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Job request: 8131

Organisation:
Bennett Institute
Workspace:
hepatitis_in_children
ID:
d5uv4q2mfrm7zr7z
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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_study_population_monthly_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2017-04-01 to 2018-04-01 by month" --output-dir=output/monthly --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/monthly/input_*.csv.gz
  
  generate_study_population_monthly_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-05-01 to 2019-04-01 by month" --output-dir=output/monthly --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/monthly/input*.csv.gz

  generate_study_population_monthly_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-05-01 to 2020-04-01 by month" --output-dir=output/monthly --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/monthly/inpu*.csv.gz

  generate_study_population_monthly_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-05-01 to 2021-04-01 by month" --output-dir=output/monthly --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/monthly/inp*.csv.gz
  
  generate_study_population_monthly_5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-05-01 to 2022-03-01 by month" --output-dir=output/monthly --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/monthly/in*.csv.gz

  generate_study_population_weekly_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_weekly --index-date-range "2021-04-01 to 2021-09-02 by week" --output-dir=output/weekly --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/weekly/input_*.csv.gz
  
  generate_study_population_weekly_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_weekly --index-date-range "2021-09-09 to 2022-04-14 by week" --output-dir=output/weekly --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/weekly/input*.csv.gz
  
  generate_study_population_weekly_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_weekly --index-date-range "2022-04-21 to 2022-05-05 by week" --output-dir=output/weekly --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/weekly/inpu*.csv.gz

  generate_study_population_dob:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_dob --output-dir=output --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_dob.csv.gz

  join_cohorts_monthly:
    run: >
      cohort-joiner:v0.0.9
        --lhs output/monthly/input_20*.csv.gz
        --rhs output/input_dob.csv.gz
        --output-dir output/monthly/joined
    needs: [
      generate_study_population_monthly_1,
      generate_study_population_monthly_2,
      generate_study_population_monthly_3,
      generate_study_population_monthly_4,
      generate_study_population_monthly_5,
      generate_study_population_dob]
    outputs:
      highly_sensitive:
        cohort: output/monthly/joined/input_20*.csv.gz

  join_cohorts_weekly:
    run: >
      cohort-joiner:v0.0.9
        --lhs output/weekly/input_weekly_20*.csv.gz
        --rhs output/input_dob.csv.gz
        --output-dir output/weekly/joined
    needs: [
      generate_study_population_weekly_1,
      generate_study_population_weekly_2,
      generate_study_population_weekly_3,
      generate_study_population_dob]
    outputs:
      highly_sensitive:
        cohort: output/weekly/joined/input_weekly_20*.csv.gz

  get_age_months:
    run: >
      python:latest python analysis/get_age_months.py
    needs: [join_cohorts_monthly, join_cohorts_weekly, generate_study_population_dob]
    outputs:
      highly_sensitive:
        cohorts_monthly: output/monthly/joined/input_2*.csv.gz
        cohorts_weekly: output/weekly/joined/input_weekly*.csv.gz
  
  isaric_preprocess:
    run: >
      python:latest python analysis/isaric_preprocess.py
    needs: [get_age_months]
    outputs:
      highly_sensitive:
        monthly: output/weekly/joined/isaric/input.csv.gz

  isaric_process:
    run: >
      python:latest python analysis/isaric_process_data.py
      --filename output/weekly/joined/isaric/input.csv.gz
      --output_filename output/weekly/joined/isaric/summary_table.csv
    needs: [isaric_preprocess]
    outputs:
      moderately_sensitive:
        monthly: output/weekly/joined/isaric/summary_table.csv

  mean_values_by_age:
    run: >
      python:latest python analysis/mean_values.py
    needs: [get_age_months]
    outputs:
      moderately_sensitive:
        monthly: output/monthly/joined/mean_test_value_*_by_age.csv

  generate_measures:
    run: cohortextractor:latest generate_measures 
      --study-definition study_definition
      --output-dir=output/monthly/joined
    needs: [
      get_age_months
      ]
    outputs:
      moderately_sensitive:
        measure_csv_monthly: output/monthly/joined/measure_*_rate.csv

  generate_measures_weekly:
    run: cohortextractor:latest generate_measures 
      --skip-existing
      --study-definition study_definition_weekly
      --output-dir=output/weekly/joined
    needs: [get_age_months]
    outputs:
      moderately_sensitive:
        measure_csv: output/weekly/joined/measure_*_rate.csv

  generate_plots:
    run: python:latest python analysis/plots.py
    needs: [generate_measures, generate_measures_weekly, mean_values_by_age]
    outputs:
      moderately_sensitive:
        counts: output/*/joined/plot_*.png
        deciles_charts: output/*/joined/deciles_chart_*.png
        measure_csv: output/*/joined/redacted/measure_*_rate.csv
        num_practices: output/*/joined/practice_count*.json

  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

Timeline

  • Created:

  • Finished:

  • Runtime:

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

Job information

Status
Failed
Backend
TPP
Workspace
hepatitis_in_children
Requested by
Louis Fisher
Branch
main
Force run dependencies
No
Git commit hash
faa40c6
Requested actions
  • get_age_months
  • isaric_preprocess
  • isaric_process
  • mean_values_by_age
  • generate_measures
  • generate_measures_weekly
  • generate_plots
  • generate_notebook

Code comparison

Compare the code used in this Job Request