@sjcrh/proteinpaint-server 2.138.3-7 → 2.139.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.138.3-7",
+  "version": "2.139.1",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -60,11 +60,11 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.136.0",
-    "@sjcrh/proteinpaint-python": "2.135.2-0",
+    "@sjcrh/proteinpaint-python": "2.139.1",
     "@sjcrh/proteinpaint-r": "2.137.2-0",
     "@sjcrh/proteinpaint-rust": "2.138.3-7",
     "@sjcrh/proteinpaint-shared": "2.138.3-7",
-    "@sjcrh/proteinpaint-types": "2.138.3-7",
+    "@sjcrh/proteinpaint-types": "2.139.1",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/grin2.js

@@ -23,6 +23,7 @@ function init({ genomes }) {
   return async (req, res) => {
     try {
       const request = req.query;
+      console.log("[GRIN2] request:", request);
       const g = genomes[request.genome];
       if (!g)
         throw new Error("genome missing");
@@ -59,7 +60,7 @@ async function runGrin2(g, ds, request) {
   }
   mayLog("[GRIN2] Processing sample data...");
   const processingStartTime = Date.now();
-  const { lesionData, processingSummary } = await processSampleData(samples, ds, request);
+  const { lesions, processingSummary } = await processSampleData(samples, ds, request);
   const processingTime = Date.now() - processingStartTime;
   const processingTimeToPrint = Math.round(processingTime / 1e3);
   mayLog(`[GRIN2] Data processing took ${processingTimeToPrint} seconds`);
@@ -69,13 +70,13 @@ async function runGrin2(g, ds, request) {
   if (processingSummary && processingSummary.failedSamples > 0) {
     mayLog(`[GRIN2] Warning: ${processingSummary.failedSamples} samples failed to process`);
   }
-  if (lesionData.length === 0) {
+  if (lesions.length === 0) {
     throw new Error("No lesions found after processing all samples. Check filter criteria and input data.");
   }
   const pyInput = {
     genedb: path.join(serverconfig.tpmasterdir, g.genedb.dbfile),
     chromosomelist: {},
-    lesion: JSON.stringify(lesionData)
+    lesion: JSON.stringify(lesions)
   };
   for (const c in g.majorchr) {
     if (ds.queries.singleSampleMutation.discoPlot?.skipChrM) {
@@ -84,7 +85,7 @@ async function runGrin2(g, ds, request) {
     }
     pyInput.chromosomelist[c] = g.majorchr[c];
   }
-  mayLog(`[GRIN2] Prepared ${lesionData.length.toLocaleString()} lesions for analysis`);
+  mayLog(`[GRIN2] Prepared ${lesions.length.toLocaleString()} lesions for analysis`);
   const grin2AnalysisStart = Date.now();
   const pyResult = await run_python("grin2PpWrapper.py", JSON.stringify(pyInput));
   if (pyResult.stderr?.trim()) {
@@ -96,7 +97,7 @@ async function runGrin2(g, ds, request) {
   const grin2AnalysisTime = Date.now() - grin2AnalysisStart;
   const grin2AnalysisTimeToPrint = Math.round(grin2AnalysisTime / 1e3);
   mayLog(`[GRIN2] Python processing took ${grin2AnalysisTimeToPrint} seconds`);
-  const resultData = JSON.parse(pyResult.stdout);
+  const resultData = JSON.parse(pyResult);
   if (!resultData?.png?.[0]) {
     throw new Error("Invalid Python output: missing PNG data");
   }
@@ -131,10 +132,13 @@ async function processSampleData(samples, ds, request) {
       const filepath = path.join(serverconfig.tpmasterdir, ds.queries.singleSampleMutation.folder, sample.name);
       await file_is_readable(filepath);
       const mlst = JSON.parse(await read_file(filepath));
-      const sampleLesions = await processSampleMlst(sample.name, mlst, lesionId, request);
+      const { sampleLesions } = await processSampleMlst(sample.name, mlst, lesionId, request);
       lesions.push(...sampleLesions);
       lesionId += sampleLesions.length;
+      processingSummary.successfulSamples++;
     } catch (error) {
+      processingSummary.failedSamples++;
+      processingSummary.failedFiles?.push(sample.name);
       mayLog(
         `[GRIN2] Error processing sample ${sample.name}: ${typeof error === "object" && error !== null && "message" in error ? error.message : String(error)}`
       );
@@ -142,7 +146,7 @@ async function processSampleData(samples, ds, request) {
   }
   mayLog(`[GRIN2] Total lesions processed: ${lesions.length.toLocaleString()}`);
   return {
-    lesionData: lesions,
+    lesions,
     processingSummary
   };
 }
@@ -154,91 +158,69 @@ async function processSampleMlst(sampleName, mlst, startId, request) {
         if (!request.snvindelOptions)
           break;
         const snvIndelLesion = filterAndConvertSnvIndel(sampleName, m, request.snvindelOptions);
-        if (snvIndelLesion)
+        if (snvIndelLesion) {
           lesions.push(snvIndelLesion);
+        }
         break;
       }
       case dtcnv: {
         if (!request.cnvOptions)
           break;
         const cnvLesion = filterAndConvertCnv(sampleName, m, request.cnvOptions);
-        if (cnvLesion)
+        if (cnvLesion) {
           lesions.push(cnvLesion);
+        }
         break;
       }
       case dtfusionrna: {
         if (!request.fusionOptions)
           break;
         const fusionLesion = filterAndConvertFusion(sampleName, m, request.fusionOptions);
-        if (fusionLesion)
+        if (fusionLesion) {
           lesions.push(fusionLesion);
+        }
         break;
       }
-      default:
-        mayLog(`[GRIN2] Unknown data type "${m.dt}" in sample ${sampleName}, skipping entry`);
+      default: {
         break;
+      }
     }
   }
-  return lesions;
+  return {
+    sampleLesions: lesions
+  };
 }
 function filterAndConvertSnvIndel(sampleName, entry, options) {
-  const opts = {
-    minTotalDepth: options?.minTotalDepth ?? 10,
-    minAltAlleleCount: options?.minAltAlleleCount ?? 2,
-    consequences: options?.consequences ?? [],
-    hyperMutator: options?.hyperMutator ?? 1e3
-  };
-  if (opts.consequences.length > 0 && entry.consequence && !opts.consequences.includes(entry.consequence)) {
+  if (!options?.consequences) {
+    return null;
+  }
+  if (options.consequences.length > 0 && entry.class && !options.consequences.includes(entry.class)) {
+    return null;
+  }
+  if (!Number.isInteger(entry.pos)) {
     return null;
   }
-  return [
-    sampleName,
-    normalizeChromosome(entry.chromosome || entry.chr),
-    String(entry.start || entry.position),
-    String(entry.end || entry.position),
-    "mutation"
-  ];
+  return [sampleName, entry.chr, entry.pos, entry.pos, "mutation"];
 }
 function filterAndConvertCnv(sampleName, entry, options) {
-  const opts = {
-    lossThreshold: options?.lossThreshold ?? -0.4,
-    gainThreshold: options?.gainThreshold ?? 0.3,
-    maxSegLength: options?.maxSegLength ?? 0,
-    minSegLength: options?.minSegLength ?? 0,
-    hyperMutator: options?.hyperMutator ?? 500
-  };
-  const isGain = entry.log2Ratio >= opts.gainThreshold;
-  const isLoss = entry.log2Ratio <= opts.lossThreshold;
+  if (!options || options.gainThreshold === void 0 || options.lossThreshold === void 0) {
+    return null;
+  }
+  const isGain = entry.value >= options.gainThreshold;
+  const isLoss = entry.value <= options.lossThreshold;
   if (!isGain && !isLoss)
     return null;
-  const lesionType = entry.log2Ratio >= opts.gainThreshold ? "gain" : "loss";
-  return [
-    sampleName,
-    normalizeChromosome(entry.chromosome || entry.chr),
-    String(entry.start || entry.begin),
-    String(entry.end || entry.stop),
-    lesionType
-  ];
-}
-function filterAndConvertFusion(sampleName, entry, options) {
-  const opts = {
-    fusionTypes: options?.fusionTypes ?? ["gene-gene", "gene-intergenic", "readthrough"],
-    minConfidence: options?.minConfidence ?? 0.7
-  };
-  if (entry.fusionType && !opts.fusionTypes.includes(entry.fusionType))
+  const lesionType = isGain ? "gain" : "loss";
+  if (!Number.isInteger(entry.start)) {
     return null;
-  if (entry.confidence && entry.confidence < opts.minConfidence)
+  }
+  if (!Number.isInteger(entry.stop)) {
     return null;
-  return [
-    sampleName,
-    normalizeChromosome(entry.chromosome || entry.chr),
-    String(entry.start || entry.position),
-    String(entry.end || entry.position),
-    "fusion"
-  ];
+  }
+  return [sampleName, entry.chr, entry.start, entry.stop, lesionType];
 }
-function normalizeChromosome(chrom) {
-  return chrom.startsWith("chr") ? chrom : `chr${chrom}`;
+function filterAndConvertFusion(sampleName, entry, _options) {
+  return [sampleName, entry.chrA, entry.posA, entry.posB, "fusion"];
 }
 export {
   api

