sapiopycommons 2025.10.17a787__py3-none-any.whl → 2025.10.20a789__py3-none-any.whl

sapiopycommons/files/temp_files.py

@@ -0,0 +1,82 @@
+import os
+import shutil
+import tempfile
+from typing import Callable, Any
+
+
+# FR-47422: Created class.
+class TempFileHandler:
+    """
+    A utility class to manage temporary files and directories.
+    """
+    directories: list[str]
+    files: list[str]
+
+    def __init__(self):
+        self.directories = []
+        self.files = []
+
+    def create_temp_directory(self) -> str:
+        """
+        Create a temporary directory.
+
+        :return: The path to a newly created temporary directory.
+        """
+        directory: str = tempfile.mkdtemp()
+        self.directories.append(directory)
+        return directory
+
+    def create_temp_file(self, data: str | bytes, suffix: str = "") -> str:
+        """
+        Create a temporary file with the specified data and optional suffix.
+
+        :param data: The data to write to the temporary file.
+        :param suffix: An optional suffix for the temporary file.
+        :return: The path to a newly created temporary file containing the provided data.
+        """
+        mode: str = 'w' if isinstance(data, str) else 'wb'
+        with tempfile.NamedTemporaryFile(mode=mode, suffix=suffix, delete=False) as tmp_file:
+            tmp_file.write(data)
+            file_path: str = tmp_file.name
+            self.files.append(file_path)
+        return file_path
+
+    def create_temp_file_from_func(self, func: Callable, params: dict[str, Any], suffix: str = "",
+                                   is_binary: bool = True) -> str:
+        """
+        Create a temporary file and populate it using the provided function. The function should accept parameters as
+        specified in the `params` dictionary.
+
+        :param func: The function to call with the temporary file path that will populate the file.
+        :param params: Keyword arguments to pass to the function. If "<NEW_FILE>" is used as a value, it will be
+            replaced with the temporary file object. If "<NEW_FILE_PATH>" is used as a value, it will be replaced with
+            the temporary file path.
+        :param suffix: An optional suffix for the temporary file.
+        :param is_binary: Whether to open the temporary file in binary mode.
+        :return: The path to the newly created temporary file.
+        """
+        mode: str = 'wb' if is_binary else 'w'
+        with tempfile.NamedTemporaryFile(mode, suffix=suffix, delete=False) as tmp_file:
+            for key, value in params.items():
+                if value == "<NEW_FILE>":
+                    params[key] = tmp_file
+                elif value == "<NEW_FILE_PATH>":
+                    params[key] = tmp_file.name
+            func(**params)
+            file_path: str = tmp_file.name
+            self.files.append(file_path)
+        return file_path
+
+    def cleanup(self) -> None:
+        """
+        Delete all temporary files and directories created by this handler.
+        """
+        for directory in self.directories:
+            if os.path.exists(directory):
+                shutil.rmtree(directory)
+        self.directories.clear()
+
+        for file_path in self.files:
+            if os.path.exists(file_path):
+                os.remove(file_path)
+        self.files.clear()

sapiopycommons/general/aliases.py

@@ -224,11 +224,8 @@ class AliasUtil:
             fields: FieldMap = {f: record.fields.get(f) for f in record.fields}
         # PR-47457: Only include the record ID if the caller requests it, since including the record ID can break
         # callbacks in certain circumstances if the record ID is negative.
-        # PR-47894: Also remove the RecordId key if it exists and the caller doesn't want it included.
         if include_record_id:
             fields["RecordId"] = AliasUtil.to_record_id(record)
-        elif "RecordId" in fields:
-            del fields["RecordId"]
         return fields
 
     @staticmethod

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-2025.10.17a787.dist-info → sapiopycommons-2025.10.20a789.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2025.10.17a787
+Version: 2025.10.20a789
 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>

{sapiopycommons-2025.10.17a787.dist-info → sapiopycommons-2025.10.20a789.dist-info}/RECORD

