@sjcrh/proteinpaint-server 2.137.2-2 → 2.137.2

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": "2.137.2",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -64,7 +64,7 @@
     "@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-types": "2.137.2",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",