VERSION

-0.2.3
+0.2.4-rc3

arkindex_worker/cache.py

@@ -68,6 +68,7 @@ class CachedElement(Model):
     mirrored = BooleanField(default=False)
     initial = BooleanField(default=False)
     worker_version_id = UUIDField(null=True)
+    confidence = FloatField(null=True)
 
     class Meta:
         database = db

arkindex_worker/worker/element.py

 # -*- coding: utf-8 -*-
 
 import uuid
+from typing import Dict, List, Optional, Union
 
 from peewee import IntegrityError
 
@@ -40,10 +41,26 @@ class ElementMixin(object):
 
         return True
 
-    def create_sub_element(self, element, type, name, polygon):
+    def create_sub_element(
+        self,
+        element: Element,
+        type: str,
+        name: str,
+        polygon: List[List[Union[int, float]]],
+        confidence: Optional[float] = None,
+    ) -> str:
         """
-        Create a child element on the given element through API
-        Return the ID of the created sub element
+        Create a child element on the given element through the API.
+
+        :param Element element: The parent element.
+        :param str type: Slug of the element type for this child element.
+        :param str name: Name of the child element.
+        :param polygon: Polygon of the child element.
+        :type polygon: list(list(int or float))
+        :param confidence: Optional confidence score, between 0.0 and 1.0.
+        :type confidence: float or None
+        :returns: UUID of the created element.
+        :rtype: str
         """
         assert element and isinstance(
             element, Element
@@ -64,6 +81,10 @@ class ElementMixin(object):
         assert all(
             isinstance(coord, (int, float)) for point in polygon for coord in point
         ), "polygon points should be lists of two numbers"
+        assert confidence is None or (
+            isinstance(confidence, float) and 0 <= confidence <= 1
+        ), "confidence should be None or a float in [0..1] range"
+
         if self.is_read_only:
             logger.warning("Cannot create element as this worker is in read-only mode")
             return
@@ -78,16 +99,43 @@ class ElementMixin(object):
                 "polygon": polygon,
                 "parent": element.id,
                 "worker_version": self.worker_version_id,
+                "confidence": confidence,
             },
         )
         self.report.add_element(element.id, type)
 
         return sub_element["id"]
 
-    def create_elements(self, parent, elements):
+    def create_elements(
+        self,
+        parent: Union[Element, CachedElement],
+        elements: List[
+            Dict[str, Union[str, List[List[Union[int, float]]], float, None]]
+        ],
+    ) -> List[Dict[str, str]]:
         """
-        Create children elements on the given element through API
-        Return the IDs of created elements
+        Create child elements on the given element in a single API request.
+
+        :param parent: Parent element for all the new child elements. The parent must have an image and a polygon.
+        :type parent: Element or CachedElement
+        :param elements: List of dicts, one per element. Each dict can have the following keys:
+
+            name (str)
+               Required. Name of the element.
+
+            type (str)
+               Required. Slug of the element type for this element.
+
+            polygon (list(list(int or float)))
+               Required. Polygon for this child element. Must have at least three points, with each point
+               having two non-negative coordinates and being inside of the parent element's image.
+
+            confidence (float or None)
+                Optional confidence score, between 0.0 and 1.0.
+
+        :type elements: list(dict(str, Any))
+        :return: List of dicts, with each dict having a single key, ``id``, holding the UUID of each created element.
+        :rtype: list(dict(str, str))
         """
         if isinstance(parent, Element):
             assert parent.get(
@@ -135,6 +183,11 @@ class ElementMixin(object):
                 isinstance(coord, (int, float)) for point in polygon for coord in point
             ), f"Element at index {index} in elements: polygon points should be lists of two numbers"
 
