Merge pull request #1 from jay-m-dev/add-alzkb-site

Add alzkb-site directory with neo4j and website

Author: nickotto

.gitignore

@@ -234,4 +234,12 @@ dmypy.json
 # Cython debug symbols
 cython_debug/
 
-# End of https://www.toptal.com/developers/gitignore/api/python,macos,emacs,linux
+# End of https://www.toptal.com/developers/gitignore/api/python,macos,emacs,linux
+
+# Ignore files from the alzkb-site
+node_modules
+default.conf
+*.dump
+*.key
+*.pem
+*.crt

alzkb-site/.dockerignore

@@ -0,0 +1,2 @@
+node_modules
+npm-debug.log

alzkb-site/.env_sample

@@ -0,0 +1,73 @@
+COMPOSE_PROJECT_NAME=alzkb
+ALZKB_NEO4J_BROWSER_HTTP_PORT=7474
+ALZKB_NEO4J_BROWSER_HTTPS_PORT=7473
+ALZKB_APP_SERVICE=app
+ALZKB_PORT=5000
+ALZKB_DATA_ROOT=/data
+NEO4J_server_databases_default__to__read__only=true
+NEO4J_dbms_security_auth__enabled=false
+NEO4J_server_default__listen__address=0.0.0.0
+NEO4J_internal_dbms_cypher__ip__blocklist=0.0.0.0/0,::/0
+NEO4J_dbms_security_allow__csv__import__from__file__urls=false
+NEO4J_dbms_security_procedures_allowlist=gds.*,apoc.algo.*,apoc.atomic.*,apoc.bolt.*,apoc.case,apoc.cluster.*apoc.coll.*,apoc.config.*,apoc.convert.*,apoc.couchbase.*,apoc.create.*,apoc.custom.*,apoc.cypher.*,apoc.date.*,apoc.diff.*,apoc.do.*,apoc.dv.*,apoc.es.*,apoc.example.*,apoc.export.*,apoc.generate.*,apoc.gephi.*,apoc.get.*,apoc.graph.*,apoc.help,apoc.import.*,apoc.json.*,apoc.lock.*,apoc.log.*,apoc.math.*,apoc.merge.*,apoc.meta.*,apoc.metrics.*,apoc.model.*,apoc.mongo.*,apoc.mongodb.*,apoc.monitor.*,apoc.neighbors.*,apoc.nlp.*,apoc.nodes.*,apoc.path.*,apoc.periodic.*,apoc.redis.*,apoc.refactor.*,apoc.schema.*,apoc.search.*,apoc.spatial.*,apoc.static.*,apoc.stats.*,apoc.systemdb.*,apoc.text.*,apoc.trigger.*,apoc.ttl.*,apoc.util.*,apoc.uuid.*,apoc.warmup.*,apoc.when,apoc.xml.*
+# dbms.security.procedures.unrestricted is added automatically when the plugins are installed on the docker image
+NEO4J_dbms_security_procedures_unrestricted=gds.*,apoc.*
+NEO4J_server_directories_import=/var/lib/neo4j/import
+NEO4J_server_directories_data=/var/lib/neo4j/data
+NEO4J_server_directories_logs=/var/lib/neo4j/logs
+NEO4J_server_directories_plugins=/var/lib/neo4j/plugins
+NEO4J_PLUGINS='["apoc", "graph-data-science", "n10s"]'
+############################################################################################################
+# PRODUCTION SETTINGS
+# - uncomment the following lines in production
+# - comment the corresponding lines in development
+# ##########################################################################################################
+# ALZKB_HOST=alzkb.ai
+# ALZKB_HOST2=www.alzkb.ai
+# ALIRO_HOST=aliro.ai
+# ALIRO_HOST2=www.aliro.ai
+# ALZKB_NEO4J_BROWSER=neo4j.alzkb.ai
+# ALZKB_CERT=cert_file_name
+# ALZKB_CERT_KEY=cert_key_file_name
+# ALIRO_CERT=cert_file_name
+# ALIRO_CERT_KEY=cert_key_file_name
+# NEO4J_server_memory_heap_initial__size=1G
+# NEO4J_server_memory_heap_max__size=8G
+# NEO4J_server_default__advertised__address=neo4j.alzkb.ai
+# NEO4J_server_http_enabled=false
+# NEO4J_server_https_enabled=true
+# NEO4J_server_bolt_tls__level=OPTIONAL
+# NEO4J_dbms_ssl_policy_https_enabled=true
+# NEO4J_dbms_ssl_policy_https_base__directory==certificates/https
+# NEO4J_dbms_ssl_policy_https_private__key=cert_key_file_name
+# NEO4J_dbms_ssl_policy_https_public__certificate=cert_file_name
+# NEO4J_dbms_ssl_policy_https_client__auth=NONE
+# NEO4J_dbms_ssl_policy_bolt_enabled=true
+# NEO4J_dbms_ssl_policy_bolt_base__directory=certificates/bolt
+# NEO4J_dbms_ssl_policy_bolt_private__key=cert_key_file_name
+# NEO4J_dbms_ssl_policy_bolt_public__certificate=cert_file_name
+# NEO4J_dbms_ssl_policy_bolt_client__auth=NONE
+# NEO4J_browser_remote__content__hostname__whitelist=*
+# NEO4J_browser_post__connect__cmd=guide intro;play https://${ALZKB_HOST}/alzkb;play https://${ALZKB_HOST}/samples
+# NODE_ENV=prod
+############################################################################################################
+# DEVELOPMENT SETTINGS
+# - uncomment the following lines in development
+# - comment the corresponding lines in production
+# ##########################################################################################################
+ALZKB_HOST=127.0.0.1
+ALZKB_HOST2=localhost
+ALIRO_HOST=localhost
+ALIRO_HOST2=localhost
+ALZKB_NEO4J_BROWSER=127.0.0.1
+# # SSL is not used in development
+# # so these lines are should not be uncommented
+# # ALZKB_CERT=cert_file_name
+# # ALZKB_CERT_KEY=cert_key_file_name
+# # ALIRO_CERT=cert_file_name
+# # ALIRO_CERT_KEY=cert_key_file_name
+NEO4J_server_default__advertised__address=localhost
+NEO4J_server_http_enabled=true
+NEO4J_server_https_enabled=false
+NEO4J_browser_post__connect__cmd=guide intro
+NODE_ENV=dev

