@molgenis/vip-report-template 3.1.2 → 3.1.4

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Files changed (15) hide show
  1. package/package.json +21 -21
  2. package/src/components/SampleTable.tsx +1 -1
  3. package/src/components/Sort.tsx +1 -1
  4. package/src/components/VariantsTable.tsx +6 -3
  5. package/src/components/record/RecordDownload.tsx +14 -3
  6. package/src/components/record/info/Gene.tsx +2 -2
  7. package/src/mocks/GRCh37/vcf/family.vcf.blob +8 -2
  8. package/src/mocks/GRCh37/vcf/samples_1.vcf.blob +1 -1
  9. package/src/mocks/MockApiClient.ts +1 -1
  10. package/src/store/index.tsx +41 -27
  11. package/src/utils/query.ts +0 -1
  12. package/src/views/SampleVariantConsequence.tsx +4 -1
  13. package/src/views/SampleVariants.tsx +1 -1
  14. package/src/views/Samples.tsx +97 -38
  15. package/src/views/VariantConsequence.tsx +15 -11
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@molgenis/vip-report-template",
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- "version": "3.1.2",
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+ "version": "3.1.4",
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  "description": "Report Template for Variant Call Format (VCF) Report Generator",
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  "scripts": {
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  "build": "vite build",
@@ -15,32 +15,32 @@
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  },
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  "license": "LGPL-3.0",
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  "devDependencies": {
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- "@molgenis/vite-plugin-inline": "^1.0.7",
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- "@typescript-eslint/eslint-plugin": "^5.28.0",
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- "@typescript-eslint/parser": "^5.28.0",
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+ "@molgenis/vite-plugin-inline": "^1.0.8",
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+ "@typescript-eslint/eslint-plugin": "^5.35.1",
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+ "@typescript-eslint/parser": "^5.35.1",
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+ "@vitest/coverage-c8": "^0.22.1",
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  "bulma": "^0.9.4",
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- "c8": "^7.11.3",
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- "eslint": "^8.17.0",
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+ "eslint": "^8.22.0",
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  "eslint-config-prettier": "^8.5.0",
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- "eslint-plugin-prettier": "^4.0.0",
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- "eslint-plugin-solid": "^0.7.0",
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+ "eslint-plugin-prettier": "^4.2.1",
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+ "eslint-plugin-solid": "^0.7.1",
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  "husky": "^8.0.1",
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- "prettier": "^2.7.0",
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- "sass": "^1.52.3",
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- "typescript": "^4.7.3",
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- "vite": "^2.9.12",
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- "vite-plugin-solid": "^2.2.6",
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- "vitest": "^0.14.2"
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+ "prettier": "^2.7.1",
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+ "sass": "^1.54.5",
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+ "typescript": "^4.7.4",
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+ "vite": "^3.0.9",
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+ "vite-plugin-solid": "^2.3.0",
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+ "vitest": "^0.22.1"
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  },
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  "dependencies": {
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- "@fortawesome/fontawesome-svg-core": "^6.1.1",
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- "@fortawesome/free-solid-svg-icons": "^6.1.1",
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- "@molgenis/vip-report-api": "^3.5.2",
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- "@molgenis/vip-report-vcf": "^1.2.2",
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+ "@fortawesome/fontawesome-svg-core": "^6.1.2",
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+ "@fortawesome/free-solid-svg-icons": "^6.1.2",
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+ "@molgenis/vip-report-api": "^3.5.4",
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+ "@molgenis/vip-report-vcf": "^1.2.3",
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  "base64-js": "^1.5.1",
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- "igv": "^2.12.6",
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- "solid-app-router": "^0.3.3",
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- "solid-js": "^1.4.4"
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+ "igv": "^2.13.1",
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+ "solid-app-router": "^0.4.2",
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+ "solid-js": "^1.4.8"
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  },
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  "lint-staged": {
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  "src/**/*.{tsx,ts}": [
package/src/components/SampleTable.tsx CHANGED
@@ -76,7 +76,7 @@ export const SampleTable: Component<{
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  <For each={props.samples}>
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  {(sample) => (
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  <tr>
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- <td>{sample.id}</td>
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+ <td>{sample.data.person.familyId}</td>
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  <td>
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  <Link href={`/samples/${sample.id}`}>{sample.data.person.individualId}</Link>
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  </td>
package/src/components/Sort.tsx CHANGED
@@ -40,7 +40,7 @@ export const Sort: Component<{
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  <div class="field">
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  <div class="select">
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  <select onChange={onSortChange}>
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- <option value="-1" />
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+ <option value="-1">Position</option>
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  <For each={sortableOptions()}>
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  {(option, i) => (
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  <option value={i()} selected={option.selected === true}>
package/src/components/VariantsTable.tsx CHANGED
@@ -56,9 +56,12 @@ export const VariantsTable: Component<{
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  <tr>
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  <For each={infoFieldsNested()}>
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  {(infoField) => (
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- <For each={infoField.nested?.items}>
