sapiopycommons 2025.8.15a706__py3-none-any.whl → 2025.8.18a709__py3-none-any.whl

sapiopycommons/callbacks/callback_util.py

@@ -1765,11 +1765,8 @@ class CallbackUtil:
             blank_result_handling = BlankResultHandling.REPEAT
         def not_blank_func(r: list[DataRecord]) -> bool:
             return bool(r)
-        response: list[DataRecord] = self.__send_dialog_blank_results(request,
-                                                                      self.callback.show_input_selection_dialog,
-                                                                      not_blank_func, blank_result_handling,
-                                                                      repeat_message, cancel_message)
-        return self.rec_handler.wrap_models(response, wrapper_type)
+        return self.__send_dialog_blank_results(request, self.callback.show_input_selection_dialog, not_blank_func,
+                                                blank_result_handling, repeat_message, cancel_message)
 
     # FR-47690: Deprecated the require_authentication parameter.
     # noinspection PyUnusedLocal
@@ -1815,8 +1812,7 @@ class CallbackUtil:
         return response
 
     def request_file(self, title: str, exts: Iterable[str] | None = None,
-                     show_image_editor: bool = False, show_camera_button: bool = False,
-                     *, enforce_file_extensions: bool = True) -> tuple[str, bytes]:
+                     show_image_editor: bool = False, show_camera_button: bool = False) -> tuple[str, bytes]:
         """
         Request a single file from the user.
 
@@ -1826,8 +1822,6 @@ class CallbackUtil:
         :param show_image_editor: Whether the user will see an image editor when image is uploaded in this file prompt.
         :param show_camera_button: Whether the user will be able to use camera to take a picture as an upload request,
             rather than selecting an existing file.
-        :param enforce_file_extensions: If true, then the file extensions provided in the exts parameter will be
-            enforced. If false, then the user may upload any file type.
         :return: The file name and bytes of the uploaded file.
         """
         # If no extensions were provided, use an empty list for the extensions instead.
@@ -1847,12 +1841,11 @@ class CallbackUtil:
             file_path: str = self.__send_dialog(request, self.callback.show_file_dialog, data_sink=do_consume)
 
         # Verify that each of the file given matches the expected extension(s).
-        self.__verify_file(file_path, sink.data, exts if enforce_file_extensions else None)
+        self.__verify_file(file_path, sink.data, exts)
         return file_path, sink.data
 
     def request_files(self, title: str, exts: Iterable[str] | None = None,
-                      show_image_editor: bool = False, show_camera_button: bool = False,
-                      *, enforce_file_extensions: bool = True) -> dict[str, bytes]:
+                      show_image_editor: bool = False, show_camera_button: bool = False) -> dict[str, bytes]:
         """
         Request multiple files from the user.
 
@@ -1862,8 +1855,6 @@ class CallbackUtil:
         :param show_image_editor: Whether the user will see an image editor when image is uploaded in this file prompt.
         :param show_camera_button: Whether the user will be able to use camera to take a picture as an upload request,
             rather than selecting an existing file.
-        :param enforce_file_extensions: If true, then the file extensions provided in the exts parameter will be
-            enforced. If false, then the user may upload any file type.
         :return: A dictionary of file name to file bytes for each file the user uploaded.
         """
         # If no extensions were provided, use an empty list for the extensions instead.
@@ -1879,7 +1870,7 @@ class CallbackUtil:
         for file_path in file_paths:
             sink = InMemoryRecordDataSink(self.user)
             sink.consume_client_callback_file_path_data(file_path)
-            self.__verify_file(file_path, sink.data, exts if enforce_file_extensions else None)
+            self.__verify_file(file_path, sink.data, exts)
             ret_dict.update({file_path: sink.data})
 
