Job request: 10865

Organisation:: Nuffield Trust
Workspace:: deaths-at-home-during-covid-19
ID:: wkbqmt2ttq6pazfv

This page shows the technical details of what happened when the authorised researcher Eilís Keeble 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

Action:

service_use_models

Status:

Status: Succeeded

Job identifier:

2beq5hbfimo7ctik
Action:

service_use_home_models

Status:

Status: Succeeded

Job identifier:

gf6c2uyvixtggjk6

Pipeline

Show project.yaml

version: '3.0'

expectations:
  population_size: 10000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  generate_flow_chart_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_flow_chart.feather


  generate_study_population_measures:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_measures --output-format feather --index-date-range "2019-03-01 to 2021-02-01 by month" --skip-existing --output-dir=output/practice_measures
    outputs:
      highly_sensitive:
        cohort: output/practice_measures/input_*.feather

  generate_practice_measures:
      run: cohortextractor:latest generate_measures --study-definition study_definition_practice_measures --skip-existing --output-dir=output/practice_measures
      needs: [generate_study_population_measures]
      outputs:
        moderately_sensitive:
          measure_binary_csv: output/practice_measures/measure_*_binary.csv
          measure_csv: output/practice_measures/measure_*_rate.csv

  generate_report:
    run: cohort-report:v3.0.0 output/input.feather
    needs: [generate_study_population]
    config:
      output_path: output/cohort_reports_outputs
    outputs: 
      moderately_sensitive:
        report: output/cohort_reports_outputs/descriptives_input.html
        report_charts: output/cohort_reports_outputs/*.png

  flow_chart:
    run: r:latest analysis/00_flow_chart_data.R
    needs: [generate_flow_chart_population]
    outputs:
      moderately_sensitive:
        flow_data: output/flow_chart_data/flow_chart_data.csv

  describe_cohorts:
    run: r:latest analysis/01_describe_cohorts.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        deaths_data: output/describe_cohorts/overall_death_counts/deaths_data.csv
        deaths_cohort: output/describe_cohorts/overall_death_counts/deaths_cohort.csv
        deaths_quarter: output/describe_cohorts/overall_death_counts/deaths_quarter.csv
        deaths_quarter_figure: output/describe_cohorts/overall_death_counts/deaths_quarter.png
        deaths_data_pod: output/describe_cohorts/overall_death_counts/deaths_data_pod.csv
        deaths_cohort_pod: output/describe_cohorts/overall_death_counts/deaths_cohort_pod*.csv
        deaths_quarter_pod: output/describe_cohorts/overall_death_counts/deaths_quarter_pod.csv
        deaths_pod_figures: output/describe_cohorts/overall_death_counts/deaths_pod_cohort*.png
        deaths_quarter_characteristic: output/describe_cohorts/quarter_death_counts/deaths_quarter_*.csv
        quarter_summary_table: output/describe_cohorts/quarter_summary_table.csv
        quarter_pod_summary_table: output/describe_cohorts/quarter_pod_summary_table.csv
        deaths_quarter_ons: output/describe_cohorts/ons_death_comparisons/deaths_ons_quarter*.csv
        deaths_month_ons: output/describe_cohorts/ons_death_comparisons/deaths_ons_month*.csv
        deaths_ons_plots: output/describe_cohorts/ons_death_comparisons/deaths_ons*.png
        cohort_summary_table: output/describe_cohorts/cohorts_summary_table.csv
        cohort_pod_summary_table: output/describe_cohorts/cohorts_pod_summary_table*.csv
        death_ratios_cohort: output/describe_cohorts/death_ratios_cohort/death_ratio_cohort*.csv
        death_ratios_pod_cohort: output/describe_cohorts/death_ratios_pod_cohort/death_ratio_pod_cohort*.csv
        deaths_region_ethnicity: output/describe_cohorts/overall_death_counts/deaths_region*.csv
        deaths_characteristic_crosstabs: output/describe_cohorts/overall_death_counts/deaths_characteristic_crosstabs*.csv

