pybiolib 1.1.1626__py3-none-any.whl → 1.1.1629__py3-none-any.whl

biolib/compute_node/job_worker/executors/docker_executor.py

@@ -1,4 +1,5 @@
 import json
+import subprocess
 import tempfile
 import time
 import tarfile
@@ -490,6 +491,34 @@ class DockerExecutor:
                 self._send_system_exception,
             ) from exception
 
+    def _get_container_upper_dir_path(self) -> Optional[str]:
+        data = self._container.attrs['GraphDriver']['Data']
+        upper_dir: Optional[str] = data['UpperDir'] if data else None
+
+        if not upper_dir and utils.IS_RUNNING_IN_CLOUD:
+            # Get upperdir from containerd ctr CLI
+            result = subprocess.run(
+                args=[
+                    'ctr',
+                    '--namespace', 'moby',
+                    'snapshots',
+                    '--snapshotter', 'nydus',
+                    'mounts',
+                    '/some_arbitrary_path',
+                    str(self._container.id),
+                ],
+                check=False,
+                capture_output=True,
+            )
+            if result.returncode == 0:
+                match = re.search(r'upperdir=([^,]+)', result.stdout.decode('utf-8'))
+                upper_dir = match.group(1) if match else None
+
+        if upper_dir and os.path.exists(upper_dir):
+            return upper_dir
+
+        return None
+
     def _get_changed_files_in_docker_container(self, pre_start_diff: List[Dict]) -> 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]
@@ -516,11 +545,10 @@ class DockerExecutor:
                     return True
             return False
 
-        data = self._container.attrs['GraphDriver']['Data']
-        overlay_upper_dir_path = data['UpperDir'] if data and os.path.exists(data['UpperDir']) else None
+        overlay_upper_dir_path = self._get_container_upper_dir_path()
         if not overlay_upper_dir_path:
             logger_no_user_data.debug(
-                'Docker Overlay2 UpperDir not available. Falling back to container.get_archive() for file extraction'
+                'Docker UpperDir not available. Falling back to container.get_archive() for file extraction'
             )
 
         logger.debug(f'overlay_upper_dir_path={overlay_upper_dir_path}')

{pybiolib-1.1.1626.dist-info → pybiolib-1.1.1629.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1626
+Version: 1.1.1629
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.1626.dist-info → pybiolib-1.1.1629.dist-info}/RECORD

@@ -54,7 +54,7 @@ biolib/compute_node/job_worker/cache_state.py,sha256=N2AxvvgfizKx9P_ysM0GDCmueMU
 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=XMtU9wSM83c5tqQrITj5-MT_Gr58_d7zCW0BRizoVME,25403
+biolib/compute_node/job_worker/executors/docker_executor.py,sha256=74wUy5piILgCY-eFu2LuEOWDqmuYkaijy-ZW83S6WKw,26335
 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=yP5gG39hr-DLnw9bOE--VHi-1arDbIYiGuV1rlTbbHI,1466
@@ -101,8 +101,8 @@ biolib/utils/cache_state.py,sha256=BFrZlV4XZIueIFzAFiPidX4hmwADKY5Y5ZuqlerF5l0,3
 biolib/utils/multipart_uploader.py,sha256=PEorMsTNg5f72e3Y-KA3LrI-F6EAnsD9vENV-5EuiX0,9896
 biolib/utils/seq_util.py,sha256=hudZ7o1LI7xdpjb1OFKPBZvGVxjiqKez8zMwjtWT0TY,3269
 biolib/utils/zip/remote_zip.py,sha256=NCdUnVbGCv7SfXCI-yVU-is_OnyWmLAnVpIdSvo-W4k,23500
-pybiolib-1.1.1626.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.1626.dist-info/METADATA,sha256=XhdXYsvqSHrrj59CBCNtJO3bTUAIAUJ72NfI7HqICW0,1543
-pybiolib-1.1.1626.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-pybiolib-1.1.1626.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.1626.dist-info/RECORD,,
+pybiolib-1.1.1629.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.1629.dist-info/METADATA,sha256=grvWM24XHQjGcGXpjHv79ba0vY8PzvyTce4CUjkQ3wk,1543
+pybiolib-1.1.1629.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
+pybiolib-1.1.1629.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.1629.dist-info/RECORD,,