@sjcrh/proteinpaint-server 2.180.1 → 2.181.1

package/dataset/termdb.test.js

@@ -60,7 +60,9 @@ function termdb_test_default() {
                   }
                 }
               ]
-            }
+            },
+            /** Test by commenting out cohort.termdb.cohort.termdb.selectCohort */
+            html: "<div>Demo HTML Tab Content</div>"
           }
         }
       },
@@ -383,6 +385,10 @@ function termdb_test_default() {
         file: "files/hg38/TermdbTest/rnaseq/TermdbTest.fpkm.matrix.new.h5",
         unit: "FPKM"
       },
+      isoformExpression: {
+        file: "files/hg38/TermdbTest/rnaseq/TermdbTest.isoform.tpm.h5",
+        unit: "TPM"
+      },
       ssGSEA: {
         file: "files/hg38/TermdbTest/rnaseq/TermdbTest.ssgsea.h5"
       },

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.180.1",
+  "version": "2.181.1",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -61,12 +61,12 @@
     "typescript": "^5.6.3"
   },
   "dependencies": {
-    "@sjcrh/augen": "2.143.0",
-    "@sjcrh/proteinpaint-python": "2.179.0",
-    "@sjcrh/proteinpaint-r": "2.180.1-0",
-    "@sjcrh/proteinpaint-rust": "2.180.1-0",
-    "@sjcrh/proteinpaint-shared": "2.180.1",
-    "@sjcrh/proteinpaint-types": "2.180.1",
+    "@sjcrh/augen": "2.181.1",
+    "@sjcrh/proteinpaint-python": "2.181.0",
+    "@sjcrh/proteinpaint-r": "2.181.0",
+    "@sjcrh/proteinpaint-rust": "2.181.0",
+    "@sjcrh/proteinpaint-shared": "2.181.0",
+    "@sjcrh/proteinpaint-types": "2.181.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",

package/routes/profile.polar2.js

@@ -0,0 +1,101 @@
+import { ProfileScoresPayload } from "#types/checkers";
+import { getData } from "../src/termdb.matrix.js";
+const api = {
+  endpoint: "termdb/profilePolar2Scores",
+  methods: {
+    get: {
+      ...ProfileScoresPayload,
+      init
+    },
+    post: {
+      ...ProfileScoresPayload,
+      init
+    }
+  }
+};
+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 getScores(req.query, ds);
+      res.send(result);
+    } catch (e) {
+      console.log(e);
+      res.send({ status: "error", error: e.message || e });
+    }
+  };
+}
+function derivePrefix(query) {
+  const firstScoreId = query.scoreTerms?.[0]?.score?.term?.id;
+  if (firstScoreId?.startsWith("F")) return "F";
+  if (firstScoreId?.startsWith("A")) return "A";
+  for (const entry of query.filter?.lst || []) {
+    const id = entry.tvs?.term?.id;
+    if (id?.startsWith("F")) return "F";
+    if (id?.startsWith("A")) return "A";
+  }
+  throw "cannot determine cohort prefix from scoreTerms or filter term IDs";
+}
+async function getScores(query, ds) {
+  const { activeCohort, clientAuthResult } = query.__protected__;
+  const prefix = derivePrefix(query);
+  const facilityTermId = `${prefix}UNIT`;
+  const facilityTW = { term: { id: facilityTermId }, q: {} };
+  const terms = [facilityTW];
+  for (const t of query.scoreTerms) {
+    terms.push(t.score);
+    if (t.maxScore?.term) terms.push(t.maxScore);
+  }
+  if (!query.filterByUserSites) {
+    query.__protected__.ignoredTermIds.push(facilityTermId);
+  }
+  const cohortAuth = clientAuthResult[activeCohort];
+  const isPublic = !cohortAuth?.role || cohortAuth.role === "public";
+  const userSites = cohortAuth?.sites;
+  const raw = await getData(
+    {
+      terms,
+      filter: query.filter,
+      __protected__: query.__protected__
+    },
+    ds
+  );
+  if (raw.error) throw raw.error;
+  const sampleList = Object.values(raw.samples);
+  let sites = sampleList.map((s) => {
+    const val = s[facilityTW.$id].value;
+    let label = facilityTW.term.values?.[val]?.label || val;
+    if (label.length > 50) label = label.slice(0, 47) + "...";
+    return { 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 samples = Object.values(raw.samples);
+  const eligibleSamples = userSites && query.filterByUserSites ? samples.filter((s) => userSites.includes(s[facilityTW.$id].value)) : samples;
+  const term2Score = {};
+  for (const d of query.scoreTerms) {
+    const score = computeMedianPercentage(d, eligibleSamples);
+    if (score !== null) term2Score[d.score.term.id] = score;
+  }
+  return {
+    term2Score,
+    // Public users see only aggregated scores — do not expose site IDs or names
+    sites: isPublic ? [] : sites,
+    n: eligibleSamples.length
+  };
+}
+function computeMedianPercentage(d, samples) {
+  const percentages = samples.filter((s) => s[d.score.$id]?.value).map((s) => s[d.score.$id].value / (s[d.maxScore.$id]?.value || d.maxScore) * 100);
+  if (percentages.length === 0) return null;
+  percentages.sort((a, b) => a - b);
+  const mid = Math.floor(percentages.length / 2);
+  const median = percentages.length % 2 !== 0 ? percentages[mid] : (percentages[mid - 1] + percentages[mid]) / 2;
+  return Math.round(median);
+}
+export {
+  api
+};

