pybiolib 1.2.561__py3-none-any.whl → 1.2.565__py3-none-any.whl

biolib/compute_node/job_worker/executors/docker_executor.py

@@ -201,9 +201,6 @@ class DockerExecutor:
             stream=True,
         )
 
-        logger_no_user_data.debug(f'Running diff for Docker container for {job_uuid}')
-        pre_start_diff = self._container.diff()
-
         logger_no_user_data.debug(f'Starting Docker container for {job_uuid}')
         startup_error_string: Optional[str] = None
         try:
@@ -218,7 +215,6 @@ class DockerExecutor:
         self._metadata_for_save_output_on_cancel = MetadataToSaveOutput(
             arguments=module_input['arguments'],
             startup_error_string=startup_error_string,
-            pre_start_diff=pre_start_diff,
         )
 
         if self._options['job']['app_version'].get('stdout_render_type') != 'markdown':
@@ -264,7 +260,6 @@ class DockerExecutor:
             module_output_path=self._options['module_output_path'],
             stderr=full_stderr,
             stdout=full_stdout,
-            pre_start_diff=metadata['pre_start_diff'],
         )
 
     def cleanup(self):
@@ -532,12 +527,11 @@ class DockerExecutor:
         module_output_path: str,
         stderr: bytes,
         stdout: bytes,
-        pre_start_diff: List[Dict],
     ) -> None:
         mapped_files: List[FileInContainer] = []
         try:
             mappings = Mappings(mappings_list=self._options['module']['output_files_mappings'], arguments=arguments)
-            changed_files: List[FileInContainer] = self._get_changed_files_in_docker_container(pre_start_diff)
+            changed_files: List[FileInContainer] = self._get_changed_files_in_docker_container()
 
             for file in changed_files:
                 if file.is_file():
@@ -602,15 +596,13 @@ class DockerExecutor:
 
         return None
 
-    def _get_changed_files_in_docker_container(self, pre_start_diff: List[Dict]) -> List[FileInContainer]:
+    def _get_changed_files_in_docker_container(self) -> List[FileInContainer]:
         from_mappings = [mapping['from_path'] for mapping in self._options['module']['output_files_mappings']]
-        pre_start_diff_paths = [obj['Path'] for obj in pre_start_diff]
         post_run_diff = self._container.diff()
         run_diff_paths: List[str] = [
             obj['Path']
             for obj in post_run_diff
             if obj['Kind'] in (DockerDiffKind.CHANGED.value, DockerDiffKind.ADDED.value)
-            and obj['Path'] not in pre_start_diff_paths
         ]
 
         known_directories = set()

biolib/compute_node/job_worker/executors/types.py

@@ -46,4 +46,3 @@ class LocalExecutorOptions(TypedDict):
 class MetadataToSaveOutput(TypedDict):
     arguments: List[str]
     startup_error_string: Optional[str]
-    pre_start_diff: List[Dict]

{pybiolib-1.2.561.dist-info → pybiolib-1.2.565.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.561
+Version: 1.2.565
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.561.dist-info → pybiolib-1.2.565.dist-info}/RECORD

@@ -76,10 +76,10 @@ biolib/compute_node/job_worker/cache_state.py,sha256=MwjSRzcJJ_4jybqvBL4xdgnDYSI
 biolib/compute_node/job_worker/cache_types.py,sha256=ajpLy8i09QeQS9dEqTn3T6NVNMY_YsHQkSD5nvIHccQ,818
 biolib/compute_node/job_worker/docker_image_cache.py,sha256=ansHIkJIq_EMW1nZNlW-RRLVVeKWTbzNICYaOHpKiRE,7460
 biolib/compute_node/job_worker/executors/__init__.py,sha256=bW6t1qi3PZTlHM4quaTLa8EI4ALTCk83cqcVJfJfJfE,145
-biolib/compute_node/job_worker/executors/docker_executor.py,sha256=UxWUSk15mM_H73q2k5_kBB1IWGYGphyXbyC-Bm0QneU,31550
+biolib/compute_node/job_worker/executors/docker_executor.py,sha256=RBBPjxL-zqI77vHWG7ssrFGFSsHVob7TuIMw36URPQ0,31111
 biolib/compute_node/job_worker/executors/docker_types.py,sha256=VhsU1DKtJjx_BbCkVmiPZPH4ROiL1ygW1Y_s1Kbpa2o,216
 biolib/compute_node/job_worker/executors/tars/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biolib/compute_node/job_worker/executors/types.py,sha256=gw_T-oq0lty8Hg8WsTrqhtV-kyOF_l5nr9Xe8-kzetc,1657
+biolib/compute_node/job_worker/executors/types.py,sha256=wbjWZZ2f9FttjqUCCOeZmn7n3L3Hu-7-2PZJ3BVf_Ps,1626
 biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py,sha256=_cvEiZbOwfkv6fYmfrvdi_FVviIEYr_dSClQcOQaUWM,1198
 biolib/compute_node/job_worker/job_max_runtime_timer_thread.py,sha256=K_xgz7IhiIjpLlXRk8sqaMyLoApcidJkgu29sJX0gb8,1174
 biolib/compute_node/job_worker/job_storage.py,sha256=lScHI3ubcHKagSEW243tgbIWXUfbWDHDjEOPMvXxJE8,4603
@@ -119,8 +119,8 @@ 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=Ozk0blGtPur_D9MwShD02r_mphyQmgZkx-lOHOwnlIM,6730
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.2.561.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.561.dist-info/METADATA,sha256=vK5utD-3vpUDsQfgH-j7GEhFqqRpCmHWxS1D7uz3jRM,1570
-pybiolib-1.2.561.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
-pybiolib-1.2.561.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.561.dist-info/RECORD,,
+pybiolib-1.2.565.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.565.dist-info/METADATA,sha256=_CM-jsOMgyM_KMENpfQz0auad3iMgTcoiGDKlvfTcC8,1570
+pybiolib-1.2.565.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+pybiolib-1.2.565.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.565.dist-info/RECORD,,