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:
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 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 WildFly Server | Yes | The name of the machine where WildFly is installed |
FRPort | Example: 22 | No | The port to be used when retrieving files |
Steps to Add Parameters to File Repository Cell
Important
If the CRC is on the same WildFly 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.
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.
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 WildFly installation.
Location of New "FRC" Directory
- The new directory will reside in the /opt/ directory.
- 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.
Important
When creating the new directory you need to log onto the server with the same user that will be running WildFly.
