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Job request: 15413

Organisation:
University of Surrey
Workspace:
prostate_ca_incidence
ID:
uwbyv4zrzfbkatwn
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher AgzLeman requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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: 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_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_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
        Fig8: output/prevalenc_by_age_group.png
        Fig9: output/prevalenc_by_ethnicity.png
        Fig10: output/prevalenc_by_imd_cat.png
        csv1: output/Rates_rounded_prevalence.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
        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:

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

Job information

Status
Failed 
GitRepoNotReachableError: Could not read from https://github.com/opensafely/ProstateCancerPrevalence
Backend
TPP
Workspace
prostate_ca_incidence
Requested by
AgzLeman
Branch
main
Force run dependencies
Yes
Git commit hash
36cea08
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request