@sjcrh/proteinpaint-server 2.178.0 → 2.178.1-0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.178.0",
+  "version": "2.178.1-0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -65,8 +65,8 @@
     "@sjcrh/proteinpaint-python": "2.178.0",
     "@sjcrh/proteinpaint-r": "2.178.0",
     "@sjcrh/proteinpaint-rust": "2.178.0",
-    "@sjcrh/proteinpaint-shared": "2.178.0",
-    "@sjcrh/proteinpaint-types": "2.178.0",
+    "@sjcrh/proteinpaint-shared": "2.178.1-0",
+    "@sjcrh/proteinpaint-types": "2.178.1-0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",

package/routes/termdb.boxplot.js

@@ -22,14 +22,14 @@ const api = {
 function init({ genomes }) {
   return async (req, res) => {
     const q = req.query;
-    const genome = genomes[q.genome];
-    if (!genome) throw new Error("invalid genome name");
-    const ds = genome.datasets?.[q.dslabel];
-    if (!ds) throw new Error("invalid ds");
-    const terms = [q.tw];
-    if (q.overlayTw) terms.push(q.overlayTw);
-    if (q.divideTw) terms.push(q.divideTw);
     try {
+      const genome = genomes[q.genome];
+      if (!genome) throw new Error("invalid genome name");
+      const ds = genome.datasets?.[q.dslabel];
+      if (!ds) throw new Error("invalid dslabel");
+      const terms = [q.tw];
+      if (q.overlayTw) terms.push(q.overlayTw);
+      if (q.divideTw) terms.push(q.divideTw);
       const data = await getData(
         { filter: q.filter, filter0: q.filter0, terms, __protected__: q.__protected__, __abortSignal: q.__abortSignal },
         ds

package/routes/termdb.chat2.js

@@ -7,6 +7,7 @@ import { extract_DE_search_terms_from_query } from "./chat/DEagent.ts";
 import { extract_summary_terms } from "./chat/summaryagent.ts";
 import { extract_matrix_search_terms_from_query } from "./chat/matrixagent.ts";
 import { extract_samplescatter_terms_from_query } from "./chat/samplescatteragent.ts";
+import { extract_hiercluster_terms_from_query } from "./chat/hierclusteragent.ts";
 import { parse_dataset_db, parse_geneset_db, getGenesetNames } from "./chat/utils.ts";
 import serverconfig from "../src/serverconfig.js";
 import { mayLog } from "#src/helpers.ts";
@@ -50,7 +51,6 @@ function init({ genomes }) {
       const ai_output_json = await run_chat_pipeline(
         q.prompt,
         llm,
-        serverconfig.aiRoute,
         dataset_json,
         testing,
         dataset_db,
@@ -65,7 +65,7 @@ function init({ genomes }) {
     }
   };
 }
-async function run_chat_pipeline(user_prompt, llm, aiRoute, dataset_json, testing, dataset_db, genedb, ds, genesetNames = []) {
+async function run_chat_pipeline(user_prompt, llm, dataset_json, testing, dataset_db, genedb, ds, genesetNames = []) {
   const time1 = (/* @__PURE__ */ new Date()).valueOf();
   const class_response = await classifyQuery(user_prompt, llm);
   let ai_output_json;
@@ -84,9 +84,8 @@ async function run_chat_pipeline(user_prompt, llm, aiRoute, dataset_json, testin
     }
   } else if (class_response.type == "plot") {
     const classResult = await classifyPlotType(user_prompt, llm);
-    mayLog("classResult:", classResult);
     const dataset_db_output = await parse_dataset_db(dataset_db);
-    const genes_list = dataset_json.hasGeneExpression ? await parse_geneset_db(genedb) : [];
+    const genes_list = await parse_geneset_db(genedb);
     if (classResult == "summary") {
       const time12 = (/* @__PURE__ */ new Date()).valueOf();
       ai_output_json = await extract_summary_terms(
@@ -139,6 +138,19 @@ async function run_chat_pipeline(user_prompt, llm, aiRoute, dataset_json, testin
         genesetNames
       );
       mayLog("Time taken for sampleScatter agent:", formatElapsedTime(Date.now() - time12));
+    } else if (classResult == "hiercluster") {
+      const time12 = (/* @__PURE__ */ new Date()).valueOf();
+      ai_output_json = await extract_hiercluster_terms_from_query(
+        user_prompt,
+        llm,
+        dataset_db_output,
+        dataset_json,
+        genes_list,
+        ds,
+        testing,
+        genesetNames
+      );
+      mayLog("Time taken for hierCluster agent:", formatElapsedTime(Date.now() - time12));
     } else {
       ai_output_json = { type: "text", text: "Unknown classification value" };
     }

