chore: work on fixing server img + prod deployment

epivar-prod/README.md

@@ -16,3 +16,10 @@ Genes and gene-peak pairs:
 docker compose exec -iT epivar-node-1-server node ./scripts/import-genes.mjs < /opt/epivar/input-files/flu-infection-gene-peaks.csv
 docker compose exec -iT epivar-node-2-server node ./scripts/import-genes.mjs < TODO
 ```
+
+Peaks:
+
+```bash
+docker compose exec epivar-node-1-server node ./scripts/import-peaks.js
+docker compose exec epivar-node-2-server node ./scripts/import-peaks.js
+```

epivar-prod/docker-compose.yml

@@ -18,7 +18,7 @@ services:
   # Node 1: hg19 data --------------------------------------------------------------------------------------------------
 
   epivar-node-1-server:
-    user: $EPIVAR_UID:$EPIVAR_UID
+    # user: $EPIVAR_UID:$EPIVAR_UID
     image: ghcr.io/c3g/epivar-server:pr-13
     networks:
       - epivar-node-1-server-net
@@ -82,7 +82,7 @@ services:
   # Node 2: hg38 data (lifted over) ------------------------------------------------------------------------------------
 
   # epivar-node-2-server:
-  #   user: $USER:$USER
+  #   # user: $USER:$USER
   #   image: ghcr.io/c3g/epivar-server:latest
   #   networks:
   #     - epivar-node-2-server-net
@@ -143,7 +143,6 @@ services:
 networks:
   epivar-node-1-server-net:
     driver: bridge
-    internal: true
   epivar-node-1-redis-net:
     driver: bridge
     internal: true

models/genes.mjs

@@ -2,7 +2,19 @@
  * genes.js
  */
 
-export const normalizeGeneName = name => name.replace(/[^a-zA-Z\d]/g, '-');
+const GENE_RENAMES = {
+  CCDC132: "VPS50",
+  CCDC109B: "MCUB",
+  FAM214B: "ATOSB",
+  BZRAP1: "TSPOAP1",
+  C19orf60: "REX1BD",
+};
+
+export const normalizeGeneName = name => {
+  const nameNorm = name.replace(/[^a-zA-Z\d]/g, '-');
+  if (nameNorm in GENE_RENAMES) return GENE_RENAMES[nameNorm];
+  return nameNorm;
+}
 
 export default {
   normalizeGeneName,

scripts/import-peaks.js

@@ -12,12 +12,18 @@ console.log("Loading peaks");
 // --------------------------------------------------------------------------
 
 (async () => {
-  const {ASSAYS, loadingPrecomputedPoints, precomputedPoints} = await import('./_common.mjs');
+  const {loadingPrecomputedPoints, precomputedPoints} = await import('./_common.mjs');
 
   const db = await import("../models/db.mjs");
   const Gene = await import('../models/genes.mjs');
 
-  const datasetPaths = ASSAYS.map(assay => envConfig.QTLS_TEMPLATE.replace(/\$ASSAY/g, assay));
+  const client = await db.connect();
+
+  const assays = Object.fromEntries(
+    (await client.query("SELECT * FROM assays")).rows.map(r => [r.name, r]));
+
+  const datasetPaths = Object.keys(assays).map(assay => envConfig.QTLS_TEMPLATE.replace(/\$ASSAY/g, assay));
+  console.log(`Found paths:`, datasetPaths);
 
   // Clear relevant tables of existing data
   await db.run("TRUNCATE TABLE snps RESTART IDENTITY CASCADE");
@@ -26,11 +32,7 @@ console.log("Loading peaks");
   const featureCache = Object.fromEntries(
     (await db.findAll("SELECT * FROM features")).map(row => [row.nat_id, row.id]));
 
-  const client = await db.connect();
   try {
-    const assays = Object.fromEntries(
-      (await client.query("SELECT * FROM assays")).rows.map(r => [r.name, r]));
-
     // Preload all gene features
     process.stdout.write("Preloading gene features...");
     const geneCache = Object.fromEntries(

spec/run_server.bash

@@ -1,8 +1,5 @@
 #!/bin/bash
 
-export HOME=/app
-
-npm install -g pm2
 pipx ensurepath
-source $HOME/.profile
+source /root/.profile
 pm2-runtime /app/bin/www --name epivar -i 0

spec/server.Dockerfile

@@ -18,6 +18,8 @@ COPY spec/run_server.bash /
 
 RUN mkdir -p /tracks; \
     mkdir -p /mergedTracks
+
+HOME=/app
 WORKDIR /app
 
 # Copy source code + file directories
@@ -42,6 +44,9 @@ RUN wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigSummary -O
 # Uninstall compilation dependencies + wget since we don't need them anymore
 RUN apt-get purge -y build-essential python3-dev wget
 
+# Install PM2 to manage multiple processes
+RUN npm install -g pm2
+
 # Install Node dependencies
 RUN npm ci