Job request: 11732

Organisation:: University of Bristol
Workspace:: vaccine-effectiveness-in-children
ID:: 6g5w6s2yxg2zp252

This page shows the technical details of what happened when the 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 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:

extract_controlpotential_over12_1

Status:

Status: Succeeded

Job identifier:

r4bd3yrdfyzpl4r2
Action:

extract_treated_over12

Status:

Status: Succeeded

Job identifier:

mb3stdrlxxokxaaf
Action:

process_treated_over12

Status:

Status: Succeeded

Job identifier:

5kdzyf5wkhcojxc7
Action:

process_controlpotential_over12_1

Status:

Status: Failed

Job identifier:

dfrv3ryw3ar42mxw
Action:

process_controlactual_over12_1

Status:

Status: Failed

Job identifier:

k6xfjz5ke6f34ji4
Action:

process_controlpotential_over12_2

Status:

Status: Failed

Job identifier:

ea7ryegbrh2mdehp
Action:

km_over12_all_postest

Status:

Status: Failed

Job identifier:

sobu3wrs5uozpoho
Action:

km_over12_all_emergency

Status:

Status: Failed

Job identifier:

rihahdy7mx7dwzz4
Action:

km_over12_all_covidemergency

Status:

Status: Failed

Job identifier:

2sr5w5xtludxto4o
Action:

km_over12_all_covidadmitted

Status:

Status: Failed

Job identifier:

6wb4ym4yi6wzinzx
Action:

km_over12_all_covidcritcare

Status:

Status: Failed

Job identifier:

p5w7x76zil6j774j
Action:

km_over12_all_coviddeath

Status:

Status: Failed

Job identifier:

6g7ruwsl4m42ns7i
Action:

km_over12_all_noncoviddeath

Status:

Status: Failed

Job identifier:

gf3tgo6jw74tgqxu
Action:

process_controlactual_over12_2

Status:

Status: Failed

Job identifier:

6ff3qujedn2z6rfm
Action:

extract_controlfinal_over12

Status:

Status: Failed

Job identifier:

667c24u5on7zkby3
Action:

process_controlfinal_over12

Status:

Status: Failed

Job identifier:

w5q2djkqvwolusc5
Action:

extract_controlpotential_over12_2

Status:

Status: Failed

Job identifier:

ls4aa3l4i2famnkh
Action:

extract_controlactual_over12_2

Status:

Status: Failed

Job identifier:

ranb5vc2bqjmsy7l
Action:

match_potential_over12_2

Status:

Status: Failed

Job identifier:

5ao4lnf5xrl7zdec
Action:

match_potential_over12_1

Status:

Status: Failed

Job identifier:

qs3az6awbt73fjgk
Action:

extract_controlactual_over12_1

Status:

Status: Failed

Job identifier:

qzeevm3rnssg4cwi

Pipeline

Show project.yaml

version: '3.0'

expectations:

  population_size: 100000

actions:

  ## # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create-project.R 
  ## Edit and run create-project.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # 
  ##   
  ## # # # # # # # # # # # # # # # # # # # 
  ## Over 12s cohort 
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 
  ## Extract and match 
  ## # # # # # # # # # # # # # # # # # # # 

  extract_treated_over12:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_treated
      --output-file output/over12/extract/input_treated.feather --param cohort=over12
    outputs:
      highly_sensitive:
        extract: output/over12/extract/input_treated.feather

  process_treated_over12:
    run: r:latest analysis/treated/process_treated.R over12
    needs:
    - extract_treated_over12
    outputs:
      highly_sensitive:
        rds: output/over12/treated/*.rds

  extract_controlpotential_over12_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/over12/matchround1/extract/input_controlpotential.feather
      --param cohort=over12 --param matching_round=1 --param index_date=2021-09-20
    needs: []
    outputs:
      highly_sensitive:
        cohort: output/over12/matchround1/extract/input_controlpotential.feather

  process_controlpotential_over12_1:
    run: r:latest analysis/matching/process_controlpotential.R over12 1
    needs:
    - extract_controlpotential_over12_1
    outputs:
      highly_sensitive:
        rds: output/over12/matchround1/process/*.rds

  match_potential_over12_1:
    run: r:latest analysis/matching/match_potential.R over12 1
    needs:
    - process_treated_over12
    - process_controlpotential_over12_1
    outputs:
      highly_sensitive:
        rds: output/over12/matchround1/potential/*.rds
        csv: output/over12/matchround1/potential/*.csv.gz

  extract_controlactual_over12_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/over12/matchround1/extract/input_controlactual.feather
      --param cohort=over12 --param matching_round=1
    needs:
    - match_potential_over12_1
    outputs:
      highly_sensitive:
        cohort: output/over12/matchround1/extract/input_controlactual.feather

  process_controlactual_over12_1:
    run: r:latest analysis/matching/process_controlactual.R over12 1
    needs:
    - process_treated_over12
    - match_potential_over12_1
    - extract_controlpotential_over12_1
    - extract_controlactual_over12_1
    outputs:
      highly_sensitive:
        rds: output/over12/matchround1/actual/*.rds
        csv: output/over12/matchround1/actual/*.csv.gz

