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Job request: 16160

Organisation:
PrescQIPP
Workspace:
the_effects_of_covid-19_on_dfms_prescribing
ID:
cspxdx3oyqaw7fxi
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Rachel Seeley 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_study_population
    Status:
    Status: Failed
    Job identifier:
    j7vjwaurwmdvgaiu
    Error:
    nonzero_exit: Job exited with an error: Something went wrong with the database, please contact tech support
  • Action:
    generate_measures
    Status:
    Status: Failed
    Job identifier:
    5wijohd3x6a5kglq
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_report
    Status:
    Status: Failed
    Job identifier:
    nu6q5n6dcc5yqnoq
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 10000

actions:
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2022-02-01 to 2023-01-01 by month" --output-dir=output --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/input*.csv

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
    needs: [generate_study_population]
    outputs: 
      moderately_sensitive:
        measure_csv: output/measure_*_rate.csv

  generate_report:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/report*.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        notebook: output/report*.html
        plots: output/*.png
        tables: output/*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:08:54

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

Job request

Status
Failed
Backend
TPP
Workspace
the_effects_of_covid-19_on_dfms_prescribing
Requested by
Rachel Seeley
Branch
main
Force run dependencies
Yes
Git commit hash
6aa7e3c
Requested actions
  • run_all

Code comparison

Compare the code used in this job request