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Job request: 22589

Organisation:
Nuffield Trust
Workspace:
end-of-life-carequality
ID:
4yffpq3vclmiay4q
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Miranda Davies 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: 10000

actions:   

  generate_study_population_os_reports:
    run: ehrql:v0 generate-dataset analysis/os_reports/dataset_definition_os_reports.py --output output/os_reports/input_os_reports.csv.gz
    outputs:
      highly_sensitive:
        cohort: output/os_reports/input_os_reports.csv.gz
           
  os_report_csvs:
    run: r:latest analysis/os_reports/01_eol_service_Descriptives_csvs.R
    needs: [generate_study_population_os_reports]
    outputs:
      moderately_sensitive:
        monthly_deaths_Number: output/os_reports/eol_service/deaths_month*.csv
        monthly_gp_CSV: output/os_reports/eol_service/gp_month*.csv
        monthly_gp_Count: output/os_reports/eol_service/gp_count*.csv
        monthly_med_CSV: output/os_reports/eol_service/eol_med*.csv
        monthly_med_Count: output/os_reports/eol_service/eol_med_count*.csv
        monthly_aevis_CSV: output/os_reports/eol_service/aevis_month*.csv
        monthly_aevis_Count: output/os_reports/eol_service/aevis_count*.csv        
        monthly_op_CSV: output/os_reports/eol_service/opapp_month*.csv
        monthly_op_Count: output/os_reports/eol_service/opapp_count*.csv  
        monthly_eladm_CSV: output/os_reports/eol_service/eladm_month*.csv
        monthly_eladm_Count: output/os_reports/eol_service/eladm_count*.csv
        quarterly_eladm_Count: output/os_reports/eol_service/eladm_quarter*.csv  
        monthly_emadm_CSV: output/os_reports/eol_service/emadm_month*.csv
        monthly_emadm_Count: output/os_reports/eol_service/emadm_count*.csv
        monthly_nursing_CSV: output/os_reports/eol_service/nursing_month*.csv 
        montly_nursing_Count: output/os_reports/eol_service/nursing_count*.csv
        quarterly_nursing_Count: output/os_reports/eol_service/nursing_quarter*.csv

  os_report_charts:
    run: r:latest analysis/os_reports/02_eol_service_Descriptive_outputs.R
    needs: [os_report_csvs]
    outputs:
      moderately_sensitive:
        monthly_deaths_cod: output/os_reports/eol_service/charts/deaths_cod*.png
        monthly_deaths_place: output/os_reports/eol_service/charts/deaths_place*.png
        monthly_gp_cod: output/os_reports/eol_service/charts/gp_cod*.png
        monthly_gp_place: output/os_reports/eol_service/charts/gp_place*.png
        monthly_med_cod: output/os_reports/eol_service/charts/eol_med_cod*.png
        monthly_med_place: output/os_reports/eol_service/charts/eol_med_place*.png
        monthly_aevis_cod: output/os_reports/eol_service/charts/aevis_cod*.png 
        monthly_aevis_place: output/os_reports/eol_service/charts/aevis_place*.png 
        monthly_op_cod: output/os_reports/eol_service/charts/opapp_cod*.png
        monthly_op_place: output/os_reports/eol_service/charts/opapp_place*.png
        monthly_eladm_cod: output/os_reports/eol_service/charts/eladm_cod*.png
        monthly_eladm_place: output/os_reports/eol_service/charts/eladm_place*.png      
        monthly_emadm_cod: output/os_reports/eol_service/charts/emadm_cod*.png
        monthly_emadm_place: output/os_reports/eol_service/charts/emadm_place*.png
        monthly_nursing_cod: output/os_reports/eol_service/charts/nursing_cod*.png 
        monthly_nursing_place: output/os_reports/eol_service/charts/nursing_place*.png
        
  WP2_outputs:
    run: r:latest analysis/os_reports/03_eol_WP2_quality_indicators.R
    needs: [generate_study_population_os_reports]
    outputs:
      moderately_sensitive:
        proportion_palcare_code: output/os_reports/WP2_quality_indicators/palcare*.csv
        proportion_aeviv1: output/os_reports/WP2_quality_indicators/aevis1*.csv
        proportion_aevis3: output/os_reports/WP2_quality_indicators/aevis3*.csv
        proportion_eolmed: output/os_reports/WP2_quality_indicators/eolmed*.csv
        proportion_specpal_code: output/os_reports/WP2_quality_indicators/specpal*.csv
        proportion_cancer_palcare: output/os_reports/WP2_quality_indicators/cancer*.csv   

  WP2_outputs_advance_care_plan:
    run: r:latest analysis/os_reports/05_eol_WP2_advance_care_plan_measures.R
    needs: [generate_study_population_os_reports]
    outputs:
      moderately_sensitive:
        acp_code: output/os_reports/WP2_quality_indicators/acp*.csv
        acp3m_code: output/os_reports/WP2_quality_indicators/acp3m*.csv
        acpdur_code: output/os_reports/WP2_quality_indicators/acpdur*.csv

  WP3_descriptive_outputs:
    run: r:latest analysis/os_reports/07_eol_WP3_MAIHDA.R
    needs: [generate_study_population_os_reports]
    outputs:
      moderately_sensitive:
        descriptive_stats: output/os_reports/WP3/count*.csv
        descriptive_means: output/os_reports/WP3/GLM*.csv

  WP3_ethnicity_outputs:
    run: r:latest analysis/os_reports/09_eol_Ethnicity_breakdown.R
    needs: [generate_study_population_os_reports]
    outputs:
      moderately_sensitive:
        descriptive_ethnicity: output/os_reports/WP3/ethnicity*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:06:08

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

Job information

Status
Succeeded
Backend
TPP
Workspace
end-of-life-carequality
Requested by
Miranda Davies
Branch
main
Force run dependencies
No
Git commit hash
1c50a4a
Requested actions
  • generate_study_population_os_reports
  • WP3_ethnicity_outputs

Code comparison

Compare the code used in this Job Request