Job request: 8890

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Ali requested one or more actions to be run against real patient data in the BRIT Antibiotic Research project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

ID Status Action
gah23i74cxsmdzf6 succeeded generate_notebook_hospitalisation_rate

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 1000

actions:

  study_definition_hospitalisation_rate:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation_rate --index-date-range "2019-01-01 to 2022-02-01 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv.gz

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_hospitalisation_rate --skip-existing --output-dir=output/measures
    needs: [study_definition_hospitalisation_rate]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_*.csv

  generate_notebook_hospitalisation_rate:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_rate.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_rate --ExecutePreprocessor.timeout=86400
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        notebook: output/hospitalisation_rate/hospitalisation_rate.html 
        figures: output/hospitalisation_rate/*

  
  # study_definition_hospitalisation_rate_hxdx:
  #   run: cohortextractor:latest generate_cohort --study-definition study_definition_hospitalisation_rate_hxdx --index-date-range "2019-01-01 to 2022-02-01 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/measures/input*.csv.gz

  # generate_measures_hxdx:
  #   run: cohortextractor:latest generate_measures --study-definition study_definition_hospitalisation_rate_hxdx --skip-existing --output-dir=output/measures
  #   needs: [study_definition_hospitalisation_rate_hxdx]
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: output/measures/measur_*.csv

  # generate_notebook_hospitalisation_rate_hxdx:
  #   run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_rate_hxdx.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_rate_hxdx --ExecutePreprocessor.timeout=86400
  #   needs: [generate_measures_hxdx]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/hospitalisation_rate_hxdx/hospitalisation_rate_hxdx.html 
  #       figures: output/hospitalisation_rate_hxdx/*

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 00:00:58

Config

  • Backend:
    TPP
  • Workspace:
    hosp_rate
  • Branch:
    hospitalisation_rate
  • Creator:
    ali-fahmi
  • Force run dependencies:
    False
  • Git Commit Hash:
    6fbb9b6
  • Requested actions:
    • generate_notebook_hospitalisation_rate