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Job request: 325

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
carehomes_mortality
ID:
dxccxg6de7vcfiis
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Anna Schultze 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:
    generate_cohort_coverage
    Status:
    Status: Succeeded
    Job identifier:
    oddvkbzjkjol7dc2
  • Action:
    calculate_coverage
    Status:
    Status: Failed
    Job identifier:
    5iny4qecm7etvkux
    Error:
    Job exited with an error code
  • Action:
    feasibility_checks
    Status:
    Status: Failed
    Job identifier:
    ddebttjvons3emc6
    Error:
    Not starting as dependency failed
  • Action:
    generate_cohort
    Status:
    Status: Succeeded
    Job identifier:
    3pqm5yhsmkgkr5em

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:

  • Finished:

  • Runtime: 00:00:15

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

Job request

Status
Failed
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

Compare the code used in this job request