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Job request: 7976

Organisation:
Bennett Institute
Workspace:
hepatitis_in_children
ID:
2aazfslcvyrcnqpu
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

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_dob]
    outputs:
      highly_sensitive:
        cohort: output/weekly/joined/input_weekly_20*.csv.gz

  join_cohorts_weekly_2:
    run: >
      cohort-joiner:v0.0.9
        --lhs output/weekly/input_weekly_2022-04*.csv.gz
        --rhs output/input_dob.csv.gz
        --output-dir output/weekly/joined
    needs: [
      generate_study_population_weekly_3,
      generate_study_population_dob]
    outputs:
      highly_sensitive:
        cohort: output/weekly/joined/input_weekly_2022*.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:

  • Started:

  • Finished:

  • Runtime: 52:47:45

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

Job request

Status
Succeeded
Backend
TPP
Workspace
hepatitis_in_children
Requested by
Louis Fisher
Branch
main
Force run dependencies
No
Git commit hash
a4a2aba
Requested actions
  • 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_weekly_1
  • generate_study_population_weekly_2
  • generate_study_population_weekly_3

Code comparison

Compare the code used in this job request