Using the metaImport Script

Importing Data into cBioPortal
The metaImport script should be used to automate the process of validating and loading datasets. It also has some nice features like an extra option to only load datasets that completely pass validation (i.e. with no errors, while warnings can be explicitly allowed by the user).
Running the metaImport Script
To run the metaImport script first go to the importer folder <your_cbioportal_dir>/core/src/main/scripts/importer and then run the following command:
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./metaImport.py -h
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This will tell you the parameters you can use:
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$./metaImport.py -h
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usage: metaImport.py [-h] -s STUDY_DIRECTORY
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                     [-u URL_SERVER | -p PORTAL_INFO_DIR | -n]
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                     [-jar JAR_PATH] [-html HTML_TABLE]
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                     [-v] [-o] [-r] [-m]
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​
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cBioPortal meta Importer
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​
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optional arguments:
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  -h, --help            show this help message and exit
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  -s STUDY_DIRECTORY, --study_directory STUDY_DIRECTORY
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                        path to directory.
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  -u URL_SERVER, --url_server URL_SERVER
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                        URL to cBioPortal server. You can set this if your URL
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                        is not http://localhost/cbioportal
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  -p PORTAL_INFO_DIR, --portal_info_dir PORTAL_INFO_DIR
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                        Path to a directory of cBioPortal info files to be
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                        used instead of contacting the web API
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  -n, --no_portal_checks
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                        Skip tests requiring information from the cBioPortal
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                        installation
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  -jar JAR_PATH, --jar_path JAR_PATH
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                        Path to scripts JAR file (default: locate it relative
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                        to the import script)
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  -html HTML_TABLE, --html_table HTML_TABLE
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                        path to html report
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  -v, --verbose         report status info messages while validating
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  -o, --override_warning
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                        override warnings and continue importing
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  -r, --relaxed_clinical_definitions
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                        Option to enable relaxed mode for validator when
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                        validating clinical data without header definitions
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  -m, --strict_maf_checks
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                        Option to enable strict mode for validator when
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                        validating mutation data
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Example of Importing a study
Export PORTAL_HOME as explained here, e.g.
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export PORTAL_HOME=<cbioportal_configuration_folder>
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and then run (this simple command only works if your cBioPortal is running at http://localhost/cbioportal - if this is not the case, follow the advanced example):
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./metaImport.py -s ../../../test/scripts/test_data/study_es_0/
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Advanced Example
This example imports the study to the localhost, creates an html report and shows status messages.
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./metaImport.py -s ../../../test/scripts/test_data/study_es_0/ -u http://localhost:8080 -html myReport.html -v
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By adding -o, warnings will be overridden and import will start after validation.
Development / debugging mode
For developers and specific testing purposes, an extra script, cbioportalImporter.py, is available which imports data regardless of validation results. Check this page for more information on how to use it.

Using the Dataset Validator

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Contents

Importing Data into cBioPortal

Running the metaImport Script

Example of Importing a study

Advanced Example

Development / debugging mode