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Job request: 27128

Organisation:
University of Bristol
Workspace:
zostavax-dementia
ID:
fimac4vmutjjjqto
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Andrea Schaffer 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:
    generate_dataset_zostavax_main
    Status:
    Succeeded
    Job identifier:
    jo7kxq3xcrs2urjz
  • Action:
    process_zostavax
    Status:
    Succeeded
    Job identifier:
    6qwxkosxmy3g4rx7
  • Action:
    flow_chart_zostavax
    Status:
    Succeeded
    Job identifier:
    24vyeyggq2ylcxxa
  • Action:
    descriptives_zostavax
    Status:
    Succeeded
    Job identifier:
    onnzw2p2xxyuaqdt

Pipeline

Show project.yaml 
version: '5.0'

actions:

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create_project_actions.R 
  ## Edit and run create_project_actions.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Generate dataset 

  generate_dataset_zostavax_main:
    run: ehrql:v1 generate-dataset analysis/dataset_definition.py --output output/zostavax/dataset_zostavax_main.arrow
      --dummy-data-file analysis/dummy_data/dummy_dataset_zostavax.arrow -- --threshold_date
      2013-09-01 --min_dob 1920-09-01 --max_dob 1948-09-01
      --vaccine_name zostavax
    outputs:
      highly_sensitive:
        data: output/zostavax/dataset_zostavax_main.arrow

  ## Process dataset 

  process_zostavax:
    run: r:v2 analysis/zostavax/0_zostavax_processing.R
    needs:
    - generate_dataset_zostavax_main
    outputs:
      highly_sensitive:
        processed_data: output/zostavax/processed/dataset_processed_zostavax_main.arrow

  ## Flow chart 

  flow_chart_zostavax:
    run: r:v2 analysis/zostavax/1_zostavax_flow_chart.R
    needs:
    - process_zostavax
    outputs:
      moderately_sensitive:
        flow_chart: output/zostavax/processed/flow_chart_zostavax_main.csv

  ## Descriptives 

  descriptives_zostavax:
    run: r:v2 analysis/zostavax/2_zostavax_descriptives.R
    needs:
    - process_zostavax
    outputs:
      moderately_sensitive:
        txt: output/zostavax/descriptives/main/*.txt
        csv: output/zostavax/descriptives/main/*.csv
        png: output/zostavax/descriptives/main/*.png

  ## Define populations 

  rd_populations_general:
    run: r:v2 analysis/zostavax/3_zostavax_rd_populations.R general
    needs:
    - process_zostavax
    outputs:
      highly_sensitive:
        population: output/zostavax/populations/dataset_analysis_zostavax_main_general.arrow

  rd_populations_aged77_82:
    run: r:v2 analysis/zostavax/3_zostavax_rd_populations.R aged77_82
    needs:
    - process_zostavax
    outputs:
      highly_sensitive:
        population: output/zostavax/populations/dataset_analysis_zostavax_main_aged77_82.arrow

  rd_populations_aged78_81:
    run: r:v2 analysis/zostavax/3_zostavax_rd_populations.R aged78_81
    needs:
    - process_zostavax
    outputs:
      highly_sensitive:
        population: output/zostavax/populations/dataset_analysis_zostavax_main_aged78_81.arrow

  rd_populations_reduced_excl:
    run: r:v2 analysis/zostavax/3_zostavax_rd_populations.R reduced_excl
    needs:
    - process_zostavax
    outputs:
      highly_sensitive:
        population: output/zostavax/populations/dataset_analysis_zostavax_main_reduced_excl.arrow

  rd_populations_cogimp_no:
    run: r:v2 analysis/zostavax/3_zostavax_rd_populations.R cogimp_no
    needs:
    - process_zostavax
    outputs:
      highly_sensitive:
        population: output/zostavax/populations/dataset_analysis_zostavax_main_cogimp_no.arrow

