ChemCLI

ChemCLI, short for Chemotion CLI, is a tool to help you manage Chemotion ELN on a machine. The goal is to make installation, maintenance and upgradation of (multiple instances of) Chemotion as easy as possible.

Important Announcements

1. You must manually update to version 0.2.12 of the CLI. This is because GitHub is blocking download of the docker-compose.yml file causing versions 0.2.11 and below to fail on start. To do so, go to Releases and download the required executable. See Updating the Tool for more.

   Manually updating the tool will trigger a warning about version mismatch whenever you run ChemCLI. To get around it, run ./chemCLI advanced update --force after putting the new executable in place.

2. Have a bug that looks as follows when trying to update an instance?

   pg_dump: error: connection to server at "db" (172.21.0.2), port 5432 failed: FATAL:  database "chemotion" does not exist

   Then please have a look at the docker-compose.cli.yml files in the instances folder. The section services.executor.image should be changed so that it matches services.eln.image in the docker-compose.yml file.

3. If you are using ChemCLI versions 0.2.0 to 0.2.3, you will have to run the following command to (force) run the auto-update feature: ./chemCLI advanced update --force. You can also (always) download a new executable of ChemCLI to manually update the tool. (Apologies for the bug!)

4. Please note that support for version 0.1.x will be completely deprecated on 31.12.2023. The codes that help you migrate from version 0.1 to 0.2 will be removed in releases after 31.12.2023.

Compatibility with Chemotion ELN

ChemCLI tool supports the following versions of Chemotion ELN:

ELN Version	docker-compose.yml file
v2.2.x	eln-2.2.0
v1.10.x	eln-1.10.5
v1.9.x	eln-1.9.3

Chemotion ELN versions 1.8.x and below are no longer supported. Kindly update your instance as soon as possible. If required, please contact the helpdesk.

Concept for chemCLI

The commands have the following general layout:

general: cli-executable  <resource>  <command>  <flags>
         └─────┬──────┘  └───┬────┘  └───┬───┘  └──┬──┘
example:    chemCLI       instance     logs     --all

Following features have been implemented:

• ✔ Installation & Deployment: ./chemCLI > install installs a production instance that is ready to use.
• ✔ Instance life cycle commands: ./chemCLI > on|off|restart and ./chemCLI > instance > stats|ping|logs.
• ✔ Upgrade: ./chemCLI > instance > upgrade to upgrade an existing Chemotion instance.
• ✔ Backups: ./chemCLI > instance > backup to save the data associated with an instance.
• ✔ Restore: ./chemCLI > instance > restore to save the data associated with an instance into a new instance.
• ✔ Multiple instances: ./chemCLI > instance > new|list|switch|remove can be used to manage multiple instances.
• ✔ Administrative consoles: ./chemCLI > instance > consoles > <console_name> to drop into shell, postgreSQL and rails consoles.
• ✔ Users: ./chemCLI > instance > users > create|list|update|describe|delete to manage users in an instance. Particularly, ./chemCLI > instance > users > update can be used to modify password for users who forget theirs.

Download

Getting the tool

The ChemCLI tool is a binary file called chemCLI and needs no installation. The only prerequisite is that you install Docker Engine on Linux. In the rare scenario that your server is running Windows or Mac, you can make use of Docker Desktop which comes with a GUI. Builds for the following systems are available:

Depending on your OS, you can go to GitHub and download the latest release of the CLI.

• Linux, amd64
• Windows, amd64
• macOS, apple-silicon
• macOS, amd64

Please be sure that you have both, docker and docker compose commands. This should be the case if you installed Docker Desktop. If you choose to install only Docker Engine, then please make sure that you also have docker compose as a command (as opposed to docker-compose). On Linux, you might have to install the docker-compose-plugin to achieve this.

These binary builds should not rely on libraries of the underlying operating system: if they still do not work on your system for some reason, please create an issue here and we will try to provide you a binary build as soon as possible. If you feel like it, you can always compile the go source code on your own.

