Skip to content

Job request: 5344

Organisation:
Bennett Institute
Workspace:
mabs-draft-report
ID:
sfsqdc2n77zckus6
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Millie Green requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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

  • Action:
    data_process3
    Status:
    Status: Succeeded
    Job identifier:
    zv3wedbuy5elbz2b

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 ----

  ## Cohort 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 ----

  ## Process data
  data_process:
    run: r:latest analysis/process/process_data.R
    needs: [extract_data]
    outputs:
      highly_sensitive:
        data: output/data/data_processed.rds
  
  data_process2:
    run: r:latest analysis/process/process_data2.R
    needs: [data_process]
    outputs:
      highly_sensitive:
        data: output/data/data_processed_clean.rds
        
  data_process3:
    run: r:latest analysis/process/process_data3.R
    needs: [data_process]
    outputs:
      highly_sensitive:
        data: output/data/data_processed_clean_test.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/tables/table_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:12:31

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

Job information

Status
Succeeded
Backend
TPP
Workspace
mabs-draft-report
Requested by
Millie Green
Branch
draft-report
Force run dependencies
No
Git commit hash
153c4cc
Requested actions
  • data_process3

Code comparison

Compare the code used in this Job Request