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- {(nestedInfoField) => <FieldHeader field={nestedInfoField} />}
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- </For>
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+ <>
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+ {infoField.number.count !== 1 && <th />}
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+ <For each={infoField.nested?.items}>
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+ {(nestedInfoField) => <FieldHeader field={nestedInfoField} />}
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+ </For>
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+ </>
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  )}
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  </For>
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  </tr>
package/src/components/record/RecordDownload.tsx CHANGED
@@ -1,13 +1,18 @@
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  import { Component } from "solid-js";
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- import { Query, Sample } from "@molgenis/vip-report-api/src/Api";
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+ import { HtsFileMetadata, Query, Sample } from "@molgenis/vip-report-api/src/Api";
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  import { Metadata } from "@molgenis/vip-report-vcf/src/Vcf";
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  import api from "../../Api";
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  import { Filter, writeVcf } from "@molgenis/vip-report-vcf/src/VcfWriter";
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+ const DOWNLOAD_POSTFIX = "_report.vcf";
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  export const RecordDownload: Component<{ recordsMetadata: Metadata; query?: Query; samples?: Sample[] }> = (props) => {
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  const filter = (): Filter | undefined =>
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  props.samples ? { samples: props.samples.map((sample) => sample.person.individualId) } : undefined;
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+ function parseFilename(htsFile: HtsFileMetadata) {
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+ return htsFile.uri.split("\\").pop()?.split("/").pop()?.split(".").shift();
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+ }
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+
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  function onClick() {
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  const handler = async () => {
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  const records = await api.getRecords({ query: props.query, size: Number.MAX_SAFE_INTEGER });
@@ -16,7 +21,9 @@ export const RecordDownload: Component<{ recordsMetadata: Metadata; query?: Quer
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  const url = window.URL.createObjectURL(new Blob([vcf]));
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  const link = document.createElement("a");
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  link.href = url;
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- link.setAttribute("download", "data.vcf");
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+ const htsFile = await api.getHtsFileMetadata();
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+ const filename = parseFilename(htsFile) as string;
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+ link.setAttribute("download", filename + DOWNLOAD_POSTFIX);
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  document.body.appendChild(link);
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  link.click();
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  document.body.removeChild(link);
@@ -26,7 +33,11 @@ export const RecordDownload: Component<{ recordsMetadata: Metadata; query?: Quer
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  return (
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  <div class="control">
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- <button class="button is-info" onClick={onClick}>
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+ <button
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+ class="button is-info"
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+ onClick={onClick}
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+ title="Download vcf file with records matching filters and search queries"
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+ >
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  <span class="icon is-small">
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  <i class="fas fa-download" />
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  </span>
package/src/components/record/info/Gene.tsx CHANGED
@@ -45,9 +45,9 @@ export const Gene: Component<FieldProps> = (props) => {
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  <span>{symbol}</span>
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  </Anchor>
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  {incompletePenetrance() && (
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- <sup class="ml-1">
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+ <span class="ml-1">
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  <Abbr title="gene is known for incomplete penetrance" value="IP" />
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- </sup>
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+ </span>
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  )}
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  </>
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  )}
package/src/mocks/GRCh37/vcf/family.vcf.blob CHANGED
@@ -29,6 +29,9 @@
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  ##INFO=<ID=gnomAD,Number=.,Type=String,Description="/groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz (exact)">
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  ##INFO=<ID=gnomAD_AF,Number=.,Type=String,Description="AF field from /groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz">
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  ##INFO=<ID=gnomAD_HN,Number=.,Type=String,Description="HN field from /groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz">
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+ ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
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+ ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
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+ ##INFO=<ID=VIPC_S,Number=.,Type=String,Description="VIP decision tree classification (samples).">
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  ##IncompletePenetrance=Boolean indicating if the gene is known for incomplete penetrance.
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  ##InheritanceModesGene=List of inheritance modes for the gene
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  ##SpliceAI_pred_DP_AG=SpliceAI predicted effect on splicing. Delta position for acceptor gain
@@ -76,13 +79,16 @@
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  ##contig=<ID=MT,length=16569,assembly=b37>
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  ##fileDate=20200320
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  #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Patient Father Mother Sister Nephew Unrelated
