Merge pull request #47 from Waltham-Data-Science/claude/fix-sqlite-dependencies-6hZou

Normalize bare dict depends_on to list for MATLAB compatibility

Author: stevevanhooser

src/ndi/document.py

@@ -73,12 +73,14 @@ def __init__(self, document_type: Union[str, dict, "ndi_document"] = "base", **k
         if isinstance(document_type, dict):
             # Loading from existing properties
             self._document_properties = deepcopy(document_type)
+            self._normalize_depends_on()
         elif isinstance(document_type, ndi_document):
             # Copy from another ndi_document
             self._document_properties = deepcopy(document_type.document_properties)
         elif DIDDocument is not None and isinstance(document_type, DIDDocument):
             # Convert from DIDDocument
             self._document_properties = deepcopy(document_type.document_properties)
+            self._normalize_depends_on()
         else:
             # Create new from schema
             self._document_properties = self.read_blank_definition(document_type)
@@ -92,6 +94,27 @@ def __init__(self, document_type: Union[str, dict, "ndi_document"] = "base", **k
             for key, value in kwargs.items():
                 self._set_nested_property(key, value)
 
+    def _normalize_depends_on(self):
+        """Ensure depends_on and files.file_info are always lists.
+
+        MATLAB's jsonencode converts single-element cell arrays to scalars,
+        so documents downloaded from the cloud (or created by MATLAB) may
+        have ``depends_on`` or ``files.file_info`` as a bare dict instead
+        of a list.  Normalizing here guarantees that downstream code
+        (including DID-python's ``doc_to_sql`` / ``_serialize_depends_on``
+        and all NDI code that iterates over ``file_info``) always sees
+        a list.
+        """
+        dep = self._document_properties.get("depends_on")
+        if isinstance(dep, dict):
+            self._document_properties["depends_on"] = [dep]
+
+        files = self._document_properties.get("files")
+        if isinstance(files, dict):
+            fi = files.get("file_info")
+            if isinstance(fi, dict):
+                files["file_info"] = [fi]
+
     @property
     def document_properties(self) -> dict:
         """The document's properties as a nested dictionary."""

tests/test_database.py

@@ -388,6 +388,51 @@ def test_find_dependencies(self, temp_session):
         assert deps[0].id == parent_ido.id
 
 
+class TestDatabaseDependsSQLite:
+    """Test that depends_on is correctly stored in SQLite doc_data table."""
+
+    def test_depends_on_bare_dict_stored_in_doc_data(self, temp_session):
+        """Test that a bare dict depends_on (MATLAB-style) is stored in doc_data."""
+        db = ndi_database(temp_session)
+
+        parent_ido = ndi_ido()
+        parent = ndi_document(
+            {
+                "base": {
+                    "id": parent_ido.id,
+                    "datestamp": timestamp(),
+                    "name": "parent",
+                    "session_id": "",
+                },
+                "document_class": {"class_name": "base", "superclasses": []},
+            }
+        )
+        db.add(parent)
+
+        child_ido = ndi_ido()
+        # Use bare dict (MATLAB-style) for depends_on
+        child = ndi_document(
+            {
+                "base": {
+                    "id": child_ido.id,
+                    "datestamp": timestamp(),
+                    "name": "child",
+                    "session_id": "",
+                },
+                "document_class": {"class_name": "base", "superclasses": []},
+                "depends_on": {"name": "parent_doc", "value": parent_ido.id},
+            }
+        )
+        db.add(child)
+
+        # Verify depends_on was stored in doc_data by querying with depends_on
+        from ndi.query import ndi_query
+
+        results = db.search(ndi_query("").depends_on("parent_doc", parent_ido.id))
+        assert len(results) == 1
+        assert results[0].id == child_ido.id
+
+
 class TestDatabasePaths:
     """Test ndi_database path properties."""
 

tests/test_document.py

@@ -178,6 +178,37 @@ def test_dependency_with_deps(self):
         assert "element_id" in names
         assert len(deps) == 2
 
+    def test_depends_on_bare_dict_normalized_to_list(self):
+        """Test that a bare dict depends_on (MATLAB-style) is normalized to a list."""
+        props = {
+            "base": {"id": "id", "datestamp": "", "session_id": ""},
+            "document_class": {"class_name": "base", "superclasses": []},
+            "depends_on": {"name": "element_id", "value": "abc123"},
+        }
+        doc = ndi_document(props)
+        # Should be normalized to a list
+        assert isinstance(doc.document_properties["depends_on"], list)
+        assert len(doc.document_properties["depends_on"]) == 1
+        assert doc.dependency_value("element_id") == "abc123"
+
+    def test_file_info_bare_dict_normalized_to_list(self):
+        """Test that a bare dict file_info (MATLAB-style) is normalized to a list."""
+        props = {
+            "base": {"id": "id", "datestamp": "", "session_id": ""},
+            "document_class": {"class_name": "base", "superclasses": []},
+            "files": {
+                "file_info": {
+                    "name": "data.bin",
+                    "locations": {"location": "/tmp/data.bin"},
+                }
+            },
+        }
+        doc = ndi_document(props)
+        fi = doc.document_properties["files"]["file_info"]
+        assert isinstance(fi, list)
+        assert len(fi) == 1
+        assert fi[0]["name"] == "data.bin"
+
     def test_dependency_value(self):
         """Test dependency_value returns correct value."""
         props = {