@sjcrh/proteinpaint-server 2.198.0 → 2.200.0

package/dataset/termdb.test.js

@@ -359,7 +359,6 @@ function termdb_test_default() {
         file: "files/hg38/TermdbTest/TermdbTest_ITD.gz"
       },
       singleSampleMutation: {
-        src: "native",
         sample_id_key: "sample_id",
         folder: "files/hg38/TermdbTest/mutationpersample/"
       },
@@ -389,7 +388,6 @@ function termdb_test_default() {
         }
       },
       geneExpression: {
-        src: "native",
         file: "files/hg38/TermdbTest/rnaseq/TermdbTest.fpkm.matrix.new.h5",
         unit: "FPKM"
       },
@@ -419,7 +417,6 @@ function termdb_test_default() {
         },
         data: {
           sameLegend: true,
-          src: "native",
           plots: [
             {
               name: "UMAP",
@@ -437,7 +434,6 @@ function termdb_test_default() {
           ]
         },
         geneExpression: {
-          src: "native",
           folder: "files/hg38/TermdbTest/scrna/geneExpHdf5"
         }
       },

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.198.0",
+  "version": "2.200.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -36,7 +36,6 @@
   "license": "SEE LICENSE IN ./LICENSE",
   "devDependencies": {
     "@babel/core": "^7.9.6",
-    "@babel/plugin-proposal-optional-chaining": "^7.9.0",
     "@babel/plugin-transform-runtime": "^7.14.5",
     "@babel/preset-env": "^7.9.6",
     "@babel/preset-typescript": "^7.21.4",
@@ -59,11 +58,11 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.190.0",
-    "@sjcrh/proteinpaint-python": "2.196.0",
-    "@sjcrh/proteinpaint-r": "2.197.0",
+    "@sjcrh/proteinpaint-python": "2.199.0",
+    "@sjcrh/proteinpaint-r": "2.199.0",
     "@sjcrh/proteinpaint-rust": "2.198.0",
-    "@sjcrh/proteinpaint-shared": "2.198.0",
-    "@sjcrh/proteinpaint-types": "2.198.0",
+    "@sjcrh/proteinpaint-shared": "2.200.0",
+    "@sjcrh/proteinpaint-types": "2.200.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",
@@ -103,7 +102,6 @@
     "start.js",
     "src/app.js",
     "src/serverconfig.js",
-    "src/mds3.gdc.filter.js",
     "src/checkReadingFrame.js",
     "src/bedj.parseBed.js",
     "LICENSE/*"

