Add CLI-based validation of JSON-LD contexts

src/bioregistry/cli.py

@@ -11,6 +11,7 @@
 from .export.cli import export
 from .lint import lint
 from .utils import OLSBroken, get_hexdigests, secho
+from .validate.cli import validate
 from .version import VERSION
 
 
@@ -79,6 +80,7 @@ def align(skip_fairsharing: bool, skip_re3data: bool, skip_slow: bool, no_force:
 main.add_command(lint)
 main.add_command(compare)
 main.add_command(export)
+main.add_command(validate)
 main.add_command(web)
 
 

src/bioregistry/validate/__init__.py

@@ -0,0 +1 @@
+"""Validation utilities."""

src/bioregistry/validate/cli.py

@@ -0,0 +1,66 @@
+"""Validation command line interface.
+
+JSON-LD Validation
+
+1. Passes ``bioregistry validate jsonld "https://bioregistry.io/api/collection/0000002?format=context"``
+1. Fails ``bioregistry validate jsonld "https://raw.githubusercontent.com/prefixcommons/prefixcommons-py/master/prefixcommons/registry/go_context.jsonld"``
+2.
+"""
+
+import json
+import sys
+from pathlib import Path
+
+import click
+import requests
+
+from .utils import validate_jsonld
+
+__all__ = [
+    "validate",
+]
+
+
+@click.group()
+def validate():
+    """Validate data with the Bioregistry."""
+
+
+@validate.command()
+@click.argument("location")
+@click.option("--relax", is_flag=True)
+def jsonld(location: str, relax: bool):
+    """Validate a JSON-LD file."""
+    if location.startswith("http://") or location.startswith("https://"):
+        res = requests.get(location)
+        res.raise_for_status()
+        obj = res.json()
+    else:
+        path = Path(location).resolve()
+        if not path.is_file():
+            raise ValueError
+        obj = json.loads(path.read_text())
+
+    messages = validate_jsonld(obj, strict=not relax)
+    for message in messages:
+        error, prefix, solution, level = (
+            message["error"],
+            message["prefix"],
+            message["solution"],
+            message["level"],
+        )
+        click.secho(f"{prefix} - {error}", fg=LEVEL_TO_COLOR[level], nl=False)
+        if solution:
+            click.echo(" > " + solution)
+        else:
+            click.echo("")
+
+    if any(message["level"] == "error" for message in messages):
+        click.secho("failed", fg="red")
+        sys.exit(1)
+
+
+LEVEL_TO_COLOR = {
+    "warning": "yellow",
+    "error": "red",
+}

src/bioregistry/validate/utils.py

@@ -0,0 +1,41 @@
+"""Validation utilities."""
+
+from typing import Mapping
+
+import bioregistry
+
+__all__ = [
+    "validate_jsonld",
+]
+
+
+def validate_jsonld(obj: Mapping[str, Mapping[str, str]], strict: bool = True):
+    if not isinstance(obj, dict):
+        raise TypeError(f"data is not a dictionary")
+    context = obj.get("@context")
+    if context is None:
+        raise TypeError(f"data is missing a @context field")
+    if not isinstance(context, dict):
+        raise TypeError(f"@context is not a dictionary: {context}")
+    messages = []
+    for prefix, uri_prefix in context.items():
+        norm_prefix = bioregistry.normalize_prefix(prefix)
+        if norm_prefix is None:
+            messages.append(
+                {
+                    "prefix": prefix,
+                    "error": "invalid",
+                    "solution": None,
+                    "level": "error",
+                }
+            )
+        elif norm_prefix != prefix:
+            messages.append(
+                {
+                    "prefix": prefix,
+                    "error": "nonstandard",
+                    "solution": f"Switch to standard prefix: {norm_prefix}",
+                    "level": "error" if strict else "warning",
+                }
+            )
+    return messages

tests/test_validation.py

@@ -0,0 +1,32 @@
+"""Test for validation utilities."""
+
+import unittest
+
+from bioregistry.validate.utils import validate_jsonld
+
+
+class TestValidation(unittest.TestCase):
+    """Test case for validation utilities."""
+
+    def test_validate_jsonld(self):
+        """Test validating JSON-LD."""
+        with self.assertRaises(TypeError):
+            validate_jsonld(None)
+        with self.assertRaises(TypeError):
+            validate_jsonld({})
+        with self.assertRaises(TypeError):
+            validate_jsonld({"@context": None})
+
+        test_context = {
+            "@context": {
+                "GO": ...,
+                "nope": ...,
+            }
+        }
+        warnings, errors = validate_jsonld(test_context, strict=True)
+        self.assertEqual([("GO", "nonstandard"), ("nope", "invalid")], errors)
+        self.assertEqual([], warnings)
+
+        warnings, errors = validate_jsonld(test_context, strict=False)
+        self.assertEqual([("nope", "invalid")], errors)
+        self.assertEqual([("GO", "nonstandard")], warnings)