Skip to content

Job request: 2210

Organisation:
Workspace:
antipsychotics-prescribing-during-covid-19
ID:
pwigi7aba745j3ti
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Millie Green 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 
######################################

# This script defines the project pipeline - it specifys the execution orders for all the code in this
# repo using a series of actions.

######################################

version: '3.0'

expectations:
  population_size: 1000

actions:

  # Extract study cohort data
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2021-04-01 by month" --output-dir=output/data
    outputs:
      highly_sensitive:
        cohort: output/data/input_*.csv
  
  # Patient to practice lookup
  generate_study_population_practice_count:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --output-dir=output/data
    outputs:
      highly_sensitive:
        cohort: output/data/input_practice_count.csv
  
  # Generate measures data
  generate_measures:
      run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/data
      needs: [generate_study_population]
      outputs:
        moderately_sensitive:
          measure_csv: output/data/measure_*.csv
          
  # Practice counts
  get_practice_count:
    run: python:latest python analysis/python/scripts/get_practice_count.py --output-dir=output/data
    needs: [generate_study_population_practice_count]
    outputs:
      moderately_sensitive:
        text: output/data/practice_count.json
  
  # Patient counts
  get_patient_count:
    run: python:latest python analysis/python/scripts/get_patients_counts.py --output-dir=output/data
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        text: output/data/patient_count.json
        
  # Measures notebook
  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/python/notebooks/antipsychotics_measures.ipynb --execute --to html --output-dir=/workspace/output/results --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_measures, get_practice_count, get_patient_count]
    outputs:
      moderately_sensitive:
        notebook: output/results/antipsychotics_measures.html
  
  # Process data
  data_process:
    run: r:latest analysis/r/scripts/00_process_data.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        data: output/data/data_total_antipsychotics_issued.rds

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 28:54:21

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

Job request

Status
Succeeded
Backend
TPP
Workspace
antipsychotics-prescribing-during-covid-19
Requested by
Millie Green
Branch
study-def
Force run dependencies
No
Git commit hash
24bcde2
Requested actions
  • generate_study_population
  • generate_study_population_practice_count
  • generate_measures
  • get_practice_count
  • get_patient_count
  • generate_notebook

Code comparison

Compare the code used in this job request