Skip to content

Job request: 4258

Organisation:
NHSE/I
Workspace:
prostate_cancer_psa_testing_2021
ID:
pppon6zuuxiublud

This page shows the technical details of what happened when authorised researcher Pedro Oliveira 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
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-04-01 to 2021-09-30 by month" --output-dir=output --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv.gz
        #This has been taken from https://github.com/opensafely/sro-template/blob/master/project.yaml
        #The output files are not there, but assume it will give the 30 input files witht the suffices being the months
        #The .gz extension code above is to turn it into a compressed file


  generate_measures:
      run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
      #Give errors if used: --index-date-range "2019-04-01 to 2021-09-30 by month" --output-format csv
      needs: [generate_study_population]
      outputs:
        moderately_sensitive:
          measure_csv: output/measure_*.csv


  # run_model:
  #   run: python:analysis/PSA_graphs.py
  #   needs: [generate_measures]
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: output/PSA_test_total_table.csv
  
  #Code below functioning as of 2021 10 27
  #New 2021/10/11 - PSA_graphs.py working in ypnb book locally, but gives error whem running model
  run_model:
    #python:latest is in principle needed. All slashes in paths should be forward slashes
    run: python:latest python analysis/PSA_graphs.py
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        plots: output/*.jpg #Tests_long_list.jpg, output/Tests_short_list.jpg - comma to separate lists may not work
        #Putting a second line with plots and a different output gives duplicate key error

Timeline

  • Created:

  • Finished:

  • Runtime:

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

Job information

Status
Succeeded
Backend
TPP
Requested by
Pedro Oliveira
Branch
main
Force run dependencies
No
Git commit hash
f9a24a4
Requested actions
  • generate_study_population
  • generate_measures

Code comparison

Compare the code used in this Job Request