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Job request: 26561

Organisation:
University of Oxford
Workspace:
gbd-estimates-testing
ID:
yjgzjz7k34sdsu52
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Arina Tamborska 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_test_dataset
    Status:
    Succeeded
    Job identifier:
    gfejo34hcelxuwqa
  • Action:
    generate_denominators
    Status:
    Succeeded
    Job identifier:
    t6al5s6tx3z6qblq
  • Action:
    generate_gbs_estimates
    Status:
    Succeeded
    Job identifier:
    geynhacttr7foshy
  • Action:
    generate_ms_estimates
    Status:
    Running
    Job identifier:
    6giy2ymd53sxfxqh
  • Action:
    generate_gbs_processing
    Status:
    Succeeded
    Job identifier:
    bllimdwyydq62ij4
  • Action:
    generate_dementia_estimates
    Status:
    Pending
    Job identifier:
    ife3jhk2ak5jqclb
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    generate_ms_test_processing
    Status:
    Pending
    Job identifier:
    ng4p7gpgcvrrpkbd
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    generate_encephalitis_processing
    Status:
    Pending
    Job identifier:
    atiovadwwejln5q4
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    generate_pd_processing
    Status:
    Pending
    Job identifier:
    mwr4wx3mzqlsdegu
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    generate_falls_processing
    Status:
    Pending
    Job identifier:
    ljiscwhp2zixngwz
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    generate_dm_processing
    Status:
    Pending
    Job identifier:
    j5ydlpgbyil62lbw
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    generate_ms_test_estimates
    Status:
    Pending
    Job identifier:
    anuyj6oxtwgnd2gg
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    generate_cvd_estimates
    Status:
    Pending
    Job identifier:
    7hqpfls237ykh4g2
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    generate_encephalitis_estimates
    Status:
    Pending
    Job identifier:
    qgngdshx5h2bxud5
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    generate_dm_estimates
    Status:
    Pending
    Job identifier:
    eesix3pmp65cz6d2
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    generate_cvd_processing
    Status:
    Pending
    Job identifier:
    gl4jfc2hslqzqvbh
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    generate_ms_processing
    Status:
    Pending
    Job identifier:
    hwufs5giutbefzdm
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    generate_pd_estimates
    Status:
    Pending
    Job identifier:
    wizm3bsqhzaw3h7c
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    generate_falls_estimates
    Status:
    Pending
    Job identifier:
    ps35kajtvhndeohc
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    generate_dementia_processing
    Status:
    Pending
    Job identifier:
    skntlxbccyjtz2f7
    Status message:
    waiting_on_dependencies: Waiting on dependencies

Pipeline

Show project.yaml 
# This file is autogenerated by generate_yaml.py. Do not edit this file directly.
    
version: '4.0'

actions:

  generate_ms_estimates:
    run: ehrql:v1 generate-measures analysis/generate_gbd_estimates.py
      --output output/raw_estimates/ms_estimates.arrow
      --dummy-tables dummy-tables
      --
      --disease "ms"
    outputs:
      highly_sensitive:
        measures: output/raw_estimates/ms_estimates.arrow

  generate_ms_test_estimates:
    run: ehrql:v1 generate-measures analysis/generate_gbd_estimates.py
      --output output/raw_estimates/ms_test_estimates.arrow
      --dummy-tables dummy-tables
      --
      --disease "ms_test"
    outputs:
      highly_sensitive:
        measures: output/raw_estimates/ms_test_estimates.arrow

  generate_gbs_estimates:
    run: ehrql:v1 generate-measures analysis/generate_gbd_estimates.py
      --output output/raw_estimates/gbs_estimates.arrow
      --dummy-tables dummy-tables
      --
      --disease "gbs"
    outputs:
      highly_sensitive:
        measures: output/raw_estimates/gbs_estimates.arrow

