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Job request: 20898

Organisation:
Bennett Institute
Workspace:
waiting-list
ID:
gbrb4mv62qygexek
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Andrea Schaffer 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_clockstops
    Status:
    Status: Failed
    Job identifier:
    sgfospv27dteo7x7
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    measures_any_opioid
    Status:
    Status: Failed
    Job identifier:
    foqm3v75k7foyro2
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    measures_hi_opioid
    Status:
    Status: Failed
    Job identifier:
    cnc3tz4f72jbegyk
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    checks_clockstops
    Status:
    Status: Failed
    Job identifier:
    dy3dc4zl7uciczia
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    opioids_by_week
    Status:
    Status: Failed
    Job identifier:
    qqp3m6etukuoi5hb
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  # Closed (completed) RTT pathways
  generate_dataset_clockstops:
    run: ehrql:v0 generate-dataset analysis/dataset_definition_clockstops.py 
      --output output/data/dataset_clockstops.csv.gz
    outputs:
      highly_sensitive:
        cohort: output/data/dataset_clockstops.csv.gz  

  measures_any_opioid:
    run: ehrql:v0 generate-measures analysis/measures_any_opioid.py 
      --output output/measures/measures_any_opioid.csv
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_any_opioid.csv
  
  measures_hi_opioid:
    run: ehrql:v0 generate-measures analysis/measures_hi_opioid.py 
      --output output/measures/measures_hi_opioid.csv
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_hi_opioid.csv
        
  # Open (incomplete) RTT pathways
  # generate_dataset_openpathways:
  #   run: ehrql:v0 generate-dataset analysis/dataset_definition_openpathways.py 
  #     --output output/data/dataset_table_openpathways.csv.gz
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/data/dataset_openpathways.csv.gz  
  
  checks_clockstops:
   run: r:latest analysis/clockstops/checks_clockstops.R
   needs: [generate_dataset_clockstops]
   outputs:
      moderately_sensitive:
        data: output/clockstops/*.csv
        plots: output/clockstops/*.png

  opioids_by_week:
   run: r:latest analysis/clockstops/opioids_by_week.R
   needs: [measures_any_opioid, measures_hi_opioid]
   outputs:
      moderately_sensitive:
        data: output/clockstops/opioid*.csv
       # plots: output/clockstops/plot*.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:29

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

Job request

Status
Failed
Backend
TPP
Workspace
waiting-list
Requested by
Andrea Schaffer
Branch
main
Force run dependencies
Yes
Git commit hash
470eeff
Requested actions
  • run_all

Code comparison

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