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Job request: 2097

Organisation:
Bennett Institute
Workspace:
long-covid-historical-health
ID:
dik55ahhnf5kv7t3
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
    Status:
    Status: Succeeded
    Job identifier:
    i24xbeazffgog6yv
  • Action:
    select_cohorts
    Status:
    Status: Failed
    Job identifier:
    sfmc7y666hlcwxag
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    count_by_strata
    Status:
    Status: Succeeded
    Job identifier:
    cyrag3avfpxy6vdp
  • Action:
    logistic_models
    Status:
    Status: Succeeded
    Job identifier:
    f7t5iwsnjkz4q6ed
  • Action:
    logistic_models_after_may
    Status:
    Status: Failed
    Job identifier:
    bmf624c3vyu5txcr
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    logistic_models_before_may
    Status:
    Status: Failed
    Job identifier:
    6s4ruzpo3uf7v23j
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 5000

actions:

  generate_cohort:
    run: cohortextractor:latest generate_cohort --output-format dta
    outputs:
      highly_sensitive:
        cohort: output/input.dta

  count_by_strata:
    run: python:latest python analysis/all_time_counts.py
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        table: output/counts_table.csv

  logistic_models:
    run: stata-mp:latest analysis/model.do ""
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        table: output/model_summary.csv

  select_cohorts:
    run: stata-mp:latest analysis/select_cohorts.do ""
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        cohort_before_may: output/input_before_may.dta
        cohort_after_may: output/input_after_may.dta

  logistic_models_before_may:
    run: stata-mp:latest analysis/model.do "_before_may"
    needs: [select_cohorts]
    outputs:
      moderately_sensitive:
        table: output/model_summary_before_may.csv

  logistic_models_after_may:
    run: stata-mp:latest analysis/model.do "_after_may"
    needs: [select_cohorts]
    outputs:
      moderately_sensitive:
        table: output/model_summary_after_may.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:02:22

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

Job request

Status
Failed
Backend
TPP
Workspace
long-covid-historical-health
Requested by
Alex Walker
Branch
main
Force run dependencies
Yes
Git commit hash
0b8ba2a
Requested actions
  • run_all

Code comparison

Compare the code used in this job request