package/routes/termdb.sampleScatter.js

@@ -23,15 +23,15 @@ const api = {
 const refColor = "#F5F5DC";
 function init({ genomes }) {
   return async function(req, res) {
-    const q = req.query;
-    if (!q.genome || !q.dslabel) {
-      throw new Error("Genome and dataset label are required for termdb/sampleScatter request.");
-    }
-    const g = genomes[q.genome];
-    const ds = g.datasets[q.dslabel];
-    if (q.singleCellPlot)
-      return getSingleCellScatter(req, res, ds);
     try {
+      const q = req.query;
+      if (!q.genome || !q.dslabel) {
+        throw new Error("Genome and dataset label are required for termdb/sampleScatter request.");
+      }
+      const g = genomes[q.genome];
+      const ds = g.datasets[q.dslabel];
+      if (q.singleCellPlot)
+        return getSingleCellScatter(req, res, ds);
       let refSamples = [], cohortSamples;
       const terms = [];
       if (q.colorTW) terms.push(q.colorTW);

package/routes/termdb.violin.js

@@ -190,9 +190,10 @@ async function createCanvasImg(q, result, ds) {
     const chart = result.charts[k];
     const plot2Values = {};
     for (const plot of chart.plots) plot2Values[plot.label] = plot.values;
-    const densities = await getDensities(plot2Values);
-    let axisScale;
     const useLog = q.unit == "log";
+    const logBase = ds.cohort.termdb.logscaleBase2 ? 2 : 10;
+    const densities = await getDensities(plot2Values, useLog, logBase);
+    let axisScale;
     if (useLog) {
       axisScale = scaleLog().base(ds.cohort.termdb.logscaleBase2 ? 2 : 10).domain([result.min, result.max]).range(isH ? [0, q.svgw] : [q.svgw, 0]);
     } else {
@@ -241,8 +242,16 @@ async function getDensity(values) {
   const result = await getDensities({ plot: values });
   return result.plot;
 }
-async function getDensities(plot2Values) {
-  const plot2Density = JSON.parse(await run_R("density.R", JSON.stringify({ plot2Values })));
+async function getDensities(plot2Values, useLog = false, logBase = 10) {
+  let transformedPlot2Values = {};
+  if (useLog) {
+    for (const plot in plot2Values) {
+      transformedPlot2Values[plot] = plot2Values[plot].filter((v) => v > 0).map((v) => Math.log(v) / Math.log(logBase));
+    }
+  } else {
+    transformedPlot2Values = plot2Values;
+  }
+  const plot2Density = JSON.parse(await run_R("density.R", JSON.stringify({ plot2Values: transformedPlot2Values })));
   const densities = {};
   for (const plot in plot2Density) {
     const result = plot2Density[plot];
@@ -253,11 +262,12 @@ async function getDensities(plot2Values) {
     let xMax = -Infinity;
     for (const [i, x] of Object.entries(result.x)) {
       const density2 = result.y[i];
-      xMin = Math.min(xMin, x);
-      xMax = Math.max(xMax, x);
+      const x0 = useLog ? Math.pow(logBase, x) : x;
+      xMin = Math.min(xMin, x0);
+      xMax = Math.max(xMax, x0);
       densityMin = Math.min(densityMin, density2);
       densityMax = Math.max(densityMax, density2);
-      bins.push({ x0: x, density: density2 });
+      bins.push({ x0, density: density2 });
     }
     bins.unshift({ x0: xMin, density: densityMin });
     bins.push({ x0: xMax, density: densityMin });