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Job request: 498

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
carehome-noncarehome-death-research
ID:
mwq6ey7gtub2l6i5
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: 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 week"
    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

  010_data_management_2019:
    run: r:latest analysis/010_data_management.R ./output/input_2019.csv 20190201 ./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 20200201 ./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_2a: analysis/outfiles/table_5a.txt
        table_2b: analysis/outfiles/table_5b.txt
        table_2c: analysis/outfiles/table_5c.txt
        table_2d: analysis/outfiles/table_5d.txt
        table_3a: analysis/outfiles/table_6a.txt
        table_3b: analysis/outfiles/table_6b.txt
        table_3c: analysis/outfiles/table_6c.txt
        table_3d: analysis/outfiles/table_6d.txt
        table_4a: analysis/outfiles/table_7a.txt
        table_4b: analysis/outfiles/table_7b.txt
        table_4c: analysis/outfiles/table_7c.txt
        table_4d: analysis/outfiles/table_7d.txt
        plot_1a: analysis/outfiles/plot_4a.png
        plot_1b: analysis/outfiles/plot_4b.png
        plot_1c: analysis/outfiles/plot_4c.png
        plot_2a: analysis/outfiles/plot_5a.png
        plot_2b: analysis/outfiles/plot_5b.png
        plot_2c: analysis/outfiles/plot_5c.png
        plot_3a: analysis/outfiles/plot_6a.png
        plot_3b: analysis/outfiles/plot_6b.png
        plot_3c: analysis/outfiles/plot_6c.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:05:20

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
29ed975
Requested actions
  • 030_descriptive_mortality_rates.R
  • 035_comparative_mortality_rates.R

Code comparison

Compare the code used in this Job Request