@sjcrh/proteinpaint-server 2.204.0 → 2.205.1

package/dataset/termdb.test.js

@@ -437,10 +437,6 @@ function termdb_test_default() {
           folder: "files/hg38/TermdbTest/scrna/geneExpHdf5"
         }
       },
-      WSImages: {
-        type: "H&E",
-        imageBySampleFolder: "files/hg38/TermdbTest/wsimages"
-      },
       // w2 plot. folder: spatial images, one per subfolder of the sample's
       // directory (folder/<sample>/<imageName>/), files inside found by the
       // *FileSuffix fields. wsiFolder: plain whole-slide images, laid out as

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.204.0",
+  "version": "2.205.1",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -59,30 +59,26 @@
     "@sjcrh/augen": "2.204.0",
     "@sjcrh/proteinpaint-python": "2.204.0",
     "@sjcrh/proteinpaint-r": "2.204.0",
-    "@sjcrh/proteinpaint-rust": "2.204.0",
-    "@sjcrh/proteinpaint-shared": "2.204.0",
-    "@sjcrh/proteinpaint-types": "2.204.0",
+    "@sjcrh/proteinpaint-rust": "2.205.1",
+    "@sjcrh/proteinpaint-shared": "2.205.0",
+    "@sjcrh/proteinpaint-types": "2.205.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~3.2.0",
     "compression": "^1.6.2",
-    "connect-redis": "^6.1.3",
     "cookie-parser": "^1.4.5",
     "d3": "^7.6.1",
     "deep-object-diff": "^1.1.0",
     "express": "^4.17.1",
     "express-basic-auth": "^1.1.5",
     "express-session": "^1.18.1",
-    "got": "^14.2.0",
     "jsonwebtoken": "^9.0.3",
     "ky": "^1.2.1",
     "micromatch": "^4.0.5",
     "minimatch": "^10.0.1",
-    "node-fetch": "^2.6.1",
     "partjson": "^0.58.2",
-    "redis": "^4.7.0",
     "skia-canvas": "~3.0.8",
     "tiny-async-pool": "^1.2.0",
     "tough-cookie": "^4.1.4"

package/routes/termdb.diffMeth.js

@@ -20,9 +20,9 @@ function init({ genomes }) {
         res.send({
           data: {
             [group1Name]: groups.group1names.length,
-            [group2Name]: groups.group2names.length,
-            ...groups.alerts.length ? { alert: groups.alerts.join(" | ") } : {}
-          }
+            [group2Name]: groups.group2names.length
+          },
+          ...groups.alerts.length ? { alert: groups.alerts.join(" | ") } : {}
         });
         return;
       }

package/routes/termdb.proteome.js

@@ -1,13 +1,22 @@
+import path from "path";
 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 "";
-  const parts = acc.split("|");
-  const id = parts.length >= 2 ? parts[1] : acc;
-  const dash = id.indexOf("-");
-  return dash > 0 ? id.slice(0, dash) : id;
+  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;
 }
+const missingDapWarned = /* @__PURE__ */ new Set();
 function init({ genomes }) {
   return async (req, res) => {
     const q = req.query;
@@ -15,63 +24,99 @@ function init({ genomes }) {
       const genome = genomes[q.genome];
       if (!genome) throw "invalid genome";
       const [ds] = get_ds_tdb(genome, q);
-      if (!ds.queries?.proteome?.get) throw "queries.proteome.get() missing";
+      if (!ds.queries?.proteome?.organisms) throw "queries.proteome not configured";
       const term = q.term?.term || q.term;
       if (!term?.name) throw "term.name missing";
       const cohorts = [];
       const brConfig = ds.queries.proteome.brainRegions;
       const regionRemap = brConfig?.regionValueRemap || {};
       const sampleRegions = {};
+      const identifierAnno = /* @__PURE__ */ new Map();
       for (const organismName in ds.queries.proteome.organisms) {
         const organism = ds.queries.proteome.organisms[organismName];
         for (const assayName in organism.assays) {
           const assay = organism.assays[assayName];
           for (const cohortName in assay.cohorts || {}) {
-            const details = {
-              dbfile: ds.queries.proteome.dbfile,
-              organism: organismName,
-              assay: assayName,
-              cohort: cohortName
