For Developers

In some cases, for example during development, it may be useful to import a single data file into an existing study. To import one data file at a time, you can use the following command. Note that this process will not validate the data.

This can be done by running cbioportalImporter.py from <cbioportal_source_folder>/core/src/main/scripts/importer/.

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>

Workflow

First, if your cancer type does not yet exist, you need to create it:

./cbioportalImporter.py -c import-cancer-type -data <path to study directory>/<name of data file>

Next, create the study using

./cbioportalImporter.py -c import-study -meta <path to study directory>/<name of meta file>

The meta file has to contain the study information.

Now you can import your data file(s):

./cbioportalImporter.py -c import-study-data -meta <path to study directory>/<name of meta file> -data <path to study directory>/<name of data file>

:warning: Your first data file should always be the clinical data!

Finally, after you've imported all data, import your case lists:

./cbioportalImporter.py -c import-case-list -meta <path to study directory>/<path to case lists>

Example:

./cbioportalImporter.py -c import-cancer-type -data /data/brca_small/data_cancer_type.txt
./cbioportalImporter.py -c import-study -meta /data/brca_small/meta_study.txt
./cbioportalImporter.py -c import-study-data -meta /data/brca_small/meta_clinical.txt -data /data/brca_small/data_clinical.txt
./cbioportalImporter.py -c import-study-data -meta /data/brca_small/meta_expression.txt -data /data/brca_small/data_expression.txt
./cbioportalImporter.py -c import-case-list -meta /data/brca_small/case_lists