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Job request: 7043

Organisation:
Bennett Institute
Workspace:
asthma_sro
ID:
fisl6oaol3ych6xb
View repo View project.yaml

This page shows the technical details of what happened when the 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 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 
version: '3.0'

expectations:
  population_size: 1000

actions:

  
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-03-01 to 2022-03-31 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_*.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:
    run: python:latest python analysis/join_ethnicity.py
    needs: [generate_study_population, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/input*.csv

  generate_study_population_practice_count:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --index-date-range "2019-03-01 to 2022-03-31 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_practice_count_*.csv

  generate_measures:
      run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
      needs: [join_ethnicity]
      outputs:
        moderately_sensitive:
          measure_csv: output/measure_*_rate.csv
  
  calculate_rates:
      run: python:latest python analysis/rate_calculations.py
      needs: [generate_measures]
      outputs:
        moderately_sensitive:
          tables: output/rate_table_*.csv
          plots: output/plot_*.png
          decile_chart: output/decile_chart.png

  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/qof_notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [calculate_rates, generate_study_population_practice_count]
    outputs:
      moderately_sensitive:
        notebook: output/qof_notebook.html


# Asthma register (ast_reg)
  generate_study_population_ast_reg:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_ast_reg 
      --index-date-range "2021-04-01 to 2022-03-01 by month" 
      --output-dir=output
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/input_ast_reg*.csv
  
  join_ethnicity_ast_reg:
    run: >
      cohort-joiner:v0.0.12 
        --lhs output/input_ast*.csv
        --rhs output/input_ethnicity*.csv
        --output-dir output/joined
    needs: [generate_study_population_ethnicity, generate_study_population_ast_reg]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_ast*.csv

  generate_measures_ast_reg:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_ast_reg 
       --output-dir=output/joined
     needs: [join_ethnicity_ast_reg]
     outputs:
       moderately_sensitive:
         measure_csv: output/joined/measure_ast_reg_*_rate.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 22:05:48

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

Job information

Status
Succeeded
Backend
TPP
Workspace
asthma_sro
Requested by
Rose Higgins
Branch
master
Force run dependencies
No
Git commit hash
96e1513
Requested actions
  • generate_study_population
  • generate_study_population_ethnicity
  • join_ethnicity
  • generate_study_population_practice_count
  • generate_measures
  • calculate_rates

Code comparison

Compare the code used in this Job Request