This project is intended to download, upload images files from multiple sources including Omero, Climb and PFS to SFTP Server(for submitting to DCC). The backgroud of this project is that the old image uploading application broke recently, and it has been running for over 10 years, making a new app will be easier for engineers to use and maintain in the future. As of today, Omero and Climb part have been finished and well-tested, PFS part will be soon as the KOMP team switch from JaxLims to PFS.
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Assume that you alhready have the python install, first, create a virtual environment for running the application, I use venv, you can pick whatever suites you.
python -m venv .env/ENV_NAME
After creating the enviroment, activate it use the following coomand
. . env/ENV_NAME/bin/activate
Then use the following command to install the package to the venv you just created:
pip install git+https://github.com/TheJacksonLaboratory/KOMP_Images_ETL.git
To use, simply type python download_from_omero.py to start download and upload images from OMERO; type python download_from_drive.py to download and upload images from phenotype drive; python report_missing_images.py to create a report of missing images. For more details, please check the word document contained in this repositiory.
This project use the Jean-Paul Calderone's classic Filesystem of a Python project, for more info, please see the link below:
Filesystem of a Python project
The project is created by:
- Tianyu Chen contact:[email protected]
- Michael McFarland contact:[email protected]