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Job request: 5094

Organisation:
Bennett Institute
Workspace:
tpp_representativeness
ID:
p2xhdfv7qgjdx4p2
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

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

  counts:
    run: r:latest analysis/counts.r
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        death_count: output/tables/death_count.csv
        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:
        figure1: output/plots/Cause_of_Death_count.jpg
        figure2: output/plots/imd_count.jpg
        figure3: output/plots/age_sex_count.jpg
        figure4: output/plots/age_count.jpg
        figure5: output/plots/sex_count.jpg
        figure6: output/plots/Cause_of_Death_count_eng.jpg
        figure7: output/plots/age_sex_count_eng.jpg
        figure8: output/plots/age_count_eng.jpg
        figure9: output/plots/sex_count_eng.jpg
        figure10: output/plots/ethnicity_count_eng.jpg
        figure11: output/plots/ethnicity_count.jpg
        figure12: output/plots/ethnicity16_count_eng.jpg
        figure13: output/plots/ethnicity16_count.jpg
        figure14: output/plots/na_removed/imd_count_NA.jpg
        figure15: output/plots/na_removed/ethnicity_count_na.jpg
        figure16: output/plots/na_removed/ethnicity_count_eng_na.jpg
        figure17: output/plots/na_removed/ethnicity16_count_eng_na.jpg
        figure18: output/plots/na_removed/ethnicity16_count_na.jpg
        

  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.jpg
        region_map_2: output/plots/tpp_coverage_map_2.jpg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:03:04

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
97ab169
Requested actions
  • calculate_tpp_coverage

Code comparison

Compare the code used in this Job Request