Job request: 4788

Organisation:: University of Bristol
Workspace:: covid-ve-change-over-time--process-data-for-models
ID:: lpngiuu56g3or2hf

This page shows the technical details of what happened when the authorised researcher Elsie Horne 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

Action:

design

Status:

Status: Succeeded

Job identifier:

k4ciz5uxepbszy7m
Action:

dummy_data

Status:

Status: Succeeded

Job identifier:

2ekhzvi55cwq2ojy
Action:

generate_study_population

Status:

Status: Succeeded

Job identifier:

vvsk33livjwdc2jy
Action:

data_input_process

Status:

Status: Succeeded

Job identifier:

rngfleacn35ixnbw
Action:

data_long_process

Status:

Status: Succeeded

Job identifier:

rzcv3m6u47zzh2me
Action:

data_eligible_ab

Status:

Status: Succeeded

Job identifier:

quzvpssrrwmb4qqn
Action:

data_2nd_vax_dates

Status:

Status: Succeeded

Job identifier:

7edgjjrt6pql6hnt
Action:

plot_2nd_vax_dates

Status:

Status: Succeeded

Job identifier:

rmtvdqgxx55skaph
Action:

data_eligible_cd

Status:

Status: Succeeded

Job identifier:

ocohx4urjr6bympm
Action:

data_comparisons_process_02

Status:

Status: Succeeded

Job identifier:

r4rmcnsrdbfegvy7
Action:

data_outcomes_process_02

Status:

Status: Succeeded

Job identifier:

eolyetxup32pmgvk
Action:

data_tte_process_02_postest

Status:

Status: Succeeded

Job identifier:

cp7qrtwu6w5xey6g
Action:

check_combine_outcomes_02

Status:

Status: Succeeded

Job identifier:

phrjbihd6viducpe
Action:

apply_model_cox_02_postest

Status:

Status: Succeeded

Job identifier:

nygq7baz4ovse2tl

Pipeline

Show project.yaml

version: '3.0'

expectations:

  population_size: 100000

actions:

  ## #################################### 
  ## preliminaries 
  ## #################################### 

  design:
    run: r:latest analysis/design.R
    outputs:
      moderately_sensitive:
        study_dates_json: output/lib/study_parameters.json
        study_dates_rds: output/lib/study_parameters.rds
        jcvi_groups: output/lib/jcvi_groups.csv
        elig_dates: output/lib/elig_dates.csv
        regions: output/lib/regions.csv
        model_varlist: output/lib/model_varlist.rds

  ## #################################### 
  ## study definition 
  ## #################################### 
  ## generate dummy data for study_definition 

  dummy_data:
    run: r:latest analysis/dummy_data.R
    needs:
    - design
    outputs:
      moderately_sensitive:
        dummy_data: analysis/dummy_data.feather

  ## study definition 

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
      --output-format feather
    dummy_data_file: analysis/dummy_data.feather
    needs:
    - design
    - dummy_data
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  ## #################################### 
  ## preprocessing 
  ## #################################### 
  ## process data from study_definition 

  data_input_process:
    run: r:latest analysis/preprocess/data_input_process.R
    needs:
    - design
    - dummy_data
    - generate_study_population
    outputs:
      highly_sensitive:
        data_covs: output/data/data_covs.rds
        data_vax_dates: output/data/data_*_vax_dates.rds
      moderately_sensitive:
        data_properties: output/tables/data_processed_tabulate.txt

  ## process recurring variables as long data 

  data_long_process:
    run: r:latest analysis/preprocess/data_long_process.R
    needs:
    - design
    - data_input_process
    outputs:
      highly_sensitive:
        data_long_dates: output/data/data_long_*_dates.rds

  ## apply eligiblity criteria from boxes a and b 

  data_eligible_ab:
    run: r:latest analysis/preprocess/data_eligible_ab.R
    needs:
    - design
    - data_input_process
    outputs:
      highly_sensitive:
        data_eligible_a: output/data/data_eligible_a.rds
        data_eligible_b: output/data/data_eligible_b.rds
      moderately_sensitive:
        eligibility_count: output/lib/eligibility_count_ab.csv
        group_age_ranges: output/lib/group_age_ranges.csv

