@sjcrh/proteinpaint-server 2.87.0 → 2.88.0

package/dataset/termdb.test.js

@@ -26,17 +26,6 @@ var termdb_test_default = {
     db: {
       file: "files/hg38/TermdbTest/db"
     },
-    allowedChartTypes: [
-      "summary",
-      "survival",
-      "matrix",
-      "sampleScatter",
-      "cuminc",
-      "dataDownload",
-      "sampleView",
-      "regression",
-      "facet"
-    ],
     termdb: {
       displaySampleIds: true,
       // allow to display sample-level data

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.87.0",
+  "version": "2.88.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -60,8 +60,8 @@
   "dependencies": {
     "@sjcrh/augen": "2.87.0",
     "@sjcrh/proteinpaint-rust": "2.84.0",
-    "@sjcrh/proteinpaint-shared": "2.87.0",
-    "@sjcrh/proteinpaint-types": "2.87.0",
+    "@sjcrh/proteinpaint-shared": "2.87.1",
+    "@sjcrh/proteinpaint-types": "2.88.0",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/termdb.boxplot.js

@@ -2,7 +2,7 @@ import { boxplotPayload } from "#types/checkers";
 import { getData } from "../src/termdb.matrix.js";
 import { boxplot_getvalue } from "../src/utils.js";
 import { sortKey2values } from "../src/termdb.violin.js";
-import { roundValue } from "#shared/roundValue.js";
+import { roundValueAuto } from "#shared/roundValue.js";
 const api = {
   endpoint: "termdb/boxplot",
   methods: {
@@ -147,6 +147,8 @@ function setHiddenPlots(term, plots) {
   return plots;
 }
 function setDescrStats(boxplot, sortedValues) {
+  if (sortedValues.length < 5)
+    return [{ id: "total", label: "Total", value: sortedValues.length }];
   const mean = sortedValues.reduce((s2, i) => s2 + i, 0) / sortedValues.length;
   let s = 0;
   for (const v of sortedValues) {
@@ -157,15 +159,15 @@ function setDescrStats(boxplot, sortedValues) {
   const variance = squareDiffs / (sortedValues.length - 1);
   return [
     { id: "total", label: "Total", value: sortedValues.length },
-    { id: "min", label: "Minimum", value: roundValue(sortedValues[0], 2) },
-    { id: "p25", label: "1st quartile", value: roundValue(boxplot.p25, 2) },
-    { id: "median", label: "Median", value: roundValue(boxplot.p50, 2) },
-    { id: "mean", label: "Mean", value: roundValue(mean, 2) },
-    { id: "p75", label: "3rd quartile", value: roundValue(boxplot.p75, 2) },
-    { id: "max", label: "Maximum", value: roundValue(sortedValues[sortedValues.length - 1], 2) },
-    { id: "sd", label: "Standard deviation", value: isNaN(sd) ? null : roundValue(sd, 2) },
-    { id: "variance", label: "Variance", value: roundValue(variance, 2) },
-    { id: "iqr", label: "Inter-quartile range", value: roundValue(boxplot.iqr, 2) }
+    { id: "min", label: "Minimum", value: roundValueAuto(sortedValues[0]) },
+    { id: "p25", label: "1st quartile", value: roundValueAuto(boxplot.p25) },
+    { id: "median", label: "Median", value: roundValueAuto(boxplot.p50) },
+    { id: "mean", label: "Mean", value: roundValueAuto(mean) },
+    { id: "p75", label: "3rd quartile", value: roundValueAuto(boxplot.p75) },
+    { id: "max", label: "Maximum", value: roundValueAuto(sortedValues[sortedValues.length - 1]) },
+    { id: "sd", label: "Standard deviation", value: isNaN(sd) ? null : roundValueAuto(sd) },
+    { id: "variance", label: "Variance", value: roundValueAuto(variance) },
+    { id: "iqr", label: "Inter-quartile range", value: roundValueAuto(boxplot.iqr) }
   ];
 }
 function setUncomputableValues(values) {

