Merge branch 'main' into feature/168-Experimental-JSON-CAS-support

* main:
  #174 - FSes that are only transitively referenced cannot be serialized (#179)
  #174 - FSes that are only transitively referenced cannot be serialized (#179)

cassis/cas.py

@@ -631,7 +631,7 @@ def typecheck(self) -> List[TypeCheckError]:
 
         return all_errors
 
-    def _find_all_fs(self, generate_missing_ids: bool = False) -> Iterable[FeatureStructure]:
+    def _find_all_fs(self, generate_missing_ids: bool = True) -> Iterable[FeatureStructure]:
         """This function traverses the whole CAS in order to find all directly and indirectly referenced
         feature structures. Traversing is needed as it can be that a feature structure is not added to the sofa but
         referenced by another feature structure as a feature."""
@@ -645,8 +645,25 @@ def _find_all_fs(self, generate_missing_ids: bool = False) -> Iterable[FeatureSt
         ts = self.typesystem
         while openlist:
             fs = openlist.pop(0)
-            if generate_missing_ids and fs.xmiID is None:
-                fs.xmiID = self._get_next_xmi_id()
+
+            # We do not want to return cas:NULL here as we handle serializing it later
+            if fs.xmiID == 0:
+                continue
+
+            if fs.xmiID is None:
+                if generate_missing_ids:
+                    fs.xmiID = self._get_next_xmi_id()
+                else:
+                    raise ValueError("FS has no ID and ID generation is disabled! {fs}".format(fs=fs))
+
+            existing_fs = all_fs.get(fs.xmiID)
+            if existing_fs is not None and existing_fs is not fs:
+                raise ValueError(
+                    "Duplicate FS id [{fsId}] used for [{fs1}] and [{fs2}]".format(
+                        fsId=fs.xmiID, fs1=existing_fs, fs2=fs
+                    )
+                )
+
             all_fs[fs.xmiID] = fs
 
             t = ts.get_type(fs.type)
@@ -678,8 +695,6 @@ def _find_all_fs(self, generate_missing_ids: bool = False) -> Iterable[FeatureSt
                     if referenced_fs.xmiID not in all_fs:
                         openlist.append(referenced_fs)
 
-        # We do not want to return cas:NULL here as we handle serializing it later
-        all_fs.pop(0, None)
         yield from all_fs.values()
 
     def _get_next_xmi_id(self) -> int:

cassis/xmi.py

@@ -343,7 +343,7 @@ def serialize(self, sink: Union[IO, str], cas: Cas, pretty_print=True):
         self._serialize_cas_null(root)
 
         # Find all fs, even the ones that are not directly added to a sofa
-        for fs in sorted(cas._find_all_fs(generate_missing_ids=True), key=lambda a: a.xmiID):
+        for fs in sorted(cas._find_all_fs(), key=lambda a: a.xmiID):
             self._serialize_feature_structure(cas, root, fs)
 
         for sofa in cas.sofas:

tests/test_cas.py

@@ -443,3 +443,14 @@ def test_removing_throws_if_fs_in_other_view(small_typesystem_xml, tokens, sente
 
     with pytest.raises(ValueError):
         view.remove(tokens[0])
+
+
+def test_fail_on_duplicate_fs_id(small_typesystem_xml):
+    cas = Cas(typesystem=load_typesystem(small_typesystem_xml))
+
+    TokenType = cas.typesystem.get_type("cassis.Token")
+    cas.add_annotation(TokenType(xmiID=10, begin=0, end=0))
+    cas.add_annotation(TokenType(xmiID=10, begin=10, end=10))
+
+    with pytest.raises(ValueError):
+        list(cas._find_all_fs())

tests/test_xmi.py

@@ -198,7 +198,7 @@ def test_serializing_xmi_ignores_none_features(small_xmi, small_typesystem_xml):
     typesystem = load_typesystem(small_typesystem_xml)
     cas = load_cas_from_xmi(small_xmi, typesystem=typesystem)
     TokenType = typesystem.get_type("cassis.Token")
-    cas.add(TokenType(xmiID=13, sofa=1, begin=0, end=3, id=None, pos=None))
+    cas.add(TokenType(begin=0, end=3, id=None, pos=None))
 
     actual_xml = cas.to_xmi()