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Job request: 2454

Organisation:
Workspace:
antipsychotics-prescribing-during-covid-19-master
ID:
wzuu3tz3cz2rpyk2
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

  • Action:
    data_process
    Status:
    Status: Failed
    Job identifier:
    oy7wcs2h64joi3xd
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    summary_figures
    Status:
    Status: Failed
    Job identifier:
    mnj6sr4rksuxvng2
    Error:
    dependency_failed: Not starting as dependency failed

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: 100000

actions:

  # Extract data ----
  
  ## Cohort data
  extract_data:
    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 --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_*.feather
  
  ## Ethnicity      
  extract_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
        
  ## Patient to practice lookup
  patient_practice_lookup:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --output-dir=output/data --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_practice_count.feather
        
  
  # Data processing ----

  ## Patient counts
  get_patient_count:
    run: python:latest python analysis/get_patient_counts.py --output-dir=output/data
    needs: [extract_data]
    outputs:
       moderately_sensitive:
         text: output/data/patient_count.json
         
  ## Practice count
  get_practice_count:
    run: python:latest python analysis/get_practice_count.py --output-dir=output/data
    needs: [patient_practice_lookup]
    outputs:
      moderately_sensitive:
        text: output/data/practice_count.json
  
  ## Add ethnicity
  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py
    needs: [extract_data, extract_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/data/input*.feather
  
  ## Process data
  data_process:
    run: r:latest analysis/process_data.R
    needs: [extract_ethnicity, join_ethnicity]
    outputs:
      highly_sensitive:
        tables: output/data/data_*.rds
      moderately_sensitive:
        tables: output/data/custom_measures_*.csv
        
  ## Generate measures
  generate_measures:
      run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/data
      needs: [join_ethnicity]
      outputs:
        moderately_sensitive:
          measure_csv: output/data/measure_*.csv
  
  # ### Generate measures, by group
  # generate_measures_demographics:
  #   run: python:latest python analysis/calculate_measures.py
  #   needs: [join_ethnicity]
  #   outputs:
  #     moderately_sensitive:
  #       measure: output/combined_measure_*.csv
  # 
  #   ### Generate measures, by group and demographic
  # generate_measures_demographics:
  #   run: python:latest python analysis/calculate_measures.py
  #   needs: [join_ethnicity]
  #   outputs:
  #     moderately_sensitive:
  #       measure: output/combined_measure_*.csv
  
  

  # Results ----
  
  ## Figures
  summary_figures:
    run: r:latest analysis/summary_plots.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        plots: output/figures/plot*.svg
  
  ## Whole population notebook
  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/antipsychotic_measures.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_measures, get_practice_count, get_patient_count]
    outputs:
      moderately_sensitive:
        notebook: output/antipsychotic_measures.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:31:57

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

Job request

Status
Failed
Backend
TPP
Workspace
antipsychotics-prescribing-during-covid-19-master
Requested by
Millie Green
Branch
master
Force run dependencies
No
Git commit hash
d3f51c8
Requested actions
  • data_process
  • summary_figures

Code comparison

Compare the code used in this job request