         return ret_dict
@@ -1896,17 +1887,16 @@ class CallbackUtil:
         """
         if file_path is None or len(file_path) == 0 or file_bytes is None or len(file_bytes) == 0:
             raise SapioUserErrorException("Empty file provided or file unable to be read.")
-        if not allowed_extensions:
-            return
-        matches: bool = False
-        for ext in allowed_extensions:
-            # FR-47690: Changed to a case-insensitive match.
-            if file_path.casefold().endswith("." + ext.lstrip(".").casefold()):
-                matches = True
-                break
-        if not matches:
-            raise SapioUserErrorException("Unsupported file type. Expecting the following extension(s): "
-                                          + (",".join(allowed_extensions)))
+        if allowed_extensions:
+            matches: bool = False
+            for ext in allowed_extensions:
+                # FR-47690: Changed to a case-insensitive match.
+                if file_path.casefold().endswith("." + ext.lstrip(".").casefold()):
+                    matches = True
+                    break
+            if matches is False:
+                raise SapioUserErrorException("Unsupported file type. Expecting the following extension(s): "
+                                              + (",".join(allowed_extensions)))
 
     def write_file(self, file_name: str, file_data: str | bytes) -> None:
         """

sapiopycommons/flowcyto/flow_cyto.py

@@ -4,16 +4,38 @@ from weakref import WeakValueDictionary
 
 from databind.json import dumps
 from sapiopylib.rest.User import SapioUser
-from sapiopylib.rest.utils.singletons import SapioContextManager
 
 from sapiopycommons.flowcyto.flowcyto_data import FlowJoWorkspaceInputJson, UploadFCSInputJson, \
     ComputeFlowStatisticsInputJson
 
 
-class FlowCytoManager(SapioContextManager):
+class FlowCytoManager:
     """
     This manager includes flow cytometry analysis tools that would require FlowCyto license to use.
     """
+    _user: SapioUser
+
+    __instances: WeakValueDictionary[SapioUser, FlowCytoManager] = WeakValueDictionary()
+    __initialized: bool
+
+    def __new__(cls, user: SapioUser):
+        """
+        Observes singleton pattern per record model manager object.
+
+        :param user: The user that will make the webservice request to the application.
+        """
+        obj = cls.__instances.get(user)
+        if not obj:
+            obj = object.__new__(cls)
+            obj.__initialized = False
+            cls.__instances[user] = obj
+        return obj
+
+    def __init__(self, user: SapioUser):
+        if self.__initialized:
+            return
+        self._user = user
+        self.__initialized = True
 
     def create_flowjo_workspace(self, workspace_input: FlowJoWorkspaceInputJson) -> int:
         """

sapiopycommons/general/accession_service.py

@@ -5,7 +5,6 @@ from typing import Any
 from weakref import WeakValueDictionary
 
 from sapiopylib.rest.User import SapioUser
-from sapiopylib.rest.utils.singletons import SapioContextManager
 
 _STR_JAVA_TYPE = "java.lang.String"
 _INT_JAVA_TYPE = "java.lang.Integer"
@@ -275,10 +274,37 @@ class AccessionServiceDescriptor:
         }
 
 
-class AccessionService(SapioContextManager):
+class AccessionService:
     """
     Provides Sapio Foundations Accession Service functionalities.
     """
+    _user: SapioUser
+
+    __instances: WeakValueDictionary[SapioUser, AccessionService] = WeakValueDictionary()
+    __initialized: bool
+
+    @property
+    def user(self) -> SapioUser:
+        return self._user
+
+    def __new__(cls, user: SapioUser):
+        """
+        Observes singleton pattern per record model manager object.
+
+        :param user: The user that will make the webservice request to the application.
+        """
+        obj = cls.__instances.get(user)
+        if not obj:
+            obj = object.__new__(cls)
+            obj.__initialized = False
+            cls.__instances[user] = obj
+        return obj
+
+    def __init__(self, user: SapioUser):
+        if self.__initialized:
+            return
+        self._user = user
+        self.__initialized = True
 
     def accession_with_config(self, data_type_name: str, data_field_name: str, num_ids: int) -> list[str]:
         """

sapiopycommons/multimodal/multimodal.py

@@ -7,13 +7,35 @@ from weakref import WeakValueDictionary
 from databind.json import dumps, loads
 from sapiopylib.rest.User import SapioUser
 from sapiopylib.rest.pojo.DataRecord import DataRecord
-from sapiopylib.rest.utils.singletons import SapioContextManager
 
 from sapiopycommons.general.exceptions import SapioException
 from sapiopycommons.multimodal.multimodal_data import *
 
