refactor: remove last traces of 'update_uncontained'

src/features/document/document_feature.py

@@ -56,7 +56,6 @@ def update(
     id_address: str,
     data: Json = Form(...),
     files: Optional[List[UploadFile]] = File(None),
-    update_uncontained: Optional[bool] = False,
     user: User = Depends(auth_w_jwt_or_pat),
 ):
     """Update an Existing Document in the Database.
@@ -71,7 +70,6 @@ def update(
       - The PROTOCOL is optional, and the default is dmss.
     - document (dict): The document to replace the previous version.
     - files: Optional list of files to be stored as part of this document.
-    - update_uncontained (bool): Optional flag specifying whether to also update uncontained attributes in the document.
     - user (User): The authenticated user accessing the endpoint, automatically generated from provided bearer token or Access-Key.
 
     Returns:
@@ -89,7 +87,6 @@ def update(
         address=Address.from_absolute(id_address),
         data=data,
         files=files,
-        update_uncontained=update_uncontained,
         document_service=document_service,
     )
 
@@ -100,7 +97,6 @@ def add_document(
     address: str,
     document: Json = Form(...),
     files: Optional[List[UploadFile]] = File(None),
-    update_uncontained: Optional[bool] = False,
     user: User = Depends(auth_w_jwt_or_pat),
 ):
     """Add a document to a package or a data source using an address.
@@ -118,7 +114,6 @@ def add_document(
       - The PROTOCOL is optional, and the default is dmss.
     - document (dict): The document that is to be stored.
     - files: Optional list of files to be stored as part of this document.
-    - update_uncontained (bool): Optional flag specifying whether to also update uncontained attributes in the document.
     - user (User): The authenticated user accessing the endpoint, automatically generated from provided bearer token or Access-Key.
 
     Returns:
@@ -137,7 +132,6 @@ def add_document(
         address=Address.from_absolute(address),
         document=document,
         files=files,
-        update_uncontained=update_uncontained,
         document_service=document_service,
     )
 

src/features/document/use_cases/add_document_use_case.py

@@ -18,15 +18,12 @@
 from services.document_service import DocumentService
 
 
-def _add_document_to_data_source(
-    data_source_id: str, document: dict, update_uncontained: Optional[bool], document_service: DocumentService
-) -> dict:
+def _add_document_to_data_source(data_source_id: str, document: dict, document_service: DocumentService) -> dict:
     """Add the document to an existing data source.
 
     Args:
        data_source_id: The data source ID
        document: The entity to be added
-       update_uncontained: Whether to update uncontained children (deprecated)
        document_service: The document service
 
     Returns:
@@ -53,7 +50,7 @@ def _add_document_to_data_source(
 
     new_node.set_uid(new_node.generate_id())
 
-    document_service.save(new_node, data_source_id, update_uncontained=update_uncontained)
+    document_service.save(new_node, data_source_id)
 
     return {"uid": new_node.node_id}
 
@@ -62,7 +59,6 @@ def _add_document_to_entity_or_list(
     address: Address,
     document: dict,
     files: dict[str, BinaryIO] | None,
-    update_uncontained: Optional[bool],
     document_service: DocumentService,
 ) -> dict:
     """Add the document to an existing entity.
@@ -71,7 +67,6 @@ def _add_document_to_entity_or_list(
        address: Reference to an existing entity or to an attribute (complex or list attribute) inside an entity.
        document: The entity to be added
        files: Dict with names and files of the files contained in the document
-       update_uncontained: Whether to update uncontained children (deprecated)
 
     Returns:
        A dict that contains the ID of the added document.
@@ -131,16 +126,12 @@ def _add_document_to_entity_or_list(
             )
             parent_node.add_child(list_node)
             list_node.add_child(new_node)
-            document_service.save(
-                parent_node, address.data_source, update_uncontained=update_uncontained, initial=True
-            )
+            document_service.save(parent_node, address.data_source, initial=True)
             return {"uid": f"{list_node.node_id}"}
         else:
             parent_node.add_child(new_node)
 
