A simple Python package to download files from LabCAS
Project description
📀 LabCAS Downloader
This is a simple downloader script for LabCAS, the Laboratory Catalog and Archive System. This script enables you to "bulk download" data from a LabCAS installation such as
- Early Detection Research Network's LabCAS
- The Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions's LabCAS
- Or any other LabCAS installation that supports the LabCAS API.
🖥 Prerequisites
This software works with Python 3.8, 3.9, or 3.10. Other versions may work but have not been tested.
💿 Installation
To install the LabCAS downloader, simply use the Python package installer, pip
, i.e.:
pip install jpl.labcas.downloader
You'll probably want to do this in a virtual environment so the package doesn't conflict with other Python usage on your system. For example, on a typical Unix (or macOS) system, you'd run (where $
is the command-line prompt):
$ python3 -m venv venv
$ cd venv
$ bin/pip install jpl.labcas.downloader
Then use the bin/jpl-labcas-downloader
program out of the venv
directory.
💁♀️ Usage
To use the LabCAS Downloader, you'll need to have the following information at the ready:
- The collection ID or the collection/dataset ID of the data you want to download. For example, if you're after the entire Automated Quantitative Measures of Breast Density Data, use the collection ID
Automated_Quantitative_Measures_of_Breast_Density_Data
. However, if you want just theC0250
dataset from that collection, useAutomated_Quantitative_Measures_of_Breast_Density_Data/C02520
. You can append more/
s for nested datasets as needed. - Your assigned LabCAS username and the password that authenticates your account.
- Lastly, the API endpoint you want to use:
- For EDRN, that's
https://edrn-labcas.jpl.nasa.gov/data-access-api/
- For the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions, it's
https://edrn-labcas.jpl.nasa.gov/data-access-api/
- For EDRN, that's
Then, run the jpl-labcas-downloader
as follows:
jpl-labcas-downloader --username USERNAME --api URL DATA-ID
For example, to download the Automated_Quantitative_Measures_of_Breast_Density_Data
from the API at https://edrn-labcas.jpl.nasa.gov/data-access-api/
using username jane
, run:
jpl-labcas-downloader --username jane --api https://edrn-labcas.jpl.nasa.gov/data-access-api/ Automated_Quantitative_Measures_of_Breast_Density_Data
You'll be prompted for your password, and files will be written to the current directory.
👉 Note: Any existing files will be overwritten.
🎨 Customization
The jpl-labcas-downloader
supports several options as well as environment variables to customize its behavior.
--username USERNAME
tells the username to use to authenticate to the API. You can set theLABCAS_USERNAME
environment variable to serve as a default. Leave this out to use no authentication.--password PASSWORD
indicates the password to use, but this is insecure as password should not be put on command-lines. TheLABCAS_PASSWORD
can provide the default password. However, if neither the option nor the environment variable is given, you will be prompted for a password.--api URL
tells the URL of the LabCAS API to query. It defaults to theLABCAS_API_URL
environment variable. If neither is given,https://edrn-labcas.jpl.nasa.gov/data-access-api/
is the fallback value.--TARGET DIR
tells in what directory to write output files. It defaults to the current directory.
You can see all the options at a glance by running jpl-labcas-downloader --help
.
👥 Contributing
Within the JPL Informatics Center, we value the health of our community as much as the code, and that includes participation in creating and refining this software. Towards that end, we ask that you read and practice what's described in these documents:
- Our contributor's guide delineates the kinds of contributions we accept.
- Our code of conduct outlines the standards of behavior we practice and expect by everyone who participates with our software.
🔧 Development
If you're a developer of this package, you'll probably do something like the following:
$ git clone https://github.com/EDRN/labcas-downloader.git
$ cd labcas-downloader
$ python3 -m venv venv
$ venv/bin/pip install --quiet --upgrade pip setuptools
$ venv/bin/pip install --editable '.[dev]'
Then, changes you make to files under src
will be immediately reflected in venv/bin/jpl-labcas-downloader
when run. venv/bin
will also contain supporting development tools.
🔢 Versioning
We use the SemVer philosophy for versioning this software.
📃 License
The project is licensed under the Apache version 2 license.
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