Making it an executable

OS	How to make it an executable	How to run the executable
Linux (Ubuntu, WSL etc.)	chmod u+x chemCLI	./chemCLI
Windows (Powershell)*	(nothing to do)	.\chemCLI.exe
macOS (intel/amd64)^	chmod u+x chemCLI.amd.osx	./chemCLI.amd.osx
macOS (apple-silicon)^	chmod u+x chemCLI.arm.osx	./chemCLI.arm.osx

*On Windows, it is recommended to use Powershell 7 instead of the one provided natively (confusingly called Windows Powershell). In any case, it is necessary to have pwsh in your $PATH.

^On macOS, if the there is a security pop-up when running the command, please also Allow the executable in System Preferences > Security & Privacy.

Important Notes

• All commands here, and all the documentation of the tool, use ./chemCLI when describing how to run the executable. However, your specific command to run the executable is given in the table above.
• If possible, do not rename the executable, or rename/remove files and folders created by it. All reasonable operations can be done using chemCLI; manual operations might break the chemCLI's ability to understand how things are laid out on your machine.

First run

Make a dedicated folder

Make a folder where you want to store installation(s) of Chemotion ELN. Ideally this folder should be in the largest drive (in terms of free space) of your system. Remember that Chemotion also uses space via Docker (docker containers, volumes etc.) and therefore you need to make sure that your system partition has abundant free space.

Install

To begin with installation, run the executable (./chemCLI) and follow the prompt. The first installation can take really long time (15-30 minutes depending on your download and processor speeds). Please be aware that instance names must be lowercase and cannot contain periods (.).

This will create the first (production-grade) instance of Chemotion on your system. Generally, this is suffice if you want to use Chemotion in a single scientific group/lab. By default

• this first instance will be available on port 4000
• this first instance will be the selected instance.

⚠️ chem_cli.yml: Installation also creates a file called chem_cli.yml. This file is critical as it contains information regarding existing installations. Removing the file will render chemCLI clueless about existing installations and it will behave as if Chemotion was never installed. Please do not remove the file. Ideally there should be no need for you to modify it manually.

The selected instance

Once you install multiple instances of Chemotion, the actions of chemCLI pertain to only one of them i.e. you actively operate only one of them when you run a command in the ./chemCLI > instance section. This instance is referred to as the selected instance and its name is stored in a local file (chem_cli.yml). You can do ./chemCLI instance switch to switch to another instance if you have more than one instance.

You can also select an instance temporarily by giving its name to the CLI as a flag e.g. ./chemCLI instance status -i my-other-instance.

Start and Stop Chemotion

To turn on, and off, the selected instance, issue the commands:

• ./chemCLI on, and
• ./chemCLI off.

Backup an instance

:::caution WARNING This backup process does not backup data that reside out docker e.g. services and shared folders. These folder need to be backed up by you separately. :::

You can backup an instance of the ELN, installed using the CLI, by running the following command: ./chemCLI instance backup -i <name_of_instance> -q. This command must be run individually for every instance of Chemotion ELN that you have. Two new backup files are created for each execution of the command inside the instances/<name_of_instance-xxxxxxx>/shared/backup folder. (These two files can be used to restore data into a new instance using the ./chemCLI instance restore command.)

If running this as a cron job, remember to change into the folder where the ChemCLI executable exists. To do this, include cd path/to/the/folder in your job script. Therefore an example crontab file that runs at 03:00 on every day-of-week from Tuesday through Saturday would look like as follows:

0 3 * * 2-6 cd /home/admin/installations/chemotion_ELN && ./chemCLI instance backup -i prodinstance -q

Please also refer to the notes on manual installation for a better understanding of the backup process.

Upgrading an instance (for ELN versions 1.3 and above)

As long as you installed an instance of Chemotion using this tool, the upgrade process is quite straightforward:

• First make sure that you have the latest version of this tool.
• Prepare for update by running ./chemCLI > instance > upgrade > pull image only. This will download the latest Chemotion image from the internet if not already present on the system. Doing this saves you time later (during scheduled downtime).
• Schedule a downtime of at least 15 minutes; more if you have a lot of data that needs to backed up. During the downtime, run ./chemCLI > instance > all actions to backup your data followed by an upgrade of the instance.