-            document_service.save(
-                parent_node, address.data_source, update_uncontained=update_uncontained, initial=True
-            )
+            document_service.save(parent_node, address.data_source, initial=True)
             return {"uid": f"{new_node.node_id}"}
 
     if target.type != SIMOS.PACKAGE.value and target.type != "object":
@@ -180,13 +171,13 @@ def _add_document_to_entity_or_list(
         if new_node.should_have_id():
             new_node.set_uid(new_node.generate_id())
         target.add_child(new_node)
-        document_service.save(target.find_parent(), address.data_source, update_uncontained=False)
+        document_service.save(target.find_parent(), address.data_source)
     else:
         new_node.parent = target.parent
         target.parent.replace(new_node.node_id, new_node)
-        document_service.save(target.find_parent(), address.data_source, update_uncontained=False)
+        document_service.save(target.find_parent(), address.data_source)
 
-    document_service.save(new_node, address.data_source, update_uncontained=update_uncontained)
+    document_service.save(new_node, address.data_source)
 
     return {"uid": new_node.node_id}
 
@@ -196,7 +187,6 @@ def add_document_use_case(
     address: Address,
     document_service: DocumentService,
     files: Optional[List[UploadFile]] = None,
-    update_uncontained: Optional[bool] = False,
 ) -> dict:
     """Add document to a data source or existing entity. Can also be used to add (complex) items to a list.
 
@@ -205,20 +195,18 @@ def add_document_use_case(
         address: Reference to a package, attribute inside an entity (either a list or a complex attribute) or a data source
         document_service: The document service
         files: Dict with names and files of the files contained in the document
-        update_uncontained: Whether to update uncontained children (deprecated)
 
     Returns:
         A dict that contains the ID of the added document.
     """
     validate_entity_against_self(document, document_service.get_blueprint)
 
     if not address.path:
-        return _add_document_to_data_source(address.data_source, document, update_uncontained, document_service)
+        return _add_document_to_data_source(address.data_source, document, document_service)
 
     return _add_document_to_entity_or_list(
         address=address,
         document=document,
         files={f.filename: f.file for f in files} if files else None,
-        update_uncontained=update_uncontained,
         document_service=document_service,
     )

src/features/document/use_cases/update_document_use_case.py

@@ -18,7 +18,6 @@ def _update_document(
     data: Union[dict, list],
     document_service: DocumentService,
     files: dict[str, BinaryIO] | None,
-    update_uncontained: Optional[bool],
 ):
     """
     Update a document.
@@ -50,7 +49,7 @@ def _update_document(
     if files:
         merge_entity_and_files(node, files)
 
-    document_service.save(node, address.data_source, update_uncontained=update_uncontained, initial=True)
+    document_service.save(node, address.data_source, initial=True)
     logger.info(f"Updated entity '{address}'")
     return {"data": tree_node_to_dict(node)}
 
@@ -60,7 +59,6 @@ def update_document_use_case(
     data: Union[dict, list],
     document_service: DocumentService,
     files: Optional[List[UploadFile]] = None,
-    update_uncontained: Optional[bool] = True,
 ):
     """Update document.
 
@@ -69,7 +67,6 @@ def update_document_use_case(
         data: The data to be updated
         document_service: The document service
         files: Dict with names and files of the files contained in the document
-        update_uncontained: Whether to update uncontained children (deprecated)
     Returns:
         A dict that contains the updated document.
     """
@@ -79,7 +76,6 @@ def update_document_use_case(
         data=data,
         document_service=document_service,
         files={f.filename: f.file for f in files} if files else None,
-        update_uncontained=update_uncontained,
     )
     # Do not invalidate the blueprint cache if it was not a blueprint that was changed
     if "type" in document["data"] and document["data"]["type"] == SIMOS.BLUEPRINT.value:

