pybiolib 1.1.1325__py3-none-any.whl → 1.1.1338__py3-none-any.whl

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):

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,
                 )

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.dist-info → pybiolib-1.1.1338.dist-info}/METADATA

@@ -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.dist-info → pybiolib-1.1.1338.dist-info}/RECORD

@@ -29,7 +29,7 @@ biolib/biolib_binary_format/saved_job.py,sha256=nFHVFRNTNcAFGODLSiBntCtMk55QKwre
 biolib/biolib_binary_format/stdout_and_stderr.py,sha256=WfUUJFFCBrtfXjuWIaRPiWCpuBLxfko68oxoTKhrwx8,1023
 biolib/biolib_binary_format/system_exception.py,sha256=T3iL4_cSHAHim3RSDPS8Xyb1mfteaJBZonSXuRltc28,853
 biolib/biolib_binary_format/system_status_update.py,sha256=aOELuQ0k-GtpaZTUxYd0GFomP_OInmrK585y6fuQuKE,1191
-biolib/biolib_binary_format/utils.py,sha256=ulsXi-qTBSYbWkYTgBbgI1TdAlBc5GY4IqwkOE_79fM,4449
+biolib/biolib_binary_format/utils.py,sha256=JEYJgH3vvf_Iz0rcZjuZ85koex_KByeQaTXgFxDT1rQ,5069
 biolib/biolib_docker_client/__init__.py,sha256=aBfA6mtWSI5dBEfNNMD6bIZzCPloW4ghKm0wqQiljdo,1481
 biolib/biolib_errors.py,sha256=5m4lK2l39DafpoXBImEBD4EPH3ayXBX0JgtPzmGClow,689
 biolib/biolib_logging.py,sha256=J3E5H_LL5k6ZUim2C8gqN7E6lCBZMTpO4tnMpOPwG9U,2854
@@ -44,7 +44,7 @@ biolib/cli/start.py,sha256=TpZq1VHVkLTW1_PyjIGkJg44E3PzxSaGrN2D_rNJL0c,1736
 biolib/compute_node/.gitignore,sha256=GZdZ4g7HftqfOfasFpBC5zV1YQAbht1a7EzcXD6f3zg,45
 biolib/compute_node/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/compute_node/cloud_utils/__init__.py,sha256=VZSScLqaz5tg_gpMvWgwkAu9Qf-vgW_QHRoDOaAmU44,67
-biolib/compute_node/cloud_utils/cloud_utils.py,sha256=ab_RwoVd0LaMox60a17UP0IJytEf8h8lKi7yGRsDqpo,8409
+biolib/compute_node/cloud_utils/cloud_utils.py,sha256=bvteEsy-rZ-AkMaSiM_UdnaE0SNP2U1mF9Ak0qQSscE,8486
 biolib/compute_node/job_worker/__init__.py,sha256=ipdPWaABKYrltxny15e2kK8PWdEE7VzXbkKK6wM_zDk,71
 biolib/compute_node/job_worker/cache_state.py,sha256=N2AxvvgfizKx9P_ysM0GDCmueMUlgcveA4xSdz_Z2IQ,4822
 biolib/compute_node/job_worker/cache_types.py,sha256=4EIF2bohizsuaF61F0ufedBn6zI4SkvclRIFIxhxZuE,891
@@ -70,7 +70,7 @@ biolib/compute_node/webserver/gunicorn_flask_application.py,sha256=jPfR_YvNBekLU
 biolib/compute_node/webserver/webserver.py,sha256=15PkRyhtdtSgFDxa0z78aPO4ciZURsFqJYi-HtUmZF8,6494
 biolib/compute_node/webserver/webserver_types.py,sha256=Vmt1ZDecYhGBVEYWcW1DVxee1DEPqkqyxQzbsObXWbI,420
 biolib/compute_node/webserver/webserver_utils.py,sha256=XWvwYPbWNR3qS0FYbLLp-MDDfVk0QdaAmg3xPrT0H2s,4234
-biolib/compute_node/webserver/worker_thread.py,sha256=JngK_wVADJnrX04KZ99o4BzZWaozZxYl1wQElwkLYYo,9900
+biolib/compute_node/webserver/worker_thread.py,sha256=qNiwUUd6UJG2oFQuP7KCb0cCOTqyTCGUHJSAx7yLko4,10979
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/experiments/experiment.py,sha256=NjJOFktfTbgHNtIDavyQP_uL_-gSGwYHfycybPLJRKU,5939
 biolib/experiments/types.py,sha256=n9GxdFA7cLMfHvLLqLmZzX31ELeSSkMXFoEEdFsdWGY,171
@@ -95,8 +95,8 @@ biolib/utils/cache_state.py,sha256=BFrZlV4XZIueIFzAFiPidX4hmwADKY5Y5ZuqlerF5l0,3
 biolib/utils/multipart_uploader.py,sha256=Bf09MJcIOBwzG8L1i5UeQ2cNcYohxklhhWWAMpnE41I,9671
 biolib/utils/seq_util.py,sha256=QRLYIPg1yM_LF9bFuM-Ow14gTHoG3rOK6CeGHD705qw,2612
 biolib/utils/zip/remote_zip.py,sha256=NCdUnVbGCv7SfXCI-yVU-is_OnyWmLAnVpIdSvo-W4k,23500
-pybiolib-1.1.1325.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.1325.dist-info/METADATA,sha256=Lzqxpfs2PkDJgz9rYsA6Wks49LakITwwD0nJR8-SUfM,1492
-pybiolib-1.1.1325.dist-info/WHEEL,sha256=d2fvjOD7sXsVzChCqf0Ty0JbHKBaLYwDbGQDwQTnJ50,88
-pybiolib-1.1.1325.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.1325.dist-info/RECORD,,
+pybiolib-1.1.1338.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.1338.dist-info/METADATA,sha256=0jW7ZvvbQ4Tv8_9JJr0e5ShMxsFalVv3Cy06wVldzzw,1492
+pybiolib-1.1.1338.dist-info/WHEEL,sha256=d2fvjOD7sXsVzChCqf0Ty0JbHKBaLYwDbGQDwQTnJ50,88
+pybiolib-1.1.1338.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.1338.dist-info/RECORD,,