Job request: 377

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher krishnanbhaskaran requested one or more actions to be run against real patient data in the COVID-19 vs Non-COVID-19 Deaths 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.

Jobs

ID Status Action
u33qjzk7d4cvptah failed generate_cohort2019

Pipeline

Show Hide 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_datasetMAIN.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_datasetSEPT2020.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_dataset2019.log
  
  imputedataMAIN:
    run: stata-mp:latest analysis/an_impute_GENERAL.do MAIN
    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
    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
    needs: [cr2019]
    outputs:
      highly_sensitive:
        data: analysis/an_impute_imputeddata_2019.dta
      moderately_sensitive:
        log: analysis/output/an_impute_2019.log
    
  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  

  imp_modelMAIN_C_AGESEX:
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN coviddeath agesex agespl
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed_MAIN_coviddeath_agesex_agespl.log
        models: analysis/output/models/an_imputed_agesex_MAIN_coviddeath.ster  
         
  imp_modelMAIN_NC_AGESEX:
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN noncoviddeath agesex agespl
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed_MAIN_noncoviddeath_agesex_agespl.log
        models: analysis/output/models/an_imputed_agesex_MAIN_noncoviddeath.ster  
         
  imp_modelMAIN_C_FULLspl:
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN coviddeath full agespl
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
         
  imp_modelMAIN_C_FULLgrp:    
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN coviddeath full agegrp
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelMAIN_NC_FULLspl:
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN noncoviddeath full agespl
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelMAIN_NC_FULLgrp:    
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN noncoviddeath full agegrp
    needs: [imputedataSEPT2020]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelSEPT2020_C_AGESEX:
    run: stata-mp:latest analysis/an_imputed_GENERAL SEPT2020 coviddeath agesex agespl
    needs: [imputedataSEPT2020]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelSEPT2020_NC_AGESEX:
    run: stata-mp:latest analysis/an_imputed_GENERAL SEPT2020 noncoviddeath agesex agespl
    needs: [imputedataSEPT2020]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelSEPT2020_C_FULLspl:
    run: stata-mp:latest analysis/an_imputed_GENERAL SEPT2020 coviddeath full agespl
    needs: [imputedataSEPT2020]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelSEPT2020_C_FULLgrp:
    run: stata-mp:latest analysis/an_imputed_GENERAL SEPT2020 coviddeath full agegrp
    needs: [imputedataSEPT2020]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelSEPT2020_NC_FULLspl:
    run: stata-mp:latest analysis/an_imputed_GENERAL SEPT2020 noncoviddeath full agespl
    needs: [imputedataSEPT2020]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelSEPT2020_NC_FULLgrp:
    run: stata-mp:latest analysis/an_imputed_GENERAL SEPT2020 noncoviddeath full agegrp
    needs: [imputedataSEPT2020]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_model2019_AGESEX:
    run: stata-mp:latest analysis/an_imputed_GENERAL 2019 primarycaredeath agesex agespl
    needs: [imputedata2019]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_model2019_FULLspl: 
    run: stata-mp:latest analysis/an_imputed_GENERAL 2019 primarycaredeath full agespl
    needs: [imputedata2019]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_model2019_FULLgrp:
    run: stata-mp:latest analysis/an_imputed_GENERAL 2019 primarycaredeath full agegrp
    needs: [imputedata2019]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelMAIN_C_SAanywhereonDC:
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN coviddeath agesex agespl SA_anywhereonDC
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
        
  imp_modelMAIN_NC_SAanywhereonDC:
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN noncoviddeath agesex agespl SA_anywhereonDC
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
        
  imp_modelMAIN_C_SAu071only:
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN coviddeath agesex agespl SA_u071only
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
        
  imp_modelMAIN_NC_SAu071only:   
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN noncoviddeath agesex agespl SA_u071only
    needs: [imputedataMAIN]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
 
  imp_modelMAIN_DEATHSONLY:     
    run: stata-mp:latest analysis/an_imputed_GENERAL MAIN deathsonlyCvN agesex agespl
    needs: [imputedataMAIN]  
    outputs:
      moderately_sensitive:
        log: analysis/output/an_imputed*.log
        models: analysis/output/models/an_imputed*.ster  
        
  covnoncov_forestplot:
    run: stata-mp:latest analysis/an_processout_agesex_covvsnon_forestplots.do
    needs: 
      - agesexmodelsMAIN 
      - imp_modelMAIN_C_AGESEX 
      - imp_modelMAIN_NC_AGESEX
    outputs:
      moderately_sensitive:
        log: analysis/output/an_processout_agesex_covvsnon_forestplots_TABLE.txt
        graph: analysis/output/an_processout_agesex_covvsnon_forestplots_GRAPH.svg
 
  covnoncov_appxestimatestable:
    run: stata-mp:latest analysis/an_processout_agesex_covvsnon_table.do
    needs: 
      - agesexmodelsMAIN 
      - agesexmodels2019
      - imp_modelMAIN_C_AGESEX
      - imp_modelMAIN_NC_AGESEX
      - imp_model2019_AGESEX
      - imp_modelMAIN_C_FULLspl
      - imp_modelMAIN_C_FULLgrp
      - imp_modelMAIN_NC_FULLspl
      - imp_modelMAIN_NC_FULLgrp
      - imp_model2019_FULLspl
      - imp_model2019_FULLgrp
    outputs:
      moderately_sensitive:
        log: analysis/output/an_processout_agesex_covvsnon_table.txt
 
  deathsonly_ORfigure:
    run: stata-mp:latest analysis/an_processout_deathsonlyanalysis.do
    needs: 
      - deathsonly_models 
      - imp_modelMAIN_DEATHSONLY
    outputs:
      moderately_sensitive:
        log: analysis/output/an_processout_deathsonlyanalysis_TABLE.txt
        graph: analysis/output/an_processout_deathsonlyanalysis_GRAPH.svg 


  run_model:
    run: stata-mp:latest analysis/model.do
    needs: [generate_cohorts]
    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

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: -

Config

  • Backend:
    TPP
  • Workspace:
    covid-vs-non-covid-deaths-research
  • Branch:
    master
  • Creator:
    krishnanbhaskaran
  • Force run dependencies:
    False
  • Git Commit Hash:
    0a38007
  • Requested actions:
    • generate_cohort2019
    • crMAIN
    • crSEPT2020
    • cr2019
    • imputedataMAIN
    • imputedataSEPT2020
    • imputedata2019
    • descriptive_table1
    • absoluterisksbycause
    • agesexmodelsMAIN
    • agesexmodelsSEPT2020
    • agesexmodels2019
    • agesexmodelsSA_anyonDC
    • agesexmodelsSA_u071only
    • fullmodelsMAIN
    • fullmodelsSEPT2020
    • fullmodels2019
    • ethnicity_model_and_graph
    • deathsonly_models