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Job request: 25617

Organisation:
Bennett Institute
Workspace:
death-report
ID:
vr7xfa7qgs2xeb3o
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Martina Pesce 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: '4.0'

actions:
#Dataset for diff time
  dataset_death_TPP_ONS:
    run: ehrql:v1 generate-dataset analysis/dataset_def/dataset_definition.py --output output/highly_sensitive/dataset_death_TPP_ONS.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/highly_sensitive/dataset_death_TPP_ONS.csv.gz
  
  summary_stat:
    run: r:v2 analysis/1_summary_stats.R
      --output output/summary_stats/*.csv 
    needs: [dataset_death_TPP_ONS]
    outputs:
      moderately_sensitive:
        tables: output/summary_stats/*.csv

  reg_dereg_ONS_TPP:
    run: r:v2 analysis/2_tables_ONS_TPP_reg_dereg.R 
      --output output/report/reg_dereg_ONS_TPP/*.csv 
    needs: [dataset_death_TPP_ONS]
    outputs:
      moderately_sensitive:
        csv: output/report/reg_dereg_ONS_TPP/*.csv

  Dataset_source_dod_diff_processed:
    run: r:v2 analysis/3_dataset_DoD_TPP_ONS_with_grace_period.R
      --output output/highly_sensitive/DoD_TPP_ONS_with_grace_period.csv
    needs: [dataset_death_TPP_ONS]
    outputs:
      highly_sensitive:
        csv: output/highly_sensitive/DoD_TPP_ONS_with_grace_period.csv

  death_source:
    run: r:v2 analysis/4_source_prop.R
      --output output/report/by_source/*.csv 
    needs: [Dataset_source_dod_diff_processed]
    outputs:
      moderately_sensitive:
        csv: output/report/by_source/*.csv

  DoD_difference:
    run: r:v2 analysis/5_DoD_diff.R
      --output output/report/DoD_diff/*.csv 
    needs: [Dataset_source_dod_diff_processed]
    outputs:
      moderately_sensitive:
        csv: output/report/DoD_diff/*.csv
        
# Measures
  # measures_overall:
  #   run: ehrql:v1 generate-measures analysis/measure_def.py 
  #     --output output/measures/measures_overall.csv
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: output/measures/measures_overall.csv
  
  # table_measure_rate:
  #   run: r:v2 analysis/Table_measure_rate.R
  #     --output output/report/*.csv 
  #   needs: [measures_overall]
  #   outputs:
  #     moderately_sensitive:
  #       categorical: output/report/collate_measures_rate_table.csv

  measures_by_practice:
    run: ehrql:v1 generate-measures analysis/dataset_def/measure_practice.py 
      --output output/highly_sensitive/measures_by_practice.csv
    outputs:
      highly_sensitive:
        measure_csv: output/highly_sensitive/measures_by_practice.csv

  decile_table_figure:
    run:  r:v2 analysis/6_practice_by_source.R
    needs: [measures_by_practice]
    outputs:
      moderately_sensitive:
        csv: output/report/source_by_practice/*.csv
        png: output/report/source_by_practice/*.png  


  # visualization:
  #   run:  r:v2 Final-visualizations.R
  #   needs: [table_DoD]
  #   outputs:
  #     moderately_sensitive:
  #       csv: output/final_visualization/*.csv
  #       png: output/final_visualization/*.png 

#

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:13

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

Job request

Status
Succeeded
Backend
TPP
Workspace
death-report
Requested by
Martina Pesce
Branch
main
Force run dependencies
No
Git commit hash
6abcf63
Requested actions
  • reg_dereg_ONS_TPP

Code comparison

Compare the code used in this job request