Job request: 17105

Organisation:: Bennett Institute
Workspace:: pincer-measures
ID:: 4x2an4hptdtud5o6

This page shows the technical details of what happened when the authorised researcher Rose Higgins 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_population_5

Status:

Status: Succeeded

Job identifier:

vusqqw25ripctuy3
Action:

join_ethnicity_region

Status:

Status: Succeeded

Job identifier:

vcrqikyc4bmj4733
Action:

filter_population

Status:

Status: Succeeded

Job identifier:

22elcf7r32wsbqtn
Action:

calculate_numerators

Status:

Status: Succeeded

Job identifier:

vxtvno4ljtlhxxsr
Action:

generate_measures

Status:

Status: Succeeded

Job identifier:

xxp5ozh5zfyy37yn
Action:

generate_summary_counts

Status:

Status: Succeeded

Job identifier:

nmnxxwaj7axpmfiu
Action:

calculate_composite_indicators

Status:

Status: Succeeded

Job identifier:

s2hlbwzqukr7c3px
Action:

generate_plots

Status:

Status: Succeeded

Job identifier:

wikoxb3rylyrywe4
Action:

generate_notebook_updating

Status:

Status: Succeeded

Job identifier:

ofwnwxxhrhtiplyu

Pipeline

Show project.yaml

version: "3.0"

expectations:
  population_size: 5000

actions:
  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-09-01 to 2020-05-01 by month" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_*.feather

  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-06-01 to 2021-02-01 by month" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input*.feather

  generate_study_population_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-03-01 to 2021-09-01 by month" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/inpu*.feather

  generate_study_population_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-10-01 to 2022-02-01 by month" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/in*.feather
        
  generate_study_population_5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2022-03-01 to 2023-03-01 by month" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/i*.feather

  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.feather

  join_ethnicity_region:
    run: python:latest python analysis/join_ethnicity_region.py
    needs:
      [
        generate_study_population_1,
        generate_study_population_2,
        generate_study_population_3,
        generate_study_population_4,
        generate_study_population_5,
        generate_study_population_ethnicity,
      ]
    outputs:
      highly_sensitive:
        cohort: output/inp*.feather

  filter_population:
    run: python:latest python analysis/filter_population.py
    needs: [join_ethnicity_region]
    outputs:
      highly_sensitive:
        cohort: output/input_filtered_*.feather
  
  check_asthma:
    run: python:latest python analysis/asthma_check.py
    needs: [filter_population]
    outputs:
      moderately_sensitive:
        check: output/asthma_check.json

  calculate_numerators:
    run: python:latest python analysis/calculate_numerators.py
    needs: [filter_population]
    outputs:
      highly_sensitive:
        cohort: output/indicator_e_f_*.feather

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

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

  generate_measures_demographics:
    run: python:latest python analysis/calculate_measures.py
    needs: [calculate_numerators, filter_population]
    outputs:
      moderately_sensitive:
        counts: output/indicator_measure_*.csv
        measure_csv: output/measure*_rate.csv
        demographics: output/demographics_summary_*.csv
  
  produce_stripped_measures:
    run: python:latest python analysis/stripped_measures.py
    needs:
      [
        generate_measures,
        generate_measures_demographics
      ]
    outputs:
      moderately_sensitive:
        measures: output/measure_stripped_*.csv

  generate_summary_counts:
    run: python:latest python analysis/summary_statistics.py
    needs:
      [
        filter_population,
        generate_measures,
        generate_measures_demographics,
        calculate_numerators,
      ]
    outputs:
      moderately_sensitive:
        patient_count: output/patient_count_*.json
        practice_count: output/practice_count_*.json
        summary: output/indicator_summary_statistics_*.json

  generate_plots:
    run: python:latest python analysis/plot_measures.py
    needs:
      [
        generate_measures,
        generate_measures_demographics,
        calculate_composite_indicators,
      ]
    outputs:
      moderately_sensitive:
        counts: output/figures/plot_*.jpeg
        combined: output/figures/combined_plot_*.png
        demographics: output/demographic_aggregates.csv
        medians: output/medians.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, generate_summary_counts]
    outputs:
      moderately_sensitive:
        notebook: output/report.html

  generate_notebook_updating:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/report_updating.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_plots, generate_summary_counts]
    outputs:
      moderately_sensitive:
        notebook: output/report_updating.html

  generate_dem_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/demographic_report.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_plots]
    outputs:
      moderately_sensitive:
        notebook: output/demographic_report.html

  plot_Q1_comparisons:
    run: r:latest analysis/generate_demographic_slope_plot.R
    needs: [generate_plots]
    outputs:
      moderately_sensitive:
        plots: output/figures/SLOPE_*.png

  run_tests:
    run: python:latest python -m pytest --junit-xml=output/pytest.xml --verbose
    outputs:
      moderately_sensitive:
        log: output/pytest.xml

  test_population:
    run: python:latest python analysis/test_population.py
    needs: [filter_population]
    outputs:
      moderately_sensitive:
        counts: output/population_counts.csv
        count: output/patient_count_check.json

Timeline

Created: 1 year, 8 months ago 12 Apr 2023 15:47:37 UTC
Started: 1 year, 8 months ago 12 Apr 2023 21:51:07 UTC
Finished: 1 year, 8 months ago 14 Apr 2023 07:21:16 UTC
Runtime: 33:23:26

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

Job information

Status: Succeeded
Backend: TPP
Workspace: pincer-measures
Requested by: Rose Higgins
Branch: main
Force run dependencies: No
Git commit hash: 421f8d7
Requested actions: generate_study_population_5

join_ethnicity_region

filter_population

calculate_numerators

calculate_composite_indicators

generate_measures

generate_summary_counts

generate_plots

generate_notebook_updating

Code comparison

Compare the code used in this Job Request