+            confidence = element.get("confidence")
+            assert confidence is None or (
+                isinstance(confidence, float) and 0 <= confidence <= 1
+            ), f"Element at index {index} in elements: confidence should be None or a float in [0..1] range"
+
         if self.is_read_only:
             logger.warning("Cannot create elements as this worker is in read-only mode")
             return
@@ -176,6 +229,7 @@ class ElementMixin(object):
                         "image_id": image_id,
                         "polygon": element["polygon"],
                         "worker_version_id": self.worker_version_id,
+                        "confidence": element.get("confidence"),
                     }
                     for idx, element in enumerate(elements)
                 ]

requirements.txt

@@ -4,5 +4,5 @@ Pillow==9.1.0
 python-gitlab==2.7.1
 python-gnupg==0.4.8
 sh==1.14.2
-shapely==1.8.1.post1
+shapely==1.8.2
 tenacity==8.0.1

tests/test_cache.py

@@ -59,7 +59,7 @@ def test_create_tables(tmp_path):
     create_tables()
 
     expected_schema = """CREATE TABLE "classifications" ("id" TEXT NOT NULL PRIMARY KEY, "element_id" TEXT NOT NULL, "class_name" TEXT NOT NULL, "confidence" REAL NOT NULL, "state" VARCHAR(10) NOT NULL, "worker_version_id" TEXT NOT NULL, FOREIGN KEY ("element_id") REFERENCES "elements" ("id"))
-CREATE TABLE "elements" ("id" TEXT NOT NULL PRIMARY KEY, "parent_id" TEXT, "type" VARCHAR(50) NOT NULL, "image_id" TEXT, "polygon" text, "rotation_angle" INTEGER NOT NULL, "mirrored" INTEGER NOT NULL, "initial" INTEGER NOT NULL, "worker_version_id" TEXT, FOREIGN KEY ("image_id") REFERENCES "images" ("id"))
+CREATE TABLE "elements" ("id" TEXT NOT NULL PRIMARY KEY, "parent_id" TEXT, "type" VARCHAR(50) NOT NULL, "image_id" TEXT, "polygon" text, "rotation_angle" INTEGER NOT NULL, "mirrored" INTEGER NOT NULL, "initial" INTEGER NOT NULL, "worker_version_id" TEXT, "confidence" REAL, FOREIGN KEY ("image_id") REFERENCES "images" ("id"))
 CREATE TABLE "entities" ("id" TEXT NOT NULL PRIMARY KEY, "type" VARCHAR(50) NOT NULL, "name" TEXT NOT NULL, "validated" INTEGER NOT NULL, "metas" text, "worker_version_id" TEXT NOT NULL)
 CREATE TABLE "images" ("id" TEXT NOT NULL PRIMARY KEY, "width" INTEGER NOT NULL, "height" INTEGER NOT NULL, "url" TEXT NOT NULL)
 CREATE TABLE "transcription_entities" ("transcription_id" TEXT NOT NULL, "entity_id" TEXT NOT NULL, "offset" INTEGER NOT NULL CHECK (offset >= 0), "length" INTEGER NOT NULL CHECK (length > 0), "worker_version_id" TEXT NOT NULL, "confidence" REAL, PRIMARY KEY ("transcription_id", "entity_id"), FOREIGN KEY ("transcription_id") REFERENCES "transcriptions" ("id"), FOREIGN KEY ("entity_id") REFERENCES "entities" ("id"))

tests/test_elements_worker/test_elements.py

@@ -424,6 +424,19 @@ def test_create_sub_element_wrong_polygon(mock_elements_worker):
     assert str(e.value) == "polygon points should be lists of two numbers"
 
