Skip to content

Job request: 2312

Organisation:
Workspace:
antipsychotics-prescribing-during-covid-19-isd
ID:
pryykyhtzhnkdbvj
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
  
  ## 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

  # # 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_processed.rds
  #

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 23:46:15

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-isd
Requested by
Millie Green
Branch
individual-study-defs
Force run dependencies
No
Git commit hash
5289e71
Requested actions
  • generate_LD_cohort

Code comparison

Compare the code used in this job request

  • No previous job request available for comparison