Job request: 4464

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Vicki Palin UoM 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
a75ntaue4nf2qw7j succeeded describe_ab_type_brit
iimyeqcoxta4tesi succeeded describe_ab_type_brit_os
mzr7wx6iead4i5c5 succeeded describe_b_n_brit
yhkrlcnbvwxikzwq succeeded describe_b_n_brit_os
5jueyoihp7h3dvlc succeeded describe_overall_OS
lkuwmnqthgpk3u47 succeeded describe_overall_brit
eit57y3vpluxq3h4 succeeded describe_overall_brit_os
lhykencjntx67rug succeeded describe_percentile_brit
ujwrylrbvrbn4wlb succeeded describe_percentile_brit_os
7ausqhb436omfhia succeeded describe_percentile_os
baoyht4ev6jbtdnw succeeded describe_starpu_brit
vjzsdaehfiyi4q5x succeeded describe_starpu_brit_os
bwrwkdneyglilhvf succeeded describe_starpu_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_boxplot_os.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        boxplot: output/overallbox_os.jpeg
  
  describe_overall_brit:
    run: r:latest analysis/plot/overall_ab_boxplot_brit.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        boxplot: output/overallbox_brit.jpeg

  describe_overall_brit_os:
    run: r:latest analysis/plot/overall_ab_boxplot_brit_os.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        boxplot: output/overallbox_brit_os.jpeg

  describe_ab_type_brit:
    run: r:latest analysis/plot/stacked_bar_chart_top_10_abtype_brit.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        linechart: output/linechart_abtype_brit.jpeg
        barchart: output/barchart_abtype_brit.jpeg
        table: output/abtype_top10_bymonth_brit.csv

  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:
        linechart: output/linechart_abtype_brit_os.jpeg
        barchart: output/barchart_abtype_brit_os.jpeg
        table: output/abtype_top10_bymonth_brit_os.csv

  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.jpeg
        table: output/pres_number_os.csv
  
  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.jpeg
        table: output/pres_number_brit.csv

  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.jpeg
        table: output/pres_number_brit_os.csv

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

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

  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.jpeg

  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.jpeg

  #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: 03:24:21

Config

  • Backend:
    TPP
  • Workspace:
    abrx_os_brit
  • Branch:
    ABRX_comparison_OS_v_brit
  • Creator:
    v1kki213
  • Force run dependencies:
    False
  • Git Commit Hash:
    94409a2
  • Requested actions:
    • describe_overall_OS
    • describe_overall_brit
    • describe_overall_brit_os
    • describe_ab_type_brit
    • describe_ab_type_brit_os
    • describe_percentile_os
    • describe_percentile_brit
    • describe_percentile_brit_os
    • describe_starpu_os
    • describe_starpu_brit
    • describe_starpu_brit_os
    • describe_b_n_brit
    • describe_b_n_brit_os