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Job request: 23062

Organisation:
Nuffield Trust
Workspace:
end-of-life-carequality
ID:
cchnordc6cnv36ph
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

  • Action:
    generate_study_population_os_reports
    Status:
    Status: Failed
    Job identifier:
    c7rozemqq3adif6n
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    WP3_descriptives
    Status:
    Status: Failed
    Job identifier:
    cgdhsj5rqstnb37q
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    WP3_MAIHDA_outputs_AE
    Status:
    Status: Failed
    Job identifier:
    nhn57tvktpmmmarm
    Error:
    cancelled_by_user: Cancelled by user

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_descriptives:
    run: r:latest analysis/os_reports/07_WP3_Additional_Descriptives.R
    needs: [generate_study_population_os_reports]
    outputs:
      moderately_sensitive:
        descriptive_codeGP: output/os_reports/WP3/gp*.csv
        descriptive_codeAE: output/os_reports/WP3/aevis*.csv

  WP3_MAIHDA_outputs_AE:
    run: r:latest analysis/os_reports/06_WP3_MAIHDA_A&E.R
    needs: [generate_study_population_os_reports]
    outputs:
      moderately_sensitive:
        descriptive_AEMAIHDA: output/os_reports/WP3/AE*.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
      
  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:
        model_outputs: output/os_reports/WP3/OP*.csv
        model_graph_outputs: output/os_reports/WP3/OP*.png

Timeline

  • Created:

  • Finished:

  • Runtime:

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
7c8e3fc
Requested actions
  • generate_study_population_os_reports
  • WP3_descriptives
  • WP3_MAIHDA_outputs_AE

Code comparison

Compare the code used in this job request