cBioPortal
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2.4 Integration with Other Webservices
5.2 Datasets
6. Web API and Clients
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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:
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export PORTAL_HOME=<cbioportal_configuration_folder>
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Workflow

First, if your cancer type does not yet exist, you need to create it:
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./cbioportalImporter.py -c import-cancer-type -data <path to study directory>/<name of data file>
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Next, create the study using
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./cbioportalImporter.py -c import-study -meta <path to study directory>/<name of meta file>
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The meta file has to contain the study information.
Now you can import your data file(s):
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./cbioportalImporter.py -c import-study-data -meta <path to study directory>/<name of meta file> -data <path to study directory>/<name of data file>
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:warning: Your first data file should always be the clinical data!
Finally, after you've imported all data, import your case lists:
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./cbioportalImporter.py -c import-case-list -meta <path to study directory>/<path to case lists>
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Example:

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