@sjcrh/proteinpaint-server 2.137.2-2 → 2.137.3

package/dataset/termdb.test.js

@@ -1,7 +1,3 @@
-import serverconfig from "@sjcrh/proteinpaint-server/src/serverconfig.js";
-import * as path from "path";
-import { existsSync, unlinkSync, symlinkSync, access, constants } from "fs";
-copyDataFilesFromRepo2Tp();
 function termdb_test_default() {
   return {
     isMds3: true,
@@ -141,7 +137,7 @@ function termdb_test_default() {
                     {
                       chartType: "barchart",
                       term: { id: "diaggrp" },
-                      settings: { barchart: { colorBars: true, showPercent: true, colorUsing: "generated" } }
+                      settings: { barchart: { colorBars: true, showPercent: true, colorUsing: "present" } }
                     }
                   ]
                 },
@@ -345,27 +341,6 @@ function termdb_test_default() {
     }
   };
 }
-function copyDataFilesFromRepo2Tp() {
-  if (existsSync("/home/root/pp"))
-    return;
-  const targetDir = path.join(serverconfig.binpath, "test/tp/files/hg38/TermdbTest");
-  const datadir = path.join(serverconfig.tpmasterdir, "files/hg38/TermdbTest");
-  if (datadir == `${serverconfig.binpath}/test/tp`) {
-    access(datadir, constants.R_OK | constants.W_OK, (err) => {
-      if (!err) {
-        try {
-          if (!existsSync(datadir))
-            unlinkSync(datadir);
-          symlinkSync(targetDir, datadir);
-        } catch (error) {
-          console.warn("Error while coping data files from Repo to Tp: " + error);
-        }
-      } else {
-        console.warn(`user doesn't have sufficient permissions for `);
-      }
-    });
-  }
-}
 export {
   termdb_test_default as default
 };

package/genome/copyDataFilesFromRepo2Tp.js

@@ -0,0 +1,57 @@
+import serverconfig from '@sjcrh/proteinpaint-server/src/serverconfig.js'
+import * as path from 'path'
+import fs from 'fs'
+import { spawnSync } from 'child_process'
+
+/*
+	copyDataFilesFromRepo2Tp()
+	- does not work when tp is not writable, such as when the tp dir is mounted as read-only onto a container
+	- must be called before genome and dataset init steps in initGenomeDs(), 
+	  such as by calling in the genome js file like in genome/hg38.test.ts
+*/
+export async function copyDataFilesFromRepo2Tp(testPath) {
+	// when running tests where the tp directory is not writable (such as from inside a container),
+	// the workflow script should copy the server/test/tp dir as serverconfig.tpmasterdir
+	// and not trigger the symlinks below
+	if (fs.existsSync('/home/root/pp')) {
+		console.warn('skipped TermdbTest copying, assumed the mounted host tp dir is not writable from within a container')
+		return
+	}
+
+	const targetDir = path.join(serverconfig.binpath, 'test/tp', testPath)
+	const datadir = path.join(serverconfig.tpmasterdir, testPath)
+
+	// no need to copy files or set the symlink when the target TermdbTest dir
+	// already equals the datadir under serverconfig.tpmasterdir
+	if (targetDir === datadir) return
+
+	try {
+		await fs.promises.access(serverconfig.tpmasterdir)
+	} catch {
+		// the tp dir is not readable and/or writable,
+		// may still be okay if the tp/files/hg38/TermdbTest already exists and is up-to-date
+		console.log(`!!! insufficient permissions to create or update TermdbTest directory or symlink !!!`)
+		return
+	}
+
+	try {
+		if (!fs.existsSync(datadir)) {
+			fs.symlinkSync(targetDir, datadir)
+		} else if (fs.statSync(datadir).isDirectory()) {
+			// support an option to have an actual TermdbTest dir locally instead of a symlink,
+			// to make it easier to switch between native or container dev/test process,
+			// since a local symlink will not work as a container mount
+			console.log(`copying TermdbTest files to tp dir ...`)
+			// do not delete, copy files from repo to tp
+			const ps = spawnSync(`rsync`, ['-av', `${targetDir}/`, datadir], { encoding: 'utf-8' })
+			if (ps.stderr) throw ps.stderr
+			//console.log(421, [ps.stdout, ps.stderr])
+		} else {
+			console.log('replacing the TermdbTest symlink ...')
+			fs.unlinkSync(datadir)
+			fs.symlinkSync(targetDir, datadir)
+		}
+	} catch (error) {
+		console.warn('Error while copying data files from Repo to Tp: ', error)
+	}
+}