  generate_cvd_estimates:
    run: ehrql:v1 generate-measures analysis/generate_gbd_estimates.py
      --output output/raw_estimates/cvd_estimates.arrow
      --dummy-tables dummy-tables
      --
      --disease "cvd"
    outputs:
      highly_sensitive:
        measures: output/raw_estimates/cvd_estimates.arrow

  generate_encephalitis_estimates:
    run: ehrql:v1 generate-measures analysis/generate_gbd_estimates.py
      --output output/raw_estimates/encephalitis_estimates.arrow
      --dummy-tables dummy-tables
      --
      --disease "encephalitis"
    outputs:
      highly_sensitive:
        measures: output/raw_estimates/encephalitis_estimates.arrow

  generate_pd_estimates:
    run: ehrql:v1 generate-measures analysis/generate_gbd_estimates.py
      --output output/raw_estimates/pd_estimates.arrow
      --dummy-tables dummy-tables
      --
      --disease "pd"
    outputs:
      highly_sensitive:
        measures: output/raw_estimates/pd_estimates.arrow

  generate_falls_estimates:
    run: ehrql:v1 generate-measures analysis/generate_gbd_estimates.py
      --output output/raw_estimates/falls_estimates.arrow
      --dummy-tables dummy-tables
      --
      --disease "falls"
    outputs:
      highly_sensitive:
        measures: output/raw_estimates/falls_estimates.arrow

  generate_dm_estimates:
    run: ehrql:v1 generate-measures analysis/generate_gbd_estimates.py
      --output output/raw_estimates/dm_estimates.arrow
      --dummy-tables dummy-tables
      --
      --disease "dm"
    outputs:
      highly_sensitive:
        measures: output/raw_estimates/dm_estimates.arrow

  generate_dementia_estimates:
    run: ehrql:v1 generate-measures analysis/generate_gbd_estimates.py
      --output output/raw_estimates/dementia_estimates.arrow
      --dummy-tables dummy-tables
      --
      --disease "dementia"
    outputs:
      highly_sensitive:
        measures: output/raw_estimates/dementia_estimates.arrow

  generate_denominators:
    run: ehrql:v1 generate-measures analysis/generate_denominators.py
      --output output/denominators/denominators.arrow
      --dummy-tables dummy-tables
    outputs:
      highly_sensitive:
        measures: output/denominators/denominators.arrow

  generate_ms_processing:
    run: python:v2 analysis/process_estimates.py 
      --disease "ms"
    needs: [generate_ms_estimates, generate_denominators]
    outputs:
      moderately_sensitive:
        sex_summary_table: output/summary_checks/ms/ms_sex_summary.csv
        age_summary_table: output/summary_checks/ms/ms_age_summary.csv
        processed_measures: output/processed_estimates/ms_estimates_processed.csv
        plot: output/summary_checks/ms/ms_trends.png

  generate_ms_test_processing:
    run: python:v2 analysis/process_estimates.py 
      --disease "ms_test"
    needs: [generate_ms_test_estimates, generate_denominators]
    outputs:
      moderately_sensitive:
        sex_summary_table: output/summary_checks/ms_test/ms_test_sex_summary.csv
        age_summary_table: output/summary_checks/ms_test/ms_test_age_summary.csv
        processed_measures: output/processed_estimates/ms_test_estimates_processed.csv
        plot: output/summary_checks/ms_test/ms_test_trends.png

  generate_gbs_processing:
    run: python:v2 analysis/process_estimates.py 
      --disease "gbs"
    needs: [generate_gbs_estimates, generate_denominators]
    outputs:
      moderately_sensitive:
        sex_summary_table: output/summary_checks/gbs/gbs_sex_summary.csv
        age_summary_table: output/summary_checks/gbs/gbs_age_summary.csv
        processed_measures: output/processed_estimates/gbs_estimates_processed.csv
        plot: output/summary_checks/gbs/gbs_trends.png

