pybiolib 1.1.1325__tar.gz → 1.1.1338__tar.gz

{pybiolib-1.1.1325 → pybiolib-1.1.1338}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1325
+Version: 1.1.1338
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.1325 → pybiolib-1.1.1338}/biolib/biolib_binary_format/utils.py

@@ -86,6 +86,28 @@ def _get_request_with_retries_for_timeout(
     raise Exception(f'Failed to complete HTTP GET request for "{url}" after {retries} retries')
 
 
+class LocalFileIndexableBuffer(IndexableBuffer):
+
+    def __init__(self, filename: str):
+        super().__init__()
+        self._filehandle = open(filename, 'rb')
+
+    def get_data(self, start: int, length: int) -> bytes:
+        if length < 0:
+            raise Exception('get_data length must be positive')
+
+        if length == 0:
+            return bytes(0)
+
+        self._filehandle.seek(start)
+        data: bytes = self._filehandle.read(length)
+
+        if len(data) != length:
+            raise Exception(f'get_data got response of unexpected length. Got {len(data)} expected {length}.')
+
+        return data
+
+
 class RemoteIndexableBuffer(IndexableBuffer):
 
     def __init__(self, endpoint: RemoteEndpoint):

{pybiolib-1.1.1325 → pybiolib-1.1.1338}/biolib/compute_node/cloud_utils/cloud_utils.py

@@ -102,7 +102,7 @@ class CloudUtils:
             logger_no_user_data.error("Not deregistering as environment is not cloud")
 
     @staticmethod
-    def finish_cloud_job(cloud_job_id: str, system_exception_code: Optional[int]) -> None:
+    def finish_cloud_job(cloud_job_id: str, system_exception_code: Optional[int], exit_code: Optional[int]) -> None:
         if not cloud_job_id:
             logger_no_user_data.error(
                 'Finish cloud job was called but no cloud job was supplied. '
@@ -120,6 +120,7 @@ class CloudUtils:
                         'auth_token': config["compute_node_info"]["auth_token"],
                         'cloud_job_id': cloud_job_id,
                         'system_exception_code': system_exception_code,
+                        'job_exit_code': exit_code
                     },
                     timeout=10,
                 )

{pybiolib-1.1.1325 → pybiolib-1.1.1338}/biolib/compute_node/webserver/worker_thread.py

@@ -9,13 +9,14 @@ import socket
 from queue import Queue
 
 from biolib import utils
+from biolib.biolib_binary_format.utils import LocalFileIndexableBuffer
 from biolib.compute_node.cloud_utils import CloudUtils
 from biolib.compute_node.job_worker import JobWorkerProcess
 from biolib.compute_node.job_worker.job_storage import JobStorage
 from biolib.compute_node.socker_listener_thread import SocketListenerThread
 from biolib.compute_node.socket_sender_thread import SocketSenderThread
 from biolib.compute_node.webserver import webserver_utils
-from biolib.biolib_binary_format import SystemStatusUpdate, SystemException
+from biolib.biolib_binary_format import SystemStatusUpdate, SystemException, ModuleOutputV2
 from biolib.compute_node.utils import get_package_type, WorkerThreadException, SystemExceptionCodes
 from biolib.biolib_logging import logger, logger_no_user_data
 
@@ -76,6 +77,22 @@ 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()
+
+                        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,
@@ -184,11 +201,14 @@ class WorkerThread(threading.Thread):
         if system_exception_code and os.path.exists(self._job_temporary_dir):
             shutil.rmtree(self._job_temporary_dir)
 
+        exit_code = self.compute_state.get('exit_code')
+
         if utils.IS_RUNNING_IN_CLOUD:
-            # Get and send exception code if present
+            # Get and send compute node exception code and job exit code if present
             CloudUtils.finish_cloud_job(
                 cloud_job_id=self.compute_state['cloud_job_id'],
-                system_exception_code=system_exception_code
+                system_exception_code=system_exception_code,
+                exit_code=exit_code
             )
 
         if self._socket:

{pybiolib-1.1.1325 → pybiolib-1.1.1338}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.1.1325"
+version = "1.1.1338"
 description = "BioLib Python Client"
 readme = "README.md"
 license = "MIT"