  extract_controlpotential_over12_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/over12/matchround2/extract/input_controlpotential.feather
      --param cohort=over12 --param matching_round=2 --param index_date=2021-10-04
    needs:
    - process_controlactual_over12_1
    outputs:
      highly_sensitive:
        cohort: output/over12/matchround2/extract/input_controlpotential.feather

  process_controlpotential_over12_2:
    run: r:latest analysis/matching/process_controlpotential.R over12 2
    needs:
    - extract_controlpotential_over12_2
    outputs:
      highly_sensitive:
        rds: output/over12/matchround2/process/*.rds

  match_potential_over12_2:
    run: r:latest analysis/matching/match_potential.R over12 2
    needs:
    - process_treated_over12
    - process_controlpotential_over12_2
    - process_controlactual_over12_1
    outputs:
      highly_sensitive:
        rds: output/over12/matchround2/potential/*.rds
        csv: output/over12/matchround2/potential/*.csv.gz

  extract_controlactual_over12_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/over12/matchround2/extract/input_controlactual.feather
      --param cohort=over12 --param matching_round=2
    needs:
    - match_potential_over12_2
    outputs:
      highly_sensitive:
        cohort: output/over12/matchround2/extract/input_controlactual.feather

  process_controlactual_over12_2:
    run: r:latest analysis/matching/process_controlactual.R over12 2
    needs:
    - process_treated_over12
    - match_potential_over12_2
    - extract_controlpotential_over12_2
    - extract_controlactual_over12_2
    - process_controlactual_over12_1
    outputs:
      highly_sensitive:
        rds: output/over12/matchround2/actual/*.rds
        csv: output/over12/matchround2/actual/*.csv.gz

  extract_controlfinal_over12:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlfinal
      --output-file output/over12/extract/input_controlfinal.feather --param cohort=over12
      --param n_matching_rounds=2
    needs:
    - process_controlactual_over12_2
    outputs:
      highly_sensitive:
        extract: output/over12/extract/input_controlfinal.feather

  process_controlfinal_over12:
    run: r:latest analysis/matching/process_controlfinal.R over12
    needs:
    - process_controlactual_over12_1
    - process_controlactual_over12_2
    - extract_controlfinal_over12
    - process_treated_over12
    outputs:
      highly_sensitive:
        extract: output/over12/match/*.rds

  ## # # # # # # # # # # # # # # # # # # # 
  ## Model 
  ## # # # # # # # # # # # # # # # # # # # 

  km_over12_all_postest:
    run: r:latest analysis/km.R over12 all postest
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        csv: output/over12/models/km/all/postest/*.csv
        rds: output/over12/models/km/all/postest/*.rds
        png: output/over12/models/km/all/postest/*.png

  km_over12_all_emergency:
    run: r:latest analysis/km.R over12 all emergency
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        csv: output/over12/models/km/all/emergency/*.csv
        rds: output/over12/models/km/all/emergency/*.rds
        png: output/over12/models/km/all/emergency/*.png

  km_over12_all_covidemergency:
    run: r:latest analysis/km.R over12 all covidemergency
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        csv: output/over12/models/km/all/covidemergency/*.csv
        rds: output/over12/models/km/all/covidemergency/*.rds
        png: output/over12/models/km/all/covidemergency/*.png

  km_over12_all_covidadmitted:
    run: r:latest analysis/km.R over12 all covidadmitted
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        csv: output/over12/models/km/all/covidadmitted/*.csv
        rds: output/over12/models/km/all/covidadmitted/*.rds
        png: output/over12/models/km/all/covidadmitted/*.png

  km_over12_all_covidcritcare:
    run: r:latest analysis/km.R over12 all covidcritcare
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        csv: output/over12/models/km/all/covidcritcare/*.csv
        rds: output/over12/models/km/all/covidcritcare/*.rds
        png: output/over12/models/km/all/covidcritcare/*.png

  km_over12_all_coviddeath:
    run: r:latest analysis/km.R over12 all coviddeath
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        csv: output/over12/models/km/all/coviddeath/*.csv
        rds: output/over12/models/km/all/coviddeath/*.rds
        png: output/over12/models/km/all/coviddeath/*.png

  km_over12_all_noncoviddeath:
    run: r:latest analysis/km.R over12 all noncoviddeath
    needs:
    - process_controlfinal_over12
    outputs:
      moderately_sensitive:
        csv: output/over12/models/km/all/noncoviddeath/*.csv
        rds: output/over12/models/km/all/noncoviddeath/*.rds
        png: output/over12/models/km/all/noncoviddeath/*.png

  ## #### End ####

Timeline

Created: 2 years, 3 months ago 13 Sep 2022 21:43:00 UTC
Started: 2 years, 3 months ago 13 Sep 2022 21:41:54 UTC
Finished: 2 years, 3 months ago 13 Sep 2022 23:53:22 UTC
Runtime: 03:21:03

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

Job information

Status: Failed
Backend: TPP
Workspace: vaccine-effectiveness-in-children
Requested by: Will Hulme
Branch: main
Force run dependencies: No
Git commit hash: afb5e2c
Requested actions: run_all

Code comparison

Compare the code used in this Job Request