 
-class MultiModalManager(SapioContextManager):
+class MultiModalManager:
+    _user: SapioUser
+
+    __instances: WeakValueDictionary[SapioUser, MultiModalManager] = WeakValueDictionary()
+    __initialized: bool
+
+    def __new__(cls, user: SapioUser):
+        """
+        Observes singleton pattern per record model manager object.
+
+        :param user: The user that will make the webservice request to the application.
+        """
+        obj = cls.__instances.get(user)
+        if not obj:
+            obj = object.__new__(cls)
+            obj.__initialized = False
+            cls.__instances[user] = obj
+        return obj
+
+    def __init__(self, user:SapioUser):
+        if self.__initialized:
+            return
+        self._user = user
+        self.__initialized = True
 
     def load_image_data(self, request: ImageDataRequestPojo) -> list[str]:
         """

sapiopycommons/webhook/webservice_handlers.py

@@ -140,7 +140,7 @@ class AbstractWebserviceHandler(AbstractWebhookHandler):
         # Get the login credentials from the headers.
         auth: str = headers.get("Authorization")
         if auth and auth.startswith("Basic "):
-            credentials: list[str] = b64decode(auth.split("Basic ")[1]).decode().split(":")
+            credentials: list[str] = b64decode(auth.split("Basic ")[1]).decode().split(":", 1)
             user = self.basic_auth(url, credentials[0], credentials[1])
         elif auth and auth.startswith("Bearer "):
             user = self.bearer_token_auth(url, auth.split("Bearer ")[1])

{sapiopycommons-2025.8.15a706.dist-info → sapiopycommons-2025.8.18a709.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2025.8.15a706
+Version: 2025.8.18a709
 Summary: Official Sapio Python API Utilities Package
 Project-URL: Homepage, https://github.com/sapiosciences
 Author-email: Jonathan Steck <jsteck@sapiosciences.com>, Yechen Qiao <yqiao@sapiosciences.com>
@@ -17,7 +17,7 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Requires-Python: >=3.10
 Requires-Dist: databind>=4.5
-Requires-Dist: sapiopylib>=2025.7.31a279
+Requires-Dist: sapiopylib>=2025.4.17.264
 Description-Content-Type: text/markdown
 
 

{sapiopycommons-2025.8.15a706.dist-info → sapiopycommons-2025.8.18a709.dist-info}/RECORD

