Job request: 4328

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Ali requested one or more actions to be run against real patient data in the BRIT Antibiotic Research 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

ID Status Action
qgcdtcojw4axqtgo succeeded generate_study_population
v7amriaq3vfxn372 succeeded generate_measures
vbuxddl36k6jv7hg succeeded describe_overall_OS
huy7ilw7eufmld6c succeeded describe_overall_brit
twk2kro7bfnckgsu succeeded describe_overall_brit_os
wyq4mfistiefpjol succeeded describe_ab_type_brit
yyvgshcjpaycxpo7 succeeded describe_ab_type_brit_os
7eqrum54utmjwi37 succeeded describe_percentile_os
ko46znyncnohjw5p succeeded describe_percentile_brit
cdnvyhfreqbcvpfg succeeded describe_percentile_brit_os
znqxskwf6ku3jtxy succeeded describe_starpu_os
l4zsofpzdjmwal65 succeeded describe_starpu_brit
p44tij5nhb5ovqp6 succeeded describe_starpu_brit_os
t63ouwqaubnsgkys succeeded describe_b_n_brit
vxdn2fiviqf3bwna succeeded describe_b_n_brit_os
tf5z24jr26rpyqzb succeeded generate_notebook_starpu_brit_os

Pipeline

Show Hide 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 "2020-10-01 to today by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv.gz

  generate_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_overall_OS:
    run: r:latest analysis/plot/overall_ab_prescribing_os.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        cohort: output/overall_line_os.png
        boxplot: output/overallbox_os.png
  
  describe_overall_brit:
    run: r:latest analysis/plot/overall_ab_prescribing_brit.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        cohort: output/overall_line_brit.png
        boxplot: output/overallbox_brit.png

  describe_overall_brit_os:
    run: r:latest analysis/plot/overall_ab_prescribing_brit_os.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        cohort: output/overall_line_brit_os.png
        boxplot: output/overallbox_brit_os.png

  describe_ab_type_brit:
    run: r:latest analysis/plot/stacked_bar_chart_top_10_abtype_brit.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        barchart: output/barchart_abtype_brit.png

  describe_ab_type_brit_os:
    run: r:latest analysis/plot/stacked_bar_chart_top_10_abtype_brit_os.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        barchart: output/barchart_abtype_brit_os.png

  describe_percentile_os:
    run: r:latest analysis/plot/overall_ab_prescribing_2575percentile_os.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        percentile: output/overall_25th_75th_percent_os.png
  
  describe_percentile_brit:
    run: r:latest analysis/plot/overall_ab_prescribing_2575percentile_brit.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        percentile: output/overall_25th_75th_percent_brit.png

  describe_percentile_brit_os:
    run: r:latest analysis/plot/overall_ab_prescribing_2575percentile_brit_os.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        percentile: output/overall_25th_75th_percent_brit_os.png

  describe_starpu_os:
    run: r:latest analysis/plot/starpu_ab_prescribing_os.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        cohort: output/starpu_line_os.png
        boxplot: output/starpu_box_os.png

  describe_starpu_brit:
    run: r:latest analysis/plot/starpu_ab_prescribing_brit.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        cohort: output/starpu_line_brit.png
        boxplot: output/starpu_box_brit.png
  
  describe_starpu_brit_os:
    run: r:latest analysis/plot/starpu_ab_prescribing_brit_os.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        cohort: output/starpu_line_brit_os.png
        boxplot: output/starpu_box_brit_os.png

  describe_b_n_brit:
    run: r:latest analysis/plot/broad_narrow_bar_chart_brit.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        percentile: output/broad_narrow_bar_chart_brit.png

  describe_b_n_brit_os:
    run: r:latest analysis/plot/broad_narrow_bar_chart_brit_os.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        percentile: output/broad_narrow_bar_chart_brit_os.png

  #generate_notebook_starpu:
  #  run: jupyter:latest jupyter nbconvert /workspace/analysis/starpu.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
  #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/*


  generate_notebook_starpu_brit_os:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/starpu_brit_os.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        notebook: output/starpu_brit_os.html 
        figures: output/*

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 13:44:48

Config

  • Backend:
    TPP
  • Workspace:
    abrx_os_brit
  • Branch:
    ABRX_comparison_OS_v_brit
  • Creator:
    ali-fahmi
  • Force run dependencies:
    True
  • Git Commit Hash:
    46a9179
  • Requested actions:
    • run_all