@sjcrh/proteinpaint-server 2.170.0 → 2.171.0-0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.170.0",
+  "version": "2.171.0-0",
   "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": "2.169.0",
+    "@sjcrh/proteinpaint-python": "2.171.0-0",
     "@sjcrh/proteinpaint-r": "2.152.1-0",
-    "@sjcrh/proteinpaint-rust": "2.170.0",
-    "@sjcrh/proteinpaint-shared": "2.170.0",
-    "@sjcrh/proteinpaint-types": "2.170.0",
+    "@sjcrh/proteinpaint-rust": "2.171.0-0",
+    "@sjcrh/proteinpaint-shared": "2.171.0-0",
+    "@sjcrh/proteinpaint-types": "2.171.0-0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",

package/routes/grin2.js

@@ -6,16 +6,7 @@ import { run_rust } from "@sjcrh/proteinpaint-rust";
 import { mayLog } from "#src/helpers.ts";
 import { get_samples } from "#src/termdb.sql.js";
 import { read_file, file_is_readable } from "#src/utils.js";
-import {
-  dtsnvindel,
-  dtcnv,
-  dtfusionrna,
-  dtsv,
-  dt2lesion,
-  optionToDt,
-  formatElapsedTime,
-  MANHATTAN_LOG_QVALUE_CUTOFF
-} from "#shared";
+import { dtsnvindel, dtcnv, dtfusionrna, dtsv, dt2lesion, optionToDt, formatElapsedTime } from "#shared";
 import crypto from "crypto";
 const MAX_LESIONS_PER_TYPE = serverconfig.features.grin2maxLesionPerType || 11e4;
 const api = {
@@ -115,9 +106,6 @@ async function runGrin2(g, ds, request) {
     lesionTypeMap: buildLesionTypeMap(availableDataTypes)
   };
   for (const c in g.majorchr) {
-    if (ds.queries.singleSampleMutation.discoPlot?.skipChrM) {
-      if (c.toLowerCase() == "chrm") continue;
-    }
     pyInput.chromosomelist[c] = g.majorchr[c];
   }
   const grin2AnalysisStart = Date.now();
@@ -141,7 +129,9 @@ async function runGrin2(g, ds, request) {
     png_dot_radius: request.pngDotRadius,
     lesion_type_colors: request.lesionTypeColors,
     q_value_threshold: request.qValueThreshold,
-    log_cutoff: MANHATTAN_LOG_QVALUE_CUTOFF
+    max_capped_points: request.maxCappedPoints,
+    hard_cap: request.hardCap,
+    bin_size: request.binSize
   };
   const manhattanPlotStart = Date.now();
   const rsResult = await run_rust("manhattan_plot", JSON.stringify(rustInput));
@@ -214,12 +204,14 @@ async function processSampleData(samples, ds, request, tracker) {
       await file_is_readable(filepath);
       const mlst = JSON.parse(await read_file(filepath));
       const { sampleLesions, contributedTypes } = await processSampleMlst(sample.name, mlst, request, tracker);
-      lesions.push(...sampleLesions);
+      const skipChrM = ds.queries.singleSampleMutation.discoPlot?.skipChrM;
+      const filteredLesions = skipChrM ? sampleLesions.filter((lesion) => lesion[1].toLowerCase() !== "chrm") : sampleLesions;
+      lesions.push(...filteredLesions);
       for (const type of contributedTypes) {
         samplesPerType.get(type)?.add(sample.name);
       }
       processingSummary.processedSamples += 1;
-      processingSummary.totalLesions += sampleLesions.length;
+      processingSummary.totalLesions += filteredLesions.length;
       if (allTypesCapped(tracker)) {
         const remaining = samples.length - 1 - i;
         if (remaining > 0) processingSummary.unprocessedSamples += remaining;

package/routes/healthcheck.js

@@ -9,7 +9,8 @@ const api = {
     }
   }
 };
-function init({ genomes }) {
+function init(arg) {
+  const genomes = arg.genomes;
   return async (req, res) => {
     try {
       const q = req.query;