package/routes/termdb.cluster.js

@@ -7,7 +7,7 @@ import serverconfig from "#src/serverconfig.js";
 import { gdc_validate_query_geneExpression } from "#src/mds3.gdc.js";
 import { mayLimitSamples } from "#src/mds3.filter.js";
 import { clusterMethodLst, distanceMethodLst } from "#shared/clustering.js";
-import { TermTypes, PROTEOME_ABUNDANCE } from "#shared/terms.js";
+import { TermTypes, ISOFORM_EXPRESSION, PROTEOME_ABUNDANCE } from "#shared/terms.js";
 import { termType2label } from "#shared/terms.js";
 import { formatElapsedTime } from "#shared/time.js";
 const api = {
@@ -34,7 +34,7 @@ function init({ genomes }) {
       if (!ds) throw "invalid dataset name";
       if (ds.label === "GDC" && !ds.__gdc?.doneCaching)
         throw "The server has not finished caching the case IDs: try again in about 2 minutes.";
-      if ([TermTypes.GENE_EXPRESSION, TermTypes.METABOLITE_INTENSITY].includes(q.dataType)) {
+      if ([TermTypes.GENE_EXPRESSION, ISOFORM_EXPRESSION, TermTypes.METABOLITE_INTENSITY].includes(q.dataType)) {
         if (!ds.queries?.[q.dataType]) throw `no ${q.dataType} data on this dataset`;
         if (!q.terms) throw `missing gene list`;
         if (!Array.isArray(q.terms)) throw `gene list is not an array`;
@@ -81,7 +81,7 @@ async function getResult(q, ds) {
   for (const [term, obj] of term2sample2value) {
     if (Object.keys(obj).length === 0) {
       const tw = q.terms.find((t2) => t2.$id == term);
-      const termName = !tw ? term : tw.term.type == "geneExpression" ? tw.term.gene : tw.term.name;
+      const termName = !tw ? term : tw.term.type == "geneExpression" ? tw.term.gene : tw.term.type == "isoformExpression" ? tw.term.isoform : tw.term.name;
       noValueTerms.push(termName);
       term2sample2value.delete(term);
       delete byTermId[term];
@@ -309,7 +309,115 @@ async function validateNative(q, ds) {
     return { term2sample2value, byTermId, bySampleId };
   };
 }
+async function validateQueryIsoformExpression(ds, _genome) {
+  const q = ds.queries.isoformExpression;
+  if (!q) return;
+  q.geneExpression2bins = {};
+  if (typeof q.get == "function") return;
+  if (q.file) {
+    await validateNativeIsoform(q, ds);
+    return;
+  }
+  throw "isoformExpression requires either .get() or .file";
+}
+async function validateNativeIsoform(q, ds) {
+  q.file = path.join(serverconfig.tpmasterdir, q.file);
+  q.samples = [];
+  try {
+    await utils.file_is_readable(q.file);
+    const tmp = await run_rust("readH5", JSON.stringify({ hdf5_file: q.file, validate: true, include_items: true }));
+    const vr = JSON.parse(tmp);
+    if (vr.status !== "success") throw vr.message;
+    if (!vr.samples?.length) throw "HDF5 file has no samples, please check file.";
+    for (const sn of vr.samples) {
+      const si = ds.cohort.termdb.q.sampleName2id(sn);
+      if (si == void 0) {
+        if (ds.cohort.db) {
+          throw `unknown sample ${sn} from HDF5 ${q.file}`;
+        } else {
+          continue;
+        }
+      }
