@sjcrh/proteinpaint-server 2.178.1-0 → 2.179.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.178.1-0",
+  "version": "2.179.0",
   "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": "2.178.0",
+    "@sjcrh/proteinpaint-python": "2.179.0",
     "@sjcrh/proteinpaint-r": "2.178.0",
-    "@sjcrh/proteinpaint-rust": "2.178.0",
-    "@sjcrh/proteinpaint-shared": "2.178.1-0",
-    "@sjcrh/proteinpaint-types": "2.178.1-0",
+    "@sjcrh/proteinpaint-rust": "2.179.0",
+    "@sjcrh/proteinpaint-shared": "2.179.0",
+    "@sjcrh/proteinpaint-types": "2.179.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",

package/routes/termdb.config.js

@@ -1,7 +1,16 @@
 import serverconfig from "#src/serverconfig.js";
 import { authApi } from "#src/auth.js";
 import { get_ds_tdb } from "#src/termdb.js";
-import { TermTypes } from "#shared/terms.js";
+import {
+  TermTypeGroups,
+  SINGLECELL_CELLTYPE,
+  GENE_EXPRESSION,
+  METABOLITE_INTENSITY,
+  WHOLE_PROTEOME_ABUNDANCE,
+  SINGLECELL_GENE_EXPRESSION,
+  DNA_METHYLATION,
+  SSGSEA
+} from "#shared/terms.js";
 const api = {
   endpoint: "termdb/config",
   methods: {
@@ -255,7 +264,8 @@ function addNonDictionaryQueries(c, ds, genome) {
       q2.singleCell.DEgenes = { termId: q.singleCell.DEgenes.termId };
     }
     if (q.singleCell?.terms?.length) {
-      c.scctTerms = q.singleCell.terms;
+      if (!c.termType2terms) c.termType2terms = {};
+      c.termType2terms[TermTypeGroups.SINGLECELL_CELLTYPE] = q.singleCell.terms;
     }
   }
   if (q.images) {
@@ -270,14 +280,14 @@ function getAllowedTermTypes(ds) {
   if (ds.cohort.termdb.allowedTermTypes) {
     for (const t of ds.cohort.termdb.allowedTermTypes) typeSet.add(t);
   }
-  if (ds.queries?.geneExpression) typeSet.add(TermTypes.GENE_EXPRESSION);
-  if (ds.queries?.metaboliteIntensity) typeSet.add(TermTypes.METABOLITE_INTENSITY);
-  if (ds.queries?.proteome?.whole) typeSet.add(TermTypes.WHOLE_PROTEOME_ABUNDANCE);
-  if (ds.queries?.ssGSEA) typeSet.add(TermTypes.SSGSEA);
-  if (ds.queries?.dnaMethylation) typeSet.add(TermTypes.DNA_METHYLATION);
+  if (ds.queries?.geneExpression) typeSet.add(GENE_EXPRESSION);
+  if (ds.queries?.metaboliteIntensity) typeSet.add(METABOLITE_INTENSITY);
+  if (ds.queries?.proteome?.whole) typeSet.add(WHOLE_PROTEOME_ABUNDANCE);
+  if (ds.queries?.ssGSEA) typeSet.add(SSGSEA);
+  if (ds.queries?.dnaMethylation) typeSet.add(DNA_METHYLATION);
   if (ds.queries?.singleCell) {
-    typeSet.add(TermTypes.SINGLECELL_CELLTYPE);
-    if (ds.queries.singleCell?.geneExpression) typeSet.add(TermTypes.SINGLECELL_GENE_EXPRESSION);
+    typeSet.add(SINGLECELL_CELLTYPE);
+    if (ds.queries.singleCell?.geneExpression) typeSet.add(SINGLECELL_GENE_EXPRESSION);
   }
   if (ds.cohort.termdb.termCollections?.length) typeSet.add("termCollection");
   return [...typeSet];

package/routes/termdb.dmr.js

@@ -1,6 +1,8 @@
 import { TermdbDmrPayload } from "#types/checkers";
-import { run_R } from "@sjcrh/proteinpaint-r";
+import { run_python } from "@sjcrh/proteinpaint-python";
 import { invalidcoord } from "#shared/common.js";
+import { mayLog } from "#src/helpers.ts";
+import { formatElapsedTime } from "#shared";
 const api = {
   endpoint: "termdb/dmr",
   methods: {
@@ -22,24 +24,33 @@ function init({ genomes }) {
       if (!genome) throw new Error("invalid genome");
       const ds = genome.datasets?.[q.dslabel];
       if (!ds) throw new Error("invalid ds");
-      if (!ds.queries?.dnaMethylation) throw new Error("not supported");
+      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");
-      const arg = {
-        group1: q.group1,
-        group2: q.group2,
-        file: ds.queries.dnaMethylation.file,
-        // todo change file to mValueFile
+      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,
         chr: q.chr,
         start: q.start,
-        stop: q.stop
+        stop: q.stop,
+        group1,
+        group2,
+        annotations: q.annotations || [],
+        nan_threshold: q.nan_threshold ?? 0.5
       };
-      const result = JSON.parse(await run_R("dmr.R", JSON.stringify(arg)));
+      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));
       if (result.error) throw new Error(result.error);
-      res.send(result);
+      res.send({ status: "ok", dmrs: result.dmrs });
     } catch (e) {
-      res.send({ error: e.message || e });
+      const msg = e instanceof Error ? e.message : String(e);
+      res.send({ error: msg });
+      if (e instanceof Error && e.stack) console.log(e);
     }
   };
 }

