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Job request: 4057

Organisation:
DataLab
Workspace:
pincer-measures
ID:
6owmsdmeytxgkha6
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 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

Pipeline

Show 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 2020-12-01 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 "2021-01-01 to 2021-07-01 by month" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/inpu*.feather
  

  check_EGFR:
    run: python:latest python analysis/check_EGFR.py
    needs: [join_ethnicity_region]
    outputs:
      moderately_sensitive:
        counts: output/egfr_tabulation.csv

  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

  generate_study_population_lithium:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_lithium --index-date-range "2019-09-01 to 2021-07-01 by month" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_lithium_*.feather

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

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

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

  
  check_asthma:
    run: python:latest python analysis/check_asthma.py
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        csv: output/asthma_sum.csv
  
  generate_measures_demographics:
    run: python:latest python analysis/calculate_measures.py
    needs: [calculate_numerators, join_ethnicity_region, generate_study_population_lithium]
    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: [join_ethnicity_region, generate_measures, generate_measures_demographics, calculate_numerators, generate_study_population_lithium]
    outputs:
      highly_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

  cusum:
    run: python:latest python analysis/cusum.py
    needs: [generate_measures, generate_measures_demographics]
    outputs:
      moderately_sensitive:
        cusum: output/cusum/cusum_results.json
        alerts: output/cusum/cusum_alerts_summary.json
        by_date: output/cusum/cusum_alerts_by_date.json
  
  plot_cusum:
    run: python:latest python analysis/plot_cusum.py
    needs: [cusum, generate_measures, generate_measures_demographics]
    outputs:
      moderately_sensitive:
        cusum: output/cusum/cusum/cusum_indicator_*.jpeg
        alert: output/cusum/alerts/alerts_indicator_*.jpeg
        combined_cusum: output/cusum/combined_cusum_count.png
  
  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

  indicator_saturation_a:
    run: r:latest analysis/indicator_saturation_analysis.R -I a -T date -C practice -v -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

  indicator_saturation_b:
    run: r:latest analysis/indicator_saturation_analysis.R -I b -T date -C practice -v -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

  indicator_saturation_c:
    run: r:latest analysis/indicator_saturation_analysis.R -I c -T date -C practice -v -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

  indicator_saturation_d:
    run: r:latest analysis/indicator_saturation_analysis.R -I d -T date -C practice -v -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

  indicator_saturation_e:
    run: r:latest analysis/indicator_saturation_analysis.R -I e -T date -C practice -v -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

  indicator_saturation_f:
    run: r:latest analysis/indicator_saturation_analysis.R -I f -T date -C practice -v -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
        
  indicator_saturation_g:
    run: r:latest analysis/indicator_saturation_analysis.R -I g -T date -C practice -v -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

  indicator_saturation_i:
    run: r:latest analysis/indicator_saturation_analysis.R -I i -T date -C practice -v -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

  indicator_saturation_k:
    run: r:latest analysis/indicator_saturation_analysis.R -I k -T date -C practice -v -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

  indicator_saturation_ac:
    run: r:latest analysis/indicator_saturation_analysis.R -I ac -T date -C practice -v -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

  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 -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
        
  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 -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

  indicator_saturation_li:
    run: r:latest analysis/indicator_saturation_analysis.R -I li -T date -C practice -v -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

  indicator_saturation_am:
    run: r:latest analysis/indicator_saturation_analysis.R -I am -T date -C practice -v -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

  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:
        plots: output/indicator_saturation/combined/BREAK-COUNT_*.png
  
###
### REVERSED ANALYSIS
###

  indicator_saturation_a_rev:
    run: r:latest analysis/indicator_saturation_analysis.R -I a -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_a_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation_rev/indicator_saturation_*_a/*.csv
        
  indicator_saturation_b_rev:
    run: r:latest analysis/indicator_saturation_analysis.R -I b -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_b_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation_rev/indicator_saturation_*_b/*.csv

  indicator_saturation_c_rev:
    run: r:latest analysis/indicator_saturation_analysis.R -I c -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_c_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation_rev/indicator_saturation_*_c/*.csv

  indicator_saturation_d_rev:
    run: r:latest analysis/indicator_saturation_analysis.R -I d -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_d_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation_rev/indicator_saturation_*_d/*.csv

  indicator_saturation_e_rev:
    run: r:latest analysis/indicator_saturation_analysis.R -I e -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_e_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation_rev/indicator_saturation_*_e/*.csv


  indicator_saturation_f_rev:
    run: r:latest analysis/indicator_saturation_analysis.R -I f -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_f_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation_rev/indicator_saturation_*_f/*.csv
        
  indicator_saturation_g_rev:
    run: r:latest analysis/indicator_saturation_analysis.R -I g -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_g_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation_rev/indicator_saturation_*_g/*.csv

  indicator_saturation_i_rev:
    run: r:latest analysis/indicator_saturation_analysis.R -I i -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_i_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation_rev/indicator_saturation_*_i/*.csv

  indicator_saturation_k_rev:
    run: r:latest analysis/indicator_saturation_analysis.R -I k -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_k_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation_rev/indicator_saturation_*_k/*.csv

  indicator_saturation_ac_rev:
    run: r:latest analysis/indicator_saturation_analysis.R -I ac -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_ac_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation_rev/indicator_saturation_*_ac/*.csv

  indicator_saturation_am_rev:
    run: r:latest analysis/indicator_saturation_analysis.R -I am -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_am_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation_rev/indicator_saturation_*_am/*.csv

  indicator_saturation_li_rev:
    run: r:latest analysis/indicator_saturation_analysis.R -I li -T date -C practice -v -Q -i output -o output/indicator_saturation_rev measure_indicator_li_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation_rev/indicator_saturation_*_li/*.csv

  indicator_saturation_me_no_fbc_rev:
    run: r:latest analysis/indicator_saturation_analysis.R -I me_no_fbc -T date -C practice -B indicator_me_denominator -v -Q -i output -o output/indicator_saturation_rev measure_indicator_me_no_fbc_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation_rev/indicator_saturation_*_me_no_fbc/*.csv

  indicator_saturation_me_no_lft_rev:
    run: r:latest analysis/indicator_saturation_analysis.R -I me_no_lft -T date -C practice -B indicator_me_denominator -v -Q -i output -o output/indicator_saturation_rev measure_indicator_me_no_lft_rate.csv 
    needs: [generate_measures, generate_measures_demographics, calculate_composite_indicators]
    outputs:
      moderately_sensitive:
        out_csv: output/indicator_saturation_rev/indicator_saturation_*_me_no_lft/*.csv

  combine_indicator_saturation_data_rev:
    run: r:latest analysis/combine_indicator_saturation_output.R output/indicator_saturation_rev output/indicator_saturation_rev/combined
    needs: [indicator_saturation_a_rev, indicator_saturation_b_rev, indicator_saturation_c_rev, indicator_saturation_d_rev, indicator_saturation_e_rev, 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_rev/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_rev:
    run: r:latest analysis/generate_indicator_saturation_plots.R output/indicator_saturation_rev output/indicator_saturation_rev/combined
    needs: [combine_indicator_saturation_data_rev]
    outputs:
      moderately_sensitive:
        plots: output/indicator_saturation_rev/combined/BREAK-COUNT_*.png






  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: 00:00:40

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
Lisa Hopcroft
Branch
main
Force run dependencies
No
Git commit hash
f43a481
Requested actions
  • combine_indicator_saturation_data_rev
  • generate_indicator_saturation_plots_rev