pybiolib 1.2.437__tar.gz → 1.2.464__tar.gz

{pybiolib-1.2.437 → pybiolib-1.2.464}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.437
+Version: 1.2.464
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.437 → pybiolib-1.2.464}/biolib/compute_node/webserver/worker_thread.py

@@ -179,7 +179,10 @@ class WorkerThread(threading.Thread):
         cloud_job_uuid = self.compute_state['cloud_job_id']
         system_exception_code = self.compute_state['status'].get('error_code')
 
-        if utils.IS_RUNNING_IN_CLOUD and system_exception_code != SystemExceptionCodes.CANCELLED_BY_USER.value:
+        if utils.IS_RUNNING_IN_CLOUD and system_exception_code not in [
+            SystemExceptionCodes.CANCELLED_BY_USER.value,
+            SystemExceptionCodes.EXCEEDED_MAX_JOB_RUNTIME.value,
+        ]:
             CloudUtils.finish_cloud_job(
                 cloud_job_id=cloud_job_uuid,
                 system_exception_code=system_exception_code,
@@ -214,7 +217,10 @@ class WorkerThread(threading.Thread):
                     CloudUtils.deregister(error='job_cleanup_timed_out')
                     deregistered_due_to_error = True
 
-            elif system_exception_code == SystemExceptionCodes.CANCELLED_BY_USER.value:
+            elif system_exception_code in [
+                SystemExceptionCodes.CANCELLED_BY_USER.value,
+                SystemExceptionCodes.EXCEEDED_MAX_JOB_RUNTIME.value,
+            ]:
                 self.compute_state['exit_code'] = self._upload_module_output_and_get_exit_code()
                 CloudUtils.finish_cloud_job(
                     cloud_job_id=cloud_job_uuid,
@@ -222,7 +228,6 @@ class WorkerThread(threading.Thread):
                     exit_code=self.compute_state.get('exit_code', None),
                 )
 
-
         # Delete result as error occurred
         if system_exception_code and os.path.exists(self._job_temporary_dir):
             shutil.rmtree(self._job_temporary_dir)

{pybiolib-1.2.437 → pybiolib-1.2.464}/biolib/jobs/job.py

@@ -19,7 +19,7 @@ from biolib.biolib_errors import BioLibError, CloudJobFinishedError
 from biolib.biolib_logging import logger, logger_no_user_data
 from biolib.compute_node.job_worker.job_storage import JobStorage
 from biolib.compute_node.utils import SystemExceptionCodeMap, SystemExceptionCodes
-from biolib.jobs.job_result import JobResult
+from biolib.jobs.job_result import JobResult, PathFilter
 from biolib.jobs.types import CloudJobDict, CloudJobStartedDict, JobDict
 from biolib.tables import BioLibTable
 from biolib.typing_utils import Dict, List, Optional, Union, cast
@@ -102,11 +102,14 @@ class Job:
             state=self._job_dict['state'],
         )
 
-    def list_output_files(self, *args, **kwargs) -> List[LazyLoadedFile]:
-        return self.result.list_output_files(*args, **kwargs)
+    def list_output_files(
+        self,
+        path_filter: Optional[PathFilter] = None,
+    ) -> List[LazyLoadedFile]:
+        return self.result.list_output_files(path_filter=path_filter)
 
-    def get_output_file(self, *args, **kwargs) -> LazyLoadedFile:
-        return self.result.get_output_file(*args, **kwargs)
+    def get_output_file(self, filename: str) -> LazyLoadedFile:
+        return self.result.get_output_file(filename=filename)
 
     def load_file_as_numpy(self, *args, **kwargs):
         try:
@@ -165,8 +168,17 @@ class Job:
 
             logger.info(f'  - {destination_file_path}')
 
-    def save_files(self, *args, **kwargs) -> None:
-        self.result.save_files(*args, **kwargs)
+    def save_files(
+        self,
+        output_dir: str,
+        path_filter: Optional[PathFilter] = None,
+        skip_file_if_exists: Optional[bool] = None,
+    ) -> None:
+        self.result.save_files(
+            output_dir=output_dir,
+            path_filter=path_filter,
+            skip_file_if_exists=skip_file_if_exists,
+        )
 
     def get_status(self) -> str:
         self._refetch_job_dict()

{pybiolib-1.2.437 → pybiolib-1.2.464}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.2.437"
+version = "1.2.464"
 description = "BioLib Python Client"
 readme = "PYPI_README.md"
 license = "MIT"