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Job request: 10865

Organisation:
Nuffield Trust
Workspace:
deaths-at-home-during-covid-19
ID:
wkbqmt2ttq6pazfv
View repo View project.yaml

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 in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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: 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:

  • Started:

  • Finished:

  • Runtime: 00:51:21

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

Job information

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