@sjcrh/proteinpaint-server 2.167.2 → 2.169.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.167.2",
+  "version": "2.169.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -62,11 +62,11 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.143.0",
-    "@sjcrh/proteinpaint-python": "2.164.1",
+    "@sjcrh/proteinpaint-python": "2.169.0",
     "@sjcrh/proteinpaint-r": "2.152.1-0",
-    "@sjcrh/proteinpaint-rust": "2.167.0",
-    "@sjcrh/proteinpaint-shared": "2.167.0",
-    "@sjcrh/proteinpaint-types": "2.167.0",
+    "@sjcrh/proteinpaint-rust": "2.169.0",
+    "@sjcrh/proteinpaint-shared": "2.169.0",
+    "@sjcrh/proteinpaint-types": "2.169.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",

package/routes/saveWSIAnnotation.js

@@ -81,7 +81,12 @@ function validateQuery(ds, connection) {
 				) VALUES (?, ?, ?, ?, ?, ?, ?)
 			`;
       const insertStmt = connection.prepare(insertSql);
-      const userRow = connection.prepare(`SELECT id FROM project_users WHERE project_id = ? ORDER BY id ASC LIMIT 1`).get(projectId);
+      const userRow = connection.prepare(
+        `SELECT id
+						  FROM project_users
+						  ORDER BY id
+						  LIMIT 1`
+      ).get();
       const userId = userRow?.id;
       insertStmt.run(projectId, userId, coords, timestamp, status, classId, imageId);
       return { status: "ok" };

package/routes/termdb.boxplot.js

@@ -2,8 +2,9 @@ import { boxplotPayload } from "#types/checkers";
 import { getData } from "../src/termdb.matrix.js";
 import { boxplot_getvalue } from "../src/utils.js";
 import { sortPlot2Values } from "./termdb.violin.ts";
-import { getDescrStats } from "./termdb.descrstats.ts";
+import { getDescrStats, getStdDev, getMean } from "./termdb.descrstats.ts";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
+import { roundValueAuto } from "#shared/roundValue.js";
 const api = {
   endpoint: "termdb/boxplot",
   methods: {
@@ -20,14 +21,14 @@ 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 ds");
-      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__ }, ds);
       if (data.error) throw new Error(data.error);
       const { absMin, absMax, charts, uncomputableValues, descrStats, outlierMin, outlierMax } = await processData(
@@ -89,9 +90,13 @@ async function processData(data, q) {
     if (q.orderByMedian == true) {
       plots.sort((a, b) => a.boxplot.p50 - b.boxplot.p50);
     }
-    charts[chart] = { chartId: chart, plots };
+    const sampleCount = plots.reduce((total, p) => {
+      if (p.hidden) return total;
+      return total + p.descrStats.total.value;
+    }, 0);
+    charts[chart] = { chartId: chart, plots, sampleCount };
   }
-  if (q.showAssocTests == true && overlayTerm) await getWilcoxonData(charts);
+  if (q.showAssocTests && overlayTerm) await getWilcoxonData(charts);
   Object.keys(charts).forEach((c) => charts[c].plots.forEach((p) => delete p.tempValues));
   return { absMin, absMax, charts, uncomputableValues, descrStats, outlierMin, outlierMax };
 }
@@ -109,7 +114,7 @@ function setPlotData(plots, values, key, sampleType, descrStats, q, data, outlie
   if (!boxplot) throw new Error("boxplot_getvalue failed [termdb.boxplot init()]");
   const _plot = {
     boxplot,
-    descrStats,
+    descrStats: setIndividualBoxPlotStats(boxplot, sortedValues),
     //quick fix
     //to delete later
     tempValues: sortedValues
@@ -136,6 +141,22 @@ function setPlotData(plots, values, key, sampleType, descrStats, q, data, outlie
   }
   return [outlierMax, outlierMin];
 }
+function setIndividualBoxPlotStats(boxplot, values) {
+  const stats = {
+    total: { key: "total", label: "Total", value: values.length },
+    min: { key: "min", label: "Minimum", value: values[0] },
+    p25: { key: "p25", label: "1st quartile", value: boxplot.p25 },
+    median: { key: "median", label: "Median", value: boxplot.p50 },
+    p75: { key: "p75", label: "3rd quartile", value: boxplot.p75 },
+    mean: { key: "mean", label: "Mean", value: getMean(values) },
+    max: { key: "max", label: "Maximum", value: values[values.length - 1] },
+    stdDev: { key: "stdDev", label: "Standard deviation", value: getStdDev(values) }
+  };
+  for (const key of Object.keys(stats)) {
+    stats[key].value = roundValueAuto(stats[key].value);
+  }
+  return stats;
+}
 function setHiddenPlots(term, plots) {
   for (const v of Object.values(term.term?.values)) {
     const plot = plots.find((p) => p.key === v.label);