-            };
-            const tw = {
-              $id: "_",
-              term: {
-                name: term.name,
-                type: "proteomeAbundance",
-                dataTypeDetails: details
+            const cohortCfg = assay.cohorts[cohortName];
+            const dapPath = path.join(serverconfig.tpmasterdir, cohortCfg.DAPfile);
+            const rows = await readGeneRows(dapPath, String(term.name).toLowerCase());
+            if (!rows) {
+              if (!missingDapWarned.has(dapPath)) {
+                missingDapWarned.add(dapPath);
+                console.warn(
+                  `proteome: DAPfile missing or unreadable for ${organismName}/${assayName}/${cohortName}: ${dapPath}`
+                );
+              }
+              continue;
+            }
+            if (!rows.length) continue;
+            const organismFilter = [{ columnIdx: organism.columnIdx, columnValue: organism.columnValue }];
+            const assayFilter = [{ columnIdx: assay.columnIdx, columnValue: assay.columnValue }];
+            let caseSamples = [];
+            let controlSamples = [];
+            try {
+              caseSamples = listCohortSamples(ds.queries.proteome.db, [
+                ...organismFilter,
+                ...assayFilter,
+                ...cohortCfg.caseFilter
+              ]);
+              controlSamples = listCohortSamples(ds.queries.proteome.db, [
+                ...organismFilter,
+                ...assayFilter,
+                ...cohortCfg.controlFilter
+              ]);
+            } catch {
+            }
+            const annoKey = `${organismName}|${assayName}`;
+            if (!identifierAnno.has(annoKey)) {
+              let m = /* @__PURE__ */ new Map();
+              try {
+                m = listIdentifierAnnotations(ds.queries.proteome.db, term.name, [...organismFilter, ...assayFilter]);
+              } catch {
+              }
+              identifierAnno.set(annoKey, m);
+            }
+            const anno = identifierAnno.get(annoKey);
+            const sampleIds = brConfig ? [...caseSamples, ...controlSamples] : [];
+            if (brConfig) {
+              const regionOf = (filters) => {
+                const f = filters.find((f2) => f2.columnIdx === brConfig.regionColumnIdx);
+                if (!f) return void 0;
+                const code = regionRemap[String(f.columnValue)] ?? String(f.columnValue);
+                return brConfig.regions[code] !== void 0 ? code : void 0;
+              };
+              const caseRegion = regionOf(cohortCfg.caseFilter);
+              const controlRegion = regionOf(cohortCfg.controlFilter);
+              if (caseRegion) for (const sid of caseSamples) sampleRegions[sid] = caseRegion;
+              if (controlRegion) for (const sid of controlSamples) sampleRegions[sid] = controlRegion;
+            }
+            for (const row of rows) {
+              const entry = {
+                organism: organismName,
+                assayName,
+                cohortName,
+                uniqueIdentifier: row.identifier,
+                proteinAccession: row.acc,
+                geneName: term.name,
+                // 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.
+                fdr: row.fdr,
+                pValue: row.fdr,
+                testedN: caseSamples.length,
+                controlN: controlSamples.length
+              };
+              const a = anno.get(row.identifier);
+              if (a?.isoform) entry.isoform = a.isoform;
+              if (assay.PTMType) {
+                entry.PTMType = assay.PTMType;
+                if (a?.modsite) entry.modSites = a.modsite;
               }
-            };
-            const cohortData = await ds.queries.proteome.get({
-              terms: [tw],
-              dataTypeDetails: details,
-              filter: q.filter,
