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Job request: 21662

Organisation:
University of Manchester
Workspace:
digital-access-to-primary-care
ID:
7wxbzam4vhpwzndv
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Abodunrin Aminu 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: '3.0'

expectations:
  population_size: 1000

actions:

  generate_consultation_dataset_2019-04-01_to_2020-03-31:
    run: >
      ehrql:v1
        generate-dataset analysis/dataset_definition.py
        --output output/consultation_dataset_2019-04-01_to_2020-03-31.arrow
        --
        --start-date "2019-04-01"
        --end-date "2020-03-31"
    outputs:
      highly_sensitive:
        study_population: output/consultation_dataset_2019-04-01_to_2020-03-31.arrow

  generate_consultation_dataset_2020-04-01_to_2021-03-31:
    run: >
      ehrql:v1
        generate-dataset analysis/dataset_definition.py
        --output output/consultation_dataset_2020-04-01_to_2021-03-31.arrow
        --
        --start-date "2020-04-01"
        --end-date "2021-03-31"
    outputs:
      highly_sensitive:
        study_population: output/consultation_dataset_2020-04-01_to_2021-03-31.arrow

  generate_consultation_dataset_2021-04-01_to_2022-03-31:
    run: >
      ehrql:v1
        generate-dataset analysis/dataset_definition.py
        --output output/consultation_dataset_2021-04-01_to_2022-03-31.arrow
        --
        --start-date "2021-04-01"
        --end-date "2022-03-31"
    outputs:
      highly_sensitive:
        study_population: output/consultation_dataset_2021-04-01_to_2022-03-31.arrow

  generate_consultation_measures:
    run: >
      ehrql:v1
        generate-measures analysis/measures_definition.py
        --output output/measures/consultation_measures.csv
    outputs:
      moderately_sensitive:
        study_population: output/measures/consultation_measures.csv

  summarise_consultation_datasets:
     run: >
       r:latest analysis/summarise_consultation_dataset.R
     needs: [generate_consultation_dataset_2019-04-01_to_2020-03-31, generate_consultation_dataset_2020-04-01_to_2021-03-31, generate_consultation_dataset_2021-04-01_to_2022-03-31]
     outputs:
       moderately_sensitive:
         measure_csv: output/data/summary_consultation_dataset.csv

  binary_regression_01:
     run: >
       r:latest analysis/binary_regression.R
     needs: [generate_consultation_dataset_2019-04-01_to_2020-03-31, generate_consultation_dataset_2020-04-01_to_2021-03-31, generate_consultation_dataset_2021-04-01_to_2022-03-31]
     outputs:
       moderately_sensitive:
         measure_txt1: output/data/binary_regression_2019-20.txt
         measure_txt2: output/data/binary_regression_2020-21.txt    
         measure_txt3: output/data/binary_regression_2021-22.txt          

  # summarise_consultation_codes:
  #   run: >
  #     r:latest analysis/investigate_consultation_codes.R
  #   needs: [generate_consultation_dataset_2020-04-01_to_2021-03-31]
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: output/data/summary_consultation_codes.csv

  # visualise_consultation_datasets:
  #    run: >
  #      r:latest analysis/visualise_consultation_dataset.R
  #    needs: [generate_consultation_measures]
  #    outputs:
  #      moderately_sensitive:
  #        figure_pre2019: output/figures/figure_pre2019_consultation_measure_by_age.png
  #        figure_during2020: output/figures/figure_during2020_consultation_measure_by_age.png
  #        figure_during2021: output/figures/figure_during2021_consultation_measure_by_age.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:54:04

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

Job information

Status
Succeeded
Backend
TPP
Workspace
digital-access-to-primary-care
Requested by
Abodunrin Aminu
Branch
main
Force run dependencies
No
Git commit hash
eb8b05e
Requested actions
  • binary_regression_01

Code comparison

Compare the code used in this Job Request