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Job request: 10811

Organisation:
Bennett Institute
Workspace:
antimicrobial-stewardship
ID:
uxzxgtv26rivjynf
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: 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_nitro_trim_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nitro_trim --skip-existing --output-dir=output --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input*.csv.gz

  calculate_nitro_trim_ratio:
    run: python:latest python analysis/calculate_nitro_trim_ratio.py
    needs: [generate_nitro_trim_population]
    outputs:
      moderately_sensitive:
        ratios: output/nitro_trim_ratio.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 --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: 00:06:42

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
0fa58c2
Requested actions
  • calculate_nitro_trim_ratio

Code comparison

Compare the code used in this job request