Skip to content

Job request: 913

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
learning-disabilities-full
ID:
jewo4ci726gyg72a
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: 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:
        log: logs/001_clean_input_data.log
        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:
        log: logs/002_create_ld_analysis_dataset.log
        an_data1: analysis/data_ldanalysis_cohort1.dta
        an_data2: analysis/data_ldanalysis_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_2_coviddeath_ldr_group_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_covidadmission_ldr_group_cox_regression.log
        hrs_adult: output/output_hrs_main_2_covidadmission_ldr_group.out
        rates_adult: output/output_rates_2_covidadmission_ldr_group.out

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

  cox_regression_ar1:
    run: stata-mp:latest analysis/AAR001_1_cox_regression.do
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR001_1_cox_regression.log

  cox_regression_ar2:
    run: stata-mp:latest analysis/AAR001_2_cox_regression.do
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR001_2_cox_regression.log

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:51:21

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
35b530c
Requested actions
  • cox_regression2

Code comparison

Compare the code used in this Job Request