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Job request: 25005

Organisation:
Bennett Institute
Workspace:
pifu-data-exploration
ID:
ogpzgy7vqs5zknjs
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Andrea Schaffer 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: '4.0'

actions:
  generate_dataset_explore:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_explore.py --output output/dataset_explore.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/dataset_explore.csv.gz

  table_explore:
    run: r:latest analysis/process/data_exploration.R
    needs: [generate_dataset_explore]
    outputs:
      moderately_sensitive:
        table1: output/processed/table_explore.csv
        #table2: output/processed/table_pfu_explore.csv
        table3: output/processed/counts_explore.csv

  generate_dataset:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_everyone.py --output output/dataset_everyone.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/dataset_everyone.csv.gz
  
  generate_dataset_rheum:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_rheum.py --output output/dataset_rheum.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/dataset_rheum.csv.gz

  measures:
    run: ehrql:v1 generate-measures analysis/measures.py --output output/measures/measures.csv
    outputs:
      moderately_sensitive:
        dataset: output/measures/measures.csv

  measures_london:
    run: ehrql:v1 generate-measures analysis/measures_region.py --output output/measures/measures_london.csv 
      -- 
      --param_region London
    outputs:
      moderately_sensitive:
        dataset: output/measures/measures_london.csv

  measures_northeast:
    run: ehrql:v1 generate-measures analysis/measures_region.py --output output/measures/measures_northeast.csv 
      -- 
      --param_region 'North East'
    outputs:
      moderately_sensitive:
        dataset: output/measures/measures_northeast.csv

  measures_northwest:
    run: ehrql:v1 generate-measures analysis/measures_region.py --output output/measures/measures_northwest.csv 
      -- 
      --param_region 'North West'
    outputs:
      moderately_sensitive:
        dataset: output/measures/measures_northwest.csv

  measures_yorkshire:
    run: ehrql:v1 generate-measures analysis/measures_region.py --output output/measures/measures_yorkshire.csv 
      --
      --param_region 'Yorkshire and The Humber'
    outputs:
      moderately_sensitive:
        dataset: output/measures/measures_yorkshire.csv

  measures_eastmidlands:
    run: ehrql:v1 generate-measures analysis/measures_region.py --output output/measures/measures_eastmidlands.csv 
      --
      --param_region 'East Midlands'
    outputs:
      moderately_sensitive:
        dataset: output/measures/measures_eastmidlands.csv

  measures_westmidlands:
    run: ehrql:v1 generate-measures analysis/measures_region.py --output output/measures/measures_westmidlands.csv 
      -- 
      --param_region 'West Midlands'
    outputs:
      moderately_sensitive:
        dataset: output/measures/measures_westmidlands.csv

  measures_east:
    run: ehrql:v1 generate-measures analysis/measures_region.py --output output/measures/measures_east.csv 
      --
      --param_region East
    outputs:
      moderately_sensitive:
        dataset: output/measures/measures_east.csv

  measures_southeast:
    run: ehrql:v1 generate-measures analysis/measures_region.py --output output/measures/measures_southeast.csv 
      --
      --param_region 'South East'
    outputs:
      moderately_sensitive:
        dataset: output/measures/measures_southeast.csv

  measures_southwest:
    run: ehrql:v1 generate-measures analysis/measures_region.py --output output/measures/measures_southwest.csv 
      --
      --param_region 'South West'
    outputs:
      moderately_sensitive:
        dataset: output/measures/measures_southwest.csv

  table:
    run: r:latest analysis/process/pop_characteristics.R
    needs: [generate_dataset, generate_dataset_rheum]
    outputs:
      moderately_sensitive:
        table1: output/processed/table.csv
        table2: output/processed/table_pfu.csv
        table3: output/processed/table_rheum.csv

  time_series:
    run: r:latest analysis/process/measures_process.R
    needs: [measures]
    outputs:
      moderately_sensitive:
        timeseries1: output/processed/time_series_overall.csv
        timeseries2: output/processed/time_series_specialty.csv
  
  time_series_region:
    run: r:latest analysis/process/measures_region_process.R
    needs: [measures_london, measures_east, measures_eastmidlands, measures_northeast, measures_northwest, measures_southeast, measures_southwest, measures_westmidlands, measures_yorkshire]
    outputs:
      moderately_sensitive:
        timeseries1: output/processed/ts_*.csv
        timeseries2: output/processed/ts_sp*.csv

  visits:
    run: r:latest analysis/process/visit_stats.R
    needs: [generate_dataset_rheum]
    outputs:
      moderately_sensitive:
        table: output/processed/visit_stats.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 88:45:47

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

Job information

Status
Succeeded
Backend
TPP
Workspace
pifu-data-exploration
Requested by
Andrea Schaffer
Branch
main
Force run dependencies
No
Git commit hash
369d96f
Requested actions
  • measures_london
  • measures_northeast
  • measures_northwest
  • measures_yorkshire
  • measures_eastmidlands
  • measures_westmidlands
  • measures_east
  • measures_southeast
  • measures_southwest
  • time_series_region

Code comparison

Compare the code used in this Job Request