installation-linker.md

Steps for running the linker

Checkout the github repository for onefl-deduper

$ git checkout https://github.com/ufbmi/onefl-deduper.git
$ cd onefl-deduper

Create the database

Execute the following scripts on the SQLServer:

schema/000/upgrade.sql schema/000/data.sql

Create the partners that you need to link, these partner names will be used later.

INSERT INTO dbo.partner
    (partner_code, partner_description, partner_added_at)
VALUES
    ('SOURCE_1', 'source 1', GETDATE()),
    ('SOURCE_2', 'source 2', GETDATE())

Setup the python virtual environment

$ mkvirtualenv deduper -p `which python3`
$ pip install -r requirements-to-freeze.txt

Obtain the source files

$ cp some/long/path/file.csv data/partner_hashes.csv

Create and update the config files as needed

$ cp config/example/settings_linker.py.example config/settings_linker.py
$ cp config/example/logs.cfg.example config/logs.cfg

Before running the linker for each source, update the following parameters in the config/settings_linker.py file as needed.

IN_DELIMITER - indicates what is the record separator (comma or tab)
IN_FILE - the name of your input file (containing the PHI elements)
OUT_FILE - the name of the file which will be sent to University of Florida
DB_HOST - the name of the SQL server
DB_NAME - the name of the SQL database
DB_USER - the database service account name
DB_PASS - the database service account pasword

Run the linker

Substitute the [PARTNERNAME] by the actual value in the following command

$ PYTHONPATH=. python run/linker.py -i data -o data -p=PARTNERNAME --ask

When completed, you should be able to see new rows inserted in the database, and an output file as configured with OUT_FILE option. This output file should contain four columns:

PATID   UUID    hash_1  hash_2

To check how many rows have been insreted in the database you can run the following query:

SELECT COUNT(*) FROM LINKAGE WHERE partner_code = 'PARTNERNAME'