package/routes/termdb.boxplot.js

@@ -5,6 +5,7 @@ import { sortPlot2Values } from "./termdb.violin.ts";
 import { getDescrStats, getStdDev, getMean } from "./termdb.descrstats.ts";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import { roundValueAuto } from "#shared/roundValue.js";
+import { isNumericTerm } from "@sjcrh/proteinpaint-shared";
 const api = {
   endpoint: "termdb/boxplot",
   methods: {
@@ -31,13 +32,11 @@ function init({ genomes }) {
     try {
       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(
-        data,
-        q
-      );
+      const { absMin, absMax, bins, charts, uncomputableValues, descrStats, outlierMin, outlierMax } = await processData(data, q);
       const returnData = {
         absMin: q.removeOutliers ? outlierMin : absMin,
         absMax: q.removeOutliers ? outlierMax : absMax,
+        bins,
         charts,
         uncomputableValues: setUncomputableValues(uncomputableValues),
         descrStats
@@ -54,15 +53,15 @@ async function processData(data, q) {
   const values = samples.map((s) => s?.[q.tw.$id]?.value).filter((v) => typeof v === "number" && !q.tw.term.values?.[v]?.uncomputable);
   const descrStats = getDescrStats(values, q.removeOutliers);
   const sampleType = `All ${data.sampleType?.plural_name || "samples"}`;
-  const overlayTerm = q.overlayTw;
-  const divideTerm = q.divideTw;
+  const overlayTw = q.overlayTw;
+  const divideTw = q.divideTw;
   const { absMin, absMax, chart2plot2values, uncomputableValues } = parseValues(
     q,
     data,
     sampleType,
     q.isLogScale,
-    overlayTerm,
-    divideTerm
+    overlayTw,
+    divideTw
   );
   if (!absMin && absMin !== 0) throw new Error("absMin is undefined");
   if (!absMax && absMax !== 0) throw new Error("absMax is undefined");
@@ -70,7 +69,7 @@ async function processData(data, q) {
   let outlierMin = Number.POSITIVE_INFINITY, outlierMax = Number.NEGATIVE_INFINITY;
   for (const [chart, plot2values] of chart2plot2values) {
     const plots = [];
-    for (const [key, values2] of sortPlot2Values(data, plot2values, overlayTerm)) {
+    for (const [key, values2] of sortPlot2Values(data, plot2values, overlayTw)) {
       ;
       [outlierMax, outlierMin] = setPlotData(
         plots,
@@ -79,14 +78,14 @@ async function processData(data, q) {
         sampleType,
         descrStats,
         q,
-        data,
         outlierMin,
         outlierMax,
-        overlayTerm
+        overlayTw
       );
     }
     if (q.tw.term?.values) setHiddenPlots(q.tw, plots);
-    if (overlayTerm && overlayTerm.term?.values) setHiddenPlots(overlayTerm, plots);
+    if (overlayTw && overlayTw.term?.values) setHiddenPlots(overlayTw, plots);
+    if (divideTw && divideTw.term?.values) setHiddenPlots(divideTw, plots);
     if (q.orderByMedian == true) {
       plots.sort((a, b) => a.boxplot.p50 - b.boxplot.p50);
     }
@@ -96,11 +95,16 @@ async function processData(data, q) {
     }, 0);
     charts[chart] = { chartId: chart, plots, sampleCount };
   }
-  if (q.showAssocTests && overlayTerm) await getWilcoxonData(charts);
+  const bins = {
+    term1: numericBins(q.tw, data)
+  };
+  if (overlayTw) bins.term2 = numericBins(overlayTw, data);
+  if (divideTw) bins.term0 = numericBins(divideTw, data);
+  if (q.showAssocTests && overlayTw) await getWilcoxonData(charts);
   Object.keys(charts).forEach((c) => charts[c].plots.forEach((p) => delete p.tempValues));
-  return { absMin, absMax, charts, uncomputableValues, descrStats, outlierMin, outlierMax };
+  return { absMin, absMax, bins, charts, uncomputableValues, descrStats, outlierMin, outlierMax };
 }
-function setPlotData(plots, values, key, sampleType, descrStats, q, data, outlierMin, outlierMax, overlayTerm) {
+function setPlotData(plots, values, key, sampleType, descrStats, q, outlierMin, outlierMax, overlayTw) {
   const sortedValues = values.sort((a, b) => a - b);
   const vs = sortedValues.map((v) => {
     const value = { value: v };
@@ -112,33 +116,24 @@ function setPlotData(plots, values, key, sampleType, descrStats, q, data, outlie
   }
   const boxplot = boxplot_getvalue(vs, q.removeOutliers);
   if (!boxplot) throw new Error("boxplot_getvalue failed [termdb.boxplot init()]");
-  const _plot = {
+  const plot = {
     boxplot,
     descrStats: setIndividualBoxPlotStats(boxplot, sortedValues),
     //quick fix
     //to delete later
     tempValues: sortedValues
   };
-  if (overlayTerm) {
-    const _key = overlayTerm?.term?.values?.[key]?.label || key;
-    const plotLabel = `${_key}, n=${values.length}`;
-    const overlayBins = numericBins(overlayTerm, data);
-    const plot = Object.assign(_plot, {
-      color: overlayTerm?.term?.values?.[key]?.color || null,
-      key: _key,
-      overlayBins: overlayBins.has(key) ? overlayBins.get(key) : null,
-      seriesId: key
-    });
-    plot.boxplot.label = plotLabel;
-    plots.push(plot);
+  if (overlayTw) {
+    const _key = overlayTw?.term?.values?.[key]?.label || key;
+    plot.color = overlayTw?.term?.values?.[key]?.color || null;
+    plot.key = _key;
+    plot.seriesId = key;
+    plot.boxplot.label = `${_key}, n=${values.length}`;
   } else {
-    const plotLabel = `${sampleType}, n=${values.length}`;
-    const plot = Object.assign(_plot, {
-      key: sampleType
-    });
-    plot.boxplot.label = plotLabel;
-    plots.push(plot);
+    plot.key = sampleType;
+    plot.boxplot.label = `${sampleType}, n=${values.length}`;
   }
+  plots.push(plot);
   return [outlierMax, outlierMin];
 }
 function setIndividualBoxPlotStats(boxplot, values) {
@@ -204,7 +199,7 @@ async function getWilcoxonData(charts) {
     }
   }
 }
-function parseValues(q, data, sampleType, isLog, overlayTerm, divideTerm) {
+function parseValues(q, data, sampleType, isLog, overlayTw, divideTw) {
   const chart2plot2values = /* @__PURE__ */ new Map();
   const uncomputableValues = {};
   let absMin = Infinity, absMax = -Infinity;
@@ -219,20 +214,20 @@ function parseValues(q, data, sampleType, isLog, overlayTerm, divideTerm) {
     if (isLog && value.value <= 0) continue;
     let chart = "";
     let plot = sampleType;
-    if (divideTerm) {
-      if (!val[divideTerm?.$id]) continue;
-      const value0 = val[divideTerm.$id];
-      if (divideTerm.term?.values?.[value0.key]?.uncomputable) {
-        const label = divideTerm.term.values[value0?.key]?.label;
+    if (divideTw) {
+      if (!val[divideTw?.$id]) continue;
+      const value0 = val[divideTw.$id];
+      if (divideTw.term?.values?.[value0.key]?.uncomputable) {
+        const label = divideTw.term.values[value0?.key]?.label;
         uncomputableValues[label] = (uncomputableValues[label] || 0) + 1;
       }
       chart = value0.key;
     }
-    if (overlayTerm) {
-      if (!val[overlayTerm?.$id]) continue;
-      const value2 = val[overlayTerm.$id];
-      if (overlayTerm.term?.values?.[value2.key]?.uncomputable) {
-        const label = overlayTerm.term.values[value2?.key]?.label;
+    if (overlayTw) {
+      if (!val[overlayTw?.$id]) continue;
+      const value2 = val[overlayTw.$id];
+      if (overlayTw.term?.values?.[value2.key]?.uncomputable) {
+        const label = overlayTw.term.values[value2?.key]?.label;
         uncomputableValues[label] = (uncomputableValues[label] || 0) + 1;
       }
       plot = value2.key;
@@ -247,9 +242,13 @@ function parseValues(q, data, sampleType, isLog, overlayTerm, divideTerm) {
   }
   return { absMax, absMin, chart2plot2values, uncomputableValues };
 }
-function numericBins(overlayTerm, data) {
-  const overlayBins = data.refs.byTermId[overlayTerm?.$id]?.bins ?? [];
-  return new Map(overlayBins.map((bin) => [bin.label, bin]));
+function numericBins(tw, data) {
+  const bins = {};
+  if (!isNumericTerm(tw?.term)) return bins;
+  for (const bin of data.refs.byTermId[tw?.$id]?.bins || []) {
+    bins[bin.label] = bin;
+  }
+  return bins;
 }
 export {
   api,

