Tests passing

Author: Ubuntu

nucleus/annotation.py

@@ -582,13 +582,25 @@ def to_payload(self) -> dict:
 
         return payload
 
-    def has_files(self) -> bool:
+    def has_local_files(self) -> bool:
         if is_local_path(self.mask_url):
             if not os.path.isfile(self.mask_url):
                 raise Exception(f"Mask file {self.mask_url} does not exist.")
             return True
         return False
 
+    def __eq__(self, other):
+        if not isinstance(other, SegmentationAnnotation):
+            return False
+        self.annotations = sorted(self.annotations, key=lambda x: x.index)
+        other.annotations = sorted(other.annotations, key=lambda x: x.index)
+        return (
+            (self.annotation_id == other.annotation_id)
+            and (self.annotations == other.annotations)
+            and (self.mask_url == other.mask_url)
+            and (self.reference_id == other.reference_id)
+        )
+
 
 class AnnotationTypes(Enum):
     BOX = BOX_TYPE

nucleus/annotation_uploader.py

@@ -7,7 +7,7 @@
     FormDataContextHandler,
     make_many_form_data_requests_concurrently,
 )
-from nucleus.constants import ITEMS_KEY, SEGMENTATIONS_KEY
+from nucleus.constants import MASK_TYPE, SERIALIZED_REQUEST_KEY
 from nucleus.payload_constructor import (
     construct_annotation_payload,
     construct_segmentation_payload,
@@ -143,7 +143,7 @@ def make_batched_file_form_data_requests(
         return make_many_form_data_requests_concurrently(
             client=self._client,
             requests=requests,
-            route=f"dataset/{self.dataset_id}/annotate_segmentation_files",
+            route=f"dataset/{self.dataset_id}/annotate",
             progressbar=progressbar,
             concurrency=local_file_upload_concurrency,
         )
@@ -166,7 +166,7 @@ def fn():
             )
             form_data = [
                 FileFormField(
-                    name=ITEMS_KEY,
+                    name=SERIALIZED_REQUEST_KEY,
                     filename=None,
                     value=json.dumps(request_json),
                     content_type="application/json",
@@ -186,7 +186,7 @@ def fn():
                     )
                 form_data.append(
                     FileFormField(
-                        name=SEGMENTATIONS_KEY,
+                        name=MASK_TYPE,
                         filename=segmentation.mask_url,
                         value=mask_fp,
                         content_type="image/png",

nucleus/constants.py

@@ -99,6 +99,7 @@
 REFERENCE_ID_KEY = "reference_id"
 REQUEST_ID_KEY = "requestId"
 SCENES_KEY = "scenes"
+SERIALIZED_REQUEST_KEY = "serialized_request"
 SEGMENTATIONS_KEY = "segmentations"
 SLICE_ID_KEY = "slice_id"
 STATUS_CODE_KEY = "status_code"

tests/test_segmentation.py

@@ -1,28 +1,57 @@
 from nucleus.annotation import SegmentationAnnotation
+from nucleus.dataset import Dataset
 from tests.helpers import (
     TEST_LOCAL_MASK_URL,
     TEST_SEGMENTATION_ANNOTATIONS,
     assert_segmentation_annotation_matches_dict,
 )
 
 
-def test_single_local_semseg_gt_upload(dataset):
-    annotation = SegmentationAnnotation.from_json(
+def test_single_local_semseg_gt_upload(dataset: Dataset):
+    request_annotation = SegmentationAnnotation.from_json(
         TEST_SEGMENTATION_ANNOTATIONS[0]
     )
-    annotation.mask_url = TEST_LOCAL_MASK_URL
-    response = dataset.annotate(annotations=[annotation])
+    request_annotation.mask_url = TEST_LOCAL_MASK_URL
+    response = dataset.annotate(annotations=[request_annotation])
 
     assert response["dataset_id"] == dataset.id
     assert response["annotations_processed"] == 1
     assert response["annotations_ignored"] == 0
 
-    response_annotation = dataset.refloc(annotation.reference_id)[
+    response_annotation = dataset.refloc(request_annotation.reference_id)[
         "annotations"
     ]["segmentation"][0]
-    assert_segmentation_annotation_matches_dict(
-        response_annotation, TEST_SEGMENTATION_ANNOTATIONS[0]
-    )
+
+    assert response_annotation == request_annotation
+
+
+def test_batch_local_semseg_gt_upload(dataset: Dataset):
+
+    # This reference id is not in the dataset.
+    bad_reference_id = TEST_SEGMENTATION_ANNOTATIONS[-1]["reference_id"]
+
+    request_annotations = [
+        SegmentationAnnotation.from_json(json_data)
+        for json_data in TEST_SEGMENTATION_ANNOTATIONS
+    ]
+    for request_annotation in request_annotations:
+        request_annotation.mask_url = TEST_LOCAL_MASK_URL
+    response = dataset.annotate(annotations=request_annotations)
+
+    print(request_annotations)
+    print(response)
+
+    assert response["dataset_id"] == dataset.id
+    assert response["annotations_processed"] == 4
+    assert response["annotations_ignored"] == 0
+    assert bad_reference_id in response["errors"][0]
+
+    for request_annotation in request_annotations[:4]:
+        response_annotation = dataset.refloc(request_annotation.reference_id)[
+            "annotations"
+        ]["segmentation"][0]
+
+        assert response_annotation == request_annotation
 
 
 def test_single_semseg_gt_upload(dataset):
@@ -49,7 +78,7 @@ def test_batch_semseg_gt_upload(dataset):
     ]
     response = dataset.annotate(annotations=annotations)
     assert response["dataset_id"] == dataset.id
-    assert response["annotations_processed"] == 5
+    assert response["annotations_processed"] == 4
     assert response["annotations_ignored"] == 0
 
 
@@ -61,14 +90,14 @@ def test_batch_semseg_gt_upload_ignore(dataset):
     ]
     response = dataset.annotate(annotations=annotations)
     assert response["dataset_id"] == dataset.id
-    assert response["annotations_processed"] == 5
+    assert response["annotations_processed"] == 4
     assert response["annotations_ignored"] == 0
 
     # When we re-upload, expect them to be ignored
     response = dataset.annotate(annotations=annotations)
     assert response["dataset_id"] == dataset.id
     assert response["annotations_processed"] == 0
-    assert response["annotations_ignored"] == 5
+    assert response["annotations_ignored"] == 4
 
 
 def test_batch_semseg_gt_upload_update(dataset):
@@ -79,11 +108,11 @@ def test_batch_semseg_gt_upload_update(dataset):
     ]
     response = dataset.annotate(annotations=annotations)
     assert response["dataset_id"] == dataset.id
-    assert response["annotations_processed"] == 5
+    assert response["annotations_processed"] == 4
     assert response["annotations_ignored"] == 0
 
     # When we re-upload, expect uploads to be processed
     response = dataset.annotate(annotations=annotations, update=True)
     assert response["dataset_id"] == dataset.id
-    assert response["annotations_processed"] == 5
+    assert response["annotations_processed"] == 4
     assert response["annotations_ignored"] == 0