@sjcrh/proteinpaint-server 2.114.0 → 2.115.0

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Files changed (8) hide show
  1. package/package.json +6 -5
  2. package/routes/correlationVolcano.js +4 -1
  3. package/routes/samplewsimages.js +23 -35
  4. package/routes/termdb.topMutatedGenes.js +51 -0
  5. package/routes/wsisamples.js +74 -0
  6. package/src/app.js +501 -611
  7. package/src/serverconfig.js +1 -1
  8. package/routes/gdc.topMutatedGenes.js +0 -275
package/src/serverconfig.js CHANGED
@@ -126,7 +126,7 @@ if (serverconfig.debugmode && !serverconfig.binpath.includes('sjcrh/')) {
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  const routeSetters = []
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  const defaultDir = path.join(serverconfig.binpath, 'src/test/routes')
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  // will add testing routes as needed and if found, such as in dev environment
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- const testRouteSetters = ['gdc.js', 'specs.js', 'readme.js', 'closeCoverage.js']
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+ const testRouteSetters = ['gdc.js', 'specs.js', 'readme.js', 'coverage.js']
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  if (serverconfig.features.sse === undefined) serverconfig.features.sse = true
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  if (typeof serverconfig.features.sse !== 'boolean') {
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  throw `serverconfig.features.sse must be either undefined or boolean`
package/routes/gdc.topMutatedGenes.js DELETED
@@ -1,275 +0,0 @@
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- import { gdcTopMutatedGenePayload } from "#types/checkers";
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- import { mclasscnvgain, mclasscnvloss, dtsnvindel } from "#shared/common.js";
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- import ky from "ky";
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- const api = {
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- endpoint: "gdc/topMutatedGenes",
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- methods: {
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- get: {
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- init,
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- ...gdcTopMutatedGenePayload
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- },
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- post: {
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- init,
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- ...gdcTopMutatedGenePayload
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- }
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- }
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- };
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- function init({ genomes }) {
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- return async (req, res) => {
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- const q = req.query;
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- const g = genomes.hg38;
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- if (!g)
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- throw "hg38 missing";
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- const ds = g.datasets.GDC;
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- if (!ds)
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- throw "hg38 GDC missing";
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- try {
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- const genes = await getGenesGraphql(q, ds);
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- const payload = { genes };
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- res.send(payload);
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- } catch (e) {
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- res.send({ status: "error", error: e.message || e });
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- if (e.stack)
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- console.log(e.stack);
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- else
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- console.trace(e);
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- }
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- };
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- }
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- const queryV2 = {
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- query: `
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- query GenesTable(
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- $caseFilters: FiltersArgument
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- $genesTable_filters: FiltersArgument
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- $genesTable_size: Int
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- $genesTable_offset: Int
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- $score: String
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- $ssmCase: FiltersArgument
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- $geneCaseFilter: FiltersArgument
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- $ssmTested: FiltersArgument
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- $cnvTested: FiltersArgument
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- $cnvGainFilters: FiltersArgument
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- $cnvLossFilters: FiltersArgument
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- $sort: [Sort]
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- ) {
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- genesTableViewer: viewer {
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- explore {
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- cases {
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- hits(first: 0, case_filters: $ssmTested) {
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- total
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- }
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- }
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- filteredCases: cases {
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- hits(first: 0, case_filters: $geneCaseFilter) {
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- total
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- }
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- }
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- cnvCases: cases {
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- hits(first: 0, case_filters: $cnvTested) {
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- total
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- }
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- }
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- genes {
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- hits(
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- first: $genesTable_size
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- offset: $genesTable_offset
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- filters: $genesTable_filters
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- case_filters: $caseFilters
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- score: $score
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- sort: $sort
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- ) {
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- total
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- edges {
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- node {
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- id
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- numCases: score
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- symbol
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- name
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- cytoband
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- biotype
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- gene_id
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- is_cancer_gene_census
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- ssm_case: case {
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- hits(first: 0, filters: $ssmCase) {
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- total
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- }
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- }
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- cnv_case: case {
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- hits(first: 0, filters: $cnvTested) {
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- total
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- }
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- }
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- case_cnv_gain: case {
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- hits(first: 0, filters: $cnvGainFilters) {
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- total
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- }
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- }
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- case_cnv_loss: case {
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- hits(first: 0, filters: $cnvLossFilters) {
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- total
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- }
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- }
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- }
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- }
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- }
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- }
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- }
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- }
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- }`,
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- getVariables: (q) => {
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- const variables = {
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- caseFilters: { op: "and", content: [] },
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- genesTable_filters: { op: "and", content: [] },
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- genesTable_size: q.maxGenes || 50,
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- genesTable_offset: 0,
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- score: "case.project.project_id",
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- ssmCase: {
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- op: "and",
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- content: [
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- {
