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Job request: 9758

Organisation:
Bennett Institute
Workspace:
shared-care-monitoring
ID:
xtj45skqzmg6h6pb
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Andrew Brown 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:

  generate_study_population_1:
     run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-09-01 to 2019-12-01 by month" --output-format csv.gz
     outputs:
       highly_sensitive:
         cohort: output/input_*.csv.gz
       
  generate_study_population_ethnicity:    
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv.gz

  join_cohorts:
    run: >
      cohort-joiner:v0.0.7
        --lhs output/input_20*.csv.gz
        --rhs output/input_ethnicity.csv.gz
        --output-dir output/joined
    needs: [generate_study_population_1, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_20*.csv.gz
    
  generate_report:
     run: cohort-report:v3.0.0 output/joined/input_2019-09-01.csv.gz output/joined/input_2019-10-01.csv.gz output/joined/input_2019-11-01.csv.gz output/joined/input_2019-12-01.csv.gz
     needs: [join_cohorts]
     config:
       variable_types:
           age_band: categorical
           sex: categorical
           ethnicity: categorical
           practice: categorical
           region: categorical
           imdQ5: categorical
           rural_urban: categorical
           care_home: binary
           housebound: binary
           dementia: binary
           learning_disability: binary
           serious_mental_illness: binary
           methotrexate_3months: binary
           leflunomide_3months: binary
           azathioprine_3months: binary
           full_blood_count_3months: binary
           liver_function_test_3months: binary
           urea_electrolyte_test_3months: binary
           blood_pressure_test_3months: binary
           met_overdue_num: binary
           lef_overdue_num: binary
           aza_overdue_num: binary
           all_sc_overdue_monitoring_num: binary
           fbc_overdue_num: binary
           lft_overdue_num: binary
           u_e_overdue_num: binary
           bp_overdue_num: binary
       output_path: output/cohort_reports_outputs
     outputs:
       moderately_sensitive:
         reports: output/cohort_reports_outputs/descriptives_input_*.html
                  
  generate_measures:
     run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir output/joined
     needs: [join_cohorts]
     outputs:
       moderately_sensitive:
         measure_csv: output/joined/measure_*_rate.csv
         
  generate_deciles_charts:
     run: >
       deciles-charts:v0.0.21
         --input-files output/joined/measure_all_sc_overdue_monitoring_by_practice_rate.csv
         --output-dir output/joined
     needs: [generate_measures]
     outputs:
       moderately_sensitive:
         deciles_charts: output/joined/deciles_*_*.*

  generate_plots:
     run: python:latest python analysis/plots.py
     needs: [generate_measures]
     outputs:
       moderately_sensitive:
         counts: output/joined/plot_*.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 15:00:48

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

Job information

Status
Succeeded
Backend
TPP
Workspace
shared-care-monitoring
Requested by
Andrew Brown
Branch
main
Force run dependencies
Yes
Git commit hash
da7ac36
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request