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+ 1 1701 . T C . PASS CSQ=C|intergenic_variant|MODIFIER||||||||||||||||1||||1||||||||||||||||||||||||||||||||||||||||||||P|exip_p;DP=131 GT:AD:DP:VI:VIC:VID:VIG:VIM 1|1:0,50:50:AR:.:1:64802:1 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.
79
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  1 10042538 . C T . PASS CSQ=T|missense_variant|MODERATE|NMNAT1|64802|Transcript|NM_001297778.1|protein_coding|5/5||NM_001297778.1:c.619C>Tblablablablablabla|NP_001284707.1:p.Arg207Trp|778/3796|619/840|207/279|R/W|Cgg/Tgg|rs142968179&CM127756|1||1||1|EntrezGene|||||0.04|0.08||pathogenic||1&1|26103963&22842229&22842230|||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.16572298|||AR|LP||||1:10042538-10042538|3.88948e-05|0|37133|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,T|downstream_gene_variant|MODIFIER|NMNAT1|64802|Transcript|NM_001297779.2|protein_coding||||||||||rs142968179&CM127756|1|714|1|||EntrezGene||||||||pathogenic||1&1|26103963&22842229&22842230|||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.033541594|||AR|LP||||1:10042538-10042538|3.88948e-05|0|37133|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,T|missense_variant|MODERATE|NMNAT1|64802|Transcript|NM_022787.4|protein_coding|5/5||NM_022787.4:c.619C>T|NP_073624.2:p.Arg207Trp|716/3734|619/840|207/279|R/W|Cgg/Tgg|rs142968179&CM127756|1||1|||EntrezGene|||||0.04|0.08||pathogenic||1&1|26103963&22842229&22842230|||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.14321531|||AR|LP||||1:10042538-10042538|3.88948e-05|0|37133|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM 1|1:0,50:50:AR:.:1:64802:1 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.
80
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  1 16375583 . GA G . PASS CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|CLCNKB|1188|Transcript|NM_001165945.2|protein_coding|1/13||NM_001165945.2:c.118del|NP_001159417.2:p.Arg40GlyfsTer4|328/2174|118/1554|40/517|R/X|Agg/gg|rs751608665|1||1|||EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.9770811|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:VIS 1|0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:AR_C 1|0:25,25:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:.
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  1 16376412 n_alt G N . PASS CSQ=N|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||10/19||||||||CS1211892&CS971662|1||1||1|EntrezGene||||||||||1&1|||||||||||||||||VUS|0.373989|HP:0000951||AR||||||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_lp|,N|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_001165945.2|protein_coding||3/12||||||||CS1211892&CS971662|1||1|||EntrezGene||||||||||1&1|||||||||||||||||VUS|0.373989|HP:0000951||AR||||||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:VIS 1|0:5,45:50:AR,AD:1_16376412_G_A,1_16375583_GA_G:1:1188:1:AR_C 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:.
82
86
  1 16376412 . G A . PASS CSQ=A|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||10/19|NM_000085.5:c.968+1G>A|||||||rs201204502&CS1211892&CS971662|1||1||1|EntrezGene||||||||||0&1&1||||||||17|-36|-28|-1|0.00|0.00|0.03|0.97|CLCNKB|VUS|0.9855972|HP:0000951||AR|LP||||1:16376412-16376412|6.38086e-05|0|1285112|Pathogenic/Likely_pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp|,A|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_001165945.2|protein_coding||3/12|NM_001165945.2:c.461+1G>A|||||||rs201204502&CS1211892&CS971662|1||1|||EntrezGene||||||||||0&1&1||||||||17|-36|-28|-1|0.00|0.00|0.03|0.97|CLCNKB|VUS|0.9855972|HP:0000951||AR|LP||||1:16376412-16376412|6.38086e-05|0|1285112|Pathogenic/Likely_pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:VIS 0|1:50:50:AR:1_16375583_GA_G,1_16376412_G_N:0:1188:1:AR_C 0|0:50,0:50:.:.:.:.:.:. 1|0:25,25:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:.
83
- 1 17349219 g_ref G A . PASS CSQ=A|missense_variant|MODERATE|SDHB|6390|Transcript|NM_003000.3|protein_coding|7/8||NM_003000.3:c.649C>T|NP_002991.2:p.Arg217Cys|662/1015|649/843|217/280|R/C|Cgc/Tgc|rs200245469&CM094752&CM1210440&COSV64965760|1||-1||1|EntrezGene|||||0|1||likely_pathogenic|0&0&0&1|1&1&1&1||||||||28|6|6|5|0.00|0.00|0.00|0.00|SDHB|VUS|0.89070946|HP:0000951||AD&AR|LP|||||||183735|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM 1|1:0,50:50:AR:.:1:6390:1 1|0:45,5:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 1|0:25,25:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.
84
- 1 17355094 . C T . PASS CSQ=T|splice_donor_variant|HIGH|SDHB|6390|Transcript|NM_003000.3|protein_coding||4/7|NM_003000.3:c.423+1G>A|||||||rs398122805&CS056774&CS062098&COSV64965540|1||-1||1|EntrezGene||||||||pathogenic|0&0&0&1|1&1&1&1|21348866&17667967&17804857&16405730&21565294&15383933|||||||-49|12|26|1|0.00|0.00|0.14|0.97|SDHB|VUS|0.9641474|HP:0000951||AD&AR|LP||||1:17355094-17355094|1.19344e-05|0|29896|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM 1|0:5,45:50:AD:.:1:6390:1 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.
87
+ 1 17349219 g_ref G A . PASS CSQ=A|missense_variant|MODERATE|SDHB|6390|Transcript|NM_003000.3|protein_coding|7/8||NM_003000.3:c.649C>T|NP_002991.2:p.Arg217Cys|662/1015|649/843|217/280|R/C|Cgc/Tgc|rs200245469&CM094752&CM1210440&COSV64965760|1||-1||1|EntrezGene|||||0|1||likely_pathogenic|0&0&0&1|1&1&1&1||||||||28|6|6|5|0.00|0.00|0.00|0.00|SDHB|VUS|0.89070946|HP:0000951&HP:0003124||AD&AR|LP|||||||183735|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM 1|1:0,50:50:AR:.:1:6390:1 1|0:45,5:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 1|0:25,25:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.
88
+ 1 17355094 . C T . PASS CSQ=T|splice_donor_variant|HIGH|SDHB|6390|Transcript|NM_003000.3|protein_coding||4/7|NM_003000.3:c.423+1G>A|||||||rs398122805&CS056774&CS062098&COSV64965540|1||-1||1|EntrezGene||||||||pathogenic|0&0&0&1|1&1&1&1|21348866&17667967&17804857&16405730&21565294&15383933|||||||-49|12|26|1|0.00|0.00|0.14|0.97|SDHB|VUS|0.9641474|HP:0003124||AD&AR|LP||||1:17355094-17355094|1.19344e-05|0|29896|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM 1|0:5,45:50:AD:.:1:6390:1 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.
85
89
  1 152520788 symbolic1 A <DEL> . PASS CSQ=deletion|transcript_ablation|HIGH|LCE3D|84648|Transcript|NM_032563.2|protein_coding|||||||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_lp|,deletion|transcript_ablation|HIGH|LCE3E|353145|Transcript|NM_178435.4|protein_coding|||||||||||1||-1|||EntrezGene|||||||||||||||||||||||||||||||||||||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_lp|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00701519957||||||||||||1||||||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_vus|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00905971885||||||||||||1||||||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_vus|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00522719201||||||||||||1||||||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_vus|;SVLEN=-49314;SVTYPE=DEL GT:AD:DP:VI:VIC:VID:VIM 1|1:0,50:50:AR:.:1:0 0|0:50,0:50:.:.:.:. 0|0:50,0:50:.:.:.:. 0|0:50,0:50:.:.:.:. 0|0:50,0:50:.:.:.:. 1|0:25,25:50:.:.:.:.
90
+ 2 321682 . T <DEL> . PASS CSQ=deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|LINC01865|105373350|Transcript|NR_146953.1|lncRNA|4/3|3/3|||685-?/2100||||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||3|1A_(+0.00)%3B3A_(1_gene%2C_+0.00)%3B5F_(+0.00)|0||||||||P|exip_p;END=321887;SVLEN=-205;SVTYPE=DEL GT:AD:DP:VI:VIC:VID:VIG:VIM 1|1:0,50:50:AR:.:1:64802:1 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.
91
