From d8f1573dfd16ce7f271ff3c82abc9724ee1d5c80 Mon Sep 17 00:00:00 2001
From: Stephen C Phillips <steve@scphillips.com>
Date: Fri, 3 Apr 2020 17:07:31 +0100
Subject: [PATCH] WIP: deployment working perhaps, host:8080

---
 Vagrantfile                  |   2 +-
 docker/Dockerfile_base       |   1 +
 docker/Dockerfile_deployment |   9 +--
 docker/deploy.sh             | 106 +++++++++++++++++++++++++++++++++++
 vagrant/base.sh              | 106 ++++++++++++++++++++++++++---------
 5 files changed, 191 insertions(+), 33 deletions(-)
 create mode 100644 docker/deploy.sh

diff --git a/Vagrantfile b/Vagrantfile
index e0013d5..dc793cc 100644
--- a/Vagrantfile
+++ b/Vagrantfile
@@ -6,7 +6,7 @@ Vagrant.configure("2") do |config|
   config.vm.box = "ubuntu/bionic64"
 
   config.vm.hostname = hostname
-  config.vm.network "forwarded_port", guest: 8001, host: 8001
+  config.vm.network "forwarded_port", guest: 8080, host: 8080
 
   config.vm.synced_folder ".", "/vagrant"
   #config.vm.synced_folder ".", "/vagrant", type: "rsync", rsync__exclude: ".git/"
diff --git a/docker/Dockerfile_base b/docker/Dockerfile_base
index 2d7a290..8eaa82e 100644
--- a/docker/Dockerfile_base
+++ b/docker/Dockerfile_base
@@ -1,3 +1,4 @@
 FROM alpine:latest
 
+# apk is Alpine's apt-get equivalent
 RUN apk update && apk add curl git openjdk8 gradle nodejs libffi-dev openssl-dev git-lfs
\ No newline at end of file
diff --git a/docker/Dockerfile_deployment b/docker/Dockerfile_deployment
index de36606..2274fd6 100644
--- a/docker/Dockerfile_deployment
+++ b/docker/Dockerfile_deployment
@@ -1,21 +1,16 @@
 ARG GCP_HOST
-
 ARG GCP_PROJECT_ID
 
 FROM $GCP_HOST/$GCP_PROJECT_ID/ssm-base:alpine
 
-MAINTAINER NAJD
-
 COPY ./build ./build
-
 COPY ./docker/deploy.sh .
 
+# RUN lines are executed when the image is built
 RUN mv ./build/libs/*.war ./
-
 RUN rm -rf /build/*
-
 RUN ls -l
-
 RUN chmod +x ./deploy.sh
 