package/routes/termdb.sampleScatter.js

@@ -7,6 +7,7 @@ import { authApi } from "../src/auth.js";
 import { run_R } from "@sjcrh/proteinpaint-r";
 import { read_file } from "../src/utils.js";
 import { getDescrStats } from "#routes/termdb.descrstats.ts";
+import { SINGLECELL_GENE_EXPRESSION, isSingleCellTerm } from "#shared/terms.js";
 const api = {
   endpoint: "termdb/sampleScatter",
   methods: {
@@ -121,12 +122,11 @@ async function getSingleCellScatter(req, res, ds) {
   const { name, sample } = q.singleCellPlot;
   try {
     const tw = q.colorTW;
+    if (!tw || !isSingleCellTerm(tw.term))
+      throw new Error("colorTW must be provided and be a single cell term for single cell scatter plot");
     const arg = { plots: [name], sample };
-    if (tw) {
-      if (tw.term.type == "singleCellGeneExpression") arg.gene = tw.term.gene;
-      else if (tw.term.type == "singleCellCellType") arg.colorBy = tw.term.name;
-      else throw new Error("unsupported tw");
-    }
+    if (tw.term.type == SINGLECELL_GENE_EXPRESSION) arg.gene = tw.term.gene;
+    else arg.colorBy = tw.term.name;
     const data = await ds.queries.singleCell.data.get(arg);
     const plot = data.plots[0];
     const cells = [...plot.expCells, ...plot.noExpCells];
@@ -142,7 +142,8 @@ async function getSingleCellScatter(req, res, ds) {
         z: 0,
         category: cell.category,
         shape: "Ref",
-        hidden
+        hidden,
+        geneExp: cell.geneExp
       };
     });
     const [xMin, xMax, yMin, yMax] = samples.reduce(
@@ -151,14 +152,16 @@ async function getSingleCellScatter(req, res, ds) {
     );
     const categories = new Set(samples.map((s) => s.category));
     const colorMap = {};
-    const k2c = getColors(categories.size);
-    for (const category of categories) {
-      const color = k2c(category);
-      colorMap[category] = {
-        sampleCount: samples.filter((s) => s.category == category).length,
-        color,
-        key: category
-      };
+    if (tw.term.type != SINGLECELL_GENE_EXPRESSION) {
+      const k2c = getColors(categories.size);
+      for (const category of categories) {
+        const color = k2c(category);
+        colorMap[category] = {
+          sampleCount: samples.filter((s) => s.category == category).length,
+          color,
+          key: category
+        };
+      }
     }
     const shapeLegend = [["Ref", { sampleCount: samples.length, shape: 0, key: "Ref" }]];
     const colorLegend = Object.entries(colorMap);

package/routes/termdb.singlecellSamples.js

@@ -9,7 +9,7 @@ import { termdbSingleCellSamplesPayload } from "#types/checkers";
 import { validate_query_singleCell_DEgenes } from "./termdb.singlecellDEgenes.ts";
 import { gdc_validate_query_singleCell_data } from "#src/mds3.gdc.js";
 import ky from "ky";
-import { TermTypes } from "#shared/terms.js";
+import { SINGLECELL_CELLTYPE } from "#shared/terms.js";
 const api = {
   endpoint: "termdb/singlecellSamples",
   methods: {
@@ -252,7 +252,7 @@ function colorColumn2terms(plots, ds) {
         /** TODO: possible term may apply to multiple plots.
          * May need to change to plots: [] */
         plot: plot.name,
-        type: TermTypes.SINGLECELL_CELLTYPE,
+        type: SINGLECELL_CELLTYPE,
         groupsetting: {},
         values: baseValues.reduce((acc, v) => {
           const alias = c?.aliases?.[v];

package/routes/termdb.topVariablyExpressedGenes.js

@@ -70,7 +70,7 @@ function nativeValidateQuery(ds) {
       }
     } else {
       for (const i of gE.samples) {
-        const n = ds.cohort.termdb.q.id2sampleName(i.id);
+        const n = ds.cohort.termdb.q.id2sampleName(i);
         if (!n) throw "sample id cannot convert to string name";
         samples.push(n);
       }