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Job request: 27456

Organisation:
NHS England
Workspace:
obesity-tirzepatide
ID:
k4f2zppyuueie7th
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Amy Gimma 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

  • Action:
    run_upset_plot_comorbidities
    Status:
    Pending
    Job identifier:
    lk4q3kviaugdapix
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    generate_dataset
    Status:
    Pending
    Job identifier:
    jkz7y47yrighgf6w
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    generate_measures_categorical
    Status:
    Pending
    Job identifier:
    bvy3sgx2k2o3rmqy
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    run_time_series_main
    Status:
    Pending
    Job identifier:
    5zwku6vm6vezv3xr
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    generate_measures_cohorts
    Status:
    Pending
    Job identifier:
    o5qvneaueuzdzlbq
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    generate_measures_main
    Status:
    Pending
    Job identifier:
    trvuvfxykbwr4yef
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    run_basic_data_checks
    Status:
    Pending
    Job identifier:
    faeeqmmayabe4wjp
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    run_combination_data_checks
    Status:
    Pending
    Job identifier:
    ejhrx64qh7z3kcu4
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    run_descriptive_table
    Status:
    Pending
    Job identifier:
    bbn4ejg3h5bgnuob
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    run_time_series_categorical
    Status:
    Pending
    Job identifier:
    rxonjc5qzthw4pj4
    Status message:
    waiting_on_dependencies: Waiting on dependencies

Pipeline

Show project.yaml 
version: '5.0'

actions:
  generate_dataset:
    run: >
      ehrql:v1 generate-dataset analysis/dataset_definition.py
      --output output/dataset.csv
      --dummy-tables dummy_tables/custom
      --test-data-file analysis/tests/test-dataset_definition.py
    outputs:
      highly_sensitive:
        dataset: output/dataset.csv
  generate_measures_main:
    run: >
      ehrql:v1 generate-measures analysis/measures_main.py
      --output output/measures_main.csv
      --dummy-tables dummy_tables/custom
    outputs:
      moderately_sensitive:
        measures: output/measures_main.csv
  generate_measures_cohorts:
    run: >
      ehrql:v1 generate-measures analysis/measures_cohorts.py
      --output output/measures_cohorts.csv
      --dummy-tables dummy_tables/custom
    outputs:
      moderately_sensitive:
        measures: output/measures_cohorts.csv
  generate_measures_categorical:
    run: >
      ehrql:v1 generate-measures analysis/measures_categorical.py
      --output output/measures_categorical.csv
      --dummy-tables dummy_tables/custom
    outputs:
      moderately_sensitive:
        measures: output/measures_categorical.csv 
  run_basic_data_checks:
    needs: [generate_dataset]
    run: r:v2 analysis/data_checks/basic_data_checks.R
    outputs:
      moderately_sensitive:
        patient_categorical_checks: output/data_checks/patient_categorical_checks.csv
        continuous_checks: output/data_checks/continuous_checks_by_tirzepatide.csv
        continuous_histograms: output/data_checks/continuous_variables_histograms.png
        missing_values: output/data_checks/missing_values.csv
  run_combination_data_checks:
    needs: [generate_dataset]
    run: r:v2 analysis/data_checks/combination_data_checks.R
    outputs:
      moderately_sensitive:
        concurrency_checks: output/data_checks/concurrency_checks.csv
        consistency_checks: output/data_checks/consistency_checks.csv
  run_descriptive_table:
    needs: [generate_dataset]
    run: r:v2 analysis/descriptive/table_1.R
    outputs:
      moderately_sensitive:
          table_1_csv: output/descriptive/table_1.csv
  run_time_series_main:
    needs: [generate_measures_main]
    run: r:v2 analysis/descriptive/time_series_main.R
    outputs: 
      moderately_sensitive:
        measures_main_plot_incidence: output/descriptive/incidence_tirzepatide_time_series.png
        measures_main_plot_prevelance: output/descriptive/prevalence_tirzepatide_time_series.png
        measures_main_plot_combined: output/descriptive/tirzepatide_combined_main_time_series.png
  run_time_series_categorical:
    needs: [generate_measures_categorical]
    run: r:v2 analysis/descriptive/time_series_categorical.R
    outputs: 
      moderately_sensitive:
        measures_categorical_plot: output/descriptive/prevalence_tirzepatide_time_series_categorical.png
  run_upset_plot_comorbidities:
    needs: [generate_dataset]
    run: r:v2 analysis/descriptive/upset_plot_comorbidities.R
    outputs:
      moderately_sensitive:
        upset_plot_comorbidities: output/descriptive/upset_plot_comorbidities.png

Job statistics

Status Count Percentage
Pending 10 100%
Running 0 0%
Succeeded 0 0%
Failed 0 0%

0 / 10 (0%) complete

Timeline

  • Created:

  • Runtime:

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

Job request

Status
Pending
Backend
TPP
Workspace
obesity-tirzepatide
Requested by
Amy Gimma
Branch
main
Force run dependencies
Yes
Git commit hash
e9e0bd2
Requested actions
  • run_all

Code comparison

Compare the code used in this job request