EyeArt Streamline

What?

Once your EyeArt analysis results have been exported into a nice and clean .csv (Eyenuk Reports/Results_CSV/EyenukAnalysisResults_YYYYMMDD_HHhMMmSSs.csv), it only takes one line of code to:

1. Update your spreadsheet for ophthamology consultation referrals letters (from Eyenuk Reports/Processing Log/BioPortal-Consultletters_DATA_LABELS_YYYY-MM-DD_NNNN.csv to Eyenuk Reports/Processing Log/DATA_LABELS_YYYY-MM-DD_DATA_LABELS.xlsx);

2. Update your EyeArt analysis result tracker (Eyenuk Reports/Processing Log/Reports Processing Log.xlsx) (and duplicate the previous copy as Eyenuk Reports/Processing Log/Reports Processing Log-initial_file_YYYY-MM-DD.xlsx);

3. Generate a data file that can safely be input into REDCap (Eyenuk Reports/Results_CSV/EyenukAnalysisResults_YYYMMDD_HHhMMmSSs-REDCap.csv).

Note: throughout eyeart_streamline.py, there are several checkpoints that append information to a textfile called (EyeArt_Streamline/sanity_check_YYYY_MM_DD.txt) so that you can ensure that everything is functioning as expected. Each checkpoint is preceded by a ### Sanity check X comment in the eyeart_streamline.py code.

Getting started

1. Download Anaconda Distribution for Windows.

2. Set up your working directory (Eyenuk Reports):

└───Eyenuk Reports
     ├───EyeArt_Streamline
     │      └─── environment.yml
     │      └─── eyeart_streamline.py
     ├───Processing Log
     │      └─── BioPortal-Consultletters_DATA_LABELS_YYYY-MM-DD_NNNN.csv
     │      └─── Reports Processing Log.xlsx
     └───Results_CSV
            └─── EyenukAnalysisResults_YYYYMMDD_HHhMMmSSs.csv 

PS: automating directory tree generation

3. Open Visual Studio Code through the Anaconda Navigator.

4. Navigate to your working directory (Eyenuk Reports) and set up the following Conda environment:

cd PATH/TO/Eyenuk Reports/EyeArt_Streamline
conda env create -f environment.yml
conda activate eyeart_env

Note: if using Windows, make sure to do this through the VS Code Command Prompt (not Powershell) Note: if using Mac, you may need to: conda install openpyxl

5. Run!

python eyeart_streamline.py

Note: Which Files Contain What Columns

Eyenuk Reports/Results_CSV/EyenukAnalysisResults_YYYYMMDD_HHhMMmSSs.csv

Columns:

• PatientID: MRN:####### RAMQ:############

Eyenuk Reports/Processing Log/DDMMMYYYY_DATA_LABELS_YYYY-MM-DD_NNNN.csv

Columns:

• Record ID: number assigned to patient for the study for anonymization purposes.
• RAMQ Number: ############
• Medical Record Number (MRN): #######

Eyenuk Reports/Processing Log/Reports Processing Log.xlsx

Columns:

• Record ID: number assigned to patient for the study for anonymization purposes.