Merge pull request #85 from molgenis/feat/inheritance

Feature: add inheritance filtering

src/components/RecordTable.vue

@@ -266,9 +266,11 @@ export default Vue.extend({
       'hasCapice',
       'getAnnotation',
       'isAnnotationEnabled',
-      'isRecordsContainPhenotypes'
+      'isRecordsContainPhenotypes',
+      'isSamplesContainInheritance',
+      'isSamplesContainDenovo'
     ]),
-    ...mapState(['metadata', 'records', 'annotations', 'selectedSamplePhenotypes', 'filterRecordsByPhenotype']),
+    ...mapState(['metadata', 'records', 'annotations', 'selectedSamplePhenotypes', 'filterRecordsByPhenotype', 'filterRecordsByInheritance', 'filterRecordsByDenovo']),
     genomeAssembly(): string {
       return this.metadata.htsFile.genomeAssembly;
     },
@@ -356,6 +358,12 @@ export default Vue.extend({
       if (this.isRecordsContainPhenotypes && this.hasSamplePhenotypes() && this.filterRecordsByPhenotype) {
         queries.push(this.createSamplePhenotypesQuery());
       }
+      if (this.isSamplesContainInheritance && this.filterRecordsByInheritance) {
+        queries.push(this.createSampleInheritanceQuery());
+      }
+      if (this.isSamplesContainDenovo && this.filterRecordsByDenovo) {
+        queries.push(this.createSampleDenovoQuery());
+      }
       // todo: translate ctx filter param to query
 
       let query: Query | ComposedQuery | undefined;
@@ -378,6 +386,20 @@ export default Vue.extend({
         args: ['het', 'hom_a', 'part']
       };
     },
+    createSampleInheritanceQuery(): Query {
+      return {
+        selector: ['s', this.sample.index, 'f', 'VIM'],
+        operator: '==',
+        args:1
+      };
+    },
+    createSampleDenovoQuery(): Query {
+      return {
+        selector: ['s', this.sample.index, 'f', 'VID'],
+        operator:'==',
+        args:1
+      };
+    },
     hasSamplePhenotypes(): boolean {
       return this.selectedSamplePhenotypes !== null && this.selectedSamplePhenotypes.page.totalElements > 0;
     },
@@ -484,6 +506,14 @@ export default Vue.extend({
     '$store.state.filterRecordsByPhenotype'() {
       this.page.currentPage = 1;
       (this.$refs.table as BTable).refresh();
+    },
+    '$store.state.filterRecordsByInheritance'() {
+      this.page.currentPage = 1;
+      (this.$refs.table as BTable).refresh();
+    },
+    '$store.state.filterRecordsByDenovo'() {
+      this.page.currentPage = 1;
+      (this.$refs.table as BTable).refresh();
     }
   }
 });

src/components/RecordTableControls.vue

@@ -1,23 +1,37 @@
 <template>
-  <b-form-checkbox
-    v-if="isRecordsContainPhenotypes"
-    :checked="filterRecordsByPhenotype"
-    @change="this.setFilterRecordsByPhenotype"
-    >{{ $t('matchPhenotype') }}</b-form-checkbox
-  >
+  <div>
+    <b-form-checkbox
+        v-if="isRecordsContainPhenotypes"
+        :checked="filterRecordsByPhenotype"
+        @change="this.setFilterRecordsByPhenotype"
+    >{{ $t('matchPhenotype') }}
+    </b-form-checkbox>
+    <b-form-checkbox
+        v-if="isSamplesContainInheritance"
+        :checked="filterRecordsByInheritance"
+        @change="this.setFilterRecordsByInheritance"
+    >{{ $t('matchInheritance') }}
+    </b-form-checkbox>
+    <b-form-checkbox
+        v-if="isSamplesContainDenovo"
+        :checked="filterRecordsByDenovo"
+        @change="this.setFilterRecordsByDenovo"
+    >{{ $t('matchDenovo') }}
+    </b-form-checkbox>
+  </div>
 </template>
 
