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Job request: 3860

Organisation:
Bennett Institute
Workspace:
antimicrobial-stewardship
ID:
e6iiobknpxasxqqi

This page shows the technical details of what happened when authorised researcher Jon Massey requested one or more actions to be run against real patient data in the 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

Pipeline

Show project.yaml
######################################

# This script defines the project pipeline - it specifys the execution orders for all the code in this
# repo using a series of actions.

######################################

version: '3.0'

expectations:
  population_size: 3000

actions:

  # Extract data ----
  # generate_study_population:
  #   run: cohortextractor:latest generate_cohort --study-definition study_definition --skip-existing --output-dir=output --output-format=csv.gz
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/input*.csv.gz

  generate_measure_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-09-01 to today by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input*.csv.gz

  calculate_measures:
    run: python:latest python analysis/calculate_measures.py
    needs: [generate_measure_population]
    outputs:
      highly_sensitive:
        measures: output/measures/measure_*.csv.gz
      moderately_sensitive:
        pivot_stats: output/measures/pivotstats_*.csv

  plot_measure_deciles:
    run: python:latest python analysis/plot_deciles.py
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        figures: output/figures/*.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:02:55

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job information

Status
Succeeded
Backend
TPP
Requested by
Jon Massey
Branch
master
Force run dependencies
No
Git commit hash
383a3b7
Requested actions
  • plot_measure_deciles

Code comparison

Compare the code used in this Job Request