alzkb-site/.eslintrc.js

@@ -0,0 +1,15 @@
+module.exports = {
+  env: {
+    browser: true,
+    es2021: true
+  },
+  extends: [
+    'standard'
+  ],
+  parserOptions: {
+    ecmaVersion: 'latest',
+    sourceType: 'module'
+  },
+  rules: {
+  }
+}

alzkb-site/README.md

@@ -0,0 +1,56 @@
+# Alzheimer's Knowledgebase (AlzKB) Site
+This repository is comprised of the following components:
+
+- **Website**: site with some general information about this project. The source code for this website is found in the `app` directory
+
+- **Neo4j**: used to store the graph database for this Knowledgebase.
+
+- **Nginx**: used as a reverse proxy for the Website and the Neo4j Browser
+
+- **Docker Compose files**
+  - The `.yml` files contain definitions for building a docker image.  
+
+- **Environmental Variables**
+  - The environmental variables in .env_sample are used by the different docker services.
+
+# Installation
+## Prerequisites
+**Docker**
+- Automated Installation
+  - Run `install-docker.sh` to install **Docker Engine**
+- Manual Installation
+  - Install either [**Docker Desktop**](https://www.docker.com/products/docker-desktop/) or [**Docker Engine**](https://docs.docker.com/engine/getstarted/step_one/) based on your needs.
+  - [**Docker Compose**](https://docs.docker.com/compose/install/)
+## Building and Running
+### Building and deploying all services
+1. Get a dump file of the database [here](https://upenn.box.com/s/dalcofa8i7rkkc2h2n6bfg8nvmwi83pq) and put this file in **neo4j/dump/**, make sure the filename is alzkb.dump (rename it if necessary)
+2. Copy the **.env_sample** as **.env** and set the variable values as needed for your environment.
+3. **On the very first run**, uncomment the lines for the neo4j-admin service in the docker-compose.yml file, after the first run, the neo4j-admin service is not needed.
+4. To deploy the Website, Neo4j, Nginx and dump the database into neo4j run: `docker compose up -d --build`
+### Building and deploying the services independently
+The services can be built independently of each other as needed.  
+**First**, copy the **.env_sample** as **.env** and update the variable values as needed for your environment.
+- Website
+  - Run `docker compose -f ./app.yml up -d --build`
+- Load the database dump
+  1. Ensure that the neo4j docker container is not running, it must be stopped if it is.
+  2. Get a dump file of the database [here](https://upenn.box.com/s/dalcofa8i7rkkc2h2n6bfg8nvmwi83pq) and put this file in **neo4j/dump/**, make sure the filename is alzkb.dump (rename it if necessary)
+  3. Run `docker compose -f ./neo4j-admin.yml up -d --build`
+- Neo4j
+  - Run `docker compose -f ./neo4j.yml up -d --build`
+- Nginx
+  - Run `docker compose -f ./nginx.yml up -d --build`
+## Environmental Variables
+The **.env_sample** file contains the following environmental variables:
+- `COMPOSE_PROJECT_NAME` Base name of this project.
+  - See the docker [documentation](https://docs.docker.com/compose/reference/envvars/) for more details.
+- `ALZKB_HOST` IP address (or URL) of the host server where the **Website** will be deployed.
+- `ALZKB_NEO4J_BROWSER` URL used for the Neo4J Browser, (may be different from `ALZKB_HOST`)
+- `ALZKB_APP_SERVICE` Name of the docker service where the **Website** will run. This value is used by Nginx to forward requests to this service.
+- `ALZKB_PORT` Port used by ExpressJS to serve the **Website**, Nginx will forward requests to `ALZKB_HOST` to this port.
+- `ALZKB_DATA_ROOT` Directory where the data from **Neo4J** will be stored on the host machine (data, logs, etc.)
+- `NEO4J_*` variables to configure Neo4j
+  - For more information about these varibales, see the neo4j.conf [documenation](https://neo4j.com/docs/operations-manual/5/configuration/neo4j-conf/).
+  - More details about how these variables map to the neo4j.conf file can be found [here](https://neo4j.com/docs/operations-manual/current/docker/configuration/)
+- `NODE_ENV` Set to either **prod** or **dev** 
+  - see [here](https://docs.npmjs.com/cli/v8/commands/npm-install) for more details.

