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Job request: 23322

Organisation:
Bennett Institute
Workspace:
pharmacy-first-data-development
ID:
zqnivn7ogig2mv2d
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Milan Wiedemann requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, 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_dataset_curation:
    run: >
      ehrql:v1 generate-dataset analysis/dataset_definition_curation.py
        --test-data-file analysis/test_dataset_definition_curation.py
        --dummy-tables dummy_tables
        --output output/data_curation/data_curation.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/data_curation/data_curation.csv.gz
  
  generate_measures_codes:
    run: > 
      ehrql:v1 generate-measures analysis/measures_definition_clinical_codes.py
      --dummy-tables dummy_tables
      --output output/clinical_codes/code_counts_measures.csv
    outputs:
      moderately_sensitive:
        measure: output/clinical_codes/code_counts_measures.csv

  data_curation_medications:
    run: r:latest analysis/data_curation_medications_table.R
    needs: [generate_dataset_curation]
    outputs:
      moderately_sensitive:
        dataset: output/data_curation/medication_status_counts.csv

  data_curation_consultations:
    run: r:latest analysis/data_curation_pharmacy_first_consultations.R
    needs: [generate_dataset_curation]
    outputs:
      moderately_sensitive:
        dataset: output/data_curation/consultations_counts.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:54:58

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

Job information

Status
Succeeded
Backend
TPP
Workspace
pharmacy-first-data-development
Requested by
Milan Wiedemann
Branch
main
Force run dependencies
No
Git commit hash
1459bd7
Requested actions
  • data_curation_consultations

Code comparison

Compare the code used in this Job Request