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Job request: 21660

Organisation:
University of Manchester
Workspace:
digital-access-to-primary-care
ID:
d5qoo2ejnu2jss47
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 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_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_txt: output/data/binary_regression.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: 00:51:54

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

Job request

Status
Succeeded
Backend
TPP
Workspace
digital-access-to-primary-care
Requested by
Abodunrin Aminu
Branch
main
Force run dependencies
No
Git commit hash
c958a79
Requested actions
  • binary_regression_01

Code comparison

Compare the code used in this job request