  rd_populations_cogimp_yes:
    run: r:v2 analysis/zostavax/3_zostavax_rd_populations.R cogimp_yes
    needs:
    - process_zostavax
    outputs:
      highly_sensitive:
        population: output/zostavax/populations/dataset_analysis_zostavax_main_cogimp_yes.arrow

  rd_populations_men:
    run: r:v2 analysis/zostavax/3_zostavax_rd_populations.R men
    needs:
    - process_zostavax
    outputs:
      highly_sensitive:
        population: output/zostavax/populations/dataset_analysis_zostavax_main_men.arrow

  rd_populations_women:
    run: r:v2 analysis/zostavax/3_zostavax_rd_populations.R women
    needs:
    - process_zostavax
    outputs:
      highly_sensitive:
        population: output/zostavax/populations/dataset_analysis_zostavax_main_women.arrow

  rd_populations_thresholdm_no:
    run: r:v2 analysis/zostavax/3_zostavax_rd_populations.R thresholdm_no
    needs:
    - process_zostavax
    outputs:
      highly_sensitive:
        population: output/zostavax/populations/dataset_analysis_zostavax_main_thresholdm_no.arrow

  ## Determine MSE optimal bandwidth 

  rd_msebw_zostavax:
    run: r:v2 analysis/zostavax/4_zostavax_rd_msebw.R
    needs:
    - rd_populations_general
    outputs:
      moderately_sensitive:
        msebw: output/zostavax/setup/rd_msebw.csv

  ## Run RD analyses 

  rd_analysis_alt_kernel:
    run: r:v2 analysis/zostavax/5_zostavax_rd_analysis.R general alt_kernel
    needs:
    - rd_populations_general
    - rd_msebw_zostavax
    outputs:
      moderately_sensitive:
        results: output/zostavax/results/rd_results_alt_kernel.csv

  rd_analysis_alt_msebw:
    run: r:v2 analysis/zostavax/5_zostavax_rd_analysis.R general alt_msebw
    needs:
    - rd_populations_general
    - rd_msebw_zostavax
    outputs:
      moderately_sensitive:
        results: output/zostavax/results/rd_results_alt_msebw.csv

  rd_analysis_alt_outcome:
    run: r:v2 analysis/zostavax/5_zostavax_rd_analysis.R general alt_outcome
    needs:
    - rd_populations_general
    - rd_msebw_zostavax
    outputs:
      moderately_sensitive:
        results: output/zostavax/results/rd_results_alt_outcome.csv

  rd_analysis_alt_polynomial:
    run: r:v2 analysis/zostavax/5_zostavax_rd_analysis.R general alt_polynomial
    needs:
    - rd_populations_general
    - rd_msebw_zostavax
    outputs:
      moderately_sensitive:
        results: output/zostavax/results/rd_results_alt_polynomial.csv

  rd_analysis_annual_fup:
    run: r:v2 analysis/zostavax/5_zostavax_rd_analysis.R general annual_fup
    needs:
    - rd_populations_general
    - rd_msebw_zostavax
    outputs:
      moderately_sensitive:
        results: output/zostavax/results/rd_results_annual_fup.csv

  rd_analysis_fixed_bw_aged77_82:
    run: r:v2 analysis/zostavax/5_zostavax_rd_analysis.R aged77_82 fixed_bw_aged77_82
    needs:
    - rd_populations_aged77_82
    - rd_msebw_zostavax
    outputs:
      moderately_sensitive:
        results: output/zostavax/results/rd_results_fixed_bw_aged77_82.csv

  rd_analysis_fixed_bw_aged78_81:
    run: r:v2 analysis/zostavax/5_zostavax_rd_analysis.R aged78_81 fixed_bw_aged78_81
    needs:
    - rd_populations_aged78_81
    - rd_msebw_zostavax
    outputs:
      moderately_sensitive:
        results: output/zostavax/results/rd_results_fixed_bw_aged78_81.csv

