pybiolib 1.2.322.dev1__tar.gz → 1.2.328.dev1__tar.gz

{pybiolib-1.2.322.dev1 → pybiolib-1.2.328.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.322.dev1
+Version: 1.2.328.dev1
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.322.dev1 → pybiolib-1.2.328.dev1}/biolib/compute_node/webserver/worker_thread.py

@@ -7,6 +7,7 @@ import sys
 import threading
 import time
 from queue import Queue
+from typing import Optional
 
 from biolib import api, utils
 from biolib.biolib_binary_format import ModuleOutputV2, SystemException, SystemStatusUpdate
@@ -55,6 +56,26 @@ class WorkerThread(threading.Thread):
     def _job_temporary_dir(self):
         return self.compute_state['job_temporary_dir']
 
+    def _upload_module_output_and_get_exit_code(self) -> Optional[int]:
+        exit_code = None
+        try:
+            module_output_path = os.path.join(
+                self._job_temporary_dir,
+                JobStorage.module_output_file_name,
+            )
+            if os.path.exists(module_output_path):
+                module_output = ModuleOutputV2(buffer=LocalFileIndexableBuffer(filename=module_output_path))
+                exit_code = module_output.get_exit_code()
+                logger_no_user_data.debug(f'Got exit code: {exit_code}')
+                if utils.IS_RUNNING_IN_CLOUD:
+                    JobStorage.upload_module_output(
+                        job_temporary_dir=self._job_temporary_dir,
+                        job_uuid=self._job_uuid,
+                    )
+        except Exception as error:
+            logger_no_user_data.error(f'Could not upload module output or get exit code: {error}')
+        return exit_code
+
     def run(self):
         try:
             while True:
@@ -77,25 +98,7 @@ class WorkerThread(threading.Thread):
 
                     # If 'Computation Finished'
                     if progress == 94:
-                        # Get Job exit code
-                        try:
-                            module_output_path = os.path.join(
-                                self._job_temporary_dir,
-                                JobStorage.module_output_file_name,
-                            )
-                            module_output = ModuleOutputV2(buffer=LocalFileIndexableBuffer(filename=module_output_path))
-                            self.compute_state['exit_code'] = module_output.get_exit_code()
-                            logger_no_user_data.debug(f"Got exit code: {self.compute_state['exit_code']}")
-
-                        except Exception as error:  # pylint: disable=broad-except
-                            logger_no_user_data.error(f'Could not get exit_code from module output due to: {error}')
-
-                        if utils.IS_RUNNING_IN_CLOUD:
-                            JobStorage.upload_module_output(
-                                job_temporary_dir=self._job_temporary_dir,
-                                job_uuid=self._job_uuid,
-                            )
-
+                        self.compute_state['exit_code'] = self._upload_module_output_and_get_exit_code()
                         self._set_status_update(progress=95, log_message='Result Ready')
                         self.compute_state['is_completed'] = True
                         self.terminate()
@@ -174,13 +177,16 @@ class WorkerThread(threading.Thread):
 
     def terminate(self) -> None:
         cloud_job_uuid = self.compute_state['cloud_job_id']
-        exit_code = self.compute_state.get('exit_code')
         system_exception_code = self.compute_state['status'].get('error_code')
+
         if utils.IS_RUNNING_IN_CLOUD:
+            if system_exception_code == SystemExceptionCodes.CANCELLED_BY_USER.value:
+                self.compute_state['exit_code'] = self._upload_module_output_and_get_exit_code()
+
             CloudUtils.finish_cloud_job(
                 cloud_job_id=cloud_job_uuid,
                 system_exception_code=system_exception_code,
-                exit_code=exit_code,
+                exit_code=self.compute_state.get('exit_code', None),
             )
 
         deregistered_due_to_error = False

{pybiolib-1.2.322.dev1 → pybiolib-1.2.328.dev1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.2.322.dev1"
+version = "1.2.328.dev1"
 description = "BioLib Python Client"
 readme = "PYPI_README.md"
 license = "MIT"