-              filter0: q.filter0,
-              for: "proteinView",
-              __abortSignal: q.__abortSignal
-            });
-            const controlSampleIds = cohortData.controlSampleIds || /* @__PURE__ */ new Set();
-            const prior = assay.cohorts[cohortName].prior;
-            for (const entry of cohortData.allEntries || []) {
-              const s2v = entry.s2v;
-              const sampleRegionsRaw = entry.sampleRegionsRaw || {};
-              const stats = getCohortStats(s2v, controlSampleIds, prior);
-              delete entry.s2v;
-              delete entry.sampleRegionsRaw;
-              entry.foldChange = stats.foldChange;
-              entry.pValue = stats.pValue;
-              entry.testedN = stats.testedN;
-              entry.controlN = stats.controlN;
               if (assay.mclassOverride) entry.mclassOverride = assay.mclassOverride;
               if (organism.genomeName) entry.genomeName = organism.genomeName;
-              if (brConfig) {
-                entry.sampleIds = Object.keys(s2v);
-                for (const sid in sampleRegionsRaw) {
-                  const raw = sampleRegionsRaw[sid];
-                  if (raw == null) continue;
-                  const code = regionRemap[String(raw)] ?? String(raw);
-                  if (brConfig.regions[code] !== void 0) sampleRegions[sid] = code;
-                }
-              }
+              if (brConfig) entry.sampleIds = sampleIds.slice();
               cohorts.push(entry);
             }
           }
@@ -104,133 +149,6 @@ function init({ genomes }) {
     }
   };
 }
-function getCohortStats(allS2v, controlSampleIds, prior) {
-  if (!allS2v || typeof allS2v != "object") return { foldChange: null, pValue: null, testedN: 0, controlN: 0 };
-  const controlValues = [];
-  const testedValues = [];
-  for (const sampleId in allS2v) {
-    const v = Number(allS2v[sampleId]);
-    if (!Number.isFinite(v)) continue;
-    if (controlSampleIds.has(String(sampleId))) controlValues.push(v);
-    else testedValues.push(v);
-  }
-  const controlMean = controlValues?.length ? controlValues.reduce((sum, v) => sum + v, 0) / controlValues.length : null;
-  const testedMean = testedValues?.length ? testedValues.reduce((sum, v) => sum + v, 0) / testedValues.length : null;
-  const foldChange = testedMean != null && controlMean != null && Number.isFinite(testedMean) && Number.isFinite(controlMean) && controlMean !== 0 ? testedMean / controlMean : null;
-  if (!Number.isFinite(prior?.d0) || prior.d0 <= 0 || !Number.isFinite(prior?.s0sq) || prior.s0sq <= 0) {
-    throw "prior with finite positive d0 and s0sq is required for moderated t-test";
-  }
-  const pValue = getModeratedPValue(testedValues, controlValues, prior);
-  return {
-    foldChange,
-    pValue,
-    testedN: testedValues.length,
-    controlN: controlValues.length
-  };
-}
-function getModeratedPValue(a, b, prior) {
-  const n1 = a.length;
-  const n2 = b.length;
-  if (n1 < 2 || n2 < 2) return null;
-  const mean1 = a.reduce((s, v) => s + v, 0) / n1;
-  const mean2 = b.reduce((s, v) => s + v, 0) / n2;
-  let ss1 = 0;
-  for (const v of a) {
-    const d = v - mean1;
-    ss1 += d * d;
-  }
-  let ss2 = 0;
-  for (const v of b) {
-    const d = v - mean2;
-    ss2 += d * d;
-  }
-  const dfResidual = n1 + n2 - 2;
-  const pooledVar = (ss1 + ss2) / dfResidual;
-  const { d0, s0sq } = prior;
-  const sTildeSq = (d0 * s0sq + dfResidual * pooledVar) / (d0 + dfResidual);
-  const se = Math.sqrt(sTildeSq * (1 / n1 + 1 / n2));
-  if (!(se > 0)) {
-    if (mean1 === mean2) return 1;
-    return 1e-300;
-  }
-  const t = (mean1 - mean2) / se;
-  const df = d0 + dfResidual;
-  if (!Number.isFinite(df) || df < 0.1) return null;
-  const p = 2 * tCdfTail(Math.abs(t), df);
-  if (!Number.isFinite(p)) return null;
-  return Math.max(1e-300, Math.min(1, p));
-}
-function tCdfTail(t, df) {
