Add Experiment and Protocol Information to the HID Database

Description:

This script will set up the experiment description, protocol information, subject groups, and collection equipment into the HID database.

Installation:

1) Please run the Install.sh script and follow the directions for the LocalHumanUploadScript.sh installation (see Readme.htm)

XML configuration file:

1. Warning! The scripts use the SAX parser so the order of the XML tags is important. We also get better error processing because the scripts can tell you which lines of your XML file are incorrectly parsed.

2. A project consists of the following tags in the XML file:

2.1. <project>

2.1.1. <name>

2.1.1.1. Name of project, same as the name used to register the project with BIRN: https://portal.nbirn.net/BIRN/cgi-bin/Login/rd.cgi?location=https://portal.nbirn.net/BIRN/cgi-bin/Projects

2.1.2. <ID>

2.1.2.1. Project ID from the BIRN project registration page

2.1.3. <contactFirstName>

2.1.3.1. Name of contact for project

2.1.4. <contactLastName>

2.1.4.1. If you need a definition for this you probably won’t be able to upload the data anyway… J

2.1.5. <contactEmail>

2.1.6. <baseURI>

2.1.6.1. This is the SRB location to upload the data. If you created the project using the BIRN projects page it will be: /home/Projects/ProjectName__ProjectID/Data

2.2. <subjectGroup> - There can be N number of these tags

2.2.1. <name>

2.2.1.1. Name of this group of subjects (ie. control adults, AD patients, etc).

2.2.2. <description>

2.2.3. <subjectGroupType>

2.2.3.1. Common types are patient, control.

2.3. <visitType> - There can be N number of these tags

2.3.1. <name>

2.3.1.1. Name of the visit, common names are scan, clinical, screening, etc.

2.3.2. <description>

2.4. <seriesParadigm> - There can be N number of these tags

2.4.1. <paradigm>

2.4.1.1. A descriptive name for the paradigm with up to 64 characters and no whitespaces

2.4.2. <paradigmVersion>

2.4.2.1. Version number of this paradigm

2.4.3. <description>

2.5. <collectionEquipment> - There can be N number of these tags

2.5.1. <maker>

2.5.1.1. Manufacturer of the data collection equipment

2.5.2. <model>

2.5.2.1. Model of data collection equipment

2.5.3. <location>

2.5.3.1. Location of data collection equipment

Example: see Ped_ProjectSetup.xml file with distribution

Usage:

AddExperiment2HID.sh <XML_CONFIG_FILE>

OR (to set the HIDPRD password via the command line)

env HIDPRD=[password] AddExperiment2HID.sh <XML_CONFIG_FILE>

Dependencies:

AddExperiment2HID.sh

java/classes12.jar

Authors/Contact List:

Dingying Wei - UCI (dywei@uci.edu)

David Keator - UCI (dbkeator@uci.edu)