feat: qc values thresholds should be adjustable (#1530) (#1644)

Makefile

@@ -116,3 +116,7 @@ format-isort:
 .PHONY: format-black
 format-black:
 	black --line-length 100 --exclude '/(\.eggs|\.git|\.hg|\.mypy_cache|\.nox|\.tox|\.?v?env|_build|buck-out|build|dist|src|node_modules)/' .
+
+.PHONY: gen-api-schema
+gen-api-schema:
+	$(MANAGE) spectacular > ./varfish/tests/drf_spectacular/varfish_api_schema.yaml

cases/vueapp/src/api/caseClient.ts

@@ -217,4 +217,12 @@ export class CaseClient extends ClientBase {
       'DELETE',
     )
   }
+
+  /** Retrieve project settings. */
+  async retrieveProjectSettings(projectUuid: string) {
+    return await this.fetchHelper(
+      `/variants/ajax/project-settings/retrieve/${projectUuid}/`,
+      'GET',
+    )
+  }
 }

cases/vueapp/src/components/CaseDetail/CardVariantQc.vue

@@ -65,21 +65,23 @@ const tsTv = (member) => {
                 }}
               </td>
               <td
-                v-if="tsTv(member) >= 2.0 && tsTv(member) <= 2.9"
-                class="text-right"
-              >
-                {{ tsTv(member) }}
-              </td>
-              <td
-                v-else
+                v-if="
+                  tsTv(member) <
+                    caseDetailsStore.projectSettings.ts_tv_valid_lower ||
+                  tsTv(member) >
+                    caseDetailsStore.projectSettings.ts_tv_valid_upper
+                "
                 class="text-right text-danger font-weight-bold"
-                :title="`Ts/Tv ratio should be within 2.0-2.9 but is ${tsTv(
+                :title="`Ts/Tv ratio should be within ${caseDetailsStore.projectSettings.ts_tv_warning_lower}-${caseDetailsStore.projectSettings.ts_tv_warning_upper} but is ${tsTv(
                   member,
                 )}`"
               >
                 <i-bi-exclamation-circle />
                 {{ tsTv(member) }}
               </td>
+              <td v-else class="text-right">
+                {{ tsTv(member) }}
+              </td>
               <td class="text-right">
                 {{
                   caseDetailsStore.caseVariantStats[

cases/vueapp/src/components/CaseDetail/QcTableVarStats.vue

@@ -1,11 +1,14 @@
 <script setup>
 import { displayName, formatLargeInt } from '@varfish/helpers'
+import { useCaseDetailsStore } from '@cases/stores/caseDetails'
 import { tsTvRatio } from '@cases/common'
 
 const props = defineProps({
   // eslint-disable-next-line vue/require-default-prop
   varStats: Object,
 })
+
+const caseDetailsStore = useCaseDetailsStore()
 </script>
 
 <template>
@@ -37,11 +40,16 @@ const props = defineProps({
           </td>
           <td class="text-right">
             <span
-              v-if="tsTvRatio(entry) < 1.0 || tsTvRatio(entry) > 2.9"
+              v-if="
+                tsTvRatio(entry) <
+                  caseDetailsStore.projectSettings.ts_tv_valid_lower ||
+                tsTvRatio(entry) >
+                  caseDetailsStore.projectSettings.ts_tv_valid_upper
+              "
               class="text-danger"
             >
               <i-bi-exclamation-circle
-                :title="`On-target Ts/Tv ratio should be between 2.0 and 2.9 but was ${tsTvRatio(
+                :title="`On-target Ts/Tv ratio should be between ${caseDetailsStore.projectSettings.ts_tv_warning_lower} and ${caseDetailsStore.projectSettings.ts_tv_warning_upper} but was ${tsTvRatio(
                   entry,
                 )}.`"
               />

cases/vueapp/src/stores/caseDetails.ts

@@ -133,6 +133,11 @@ export const useCaseDetailsStore = defineStore('caseDetails', () => {
 
   const projectDefaultPresetSet = ref<any | null>(null)
 
+  const projectSettings = ref<any>({
+    ts_tv_valid_lower: 2.0,
+    ts_tv_valid_upper: 2.9,
+  })
+
   /** Promise for initialization of the store. */
   const initializeRes = ref<Promise<any> | null>(null)
 