When upgrading from ELN version 1.3, please create a backup using chemCLI version 0.2.2 or above. This is because the data backup script provided inside the container is broken and this is fixed by chemCLI tool.

Uninstallation

⚠️ be sure about what you want to do!

You can uninstall everything created by chemCLI by running: ./chemCLI > advanced > uninstall. Last you can simply delete the downloaded binary itself.

Updating the Tool

chemCLI (version 0.2 onwards) is configured to check for new releases of itself every 24 hours with the servers of GitHub. If a new version is available, it will inform you of it. You can then update the tool by going to ./chemCLI > advanced > update - chemCLI.

Respecting your privacy: You can disable this automatic checking for next 100 years by running ./chemCLI advanced update --disable-autocheck.

Updating from version 0.1.x

If you are using chemCLI version 0.1 (then called chemotion CLI), please do the following to update to the latest version:

• Download the latest version and make it an executable.
• Create copy of the file chemotion-cli.yml as chem_cli.yml by executing: cp chemotion-cli.yml chem_cli.yml.
• Run the new executable (./chemCLI). It should guide you through an automated update. After a successful update, it is safe to remove chemotion-cli.yml and chemotion-cli.log files.
• This update does not upgrade the instances

Please note that support for version 0.1.x will be completely deprecated on 31.12.2023.

Advanced Usage

Using flags

chemCLI has a lot to offer, with a few advanced features available exclusively via flags. Feel free to use --help option at the end of the command and its subcommands to explore more.

A particular construct worth noting is using the ./chemCLI instance restore command to create the first instance while restoring data from a previous instance into it. This can be useful for moving from non-docker and/or non-chemCLI based installations to a chemCLI managed installation.

For example:

./chemCLI instance restore --name first-instance --data /absolute/path/to/backup.data.tar.gz --db /absolute/path/to/backup.sql.gz --suffix 4cfcfd0c --address https://chemotion.myuni.de --use https://github.com/Chemotion/ChemCLI/releases/download/0.2.7/docker-compose.yml

Silent and Debug Use

Almost all features of chemCLI can be used in silent mode i.e. without any input/interaction from user as long as all required pieces of information have been provided using flags. In silent mode, most of the output from the CLI (but not that of docker) is logged only in the log file, and not put on screen.

To use chemCLI in silent mode, add the flag -q/--quiet to your command. The CLI will then use default values and other flags to try and accomplish the action. Examples:

./chemCLI -q instance new --name second-instance --address https://myuni.de:3000 --use ../my/path/docker-compose.yml

./chemCLI -q instance backup # for running backups silently

Similarly, the CLI can be run in Debug mode when you encounter an error. This produces a very detailed log file containing a trace of actions you undertake. Telling us about the error and sending us the log file can help us a lot when it comes to helping you. Please audit the debug file for any personal information (such as username etc.) before sending it to us.

Known limitations and bugs

• Everything happens in the folder (and subfolders) where ./chemCLI is executed. All files and folders are expected to be there; otherwise failures can happen. The user executing ChemCLI is expected to have all file permissions for this folder.
• Have a bug that looks as follows when trying to update?

pg_dump: error: connection to server at "db" (172.21.0.2), port 5432 failed: FATAL:  database "chemotion" does not exist

Then please have a look at the docker-compose.cli.yml files in the instances folder. The section services.executor.image should be changed so that it matches services.eln.image in the docker-compose.yml file.

• If you are using ChemCLI versions 0.2.0 to 0.2.3, you will have to run the following command to (force) run the auto-update feature: ./chemCLI advanced update --force. You can also (always) download a new executable of ChemCLI to manually update the tool.

Acknowledgments

This project has been funded by the DFG.

Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI4Chem project – Projektnummer 441958208 – since 2020.