hello-world

This is an example of an OGC-compliant application package for a simple Jupyter Notebook that echos and writes a string to an output file. The notebook is parameterized using papermill.

File descriptions

• hello-world.ipynb

  • Notebook/algorithm. All this notebook does is echo and write a string to an output file.

• inputs.json

  • Contains the input string to inject into the papermilled hello-world.ipynb notebook.

• hello-world.cwl

  • Notebook CWL workflow.

• main-workflow.cwl

  • Staged CWL workflow. This workflow is split into three stages: stage_in, process, and stage_out. The stage_in step is meant to execute a workflow that prepares the environment before running the process i.e. localizing input datasets. The process step executes the notebook algorithm workflow. The stage_out step could be used to execute a workflow that publishes generated datasets, or performs cleanup activities.

• hello-world.json

  • Application descriptor. This file defines the process parameters and how to execute the process, including which workflow to execute. The WPS will ingest this file to deploy a process.

For more information regarding OGC, see here.

Install

Install the CWL command line tool.

git clone https://github.com/marjo-luc/hello-world.git
cd hello-world

Execute

Execute subworkflow using the CWL runner

cwl-runner --no-read-only hello-world.cwl --input_1 "Hi!"

Execute main workflow using the CWL runner

cwl-runner --no-read-only main-workflow.cwl --input_1 "Hi!"

Execute notebook in batch mode using Docker

docker run marjoluc/hello-world:stable ./run.sh hello-world.ipynb output.ipynb -Sinput_1 "Hello!"

Execute notebook in batch mode without using Docker

conda env create --file binder/environment.yml ./run.sh hello-world.ipynb output.ipynb -Sinput_1 "Hello!"