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Job request: 394

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
covid-vs-non-covid-deaths-research
ID:
eqls6m4jz2mpkhly
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 within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

  • Action:
    crMAIN
    Status:
    Status: Succeeded
    Job identifier:
    5qoe7ggrstyynscc
  • Action:
    crSEPT2020
    Status:
    Status: Succeeded
    Job identifier:
    6i462vmvnke3zppu
  • Action:
    cr2019
    Status:
    Status: Succeeded
    Job identifier:
    wqowqzhmho42rboq
  • Action:
    imputedataMAIN
    Status:
    Status: Succeeded
    Job identifier:
    hrhgm5jm72ttipdj
  • Action:
    imputedataSEPT2020
    Status:
    Status: Failed
    Job identifier:
    eqnl2rjusa74gcom
    Error:
    ActionFailedError: crSEPT2020 failed
  • Action:
    imputedata2019
    Status:
    Status: Failed
    Job identifier:
    46hsyxwu2fvncia2
    Error:
    ActionFailedError: cr2019 failed
  • Action:
    descriptive_table1
    Status:
    Status: Succeeded
    Job identifier:
    zvual5zq5ulou547
  • Action:
    absoluterisksbycause
    Status:
    Status: Succeeded
    Job identifier:
    fa7rno27dceeo3ow
  • Action:
    agesexmodelsMAIN
    Status:
    Status: Failed
    Job identifier:
    nmdm3czwwatq534b
    Error:
    Job exited with an error code
  • Action:
    agesexmodelsSEPT2020
    Status:
    Status: Failed
    Job identifier:
    ojjn4nj4arwkdhr3
    Error:
    ActionFailedError: crSEPT2020 failed
  • Action:
    agesexmodels2019
    Status:
    Status: Failed
    Job identifier:
    tuujvxvsmax7b4mp
    Error:
    ActionFailedError: cr2019 failed
  • Action:
    agesexmodelsSA_anyonDC
    Status:
    Status: Failed
    Job identifier:
    vjl6qvthoknfa3yq
    Error:
    Job exited with an error code
  • Action:
    agesexmodelsSA_u071only
    Status:
    Status: Failed
    Job identifier:
    x3sg5waabjycy4dq
    Error:
    Job exited with an error code
  • Action:
    fullmodelsSEPT2020
    Status:
    Status: Failed
    Job identifier:
    q7h4owq43xyyhxjw
    Error:
    ActionFailedError: crSEPT2020 failed
  • Action:
    fullmodels2019
    Status:
    Status: Failed
    Job identifier:
    hs6iuysw5iqzoqzv
    Error:
    ActionFailedError: cr2019 failed
  • Action:
    ethnicity_model_and_graph
    Status:
    Status: Failed
    Job identifier:
    qz5yjx4dtxoamxdt
    Error:
    ActionNotRunError: imputedataMAIN has not been run
  • Action:
    deathsonly_models
    Status:
    Status: Failed
    Job identifier:
    mpkzkzn7phip7dy6
    Error:
    Job exited with an error code
  • Action:
    fullmodelsMAIN
    Status:
    Status: Failed
    Job identifier:
    mcjbojdvrivffwkb
    Error:
    Job exited with an error code

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
    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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:06:45

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

Job request

Status
Failed
Backend
TPP
Workspace
covid-vs-non-covid-deaths-research
Requested by
Krishnan Bhaskaran
Branch
master
Force run dependencies
No
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

Code comparison

Compare the code used in this job request