueryPartsBase):

variants/tests/factories.py

@@ -185,6 +185,9 @@ class FormDataFactory(FormDataFactoryBase):
     flag_candidate: bool = True
     flag_final_causative: bool = True
     flag_for_validation: bool = True
+    flag_no_disease_association: bool = True
+    flag_segregates: bool = True
+    flag_doesnt_segregate: bool = True
     flag_phenotype_match_empty: bool = True
     flag_phenotype_match_negative: bool = True
     flag_phenotype_match_positive: bool = True
@@ -946,6 +949,9 @@ class Meta:
     flag_candidate = False
     flag_final_causative = False
     flag_for_validation = False
+    flag_no_disease_association = False
+    flag_segregates = False
+    flag_doesnt_segregate = False
     flag_molecular = ""
     flag_visual = ""
     flag_validation = ""

variants/tests/test_file_export.py

@@ -66,7 +66,7 @@ def test_export_tsv(self):
     def _test_tabular(self, arrs, has_trailing):
         self.assertEquals(len(arrs), 4 + int(has_trailing))
         # TODO: also test without flags and comments
-        self.assertEquals(len(arrs[0]), 46)
+        self.assertEquals(len(arrs[0]), 49)
         self.assertSequenceEqual(arrs[0][:3], ["Chromosome", "Position", "Reference bases"])
         self.assertSequenceEqual(
             arrs[0][-5:],
@@ -207,7 +207,7 @@ def test_export_tsv(self):
     def _test_tabular(self, arrs, has_trailing):
         self.assertEquals(len(arrs), 5 + int(has_trailing))
         # TODO: also test without flags and comments
-        self.assertEquals(len(arrs[0]), 47)
+        self.assertEquals(len(arrs[0]), 50)
         self.assertSequenceEqual(arrs[0][:3], ["Sample", "Chromosome", "Position"])
         self.assertEqual(arrs[0][-1], "sample Alternate allele fraction")
         members = sorted(self.project.get_members())
@@ -411,7 +411,7 @@ def test_export_tsv_as_contributor_for_cohort_by_superuser(self):
     def _test_tabular(self, arrs, ref, has_trailing, smallvars):
         self.assertEquals(len(arrs), ref + int(has_trailing))
         # TODO: also test without flags and comments
-        self.assertEquals(len(arrs[0]), 47)
+        self.assertEquals(len(arrs[0]), 50)
         self.assertSequenceEqual(arrs[0][:3], ["Sample", "Chromosome", "Position"])
         self.assertEqual(arrs[0][-1], "sample Alternate allele fraction")
         for i, small_var in enumerate(sorted(smallvars, key=lambda x: (x.chromosome_no, x.start))):