 <script lang="ts">
 import Vue from 'vue';
-import { mapActions, mapGetters, mapState } from 'vuex';
+import {mapActions, mapGetters, mapState} from 'vuex';
 
 export default Vue.extend({
   computed: {
-    ...mapGetters(['isRecordsContainPhenotypes']),
-    ...mapState(['filterRecordsByPhenotype'])
+    ...mapGetters(['isRecordsContainPhenotypes', 'isSamplesContainInheritance', 'isSamplesContainDenovo']),
+    ...mapState(['filterRecordsByPhenotype', 'filterRecordsByInheritance', 'filterRecordsByDenovo'])
   },
   methods: {
-    ...mapActions(['setFilterRecordsByPhenotype'])
+    ...mapActions(['setFilterRecordsByPhenotype', 'setFilterRecordsByInheritance', 'setFilterRecordsByDenovo'])
   }
 });
 </script>

src/locales/en.json

@@ -53,5 +53,7 @@
   "open": "Open...",
   "save": "Save...",
   "exit": "Exit",
-  "matchPhenotype": "Only display records that match sample phenotype(s)"
+  "matchPhenotype": "Only display records that match sample phenotype(s)",
+  "matchInheritance": "Only display records that match inheritance",
+  "matchDenovo": "Only display records that are denovo"
 }

src/store/actions.ts

@@ -83,6 +83,12 @@ export default {
   },
   setFilterRecordsByPhenotype({ commit }: ActionContext<State, State>, value: boolean) {
     commit('setFilterRecordsByPhenotype', value);
+  },
+  setFilterRecordsByInheritance({ commit }: ActionContext<State, State>, value: boolean) {
+    commit('setFilterRecordsByInheritance', value);
+  },
+  setFilterRecordsByDenovo({ commit }: ActionContext<State, State>, value: boolean) {
+    commit('setFilterRecordsByDenovo', value);
   }
 };
 

src/store/getters.ts

@@ -119,5 +119,31 @@ export default {
       }
     }
     return hasPhenotypeAssociations;
+  },
+  /**
+   * Returns whether records contain inheritance matching information.
+   */
+  isSamplesContainInheritance: (state: State): boolean => {
+    let hasSampleInheritance;
+    if (state.metadata === null) {
+      hasSampleInheritance = false;
+    } else {
+      const vimFormat = state.metadata.records.format.find(item => item.id === 'VIM');
+      hasSampleInheritance = vimFormat !== undefined
+    }
+    return hasSampleInheritance;
+  },
+  /**
+   * Returns whether records contain denovo information.
+   */
+  isSamplesContainDenovo: (state: State): boolean => {
+    let hasSampleInheritance;
+    if (state.metadata === null) {
+      hasSampleInheritance = false;
+    } else {
+      const vimFormat = state.metadata.records.format.find(item => item.id === 'VID');
+      hasSampleInheritance = vimFormat !== undefined
+    }
+    return hasSampleInheritance;
   }
 };

src/store/mutations.ts

@@ -32,5 +32,11 @@ export default {
   },
   setFilterRecordsByPhenotype(state: State, value: boolean) {
     state.filterRecordsByPhenotype = value;
+  },
+  setFilterRecordsByInheritance(state: State, value: boolean) {
+    state.filterRecordsByInheritance = value;
+  },
+  setFilterRecordsByDenovo(state: State, value: boolean) {
+    state.filterRecordsByDenovo = value;
   }
 };

src/store/state.ts

@@ -8,6 +8,8 @@ const state: State = {
   selectedSamplePhenotypes: null,
   records: null,
   filterRecordsByPhenotype: true,
+  filterRecordsByInheritance: false,
+  filterRecordsByDenovo: false,
   annotations: null
 };
 

src/types/State.ts

@@ -10,5 +10,7 @@ export type State = {
   selectedSamplePhenotypes: PagedItems<Phenotype> | null;
   records: PagedItems<Record> | null;
   filterRecordsByPhenotype: boolean;
+  filterRecordsByInheritance: boolean;
+  filterRecordsByDenovo: boolean;
   annotations: Annotations | null;
 };

src/views/Samples.vue

@@ -20,7 +20,7 @@ export default Vue.extend({
   components: { SampleNavigation, SampleReport },
   computed: {
     ...mapGetters(['samples', 'getSampleById']),
-    ...mapState(['selectedSample', 'selectedSamplePhenotypes'])
+    ...mapState(['selectedSample', 'selectedSamplePhenotypes', 'selectedSampleInheritance', 'selectedSampleDenovo'])
   },
   methods: {
     ...mapActions(['loadMetadata', 'loadSamples', 'selectSample']),

