Skip to content

Job request: 5378

Organisation:
Bennett Institute
Workspace:
mabs-further-testing
ID:
nee5ecszsx76frys
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Helen Curtis 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:
    extract_data
    Status:
    Status: Succeeded
    Job identifier:
    vxxnmljqmd337nuv
  • Action:
    data_process
    Status:
    Status: Succeeded
    Job identifier:
    xwy7tplnofcpang5
  • Action:
    data_properties
    Status:
    Status: Succeeded
    Job identifier:
    3ym3ukvuxov7eash
  • Action:
    report_data
    Status:
    Status: Succeeded
    Job identifier:
    qv7ldv4jdgfbq53i
  • Action:
    flow_chart
    Status:
    Status: Succeeded
    Job identifier:
    rpqfvxr6uve7cky5

Pipeline

Show project.yaml 
################################################################################
#
# Description: This script defines the project pipeline - it specifys the 
#              execution orders for all the code in this repo using a series of 
#              actions.
#
# Author(s): M Green
# Date last updated: 31/01/2022
#
################################################################################

version: '3.0'

expectations:
  population_size: 100000

actions:
  
  # Extract data ----
  extract_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/data/input.csv.gz
  
  
  # Data processing ----
  data_process:
    run: r:latest analysis/process/process_data.R
    needs: [extract_data]
    outputs:
      highly_sensitive:
        data: output/data/data_processed*.rds
  
  # Data summaries ----
  flow_chart:
    run: r:latest analysis/descriptive/flow_chart.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        data: output/data/flowchart.csv

  data_properties:
    run: r:latest analysis/descriptive/data_properties.R output/data/data_processed.rds output/data_properties
    needs: [data_process]
    outputs:
      moderately_sensitive:
        cohort: output/data_properties/data_processed*.txt
  
  
  # Report ----
  report_data:
    run: r:latest analysis/descriptive/coverage_report_data.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        tables: output/reports/coverage/table_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 05:57:22

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

Job request

Status
Succeeded
Backend
TPP
Workspace
mabs-further-testing
Requested by
Helen Curtis
Branch
helen-edits2
Force run dependencies
No
Git commit hash
a6813c6
Requested actions
  • extract_data
  • data_process
  • flow_chart
  • data_properties
  • report_data

Code comparison

Compare the code used in this job request

  • No previous job request available for comparison