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Job request: 935

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
learning-disabilities-full
ID:
qnhjib6yzgaenbu5
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 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: 50000

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_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.out

  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_risk_by_age.do 1 0 covidadmission
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR002_risk_by_age_wave1_male0_covidadmission.log
        absrisk: output/ar_wave1_male0_covidadmission.out
        graph: output/ar_wave1_male0_covidadmission.svg

  ar_2:
    run: stata-mp:latest analysis/AAR002_risk_by_age.do 1 1 covidadmission
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR002_risk_by_age_wave1_male1_covidadmission.log
        absrisk: output/ar_wave1_male1_covidadmission.out
        graph: output/ar_wave1_male1_covidadmission.svg

  ar_3:
    run: stata-mp:latest analysis/AAR002_risk_by_age.do 2 0 covidadmission
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR002_risk_by_age_wave2_male0_covidadmission.log
        absrisk: output/ar_wave2_male0_covidadmission.out
        graph: output/ar_wave2_male0_covidadmission.svg

  ar_4:
    run: stata-mp:latest analysis/AAR002_risk_by_age.do 2 1 covidadmission
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR002_risk_by_age_wave2_male1_covidadmission.log
        absrisk: output/ar_wave2_male1_covidadmission.out
        graph: output/ar_wave2_male1_covidadmission.svg

  ar_5:
    run: stata-mp:latest analysis/AAR002_risk_by_age.do 1 0 coviddeath
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR002_risk_by_age_wave1_male0_coviddeath.log
        absrisk: output/ar_wave1_male0_coviddeath.out
        graph: output/ar_wave1_male0_coviddeath.svg

  ar_6:
    run: stata-mp:latest analysis/AAR002_risk_by_age.do 1 1 coviddeath
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR002_risk_by_age_wave1_male1_coviddeath.log
        absrisk: output/ar_wave1_male1_coviddeath.out
        graph: output/ar_wave1_male1_coviddeath.svg

  ar_7:
    run: stata-mp:latest analysis/AAR002_risk_by_age.do 2 0 coviddeath
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR002_risk_by_age_wave2_male0_coviddeath.log
        absrisk: output/ar_wave2_male0_coviddeath.out
        graph: output/ar_wave2_male0_coviddeath.svg

  ar_8:
    run: stata-mp:latest analysis/AAR002_risk_by_age.do 2 1 coviddeath
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR002_risk_by_age_wave2_male1_coviddeath.log
        absrisk: output/ar_wave2_male1_coviddeath.out
        graph: output/ar_wave2_male1_coviddeath.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:11:00

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

Job information

Status
Succeeded
Backend
TPP
Workspace
learning-disabilities-full
Requested by
Elizabeth (Fizz) Williamson
Branch
master
Force run dependencies
No
Git commit hash
c665887
Requested actions
  • create_analysis

Code comparison

Compare the code used in this Job Request