pybiolib 1.2.565__py3-none-any.whl → 1.2.567__py3-none-any.whl

biolib/compute_node/job_worker/executors/docker_executor.py

@@ -27,7 +27,7 @@ from biolib.compute_node import utils as compute_node_utils
 from biolib.compute_node.cloud_utils import CloudUtils
 from biolib.compute_node.job_worker.docker_image_cache import DockerImageCache
 from biolib.compute_node.job_worker.executors.docker_types import DockerDiffKind
-from biolib.compute_node.job_worker.executors.types import LocalExecutorOptions, StatusUpdate, MetadataToSaveOutput
+from biolib.compute_node.job_worker.executors.types import LocalExecutorOptions, MetadataToSaveOutput, StatusUpdate
 from biolib.compute_node.job_worker.mappings import Mappings, path_without_first_folder
 from biolib.compute_node.job_worker.utilization_reporter_thread import UtilizationReporterThread
 from biolib.compute_node.job_worker.utils import ComputeProcessException
@@ -598,12 +598,33 @@ class DockerExecutor:
 
     def _get_changed_files_in_docker_container(self) -> List[FileInContainer]:
         from_mappings = [mapping['from_path'] for mapping in self._options['module']['output_files_mappings']]
-        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)
-        ]
+        overlay_upper_dir_path = self._get_container_upper_dir_path()
+
+        if not overlay_upper_dir_path:
+            logger_no_user_data.debug(
+                'Docker UpperDir not available. Falling back to container.get_archive() for file extraction'
+            )
+            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)
+            ]
+        else:
+            logger_no_user_data.debug(f'overlay_upper_dir_path={overlay_upper_dir_path}')
+            # Recursively find all files in overlay_upper_dir_path
+            run_diff_paths = []
+            for root, _, files in os.walk(overlay_upper_dir_path):
+                # Convert absolute paths to container paths
+                rel_path = os.path.relpath(root, overlay_upper_dir_path)
+                if rel_path == '.':
+                    # Handle the root directory case
+                    for file in files:
+                        run_diff_paths.append(f'/{file}')
+                else:
+                    # Handle subdirectories
+                    for file in files:
+                        run_diff_paths.append(f'/{rel_path}/{file}')
 
         known_directories = set()
         for path in run_diff_paths:
@@ -621,14 +642,6 @@ class DockerExecutor:
                     return True
             return False
 
-        overlay_upper_dir_path = self._get_container_upper_dir_path()
-        if not overlay_upper_dir_path:
-            logger_no_user_data.debug(
-                'Docker UpperDir not available. Falling back to container.get_archive() for file extraction'
-            )
-
-        logger_no_user_data.debug(f'overlay_upper_dir_path={overlay_upper_dir_path}')
-
         files_and_empty_dirs: List[FileInContainer] = []
         for path in run_diff_paths:
             if path not in known_directories and path_is_included_in_from_mappings(path):

{pybiolib-1.2.565.dist-info → pybiolib-1.2.567.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.565
+Version: 1.2.567
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.565.dist-info → pybiolib-1.2.567.dist-info}/RECORD

@@ -76,7 +76,7 @@ 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=RBBPjxL-zqI77vHWG7ssrFGFSsHVob7TuIMw36URPQ0,31111
+biolib/compute_node/job_worker/executors/docker_executor.py,sha256=FFN4dn3mV19u6imT8e4vjpfDIxX9d3bpq9x2JPVOAus,31811
 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=wbjWZZ2f9FttjqUCCOeZmn7n3L3Hu-7-2PZJ3BVf_Ps,1626
@@ -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-1.2.565.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,,
+pybiolib-1.2.567.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.567.dist-info/METADATA,sha256=cYbTCTlMWjLsgfbKKtLkHmAn3WZ2ezprxNiAadnwqmo,1570
+pybiolib-1.2.567.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+pybiolib-1.2.567.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.567.dist-info/RECORD,,