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Job request: 8663

Organisation:
Bennett Institute
Workspace:
asthma_indicators
ID:
i7a2ocjhmpitsohb
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Rose Higgins 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 
version: '3.0'

expectations:
  population_size: 1000

actions:

# Asthma indicator (AST007) actions

  generate_study_population_ast007:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition_ast007 
      --index-date-range "2021-03-01 to 2021-05-31 by month" 
      --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_ast007*.csv
 
  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition_ethnicity 
      --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv

  join_ethnicity_ast_reg:
    run: >
      cohort-joiner:v0.0.12 
        --lhs output/input_ast007*.csv
        --rhs output/input_ethnicity*.csv
        --output-dir output/joined
    needs: [generate_study_population_ethnicity, generate_study_population_ast007]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_ast007*.csv

  generate_measures_ast007:
      run: cohortextractor:latest generate_measures 
        --study-definition study_definition_ast007 
        --output-dir=output/joined
      needs: [generate_study_population_ast007, generate_study_population_ethnicity, join_ethnicity_ast_reg]
      outputs:
        moderately_sensitive:
          measure_csv: output/joined/measure_*_rate.csv

  calculate_rates_ast007:
      run: python:latest python analysis/rate_calculations_ast007.py
      needs: [join_ethnicity_ast_reg, generate_measures_ast007]
      outputs:
        moderately_sensitive:
          tables: output/rate_table_*.csv
          plots: output/plot_*.png
          decile_chart: output/decile_chart.png

  # generate_notebook_ast007:
  #   run: jupyter:latest jupyter nbconvert /workspace/analysis/qof_notebook_ast007.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
  #   needs: [calculate_rates_ast007]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/qof_notebook_ast007.html


# Testing Asthma variables
  generate_study_population_ast007_test_variables:
    run: cohortextractor:latest generate_cohort 
        --study-definition study_definition_ast007_test_variables 
        --index-date-range "2021-03-01 to 2021-05-31 by month" 
        --output-dir=output/test
    outputs:
      highly_sensitive:
        cohort: output/test/input_ast007_test*.csv

  generate_measures_ast007_test:
      run: cohortextractor:latest generate_measures 
        --study-definition study_definition_ast007_test_variables 
        --output-dir=output/test
      needs: [generate_study_population_ast007_test_variables]
      outputs:
        moderately_sensitive:
          measure_csv: output/test/measure_*_rate.csv
  
 # Check with separate analysis script 
  # check_data:
  #   run: r:latest analysis/indicator_dates_testing.py
  #   outputs:
  #     moderately_sensitive:
  #       table_csv: output/test/test.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:47:57

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

Job information

Status
Succeeded
Backend
TPP
Workspace
asthma_indicators
Requested by
Rose Higgins
Branch
main
Force run dependencies
Yes
Git commit hash
8e1fb1b
Requested actions
  • generate_study_population_ast007
  • generate_study_population_ethnicity
  • join_ethnicity_ast_reg
  • generate_measures_ast007
  • calculate_rates_ast007

Code comparison

Compare the code used in this Job Request