pybiolib 1.2.923__tar.gz → 1.2.931__tar.gz

{pybiolib-1.2.923 → pybiolib-1.2.931}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.923
+Version: 1.2.931
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.923 → pybiolib-1.2.931}/biolib/cli/run.py

@@ -48,7 +48,7 @@ def _run(local: bool, non_blocking: bool, uri: str, args: Tuple[str]) -> None:
     )
 
     if blocking:
-        job.save_files('biolib_results')
+        job.save_files('biolib_results', overwrite=True)
 
         # Write stdout and stderr if it has not been streamed (Markdown is not streamed)
         if app.version.get('stdout_render_type') == 'markdown' or not sys.stdout.isatty():

{pybiolib-1.2.923 → pybiolib-1.2.931}/biolib/jobs/job.py

@@ -226,7 +226,7 @@ class Result:
 
         return self._cached_input_arguments
 
-    def save_input_files(self, output_dir: str) -> None:
+    def save_input_files(self, output_dir: str, overwrite: bool = False) -> None:
         logger.info('Downloading input files...')
         module_input = self._get_module_input()
 
@@ -236,7 +236,12 @@ class Result:
             # Remove leading slash of file_path
             destination_file_path = Path(output_dir) / Path(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 not overwrite:
+                    raise BioLibError(f'File {destination_file_path} already exists. Set overwrite=True to overwrite.')
+                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:
@@ -252,11 +257,13 @@ class Result:
         output_dir: str,
         path_filter: Optional[PathFilter] = None,
         skip_file_if_exists: Optional[bool] = None,
+        overwrite: bool = False,
     ) -> None:
         self.result.save_files(
             output_dir=output_dir,
             path_filter=path_filter,
             skip_file_if_exists=skip_file_if_exists,
+            overwrite=overwrite,
         )
 
     def get_status(self) -> str:

{pybiolib-1.2.923 → pybiolib-1.2.931}/biolib/jobs/job_result.py

@@ -39,6 +39,7 @@ class JobResult:
         output_dir: str,
         path_filter: Optional[PathFilter] = None,
         skip_file_if_exists: Optional[bool] = None,
+        overwrite: bool = False,
     ) -> None:
         module_output = self._get_module_output()
         output_files = module_output.get_files()
@@ -68,6 +69,8 @@ class JobResult:
                 if skip_file_if_exists:
                     print(f'Skipping {destination_file_path} as a file with that name already exists locally.')
                     continue
+                elif not overwrite:
+                    raise BioLibError(f'File {destination_file_path} already exists. Set overwrite=True to overwrite.')
                 else:
                     destination_file_path.rename(
                         f'{destination_file_path}.biolib-renamed.{time.strftime("%Y%m%d%H%M%S")}'

{pybiolib-1.2.923 → pybiolib-1.2.931}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.2.923"
+version = "1.2.931"
 description = "BioLib Python Client"
 readme = "PYPI_README.md"
 license = "MIT"