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Job request: 3429

Organisation:
Bennett Institute
Workspace:
pincer-measures
ID:
bsfgdb72vn3jbgbk
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:
    check_EGFR
    Status:
    Status: Failed
    Job identifier:
    mf4hbvgpm4n5y2ru
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    test_indicator_g
    Status:
    Status: Failed
    Job identifier:
    7scr5ko6e2yys7kt
    Error:
    nonzero_exit: Job exited with an error code

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: jupyter:latest jupyter nbconvert /workspace/analysis/test_indicator_g.ipynb --execute --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        csv: output/indicator_g_matching.csv
        

  check_EGFR:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/check_EGFR.ipynb --execute --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    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 analysis/calculate_numerators.py
    needs: [join_ethnicity_region]
    outputs:
      highly_sensitive:
        cohort: output/inpu*.csv

  calculate_composite_indicators:
    run: python:latest 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_measures_demographics:
    run: python:latest analysis/calculate_measures.py
    needs: [calculate_numerators]
    outputs:
      moderately_sensitive:
        counts: output/indicator_measure_*.csv
  
  generate_plots:
    run: python:latest 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: 00:57:09

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

Job request

Status
Failed
Backend
TPP
Workspace
pincer-measures
Requested by
Louis Fisher
Branch
main
Force run dependencies
No
Git commit hash
abee056
Requested actions
  • test_indicator_g
  • check_EGFR

Code comparison

Compare the code used in this job request