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
INCLUDED_TYPES
-- the modules to include, comma separated. Cannot be specified ifEXCLUDED_TYPES
is specified. If neither is specified, defaults to all the modules. Thefull
module that cannot be explicitly included (the only way to run it is to leaveINCLUDED_TYPES
andEXCLUDED_TYPES
blank).EXCLUDED_TYPES
-- include all the modules except those included in this comma separated list. The modulefull
is automatically excluded if this parameter is not blank. See alsoINCLUDED_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.