+      q.samples.push(si);
+    }
+    q.availableItems = vr.items || [];
+    console.log(
+      `${ds.label}: isoformExpression HDF5 file validated. Format: ${vr.format}, Samples:`,
+      q.samples.length,
+      "Items:",
+      q.availableItems.length
+    );
+  } catch (error) {
+    throw `${ds.label}: Failed to validate isoformExpression HDF5 file: ${error}`;
+  }
+  q.get = async (param) => {
+    const limitSamples = await mayLimitSamples(param, q.samples, ds);
+    if (limitSamples?.size == 0) {
+      return { term2sample2value: /* @__PURE__ */ new Map(), byTermId: {}, bySampleId: {} };
+    }
+    const bySampleId = {};
+    const samples = q.samples || [];
+    if (limitSamples) {
+      for (const sid of limitSamples) {
+        if (ds.cohort?.termdb?.q?.id2sampleRefs) {
+          bySampleId[sid] = ds.cohort.termdb.q.id2sampleRefs(sid);
+        } else {
+          bySampleId[sid] = { label: ds.cohort.termdb.q.id2sampleName(sid) };
+        }
+      }
+    } else {
+      for (const sid of samples) {
+        if (ds.cohort?.termdb?.q?.id2sampleRefs) {
+          bySampleId[sid] = ds.cohort.termdb.q.id2sampleRefs(sid);
+        } else {
+          bySampleId[sid] = { label: ds.cohort.termdb.q.id2sampleName(sid) };
+        }
+      }
+    }
+    const term2sample2value = /* @__PURE__ */ new Map();
+    const byTermId = {};
+    const isoformIds = [];
+    for (const tw of param.terms) {
+      if (tw.term.isoform) {
+        isoformIds.push(tw.term.isoform);
+      }
+    }
+    if (isoformIds.length === 0) {
+      console.log("No isoforms to query");
+      return { term2sample2value, byTermId };
+    }
+    const time1 = Date.now();
+    const isoformData = JSON.parse(await queryHDF5(q.file, isoformIds, null));
+    console.log("Time taken to run isoform query:", formatElapsedTime(Date.now() - time1));
+    const isoformsData = isoformData.query_output || {};
+    if (!isoformsData) throw "No expression data returned from HDF5 query";
+    for (const tw of param.terms) {
+      if (!tw.term.isoform) continue;
+      const isoformResult = isoformsData[tw.term.isoform];
+      if (!isoformResult) {
+        console.warn(`No data found for isoform ${tw.term.isoform} in the response`);
+        continue;
+      }
+      const samplesData = isoformResult.samples || {};
+      const s2v = {};
+      for (const sampleName in samplesData) {
+        const sampleId = ds.cohort.termdb.q.sampleName2id(sampleName);
+        if (!sampleId) continue;
+        if (limitSamples && !limitSamples.has(sampleId)) continue;
+        s2v[sampleId] = samplesData[sampleName];
+      }
+      if (Object.keys(s2v).length) {
+        term2sample2value.set(tw.$id, s2v);
+      }
+    }
+    if (term2sample2value.size == 0) {
+      throw "No data available for the input " + param.terms?.map((tw) => tw.term.isoform).join(", ");
+    }
+    return { term2sample2value, byTermId, bySampleId };
+  };
+}
 export {
   api,
+  validateQueryIsoformExpression,
   validate_query_geneExpression
 };

