@sjcrh/proteinpaint-server 2.122.0 → 2.124.0

package/dataset/termdb.test.js

@@ -5,6 +5,9 @@ copyDataFilesFromRepo2Tp();
 function termdb_test_default() {
   return {
     isMds3: true,
+    isSupportedChartOverride: {
+      runChart: () => true
+    },
     cohort: {
       massNav: {
         tabs: {
@@ -34,7 +37,7 @@ function termdb_test_default() {
       },
       termdb: {
         allowedTermTypes: ["geneVariant"],
-        displaySampleIds: true,
+        displaySampleIds: () => true,
         // allow to display sample-level data
         timeUnit: "years",
         minTimeSinceDx: 5,
@@ -123,16 +126,6 @@ function termdb_test_default() {
         ]
       }
     },
-    customTwQByType: {
-      // dataset-specific termsetting configs on certain term types
-      geneVariant: {
-        default: { cnvGainCutoff: 0.1, cnvLossCutoff: -0.1, cnvMaxLength: 0 },
-        byGene: {
-          // key is term.name, thus possible to use non-gene names e.g. C19MC
-          MYCN: { cnvGainCutoff: 0.5, cnvLossCutoff: -0.1, cnvMaxLength: 0 }
-        }
-      }
-    },
     variant2samples: {
       variantkey: "ssm_id",
       // required, tells client to return ssm_id for identifying variants

package/genome/hg38.js

@@ -14,6 +14,19 @@ var hg38_default = {
         termdb: {
           isGeneSetTermdb: true
         }
+      },
+      analysisGenesetGroups: [
+        { label: "-", value: "-" },
+        { label: "BP: subset of GO", value: "BP: subset of GO" },
+        { label: "MF: subset of GO", value: "MF: subset of GO" },
+        { label: "CC: subset of GO", value: "CC: subset of GO" },
+        { label: "WikiPathways subset of CP", value: "WikiPathways subset of CP" },
+        { label: "REACTOME subset of CP", value: "REACTOME subset of CP" },
+        { label: "H: hallmark gene sets", value: "H: hallmark gene sets" }
+      ],
+      geneORAparam: {
+        minCutoff: 15,
+        maxCutoff: 500
       }
     }
   },

package/genome/hg38.test.js

@@ -13,6 +13,14 @@ const genome = {
         termdb: {
           isGeneSetTermdb: true
         }
+      },
+      analysisGenesetGroups: [
+        { label: "-", value: "-" },
+        { label: "H: hallmark gene sets", value: "H: hallmark gene sets" }
+      ],
+      geneORAparam: {
+        minCutoff: 0,
+        maxCutoff: 500
       }
     }
   },

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.122.0",
+  "version": "2.124.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -67,9 +67,10 @@
   "dependencies": {
     "@sjcrh/augen": "2.121.0",
     "@sjcrh/proteinpaint-python": "2.118.0",
-    "@sjcrh/proteinpaint-rust": "2.122.0",
-    "@sjcrh/proteinpaint-shared": "2.121.0",
-    "@sjcrh/proteinpaint-types": "2.121.0",
+    "@sjcrh/proteinpaint-r": "2.123.0",
+    "@sjcrh/proteinpaint-rust": "2.124.0",
+    "@sjcrh/proteinpaint-shared": "2.124.0",
+    "@sjcrh/proteinpaint-types": "2.124.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",
@@ -110,12 +111,9 @@
     "start.js",
     "src/app.js",
     "src/serverconfig.js",
-    "src/run_R.js",
     "src/mds3.gdc.filter.js",
     "src/checkReadingFrame.js",
     "src/bedj.parseBed.js",
-    "utils/*.R",
-    "utils/*.py",
     "LICENSE/*"
   ],
   "bugs": {

