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Job request: 5168

Organisation:
Bennett Institute
Workspace:
tpp_representativeness
ID:
aw7w6j5niyti2slw
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:
    cpud76jllnrrjtk4
  • Action:
    generate_deaths_cohort
    Status:
    Status: Succeeded
    Job identifier:
    rwqevl6hf6xlgs4x
  • Action:
    counts_deaths
    Status:
    Status: Succeeded
    Job identifier:
    tnqg2wgqd4463jo4
  • Action:
    plots_deaths
    Status:
    Status: Succeeded
    Job identifier:
    42khkwwirvnvfvgf
  • Action:
    calculate_tpp_coverage
    Status:
    Status: Succeeded
    Job identifier:
    ucjqzvopooo4u7vb
  • Action:
    counts
    Status:
    Status: Succeeded
    Job identifier:
    bv3iwcvb4vvjvzad
  • Action:
    plots
    Status:
    Status: Succeeded
    Job identifier:
    utuppdkdc3bmwgjc

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.jpg
        figure3: output/plots/age_sex_count.jpg
        figure4: output/plots/age_count.jpg
        figure5: output/plots/sex_count.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

  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.jpg
        figure6: output/plots/Cause_of_Death_count_eng.jpg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:55:45

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
ce2fc6b
Requested actions
  • run_all

Code comparison

Compare the code used in this job request