@@ -1,8 +1,47 @@
 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/agent_service_base.py,sha256=eTJunFQoxLc0risWiQIkQK946XpHzSFO38NzzRvOn9Q,60325
+sapiopycommons/ai/converter_service_base.py,sha256=HiUXmwqv1STgyQeF9_eTFXzjIFXp5-NJ7sEhMpV3aAU,6351
+sapiopycommons/ai/external_credentials.py,sha256=ki_xIH4J843b_sSwEa8YHr8vW9erVv-jowZJXSgPQs8,4347
+sapiopycommons/ai/protobuf_utils.py,sha256=cBjbxoFAwU02kNUxEce95WnMU2CMuDD-qFaeWgvQJMQ,24599
+sapiopycommons/ai/request_validation.py,sha256=dsCZXWDSHLm7pGywArB_GRymXxo1l-eGMn6veUwSg20,25641
+sapiopycommons/ai/server.py,sha256=gutSskn_Fenq1uz0DDMvjx4QVFiKt2WVEP3-01a69eU,6384
+sapiopycommons/ai/test_client.py,sha256=IRZ-8prhg7XMDmN9aC1MQr5mSkMgfT37aLsOy-VB-MU,20495
+sapiopycommons/ai/protoapi/externalcredentials/external_credentials_pb2.py,sha256=mEonoj6Iq-AyvO4m3YsPYu85aZfD1E0a0cL8B9yPfEo,2481
+sapiopycommons/ai/protoapi/externalcredentials/external_credentials_pb2.pyi,sha256=sfExq8fFwIwFxCpV50ytdxW5ePNBjJBr_80_trq_JQw,1658
+sapiopycommons/ai/protoapi/externalcredentials/external_credentials_pb2_grpc.py,sha256=TNS1CB_QGBSa1YU9sYR_hF-pmBwv2GpxjaNQoM_r9iU,948
+sapiopycommons/ai/protoapi/fielddefinitions/fields_pb2.py,sha256=8tKXwLXcqFGdQHHSEBSi6Fd7dcaCFoOqmhjzqhenb_M,2372
+sapiopycommons/ai/protoapi/fielddefinitions/fields_pb2.pyi,sha256=FwtXmNAf7iYGEFm4kbqb04v77jNHbZg18ZmEDhle_bU,1444
+sapiopycommons/ai/protoapi/fielddefinitions/fields_pb2_grpc.py,sha256=uO25bcnfGqXpP4ggUur54Nr73Wj-DGWftExzLNcxdHI,931
+sapiopycommons/ai/protoapi/fielddefinitions/velox_field_def_pb2.py,sha256=in9iHiLPYcnLWoLeqy4nWSI0jZGHD_bMhEFRIRtJPuo,20864
+sapiopycommons/ai/protoapi/fielddefinitions/velox_field_def_pb2.pyi,sha256=U5zXrbBxsWilLTsRWJd1TqjdjLKFsr3enF9OJ8GfyWw,34028
+sapiopycommons/ai/protoapi/fielddefinitions/velox_field_def_pb2_grpc.py,sha256=Vj6qDKvsHgl25iBi3UjtTuGxihekgqCuufExvnJKzQI,940
+sapiopycommons/ai/protoapi/plan/step_output_pb2.py,sha256=EBNCzLUDwwCqDCh35zSfFdfq0RP8WrmTMXEzEPu_1_E,2655
+sapiopycommons/ai/protoapi/plan/step_output_pb2.pyi,sha256=yuxOYnDZ9DRuu-TLzaKOW_B4LUiYxTrNc2AbssXg4kE,2022
+sapiopycommons/ai/protoapi/plan/step_output_pb2_grpc.py,sha256=ebWLIfOFeVE2WuUIThMBerVweH-1phviGX195UTwYyg,924
+sapiopycommons/ai/protoapi/plan/step_pb2.py,sha256=mKTm_syaX99GzhWtGIPkxMTsfcsvW0QbRqjv06eHSM0,2433
+sapiopycommons/ai/protoapi/plan/step_pb2.pyi,sha256=QPIcsjcUvEGQkdZMUMiVzFFNDl8yOUe_qJtf5XEp5Ck,2062
+sapiopycommons/ai/protoapi/plan/step_pb2_grpc.py,sha256=1CBna5NBBxPwQhrkN8-Fim_j3FGmOfDo5C4c8sIBV8Q,917
+sapiopycommons/ai/protoapi/plan/converter/converter_pb2.py,sha256=rZYBRfR0umwDYvBdYnzxR1VZSutRqunhd3QsdtQXiCM,3593
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+sapiopycommons/ai/protoapi/plan/item/item_container_pb2.py,sha256=VIXmIw8-9jtH7peJZ16BEmGDfaVjjxTKhmlfcHWT82M,3863
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+sapiopycommons/ai/protoapi/plan/script/script_pb2.py,sha256=4TN7NlJEENAVqwfymoEDj5hhHYxHLdrHdpRUVgzVG8A,5621
