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Job request: 15335

Organisation:
University of Surrey
Workspace:
prostate_ca_incidence
ID:
56isd4dxh2ezvxeo
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher AgzLeman 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: 1000

actions:
  
  generate_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.feather

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  generate_rates_1:    
    run: cohortextractor:latest generate_cohort --study-definition study_definition_rates --index-date-range "2015-01-01 to 2018-12-01 by month" --skip-existing --output-dir=output --output-format=feather
    outputs:      
      highly_sensitive:
        cohort: output/measures/inpu*.feather
  
  generate_rates_2:    
    run: cohortextractor:latest generate_cohort --study-definition study_definition_rates --index-date-range "2019-01-01 to 2022-12-01 by month" --skip-existing --output-dir=output --output-format=feather
    outputs:      
      highly_sensitive:
        cohort: output/measures/inp*.feather

  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py
    needs:
      [
        generate_rates_1,
        generate_rates_2,
        generate_ethnicity,
      ]
    outputs:
      highly_sensitive:
        cohort: output/measures/in*.feather
  
  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_rates --skip-existing --output-dir=output/measures
    needs: 
      [
        generate_rates_1,
        generate_rates_2,
        join_ethnicity,
      ]
    outputs:
      moderately_sensitive:
        measure_csv1: output/measures/measure_prevalence*_rate.csv
        measure_csv2: output/measures/measure_prevalencebyRegion*_rate.csv
        measure_csv3: output/measures/measure_prevalencebyIMD*_rate.csv
        measure_csv4: output/measures/measure_prevalencebyEthnicity*_rate.csv
        measure_csv5: output/measures/measure_prevalencebyAge*_rate.csv
        measure_csv6: output/measures/measure_incidence*_rate.csv
        measure_csv7: output/measures/measure_incidencebyRegion*_rate.csv
        measure_csv8: output/measures/measure_incidencebyIMD*_rate.csv
        measure_csv9: output/measures/measure_incidencebyEthnicity*_rate.csv
        measure_csv10: output/measures/measure_incidencebyAge*_rate.csv
        measure_csv11: output/measures/measure_mortality*_rate.csv

  describe_trends:
    run: r:latest analysis/Descriptive_trends.R
    needs: 
      [
        generate_measures,
        generate_study_population
      ]
    outputs:
      moderately_sensitive:
        Fig1: output/incidence.png
        Fig2: output/prevalence.png
        Fig3: output/died_prostate.png
        Fig4: output/incidence_by_age_group.png
        Fig5: output/incidence_by_ethnicity.png
        Fig6: output/incidence_by_imd_cat.png
        Fig7: output/incidence_by_region.png
        Fig8: output/prevalenc_by_age_group.png
        Fig9: output/prevalenc_by_ethnicity.png
        Fig10: output/prevalenc_by_imd_cat.png
        Fig11: output/prevalenc_by_region.png
        csv1: output/Rates_rounded_prevalence.csv
        csv2: output/Rates_rounded_prevalence_by_region.csv
        csv3: output/Rates_rounded_prevalence_by_imd_cat.csv
        csv4: output/Rates_rounded_prevalence_by_ethnicity.csv
        csv5: output/Rates_rounded_prevalence_by_age_group.csv
        csv6: output/Rates_rounded_incidence.csv
        csv7: output/Rates_rounded_incidence_by_region.csv
        csv8: output/Rates_rounded_incidence_by_imd_cat.csv
        csv9: output/Rates_rounded_incidence_by_ethnicity.csv
        csv10: output/Rates_rounded_incidence_by_age_group.csv
        csv11: output/Rates_rounded_died_prostate.csv
        csv12: output/Table1.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:43

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

Job request

Status
Succeeded
Backend
TPP
Workspace
prostate_ca_incidence
Requested by
AgzLeman
Branch
main
Force run dependencies
No
Git commit hash
bcff1b2
Requested actions
  • describe_trends

Code comparison

Compare the code used in this job request