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Job request: 752

Organisation:
Bennett Institute
Workspace:
long-covid-descriptive
ID:
3yvqy72rro4ih3oh
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Alex Walker 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_1
    Status:
    Status: Failed
    Job identifier:
    oo4sk2nrgnfxfskp
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_cohort_2
    Status:
    Status: Failed
    Job identifier:
    q5n3nrjopu2o7g66
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    calculate_measures
    Status:
    Status: Failed
    Job identifier:
    v6nfgue3vab7oshl
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    standardise_and_plot
    Status:
    Status: Failed
    Job identifier:
    3wx46qlquyr6zfcg
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 500

actions:

  generate_cohort_1:
    # week 45 2020 to 20 2020 inclusive
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-11-02 to 2020-12-13 by week"
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv

  generate_cohort_2:
    # week 51 2020 to 03 2021 inclusive
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-12-14 to 2021-01-24 by week"
    outputs:
      highly_sensitive:
        cohort: output/input*.csv

  calculate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition
    needs: [generate_cohort_1, generate_cohort_2]
    outputs:
      moderately_sensitive:
        measure: output/measure_*_rate.csv

  standardise_and_plot:
    run: python:latest python analysis/time_series_plots.py
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        tables: output/*_rate.csv
        graph: output/time_series_plot.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:57

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

Job request

Status
Failed
Backend
TPP
Workspace
long-covid-descriptive
Requested by
Alex Walker
Branch
main
Force run dependencies
No
Git commit hash
8b02fe8
Requested actions
  • run_all

Code comparison

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