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Job request: 23700

Organisation:
Bennett Institute
Workspace:
pharmacy-first-data-development
ID:
76jsgq4tcgiis3lz
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Milan Wiedemann 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

Pipeline

Show project.yaml 
version: '3.0'

# Ignore this`expectation` block. It is required but not used, and will be removed in future versions.
expectations:
  population_size: 1000

actions:
  generate_pf_codes_data_development:
    run: >
      ehrql:v1 generate-dataset analysis/dataset_definition_pf_data_development.py
        --test-data-file analysis/test_dataset_definition_pf_data_development.py
        --output output/data_development/pf_codes_data_development.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/data_development/pf_codes_data_development.csv.gz

  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_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:
     run: r:latest analysis/data_development_med_status_counts.R
     needs: [generate_med_status_data_development]
     outputs:
       moderately_sensitive:
         dataset: output/data_development/med_status_counts.csv

  data_development_pf_code_distinct:
    run: r:latest analysis/data_development_pf_code_count_distinct.R
    needs: [generate_pf_codes_data_development]
    outputs:
      moderately_sensitive:
        dataset: output/data_development/pf_codes_count_distinct.csv

  data_development_pf_code_events:
    run: r:latest analysis/data_development_pf_code_count_events.R
    needs: [generate_pf_codes_data_development]
    outputs:
      moderately_sensitive:
        dataset: output/data_development/pf_codes_count_events.csv

  data_development_pf_codes_pathways:
    run: r:latest analysis/data_development_pf_code_count_pathways.R
    needs: [generate_pf_codes_data_development]
    outputs:
      moderately_sensitive:
        dataset: output/data_development/pf_codes_count_pathways.csv

  data_development_pf_codes_combine:
    run: r:latest analysis/data_development_pf_code_count_combine.R
    needs: [data_development_pf_code_distinct, data_development_pf_code_events, data_development_pf_codes_pathways]
    outputs:
      moderately_sensitive:
        dataset: output/data_development/pf_codes_count_summary.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 08:47:34

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

Job request

Status
Succeeded
Backend
TPP
Workspace
pharmacy-first-data-development
Requested by
Milan Wiedemann
Branch
main
Force run dependencies
No
Git commit hash
2330732
Requested actions
  • data_development_pf_code_distinct
  • data_development_pf_code_events
  • data_development_pf_codes_pathways
  • data_development_pf_codes_combine

Code comparison

Compare the code used in this job request