Skip to content

Job request: 18805

Organisation:
Bennett Institute
Workspace:
pax-usernonuser
ID:
nvyvit7jrez3tszt
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Linda Nab 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:
    create_flowchart
    Status:
    Status: Failed
    Job identifier:
    j2hgj3uf3h5m75pf
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    data_process
    Status:
    Status: Failed
    Job identifier:
    ymjhxm2rgurnvixi
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    data_process_flowchart
    Status:
    Status: Failed
    Job identifier:
    5wlvgh5fiduqt5yp
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    data_properties
    Status:
    Status: Failed
    Job identifier:
    j5zbpt2ldllshqwf
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_study_population
    Status:
    Status: Failed
    Job identifier:
    c5fzl2poe2gojuvh
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_study_population_flowchart
    Status:
    Status: Failed
    Job identifier:
    6t4zh52r4rs27jrg
    Error:
    cancelled_by_user: Cancelled by user

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 
  ## Data extraction 
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input.csv.gz

  generate_study_population_flowchart:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flowchart --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_flowchart.csv.gz

  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 
  ## Data cleaning and description
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 

  data_process:
    run: r:latest analysis/data_process.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data1: output/data/data_processed.rds
        data2: output/data/data_processed_grace6.rds
        data3: output/data/data_processed_grace7.rds
        data4: output/data/data_processed_grace8.rds
        rds: output/data_properties/n_excluded.rds

  data_process_flowchart:
    run: r:latest analysis/data_process_flowchart.R
    needs: [generate_study_population_flowchart]
    outputs:
      highly_sensitive:
        data: output/data/data_flowchart_processed.rds
  
  data_properties:
    run: r:latest analysis/data_properties/data_properties.R output/data/data_processed.rds output/data_properties
    needs: [data_process]
    outputs:
      moderately_sensitive:
        txt1: output/data_properties/data_processed_skim.txt
        txt2: output/data_properties/data_processed_coltypes.txt
        txt3: output/data_properties/data_processed_tabulate.txt

  create_flowchart:
    run: r:latest analysis/flowchart.R
    needs: [data_process_flowchart, data_process]
    outputs:
      moderately_sensitive:
        csv1: output/flowchart/flowchart.csv
        csv2: output/flowchart/flowchart_redacted.csv

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
pax-usernonuser
Requested by
Linda Nab
Branch
main
Force run dependencies
No
Git commit hash
8bfe162
Requested actions
  • run_all

Code comparison

Compare the code used in this job request

  • No previous job request available for comparison