tMDataLoader compatibility with i2b2 transmart

#1

On i2b2-transmart V 18.1 beta, while we are trying to load a clinical study using tMDataLoader 17.1, it is giving following error:

07/26 10:54:45 MSG === PROCESSING STUDIES IN ‘’ ===
07/26 10:54:45 MSG == Found study: Test2Study1 ==
07/26 10:54:45 MSG Processing Clinical data
07/26 10:54:45 MSG Connecting to database server
07/26 10:54:47 MSG Mapping file: Test2Study1_Mapping_File.txt
07/26 10:54:47 WAR Column index ‘3’ is already mapped in other row for row: [demographic001.txt, Ages+Demographics, 3, Age (AGE), , , ]
07/26 10:54:47 MSG Processing demographic001.txt
07/26 10:54:49 MSG Processed 3018 rows
07/26 10:54:49 MSG Job ID: 18288
07/26 10:54:49 MSG Run procedures: I2B2_LOAD_CLINICAL_DATA
07/26 10:54:49 MSG Study ID=TEST2STUDY1; Node=\Test2Study1
Jul 26, 2018 10:54:49 AM groovy.sql.Sql call
WARNING: Failed to execute: {call tm_dataloader.I2B2_LOAD_CLINICAL_DATA(?,?,?,?,?,?,?,?,?)} because: ORA-06550: line 1, column 21:
PLS-00905: object TM_DATALOADER.I2B2_LOAD_CLINICAL_DATA is invalid
ORA-06550: line 1, column 7:
PL/SQL: Statement ignored

Exception in thread “Thread-2” java.sql.SQLException: ORA-06550: line 1, column 21:
PLS-00905: object TM_DATALOADER.I2B2_LOAD_CLINICAL_DATA is invalid
ORA-06550: line 1, column 7:
PL/SQL: Statement ignored

    at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:450)
    at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:399)
    at oracle.jdbc.driver.T4C8Oall.processError(T4C8Oall.java:1059)
    at oracle.jdbc.driver.T4CTTIfun.receive(T4CTTIfun.java:522)
    at oracle.jdbc.driver.T4CTTIfun.doRPC(T4CTTIfun.java:257)

It is coming because of below procedure is invalid
i2b2_add_root_node(root_node, jobId);

This is invalid because insert into i2b2(i2b2_id) has invalid identifier . i2b2metadata.i2b2.i2b2_id is not a valid column.

Is there any iMDataLoader compatible version for this version of i2b2-transmart or any DB patch to resolve these kind of issues for compatibility?

#2

Hi sbaig,

The 18.1 stack uses an i2b2 compatible database schema. The 17.1 stack does not which is why it is expecting columns that dont exist in the 18.1 i2b2 schema, it also looks like you are missing loader specific columns used by the 17.1 leader itself.

We are very close to releasing a loader for 18.1, stay tuned.

1 Like
Is there any way to load data into this newly released instance from the publicly available data held at http://library.transmartfoundation.org/datasets/?