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Job request: 611

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
carehome-noncarehome-death-research
ID:
extzyxwpdywvovid
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 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

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 1000

actions:
  generate_cohort_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019
    outputs:
      highly_sensitive:
        cohort: output/input_2019.csv

  generate_cohort_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2020
    outputs:
      highly_sensitive:
        cohort: output/input_2020.csv

  generate_measures_cohorts:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2019-02-01 to 2020-11-30 by month"
    outputs:
      highly_sensitive:
        cohort1: 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_all.csv
        measure2: output/measure_covid_death_sex.csv
        measure3: output/measure_covid_death_age.csv
        measure4: output/measure_covid_death_sex_age.csv
        measure5: output/measure_allcause_death_all.csv
        measure6: output/measure_allcause_death_sex.csv
        measure7: output/measure_allcause_death_age.csv
        measure8: output/measure_allcause_death_sex_age.csv
        measure9: output/measure_noncovid_death_all.csv
        measure10: output/measure_noncovid_death_sex.csv
        measure11: output/measure_noncovid_death_age.csv
        measure12: output/measure_noncovid_death_sex_age.csv
        measure13: output/measure_covid_death_sex_age_five.csv
        measure14: output/measure_allcause_death_sex_age_five.csv
        measure15: output/measure_noncovid_death_sex_age_five.csv
        measure16: output/measure_covid_death_all_chdetail.csv
        measure17: output/measure_covid_death_sex_chdetail.csv
        measure18: output/measure_covid_death_age_chdetail.csv
        measure19: output/measure_covid_death_sex_age_chdetail.csv
        measure20: output/measure_allcause_death_all_chdetail.csv
        measure21: output/measure_allcause_death_sex_chdetail.csv
        measure22: output/measure_allcause_death_age_chdetail.csv
        measure23: output/measure_allcause_death_sex_age_chdetail.csv
        measure24: output/measure_noncovid_death_all_chdetail.csv
        measure25: output/measure_noncovid_death_sex_chdetail.csv
        measure26: output/measure_noncovid_death_age_chdetail.csv
        measure27: output/measure_noncovid_death_sex_age_chdetail.csv

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

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

  020_baseline_characteristics_2019:
    run: r:latest analysis/020_baseline_characteristics.R ./data/study_population_2019.csv ./analysis/outfiles/table_1a.txt
    needs: [generate_cohort_2019, 010_data_management_2019]
    outputs: 
      moderately_sensitive:
        table1a: analysis/outfiles/table_1a.txt

  020_baseline_characteristics_2020:
    run: r:latest analysis/020_baseline_characteristics.R ./data/study_population_2020.csv ./analysis/outfiles/table_1b.txt
    needs: [generate_cohort_2020, 010_data_management_2020]
    outputs: 
      moderately_sensitive:
        table1b: analysis/outfiles/table_1b.txt

  025_carehome_characteristics:
    run: r:latest analysis/025_carehome_characteristics.R ./data/study_population_2020.csv 
    needs: [010_data_management_2020]
    outputs: 
      moderately_sensitive:
        log: analysis/outfiles/carehome_characteristics.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_2a: analysis/outfiles/table_2a.txt
        table_2b: analysis/outfiles/table_2b.txt
        table_2c: analysis/outfiles/table_2c.txt
        table_2d: analysis/outfiles/table_2d.txt
        table_3a: analysis/outfiles/table_3a.txt
        table_3b: analysis/outfiles/table_3b.txt
        table_3c: analysis/outfiles/table_3c.txt
        table_3d: analysis/outfiles/table_3d.txt
        table_4a: analysis/outfiles/table_4a.txt
        table_4b: analysis/outfiles/table_4b.txt
        table_4c: analysis/outfiles/table_4c.txt
        table_4d: analysis/outfiles/table_4d.txt
        plot_1a: analysis/outfiles/plot_1a.png
        plot_1b: analysis/outfiles/plot_1b.png
        plot_1c: analysis/outfiles/plot_1c.png
        plot_2a: analysis/outfiles/plot_2a.png
        plot_2b: analysis/outfiles/plot_2b.png
        plot_2c: analysis/outfiles/plot_2c.png
        plot_3a: analysis/outfiles/plot_3a.png
        plot_3b: analysis/outfiles/plot_3b.png
        plot_3c: analysis/outfiles/plot_3c.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_5a: analysis/outfiles/table_5a.txt
        table_5b: analysis/outfiles/table_5b.txt
        table_5c: analysis/outfiles/table_5c.txt
        table_5d: analysis/outfiles/table_5d.txt
        table_6a: analysis/outfiles/table_6a.txt
        table_6b: analysis/outfiles/table_6b.txt
        table_6c: analysis/outfiles/table_6c.txt
        table_6d: analysis/outfiles/table_6d.txt
        table_7a: analysis/outfiles/table_7a.txt
        table_7b: analysis/outfiles/table_7b.txt
        table_7c: analysis/outfiles/table_7c.txt
        table_7d: analysis/outfiles/table_7d.txt
        plot_8a: analysis/outfiles/plot_4a.png
        plot_8b: analysis/outfiles/plot_4b.png
        plot_8c: analysis/outfiles/plot_4c.png
        plot_5a: analysis/outfiles/plot_5a.png
        plot_5b: analysis/outfiles/plot_5b.png
        plot_5c: analysis/outfiles/plot_5c.png
        plot_6a: analysis/outfiles/plot_6a.png
        plot_6b: analysis/outfiles/plot_6b.png
        plot_6c: analysis/outfiles/plot_6c.png

  040_cause_of_death.R:
    run: r:latest analysis/040_cause_of_death.R 
    needs: [generate_measures_cohorts]
    outputs: 
      moderately_sensitive:
        table_8a: analysis/outfiles/table_8a.txt
        table_8b: analysis/outfiles/table_8b.txt
        plot_7a: analysis/outfiles/plot_7a.png
        plot_7b: analysis/outfiles/plot_7b.png

  050_standardisation.R:
    run: r:latest analysis/050_standardisation.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        table_9a: analysis/outfiles/table_9a.txt
        table_9b: analysis/outfiles/table_9b.txt     
        table_9c: analysis/outfiles/table_9c.txt
        plot_8a: analysis/outfiles/plot_8a.png
        plot_8b: analysis/outfiles/plot_8b.png
        plot_8c: analysis/outfiles/plot_8c.png

  generate_measures_sensitivity_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures_tppdeath --index-date-range "2019-02-01 to 2020-11-30 by month"
    needs: [generate_measures]
    outputs:
      highly_sensitive:
        cohort_sensitivity: output/input_measures_tppdeath_*.csv

  generate_measures_sensitivity:
    run: cohortextractor:latest generate_measures --study-definition study_definition_measures_tppdeath
    needs: [generate_measures_sensitivity_cohort]
    outputs:
      moderately_sensitive:
        measure_sensitivity: output/measure_allcause_tppdeath_all.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:03:41

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

Job request

Status
Succeeded
Backend
TPP
Workspace
carehome-noncarehome-death-research
Requested by
Anna Schultze
Branch
master
Force run dependencies
Yes
Git commit hash
e400316
Requested actions
  • generate_measures_cohorts
  • generate_measures
  • 030_descriptive_mortality_rates.R
  • 035_comparative_mortality_rates.R
  • 040_cause_of_death.R
  • 050_standardisation.R
  • generate_measures_sensitivity_cohort
  • generate_measures_sensitivity

Code comparison

Compare the code used in this job request