elapi 2.2.0

elAPI is a powerful, extensible API client for eLabFTW.

elAPI is a powerful, extensible API client for eLabFTW developed at the University Computing Centre (URZ, FIRE division) of University of Heidelberg. It supports serving all kinds of requests documented in eLabFTW API documentation with ease. elAPI provides a simple interface via its CLI executable, and numerous advanced APIs when it is used directly as a Python package.

Example:

From the documentation:

GET /users/{id}

With elAPI you can do the following:

$ elapi get experiments --format csv --export ~/Downloads/

Once the command is run, in the background, elAPI will read host (eLab server) address, API key and various other settings (see configuration) from the configuration file elapi.yml, perform validation (e.g., whether the server address is valid), fetch all experiments list, convert them to CSV, and export them to your local ~/Downloads/ folder.

Installation

We recommend pipx for installing elAPI for use of its CLI functionalities. Pipx installs packages in isolated virtual environments, so Pipx-installed elAPI should not conflict with elAPI installed inside other virtual environments.

$ pipx install elapi

After installation with Pipx is complete, you would also be able to run elAPI just by entering the elapi command on the terminal. You can move on to "Getting started".

Advanced installation

elAPI can be used both as a CLI tool and as a Python library. If you are interested in simply using elAPI's off-the-shelf features from the command-line, install elAPI as a CLI tool (see "Installation"). If you intend to write automation script for eLabFTW, you should install elAPI as a library inside a virtual environment. Of course, if you're interested in both, you can have elAPI installed in both ways.

[!NOTE] Support for installing Python packages with pip install --user has been deprecated with the adoption of PEP 688 on many systems like Debian 12.

Installing elAPI as a library

It is recommended to install elAPI inside a Python virtual environment with your preferred package manager (pip, poetry, pipenv, rye, uv, etc.) for use of its rich APIs for working with eLabFTW. From inside a virtual environment, elAPI CLI can be invoked with python -m elapi.cli. At the moment, though, the documentation about using elAPI as a library is severely lacking.

Getting started

Once you have elAPI installed, to quickly get started, run elapi init. You will be prompted with questions about your eLabFTW server with examples to help you fill in the answers. Here's a demo:

$ elapi init

elapi init demo

That's all! Run elapi show-config to view your configuration details.

Compatibility

elAPI is compatible with the following Python versions: 3.9, 3.10, 3.11, 3.12. elAPI supports the eLabFTW REST API v2, and can be used with the following eLabFTW versions: 4.5, 4.6, 4.7, 4.8, 4.9, 4.10, 5.0, 5.1.

Configuration

elAPI needs to be configured first before you can do anything useful with it. Mainly, elAPI needs to know your eLabFTW server's API URL and your API key (or token) for access. See quick configuration method in "Getting started" before you dive into the advanced settings.

Advanced configuration

elAPI supports a YAML configuration file in the following locations.

• Current directory: ./elapi.yml
• User directory: $HOME/.config/elapi.yml
• Root directory: /etc/elapi.yml

elAPI supports configuration overloading. I.e., a keyword set in root configuration file /etc/elapi.yml can be overridden by setting a different value in user configuration file $HOME/.config/elapi.yml. In terms of precedence, configuration file present in the currently active directory has the highest priority, and configuration in root directory has the lowest.

The following parameters are currently configurable, with host and api_token being the required fields. For testing purposes, it would be safe to store everything in $HOME/.config/elapi.yml.

# elAPI configuration
# Saved in `$HOME/.config/elapi.yml`

host: <host API url>
# Example: https://demo.elabftw.net/api/v2/
# Note the host URL ends with the API endpoint
api_token: <token with at least read-access>
# "A.k.a API key". You can generate an API token from eLabFTW user panel -> API keys tab.
export_dir: ~/Downloads/elAPI
unsafe_api_token_warning: true
enable_http2: false
verify_ssl: true
timeout: 90

• export_dir is where elAPI will export response content to if no path is explicitly provided to --export/-E.
• When unsafe_api_token_warning is True, elAPI will show a warning if you're storing elapi.yml in the current working directory, as it typically happens that developers accidentally commit and push configuration files with secrets.
• enable_http2 enables HTTP/2 protocol support which by default is turned off. Be aware of known issues with HTTP/2 if you are making async requests with a heavy load.
• verify_ssl can be turned off with value False if you are trying out a development server that doesn't provide a valid SSL certificate.
• timeout can be modified to your needs. E.g., a poor internet connection might benefit from a higher timeout number. The default timeout is 90 seconds.

show-config

You can get an overview of detected configuration with elapi show-config. show-config makes it easier to verify which configuration values are actually used by elAPI, if you are working with multiple configuration files.