-  const x = df / (df + t * t);
-  return 0.5 * regularizedBetaIncomplete(df / 2, 0.5, x);
-}
-function regularizedBetaIncomplete(a, b, x) {
-  if (x <= 0) return 0;
-  if (x >= 1) return 1;
-  if (x > (a + 1) / (a + b + 2)) {
-    return 1 - regularizedBetaIncomplete(b, a, 1 - x);
-  }
-  const lnPrefactor = lnBetaPrefactor(a, b, x);
-  const maxIter = 200;
-  const eps = 1e-14;
-  let f = 1e-30;
-  let C = 1e-30;
-  let D = 0;
-  for (let m = 0; m <= maxIter; m++) {
-    let numerator;
-    if (m === 0) {
-      numerator = 1;
-    } else {
-      const k = m;
-      if (k % 2 === 1) {
-        const i = (k - 1) / 2;
-        numerator = -(a + i) * (a + b + i) * x / ((a + 2 * i) * (a + 2 * i + 1));
-      } else {
-        const i = k / 2;
-        numerator = i * (b - i) * x / ((a + 2 * i - 1) * (a + 2 * i));
-      }
-    }
-    D = 1 + numerator * D;
-    if (Math.abs(D) < 1e-30) D = 1e-30;
-    D = 1 / D;
-    C = 1 + numerator / C;
-    if (Math.abs(C) < 1e-30) C = 1e-30;
-    const delta = C * D;
-    f *= delta;
-    if (m > 0 && Math.abs(delta - 1) < eps) break;
-  }
-  return Math.exp(lnPrefactor) * f / a;
-}
-function lnBetaPrefactor(a, b, x) {
-  return a * Math.log(x) + b * Math.log(1 - x) - lnBeta(a, b);
-}
-function lnBeta(a, b) {
-  return lnGamma(a) + lnGamma(b) - lnGamma(a + b);
-}
-function lnGamma(z) {
-  if (z < 0.5) {
-    return Math.log(Math.PI / Math.sin(Math.PI * z)) - lnGamma(1 - z);
-  }
-  z -= 1;
-  const g = 7;
-  const coef = [
-    0.9999999999998099,
-    676.5203681218851,
-    -1259.1392167224028,
-    771.3234287776531,
-    -176.6150291621406,
-    12.507343278686905,
-    -0.13857109526572012,
-    9984369578019572e-21,
-    15056327351493116e-23
-  ];
-  let x = coef[0];
-  for (let i = 1; i < coef.length; i++) {
-    x += coef[i] / (z + i);
-  }
-  const t = z + g + 0.5;
-  return 0.5 * Math.log(2 * Math.PI) + (z + 0.5) * Math.log(t) - t + Math.log(x);
-}
 async function validate_query_proteome(ds) {
   const q = ds.queries.proteome;
   if (!q) return;
@@ -264,14 +182,15 @@ 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.${cohortName}`;
-          if (!cohort.DAPfile && (!cohort.prior?.d0 || !cohort.prior?.s0sq))
-            throw `Missing prior.d0 and prior.s0sq in queries.proteome.organisms.${organismName}.assays.${assayName}.cohorts.${cohortName}`;
+          if (!cohort.DAPfile)
+            throw `Missing DAPfile in queries.proteome.organisms.${organismName}.assays.${assayName}.cohorts.${cohortName}`;
         }
       } else {
         throw `Invalid assay structure for "${assayName}". Must have .cohorts`;
       }
     }
   }
+  const geneIndexHint = q.db.prepare(`SELECT 1 FROM sqlite_master WHERE type = 'index' AND name = 'proteome_abundance_gene'`).get() ? " INDEXED BY proteome_abundance_gene" : "";
   q.find = async (arg) => {
     const proteins = arg?.proteins;
     if (!Array.isArray(proteins) || proteins.length == 0) throw "queries.proteome.find arg.proteins[] missing";
@@ -307,7 +226,7 @@ async function validate_query_proteome(ds) {
       const rawRows = [];
       if (filters?.length) {
         const { conditions, params } = buildFilterClause(filters);
-        const sql = `SELECT DISTINCT gene, identifier FROM proteome_abundance WHERE gene >= ? COLLATE NOCASE AND gene < ? COLLATE NOCASE AND ${conditions.join(
+        const sql = `SELECT DISTINCT gene, identifier FROM proteome_abundance${geneIndexHint} WHERE gene >= ? COLLATE NOCASE AND gene < ? COLLATE NOCASE AND ${conditions.join(
           " AND "
         )} LIMIT ${MAX_FIND_RESULTS}`;
         rawRows.push(...q.db.prepare(sql).all(token, upperToken, ...params));
@@ -356,23 +275,36 @@ function buildFilterClause(filters) {
   }
   return { conditions, params };
 }
-function countDistinctSamples(db, filters) {
-  if (!filters?.length) throw "countDistinctSamples: filters must not be empty";
