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Job request: 11471

Organisation:
Bennett Institute
Workspace:
asthma_sro
ID:
2p5pje2mnhgtlb7j
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 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
  
  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:v0.0.46 
        --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

  join_measures_register:
      run: python:latest python analysis/join_and_round.py
           --input-list output/joined/measure_ast_reg_total_rate.csv
           --input-list output/joined/measure_ast_reg_age_band_rate.csv
           --input-list output/joined/measure_ast_reg_care_home_rate.csv
           --input-list output/joined/measure_ast_reg_ethnicity_rate.csv
           --input-list output/joined/measure_ast_reg_imd_rate.csv
           --input-list output/joined/measure_ast_reg_learning_disability_rate.csv
           --input-list output/joined/measure_ast_reg_region_rate.csv
           --input-list output/joined/measure_ast_reg_sex_rate.csv
           --output-dir output/joined/summary
           --output-name "measure_register.csv"
      needs: [generate_measures_ast_reg]
      outputs:
        moderately_sensitive:
          # Only output the single summary file
          measure_csv: output/joined/summary/measure_register.csv         
  
  calculate_rates_ast_reg:
      run: python:latest python analysis/rate_calculations.py
      needs: [generate_measures_ast_reg]
      outputs:
        moderately_sensitive:
          tables: output/rate_table_*.csv
          plots: output/plot_*.png
          decile_chart: output/decile_chart.png
 #############################
  # Plotting
  #############################
  generate_qof_deciles_charts:
    run: >
            deciles-charts:v0.0.15
            --input-files output/joined/measure_*_practice_rate.csv
            --output-dir output/joined
    config:
      show_outer_percentiles: false
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures_ast_reg]
    outputs:
      moderately_sensitive:
        cohort: output/joined/deciles_*_*.*

  generate_qof_groups:
    run: >
            python:latest python analysis/group_charts.py
            --input-files output/joined/measure_ast_reg_*.csv
            --output-dir output/joined
            --date-lines "2019-03-31" "2020-03-31" "2021-03-31"
            --scale "percentage"
    needs: [generate_measures_ast_reg]
    outputs:
      moderately_sensitive:
        cohort: output/joined/group_chart_*.png

  generate_all_breakdowns:
    run: >
            python:latest python analysis/panel_plots.py
            --input-file output/joined/summary/measure_register.csv
            --measures-pattern "*_rate"
            --output-dir output/joined/summary
            --output-name "asthma_register_by_demographic_group"
            --date-lines "2019-03-31" "2020-03-31" "2021-03-31"
            --scale "percentage"
    needs: [join_measures_register]
    outputs:
      moderately_sensitive:
        cohort: output/joined/summary/asthma_register_by_demographic_group.png

  generate_notebook_ast_reg:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/Table1_notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [join_measures_register]
    outputs:
      moderately_sensitive:
        notebook: output/Table1_notebook.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 43:57:00

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
Yes
Git commit hash
570dbbf
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request