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Job request: 20680

Organisation:
University of Surrey
Workspace:
pancreaticcancer_enzyme_rx
ID:
ypih5alzvjj7sib2
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.

Jobs

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

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

  generate_enzyme_replace_1:    
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2015-01-01 to 2018-08-01 by month" --skip-existing --output-dir=output --output-format=feather
    outputs:      
      highly_sensitive:
        cohort: output/measures/inp*.feather
  
  generate_enzyme_replace_2:    
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-09-01 to 2023-09-01 by month" --skip-existing --output-dir=output --output-format=feather
    outputs:      
      highly_sensitive:
        cohort: output/measures/in*.feather

  generate_measures_enzymeRx:
    run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
    needs: 
      [
        generate_enzyme_replace_1,
        generate_enzyme_replace_2,
      ]
    outputs:
      moderately_sensitive:
        measure_csv1: output/measures/measure_enzymeRx*_rate.csv
        measure_csv2: output/measures/measure_ExByRegion*_rate.csv

  describe_ERx_rates:
    run: r:latest analysis/analysis_enzymeRx.R
    needs: [generate_measures_enzymeRx]
    outputs:
      moderately_sensitive:
        Fig1: output/ERx_number.png
        Fig2: output/ERx_rates.png
        Fig3: output/model_rates.png
        Fig4: output/Region.png
        Fig5: output/Figure_3A_East.png
        Fig6: output/Figure_3B_East Midlands.png
        Fig7: output/Figure_3C_London.png
        Fig8: output/Figure_3D_North East.png
        Fig9: output/Figure_3E_North West.png
        Fig10: output/Figure_3F_South East.png
        Fig11: output/Figure_3G_South West.png
        Fig12: output/Figure_3H_West Midlands.png
        Fig13: output/Figure_3I_Yorkshire and The Humber.png
        csv3: output/ERx_Rates_rounded.csv
        csv4: output/Region_rounded.csv
  
  generate_report:
    run: r:latest analysis/Produce_html.R
    needs: [describe_ERx_rates]
    outputs:
      moderately_sensitive:
        cohort: output/Report_file.html

  # generate_notebook:
  #   run: jupyter:latest jupyter nbconvert /workspace/analysis/reportEx.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
  #   needs: [describe_ERx_rates]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/reportEx.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 32:46:58

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

Job information

Status
Failed
Backend
TPP
Workspace
pancreaticcancer_enzyme_rx
Requested by
AgzLeman
Branch
main
Force run dependencies
Yes
Git commit hash
fda37cc
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request