Job request: 4933

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Lisa Hopcroft requested one or more actions to be run against real patient data in the PINCER 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

ID Status Action
vpbgkgmny4kmxfmx succeeded combine_indicator_saturation_data
wt6obtjpletxjd73 succeeded generate_indicator_saturation_plots
sbyee64sriapighr succeeded indicator_saturation_a
n7bctjlbxc5hs4ud succeeded indicator_saturation_ac
hqnfnurfpy55r4cd succeeded indicator_saturation_am
62fc357vcare6msw succeeded indicator_saturation_b
wvrv43dkpzfjgkyq succeeded indicator_saturation_d
bp5ajc3effjo7jyv succeeded indicator_saturation_f
c52rlcc6x45llapn succeeded indicator_saturation_i
gng2qc3wfeb6wbkq succeeded indicator_saturation_li
rlwcz4hhga3ydv3u succeeded indicator_saturation_me_no_fbc

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 1000

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_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_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

  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
        

  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_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


  indicator_saturation_a:
    run: r:latest analysis/indicator_saturation_analysis.R -I a -T date -C practice -v -f -i output -o output/indicator_saturation measure_indicator_a_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation/indicator_saturation_*_a/summary_output.csv
        plot_csv: output/indicator_saturation/indicator_saturation_*_a/plot_data.csv
        coef_csv: output/indicator_saturation/indicator_saturation_*_a/coefficients_data.csv
        plot_png: output/indicator_saturation/indicator_saturation_*_a/figures/*.png

  indicator_saturation_b:
    run: r:latest analysis/indicator_saturation_analysis.R -I b -T date -C practice -v -f -i output -o output/indicator_saturation measure_indicator_b_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation/indicator_saturation_*_b/summary_output.csv
        plot_csv: output/indicator_saturation/indicator_saturation_*_b/plot_data.csv
        coef_csv: output/indicator_saturation/indicator_saturation_*_b/coefficients_data.csv
        plot_png: output/indicator_saturation/indicator_saturation_*_b/figures/*.png

  indicator_saturation_c:
    run: r:latest analysis/indicator_saturation_analysis.R -I c -T date -C practice -v -f -i output -o output/indicator_saturation measure_indicator_c_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation/indicator_saturation_*_c/summary_output.csv
        plot_csv: output/indicator_saturation/indicator_saturation_*_c/plot_data.csv
        coef_csv: output/indicator_saturation/indicator_saturation_*_c/coefficients_data.csv
        plot_png: output/indicator_saturation/indicator_saturation_*_c/figures/*.png

  indicator_saturation_d:
    run: r:latest analysis/indicator_saturation_analysis.R -I d -T date -C practice -v -f -i output -o output/indicator_saturation measure_indicator_d_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation/indicator_saturation_*_d/summary_output.csv
        plot_csv: output/indicator_saturation/indicator_saturation_*_d/plot_data.csv
        coef_csv: output/indicator_saturation/indicator_saturation_*_d/coefficients_data.csv
        plot_png: output/indicator_saturation/indicator_saturation_*_d/figures/*.png

  indicator_saturation_e:
    run: r:latest analysis/indicator_saturation_analysis.R -I e -T date -C practice -v -f -i output -o output/indicator_saturation measure_indicator_e_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation/indicator_saturation_*_e/summary_output.csv
        plot_csv: output/indicator_saturation/indicator_saturation_*_e/plot_data.csv
        coef_csv: output/indicator_saturation/indicator_saturation_*_e/coefficients_data.csv
        plot_png: output/indicator_saturation/indicator_saturation_*_e/figures/*.png

  indicator_saturation_f:
    run: r:latest analysis/indicator_saturation_analysis.R -I f -T date -C practice -v -f -i output -o output/indicator_saturation measure_indicator_f_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation/indicator_saturation_*_f/summary_output.csv
        plot_csv: output/indicator_saturation/indicator_saturation_*_f/plot_data.csv
        coef_csv: output/indicator_saturation/indicator_saturation_*_f/coefficients_data.csv
        plot_png: output/indicator_saturation/indicator_saturation_*_f/figures/*.png
        
  indicator_saturation_g:
    run: r:latest analysis/indicator_saturation_analysis.R -I g -T date -C practice -v -f -i output -o output/indicator_saturation measure_indicator_g_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation/indicator_saturation_*_g/summary_output.csv
        plot_csv: output/indicator_saturation/indicator_saturation_*_g/plot_data.csv
        coef_csv: output/indicator_saturation/indicator_saturation_*_g/coefficients_data.csv
        plot_png: output/indicator_saturation/indicator_saturation_*g/figures/*.png

  indicator_saturation_i:
    run: r:latest analysis/indicator_saturation_analysis.R -I i -T date -C practice -v -f -i output -o output/indicator_saturation measure_indicator_i_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation/indicator_saturation_*_i/summary_output.csv
        plot_csv: output/indicator_saturation/indicator_saturation_*_i/plot_data.csv
        coef_csv: output/indicator_saturation/indicator_saturation_*_i/coefficients_data.csv
        plot_png: output/indicator_saturation/indicator_saturation_*_i/figures/*.png

