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Job request: 399

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
covid-vs-non-covid-deaths-research
ID:
qbkmf62n4eg3rk6b
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Dave Evans 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:
    imputedataMAIN
    Status:
    Status: Succeeded
    Job identifier:
    cuoxypsxgolnzhho
  • Action:
    crSEPT2020
    Status:
    Status: Succeeded
    Job identifier:
    ok7gbnhbm55nczij
  • Action:
    cr2019
    Status:
    Status: Succeeded
    Job identifier:
    o3q6nswtpifdhbfl
  • Action:
    ethnicity_model_and_graph
    Status:
    Status: Succeeded
    Job identifier:
    wt43l5gp5ab7fjss
  • Action:
    imputedataSEPT2020
    Status:
    Status: Succeeded
    Job identifier:
    xemaylwooluf727i
  • Action:
    imputedata2019
    Status:
    Status: Succeeded
    Job identifier:
    h5wtk24lk2ltizij
  • Action:
    agesexmodelsSEPT2020
    Status:
    Status: Failed
    Job identifier:
    qq56hpi7lvi45s5u
    Error:
    Job exited with an error code
  • Action:
    agesexmodels2019
    Status:
    Status: Failed
    Job identifier:
    d2v3khlmsy3f2rmz
    Error:
    Job exited with an error code
  • Action:
    fullmodelsSEPT2020
    Status:
    Status: Failed
    Job identifier:
    gzvimwoezbtkdj2k
    Error:
    Job exited with an error code
  • Action:
    fullmodels2019
    Status:
    Status: Failed
    Job identifier:
    fpy6ojuo6lc67sdz
    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: 00:05:05

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
Dave Evans
Branch
master
Force run dependencies
No
Git commit hash
85ccd5c
Requested actions
  • crSEPT2020
  • cr2019
  • imputedataSEPT2020
  • imputedata2019
  • agesexmodelsSEPT2020
  • agesexmodels2019
  • fullmodelsSEPT2020
  • fullmodels2019
  • ethnicity_model_and_graph

Code comparison

Compare the code used in this job request