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Job request: 12263

Organisation:
Bennett Institute
Workspace:
medication_reviews
ID:
7bij3wgilnfhhjoj
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Vicky Speed 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: 3000

actions:

  generate_study_population:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition
        --index-date-range "2019-04-01 to 2022-03-01 by month"
        --output-format='csv.gz'
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv.gz

  generate_ethnicity_cohort:
    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:v0.0.44
        --lhs output/input_20*.csv.gz
        --rhs output/input_ethnicity.csv.gz
        --output-dir output/joined
    needs: [generate_study_population, generate_ethnicity_cohort]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_*.csv.gz

## generate Structured Medication Review Measures and plots

  generate_measures_all_reviews:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition 
       --output-dir=output/joined
     needs: [join_cohorts]
     outputs:
       moderately_sensitive:
         measure_csv: output/joined/measure_*_*_rate.csv
  
  smr_plots:
    run: python:latest python analysis/plots.py
    needs: [generate_measures_all_reviews]
    outputs:
      moderately_sensitive:
        cohort: output/figures/*_*_rate.jpeg

  generate_deciles_charts:
    run: >
      deciles-charts:v0.0.33
        --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_all_reviews]
    outputs:
      moderately_sensitive:
        deciles_charts: output/joined/deciles_*_*.*

  generate_table_1:
    run: python:latest python analysis/table_1.py --study_def_paths="output/joined/input_*.csv.gz" --demographics="age_band,sex,region,imdQ5,ethnicity,learning_disability,care_home_type" --outcome "had_smr"
    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        counts: output/table_1.csv
        had_outcome: output/table_1_had_outcome.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 29:41:46

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

Job request

Status
Succeeded
Backend
TPP
Workspace
medication_reviews
Requested by
Vicky Speed
Branch
main
Force run dependencies
Yes
Git commit hash
94fc1b9
Requested actions
  • generate_study_population
  • generate_ethnicity_cohort
  • join_cohorts
  • generate_measures_all_reviews
  • smr_plots
  • generate_deciles_charts
  • generate_table_1
  • run_all

Code comparison

Compare the code used in this job request