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Job request: 294

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
carehomes_mortality
ID:
gctasdxx5valpqns
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Anna Schultze requested one or more actions to be run against real patient data in the 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

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 1000

actions:
  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  generate_cohort_coverage:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_coverage
    outputs:
      highly_sensitive:
        cohort: output/input_coverage.csv

  calculate_coverage: 
    run: r:latest analysis/run_calculate_tpp_coverage.R output/input_coverage.csv data/msoa_pop.csv
    needs: [generate_cohort_coverage]
    outputs: 
      moderately_sensitive: 
        log: analysis/logfiles/calculate_tpp_coverage.txt
      highly_sensitive:
        data: data/tpp_msoa_coverage.csv
        
  feasibility_checks: 
    run: r:latest analysis/run_feasibility_checks.R output/input.csv data/tpp_msoa_coverage.csv
    needs: [generate_cohort, calculate_coverage]
    outputs: 
      moderately_sensitive: 
        log: analysis/logfiles/feasibility_checks.txt
        table1a: analysis/outfiles/table1a.txt
        table1b: analysis/outfiles/table1b.txt
        figure1a: analysis/outfiles/figure1a.png
        figure1b: analysis/outfiles/figure1b.png
        figure1c: analysis/outfiles/figure1c.png
        table2: analysis/outfiles/table2.txt
        table3: analysis/outfiles/table3.txt
        figure2: analysis/outfiles/figure2.png
        table4: analysis/outfiles/table4.txt


  run_all:
    needs: [feasibility_checks]
    # 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
Unknown
Backend
TPP
Workspace
carehomes_mortality
Requested by
Anna Schultze
Branch
master
Force run dependencies
Yes
Git commit hash
1d5f267
Requested actions
  • run_all

Code comparison

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