Adapting your code to run as a Generalized Code Object

In order for your code to successfully run on the FCP, you must make sure to comply with the following specification:

Modify Where You Are Reading and Writing From in Your Code

1. All inputs should be read from the /input folder. Datasets will be zero-indexed within the /input folder (i.e. Input Dataset 1 - /input/0/, Input Dataset 2 - /input/1/, etc.)

   ---

   • For Tabular Data: /input/0/dataset.csv. If you would like to work with the data as a Pandas DataFrame you can load the Dataset using the following example:

     df = pd.read_csv(“/input/0/dataset.csv”)

     ---

   • For file data (data that has been defined in the Data Schema as type Filename):If there is any file data associated with the Dataset, it will be under the /input/file_data/ directory, structured in the same subdirectory structure as was specified when importing the Dataset. Example:
     /input/0/file_data/.

     ---

   • For DICOM data (data that has been defined in the Data Schema as type DicomStudyUID, DicomSeriesUID, or DicomInstanceUID.): If there is any DICOM data associated with the Dataset, it will be under the /input/dicom_data/ directory, structured in the same subdirectory structure as was specified when importing the Dataset. Example:
     /input/0/dicom_data/

     ---

2. All output should be written to the /output mount.

   ---

   • For Tabular Data: /output/0/dataset.csv. To write your data as a Pandas DataFrame you can use the following example:

     df.to_csv(“/output/0/dataset.csv”, index=False)

     ---

   • For file data: /output/0/file_data/

     ---

   • For DICOM data: /output/0/dicom_data/

[If applicable] Modify where you are reading your runtime parameters

Any run parameters that have been specified shall be in a file named /input/run_params.json

Creating the Dockerfile

Create a Dockerfile with the configuration necessary for your code. You may use the example provided in the user-resources github repository as a template and make changes as needed where there are comments beginning with "# !! EDIT THIS:"

Ensure any files that might be downloaded at runtime are pre-downloaded and copied to the container in the Dockerfile

Copy files that might need to be downloaded at runtime as pre-downloaded copy statements within the Dockerfile

Optional recommendations

We recommend that you build and test your container locally. There is a utility script called docker-run.sh in the gc-docker-utils folder to assist with this. It can be used by running:

./docker-run.sh path/to/input path/to/output