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Job request: 3031

Organisation:
Bennett Institute
Workspace:
antimicrobial-stewardship
ID:
nvrwii6u6nrq73fo
View repo View project.yaml

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

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release 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: 08:46:28

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

Job request

Status
Succeeded
Backend
TPP
Workspace
antimicrobial-stewardship
Requested by
Jon Massey
Branch
master
Force run dependencies
Yes
Git commit hash
c49ddea
Requested actions
  • plot_broad_spec_deciles
  • plot_trimethoprim_nitrofurantoin_deciles

Code comparison

Compare the code used in this job request