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Job request: 27461

Organisation:
NHS England
Workspace:
obesity-tirzepatide
ID:
kjuu72alzufzke6r
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:
    generate_dataset
    Status:
    Pending
    Job identifier:
    6lpppfat7ergsduw
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    run_descriptive_table
    Status:
    Pending
    Job identifier:
    qb4jg2b7rrhgo2to
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    generate_measures_categorical
    Status:
    Pending
    Job identifier:
    zhgzs4ieogqmy3hf
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    generate_measures_cohorts
    Status:
    Pending
    Job identifier:
    ybwsh43ngvfeueqr
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    generate_measures_main
    Status:
    Pending
    Job identifier:
    2ozcus6q4op6sppo
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    run_combination_data_checks
    Status:
    Pending
    Job identifier:
    hflfqo5cvnfaucjx
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    run_upset_plot_comorbidities
    Status:
    Pending
    Job identifier:
    coaw2alhl5jddtox
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    run_basic_data_checks
    Status:
    Pending
    Job identifier:
    7i4jocvaijf7jgr3
    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 8 100%
Running 0 0%
Succeeded 0 0%
Failed 0 0%

0 / 8 (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
01f84d4
Requested actions
  • generate_dataset
  • generate_measures_main
  • generate_measures_cohorts
  • generate_measures_categorical
  • run_basic_data_checks
  • run_combination_data_checks
  • run_descriptive_table
  • run_upset_plot_comorbidities

Code comparison

Compare the code used in this job request