Rework how duplicate windows & annotations are inserted.

perch_hoplite/agile/02_agile_modeling.ipynb

@@ -170,7 +170,7 @@
         "      label=ann.label,\n",
         "      label_type=ann.label_type,\n",
         "      provenance=ann.provenance,\n",
-        "      skip_duplicates=True,\n",
+        "      handle_duplicates=\"skip\",\n",
         "  )\n",
         "\n",
         "print(\"Annotations after saving new labels:\", len(db.get_all_annotations()))"
@@ -310,7 +310,7 @@
         "      label=ann.label,\n",
         "      label_type=ann.label_type,\n",
         "      provenance=ann.provenance,\n",
-        "      skip_duplicates=True,\n",
+        "      handle_duplicates=\"skip\",\n",
         "  )\n",
         "\n",
         "print(\"Annotations after saving new labels:\", len(db.get_all_annotations()))"

perch_hoplite/agile/99_migrate_db.ipynb

@@ -244,6 +244,7 @@
         "      label=old_label,\n",
         "      label_type=interface.LabelType(old_type),\n",
         "      provenance=old_provenance,\n",
+        "      handle_duplicates=\"allow\",\n",
         "  )\n",
         "new_db.commit()"
       ],

perch_hoplite/agile/ingest_annotations.py

@@ -94,6 +94,7 @@ def ingest_dataset(
                 label=label,
                 label_type=interface.LabelType.POSITIVE,
                 provenance=provenance,
+                handle_duplicates='allow',
             )
             lbl_counts[label] += 1
     lbl_count = sum(lbl_counts.values())

perch_hoplite/agile/tests/classifier_data_test.py

@@ -211,6 +211,7 @@ def add_label(window_id, lbl_idx, lbl_type):
           label=db_test_utils.CLASS_LABELS[lbl_idx],
           label_type=lbl_type,
           provenance='test',
+          handle_duplicates='allow',
       )
 
     with self.subTest('single_positive_label'):

perch_hoplite/db/README.md

@@ -303,6 +303,20 @@ window_id = db.insert_window(
   embedding=np.random.normal(size=1280),
   extra=999,
 )
+window_id = db.insert_window(
+  recording_id=1,
+  offsets=[2, 3],
+  embedding=np.random.normal(size=1280),
+  extra=1000,
+  handle_duplicates="overwrite",
+)
+window_id = db.insert_window(
+  recording_id=1,
+  offsets=[2, 3],
+  embedding=np.random.normal(size=1280),
+  extra=1001,
+  handle_duplicates="skip",
+)
 ```
 
 Retrieving an existing window can be done like this:
@@ -373,7 +387,7 @@ annotation_id = db.insert_annotation(
   label="wolf",
   label_type=LabelType.POSITIVE,
   provenance="me",
-  skip_duplicates=True,
+  handle_duplicates="skip",
 )
 ```
 

perch_hoplite/db/db_loader.py

@@ -94,6 +94,7 @@ def duplicate_db(
   for annotation in tqdm.tqdm(source_db.get_all_annotations()):
     target_id = target_db.insert_annotation(
         window_id=window_id_mapping[annotation.window_id],
+        handle_duplicates='allow',
         **annotation.to_kwargs(skip=['id', 'window_id']),
     )
     annotation_id_mapping[annotation.id] = target_id

perch_hoplite/db/in_mem_impl.py

@@ -21,7 +21,7 @@
 import dataclasses
 import datetime as dt
 import itertools
-from typing import Any
+from typing import Any, Literal
 
 from absl import logging
 from ml_collections import config_dict
@@ -351,13 +351,22 @@ def insert_window(
       recording_id: int,
       offsets: list[float],
       embedding: np.ndarray | None = None,
+      handle_duplicates: Literal[
+          'allow', 'overwrite', 'skip', 'error'
+      ] = 'error',
       **kwargs: Any,
   ) -> int:
     """Insert a window into the database."""
 
     if recording_id not in self._recordings:
       raise ValueError(f'Recording id not found: {recording_id}')
 
+    duplicate_id = self._handle_window_duplicates(
+        recording_id, offsets, handle_duplicates
+    )
+    if duplicate_id is not None:
+      return duplicate_id
+
     window_id = self._next_window_id
     self._windows[window_id] = interface.Window(
         id=window_id,
@@ -403,29 +412,21 @@ def insert_annotation(
       label: str,
       label_type: interface.LabelType,
       provenance: str,
-      skip_duplicates: bool = False,
+      handle_duplicates: Literal[
+          'allow', 'overwrite', 'skip', 'error'
+      ] = 'error',
       **kwargs: Any,
   ) -> int:
     """Insert an annotation into the database."""
 
     if recording_id not in self._recordings:
       raise ValueError(f'Recording id not found: {recording_id}')
 
-    if skip_duplicates:
-      matches = self.get_all_annotations(
-          config_dict.create(
-              eq=dict(
-                  recording_id=recording_id,
-                  label=label,
-                  label_type=label_type,
-              ),
-              approx=dict(
-                  offsets=offsets,
-              ),
-          )
-      )
-      if matches:
-        return matches[0].id
+    duplicate_id = self._handle_annotation_duplicates(
+        recording_id, offsets, label, label_type, provenance, handle_duplicates
+    )
+    if duplicate_id is not None:
+      return duplicate_id
 
     annotation_id = self._next_annotation_id
     self._annotations[annotation_id] = interface.Annotation(