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Data loading: Importing without validation and deleting 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 Importing a study without validation Deleting a study
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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
.
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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/
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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.