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Job request: 5702

Organisation:
Bennett Institute
Workspace:
tpp_representativeness
ID:
ridgvb23h4xycafi
View repo View project.yaml

This page shows the technical details of what happened when 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 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

  • Action:
    generate_cohort
    Status:
    Status: Succeeded
    Job identifier:
    paswb4lriserxh6a
  • Action:
    counts
    Status:
    Status: Succeeded
    Job identifier:
    jbcgyr3wvpqid2j6
  • Action:
    plots
    Status:
    Status: Succeeded
    Job identifier:
    55wt7mna4xtfryln

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/cohorts --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input.csv.gz

  generate_deaths_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_deaths --output-dir=output/cohorts --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_deaths.csv.gz

  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

  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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:49:03

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
Yes
Git commit hash
038531d
Requested actions
  • plots

Code comparison

Compare the code used in this Job Request