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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 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

  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 request

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