  rd_analysis_primary:
    run: r:v2 analysis/zostavax/5_zostavax_rd_analysis.R general primary
    needs:
    - rd_populations_general
    - rd_msebw_zostavax
    outputs:
      moderately_sensitive:
        results: output/zostavax/results/rd_results_primary.csv

  rd_analysis_reduced_excl:
    run: r:v2 analysis/zostavax/5_zostavax_rd_analysis.R reduced_excl reduced_excl
    needs:
    - rd_populations_reduced_excl
    - rd_msebw_zostavax
    outputs:
      moderately_sensitive:
        results: output/zostavax/results/rd_results_reduced_excl.csv

  rd_analysis_sub_cogimp_no:
    run: r:v2 analysis/zostavax/5_zostavax_rd_analysis.R cogimp_no sub_cogimp_no
    needs:
    - rd_populations_cogimp_no
    - rd_msebw_zostavax
    outputs:
      moderately_sensitive:
        results: output/zostavax/results/rd_results_sub_cogimp_no.csv

  rd_analysis_sub_cogimp_yes:
    run: r:v2 analysis/zostavax/5_zostavax_rd_analysis.R cogimp_yes sub_cogimp_yes
    needs:
    - rd_populations_cogimp_yes
    - rd_msebw_zostavax
    outputs:
      moderately_sensitive:
        results: output/zostavax/results/rd_results_sub_cogimp_yes.csv

  rd_analysis_sub_sex_men:
    run: r:v2 analysis/zostavax/5_zostavax_rd_analysis.R men sub_sex_men
    needs:
    - rd_populations_men
    - rd_msebw_zostavax
    outputs:
      moderately_sensitive:
        results: output/zostavax/results/rd_results_sub_sex_men.csv

  rd_analysis_sub_sex_women:
    run: r:v2 analysis/zostavax/5_zostavax_rd_analysis.R women sub_sex_women
    needs:
    - rd_populations_women
    - rd_msebw_zostavax
    outputs:
      moderately_sensitive:
        results: output/zostavax/results/rd_results_sub_sex_women.csv

  rd_analysis_thresholdm_no:
    run: r:v2 analysis/zostavax/5_zostavax_rd_analysis.R thresholdm_no thresholdm_no
    needs:
    - rd_populations_thresholdm_no
    - rd_msebw_zostavax
    outputs:
      moderately_sensitive:
        results: output/zostavax/results/rd_results_thresholdm_no.csv

  ## Make output 

  rd_output_zostavax:
    run: r:v2 analysis/zostavax/6_zostavax_rd_output.R
    needs:
    - rd_analysis_alt_kernel
    - rd_analysis_alt_msebw
    - rd_analysis_alt_outcome
    - rd_analysis_alt_polynomial
    - rd_analysis_annual_fup
    - rd_analysis_fixed_bw_aged77_82
    - rd_analysis_fixed_bw_aged78_81
    - rd_analysis_primary
    - rd_analysis_reduced_excl
    - rd_analysis_sub_cogimp_no
    - rd_analysis_sub_cogimp_yes
    - rd_analysis_sub_sex_men
    - rd_analysis_sub_sex_women
    - rd_analysis_thresholdm_no
    outputs:
      moderately_sensitive:
        output: output/zostavax/output/rd_results.csv
        output_rounded: output/zostavax/output/rd_results_rounded.csv

Job statistics

Status Count Percentage
Pending 0 0%
Running 0 0%
Succeeded 4 100%
Failed 0 0%

4 / 4 (100%) complete

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:45:49

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

Job request

Status
Succeeded
Backend
TPP
Workspace
zostavax-dementia
Requested by
Andrea Schaffer
Branch
main
Force run dependencies
No
Git commit hash
57bd311
Requested actions
  • generate_dataset_zostavax_main
  • process_zostavax
  • flow_chart_zostavax
  • descriptives_zostavax

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