Developers Getting Started With i2b2
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There are additional optional configuration steps for CRC breakdowns and FR SFTP.



Important

You only need to update the QT_BREAKDOWN_PATH table if you loaded your own metadata during the Data Installation process.

  • If you loaded the data that is supplied in the metadata and crcdata (demodata) packages then no changes are necessary.
  • If you loaded your own metadata then you need to change the entries in the VALUE column of the QT_BREAKDOWN_PATH table to point to the metadata key (TABLE_CD\FULLNAME) for your analysis breakdowns.

Update the path in the QT_BREAKDOWN_PATH table

In the i2b2 users will select the type of results they would like returned when running a query (e.g. Patient set, Encounter set, Number of Patients, etc.). Some of the result types are a breakdown of pre-defined concepts such as gender, vital status, race, and age. The metadata keys for these analysis breakdowns are defined in the QT_BREAKDOWN_PATH table that was created during the CRC data installation.

  • The standard i2b2 breakdowns are the demographic concepts of gender, vital status, race, and age.
  • The metadata key is a concatenation of two columns in two different ontology tables. This key tells the CRC where the concepts for the breakdowns are located. The CRC uses this information to query the Ontology cell to retrieve the query parameters associated with the concept



METADATA KEY

The metadata key is comprised of two parts:

Part 1: the first part of the key is the TABLE_CD which is equivalent to the C_TABLE_CD column in the TABLE_ACCESS table.
Part 2: the second part of the key is the FULLNAME which is equivalent to the C_FULLNAME column in your metadata table.


The format of the metadata key is: \\TABLE_CD\FULLNAME\



EXAMPLE DATA FROM I2B2 DEMO

The following is an example of the i2b2 demo data that was loaded into the QT_BREAKDOWN, TABLE_ACCESS, and I2B2 tables during the data installation process.


Table: QT_BREAKDOWN_PATH


NAME VALUE
PATIENT_AGE_COUNT_XML \\i2b2_DEMO\i2b2\Demographics\Age\
PATIENT_GENDER_COUNT_XML \\i2b2_DEMO\i2b2\Demographics\Gender\
PATIENT_RACE_COUNT_XML \\i2b2_DEMO\i2b2\Demographics\Race\
PATIENT_VITALSTATUS_COUNT_XML \\i2b2_DEMO\i2b2\Demographics\Vital Status\


Table: TABLE_ACCESS

(Only those columns and rows that are relevant to this example are shown)


C_TABLE_CD C_TABLE_NAME C_FULLNAME C_NAME
i2b2_DEMO I2B2 \i2b2\Demographics\ Demographics


Table: I2B2

(Only those columns and rows that are relevant to this example are shown)


C_FULLNAME C_NAME
\i2b2\Demographics\Age\ Age
\i2b2\Demographics\Gender\ Gender
\i2b2\Demographics\Race\ Race
\i2b2\Demographics\VitalStatus\ Vital Status







Setting up Secure File Transfer Protocol (SFTP)

By default, the File Repository Cell uses SOAP to transfer files in i2b2. If you prefer your admin user transfer files directly via SFTP you will need to take the following steps.


Step 1:   Enter cell parameters in i2b2 Administration Module
Step 2:   Create an FRC directory

Step 1: Enter Cell Parameters in i2b2 Admin

The first step in setting up the File Repository to use SFTP is to enter a few parameters on the File Repository cell. These cell parameters will define the Method, Host and Port to be used when transferring files.


Parameter Name

Values

Required

Description

FRMethod

SFTP or local

Yes

Defines the method to be used when retrieving files

FRHost

Name of your JBoss Server  

Yes

The name of the machine where JBoss is installed  

FRPort

Example: 22

No

The port to be used when retrieving files



Steps to Add Parameters to File Repository Cell


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6. Enter the following parameter to define the method of transfer.
Parameter Name: FRMethod
Parameter Value: SFTP or local
Parameter Data Type: Text

Important

If the CRC is on the same JBoss as the File Repository then you will want to set the FRMethod to local. This will prevent the CRC Loader from accessing the File Repository via a web service call, which will result in faster responses.



7. Click on Save to save the new parameter.
8. The Parameters List page will display with the new parameter.

Note

The Navigation panel will not automatically refresh to display the new parameter. If you wish to update the list in the Navigation panel you can click on Params and it will refresh the hierarchical tree.



9. In the Parameters List page click on Add New Parameter to enter another parameter.
10. Enter the following parameter for the name of the machine where your JBoss resides.

Parameter Name: FRHost
Parameter Value: Machine_Name_Where_JBoss_Resides
Parameter Data Type: Text


11. Click on Save to save the new parameter.
12. In the Parameters List page click on Add New Parameter to enter another parameter.
13. Enter the following parameter for the port to be used by the FRC to connect. This parameter is optional. The value is usually set to 22.

Parameter Name: FRPort
Parameter Value: 22
Parameter Data Type: Text


14. Click on Save to save the new parameter.
15. The Parameters List page will display all the new parameters you have entered.
16. In the Navigation panel click on Params to refresh the hierarchical tree and display the new parameters.



Step 2: Create an FRC directory

The second and last step in setting up File Repository to use SFTP is to create a directory on the server to host the files. This new directory will be called FRC and will reside on the same server as your JBoss installation.


Location of New "FRC" Directory


Linux Server:
  • The new directory will reside in the /opt/ directory.
Example:    /opt/FRC/


Windows Server:
  • The FRC directory needs to reside in a directory called opt. Since Windows does not typically come installed with an opt directory you will need to create one in the root directory.
  • Once you have an opt directory you can create the new FRC directory within it.
Example:    C:\opt\FRC\


Important

When creating the new directory you need to log onto the server with the same user that will be running JBoss.




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