package/routes/termdb.percentile.js

@@ -1,5 +1,6 @@
 import { percentilePayload } from "#types/checkers";
-import * as termdbsql from "#src/termdb.sql.js";
+import { isNumericTerm } from "#shared/terms.js";
+import { getData } from "#src/termdb.matrix.js";
 import computePercentile from "#shared/compute.percentile.js";
 const api = {
   endpoint: "termdb/getpercentile",
@@ -33,20 +34,23 @@ function init({ genomes }) {
   };
 }
 async function trigger_getpercentile(q, res, ds) {
-  const term = ds.cohort.termdb.q.termjsonByOneid(q.tid);
+  const term = q.term;
   if (!term)
-    throw "invalid termid";
-  if (term.type != "float" && term.type != "integer")
-    throw "not numerical term";
-  const percentile_lst = q.getpercentile;
-  const perc_values = [];
+    throw "term is missing";
+  if (!isNumericTerm(term))
+    throw "not numeric term";
+  const tw = { $id: "_", term, q: { mode: "continuous" } };
+  const data = await getData({ filter: q.filter, filter0: q.filter0, terms: [tw], __protected__: q.__protected__ }, ds);
+  if (data.error)
+    throw data.error;
   const values = [];
-  const rows = await termdbsql.get_rows_by_one_key({
-    ds,
-    key: q.tid,
-    filter: q.filter ? typeof q.filter == "string" ? JSON.parse(q.filter) : q.filter : null
-  });
-  for (const { value } of rows) {
+  for (const key in data.samples) {
+    const sample = data.samples[key];
+    const v = sample[tw.$id];
+    if (!v?.value) {
+      continue;
+    }
+    const value = v.value;
     if (term.values && term.values[value] && term.values[value].uncomputable) {
       continue;
     }
@@ -55,6 +59,8 @@ async function trigger_getpercentile(q, res, ds) {
     }
     values.push(Number(value));
   }
+  const percentile_lst = q.getpercentile;
+  const perc_values = [];
   for (const percentile of percentile_lst) {
     const perc_value = computePercentile(values, percentile);
     perc_values.push(perc_value);