package/routes/profile.impressionDistribution.js

@@ -0,0 +1,176 @@
+import { getData } from "../src/termdb.matrix.js";
+const api = {
+  endpoint: "termdb/profileImpressionDistribution",
+  methods: {
+    get: {
+      init,
+      request: { typeId: "ProfileImpressionDistributionRequest" },
+      response: { typeId: "ProfileImpressionDistributionResponse" }
+    },
+    post: {
+      init,
+      request: { typeId: "ProfileImpressionDistributionRequest" },
+      response: { typeId: "ProfileImpressionDistributionResponse" }
+    }
+  }
+};
+function init({ genomes }) {
+  return async (req, res) => {
+    try {
+      const g = genomes[req.query.genome];
+      if (!g) throw "invalid genome name";
+      const ds = g.datasets?.[req.query.dslabel];
+      const result = await getDistribution(req.query, ds);
+      res.send(result);
+    } catch (e) {
+      console.log(e);
+      res.send({ status: "error", error: e.message || e });
+    }
+  };
+}
+function derivePrefix(query) {
+  const id = query.scTermId || query.pocTermId;
+  if (id?.startsWith("F")) return "F";
+  if (id?.startsWith("A")) return "A";
+  for (const entry of query.filter?.lst || []) {
+    const fid = entry.tvs?.term?.id;
+    if (fid?.startsWith("F")) return "F";
+    if (fid?.startsWith("A")) return "A";
+  }
+  throw "cannot determine cohort prefix from request term IDs";
+}
+async function getDistribution(query, ds) {
+  const { activeCohort, clientAuthResult } = query.__protected__;
+  const prefix = derivePrefix(query);
+  const facilityTermId = `${prefix}UNIT`;
+  const facilityTW = { term: { id: facilityTermId }, q: {} };
+  const scTW = { term: { id: query.scTermId }, q: { mode: "continuous" } };
+  const pocTW = query.pocTermId ? { term: { id: query.pocTermId }, q: { mode: "continuous" } } : null;
+  const responderTWs = (query.pocResponderTermIds || []).map((id) => ({ term: { id }, q: {} }));
+  const maxScore = Number(query.maxScore) || 10;
+  if (!query.filterByUserSites) {
+    query.__protected__.ignoredTermIds.push(facilityTermId);
+  }
+  const cohortAuth = clientAuthResult[activeCohort];
+  const isPublic = !cohortAuth?.role || cohortAuth.role === "public";
+  const userSites = cohortAuth?.sites;
+  const terms = [facilityTW, scTW];
+  if (pocTW) terms.push(pocTW);
+  for (const tw of responderTWs) terms.push(tw);
+  const raw = await getData(
+    {
+      terms,
+      filter: query.filter,
+      __protected__: query.__protected__
+    },
+    ds
+  );
+  if (raw.error) throw raw.error;
+  const sampleList = Object.values(raw.samples);
+  let sites = [];
+  if (!isPublic) {
+    for (const s of sampleList) {
+      const cell = s[facilityTW.$id];
+      if (!cell) continue;
+      const val = cell.value;
+      let label = facilityTW.term.values?.[val]?.label || val;
+      if (typeof label === "string" && label.length > 50) label = label.slice(0, 47) + "...";
+      sites.push({ value: val, label });
+    }
+    if (userSites && query.filterByUserSites) sites = sites.filter((s) => userSites.includes(s.value));
+    sites.sort((a, b) => a.label.localeCompare(b.label));
+  }
+  const eligibleSamples = userSites && query.filterByUserSites ? sampleList.filter((s) => userSites.includes(s[facilityTW.$id]?.value)) : sampleList;
+  const scValues = collectScalarValues(eligibleSamples, scTW.$id);
+  const responders = responderTWs.map((tw) => {
+    const values = collectResponderRatings(eligibleSamples, [tw.$id]);
+    return {
+      termId: tw.term.id,
+      label: responderLabel(tw.term?.name, tw.term.id),
+      median: median(values),
+      total: values.length,
+      distribution: buildDistribution(values, maxScore)
+    };
+  });
+  if (!responders.length && pocTW) {
+    const values = collectScalarValues(eligibleSamples, pocTW.$id);
+    responders.push({
+      termId: pocTW.term.id,
+      label: "POC Staff",
+      median: median(values),
+      total: values.length,
+      distribution: buildDistribution(values, maxScore)
+    });
+  }
+  return {
+    scMedian: median(scValues),
+    scTotal: scValues.length,
+    // Shared SC frequency distribution (site counts binned per rating), used for the SC line
+    // on the response-distribution chart. Same across every responder group's chart pair.
+    scDistribution: buildDistribution(scValues, maxScore),
+    responders,
+    sites: isPublic ? [] : sites,
+    n: eligibleSamples.length
+  };
+}
+function responderLabel(name, id) {
+  if (!name) return id;
+  const stripped = name.replace(/^Impression\s+/i, "").trim();
+  return stripped || name;
+}
+function collectScalarValues(samples, $id) {
+  const out = [];
+  for (const s of samples) {
+    const cell = s[$id];
+    if (!cell || cell.value == null) continue;
+    const n = Number(cell.value);
+    if (Number.isFinite(n)) out.push(n);
+  }
+  return out;
+}
+function collectResponderRatings(samples, $ids) {
+  const out = [];
+  for (const s of samples) {
+    for (const $id of $ids) {
+      const cell = s[$id];
+      if (!cell || cell.value == null) continue;
+      const map = typeof cell.value === "string" ? JSON.parse(cell.value) : cell.value;
+      for (const [rating, count] of Object.entries(map)) {
+        const r = Number(rating);
+        const c = Number(count);
+        if (Number.isFinite(r) && Number.isFinite(c)) for (let i = 0; i < c; i++) out.push(r);
+      }
+    }
+  }
+  return out;
+}
+function median(values) {
+  if (values.length === 0) return null;
+  const sorted = [...values].sort((a, b) => a - b);
+  const mid = Math.floor(sorted.length / 2);
+  const m = sorted.length % 2 !== 0 ? sorted[mid] : (sorted[mid - 1] + sorted[mid]) / 2;
+  return Math.round(m);
+}
+function buildDistribution(values, maxScore) {
+  const total = values.length;
+  const counts = {};
+  for (let r = 1; r <= maxScore; r++) counts[r] = 0;
+  for (const v of values) {
+    const r = Math.round(v);
+    if (r >= 1 && r <= maxScore) counts[r] += 1;
+  }
+  const out = [];
+  for (let r = 1; r <= maxScore; r++) {
+    const count = counts[r];
+    const pct = total > 0 ? count / total * 100 : 0;
+    out.push({ rating: r, count, pct: Math.round(pct * 10) / 10 });
+  }
+  return out;
+}
+export {
+  api,
+  buildDistribution,
+  collectResponderRatings,
+  collectScalarValues,
+  median
+};

package/routes/termdb.proteome.js

@@ -264,7 +264,7 @@ async function validate_query_proteome(ds) {
             throw `Missing controlFilter in queries.proteome.organisms.${organismName}.assays.${assayName}.cohorts.${cohortName}`;
           if (!cohort.caseFilter)
             throw `Missing caseFilter in queries.proteome.organisms.${organismName}.assays.${assayName}.cohorts.${cohortName}`;
-          if (!cohort.prior?.d0 || !cohort.prior?.s0sq)
+          if (!cohort.DAPfile && (!cohort.prior?.d0 || !cohort.prior?.s0sq))
             throw `Missing prior.d0 and prior.s0sq in queries.proteome.organisms.${organismName}.assays.${assayName}.cohorts.${cohortName}`;
         }
       } else {