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Job request: 4464

Organisation:
University of Manchester
Workspace:
abrx_os_brit
ID:
vruzpuukeetk4fdk
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Vicki Palin UoM 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 "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/*

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:24:21

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

Job information

Status
Succeeded
Backend
TPP
Workspace
abrx_os_brit
Requested by
Vicki Palin UoM
Branch
ABRX_comparison_OS_v_brit
Force run dependencies
No
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

Code comparison

Compare the code used in this Job Request