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OntoPortal Utilities

A set of scripts for benchmarking and troubleshooting issues with OntoPortal

Installation

  1. Clone this repo and run bundle install
  2. Copy config/config.yml.sample to config/config.yml
  3. Edit config/config.yml and replace the following attributes with your own:
   servers_to_compare:
      https://master-server: '<api key for master-server>'
      https://slave-server1: '<api key for slave-server1>'
      https://slave-server2: '<api key for slave-server2>'
      ...

Example:

  servers_to_compare:
    https://data.bioontology.org: '3c555bd8-2f80-46d4-aa04-e013bf5fd00f'
    https://data1.bioontology.org: '2b9806f2-9b21-43ca-bdf1-bbadf1358fbd'

BioPortal API key can be found here: https://bioportal.bioontology.org/account

Server Data Comparator

Retrieves a given number of ontologies from a set of API servers and compares their metadata and class artifacts. You can add any number of servers to compare against each other. The comparisons are done using every permutation of two servers from the list. The very first server on the list (master) is used to retrieve the list of ontologies to be used in the comparison tests.

Execution:

The script accepts the following parameters (all are OPTIONAL):

    -o, ACR1,ACR2,ACR3 OR NUM   An optional comma-separated list of ontologies to test 
        --ont                   OR 
                                An optional number of RANDOM ontologies to test
                                Default: 10 random ontologies
        
    -c  NUM (integer > 0)       Optional number of classes to test per ontology
        --classes               Default: 500
     
    -i  --ignore_ids            Ignore the fact that Submission IDs are different between servers and proceed with ALL checks
                                Default: if Submission IDs are different, further checks NOT PERFORMED

    -l, PATH_TO_LOG_FILE        Optional path to the log file        
        --log                   Default: logs/server_data_comparator-run.log
         
    -h  --help                  Display help screen

Usage: $ bundle exec ruby server_data_comparator.rb [options]

Run Examples:

Test 10 random ontologies with 500 classes from each:

$ bundle exec ruby server_data_comparator.rb

Test 200 classes from ontologies NCIT, DOID, and BAO:

$ bundle exec ruby server_data_comparator.rb -o NCIT,DOID,BAO -c 200

Test 20 random ontologies with 500 classes from each and ignore possible mismatch between Submission IDs:

$ bundle exec ruby server_data_comparator.rb -o 20 -i

Test 20 random ontologies with 2000 classes from each:

$ bundle exec ruby server_data_comparator.rb -o 20 -c 2000