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Job request: 15011

Organisation:
Bennett Institute
Workspace:
mabsavs-usernonuser-ccw
ID:
qj25fxsqomx4ecpg
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 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 
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

  generate_study_population_flowchart:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flowchart --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_flowchart.csv.gz
  
  generate_study_population_flowchart_ba2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flowchart_ba2 --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_flowchart_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
        rds: output/data_properties/n_excluded.rds

  data_process_ba2:
    run: r:latest analysis/data_process.R ba2
    needs: [generate_study_population_ba2]
    outputs:
      highly_sensitive:
        data: output/data/ba2_data_processed.rds
        rds: output/data_properties/ba2_n_excluded.rds

  data_process_flowchart:
    run: r:latest analysis/data_process_flowchart.R ba1
    needs: [generate_study_population_flowchart]
    outputs:
      highly_sensitive:
        data: output/data/data_flowchart_processed.rds

  data_process_flowchart_ba2:
    run: r:latest analysis/data_process_flowchart.R ba2
    needs: [generate_study_population_flowchart_ba2]
    outputs:
      highly_sensitive:
        data: output/data/ba2_data_flowchart_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

  create_flowchart:
    run: r:latest analysis/flowchart.R ba1
    needs: [data_process_flowchart, data_process]
    outputs:
      highly_sensitive:
        csv: output/tables/flowchart/flowchart.csv

  create_flowchart_ba2:
    run: r:latest analysis/flowchart.R ba2
    needs: [data_process_flowchart_ba2, data_process_ba2]
    outputs:
      highly_sensitive:
        csv: output/tables/flowchart/ba2_flowchart.csv
  
  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
  ## # # # # # # # # # # # # # # # # # # # 

  create_table1:
    run: r:latest analysis/table_1.R ba1
    needs: [data_process]
    outputs:
      moderately_sensitive:
        html: output/tables/table1_redacted.html

  create_table1_ba2:
    run: r:latest analysis/table_1.R ba2
    needs: [data_process_ba2]
    outputs:
      moderately_sensitive:
        html: output/tables/ba2_table1_redacted.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:33:11

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

Job request

Status
Failed
Backend
TPP
Workspace
mabsavs-usernonuser-ccw
Requested by
Linda Nab
Branch
ccw-analysis
Force run dependencies
No
Git commit hash
ec77f8d
Requested actions
  • generate_study_population
  • generate_study_population_ba2
  • generate_study_population_flowchart
  • generate_study_population_flowchart_ba2
  • data_process
  • data_process_ba2
  • data_process_flowchart
  • data_process_flowchart_ba2
  • data_properties
  • data_properties_ba2
  • create_flowchart
  • create_flowchart_ba2

Code comparison

Compare the code used in this job request