+ 2 6693415 . T <DEL> . PASS CSQ=deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001914803||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524064657||||||||||||1||||1||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524052275||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524121752||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524688093||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00525576244||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524108762||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524259723||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524175972||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524198224||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524134566||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00769910345||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524344258||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524278495||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524312437||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524083163||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524770333||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00829572188||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524396085||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00909212078||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524214908||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524150456||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524239498||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524095954||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00530094654||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|intergenic_variant|MODIFIER||||||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p|;END=6707844;SVLEN=-14429;SVTYPE=DEL GT:AD:DP:VI:VIC:VID:VIG:VIM 1|1:0,50:50:AR:.:1:64802:1 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.
86
92
  4 106320294 . G A . PASS CSQ=A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_006903.4|protein_coding|7/11||NM_006903.4:c.596C>T|NP_008834.3:p.Pro199Leu|616/1586|596/918|199/305|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1|||EntrezGene|||||0|0.985||pathogenic|0&0&1|1&1&1|27523597|||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.8097311|||AR|LP||||4:106320294-106320294|0.000211803|0|372226|Likely_pathogenic||criteria_provided&_single_submitter|LP|filter&vkgl&exit_lp|,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176866.2|protein_coding|4/8||NM_176866.2:c.377C>T|NP_789842.2:p.Pro126Leu|397/1367|377/699|126/232|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1|||EntrezGene|||||0|0.992||pathogenic|0&0&1|1&1&1|27523597|||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.7550335|||AR|LP||||4:106320294-106320294|0.000211803|0|372226|Likely_pathogenic||criteria_provided&_single_submitter|LP|filter&vkgl&exit_lp|,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176867.3|protein_coding|2/6||NM_176867.3:c.185C>T|NP_789843.2:p.Pro62Leu|205/1175|185/507|62/168|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1|||EntrezGene|||||0|0.995||pathogenic|0&0&1|1&1&1|27523597|||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.8145551|||AR|LP||||4:106320294-106320294|0.000211803|0|372226|Likely_pathogenic||criteria_provided&_single_submitter|LP|filter&vkgl&exit_lp|,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176869.3|protein_coding|8/12||NM_176869.3:c.683C>T|NP_789845.1:p.Pro228Leu|695/1665|683/1005|228/334|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1||1|EntrezGene|||||0|0.993||pathogenic|0&0&1|1&1&1|27523597|||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.76490384|||AR|LP||||4:106320294-106320294|0.000211803|0|372226|Likely_pathogenic||criteria_provided&_single_submitter|LP|filter&vkgl&exit_lp|,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001994744|promoter_flanking_region||||||||||rs138215926&CM1610192&COSV58994362|1|||||||||||||pathogenic|0&0&1|1&1&1|27523597|||||||||||||||||||||||||4:106320294-106320294|0.000211803|0|372226|Likely_pathogenic||criteria_provided&_single_submitter|LP|filter&vkgl&clinVar&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM 1|1:0,50:50:AR:.:1:27068:1 1|0:25,25:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 1|1:0,50:50:.:.:.:.:.
87
93
  9 107546633 . AAAGAT A . PASS CSQ=-|frameshift_variant|HIGH|ABCA1|19|Transcript|NM_005502.4|protein_coding|50/50||NM_005502.4:c.6744_6748del|NP_005493.2:p.Phe2250ThrfsTer3|7057-7061/10408|6744-6748/6786|2248-2250/2261|TSF/TX|acATCTTtt/actt||1||-1||1|EntrezGene|||||||||||||||||||||||||||VUS|0.9823047|HP:0000951||AD&AR||||||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM 1|1:0,10:10:AR:.:0:19:1 0|1:1,49:50:.:.:.:.:. 1|0:0,50:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.
88
94
  9 107584864 . AC A . PASS CSQ=-|frameshift_variant|HIGH|ABCA1|19|Transcript|NM_005502.4|protein_coding|19/50||NM_005502.4:c.2740del|NP_005493.2:p.Val914TrpfsTer8|3053/10408|2740/6786|914/2261|V/X|Gtg/tg||1||-1||1|EntrezGene||||||||||||||||||33|-42|28|1|0.00|0.00|0.10|0.00|ABCA1|VUS|0.98804027|HP:0000951||AD&AR|LP|||||||||||LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM 1|0:25,25:50:AD:.:1:19:1 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.
package/src/mocks/GRCh37/vcf/samples_1.vcf.blob CHANGED
@@ -9,7 +9,7 @@
9
9
  ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
10
10
  ##HPO=List of HPO terms for the gene
11
11
  ##INFO=<ID=BND_DEPTH,Number=1,Type=Integer,Description="Read depth at local translocation breakend">
12
- ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|SYMBOL_SOURCE|HGNC_ID|REFSEQ_MATCH|REFSEQ_OFFSET|SOURCE|SIFT|PolyPhen|HGVS_OFFSET|CLIN_SIG|SOMATIC|PHENO|PUBMED|CHECK_REF|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|SpliceAI_pred_DP_AG|SpliceAI_pred_DP_AL|SpliceAI_pred_DP_DG|SpliceAI_pred_DP_DL|SpliceAI_pred_DS_AG|SpliceAI_pred_DS_AL|SpliceAI_pred_DS_DG|SpliceAI_pred_DS_DL|SpliceAI_pred_SYMBOL|CAPICE_CL|CAPICE_SC|HPO|IncompletePenetrance|InheritanceModesGene|VKGL_CL|ASV_ACMG_class|ASV_AnnotSV_ranking_criteria|ASV_AnnotSV_ranking_score|gnomAD|gnomAD_AF|gnomAD_HN|VIPC|VIPP|VIPL">
12
+ ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|SYMBOL_SOURCE|HGNC_ID|REFSEQ_MATCH|REFSEQ_OFFSET|SOURCE|SIFT|PolyPhen|HGVS_OFFSET|CLIN_SIG|SOMATIC|PHENO|PUBMED|CHECK_REF|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|SpliceAI_pred_DP_AG|SpliceAI_pred_DP_AL|SpliceAI_pred_DP_DG|SpliceAI_pred_DP_DL|SpliceAI_pred_DS_AG|SpliceAI_pred_DS_AL|SpliceAI_pred_DS_DG|SpliceAI_pred_DS_DL|SpliceAI_pred_SYMBOL|CAPICE_CL|CAPICE_SC|HPO|IncompletePenetrance|InheritanceModesGene|VKGL_CL|ASV_ACMG_class|ASV_AnnotSV_ranking_criteria|ASV_AnnotSV_ranking_score|gnomAD|gnomAD_AF|gnomAD_HN|VIPC|VIPP_renamed|VIPL_renamed">
13
13
  ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakend">
14
14
  ##INFO=<ID=MATE_BND_DEPTH,Number=1,Type=Integer,Description="Read depth at remote translocation mate breakend">
15
15
  ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
package/src/mocks/MockApiClient.ts CHANGED
@@ -120,7 +120,7 @@ export class MockApiClient implements Api {
120
120
  args: "-i testdata_b37_vip.vcf -t /Users/user/vip-report-template/dist/vip-report-template.html -f",
121
121
  },
122
122
  htsFile: {
123
- uri: "testdata_b37_vip.vcf",
123
+ uri: "/path/to/testdata_b37_vip.vcf",
124
124
  htsFormat: "VCF",
125
125
  genomeAssembly: "GRCh37",
126
126
  },
package/src/store/index.tsx CHANGED
@@ -14,11 +14,18 @@ type AppStateVariants = {
14
14
  sort?: SortOrder | null; // null: do not sort. undefined: sort undefined
15
15
  };
16
16
 
