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Job request: 14926

Organisation:
Bennett Institute
Workspace:
mabsavs-usernonuser-ccw
ID:
gbxnyangjers6xgy
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Linda Nab 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 100000

actions:

  ## # # # # # # # # # # # # # # # # # # # 
  ## Data extraction 
  ## # # # # # # # # # # # # # # # # # # # 

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input.csv.gz

  generate_study_population_ba2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ba2 --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_ba2.csv.gz

  ## # # # # # # # # # # # # # # # # # # # 
  ## Data cleaning and description
  ## # # # # # # # # # # # # # # # # # # # 

  data_process:
    run: r:latest analysis/data_process.R ba1
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data: output/data/data_processed.rds

  data_process_ba2:
    run: r:latest analysis/data_process.R ba2
    needs: [generate_study_population_ba2]
    outputs:
      highly_sensitive:
        data1: output/data/ba2_data_processed.rds   

  data_properties:
    run: r:latest analysis/data_properties/data_properties.R output/data/data_processed.rds output/data_properties
    needs: [data_process]
    outputs:
      moderately_sensitive:
        txt1: output/data_properties/data_processed_skim.txt
        txt2: output/data_properties/data_processed_coltypes.txt
        txt3: output/data_properties/data_processed_tabulate.txt

  data_properties_ba2:
    run: r:latest analysis/data_properties/data_properties.R output/data/ba2_data_processed.rds output/data_properties
    needs: [data_process_ba2]
    outputs:
      moderately_sensitive:
        txt1: output/data_properties/ba2_data_processed_skim.txt
        txt2: output/data_properties/ba2_data_processed_coltypes.txt
        txt3: output/data_properties/ba2_data_processed_tabulate.txt
  
  sense_check:
    run: r:latest analysis/data_properties/sense_check.R ba1
    needs: [data_process]
    outputs:
      moderately_sensitive:
        csv: output/data_properties/sense_checks.txt

  sense_check_ba2:
    run: r:latest analysis/data_properties/sense_check.R ba2
    needs: [data_process_ba2]
    outputs:
      moderately_sensitive:
        csv: output/data_properties/ba2_sense_checks.txt

  ## # # # # # # # # # # # # # # # # # # # 
  ## CCW Analysis - Day 0 
  ## # # # # # # # # # # # # # # # # # # # 

  ## # # # # # # # # # # # # # # # # # # # 
  ## Tables
  ## # # # # # # # # # # # # # # # # # # #

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:07:55

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

Job information

Status
Succeeded
Backend
TPP
Workspace
mabsavs-usernonuser-ccw
Requested by
Linda Nab
Branch
ccw-analysis
Force run dependencies
No
Git commit hash
e2e1892
Requested actions
  • data_process
  • data_process_ba2
  • data_properties
  • data_properties_ba2
  • sense_check
  • sense_check_ba2

Code comparison

Compare the code used in this Job Request