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Job request: 22858

Organisation:
Nuffield Trust
Workspace:
end-of-life-carequality
ID:
dgvwgtysaucee4u5
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Sophie Julian requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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_MAIHDA_outputs:
    run: r:latest analysis/os_reports/07_eol_WP3_MAIHDA.R
    needs: [generate_study_population_os_reports]
    outputs:
      moderately_sensitive:
        descriptive_Mean_Gp: output/os_reports/WP3/GLM_GP*.csv
        descriptive_gpbeta0: output/os_reports/WP3/GPbeta0.csv
        descriptive_gpsigma2u: output/os_reports/WP3/GPsigma2u.csv
        descriptive_gpexpectation: output/os_reports/WP3/GPexpectation.csv
        descriptive_gpvariance: output/os_reports/WP3/GPvariance.csv
        descriptive_gpvariance2: output/os_reports/WP3/GPvariance2.csv
        descriptive_gpvariance1: output/os_reports/WP3/GPvariance1.csv
        descriptive_gpvpc2: output/os_reports/WP3/GPvpc2.csv
        descriptive_gpvpc1: output/os_reports/WP3/GPvpc1.csv

  WP3_MAIHDA_outputs_OP:
    run: r:latest analysis/os_reports/08_eol_WP3_MAIHDA_opapp.R
    needs: [generate_study_population_os_reports]
    outputs:
      moderately_sensitive:
        descriptive_beta0: output/os_reports/WP3/OP*.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: 00:01:38

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
Sophie Julian
Branch
main
Force run dependencies
No
Git commit hash
9709097
Requested actions
  • WP3_MAIHDA_outputs_OP

Code comparison

Compare the code used in this Job Request