read_credentials.py

Data collected and produced for each project will follow BIDS specifications to ensure community standards are upheld, to improve data integrity and conformity, and to improve data consistency and data processing optimization.

A single JSON file describes various parameters for each project/program. This file is ‘credentials.json’ and is located in the main code directory on the mounted centralized storage (/resshare/general_processing_codes). The table below outlines the keys and their associated descriptions for a project in the credentials file. Each project in the credentials file should be defined as their own key titled by their respective protocol number prescribed by their IRB of record. For pilot studies, a short name may be used in place of the IRB number.

Key descriptions for the credentials.json file.

Key	Data Type	Description
projects	list[string]	List of all project identifiers (these are referred to as <project_identifier>)
<project_identifier>	dictionary	Dictionary identifying key elements of each project described in credentials_secondary_table

Dictionary keys for the <project_identifier> elements.

Key	Data Type	Description
description	string	Text used to give a short description of the project
title	string	Full project title
database	string	MySQL database for the associated main and source tables described in the MySQL section of this document
dataDir	string	Local directory within the mounted centralized storage’s ‘projects’ folder where data shall be located.
dicom_id	string	Unique string within the DICOM filenames to help identify DICOMS within the PACS and souredata directories
searchSourceTable	string	MySQL table identifying files within the project’s sourcedata directory
searchTable	string	MySQL table identifying files within the project’s directory (excluding sourcedata)

read_credentials(inDir, basename)

Read the credential file (credentials.json) from the general_processing_codes directory.

This program returns the Project credentials into the custom creds class (NEEDS REFERENCE), which should be imported prior to calling read_credentials()

read_credentials(project)

Parameters:

project (string) – <project_identifier>. This should correspond to the projects IRB protocol number.

Raises:

Error – if credentials.json is not found

Returns:

None

Return type:

None