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Job request: 7721

Organisation:
Bennett Institute
Workspace:
test-interactive
ID:
5gxeemcshxrpmf3h
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher 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: '3.0'

expectations:
  population_size: 1000

actions:
  
  generate_codelist_report:
    run: >
      cohortextractor:latest generate_codelist_report
        --output-dir=output
        --codelist-path=codelists/opensafely-systolic-blood-pressure-qof.csv
        --start-date=2021-01-01
        --end-date=2021-12-31
    outputs:
      moderately_sensitive:
        table: output/counts_per_*.csv
        list_sizes: output/list_sizes.csv

  generate_dummy_data:
    run: python:latest python analysis/generate_dummy_data.py
    outputs:
      moderately_sensitive:
        weekly: output/dummy/counts_per_code.csv
        codes: output/dummy/counts_per_week_per_practice.csv

  generate_measures:
    run: python:latest python analysis/generate_measures.py
    needs: [generate_codelist_report]
    outputs:
      moderately_sensitive:
        measure: output/measure_counts_per_week_per_practice.csv
        event_counts: output/event_counts.csv

  generate_top_5_table:
    run: python:latest python analysis/top_codes_table.py
    needs: [generate_codelist_report]
    outputs:
      moderately_sensitive:
        table: output/top_5_code_table.csv

  generate_deciles_charts:
    run: >
      deciles-charts:v0.0.15
        --input-files output/measure_counts_per_week_per_practice.csv
        --output-dir output
    config:
      show_outer_percentiles: false
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        deciles_charts: output/deciles_*_*.*

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:18

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

Job request

Status
Succeeded
Backend
TPP
Workspace
test-interactive
Requested by
Louis Fisher
Branch
main
Force run dependencies
No
Git commit hash
70d1937
Requested actions
  • generate_top_5_table

Code comparison

Compare the code used in this job request