Job request: 394

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
5qoe7ggrstyynscc succeeded crMAIN
6i462vmvnke3zppu succeeded crSEPT2020
wqowqzhmho42rboq succeeded cr2019
hrhgm5jm72ttipdj succeeded imputedataMAIN
eqnl2rjusa74gcom failed imputedataSEPT2020
46hsyxwu2fvncia2 failed imputedata2019
zvual5zq5ulou547 succeeded descriptive_table1
fa7rno27dceeo3ow succeeded absoluterisksbycause
nmdm3czwwatq534b failed agesexmodelsMAIN
ojjn4nj4arwkdhr3 failed agesexmodelsSEPT2020
tuujvxvsmax7b4mp failed agesexmodels2019
vjl6qvthoknfa3yq failed agesexmodelsSA_anyonDC
x3sg5waabjycy4dq failed agesexmodelsSA_u071only
mcjbojdvrivffwkb failed fullmodelsMAIN
q7h4owq43xyyhxjw failed fullmodelsSEPT2020
hs6iuysw5iqzoqzv failed fullmodels2019
qz5yjx4dtxoamxdt failed ethnicity_model_and_graph
mpkzkzn7phip7dy6 failed deathsonly_models

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_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
    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  
        


  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

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 00:06:45

Config

  • Backend:
    TPP
  • Workspace:
    covid-vs-non-covid-deaths-research
  • Branch:
    master
  • Creator:
    krishnanbhaskaran
  • Force run dependencies:
    False
  • Git Commit Hash:
    85ccd5c
  • Requested actions:
    • 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