# AusTrakka CLI
Command line interface for AusTrakka V2.
## Installation
The AusTrakka CLI requires Python to run. Installation into a conda environment (see below) is the recommended method.
To install without conda, simply install with
```
python -m pip install austrakka
```
You will need to set the environment variable `AT_URI` to the value provided by the AusTrakka team.
You may wish to add this to your `.bashrc` or `.zshrc` file.
To use the CLI, you must log in by setting the `AT_TOKEN` environment variable using the
`austrakka auth user` command (see User Authentication, below). You may wish to configure
a login command for convenience:
```
alias at-login="export AT_TOKEN=\$(austrakka auth user)"
```
You may wish to add this to your `.bashrc` or `.zshrc` file.
### Install into a conda environment (optional but recommended)
If you wish to create a conda environment named `austrakka` with the necessary environment
variables set and the `at-login` alias, run:
```
conda create -n austrakka python=3.9
conda activate austrakka
python -m pip install austrakka
conda env config vars set AT_URI="[value provided by AusTrakka team]"
mkdir -p ${CONDA_PREFIX}/etc/conda/activate.d
echo "alias at-login=\"export AT_TOKEN=\\\$(austrakka auth user)\"" > ${CONDA_PREFIX}/etc/conda/activate.d/austrakka-alias.sh
```
Note that the last two lines are valid only for Linux/Mac and will not work on Windows.
You can then use
```
conda activate austrakka
at-login
```
in order to use the CLI. See _User Authentication_ below for alternative login methods.
### Updating the CLI
To update to the latest version, run
```
python -m pip install --upgrade austrakka
```
If you have installed the CLI into a conda environment, you should first activate it with `conda activate austrakka`.
## Running the CLI
Before you can use the CLI, you must log in as described below, to allow the CLI to use your AusTrakka credentials.
Your authorisation will expire after a period and you will need to log in again.
### User Authentication
Most users will want to use the CLI this way.
Set the following environment variable:
```
export AT_TOKEN=$(austrakka auth user)
```
If you have configured a login command as described above, you can instead run
```
at-login
```
In Windows, you can set the AT_TOKEN environment variable by first running
```
austrakka auth user
```
to obtain a token string, and then running
```
set AT_TOKEN=<output of previous command>
```
to set the environment variable.
For any of these methods, you should be directed to log in via a browser and enter a code to authorise the CLI.
### Process Authentication
This authentication mode is intended for long-term automated processes. Most users will not need it.
To authenticate a process, you'll need to set the following environment variables:
```bash
AT_AUTH_PROCESS_ID
AT_AUTH_PROCESS_SECRET
```
Values for `AT_AUTH_PROCESS_ID` and `AT_AUTH_PROCESS_SECRET` will be provided to you by the AusTrakka team. Note that the secret value is sensitive.
Once these variables are set, run the following to authorise:
```
export AT_TOKEN=$(austrakka auth process)
```
### Using the CLI
The CLI has a subcommand structure. Run
```
austrakka -h
```
to see available subcommands.
Run e.g.
```
austrakka metadata -h
```
to see available commands to manipulate metadata.
Run e.g.
```
austrakka metadata add -h
```
to see the usage of the `metadata add` command to upload metadata files.
## Environment Variables Reference
| Name | Description |
|-------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------|
| `AT_TOKEN` | AusTrakka auth token |
| `AT_URI` | URI for API endpoint |
| `AT_LOG_LEVEL` | Level of logging |
| `AT_LOG` | Set to `file` to redirecting logging to a temp file |
| `AT_CMD_SET` | Set to `austrakka-admin` to display admin commands (these will not actually run successfully unless you have an appropriate role on the server) |
| `AT_SKIP_CERT_VERIFY` | Skips verification of the cert used by the AusTrakka backend |
| `AT_SKIP_VERSION_CHECK` | Skips checking of new CLI version |
| `AT_USE_HTTP2` | Uses HTTP2 (experimental) |
All commands require `AT_URI` and `AT_TOKEN` to be set, except for `auth` commands.
## Project Structure
Each logical component of the system has its own package under `austrakka/`. Eg. `austrakka/job`.
Components that are children of another component are nested beneath. Eg. `austrakka/job/instance`.
