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Job request: 26498

Organisation:
University of Oxford
Workspace:
gbd-estimates-testing
ID:
vjouad5dqxoqzzpn
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_ms_estimates
    Status:
    Succeeded
    Job identifier:
    jikiyktnwgayqe5l
  • Action:
    generate_gbs_estimates
    Status:
    Succeeded
    Job identifier:
    ajpvatptr5ewtlnj
  • Action:
    generate_denominators
    Status:
    Succeeded
    Job identifier:
    bnhm63igl7ssqk5p
  • Action:
    generate_gbs_processing
    Status:
    Succeeded
    Job identifier:
    q35gyr2xw5y4hyco
  • Action:
    generate_ms_processing
    Status:
    Succeeded
    Job identifier:
    sk72lcvaw5opdjuo

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_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_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_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_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 0 0%
Running 0 0%
Succeeded 5 100%
Failed 0 0%

5 / 5 (100%) complete

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:36:02

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

Job request

Status
Succeeded
Backend
TPP
Workspace
gbd-estimates-testing
Requested by
Arina Tamborska
Branch
main
Force run dependencies
No
Git commit hash
e1ccd21
Requested actions
  • generate_ms_estimates
  • generate_gbs_estimates
  • generate_denominators
  • generate_ms_processing
  • generate_gbs_processing

Code comparison

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