@@ -1,8 +1,42 @@
 sapiopycommons/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/ai/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/ai/tool_of_tools.py,sha256=zYmQ4rNX-qYQnc-vNDnYZjtv9JgmQAmVVuHfVOdBF3w,46984
+sapiopycommons/ai/converter_service_base.py,sha256=w4_PXjlk7_F5AUMlPUhKJ9gZlxY9RNG6yH9cDDFROuo,4620
+sapiopycommons/ai/protobuf_utils.py,sha256=QdYcelIvOIKBV5u_KR_Fh06kZ0eJDIb5ZVnfqV01FeE,24601
+sapiopycommons/ai/server.py,sha256=2-Q49-JJgiymOdRJ4EWj0aKGXnly5D2Hrjo3fklNl_8,4222
+sapiopycommons/ai/test_client.py,sha256=gWmY4rT0F9hzXv0hQ_iQqDBfTRKWh_QKwWeGyU-E9ks,14582
+sapiopycommons/ai/tool_service_base.py,sha256=GR1z9qxvStlLYhBLu0W-6OI9TfNDVtYQX-I_BJiRYCg,43921
+sapiopycommons/ai/api/fielddefinitions/proto/fields_pb2.py,sha256=YcZjb_YM-XeLErM8hEC_S7vGMVGvcXAMGs2b-u5zvOE,2377
+sapiopycommons/ai/api/fielddefinitions/proto/fields_pb2.pyi,sha256=FwtXmNAf7iYGEFm4kbqb04v77jNHbZg18ZmEDhle_bU,1444
+sapiopycommons/ai/api/fielddefinitions/proto/fields_pb2_grpc.py,sha256=wPImJPdCUZNVEVoUWzsba9kGIXjEKPdUkawP5SnVyiU,932
+sapiopycommons/ai/api/fielddefinitions/proto/velox_field_def_pb2.py,sha256=nWC91vR2pMgMUyNOZRZ0YiuL1-8ntnjXLqt1daxsD34,20869
+sapiopycommons/ai/api/fielddefinitions/proto/velox_field_def_pb2.pyi,sha256=U5zXrbBxsWilLTsRWJd1TqjdjLKFsr3enF9OJ8GfyWw,34028
+sapiopycommons/ai/api/fielddefinitions/proto/velox_field_def_pb2_grpc.py,sha256=4vD4jWanaJ4uclSkFmS7JIz_lwYXDWBE3DomuPjUyII,941
+sapiopycommons/ai/api/plan/converter/proto/converter_pb2.py,sha256=dT8X_D18RRAMY5PA7tHVGlbwhH2JIH6CrkuXb6iwL4E,3401
+sapiopycommons/ai/api/plan/converter/proto/converter_pb2.pyi,sha256=LazSPiQ0fCmI_lZ5lm-871XMU-PTlAtfbjta8Aqp3Mk,4104
+sapiopycommons/ai/api/plan/converter/proto/converter_pb2_grpc.py,sha256=EvhojTeQHuLNrK1HVolQbcOsa-sJDM8ExLqqu4F_a6U,6515
+sapiopycommons/ai/api/plan/item/proto/item_container_pb2.py,sha256=qph1v5-16l_87aKH-aQixGjQthg_xXF7Lm66DCfFWIA,3822
+sapiopycommons/ai/api/plan/item/proto/item_container_pb2.pyi,sha256=K8Y0dvNY7V0MLOegC1ODXqc1g4lH1NY70EGH2UWN9vQ,4118
+sapiopycommons/ai/api/plan/item/proto/item_container_pb2_grpc.py,sha256=nNTWRJEg7MglgC1AsVBsdXo0Q1sYvvsucwX3KpzYiOw,933
+sapiopycommons/ai/api/plan/proto/step_output_pb2.py,sha256=JpBZSyoYyPTEaaXjW664PeJNK0zxV1mly_kp5re42z4,2661
+sapiopycommons/ai/api/plan/proto/step_output_pb2.pyi,sha256=yuxOYnDZ9DRuu-TLzaKOW_B4LUiYxTrNc2AbssXg4kE,2022
+sapiopycommons/ai/api/plan/proto/step_output_pb2_grpc.py,sha256=vDRY_pIIshQ4UpdW-ra1F5zBmntdsW2scySkMAA-zfc,925
+sapiopycommons/ai/api/plan/proto/step_pb2.py,sha256=nL976oTFdX4ih4gg7_J-8eFoGB69tFvERB2gT3L2-6s,2439
+sapiopycommons/ai/api/plan/proto/step_pb2.pyi,sha256=QPIcsjcUvEGQkdZMUMiVzFFNDl8yOUe_qJtf5XEp5Ck,2062