Each component package contains the following files:
| File | Purpose |
|---------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| `__init__.py` | Contains the Click commands offered by the component. Note that even if a component does not have any commands associated with it, this file must exist for the final build to include it. |
| `funcs.py` | Any functions associated with the component. |
| `opts.py` | Click command line options associated with the component. Defined here so they can be reused across the CLI. Eg. `--species` is used for multiple commands. The species CLI option is defined here and imported to all commands that use it. |
| `enums.py` | Any enumerations associated with the component. |
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"description": "# AusTrakka CLI\n\nCommand line interface for AusTrakka V2.\n\n## Installation\n\nThe AusTrakka CLI requires Python to run. Installation into a conda environment (see below) is the recommended method.\n\nTo install without conda, simply install with \n```\npython -m pip install austrakka\n```\n\nYou will need to set the environment variable `AT_URI` to the value provided by the AusTrakka team.\nYou may wish to add this to your `.bashrc` or `.zshrc` file.\n\nTo use the CLI, you must log in by setting the `AT_TOKEN` environment variable using the \n`austrakka auth user` command (see User Authentication, below). 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See _User Authentication_ below for alternative login methods.\n\n### Updating the CLI\n\nTo update to the latest version, run \n```\npython -m pip install --upgrade austrakka\n```\nIf you have installed the CLI into a conda environment, you should first activate it with `conda activate austrakka`.\n\n## Running the CLI\n\nBefore you can use the CLI, you must log in as described below, to allow the CLI to use your AusTrakka credentials. \nYour authorisation will expire after a period and you will need to log in again.\n\n### User Authentication\n\nMost users will want to use the CLI this way.\n\nSet the following environment variable:\n```\nexport AT_TOKEN=$(austrakka auth user)\n```\n\nIf you have configured a login command as described above, you can instead run \n```\nat-login\n```\n\nIn Windows, you can set the AT_TOKEN environment variable by first running\n```\naustrakka auth user\n```\nto obtain a token string, and then running \n```\nset AT_TOKEN=<output of previous command>\n```\nto set the environment variable.\n\nFor any of these methods, you should be directed to log in via a browser and enter a code to authorise the CLI.\n\n### Process Authentication\n\nThis authentication mode is intended for long-term automated processes. Most users will not need it. \n\nTo authenticate a process, you'll need to set the following environment variables:\n```bash\nAT_AUTH_PROCESS_ID\nAT_AUTH_PROCESS_SECRET\n```\nValues for `AT_AUTH_PROCESS_ID` and `AT_AUTH_PROCESS_SECRET` will be provided to you by the AusTrakka team. Note that the secret value is sensitive.\n\nOnce these variables are set, run the following to authorise:\n```\nexport AT_TOKEN=$(austrakka auth process)\n```\n\n### Using the CLI\n\nThe CLI has a subcommand structure. Run \n```\naustrakka -h\n```\nto see available subcommands.\n\nRun e.g. \n```\naustrakka metadata -h\n```\nto see available commands to manipulate metadata.\n\nRun e.g. \n```\naustrakka metadata add -h\n```\nto see the usage of the `metadata add` command to upload metadata files.\n\n## Environment Variables Reference\n\n| Name | Description |\n|-------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------|\n| `AT_TOKEN` | AusTrakka auth token |\n| `AT_URI` | URI for API endpoint |\n| `AT_LOG_LEVEL` | Level of logging |\n| `AT_LOG` | Set to `file` to redirecting logging to a temp file |\n| `AT_CMD_SET` | Set to `austrakka-admin` to display admin commands (these will not actually run successfully unless you have an appropriate role on the server) |\n| `AT_SKIP_CERT_VERIFY` | Skips verification of the cert used by the AusTrakka backend |\n| `AT_SKIP_VERSION_CHECK` | Skips checking of new CLI version |\n| `AT_USE_HTTP2` | Uses HTTP2 (experimental) |\n\nAll commands require `AT_URI` and `AT_TOKEN` to be set, except for `auth` commands.\n\n## Project Structure\n\nEach logical component of the system has its own package under `austrakka/`. 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The species CLI option is defined here and imported to all commands that use it. |\n| `enums.py` | Any enumerations associated with the component. |\n",
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