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Job request: 248

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
covid-vs-non-covid-deaths-research
ID:
eqgjw7htnpvaby44
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:
    cr2019
    Status:
    Job identifier:
    rttlzwmpikwqsszs-manually-set

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

  crmain:
    run: stata-mp:latest analysis/cr_create_analysis_dataset.do
    needs: [generate_cohorts]
    outputs:
      highly_sensitive:
        data: analysis/cr_create_analysis_dataset.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
  
  an_covid_vs_othercauses_abs_AGESEX:
    run: stata-mp:latest analysis/an_covid_vs_othercauses_abs_AGESEX.do
    needs: [crmain]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_covid_vs_othercauses_abs_AGESEX.log
        barchart: analysis/output/an_covid_vs_othercauses_abs_AGESEX_GRAPH.svg
        estimates: analysis/output/an_covid_vs_othercauses_abs_AGESEX_ESTIMATES.dta
  
  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:

  • Finished:

  • Runtime: 00:35:26

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

Job request

Status
Succeeded
Backend
TPP
Workspace
covid-vs-non-covid-deaths-research
Requested by
Krishnan Bhaskaran
Branch
master
Force run dependencies
No
Git commit hash
c4d67ed
Requested actions
  • cr2019

Code comparison

Compare the code used in this job request