package/genome/hg38.test.js

@@ -1,3 +1,5 @@
+import { copyDataFilesFromRepo2Tp } from "./copyDataFilesFromRepo2Tp.js";
+await copyDataFilesFromRepo2Tp("files/hg38/TermdbTest");
 const genome = {
   species: "human",
   genomefile: "NA",
@@ -8,8 +10,9 @@ const genome = {
     msigdb: {
       label: "MSigDB",
       cohort: {
-        db: { file: "files/hg38/TermdbTest/msigdb/db" },
+        // NOTE: in the dev environment, sjpp/start.js is
         // nest file under TermdbTest since the folder is auto symlinked
+        db: { file: "files/hg38/TermdbTest/msigdb/db" },
         termdb: {
           isGeneSetTermdb: true
         }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.137.2-2",
+  "version": "2.137.3",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -63,8 +63,8 @@
     "@sjcrh/proteinpaint-python": "2.135.2-0",
     "@sjcrh/proteinpaint-r": "2.137.2-0",
     "@sjcrh/proteinpaint-rust": "2.137.2-0",
-    "@sjcrh/proteinpaint-shared": "2.137.2-2",
-    "@sjcrh/proteinpaint-types": "2.137.2-2",
+    "@sjcrh/proteinpaint-shared": "2.137.3",
+    "@sjcrh/proteinpaint-types": "2.137.3",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/filterTermValues.js

@@ -1,5 +1,6 @@
 import { FilterTermValuesPayload } from "#types/checkers";
 import { getData, getSamplesPerFilter } from "../src/termdb.matrix.js";
+import { authApi } from "../src/auth.js";
 const api = {
   endpoint: "filterTermValues",
   methods: {
@@ -48,11 +49,14 @@ function getList(samplesPerFilter, filtersData, tw) {
   return filteredValues;
 }
 async function getFilters(query, ds, genome, res) {
+  if (!query.filterByUserSites)
+    authApi.mayAdjustFilter(query, ds, query.terms);
   try {
     const samplesPerFilter = await getSamplesPerFilter(query, ds);
     const filtersData = await getData(
       {
-        terms: query.terms
+        terms: query.terms,
+        __protected__: query.__protected__
       },
       ds,
       genome

package/routes/grin2.js

@@ -47,7 +47,7 @@ async function runGrin2(g, ds, request) {
   const startTime = Date.now();
   mayLog("[GRIN2] Getting samples from cohort filter...");
   const samples = await get_samples(
-    request.filter,
+    request,
     ds,
     true
     // must set to true to return sample name to be able to access file. FIXME this can let names revealed to grin2 client, may need to apply access control

package/routes/profileFormScores.js

@@ -29,14 +29,17 @@ function init({ genomes }) {
   };
 }
 async function getScoresDict(query, ds, genome) {
+  if (!query.filterByUserSites)
+    query.__protected__.ignoredTermIds.push(query.facilityTW.term.id);
   const terms = [...query.scoreTerms, query.facilityTW];
   if (query.scScoreTerms)
     terms.push(...query.scScoreTerms);
   const data = await getData(
     {
       terms,
-      filter: query.site || !query.isAggregate ? void 0 : query.filter
+      filter: query.site || !query.isAggregate ? void 0 : query.filter,
       //if isRadarFacility and site is specified, do not apply the filter
+      __protected__: query.__protected__
     },
     ds,
     genome
@@ -48,6 +51,9 @@ async function getScoresDict(query, ds, genome) {
   sites = lst.map((s) => {
     return { label: data.refs.bySampleId[s.sample].label, value: s.sample };
   });
+  if (query.userSites) {
+    sites = sites.filter((s) => query.userSites.includes(s.label));
+  }
   let sitesSelected = [];
   if (query.site)
     sitesSelected = [query.site];
@@ -56,18 +62,18 @@ async function getScoresDict(query, ds, genome) {
   else
     sitesSelected = query.sites;
   const sampleData = sitesSelected?.length == 1 ? data.samples[sitesSelected[0]] : null;
-  const samples = Object.values(data.samples);
+  let samples = sampleData ? [sampleData] : Object.values(data.samples);
+  if (sitesSelected?.length > 0)
+    samples = samples.filter((s) => sitesSelected.includes(s.sample));
   const term2Score = {};
   for (const d of query.scoreTerms) {
-    const samples2 = sampleData ? [sampleData] : Object.values(data.samples);
     const getDictFunc = (sample) => getDict(d.$id, sample);
-    const percents = getPercentsDict(getDictFunc, samples2);
+    const percents = getPercentsDict(getDictFunc, samples);
     term2Score[d.term.id] = percents;
   }
   if (query.scScoreTerms)
     for (const d of query.scScoreTerms) {
-      const samples2 = sampleData ? [sampleData] : Object.values(data.samples);
-      const percents = getSCPercentsDict(d, samples2);
+      const percents = getSCPercentsDict(d, samples);
       term2Score[d.term.id] = percents;
     }
   const facilityValue = sampleData?.[query.facilityTW.$id];

