Job request: 4258

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher PedroOliveira28 requested one or more actions to be run against real patient data in the Prostate Cancer PSA Testing 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
qhjdtoce5grwi33g succeeded generate_measures
ae4ae2pkijrvub4b succeeded generate_study_population

Pipeline

Show Hide 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

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: -

Config