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Job request: 27372

Organisation:
Bennett Institute
Workspace:
pharmacy-first-data-development
ID:
r7uweympdq37qtbx
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Viveck Kingsley 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:
    data_development_med_status_combine
    Status:
    Pending
    Job identifier:
    66gwizyovry2p6y3
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    data_development_med_status_post
    Status:
    Pending
    Job identifier:
    j2wjxxy6w3wafn5t
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    generate_med_status_data_development
    Status:
    Pending
    Job identifier:
    p6p6ahxfwgixmyi3
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    generate_med_status_data_development_fixed
    Status:
    Pending
    Job identifier:
    7je7qrd4y353iqpz
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    generate_pf_med_counts_measures
    Status:
    Pending
    Job identifier:
    2wjyhwalgiotwhn2
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    generate_study_population
    Status:
    Pending
    Job identifier:
    gdk464j7dcyn3o3t
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    data_development_med_status_pre
    Status:
    Pending
    Job identifier:
    nujrjig7oqi3hdbg
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    describe_study_population
    Status:
    Pending
    Job identifier:
    xchhwlkt3dvzjejs
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    generate_measures_pf_codes
    Status:
    Pending
    Job identifier:
    wjxpsmkv2ts4nfgb
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    generate_med_status_counts_measures
    Status:
    Pending
    Job identifier:
    wd27mjizip4vvfzs
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    data_development_med_status_post_fixed
    Status:
    Pending
    Job identifier:
    st7esbnqp3kwf7is
    Status message:
    waiting_on_dependencies: Waiting on dependencies

Pipeline

Show project.yaml 
version: '5.0'

actions:

  generate_med_status_data_development:
    run: >
      ehrql:v1 generate-dataset analysis/dataset_definition_med_status_data_development.py
        --output output/data_development/med_status_data_development.arrow
    outputs:
      highly_sensitive:
        dataset: output/data_development/med_status_data_development.arrow

  generate_med_status_data_development_fixed:
    run: >
      ehrql:v1 generate-dataset analysis/dataset_definition_med_status_data_development_fixed.py
        --output output/data_development/med_status_data_development_fixed.arrow
    outputs:
      highly_sensitive:
        dataset: output/data_development/med_status_data_development_fixed.arrow

  generate_measures_pf_codes:
    run: > 
      ehrql:v1 generate-measures analysis/measures_definition_clinical_codes.py
      --output output/clinical_codes/code_counts_measures.csv
    outputs:
      moderately_sensitive:
        measure: output/clinical_codes/code_counts_measures.csv

  data_development_med_status_pre:
     run: r:v2 analysis/data_development_med_status_pre_counts.R
     needs: [generate_med_status_data_development]
     outputs:
       moderately_sensitive:
         dataset: output/data_development/med_status_pre_counts.csv
  
  data_development_med_status_post:
     run: r:v2 analysis/data_development_med_status_post_counts.R
     needs: [generate_med_status_data_development]
     outputs:
       moderately_sensitive:
         dataset: output/data_development/med_status_post_counts.csv
    
  data_development_med_status_post_fixed:
      run: r:v2 analysis/data_development_med_status_post_counts_fixed.R
      needs: [generate_med_status_data_development_fixed]
      outputs:
        moderately_sensitive:
          dataset: output/data_development/med_status_post_counts_fixed.csv

  data_development_med_status_combine:
     run: r:v2 analysis/data_development_med_status_combine.R
     needs: [data_development_med_status_pre, data_development_med_status_post]
     outputs:
       moderately_sensitive:
         dataset: output/data_development/med_status_counts.csv

  generate_pf_med_counts_measures:
    run: >
      ehrql:v1 generate-measures analysis/measures_definition_pf_consultation_med_counts.py
      --dummy-tables dummy_tables
      --output output/measures/consultation_med_counts_measures.csv
    outputs:
      moderately_sensitive:
        measure: output/measures/consultation_med_counts_measures.csv

  generate_med_status_counts_measures:
    run: >
      ehrql:v1 generate-measures analysis/measures_med_status_counts.py
      --output output/measures/measures_med_status_counts.csv
    outputs:
      moderately_sensitive:
        measure: output/measures/measures_med_status_counts.csv

  generate_study_population:
    run: >
      ehrql:v1 generate-dataset analysis/dataset_definition_study_population.py
        --output output/study_population/study_population.arrow
    outputs:
      highly_sensitive:
        dataset: output/study_population/study_population.arrow

  describe_study_population:
    run: r:v3 analysis/describe_study_population.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        dataset: output/study_population/study_population_summary.csv

Job statistics

Status Count Percentage
Pending 11 100%
Running 0 0%
Succeeded 0 0%
Failed 0 0%

0 / 11 (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
pharmacy-first-data-development
Requested by
Viveck Kingsley
Branch
main
Force run dependencies
Yes
Git commit hash
6bb3ba0
Requested actions
  • run_all

Code comparison

Compare the code used in this job request