+sapiopycommons/ai/api/plan/proto/step_pb2_grpc.py,sha256=DgiBYFvTNiDG_2a9Tpt5iel2fRUfePZWP41fZTC-KWk,918
+sapiopycommons/ai/api/plan/script/proto/script_pb2.py,sha256=iUjALwM3e-mwuwVTc_N0k9CF4KkwniIPcxLiQK3fOR0,5200
+sapiopycommons/ai/api/plan/script/proto/script_pb2.pyi,sha256=IsaOnZVLD91PQwQcjDxMpfcYlI6U9cwEIMl770m6HgI,6204
+sapiopycommons/ai/api/plan/script/proto/script_pb2_grpc.py,sha256=RkShHpe_d5EJHk3qp-or1JpvSEqShb7cCiaXnJ2YSww,6931
+sapiopycommons/ai/api/plan/tool/proto/entry_pb2.py,sha256=2q87XYhq_SOADuhoIyr1CHQC3SZiupjSjJLNp1np-hA,2141
+sapiopycommons/ai/api/plan/tool/proto/entry_pb2.pyi,sha256=R5apvEaENIKKG2DbqwxjgI9arkqYq928xe04WNtTniM,2365
+sapiopycommons/ai/api/plan/tool/proto/entry_pb2_grpc.py,sha256=YKkX2kexERUx4asLCShufSnZhgf339Zk8Xw1FAgLfHQ,924
+sapiopycommons/ai/api/plan/tool/proto/tool_pb2.py,sha256=WzE4-S1KXJC26RlubLkiDa3GnEhZ0pbxE3V4AuFicZM,8255
+sapiopycommons/ai/api/plan/tool/proto/tool_pb2.pyi,sha256=YU7CJkij037QJNR8VhheC-ouukUD13vyLt18YXR1HYA,16763
+sapiopycommons/ai/api/plan/tool/proto/tool_pb2_grpc.py,sha256=68u5E1ZKha5frP5GuY8Ad-c0c79vBhtfnj5Q4u-8xOY,6982
+sapiopycommons/ai/api/session/proto/sapio_conn_info_pb2.py,sha256=WKzNi-d5dqeJbmEXUVE5qJ4Qm34HmsqRXRtXih382g8,2100
+sapiopycommons/ai/api/session/proto/sapio_conn_info_pb2.pyi,sha256=vLYA8Tkzq2AwgVadoUp5vAg4HgGlgga0kzeS3e_XkCQ,1621
+sapiopycommons/ai/api/session/proto/sapio_conn_info_pb2_grpc.py,sha256=2W0YzT4SfnGTLq98AdvkyNM0n75Tkl8DervPS1ryGao,932
 sapiopycommons/callbacks/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/callbacks/callback_util.py,sha256=Z1LcXnRRjXyhmcSDUwh4NzcA6ICtcbFUMKcvAqQcS8E,153811
+sapiopycommons/callbacks/callback_util.py,sha256=OuPJ1o6jcDQ7qV-dxrjAkJerGbVI9_9P-xu0r3ODaMM,153008
 sapiopycommons/callbacks/field_builder.py,sha256=rnIP-RJafk3mZlAx1eJ8a0eSW9Ps_L6_WadCmusnENw,38772
 sapiopycommons/chem/IndigoMolecules.py,sha256=7ucCaRMLu1zfH2uPIvXwRTSdpNcS03O1P9p_O-5B4xQ,5110
 sapiopycommons/chem/Molecules.py,sha256=mVqPn32MPMjF0iZas-5MFkS-upIdoW5OB72KKZmJRJA,12523
@@ -25,19 +59,17 @@ sapiopycommons/eln/experiment_tags.py,sha256=7-fpOiSqrjbXmWIJhEhaxMgLsVCPAtKqH8x
 sapiopycommons/eln/plate_designer.py,sha256=XFazSvhTbSy47t80-jc2tyx_-fQ_IUjKd18JQKEFcsY,13939
 sapiopycommons/eln/step_creation.py,sha256=CFkGC-SxwAQpQlcs_obqLAVgmsNxKSGMqMtO_E6IVmw,10171
 sapiopycommons/files/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/files/assay_plate_reader.py,sha256=3c2PQiiAbc2QJU9ZfNLzcTmvJrUwsbkIHO7R6R52xGU,3020
 sapiopycommons/files/complex_data_loader.py,sha256=T39veNhvYl6j_uZjIIJ8Mk5Aa7otR5RB-g8XlAdkksA,1421
 sapiopycommons/files/file_bridge.py,sha256=vKbqxPexi15epr_-_qLrEfYoxNxB031mXN92iVtOMqE,9511
