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Job request: 14268

Organisation:
University of Surrey
Workspace:
pancreaticcancer_enzyme_rx
ID:
a4fjslydqzdswwm6
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 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: 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 2022-12-01 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
        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/Test1_R.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: 00:00:26

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

Job information

Status
Succeeded
Backend
TPP
Workspace
pancreaticcancer_enzyme_rx
Requested by
AgzLeman
Branch
main
Force run dependencies
No
Git commit hash
740d977
Requested actions
  • describe_ERx_rates
  • generate_report

Code comparison

Compare the code used in this Job Request