update repo with current basic deployment details

.gitignore

@@ -1,14 +1,8 @@
-# Dependencies
-marvinjs/
-piwik/
-joomla/
-webservices/
+docker_volumes/
 
 # Data
 .DS_Store
 *.sql
 
 # Admin
-PROD.*
-db.env
-public-html/custom/common/xhr/php/
+*.env

LICENSE.md

@@ -0,0 +1 @@
+Copyright 2018 - Roger Linington

README.md

@@ -1,24 +1,39 @@
-# NPAtlas_website
+# The Natural Products Atlas
 
-Reposistory for the new Dockerized deployment of the NP Atlas website www.npatlas.org.
+Hosted at www.npatlas.org
 
-Custom HTML/CSS/JS are contained in the `public-html` folder, with modules being copied into the Joomla CMS.
+AUTHOR: Jeff van Santen
 
-#### Status
+Contained is a bare bones `docker-compose` deployment for the NP Atlas.
+The required Docker images are currently not publically available.
 
-**Beta** - requires significant development and cleanup of legacy code and dependencies. Website versioning to be removed and re-factored.
+This repo exists primarily for **Issue Tracking**.
 
-#### Setup
+#### Environment files
 
-Deployment is controlled with Docker and Docker Compose. Development `docker-compose.yml` is provided with commented out dependencies (some currently missing).
+As specified in the `docker.compose.yml` two environment files need to be configured.
+Here are the required files for the REST api and the webapp, respectively.
 
-Requirements:
+api.env
 
-- a Joomla instance with the NP Atlas specific data (SQL + Filesystem, not included in this repo).
-- the JChem webservices to be installed (example in `docker-compose.yml`)
-- replace ServerName in `/sites-enabled/npatlas.conf` for Joomla Apache.
-- `public-html/marvinjs/` for chemical drawing util.
+```
+LOG_LEVEL=debug
+MODULE_NAME=atlas.main
+DATABASE_URL=postgresql://jvansan:jvansan@127.0.0.1/np_atlas_2020_06
+#AUTH_DATABASE_URL=postgresql://jvansan:jvansan@127.0.0.1/authentication # Only used with DEV_DEPLOYMENT == true
+DEV_DEPLOYMENT=false
+REDIS_URL=redis
+```
 
-`/public-html/custom/` contains Joomla modules in HTML/JS with extra CSS. These require changing of API URL from localhost to deployed URL with the correct API Key.
+app.env
 
-Set the variables in `EXAMPLE_db.env` and move to `db.env`.
+```
+ATLAS_APIKEY=<REPLACEME>
+ATLAS_URL=http://api/api/v1
+ATLAS_VERSION=2020_06
+SECRET_KEY=<REPLACEME>
+DEV=false
+ALLOWED_HOSTS=<REPLACEME>
+EMAIL_HOST_USER=<REPLACEME>
+EMAIL_HOST_PASSWORD=<REPLACEME>
+```

docker-compose.yml

@@ -1,93 +1,87 @@
 version: "3"
 
 services:
-  # traefik:
-  #   image: traefik:2.1
-  #   command:
-  #     - "--log.level=DEBUG"
-  #     - "--providers.docker"
-  #     - "--api.dashboard=true"
-  #     - "--accesslog"
-  #     - "--entrypoints.web.address=:80"
-  #     #- "--entrypoints.web.proxyProtocol.trustedIPs=127.0.0.1/32,96.54.173.75"
-  #     # - "--entrypoints.websecure.address=:443"
-  #     # - "--certificatesresolvers.myresolver.acme.email=jvansant@sfu.ca"
-  #     # - "--certificatesresolvers.myresolver.acme.storage=/etc/traefik/acme.json"
-  #     ## used during the challenge
-  #     # - "--certificatesresolvers.myresolver.acme.httpChallenge.entryPoint=websecure"
-  #     ## used during the challenge
-  #     #- "--certificatesresolvers.myresolver.acme.tlschallenge=true"
-  #     ## Staging for testing
-  #     #- "--certificatesresolvers.myresolver.acme.caServer=https://acme-staging-v02.api.letsencrypt.org/directory"
-  #   labels:
-  #     - "traefik.http.routers.api.entrypoints=web"
-  #     - "traefik.http.routers.api.rule=Host(`traefik.localhost`)"
-  #     - "traefik.http.routers.api.service=api@internal"
-  #     # - "traefik.http.routers.api.middlewares=auth"
-  #     # - "traefik.http.middlewares.auth.basicauth.users=test:$$apr1$$H6uskkkW$$IgXLP6ewTrSuBkTrqE8wj/"
-  #     # - "traefik.http.middlewares.redirect-to-https.redirectscheme.scheme=https"
-  #     # - "traefik.http.routers.http-catchall.rule=hostregexp(`{host:.+}`)"
-  #     # - "traefik.http.routers.http-catchall.entrypoints=web"
-  #     # - "traefik.http.routers.http-catchall.middlewares=redirect-to-https"
-  #   ports:
-  #     # The HTTP port
-  #     - "80:80"
-  #     # The HTTPS port
-  #     - "443:443"
-  #     # - "8080:8080"
-  #   volumes:
-  #     # So that Traefik can listen to the Docker events
-  #     - /var/run/docker.sock:/var/run/docker.sock
-  #   logging:
-  #     driver: "json-file"
-  #     options:
-  #       max-size: "200k"
-  #       max-file: "10"
+  traefik:
+    image: traefik:2.2
+    restart: always
+    command:
+      --api.insecure=true
+      --providers.docker
+      --entryPoints.web.address=:80
+      --entryPoints.websecure.address=:443
+      --certificatesResolvers.le.acme.email=jvansant@sfu.ca
+      --certificatesResolvers.le.acme.storage=/acme/acme.json
+      --certificatesResolvers.le.acme.tlsChallenge=true
+      --entrypoints.web.http.redirections.entryPoint.to=websecure
+      --entrypoints.web.http.redirections.entryPoint.scheme=https
+      # --log.level=DEBUG
+      # --certificatesResolvers.le.acme.caServer=https://acme-staging-v02.api.letsencrypt.org/directory
+    ports:
+      # The HTTP port
+      - "80:80"
+      # The HTTPS port
+      - "443:443"
+       # The Web UI enabled by --api.insecure=true
+      - "8080:8080"
+    volumes:
+      # So that Traefik can listen to the Docker events
+      - /var/run/docker.sock:/var/run/docker.sock
+      - "./docker_volumes/acme/:/acme/"
+    environment:
+      - HTTP_PROXY=http://bby-nsx-proxy.its.sfu.ca:8080
+      - HTTPS_PROXY=http://bby-nsx-proxy.its.sfu.ca:8080
+      - NO_PROXY=www.npatlas.org,127.0.0.0/8,172.24.0.0/8
 
