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Job request: 8859

Organisation:
Bennett Institute
Workspace:
asthma_sro
ID:
4uuhfexj5dbojczh
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 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 
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) Dictionary method actions
  generate_study_population_ast_reg:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_ast_reg 
      --index-date-range "2019-03-01 to 2022-03-31 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: 14:12:07

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

Job request

Status
Succeeded
Backend
TPP
Workspace
asthma_sro
Requested by
Rose Higgins
Branch
master
Force run dependencies
Yes
Git commit hash
c77942b
Requested actions
  • generate_study_population_ast_reg
  • join_ethnicity_ast_reg
  • generate_measures_ast_reg

Code comparison

Compare the code used in this job request