src/features/export/use_cases/export_use_case.py

@@ -23,13 +23,17 @@ def save_node_to_zipfile(
         if document_meta:
             document_node.entity["_meta_"] = document_meta
         storage_client = ZipFileClient(zip_file)
-        document_service.save(
-            document_node,
-            data_source_id,
-            storage_client,
-            update_uncontained=True,
-            combined_document_meta=document_meta,
-        )
+        path = ""  # Path here is used to get the proper file structure in the zip file
+        for node in document_node.traverse():
+            if not node.storage_contained and not node.is_array():
+                path = f"{path}/{node.entity['name']}/" if path else f"{node.entity['name']}"
+                document_service.save(
+                    node=node,
+                    data_source_id=data_source_id,
+                    path=path,
+                    repository=storage_client,
+                    combined_document_meta=document_meta,
+                )
 
 
 def create_zip_export(document_service: DocumentService, address: Address, user: User) -> str:

src/services/document_service.py

@@ -109,14 +109,12 @@ def save(
         data_source_id: str,
         repository=None,
         path="",
-        update_uncontained: bool = False,
         combined_document_meta: dict | None = None,
         initial: bool = False,
     ) -> Dict:
         """
-        Recursively saves a Node.
-        Digs down to the leaf children, and based on storageContained,
-        either saves the entity and returns the Reference, OR returns the entire entity.
+        Saves a Node.
+        Converting uncontained child entities to references.
 
         node: The Node to save
         path: A Filesystem equivalent path for this node. Used when writing zip-files.
@@ -132,9 +130,7 @@ def save(
 
         """
         if initial and node.storage_contained:
-            self.save(
-                node.parent, data_source_id, repository, path, update_uncontained, combined_document_meta, initial
-            )
+            self.save(node.parent, data_source_id, repository, path, combined_document_meta, initial)
         if not node.entity:
             return {}
         # If not passed a custom repository to save into, use the DocumentService's storage
@@ -144,7 +140,6 @@ def save(
         # If the node is a package, we build the path string to be used by filesystem like repositories.
         # Also, check for duplicate names in the package.
         if node.type == SIMOS.PACKAGE.value:
-            path = f"{path}/{node.entity['name']}/" if path else f"{node.entity['name']}"
             if len(node.children) > 0:
                 packageContent = node.children[0]
                 contentListNames = []
@@ -158,16 +153,6 @@ def save(
 
                         contentListNames.append(child.entity["name"])
 
-        if update_uncontained:  # If flag is set, dig down and save uncontained documents
-            for child in node.children:
-                if child.is_array():
-                    [
-                        self.save(x, data_source_id, repository, path, update_uncontained, combined_document_meta)
-                        for x in child.children
-                    ]
-                else:
-                    self.save(child, data_source_id, repository, path, update_uncontained, combined_document_meta)
-
         if node.type == SIMOS.BLOB.value:
             node.entity = self.save_blob_data(node, repository)
 

src/tests/bdd/authentication/create_entity_with_user_as_owner.feature

@@ -19,7 +19,7 @@ Feature: Set logged in user as owner when creating an entity
       """
       Given the logged in user is "johndoe" with roles "dmss-admin"
       Given authentication is enabled
-      Given i access the resource url "/api/documents/test-DS/$2.content?update_uncontained=False"
+      Given i access the resource url "/api/documents/test-DS/$2.content"
       When i make a form-data "POST" request
       """
       {

src/tests/bdd/document/add_file.feature

@@ -339,7 +339,7 @@ Feature: Explorer - Add file
     """
 
   Scenario: Add file - not contained
-    Given i access the resource url "/api/documents/test-DS/$1.content?update_uncontained=True"
+    Given i access the resource url "/api/documents/test-DS/$1.content"
     When i make a form-data "POST" request
     """
     {
@@ -502,7 +502,7 @@ Feature: Explorer - Add file
     Then the response status should be "OK"
 
   Scenario: Add Parent entity without a name attribute with -by-path endpoint
-    Given i access the resource url "/api/documents/test-DS/root_package?update_uncontained=True"
+    Given i access the resource url "/api/documents/test-DS/root_package"
     When i make a "POST" request with "1" files
     """
     {
@@ -557,7 +557,7 @@ Feature: Explorer - Add file
     And the response should have valid uid
 