+function listCohortSamples(db, filters) {
+  if (!filters?.length) throw "listCohortSamples: filters must not be empty";
+  let perDb = cohortSampleCache.get(db);
+  if (!perDb) cohortSampleCache.set(db, perDb = /* @__PURE__ */ new Map());
+  const key = JSON.stringify(filters);
+  const hit = perDb.get(key);
+  if (hit) return hit;
   const { conditions, params } = buildFilterClause(filters);
-  const row = db.prepare(`SELECT COUNT(DISTINCT sample) as cnt FROM proteome_abundance WHERE ${conditions.join(" AND ")}`).get(...params);
-  return row?.cnt || 0;
+  const samples = db.prepare(`SELECT DISTINCT sample FROM proteome_abundance WHERE ${conditions.join(" AND ")}`).all(...params).map((r) => String(r.sample));
+  perDb.set(key, samples);
+  return samples;
 }
-function queryDbRows(db, matchColumn, matchValue, filters) {
+const cohortSampleCache = /* @__PURE__ */ new WeakMap();
+function listIdentifierAnnotations(db, gene, filters) {
   const { conditions, params } = buildFilterClause(filters);
-  const allConditions = [`${matchColumn} = ? COLLATE NOCASE`, ...conditions];
+  const rows = db.prepare(
+    `SELECT identifier, modsite, isoform FROM proteome_abundance WHERE gene = ? COLLATE NOCASE${conditions.length ? " AND " + conditions.join(" AND ") : ""} GROUP BY identifier`
+  ).all(gene, ...params);
+  return new Map(rows.map((r) => [r.identifier, { modsite: r.modsite, isoform: r.isoform }]));
+}
+function queryDbRows(db, identifier, filters) {
+  const { conditions, params } = buildFilterClause(filters);
+  const allConditions = [`identifier = ? COLLATE NOCASE`, ...conditions];
   const sql = `SELECT organism, disease, identifier, protein_accession, isoform, modsite, gene, sample, value, brain_region
 		FROM proteome_abundance
 		WHERE ${allConditions.join(" AND ")}`;
-  return db.prepare(sql).all(matchValue, ...params);
+  return db.prepare(sql).all(identifier, ...params);
 }
 async function getProteomeValuesFromCohort(ds, param, q) {
   const db = ds.queries.proteome.db;
-  const hasBrainRegions = !!q.brainRegions;
   const { assay, cohort, organism } = param.dataTypeDetails;
   const organismConfig = q.organisms?.[organism];
   if (!organismConfig) throw `queries.proteome invalid organism: ${organism}`;
@@ -380,7 +312,6 @@ async function getProteomeValuesFromCohort(ds, param, q) {
   const organismColumnValue = organismConfig.columnValue;
   const assayConfig = organismConfig.assays?.[assay];
   if (!assayConfig) throw `queries.proteome.get invalid assay: ${assay}`;
-  const PTMType = assayConfig.PTMType;
   const assayColumnIdx = assayConfig.columnIdx;
   const assayColumnValue = assayConfig.columnValue;
   const cohortConfig = assayConfig?.cohorts?.[cohort];
@@ -390,27 +321,16 @@ async function getProteomeValuesFromCohort(ds, param, q) {
   const organismFilter = [{ columnIdx: organismColumnIdx, columnValue: organismColumnValue }];
   const assayFilter = [{ columnIdx: assayColumnIdx, columnValue: assayColumnValue }];
   const term2sample2value = /* @__PURE__ */ new Map();
-  const allEntries = [];
   const controlSampleIds = /* @__PURE__ */ new Set();
   for (const tw of param.terms) {
     if (!tw) continue;
     const fullGeneName = tw.term.name;
     const identifier = fullGeneName.split(":")[1]?.trim();
     const geneName = fullGeneName.split(":")[0]?.trim();
-    if (param.for === "proteinView") {
-      if (!geneName) throw "invalid term name for proteome query, gene name missing";
-    } else {
-      if (!identifier || !geneName)
-        throw "invalid term name for proteome query, must be in format geneName: uniqueIdentifier";
-    }
-    const matchColumn = param.for === "proteinView" ? "gene" : "identifier";
-    const matchValue = param.for === "proteinView" ? geneName : identifier;
-    const caseRows = queryDbRows(db, matchColumn, matchValue, [...organismFilter, ...assayFilter, ...cohortCaseFilter]);
