sapiopycommons 2025.10.1a772__py3-none-any.whl → 2025.10.2a773__py3-none-any.whl

sapiopycommons/files/file_util.py

@@ -1,4 +1,7 @@
+import gzip
 import io
+import tarfile
+import time
 import warnings
 import zipfile
 
@@ -322,7 +325,7 @@ 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.
@@ -335,6 +338,130 @@ 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/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) -> None:
+        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/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-2025.10.1a772.dist-info → sapiopycommons-2025.10.2a773.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2025.10.1a772
+Version: 2025.10.2a773
 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-2025.10.1a772.dist-info → sapiopycommons-2025.10.2a773.dist-info}/RECORD

@@ -1,6 +1,41 @@
 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=HiUXmwqv1STgyQeF9_eTFXzjIFXp5-NJ7sEhMpV3aAU,6351
+sapiopycommons/ai/protobuf_utils.py,sha256=cBjbxoFAwU02kNUxEce95WnMU2CMuDD-qFaeWgvQJMQ,24599
+sapiopycommons/ai/request_validation.py,sha256=AOpLoXYRnKf0h7MRNj6ev_rfcRxXREzQgBcbpBp5loY,24014
+sapiopycommons/ai/server.py,sha256=1ksOax2cab9MH7ESXQ5dwVNZcBKiWpNVhkzO4KkFTSg,6370
+sapiopycommons/ai/test_client.py,sha256=Um93jXmIx0YaHf-YbV5NSamPTHveJ0kU_UaAfOApnZg,16342
+sapiopycommons/ai/tool_service_base.py,sha256=_KHd9Y2C8gg3Ad-4ubP9fMf5_kMC41k5LZh8EfAW6MU,54435
+sapiopycommons/ai/protoapi/fielddefinitions/fields_pb2.py,sha256=8tKXwLXcqFGdQHHSEBSi6Fd7dcaCFoOqmhjzqhenb_M,2372
+sapiopycommons/ai/protoapi/fielddefinitions/fields_pb2.pyi,sha256=FwtXmNAf7iYGEFm4kbqb04v77jNHbZg18ZmEDhle_bU,1444
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+sapiopycommons/ai/protoapi/fielddefinitions/velox_field_def_pb2.pyi,sha256=U5zXrbBxsWilLTsRWJd1TqjdjLKFsr3enF9OJ8GfyWw,34028
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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=Z1LcXnRRjXyhmcSDUwh4NzcA6ICtcbFUMKcvAqQcS8E,153811
 sapiopycommons/callbacks/field_builder.py,sha256=rnIP-RJafk3mZlAx1eJ8a0eSW9Ps_L6_WadCmusnENw,38772
@@ -31,9 +66,10 @@ 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=i-xgh4puYLtREI1ZtKq8y5q1lRWQX_UrVyJd2yQO0hw,3183
 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
@@ -65,8 +101,8 @@ 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
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-sapiopycommons-2025.10.1a772.dist-info/RECORD,,
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