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Job request: 938

Organisation:
Bennett Institute
Workspace:
sro-smr
ID:
4lxzhastjhx7jrib
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher 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_smr:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2020-11-01 by month" --output-dir=output/measures
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv

  generate_study_population_hospital_admission:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_hospital_admission --index-date-range "2019-01-01 to 2020-11-01 by month" --output-dir=output/measures
    outputs:
      highly_sensitive:
        cohort: output/measures/input_hospital_admission_*.csv
  
  generate_study_population_falls:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_falls --index-date-range "2019-01-01 to 2020-11-01 by month" --output-dir=output/measures
    outputs:
      highly_sensitive:
        cohort: output/measures/input_falls_*.csv
  
  generate_measures_smr:
      run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/measures
      needs: [generate_study_population_smr]
      outputs:
        moderately_sensitive:
          measure_csv: output/measures/measure_*.csv

  generate_measures_hospital_admission:
      run: cohortextractor:latest generate_measures --study-definition study_definition_hospital_admission --output-dir=output/measures
      needs: [generate_study_population_hospital_admission]
      outputs:
        moderately_sensitive:
          measure_csv: output/measures/measure_smr_by_hospital_admission_*.csv
  
  generate_measures_falls:
      run: cohortextractor:latest generate_measures --study-definition study_definition_falls --output-dir=output/measures
      needs: [generate_study_population_falls]
      outputs:
        moderately_sensitive:
          measure_csv: output/measures/measure_smr_by_falls_*.csv
  
  generate_plots_smr:
    run: python:latest python analysis/generate_plots_smr.py
    needs: [generate_measures_smr, generate_measures_hospital_admission, generate_measures_falls]
    outputs:
      moderately_sensitive:
        figure1: output/figures/population_rates.jpeg
        figure2: output/figures/sex_rates.jpeg
        figure3: output/figures/region_rates.jpeg
        figure4: output/figures/age_rates.jpeg
        figure5: output/figures/care_home_status_rates.jpeg
        figure6: output/figures/smr_decile_chart_falls.jpeg
        figure7: output/figures/smr_decile_chart.jpeg
        figure8: output/figures/smr_decile_chart_hospital_admission.jpeg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:09:58

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

Job information

Status
Succeeded
Backend
TPP
Workspace
sro-smr
Requested by
Louis Fisher
Branch
master
Force run dependencies
No
Git commit hash
db37485
Requested actions
  • generate_study_population_hospital_admission

Code comparison

Compare the code used in this Job Request