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Job request: 9339

Organisation:
Bennett Institute
Workspace:
opensafely-interactive
ID:
yxegyr6guoufruy7
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Lucy Bridges requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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: '3.0'

expectations:
  population_size: 1000

actions:

  codelist_report_02q87lMmz98GXYLAAzgj0I:
    run: >
      cohortextractor:latest generate_codelist_report
        --codelist-path=codelist.csv
        --start-date=2019-09-01
        --end-date=2022-06-08
        --output-dir output/02q87lMmz98GXYLAAzgj0I
    outputs:
      moderately_sensitive:
        table: output/02q87lMmz98GXYLAAzgj0I/counts_per_*.csv
        list_sizes: output/02q87lMmz98GXYLAAzgj0I/list_sizes.csv
        patient_count_table: output/02q87lMmz98GXYLAAzgj0I/patient_count.csv

  measures_02q87lMmz98GXYLAAzgj0I:
    run: python:latest python analysis/generate_measures.py output/02q87lMmz98GXYLAAzgj0I
    needs: [codelist_report_02q87lMmz98GXYLAAzgj0I]
    outputs:
      moderately_sensitive:
        measure: output/02q87lMmz98GXYLAAzgj0I/measure_counts_per_week_per_practice.csv
        events_count_table: output/02q87lMmz98GXYLAAzgj0I/event_counts.csv
        practice_count_table: output/02q87lMmz98GXYLAAzgj0I/practice_count.csv

  top_5_table_02q87lMmz98GXYLAAzgj0I:
    run: python:latest python analysis/top_codes_table.py output/02q87lMmz98GXYLAAzgj0I
    needs: [codelist_report_02q87lMmz98GXYLAAzgj0I]
    outputs:
      moderately_sensitive:
        table: output/02q87lMmz98GXYLAAzgj0I/top_5_code_table.csv

  deciles_charts_02q87lMmz98GXYLAAzgj0I:
    run: >
      deciles-charts:v0.0.24
        --input-files output/02q87lMmz98GXYLAAzgj0I/measure_counts_per_week_per_practice.csv
        --output-dir output/02q87lMmz98GXYLAAzgj0I
    config:
      show_outer_percentiles: false
      tables:
        output: true
      charts:
        output: true
    needs: [measures_02q87lMmz98GXYLAAzgj0I]
    outputs:
      moderately_sensitive:
        deciles_charts: output/02q87lMmz98GXYLAAzgj0I/deciles_*.*

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:06:07

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

Job information

Status
Succeeded
Backend
TPP
Workspace
opensafely-interactive
Requested by
Lucy Bridges
Branch
main
Force run dependencies
No
Git commit hash
03550a3
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request