sapiopycommons 2025.10.15a782__py3-none-any.whl → 2025.10.17a787__py3-none-any.whl

sapiopycommons/callbacks/callback_util.py

@@ -858,9 +858,9 @@ class CallbackUtil:
             raise SapioException("No records provided.")
         data_type: str = AliasUtil.to_singular_data_type_name(records)
         if index_field is not None:
-            field_map_list: list[FieldMap] = self.__get_indexed_field_maps(records, index_field)
+            field_map_list: list[FieldMap] = self.__get_indexed_field_maps(records, index_field, True)
         else:
-            field_map_list: list[FieldMap] = AliasUtil.to_field_map_list(records)
+            field_map_list: list[FieldMap] = AliasUtil.to_field_map_list(records, True)
 
         # Convert the group_by parameter to a field name.
         if group_by is not None:
@@ -882,6 +882,18 @@ class CallbackUtil:
             temp_dt = self.__temp_dt_from_field_names(data_type, fields, None, default_modifier, field_modifiers)
         temp_dt.record_image_assignable = bool(image_data)
 
+        # PR-47894: If the RecordId field is not present in the layout, then it should not be included in the field
+        # maps, as otherwise selection list fields can break.
+        remove_record_id: bool = True
+        for field_def in temp_dt.get_field_def_list():
+            if field_def.data_field_name == "RecordId":
+                remove_record_id = False
+                break
+        if remove_record_id:
+            for field_map in field_map_list:
+                if "RecordId" in field_map:
+                    del field_map["RecordId"]
+
         # Send the request to the user.
         request = TableEntryDialogRequest(title, msg, temp_dt, field_map_list,
                                           record_image_data_list=image_data, group_by_field=group_by,
@@ -1928,7 +1940,8 @@ class CallbackUtil:
         self.write_file(zip_name, FileUtil.zip_files(files))
 
     @staticmethod
-    def __get_indexed_field_maps(records: Iterable[SapioRecord], index_field: str) -> list[FieldMap]:
+    def __get_indexed_field_maps(records: Iterable[SapioRecord], index_field: str, include_record_id: bool = False) \
+            -> list[FieldMap]:
         """
         For dialogs that accept multiple records, we may want to be able to match the returned results back to the
         records that they're for. In this case, we need to add an index to each record so that we can match them back
@@ -1938,12 +1951,13 @@ class CallbackUtil:
         :param records: The records to return indexed field maps of.
         :param index_field: The name of the field to use as the index. Make sure that this field doesn't exist on the
             records, as then it will overwrite the existing value.
+        :param include_record_id: Whether to include the RecordId field in the field maps.
         :return: A list of field maps for the records, with an index field added to each. The value of the index on
             each field map is the record's record ID (even if it's a record model with a negative ID).
         """
         ret_val: list[FieldMap] = []
         for record in records:
-            field_map: FieldMap = AliasUtil.to_field_map(record)
+            field_map: FieldMap = AliasUtil.to_field_map(record, include_record_id)
             field_map[index_field] = AliasUtil.to_record_id(record)
             ret_val.append(field_map)
         return ret_val

sapiopycommons/files/file_util.py

@@ -1,7 +1,4 @@
-import gzip
 import io
-import tarfile
-import time
 import warnings
 import zipfile
 
@@ -325,7 +322,7 @@ class FileUtil:
     @staticmethod
     def zip_files(files: dict[str, str | bytes]) -> bytes:
         """
-        Create a .zip file for a collection of files.
+        Create a zip file for a collection of files.
 
         :param files: A dictionary of file name to file data as a string or bytes.
         :return: The bytes for a zip file containing the input files.
@@ -338,130 +335,6 @@ class FileUtil:
             # throws an I/O exception.
             return zip_buffer.getvalue()
 
