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Job request: 4428

Organisation:
NHSE/I
Workspace:
carehomeprescribing
ID:
bcg2ybnbrviozuty
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 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 
version: '3.0'

expectations:
  population_size: 10000

actions:


  generate_study_population:
    run: cohortextractor:latest generate_cohort --index-date-range "2020-05-01 to 2020-12-01 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 "2020-05-01 to 2020-12-01 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: 02:32:34

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

Job information

Status
Succeeded
Backend
TPP
Workspace
carehomeprescribing
Requested by
Greg Eydmann
Branch
main
Force run dependencies
No
Git commit hash
4b9d662
Requested actions
  • generate_study_population
  • generate_study_population_control
  • generate_study_population_ethnicity
  • join_ethnicity
  • join_ethnicity_control
  • generate_measures_control
  • generate_measures
  • describe

Code comparison

Compare the code used in this Job Request