   Scenario: Add Comment entity without a name attribute with -by-path endpoint
-    Given i access the resource url "/api/documents/test-DS/root_package?update_uncontained=True"
+    Given i access the resource url "/api/documents/test-DS/root_package"
     When i make a "POST" request with "1" files
     """
     {
@@ -572,7 +572,7 @@ Feature: Explorer - Add file
     Then the response status should be "OK"
 
   Scenario: Add blueprint without a name attribute with -by-path endpoint should fail
-    Given i access the resource url "/api/documents/test-DS/root_package?update_uncontained=True"
+    Given i access the resource url "/api/documents/test-DS/root_package"
     When i make a "POST" request with "1" files
     """
     {
@@ -596,7 +596,7 @@ Feature: Explorer - Add file
     """
 
   Scenario: Add package without a name attribute with -by-path endpoint should fail
-    Given i access the resource url "/api/documents/test-DS/root_package?update_uncontained=True"
+    Given i access the resource url "/api/documents/test-DS/root_package"
     When i make a "POST" request with "1" files
     """
     {
@@ -620,7 +620,7 @@ Feature: Explorer - Add file
     """
 
   Scenario: Add parent entity without a name attribute with add_by_parent_id endpoint
-    Given i access the resource url "/api/documents/test-DS/1.content?update_uncontained=True"
+    Given i access the resource url "/api/documents/test-DS/1.content"
     When i make a form-data "POST" request
     """
     {
@@ -643,7 +643,7 @@ Feature: Explorer - Add file
     """
 
   Scenario: Add comment entity without a name attribute with add_by_parent_id endpoint
-    Given i access the resource url "/api/documents/test-DS/$1.content?update_uncontained=True"
+    Given i access the resource url "/api/documents/test-DS/$1.content"
     When i make a form-data "POST" request
     """
     {
@@ -703,7 +703,7 @@ Feature: Explorer - Add file
     """
 
   Scenario: Add file with multiple PDFs
-    Given i access the resource url "/api/documents/test-DS/root_package?update_uncontained=True"
+    Given i access the resource url "/api/documents/test-DS/root_package"
     When i make a "POST" request with "4" files
     """
     {

src/tests/bdd/document/remove.feature

@@ -19,7 +19,7 @@ Feature: Explorer - Remove
       | 4   | 1          | sub_package_2 |             | dmss://system/SIMOS/Package     |
       | 3   | 2          | document_1    |             | dmss://system/SIMOS/Blueprint |
 
-  Scenario: Remove root package
+  Scenario: Remove root package by id
     Given i access the resource url "/api/documents/data-source-name/$1"
     When i make a "DELETE" request
     Then the response status should be "OK"

src/tests/bdd/document/remove_2.feature

@@ -13,7 +13,7 @@ Feature: Explorer - Remove by path
       | 4   | 1          | sub_package_2 |             | dmss://system/SIMOS/Package   |
       | 3   | 2          | document_1    |             | dmss://system/SIMOS/Blueprint |
 
-  Scenario: Remove root package
+  Scenario: Remove root package by name
     Given i access the resource url "/api/documents/data-source-name/blueprints"
     When i make a "DELETE" request
     Then the response status should be "OK"

src/tests/bdd/steps/domain.py

@@ -93,7 +93,9 @@ def step_impl_documents(context, data_source_id: str, collection: str):
     document_service = DocumentService(get_data_source, user=context.user)
     tree: Node = generate_tree(data_source_id, context.table, document_service)
     tree.show_tree()
-    document_service.save(node=tree, data_source_id=data_source_id, update_uncontained=True)
+    for node in tree.traverse():
+        if not node.storage_contained and not node.is_array():
+            document_service.save(node=node, data_source_id=data_source_id)
 
 
 @given('AccessControlList for document "{document_id}" in data-source "{data_source}" is')