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- op: "in",
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- content: {
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- field: "cases.available_variation_data",
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- value: ["ssm"]
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- }
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- },
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- {
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- op: "NOT",
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- content: {
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- field: "genes.case.ssm.observation.observation_id",
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- value: "MISSING"
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- }
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- }
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- ]
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- },
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- geneCaseFilter: {
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- content: [
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- {
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- content: {
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- field: "cases.available_variation_data",
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- value: ["ssm"]
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- },
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- op: "in"
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- }
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- ],
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- op: "and"
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- },
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- ssmTested: {
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- content: [
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- {
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- content: {
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- field: "cases.available_variation_data",
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- value: ["ssm"]
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- },
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- op: "in"
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- }
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- ],
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- op: "and"
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- },
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- cnvTested: {
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- op: "and",
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- content: [
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- {
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- content: {
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- field: "cases.available_variation_data",
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- value: ["cnv"]
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- },
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- op: "in"
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- }
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- ]
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- },
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- cnvGainFilters: {
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- op: "and",
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- content: [
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- {
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- content: {
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- field: "cases.available_variation_data",
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- value: ["cnv"]
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- },
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- op: "in"
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- },
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- {
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- content: {
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- field: "cnvs.cnv_change",
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- value: ["Gain"]
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- },
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- op: "in"
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- }
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- ]
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- },
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- cnvLossFilters: {
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- op: "and",
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- content: [
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- {
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- content: {
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- field: "cases.available_variation_data",
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- value: ["cnv"]
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- },
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- op: "in"
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- },
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- {
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- content: {
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- field: "cnvs.cnv_change",
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- value: ["Loss"]
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- },
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- op: "in"
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- }
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- ]
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- }
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- };
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- if (q.filter0) {
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- variables.ssmCase.content.push(JSON.parse(JSON.stringify(q.filter0)));
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- variables.caseFilters.content.push(JSON.parse(JSON.stringify(q.filter0)));
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- variables.geneCaseFilter.content.push(JSON.parse(JSON.stringify(q.filter0)));
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- variables.cnvLossFilters.content.push(JSON.parse(JSON.stringify(q.filter0)));
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- variables.cnvGainFilters.content.push(JSON.parse(JSON.stringify(q.filter0)));
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- variables.cnvTested.content.push(JSON.parse(JSON.stringify(q.filter0)));
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- }
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- if (q.geneFilter == "CGC") {
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- variables.genesTable_filters.content.push(geneCGC());
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- variables.cnvLossFilters.content.push(geneCGC());
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- variables.cnvGainFilters.content.push(geneCGC());
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- }
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- return variables;
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- }
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- };
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- async function getGenesGraphql(q, ds) {
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- const { host, headers } = ds.getHostHeaders(q);
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- const query = queryV2.query;
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- const variables = queryV2.getVariables(q);
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- const re = await ky.post(host.graphql, {
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- timeout: false,
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- // do not let ky timeout
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- headers,
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- json: { query, variables }
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- }).json();
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- const genes = [];
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- for (const g of re.data.genesTableViewer.explore.genes.hits.edges) {
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- if (typeof g.node != "object")
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- throw "node missing from re.data.genesTableViewer.explore.genes.hits.edges[]";
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- const mutationStat = [];
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- if (Number.isInteger(g.node.case_cnv_gain?.hits?.total) && g.node.case_cnv_gain.hits.total > 0)
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- mutationStat.push({ class: mclasscnvgain, count: g.node.case_cnv_gain.hits.total });
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- if (Number.isInteger(g.node.case_cnv_loss?.hits?.total) && g.node.case_cnv_loss.hits.total > 0)
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- mutationStat.push({ class: mclasscnvloss, count: g.node.case_cnv_loss.hits.total });
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- if (Number.isInteger(g.node.ssm_case?.hits?.total) && g.node.ssm_case.hits.total > 0)
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- mutationStat.push({ dt: dtsnvindel, count: g.node.ssm_case.hits.total });
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- genes.push({
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- gene: g.node.symbol,
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- mutationStat
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- });
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- }
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- return genes;
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- }
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- function geneCGC() {
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- return {
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- content: {
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- field: "genes.is_cancer_gene_census",
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- value: ["true"]
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- },
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- op: "in"
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- };
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- }
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- export {
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- api
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- };