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Job request: 22771

Organisation:
University of Manchester
Workspace:
digital-access-to-primary-care
ID:
tcuew6vtdpe34top
View repo View project.yaml

This page shows the technical details of what happened when 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 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_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

  logit_regression:
     run: >
       r:latest analysis/logit_regression.R
     needs: [generate_dataset_fy19to20, generate_dataset_fy20to21, generate_dataset_fy21to22]
     outputs:
       moderately_sensitive:
         results: output/results/combined_regression_result.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: 62:06:46

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

Job information

Status
Failed
Backend
TPP
Workspace
digital-access-to-primary-care
Requested by
Abodunrin Aminu
Branch
main
Force run dependencies
No
Git commit hash
f841243
Requested actions
  • logit_regression
  • summarise_codes

Code comparison

Compare the code used in this Job Request