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Job request: 24275

Organisation:
University of Bristol
Workspace:
post-covid-neurodegenerative-v1
ID:
fgh5qjomvaiobzzu
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Harry T Mason 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: 1000

actions:

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create_project_actions.R 
  ## Edit and run create_project_actions.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Define study dates 

  study_dates:
    run: r:latest analysis/study_dates.R
    outputs:
      highly_sensitive:
        study_dates_json: output/study_dates.json

  ## Generate dates for all cohorts 

  generate_dates:
    run: ehrql:v1 generate-dataset analysis/dataset_definition/dataset_definition_dates.py
      --output output/dataset_definition/index_dates.csv.gz
    needs:
    - study_dates
    outputs:
      highly_sensitive:
        dataset: output/dataset_definition/index_dates.csv.gz

  ## Generate cohort - prevax 

  generate_cohort_prevax:
    run: ehrql:v1 generate-dataset analysis/dataset_definition/dataset_definition_prevax.py
      --output output/dataset_definition/input_prevax.csv.gz
    needs:
    - generate_dates
    outputs:
      highly_sensitive:
        cohort: output/dataset_definition/input_prevax.csv.gz

  ## Generate cohort - vax 

  generate_cohort_vax:
    run: ehrql:v1 generate-dataset analysis/dataset_definition/dataset_definition_vax.py
      --output output/dataset_definition/input_vax.csv.gz
    needs:
    - generate_dates
    outputs:
      highly_sensitive:
        cohort: output/dataset_definition/input_vax.csv.gz

  ## Generate cohort - unvax 

  generate_cohort_unvax:
    run: ehrql:v1 generate-dataset analysis/dataset_definition/dataset_definition_unvax.py
      --output output/dataset_definition/input_unvax.csv.gz
    needs:
    - generate_dates
    outputs:
      highly_sensitive:
        cohort: output/dataset_definition/input_unvax.csv.gz

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 134:49:53

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

Job information

Status
Succeeded
Backend
TPP
Workspace
post-covid-neurodegenerative-v1
Requested by
Harry T Mason
Branch
main
Force run dependencies
No
Git commit hash
c0de683
Requested actions
  • run_all

Code comparison

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