-  webservices:
-    image: webservices:latest
-    build: ./webservices
+  # separate static file server
+  static:
+    image: nginx
+    restart: always
+    # pass location of static files
     volumes:
-      - ${PWD}/webservices/ws-config.xml:/usr/local/tomcat/.chemaxon/ws-config.xml
+      - "./static_deploy:/usr/share/nginx/html/static"
     labels:
-      - "traefik.http.routers.webservice.entrypoints=web"
-      - "traefik.http.routers.webservice.rule=Host(`${DOMAIN?Variable DOMAIN not set}`) && PathPrefix(`/webservices2`)"
+      - traefik.http.routers.static.rule=Host(`www.npatlas.org`)&&PathPrefix(`/static`)
+      - traefik.http.routers.static.tls=true
+      - traefik.http.routers.static.tls.certresolver=le
 
-  site:
-    build: .
-    image: joomla-site
+  api:
+    image: npatlas_api:0.0.11
     restart: always
-    volumes:
-      - ./public-html:/var/www/html:cached
-      - ./sites-enabled:/etc/apache2/sites-enabled
-    environment:
-      - JOOMLA_DB_HOST=mysqlserver
     env_file:
-      - ./db.env
+      - api.env
     labels:
-      - "traefik.http.routers.joomla.entrypoints=web"
-      - "traefik.http.routers.joomla.rule=Host(`${DOMAIN?Variable DOMAIN not set}`) && (PathPrefix(`/joomla`) || PathPrefix(`/custom`) || PathPrefix(`/marvinjs`)  || Path(`/`) || Path(`/robots.txt`))"
-      - "traefik.http.middlewares.joomla-gzip.compress=true"
-      - "traefik.http.routers.joomla.middlewares=joomla-gzip@docker"
+      - traefik.http.routers.atlas-api.rule=Host(`www.npatlas.org`)&&PathPrefix(`/api`)
+      - traefik.http.routers.atlas-api.tls=true
+      - traefik.http.routers.atlas-api.tls.certresolver=le
+
+  # Dont expose ports - no auth
+  redis:
+    image: redis
+    # Enable persistent data
+    volumes:
+      - "./docker_volumes/redis:/data"
+    command: ["redis-server", "--appendonly", "yes"]
 
-  # analytic:
-  #   image: matomo
-  #   volumes:
-  #     - /data/docker/matomo:/var/www/html
-  #   environment:
-  #     - MATOMO_DATABASE_HOST=mysql
-  #     - MATOMO_ENABLE_PROXY_URI_HEADER=yes
-  #     - VIRUAL_HOST=
-  #   env_file:
-  #     - ./db.env
-  #   labels:
-  #     - "traefik.http.routers.matomo.entrypoints=web"
-  #     - "traefik.http.routers.matomo.rule=Host(`${DOMAIN?Variable DOMAIN not set}`) && PathPrefix(`/piwik`)"
-  #     - "traefik.http.middlewares.matomo-path.stripprefix.prefixes=/piwik"
-  #     - "traefik.http.middlewares.matomo-path.stripprefix.forceslash=true"
-  #     - "traefik.http.routers.matomo.middlewares=matomo-path@docker"
 
-networks:
-  default:
-    external:
-      name: atlas_network
+  marvinws:
+    image: marvinws:latest
+    restart: always
+    labels:
+      - "traefik.http.routers.webservice.rule=Host(`www.npatlas.org`)&&PathPrefix(`/webservices2`)"
+      - "traefik.http.middlewares.wsstrip.stripprefix.prefixes=/webservices2"
+      - traefik.http.routers.webservice.middlewares=wsstrip@docker
+      - traefik.http.routers.webservice.tls=true
+      - traefik.http.routers.webservice.tls.certresolver=le
+
+  app:
+    image: npatlas:2.0.6
+    restart: always
+    env_file:
+      - app.env
+    # Persistent SQLite DB
+    volumes:
+        - "./db:/usr/src/app/db"
+    labels:
+      - traefik.http.routers.atlas.rule=Host(`www.npatlas.org`)&&PathPrefix(`/`)
+      - traefik.http.routers.atlas.tls=true
+      - traefik.http.routers.atlas.tls.certresolver=le