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Job request: 951

Organisation:
Bennett Institute
Workspace:
sro-smr
ID:
q6ni3sujxv5mup4j
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 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.

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: 01:25:04

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

Job request

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

Code comparison

Compare the code used in this job request