17
+ type AppStateSamples = {
18
+ page?: number;
19
+ searchQuery?: string;
20
+ probandFilterValue?: boolean;
21
+ };
22
+
17
23
  export type AppState = {
18
24
  variants?: AppStateVariants;
19
- samples?: {
25
+ sampleVariants?: {
20
26
  [key: number]: { variants: AppStateVariants };
21
27
  };
28
+ samples?: AppStateSamples;
22
29
  };
23
30
 
24
31
  export type AppActions = {
@@ -26,22 +33,23 @@ export type AppActions = {
26
33
  setVariantsPage(page: number): void;
27
34
  setVariantsPageSize(pageSize: number): void;
28
35
  setVariantsSearchQuery(searchQuery: string): void;
29
- clearVariantsSearchQuery(): void;
30
36
  setVariantsFilterQuery(query: QueryClause): void;
31
37
  clearVariantsFilterQuery(selector: Selector): void;
32
38
  setVariantsSort(sort: SortOrder | null): void;
33
39
  setSampleVariantsPage(sample: Item<Sample>, page: number): void;
34
40
  setSampleVariantsPageSize(sample: Item<Sample>, pageSize: number): void;
35
41
  setSampleVariantsSearchQuery(sample: Item<Sample>, searchQuery: string): void;
36
- clearSampleVariantsSearchQuery(sample: Item<Sample>): void;
37
42
  setSampleVariantsFilterQuery(sample: Item<Sample>, query: QueryClause): void;
38
43
  clearSampleVariantsFilterQuery(sample: Item<Sample>, selector: Selector): void;
39
44
  setSampleVariantsSort(sample: Item<Sample>, sort: SortOrder | null): void;
45
+ setSamplePage(page: number): void;
46
+ setSampleSearchQuery(searchQuery: string): void;
47
+ setSampleProbandFilterValue(probandFilterValue: boolean): void;
40
48
  };
41
49
 
