i2b2 HowTo Create a Project

Tags: i2b2 HowTo

This is the procedure to create a new project in i2b2. Most of the process is carried out by Jeff's create project scripts, but there is some preparation work that could perhaps be incorporated into the scripts at some point.

Procesdure

1. Create Databases

[i2b2ClinDataIntegration].[dbo].[CREATE_i2b2Project] 
   '{study name}'
  ,'{password}'
GO

2. Edit Project Creation Config and Scripts

1. As the scripts have some hard coded elements it is necessary to take a copy of the procedures directory and change the hard coded values. Therefore, copy the /usr/local/i2b2-procedures-1.1-production directory.
2. In the new procedures directory, amend the file config/config.properties.

The following values need amending:

• project.name
• crc.ds.jndi.name
• ont.ds.jndi.name
• work.ds.jndi.name
• db.project.data.databasename
• db.project.data.username
• db.project.data.password
• db.project.meta.databasename [1]
• db.project.meta.username
• db.project.meta.password
• db.project.work.databasename
• db.project.work.username
• db.project.work.password
• import.user
• import.password
• import.pmURL
• import.domainID
• import.projectID

1. Edit the file config/defaults.sh.

The following values need amending:

• CRC_DS
• ONT_DS
• WORK_DS

Also, ensure that the following variables contain the correct directories:

• JBOSS_HOME
• ANT_HOME
• JAVA_HOME

3. Run the project creation scripts

Whilst in the procedures directory do the following commands:

• sudo su root (And enter your password)
• export I2B2_PROCEDURES_HOME=$PWD
• bin/project-install/1-project-install.sh [Project Name]
• bin/project-install/2-update-datasources.sh [Project Name]

6. Update the ETL Reset i2b2 databases SQL Agent job

Open up the SQL Agent job ETL Reset i2b2 databases and create a new step with the single line of code as below, The starting database MUST be the project / database you've just created e.g. i2b2_app03_scad_Data.
EXECUTE LOAD_All

7. Create the ontology

See: i2b2 HowTo Create an Ontology

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