@molgenis/vip-report-template 2.7.3 → 3.0.0

package/src/plugins/bootstrap-vue.ts

@@ -1,68 +0,0 @@
-import Vue from 'vue';
-import {
-  AlertPlugin,
-  BIcon,
-  BIconBoxArrowInUpRight,
-  BIconChevronDown,
-  BIconChevronUp,
-  BIconCircle,
-  BIconCircleFill,
-  BIconDiamond,
-  BIconDiamondFill,
-  BIconExclamationCircle,
-  BIconQuestionCircle,
-  BIconQuestionDiamond,
-  BIconQuestionSquare,
-  BIconSearch,
-  BIconSquare,
-  BIconSquareFill,
-  ButtonPlugin,
-  CollapsePlugin,
-  FormCheckboxPlugin,
-  FormInputPlugin,
-  FormSelectPlugin,
-  FormTextareaPlugin,
-  InputGroupPlugin,
-  LayoutPlugin,
-  ModalPlugin,
-  NavbarPlugin,
-  NavPlugin,
-  PaginationPlugin,
-  TablePlugin,
-  TabsPlugin,
-  VBTooltipPlugin
-} from 'bootstrap-vue';
-import 'bootstrap/dist/css/bootstrap.min.css';
-import 'bootstrap-vue/dist/bootstrap-vue.css';
-
-Vue.use(AlertPlugin);
-Vue.use(ButtonPlugin);
-Vue.use(CollapsePlugin);
-Vue.use(FormCheckboxPlugin);
-Vue.use(FormInputPlugin);
-Vue.use(FormSelectPlugin);
-Vue.use(FormTextareaPlugin);
-Vue.use(InputGroupPlugin);
-Vue.use(LayoutPlugin);
-Vue.use(ModalPlugin);
-Vue.use(NavbarPlugin);
-Vue.use(NavPlugin);
-Vue.use(PaginationPlugin);
-Vue.use(TablePlugin);
-Vue.use(TabsPlugin);
-Vue.use(VBTooltipPlugin);
-Vue.component('BIcon', BIcon);
-Vue.component('BIconBoxArrowInUpRight', BIconBoxArrowInUpRight);
-Vue.component('BIconChevronDown', BIconChevronDown);
-Vue.component('BIconChevronUp', BIconChevronUp);
-Vue.component('BIconCircle', BIconCircle);
-Vue.component('BIconCircleFill', BIconCircleFill);
-Vue.component('BIconDiamond', BIconDiamond);
-Vue.component('BIconDiamondFill', BIconDiamondFill);
-Vue.component('BIconExclamationCircle', BIconExclamationCircle);
-Vue.component('BIconSearch', BIconSearch);
-Vue.component('BIconSquare', BIconSquare);
-Vue.component('BIconSquareFill', BIconSquareFill);
-Vue.component('BIconQuestionCircle', BIconQuestionCircle);
-Vue.component('BIconQuestionDiamond', BIconQuestionDiamond);
-Vue.component('BIconQuestionSquare', BIconQuestionSquare);

package/src/router/index.ts

@@ -1,48 +0,0 @@
-import Vue from 'vue';
-import VueRouter, { RouteConfig } from 'vue-router';
-import About from '@/views/About.vue';
-import Samples from '@/views/Samples.vue';
-import VcfViewer from '@/views/VcfViewer.vue';
-import DecisionTreeViewer from '@/views/DecisionTreeViewer.vue';
-
-Vue.use(VueRouter);
-
-const routes: Array<RouteConfig> = [
-  {
-    path: '/',
-    name: 'home',
-    redirect: { name: 'samples' }
-  },
-  {
-    path: '/samples/:id?',
-    name: 'samples',
-    component: Samples
-  },
-  {
-    path: '/about',
-    name: 'about',
-    component: About
-  },
-  {
-    path: '/decision-tree',
-    name: 'decision-tree',
-    component: DecisionTreeViewer
-  },
-  {
-    path: '/data/vcf',
-    name: 'vcf',
-    component: VcfViewer
-  },
-  {
-    path: '*',
-    redirect: '/'
-  }
-];
-
-const router = new VueRouter({
-  mode: 'hash',
-  base: process.env.BASE_URL,
-  routes
-});
-
-export default router;

