Maintaining Studies

For data curators and developers cbioportalImporter.py is available. This script can import data regardless of validation results. If data format is incorrect, the importer may stop with an error or crash, or leave the database in an inconsistent state.

This script can also be used to delete studies.

Requirements

This script requires $PORTAL_HOME to point to the folder containing your cBioPortal configuration. This can be done with:

export PORTAL_HOME=<cbioportal_configuration_folder>

The script itself can be found in <cbioportal_source_folder>/core/src/main/scripts/importer.

Importing a study without validation

To import a study without validation, run:

./cbioportalImporter.py -s <path to study directory>

For example:

./cbioportalImporter.py -s ../../../test/scripts/test_data/study_es_0/

Deleting a study

To remove a study, run:

./cbioportalImporter.py -c remove-study -meta <path to study directory>/meta_study.txt

The meta_study.txt file should contain the study ID in cancer_study_identifier: of the study you would like to remove.

For example:

./cbioportalImporter.py -c remove-study -meta /data/brca_small/meta_study.txt

If you have the Cancer Study Id of the study, or studies you want to remove, you can also use:

./cbioportalImporter.py -c remove-study -id study1_id

Where study1_id is the Cancer Study Id of the study you would like to remove.

You can also remove multiple studies at once by passing the Cancer Study Ids separated by commas:

./cbioportalImporter.py -c remove-study -id study1_id,study2_id,study3_id

Where study1_id, study2_id and study3_id are the Cancer Study IDs of the studies you would like to remove.