@sjcrh/proteinpaint-server 2.205.1 → 2.206.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.205.1",
+  "version": "2.206.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -59,9 +59,9 @@
     "@sjcrh/augen": "2.204.0",
     "@sjcrh/proteinpaint-python": "2.204.0",
     "@sjcrh/proteinpaint-r": "2.204.0",
-    "@sjcrh/proteinpaint-rust": "2.205.1",
-    "@sjcrh/proteinpaint-shared": "2.205.0",
-    "@sjcrh/proteinpaint-types": "2.205.0",
+    "@sjcrh/proteinpaint-rust": "2.206.0",
+    "@sjcrh/proteinpaint-shared": "2.206.0",
+    "@sjcrh/proteinpaint-types": "2.206.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",

package/routes/termdb.geneRanking.js

@@ -26,7 +26,7 @@ function stripQuotes(s) {
 async function parseTsv(absPath) {
   const text = await fs.promises.readFile(absPath, "utf8");
   const lines = text.split(/\r?\n/).filter((l) => l.length > 0);
-  if (lines.length === 0) return { columns: [], rows: [] };
+  if (lines.length === 0) return { columns: [], rows: [], counts: [], geneIndex: /* @__PURE__ */ new Map() };
   const columns = lines[0].split("	").map(stripQuotes);
   const rows = [];
   for (let i = 1; i < lines.length; i++) {
@@ -39,7 +39,17 @@ async function parseTsv(absPath) {
     });
     rows.push(row);
   }
-  return { columns, rows };
+  const counts = columns.map(
+    (_, c) => c === 0 ? rows.length : rows.filter((r) => r[c] !== null && r[c] !== void 0).length
+  );
+  const geneIndex = /* @__PURE__ */ new Map();
+  for (const [i, r] of rows.entries()) {
+    if (typeof r[0] === "string") {
+      const g = r[0].toLowerCase();
+      if (!geneIndex.has(g)) geneIndex.set(g, i);
+    }
+  }
+  return { columns, rows, counts, geneIndex };
 }
 function zscorePerColumnIgnoringNull(matrix, ncol) {
   const out = matrix.map((r) => [...r]);
@@ -67,24 +77,53 @@ async function handleData(q, res, genomes) {
   if (!ds) throw "invalid dslabel";
   const cfg = ds.queries?.geneRanking;
   if (!cfg || !cfg.rankings) throw "geneRanking not configured for this dataset";
+  if (q.gene) {
+    const wanted = String(q.gene).trim().toLowerCase();
+    const geneRanks = {};
+    const keys = Object.keys(cfg.rankings);
+    const loaded = await Promise.all(
+      keys.map(
+        (key) => loadRanking(q, cfg.rankings[key], key).catch((e) => {
+          console.log(`geneRanking: cannot load ranking "${key}": ${e?.message || e}`);
+          return null;
+        })
+      )
+    );
+    for (const [i, parsed2] of loaded.entries()) {
+      if (!parsed2) continue;
+      const ri = parsed2.geneIndex.get(wanted);
+      geneRanks[keys[i]] = {
+        columns: parsed2.columns,
+        row: ri === void 0 ? null : parsed2.rows[ri],
+        counts: parsed2.counts,
+        total: parsed2.rows.length
+      };
+    }
+    res.send({ geneRanks });
+    return;
+  }
   if (!q.key) {
     res.send({ keys: Object.keys(cfg.rankings) });
     return;
   }
   const relPath = cfg.rankings[q.key];
   if (!relPath) throw "invalid key";
+  const parsed = await loadRanking(q, relPath, q.key);
+  res.send({ columns: parsed.columns, rows: parsed.rows });
+}
+async function loadRanking(q, relPath, key) {
   if (path.isAbsolute(relPath) || relPath.split(/[\\/]/).includes("..")) throw "invalid file path";
   const absPath = path.resolve(serverconfig.tpmasterdir, relPath);
   const tpRoot = path.resolve(serverconfig.tpmasterdir) + path.sep;
   if (!absPath.startsWith(tpRoot)) throw "invalid file path";
   const stat = await fs.promises.stat(absPath);
-  const cacheKey = `${q.genome}|${q.dslabel}|${q.key}`;
+  const cacheKey = `${q.genome}|${q.dslabel}|${key}`;
   let entry = fileCache.get(cacheKey);
   if (!entry || entry.mtimeMs !== stat.mtimeMs) {
     entry = { parsed: await parseTsv(absPath), mtimeMs: stat.mtimeMs };
     fileCache.set(cacheKey, entry);
   }
-  res.send({ columns: entry.parsed.columns, rows: entry.parsed.rows });
+  return entry.parsed;
 }
 async function handleCluster(q, res) {
   const { row_names, col_names } = q;

package/routes/termdb.proteome.js

@@ -3,19 +3,7 @@ import { get_ds_tdb } from "#src/termdb.js";
 import * as utils from "#src/utils.js";
 import { mayLimitSamples } from "#src/mds3.filter.js";
 import serverconfig from "#src/serverconfig.js";
-import { readGeneRows } from "../src/routes/termdb.bubbleHeatmap.ts";
-function baseUniProtAcc(acc) {
-  if (!acc) return "";
-  if (acc.includes("|")) {
-    const parts2 = acc.split("|");
-    const id = parts2.length >= 2 ? parts2[1] : acc;
-    const dash = id.indexOf("-");
-    return dash > 0 ? id.slice(0, dash) : id;
-  }
-  const parts = acc.split(".");
-  if (parts.length >= 3 && (parts[0] === "sp" || parts[0] === "tr")) return parts[1];
-  return acc;
-}
+import { readGeneRows, baseUniProtAcc } from "../src/routes/termdb.bubbleHeatmap.ts";
 const missingDapWarned = /* @__PURE__ */ new Set();
 function init({ genomes }) {
   return async (req, res) => {
@@ -93,6 +81,8 @@ function init({ genomes }) {
             for (const row of rows) {
               const entry = {
                 organism: organismName,
+                // the study catalog (dataset config) is the authority on disease
+                disease: cohortCfg.catalog?.disease,
                 assayName,
                 cohortName,
                 uniqueIdentifier: row.identifier,
@@ -101,8 +91,8 @@ function init({ genomes }) {
                 // client computes log2(foldChange); DAP stores log2FC directly
                 foldChange: Math.pow(2, row.fc),
                 // significance is the DAP file's FDR (BH-adjusted p), consistent with
-                // the other DAP-driven tools. pValue is a deprecated alias of fdr kept
-                // for existing clients; new code should read fdr.
+                // the other DAP-driven tools; a nominal p is only present when the
+                // DAP file carries one (6th column)
                 fdr: row.fdr,
                 pValue: row.fdr,
                 testedN: caseSamples.length,
@@ -130,7 +120,7 @@ function init({ genomes }) {
           const baseAcc = baseUniProtAcc(e.proteinAccession);
           if (!baseAcc) continue;
           const key = `${e.organism}|${e.cohortName}|${baseAcc}`;
-          const p = Number.isFinite(e.pValue) ? e.pValue : Infinity;
+          const p = Number.isFinite(e.fdr) ? e.fdr : Infinity;
           const cur = refFcByKey.get(key);
           if (!cur || p < cur.p) refFcByKey.set(key, { fc: e.foldChange, p });
         }