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Job request: 25341

Organisation:
Bennett Institute
Workspace:
winter_pressures_inequalities
ID:
zrvxln6zz64364m3
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Ruth Costello 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: '4.0'
# Generates cohorts for COVID outcome.
actions:  
  generate_dataset_covid_2021:
      run: >
        ehrql:v1 generate-dataset analysis/dataset_definition_covid.py 
        --output output/dataset_covid_2021.arrow
        --
        --start_date 2021-03-01
      outputs:
        highly_sensitive:
          population: output/dataset_covid_2021.arrow

  generate_dataset_covid_2022:
      run: >
        ehrql:v1 generate-dataset analysis/dataset_definition_covid.py 
        --output output/dataset_covid_2022.arrow
        --test-data-file analysis/test_dataset_definition_covid.py
        --
        --start_date 2022-03-01
      outputs:
        highly_sensitive:
          population: output/dataset_covid_2022.arrow

  generate_dataset_covid_2023:
      run: >
        ehrql:v1 generate-dataset analysis/dataset_definition_covid.py 
        --output output/dataset_covid_2023.arrow
        --
        --start_date 2023-03-01
      outputs:
        highly_sensitive:
          population: output/dataset_covid_2023.arrow

  generate_dataset_covid_2024:
      run: >
        ehrql:v1 generate-dataset analysis/dataset_definition_covid.py 
        --output output/dataset_covid_2024.arrow
        --
        --start_date 2024-03-01
      outputs:
        highly_sensitive:
          population: output/dataset_covid_2024.arrow

  generate_dataset_flu_rsv_2018:
      run: >
        ehrql:v1 generate-dataset analysis/dataset_definition_flu_rsv.py 
        --output output/dataset_flu_rsv_2018.arrow
        --test-data-file analysis/test_dataset_definition_flu_rsv.py
        --
        --start_date 2018-09-01
      outputs:
        highly_sensitive:
          population: output/dataset_flu_rsv_2018.arrow

  generate_dataset_flu_rsv_2019:
      run: >
        ehrql:v1 generate-dataset analysis/dataset_definition_flu_rsv.py 
        --output output/dataset_flu_rsv_2019.arrow
        --test-data-file analysis/test_dataset_definition_flu_rsv.py
        --
        --start_date 2019-09-01
      outputs:
        highly_sensitive:
          population: output/dataset_flu_rsv_2019.arrow

  generate_dataset_flu_rsv_2021:
      run: >
        ehrql:v1 generate-dataset analysis/dataset_definition_flu_rsv.py 
        --output output/dataset_flu_rsv_2021.arrow
        --test-data-file analysis/test_dataset_definition_flu_rsv.py
        --
        --start_date 2021-09-01
      outputs:
        highly_sensitive:
          population: output/dataset_flu_rsv_2021.arrow

  generate_dataset_flu_rsv_2022:
      run: >
        ehrql:v1 generate-dataset analysis/dataset_definition_flu_rsv.py 
        --output output/dataset_flu_rsv_2022.arrow
        --test-data-file analysis/test_dataset_definition_flu_rsv.py
        --
        --start_date 2022-09-01
      outputs:
        highly_sensitive:
          population: output/dataset_flu_rsv_2022.arrow

  generate_dataset_flu_rsv_2023:
      run: >
        ehrql:v1 generate-dataset analysis/dataset_definition_flu_rsv.py 
        --output output/dataset_flu_rsv_2023.arrow
        --test-data-file analysis/test_dataset_definition_flu_rsv.py
        --
        --start_date 2023-09-01
      outputs:
        highly_sensitive:
          population: output/dataset_flu_rsv_2023.arrow

  generate_dataset_flu_rsv_2024:
      run: >
        ehrql:v1 generate-dataset analysis/dataset_definition_flu_rsv.py 
        --output output/dataset_flu_rsv_2024.arrow
        --test-data-file analysis/test_dataset_definition_flu_rsv.py
        --
        --start_date 2024-09-01
      outputs:
        highly_sensitive:
          population: output/dataset_flu_rsv_2024.arrow

  measures_covid: 
      run: >
        ehrql:v1 generate-measures analysis/measures_covid.py
        --output output/measures/measures_covid.csv 
        --
        --start-date 2021-03-01
        --intervals 48
      outputs:
        highly_sensitive:
          measures_csv: output/measures/measures_covid.csv

  measures_flu_rsv_2018: 
      run: >
        ehrql:v1 generate-measures analysis/measures_flu_rsv.py
        --output output/measures/measures_flu_rsv_2018.csv 
        --
        --start-date 2018-09-01
        --intervals 24
      outputs:
        highly_sensitive:
          measures_csv: output/measures/measures_flu_rsv_2018.csv

  measures_flu_rsv_2021: 
      run: >
        ehrql:v1 generate-measures analysis/measures_flu_rsv.py
        --output output/measures/measures_flu_rsv_2021.csv 
        --
        --start-date 2021-09-01
        --intervals 48
      outputs:
        highly_sensitive:
          measures_csv: output/measures/measures_flu_rsv_2021.csv

  data_process_covid:
      run: r:latest analysis/data_processing_covid.R 
      needs: 
      - generate_dataset_covid_2021
      - generate_dataset_covid_2022
      - generate_dataset_covid_2023
      - generate_dataset_covid_2024
      - generate_dataset_flu_rsv_2018
      - generate_dataset_flu_rsv_2019
      - generate_dataset_flu_rsv_2021
      - generate_dataset_flu_rsv_2022
      - generate_dataset_flu_rsv_2023
      - generate_dataset_flu_rsv_2024
      outputs: 
        highly_sensitive:
          data: output/an_bl_data_covid.arrow
          data_flu_rsv: output/an_bl_data_flu_rsv.arrow

  tables:
      run: r:latest analysis/descriptive_analysis.R 
      needs: 
        - data_process_covid
      outputs: 
        moderately_sensitive:
          table: output/tables/baseline_table_covid.csv
          table_flu_rsv: output/tables/baseline_table_flu_rsv.csv
          table_s: output/tables/baseline_table_covid_strata.csv
          table_flu_rsv_s: output/tables/baseline_table_flu_rsv_strata.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 05:30:31

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

Job request

Status
Succeeded
Backend
TPP
Workspace
winter_pressures_inequalities
Requested by
Ruth Costello
Branch
main
Force run dependencies
No
Git commit hash
8aef097
Requested actions
  • generate_dataset_covid_2021
  • generate_dataset_covid_2022
  • generate_dataset_covid_2023
  • generate_dataset_covid_2024

Code comparison

Compare the code used in this job request