package/routes/termdb.cohort.summary.js

@@ -19,7 +19,7 @@ function init({ genomes }) {
       if (!genome)
         throw "invalid genome";
       const [ds] = get_ds_tdb(genome, q);
-      const count = ds.cohort.termdb.q.getCohortSampleCount(q.cohort);
+      const count = ds.cohort.termdb.q?.getCohortSampleCount?.(q.cohort) || 1;
       res.send({ count });
     } catch (e) {
       res.send({ error: e.message || e });

package/routes/termdb.cohorts.js

@@ -31,6 +31,8 @@ function init({ genomes }) {
   };
 }
 function getCohortsData(ds) {
+  if (!ds.cohort.db)
+    return { cohorts: [], features: [], cfeatures: [] };
   const features = ds.cohort.db.connection.prepare("select * from features").all();
   const cohorts = ds.cohort.db.connection.prepare(
     `select * from cohorts where cohort in (select distinct(cohort) from cohort_features)

package/routes/termdb.config.js

@@ -2,7 +2,7 @@ import serverconfig from "#src/serverconfig.js";
 import { authApi } from "#src/auth.js";
 import { get_ds_tdb } from "#src/termdb.js";
 import { mayCopyFromCookie } from "#src/utils.js";
-import { mayComputeTermtypeByCohort } from "#src/termdb.server.init.js";
+import { mayComputeTermtypeByCohort } from "#src/termdb.server.init.ts";
 import { TermTypes } from "#shared/terms.js";
 const api = {
   endpoint: "termdb/config",
@@ -39,12 +39,11 @@ function init({ genomes }) {
 }
 function make(q, res, ds, genome) {
   const tdb = ds.cohort.termdb;
+  const auth = { embedder: q.embedder };
   const c = {
     selectCohort: tdb.selectCohort,
     // optional
-    supportedChartTypes: tdb.q?.getSupportedChartTypes(q.embedder),
-    allowedChartTypes: ds.cohort.allowedChartTypes,
-    hiddenChartTypes: ds.cohort.hiddenChartTypes,
+    supportedChartTypes: tdb.q?.getSupportedChartTypes(auth),
     renamedChartTypes: ds.cohort.renamedChartTypes,
     allowedTermTypes: getAllowedTermTypes(ds),
     termMatch2geneSet: tdb.termMatch2geneSet,
@@ -242,8 +241,8 @@ function getAllowedTermTypes(ds) {
   mayComputeTermtypeByCohort(ds);
   const typeSet = /* @__PURE__ */ new Set();
   for (const r of ds.cohort.termdb.termtypeByCohort) {
-    if (r.type)
-      typeSet.add(r.type);
+    if (r.termType)
+      typeSet.add(r.termType);
   }
   if (ds.cohort.termdb.allowedTermTypes) {
     for (const t of ds.cohort.termdb.allowedTermTypes)

package/routes/termdb.singlecellSamples.js

@@ -2,6 +2,7 @@ import fs from "fs";
 import path from "path";
 import { read_file } from "#src/utils.js";
 import run_R from "#src/run_R.js";
+import { joinUrl } from "#src/helpers.ts";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import serverconfig from "#src/serverconfig.js";
 import { termdbSingleCellSamplesPayload } from "#types/checkers";
@@ -228,15 +229,19 @@ function gdc_validateGeneExpression(G, ds, genome) {
     try {
       const uuid = ds.__gdc.map2caseid.get(q.sample.sID);
       const fileid = q.sample.eID;
+      const hdf5id = ds.__gdc.scrnaAnalysis2hdf5.get(fileid);
+      if (!hdf5id)
+        throw "cannot map eID to hdf5 id";
       const aliasLst = genome.genedb.getAliasByName.all(q.gene);
       const gencodeId = aliasLst.find((a) => a?.alias.toUpperCase().startsWith("ENSG"))?.alias;
+      if (!gencodeId)
+        throw "cannot map gene symbol to GENCODE";
       const body = {
-        case_id: uuid,
         gene_ids: [gencodeId],
-        file_id: fileid
+        file_id: hdf5id
       };
       const { host } = ds.getHostHeaders(q);
-      const out = await ky.post(path.join(host.rest, "scrna_seq/gene_expression"), { timeout: false, json: body }).json();
+      const out = await ky.post(joinUrl(host.rest, "scrna_seq/gene_expression"), { timeout: false, json: body }).json();
       const result = out.data[0].cells;
       const data = {};
       for (const r of result) {