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Job request: 4565

Organisation:
NHSE/I
Workspace:
carehomeprescribing
ID:
5wnqqm6w5iel3kjv
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Greg Eydmann 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.

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:


  generate_study_population:
    run: cohortextractor:latest generate_cohort --index-date-range "2019-03-01 to 2021-03-01 by month" --study-definition study_definition --output-dir=output/inputs
    outputs:
      highly_sensitive:
        cohort: output/inputs/input_*.csv

  generate_study_population_control:
    run: cohortextractor:latest generate_cohort --index-date-range "2019-03-01 to 2021-03-01 by month" --study-definition study_definition_control --output-dir=output/control
    outputs:
      highly_sensitive:
        cohort: output/control/input_control_*.csv
        
        
  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output/inputs 
    outputs:
      highly_sensitive:     
        cohort: output/inputs/input_ethnicity.csv

  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py    
    needs: [generate_study_population, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/inputs/input*.csv


  join_ethnicity_control:
    run: python:latest python analysis/join_ethnicity_control.py    
    needs: [generate_study_population_control, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/control/input*.csv
        
          # Generate measures
          
  generate_measures_control:
      run: cohortextractor:latest generate_measures --study-definition study_definition_control --output-dir=output/control
      needs: [join_ethnicity_control]
      outputs:
        moderately_sensitive:
          measure_csv: output/control/measure_control_*.csv


  generate_measures:
      run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/inputs
      needs: [join_ethnicity]
      outputs:
        moderately_sensitive:
          measure_csv: output/inputs/measure_a*.csv
               
  describe:
    run: python:latest python analysis/descriptives.py
    needs: [generate_measures,join_ethnicity,generate_measures_control]
    outputs:
      moderately_sensitive:
        cohort: output/graphs/*.html
        tables: output/descriptives/descriptive_statistics_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job request

Status
Failed 
JobRequestError: generate_study_population failed on a previous run and must be re-run
Backend
TPP
Workspace
carehomeprescribing
Requested by
Greg Eydmann
Branch
main
Force run dependencies
No
Git commit hash
e3a846b
Requested actions
  • run_all

Code comparison

Compare the code used in this job request