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Job request: 1056

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
carehome-noncarehome-death-research
ID:
ndsv554eknnpingi
View repo View project.yaml

This page shows the technical details of what happened when the 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 list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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:

# PRIMARY ANALYSES 
    
  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

  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


  055_standardisation_smaller_age.R:
    run: r:latest analysis/055_standardisation_smaller_age.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        table_standardised_allcause_age: output/tables/table_standardised_allcause_age.txt
        table_standardised_covid_age: output/tables/table_standardised_covid_age.txt
        table_standardised_noncovid_age: output/tables/table_standardised_noncovid_age.txt     
        plot_standardised_allcause_age_m: output/plots/plot_standardised_allcause_age_m.png
        plot_standardised_covid_age_m: output/plots/plot_standardised_covid_age_m.png
        plot_standardised_noncovid_age_m: output/plots/plot_standardised_noncovid_age_m.png
        plot_standardised_allcause_age_f: output/plots/plot_standardised_allcause_age_f.png
        plot_standardised_covid_age_f: output/plots/plot_standardised_covid_age_f.png
        plot_standardised_noncovid_age_f: output/plots/plot_standardised_noncovid_age_f.png
        table_cmr_allcause_age: output/tables/table_cmr_allcause_age.txt
        table_cmr_covid_age: output/tables/table_cmr_covid_age.txt
        table_cmr_noncovid_age: output/tables/table_cmr_noncovid_age.txt
        plot_cmr_allcause_age_m: output/plots/plot_cmr_allcause_age_m.png
        plot_cmr_covid_age_m: output/plots/plot_cmr_covid_age_m.png
        plot_cmr_noncovid_age_m: output/plots/plot_cmr_noncovid_age_m.png
        plot_cmr_allcause_age_f: output/plots/plot_cmr_allcause_age_f.png
        plot_cmr_covid_age_f: output/plots/plot_cmr_covid_age_f.png
        plot_cmr_noncovid_age_f: output/plots/plot_cmr_noncovid_age_f.png

# SENSITIVITY ANALYSES 

  generate_sensitivity_measures_cohorts:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sensitivity --index-date-range "2016-02-01 to 2021-02-01 by month"
    outputs:
      highly_sensitive:
        cohort_measures: output/input_sensitivity_*.csv

  generate_sensitivity_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_sensitivity
    needs: [generate_sensitivity_measures_cohorts]
    outputs:
      moderately_sensitive:
        measure1: output/measure_tpp_death_age.csv

  S020_sensitivity_baseline_characteristics_chdetail:
    run: r:latest analysis/S020_sensitivity_baseline_characteristics_chdetail.R ./output/study_population_2019.csv ./output/tables/S_table_one_chdetail_2019.txt
    needs: [generate_cohort_2019, 010_data_management_2019]
    outputs: 
      moderately_sensitive:
        S_table1: output/tables/S_table_one_chdetail_2019.txt

  S050_sensitivity_standardisation_chdetail:
    run: r:latest analysis/S050_sensitivity_standardisation_chdetail.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        S_table_standardised_allcause_chdetail: output/tables/S_table_standardised_allcause_chdetail.txt
        S_table_standardised_covid_chdetail: output/tables/S_table_standardised_covid_chdetail.txt
        S_table_standardised_noncovid_chdetail: output/tables/S_table_standardised_noncovid_chdetail.txt     
        S_plot_standardised_allcause_chdetail_m: output/plots/S_plot_standardised_allcause_chdetail_m.png
        S_plot_standardised_covid_chdetail_m: output/plots/S_plot_standardised_covid_chdetail_m.png
        S_plot_standardised_noncovid_chdetail_m: output/plots/S_plot_standardised_noncovid_chdetail_m.png
        S_plot_standardised_allcause_chdetail_f: output/plots/S_plot_standardised_allcause_chdetail_f.png
        S_plot_standardised_covid_chdetail_f: output/plots/S_plot_standardised_covid_chdetail_f.png
        S_plot_standardised_noncovid_chdetail_f: output/plots/S_plot_standardised_noncovid_chdetail_f.png

  S030_sensitivity_descriptive_mortality_rates_tpp:
    run: r:latest analysis/S030_sensitivity_descriptive_mortality_rates_tpp.R 
    needs: [generate_sensitivity_measures_cohorts, generate_sensitivity_measures]
    outputs: 
      moderately_sensitive:
        S_table_descriptive_allcause: output/tables/S_table_descriptive_allcause_tpp.txt
        S_plot_descriptive_noncovid: output/plots/S_plot_descriptive_allcause_tpp.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:58:43

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
No
Git commit hash
58c3efc
Requested actions
  • 030_descriptive_mortality_rates.R
  • 035_comparative_mortality_rates.R
  • 040_cause_of_death.R
  • 050_standardisation.R
  • 055_standardisation_smaller_age.R
  • generate_sensitivity_measures_cohorts
  • generate_sensitivity_measures
  • S020_sensitivity_baseline_characteristics_chdetail
  • S050_sensitivity_standardisation_chdetail
  • S030_sensitivity_descriptive_mortality_rates_tpp

Code comparison

Compare the code used in this Job Request