package/routes/termdb.config.js

@@ -5,6 +5,7 @@ import {
   TermTypeGroups,
   SINGLECELL_CELLTYPE,
   GENE_EXPRESSION,
+  ISOFORM_EXPRESSION,
   METABOLITE_INTENSITY,
   PROTEOME_ABUNDANCE,
   SINGLECELL_GENE_EXPRESSION,
@@ -162,7 +163,8 @@ function addNonDictionaryQueries(c, ds, genome) {
       "cnvCutoffsByGene",
       "absoluteValueRenderMax",
       "gainColor",
-      "lossColor"
+      "lossColor",
+      "requiresHardcodeCnvOnlyFlag"
     ]) {
       if (k in q.cnv) q2.cnv[k] = q.cnv[k];
     }
@@ -187,6 +189,9 @@ function addNonDictionaryQueries(c, ds, genome) {
   if (q.geneExpression) {
     q2.geneExpression = { unit: q.geneExpression.unit };
   }
+  if (q.isoformExpression) {
+    q2.isoformExpression = { unit: q.isoformExpression.unit };
+  }
   if (q.proteome) {
     q2.proteome = {};
     if (q.proteome.assays) {
@@ -197,10 +202,12 @@ function addNonDictionaryQueries(c, ds, genome) {
           q2.proteome.assays[assay].cohorts = {};
           for (const cohort in q.proteome.assays[assay].cohorts) {
             q2.proteome.assays[assay].cohorts[cohort] = {};
-            if ("filter" in q.proteome.assays[assay].cohorts[cohort]) {
-              q2.proteome.assays[assay].cohorts[cohort].filter = JSON.parse(
-                JSON.stringify(q.proteome.assays[assay].cohorts[cohort].filter)
-              );
+            const src = q.proteome.assays[assay].cohorts[cohort];
+            if ("filter" in src) {
+              q2.proteome.assays[assay].cohorts[cohort].filter = JSON.parse(JSON.stringify(src.filter));
+            }
+            if ("overlayTerm" in src) {
+              q2.proteome.assays[assay].cohorts[cohort].overlayTerm = JSON.parse(JSON.stringify(src.overlayTerm));
             }
           }
         }
@@ -292,6 +299,7 @@ function getAllowedTermTypes(ds) {
     for (const t of ds.cohort.termdb.allowedTermTypes) typeSet.add(t);
   }
   if (ds.queries?.geneExpression) typeSet.add(GENE_EXPRESSION);
+  if (ds.queries?.isoformExpression) typeSet.add(ISOFORM_EXPRESSION);
   if (ds.queries?.metaboliteIntensity) typeSet.add(METABOLITE_INTENSITY);
   if (ds.queries?.proteome?.assays) typeSet.add(PROTEOME_ABUNDANCE);
   if (ds.queries?.ssGSEA) typeSet.add(SSGSEA);

