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Job request: 5058

Organisation:
Bennett Institute
Workspace:
med-safety-poc
ID:
b2ykrpif7o7lq24o
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Emmanuel Bessah 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: 5000

actions:

  # generate_study_population_ce1:
  #   run: cohortextractor:latest generate_cohort --study-definition study_definition_ce1_for_ce2 --index-date-range "2020-01-01 to 2020-12-01 by month"
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/ce1/input_ce1_for_ce2_*.csv

  generate_study_population_ce2:
    run: cohortextractor-v2:latest generate_cohort --cohort-definition analysis/study_definition_ce2.py --output output/ce2/input_ce2_*.csv --dummy-data-file output/ce1/input_expanded_ce1_for_ce2_*.csv
    outputs:
      highly_sensitive:
        cohort: output/ce2/input_ce2_*.csv


  validate_cohort_v2:
    run: cohortextractor-v2:latest validate_cohort databricks --cohort-definition analysis/study_definition_ce2.py --output output/ce2/sql/generated_sql_*.sql
    outputs:
      moderately_sensitive:
        cohort: output/ce2/sql/generated_sql_*.sql


  add_practice_ids:
    run: python:latest python analysis/add_practice_ids.py
    needs: [generate_study_population_ce2]
    outputs:
      moderately_sensitive:
        cohort: output/ce2/input_expanded_ce2_*.csv


  generate_measures:
    run: cohortextractor-v2:latest generate_measures --cohort-definition analysis/study_definition_ce2.py --output output/ce2/measure_ce2_*.csv --input output/ce2/input_expanded_ce2_*.csv
    needs: [add_practice_ids]
    outputs:
        moderately_sensitive:
          measure_csv: output/ce2/measure_ce2_*.csv


  # generate_report:
  #   run: cohort-report:v2.0.2 output/ce1/input_2019-09-01.feather
  #   needs: [generate_study_population_ce1]
  #   config:
  #     output_path: output/ce1/cohort_reports_outputs
  #   outputs:
  #     moderately_sensitive:
  #       reports: output/ce1/cohort_reports_outputs/*.html

    
  generate_plots:
    run: python:latest python analysis/plot_measures.py
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        counts: output/ce2/figures/plot_*.jpeg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:06:01

These timestamps are generated and stored using the UTC timezone on the NHSD-REF backend.

Job information

Status
Succeeded
Backend
NHSD-REF
Workspace
med-safety-poc
Requested by
Emmanuel Bessah
Branch
main
Force run dependencies
No
Git commit hash
24201b0
Requested actions
  • generate_study_population_ce2

Code comparison

Compare the code used in this Job Request