pybiolib 1.1.1558__tar.gz → 1.1.1564__tar.gz

{pybiolib-1.1.1558 → pybiolib-1.1.1564}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1558
+Version: 1.1.1564
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

pybiolib-1.1.1564/biolib/biolib_binary_format/file_in_container.py

@@ -0,0 +1,105 @@
+import os.path
+import tarfile
+import tempfile
+
+from docker.models.containers import Container  # type: ignore
+
+from biolib.typing_utils import Iterable, Optional
+
+
+class FileInContainer:
+    def __init__(self, container: Container, path_in_container: str, overlay_upper_dir_path: Optional[str]):
+        self._container: Container = container
+        self._path_on_disk: Optional[str] = overlay_upper_dir_path + path_in_container if overlay_upper_dir_path \
+            else None
+
+        self._path_in_container: str = path_in_container
+        self._path: str = path_in_container
+        self._buffered_file_data: Optional[bytes] = None
+
+    def __repr__(self) -> str:
+        return f'FileInContainer({self.path})'
+
+    @property
+    def path(self) -> str:
+        return self._path
+
+    @path.setter
+    def path(self, value: str) -> None:
+        self._path = value
+
+    def is_file(self) -> bool:
+        if self._path_on_disk:
+            return os.path.isfile(self._path_on_disk)
+        else:
+            tmp_file = self._get_temp_file_from_container_via_tar()
+            if tmp_file:
+                os.remove(tmp_file)
+                return True
+            else:
+                return False
+
+    def get_data_size_in_bytes(self) -> int:
+        if self._path_on_disk:
+            return os.path.getsize(self._path_on_disk)
+        else:
+            tmp_file = self._get_temp_file_from_container_via_tar()
+            if tmp_file:
+                file_length = os.path.getsize(tmp_file)
+                os.remove(tmp_file)
+                return file_length
+            else:
+                return 0
+
+    def get_data_stream(self) -> Iterable[bytes]:
+        if self._path_on_disk:
+            with open(self._path_on_disk, mode='rb') as file:
+                while True:
+                    chunk = file.read(1_000_000)
+                    if not chunk:
+                        return
+
+                    yield chunk
+        else:
+            tmp_file = self._get_temp_file_from_container_via_tar()
+            if not tmp_file:
+                yield bytes()
+                return
+            else:
+                file = open(tmp_file, mode='rb')
+                while True:
+                    chunk = file.read(1_000_000)
+                    if not chunk:
+                        file.close()
+                        os.remove(tmp_file)
+                        return
+
+                    yield chunk
+
+    def _get_temp_file_from_container_via_tar(self) -> Optional[str]:
+        with tempfile.NamedTemporaryFile(mode='w+', delete=True) as tmp_io:
+            stream, _ = self._container.get_archive(path=self._path_in_container)
+            for chunk in stream:
+                tmp_io.write(chunk)
+
+            tmp_io.seek(0)
+            with tarfile.open(tmp_io.name) as tar:
+                members = tar.getmembers()
+                file_members = [member for member in members if member.isfile()]
+                if not file_members:
+                    # Path was not a file
+                    return None
+
+                assert len(file_members) == 1
+                file_obj = tar.extractfile(member=file_members[0])
+                if not file_obj:
+                    # Path was not a file
+                    return None
+                tmp_io_2 = tempfile.NamedTemporaryFile(mode='w+', delete=False)
+                while True:
+                    chunk = file_obj.read(1_000_000)
+                    if not chunk:
+                        break
+                    tmp_io_2.write(chunk)
+                tmp_io_2.close()
+                return tmp_io_2.name

{pybiolib-1.1.1558 → pybiolib-1.1.1564}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.1.1558"
+version = "1.1.1564"
 description = "BioLib Python Client"
 readme = "README.md"
 license = "MIT"

pybiolib-1.1.1558/biolib/biolib_binary_format/file_in_container.py

@@ -1,79 +0,0 @@
-import io
-import os.path
-import tarfile
-
-from docker.models.containers import Container  # type: ignore
-
-from biolib.typing_utils import Iterable, Optional
-
-
-class FileInContainer:
-    def __init__(self, container: Container, path_in_container: str, overlay_upper_dir_path: Optional[str]):
-        self._container: Container = container
-        self._path_on_disk: Optional[str] = overlay_upper_dir_path + path_in_container if overlay_upper_dir_path \
-            else None
-
-        self._path_in_container: str = path_in_container
-        self._path: str = path_in_container
-        self._buffered_file_data: Optional[bytes] = None
-
-    def __repr__(self) -> str:
-        return f'FileInContainer({self.path})'
-
-    @property
-    def path(self) -> str:
-        return self._path
-
-    @path.setter
-    def path(self, value: str) -> None:
-        self._path = value
-
-    def is_file(self) -> bool:
-        if self._path_on_disk:
-            return os.path.isfile(self._path_on_disk)
-        else:
-            return self._get_file_data_from_container_via_tar() is not None
-
-    def get_data_size_in_bytes(self) -> int:
-        if self._path_on_disk:
-            return os.path.getsize(self._path_on_disk)
-        else:
-            file_data = self._get_file_data_from_container_via_tar()
-            return len(file_data) if file_data else 0
-
-    def get_data_stream(self) -> Iterable[bytes]:
-        if self._path_on_disk:
-            with open(self._path_on_disk, mode='rb') as file:
-                while True:
-                    chunk = file.read(1_024)
-                    if not chunk:
-                        return
-
-                    yield chunk
-        else:
-            yield self._get_file_data_from_container_via_tar() or bytes()
-
-    def _get_file_data_from_container_via_tar(self) -> Optional[bytes]:
-        if not self._buffered_file_data:
-            with io.BytesIO() as tmp_io:
-                stream, _ = self._container.get_archive(path=self._path_in_container)
-                for chunk in stream:
-                    tmp_io.write(chunk)
-
-                tmp_io.seek(0)
-                with tarfile.open(fileobj=tmp_io) as tar:
-                    members = tar.getmembers()
-                    file_members = [member for member in members if member.isfile()]
-                    if not file_members:
-                        # Path was not a file
-                        return None
-
-                    assert len(file_members) == 1
-                    file_obj = tar.extractfile(member=file_members[0])
-                    if not file_obj:
-                        # Path was not a file
-                        return None
-
-                    self._buffered_file_data = file_obj.read()
-
-        return self._buffered_file_data