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Job request: 5941

Organisation:
Bennett Institute
Workspace:
mabs-outcomes
ID:
jio747m56rmwvelp
View repo View project.yaml

This page shows the technical details of what happened when the 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 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

  • Action:
    extract_data
    Status:
    Status: Succeeded
    Job identifier:
    awv5jtjlomy7fy3s

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: 11/02/2022
#
################################################################################

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 ----
  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
        
  # Sensitivity anslysis ----
  sa_symptomatic_test:
    run: r:latest -e 'rmarkdown::render("analysis/descriptive/sa_symptomatic_test.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/coverage")'
    needs: [data_process]
    outputs:
      moderately_sensitive:
        html: output/coverage/sa_symptomatic_test.html
  
  
  # Report ----
  report_data:
    run: r:latest analysis/descriptive/coverage_report_data.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        redacted_tables: output/coverage/table_*.csv
        unredacted_tables: output/coverage/for-checks/table_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 09:14:47

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

Job information

Status
Succeeded
Backend
TPP
Workspace
mabs-outcomes
Requested by
Millie Green
Branch
outcomes
Force run dependencies
No
Git commit hash
d3079e7
Requested actions
  • extract_data

Code comparison

Compare the code used in this Job Request