package/routes/termdb.violin.js

@@ -150,6 +150,7 @@ function sortPlot2Values(data, plot2values, overlayTerm) {
 function setResponse(valuesObject, data, q) {
   const charts = {};
   const overlayTerm = q.overlayTw;
+  const divideTw = q.divideTw;
   for (const [chart, plot2values] of valuesObject.chart2plot2values) {
     const plots = [];
     for (const [plot, values] of sortPlot2Values(data, plot2values, overlayTerm)) {
@@ -157,16 +158,23 @@ function setResponse(valuesObject, data, q) {
         label: overlayTerm?.term?.values?.[plot]?.label || plot,
         values,
         seriesId: plot,
+        chartId: chart,
+        //quick fix to get list samples working
         plotValueCount: values?.length,
-        color: overlayTerm?.term?.values?.[plot]?.color || null,
-        overlayTwBins: isNumericTerm(overlayTerm?.term) ? numericBins(overlayTerm, data) : null
+        color: overlayTerm?.term?.values?.[plot]?.color || null
       });
     }
     charts[chart] = { chartId: chart, plots };
   }
+  const bins = {
+    term1: numericBins(q.tw, data)
+  };
+  if (overlayTerm) bins.term2 = numericBins(overlayTerm, data);
+  if (divideTw) bins.term0 = numericBins(divideTw, data);
   const result = {
     min: valuesObject.min,
     max: valuesObject.max,
+    bins,
     charts,
     uncomputableValues: Object.keys(valuesObject.uncomputableValues).length > 0 ? valuesObject.uncomputableValues : null
   };