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Job request: 2204

Organisation:
Workspace:
antipsychotics-prescribing-during-covid-19
ID:
aa7f42eit74emgnc
View repo View project.yaml

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

# 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: 00:01:17

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

Job information

Status
Failed
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

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