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Job request: 253

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
covid-vs-non-covid-deaths-research
ID:
2u3iqvyg4iutnymf
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: 10000

actions:
  generate_cohorts:
    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_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.do
    needs: [generate_cohorts]
    outputs:
      highly_sensitive:
        data: analysis/cr_create_analysis_dataset.dta
        stsetdata: analysis/cr_create_analysis_dataset_STSET_ONSCSDEATH.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset.log
  
  cr2019:
    run: stata-mp:latest analysis/cr_create_analysis_dataset_2019.do
    needs: [generate_cohort2019]
    outputs:
      highly_sensitive:
        data: analysis/cr_create_analysis_dataset_2019.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset_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

  covnoncov_logisticmodels:
    run: stata-mp:latest analysis/an_covidvsnoncovid_agesex.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covidvsnoncovid_agesex.log
        models: analysis/output/models/an_covidvsnoncovid_agesex_*.ster
  
  covnoncov_forestplot:
    run: stata-mp:latest analysis/an_processout_agesex_covvsnon_forestplots.do
    needs: [covnoncov_logisticmodels]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_processout_agesex_covvsnon_forestplots_TABLE.txt
        graph: analysis/output/an_processout_agesex_covvsnon_forestplots_GRAPH.svg
 
  ethnicity_model:
    run: stata-mp:latest analysis/an_ethnicitybycod.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_ethnicitybycod.log
        graph: analysis/output/an_ethnicitybycod.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

Timeline

  • Created:

  • Started:

  • Runtime:

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

Job information

Status
Failed
Backend
TPP
Workspace
covid-vs-non-covid-deaths-research
Requested by
Krishnan Bhaskaran
Branch
master
Force run dependencies
No
Git commit hash
a18eb5a
Requested actions
  • covnoncov_logisticmodels

Code comparison

Compare the code used in this Job Request