package/src/shims-tsx.d.ts

@@ -1,13 +0,0 @@
-import Vue, { VNode } from 'vue';
-
-declare global {
-  namespace JSX {
-    // tslint:disable no-empty-interface
-    interface Element extends VNode {}
-    // tslint:disable no-empty-interface
-    interface ElementClass extends Vue {}
-    interface IntrinsicElements {
-      [elem: string]: any;
-    }
-  }
-}

package/src/shims-vue.d.ts

@@ -1,4 +0,0 @@
-declare module '*.vue' {
-  import Vue from 'vue';
-  export default Vue;
-}

package/src/store/actions.ts

@@ -1,131 +0,0 @@
-import { Alert } from '@/types/Alert';
-import { ActionContext } from 'vuex';
-import { State } from '@/types/State';
-import { apiData } from '@/mocks/apiDataMock';
-import { Annotation, Annotations } from '@/types/Annotations';
-import { Api, ApiClient, ApiData, Vcf } from '@molgenis/vip-report-api';
-import { Buffer } from 'buffer';
-import { gunzipSync } from 'fflate';
-
-declare global {
-  interface Window {
-    api: ApiData.Container;
-  }
-}
-
-const inputData = process.env.NODE_ENV === 'development' || process.env.NODE_ENV === 'test' ? apiData : window.api;
-let api: ApiClient = new ApiClient(inputData);
-
-export type Locus = {
-  contig: string;
-  pos: number;
-};
-
-export default {
-  async loadMetadata({ commit }: ActionContext<State, State>): Promise<void> {
-    const response = await api.getMeta();
-    commit('setMetadata', response);
-  },
-  async validateSamples({ commit }: ActionContext<State, State>): Promise<void> {
-    const params: Api.Params = { size: 0 };
-    const response = await api.getSamples(params);
-    if (response.total > response.page.totalElements) {
-      commit('addAlert', {
-        type: 'warning',
-        messageId: 'sampleWarning',
-        messageArgs: [response.page.totalElements, response.total]
-      });
-    }
-  },
-  async loadSamples({ commit }: ActionContext<State, State>): Promise<void> {
-    const params: Api.Params = { size: Number.MAX_VALUE };
-    const response = await api.getSamples(params);
-    commit('setSamples', response);
-  },
-  async selectSample({ commit }: ActionContext<State, State>, sample: Api.Sample): Promise<void> {
-    const response = await api.getPhenotypes({
-      query: {
-        selector: ['subject', 'id'],
-        operator: '==',
-        args: sample.person.individualId
-      }
-    });
-
-    commit('setSelectedSample', sample);
-    commit('setSelectedSamplePhenotypes', response);
-  },
-  async validateRecords({ commit }: ActionContext<State, State>): Promise<void> {
-    const response = await api.getRecords({ size: 0 });
-    if (response.total > response.page.totalElements) {
-      commit('addAlert', {
-        type: 'warning',
-        messageId: 'recordWarning',
