Addition of the argument

darwin/cli.py

@@ -124,6 +124,7 @@ def _run(args: Namespace, parser: ArgumentParser) -> None:
                 args.path,
                 args.frames,
                 args.extract_views,
+                args.handle_as_slices,
                 args.preserve_folders,
                 args.verbose,
                 args.item_merge_mode,

darwin/cli_functions.py

@@ -655,6 +655,7 @@ def upload_data(
     path: Optional[str],
     frames: bool,
     extract_views: bool = False,
+    handle_as_slices: bool = False,
     preserve_folders: bool = False,
     verbose: bool = False,
     item_merge_mode: Optional[str] = None,
@@ -682,6 +683,8 @@ def upload_data(
         Specify whether the files will be uploaded as a list of frames or not.
     extract_views : bool
         If providing a volume, specify whether to extract the orthogonal views or not.
+    handle_as_slices : bool
+        Whether to upload DICOM files as slices
     preserve_folders : bool
         Specify whether or not to preserve folder paths when uploading.
     verbose : bool
@@ -779,6 +782,7 @@ def file_upload_callback(
                 fps=fps,
                 as_frames=frames,
                 extract_views=extract_views,
+                handle_as_slices=handle_as_slices,
                 path=path,
                 preserve_folders=preserve_folders,
                 progress_callback=progress_callback,

darwin/dataset/remote_dataset_v2.py

@@ -171,6 +171,7 @@ def push(
         fps: int = 0,
         as_frames: bool = False,
         extract_views: bool = False,
+        handle_as_slices: Optional[bool] = False,
         files_to_exclude: Optional[List[PathLike]] = None,
         path: Optional[str] = None,
         preserve_folders: bool = False,
@@ -199,6 +200,8 @@ def push(
             When the uploading file is a video, specify whether it's going to be uploaded as a list of frames.
         extract_views: bool, default: False
             When the uploading file is a volume, specify whether it's going to be split into orthogonal views.
+        handle_as_slices: Optioonal[bool], default: False
+            Whether to upload DICOM files as slices
         files_to_exclude : Optional[PathLike]], default: None
             Optional list of files to exclude from the file scan. These can be folders.
         path: Optional[str], default: None
@@ -267,7 +270,9 @@ def push(
             local_files, multi_file_items = _find_files_to_upload_as_multi_file_items(
                 search_files, files_to_exclude, fps, item_merge_mode
             )
-            handler = UploadHandlerV2(self, local_files, multi_file_items)
+            handler = UploadHandlerV2(
+                self, local_files, multi_file_items, handle_as_slices=handle_as_slices
+            )
         else:
             local_files = _find_files_to_upload_as_single_file_items(
                 search_files,
@@ -279,7 +284,9 @@ def push(
                 extract_views,
                 preserve_folders,
             )
-            handler = UploadHandlerV2(self, local_files)
+            handler = UploadHandlerV2(
+                self, local_files, handle_as_slices=handle_as_slices
+            )
         if blocking:
             handler.upload(
                 max_workers=max_workers,
@@ -883,10 +890,10 @@ def _find_files_to_upload_as_multi_file_items(
         List of directories to search for files.
     files_to_exclude : List[PathLike]
         List of files to exclude from the file scan.
-    item_merge_mode : str
-        Mode to merge the files in the folders. Valid options are: 'slots', 'series', 'channels'.
     fps : int
         When uploading video files, specify the framerate
+    item_merge_mode : str
+        Mode to merge the files in the folders. Valid options are: 'slots', 'series', 'channels'.
 
     Returns
     -------

darwin/dataset/upload_manager.py

@@ -382,6 +382,7 @@ def __init__(
         dataset: "RemoteDataset",
         local_files: List[LocalFile],
         multi_file_items: Optional[List[MultiFileItem]] = None,
+        handle_as_slices: Optional[bool] = False,
     ):
         self._progress: Optional[
             Iterator[Callable[[Optional[ByteReadCallback]], None]]
@@ -391,11 +392,17 @@ def __init__(
         self.dataset: RemoteDataset = dataset
         self.errors: List[UploadRequestError] = []
         self.skip_existing_full_remote_filepaths()
-        self.blocked_items, self.pending_items = self._request_upload()
+        self.blocked_items, self.pending_items = self._request_upload(
+            handle_as_slices=handle_as_slices
+        )
 
     @staticmethod
-    def build(dataset: "RemoteDataset", local_files: List[LocalFile]):
-        return UploadHandlerV2(dataset, local_files)
+    def build(
+        dataset: "RemoteDataset",
+        local_files: List[LocalFile],
+        handle_as_slices: Optional[bool] = False,
+    ):
+        return UploadHandlerV2(dataset, local_files, handle_as_slices=handle_as_slices)
 
     @property
     def client(self) -> "Client":
@@ -542,7 +549,9 @@ def callback(file_name, file_total_bytes, file_bytes_sent):
                 file_to_upload(callback)
 
     @abstractmethod
-    def _request_upload(self) -> Tuple[List[ItemPayload], List[ItemPayload]]:
+    def _request_upload(
+        self, handle_as_slices: Optional[bool] = False
+    ) -> Tuple[List[ItemPayload], List[ItemPayload]]:
         pass
 
     @abstractmethod
@@ -565,14 +574,18 @@ def __init__(
         dataset: "RemoteDataset",
         local_files: List[LocalFile],
         multi_file_items: Optional[List[MultiFileItem]] = None,
+        handle_as_slices: Optional[bool] = False,
     ):
         super().__init__(
             dataset=dataset,
             local_files=local_files,
             multi_file_items=multi_file_items,
+            handle_as_slices=handle_as_slices,
         )
 