package/routes/burden.js

@@ -1,5 +1,5 @@
 import { burdenPayload } from "#types/checkers";
-import run_R from "#src/run_R.js";
+import { run_R } from "@sjcrh/proteinpaint-r";
 import path from "path";
 import serverconfig from "#src/serverconfig.js";
 const api = {
@@ -57,7 +57,7 @@ async function getBurdenResult(q, cumburden) {
   let result = cumburden.db.connection.prepare("SELECT * FROM estimates WHERE id=?").get(id);
   if (!result) {
     result = { id, status: null, input: jsonInput };
-    const estJson = await run_R(path.join(serverconfig.binpath, "utils", "burden-main.R"), jsonInput, []);
+    const estJson = await run_R("burden-main.R", jsonInput, []);
     const estimate = JSON.parse(estJson);
     const ages = Object.keys(estimate[0]).filter((k) => k.startsWith("["));
     const overall = { chc: 0 };
@@ -92,7 +92,6 @@ function normalizeInput(q, cumburden) {
     files: cumburden.files,
     boosubdir: cumburden.bootsubdir
   };
-  normalized.binpath = serverconfig.binpath;
   const jsonInput = JSON.stringify(normalized);
   return { id, jsonInput };
 }
@@ -102,7 +101,7 @@ async function compute95ci(result, cumburden) {
       throw "result{} does not have .input";
     const input = structuredClone(result.input);
     input.burden = Object.values(result.estimate).filter((est) => est.chc !== 0);
-    const lowup = await run_R(path.join(serverconfig.binpath, "utils", "burden-ci95.R"), JSON.stringify(input), []);
+    const lowup = await run_R("burden-ci95.R", JSON.stringify(input), []);
     const { low, up, overall } = JSON.parse(lowup);
     const ci95 = { 0: {} };
     for (const est of Object.values(result.estimate)) {

package/routes/correlationVolcano.js

@@ -1,9 +1,7 @@
 import { CorrelationVolcanoPayload } from "#types/checkers";
 import { getData } from "../src/termdb.matrix.js";
-import run_R from "../src/run_R.js";
-import serverconfig from "../src/serverconfig.js";
+import { run_R } from "@sjcrh/proteinpaint-r";
 import { mayLog } from "#src/helpers.ts";
-import path from "path";
 import { getStdDev } from "#shared/descriptive.stats.js";
 import { formatElapsedTime } from "#shared/time.js";
 const minArrayLength = 3;
@@ -91,7 +89,7 @@ async function compute(q, ds, genome) {
   };
   const time1 = Date.now();
   const output = {
-    terms: JSON.parse(await run_R(path.join(serverconfig.binpath, "utils", "corr.R"), JSON.stringify(input)))
+    terms: JSON.parse(await run_R("corr.R", JSON.stringify(input)))
   };
   const elapsedMs = Date.now() - time1;
   const formattedTime = formatElapsedTime(elapsedMs);

package/routes/genesetOverrepresentation.js

@@ -42,13 +42,7 @@ async function run_genesetOverrepresentation_analysis(q, genomes) {
   const rust_output = await run_rust("genesetORA", JSON.stringify(gene_overrepresentation_input_type));
   const time2 = (/* @__PURE__ */ new Date()).valueOf();
   console.log("Time taken to run rust gene over representation pipeline:", time2 - time1, "ms");
-  let result;
-  for (const line of rust_output.split("\n")) {
-    if (line.startsWith("pathway_p_values:")) {
-      result = JSON.parse(line.replace("pathway_p_values:", ""));
-    } else {
-    }
-  }
+  const result = JSON.parse(rust_output);
   return result;
 }
 export {

package/routes/genomes.js

@@ -93,7 +93,11 @@ function clientcopy_genome(genomename, genomes) {
   if (g.termdbs) {
     g2.termdbs = {};
     for (const k in g.termdbs) {
-      g2.termdbs[k] = { label: g.termdbs[k].label };
+      g2.termdbs[k] = {
+        label: g.termdbs[k].label,
+        analysisGenesetGroups: g.termdbs[k].analysisGenesetGroups,
+        geneORAparam: g.termdbs[k].geneORAparam
+      };
     }
   }
   for (const dsname in g.datasets) {