@@ -235,6 +240,9 @@ export const useCaseDetailsStore = defineStore('caseDetails', () => {
         .then((res) => {
           projectDefaultPresetSet.value = res
         }),
+      caseClient.retrieveProjectSettings(projectUuid.value).then((res) => {
+        projectSettings.value = res
+      }),
     ])
       .then(() => {
         storeState.serverInteractions -= 1
@@ -460,6 +468,7 @@ export const useCaseDetailsStore = defineStore('caseDetails', () => {
     caseSvAnnotationReleaseInfos,
     genotypeMapping,
     projectDefaultPresetSet,
+    projectSettings,
     // functions
     initialize,
     updateCase,

cases/vueapp/tests/unit/cases/CaseDetail/QcTableVarStats.spec.js

@@ -1,16 +1,8 @@
 import QcTableVarStats from '@cases/components/CaseDetail/QcTableVarStats.vue'
-import { mount } from '@vue/test-utils'
 import { beforeAll, describe, expect, test, vi } from 'vitest'
 
 import caseDetailsStoreData from '../../../data/caseDetailsStoreData.json'
-
-const makeWrapper = (varStats) => {
-  return mount(QcTableVarStats, {
-    props: {
-      varStats: varStats,
-    },
-  })
-}
+import { makeWrapper } from '../CaseDetailApp.common'
 
 describe('QcTableVarStats.vue', () => {
   beforeAll(() => {
@@ -19,13 +11,15 @@ describe('QcTableVarStats.vue', () => {
   })
 
   test('test with null data', async () => {
-    const wrapper = makeWrapper(null)
+    const wrapper = makeWrapper(QcTableVarStats)
 
     expect(wrapper.findAll('table').length).toBe(1)
     expect(wrapper.html()).toMatch(/No variant statistics to display./)
   })
 
+  // TODO Fix me
   test('test with data data', async () => {
+    // console.log(caseDetailsStoreData.caseVariantStats)
     const varStats = Object.entries(caseDetailsStoreData.caseVariantStats).map(
       ([name, stats]) => {
         return {
@@ -34,7 +28,10 @@ describe('QcTableVarStats.vue', () => {
         }
       },
     )
-    const wrapper = makeWrapper(varStats)
+
+    const wrapper = makeWrapper(QcTableVarStats, caseDetailsStoreData, {
+      varStats: varStats,
+    })
 
     expect(wrapper.findAll('table').length).toBe(1)
     expect(wrapper.html()).toMatch(/<td>NA12878<\/td>/)

varfish/tests/drf_spectacular/varfish_api_schema.yaml

@@ -5870,6 +5870,38 @@ paths:
               schema:
                 $ref: '#/components/schemas/PresetSet'
           description: ''
+  /variants/ajax/project-settings/retrieve/{project}/:
+    get:
+      operationId: variants_ajax_project_settings_retrieve_retrieve
+      description: |-
+        A view that returns project settings for the given project.
+
+        **URL:** ``/variants/ajax/project-settings/retrieve/{project.uuid}``
+
+        **Methods:** ``GET``
+
+        **Returns:** {
+            ts_tv_warning_upper,
+            ts_tv_warning_lower
+        }
+      parameters:
+      - in: path
+        name: project
+        schema:
+          type: string
+          pattern: ^[0-9a-f-]+$
+        required: true
+      tags:
+      - variants
+      security:
+      - cookieAuth: []
+      responses:
+        '200':
+          content:
+            application/vnd.bihealth.varfish+json:
+              schema:
+                $ref: '#/components/schemas/ProjectSettings'
+          description: ''
   /variants/ajax/project/qc/{project}/:
     get:
       operationId: variants_ajax_project_qc_retrieve
@@ -7660,6 +7692,40 @@ paths:
                 items:
                   $ref: '#/components/schemas/HpoTerm'
           description: ''
+  /variants/api/project-settings/retrieve/{project}/:
+    get:
+      operationId: variants_api_project_settings_retrieve_retrieve
+      description: |-
+        A view that returns project settings for the given project.
+
+        **URL:** ``/variants/api/project-settings/retrieve/{project.uuid}``
+
+        **Methods:** ``GET``
+
+        **Returns:** {
+            ts_tv_warning_upper,
+            ts_tv_warning_lower
+        }
+      parameters:
+      - in: path
+        name: project
+        schema:
+          type: string
+          pattern: ^[0-9a-f-]+$
+        required: true
+      tags:
+      - variants
+      security:
+      - basicAuth: []
+      - cookieAuth: []
+      - knoxApiToken: []
+      responses:
+        '200':
+          content:
+            application/vnd.bihealth.varfish+json:
+              schema:
+                $ref: '#/components/schemas/ProjectSettings'
+          description: ''
   /variants/api/project/qc/{project}/:
     get:
       operationId: variants_api_project_qc_retrieve
@@ -13258,6 +13324,19 @@ components:
       - qualitypresets_set
       - quickpresets_set
       - sodar_uuid
+    ProjectSettings:
+      type: object
+      description: Serializer for project settings.
+      properties:
+        ts_tv_valid_upper:
+          type: number
+          format: double
+        ts_tv_valid_lower:
+          type: number
+          format: double
+      required:
+      - ts_tv_valid_lower
+      - ts_tv_valid_upper
     QualityPresets:
       type: object
       description: Serializer for ``QualityPresets``.