package/routes/termdb.diffMeth.js

@@ -1,6 +1,5 @@
 import { diffMethPayload } from "#types/checkers";
 import { getData } from "../src/termdb.matrix.js";
-import { get_ds_tdb } from "../src/termdb.js";
 import { run_R } from "@sjcrh/proteinpaint-r";
 import { mayLog } from "#src/helpers.ts";
 import { formatElapsedTime } from "#shared";
@@ -22,8 +21,9 @@ function init({ genomes }) {
     try {
       const q = req.query;
       const genome = genomes[q.genome];
-      if (!genome) throw new Error("invalid genome");
-      const [ds] = get_ds_tdb(genome, q);
+      if (!genome) throw "unknown genome";
+      const ds = genome.datasets?.[q.dslabel];
+      if (!ds) throw "unknown ds";
       let term_results = [];
       if (q.tw) {
         term_results = await getData({ filter: q.filter, filter0: q.filter0, terms: [q.tw] }, ds);
@@ -35,7 +35,12 @@ function init({ genomes }) {
         if (term_results2.error) throw new Error(term_results2.error);
       }
       const results = await run_diffMeth(req.query, ds, term_results, term_results2);
-      if (!results || !results.data) throw new Error("No data available");
+      if (!results || !results.data)
+        throw new Error(
+          "Differential methylation analysis returned no data. Please verify sample selections and try again."
+        );
+      if (Array.isArray(results.data) && !results.data.length)
+        throw new Error("No promoters passed filtering. Try relaxing group criteria or selecting more samples.");
       res.send(results);
     } catch (e) {
       res.send({ status: "error", error: e.message || e });
@@ -44,12 +49,15 @@ function init({ genomes }) {
   };
 }
 async function run_diffMeth(param, ds, term_results, term_results2) {
-  if (param.samplelst?.groups?.length != 2) throw new Error(".samplelst.groups.length!=2");
-  if (param.samplelst.groups[0].values?.length < 1) throw new Error("samplelst.groups[0].values.length<1");
-  if (param.samplelst.groups[1].values?.length < 1) throw new Error("samplelst.groups[1].values.length<1");
+  if (param.samplelst?.groups?.length != 2)
+    throw new Error("Exactly 2 sample groups are required for differential methylation analysis.");
+  if (param.samplelst.groups[0].values?.length < 1)
+    throw new Error("Group 1 has no samples. Please select at least one sample.");
+  if (param.samplelst.groups[1].values?.length < 1)
+    throw new Error("Group 2 has no samples. Please select at least one sample.");
   const q = ds.queries.dnaMethylation?.promoter;
-  if (!q) throw new Error("ds.queries.dnaMethylation.promoter is not configured");
-  if (!q.file) throw new Error("ds.queries.dnaMethylation.promoter.file is missing");
+  if (!q) throw new Error("This dataset does not have promoter-level methylation data configured.");
+  if (!q.file) throw new Error("Promoter methylation data file is not configured for this dataset.");
   const group1names = [];
   const conf1_group1 = [];
   const conf2_group1 = [];
@@ -169,10 +177,13 @@ async function run_diffMeth(param, ds, term_results, term_results2) {
 }
 function validateGroups(sample_size1, sample_size2, group1names, group2names) {
   const alerts = [];
-  if (sample_size1 < 1) alerts.push("sample size of group1 < 1");
-  if (sample_size2 < 1) alerts.push("sample size of group2 < 1");
+  if (sample_size1 < 1) alerts.push("No samples in group 1 have methylation data available.");
+  if (sample_size2 < 1) alerts.push("No samples in group 2 have methylation data available.");
   const commonnames = group1names.filter((x) => group2names.includes(x));
-  if (commonnames.length) alerts.push(`Common elements found between both groups: ${commonnames.join(", ")}`);
+  if (commonnames.length)
+    alerts.push(
+      `${commonnames.length} sample(s) appear in both groups: ${commonnames.join(", ")}. Please remove duplicates.`
+    );
   return alerts;
 }
 export {

