为何有效URI在LinkML中验证失败？升级runtime仍报错

Problem #

When setting a valid, accessible URI (https://ceur-ws.org/Vol-2931/ICBO_2019_paper_20.pdf) in Python code generated from a LinkML YAML file, a ValueError is thrown claiming the URI is invalid. Upgrading linkml-runtime from version 1.4.5 to 1.4.10 and regenerating the code does not resolve the issue. Debugging identifies the root cause as the URI.is_valid() method using the overly simplistic regex ^\S+$ for validation.

Possible Causes & Fixes #

1. Hidden Whitespace in the URI String #

The regex ^\S+$ rejects any string containing whitespace (spaces, tabs, newlines, non-breaking spaces, etc.). Even an invisible trailing space or non-breaking space in your URI string would trigger the error.

Fix:

• Trim the URI string before passing it to the generated class:

  uri = "https://ceur-ws.org/Vol-2931/ICBO_2019_paper_20.pdf".strip()
  # Or remove all whitespace characters:
  import re
  uri = re.sub(r"\s+", "", uri)
  

• Verify the string has no hidden whitespace by printing its raw representation:

  print(repr(uri))
  

  This will expose invisible characters (e.g., 'https://ceur-ws.org/Vol-2931/ICBO_2019_paper_20.pdf ' with a trailing space).

2. Override the Faulty URI Validation #

The ^\S+$ regex is not a proper URI validator—it’s overly permissive for invalid URIs with no whitespace and can incorrectly reject valid URIs if hidden whitespace is present. Replace it with a robust validation method using Python’s built-in libraries.

Fix:
Subclass the generated URI class and override the is_valid method to use proper URI parsing:

from linkml_runtime.utils.formatutils import URI
import urllib.parse

class ValidURI(URI):
    @classmethod
    def is_valid(cls, value: str) -> bool:
        try:
            parsed = urllib.parse.urlparse(value)
            # Ensure scheme (http/https) and domain are present
            return bool(parsed.scheme and parsed.netloc)
        except ValueError:
            return False

# Use this subclass instead of the auto-generated URI type in your code

3. Report the Bug to LinkML #

The simplistic regex used in linkml-runtime versions 1.4.5–1.4.10 is inadequate for proper URI validation. The project should use standard URI parsing logic instead of a regex for this check.

Content of the question originates from Stack Exchange, question author: Wolfgang Fahl