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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 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 indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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:
    check_EGFR
    Status:
    Status: Failed
    Job identifier:
    mf4hbvgpm4n5y2ru
  • Action:
    test_indicator_g
    Status:
    Status: Failed
    Job identifier:
    7scr5ko6e2yys7kt

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 information

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