pybiolib 1.1.2003__py3-none-any.whl → 1.1.2011__py3-none-any.whl

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.dist-info → pybiolib-1.1.2011.dist-info}/METADATA

@@ -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.dist-info → pybiolib-1.1.2011.dist-info}/RECORD

@@ -90,7 +90,7 @@ biolib/experiments/experiment.py,sha256=_ied3A3U6NFa6_ewEYn2TCozqeHvDxDqdRhMtZbF
 biolib/experiments/types.py,sha256=n9GxdFA7cLMfHvLLqLmZzX31ELeSSkMXFoEEdFsdWGY,171
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
 biolib/jobs/job.py,sha256=aWKnf_2pYdr76gh3hxPiVs2iuXlpwZkKPTK81Pz4G2U,19072
-biolib/jobs/job_result.py,sha256=UGxE9MNLtwJiWmhw2UNjOQW7EZi7B-e2lL0PXYvsXeA,4925
+biolib/jobs/job_result.py,sha256=IaSKb9B33zTnMq8CQBRB8_FTc8uYqJU8Amag8bcwyvE,5799
 biolib/jobs/types.py,sha256=qhadtH2KDC2WUOOqPiwke0YgtQY4FtuB71Stekq1k48,970
 biolib/lfs/__init__.py,sha256=Qv8vdYeK43JecT4SsE93ZYE2VmNiZENdNpW8P9-omxs,115
 biolib/lfs/cache.py,sha256=pQS2np21rdJ6I3DpoOutnzPHpLOZgUIS8TMltUJk_k4,2226
@@ -109,8 +109,8 @@ biolib/utils/cache_state.py,sha256=u256F37QSRIVwqKlbnCyzAX4EMI-kl6Dwu6qwj-Qmag,3
 biolib/utils/multipart_uploader.py,sha256=XvGP1I8tQuKhAH-QugPRoEsCi9qvbRk-DVBs5PNwwJo,8452
 biolib/utils/seq_util.py,sha256=jC5WhH63FTD7SLFJbxQGA2hOt9NTwq9zHl_BEec1Z0c,4907
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.1.2003.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.2003.dist-info/METADATA,sha256=OllzY7bgzHEQu23N9rHAK3GyFKRCycBbpcwD3q0Xjq8,1508
-pybiolib-1.1.2003.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pybiolib-1.1.2003.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.2003.dist-info/RECORD,,
+pybiolib-1.1.2011.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.2011.dist-info/METADATA,sha256=nzajC4HmYF0zf_amvrcgobGbTs-_DAp2pmfKkoRvG50,1508
+pybiolib-1.1.2011.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.1.2011.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.2011.dist-info/RECORD,,