+# CMD is run when a container (created from the image) boots
 CMD ./deploy.sh
diff --git a/docker/deploy.sh b/docker/deploy.sh
new file mode 100644
index 0000000..50572c5
--- /dev/null
+++ b/docker/deploy.sh
@@ -0,0 +1,106 @@
+apk update
+apk upgrade
+
+#Setting Java OpenJDK runtime environment variables
+export JAVA_HOME="/usr/lib/jvm/java-1.8-openjdk/"
+export JAVA_OPTS="-Xmx2G"
+export CATALINA_HOME="/var/lib/tomcat"
+export CATALINA_BASE="/var/lib/tomcat"
+
+if [ ! -d "/var/lib/tomcat" ]; then
+echo "First boot of container: downloading tomcat!"
+
+#Download tomcat 7.0.96
+curl -s -o "tomcat7.tar.gz" https://archive.apache.org/dist/tomcat/tomcat-7/v7.0.96/bin/apache-tomcat-7.0.96.tar.gz
+echo "Tomcat7 downloaded!"
+
+#probably can be uninstalled to save space 
+#apk del curl
+
+#Make tomcat folder and unpack tomcat executable
+mv /tomcat7.tar.gz /var/lib/
+cd /var/lib/
+mkdir tomcat
+tar -C tomcat -xzf "tomcat7.tar.gz" --strip-components=1
+rm tomcat7.tar.gz
+echo "Unpacked Tomcat7!"
+
+#Make JENA folder and unpack .war
+cd tomcat
+mkdir jena-tdb
+cd webapps
+mkdir system-modeller
+mv /*.war ./system-modeller/
+cd system-modeller/
+unzip system-modeller-*.war
+
+#Setting MongoDB connection variables
+cd WEB-INF/classes/
+sed -i 's/spring.data.mongodb.host=localhost/spring.data.mongodb.host='"$MONGO_MONGODB_SERVICE_HOST"'/g' application.properties
+sed -i 's/# Mongo/# Mongo\nspring.data.mongodb.username=root\nspring.data.mongodb.password='"$MONGODB_ROOT_PASSWORD"'\nspring.data.mongodb.authentication-database=admin/g' application.properties
+
+cd /var/lib/tomcat/bin
+./catalina.sh start
+
+echo "Waiting for tomcat7 to start"
+until [ "`curl --silent --show-error --connect-timeout 1 -I http://localhost:8080 | grep 'Coyote'`" != "" ];
+do
+  echo "Waiting for tomcat7 to start..."
+  sleep 5
+done
+
+echo "Tomcat7 started!"
+echo "Setting reset.on.start to false for subsequent reboots..."
+
+cd /var/lib/tomcat/webapps/system-modeller/WEB-INF/classes/
+sed -i 's/reset.on.start=true/reset.on.start=false/g' application.properties
+sed -i 's/reset.on.start=true/reset.on.start=false/g' application-production.properties
+
+echo "Restarting tomcat7"
+
+cd /var/lib/tomcat/bin
+./catalina.sh stop
+
+sleep 5
+
+else
+echo "Tomcat already installed: the container must be restarting?"
+
+fi
+
+if test -n "$(find / -maxdepth 1 -name '*.war' -print -quit)"
+then
+ echo "This appears to be an upgrade as system-modeller.war is present at root!"
+ cd /var/lib/tomcat/webapps
+ rm -rf system-modeller
+ mkdir system-modeller
+ mv /*.war ./system-modeller/
+ cd system-modeller/
+ unzip system-modeller-*.war
+ 
+ #Setting MongoDB connection variables
+ cd WEB-INF/classes/
+ sed -i 's/spring.data.mongodb.host=localhost/spring.data.mongodb.host='"$MONGO_MONGODB_SERVICE_HOST"'/g' application.properties
+ sed -i 's/# Mongo/# Mongo\nspring.data.mongodb.username=root\nspring.data.mongodb.password='"$MONGODB_ROOT_PASSWORD"'\nspring.data.mongodb.authentication-database=admin/g' application.properties
+
+ cd /var/lib/tomcat/webapps/system-modeller/WEB-INF/classes/
+ sed -i 's/reset.on.start=true/reset.on.start=false/g' application.properties
+ sed -i 's/reset.on.start=true/reset.on.start=false/g' application-production.properties
+ 
+else
+ echo "Restart not due to upgrade: something must have crashed :("
+fi
+
+echo "Starting tomcat7"
+
+cd /var/lib/tomcat/bin
+./catalina.sh run
+
+
+#MongoDB GCloud Settings
+#spring.data.mongodb.username=root
+#spring.data.mongodb.password=0Z5XQR5IEJ
+#spring.data.mongodb.authentication-database=admin
+#spring.data.mongodb.host=10.3.246.90
+#spring.data.mongodb.port=27017
+#spring.data.mongodb.database=system-modeller
\ No newline at end of file
diff --git a/vagrant/base.sh b/vagrant/base.sh
index 547159f..49786c9 100644
--- a/vagrant/base.sh
+++ b/vagrant/base.sh
@@ -6,20 +6,31 @@ export CI_COMMIT_SHORT_SHA="12345qwerty"  # this would be set by GitLab
 export GCP_HOST="eu.gcr.io"  # these are pointing to the GCP K8s instance
 export GCP_PROJECT_ID="test"
 
