Merge pull request #771 from molgenis/RubenOPS-patch-1

Create minor-release-update.md

docs/minor-release-update.md

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+# Minor Version Upgrade Manual: Procedures for y.z Releases
+
+> Note: This manual is intended for minor version updates within the latest major release. For example, you can use it to update from version 4.1 to 4.7.1. For upgrading to a new major version, please refer to the specific manuals dedicated to major version upgrades.
+
+## Check latest version
+
+For the latest 4.y.z release check https://github.com/molgenis/molgenis-service-armadillo/releases/latest. This will redirect to a v4.y.z page.
+
+# Updating Armadillo
+
+### 1. Stop docker containers
+
+First, log in to the Armadillo UI and navigate to the Profiles tab. Now, click 'Stop' for each profile listed.
+
+Next, stop any unnecessary containers.
+
+The commands provided are indicative, so adjust them as needed.
+
+```bash
+# should return empty list (i.e. default, xenon, rock)
+docker container list
+
+# remove containers not needed
+docker container stop <id>
+```
+
+## 2. Download required files
+
+Make a note of the version number ie. `v4.7.1` as you need to download some files from the terminal using the update script.
+
+### 2.1 Update script
+
+You need to be root user.
+
+```bash
+cd /root
+
+# Make sure to change the versions number v4.y.z
+mkdir v4.y.z
+cd v4.y.z
+
+# Check directory location
+pwd
+```
+
+```bash
+# Change the version number v4.y.z then run command
+wget https://raw.githubusercontent.com/molgenis/molgenis-service-armadillo/v4.y.z/scripts/install/armadillo-check-update.sh
+```
+
+Make the script runnable
+```bash
+chmod u+x armadillo-check-update.sh
+```
+
+### 2.2 Run update script
+
+You can run the following script to download the new Armadillo version.
+
+> The output could help us to help you fix problems.
+
+```bash
+# Change the version number v4.y.z
+./armadillo-check-update.sh 4.y.z
+```
+
+Once the script has completed, you can verify that the Armadillo JAR file has been downloaded by checking the directory:
+
+```bash
+# See all jar files on your system
+ls -ltr /usr/share/armadillo/application/
+```
+
+### 3. Make backup of system config
+
+```bash
+# Still in the correct directory? (`/root/v4.y.z`)
+pwd
+```
+
+We make a backup into the same `v4.y.z` directory but that is not strictly needed.
+
+```bash
+cp -r /usr/share/armadillo/data/system ./
+```
+
+should result in:
+
+```bash
+ls system/
+# access.json  profiles.json
+```
+
+## 4. Restart application using new version
+
+Armadillo has not yet been updated, follow the following steps to do so:
+
+### 4.1 Stop Armadillo
+
+```bash
+systemctl stop armadillo
+```
+
+### 4.2 Link new version
+
+```bash
+# List application files
+ls -l /usr/share/armadillo/application/
+
+# Remove the linked file
+rm /usr/share/armadillo/application/armadillo.jar
+
+# Attach new linked file and dont forget to change the version number v4.y.z
+ln -s /usr/share/armadillo/application/armadillo-4.y.z.jar /usr/share/armadillo/application/armadillo.jar
+
+# Check result
+ls -l /usr/share/armadillo/application/
+```
+
+### 4.3 Restart Armadillo
+
+```bash
+systemctl start armadillo
+systemctl status armadillo
+```
+
+## 5. Log on to the UI
+
+Go to your armadillo website. Is the version in the left top corner updated? This means the update was successful. We're
+almost finished. 
+
+## 6. Start profiles
+
+Login into the website and go to the profiles tab. Now you can start all the profiles again.
+
+Everything should now be working correctly. You can try and login to your server via the central analysis server, using
+the `DSMolgenisArmadillo` (2.0.5 or up) package to test. 
+
+Enjoy =)
+Team Armadillo