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Job request: 18845

Organisation:
Bennett Institute
Workspace:
pax-usernonuser
ID:
l2dxapa2vxkj7thu
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: 1000

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_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_pax_trt:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pax_trt --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_pax_trt.csv.gz

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

  data_process:
    run: r:latest analysis/data_process.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data1: output/data/data_processed.rds
        data2: output/data/data_processed_grace6.rds
        data3: output/data/data_processed_grace7.rds
        data4: output/data/data_processed_grace8.rds
        rds1: output/data_properties/n_excluded.rds
        rds2: output/data_properties/n_excluded_contraindicated.rds

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

  create_flowchart:
    run: r:latest analysis/flowchart.R
    needs: [data_process_flowchart, data_process]
    outputs:
      moderately_sensitive:
        csv1: output/flowchart/flowchart.csv
        csv2: output/flowchart/flowchart_redacted.csv

  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 
  ## Descriptive analyses
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # #

  describe_distr_trt_init:
    run: r:latest analysis/descriptives/describe_distr_trt_init.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        csv1: output/descriptives/distr_pax_init.csv
        csv2: output/descriptives/distr_pax_init_red.csv

  describe_outcomes_in_trt_window:
    run: r:latest analysis/descriptives/describe_outcomes_in_trt_window.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        csv1: output/descriptives/outcomes_in_trt_window.csv
        csv2: output/descriptives/outcomes_in_trt_window_red.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:27:33

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

Job request

Status
Succeeded
Backend
TPP
Workspace
pax-usernonuser
Requested by
Linda Nab
Branch
main
Force run dependencies
No
Git commit hash
a7da1ce
Requested actions
  • data_process
  • data_process_flowchart
  • data_properties
  • create_flowchart

Code comparison

Compare the code used in this job request