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Job request: 22754

Organisation:
Nuffield Trust
Workspace:
end-of-life-carequality
ID:
36gbcpkry7zuiyfs
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_MAIHDA_outputs:
    run: r:latest analysis/os_reports/07_eol_WP3_MAIHDA.R
    needs: [generate_study_population_os_reports]
    outputs:
      moderately_sensitive:
        descriptive_beta: output/os_reports/WP3/beta.csv
        descriptive_sigma2u: output/os_reports/WP3/sigma2u.csv
        descriptive_expectation: output/os_reports/WP3/expectation.csv
        descriptive_variance: output/os_reports/WP3/variance.csv
        descriptive_variance2: output/os_reports/WP3/variance2.csv
        descriptive_variance1: output/os_reports/WP3/variance1.csv
        descriptive_vpc2: output/os_reports/WP3/vpc2.csv
        descriptive_vpc1: output/os_reports/WP3/vpc1.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: 00:10:04

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

Job information

Status
Failed
Backend
TPP
Workspace
end-of-life-carequality
Requested by
Miranda Davies
Branch
main
Force run dependencies
No
Git commit hash
7c51f51
Requested actions
  • generate_study_population_os_reports
  • WP3_MAIHDA_outputs

Code comparison

Compare the code used in this Job Request