$ elapi show-config  # system username: "culdesac" 

If both host and api_token are detected, you are good to go!

Overriding configuration

elAPI now supports --override/--OC as a global option that can be used to override the configuration parameters as detected by elapi show-cofig. All plugins will also automatically listen to the overridden configuration. This can be useful to set certain configurations temporarily. E.g., elapi --OC '{"timeout": 300"}' get info will override the timeout from the configuration files.

Usage

elAPI can be invoked from the command-line.

$ elapi --help 

GET requests

Request an overview of running eLabFTW server:

$ elapi get info -F yml
# Here -F (or --format) defines the output format

You can request a list o all active experiments and export it to a JSON file.

$ elapi get experiments --export ~/Downoads/experiments.json

Enable built-in syntax highlighting with --highlight or -H. Here, the following command will fetch team information of team with team ID 1.

$ elapi get -H teams --id 1

POST requests

Create a new user by the name 'John Doe':

$ elapi post users --id <user id> -d '{"firstname": "John", "lastname": "Doe", "email": "[e-mail]"}'

PATCH requests

Update an existing user's email address:

$ elapi patch users --id <user id> -d '{"email": "[e-mail]"}'

patch command allows us to make changes to eLabFTW server settings. E.g., you can update the time (in minutes) after which the authentication cookie will expire.

$ elapi patch config -d '{"cookie_validity_time": 43200}'

You can publish an announcement to all the members.

$ elapi patch config -d '{"announcement": "Notice: Server will be down tomorrow at midnight due to scheduled maintenance."}'

DELETE requests

Delete all the tags associated to an experiment:

$ elapi delete experiments -i <experiment ID> --sub tags

You can reset the configuration to default values.

$ elapi delete config

experiments built-in plugin

experiments plugin enables experiments-specific actions. You can download an experiment in PDF by its "Unique eLabID" to ~/Downloads directory.

$ elapi experiments get -i <experiment unique elabid> -F pdf --export ~/Downloads/

Append text in markdown to an existing experiment by its ID:

$ elapi experiments append --id <experiment ID> -M -t "**New content.**"

You can also upload an attachment to an experiment.

$ elapi experiments upload-attachment --id <experiment ID> --path <path to attachment file> --comment <comment for your attachment>

Creating a plugin

elAPI has seamless support with tight-integration for third-party plugins. A simple third-party plugin can be created in a few easy steps:

1. Create a new subfolder under ~/.local/share/elapi/plugins with the name for your new plugin (e.g, a folder named "test")
2. Create a cli.py in the subfolder with the following snippet:

from elapi.plugins.commons import Typer

app = Typer(name="test", help="Test plugin.")

3. Run elapi again to see your plugin name under Third-party plugins list

Plugins are integrated in a way such that a plugin will not fail elAPI. So, even if one erroneous plugin is loaded, all other plugins and elAPI itself will remain unaffected. elAPI will show the error message on the "Message" panel.

If you try to import a package that is not a dependency of elAPI inside cli.py, your plugin will fail. In that case, you want to create a plugin metadata file elapi_plugin_metadata.yml (notice only .yml extension is allowed), and define the virtual environment that your plugin specifically requires.

import requests  # A third-party dependency

from elapi.api import GETRequest
from elapi.plugins.commons import Typer

# Plugin metadata
app = Typer(name="awesome", help="An awesome elAPI plugin.")


@app.command(name="get-request", short_help=f"Make a GET request")
def get_request(endpoint_name):
    r = GETRequest()
    print(r(endpoint_name).json())


@app.command(name="get-wiki-status", short_help=f"Show status of Wikipedia")
def wiki_status():
    r = requests.get("https://wikipedia.org")
    print(r)

And the path to virtual environment will be defined in the metadata file:

# elapi_plugin_metadata.yml
plugin_name: awesome
cli_script: ~/awesome/cli.py  # Path to the cli.py script
venv_dir: ~/awesome/.venv  # Path to the virtual environment
project_dir: ~/awesome  # Path to the project root directory where the plugin is located

This metadata file of plugin awesome must be placed inside ~/.local/share/elapi/plugins/awesome. Notice, the plugin name must also match the parent directory name of elapi_plugin_metadata.yml. This way we ensure a plugin name remains unique.