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Job request: 25061

Organisation:
Bennett Institute
Workspace:
death-report
ID:
sxxw3duf7kfe63sp
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_date_diff:
    run: ehrql:v1 generate-dataset analysis/dataset_definition.py --output output/dataset_death_date_diff.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/dataset_death_date_diff.csv.gz
  
  summary_stat:
    run: r:v2 analysis/summary_stats.R
      --output output/DoD/summary_stats_DoD.csv 
    needs: [dataset_death_date_diff]
    outputs:
      moderately_sensitive:
        continuous: output/DoD/summary_stats_DoD.csv
        categorical: output/DoD/table_freq_DoD.csv

  table_DoD:
    run: r:v2 analysis/Table_DoD.R
      --output output/report/*.csv 
    needs: [dataset_death_date_diff]
    outputs:
      moderately_sensitive:
        categorical1: output/report/collate_death_source_table.csv
        categorical2: output/report/collate_DoD_diff_table.csv
        categorical3: output/report/collate_death_source_table_spec_periods.csv

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

# 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/measure_practice.py 
      --output output/measures/measures_by_practice.csv
    outputs:
      highly_sensitive:
        measure_csv: output/measures/measures_by_practice.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:16:30

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
Yes
Git commit hash
f787ce3
Requested actions
  • dataset_death_date_diff
  • summary_stat

Code comparison

Compare the code used in this job request