  ## #################################### 
  ## second_vax_period 
  ## #################################### 
  ## identify second vaccination time periods 
  ## create dataset for identifying second vaccination time periods 

  data_2nd_vax_dates:
    run: r:latest analysis/second_vax_period/data_2nd_vax_dates.R
    needs:
    - design
    - data_input_process
    - data_eligible_ab
    outputs:
      highly_sensitive:
        data_vax_plot: output/second_vax_period/data/data_vax_plot.rds
        second_vax_period_dates_rds: output/lib/second_vax_period_dates.rds
      moderately_sensitive:
        second_vax_period_dates_csv: output/lib/second_vax_period_dates.csv

  ## plot second vaccination time periods 

  plot_2nd_vax_dates:
    run: r:latest analysis/second_vax_period/plot_2nd_vax_dates.R
    needs:
    - design
    - data_eligible_ab
    - data_2nd_vax_dates
    outputs:
      moderately_sensitive:
        plots_by_region: output/second_vax_period/images/plot_by_region_*.png

  ## apply eligiblity criteria from boxes c and d 

  data_eligible_cd:
    run: r:latest analysis/second_vax_period/data_eligible_cd.R
    needs:
    - design
    - data_input_process
    - data_eligible_ab
    - data_2nd_vax_dates
    outputs:
      highly_sensitive:
        data_eligible_c: output/data/data_eligible_c.rds
        data_eligible_d: output/data/data_eligible_d.rds

  ## #################################### 
  ## comparisons 
  ## #################################### 
  ## process data, apply model and generate report for JCVI group 02 
  ## process covariates data 

  data_comparisons_process_02:
    run: r:latest analysis/comparisons/data_comparisons_process.R 02
    needs:
    - design
    - data_input_process
    - data_long_process
    - data_2nd_vax_dates
    - data_eligible_cd
    outputs:
      highly_sensitive:
        data_comparisons: output/jcvi_group_02/data/data_comparisons.rds

  ## process outcomes data 

  data_outcomes_process_02:
    run: r:latest analysis/comparisons/data_outcomes_process.R 02
    needs:
    - design
    - data_input_process
    - data_long_process
    - data_comparisons_process_02
    outputs:
      highly_sensitive:
        data_outcomes: output/jcvi_group_02/data/data_outcomes.rds

  ## check gap between outcomes for combining 

  check_combine_outcomes_02:
    run: r:latest analysis/comparisons/check_combine_outcomes.R 02
    needs:
    - data_outcomes_process_02
    outputs:
      highly_sensitive:
        data_check_combine_outcomes: output/jcvi_group_02/data/check_combine_outcomes.rds
      moderately_sensitive:
        plot_check_combine_outcomes: output/jcvi_group_02/images/check_combine_outcomes.png
        table_check_combine_outcomes: output/jcvi_group_02/tables/check_combine_outcomes.csv

  ## outcome = postest 
  ## process tte data for postest 

  data_tte_process_02_postest:
    run: r:latest analysis/comparisons/data_tte_process.R 02 postest
    needs:
    - data_comparisons_process_02
    - data_outcomes_process_02
    outputs:
      highly_sensitive:
        data_tte_brand_outcome: output/jcvi_group_02/data/data_tte_*_postest.rds

  ## apply cox model for postest 

  apply_model_cox_02_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R 02 postest
    needs:
    - design
    - data_comparisons_process_02
    - data_tte_process_02_postest
    outputs:
      highly_sensitive:
        modelnumber: output/jcvi_group_02/models/*_postest_model*.rds
        model_tidy_rds: output/jcvi_group_02/models/*_postest_modelcox_tidy.rds
      moderately_sensitive:
        model_glance: output/jcvi_group_02/models/*_postest_modelcox_glance.csv
        model_tidy_csv: output/jcvi_group_02/models/*_postest_modelcox_tidy.csv

Timeline

Created: 2 years, 11 months ago 23 Dec 2021 06:56:06 UTC
Started: 2 years, 11 months ago 23 Dec 2021 06:56:24 UTC
Finished: 2 years, 11 months ago 23 Dec 2021 15:16:49 UTC
Runtime: 08:29:09

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

Job information

Status: Succeeded
Backend: TPP
Workspace: covid-ve-change-over-time--process-data-for-models
Requested by: Elsie Horne
Branch: process-data-for-models
Force run dependencies: Yes
Git commit hash: b5e2555
Requested actions: run_all

Code comparison

Compare the code used in this Job Request