  describe_service_use:
    run: r:latest analysis/02_describe_service_use.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        service_use_means: output/describe_service_use/service_use_mean*.csv
        service_use_means_plots: output/describe_service_use/plots/service_use_mean*.pdf
        service_use_prop_plots: output/describe_service_use/plots/service_use_prop*.pdf
        gp_complete_service_use_means: output/describe_service_use/complete_gp_history/gp_service_use_mean*.csv
        gp_complete_service_use_means_plots: output/describe_service_use/complete_gp_history/plots/gp_service_use_mean*.pdf
        gp_complete_service_use_prop_plots: output/describe_service_use/complete_gp_history/plots/gp_service_use_prop*.pdf

  describe_service_use_home_cohort: 
    run: r:latest analysis/03_describe_service_use_home_cohort.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        service_use_cohort: output/describe_service_use_home/service_use_cohort_home*.csv     
        service_use_cohort_plots: output/describe_service_use_home/plots/service_use_cohort_home_*.pdf        
        service_use_cohort_prop_plots: output/describe_service_use_home/plots/service_prop_cohort_home_*.pdf

  describe_service_use_home_quarter: 
    run: r:latest analysis/04_describe_service_use_home_quarter.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        service_use_quarter: output/describe_service_use_home/service_use_quart_home.csv
        service_use_quarter_plots: output/describe_service_use_home/plots/service_use_quart_home*.pdf
        service_use_quarter_prop_plots: output/describe_service_use_home/plots/service_prop_quart_home*.pdf

  describe_service_use_home_gp_cohort: 
    run: r:latest analysis/05_describe_service_use_home_gp_cohort.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        gp_complete_service_use_cohort: output/describe_service_use_home/complete_gp_history/gp_service_use_cohort_home*.csv     
        gp_complete_service_use_cohort_plots: output/describe_service_use_home/complete_gp_history/plots/gp_service_use_cohort_home_*.pdf
        gp_complete_service_use_cohort_prop_plots: output/describe_service_use_home/complete_gp_history/plots/gp_service_prop_cohort_home_*.pdf

  describe_service_use_home_gp_quarter: 
    run: r:latest analysis/06_describe_service_use_home_gp_quarter.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        gp_complete_service_use_quarter: output/describe_service_use_home/complete_gp_history/gp_service_use_quart_home.csv
        gp_complete_service_use_quarter_plots: output/describe_service_use_home/complete_gp_history/plots/gp_service_use_quart_home_*.pdf
        gp_complete_service_use_quarter_prop_plots: output/describe_service_use_home/complete_gp_history/plots/gp_service_prop_quart_home_*.pdf

  practice_measures_plots:
    run: r:latest analysis/07_practice_measures_plots.R
    needs: [generate_practice_measures]
    outputs:
      moderately_sensitive:
        deciles_data: output/practice_measures/plots/deciles_*.csv
        deciles_plots: output/practice_measures/plots/deciles_*.png

  service_use_models:
    run: r:latest analysis/08_service_use_models.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        service_use_models: output/describe_service_use/models/model_*.csv
        gp_service_use_models: output/describe_service_use/complete_gp_history/models/gp_model_*.csv

  service_use_home_models: 
    run: r:latest analysis/09_home_service_use_models.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        service_use_models: output/describe_service_use_home/models/model_*.csv

Timeline

Created: 3 years, 2 months ago 15 Aug 2022 09:57:14 UTC
Started: 3 years, 2 months ago 15 Aug 2022 09:57:16 UTC
Finished: 3 years, 2 months ago 15 Aug 2022 10:25:30 UTC
Runtime: 00:51:21

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

Job request

Status: Succeeded
Backend: TPP
Workspace: deaths-at-home-during-covid-19
Requested by: Eilís Keeble
Branch: main
Force run dependencies: No
Git commit hash: 9d7a652
Requested actions: service_use_models

service_use_home_models

Code comparison

Compare the code used in this job request