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Job request: 22483

Organisation:
Nuffield Trust
Workspace:
end-of-life-carequality
ID:
vdntz2z6ldzwpkpp
View repo View project.yaml

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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:14:55

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

Job request

Status
Succeeded
Backend
TPP
Workspace
end-of-life-carequality
Requested by
Miranda Davies
Branch
main
Force run dependencies
No
Git commit hash
78008d9
Requested actions
  • generate_study_population_os_reports
  • WP3_descriptive_outputs

Code comparison

Compare the code used in this job request