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Job request: 4015

Organisation:
NHSE/I
Workspace:
carehomeprescribing
ID:
3ddvrlneofefwk5t
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.

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  generate_study_population_ad:
    run: cohortextractor:latest generate_cohort --index-date-range "2019-32-01 to 2021-03-01 by month" --study-definition study_definition_ad
    outputs:
      highly_sensitive:
        cohort: output/input_ad_*.csv

  generate_study_population_ap:
    run: cohortextractor:latest generate_cohort --index-date-range "2019-03-01 to 2021-03-01 by month" --study-definition study_definition_ap
    outputs:
      highly_sensitive:
        cohort: output/input_ap_*.csv

  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output
    outputs:
      highly_sensitive:     
        cohort: output/input_ethnicity.csv

  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py
    needs: [generate_study_population_ad, generate_study_population_ap, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/input*.csv
        
          # Generate measures
  generate_measures_ad:
      run: cohortextractor:latest generate_measures --study-definition study_definition_ad --output-dir=output
      needs: [join_ethnicity]
      outputs:
        moderately_sensitive:
          measure_csv: output/measure_ad_*.csv
          

  generate_measures_ap:
      run: cohortextractor:latest generate_measures --study-definition study_definition_ap --output-dir=output
      needs: [join_ethnicity]
      outputs:
        moderately_sensitive:
          measure_csv: output/measure_ap_*.csv
        
  describe:
    run: python:latest python analysis/descriptives.py
    needs: [generate_measures_ad, generate_measures_ap]
    outputs:
      moderately_sensitive:
        cohort: output/*.html
        tables: output/*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job information

Status
Failed 
JobRequestError: generate_measures_ad 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
be652b5
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request