-        messageArgs: [response.page.totalElements, response.total]
-      });
-    }
-  },
-  async loadRecords({ commit }: ActionContext<State, State>, params?: Api.Params): Promise<void> {
-    const response = await api.getRecords(params);
-    commit('setRecords', response);
-  },
-  selectRecord({ commit }: ActionContext<State, State>, record: Vcf.Record): void {
-    commit('setSelectedRecord', record);
-  },
-  removeAlert({ commit }: ActionContext<State, State>, alert: Alert): void {
-    commit('removeAlert', alert);
-  },
-  enableAnnotations({ commit }: ActionContext<State, State>): void {
-    commit('setAnnotations', {});
-  },
-  disableAnnotations({ commit }: ActionContext<State, State>): void {
-    commit('setAnnotations', null);
-  },
-  importAnnotations({ commit }: ActionContext<State, State>, annotations: Annotations): void {
-    commit('setAnnotations', annotations);
-  },
-  upsertAnnotation({ commit, state }: ActionContext<State, State>, annotation: Annotation): void {
-    const annotations = Object.assign({}, state.annotations);
-    const key = `${annotation.sampleId}_${annotation.chr}_${annotation.pos}_${annotation.ref}_${annotation.alt.join(
-      ','
-    )}`;
-    annotations[key] = annotation;
-    commit('setAnnotations', annotations);
-  },
-  setFilterRecordsByPhenotype({ commit }: ActionContext<State, State>, value: boolean): void {
-    commit('setFilterRecordsByPhenotype', value);
-  },
-  setFilterRecordsByInheritance({ commit }: ActionContext<State, State>, value: boolean): void {
-    commit('setFilterRecordsByInheritance', value);
-  },
-  setFilterRecordsByDenovo({ commit }: ActionContext<State, State>, value: boolean): void {
-    commit('setFilterRecordsByDenovo', value);
-  },
-  setFilterRecordsByDepth({ commit }: ActionContext<State, State>, value: boolean): void {
-    commit('setFilterRecordsByDepth', value);
-  },
-  getVcfGz(): Promise<Buffer> {
-    return api.getVcfGz();
-  },
-  // eslint-disable-next-line @typescript-eslint/no-unused-vars
-  getFastaGz({ commit }: ActionContext<State, State>, locus: Locus): Promise<Buffer | null> {
-    return api.getFastaGz(locus.contig, locus.pos);
-  },
-  getGenesGz(): Promise<Buffer | null> {
-    return api.getGenesGz();
-  },
-  // eslint-disable-next-line @typescript-eslint/no-unused-vars
-  getBam({ commit }: ActionContext<State, State>, sampleId: string): Promise<Buffer | null> {
-    return api.getBam(sampleId);
-  },
-  async getDecisionTree(): Promise<string | undefined> {
-    const zippedDecisionTree = await api.getDecisionTreeGz();
-    if (zippedDecisionTree) {
-      return Buffer.from(gunzipSync(zippedDecisionTree).buffer).toString();
-    }
-  }
-};
-
-// testability
-export function setTestApi(testApi: ApiClient): void {
-  api = testApi;
-}