42
50
  export type AppStore = [state: AppState, actions: AppActions];
43
51
 
44
- const defaultState: AppState = { variants: {}, samples: {} };
52
+ const defaultState: AppState = { variants: {}, sampleVariants: {} };
45
53
 
46
54
  const StoreContext = createContext<AppStore>() as Context<AppStore>;
47
55
 
@@ -49,12 +57,12 @@ export const Provider: ParentComponent = (props) => {
49
57
  const [state, setState] = createStore(defaultState);
50
58
 
51
59
  function getVariants(sample: Item<Sample>) {
52
- return state.samples ? state.samples[sample.id]?.variants || {} : {};
60
+ return state.sampleVariants ? state.sampleVariants[sample.id]?.variants || {} : {};
53
61
  }
54
62
 
55
63
  const actions: AppActions = {
56
64
  reset() {
57
- setState({ variants: undefined, samples: undefined });
65
+ setState({ variants: undefined, sampleVariants: undefined, samples: undefined });
58
66
  },
59
67
  setVariantsPage(page: number) {
60
68
  setState({ variants: { ...(state.variants || {}), page } });
@@ -65,9 +73,6 @@ export const Provider: ParentComponent = (props) => {
65
73
  setVariantsSearchQuery(searchQuery: string) {
66
74
  setState({ variants: { ...(state.variants || {}), searchQuery } });
67
75
  },
68
- clearVariantsSearchQuery() {
69
- setState({ variants: { ...(state.variants || {}), searchQuery: undefined } });
70
- },
71
76
  setVariantsFilterQuery(query: QueryClause) {
72
77
  setState({
73
78
  variants: {
@@ -93,37 +98,34 @@ export const Provider: ParentComponent = (props) => {
93
98
  });
94
99
  },
95
100
  setSampleVariantsPage(sample: Item<Sample>, page: number) {
96
- setState({ samples: { ...(state.samples || {}), [sample.id]: { variants: { ...getVariants(sample), page } } } });
101
+ setState({
102
+ sampleVariants: {
103
+ ...(state.sampleVariants || {}),
104
+ [sample.id]: { variants: { ...getVariants(sample), page } },
105
+ },
106
+ });
97
107
  },
98
108
  setSampleVariantsPageSize(sample: Item<Sample>, pageSize: number) {
99
109
  setState({
100
- samples: {
101
- ...(state.samples || {}),
110
+ sampleVariants: {
111
+ ...(state.sampleVariants || {}),
102
112
  [sample.id]: { variants: { ...getVariants(sample), pageSize, page: undefined } },
103
113
  },
104
114
  });
105
115
  },
106
116
  setSampleVariantsSearchQuery(sample: Item<Sample>, searchQuery: string) {
107
117
  setState({
108
- samples: {
109
- ...(state.samples || {}),
118
+ sampleVariants: {
119
+ ...(state.sampleVariants || {}),
110
120
  [sample.id]: { variants: { ...getVariants(sample), searchQuery, page: undefined } },
111
121
  },
112
122
  });
113
123
  },
114
- clearSampleVariantsSearchQuery(sample: Item<Sample>) {
115
- setState({
116
- samples: {
117
- ...(state.samples || {}),
118
- [sample.id]: { variants: { ...getVariants(sample), searchQuery: undefined, page: undefined } },
119
- },
120
- });
121
- },
122
124
  setSampleVariantsFilterQuery(sample: Item<Sample>, query: QueryClause) {
123
125
  const variants = getVariants(sample);
124
126
  setState({
125
- samples: {
126
- ...(state.samples || {}),
127
+ sampleVariants: {
128
+ ...(state.sampleVariants || {}),
127
129
  [sample.id]: {
128
130
  variants: {
129
131
  ...variants,
@@ -137,8 +139,8 @@ export const Provider: ParentComponent = (props) => {
137
139
  clearSampleVariantsFilterQuery(sample: Item<Sample>, selector: Selector) {
138
140
  const variants = getVariants(sample);
139
141
  setState({
140
- samples: {
141
- ...(state.samples || {}),
142
+ sampleVariants: {
143
+ ...(state.sampleVariants || {}),
142
144
  [sample.id]: {
143
145
  variants: {
144
146
  ...getVariants(sample),
@@ -151,9 +153,21 @@ export const Provider: ParentComponent = (props) => {
151
153
  },
152
154
  setSampleVariantsSort(sample: Item<Sample>, sort: SortOrder | null) {
153
155
  setState({
154
- samples: { ...(state.samples || {}), [sample.id]: { variants: { ...getVariants(sample), sort } } },
156
+ sampleVariants: {
157
+ ...(state.sampleVariants || {}),
158
+ [sample.id]: { variants: { ...getVariants(sample), sort } },
159
+ },
155
160
  });
156
161
  },
162
+ setSamplePage(page: number) {
163
+ setState({ samples: { ...(state.samples || {}), page } });
164
+ },
165
+ setSampleSearchQuery(searchQuery: string) {
166
+ setState({ samples: { ...(state.samples || {}), searchQuery } });
167
+ },
168
+ setSampleProbandFilterValue(probandFilterValue: boolean) {
169
+ setState({ samples: { ...(state.samples || {}), probandFilterValue } });
170
+ },
157
171
  };
158
172
  const store: AppStore = [state, actions];
159
173
 