package/routes/termdb.chat.js

@@ -59,15 +59,19 @@ function init({ genomes }) {
         throw "llm_backend either needs to be 'SJ' or 'ollama'";
       }
       const chatbot_input = {
-        // Just hardcoding variables here, these will later be defined in more appropriate places
         user_input: q.prompt,
         apilink,
         tpmasterdir: serverconfig.tpmasterdir,
         comp_model_name,
         embedding_model_name,
+        dataset_db: ds.cohort.db.file,
+        genedb: g.genedb.dbfile,
+        aiRoute: serverconfig.aiRoute,
+        // Route file for classifying chat request into various routes
         llm_backend_name: serverconfig.llm_backend,
         // The type of backend (engine) used for running the embedding and completion model. Currently "SJ" and "Ollama" are supported
         aifiles: serverconfig_ds_entries.aifiles,
+        // Dataset specific data containing data-specific routes, system prompts for agents and few-shot examples
         binpath: serverconfig.binpath
       };
       const time1 = (/* @__PURE__ */ new Date()).valueOf();
@@ -87,23 +91,48 @@ function init({ genomes }) {
         if (ai_output_json.plot.simpleFilter) {
           if (!Array.isArray(ai_output_json.plot.simpleFilter)) throw "ai_output_json.plot.simpleFilter is not array";
           const localfilter = { type: "tvslst", in: true, join: "", lst: [] };
+          if (ai_output_json.plot.simpleFilter.length > 1) localfilter.join = "and";
           for (const f of ai_output_json.plot.simpleFilter) {
             const term = ds.cohort.termdb.q.termjsonByOneid(f.term);
             if (!term) throw "invalid term id from simpleFilter[].term";
-            if (term.type != "categorical") throw "term not categorical";
-            let cat;
-            for (const ck in term.values) {
-              if (ck == f.category) cat = ck;
-              else if (term.values[ck].label == f.category) cat = ck;
-            }
-            if (!cat) throw "invalid category from " + JSON.stringify(f);
-            localfilter.lst.push({
-              type: "tvs",
-              tvs: {
-                term,
-                values: [{ key: cat }]
+            if (term.type == "categorical") {
+              let cat;
+              for (const ck in term.values) {
+                if (ck == f.category) cat = ck;
+                else if (term.values[ck].label == f.category) cat = ck;
+              }
+              if (!cat) throw "invalid category from " + JSON.stringify(f);
+              localfilter.lst.push({
+                type: "tvs",
+                tvs: {
+                  term,
+                  values: [{ key: cat }]
+                }
+              });
+            } else if (term.type == "float" || term.type == "integer") {
+              const numeric = {
+                type: "tvs",
+                tvs: {
+                  term,
+                  ranges: []
+                }
+              };
+              const range = {};
+              if (f.gt && !f.lt) {
+                range.start = Number(f.gt);
+                range.stopunbounded = true;
+              } else if (f.lt && !f.gt) {
+                range.stop = Number(f.lt);
+                range.startunbounded = true;
+              } else if (f.gt && f.lt) {
+                range.start = Number(f.gt);
+                range.stop = Number(f.lt);
+              } else {
+                throw "Neither greater or lesser defined";
               }
-            });
+              numeric.tvs.ranges.push(range);
+              localfilter.lst.push(numeric);
+            }
           }
           delete ai_output_json.plot.simpleFilter;
           ai_output_json.plot.filter = localfilter;