pybiolib 1.1.2003__tar.gz → 1.1.2011__tar.gz

{pybiolib-1.1.2003 → pybiolib-1.1.2011}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.2003
+Version: 1.1.2011
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.2003 → pybiolib-1.1.2011}/biolib/jobs/job_result.py

@@ -34,7 +34,9 @@ class JobResult:
     def get_exit_code(self) -> int:
         return self._get_module_output().get_exit_code()
 
-    def save_files(self, output_dir: str, path_filter: Optional[PathFilter] = None) -> None:
+    def save_files(
+        self, output_dir: str, path_filter: Optional[PathFilter] = None, skip_file_if_exists: Optional[bool] = None
+    ) -> None:
         module_output = self._get_module_output()
         output_files = module_output.get_files()
         filtered_output_files = self._get_filtered_files(output_files, path_filter) if path_filter else output_files
@@ -60,15 +62,33 @@ class JobResult:
             # Remove leading slash of file_path
             destination_file_path = Path(output_dir) / Path(file.path.lstrip('/'))
             if destination_file_path.exists():
-                destination_file_path.rename(f'{destination_file_path}.biolib-renamed.{time.strftime("%Y%m%d%H%M%S")}')
+                if skip_file_if_exists:
+                    print(f'Skipping {destination_file_path} as a file with that name already exists locally.')
+                    continue
+                else:
+                    destination_file_path.rename(
+                        f'{destination_file_path}.biolib-renamed.{time.strftime("%Y%m%d%H%M%S")}'
+                    )
 
             dir_path = destination_file_path.parent
             if dir_path:
                 dir_path.mkdir(parents=True, exist_ok=True)
 
-            with open(destination_file_path, mode='wb') as destination_file:
-                for chunk in stream_seeker.seek_and_read(file_start=file.start, file_length=file.length):
-                    destination_file.write(chunk)
+            # write content to temporary (partial) file
+            partial_path = destination_file_path.with_suffix(f'.{self._job_uuid}.partial_biolib_download')
+            file_start = file.start
+            data_to_download = file.length
+            if partial_path.exists():
+                data_already_downloaded = partial_path.stat().st_size
+                file_start += data_already_downloaded
+                data_to_download -= data_already_downloaded
+
+            with open(partial_path, mode='ab') as partial_file:
+                for chunk in stream_seeker.seek_and_read(file_start=file_start, file_length=data_to_download):
+                    partial_file.write(chunk)
+
+            # rename partial file to actual file name
+            partial_path.rename(destination_file_path)
 
     def get_output_file(self, filename) -> LazyLoadedFile:
         files = self._get_module_output().get_files()

{pybiolib-1.1.2003 → pybiolib-1.1.2011}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.1.2003"
+version = "1.1.2011"
 description = "BioLib Python Client"
 readme = "README.md"
 license = "MIT"