This job removes data from the database. This job is modular; you can choose what data to delete.

This job will refuse to fully remove a study if it the study has data that this job does not support removing. Beware of this limitation, as it limits the useful of this job pending the implementation of the remaining modules.

Note that running this job requires a backout.params file, which is not very convenient. You can still create an empty backout.params file and specify all the parameters on the command line. E.g.:

touch /tmp/backout.params
./transmart-batch-capsule.jar -p /tmp/backout.params -d STUDY_ID=GSE8581

Available parameters

  • INCLUDED_TYPES – the modules to include, comma separated. Cannot be specified if EXCLUDED_TYPES is specified. If neither is specified, defaults to all the modules. The full module that cannot be explicitly included (the only way to run it is to leave INCLUDED_TYPES and EXCLUDED_TYPES blank).
  • EXCLUDED_TYPES – include all the modules except those included in this comma separated list. The module full is automatically excluded if this parameter is not blank. See also INCLUDED_TYPES.

You could also use the study-specific parameters.


This job will run a few common steps at the beginning and at the end. In the middle, it will run sequentially the specified modules. Each module has two phases – in the first, it determines whether data whose deletion it handles exists on the database; the second phase is only invoked if such data indeed exists and it handles the data’s deletion.

The full module is special. It always runs last and it aborts the job if it finds concepts or assays belonging to the study in question (apart from the top node). If it doesn’t, it proceeds to the deletion of the top node and the study patients. No other module deletes patients, since data for all of the data types depends on them being present.


Available modules at this point:

  • clinical – deletes clinical data and clinical data related only concepts. Does not delete patients.
  • full – deletes the study top node and the study patients, provided no other data remains.