package/src/utils/query.ts CHANGED
@@ -29,7 +29,6 @@ export function createSampleQuery(
29
29
  const searchFilterQuery = createQuery(search, filters, metadata);
30
30
  const query: Query =
31
31
  searchFilterQuery !== null ? { operator: "and", args: [sampleQuery, searchFilterQuery] } : sampleQuery;
32
- console.log(query);
33
32
  return query;
34
33
  }
35
34
 
package/src/views/SampleVariantConsequence.tsx CHANGED
@@ -63,6 +63,9 @@ export const SampleVariantConsequence: Component<{
63
63
  consequenceId: number;
64
64
  decisionTree: DecisionTree | null;
65
65
  }> = (props) => {
66
+ const hasDecisionTreePathMeta = () =>
67
+ (props.recordsMeta.info.CSQ?.nested?.items || []).findIndex((csq) => csq.id === "VIPP") !== -1;
68
+
66
69
  return (
67
70
  <>
68
71
  <div class="columns">
@@ -74,7 +77,7 @@ export const SampleVariantConsequence: Component<{
74
77
  record={props.variant}
75
78
  />
76
79
  </div>
77
- {props.decisionTree !== null && (
80
+ {props.decisionTree !== null && hasDecisionTreePathMeta() && (
78
81
  <div class="column">
79
82
  <h1 class="title is-5">Classification tree path</h1>
80
83
  <DecisionTreePath
package/src/views/SampleVariants.tsx CHANGED
@@ -66,7 +66,7 @@ export const SampleVariants: Component<{
66
66
  const [state, actions] = useStore();
67
67
 
68
68
  function getStateVariants() {
69
- return state.samples ? state.samples[props.sample.id]?.variants : undefined;
69
+ return state.sampleVariants ? state.sampleVariants[props.sample.id]?.variants : undefined;
70
70
  }
71
71
 
72
72
  // state initialization - start
package/src/views/Samples.tsx CHANGED
@@ -1,57 +1,116 @@
1
- import { Component, createResource, createSignal } from "solid-js";
1
+ import { Component, createResource, Show } from "solid-js";
2
2
  import { SampleTable } from "../components/SampleTable";
3
3
  import { Pager } from "../components/record/Pager";
4
4
  import { SearchBox } from "../components/SearchBox";
5
5
  import { Checkbox, CheckboxEvent } from "../components/Checkbox";
6
6
  import { Breadcrumb } from "../components/Breadcrumb";
7
- import { EMPTY_PARAMS, EMPTY_PHENOTYPES, EMPTY_SAMPLES_PAGE, fetchPhenotypes, fetchSamples } from "../utils/ApiUtils";
7
+ import { EMPTY_PARAMS, EMPTY_PHENOTYPES, fetchPhenotypes, fetchSamples } from "../utils/ApiUtils";
8
+ import { useStore } from "../store";
9
+ import { Params, Query, QueryClause } from "@molgenis/vip-report-api/src/Api";
10
+ import { Loader } from "../components/Loader";
8
11
 
9
12
  export const Samples: Component = () => {
10
- const [params, setParams] = createSignal(EMPTY_PARAMS);
11
- const [samples] = createResource(params, fetchSamples, { initialValue: EMPTY_SAMPLES_PAGE });
13
+ const [state, actions] = useStore();
12
14
  const [phenotypes] = createResource(EMPTY_PARAMS, fetchPhenotypes, { initialValue: EMPTY_PHENOTYPES });
13
15
 
14
- const onPageChange = (page: number) => setParams({ page });
15
- const onSearchChange = (search: string) =>
16
- setParams({
17
- page: 0,
18
- query: search !== "" ? { selector: ["person", "individualId"], operator: "~=", args: search } : undefined,
19
- });
16
+ function getStateSamples() {
17
+ return state.samples ? state.samples : undefined;
18
+ }
19
+
20
+ if (getStateSamples()?.page === undefined) {
21
+ actions.setSamplePage(0);
22
+ }
23
+
24
+ const onPageChange = (page: number) => actions.setSamplePage(page);
25
+ const onSearchChange = (search: string) => {
26
+ actions.setSampleSearchQuery(search);
27
+ actions.setSamplePage(0);
28
+ };
20
29
  const onProbandFilterChange = (event: CheckboxEvent) => {
21
- setParams({
22
- page: 0,
23
- query: event.checked ? { selector: ["proband"], operator: "==", args: event.checked } : undefined,
24
- });
30
+ actions.setSampleProbandFilterValue(event.checked);
31
+ actions.setSamplePage(0);
32
+ };
33
+
34
+ function createQuery(search: string | undefined, probandFilterValue: boolean | undefined): Query | null {
35
+ const searchQuery: QueryClause | undefined =
36
+ search !== undefined && search !== ""
37
+ ? { selector: ["person", "individualId"], operator: "~=", args: search }
38
+ : undefined;
39
+ const probandQuery: QueryClause | undefined =
40
+ probandFilterValue !== undefined && probandFilterValue
41
+ ? { selector: ["proband"], operator: "==", args: probandFilterValue }
42
+ : undefined;
43
+ if (searchQuery !== undefined || probandQuery != undefined) {
44
+ const args: QueryClause[] = [];
45
+ if (searchQuery !== undefined) {
46
+ args.push(searchQuery);
47
+ }
48
+ if (probandQuery !== undefined) {
49
+ args.push(probandQuery);
50
+ }
51
+ if (args.length > 0) {
52
+ const query: Query = {
53
+ operator: "and",
54
+ args: args,
55
+ };
56
+ return query;
57
+ }
58
+ }
59
+ return null;
60
+ }
61
+
62
+ const params = (): Params => {
63
+ return {
64
+ query: createQuery(searchQuery(), probandFilterValue()) || undefined,
65
+ page: page() || undefined,
66
+ };
25
67
  };
26
68
 