package/src/store/getters.ts

@@ -1,207 +0,0 @@
-import { State } from '@/types/State';
-import { GenomeBrowserDb } from '@/types/GenomeBrowserDb';
-import { Annotation } from '@/types/Annotations';
-import { Api, Vcf } from '@molgenis/vip-report-api';
-
-export default {
-  samples: (state: State): Array<Api.Sample> => {
-    if (state.samples === null) {
-      return [];
-    }
-
-    const items = state.samples.items.slice();
-    return items.sort(function (thisSample, thatSample) {
-      if (thisSample.person.individualId < thatSample.person.individualId) {
-        return -1;
-      }
-      if (thisSample.person.individualId > thatSample.person.individualId) {
-        return 1;
-      }
-      return 0;
-    });
-  },
-  getSampleById:
-    (state: State) =>
-    (id: string): Api.Sample | null => {
-      if (state.samples === null) {
-        return null;
-      }
-      return state.samples.items.find((sample) => sample.person.individualId === id) || null;
-    },
-  sampleMaternal: (state: State): Api.Sample | null => {
-    if (state.selectedSample === null) {
-      return null;
-    }
-    const maternalId = state.selectedSample.person.maternalId;
-    if (maternalId === '0') {
-      return null;
-    }
-    if (state.samples === null) {
-      return null;
-    }
-    return state.samples.items.find((sample) => sample.person.individualId === maternalId) || null;
-  },
-  samplePaternal: (state: State): Api.Sample | null => {
-    if (state.selectedSample === null) {
-      return null;
-    }
-    const paternalId = state.selectedSample.person.paternalId;
-    if (paternalId === '0') {
-      return null;
-    }
-    if (state.samples === null) {
-      return null;
-    }
-    return state.samples.items.find((sample) => sample.person.individualId === paternalId) || null;
-  },
-  genomeBrowserDb: (state: State): GenomeBrowserDb | null => {
-    if (state.metadata === null) {
-      return null;
-    }
-
-    let genomeBrowserDb: GenomeBrowserDb | null;
-    switch (state.metadata.htsFile.genomeAssembly) {
-      case 'NCBI34':
-        genomeBrowserDb = GenomeBrowserDb.hg16;
-        break;
-      case 'NCBI35':
-        genomeBrowserDb = GenomeBrowserDb.hg17;
-        break;
-      case 'NCBI36':
-        genomeBrowserDb = GenomeBrowserDb.hg18;
-        break;
-      case 'GRCh37':
-        genomeBrowserDb = GenomeBrowserDb.hg19;
-        break;
-      case 'GRCh38':
-        genomeBrowserDb = GenomeBrowserDb.hg38;
-        break;
-      case 'UNKNOWN':
-      default:
-        genomeBrowserDb = null;
-        break;
-    }
-
-    return genomeBrowserDb;
-  },
-  hasCapice: (state: State): boolean => {
-    return state.metadata !== null && state.metadata.records.info['CAP'] !== undefined;
-  },
-  hasConsequences: (state: State): boolean => {
-    return (
-      state.metadata !== null &&
-      (state.metadata.records.info['CSQ'] !== undefined || state.metadata.records.info['ANN']) !== undefined
-    );
-  },
-  isAnnotationEnabled: (state: State): boolean => {
-    return state.annotations !== null;
-  },
-  getAnnotation:
-    (state: State) =>
-    (record: Vcf.Record): Annotation => {
-      if (state.annotations === null) {
-        throw 'Annotations disabled';
-      }
-      if (state.selectedSample == null) {
-        throw 'No sample selected';
-      }
-
-      const sampleId = state.selectedSample.person.individualId;
-      const key = `${sampleId}_${record.c}_${record.p}_${record.r}_${record.a.join(',')}`;
-      let annotation = state.annotations[key];
-      if (annotation === undefined) {
-        annotation = {
-          sampleId: sampleId,
-          chr: record.c,
-          pos: record.p,
-          ref: record.r,
-          alt: record.a,
-          geneMatch: null,
-          class: null,
-          txt: null
-        };
-      }
-      return annotation;
-    },
-  /**
-   * Returns whether records contain mvl annotations.
-   */
-  isRecordsContainMvl: (state: State): boolean => {
-    let hasMvl;
-    if (state.metadata === null) {
-      hasMvl = false;
-    } else {
-      const csqInfo = state.metadata.records.info['CSQ'];
-      if (csqInfo === undefined) {
-        hasMvl = false;
-      } else {
-        if (csqInfo.nested === undefined) {
-          hasMvl = false;
-        } else {
-          hasMvl = csqInfo.nested.items.some((item) => item.id === 'VKGL_UMCG');
-        }
-      }
-    }
-    return hasMvl;
-  },
-  /**
-   * Returns whether records contain phenotype associations.
-   */
-  isRecordsContainPhenotypes: (state: State): boolean => {
-    let hasPhenotypeAssociations;
-    if (state.metadata === null) {
-      hasPhenotypeAssociations = false;
-    } else {
-      const csqInfo = state.metadata.records.info['CSQ'];
-      if (csqInfo === undefined) {
-        hasPhenotypeAssociations = false;
-      } else {
-        if (csqInfo.nested === undefined) {
-          hasPhenotypeAssociations = false;
-        } else {
-          hasPhenotypeAssociations = csqInfo.nested.items.some((item) => item.id === 'HPO');
-        }
-      }
-    }
-    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['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['VID'];
-      hasSampleInheritance = vimFormat !== undefined;
-    }
-    return hasSampleInheritance;
-  },
-  /**
-   * Returns whether records contain read depth information.
-   */
-  isSamplesContainDepth: (state: State): boolean => {
-    let hasReadDepth;
-    if (state.metadata === null) {
-      hasReadDepth = false;
-    } else {
-      const dpFormat = state.metadata.records.format['DP'];
-      hasReadDepth = dpFormat !== undefined;
-    }
-    return hasReadDepth;
-  }
-};

