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Job request: 2942

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
covid-vs-non-covid-deaths-research
ID:
5hs5xjvh6jeak7pn
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Krishnan Bhaskaran 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: 100000

actions:
  generate_cohortMAIN:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  generate_cohort2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019
    outputs:
      highly_sensitive:
        cohort: output/input_2019.csv
  
  generate_cohortSEPT2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_SEPT2020
    outputs:
      highly_sensitive:
        cohort: output/input_SEPT2020.csv
        
  generate_flowchartdata:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart
    outputs:
      highly_sensitive:
        cohort: output/input_flow_chart.csv

  crMAIN:
    run: stata-mp:latest analysis/cr_create_analysis_dataset_GENERAL.do MAIN
    needs: [generate_cohortMAIN]
    outputs:
      highly_sensitive:
        data: analysis/cr_create_analysis_dataset_MAIN_STSET.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset.log
  
  crSEPT2020:
    run: stata-mp:latest analysis/cr_create_analysis_dataset_GENERAL.do SEPT2020
    needs: [generate_cohortSEPT2020]
    outputs:
      highly_sensitive:
        data: analysis/cr_create_analysis_dataset_SEPT2020_STSET.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset_SEPT2020.log
  
  cr2019:
    run: stata-mp:latest analysis/cr_create_analysis_dataset_GENERAL.do 2019
    needs: [generate_cohort2019]
    outputs:
      highly_sensitive:
        data: analysis/cr_create_analysis_dataset_2019_STSET.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset_2019.log
  
  imputedataMAIN:
    run: stata-mp:latest analysis/an_impute_GENERAL.do MAIN 9572
    needs: [crMAIN]
    outputs:
      highly_sensitive:
        data: analysis/an_impute_imputeddata_MAIN.dta
      moderately_sensitive:
        log: analysis/output/an_impute_MAIN.log

  imputedataSEPT2020:
    run: stata-mp:latest analysis/an_impute_GENERAL.do SEPT2020 394
    needs: [crSEPT2020]
    outputs:
      highly_sensitive:
        data: analysis/an_impute_imputeddata_SEPT2020.dta
      moderately_sensitive:
        log: analysis/output/an_impute_SEPT2020.log
  
  imputedata2019:
    run: stata-mp:latest analysis/an_impute_GENERAL.do 2019 9374
    needs: [cr2019]
    outputs:
      highly_sensitive:
        data: analysis/an_impute_imputeddata_2019.dta
      moderately_sensitive:
        log: analysis/output/an_impute_2019.log
    
  ethnicity_deprivation_cov_agesex:
    run: stata-mp:latest analysis/an_imputed_GENERAL_ETHxDEPR.do MAIN coviddeath agesex 
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed_GENERAL_ETHxDEPR_MAIN_coviddeath_agesex_agespl.log        
        models: analysis/output/models/an_imputed_ETHxDEPR_agesex_MAIN_coviddeath.ster        

  ethnicity_deprivation_cov_full:
    run: stata-mp:latest analysis/an_imputed_GENERAL_ETHxDEPR.do MAIN coviddeath full
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed_GENERAL_ETHxDEPR_MAIN_coviddeath_full_agespl.log        
        models: analysis/output/models/an_imputed_ETHxDEPR_full_MAIN_coviddeath_agespl.ster        

  ethnicity_deprivation_noncov_agesex:
    run: stata-mp:latest analysis/an_imputed_GENERAL_ETHxDEPR.do MAIN noncoviddeath agesex 
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed_GENERAL_ETHxDEPR_MAIN_noncoviddeath_agesex_agespl.log        
        models: analysis/output/models/an_imputed_ETHxDEPR_agesex_MAIN_noncoviddeath.ster        

  ethnicity_deprivation_noncov_full:
    run: stata-mp:latest analysis/an_imputed_GENERAL_ETHxDEPR.do MAIN noncoviddeath full
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed_GENERAL_ETHxDEPR_MAIN_noncoviddeath_full_agespl.log        
        models: analysis/output/models/an_imputed_ETHxDEPR_full_MAIN_noncoviddeath_agespl.ster        
  
  ethnicity_deprivation_figure:
    run: stata-mp:latest analysis/an_processout_ethxdepr.do    
    needs:
      - imputedataMAIN
      - ethnicity_deprivation_cov_agesex
      - ethnicity_deprivation_cov_full
      - ethnicity_deprivation_noncov_agesex
      - ethnicity_deprivation_noncov_full
    outputs:
      moderately_sensitive:
        graph: analysis/output/an_processout_ethxdepr.svg      
    