69
+ const page = () => getStateSamples()?.page;
70
+ const searchQuery = () => getStateSamples()?.searchQuery;
71
+ const probandFilterValue = () => getStateSamples()?.probandFilterValue;
72
+
73
+ const [samples] = createResource(params, fetchSamples);
74
+
27
75
  return (
28
76
  <>
29
77
  <Breadcrumb items={[{ text: "Samples" }]} />
30
- <div class="columns">
31
- <div class="column is-4 is-offset-3">
32
- {!samples.loading && <Pager page={samples().page} onPageChange={onPageChange} />}
33
- </div>
34
- <div class="column is-2 is-offset-1">
35
- {!samples.loading && <span class="is-pulled-right">{samples().page.totalElements} records</span>}
36
- </div>
37
- </div>
38
-
39
- <div class="columns">
40
- <div class="column is-1-fullhd is-2">
41
- <SearchBox onInput={onSearchChange} />
42
- <p class="has-text-weight-semibold">Proband</p>
43
- <div class="field">
44
- <div class="control">
45
- <Checkbox value={"proband"} label="" onChange={onProbandFilterChange} />
78
+ <Show when={samples()} fallback={<Loader />}>
79
+ {(samples) => (
80
+ <>
81
+ <div class="columns">
82
+ <div class="column is-4 is-offset-3">{<Pager page={samples.page} onPageChange={onPageChange} />}</div>
83
+ <div class="column is-2 is-offset-1">
84
+ {<span class="is-pulled-right">{samples.page.totalElements} records</span>}
85
+ </div>
86
+ </div>
87
+
88
+ <div class="columns">
89
+ <div class="column is-1-fullhd is-2">
90
+ <SearchBox onInput={onSearchChange} value={state.samples?.searchQuery} />
91
+ <p class="has-text-weight-semibold">Proband</p>
92
+ <div class="field">
93
+ <div class="control">
94
+ <Checkbox
95
+ value={"proband"}
96
+ label=""
97
+ onChange={onProbandFilterChange}
98
+ checked={state.samples?.probandFilterValue}
99
+ />
100
+ </div>
101
+ </div>
102
+ </div>
103
+ <div class="column">
104
+ <span class="is-italic">
105
+ Click on an individual id for detailed information for this sample. In this screen a link to the
106
+ variants for this sample is available.
107
+ </span>
108
+ {!phenotypes.loading && <SampleTable samples={samples.items} phenotypes={phenotypes().items} />}
109
+ </div>
46
110
  </div>
47
- </div>
48
- </div>
49
- <div class="column">
50
- {!samples.loading && !phenotypes.loading && (
51
- <SampleTable samples={samples().items} phenotypes={phenotypes().items} />
52
- )}
53
- </div>
54
- </div>
111
+ </>
112
+ )}
113
+ </Show>
55
114
  </>
56
115
  );
57
116
  };
package/src/views/VariantConsequence.tsx CHANGED
@@ -28,6 +28,8 @@ export const VariantConsequence: Component = () => {
28
28
 
29
29
  const csqFields = (): FieldMetadata[] => recordsMetadata().info.CSQ?.nested?.items || [];
30
30
  const csqValues = (): ValueArray => getSpecificConsequence(variant().data.n.CSQ as ValueArray, consequenceId);
31
+
32
+ const hasDecisionTreePathMeta = () => csqFields().findIndex((csq) => csq.id === "VIPP") !== -1;
31
33
  return (
32
34
  <Show when={!variant.loading} fallback={<Loader />}>
33
35
  <Breadcrumb
@@ -42,17 +44,19 @@ export const VariantConsequence: Component = () => {
42
44
  <h1 class="title is-5">Consequence</h1>
43
45
  <ConsequenceTable csqMetadata={csqFields()} csqValues={csqValues()} record={variant()} />
44
46
  </div>
45
- <Show when={!recordsMetadata.loading && !decisionTree.loading && (decisionTree() as DecisionTree)}>
46
- {(decisionTree) => (
47
- <div class="column">
48
- <h1 class="title is-5">Classification tree path</h1>
49
- <DecisionTreePath
50
- decisionTree={decisionTree}
51
- path={getDecisionTreePath(recordsMetadata(), variant(), consequenceId)}
52
- />
53
- </div>
54
- )}
55
- </Show>
47
+ {hasDecisionTreePathMeta() && (
48
+ <Show when={!recordsMetadata.loading && !decisionTree.loading && (decisionTree() as DecisionTree)}>
49
+ {(decisionTree) => (
50
+ <div class="column">
51
+ <h1 class="title is-5">Classification tree path</h1>
52
+ <DecisionTreePath
53
+ decisionTree={decisionTree}
54
+ path={getDecisionTreePath(recordsMetadata(), variant(), consequenceId)}
55
+ />
56
+ </div>
57
+ )}
58
+ </Show>
59
+ )}
56
60
  </div>
57
61
  <div class="columns">
58
62
  <div class="column is-6">