package/routes/samplewsimages.js

@@ -30,6 +30,15 @@ function init({ genomes }) {
           if (annotations) {
             wsimage.overlays = annotations;
           }
+          if (ds.queries.WSImages.getZoomInPoints) {
+            const zoomInPoints = await ds.queries.WSImages.getZoomInPoints(
+              sampleId,
+              wsimage.filename
+            );
+            if (zoomInPoints) {
+              wsimage.zoomInPoints = zoomInPoints;
+            }
+          }
         }
       }
       res.send({ sampleWSImages: wsimages });

package/routes/termdb.DE.js

@@ -4,7 +4,7 @@ import { diffExpPayload } from "#types/checkers";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import { getData } from "../src/termdb.matrix.js";
 import { get_ds_tdb } from "../src/termdb.js";
-import run_R from "../src/run_R.js";
+import { run_R } from "@sjcrh/proteinpaint-r";
 import { mayLog } from "#src/helpers.ts";
 import serverconfig from "../src/serverconfig.js";
 import imagesize from "image-size";
@@ -223,9 +223,7 @@ async function run_DE(param, ds, term_results, term_results2) {
   const sample_size_limit = 8;
   if (group1names.length <= sample_size_limit && group2names.length <= sample_size_limit || param.method == "edgeR" || param.method == "limma") {
     const time12 = (/* @__PURE__ */ new Date()).valueOf();
-    const result2 = JSON.parse(
-      await run_R(path.join(serverconfig.binpath, "utils", "edge.R"), JSON.stringify(expression_input))
-    );
+    const result2 = JSON.parse(await run_R("edge.R", JSON.stringify(expression_input)));
     mayLog("Time taken to run edgeR:", formatElapsedTime(Date.now() - time12));
     param.method = "edgeR";
     const ql_imagePath = path.join(serverconfig.cachedir, result2.edgeR_ql_image_name[0]);

package/routes/termdb.cluster.js

@@ -1,5 +1,5 @@
 import path from "path";
-import run_R from "#src/run_R.js";
+import { run_R } from "@sjcrh/proteinpaint-r";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import { termdbClusterPayload } from "#types/checkers";
 import * as utils from "#src/utils.js";
@@ -172,9 +172,7 @@ async function doClustering(data, q, numCases = 1e3) {
   }
   if (inputData.matrix.length == 0)
     throw "Clustering matrix is empty";
-  const Routput = JSON.parse(
-    await run_R(path.join(serverconfig.binpath, "utils", "hclust.R"), JSON.stringify(inputData))
-  );
+  const Routput = JSON.parse(await run_R("hclust.R", JSON.stringify(inputData)));
   const row_names_index = Routput.RowOrder.map((row) => inputData.row_names.indexOf(row.name));
   const col_names_index = Routput.ColOrder.map((col) => inputData.col_names.indexOf(col.name));
   const output_matrix = [];

package/routes/termdb.config.js

@@ -41,7 +41,6 @@ function make(q, req, res, ds, genome) {
   const c = {
     selectCohort: getSelectCohort(ds, req),
     supportedChartTypes: tdb.q?.getSupportedChartTypes(req),
-    hiddenTermIds: tdb.hiddenTermIds,
     renamedChartTypes: ds.cohort.renamedChartTypes,
     allowedTermTypes: getAllowedTermTypes(ds),
     termMatch2geneSet: tdb.termMatch2geneSet,
@@ -76,8 +75,6 @@ function make(q, req, res, ds, genome) {
     c.timeUnit = tdb.timeUnit;
   if (tdb.cohortStartTimeMsg)
     c.cohortStartTimeMsg = tdb.cohortStartTimeMsg;
-  if (tdb.displaySampleIds)
-    c.displaySampleIds = tdb.displaySampleIds;
   if (tdb.hasAncestry)
     c.hasAncestry = tdb.hasAncestry;
   if (tdb.logscaleBase2)
@@ -92,8 +89,6 @@ function make(q, req, res, ds, genome) {
     c.regression = tdb.regression;
   if (ds.assayAvailability)
     c.assayAvailability = ds.assayAvailability;
-  if (ds.customTwQByType)
-    c.customTwQByType = ds.customTwQByType;
   if (ds.cohort.correlationVolcano)
     c.correlationVolcano = ds.cohort.correlationVolcano;
   c.requiredAuth = authApi.getRequiredCredForDsEmbedder(q.dslabel, q.embedder);
@@ -104,6 +99,8 @@ function make(q, req, res, ds, genome) {
   c.requiredAuth = authApi.getRequiredCredForDsEmbedder(q.dslabel, q.embedder);
   const info = authApi.getNonsensitiveInfo(req);
   c.clientAuthResult = info?.clientAuthResult || {};
+  if (tdb.displaySampleIds)
+    c.displaySampleIds = tdb.displaySampleIds(c.clientAuthResult);
   res.send({ termdbConfig: c });
 }
 function addRestrictAncestries(c, tdb) {

