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Job request: 4443

Organisation:
Bennett Institute
Workspace:
tpp_representativeness
ID:
d4sqrch25jxrwqya
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 within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

  • Action:
    generate_cohort
    Status:
    Status: Succeeded
    Job identifier:
    ofv6c7hmfgdbvmaz
  • Action:
    counts
    Status:
    Status: Succeeded
    Job identifier:
    murjwi6bykmb3uat
  • Action:
    calculate_tpp_coverage
    Status:
    Status: Succeeded
    Job identifier:
    plmd5sugucztphw4
  • Action:
    plots
    Status:
    Status: Succeeded
    Job identifier:
    q5lddgougfrypkby

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.svg
        figure2: output/plots/imd_count.svg
        figure3: output/plots/age_sex_count.svg
        figure4: output/plots/age_count.svg
        figure5: output/plots/sex_count.svg
        figure6: output/plots/Cause_of_Death_count_eng.svg
        figure7: output/plots/age_sex_count_eng.svg
        figure8: output/plots/age_count_eng.svg
        figure9: output/plots/sex_count_eng.svg
        figure10: output/plots/ethnicity_count_eng.svg
        figure11: output/plots/ethnicity_count.svg
        figure12: output/plots/ethnicity16_count_eng.svg
        figure13: output/plots/ethnicity16_count.svg

  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.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:47:22

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

Job request

Status
Succeeded
Backend
TPP
Workspace
tpp_representativeness
Requested by
Colm Andrews
Branch
master
Force run dependencies
Yes
Git commit hash
f620ce1
Requested actions
  • run_all

Code comparison

Compare the code used in this job request