From a5bf90596af550d50e851776e0c41b6f0ea01637 Mon Sep 17 00:00:00 2001
From: hsolbrig <solbrig@jhu.edu>
Date: Thu, 3 Jun 2021 12:51:36 -0500
Subject: [PATCH] Fix for issue #6

Deprecated loc function in preference to internal _loc and do a few more tests on yaml_loc and the new suffix
---
 Pipfile                           |  1 +
 linkml_runtime/utils/yamlutils.py | 12 ++++++----
 tests/test_issues/test_issue_6.py | 39 +++++++++++++++++++++++++++++++
 3 files changed, 48 insertions(+), 4 deletions(-)
 create mode 100644 tests/test_issues/test_issue_6.py

diff --git a/Pipfile b/Pipfile
index bed30eff..1141f915 100644
--- a/Pipfile
+++ b/Pipfile
@@ -18,6 +18,7 @@ rdflib-jsonld = "~=0.5"
 click = "*"
 prefixcommons = "*"
 shexjsg = "~=0.7"
+deprecated = "*"
 
 [dev-packages]
 
diff --git a/linkml_runtime/utils/yamlutils.py b/linkml_runtime/utils/yamlutils.py
index c379c0cb..597c9ef4 100644
--- a/linkml_runtime/utils/yamlutils.py
+++ b/linkml_runtime/utils/yamlutils.py
@@ -1,9 +1,9 @@
 from copy import copy
-from dataclasses import dataclass
 from json import JSONDecoder
 from typing import Union, Any, List, Optional, Type, Callable, Dict
 
 import yaml
+from deprecated.classic import deprecated
 from jsonasobj2 import JsonObj, as_json, as_dict, JsonObjTypes, items
 from rdflib import Graph
 from yaml.constructor import ConstructorError
@@ -291,14 +291,18 @@ def add_node(self, node):
         self._len = node.end_mark.index - node.start_mark.index
         return self
 
+    @deprecated(reason="Use yaml_loc instead")
     def loc(self) -> str:
+        return self._loc()
+
+    def _loc(self) -> str:
         return f'File "{self._s.name}", line {self._s.line + 1}, col {self._s.column + 1}' if self._s else ''
 
     @staticmethod
-    def yaml_loc(loc_str: Optional[Union["TypedNode", str]] = None) -> str:
+    def yaml_loc(loc_str: Optional[Union["TypedNode", str]] = None, suffix: Optional[str] = ": ") -> str:
         """ Return the yaml file and location of loc_str if it exists """
-        return '' if loc_str is None or not hasattr(loc_str, "loc" or not callable(loc_str.loc)) else\
-            (loc_str.loc() + ": ")
+        return '' if loc_str is None or not hasattr(loc_str, "_loc" or not callable(loc_str._loc)) else\
+            (loc_str._loc() + suffix)
 
 
 class extended_str(str, TypedNode):
diff --git a/tests/test_issues/test_issue_6.py b/tests/test_issues/test_issue_6.py
new file mode 100644
index 00000000..f31294cb
--- /dev/null
+++ b/tests/test_issues/test_issue_6.py
@@ -0,0 +1,39 @@
+import unittest
+from contextlib import redirect_stderr
+from io import StringIO
+
+import hbreader
+import yaml
+
+from utils.yamlutils import DupCheckYamlLoader, TypedNode
+
+inp_yaml = """
+foo:
+    x: 17
+    y: I yam that I yam
+    z: 12.43
+"""
+
+
+class Issue6TestCase(unittest.TestCase):
+    def test_loc_function(self):
+        inp = yaml.load(hbreader.hbread(inp_yaml), DupCheckYamlLoader)
+        self.assertEqual('File "<unicode string>", line 3, col 8: ', TypedNode.yaml_loc(inp['foo']['x']))
+        self.assertEqual('File "<unicode string>", line 3, col 8', TypedNode.yaml_loc(inp['foo']['x'], suffix=''))
+        self.assertEqual('File "<unicode string>", line 4, col 8: ', TypedNode.yaml_loc(inp['foo']['y']))
+        self.assertEqual('File "<unicode string>", line 4, col 8I yam that I yam',
+                         TypedNode.yaml_loc(inp['foo']['y'], suffix=inp['foo']['y']))
+        self.assertEqual('File "<unicode string>", line 5, col 8: ', TypedNode.yaml_loc(inp['foo']['z']))
+
+        outs = StringIO()
+        with redirect_stderr(outs):
+            self.assertEqual('File "<unicode string>", line 3, col 8', TypedNode.loc(inp['foo']['x']))
+        self.assertIn('Call to deprecated method loc. (Use yaml_loc instead)', outs.getvalue())
+
+        self.assertEqual('', TypedNode.yaml_loc(None))
+        self.assertEqual('', TypedNode.yaml_loc("abc"))
+        self.assertEqual('', TypedNode.yaml_loc(['a', 'b']))
+
+
+if __name__ == '__main__':
+    unittest.main()