3.2 Data Installation Overview
In this chapter we will be using the scripts provided in the data package to create tables and load them with sample data.
Assumptions
The data in this package provides data for a domain of i2b2demo and a project of Demo. The assumption is that the PM Service will be configured as such when installing the PM Cell.
Order of Installation
The basic steps that will be taken during this installation are as follows:
Step 1: Extract the i2b2 data package
Step 2: Create database user accounts
Step 3: Install the Crcdata Tables and Stored Procedures
Step 4: Install the Hivedata Tables
Step 5: Install the Imdata Tables (only if installing the IM Cell which is optional)
Step 6: Install the Metadata Tables
Step 7: Install the PM Tables and Triggers
Step 8: Install the Workdata Tables
| Important |
| The details of what is to be done for each step are defined in the different sections within this chapter. It is important to follow steps in the order they are defined and not to skip any of them unless otherwise noted. |
3.2.1 Extract the i2b2 Data Package
In the Requirements Chapter of this install document you downloaded a zip file that contained the i2b2 data package. This zip file contains all the data installation scripts needed to create the i2b2 tables and load the sample data provided.
Steps to extract the code
- Set up a target source directory for the i2b2 data.
- Locate the i2b2create_db_1700.zip file you downloaded in the Requirements chapter.
- Extract the data package into the target source directory you just created.
| Tip |
|
You will want to make note of the location as it will be needed further along in the i2b2 installation. In the installation document whenever you see YOUR_I2B2_DATA_DIR it will need to be replaced with the location of your i2b2 Data files. For your convenience an installation Worksheet to track the setup locations has been provided in the Appendices Chapter. |
3.2.2 Directory Structure and Schema Mapping
Directory Structure for the i2b2 demo data package
Once you have extracted the files from the i2b2 data package you will notice the following directory structure in your i2b2 data directory:
Main Directory for New Data Installs: YOUR_I2B2_DATA_DIR\edu.harvard.i2b2.data\Release_1-7\NewInstall
|
Directory |
Description |
|
|
Crcdata |
Contains the data installation files for the Data Repository (CRC) Cell. |
|
|
Hivedata |
Contains the data installation files for the i2b2 Hive. |
|
|
Imdata |
Contains the data installation files for the Identity Management (IM) Cell. |
|
|
Metadata |
Contains the data installation files for the Ontology Management (ONT) Cell. |
|
|
Pmdata |
Contains the data installation files for the Project Management (PM) Cell. |
|
|
Workdata |
Contains the data installation files for the Workplace Framework (WORK) Cell. |
|
In each of the above directories you will find the following:
|
Directory or File |
Description |
|
|
Scripts |
This directory contains all the scripts used during the data installation (create and load) |
|
|
db.properties |
Properties file to define the database setup parameters (type, username, driver, etc.) |
|
Schema Mapping
As stated previous the main directory for your data installation is YOUR_I2B2_DATA_DIR\edu.harvard.i2b2.data\Release_1-7\NewInstall and within it are several folders contains the install scripts. These folder and the appropriate schema to which they are mapped are outlined in the following table.
|
Directory Folder |
Schema |
Project |
|
|
Crcdata |
i2b2demodata |
Demo |
|
|
Hivedata |
i2b2hive |
||
|
Imdata |
i2b2imdata |
||
|
Metadata |
i2b2metadata |
Demo |
|
|
Pmdata |
i2b2pm |
||
|
Workdata |
i2b2workdata |
Demo |
|
Comments
0 comments
Please sign in to leave a comment.