Skip to content

Job request: 927

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
absolute-risks
ID:
s5rnelexa4nfrjdu
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Elizabeth (Fizz) Williamson 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.

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_cohort1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-03-01"
    outputs:
      highly_sensitive:
        cohort: output/input_2020-03-01.csv

  generate_cohort2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-09-01"
    outputs:
      highly_sensitive:
        cohort: output/input_2020-09-01.csv

  clean:
    run: stata-mp:latest analysis/001_clean_input_data.do
    needs: [generate_cohort1, generate_cohort2]
    outputs:
     highly_sensitive:
        clean1: analysis/data_base_cohort1.dta
        clean2: analysis/data_base_cohort2.dta

  create_analysis:
    run: stata-mp:latest analysis/002_create_ld_analysis_dataset.do
    needs: [clean]
    outputs:
     highly_sensitive:
        an_data1: analysis/data_ldanalysis_cohort1.dta
        an_data2: analysis/data_ldanalysis_cohort2.dta


  create_analysis_ar:
    run: stata-mp:latest analysis/003_create_ar_analysis_dataset.do
    needs: [clean]
    outputs:
     highly_sensitive:
        an_data1: analysis/data_aranalysis_cohort1.dta
        an_data2: analysis/data_aranalysis_cohort2.dta


  describe_cohort:
    run: stata-mp:latest analysis/AL001_describe_cohort.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL001_describe_cohort.log

  tabulate_cohort:
    run: stata-mp:latest analysis/AL002_tabulate_cohort_descriptives.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL002_tabulate_cohort_descriptives.log
        model: output/basetable1.txt

  cox_regression:
    run: stata-mp:latest analysis/AL004_cox_regression.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression.log
        hrs_adult: output/output_hrs_main.out
        rates_adult: output/output_rates.out

  cox_regression_child:
    run: stata-mp:latest analysis/AL005_cox_regression_child.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL005_cox_regression_child.log
        hrs_child: output/output_hrs_main_child.out
        rates_child: output/output_rates_child.out

  cumulative_incidence:
    run: stata-mp:latest analysis/AL003_cumulative_incidence.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL003_cumulative_incidence.log
        graph1: output/cumincidence_coviddeath.svg
        graph2: output/cumincidence_composite.svg

  cox_regression1:
    run: stata-mp:latest analysis/AL004_1_cox_regression.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_1_cox_regression.log
        hrs_adult: output/output_hrs_main_2_coviddeath_ldr_group.out
        rates_adult: output/output_rates_2_coviddeath_ldr_group.out

  cox_regression2:
    run: stata-mp:latest analysis/AL004_2_cox_regression.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_2_cox_regression.log
        hrs_adult: output/output_hrs_main_2_covidadmission_ldr_group.out
        rates_adult: output/output_rates_2_covidadmission_ldr_group.out

  cox_regression3:
    run: stata-mp:latest analysis/AL004_3_cox_regression.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_3_cox_regression.log
        hrs_adult: output/output_hrs_main_1_coviddeath_ldr_group.out
        rates_adult: output/output_rates_1_coviddeath_ldr_group.out

  cox_regression4:
    run: stata-mp:latest analysis/AL004_4_cox_regression.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_4_cox_regression.log
        hrs_adult: output/output_hrs_main_1_covidadmission_ldr_group.out
        rates_adult: output/output_rates_1_covidadmission_ldr_group.out4

  cox_regression3_ar:
    run: stata-mp:latest analysis/AAR001_3_cox_regression.do
    needs: [create_analysis_ar]
    outputs:
    moderately_sensitive:
      log: logs/AAR001_3_cox_regression.log
      hrfemale: output/hr_coviddeath_wave1_male0.txt
      hrmale: output/hr_coviddeath_wave1_male1.txt

  cox_regression4_ar:
    run: stata-mp:latest analysis/AAR001_4_cox_regression.do
    needs: [create_analysis_ar]
    outputs:
    moderately_sensitive:
      log: logs/AAR001_4_cox_regression.log
      hrfemale: output/hr_coviddeath_wave2_male0.txt
      hrmale: output/hr_coviddeath_wave2_male1.txt

  cox_regression1_ar:
    run: stata-mp:latest analysis/AAR001_1_cox_regression.do
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR001_1_cox_regression.log
        hrfemale: output/hr_covidadmission_wave1_male0.txt
        hrmale: output/hr_covidadmission_wave1_male1.txt

  cox_regression2_ar:
    run: stata-mp:latest analysis/AAR001_2_cox_regression.do
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR001_2_cox_regression.log
        hrfemale: output/hr_covidadmission_wave2_male0.txt
        hrmale: output/hr_covidadmission_wave2_male1.txt


  ar_1:
    run: stata-mp:latest analysis/AAR002_1_risk_by_age.do
    needs: [create_analysis_ar]
    outputs:
    moderately_sensitive:
      log: logs/AAR002_1_risk_by_age.log
      arfemale: output/ar_wave1_male0_covidadmission.out
      armale: output/ar_wave1_male1_covidadmission.out
      garfemale: output/ar_wave1_male0_covidadmission.svg
      garmale: output/ar_wave1_male1_covidadmission.svg

  ar_2:
    run: stata-mp:latest analysis/AAR002_2_risk_by_age.do
    needs: [create_analysis_ar]
    outputs:
    moderately_sensitive:
      log: logs/AAR002_2_risk_by_age.log
      arfemale: output/ar_wave2_male0_covidadmission.out
      armale: output/ar_wave2_male1_covidadmission.out
      garfemale: output/ar_wave2_male0_covidadmission.svg
      garmale: output/ar_wave2_male1_covidadmission.svg

  ar_3:
    run: stata-mp:latest analysis/AAR002_3_risk_by_age.do
    needs: [create_analysis_ar]
    outputs:
    moderately_sensitive:
      log: logs/AAR002_3_risk_by_age.log
      arfemale: output/ar_wave1_male0_coviddeath.out
      armale: output/ar_wave1_male1_coviddeath.out
      garfemale: output/ar_wave1_male0_coviddeath.svg
      garmale: output/ar_wave1_male1_coviddeath.svg

  ar_4:
    run: stata-mp:latest analysis/AAR002_4_risk_by_age.do
    needs: [create_analysis_ar]
    outputs:
    moderately_sensitive:
      log: logs/AAR002_4_risk_by_age.log
      arfemale: output/ar_wave2_male0_coviddeath.out
      armale: output/ar_wave2_male1_coviddeath.out
      garfemale: output/ar_wave2_male0_coviddeathn.svg
      garmale: output/ar_wave2_male1_coviddeath.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job request

Status
Failed 
JobRequestError: Internal error
Backend
TPP
Workspace
absolute-risks
Requested by
Elizabeth (Fizz) Williamson
Branch
master
Force run dependencies
No
Git commit hash
cd3940a
Requested actions
  • create_analysis_ar

Code comparison

Compare the code used in this job request