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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 authorised researcher Helen Curtis 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:
    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 information

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

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  • No previous Job Request available for comparison