-    # FR-47422: Add a function for unzipping files that may have been zipped by the above function.
-    @staticmethod
-    def unzip_files(zip_file: bytes) -> dict[str, bytes]:
-        """
-        Decompress a .zip file from an in-memory bytes object and extracts all files into a dictionary.
-
-        :param zip_file: The bytes of the zip file to be decompressed.
-        :return: A dictionary of file name to file bytes for each file in the zip.
-        """
-        extracted_files: dict[str, bytes] = {}
-        with io.BytesIO(zip_file) as zip_buffer:
-            with zipfile.ZipFile(zip_buffer, "r") as zip_file:
-                for file_name in zip_file.namelist():
-                    with zip_file.open(file_name) as file:
-                        extracted_files[file_name] = file.read()
-        return extracted_files
-
-    # FR-47422: Add functions for compressing and decompressing .gz, .tar, and .tar.gz files.
-    @staticmethod
-    def gzip_file(file_data: bytes | str) -> bytes:
-        """
-        Create a .gz file for a single file.
-
-        :param file_data: The file data to be compressed as bytes or a string.
-        :return: The bytes of the gzip-compressed file.
-        """
-        return gzip.compress(file_data.encode() if isinstance(file_data, str) else file_data)
-
-    @staticmethod
-    def ungzip_file(gzip_file: bytes) -> bytes:
-        """
-        Decompress a .gz file.
-
-        :param gzip_file: The bytes of the gzip-compressed file.
-        :return: The decompressed file data as bytes.
-        """
-        return gzip.decompress(gzip_file)
-
-    @staticmethod
-    def tar_files(files: dict[str, str | bytes]) -> bytes:
-        """
-        Create a .tar file for a collection of files.
-
-        :param files: A dictionary of file name to file data as a string or bytes.
-        :return: The bytes for a tar file containing the input files.
-        """
-        with io.BytesIO() as tar_buffer:
-            with tarfile.open(fileobj=tar_buffer, mode="w") as tar:
-                for name, data in files.items():
-                    if isinstance(data, str):
-                        data: bytes = data.encode('utf-8')
-
-                    tarinfo = tarfile.TarInfo(name=name)
-                    tarinfo.size = len(data)
-                    tarinfo.mtime = int(time.time())
-
-                    with io.BytesIO(data) as file:
-                        tar.addfile(tarinfo=tarinfo, fileobj=file)
-
-            tar_buffer.seek(0)
-            return tar_buffer.getvalue()
-
-    @staticmethod
-    def untar_files(tar_file: bytes) -> dict[str, bytes]:
-        """
-        Decompress a .tar file from an in-memory bytes object and extracts all files into a dictionary.
-
-        :param tar_file: The bytes of the tar file to be decompressed.
-        :return: A dictionary of file name to file bytes for each file in the tar.
-        """
-        extracted_files: dict[str, bytes] = {}
-        with io.BytesIO(tar_file) as tar_buffer:
-            with tarfile.open(fileobj=tar_buffer, mode="r") as tar:
-                for member in tar.getmembers():
-                    if member.isfile():
-                        file_obj = tar.extractfile(member)
-                        if file_obj:
-                            with file_obj:
-                                extracted_files[member.name] = file_obj.read()
-        return extracted_files
-
-    @staticmethod
-    def tar_gzip_files(files: dict[str, str | bytes]) -> bytes:
-        """
-        Create a .tar.gz file for a collection of files.
-
-        :param files: A dictionary of file name to file data as a string or bytes.
-        :return: The bytes for a tar.gz file containing the input files.
-        """
-        with io.BytesIO() as tar_buffer:
-            with tarfile.open(fileobj=tar_buffer, mode="w:gz") as tar:
-                for name, data in files.items():
-                    if isinstance(data, str):
-                        data: bytes = data.encode('utf-8')
-
-                    tarinfo = tarfile.TarInfo(name=name)
-                    tarinfo.size = len(data)
-                    tarinfo.mtime = int(time.time())
-
-                    with io.BytesIO(data) as file:
-                        tar.addfile(tarinfo=tarinfo, fileobj=file)
-
-            tar_buffer.seek(0)
-            return tar_buffer.getvalue()
-
-    @staticmethod
-    def untar_gzip_files(tar_gzip_file: bytes) -> dict[str, bytes]:
-        """
-        Decompress a .tar.gz file from an in-memory bytes object and extracts all files into a dictionary.
-
-        :param tar_gzip_file: The bytes of the tar.gz file to be decompressed.
-        :return: A dictionary of file name to file bytes for each file in the tar.gz
-        """
-        extracted_files: dict[str, bytes] = {}
-        with io.BytesIO(tar_gzip_file) as tar_buffer:
-            with tarfile.open(fileobj=tar_buffer, mode="r:gz") as tar:
-                for member in tar.getmembers():
-                    if member.isfile():
-                        file_obj = tar.extractfile(member)
-                        if file_obj:
-                            with file_obj:
-                                extracted_files[member.name] = file_obj.read()
-        return extracted_files
-
     # Deprecated functions:
 
     # FR-46097 - Add write file request shorthand functions to FileUtil.

sapiopycommons/general/aliases.py

@@ -224,8 +224,11 @@ 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(":", 1)
+            credentials: list[str] = b64decode(auth.split("Basic ")[1]).decode().split(":")
             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-2025.10.15a782.dist-info → sapiopycommons-2025.10.17a787.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2025.10.15a782
+Version: 2025.10.17a787
 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-2025.10.15a782.dist-info → sapiopycommons-2025.10.17a787.dist-info}/RECORD

