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  • FCL4tranSMART is superseded by transmart-ICE which has the latest released code from Sanofi for their ICE tool data loader (formerly FCL4tranSMART).
  • The V1.2_Hackathon directory contents were unused
  • The loader is now superseded by the coipuy copy built from the src directory
  • The src-old directory is clearly redundant
  • The duplicate Kettle scripts under Kettle-GPL, Oracle and Postgres are removed. Since the start of the release 16 series the release copy of these scripts has been in the database-specific directories under the Kettle directory. These are used by the make targets in transmart-data and should be used by any local ETL pipelines.

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This release has been tested on Postgres up to 9.6, and on Postgres 10, Postgres 11 and Postgres 1112. No version-specific issues have been identified.

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Ubuntu 20 support

TranSMART 19 will be is being tested on Ubuntu 20 when it is (released in Spring 2020. Target release date is Thursday 23rd April 2020.).

Fedora support

TranSMART 19 will be is being tested on Fedora 32 , schedules for release (released end-April 2020). Code has been built and tested on Fedora 31.

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Only minor updates to Kettle scripts were needed to satisfy an additional validation. These had prevented upgrading Kettel Kettle in earlier tranSMART releases.

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Although tranSMART ETL procedures log each step to the audit tables, this logging is part of the ETL transaction. If the transaction should fail or if the ETL job is cancelled canceled the logging data will also be lost.

The audit log utilities in tranSMART 19 can also write to the database log file. This is an immediate write and output can be followed while the ETRL ETL job is running. An added benefit is that when run from the command line the log output is also printed to the console. This provides an immediate report of the audit messages so an inspection of the code can indicate which step is currently running.

To set up this additional logging, create a row in the new tm_cz.etl_settings table:

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The names are defined interbally in several places in the source code. They have been made clearer in tranSMART 19. The internal name RNASEQ_COG (developed by Cognizant for Sanofi) is used by RNAseq expression counts.

Renaming/moving a study

The postgresql script tm_cz.i2b2_move_study missed many of the changes needed to rename or move a study. The updated script requires two inputs: the original path of the top node for the study and the new path. Any new nodes are automatically created. The function takes an additional jobId parameter which is NULL when run from the command line.

Example:

psql -U tm_cz -W -c "select* from tm_cz.i2b2_move_study('\Public Studies\Asthma_Barczak GSE34466\', '\Public Studies\Asthma\Barczak GSE34466', NULL)"