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Job request: 19007

Organisation:
Bennett Institute
Workspace:
tpp_representativeness
ID:
ianepbhkg5tinwjf
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Colm Andrews 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: 10000

actions:
  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/04_2023/cohorts --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/4_2023/cohorts/input.csv.gz

  generate_dataset_report:
    run: >
      dataset-report:v0.0.26
        --input-files output/4_2023/cohorts/input.csv.gz
        --output-dir output/4_2023/cohorts/
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        dataset_report: output/4_2023/cohorts/input.html
        
  generate_deaths_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_deaths --output-dir=output/4_2023/cohorts --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/4_2023/cohorts/input_deaths.csv.gz
  
  generate_dataset_deaths_report:
    run: >
      dataset-report:v0.0.26
        --input-files output/4_2023/cohorts/input_deaths.csv.gz
        --output-dir output/4_2023/cohorts/
    needs: [generate_deaths_cohort]
    outputs:
      moderately_sensitive:
        dataset_report: output/4_2023/cohorts/input_deaths.html

  counts:
    run: r:latest analysis/counts.r
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        imd_table: output/tables/imd_count.csv
        imd_table_NA: output/tables/imd_count_NA.csv
        age_sex_table: output/tables/age_sex_count.csv
        age_table: output/tables/age_count.csv
        ethnicity_table: output/tables/ethnic_group.csv
        ethnicity_table_NA: output/tables/ethnic_group_NA.csv

  plots:
    run: r:latest analysis/plots.R
    needs: [counts]
    outputs:
      moderately_sensitive:
        figure2: output/plots/imd_count.png
        figure3: output/plots/age_sex_count.png
        figure4: output/plots/age_count.png
        figure5: output/plots/sex_count.png
        figure7: output/plots/age_sex_count_eng.png
        figure8: output/plots/age_count_eng.png
        figure9: output/plots/sex_count_eng.png
        figure10: output/plots/ethnicity_count_eng.png
        figure11: output/plots/ethnicity_count.png
        figure12: output/plots/ethnicity16_count_eng.png
        figure13: output/plots/ethnicity16_count.png
        figure14: output/plots/na_removed/imd_count_NA.png
        figure15: output/plots/na_removed/ethnicity_count_na.png
        figure16: output/plots/na_removed/ethnicity_count_eng_na.png
        figure17: output/plots/na_removed/ethnicity16_count_eng_na.png
        figure18: output/plots/na_removed/ethnicity16_count_na.png
        figure19: output/plots/ethnicity_5_16_comb.png
        figure20: output/plots/agesex_comb_plot.png
        figure21: output/plots/age_cum_plot_eng.png
        figure22: output/plots/age_cum_plot.png
        figure23: output/plots/ethnicity_count_eng_nw.png
        figure24: output/plots/ethnicity_count_nw.png
        figure25: output/plots/ethnicity16_count_eng_nw.png
        figure26: output/plots/ethnicity16_count_nw.png

  calculate_tpp_coverage:
    run: r:latest analysis/calculate_tpp_coverage.R
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        region_table: output/tables/tpp_pop_all.csv
        region_map: output/plots/tpp_coverage_map.png

  counts_deaths:
    run: r:latest analysis/death_counts.R
    needs: [generate_deaths_cohort]
    outputs:
      moderately_sensitive:
        death_count: output/tables/death_count.csv

  plots_deaths:
    run: r:latest analysis/death_plots.R
    needs: [counts_deaths]
    outputs:
      moderately_sensitive:
        figure1: output/plots/Cause_of_Death_count.png
        figure6: output/plots/Cause_of_Death_count_eng.png

  immortal:
    run: r:latest analysis/immortal_check.R
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        immmortal_table: output/tables/immortal.csv
        immmortal_table_rounded: output/tables/immort_rounded.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:03:57

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

Job information

Status
Succeeded
Backend
TPP
Workspace
tpp_representativeness
Requested by
Colm Andrews
Branch
master
Force run dependencies
No
Git commit hash
cd1bb2b
Requested actions
  • generate_dataset_report
  • generate_dataset_deaths_report

Code comparison

Compare the code used in this Job Request