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Job request: 5905

Organisation:
QMUL
Workspace:
bmi-and-metabolic-markers
ID:
mm3dis6s4v5od72z
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Miriam Samuel 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:



  ## use the Measure function to allow data for different time periods to be extracted in the same study population:  --index-date-range ""yyyy-mm-dd"" --output-format feather 
  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2015-03-01" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_all_2015-03-01.feather  

  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2016-03-01" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_all_2016-03-01.feather  

  generate_study_population_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2017-03-01" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_all_2017-03-01.feather  
        
  generate_study_population_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2018-03-01" --output-format feather 
    outputs:
      highly_sensitive:
        cohort: output/data/input_all_2018-03-01.feather  
        
        
  generate_study_population_5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2019-03-01" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_all_2019-03-01.feather        
        
  generate_study_population_6:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2020-03-01" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_all_2020-03-01.feather  
   
  generate_study_population_7:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2021-03-01" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_all_2021-03-01.feather  
 
 

  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output/data --output-format=feather 
    outputs:
      highly_sensitive:
        cohort: output/data/input_ethnicity.feather
        
      
        
  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py --output-dir=output/data --output-format feather
    needs: [generate_study_population_1, generate_study_population_2, generate_study_population_3, generate_study_population_4, generate_study_population_5, generate_study_population_6, generate_study_population_7, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/data/input*.feather



  
  generate_BMI_complete_categories:
    run: r:latest analysis/BMI.R --output-dir=output/data
    needs: [join_ethnicity]
    outputs:
      highly_sensitive:
        cohort1: output/data/BMI_complete_categories.csv
        cohort2: output/data/BMI_complete_long.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 321:35:15

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

Job request

Status
Failed
Backend
TPP
Workspace
bmi-and-metabolic-markers
Requested by
Miriam Samuel
Branch
main
Force run dependencies
Yes
Git commit hash
f61be4a
Requested actions
  • generate_study_population_1
  • generate_study_population_2
  • generate_study_population_3
  • generate_study_population_4
  • generate_study_population_5
  • generate_study_population_6
  • generate_study_population_7
  • generate_study_population_ethnicity
  • join_ethnicity

Code comparison

Compare the code used in this job request