varfish/vueapp/components.d.ts

@@ -105,6 +105,7 @@ declare module 'vue' {
     IMdiPlusCircle: typeof import('~icons/mdi/plus-circle')['default']
     IMdiPodium: typeof import('~icons/mdi/podium')['default']
     IMdiRefresh: typeof import('~icons/mdi/refresh')['default']
+    IMdiSettings: typeof import('~icons/mdi/settings')['default']
     IMdiSquareEditOutline: typeof import('~icons/mdi/square-edit-outline')['default']
     IMdiStar: typeof import('~icons/mdi/star')['default']
     IMdiTableColumnWidth: typeof import('~icons/mdi/table-column-width')['default']

variants/plugins.py

@@ -139,6 +139,16 @@ class ProjectAppPlugin(ProjectAppPluginPoint):
                 "database (such as no variant of a case showing up because being in the in-house database many times)."
             ),
         },
+        "ts_tv_valid_range": {
+            "scope": SODAR_CONSTANTS["APP_SETTING_SCOPE_PROJECT"],
+            "type": "STRING",
+            "default": "2.0-2.9",
+            "label": "Ts/Tv valid range",
+            "description": (
+                "Variants with a Ts/Tv ratio outside this range will be highlighted as a warning. "
+                "The recommended value is <code>2.0-2.9</code>"
+            ),
+        },
     }
 
     #: Additional columns to display for the projects.

variants/serializers/__init__.py

@@ -779,3 +779,18 @@ class CaseListQcStatsSerializer(serializers.Serializer):
     dpQuantiles = serializers.JSONField()
     hetRatioQuantiles = serializers.JSONField()
     dpHetData = serializers.JSONField()
+
+
+@attrs.define
+class ProjectSettings:
+    """Helper class that contains the results of the settings shortcuts"""
+
+    ts_tv_valid_upper: float
+    ts_tv_valid_lower: float
+
+
+class ProjectSettingsSerializer(serializers.Serializer):
+    """Serializer for project settings."""
+
+    ts_tv_valid_upper = serializers.FloatField()
+    ts_tv_valid_lower = serializers.FloatField()

variants/urls/__init__.py

@@ -298,6 +298,11 @@
         view=views_ajax.HpoTermsAjaxView.as_view(),
         name="ajax-hpo-terms",
     ),
+    url(
+        regex=r"^ajax/project-settings/retrieve/(?P<project>[0-9a-f-]+)/?$",
+        view=views_ajax.ProjectSettingsRetrieveAjaxView.as_view(),
+        name="ajax-project-settings-retrieve",
+    ),
 ]
 
 api_urlpatterns = [
@@ -457,6 +462,11 @@
         name="api-extra-anno-fields",
     ),
     url(regex=r"^api/hpo-terms/?$", view=views_api.HpoTermsApiView.as_view(), name="api-hpo-terms"),
+    url(
+        regex=r"^api/project-settings/retrieve/(?P<project>[0-9a-f-]+)/?$",
+        view=views_api.ProjectSettingsRetrieveApiView.as_view(),
+        name="api-project-settings-retrieve",
+    ),
 ]
 
 

variants/views/ajax/__init__.py

@@ -8,6 +8,7 @@
     CaseRetrieveApiView,
     ExtraAnnoFieldsApiView,
     HpoTermsApiView,
+    ProjectSettingsRetrieveApiView,
     SmallVariantCommentDeleteApiView,
     SmallVariantCommentListCreateApiView,
     SmallVariantCommentListProjectApiView,
@@ -434,3 +435,19 @@ class CaseListQcStatsAjaxView(CaseListQcStatsApiView):
     """
 
     authentication_classes = [SessionAuthentication]
+
+
+class ProjectSettingsRetrieveAjaxView(ProjectSettingsRetrieveApiView):
+    """A view that returns project settings for the given project.
+
+    **URL:** ``/variants/ajax/project-settings/retrieve/{project.uuid}``
+
+    **Methods:** ``GET``
+
+    **Returns:** {
+        ts_tv_warning_upper,
+        ts_tv_warning_lower
+    }
+    """
+
+    authentication_classes = [SessionAuthentication]