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Job request: 3458

Organisation:
Bennett Institute
Workspace:
pincer-measures
ID:
ihxe2d4poo2aljr6
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 in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

  • Action:
    generate_study_asthma
    Status:
    Status: Succeeded
    Job identifier:
    mwfxu6fv23csdz5l
  • Action:
    generate_measures_asthma
    Status:
    Status: Succeeded
    Job identifier:
    oj3latdqzj6zqcbg
  • Action:
    calculate_numerators
    Status:
    Status: Failed
    Job identifier:
    qka2l4oqzkogxkl2
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_measures
    Status:
    Status: Failed
    Job identifier:
    do24v7dn7sh7ck4k
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    check_asthma
    Status:
    Status: Failed
    Job identifier:
    hyqinkn7kdesp6ca
    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 "2019-09-01 to 2021-07-01 by month" --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv
  
  test_indicator_g:
    run: python:latest python analysis/test_indicator_g.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        csv: output/indicator_g_matching.csv
        

  check_EGFR:
    run: python:latest python analysis/check_EGFR.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        plots: output/BOXPLOT_*.png
        counts: output/CROSSTAB_*.csv
        
  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv
      
  join_ethnicity_region:
    run: python:latest python analysis/join_ethnicity_region.py
    needs: [generate_study_population, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/input*.csv

  calculate_numerators:
    run: python:latest python analysis/calculate_numerators.py
    needs: [join_ethnicity_region]
    outputs:
      highly_sensitive:
        cohort: output/inpu*.csv

  calculate_composite_indicators:
    run: python:latest python analysis/composite_indicators.py
    needs: [calculate_numerators]
    outputs:
      moderately_sensitive:
        counts: output/*_composite_measure.csv

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

  generate_study_asthma:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_asthma --index-date-range "2019-09-01 to 2021-07-01 by month" --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/input_asthma_*.csv
  
  generate_measures_asthma:
    run: cohortextractor:latest generate_measures --study-definition study_definition_asthma --output-dir=output
    needs: [generate_study_asthma]
    outputs:
        moderately_sensitive:
          measure_csv: output/measure_no_asthma_resolved_rate.csv
  
  check_asthma:
    run: python:latest python analysis/check_asthma.py
    needs: [generate_measures, generate_measures_asthma]
    outputs:
      moderately_sensitive:
        csv: output/asthma_sum.csv
  
  generate_measures_demographics:
    run: python:latest python analysis/calculate_measures.py
    needs: [calculate_numerators]
    outputs:
      moderately_sensitive:
        counts: output/indicator_measure_*.csv
  
  generate_plots:
    run: python:latest python analysis/plot_measures.py
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        counts: output/plot_*.jpeg

  generate_notebook:
    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_plots]
    outputs:
      moderately_sensitive:
        notebook: output/report.html
  
  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: 23:03:58

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

Job information

Status
Failed
Backend
TPP
Workspace
pincer-measures
Requested by
Louis Fisher
Branch
main
Force run dependencies
No
Git commit hash
60b4393
Requested actions
  • generate_study_asthma
  • generate_measures_asthma
  • check_asthma

Code comparison

Compare the code used in this Job Request