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Job request: 22503

Organisation:
University of Manchester
Workspace:
digital-access-to-primary-care
ID:
4dfgwuc7htw4m5k7
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: 5000

actions:

  generate_dataset_fy19to20:
    run: >
      ehrql:v1
        generate-dataset analysis/dataset_definition.py
        --output output/consultation_dataset_2019-03-23_to_2020-03-22.arrow
        --
        --start-date "2019-03-23"
        --end-date "2020-03-22"
    outputs:
      highly_sensitive:
        study_population: output/consultation_dataset_2019-03-23_to_2020-03-22.arrow

  generate_dataset_fy20to21:
    run: >
      ehrql:v1
        generate-dataset analysis/dataset_definition.py
        --output output/consultation_dataset_2020-03-23_to_2021-03-22.arrow
        --
        --start-date "2020-03-23"
        --end-date "2021-03-22"
    outputs:
      highly_sensitive:
        study_population: output/consultation_dataset_2020-03-23_to_2021-03-22.arrow

  generate_dataset_fy21to22:
    run: >
      ehrql:v1
        generate-dataset analysis/dataset_definition.py
        --output output/consultation_dataset_2021-03-23_to_2022-03-22.arrow
        --
        --start-date "2021-03-23"
        --end-date "2022-03-22"
    outputs:
      highly_sensitive:
        study_population: output/consultation_dataset_2021-03-23_to_2022-03-22.arrow

  generate_measures:
    run: >
      ehrql:v1
        generate-measures analysis/measures_definition.py
        --dummy-tables dummy_tables
        --output output/measures/consultation_measures.csv
    outputs:
      moderately_sensitive:
        study_population: output/measures/consultation_measures.csv

  tidy_measures:
    run: >
      r:latest analysis/tidy_consultation_measures.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        study_population: output/measures/tidy_consultation_measures.csv

  summarise_datasets:
     run: >
       r:latest analysis/summarise_consultation_dataset.R
     needs: [generate_dataset_fy19to20, generate_dataset_fy20to21, generate_dataset_fy21to22]
     outputs:
       moderately_sensitive:
         datasets_summary: output/data/summary_consultation_datasets.csv

  nb_regression:
     run: >
       r:latest analysis/negative_binomial_model.R
     needs: [generate_dataset_fy19to20, generate_dataset_fy20to21, generate_dataset_fy21to22]
     outputs:
       moderately_sensitive:
         results: output/results/nb_regression.txt        

  summarise_codes:
    run: >
      r:latest analysis/investigate_consultation_codes.R
    needs: [generate_dataset_fy20to21]
    outputs:
      moderately_sensitive:
        codes_summary: output/data/summary_consultation_codes.csv

  summarise_appointment_status:
    run: >
      r:latest analysis/investigate_appointment_status.R
    needs: [generate_dataset_fy20to21]
    outputs:
      moderately_sensitive:
        codes_summary: output/data/summary_last_appointment_status.csv

  # visualise_measures:
  #    run: >
  #      r:latest analysis/visualise_consultation_measures.R
  #    needs: [generate_measures]
  #    outputs:
  #      moderately_sensitive:
  #        figure_ratio: output/figures/plot_ratio_has_consultations.png
  #        figure_count: output/figures/plot_ratio_count_consultations.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:48:19

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
1f695a6
Requested actions
  • summarise_datasets

Code comparison

Compare the code used in this job request