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Job request: 7932

Organisation:
University of Bristol
Workspace:
covid-ve-change-over-time--include-prev-infection
ID:
dawmmwzaoxarimbu
View repo View project.yaml

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 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_study_population
    Status:
    Status: Failed
    Job identifier:
    sa33upfgzy4bqmwf
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    check_prior_covid
    Status:
    Status: Failed
    Job identifier:
    fbndb2rhox37pbb4
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    dummy_data_vax
    Status:
    Status: Failed
    Job identifier:
    3dtntwce6kbheozm
    Error:
    Internal error
  • Action:
    data_input_process
    Status:
    Status: Failed
    Job identifier:
    6tptqg7qwnla674f
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:

  population_size: 100000

actions:

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml 
  ## This file is created by create_project.R 
  ## Edit and run create_project.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## #################################### 
  ## study definition 
  ## #################################### 
  ## generate dummy data for study_definition 

  dummy_data_vax:
    run: r:latest analysis/dummy_data_vax.R
    outputs:
      moderately_sensitive:
        dummy_data: analysis/dummy_data_vax.feather

  ## study definition 

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vax
      --output-format feather
    dummy_data_file: analysis/dummy_data_vax.feather
    needs:
    - dummy_data_vax
    outputs:
      highly_sensitive:
        cohort: output/input_vax.feather

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

  data_input_process:
    run: r:latest analysis/preprocess/data_input_process.R
    needs:
    - dummy_data_vax
    - generate_study_population
    outputs:
      highly_sensitive:
        data_wide_vax_dates: output/data/data_wide_vax_dates.rds
        data_processed: output/data/data_processed.rds
      moderately_sensitive:
        data_properties: output/tables/data_*_tabulate.txt

  ## check number of events for defining prior covid 

  check_prior_covid:
    run: r:latest analysis/preprocess/check_prior_covid.R
    needs:
    - data_input_process
    outputs:
      moderately_sensitive:
        prior_covid_outcomes_n: output/eda/prior_covid_outcomes_n.png

Timeline

  • Created:

  • Finished:

  • Runtime:

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

Job request

Status
Failed
Backend
TPP
Workspace
covid-ve-change-over-time--include-prev-infection
Requested by
Elsie Horne
Branch
include-prev-infection
Force run dependencies
No
Git commit hash
02c1fc4
Requested actions
  • run_all

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