package/routes/termdb.dmr.js

@@ -1,7 +1,9 @@
 import { TermdbDmrPayload } from "#types/checkers";
-import { run_python } from "@sjcrh/proteinpaint-python";
+import { run_rust } from "@sjcrh/proteinpaint-rust";
+import { run_R } from "@sjcrh/proteinpaint-r";
 import { invalidcoord } from "#shared/common.js";
 import { mayLog } from "#src/helpers.ts";
+import serverconfig from "#src/serverconfig.js";
 import { formatElapsedTime } from "#shared";
 const api = {
   endpoint: "termdb/dmr",
@@ -21,32 +23,64 @@ function init({ genomes }) {
     try {
       const q = req.query;
       const genome = genomes[q.genome];
-      if (!genome) throw new Error("invalid genome");
+      if (!genome) throw "unknown genome";
       const ds = genome.datasets?.[q.dslabel];
-      if (!ds) throw new Error("invalid ds");
-      if (!ds.queries?.dnaMethylation) throw new Error("analysis not supported");
-      if (!Array.isArray(q.group1) || q.group1.length == 0) throw new Error("group1 not non empty array");
-      if (!Array.isArray(q.group2) || q.group2.length == 0) throw new Error("group2 not non empty array");
-      if (invalidcoord(genome, q.chr, q.start, q.stop)) throw new Error("invalid chr/start/stop");
+      if (!ds) throw "unknown ds";
+      if (!ds.queries?.dnaMethylation) throw new Error("This dataset does not support DNA methylation analysis.");
+      if (!Array.isArray(q.group1) || q.group1.length == 0)
+        throw new Error("Group 1 has no samples. Please select at least one sample.");
+      if (!Array.isArray(q.group2) || q.group2.length == 0)
+        throw new Error("Group 2 has no samples. Please select at least one sample.");
+      if (invalidcoord(genome, q.chr, q.start, q.stop))
+        throw new Error(`Invalid genomic coordinates: ${q.chr}:${q.start}-${q.stop}`);
+      const SERVER_MAX_REGION_BP = 1e7;
+      const span = q.stop - q.start;
+      if (span > SERVER_MAX_REGION_BP)
+        throw new Error(
+          `Region too large (${(span / 1e6).toFixed(1)} Mb). Server maximum is ${SERVER_MAX_REGION_BP / 1e6} Mb.`
+        );
       const group1 = q.group1.map((s) => s.sample).filter(Boolean);
       const group2 = q.group2.map((s) => s.sample).filter(Boolean);
-      if (group1.length < 3) throw new Error(`Need at least 3 samples in group1, got ${group1.length}`);
-      if (group2.length < 3) throw new Error(`Need at least 3 samples in group2, got ${group2.length}`);
-      const gpdmInput = {
-        h5file: ds.queries.dnaMethylation.file,
+      if (group1.length < 3)
+        throw new Error(`Group 1 needs at least 3 samples with methylation data, got ${group1.length}.`);
+      if (group2.length < 3)
+        throw new Error(`Group 2 needs at least 3 samples with methylation data, got ${group2.length}.`);
+      const useR = q.backend === "r";
+      const dmrInput = {
+        probe_h5_file: ds.queries.dnaMethylation.file,
+        cachedir: serverconfig.cachedir,
+        genome: q.genome,
         chr: q.chr,
         start: q.start,
         stop: q.stop,
-        group1,
-        group2,
-        annotations: q.annotations || [],
-        nan_threshold: q.nan_threshold ?? 0.5
+        case: group2.join(","),
+        control: group1.join(","),
+        fdr_cutoff: q.fdr_cutoff,
+        lambda: q.lambda,
+        C: q.C,
+        blockWidth: q.blockWidth,
+        devicePixelRatio: q.devicePixelRatio,
+        maxLoessRegion: q.maxLoessRegion,
+        colors: q.colors
       };
       const time1 = Date.now();
-      const result = JSON.parse(await run_python("gpdm_analysis.py", JSON.stringify(gpdmInput)));
-      mayLog("DMR analysis time:", formatElapsedTime(Date.now() - time1));
+      const result = useR ? JSON.parse(await run_R("dmrcate_full.R", JSON.stringify(dmrInput))) : JSON.parse(await run_rust("dmrcate", JSON.stringify(dmrInput)));
+      mayLog(`DMR analysis (${useR ? "R" : "Rust"}) time:`, formatElapsedTime(Date.now() - time1));
       if (result.error) throw new Error(result.error);
-      res.send({ status: "ok", dmrs: result.dmrs });
+      if (result.diagnostic?.probes) {
+        const p = result.diagnostic.probes;
+        mayLog(
+          `${useR ? "R" : "Rust"} probes logFC:`,
+          p.logFC,
+          "fdr:",
+          p.fdr?.map((f) => f.toExponential(4))
+        );
+      }
+      res.send({
+        status: "ok",
+        dmrs: result.dmrs,
+        diagnostic: result.diagnostic
+      });
     } catch (e) {
       const msg = e instanceof Error ? e.message : String(e);
       res.send({ error: msg });

