Merge branch 'k8s-prep' into develop

.gitignore

@@ -6,3 +6,4 @@ wsm.rest.sock
 logs
 .project
 .pydevproject
+.vscode
\ No newline at end of file

.gitlab-ci.yml

+default:
+  interruptible: false
+stages:
+  - tag
+  - publish
+
+# tag release
+tag:
+  image: node:12-buster-slim
+  stage: tag
+  before_script:
+    - apt-get update && apt-get install -y --no-install-recommends git-core ca-certificates
+    - npm install -g semantic-release @semantic-release/changelog @semantic-release/commit-analyzer @semantic-release/gitlab @semantic-release/git @semantic-release/npm @semantic-release/release-notes-generator conventional-changelog conventional-changelog-conventionalcommits 
+  script:
+    - semantic-release
+  when: on_success
+  only:
+    - master
+  except:
+    refs:
+      - tags
+    variables:
+      - $CI_COMMIT_TITLE =~ /^RELEASE:.+$/
+
+# build a new container
+build:
+  stage: publish
+  image:
+    name: gcr.io/kaniko-project/executor:debug
+    entrypoint: [""]
+  when: on_success
+  script:
+    - mkdir -p /kaniko/.docker
+    - echo "{\"auths\":{\"$HARBOR_REGISTRY\":{\"username\":\"$HARBOR_USER\",\"password\":\"$HARBOR_PASSWORD\"}}}" > /kaniko/.docker/config.json
+    - if [ -z $flag ]; then /kaniko/executor --context $CI_PROJECT_DIR --dockerfile $CI_PROJECT_DIR/Dockerfile --destination $HARBOR_REGISTRY/$HARBOR_PROJECT/$CI_PROJECT_NAME:$CI_COMMIT_SHORT_SHA; else /kaniko/executor --context $CI_PROJECT_DIR --dockerfile $CI_PROJECT_DIR/Dockerfile --destination $HARBOR_REGISTRY/$HARBOR_PROJECT/$CI_PROJECT_NAME:$CI_COMMIT_TAG --destination $HARBOR_REGISTRY/$HARBOR_PROJECT/$CI_PROJECT_NAME:latest; fi
+  only:
+    - tags
+    - develop

.releaserc.yaml

+plugins:
+  - "@semantic-release/gitlab"
+branches: ['master']
+ci: true
+debug: true
+dryRun: false
+tagFormat: '${version}'
+
+# Global plugin options (will be passed to all plugins)
+preset: 'conventionalcommits'
+gitlabUrl: 'http://git.wur.nl/' # your gitlab url
+# slackWebhook: 'https://slack.xxx.com/hooks/q3dtkec6yjyg9x6616o3atgkkr' # if you need slack notifies
+
+# Responsible for verifying conditions necessary to proceed with the release:
+# configuration is correct, authentication token are valid, etc...
+verifyConditions:
+  - '@semantic-release/changelog'
+  - '@semantic-release/git'
+  - '@semantic-release/gitlab'
+
+# Responsible for determining the type of the next release (major, minor or patch).
+# If multiple plugins with a analyzeCommits step are defined, the release type will be
+# the highest one among plugins output.
+# Look details at: https://github.com/semantic-release/commit-analyzer#configuration
+analyzeCommits:
+  - path: '@semantic-release/commit-analyzer'
+
+# Responsible for generating the content of the release note.
+# If multiple plugins with a generateNotes step are defined,
+# the release notes will be the result of the concatenation of each plugin output.
+generateNotes:
+  - path: '@semantic-release/release-notes-generator'
+    writerOpts:
+      groupBy: 'type'
+      commitGroupsSort: 'title'
+      commitsSort: 'header'
+    linkCompare: true
+    linkReferences: true
+
+# Responsible for preparing the release, for example creating or updating files
+# such as package.json, CHANGELOG.md, documentation or compiled assets
+# and pushing a commit.
+prepare:
+  - path: '@semantic-release/changelog'
+  - path: '@semantic-release/git'
+    message: 'RELEASE: ${nextRelease.version}'
+    assets: ['CHANGELOG.md']
+
+# Responsible for publishing the release.
+publish:
+  - path: '@semantic-release/gitlab'

Dockerfile

-FROM ubuntu:16.04
-MAINTAINER Luís de Sousa <luis.desousa@wur.nl>
+FROM ubuntu:18.04
+LABEL MAINTAINER Luís de Sousa <luis.desousa@wur.nl>
 
-RUN apt update
-RUN apt -y install python-pip python-dev nginx
+RUN apt update && apt -y install python-pip python-dev nginx curl && rm -rf /var/lib/apt/lists/*
+RUN mkdir -p /var/www/wsm.rest
 
-COPY ./requirements.txt /tmp/requirements.txt
-RUN pip install -r /tmp/requirements.txt
+WORKDIR /var/www/wsm.rest
+
+COPY . .
+
+RUN chmod +x configs/startup.sh
+RUN pip install -r requirements.txt
+
+ENTRYPOINT [ "configs/startup.sh" ]
 
-# Expose port 80
 EXPOSE 80
+STOPSIGNAL SIGQUIT
 
+HEALTHCHECK CMD curl --fail http://localhost:80 || exit 1
+CMD ["nginx", "-g", "daemon off;"]
 ################### Usage #####################
 
