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Job request: 1738

Organisation:
Bennett Institute
Workspace:
covid_vaccine_decline_variation
ID:
geo7cayucqmz4rzo
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Helen Curtis 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_ethnicity
    Status:
    Status: Succeeded
    Job identifier:
    rxahlvtc5tdfaxo3
  • Action:
    generate_study_population
    Status:
    Status: Failed
    Job identifier:
    qimg4z5jww7t4zho
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_study_population_practice_count
    Status:
    Status: Succeeded
    Job identifier:
    f77b7aj6mejxi63j
  • Action:
    get_patient_count
    Status:
    Status: Failed
    Job identifier:
    ptwzuaa32m4zb5bu
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    create_notebook
    Status:
    Status: Failed
    Job identifier:
    g4h6dflbbaksx2qy
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_measures
    Status:
    Status: Failed
    Job identifier:
    zihoqyp5jgncgund
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_notebook
    Status:
    Status: Failed
    Job identifier:
    ucar5ll6otnz2j3b
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    join_ethnicity
    Status:
    Status: Failed
    Job identifier:
    k732x23dqcq6waff
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_measure_ethnicity
    Status:
    Status: Failed
    Job identifier:
    eczaw3ig5noz4bus
    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 "2020-12-01 to 2021-04-01 by month" --output-dir=output --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv.gz

  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv.gz

  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py
    needs: [generate_study_population, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/input*.csv.gz

  generate_study_population_practice_count:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --output-dir=output --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_practice_count.csv.gz

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

  generate_measure_ethnicity:
    run: python:latest python analysis/generate_measure_ethnicity.py
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        measure: output/measure_ethnicity.csv

  get_patient_count:
    run: python:latest python analysis/get_patients_counts.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        text: output/patient_count.json

  create_notebook:
    run: python:latest python analysis/create_notebook.py
    needs: [get_patient_count, join_ethnicity]
    outputs:
      moderately_sensitive:
        notebook: analysis/SRO_Notebook.ipynb


  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/SRO_Notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [create_notebook, generate_measures, generate_measure_ethnicity, generate_study_population_practice_count, generate_study_population, join_ethnicity]
    outputs:
      moderately_sensitive:
        notebook: output/SRO_Notebook.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:44:28

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

Job request

Status
Failed
Backend
TPP
Workspace
covid_vaccine_decline_variation
Requested by
Helen Curtis
Branch
master
Force run dependencies
No
Git commit hash
e23428a
Requested actions
  • run_all

Code comparison

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