@sjcrh/proteinpaint-server 2.124.0 → 2.125.0

package/README.md

@@ -1,4 +1,4 @@
-# Proteinpaint Server
+# ProteinPaint Server
 
 The data server backend for the ProteinPaint application
 
@@ -6,26 +6,38 @@ The data server backend for the ProteinPaint application
 
 The client dependencies should be installed as a workspace, follow the README at the project root.
 
-You can either:
-- use a docker container for development, see ../build/dev/README.md
-- or install the [system depedencies](https://docs.google.com/document/d/1tkEHG_vYtT-OifPV-tlPeWQUMsEd3aWAKf5ExOT8G34/edit#heading=h.jy5sdrb1zkut)
-as listed in the [installation instructions](https://docs.google.com/document/d/1tkEHG_vYtT-OifPV-tlPeWQUMsEd3aWAKf5ExOT8G34/edit#heading=h.6nxua6c3ik9l).
+You can either use a docker container for development (../build/dev/README.md), or build from source.
+See https://github.com/stjude/proteinpaint/wiki.
 
 
-## Develop
+## Serverconfig
+
+`server/serverconfig.json` is used:
+- when running any server or test scripts from the pp/server directory
+- if `${process.cwd()/serverconfig.json` does not exist wherever `@sjcrh/proteinpaint-server` is called (if can give example of this usecase)
 
-From the proteinpaint/server/ directory:
+If no `test:unit` code uses serverconfig, then it would have been okay to not have `server/serverconfig.json`.
+However, it's safer to simply have that file available just in case any imported server code uses serverconfig
+and runs as part of test:unit, and that's why `server/emitImports.js` creates one if it doesn't exist by
+copying `container/ci/serverconfig.json`.
 
-`npm run dev` rebundles backend code
 
-`npm start` runs the proteinpaint server
+## Develop
 
+The local development environment is usually triggered following one of these:
+- follow the `Develop` section in [proteinpaint/README.md](https://github.com/stjude/proteinpaint/blob/master/README.md) (preferred)
+- `npm start` from the `server` dir
 
 ## Test
 
-```bash
-npm test
-```
+To run both type checks and test:unit: `npm run test`.
+
+To run type check only: `npx tsc`.
+
+To run unit tests only: `npm run test:unit`
+
+To run specific test file: `npx tsx path/to/spec.ts` 
+
 
 ## Build
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.124.0",
+  "version": "2.125.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -16,8 +16,9 @@
   "scripts": {
     "dev": "npm run start",
     "prestart": "tsx emitImports.js dev > server.js",
-    "start": "tsx watch . /start.js",
+    "start": "tsx watch ./start.js",
     "test:unit": "tsx emitImports.js unit > serverTests.js && c8 tsx serverTests.js && rm -rf ./cache",
+    "test": "tsc && npm run test:unit",
     "precombined:coverage": "tsx emitImports.js unit > serverTests.js",
     "combined:coverage": "coverageKey=test c8 --all --src=proteinpaint/server --experimental-monocart -r=v8 -r=html -r=json -r=markdown-summary -r=markdown-details -o=./.coverage tsx ./coverage.js & ",
     "postcombined:coverage": "rm -rf ./cache",
@@ -29,13 +30,7 @@
     "build": "./build.sh",
     "prepack": "npm run build",
     "postpack": "./dedupjs.sh",
-    "dedup": "./dedupjs.sh",
-    "//todo": "refactor or deprecate the scripts below",
-    "pretest": "tsc && ./test/pretest.js",
-    "pretest:type": "npm run checkers",
-    "pretest:integration": "tsc",
-    "test:integration": "echo 'TODO: server integration tests'",
-    "test:tsc": "tsc --esModuleInterop --noEmit --allowImportingTsExtensions ./shared/types/test/*.type.spec.ts"
+    "dedup": "./dedupjs.sh"
   },
   "author": "",
   "license": "SEE LICENSE IN ./LICENSE",
@@ -67,10 +62,10 @@
   "dependencies": {
     "@sjcrh/augen": "2.121.0",
     "@sjcrh/proteinpaint-python": "2.118.0",
-    "@sjcrh/proteinpaint-r": "2.123.0",
-    "@sjcrh/proteinpaint-rust": "2.124.0",
+    "@sjcrh/proteinpaint-r": "2.125.0",
+    "@sjcrh/proteinpaint-rust": "2.125.0",
     "@sjcrh/proteinpaint-shared": "2.124.0",
-    "@sjcrh/proteinpaint-types": "2.124.0",
+    "@sjcrh/proteinpaint-types": "2.125.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/burden.js

@@ -24,7 +24,7 @@ function init({ genomes }) {
       const q = req.query;
       const ds = genome.datasets[q.dslabel];
       if (!ds)
-        throw `invalid q.genome=${req.query.dslabel}`;
+        throw `invalid q.dslabel=${req.query.dslabel}`;
       if (!ds.cohort.cumburden?.files)
         throw `missing ds.cohort.cumburden.files`;
       if (!ds.cohort?.cumburden?.db)

package/routes/genesetEnrichment.js

@@ -4,7 +4,6 @@ import path from "path";
 import serverconfig from "#src/serverconfig.js";
 import { run_python } from "@sjcrh/proteinpaint-python";
 import { mayLog } from "#src/helpers.ts";
-import { DeleteCacheFiles } from "#src/DeleteCacheFiles.ts";
 const api = {
   endpoint: "genesetEnrichment",
   methods: {
@@ -18,6 +17,7 @@ const api = {
     }
   }
 };
+const cachedir_gsea = path.join(serverconfig.cachedir, "gsea");
 function init({ genomes }) {
   return async (req, res) => {
     try {
@@ -48,19 +48,13 @@ function init({ genomes }) {
 async function run_genesetEnrichment_analysis(q, genomes) {
   if (!genomes[q.genome].termdbs)
     throw "termdb database is not available for " + q.genome;
-  const cache = new DeleteCacheFiles({
-    cachedir: serverconfig.cachedir_gsea,
-    fileExtensions: [".pkl"],
-    maxSize: 1e6
-  });
-  await cache.mayResetCacheCheckTimeout(cache.checkWait);
   const genesetenrichment_input = {
     genes: q.genes,
     fold_change: q.fold_change,
     db: genomes[q.genome].termdbs.msigdb.cohort.db.connection.name,
     // For now msigdb has been added, but later databases other than msigdb may be used
     geneset_group: q.geneSetGroup,
-    cachedir: serverconfig.cachedir_gsea,
+    cachedir: cachedir_gsea,
     geneset_name: q.geneset_name,
     pickle_file: q.pickle_file,
     num_permutations: q.num_permutations,
@@ -85,7 +79,7 @@ async function run_genesetEnrichment_analysis(q, genomes) {
   if (data_found)
     return result;
   if (image_found)
-    return path.join(serverconfig.cachedir_gsea, result.image_file);
+    return path.join(cachedir_gsea, result.image_file);
   throw "data or image not found in gsea output; this should not happen";
 }
 export {

package/routes/termdb.config.js

@@ -171,6 +171,7 @@ function addNonDictionaryQueries(c, ds, genome) {
       "cnvMaxLength",
       "cnvGainCutoff",
       "cnvLossCutoff",
+      "cnvCutoffsByGene",
       "absoluteValueRenderMax",
       "gainColor",
       "lossColor"