-    const controlRows = queryDbRows(db, matchColumn, matchValue, [
-      ...organismFilter,
-      ...assayFilter,
-      ...cohortControlFilter
-    ]);
+    if (!identifier || !geneName)
+      throw "invalid term name for proteome query, must be in format geneName: uniqueIdentifier";
+    const caseRows = queryDbRows(db, identifier, [...organismFilter, ...assayFilter, ...cohortCaseFilter]);
+    const controlRows = queryDbRows(db, identifier, [...organismFilter, ...assayFilter, ...cohortControlFilter]);
     for (const row of controlRows) {
       const sid = ds.cohort.termdb.q.sampleName2id(row.sample);
       if (sid !== void 0) controlSampleIds.add(String(sid));
@@ -426,59 +346,18 @@ async function getProteomeValuesFromCohort(ds, param, q) {
     if (allowedSampleIds?.size == 0) {
       return { term2sample2value: /* @__PURE__ */ new Map(), byTermId: {}, bySampleId: {} };
     }
-    if (param.for === "proteinView") {
-      const entryMap = /* @__PURE__ */ new Map();
-      for (const row of allRows) {
-        const sid = ds.cohort.termdb.q.sampleName2id(row.sample);
-        if (sid === void 0) continue;
-        if (allowedSampleIds && !allowedSampleIds.has(sid)) continue;
-        if (!entryMap.has(row.identifier)) {
-          entryMap.set(row.identifier, {
-            organism: row.organism,
-            disease: row.disease,
-            uniqueIdentifier: row.identifier,
-            assayName: assay,
-            cohortName: cohort,
-            PTMType,
-            modSites: PTMType ? row.modsite || void 0 : void 0,
-            proteinAccession: row.protein_accession,
-            isoform: row.isoform,
-            // refSeq transcript ID mapped from protein_accession
-            geneName: row.gene,
-            s2v: {},
-            // raw brain_region per sample id (only when brainRegions is configured);
-            // remapped + finalized into entry.sampleRegions in the route's init().
-            sampleRegionsRaw: hasBrainRegions ? {} : void 0
-          });
-        }
-        entryMap.get(row.identifier).s2v[sid] = row.value;
-        if (hasBrainRegions) entryMap.get(row.identifier).sampleRegionsRaw[sid] = row.brain_region;
-      }
-      for (const entry of entryMap.values()) allEntries.push(entry);
-    } else {
-      const s2v = {};
-      for (const row of allRows) {
-        const sid = ds.cohort.termdb.q.sampleName2id(row.sample);
-        if (sid === void 0) continue;
-        if (allowedSampleIds && !allowedSampleIds.has(sid)) continue;
-        s2v[sid] = row.value;
-      }
-      if (Object.keys(s2v).length) {
-        term2sample2value.set(tw.$id, s2v);
-      }
-    }
-  }
-  const bySampleId = {};
-  if (param.for === "proteinView") {
-    const sampleIds = /* @__PURE__ */ new Set();
-    for (const entry of allEntries) {
-      for (const sid of Object.keys(entry.s2v)) sampleIds.add(Number(sid));
+    const s2v = {};
+    for (const row of allRows) {
+      const sid = ds.cohort.termdb.q.sampleName2id(row.sample);
+      if (sid === void 0) continue;
+      if (allowedSampleIds && !allowedSampleIds.has(sid)) continue;
+      s2v[sid] = row.value;
     }
-    for (const sid of sampleIds) {
-      bySampleId[sid] = { label: ds.cohort.termdb.q.id2sampleName(sid) };
+    if (Object.keys(s2v).length) {
+      term2sample2value.set(tw.$id, s2v);
     }
-    return { allEntries, controlSampleIds, bySampleId };
   }
+  const bySampleId = {};
   if (term2sample2value.size == 0) {
     throw `No data available for: ${param.terms?.map((t) => t.term.name).join(", ")}`;
   }
@@ -490,9 +369,9 @@ async function getProteomeValuesFromCohort(ds, param, q) {
   return { term2sample2value, controlSampleIds, bySampleId };
 }
 export {
-  countDistinctSamples,
-  getCohortStats,
   init,
+  listCohortSamples,
+  listIdentifierAnnotations,
   queryDbRows,
   validate_query_proteome
 };