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+sapiopycommons/ai/protoapi/plan/tool/entry_pb2.py,sha256=yNyyyVvz94ewjGaHw3t0pUP-KH7ACg5hLC0QzrsFPis,2130
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+sapiopycommons/ai/protoapi/plan/tool/tool_pb2.py,sha256=aLD5j60lWUxhHW8b1AoUOClLOjFPjEMmM1KrY337-gI,9095
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+sapiopycommons/ai/protoapi/session/sapio_conn_info_pb2.py,sha256=MhWzTyJz3xZgpdW8_LCVKuzKXT0cv6iHMRB-UNCUNzM,2094
+sapiopycommons/ai/protoapi/session/sapio_conn_info_pb2.pyi,sha256=vLYA8Tkzq2AwgVadoUp5vAg4HgGlgga0kzeS3e_XkCQ,1621
+sapiopycommons/ai/protoapi/session/sapio_conn_info_pb2_grpc.py,sha256=imcciy_kbmm7OV_W3jYZ53R6GQ6Yh-eUcVW0A9GkWdg,931
 sapiopycommons/callbacks/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/callbacks/callback_util.py,sha256=aLkH5p5PMI74MN7tdrJ3Xy6LDDggHpCf4Lhr9XuOreA,154535
+sapiopycommons/callbacks/callback_util.py,sha256=Z1LcXnRRjXyhmcSDUwh4NzcA6ICtcbFUMKcvAqQcS8E,153811
 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
@@ -31,14 +70,15 @@ sapiopycommons/files/file_bridge.py,sha256=vKbqxPexi15epr_-_qLrEfYoxNxB031mXN92i
 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_util.py,sha256=WBA3FYG8R2HtfxjWSzQhZKW6_1s6JSxTo9lk3SeNDu8,37140
 sapiopycommons/files/file_validator.py,sha256=ryg22-93csmRO_Pv0ZpWphNkB74xWZnHyJ23K56qLj0,28761
 sapiopycommons/files/file_writer.py,sha256=hACVl0duCjP28gJ1NPljkjagNCLod0ygUlPbvUmRDNM,17605
+sapiopycommons/files/temp_files.py,sha256=s2sGvn9uh2dTI8AVAQJWOf6RAZ0xZs7DSccCi4AGmlw,3175
 sapiopycommons/flowcyto/flow_cyto.py,sha256=B6DFquLi-gcWfJWyP4vYfwTXXJKl6O9W5-k8FzkM0Oo,2610
 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/aliases.py,sha256=pHfpH5veukVdjlR62_INCy2ItZG1omQv4dCoo8NeGlM,14869
+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
 sapiopycommons/general/data_structure_util.py,sha256=fbQR_Fh4Scg67IpFPbQW9wVLw1oxlYxqp4LjBRTpjgU,4702
@@ -65,8 +105,8 @@ 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
-sapiopycommons/webhook/webservice_handlers.py,sha256=tyaYGG1-v_JJrJHZ6cy5mGCxX9z1foLw7pM4MDJlFxs,14297
-sapiopycommons-2025.10.17a787.dist-info/METADATA,sha256=3mZft6DRxhP-QWhIDnysHuAHlxoYaghDr4kWHRpUG9g,3143
-sapiopycommons-2025.10.17a787.dist-info/WHEEL,sha256=C2FUgwZgiLbznR-k0b_5k3Ai_1aASOXDss3lzCUsUug,87
-sapiopycommons-2025.10.17a787.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
-sapiopycommons-2025.10.17a787.dist-info/RECORD,,
+sapiopycommons/webhook/webservice_handlers.py,sha256=cvW6Mk_110BzYqkbk63Kg7jWrltBCDALOlkJRu8h4VQ,14300
+sapiopycommons-2025.10.20a789.dist-info/METADATA,sha256=LW1ECHFl-cG6BPslNdeFfIGKFHCxPgtivYUg9mqsnSQ,3143
+sapiopycommons-2025.10.20a789.dist-info/WHEEL,sha256=C2FUgwZgiLbznR-k0b_5k3Ai_1aASOXDss3lzCUsUug,87
+sapiopycommons-2025.10.20a789.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
+sapiopycommons-2025.10.20a789.dist-info/RECORD,,