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Job request: 11865

Organisation:
University of Liverpool
Workspace:
flucats
ID:
v7slon4t6wngtwmo
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher 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_dataset_report_test
    Status:
    Status: Failed
    Job identifier:
    xwldx4nx3hn2fb5b
    Error:
    nonzero_exit: Job exited with error code 137: likely means it ran out of memory

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  test_action:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-03-01 to 2020-03-01 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/inp*.csv.gz

  generate_dataset_report_test:
    run: >
      dataset-report:v0.0.24
        --input-files output/input_2020-03-01.csv.gz
        --output-dir output
    needs: [test_action]
    outputs:
      moderately_sensitive:
        dataset_report: output/input_2020-03-01.html

  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-03-01 to 2021-03-07 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv.gz

  # gives until 2022-03-27. Only have ONS deaths until 2021-07-01
  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-03-14 to 2022-03-20 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input*.csv.gz
  

  generate_study_population_end:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_end --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_end.csv.gz

  join_cohorts_weekly:
    run: >
      cohort-joiner:v0.0.44
        --lhs output/input_20*.csv.gz
        --rhs output/input_end.csv.gz
        --output-dir output/joined
    needs: [
      generate_study_population_1,
      generate_study_population_2,
      generate_study_population_end]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_20*.csv.gz


  generate_dataset_report:
    run: >
      dataset-report:v0.0.24
        --input-files output/joined/input_2022-03-20.csv.gz
        --output-dir output/joined
    needs: [join_cohorts_weekly]
    outputs:
      moderately_sensitive:
        dataset_report: output/joined/input_2022-03-20.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:04:54

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

Job request

Status
Failed
Backend
EMIS
Workspace
flucats
Requested by
Louis Fisher
Branch
main
Force run dependencies
No
Git commit hash
26af8ee
Requested actions
  • generate_dataset_report_test

Code comparison

Compare the code used in this job request