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 Antipsychotics Prescribing During Covid-19 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

ID Status Action
3h3keghwxspf2tqv succeeded data_summaries

Pipeline

Show Hide 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: 100000

actions:

  # Extract cohort data
  
  ## Learning disability
  generate_ld_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ld --index-date-range "2019-01-01 to 2021-04-01 by month" --output-dir=output/data --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_ld_*.feather
  
  ## Autism
  generate_autism_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_autism --index-date-range "2019-01-01 to 2021-04-01 by month" --output-dir=output/data --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_autism_*.feather
  
  ## Serious Mental Illness
  generate_smi_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_smi --index-date-range "2019-01-01 to 2021-04-01 by month" --output-dir=output/data --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_smi_*.feather
  
  ## Care home
  generate_care_home_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_care_home --index-date-range "2019-01-01 to 2021-04-01 by month" --output-dir=output/data --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_care_home_*.feather
  
  ## Dementia
  generate_dementia_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_dementia --index-date-range "2019-01-01 to 2021-04-01 by month" --output-dir=output/data --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_dementia_*.feather
  
  ## Ethnicity      
  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output/data --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_ethnicity.feather
        
  
  # Data processing
  
  ## Add ethnicity
  join_ethnicity:
    run: python:latest python analysis/python/scripts/join_ethnicity.py
    needs: [generate_ld_cohort, generate_autism_cohort, generate_smi_cohort, generate_care_home_cohort, generate_dementia_cohort, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/data/input*.feather
        
  
  # Generate measures data
  
  ## Learning disability
  generate_measures_ld:
      run: cohortextractor:latest generate_measures --study-definition study_definition_ld --output-dir=output/data
      needs: [join_ethnicity]
      outputs:
        moderately_sensitive:
          measure_csv: output/data/measure_ld_*.csv
          
  ## Autism
  generate_measures_autism:
      run: cohortextractor:latest generate_measures --study-definition study_definition_autism --output-dir=output/data
      needs: [join_ethnicity]
      outputs:
        moderately_sensitive:
          measure_csv: output/data/measure_autism_*.csv

  ## Serious Mental Illness
  generate_measures_smi:
      run: cohortextractor:latest generate_measures --study-definition study_definition_smi --output-dir=output/data
      needs: [join_ethnicity]
      outputs:
        moderately_sensitive:
          measure_csv: output/data/measure_smi_*.csv

  ## Care home
  generate_measures_care_home:
      run: cohortextractor:latest generate_measures --study-definition study_definition_care_home --output-dir=output/data
      needs: [join_ethnicity]
      outputs:
        moderately_sensitive:
          measure_csv: output/data/measure_care_home_*.csv

  ## Dementia
  generate_measures_dementia:
      run: cohortextractor:latest generate_measures --study-definition study_definition_dementia --output-dir=output/data
      needs: [join_ethnicity]
      outputs:
        moderately_sensitive:
          measure_csv: output/data/measure_dementia_*.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
  # 
  #         
  # # 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_ld]
    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_ld_cohort, generate_measures_ld]
#     outputs:
#       highly_sensitive:
#         data: output/data/data_processed.rds
        
  # Data summaries
  data_summaries:
    run: r:latest -e 'rmarkdown::render("analysis/r/markdown/data_summaries.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [generate_ld_cohort]
    outputs:
      moderately_sensitive:
        html: output/data_summaries.html

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 00:06:39

Config