package/routes/termdb.rootterm.js

@@ -25,7 +25,7 @@ function init({ genomes }) {
         throw "invalid dataset name";
       if (!tdb)
         throw "invalid termdb object";
-      await trigger_rootterm(q, res, tdb);
+      await trigger_rootterm(req, q, res, tdb);
     } catch (e) {
       res.send({ error: e instanceof Error ? e.message : e });
       if (e instanceof Error && e.stack)
@@ -33,10 +33,10 @@ function init({ genomes }) {
     }
   };
 }
-async function trigger_rootterm(q, res, tdb) {
+async function trigger_rootterm(req, q, res, tdb) {
   const cohortValues = q.cohortValues ? q.cohortValues : "";
   const treeFilter = q.treeFilter ? q.treeFilter : "";
-  res.send({ lst: await tdb.q.getRootTerms(cohortValues, treeFilter) });
+  res.send({ lst: await tdb.q.getRootTerms(req, cohortValues, treeFilter) });
 }
 export {
   api

package/routes/termdb.termchildren.js

@@ -25,7 +25,7 @@ function init({ genomes }) {
         throw "invalid dataset name";
       if (!tdb)
         throw "invalid termdb object";
-      const result = await trigger_children(q, tdb);
+      const result = await trigger_children(req, q, tdb);
       res.send(result);
     } catch (e) {
       res.send({ error: e instanceof Error ? e.message : e });
@@ -34,12 +34,12 @@ function init({ genomes }) {
     }
   };
 }
-async function trigger_children(q, tdb) {
+async function trigger_children(req, q, tdb) {
   if (!q.tid)
     throw "no parent term id";
   const cohortValues = q.cohortValues ? q.cohortValues : "";
   const treeFilter = q.treeFilter ? q.treeFilter : "";
-  const terms = await tdb.q.getTermChildren(q.tid, cohortValues, treeFilter);
+  const terms = await tdb.q.getTermChildren(req, q.tid, cohortValues, treeFilter);
   return { lst: terms.map(copy_term) };
 }
 export {

package/routes/termdb.violin.js

@@ -7,9 +7,7 @@ import { getOrderedLabels } from "../src/termdb.barchart.js";
 import { summaryStats } from "#shared/descriptive.stats.js";
 import { isNumericTerm } from "#shared/terms.js";
 import { numericBins, parseValues } from "./termdb.boxplot.ts";
-import serverconfig from "../src/serverconfig.js";
-import run_R from "../src/run_R.js";
-import path from "path";
+import { run_R } from "@sjcrh/proteinpaint-r";
 const api = {
   endpoint: "termdb/violin",
   methods: {
@@ -238,8 +236,7 @@ async function getDensity(values) {
   return result.plot;
 }
 async function getDensities(plot2Values, min, max) {
-  const densityScript = path.join(serverconfig.binpath, "utils", "density.R");
-  const plot2Density = JSON.parse(await run_R(densityScript, JSON.stringify({ plot2Values, min, max })));
+  const plot2Density = JSON.parse(await run_R("density.R", JSON.stringify({ plot2Values, min, max })));
   const densities = {};
   for (const plot in plot2Density) {
     const result = plot2Density[plot];