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Job request: 4860

Organisation:
Bennett Institute
Workspace:
mabs-codecounts
ID:
r32brpb45rvln6ng
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 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

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: 05/01/2022
#
################################################################################

version: '3.0'

expectations:
  population_size: 100000

actions:

  # Extract data ----
  
  ## Cohort data
  extract_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-01-01 to 2022-01-01 by week" --output-dir=output/data --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/data/input_*.csv.gz
        
  
  # Data processing ----
  
  ## Generate measures
  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/data
    needs: [extract_data]
    outputs:
      moderately_sensitive:
        measure_csv: output/data/measure_*.csv
  
  ## Calculate weekly counts
  code_counts:
    run: r:latest analysis/process/weekly_code_counts.R
    needs: [extract_data]
    outputs:
      moderately_sensitive:
        data: output/data/data_weekly_counts.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:33:55

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

Job request

Status
Succeeded
Backend
TPP
Workspace
mabs-codecounts
Requested by
Millie Green
Branch
code-counts
Force run dependencies
No
Git commit hash
200545c
Requested actions
  • generate_measures

Code comparison

Compare the code used in this job request