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Job request: 4302

Organisation:
University of Manchester
Workspace:
amr-uom-brit-main
ID:
oyxbibphtm65h53i
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Simon Davy 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 --index-date-range "2019-01-01 to today by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv.gz

  generate_study_population_elderly:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_elderly 
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_elderly.csv.gz

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_*.csv
        
  describe_elderly_agedis:
    run: r:latest analysis/tables/gen_csv_age_check.R
    needs: [generate_study_population_elderly]
    outputs:
      moderately_sensitive:
        agetable: output/age_quant.csv

  describe:
    run: r:latest analysis/plot/overall_ab_prescribing.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        cohort: output/overall.png
        boxplot: output/overallbox.png

  describe_percentile:
    run: r:latest analysis/plot/overall_ab_prescribing_2575percentile.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        percentile: output/overall_25th_75th_percentile.png

  describe_starpu:
    run: r:latest analysis/plot/starpu_ab_prescribing.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        cohort: output/starpuline.png
        boxplot: output/starpubox.png
  
  generate_notebook_starpu:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/starpu.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        notebook: output/starpu.html 
        figures: output/*
        #tables: output/tables/*
        #csvs: output/*/* # two possible subfolders
        #text: output/text/*
  
  describe_infection_ab_UTI:
    run: r:latest analysis/plot/infection_ab_UTI.R
    needs: [generate_study_population, generate_measures]
    outputs:
       moderately_sensitive:
        plot: output/UTI.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:13:51

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

Job information

Status
Succeeded
Backend
TEST
Workspace
amr-uom-brit-main
Requested by
Simon Davy
Branch
main
Force run dependencies
No
Git commit hash
cc7eeeb
Requested actions
  • run_all

Code comparison

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