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Job request: 5897

Organisation:
QMUL
Workspace:
bmi-and-metabolic-markers
ID:
ogsxrt7fl43axecr
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

  • Action:
    generate_study_population_2
    Status:
    Failed
    Job identifier:
    byn6t7ao7q5bae4c
    Error:
    Internal error
  • Action:
    generate_study_population_7
    Status:
    Failed
    Job identifier:
    4xppd663lyyxoifb
    Error:
    Internal error
  • Action:
    generate_study_population_3
    Status:
    Failed
    Job identifier:
    ktz5ragptuw5k6ci
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    generate_study_population_4
    Status:
    Failed
    Job identifier:
    l7hmn3bwyi4xde4c
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    generate_study_population_ethnicity
    Status:
    Failed
    Job identifier:
    kn4ndwnrsu4p332c
    Error:
    Internal error
  • Action:
    generate_study_population_1
    Status:
    Failed
    Job identifier:
    mzvuovzhfatlpnny
    Error:
    Internal error
  • Action:
    generate_study_population_5
    Status:
    Failed
    Job identifier:
    7xymh2o6r62mavsf
    Error:
    Internal error
  • Action:
    generate_study_population_6
    Status:
    Failed
    Job identifier:
    ugpqzgriepgpurs7
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    join_ethnicity
    Status:
    Failed
    Job identifier:
    f3a4l765usjvfgtq
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_BMI_complete_categories
    Status:
    Failed
    Job identifier:
    zidwyk75onpn4nww
    Error:
    Internal error

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: 30:02:32

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_BMI_complete_categories

Code comparison

Compare the code used in this job request