-### clone system-modeller repo (putting this first as it is likely to fail with SSH issues)
-# add host keys to the end of the known_hosts file (keys generated using `ssh-keyscan iglab.it-innovation.soton.ac.uk`)
+export BASE_IMAGE=$GCP_HOST/$GCP_PROJECT_ID/ssm-base:alpine
+export BUILD_IMAGE=build-img:$CI_COMMIT_SHORT_SHA
+export BUILD_CONTAINER=build-cont-$CI_COMMIT_SHORT_SHA
+export TEST_IMAGE=test-img:$CI_COMMIT_SHORT_SHA
+export DEPLOYMENT_IMAGE=$GCP_HOST/$GCP_PROJECT_ID/ssm-deployment:$CI_COMMIT_SHORT_SHA
+
+### Clone system-modeller repo (putting this first as it is likely to fail with SSH issues)
+
+# This would not be needed when all these mechanisms are included in the repo.
+# Add host keys to the end of the known_hosts file (keys generated using `ssh-keyscan iglab.it-innovation.soton.ac.uk`)
 cat << KEYS >> ~/.ssh/known_hosts
 iglab.it-innovation.soton.ac.uk ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDAUhlAKXym/8PWBqq76jUAldx7GADjUAuJo2czqtxN4fAvJRxF/Bfw2JEUHOX22t7ABY7m/8YyHL/7YJVSdXTK78DLsAX8EbXm0kVIXkG+dm38GGqvPx2mIJU3o1tLe6R9w4pZX9ft3oqCtfmJco7mPj/5hAcQulPWr8yUZ5c+OwwWXYp7ukoPVBPVjBa1TiDae7Bz/TE+iuvCe6n4Vot1uzauZo9rBTPeIeW2kH/TVJRorfPaM/Ci+AHnJTPnrwJdR+FKgxUb56goJVkhBo2mH4gYY5We+rxOPMEpUTczM6wJbDnMPidaJimb613lghlHtveil9yiXjy7KShZ1QhL
 iglab.it-innovation.soton.ac.uk ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBBF5S+PBRXgdN/6HD90uKVdJK8zv4uNRB2vEPXUhHHkcpF8OiR8CRDrL++eTQsPP/VH1UF4fIcODQnD+AVuMXlE=
 iglab.it-innovation.soton.ac.uk ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIPOm5Jmu8yQhyBFrHbIAqOl4rk+KV3NSb4HCYlRoa0MB
 KEYS
+
 # access vagrant user's SSH_AUTH_SOCK as root in order to use the SSH agent on the host
 # also need 'config.ssh.forward_agent' = true in Vagrantfile
 SOCKET=$(ls -1 --sort t /tmp/ssh-*/agent.* | head -1)
 export SSH_AUTH_SOCK="${SOCKET}"
+
 # clone (requires your private key to be available inside the Vagrant VM, can be done with a key agent)
 git clone git@iglab.it-innovation.soton.ac.uk:Security/system-modeller.git
 
+### Update VM
 apt-get update
 apt-get -y upgrade
 
@@ -54,38 +65,39 @@ usermod -aG docker vagrant
 ### Build base docker image
 
 # the name of the image (arg "-t") includes context to do with GCP
-docker build -t "$GCP_HOST/$GCP_PROJECT_ID/ssm-base:alpine" -f /vagrant/docker/Dockerfile_base .
+docker build -t $BASE_IMAGE -f /vagrant/docker/Dockerfile_base .
 
 # log in to docker registry
 #cat keyfile.json | docker login -u _json_key --password-stdin "https://$GCP_HOST"
 
 # push image to registry
-#docker push "$GCP_HOST/$GCP_PROJECT_ID/ssm-base:alpine"
+#docker push $BASE_IMAGE
 
 ### Build SSM inside base image
 
 # The "system-modeller" arg sets the "context" to that folder so that it picks up the right files;
 # The name of the image includes the SHA of the git commit plus some context to do with GCP
+# TODO: pass in the image name ising $BASE_IMAGE instead of the individual variable parts
 # # Log in to registry so that build step below can retrieve ssm-base from there
 # cat keyfile.json | docker login -u _json_key --password-stdin "https://$GCP_HOST"
-docker build -t "build-img:$CI_COMMIT_SHORT_SHA" \
-    --build-arg GCP_HOST="$GCP_HOST" \
-    --build-arg GCP_PROJECT_ID="$GCP_PROJECT_ID" \
+docker build -t $BUILD_IMAGE \
+    --build-arg GCP_HOST=$GCP_HOST \
+    --build-arg GCP_PROJECT_ID=$GCP_PROJECT_ID \
     -f /vagrant/docker/Dockerfile_build system-modeller
 
