Job request: 7339

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Milan Wiedemann requested one or more actions to be run against real patient data in the Blood Pressure - Quality and Outcomes Framework (QOF) 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

ID Status Action
zqfpvost743ye7x3 succeeded generate_study_population_ethnicity
fav7ut744mk2g4x4 succeeded generate_study_population_bp002
6rlqpvmbpfu7t576 succeeded join_ethnicity_bp002
562cgid26e7k72i5 succeeded generate_measures_bp002
bs63xbpsdrsbw4qg succeeded generate_deciles_charts

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 1000

actions:

  # Generate ethnicity study population
  generate_study_population_ethnicity:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_ethnicity 
      --output-dir=output
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv

  generate_study_population_bp002:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_bp002 
      --index-date-range "2019-03-01 to 2022-03-01 by month" 
      --output-dir=output
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/input_bp002*.csv
  
  join_ethnicity_bp002:
    run: >
      cohort-joiner:v0.0.12 
        --lhs output/input_bp002*.csv
        --rhs output/input_ethnicity.csv
        --output-dir output/joined
    needs: [generate_study_population_ethnicity, generate_study_population_bp002]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_bp002*.csv

  generate_measures_bp002:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_bp002 
       --output-dir=output/joined
     needs: [join_ethnicity_bp002]
     outputs:
       moderately_sensitive:
         measure_csv: output/joined/measure_bp002_*_rate.csv

  generate_deciles_charts:
    run: >
      deciles-charts:v0.0.15
        --input-files output/joined/measure_*.csv
        --output-dir output
    config:
      show_outer_percentiles: false
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures_bp002]
    outputs:
      moderately_sensitive:
        deciles_charts: output/deciles_*_*.*

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 25:22:36

Config

  • Backend:
    TPP
  • Workspace:
    blood-pressure-qof
  • Branch:
    master
  • Creator:
    milanwiedemann
  • Force run dependencies:
    False
  • Git Commit Hash:
    dc94a87
  • Requested actions:
    • generate_study_population_ethnicity
    • generate_study_population_bp002
    • join_ethnicity_bp002
    • generate_measures_bp002
    • generate_deciles_charts
    • run_all