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Job request: 2058

Organisation:
Bennett Institute
Workspace:
sro-measures-demographics
ID:
bieri4gub2rldfa2
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher 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:
    run_tests
    Status:
    Status: Succeeded
    Job identifier:
    oow4jeolot7p62l4
  • Action:
    get_practice_count
    Status:
    Status: Succeeded
    Job identifier:
    zhu34zzaq6wqvjyd
  • Action:
    get_patient_count
    Status:
    Status: Succeeded
    Job identifier:
    2lxkbvgqzxqq3w2p
  • Action:
    generate_measure_ethnicity
    Status:
    Status: Failed
    Job identifier:
    mrap5mh5pek5guoe
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_measures
    Status:
    Status: Failed
    Job identifier:
    4367ooj3h5xgnyfk
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    get_event_summary
    Status:
    Status: Failed
    Job identifier:
    yybzit2zcfolehdj
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_notebook
    Status:
    Status: Failed
    Job identifier:
    ax7ujpoyaycc557c
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_notebook_demographics
    Status:
    Status: Failed
    Job identifier:
    qzinqh5thzlb3rb4
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000
   
    
actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2021-04-01 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv

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

  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

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

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


   
  
  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/sentinel_measures.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_measures, get_practice_count, get_patient_count, generate_measure_ethnicity, join_ethnicity]
    outputs:
      moderately_sensitive:
        notebook: output/sentinel_measures.html
    
  generate_notebook_demographics:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/sentinel_measures_demographics.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_measures, get_practice_count, get_patient_count, generate_measure_ethnicity, join_ethnicity]
    outputs:
      moderately_sensitive:
        notebook: output/sentinel_measures_demographics.html
     
  # generate_notebook_practice:
  #   run: jupyter:latest jupyter nbconvert /workspace/notebooks/sentinel_measures_by_practice.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
  #   needs: [generate_measures, get_practice_count, get_patient_count]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/sentinel_measures_by_practice.html
  #       csvs: output/*_check.csv

  get_event_summary:
    run: python:latest python analysis/get_event_summary.py
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        text: output/*_event_summary.csv

  run_tests:
    run: python:latest python -m pytest --junit-xml=output/pytest.xml --verbose
    outputs:
      moderately_sensitive:
        log: output/pytest.xml

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 13:34:11

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

Job request

Status
Failed
Backend
TPP
Workspace
sro-measures-demographics
Requested by
Louis Fisher
Branch
demographics-notebook
Force run dependencies
No
Git commit hash
601f7e6
Requested actions
  • generate_measures
  • generate_measure_ethnicity
  • get_practice_count
  • get_patient_count
  • generate_notebook
  • generate_notebook_demographics
  • get_event_summary
  • run_tests

Code comparison

Compare the code used in this job request