 ### Extract the build artifacts
 
 # Create an instance of the build-img (same as docker run, but the container is not started)
-docker create --name "build-cont-$CI_COMMIT_SHORT_SHA" "build-img:$CI_COMMIT_SHORT_SHA"
+docker create --name $BUILD_CONTAINER $BUILD_IMAGE
 
 # Copy out the build folder
-docker cp "build-cont-$CI_COMMIT_SHORT_SHA:/build" .
+docker cp $BUILD_CONTAINER:/build .
 
 # Delete the instance and the image (after testing they exist)
-test ! -z "$(docker ps -a | grep build-cont-$CI_COMMIT_SHORT_SHA)" && docker rm "build-cont-$CI_COMMIT_SHORT_SHA"
-#test ! -z "$(docker images -q test-img:$CI_COMMIT_SHORT_SHA)" && docker rmi "build-img:$CI_COMMIT_SHORT_SHA"
+test ! -z "$(docker ps -a | grep $BUILD_CONTAINER)" && docker rm $BUILD_CONTAINER
+#test ! -z "$(docker images -q test-img:$CI_COMMIT_SHORT_SHA)" && docker rmi $BUILD_IMAGE
 
-### run tests
+### Run tests
 
 # Create a network
 docker network create "test-network-$CI_COMMIT_SHORT_SHA" --driver bridge
@@ -97,30 +109,74 @@ docker network create "test-network-$CI_COMMIT_SHORT_SHA" --driver bridge
 export MONGO_MONGODB_SERVICE_HOST="mongo-server-$CI_COMMIT_SHORT_SHA"
 export MONGODB_ROOT_PASSWORD="root"
 docker run -d --name "$MONGO_MONGODB_SERVICE_HOST" \
-    -e MONGODB_ROOT_PASSWORD=$MONGODB_ROOT_PASSWORD \
+    --env MONGODB_ROOT_PASSWORD=$MONGODB_ROOT_PASSWORD \
     --network "test-network-$CI_COMMIT_SHORT_SHA" bitnami/mongodb:latest
 
 # # Log in to registry so that build step below can retrieve ssm-base from there
 # cat keyfile.json | docker login -u _json_key --password-stdin "https://$GCP_HOST"
 
-# Make a test-img (based on build-img, see Dockerfile_test), connect it to the network
-docker build -t "test-img:$CI_COMMIT_SHORT_SHA" \
-    --network "test-network-$CI_COMMIT_SHORT_SHA" \
-    --build-arg GCP_HOST="$GCP_HOST" \
-    --build-arg GCP_PROJECT_ID="$GCP_PROJECT_ID" \
-    --build-arg CI_COMMIT_SHORT_SHA="$CI_COMMIT_SHORT_SHA" \
-    --build-arg MONGO_MONGODB_SERVICE_HOST="$MONGO_MONGODB_SERVICE_HOST" \
+# Make a test-img (based on build-img, see Dockerfile_test), connect it to the network.
+# NB: the " || true" on the end of the command is there to make the line return no error: the tests are failing so if we did not have this then the script would exit here (because of the options set on line 1)
+docker build -t $TEST_IMAGE \
+    --network test-network-$CI_COMMIT_SHORT_SHA \
+    --build-arg GCP_HOST=$GCP_HOST \
+    --build-arg GCP_PROJECT_ID=$GCP_PROJECT_ID \
+    --build-arg CI_COMMIT_SHORT_SHA=$CI_COMMIT_SHORT_SHA \
+    --build-arg MONGO_MONGODB_SERVICE_HOST=$MONGO_MONGODB_SERVICE_HOST \
     --build-arg MONGODB_ROOT_PASSWORD="$MONGODB_ROOT_PASSWORD" \
-    -f /vagrant/docker/Dockerfile_test .
+    -f /vagrant/docker/Dockerfile_test . || true
 
