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Job request: 925

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
absolute-risks
ID:
oxxfe7fnli6ujssq
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Elizabeth (Fizz) Williamson requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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.

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 information

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
  • ar_1
  • ar_2
  • ar_3
  • ar_4

Code comparison

Compare the code used in this Job Request