Merge pull request #384 from biolink/issue_381

Issue 381

biolinkml/generators/rdfgen.py

@@ -5,6 +5,7 @@
 
 """
 import os
+import urllib.parse as urlparse
 from typing import Union, TextIO, Optional
 
 import click
@@ -32,7 +33,12 @@ def _data(self, g: Graph) -> str:
     def end_schema(self, output: Optional[str] = None, context: str = METAMODEL_CONTEXT_URI, **_) -> None:
         gen = JSONLDGenerator(self, fmt=JSONLDGenerator.valid_formats[0], emit_metadata=self.emit_metadata,
                               importmap=self.importmap)
+        # Iterate over permissible text strings making them URI compatible
+        for e in gen.schema.enums.values():
+            for pv in e.permissible_values.values():
+                pv.text = urlparse.quote(pv.text)
         jsonld_str = gen.serialize(context=context)
+
         graph = Graph()
         graph.parse(data=jsonld_str, format="json-ld", base=self.namespaces._base, prefix=True)
         if output:

tests/test_issues/test_issue_167.py

@@ -33,12 +33,12 @@ def test_issue_167b_python(self):
         """ Annotations python example """
         env.generate_single_file('issue_167b.py',
                                  lambda: PythonGenerator(env.input_path('issue_167b.yaml'),
-                                                         importmap=env.import_map).serialize(),
+                                                         importmap=env.import_map, emit_metadata=False).serialize(),
                                  comparator=lambda exp, act: compare_python(exp, act, self.env.expected_path('issue_167b.py')),
                                  value_is_returned=True)
-        env.generate_single_file('issue_167b.py',
+        env.generate_single_file('issue_167b2.py',
                                  lambda: PythonGenerator(env.input_path('issue_167b.yaml'),
-                                                         importmap=env.import_map, mergeimports=False).serialize(),
+                                                         importmap=env.import_map, mergeimports=False, emit_metadata=False).serialize(),
                                  comparator=lambda exp, act: compare_python(exp, act, self.env.expected_path('issue_167b_nomerged.py')),
                                  value_is_returned=True)
 

tests/test_issues/test_issue_344.py

@@ -7,15 +7,16 @@
 from tests.test_issues.environment import env
 
 
-class Issue167TestCase(TestEnvironmentTestCase):
+class Issue344TestCase(TestEnvironmentTestCase):
     env = env
 
     def test_issue_344(self):
         """ Test to check if prefixes of CURIEs from granular mappings show up in the json-ld context """
         x = env.generate_single_file('issue_344_context.json',
                                  lambda: ContextGenerator(env.input_path('issue_344.yaml'),
-                                 importmap=env.import_map).serialize(), value_is_returned=True)
-        context = json.load(open(os.path.join(env.outdir, 'issue_344_context.json')))
+                                 importmap=env.import_map, emit_metadata=False).serialize(), value_is_returned=True)
+        with open(os.path.join(env.outdir, 'issue_344_context.json')) as f:
+            context = json.load(f)
         self.assertIn('PCO', context['@context'])
         self.assertIn('PATO', context['@context'])
         self.assertIn('GO', context['@context'])

tests/test_issues/test_issue_381.py

@@ -0,0 +1,32 @@
+import unittest
+
+from rdflib import Graph, Namespace
+
+from biolinkml.generators.jsonldgen import JSONLDGenerator
+from biolinkml.generators.rdfgen import RDFGenerator
+from biolinkml.meta import META
+from tests.utils.test_environment import TestEnvironmentTestCase
+from tests.test_issues.environment import env
+
+NS = Namespace('https://example.org/test/')
+
+schema = f'''id: {NS}
+enums:
+  test_enum:
+    permissible_values:
+      a b:
+'''
+
+
+class Issue381TestCase(TestEnvironmentTestCase):
+    """ Test URL generation w/ non-mangled values """
+    env = env
+
+    def test_non_url_pv(self):
+        g = Graph()
+        g.parse(data=RDFGenerator(schema).serialize(), format="ttl")
+        self.assertEqual('https://example.org/test/a%20b', str(g.value(NS.test_enum, META.permissible_values)))
+
+
+if __name__ == '__main__':
+    unittest.main()