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Job request: 11679

Organisation:
University of Bristol
Workspace:
vaccine-effectiveness-in-children
ID:
fvf22iuynz5qeu7y
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Will Hulme requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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: 1000

actions:

  extract_treated:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition_treated
      --output-file output/input_treated.feather
    outputs:
      highly_sensitive:
        cohort: output/input_treated.feather

  data_process_treated:
    run: r:latest analysis/data_process_treated.R over12
    needs:
    - extract_treated
    outputs:
      highly_sensitive:
        rds: output/data/data_treated_eligible.rds
      moderately_sensitive:
        flowchart: output/data/flowchart_treated_eligible.csv

# Skim data
  skim_data_treated:
    run: r:latest analysis/data_skim.R output/data/data_treated_eligible.rds output/data_properties
    needs: [data_process_treated]
    outputs: 
      moderately_sensitive:
        txt1: output/data_properties/data_treated_eligible_skim.txt
        txt2: output/data_properties/data_treated_eligible_coltypes.txt
        txt3: output/data_properties/data_treated_eligible_tabulate.txt

  ## matching round 1
  
  extract_control_potential1:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_control_potential
      --output-file output/input_control_potential1.feather
      --output-format feather
      --param agegroup=over12
      --param matching_round=1
      --param index_date='2021-09-20'
    outputs:
      highly_sensitive:
        cohort: output/input_control_potential1.feather

 
  data_process_control_potential1:
    run: r:latest analysis/data_process_control.R over12 1
    needs:
    - extract_control_potential1
    outputs:
      highly_sensitive:
        rds: output/data/data_control_potential1.rds
 
  matching1:
    run: r:latest analysis/matching.R over12 1
    needs:
    - data_process_treated
    - data_process_control_potential1
    outputs:
      highly_sensitive:
        rds: output/match/data_potential_matchstatus1.rds
        #rds: output/match/data_potential_matched1.rds
        csv: output/match/potential_matchedcontrols1.csv.gz
 
  # skim_control_potential1:
  #   run: r:latest analysis/data_skim.R output/match/data_potential_matched1.rds output/data_properties
  #   needs: [matching1]
  #   outputs: 
  #     moderately_sensitive:
  #       txt1: output/data_properties/data_potential_matched1_skim.txt
  #       txt2: output/data_properties/data_potential_matched1_coltypes.txt
  #       txt3: output/data_properties/data_potential_matched1_tabulate.txt
 
  extract_control_match1:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition_control_match
      --output-file output/input_control_match1.feather 
      --param agegroup=over12
      --param matching_round=1
      --param index_date='2021-09-20'
    needs:
    - matching1
    outputs:
      highly_sensitive:
        cohort: output/input_control_match1.feather 

  matching_filter1:
    run: r:latest analysis/matching_filter.R over12 1
    needs:
    - matching1
    - data_process_treated
    - extract_control_match1
    - extract_control_potential1 # this is only necessary for the dummy data
    outputs:
      highly_sensitive:
        rds1: output/match/data_matchstatus_allrounds1.rds
        rds2: output/match/data_successful_matchedcontrols1.rds
        csv: output/match/cumulative_matchedcontrols1.csv.gz
        

  extract_finalmatched:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition_finalmatched 
      --output-file output/input_finalmatched.feather
    needs:
    - matching_filter1
    #- matching_filter2
    outputs:
      highly_sensitive:
        cohort: output/input_finalmatched.feather 
        
  data_process_finalmatched:
    run: r:latest analysis/data_process_finalmatched.R over12
    needs:
    - data_process_treated
    - extract_finalmatched
    - matching_filter1
    #- matching_filter2
    outputs:
      highly_sensitive:
        rds: output/data/data_finalmatched.rds
        
  model_km_over12_all_postest:
    run: r:latest analysis/km.R over12 all postest
    needs:
    - data_process_finalmatched
    outputs:
      moderately_sensitive:
        csv: output/comparison/over12/all/postest/*csv
        png: output/comparison/over12/all/postest/*png
        
  model_km_over12_all_covidemergency:
    run: r:latest analysis/km.R over12 all covidemergency
    needs:
    - data_process_finalmatched
    outputs:
      moderately_sensitive:
        csv: output/comparison/over12/all/covidemergency/*csv
        png: output/comparison/over12/all/covidemergency/*png
        
  model_km_over12_all_covidadmitted:
    run: r:latest analysis/km.R over12 all covidadmitted
    needs:
    - data_process_finalmatched
    outputs:
      moderately_sensitive:
        csv: output/comparison/over12/all/covidadmitted/*csv
        png: output/comparison/over12/all/covidadmitted/*png
        
  model_km_over12_all_emergency:
    run: r:latest analysis/km.R over12 all emergency
    needs:
    - data_process_finalmatched
    outputs:
      moderately_sensitive:
        csv: output/comparison/over12/all/emergency/*csv
        png: output/comparison/over12/all/emergency/*png
        
  model_km_over12_all_covidcritcare:
    run: r:latest analysis/km.R over12 all covidcritcare
    needs:
    - data_process_finalmatched
    outputs:
      moderately_sensitive:
        csv: output/comparison/over12/all/covidcritcare/*csv
        png: output/comparison/over12/all/covidcritcare/*png
        
  model_km_over12_all_coviddeath:
    run: r:latest analysis/km.R over12 all coviddeath
    needs:
    - data_process_finalmatched
    outputs:
      moderately_sensitive:
        csv: output/comparison/over12/all/coviddeath/*csv
        png: output/comparison/over12/all/coviddeath/*png
        
  model_km_over12_all_death:
    run: r:latest analysis/km.R over12 all death
    needs:
    - data_process_finalmatched
    outputs:
      moderately_sensitive:
        csv: output/comparison/over12/all/death/*csv
        png: output/comparison/over12/all/death/*png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:04:26

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

Job information

Status
Succeeded
Backend
TPP
Workspace
vaccine-effectiveness-in-children
Requested by
Will Hulme
Branch
main
Force run dependencies
No
Git commit hash
f6f402c
Requested actions
  • model_km_over12_all_covidemergency
  • model_km_over12_all_covidadmitted
  • model_km_over12_all_emergency
  • model_km_over12_all_covidcritcare
  • model_km_over12_all_coviddeath
  • model_km_over12_all_death

Code comparison

Compare the code used in this Job Request