add subpath logic

biogenome-client/Dockerfile

@@ -2,8 +2,6 @@ FROM node:17 as build-stage
 
 ARG ROOT_NODE
 
-ARG PROJECT_ACCESSION
-
 ARG CESIUM_TOKEN
 
 ARG BASE_PATH
@@ -19,7 +17,6 @@ COPY . .
 COPY ./ducd node_modules/ducd 
 
 ENV VITE_ROOT_NODE=${ROOT_NODE}
-ENV VITE_PROJECT_ACCESSION=${PROJECT_ACCESSION}
 ENV VITE_CESIUM_TOKEN=${CESIUM_TOKEN}
 ENV VITE_BASE_PATH=${BASE_PATH}
 
@@ -29,8 +26,19 @@ RUN npm run build
 # production stage
 FROM nginx:stable-alpine
 
-#  copy the nginx.conf in our filesystem into the image filesystem
-COPY default.conf.template /etc/nginx/templates/default.conf.template
+ARG BASE_PATH
+
+# Copy the nginx templates
+COPY root.template /etc/nginx/templates/root.template
+COPY subpath.template /etc/nginx/templates/subpath.template
+
+# Copy the script
+COPY select-template.sh /usr/local/bin/select-template.sh
+
+RUN chmod +x /usr/local/bin/select-template.sh
+
+# Set the config file based on the build argument
+RUN /usr/local/bin/select-template.sh
 
 COPY --from=build-stage /client/dist /usr/share/nginx/html
 

biogenome-client/select-template.sh

@@ -0,0 +1,12 @@
+#!/bin/sh
+
+# Print the value of BASE_PATH for debugging
+echo "BASE_PATH is: $BASE_PATH"
+
+if [ -z "$BASE_PATH" ]; then
+    echo "BASE_PATH is empty or not set. Using root.template."
+    cp /etc/nginx/templates/root.template /etc/nginx/templates/default.conf.template
+else
+    echo "BASE_PATH is set to: $BASE_PATH. Using subpath.template."
+    cp /etc/nginx/templates/subpath.template /etc/nginx/templates/default.conf.template
+fi

biogenome-client/src/components/genome-browser/Jbrowse2.vue

@@ -11,7 +11,7 @@ import RefGetPlugin from 'jbrowse-plugin-refget-api'
 import { Assembly, AssemblyAdapter, TrackData } from '../../data/types'
 // import '@fontsource/roboto'
 const wrapper = ref(null)
-const baseURL = import.meta.env.VITE_BASE_PATH? import.meta.env.VITE_BASE_PATH + 'api' : '/api'
+const baseURL = import.meta.env.VITE_BASE_PATH ? import.meta.env.VITE_BASE_PATH + '/api' : '/api'
 const props = defineProps<{
   defaultSession?: Record<string, any>
   configuration?: Record<string, any>
@@ -52,13 +52,13 @@ function parseAssembly(assembly: Assembly) {
       },
     },
   }
-  if(assembly.has_chromosomes_aliases){
+  if (assembly.has_chromosomes_aliases) {
     assemblyAdapter.refNameAliases = {
-      adapter : {
+      adapter: {
         type: "RefNameAliasAdapter",
         location: {
-          uri:`${baseURL}/assemblies/${assembly.accession}/chr_aliases`,
-          locationType:"UriLocation"
+          uri: `${baseURL}/assemblies/${assembly.accession}/chr_aliases`,
+          locationType: "UriLocation"
         }
       }
     }

biogenome-client/src/http-axios.js

@@ -1,14 +1,14 @@
 import axios from 'axios'
 
-const baseURL = import.meta.env.VITE_BASE_PATH? import.meta.env.VITE_BASE_PATH + 'api' : '/api'
+const baseURL = import.meta.env.VITE_BASE_PATH  ?  import.meta.env.VITE_BASE_PATH + '/api' : '/api' 
 const base = axios.create({
   baseURL: baseURL,
   headers: {
     'Content-type': 'application/json',
   },
 })
 
-const download =  axios.create({
+const download = axios.create({
   baseURL: baseURL,
   responseType: 'blob'
 })
@@ -47,5 +47,5 @@ export default {
   base: base,
   ena: ena,
   ncbi: ncbi,
-  download:download
+  download: download
 }

biogenome-client/src/router/index.ts

@@ -4,10 +4,6 @@ import { models, maps, cms } from '../../config.json'
 import { cmsRoutes } from './cms-routes'
 import { modelRoutes, mapRoutes } from './custom-routes'
 
-const rootNode = import.meta.env.VITE_ROOT_NODE ?
-  import.meta.env.VITE_ROOT_NODE : '131567'
-
-
 const defaultRoutes: Array<RouteRecordRaw> = [
   {
     path: '/:catchAll(.*)',
@@ -76,7 +72,7 @@ function createRoutes() {
 const routes = [...createRoutes()]
 
 const router = createRouter({
-  history: createWebHistory(import.meta.env.BASE_URL),
+  history: createWebHistory(import.meta.env.VITE_BASE_PATH ? import.meta.env.VITE_BASE_PATH : import.meta.env.BASE_URL),
   routes,
 })
 

biogenome-client/subpath.template

@@ -0,0 +1,34 @@
+proxy_cache_path /var/cache/nginx levels=1:2 keys_zone=my_cache:10m max_size=10g inactive=60m;
+
+server {
+
+    root /usr/share/nginx/html;
+
+    listen ${API_PORT};
+    location ${BASE_PATH} {
+        rewrite ${BASE_PATH}/(.*) /$1 break;
+        try_files $uri $uri/ /index.html;
+        client_max_body_size 1000M;
+    }
+
+    location  ${BASE_PATH}/files/ {
+        rewrite ${BASE_PATH}/(.*) /$1 break;
+        alias /var/www/statics/;
+    }
+
+    location ${BASE_PATH}/api {
+        rewrite ${BASE_PATH}/(.*) /$1 break;
+
+        # Define cache parameters
+        proxy_cache my_cache;
+        proxy_cache_valid 200 10m;
+        proxy_cache_methods GET HEAD;
+        proxy_cache_key $scheme$proxy_host$request_uri;
+
+
+        include uwsgi_params;
+        uwsgi_pass ${API_HOST}:${API_PORT};
+        client_max_body_size 1000M;
+        uwsgi_read_timeout 600;
+    }
+}

biogenome-client/vite.config.ts

@@ -11,9 +11,10 @@ export default ({ mode }) => {
 
   // import.meta.env.VITE_NAME available here with: process.env.VITE_NAME
   // import.meta.env.VITE_PORT available here with: process.env.VITE_PORT
-
+  const basePath = env.VITE_BASE_PATH ? env.VITE_BASE_PATH + '/': undefined
+  console.log(basePath)
   return defineConfig({
-    base: env.VITE_BASE_PATH ? env.VITE_BASE_PATH : '/',
+    base: basePath,
     resolve: {
       alias: {
         stream: 'stream-browserify',