 sapiopycommons/files/file_bridge_handler.py,sha256=SEYDIQhSCmjI6qyLdDJE8JVKSd0WYvF7JvAq_Ahp9Do,25503
 sapiopycommons/files/file_data_handler.py,sha256=f96MlkMuQhUCi4oLnzJK5AiuElCp5jLI8_sJkZVwpws,36779
-sapiopycommons/files/file_text_converter.py,sha256=Gaj_divTiKXWd6flDOgrxNXpcn9fDWqxX6LUG0joePk,7516
 sapiopycommons/files/file_util.py,sha256=djouyGjsYgWzjz2OBRnSeMDgj6NrsJUm1a2J93J8Wco,31915
 sapiopycommons/files/file_validator.py,sha256=ryg22-93csmRO_Pv0ZpWphNkB74xWZnHyJ23K56qLj0,28761
 sapiopycommons/files/file_writer.py,sha256=hACVl0duCjP28gJ1NPljkjagNCLod0ygUlPbvUmRDNM,17605
-sapiopycommons/flowcyto/flow_cyto.py,sha256=B6DFquLi-gcWfJWyP4vYfwTXXJKl6O9W5-k8FzkM0Oo,2610
+sapiopycommons/flowcyto/flow_cyto.py,sha256=vs9WhXXKz3urpjL8QKSk56B-NSmQR3O3x_WFBKoeO10,3227
 sapiopycommons/flowcyto/flowcyto_data.py,sha256=mYKFuLbtpJ-EsQxLGtu4tNHVlygTxKixgJxJqD68F58,2596
 sapiopycommons/general/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/general/accession_service.py,sha256=ZvtvZg7d_siMJUedjrF14mcqo5ZqVA5IJxDa5enlB-8,12792
+sapiopycommons/general/accession_service.py,sha256=3e__bVs7CYZ1CduLlGA9plnK7nCtdy7GXjCrNObPFgo,13484
 sapiopycommons/general/aliases.py,sha256=VwnWf_P803pcteoAIs0DkLScVChCS5XNgryTp8FzaNc,14696
 sapiopycommons/general/audit_log.py,sha256=sQAMcJx0cNkgZm7nTZSaGPxWvHG0_x6dBtU0jESavb4,9131
 sapiopycommons/general/custom_report_util.py,sha256=9elLEUSgfM0gli8nRPz1uYkhaXN4Vnx3piSiNHv5IBs,19156
@@ -49,7 +81,7 @@ sapiopycommons/general/popup_util.py,sha256=HKILegU1uCL_6abNlNL0Wn3xgX2JNa_kJeq7
 sapiopycommons/general/sapio_links.py,sha256=YkcVKNLrSGoM7tCCXBAsIbIxylctwdcEyhePrRMODe0,2859
 sapiopycommons/general/storage_util.py,sha256=ovmK_jN7v09BoX07XxwShpBUC5WYQOM7dbKV_VeLXJU,8892
 sapiopycommons/general/time_util.py,sha256=jU1urPoZRv6evNucR0-288EyT4PrsDpCr-H1-7BKq9A,12363
-sapiopycommons/multimodal/multimodal.py,sha256=EP9WYzx1CvidmEBlvzO6tiF4HJwsPB1FgxpnbWzxnpA,6161
+sapiopycommons/multimodal/multimodal.py,sha256=PFaGJPbKvW__tnxb8KkgkJZOKjQdgxF_kGfD5chet1s,6779
 sapiopycommons/multimodal/multimodal_data.py,sha256=0BeVPr9HaC0hNTF1v1phTIKGruvNnwerHsD994qJKBg,15099
 sapiopycommons/processtracking/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/processtracking/custom_workflow_handler.py,sha256=eYKdYlwo8xx-6AkB_iPUBNV9yDoNvW2h_Sm3i8JpmRU,25844
@@ -65,8 +97,8 @@ sapiopycommons/sftpconnect/sftp_builder.py,sha256=lFK3FeXk-sFLefW0hqY8WGUQDeYiGa
 sapiopycommons/webhook/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/webhook/webhook_context.py,sha256=D793uLsb1691SalaPnBUk3rOSxn_hYLhdvkaIxjNXss,1909
 sapiopycommons/webhook/webhook_handlers.py,sha256=7o_wXOruhT9auNh8OfhJAh4WhhiPKij67FMBSpGPICc,39939
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