-    def _request_upload(self) -> Tuple[List[ItemPayload], List[ItemPayload]]:
+    def _request_upload(
+        self, handle_as_slices: Optional[bool] = False
+    ) -> Tuple[List[ItemPayload], List[ItemPayload]]:
         blocked_items = []
         items = []
         chunk_size: int = _upload_chunk_size()
@@ -585,7 +598,10 @@ def _request_upload(self) -> Tuple[List[ItemPayload], List[ItemPayload]]:
                         "items": [
                             file.serialize_darwin_json_v2() for file in file_chunk
                         ],
-                        "options": {"ignore_dicom_layout": True},
+                        "options": {
+                            "ignore_dicom_layout": True,
+                            "handle_as_slices": handle_as_slices,
+                        },
                     }
                     for file_chunk in chunk(self.multi_file_items, chunk_size)
                 ]
@@ -603,7 +619,10 @@ def _request_upload(self) -> Tuple[List[ItemPayload], List[ItemPayload]]:
 
         upload_payloads.extend(
             [
-                {"items": [file.serialize_darwin_json_v2() for file in file_chunk]}
+                {
+                    "items": [file.serialize_darwin_json_v2() for file in file_chunk],
+                    "options": {"handle_as_slices": handle_as_slices},
+                }
                 for file_chunk in chunk(single_file_items, chunk_size)
             ]
         )

darwin/options.py

@@ -168,6 +168,11 @@ def __init__(self) -> None:
             action="store_true",
             help="Upload a volume with all 3 orthogonal views.",
         )
+        parser_push.add_argument(
+            "--handle_as_slices",
+            action="store_true",
+            help="Upload DICOM files as slices",
+        )
 
         parser_push.add_argument(
             "--path", type=str, default=None, help="Folder to upload the files into."

tests/darwin/cli_functions_test.py

@@ -229,6 +229,7 @@ def test_with_verbose_flag(
                         None,
                         False,
                         False,
+                        False,
                         True,
                     )
                     get_remote_dataset_mock.assert_called_once()

tests/darwin/dataset/upload_manager_test.py

@@ -3,6 +3,8 @@
 
 import pytest
 import responses
+import inspect
+
 
 from darwin.client import Client
 from darwin.config import Config
@@ -416,7 +418,98 @@ def test_upload_files(dataset: RemoteDataset, request_upload_endpoint: str):
     assert upload_handler.error_count == 0
 
 
+@pytest.mark.usefixtures("file_read_write_test")
+@responses.activate
+def test_upload_files_adds_handle_as_slices_option_to_upload_payload(
+    dataset: RemoteDataset, request_upload_endpoint: str
+):
+    request_upload_response = {
+        "blocked_items": [],
+        "items": [
+            {
+                "id": "3b241101-e2bb-4255-8caf-4136c566a964",
+                "name": "test.dcm",
+                "path": "/",
+                "slots": [
+                    {
+                        "type": "image",
+                        "file_name": "test.dcm",
+                        "slot_name": "0",
+                        "upload_id": "123e4567-e89b-12d3-a456-426614174000",
+                        "as_frames": False,
+                        "extract_views": False,
+                    }
+                ],
+            }
+        ],
+    }
+    responses.add(
+        responses.POST,
+        request_upload_endpoint,
+        json=request_upload_response,
+        status=200,
+    )
+    Path("test.dcm").touch()
+    local_file = LocalFile(local_path=Path("test.dcm"))
+    with patch("darwin.backend_v2.BackendV2.register_data") as mock_register_data:
+        with patch.object(dataset, "fetch_remote_files", return_value=[]):
+            UploadHandler.build(dataset, [local_file], handle_as_slices=True)
+            assert mock_register_data.call_count == 1
+            assert mock_register_data.call_args[0][1]["options"] == {
+                "handle_as_slices": True
+            }
+
+
+@pytest.mark.usefixtures("file_read_write_test")
+@responses.activate
+def test_upload_files_does_not_add_handle_as_slices_option_to_upload_payload(
+    dataset: RemoteDataset, request_upload_endpoint: str
+):
+    request_upload_response = {
+        "blocked_items": [],
+        "items": [
+            {
+                "id": "3b241101-e2bb-4255-8caf-4136c566a964",
+                "name": "test.dcm",
+                "path": "/",
+                "slots": [
+                    {
+                        "type": "image",
+                        "file_name": "test.dcm",
+                        "slot_name": "0",
+                        "upload_id": "123e4567-e89b-12d3-a456-426614174000",
+                        "as_frames": False,
+                        "extract_views": False,
+                    }
+                ],
+            }
+        ],
+    }
+    responses.add(
+        responses.POST,
+        request_upload_endpoint,
+        json=request_upload_response,
+        status=200,
+    )
+    Path("test.dcm").touch()
+    local_file = LocalFile(local_path=Path("test.dcm"))
+    with patch("darwin.backend_v2.BackendV2.register_data") as mock_register_data:
+        with patch.object(dataset, "fetch_remote_files", return_value=[]):
+            UploadHandler.build(dataset, [local_file], handle_as_slices=False)
+            assert mock_register_data.call_count == 1
+            assert mock_register_data.call_args[0][1]["options"] == {
+                "handle_as_slices": False
+            }
+
+
+def test_default_value_for_handle_as_slices():
+    signature = inspect.signature(UploadHandlerV2._request_upload)
+    handle_as_slices_default_value = signature.parameters["handle_as_slices"].default
+    assert handle_as_slices_default_value is False
+
+
 class TestUploadChunkSize:
+
     def test_default_value_when_env_var_is_not_set(self):
         assert _upload_chunk_size() == 500