  descriptive_table1:
    run: stata-mp:latest analysis/an_tablecontent_PublicationDescriptivesTable.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_tablecontent_PublicationDescriptivesTable.txt
  
  absoluterisksbycause:
    run: stata-mp:latest analysis/an_covid_vs_othercauses_abs_AGE.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covid_vs_othercauses_abs_AGE.log
        graph: analysis/output/an_covid_vs_othercauses_abs_AGE_GRAPH.svg
        estimates: analysis/output/an_covid_vs_othercauses_abs_AGE_ESTIMATES.dta

  agesexmodelsMAIN:
    run: stata-mp:latest analysis/an_covidvsnoncovid_agesex_GENERAL.do MAIN
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covidvsnoncovid_agesex_MAIN.log
        models: analysis/output/models/an_covidvsnoncovid_agesex_MAIN*.ster

  agesexmodelsSEPT2020:
    run: stata-mp:latest analysis/an_covidvsnoncovid_agesex_GENERAL.do SEPT2020
    needs: [crSEPT2020]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covidvsnoncovid_agesex_SEPT2020.log
        models: analysis/output/models/an_covidvsnoncovid_agesex_SEPT2020*.ster
 
  agesexmodels2019:
    run: stata-mp:latest analysis/an_covidvsnoncovid_agesex_GENERAL.do 2019
    needs: [cr2019]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covidvsnoncovid_agesex_2019.log
        models: analysis/output/models/an_covidvsnoncovid_agesex_2019*.ster
 
  agesexmodelsSA_anyonDC:
    run: stata-mp:latest analysis/an_covidvsnoncovid_agesex_GENERAL.do MAIN SA_anywhereonDC
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covidvsnoncovid_agesex_MAINSA_anywhereonDC.log
        models: analysis/output/models/an_covidvsnoncovid_agesex_MAINSA_anywhereonDC*.ster

  agesexmodelsSA_u071only:
    run: stata-mp:latest analysis/an_covidvsnoncovid_agesex_GENERAL.do MAIN SA_u071only
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covidvsnoncovid_agesex_MAINSA_u071only.log
        models: analysis/output/models/an_covidvsnoncovid_agesex_MAINSA_u071only*.ster

  fullmodelsMAIN:
    run: stata-mp:latest analysis/an_covidvsnoncovid_full_GENERAL.do MAIN
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covidvsnoncovid_full_MAIN.log
        models: analysis/output/models/an_covidvsnoncovid_full_MAIN*.ster

  fullmodelsSEPT2020:
    run: stata-mp:latest analysis/an_covidvsnoncovid_full_GENERAL.do SEPT2020
    needs: [crSEPT2020]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covidvsnoncovid_full_SEPT2020.log
        models: analysis/output/models/an_covidvsnoncovid_full_SEPT2020*.ster

  fullmodels2019:
    run: stata-mp:latest analysis/an_covidvsnoncovid_full_GENERAL.do 2019
    needs: [cr2019]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covidvsnoncovid_full_2019.log
        models: analysis/output/models/an_covidvsnoncovid_full_2019*.ster
  
  ethnicity_model_and_graph:
    run: stata-mp:latest analysis/an_ethnicitybycod_logisticversion.do
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_ethnicitybycod_logisticversion.log
        graph: analysis/output/an_ethnicitybycod_logisticversion.svg
 
  deathsonly_models:
    run: stata-mp:latest analysis/an_deathsonlyanalysis.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_deathsonlyanalysis.log
        models: analysis/output/models/an_deathsonlyanalysis_*.ster  
  
  cox_models_agesex:
    run: stata-mp:latest analysis/an_cox_covnoncov_agesex.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_covnoncov_agesex.log
        models: analysis/output/models/an_cox_covnoncov_agesex*.ster  
            
  run_model:
    run: stata-mp:latest analysis/model.do
    needs: [generate_cohortMAIN]
    outputs:
      moderately_sensitive:
        log: logs/model.log

  run_all:
    needs:
      - run_model
    # In order to be valid this action needs to define a run commmand and some
    # output. We don't really care what these are but the below does the trick.
    # In a future release of the platform, this special action won't need to be
    # defined at all.
    run: cohortextractor:latest --version
    outputs:
      moderately_sensitive:
        whatever: project.yaml

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:50

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

Job information

Status
Succeeded
Backend
TPP
Workspace
covid-vs-non-covid-deaths-research
Requested by
Krishnan Bhaskaran
Branch
master
Force run dependencies
No
Git commit hash
6ac873c
Requested actions
  • ethnicity_deprivation_figure

Code comparison

Compare the code used in this Job Request