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Introduction

Welcome to the SBOL Validation/Conversion API! This API allows for the validation of documents encoded using the SBOL data standard.

Validate/Convert File

HTTP Request

POST https://validator.sbolstandard.org/validate/

import requests


file = open("sequence1.xml").read()

request = { 'options': {'language' : 'GenBank',
                        'test_equality': False,
                        'check_uri_compliance': False,
                        'check_completeness': False,
                        'check_best_practices': False,
                        'fail_on_first_error': False,
                        'provide_detailed_stack_trace': False,
                        'subset_uri': '',
                        'uri_prefix': '',
                        'version': '',
                        'insert_type': False,
                        'main_file_name': 'main file',
                        'diff_file_name': 'comparison file',
                                },
            'return_file': True,
            'main_file': file
          }


resp = requests.post("https://validator.sbolstandard.org/validate/", json=request)

request({ method: 'POST',
              uri: 'https://validator.sbolvalidator.org/validate/',
              'content-type': 'application/json',
              json: { 'options': {  'language' : 'GenBank',
                                'test_equality': false,
                                'check_uri_compliance': false,
                                'check_completeness': false,
                                'check_best_practices': false,
                                'fail_on_first_error': false,
                                'provide_detailed_stack_trace': false,
                                'subset_uri': '',
                                'uri_prefix': '',
                                'version': '',
                                'insert_type': false,
                                'main_file_name': 'main file',
                                'diff_file_name': 'comparison file',
                            },
                'return_file': true,
                'main_file': file
                }
            }, function(err, response, body) {}
        );

The above command returns JSON structured like this

{
  "valid": true,
  "equality": false,
  "errors": [""],
  "output_file": "http://www.async.ece.utah.edu/work/sequence1.gb"
}

Query Parameters

Parameter Required Default Description
options yes N/A A dictionary containing the validation/conversion options, detailed below
return_file no false Whether or not to return the file contents as a string
main_file yes N/A A string containing the contents for the main file of the validation request
diff_file no N/A A string containing the contents for the file to be compared against the main_file

Options

Parameter Default Description
language “SBOL2” Selects the output file format from “SBOL2”, “SBOL1”, “GenBank”, “FASTA”, and “GFF3”
test_equality false If set to true, a diff_file is required and the main_file and diff_file will be compared
check_uri_compliance true If set to false, URIs in the file will not be checked for compliance with the SBOL specification
check_completeness true If set to false, not all referenced objects must be described within the given main_file
check_best_practices false If set to true, the file is checked for the best practice rules set in the SBOL specification
fail_on_first_error false If set to true, the validator will fail at the first error
provide_detailed_stack_trace false If set to true (and fail_on_first_error is true) the validator will provide a stack trace for the first validation error
subset_uri none A URI of a TopLevel described in the given SBOL file – the output will be only that TopLevel and its described children
uri_prefix none Required for conversion from FASTA and GenBank to SBOL1 or SBOL2, used to generate URIs
version none Adds the version to all URIs and to the document
insert_type false Inserts type into the URIs of objects
main_file_name “main file” The name of the main file, only used for reporting differences between two files when test_equality is true
diff_file_name “comparison file” The name of the secondary file (diff_file), only used in reporting differences between two files when test_equality is true

Response

Parameter Default Description
valid false Returns true if the file given is valid SBOL, or can be converted to valid SBOL
check_equality false Returns true if a comparison was run
equality false Returns true if the two files are equal, false otherwise. Only returned if check_equality is true
errors [“] ‘errors’ is a bit of a misnomer, this is simply the output of running the validation split by lines
output_file N/A The URI of the file requested
result file contents The value of the output file, Only returned if return_file is true in the validation request
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