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Job request: 14900

Organisation:
Bennett Institute
Workspace:
mabsavs-usernonuser-ccw
ID:
brtgv4gkckdqhdjg
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

  ## # # # # # # # # # # # # # # # # # # # 
  ## 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_day*.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_day*.rds   

  data_properties_process_day0:
    run: r:latest analysis/data_properties.R output/data/data_processed_day0.rds output/data_properties
    needs: [data_process]
    outputs:
      moderately_sensitive:
        txt1: output/data_properties/data_processed_day0_skim.txt
        txt2: output/data_properties/data_processed_day0_coltypes.txt
        txt3: output/data_properties/data_processed_day0_tabulate.txt

  data_properties_process_day0_ba2:
    run: r:latest analysis/data_properties.R output/data/ba2_data_processed_day0.rds output/data_properties
    needs: [data_process_ba2]
    outputs:
      moderately_sensitive:
        txt1: output/data_properties/ba2_data_processed_day0_skim.txt
        txt2: output/data_properties/ba2_data_processed_day0_coltypes.txt
        txt3: output/data_properties/ba2_data_processed_day0_tabulate.txt
  
  crosstab_trt_outcomes:
    run: r:latest analysis/crosstab_trt_outcomes.R ba1
    needs: [data_process]
    outputs:
      moderately_sensitive:
        csvsdays: output/data_properties/day*.csv

  crosstab_trt_outcomes_ba2:
    run: r:latest analysis/crosstab_trt_outcomes.R ba2
    needs: [data_process_ba2]
    outputs:
      moderately_sensitive:
        csvsdays: output/data_properties/ba2_day*.csv

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

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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:25:20

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

Job request

Status
Succeeded
Backend
TPP
Workspace
mabsavs-usernonuser-ccw
Requested by
Linda Nab
Branch
ccw-analysis
Force run dependencies
No
Git commit hash
fd0d432
Requested actions
  • generate_study_population
  • generate_study_population_ba2

Code comparison

Compare the code used in this job request