package/src/store/mutations.ts

@@ -1,50 +0,0 @@
-import { State } from '@/types/State';
-import { Api, Vcf } from '@molgenis/vip-report-api';
-import { Alert } from '@/types/Alert';
-import { Annotations } from '@/types/Annotations';
-
-export default {
-  setMetadata(state: State, metadata: Api.Metadata): void {
-    state.metadata = metadata;
-  },
-  setSamples(state: State, samples: Api.PagedItems<Api.Sample>): void {
-    state.samples = samples;
-  },
-  setSelectedSample(state: State, sample: Api.Sample): void {
-    state.selectedSample = sample;
-    state.selectedRecord = null;
-  },
-  setSelectedSamplePhenotypes(state: State, phenotypes: Api.PagedItems<Api.Phenotype>): void {
-    state.selectedSamplePhenotypes = phenotypes;
-  },
-  setRecords(state: State, records: Api.PagedItems<Vcf.Record>): void {
-    state.records = records;
-    state.selectedRecord = null;
-  },
-  setSelectedRecord(state: State, record: Vcf.Record): void {
-    state.selectedRecord = record;
-  },
-  addAlert(state: State, alert: Alert): void {
-    const alerts = state.alerts.slice();
-    alerts.push(alert);
-    state.alerts = alerts;
-  },
-  removeAlert(state: State, alert: Alert): void {
-    state.alerts = state.alerts.filter((anAlert) => anAlert !== alert);
-  },
-  setAnnotations(state: State, annotations: Annotations): void {
-    state.annotations = annotations;
-  },
-  setFilterRecordsByPhenotype(state: State, value: boolean): void {
-    state.filterRecordsByPhenotype = value;
-  },
-  setFilterRecordsByInheritance(state: State, value: boolean): void {
-    state.filterRecordsByInheritance = value;
-  },
-  setFilterRecordsByDenovo(state: State, value: boolean): void {
-    state.filterRecordsByDenovo = value;
-  },
-  setFilterRecordsByDepth(state: State, value: boolean): void {
-    state.filterRecordsByDepth = value;
-  }
-};

package/src/store/state.ts

@@ -1,18 +0,0 @@
-import { State } from '@/types/State';
-
-const state: State = {
-  alerts: [],
-  metadata: null,
-  samples: null,
-  selectedSample: null,
-  selectedSamplePhenotypes: null,
-  records: null,
-  selectedRecord: null,
-  filterRecordsByPhenotype: true,
-  filterRecordsByInheritance: true,
-  filterRecordsByDenovo: false,
-  filterRecordsByDepth: false,
-  annotations: null
-};
-
-export default state;

package/src/store/store.ts

@@ -1,16 +0,0 @@
-import Vue from 'vue';
-import Vuex from 'vuex';
-import state from '@/store/state';
-import actions from '@/store/actions';
-import getters from '@/store/getters';
-import mutations from '@/store/mutations';
-
-Vue.use(Vuex);
-
-export default new Vuex.Store({
-  strict: process.env.NODE_ENV !== 'production',
-  state,
-  getters,
-  mutations,
-  actions
-});

package/src/types/Alert.ts

@@ -1,5 +0,0 @@
-export interface Alert {
-  type: 'success' | 'info' | 'warning' | 'error';
-  messageId: string;
-  messageArgs: Array<string>;
-}

package/src/types/Annotations.ts

@@ -1,14 +0,0 @@
-export interface Annotations {
-  [key: string]: Annotation;
-}
-
-export interface Annotation {
-  sampleId: string;
-  chr: string;
-  pos: number;
-  ref: string;
-  alt: (string | null)[];
-  geneMatch: string | null;
-  class: string | null;
-  txt: string | null;
-}

package/src/types/Consequence.ts

@@ -1,36 +0,0 @@
-import { Vcf } from '@molgenis/vip-report-api';
-
-export interface ConsequenceMetadata {
-  effect: Vcf.InfoMetadata;
-  symbol: Vcf.InfoMetadata;
-  incompletePenetrance: Vcf.InfoMetadata;
-  inheritance: Vcf.InfoMetadata;
-  hgvsC: Vcf.InfoMetadata;
-  hgvsP: Vcf.InfoMetadata;
-  pubMed: Vcf.InfoMetadata;
-  clinVar: Vcf.InfoMetadata;
-  gnomAD: Vcf.InfoMetadata;
-  mvl: Vcf.InfoMetadata;
-  vkgl: Vcf.InfoMetadata;
-}
-
-export interface Consequence {
-  alleleIndex: number | null;
-  effect: string[];
-  symbol: string | null;
-  incompletePenetrance: boolean | false;
-  inheritance: string[];
-  hgvsC: string | null;
-  hgvsP: string | null;
-  pubMed: number[];
-  clinVar: string[];
-  gnomAD: number | null;
-  mvl: string | null;
-  vkgl: string | null;
-  primary: string | null;
-}
-
-export interface Consequences {
-  metadata: ConsequenceMetadata;
-  items: Consequence[];
-}