@@ -1,47 +1,8 @@
 sapiopycommons/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/ai/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/ai/agent_service_base.py,sha256=LVZg_4Kw5WTcIB7ru5hEqJoMWQr2eTDYjMrX8pzpn9I,56301
-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=TD2EUi_G5cy1OOVK1AmY2SQc3PEoAKGWs2pT8Qnp2Oo,25092
-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
-sapiopycommons/ai/protoapi/plan/converter/converter_pb2.pyi,sha256=_35yHfKTJH3SMdA5_c6qF6OZG6UwFWXpNh6dwRFDKkk,4250
-sapiopycommons/ai/protoapi/plan/converter/converter_pb2_grpc.py,sha256=6T5FCmT_vEFSywUVlAlWWfBDPaILb0Dq8yCGuO_Q-BU,6448
-sapiopycommons/ai/protoapi/plan/item/item_container_pb2.py,sha256=VIXmIw8-9jtH7peJZ16BEmGDfaVjjxTKhmlfcHWT82M,3863
-sapiopycommons/ai/protoapi/plan/item/item_container_pb2.pyi,sha256=bbPNQDwfFDd7_S7yU99Co1O7sRhxjle-RM0_nK8jgjc,4246
-sapiopycommons/ai/protoapi/plan/item/item_container_pb2_grpc.py,sha256=1NzBWBUINC0Rk-NGYZ-97BVKvVUxcn_I44IjQO2h-nQ,932
-sapiopycommons/ai/protoapi/plan/script/script_pb2.py,sha256=4TN7NlJEENAVqwfymoEDj5hhHYxHLdrHdpRUVgzVG8A,5621
-sapiopycommons/ai/protoapi/plan/script/script_pb2.pyi,sha256=l250ak1sOfm7Ue-PyBQC-7j7-p4DeBxltnOzwDsQIYc,6870
-sapiopycommons/ai/protoapi/plan/script/script_pb2_grpc.py,sha256=ginPYpsiI6U6dB6gfWHJM8LWjSHUgcqz_gR7Dmdsyck,6864
-sapiopycommons/ai/protoapi/plan/tool/entry_pb2.py,sha256=yNyyyVvz94ewjGaHw3t0pUP-KH7ACg5hLC0QzrsFPis,2130
-sapiopycommons/ai/protoapi/plan/tool/entry_pb2.pyi,sha256=2vI0WSy0KGFHDewMSRyX5rUkmmmSaMBLvFO7txqA6Ug,2354
-sapiopycommons/ai/protoapi/plan/tool/entry_pb2_grpc.py,sha256=i24BfJEt7LtyROxHVEyS9RLYqLZKPvyJMKRFZj6NUTg,923
-sapiopycommons/ai/protoapi/plan/tool/tool_pb2.py,sha256=aLD5j60lWUxhHW8b1AoUOClLOjFPjEMmM1KrY337-gI,9095
-sapiopycommons/ai/protoapi/plan/tool/tool_pb2.pyi,sha256=HGNou2THKPk8o9G_ZPvbGXDb6cBnv8L1R_l10i9ceHI,18441
-sapiopycommons/ai/protoapi/plan/tool/tool_pb2_grpc.py,sha256=CLSGEgSpN4D6wcE-P_5lzb2Nttjr4XjumxGUrZQSip0,6915
-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/ai/tool_of_tools.py,sha256=zYmQ4rNX-qYQnc-vNDnYZjtv9JgmQAmVVuHfVOdBF3w,46984
 sapiopycommons/callbacks/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/callbacks/callback_util.py,sha256=Z1LcXnRRjXyhmcSDUwh4NzcA6ICtcbFUMKcvAqQcS8E,153811
+sapiopycommons/callbacks/callback_util.py,sha256=aLkH5p5PMI74MN7tdrJ3Xy6LDDggHpCf4Lhr9XuOreA,154535
 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
@@ -70,15 +31,14 @@ 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=WBA3FYG8R2HtfxjWSzQhZKW6_1s6JSxTo9lk3SeNDu8,37140
+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/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=VwnWf_P803pcteoAIs0DkLScVChCS5XNgryTp8FzaNc,14696
+sapiopycommons/general/aliases.py,sha256=pHfpH5veukVdjlR62_INCy2ItZG1omQv4dCoo8NeGlM,14869
 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
@@ -105,8 +65,8 @@ 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=cvW6Mk_110BzYqkbk63Kg7jWrltBCDALOlkJRu8h4VQ,14300
-sapiopycommons-2025.10.15a782.dist-info/METADATA,sha256=DIeUTx52EZpA1ZIecBFRA4_LsTMKBwOZLzB6i2iBgxs,3143
-sapiopycommons-2025.10.15a782.dist-info/WHEEL,sha256=C2FUgwZgiLbznR-k0b_5k3Ai_1aASOXDss3lzCUsUug,87
-sapiopycommons-2025.10.15a782.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
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