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Job request: 5105

Organisation:
University of Bristol
Workspace:
covid-ve-change-over-time--add-covid-test-data
ID:
2mvjzjuyme3qsm6w
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 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

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
        outcomes: output/lib/outcomes.rds
        subgroups: output/lib/subgroups.rds

  ## #################################### 
  ## study definition 
  ## #################################### 
 

  ## study definition 

  generate_study_population_tests:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_tests
      --output-format csv
    needs:
    - design
    outputs:
      highly_sensitive:
        cohort: output/input_tests.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:49:36

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

Job information

Status
Failed
Backend
TPP
Workspace
covid-ve-change-over-time--add-covid-test-data
Requested by
Elsie Horne
Branch
add-covid-test-data
Force run dependencies
No
Git commit hash
b21102b
Requested actions
  • generate_study_population_tests

Code comparison

Compare the code used in this Job Request