 # Build it
 # docker build -t ldesousa/wsm.rest .
 
-# Run command
-# docker run -dit -v /var/www/wsm.rest:/var/www/wsm.rest -v /data/monoliths:/data/monoliths --name wsm.rest -p 8081:80 ldesousa/wsm.rest
-
-# Set the correct database connection in common/secret.py
+# Set the correct database connection in using environment variables or an env-file:
 
-# Attach to the container and run the startup script
-# docker attach wsm.rest
-# sh /var/www/wsm.rest/configs/startup.sh
-# Ctrl+P Ctrl+Q
+# Run command with envfile
+# docker run -dit --env-file /path/to/envfile -v /data/monoliths:/data/monoliths --name wsm.rest -p 8081:80 ldesousa/wsm.rest
 
+# Declaring variables inline:
+# docker run -dit -e DB_HOST=scomp1270.wurnet.nl -e DB_NAME=isric  -e DB_USER=haas005  -e DB_PASSWORD=wur -e DB_PORT=5479 -v /data/monoliths:/data/monoliths --name wsm.rest -p 8081:80 ldesousa/wsm.rest
\ No newline at end of file

README.md

@@ -102,23 +102,19 @@ To build the container image change to the project folder and run:
 
 `docker build -t ldesousa/wsm.rest .`
 
-The resulting image is named `ldesousa/wsm.rest`. To run the image it is 
-necessary to map the source code folder and port 80 (where nginx listens):
+The resulting image is named `ldesousa/wsm.rest`. 
+To run the image it is necessary to map the right environment variables to connect to the database as well as mount the source code folder and bind port 80 (where nginx listens):
 
-`docker run -dit -v /var/www/wsm.rest:/var/www/wsm.rest --name wsm.rest -p 8081:80 ldesousa/wsm.rest`
-
-Gunicorn can only be started after the source code folder has been mapped. To
-do so attach to the running container (named `wsm.rest`):
-
-`docker attach wsm.rest`
-	
-And then run the startup script:
-
-`sh /var/www/wsm.rest/configs/startup.sh`
-	
-Finally, detach orderly from the running container with the escape sequence:
+Docker run command with envfile:
+```bash
+docker run -dit --env-file /path/to/envfile -v /data/monoliths:/data/monoliths --name wsm.rest -p 8081:80 ldesousa/wsm.rest
+```
+Docker run command with variables inline:
+```bash
+docker run -dit -e DB_HOST=scomp1270.wurnet.nl -e DB_NAME=isric  -e DB_USER=haas005  -e DB_PASSWORD=wur -e DB_PORT=5479 -v /data/monoliths:/data/monoliths --name wsm.rest -p 8081:80 ldesousa/wsm.rest
+```
 
-`Ctrl+P Ctrl+Q`
+Your container will now be available on [localhost:8081](http://localhost:8081)
 
 OC deployment
 =============

common/secret.py

 """Password of database"""
-"""This is just an example, change to the correct values and rename the file to
-   secret.py"""
-DB={"host":"scomp1270.wurnet.nl","database":"isric", "user":"haas005", "password":"1515NewPW","port":"5479"}
+"""Secrets will be read from environment variables, and have some example default values set."""
+
+from os import environ
+# Get environment variables and set default if none specified:
+DB_HOST = environ.get("DB_HOST", "scomp1270.wurnet.nl")
+DB_NAME = environ.get("DB_NAME", "isric")
+DB_USER = environ.get("DB_USER", "haas005")
+DB_PASSWORD = environ.get("DB_PASSWORD", "1515NewPW")
+DB_PORT = environ.get("DB_PORT", "5479")
+
+DB={"host":DB_HOST,"database":DB_NAME, "user":DB_USER, "password":DB_PASSWORD,"port":DB_PORT}

configs/startup.sh

@@ -2,6 +2,7 @@
 
 cd /var/www/wsm.rest
 mkdir logs
+
 echo "Launching Gunicorn..."
 nohup /usr/local/bin/gunicorn wsgi:app --workers 3 --bind unix:wsm.rest.sock -m 007 </dev/null >logs/gunicorn.log 2>&1 &
 
@@ -9,9 +10,6 @@ echo "Setting up nginx config."
 rm -f /etc/nginx/sites-enabled/default
 cp /var/www/wsm.rest/configs/wsm.rest.nginx /etc/nginx/sites-enabled/wsm.rest
 
-echo "Launching nginx..."
-nohup nginx </dev/null >logs/nginx.log 2>&1 &
-
 # Wait a little for Gunicorn to set up
 sleep 2
 
@@ -19,3 +17,4 @@ echo "Fixing access to socket."
 chown www-data:www-data /var/www/wsm.rest/wsm.rest.sock
 
 echo "All done. Good to go!"
+exec "$@"
\ No newline at end of file

configs/wsm.rest.nginx

 server {
     listen 80;
-    server_name server_domain_or_IP;
+    server_name localhost;
+    
+    access_log /dev/stdout;
+    error_log /dev/stderr;
 
     location / {
         include proxy_params;