Job request: 337

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
g4s7ljbv3fqqrjca succeeded generate_cohorts
4fpcr44q23e3q6pv succeeded generate_flowchartdata
nhpt344xe6p5vkv7 succeeded generate_sep2020data

Pipeline

Show Hide 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

  generate_sep2020data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sept2020
    outputs:
      highly_sensitive:
        cohort: output/input_sept2020.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

  agesexmodels:
    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
  
  fulladjmodels:
    run: stata-mp:latest analysis/an_covidvsnoncovid_full.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covidvsnoncovid_full.log
        models: analysis/output/models/an_covidvsnoncovid_full_*.ster  
  
  agesex2019models:
    run: stata-mp:latest analysis/an_noncovid_2019_agesex.do
    needs: [cr2019]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_noncovid_2019_agesex.log
        models: analysis/output/models/an_noncovid_2019_agesex_*.ster  
  
  
  fulladj2019models:
    run: stata-mp:latest analysis/an_noncovid_2019_full.do
    needs: [cr2019]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_noncovid_2019_full.log
        models: analysis/output/models/an_noncovid_2019_full_*.ster  
    
  covnoncov_forestplot:
    run: stata-mp:latest analysis/an_processout_agesex_covvsnon_forestplots.do
    needs: [agesexmodels]
    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: 
      - agesexmodels 
      - fulladjmodels 
      - agesex2019models 
      - fulladj2019models
    outputs:
      moderately_sensitive:
        log: analysis/output/an_processout_agesex_covvsnon_table.txt
 
 
  ethnicity_model_and_graph:
    run: stata-mp:latest analysis/an_ethnicitybycod_logisticversion.do
    needs: [crmain]
    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  
   
  deathsonly_ORfigure:
    run: stata-mp:latest analysis/an_processout_deathsonlyanalysis.do
    needs: [deathsonly_models]
    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: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 00:01:21

Config

  • Backend:
    TPP
  • Workspace:
    covid-vs-non-covid-deaths-research
  • Branch:
    master
  • Creator:
    krishnanbhaskaran
  • Force run dependencies:
    False
  • Git Commit Hash:
    ae77507
  • Requested actions:
    • generate_cohorts
    • generate_flowchartdata
    • generate_sep2020data