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Job request: 10898

Organisation:
University of Liverpool
Workspace:
flucats
ID:
pzztw7wladpqkpqb
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Simon Davy 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:
    test_action
    Status:
    Status: Failed
    Job identifier:
    6nhad5m5vkyxqf4z
    Error:
    cancelled_by_user: Cancelled by user

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_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: 18:21:28

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

Job request

Status
Failed
Backend
EMIS
Workspace
flucats
Requested by
Simon Davy
Branch
main
Force run dependencies
No
Git commit hash
0478b82
Requested actions
  • test_action

Code comparison

Compare the code used in this job request