Cbio Importer

A arbitrary CSV convertor to cBioPortal-compatible csv study set. It is using the offline study import for cbioportal docker deployment. This importer expects cbioportal usage with docker compose, and uses this to automate study validation & import.

Important

Still under development!

On more information, see example/ folder. To run app on your machine use:

poetry install && poetry build && poetry run python -m cbio_importer --help

which will print usage information.

Example study generation from the host machine:

poetry run python -m cbio_importer \
  --csv_path_prefix=example \
  --functions=example/functions.py \
  --output_path_prefix=example/output \
  example/study.yaml

Or, provide arguments as .env configuration and run instead:

set -a && source .env && set +a && poetry run python -m cbio_importer

Or, run (once poetry is configured)

`generate.sh`

Using the scripts has the advantage of executing custom env configuration at desired location. Example: project file structure looks like

project
  - functions.py
  - study.yml
  - .env
  ...

and the .env file contents is among other:

CBIO_CSV_PATH_PREFIX=.
CBIO_FUNCTIONS=functions.py
CBIO_STUDY_DEFINITION=study.yaml
...

you can simply run path/to/generate.sh and pahts will be correctly resolved for you, if you execute from the project folder.

Once ready, you can import your data using import.sh:

# you have to provide these in `.env` file or manually export in your shell
CBIO_DEPLOY_FOLDER=../../cbioportal-deployment               # path to cbioportal docker-compose.yml
CBIO_IMAGE_NAME=cbioportal-6.0.17-7-g631429dbb8-dirty-bbmri  # docker image name to use
CBIO_TEMP_FOLDER=temp                                        # any folder (best non-existent) to use for temp data
CBIO_STUDY_FOLDER=example/output                             # study folder where .csv files for import exist

and run ./import.sh

Features:

Supported cbioportal entities:

• study
  • patient
  • sample
  • resource
    • sample resource
    • patient resource
    • study resource

Supported operations:

• custom functions
• filtering
• joins
• grouping