README.md

DataModelingGeneExpressions

Setup

Clone this repository into the directory of your choosing. Ensure that you have php and the necessary depencies installed. Once done, ensure the necessary mySQL username and password information in the following files:

1. src/connection.php
2. scripts/addGSE.py
3. scripts/cohortPairQuerier.py
4. scripts/cohortQuery.py
5. scripts/populationQuery.py
6. scripts/Querier.py
7. scripts/setup.py
8. scripts/truncate.py

Once the correct information is filled your, create a database with the name dataModelingGeneExpressions. Then, in the src directory, run the setup.py script. This will create the necessary tables, and populate the Concept Hierarchy Tree used in the querying scripts.

Using Application

Once setup, begin the application. From here, click register, enter information to your desires, and login. Utilize the add GSE page to populate database.

Quickly Populate Database

Navigate to scripts/addGSE.py. You will find the following code at the bottom:

if __name__ == '__main__':
    import sys
    arg = sys.argv[1]
    main(arg)
    # for i in range(70093, 70100):
    #     gse = "GSE" + str(i)
    #     main(gse)

Comment the first three lines within the if statement, and uncomment the last thre lines like so:

if __name__ == '__main__':
    # import sys
    # arg = sys.argv[1]
    # main(arg)
    for i in range(70093, 70100):
        gse = "GSE" + str(i)
        main(gse)

Change the range values as needed, and run the script. Be sure to revert the changes once done.