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Job request: 1046

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
carehome-noncarehome-death-research
ID:
xup4yiw2l6nbjomj
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Anna Schultze 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: 100000

actions:
  generate_cohort_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-02-01" 
    outputs:
      highly_sensitive:
        cohort: output/input_2019-02-01.csv

  generate_cohort_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-02-01" 
    outputs:
      highly_sensitive:
        cohort: output/input_2020-02-01.csv

  generate_measures_cohorts:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2019-02-01 to 2021-02-01 by month"
    outputs:
      highly_sensitive:
        cohort_measures: output/input_measures_*.csv

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_measures
    needs: [generate_measures_cohorts]
    outputs:
      moderately_sensitive:
        measure1: output/measure_covid_death_age.csv
        measure2: output/measure_allcause_death_age.csv
        measure3: output/measure_noncovid_death_age.csv
        measure4: output/measure_covid_death_sex_age_five.csv
        measure5: output/measure_allcause_death_sex_age_five.csv
        measure6: output/measure_noncovid_death_sex_age_five.csv
        measure7: output/measure_covid_death_age_chdetail.csv
        measure8: output/measure_allcause_death_age_chdetail.csv
        measure9: output/measure_noncovid_death_age_chdetail.csv
        measure10: output/measure_tpp_death_age.csv

  010_data_management_2019:
    run: r:latest analysis/010_data_management.R ./output/input_2019-02-01.csv ./output/study_population_2019.csv
    needs: [generate_cohort_2019]
    outputs: 
      highly_sensitive:
        data1: output/study_population_2019.csv

  010_data_management_2020:
    run: r:latest analysis/010_data_management.R ./output/input_2020-02-01.csv ./output/study_population_2020.csv
    needs: [generate_cohort_2020]
    outputs: 
      highly_sensitive:
        data2: output/study_population_2020.csv

  020_baseline_characteristics_2019:
    run: r:latest analysis/020_baseline_characteristics.R ./output/study_population_2019.csv ./output/tables/table_1_2019.txt
    needs: [generate_cohort_2019, 010_data_management_2019]
    outputs: 
      moderately_sensitive:
        table1a: output/tables/table_1_2019.txt

  020_baseline_characteristics_2020:
    run: r:latest analysis/020_baseline_characteristics.R ./output/study_population_2020.csv ./output/tables/table_one_2020.txt
    needs: [generate_cohort_2020, 010_data_management_2020]
    outputs: 
      moderately_sensitive:
        table1b: output/tables/table_one_2020.txt

  030_descriptive_mortality_rates.R:
    run: r:latest analysis/030_descriptive_mortality_rates.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        table_descriptive_allcause: output/tables/table_descriptive_allcause.txt
        table_descriptive_covid: output/tables/table_descriptive_covid.txt
        table_descriptive_noncovid: output/tables/table_descriptive_noncovid.txt
        plot_descriptive_allcause: output/plots/plot_descriptive_allcause.png
        plot_descriptive_covid: output/plots/plot_descriptive_covid.png
        plot_descriptive_noncovid: output/plots/plot_descriptive_noncovid.png


  035_comparative_mortality_rates.R:
    run: r:latest analysis/035_comparative_mortality_rates.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        table_comparative_allcause: output/tables/table_comparative_allcause.txt
        table_comparative_covid: output/tables/table_comparative_covid.txt
        table_noncomparative_covid: output/tables/table_noncomparative_covid.txt
        plot_comparative_allcause: output/plots/plot_comparative_allcause.png
        plot_comparative_covid: output/plots/plot_comparative_covid.png
        plot_comparative_noncovid: output/plots/plot_comparative_noncovid.png

  040_cause_of_death.R:
    run: r:latest analysis/040_cause_of_death.R 
    needs: [generate_measures_cohorts]
    outputs: 
      moderately_sensitive:
        table_allcauses_ch: output/tables/table_allcauses_ch.txt
        table_allcauses_ph: output/tables/table_allcauses_ph.txt
        table_nccauses_ch: output/tables/table_nccauses_ch.txt
        table_nccauses_ph: output/tables/table_nccauses_ph.txt
        plot_allcauses_ch: output/plots/plot_allcauses_ch.png
        plot_allcauses_ph: output/plots/plot_allcauses_ph.png
        plot_nccauses_ch: output/plots/plot_nccauses_ch.png
        plot_nccauses_ph: output/plots/plot_nccauses_ph.png

  050_standardisation.R:
    run: r:latest analysis/050_standardisation.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        table_standardised_allcause: output/tables/table_standardised_allcause.txt
        table_standardised_covid: output/tables/table_standardised_covid.txt
        table_standardised_noncovid: output/tables/table_standardised_noncovid.txt     
        plot_standardised_allcause: output/plots/plot_standardised_allcause.png
        plot_standardised_covid: output/plots/plot_standardised_covid.png
        plot_standardised_noncovid: output/plots/plot_standardised_noncovid.png
        table_cmr_allcause: output/tables/table_cmr_allcause.txt
        table_cmr_covid: output/tables/table_cmr_covid.txt
        table_cmr_noncovid: output/tables/table_cmr_noncovid.txt
        plot_cmr_allcause: output/plots/plot_cmr_allcause.png
        plot_cmr_covid: output/plots/plot_cmr_covid.png
        plot_cmr_noncovid: output/plots/plot_cmr_noncovid.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:45:07

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

Job information

Status
Succeeded
Backend
TPP
Workspace
carehome-noncarehome-death-research
Requested by
Anna Schultze
Branch
master
Force run dependencies
Yes
Git commit hash
4baf7af
Requested actions
  • generate_cohort_2019
  • generate_cohort_2020
  • generate_measures_cohorts
  • generate_measures
  • 010_data_management_2019
  • 010_data_management_2020
  • 020_baseline_characteristics_2019
  • 020_baseline_characteristics_2020

Code comparison

Compare the code used in this Job Request