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Job request: 4680

Organisation:
Bennett Institute
Workspace:
tpp_representativeness
ID:
5vygmkzbdn67b5ws
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:
    plots
    Status:
    Status: Succeeded
    Job identifier:
    xf5ibptw6m6risxb
  • Action:
    calculate_tpp_coverage
    Status:
    Status: Succeeded
    Job identifier:
    htisfkcj5lhkpnle

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
        age_sex_table: output/tables/age_sex_count.csv
        age_table: output/tables/age_count.csv
        ethnicity_table: output/tables/ethnic_group.csv


  plots:
    run: r:latest analysis/plots.R
    needs: [counts]
    outputs:
      moderately_sensitive:
        figure1: output/plots/Cause_of_Death_count.tiff
        figure2: output/plots/imd_count.tiff
        figure3: output/plots/age_sex_count.tiff
        figure4: output/plots/age_count.tiff
        figure5: output/plots/sex_count.tiff
        figure6: output/plots/Cause_of_Death_count_eng.tiff
        figure7: output/plots/age_sex_count_eng.tiff
        figure8: output/plots/age_count_eng.tiff
        figure9: output/plots/sex_count_eng.tiff
        figure10: output/plots/ethnicity_count_eng.tiff
        figure11: output/plots/ethnicity_count.tiff
        figure12: output/plots/ethnicity16_count_eng.tiff
        figure13: output/plots/ethnicity16_count.tiff

  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.tiff

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:04:42

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
c485d54
Requested actions
  • plots
  • calculate_tpp_coverage

Code comparison

Compare the code used in this Job Request