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Job request: 456

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
carehome-noncarehome-death-research
ID:
jz3aptqkb2gh5lh6
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:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  generate_measures_cohorts:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2019-02-01 to 2020-10-01 by month"
    outputs:
      highly_sensitive:
        cohort1: output/input_measures_2019-02-01.csv
        cohort2: output/input_measures_2019-03-01.csv
        cohort3: output/input_measures_2019-04-01.csv
        cohort4: output/input_measures_2019-05-01.csv
        cohort5: output/input_measures_2019-06-01.csv
        cohort6: output/input_measures_2019-07-01.csv
        cohort7: output/input_measures_2019-08-01.csv
        cohort8: output/input_measures_2019-09-01.csv
        cohort9: output/input_measures_2019-10-01.csv
        cohort10: output/input_measures_2019-11-01.csv
        cohort11: output/input_measures_2019-12-01.csv
        cohort12: output/input_measures_2020-01-01.csv
        cohort13: output/input_measures_2020-02-01.csv
        cohort14: output/input_measures_2020-03-01.csv
        cohort15: output/input_measures_2020-04-01.csv
        cohort16: output/input_measures_2020-05-01.csv
        cohort17: output/input_measures_2020-06-01.csv
        cohort18: output/input_measures_2020-07-01.csv
        cohort19: output/input_measures_2020-08-01.csv
        cohort20: output/input_measures_2020-09-01.csv
        cohort21: output/input_measures_2020-10-01.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

  01_data_management: 
    run: r:latest analysis/01_data_management.R 
    needs: [generate_cohort]
    outputs: 
      highly_sensitive:
        data: data/study_population.csv 
        
  02_baseline_characteristics: 
    run: r:latest analysis/02_baseline_characteristics.R
    needs: [generate_cohort, 01_data_management]
    outputs: 
      moderately_sensitive: 
        table_1: analysis/outfiles/table_1.txt

  03_descriptive_mortality_rates: 
    run: r:latest analysis/03_descriptive_mortality_rates.R 
    needs: [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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:02

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

Job request

Status
Failed
Backend
TPP
Workspace
carehome-noncarehome-death-research
Requested by
Anna Schultze
Branch
master
Force run dependencies
No
Git commit hash
304f967
Requested actions
  • 03_descriptive_mortality_rates

Code comparison

Compare the code used in this job request