package/routes/termdb.isoformAvailability.js

@@ -0,0 +1,35 @@
+import { TermdbIsoformAvailabilityPayload } from "#types/checkers";
+const api = {
+  endpoint: "termdb/isoformAvailability",
+  methods: {
+    get: {
+      ...TermdbIsoformAvailabilityPayload,
+      init
+    },
+    post: {
+      ...TermdbIsoformAvailabilityPayload,
+      init
+    }
+  }
+};
+function init({ genomes }) {
+  return (req, res) => {
+    try {
+      const q = req.query;
+      const genome = genomes[q.genome];
+      if (!genome) throw "invalid genome";
+      const ds = genome.datasets?.[q.dslabel];
+      if (!ds) throw "invalid dslabel";
+      const isoQ = ds.queries?.isoformExpression;
+      if (!isoQ) throw "isoformExpression not configured for this dataset";
+      const itemSet = new Set(isoQ.availableItems || []);
+      const available = (q.isoforms || []).filter((id) => itemSet.has(id));
+      res.send({ available });
+    } catch (e) {
+      res.send({ error: e.message || e });
+    }
+  };
+}
+export {
+  api
+};

package/routes/termdb.profileFormScores.js

@@ -42,10 +42,21 @@ async function getScoresDict(query, ds) {
       const percents = getSCPercentsDict(d, data.samples);
       term2Score[d.term.id] = percents;
     }
-  const facilityValue = data.sampleData?.[query.facilityTW.$id];
-  const termValue = query.facilityTW.term.values[facilityValue?.value];
-  const hospital = termValue?.label || termValue?.key;
-  return { term2Score, sites: data.sites, hospital, n: data.sampleData ? 1 : data.samples.length };
+  const { clientAuthResult, activeCohort } = query.__protected__;
+  const isPublic = !clientAuthResult[activeCohort]?.role || clientAuthResult[activeCohort].role === "public";
+  let hospital;
+  if (!isPublic && data.sampleData) {
+    const facilityValue = data.sampleData[query.facilityTW.$id];
+    const termValue = query.facilityTW.term.values[facilityValue?.value];
+    hospital = termValue?.label || termValue?.key;
+  }
+  return {
+    term2Score,
+    // Do not expose individual site IDs, names, or hospital to public-role users
+    sites: isPublic ? [] : data.sites,
+    hospital,
+    n: data.sampleData ? 1 : data.samples.length
+  };
 }
 function getDict(key, sample) {
   if (!sample[key]) return null;

package/routes/termdb.profileScores.js

@@ -81,7 +81,15 @@ async function getScores(query, ds) {
   for (const d of query.scoreTerms) {
     term2Score[d.score.term.id] = getPercentage(d, data.samples, data.sampleData);
   }
-  return { term2Score, sites: data.sites, site: data.site, n: data.sampleData ? 1 : data.samples.length };
+  const { clientAuthResult, activeCohort } = query.__protected__;
+  const isPublic = !clientAuthResult[activeCohort]?.role || clientAuthResult[activeCohort].role === "public";
+  return {
+    term2Score,
+    // Do not expose individual site IDs or names to public-role users
+    sites: isPublic ? [] : data.sites,
+    site: isPublic ? void 0 : data.site,
+    n: data.sampleData ? 1 : data.samples.length
+  };
 }
 function getPercentage(d, samples, sampleData) {
   if (!d) return null;

package/routes/termdb.sampleScatter.js

@@ -131,9 +131,21 @@ async function getSingleCellScatter(req, res, ds) {
     const data = await ds.queries.singleCell.data.get(arg);
     const plot = data.plots[0];
     const cells = [...plot.expCells, ...plot.noExpCells];
+    const groups = tw.q?.customset?.groups;
+    const cat2GrpName = /* @__PURE__ */ new Map();
+    if (groups) {
+      for (const group of groups) {
+        for (const value of Object.values(group.values)) {
+          cat2GrpName.set(value.key, group.name);
+        }
+      }
+    }
     const samples = cells.map((cell) => {
+      let category = cell.category;
+      const groupName = cat2GrpName.get(category);
+      if (groupName !== void 0) category = groupName;
       const hidden = {
-        category: tw?.q?.hiddenValues ? cell.category in tw.q.hiddenValues : false
+        category: tw?.q?.hiddenValues ? category in tw.q.hiddenValues : false
       };
       return {
         sample: cell.cellId,
@@ -141,7 +153,7 @@ async function getSingleCellScatter(req, res, ds) {
         x: cell.x,
         y: cell.y,
         z: 0,
-        category: cell.category,
+        category,
         shape: "Ref",
         hidden,
         geneExp: cell.geneExp