 
+@pytest.mark.parametrize("confidence", ["lol", "0.2", -1.0, 1.42, float("inf")])
+def test_create_sub_element_wrong_confidence(mock_elements_worker, confidence):
+    with pytest.raises(AssertionError) as e:
+        mock_elements_worker.create_sub_element(
+            element=Element({"zone": None}),
+            type="something",
+            name="blah",
+            polygon=[[0, 0], [0, 10], [10, 10], [10, 0], [0, 0]],
+            confidence=confidence,
+        )
+    assert str(e.value) == "confidence should be None or a float in [0..1] range"
+
+
 def test_create_sub_element_api_error(responses, mock_elements_worker):
     elt = Element(
         {
@@ -495,6 +508,49 @@ def test_create_sub_element(responses, mock_elements_worker):
         "polygon": [[1, 1], [2, 2], [2, 1], [1, 2]],
         "parent": "12341234-1234-1234-1234-123412341234",
         "worker_version": "12341234-1234-1234-1234-123412341234",
+        "confidence": None,
+    }
+    assert sub_element_id == "12345678-1234-1234-1234-123456789123"
+
+
+def test_create_sub_element_confidence(responses, mock_elements_worker):
+    elt = Element(
+        {
+            "id": "12341234-1234-1234-1234-123412341234",
+            "corpus": {"id": "11111111-1111-1111-1111-111111111111"},
+            "zone": {"image": {"id": "22222222-2222-2222-2222-222222222222"}},
+        }
+    )
+    responses.add(
+        responses.POST,
+        "http://testserver/api/v1/elements/create/",
+        status=200,
+        json={"id": "12345678-1234-1234-1234-123456789123"},
+    )
+
+    sub_element_id = mock_elements_worker.create_sub_element(
+        element=elt,
+        type="something",
+        name="0",
+        polygon=[[1, 1], [2, 2], [2, 1], [1, 2]],
+        confidence=0.42,
+    )
+
+    assert len(responses.calls) == len(BASE_API_CALLS) + 1
+    assert [
+        (call.request.method, call.request.url) for call in responses.calls
+    ] == BASE_API_CALLS + [
+        ("POST", "http://testserver/api/v1/elements/create/"),
+    ]
+    assert json.loads(responses.calls[-1].request.body) == {
+        "type": "something",
+        "name": "0",
+        "image": "22222222-2222-2222-2222-222222222222",
+        "corpus": "11111111-1111-1111-1111-111111111111",
+        "polygon": [[1, 1], [2, 2], [2, 1], [1, 2]],
+        "parent": "12341234-1234-1234-1234-123412341234",
+        "worker_version": "12341234-1234-1234-1234-123412341234",
+        "confidence": 0.42,
     }
     assert sub_element_id == "12345678-1234-1234-1234-123456789123"
 
@@ -740,6 +796,26 @@ def test_create_elements_wrong_elements_polygon(mock_elements_worker):
     )
 
