KOMP Images Import

Description

This project is intend to import pictures taken from lab to Omero and LIMS. This project is made up by 2 parts: transfer-to_omero, which generates the omero submission form and drop it along with images into the drop box, and transfer_to_lims, which creates and drops the desired .csv file to the folder, which will be later collected by technicians. It contains the following features:

• Real-time file structure moniroting
• Trace, catch run-time errors and report to developer on time
• More pending implementations

Prerequisite

• Python 3.9 +
• Git
• MySQL
• pip
• conda

Installation

To install the app, cd to your work directory, then create a virtual environment in Python 3.9+. Normally I would suggest to use venv, but since this requires ezomero package and it has a conflicting bug when installing using venv or pyenv, be sure to only use conda to avoid it.

conda creates -n yourenvname

Now, activate the virtual environment you just created use the following command:

conda activate yourenvname

Make sure you have git installed on your computer, use this command to pull the repository to your end:

git clone https://github.com/TheJacksonLaboratory/OMERO_Import_Strategy.git

Then use this command to install the dependency for the project:

pip install -r requirements.txt

Now everything is setup, you should be ready to this the app.

Usage

Before you start running the program, make a configuration file named config.yml in your project folder in the following format:

database:
  name: database name(schema)
  user: database username
  password: database password
  host: host of the database

user:
   username: omero username
   password: omero password

azure:
    email: [email protected]
    access token: your-personal-access-token
    base_url: https://dev.azure.com/jacksonlaboratory
    team: Teams\\Of\\Yours\\On\\Azure

transfer_to_omero:
    src: \\jax.org\jax\phenotype\OMERO\KOMP\ImagesToBeImportedIntoOmero
    dest: \\jax.org\jax\omero-drop\dropbox
    log_path: C:/Program Files/KOMP/SoftwareUtilities/exec_logs/import_to_omero_log
    submission_form_name: OMERO_submission_form.xlsx
    group_owner: whitej
    wk_group: komp_eye

    Eye:
      OD: "Right eye"
      OS: "Left Eye"
      OU: "Both"

transfer_to_lims:
    log_path: C:/Program Files/KOMP/SoftwareUtilities/exec_logs/import_to_jaxlims_log
    TEST:
      fundus2: Eye Morphology
      path: Gross Pathology
      fundus: ERG
      Slit: Eye Morphology

    procedureDefVersionKey:
      Gross Pathology: 230
      Eye Morphology: 231
      ERG: 254

    dest:
      Eye Morphology: \\jax.org\jax\phenotype\EYE-MORPHOLOGY\KOMP\images-omero
      Gross Pathology: \\jax.org\jax\phenotype\GrossPathology\KOMP\images-omero
      ERG: \\jax.org\jax\phenotype\ERG-V2\KOMP\images-omero

Now you are good to go, running the app is simply like running any other python applicationd, open the terminal/command prompt, then type the following command:

python /path/to/your/directory/transform_to_omero.py
python /path/to/your/directory/ import_to_lims.py

That's it, you can customize the run of the app by creating a bash/shell script or Windows Batchfile.