package/routes/profileScores.js

@@ -29,6 +29,8 @@ function init({ genomes }) {
   };
 }
 async function getScores(query, ds, genome) {
+  if (!query.filterByUserSites)
+    query.__protected__.ignoredTermIds.push(query.facilityTW.term.id);
   const terms = [query.facilityTW];
   for (const term of query.scoreTerms) {
     terms.push(term.score);
@@ -39,8 +41,9 @@ async function getScores(query, ds, genome) {
   const data = await getData(
     {
       terms,
-      filter: query.site || !query.isAggregate ? void 0 : query.filter
+      filter: query.site || !query.isAggregate ? void 0 : query.filter,
       //if site is specified, do not apply the filter that is for the aggregation
+      __protected__: query.__protected__
     },
     ds,
     genome

package/routes/termdb.categories.js

@@ -45,8 +45,9 @@ async function trigger_getcategories(q, res, tdb, ds, genome) {
     terms: [q.tw],
     currentGeneNames: q.currentGeneNames,
     // optional, from mds3 mayAddGetCategoryArgs()
-    rglst: q.rglst
+    rglst: q.rglst,
     // optional, from mds3 mayAddGetCategoryArgs()
+    __protected__: q.__protected__
   };
   const data = await getData(arg, ds, genome);
   if (data.error)

package/routes/termdb.config.js

@@ -62,7 +62,8 @@ function make(q, req, res, ds, genome) {
     defaultChartType: ds.cohort.defaultChartType,
     invalidTokenErrorHandling: tdb.invalidTokenErrorHandling,
     colorMap: tdb.colorMap,
-    defaultTw4correlationPlot: tdb.defaultTw4correlationPlot
+    defaultTw4correlationPlot: tdb.defaultTw4correlationPlot,
+    authFilter: req.query.filter
   };
   if (tdb.plotConfigByCohort)
     c.plotConfigByCohort = tdb.plotConfigByCohort;
@@ -92,7 +93,6 @@ function make(q, req, res, ds, genome) {
     c.assayAvailability = ds.assayAvailability;
   if (ds.cohort.correlationVolcano)
     c.correlationVolcano = ds.cohort.correlationVolcano;
-  c.requiredAuth = authApi.getRequiredCredForDsEmbedder(q.dslabel, q.embedder);
   addRestrictAncestries(c, tdb);
   addScatterplots(c, ds);
   addMatrixplots(c, ds);
@@ -102,6 +102,7 @@ function make(q, req, res, ds, genome) {
   c.clientAuthResult = info?.clientAuthResult || {};
   if (tdb.displaySampleIds)
     c.displaySampleIds = tdb.displaySampleIds(c.clientAuthResult);
+  c.authFilter = req.query.filter;
   res.send({ termdbConfig: c });
 }
 function addRestrictAncestries(c, tdb) {

package/routes/termdb.descrstats.js

@@ -30,7 +30,11 @@ function init({ genomes }) {
         throw "invalid termdb object";
       if (!q.tw.$id)
         q.tw.$id = "_";
-      const data = await getData({ filter: q.filter, filter0: q.filter0, terms: [q.tw] }, ds, genome);
+      const data = await getData(
+        { filter: q.filter, filter0: q.filter0, terms: [q.tw], __protected__: q.__protected__ },
+        ds,
+        genome
+      );
       if (data.error)
         throw data.error;
       const values = [];

package/routes/termdb.topMutatedGenes.js

@@ -93,7 +93,7 @@ function validate_query_getTopMutatedGenes(ds) {
   q.get = async (param) => {
     let sampleStatement = "";
     if (param.filter) {
-      const lst = await get_samples(param.filter, ds);
+      const lst = await get_samples(param, ds);
       if (lst.length == 0)
         throw "empty sample filter";
       sampleStatement = `WHERE sample IN (${lst.map((i) => i.id).join(",")})`;

package/routes/termdb.topTermsByType.js

@@ -56,7 +56,7 @@ function nativeValidateQuery(ds, type) {
     const typeQuery = ds.queries[type];
     const samples = [];
     if (q.filter) {
-      const sidlst = await get_samples(q.filter, ds);
+      const sidlst = await get_samples(q, ds);
       for (const i of sidlst) {
         if (typeQuery.samples.includes(i.id)) {
           const n = ds.cohort.termdb.q.id2sampleName(i.id);

package/routes/termdb.topVariablyExpressedGenes.js

@@ -66,7 +66,7 @@ function nativeValidateQuery(ds) {
   ds.queries.topVariablyExpressedGenes.getGenes = async (q) => {
     const samples = [];
     if (q.filter) {
-      const sidlst = await get_samples(q.filter, ds);
+      const sidlst = await get_samples(q, ds);
       for (const i of sidlst) {
         if (gE.samples.includes(i.id)) {
           const n = ds.cohort.termdb.q.id2sampleName(i.id);