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Job request: 11009

Organisation:
Bennett Institute
Workspace:
antimicrobial-stewardship
ID:
uodwbl2exgyalbdb
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 in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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

  check_broad_spec_codelists:
    run: python:latest python analysis/check_broad_spec_codelists.py
    outputs:
      moderately_sensitive:
        report: output/broad_spectrum_codelist_report.txt

  generate_broad_spec_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_broad_spec --skip-existing --output-dir=output --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_broad*.csv.gz

  calculate_broad_spec_ratio:
    run: python:latest python analysis/calculate_broad_spec.py
    needs: [generate_broad_spec_population]
    outputs:
      moderately_sensitive:
        ratios: output/broad_spec_ratio.csv

  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: 00:09:13

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
4b35f1a
Requested actions
  • generate_broad_spec_population

Code comparison

Compare the code used in this Job Request