  indicator_saturation_k:
    run: r:latest analysis/indicator_saturation_analysis.R -I k -T date -C practice -v -f -i output -o output/indicator_saturation measure_indicator_k_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation/indicator_saturation_*_k/summary_output.csv
        plot_csv: output/indicator_saturation/indicator_saturation_*_k/plot_data.csv
        coef_csv: output/indicator_saturation/indicator_saturation_*_k/coefficients_data.csv
        plot_png: output/indicator_saturation/indicator_saturation_*_k/figures/*.png

  indicator_saturation_ac:
    run: r:latest analysis/indicator_saturation_analysis.R -I ac -T date -C practice -v -f -i output -o output/indicator_saturation measure_indicator_ac_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation/indicator_saturation_*_ac/summary_output.csv
        plot_csv: output/indicator_saturation/indicator_saturation_*_ac/plot_data.csv
        coef_csv: output/indicator_saturation/indicator_saturation_*_ac/coefficients_data.csv
        plot_png: output/indicator_saturation/indicator_saturation_*_ac/figures/*.png

  indicator_saturation_me_no_fbc:
    run: r:latest analysis/indicator_saturation_analysis.R -I me_no_fbc -T date -C practice -B indicator_me_denominator -v -f -i output -o output/indicator_saturation measure_indicator_me_no_fbc_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation/indicator_saturation_*_me_no_fbc/summary_output.csv
        plot_csv: output/indicator_saturation/indicator_saturation_*_me_no_fbc/plot_data.csv
        coef_csv: output/indicator_saturation/indicator_saturation_*_me_no_fbc/coefficients_data.csv
        plot_png: output/indicator_saturation/indicator_saturation_*_me_no_fbc/figures/*.png
        
  indicator_saturation_me_no_lft:
    run: r:latest analysis/indicator_saturation_analysis.R -I me_no_lft -T date -C practice -B indicator_me_denominator -v -f -i output -o output/indicator_saturation measure_indicator_me_no_lft_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation/indicator_saturation_*_me_no_lft/summary_output.csv
        plot_csv: output/indicator_saturation/indicator_saturation_*_me_no_lft/plot_data.csv
        coef_csv: output/indicator_saturation/indicator_saturation_*_me_no_lft/coefficients_data.csv
        plot_png: output/indicator_saturation/indicator_saturation_*_me_no_lft/figures/*.png

  indicator_saturation_li:
    run: r:latest analysis/indicator_saturation_analysis.R -I li -T date -C practice -v -f -i output -o output/indicator_saturation measure_indicator_li_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation/indicator_saturation_*_li/summary_output.csv
        plot_csv: output/indicator_saturation/indicator_saturation_*_li/plot_data.csv
        coef_csv: output/indicator_saturation/indicator_saturation_*_li/coefficients_data.csv
        plot_png: output/indicator_saturation/indicator_saturation_*_li/figures/*.png

  indicator_saturation_am:
    run: r:latest analysis/indicator_saturation_analysis.R -I am -T date -C practice -v -f -i output -o output/indicator_saturation measure_indicator_am_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation/indicator_saturation_*_am/summary_output.csv
        plot_csv: output/indicator_saturation/indicator_saturation_*_am/plot_data.csv
        coef_csv: output/indicator_saturation/indicator_saturation_*_am/coefficients_data.csv
        plot_png: output/indicator_saturation/indicator_saturation_*_am/figures/*.png

  combine_indicator_saturation_data:
    run: r:latest analysis/combine_indicator_saturation_output.R output/indicator_saturation output/indicator_saturation/combined
    needs: [indicator_saturation_a, indicator_saturation_b, indicator_saturation_c, indicator_saturation_d, indicator_saturation_e, indicator_saturation_f, indicator_saturation_g, indicator_saturation_i, indicator_saturation_k, indicator_saturation_ac, indicator_saturation_me_no_fbc, indicator_saturation_me_no_lft, indicator_saturation_li, indicator_saturation_am]
    outputs:
      moderately_sensitive:
        counts: output/indicator_saturation/combined/*.csv
        # plots: output/indicator_saturation/combined/CDPLOT_*.png
        # summary: output/indicator_saturation/combined/SUMMARY_*.png
        # Rdat: output/indicator_saturation/combined/ANALYSIS_OUTPUT.Rdat
  
  generate_indicator_saturation_plots:
    run: r:latest analysis/generate_indicator_saturation_plots.R output/indicator_saturation output/indicator_saturation/combined
    needs: [combine_indicator_saturation_data]
    outputs:
      moderately_sensitive:
        breakcount_plots: output/indicator_saturation/combined/BREAK-COUNT_*.png
        breakmagnitude_plots: output/indicator_saturation/combined/BREAK-MAGNITUDE_*.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

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 25:01:48

Config

  • Backend:
    TPP
  • Workspace:
    pincer-measures-change-detection
  • Branch:
    main
  • Creator:
    LisaHopcroft
  • Force run dependencies:
    False
  • Git Commit Hash:
    8fd2867
  • Requested actions:
    • indicator_saturation_a
    • indicator_saturation_b
    • indicator_saturation_d
    • indicator_saturation_f
    • indicator_saturation_i
    • indicator_saturation_ac
    • indicator_saturation_me_no_fbc
    • indicator_saturation_li
    • indicator_saturation_am
    • combine_indicator_saturation_data
    • generate_indicator_saturation_plots