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CHANGELOG.md

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CHANGELOG of Chemotion CLI tool

Version 0.2

The main changes are as follows:

  • ./chemCLI instance consoles command that allows you to enter the console of a running instance.
  • ./chemCLI instance ping command that checks if the instance is up, running and available at the specified URL.
  • ./chemCLI instance restore command to restore your data into a new instance of Chemotion ELN.
  • ./chemCLI advanced update command that updates the CLI tool itself. The tool now also checks (once a day) if an update to itself is available and displays a reminder if this is the case.
  • ./chemCLI instance new now uses the latest available docker-compose.yml file, not a hard-coded one.
  • ./chemCLI instance status is now merged into ./chemCLI instance stats.
  • Responsive menus: only actions that make sense are displayed e.g. the main menu shows an off option if the selected instance is already running.
  • Back option: It is now possible to go to the menu above using a back option. The tool exits once a task is completed -- this is an intended feature.
  • The tool is (milliseconds) slower to start now precisely because it now checks on the status of the instance on launch.
  • Bugfixes
  • Changes that effect the user's files are as follows.:

chemotion-cli.yml is now called chem_cli.yml. chemotion-cli.log is called chem_cli.log. The executable is called chemCLI instead of chemotion.

The second difference is formatting of the chem_cli.yml file.

  • The global keys that handle state of the tool i.e. selected, quiet and debug have now been moved to cli_state.selected, cli_state.quiet and cli_state.debug respectively.

  • The instances.<instance_name>.address and instances.<instance_name>.protocol keys have been removed. Instead, we have instances.<instance_name>.accessaddress which stores the full URL that is used to access the ELN instance.

  • We have new keys: cli_state.version, cli_state.version_checked_on

  • With these changes, the version of this YAML file has been changed from "1.0" to "2.0".

Therefore, if your file looked as follows:

instances:
  main:
    address: mynotebook.kit.edu
    debug: false
    kind: Production
    name: main-ee5e5424
    port: 4000
    protocol: http
    quiet: false
  second:
    address: localhost
    debug: false
    kind: Production
    name: second-ff6f6535
    port: 4100
    protocol: http
    quiet: false
selected: main
version: "1.0"

It should now look as follows:

cli_state:
  debug: false
  quiet: false
  selected: main
  version: 0.2.2
  version_checked_on: 2023-04-06T10:54:40.818796948+02:00
instances:
  main:
    accessaddress: http://mynotebook.kit.edu
    image: ptrxyz/eln-1.3.1p220712
    kind: Production
    name: main-ee5e5044
    port: 4000
  second:
    accessaddress: http://localhost:4100
    image: ptrxyz/chemotion:eln-1.5.1
    kind: Production
    name: second-ff6f6535
    port: 4100
version: "2.0"

The third difference is splitting of docker-compose.yml file into two files.

So far dockerized installations of Chemotion have relied on docker-compose.yml file from here.

The CLI in version 0.1.x-alpha diverged from this by modifying the file to suit the needs of the CLI by

  1. changing the services:eln:ports key
  2. including this label on networks, services and volumes: `net.chemotion.cli.project: <instance_name>-<instance_uniqueID>
  3. including names on the volumes so that they are named the following: <instance_name>-<instance_uniqueID>_chemotion_<app|data|db|spectra>.

Version 0.2.x onwards, we refrain from modifying the docker-compose.yml file, making only one change in it (Change 1. is still done.). Changes 2. and 3. are included in the configuration by adding a new file called docker-compose.cli.yml (that we use in addition to the docker-compose.yml file). The docker compose tool seamlessly merges the two files when reading them.

The extended file also includes an extra service called executor to ease running commands in the eln (primary service) without switching on all other services.