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Job request: 2898

Organisation:
Bennett Institute
Workspace:
antimicrobial-stewardship
ID:
4avqeu4h7ekc4qg6
View repo View project.yaml

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: 1000000

actions:

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

  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
    outputs:
      highly_sensitive:
        cohort: output/measures/input*.csv

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

  plot_broad_spec_deciles:
    run: python:latest python analysis/plot_deciles.py broad_spectrum_proportion
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        cohort: output/figures/broad_spectrum_proportion_decile_chart.png

  plot_trimethoprim_nitrofurantoin_deciles:
    run: python:latest python analysis/plot_deciles.py trimethoprim_prescription_proportion
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        cohort: output/figures/trimethoprim_prescription_proportion_decile_chart.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 05:05:55

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

Job information

Status
Succeeded
Backend
TPP
Workspace
antimicrobial-stewardship
Requested by
Jon Massey
Branch
master
Force run dependencies
Yes
Git commit hash
dafa9b6
Requested actions
  • plot_broad_spec_deciles
  • plot_trimethoprim_nitrofurantoin_deciles

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