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Job request: 26981

Organisation:
University of Nottingham
Workspace:
p3-measure-validation
ID:
o3p37bmsnk72wqy6
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Weiyao Meng 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:
    postprocess_safety_count_by_outcome_source
    Status:
    Succeeded
    Job identifier:
    blpy24wgedjiuxiu
  • Action:
    postprocess_safety_rate_by_outcome_source
    Status:
    Succeeded
    Job identifier:
    tar3wjsfg27vfmm6

Pipeline

Show project.yaml 
version: '4.0'

actions:
  generate_dataset:
    run: ehrql:v1 generate-dataset analysis_protocol3/protocol3_dataset_definition_patients.py --output output/dataset_patients.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/dataset_patients.csv.gz
  
  generate_patient_measures_consultation_validation:
    run: ehrql:v1 generate-measures analysis_protocol3/validation/measures_patient_consultations_validation.py --output output/patient_measures_consultation_validation.csv
    outputs:
      moderately_sensitive:
        measure_tables: output/patient_measures_consultation_validation.csv

  process_patient_measures_consultation_validation:
    run: python:v2 analysis_protocol3/validation/process_measure_consultation_validation.py --output output/patient_measures_consultation_validation_ordered.csv
    needs: [generate_patient_measures_consultation_validation]
    outputs:
      moderately_sensitive:
        measure_tables: output/patient_measures_consultation_validation_ordered.csv
        summary_tables: output/patient_measures_consultation_validation_summary.csv
        pf_consultation_chart: output/patient_measures_pf_consultations_by_condition.png
        gp_consultation_chart: output/patient_measures_gp_consultation_by_condition.png

  generate_safety_outcome_measures_count_validation:
    run: ehrql:v1 generate-measures analysis_protocol3/validation/measures_safety_count_validation.py --output output/safety_measures_count_validation.csv
    outputs:
      moderately_sensitive:
        measure_tables: output/safety_measures_count_validation.csv
  
  process_safety_count_validation:
    run: python:latest analysis_protocol3/validation/process_safety_count_validation.py
    needs: [generate_safety_outcome_measures_count_validation]
    outputs:
      moderately_sensitive:
        safety_count_validation_summary: output/safety_count_validation_summary.csv
        safety_count_validation_flags: output/safety_count_validation_flags.csv
  
  generate_safety_outcome_measures_rate_validation:
    run: ehrql:v1 generate-measures analysis_protocol3/validation/measures_safety_rate_validation.py --output output/safety_measures_rate_validation.csv
    outputs:
      moderately_sensitive:
        measure_tables: output/safety_measures_rate_validation.csv
  
  process_safety_rate_validation:
    run: python:latest analysis_protocol3/validation/process_safety_rate_validation.py
    needs: [generate_safety_outcome_measures_rate_validation]
    outputs:
      moderately_sensitive:
        safety_rate_validation_summary: output/safety_rate_validation_summary.csv
        safety_rate_validation_flags: output/safety_rate_validation_flags.csv
  
  postprocess_safety_count_by_outcome_source:
    run: python:latest analysis_protocol3/validation/postprocess_count_by_outcome_source.py
    needs: [generate_safety_outcome_measures_count_validation]
    outputs:
      moderately_sensitive:
        safety_count_by_outcome_source: output/safety_count_by_outcome_source.csv

  postprocess_safety_rate_by_outcome_source:
    run: python:latest analysis_protocol3/validation/postprocess_rate_by_outcome_source.py
    needs: [generate_safety_outcome_measures_rate_validation]
    outputs:
      moderately_sensitive:
        safety_rate_by_outcome_source: output/safety_rate_by_outcome_source.csv
        safety_numerator_gp_consultation_by_month: output/safety_numerator_gp_consultation_by_month.png
        safety_numerator_ae_primary_non_primary_by_month: output/safety_numerator_ae_primary_non_primary_by_month.png
        safety_numerator_hes_primary_non_primary_by_month: output/safety_numerator_hes_primary_non_primary_by_month.png

Job statistics

Status Count Percentage
Pending 0 0%
Running 0 0%
Succeeded 2 100%
Failed 0 0%

2 / 2 (100%) complete

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:03:22

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

Job request

Status
Succeeded
Backend
TPP
Workspace
p3-measure-validation
Requested by
Weiyao Meng
Branch
main
Force run dependencies
No
Git commit hash
a216bd3
Requested actions
  • postprocess_safety_count_by_outcome_source
  • postprocess_safety_rate_by_outcome_source

Code comparison

Compare the code used in this job request