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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 in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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
  
  ## 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 information

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

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