pybiolib 1.2.322.dev1__py3-none-any.whl → 1.2.334.dev1__py3-none-any.whl

biolib/_internal/utils/multinode.py

@@ -71,7 +71,7 @@ def run_locally(command_list, args):
         print(f'Error: {result.stderr}')
 
 
-def fasta_batch_records(fasta_file, work_per_batch_min, work_per_residue=1, verbose=False):
+def fasta_batch_records(records, work_per_batch_min, work_per_residue=1, verbose=False):
     """Converts FASTA records to batches of records, based on thresholds"""
 
     def log_batches(batches):
@@ -84,7 +84,7 @@ def fasta_batch_records(fasta_file, work_per_batch_min, work_per_residue=1, verb
             n_seqs, n_res = batch_dict['records'], batch_dict['residues']
             print(f'Batch {i+1}: {n_res} residues from {n_seqs} sequences')
 
-    records = SeqUtil.parse_fasta(fasta_file)
+    # records = SeqUtil.parse_fasta(fasta_file)
 
     batches = []
     batch = []

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.dist-info → pybiolib-1.2.334.dev1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.322.dev1
+Version: 1.2.334.dev1
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.322.dev1.dist-info → pybiolib-1.2.334.dev1.dist-info}/RECORD

@@ -24,7 +24,7 @@ biolib/_internal/types/resource.py,sha256=G-vPkZoe4Um6FPxsQZtRzAlbSW5sDW4NFkbjn2
 biolib/_internal/types/resource_version.py,sha256=sLxViYXloDDUhTDFgjegiQCj097OM1Ih1-uqlC_4ULA,174
 biolib/_internal/types/typing.py,sha256=D4EKKEe7kDx0K6lJi-H_XLtk-8w6nu2fdqn9bvzI-Xo,288
 biolib/_internal/utils/__init__.py,sha256=p5vsIFyu-zYqBgdSMfwW9NC_jk7rXvvCbV4Bzd3As7c,630
-biolib/_internal/utils/multinode.py,sha256=zWrQhcVK5u_xdWX2oIM-D_2fINqNPlqF_h71fu4K8LY,8279
+biolib/_internal/utils/multinode.py,sha256=G0t7dkHtoxIfdCD0vjG8eyQwRxQ0zWazOWZUFQ3hQxw,8278
 biolib/_runtime/runtime.py,sha256=bZQ0m39R9jOBVAtlyvzDnOobKueOAQUCwMUZjDQnO7E,4439
 biolib/api/__init__.py,sha256=mQ4u8FijqyLzjYMezMUUbbBGNB3iFmkNdjXnWPZ7Jlw,138
 biolib/api/client.py,sha256=_kmwaGI_-u7kOeWVCYmo-pD2K1imwEv9n2gNZRb5F-I,3790
@@ -97,7 +97,7 @@ biolib/compute_node/webserver/gunicorn_flask_application.py,sha256=jPfR_YvNBekLU
 biolib/compute_node/webserver/webserver.py,sha256=o4kOAStsqThUtKlnRE-U5TP0JIYntuySDjU7PH310xg,6620
 biolib/compute_node/webserver/webserver_types.py,sha256=2t8EaFKESnves3BA_NBdnS2yAdo1qwamCFHiSt888nE,380
 biolib/compute_node/webserver/webserver_utils.py,sha256=XWvwYPbWNR3qS0FYbLLp-MDDfVk0QdaAmg3xPrT0H2s,4234
-biolib/compute_node/webserver/worker_thread.py,sha256=GRRBUqXdMKvbjyLQhYlqGIbFKeU2iiEXIe5IXi9wgdg,11806
+biolib/compute_node/webserver/worker_thread.py,sha256=jakGi-libQJfD7rcB525XbTVIAmI4uZ-xwvzvqFSWgw,11961
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/experiments/experiment.py,sha256=m7FB7hot8CMOVrNyWGPB6FTkWQJwI0ytpIvtPxfoPME,7684
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
@@ -118,8 +118,8 @@ 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-1.2.322.dev1.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.322.dev1.dist-info/METADATA,sha256=WDLf3UFbGCBrYk9XZwtFOe8DyTiBltMdpI98sWlqaS8,1575
-pybiolib-1.2.322.dev1.dist-info/WHEEL,sha256=IYZQI976HJqqOpQU6PHkJ8fb3tMNBFjg-Cn-pwAbaFM,88
-pybiolib-1.2.322.dev1.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.322.dev1.dist-info/RECORD,,
+pybiolib-1.2.334.dev1.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.334.dev1.dist-info/METADATA,sha256=AXuQRU7aU2ktbCRoVoprdenRGFhL6B5pJ4zQhVH3lu4,1575
+pybiolib-1.2.334.dev1.dist-info/WHEEL,sha256=IYZQI976HJqqOpQU6PHkJ8fb3tMNBFjg-Cn-pwAbaFM,88
+pybiolib-1.2.334.dev1.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.334.dev1.dist-info/RECORD,,