 # Delete the test-img, mongo instance and network
-# test ! -z "$(docker images -q test-img:$CI_COMMIT_SHORT_SHA)" && docker rmi "test-img:$CI_COMMIT_SHORT_SHA"
+test ! -z "$(docker images -q $TEST_IMAGE)" && docker rmi $TEST_IMAGE
 docker top "mongo-server-$CI_COMMIT_SHORT_SHA" && docker stop "mongo-server-$CI_COMMIT_SHORT_SHA" && docker rm "mongo-server-$CI_COMMIT_SHORT_SHA"
 docker network rm "test-network-$CI_COMMIT_SHORT_SHA"
 
-## Docker commands
+### Build deployment image
+
+# Copy in docker folder from host to VM to make deploy script available to container (will not be needed when this is integrated into the SSM repo)
+cp -a /vagrant/docker/ .
+
+# Dockerfile_deployment starts with ssm-base and copies in the built WAR file and the deploy script.
+
+# # Log in to registry so that the push step below can upload the image
+# cat keyfile.json | docker login -u _json_key --password-stdin "https://$GCP_HOST"
+# Not sure why, but Niall's build also had     --build-arg CI_JOB_ID="$CI_JOB_ID" \
+docker build -t $DEPLOYMENT_IMAGE \
+    --build-arg GCP_HOST=$GCP_HOST \
+    --build-arg GCP_PROJECT_ID=$GCP_PROJECT_ID \
+    -f /vagrant/docker/Dockerfile_deployment .
+#docker push "$DEPLOYMENT_IMAGE"
+#echo "Pushed new image to private container registry under the tag: $CI_COMMIT_SHORT_SHA. If you have thoroughly tested this version, run update-deployment to push these changes to GCP."
+#  after_script:
+#    - docker system prune -f # this removes any dead containers etc to minimise storage needed
+
+### Deploy SSM with MongoDB
+
+docker network create "deploy-network-$CI_COMMIT_SHORT_SHA" --driver bridge
+
+export MONGO_MONGODB_SERVICE_HOST="mongo-server-$CI_COMMIT_SHORT_SHA"
+export MONGODB_ROOT_PASSWORD="root"
+docker run -d --name "$MONGO_MONGODB_SERVICE_HOST" \
+    --env MONGODB_ROOT_PASSWORD=$MONGODB_ROOT_PASSWORD \
+    --network "deploy-network-$CI_COMMIT_SHORT_SHA" \
+    bitnami/mongodb:latest
+
+# Expose port 8080 of the ssm container as 8080 in the host
+# If running this through vagrant then a port forward is needed there as well
+docker run -d --name "ssm-$CI_COMMIT_SHORT_SHA" \
+    --env MONGO_MONGODB_SERVICE_HOST="$MONGO_MONGODB_SERVICE_HOST" \
+    --env MONGODB_ROOT_PASSWORD="$MONGODB_ROOT_PASSWORD" \
+    --network "deploy-network-$CI_COMMIT_SHORT_SHA" \
+    --publish 8080:8080 \
+    $DEPLOYMENT_IMAGE
+
+
+### Docker stuff
+
 # "docker container ls" only shows running containers ffs
 # "docker container ls -a" shows all
-# "docker rm <containerID>" to delete them
+# "docker rm <containerID>" to delete them (may need to do "docker stop <containerID>" first)
 # "docker run --name <container name> -it <image name>" to create and run container and log in (obviously). "i" for interactive, "t" for attaching a pseudo TTY
-# "docker build --no-cache ..." is useful when debugging
\ No newline at end of file
+# "docker build --no-cache ..." is useful when debugging
+# "docker exec -ti <CONTAINER_ID> bash" to attach to a running container with bash shell so you can look around
+# In a Dockerfile, any ARG declared before a FROM is undefined after FROM
\ No newline at end of file
-- 
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