dataset-report

dataset-report generates a report for each dataset in an input directory. Datasets are extracted by cohort-extractor.

Usage

In summary:

Use cohort-extractor to extract one or more datasets.
Use dataset-report to generate a report for each dataset.

Let's walk through an example project.yaml.

The following cohort-extractor action extracts a dataset:

generate_cohort:
  run: >
    cohortextractor:latest generate_cohort
      --study-definition study_definition
  outputs:
    highly_sensitive:
      cohort: output/input.csv

Finally, the following dataset-report reusable action generates a report for the dataset. Remember to replace [version] with a dataset-report version:

generate_dataset_report:
  run: >
    dataset-report:[version]
      --input-files output/input.csv
      --output-dir output
  needs: [generate_cohort]
  outputs:
    moderately_sensitive:
      dataset_report: output/input.md

Notes for developers

Please see DEVELOPERS.md.