tests/unit/store/actions.spec.ts

@@ -136,3 +136,17 @@ test('set filter records by phenotype', async done => {
   expect(commit).toHaveBeenCalledWith('setFilterRecordsByPhenotype', true);
   done();
 });
+
+test('set filter records by inheritance', async done => {
+  const commit = jest.fn() as Commit;
+  actions.setFilterRecordsByInheritance({ commit } as ActionContext<State, State>, true);
+  expect(commit).toHaveBeenCalledWith('setFilterRecordsByInheritance', true);
+  done();
+});
+
+test('set filter records by denovo status', async done => {
+  const commit = jest.fn() as Commit;
+  actions.setFilterRecordsByDenovo({ commit } as ActionContext<State, State>, true);
+  expect(commit).toHaveBeenCalledWith('setFilterRecordsByDenovo', true);
+  done();
+});

tests/unit/store/getters.spec.ts

@@ -4,6 +4,7 @@ import { State } from '@/types/State';
 import { GenomeBrowserDb } from '@/types/GenomeBrowserDb';
 import { mock } from 'ts-mockito';
 import {
+  FormatMetadata,
   HtsFileMetadata,
   InfoMetadata,
   Metadata,
@@ -403,3 +404,91 @@ test('whether records contain phenotype associations without VEP', () => {
   };
   expect(getters.isRecordsContainPhenotypes(testState)).toEqual(false);
 });
+
+test('whether records contain inheritance matching information. true.', () => {
+  const formatMetadata = mock<FormatMetadata>();
+  formatMetadata.id = 'VIM';
+
+  const recordsMetadata = mock<RecordsMetadata>();
+  recordsMetadata.format = [formatMetadata];
+
+  const metadata = mock<Metadata>();
+  metadata.records = recordsMetadata;
+
+  const testState: State = {
+    ...initialState,
+    metadata: metadata
+  };
+  expect(getters.isSamplesContainInheritance(testState)).toEqual(true);
+});
+
+test('whether records contain inheritance matching information. false.', () => {
+  const formatMetadata = mock<FormatMetadata>();
+  formatMetadata.id = 'OTHER';
+
+  const recordsMetadata = mock<RecordsMetadata>();
+  recordsMetadata.format = [formatMetadata];
+
+  const metadata = mock<Metadata>();
+  metadata.records = recordsMetadata;
+
+  const testState: State = {
+    ...initialState,
+    metadata: metadata
+  };
+  expect(getters.isSamplesContainInheritance(testState)).toEqual(false);
+});
+
+test('whether records contain inheritance matching information. null.', () => {
+  const metadata =null;
+
+  const testState: State = {
+    ...initialState,
+    metadata: metadata
+  };
+  expect(getters.isSamplesContainInheritance(testState)).toEqual(false);
+});
+
+test('whether records contain denovo information. true.', () => {
+  const formatMetadata = mock<FormatMetadata>();
+  formatMetadata.id = 'VID';
+
+  const recordsMetadata = mock<RecordsMetadata>();
+  recordsMetadata.format = [formatMetadata];
+
+  const metadata = mock<Metadata>();
+  metadata.records = recordsMetadata;
+
+  const testState: State = {
+    ...initialState,
+    metadata: metadata
+  };
+  expect(getters.isSamplesContainDenovo(testState)).toEqual(true);
+});
+
+test('whether records contain denovo information. false.', () => {
+  const formatMetadata = mock<FormatMetadata>();
+  formatMetadata.id = 'OTHER';
+
+  const recordsMetadata = mock<RecordsMetadata>();
+  recordsMetadata.format = [formatMetadata];
+
+  const metadata = mock<Metadata>();
+  metadata.records = recordsMetadata;
+
+  const testState: State = {
+    ...initialState,
+    metadata: metadata
+  };
+  expect(getters.isSamplesContainDenovo(testState)).toEqual(false);
+});
+
+test('whether records contain denovo information. null.', () => {
+  const metadata =null;
+
+  const testState: State = {
+    ...initialState,
+    metadata: metadata
+  };
+  expect(getters.isSamplesContainDenovo(testState)).toEqual(false);
+});

tests/unit/store/mutations.spec.ts

@@ -52,3 +52,15 @@ test('set filter records by phenotype', () => {
   mutations.setFilterRecordsByPhenotype(testState, false);
   expect(testState.filterRecordsByPhenotype).toBe(false);
 });
+
+test('set filter records by inheritance', () => {
+  const testState: State = { ...initialState };
+  mutations.setFilterRecordsByInheritance(testState, false);
+  expect(testState.filterRecordsByInheritance).toBe(false);
+});
+
+test('set filter records by denovo', () => {
+  const testState: State = { ...initialState };
+  mutations.setFilterRecordsByDenovo(testState, false);
+  expect(testState.filterRecordsByDenovo).toBe(false);
+});