fix: testable and functional view manager (#1192)

* feat: local rest-on-couch instance

* fix: fix fancytree regressions

* chore: limit exposed network interfaces

* chore: cleanup

* docs: provide instructions for testing the view manager

Author: stropitek

.env.example

@@ -0,0 +1 @@
+ALLOWED_ORIGINS=http://localhost:63342

.gitignore

@@ -17,3 +17,6 @@ src/usr/config/default.json
 
 .eslintcache
 .sass-cache
+.env
+
+couchdb-data

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "rest-on-couch/home/visualizer"]
+	path = rest-on-couch/home/visualizer
+	url = https://github.com/cheminfo/roc-visualizer-config.git

README.md

@@ -28,3 +28,16 @@ The visualizer allows the modules to comminucate via a central repository of var
 
 To install the development version of the visualizer, you need Node.js.  
 Run `npm install` and all the dependencies will be downloaded.
+
+## View manager
+
+To test the view manager, run a local instance of couchdb with rest-on-couch:
+
+```bash
+# Edit the .env file if needed, making sure the allowed origin is the dev URL serving the visualizer
+cp .env.example .env
+git submodule init
+docker compose up -d --build
+```
+
+Open

bower.json

@@ -42,6 +42,7 @@
     "spectrum": "101b05c1d977fbc529ae4c3b6865b1f7ab70c6e0",
     "sprintf": "1.1.3",
     "threejs": "r71",
+    "ui-contextmenu": "1.18.1",
     "uri.js": "1.18.4",
     "web-animations-js": "2.2.2",
     "x2js": "1.2.0",

compose.yml

@@ -0,0 +1,22 @@
+services:
+  rest-on-couch:
+    build: ./rest-on-couch
+    environment:
+      COUCHDB_USER: admin
+      COUCHDB_PASSWORD: 1234
+      DEBUG: couch:*
+      ALLOWED_ORIGINS: ${ALLOWED_ORIGINS:?Provide the origins in your .env file}
+    depends_on:
+      - couchdb
+    restart: unless-stopped
+    ports:
+      - 127.0.0.1:3000:3000
+  couchdb:
+    image: docker.io/couchdb:3.4
+    environment:
+      COUCHDB_USER: admin
+      COUCHDB_PASSWORD: 1234
+    volumes:
+      - ./couchdb-data:/opt/couchdb/data
+      - ./config/couch.ini:/opt/couchdb/etc/local.d/couch.ini
+    restart: unless-stopped

config/couch.ini

@@ -0,0 +1,10 @@
+[couchdb]
+max_document_size = 4294967296 ; 4 GB
+js_engine = quickjs
+single_node=true
+
+[chttpd]
+bind_address = 0.0.0.0
+
+[uuids]
+algorithm = random

gruntfile.js

@@ -212,6 +212,7 @@ module.exports = function (grunt) {
               './sprintf/dist/**',
               './x2js/xml2json*',
               './jit/Jit/**/*',
+              './ui-contextmenu/jquery.ui-contextmenu*',
               './colors/css/colors.min.css',
               './uri.js/src/*.js',
               './onde/src/*',

rest-on-couch/Dockerfile

@@ -0,0 +1,19 @@
+FROM ghcr.io/cheminfo/rest-on-couch:19
+
+RUN apt-get update && \
+    apt-get install -y jq
+
+COPY /wait.sh /start.sh /create_db.sh /
+RUN chmod +x /wait.sh /start.sh /create_db.sh
+
+# Copy config files
+
+# By default /rest-on-couch is the home directory the rest-on-couch image expects.
+# Can be overridden by overriding the REST_ON_COUCH_HOME_DIR environment variable.
+COPY home /rest-on-couch/
+
+RUN cd /rest-on-couch
+
+WORKDIR /app
+
+CMD ["/start.sh"]

rest-on-couch/create_db.sh

@@ -0,0 +1,47 @@
+#!/bin/sh
+
+/wait.sh
+
+response=$(curl --write-out %{http_code} --silent --output /dev/null http://couchdb:5984/visualizer)
+
+if [ ${response} = "404" ]
+then
+
+echo "Database is not instantiated. Create it."
+
+curl -X POST -H "Content-Type: application/json" http://${COUCHDB_USER}:${COUCHDB_PASSWORD}@couchdb:5984/_cluster_setup -d '{"action": "finish_cluster"}'
+
+# Init rest-on-couch users
+curl -X POST http://${COUCHDB_USER}:${COUCHDB_PASSWORD}@couchdb:5984/_users \
+     -H 'Content-Type: application/json' \
+     -d '{ "_id": "org.couchdb.user:rest-on-couch", "name": "rest-on-couch", "type": "user", "roles": [], "password": "'${COUCHDB_PASSWORD}'" }'
+
+curl -X POST http://${COUCHDB_USER}:${COUCHDB_PASSWORD}@couchdb:5984/_users \
+     -H 'Content-Type: application/json' \
+     -d '{ "_id": "org.couchdb.user:[email protected]", "name": "[email protected]", "type": "user", "roles": [], "password": "'${COUCHDB_PASSWORD}'" }'
+
+
+# Init couchdb databases and security setup, and create rest-on-couch groups (they all can be edited later)
+
+echo "Create visualizer database"
+curl -X PUT http://${COUCHDB_USER}:${COUCHDB_PASSWORD}@couchdb:5984/visualizer
+echo "Create groups in visualizer database"
+curl -X POST http://${COUCHDB_USER}:${COUCHDB_PASSWORD}@couchdb:5984/visualizer \
+     -H 'Content-Type: application/json' \
+     -d '{"$type": "group", "$owners": ["[email protected]"], "name": "anonymousRead", "users": [], "rights": ["read"], "$lastModification": "[email protected]", "$modificationDate": 0, "$creationDate": 0}';
+curl -X POST http://${COUCHDB_USER}:${COUCHDB_PASSWORD}@couchdb:5984/visualizer \
+     -H 'Content-Type: application/json' \
+     -d '{"$type": "group", "$owners": ["[email protected]"], "name": "anyuserRead", "users": [], "rights": ["read"], "$lastModification": "[email protected]", "$modificationDate": 0, "$creationDate": 0}';
+
+echo "Create default groups in visualizer"
+curl -X PUT http://${COUCHDB_USER}:${COUCHDB_PASSWORD}@couchdb:5984/visualizer/defaultGroups \
+     -H 'Content-Type: application/json' \
+     -d '{"_id": "defaultGroups","$type": "db","anonymous": ["anonymousRead"],"anyuser": ["anyuserRead"]}'
+
+echo "Setup visualizer database _security"
+curl -X PUT http://${COUCHDB_USER}:${COUCHDB_PASSWORD}@couchdb:5984/visualizer/_security \
+     -H 'Content-Type: application/json' \
+     -d '{ "admins": { "names": ["rest-on-couch"], "roles": [] }, "members": { "names": ["rest-on-couch"], "roles": [] } }'
+
+
+fi