alzkb-site/app.yml

@@ -0,0 +1,9 @@
+version: '3.8'
+
+services:
+  app:
+    build:
+      context: ./app
+    env_file: .env
+    ports:
+      - 5000:5000

alzkb-site/app/.dockerignore

@@ -0,0 +1,2 @@
+node_modules
+npm-debug.log

alzkb-site/app/Dockerfile

@@ -0,0 +1,17 @@
+FROM node:18.12.1-bullseye-slim
+# FROM node:latest
+
+# Create app directory
+WORKDIR /usr/src/app
+
+# Install app dependencies
+# Copy both package.json and package-lock.json
+COPY package*.json ./
+
+RUN npm install
+RUN npm install pm2 --location=global
+
+# Bundle app source
+COPY . .
+
+CMD ["pm2-runtime", "alzkb.js"]

alzkb-site/app/alzkb.js

@@ -0,0 +1,37 @@
+const express = require('express')
+require('dotenv').config()
+// const path = require('path')
+const config = require('./config/config')
+
+const app = express()
+const cors = require('cors')
+const compression = require('compression')
+// const helmet = require('helmet')
+// const ejs = require('ejs')
+require('ejs')
+
+app.use(cors())
+app.use(compression())
+app.use(express.static('public', { maxAge: 3600000 }))
+app.set('view engine', 'ejs')
+// app.use(helmet())
+
+app.get('/', (req, res) => {
+  res.render('alzkb', config)
+})
+
+app.get('/about', (req, res) => {
+  res.render('about', config)
+})
+
+app.get('/alzkb', (req, res) => {
+  res.render('alzkb_about')
+})
+
+app.get('/samples', (req, res) => {
+  res.render('samples')
+})
+
+app.listen(process.env.ALZKB_PORT, () => {
+  console.log("port", process.env.ALZKB_PORT)
+})

alzkb-site/app/config/config.js

@@ -0,0 +1,14 @@
+const config = {
+  dev: {
+    neo_browser: 'http://' + process.env.ALZKB_NEO4J_BROWSER + ':' + process.env.ALZKB_NEO4J_BROWSER_HTTP_PORT + '/browser/',
+  },
+  prod: {
+    neo_browser: 'https://' + process.env.ALZKB_NEO4J_BROWSER + '/browser/'
+  }
+}
+
+if (process.env.NODE_ENV === "prod") {
+  module.exports = config.prod
+} else {
+  module.exports = config.dev
+}