  generate_cvd_processing:
    run: python:v2 analysis/process_estimates.py 
      --disease "cvd"
    needs: [generate_cvd_estimates, generate_denominators]
    outputs:
      moderately_sensitive:
        sex_summary_table: output/summary_checks/cvd/cvd_sex_summary.csv
        age_summary_table: output/summary_checks/cvd/cvd_age_summary.csv
        processed_measures: output/processed_estimates/cvd_estimates_processed.csv
        plot: output/summary_checks/cvd/cvd_trends.png

  generate_encephalitis_processing:
    run: python:v2 analysis/process_estimates.py 
      --disease "encephalitis"
    needs: [generate_encephalitis_estimates, generate_denominators]
    outputs:
      moderately_sensitive:
        sex_summary_table: output/summary_checks/encephalitis/encephalitis_sex_summary.csv
        age_summary_table: output/summary_checks/encephalitis/encephalitis_age_summary.csv
        processed_measures: output/processed_estimates/encephalitis_estimates_processed.csv
        plot: output/summary_checks/encephalitis/encephalitis_trends.png

  generate_pd_processing:
    run: python:v2 analysis/process_estimates.py 
      --disease "pd"
    needs: [generate_pd_estimates, generate_denominators]
    outputs:
      moderately_sensitive:
        sex_summary_table: output/summary_checks/pd/pd_sex_summary.csv
        age_summary_table: output/summary_checks/pd/pd_age_summary.csv
        processed_measures: output/processed_estimates/pd_estimates_processed.csv
        plot: output/summary_checks/pd/pd_trends.png

  generate_falls_processing:
    run: python:v2 analysis/process_estimates.py 
      --disease "falls"
    needs: [generate_falls_estimates, generate_denominators]
    outputs:
      moderately_sensitive:
        sex_summary_table: output/summary_checks/falls/falls_sex_summary.csv
        age_summary_table: output/summary_checks/falls/falls_age_summary.csv
        processed_measures: output/processed_estimates/falls_estimates_processed.csv
        plot: output/summary_checks/falls/falls_trends.png

  generate_dm_processing:
    run: python:v2 analysis/process_estimates.py 
      --disease "dm"
    needs: [generate_dm_estimates, generate_denominators]
    outputs:
      moderately_sensitive:
        sex_summary_table: output/summary_checks/dm/dm_sex_summary.csv
        age_summary_table: output/summary_checks/dm/dm_age_summary.csv
        processed_measures: output/processed_estimates/dm_estimates_processed.csv
        plot: output/summary_checks/dm/dm_trends.png

  generate_dementia_processing:
    run: python:v2 analysis/process_estimates.py 
      --disease "dementia"
    needs: [generate_dementia_estimates, generate_denominators]
    outputs:
      moderately_sensitive:
        sex_summary_table: output/summary_checks/dementia/dementia_sex_summary.csv
        age_summary_table: output/summary_checks/dementia/dementia_age_summary.csv
        processed_measures: output/processed_estimates/dementia_estimates_processed.csv
        plot: output/summary_checks/dementia/dementia_trends.png

  generate_test_dataset:
    run: ehrql:v1 generate-dataset analysis/testing/test_dataset_definition.py 
     --output output/testing/dataset.csv
     --dummy-tables dummy-tables
    outputs:
     highly_sensitive:
       test_dataset: output/testing/dataset.csv

Job statistics

Status Count Percentage
Pending 15 75%
Running 1 5%
Succeeded 4 20%
Failed 0 0%

4 / 20 (20%) complete

Timeline

  • Created:

  • Started:

  • Runtime: 07:02:17

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

Job request

Status
Running
Backend
TPP
Workspace
gbd-estimates-testing
Requested by
Arina Tamborska
Branch
main
Force run dependencies
Yes
Git commit hash
dde2878
Requested actions
  • generate_ms_estimates
  • generate_denominators
  • generate_ms_processing
  • run_all

Code comparison

Compare the code used in this job request