 
+@pytest.mark.parametrize("confidence", ["lol", "0.2", -1.0, 1.42, float("inf")])
+def test_create_elements_wrong_elements_confidence(mock_elements_worker, confidence):
+    with pytest.raises(AssertionError) as e:
+        mock_elements_worker.create_elements(
+            parent=Element({"zone": {"image": {"id": "image_id"}}}),
+            elements=[
+                {
+                    "name": "a",
+                    "type": "something",
+                    "polygon": [[0, 0], [0, 10], [10, 10], [10, 0], [0, 0]],
+                    "confidence": confidence,
+                }
+            ],
+        )
+    assert (
+        str(e.value)
+        == "Element at index 0 in elements: confidence should be None or a float in [0..1] range"
+    )
+
+
 def test_create_elements_api_error(responses, mock_elements_worker):
     elt = Element(
         {
@@ -930,6 +1006,80 @@ def test_create_elements(responses, mock_elements_worker_with_cache, tmp_path):
             image_id="c0fec0fe-c0fe-c0fe-c0fe-c0fec0fec0fe",
             polygon=[[1, 1], [2, 2], [2, 1], [1, 2]],
             worker_version_id=UUID("12341234-1234-1234-1234-123412341234"),
+            confidence=None,
+        )
+    ]
+
+
+def test_create_elements_confidence(
+    responses, mock_elements_worker_with_cache, tmp_path
+):
+    elt = Element(
+        {
+            "id": "12341234-1234-1234-1234-123412341234",
+            "zone": {
+                "image": {
+                    "id": "c0fec0fe-c0fe-c0fe-c0fe-c0fec0fec0fe",
+                    "width": 42,
+                    "height": 42,
+                    "url": "http://aaaa",
+                }
+            },
+        }
+    )
+    responses.add(
+        responses.POST,
+        "http://testserver/api/v1/element/12341234-1234-1234-1234-123412341234/children/bulk/",
+        status=200,
+        json=[{"id": "497f6eca-6276-4993-bfeb-53cbbbba6f08"}],
+    )
+
+    created_ids = mock_elements_worker_with_cache.create_elements(
+        parent=elt,
+        elements=[
+            {
+                "name": "0",
+                "type": "something",
+                "polygon": [[1, 1], [2, 2], [2, 1], [1, 2]],
+                "confidence": 0.42,
+            }
+        ],
+    )
+
+    assert len(responses.calls) == len(BASE_API_CALLS) + 1
+    assert [
+        (call.request.method, call.request.url) for call in responses.calls
+    ] == BASE_API_CALLS + [
+        (
+            "POST",
+            "http://testserver/api/v1/element/12341234-1234-1234-1234-123412341234/children/bulk/",
+        ),
+    ]
+    assert json.loads(responses.calls[-1].request.body) == {
+        "elements": [
+            {
+                "name": "0",
+                "type": "something",
+                "polygon": [[1, 1], [2, 2], [2, 1], [1, 2]],
+                "confidence": 0.42,
+            }
+        ],
+        "worker_version": "12341234-1234-1234-1234-123412341234",
+    }
+    assert created_ids == [{"id": "497f6eca-6276-4993-bfeb-53cbbbba6f08"}]
+
+    # Check that created elements were properly stored in SQLite cache
+    assert (tmp_path / "db.sqlite").is_file()
+
+    assert list(CachedElement.select()) == [
+        CachedElement(
+            id=UUID("497f6eca-6276-4993-bfeb-53cbbbba6f08"),
+            parent_id=UUID("12341234-1234-1234-1234-123412341234"),
+            type="something",
+            image_id="c0fec0fe-c0fe-c0fe-c0fe-c0fec0fec0fe",
+            polygon=[[1, 1], [2, 2], [2, 1], [1, 2]],
+            worker_version_id=UUID("12341234-1234-1234-1234-123412341234"),
+            confidence=0.42,
         )
     ]
 

tests/test_elements_worker/test_transcriptions.py

@@ -345,6 +345,7 @@ def test_create_transcription_orientation_with_cache(
                 "mirrored": False,
                 "initial": False,
                 "worker_version_id": None,
+                "confidence": None,
             },
             "text": "Animula vagula blandula",
             "confidence": 0.42,
@@ -809,6 +810,7 @@ def test_create_transcriptions_orientation(responses, mock_elements_worker_with_
                 "mirrored": False,
                 "initial": False,
                 "worker_version_id": None,
+                "confidence": None,
             },
             "text": "Animula vagula blandula",
             "confidence": 0.12,
@@ -827,6 +829,7 @@ def test_create_transcriptions_orientation(responses, mock_elements_worker_with_
                 "mirrored": False,
                 "initial": False,
                 "worker_version_id": None,
+                "confidence": None,
             },
             "text": "Hospes comesque corporis",
             "confidence": 0.21,
@@ -1585,6 +1588,7 @@ def test_create_transcriptions_orientation_with_cache(
                 "mirrored": False,
                 "initial": False,
                 "worker_version_id": UUID("12341234-1234-1234-1234-123412341234"),
+                "confidence": None,
             },
             "text": "Animula vagula blandula",
             "confidence": 0.5,
@@ -1603,6 +1607,7 @@ def test_create_transcriptions_orientation_with_cache(
                 "mirrored": False,
                 "initial": False,
                 "worker_version_id": UUID("12341234-1234-1234-1234-123412341234"),
+                "confidence": None,
             },
             "text": "Hospes comesque corporis",
             "confidence": 0.75,
@@ -1621,6 +1626,7 @@ def test_create_transcriptions_orientation_with_cache(
                 "mirrored": False,
                 "initial": False,
                 "worker_version_id": UUID("12341234-1234-1234-1234-123412341234"),
+                "confidence": None,
             },
             "text": "Quae nunc abibis in loca",
             "confidence": 0.9,