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Job request: 14691

Organisation:
University of Surrey
Workspace:
mh_emergencies
ID:
7o26bylpkcxskvww
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_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_self_harmAE*_rate.csv
        measure_csv2: output/measures/measure_self_harmAEbyRegion*_rate.csv
        measure_csv3: output/measures/measure_self_harmAEbyIMD*_rate.csv
        measure_csv4: output/measures/measure_self_harmAEbyEthnicity*_rate.csv
        measure_csv5: output/measures/measure_self_harmAEbyAge*_rate.csv

  describe_trends:
    run: r:latest analysis/Descriptive_trends.R
    needs: 
      [
        generate_measures,
      ]
    outputs:
      moderately_sensitive:
        fig1: output/self_harmAE.png
        fig2: output/self_harmAEbyReg.png
        fig3: output/self_harmAEbyIMD.png
        fig4: output/self_harmAEbyEth.png
        fig5: output/self_harmAEbyAge.png   
        csv1: output/self_harmAE_rounded.csv
        csv2: output/self_harmAEbyReg_rounded.csv
        csv3: output/self_harmAEbyIMD_rounded.csv
        csv4: output/self_harmAEbyEth_rounded.csv
        csv5: output/self_harmAEbyAge_rounded.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 29:10:36

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

Job information

Status
Succeeded
Backend
TPP
Workspace
mh_emergencies
Requested by
AgzLeman
Branch
main
Force run dependencies
Yes
Git commit hash
cd281ea
Requested actions
  • run_all

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