pybiolib 1.1.2097__py3-none-any.whl → 1.1.2112__py3-none-any.whl

biolib/app/app.py

@@ -56,6 +56,7 @@ class BioLibApp:
         result_prefix: Optional[str] = None,
         timeout: Optional[int] = None,
         notify: bool = False,
+        machine_count: Optional[int] = None,
     ) -> Job:
         if not experiment_id:
             experiment = Experiment.get_experiment_in_context()
@@ -85,6 +86,7 @@ class BioLibApp:
             override_command=override_command,
             result_prefix=result_prefix,
             timeout=timeout,
+            requested_machine_count=machine_count,
         )
         if blocking:
             # TODO: Deprecate utils.STREAM_STDOUT and always stream logs by simply calling job.stream_logs()

biolib/biolib_api_client/biolib_job_api.py

@@ -46,6 +46,7 @@ class BiolibJobApi:
             experiment_uuid: Optional[str] = None,
             timeout: Optional[int] = None,
             notify: bool = False,
+            requested_machine_count: Optional[int] = None,
     ):
         data = {
             'app_version_id': app_version_id,
@@ -73,6 +74,9 @@ class BiolibJobApi:
                 'requested_machine': machine
             })
 
+        if requested_machine_count:
+            data.update({'requested_machine_count': requested_machine_count})
+
         if experiment_uuid:
             data['experiment_uuid'] = experiment_uuid
 
@@ -156,6 +160,7 @@ class BiolibJobApi:
             caller_job_uuid: Optional[str] = None,
             requested_timeout_seconds: Optional[int] = None,
             notify: bool = False,
+            requested_machine_count: Optional[int] = None,
     ) -> Dict:
         job_dict: Dict = biolib.api.client.post(
             path='/jobs/create_job_with_data/',
@@ -171,6 +176,7 @@ class BiolibJobApi:
                 'client-version': BIOLIB_PACKAGE_VERSION,
                 'experiment-uuid': experiment_uuid,
                 'requested-machine': requested_machine,
+                'requested-machine-count': str(requested_machine_count) if requested_machine_count else None,
                 'result-name-prefix': result_name_prefix,
                 'requested-timeout-seconds': str(requested_timeout_seconds) if requested_timeout_seconds else None,
                 'notify': 'true' if notify else 'false',

biolib/compute_node/job_worker/executors/docker_executor.py

@@ -270,6 +270,8 @@ class DockerExecutor:
     # TODO: type this method
     def _initialize_docker_container(self, module_input):
         try:
+            job_uuid = self._options['job']['public_id']
+            logger_no_user_data.debug(f'Job "{job_uuid}" initializing Docker container...')
             module = self._options['module']
             logger.debug(f"Initializing docker container with command: {module['command']}")
 
@@ -314,6 +316,7 @@ class DockerExecutor:
                     }
                 )
 
+            logger_no_user_data.debug(f'Job "{job_uuid}" initializing Docker container. Getting IPs for proxies...')
             for proxy in self._options['remote_host_proxies']:
                 proxy_ip = proxy.get_ip_address_on_network(internal_network)
                 if proxy.is_app_caller_proxy:
@@ -332,6 +335,7 @@ class DockerExecutor:
                 else:
                     extra_hosts[proxy.hostname] = proxy_ip
 
+            logger_no_user_data.debug(f'Job "{job_uuid}" initializing Docker container. Constructing container args...')
             create_container_args = {
                 'environment': environment_vars,
                 'extra_hosts': extra_hosts,
@@ -368,9 +372,10 @@ class DockerExecutor:
             if docker_runtime is not None:
                 create_container_args['runtime'] = docker_runtime
 
-            self._docker_container = BiolibDockerClient.get_docker_client().containers.create(**create_container_args)
-
-            logger_no_user_data.debug('Finished initializing docker container')
+            docker_client = BiolibDockerClient.get_docker_client()
+            logger_no_user_data.debug(f'Job "{job_uuid}" initializing Docker container. Creating container...')
+            self._docker_container = docker_client.containers.create(**create_container_args)
+            logger_no_user_data.debug(f'Job "{job_uuid}" finished initializing Docker container.')
         except Exception as exception:
             raise ComputeProcessException(
                 exception, SystemExceptionCodes.FAILED_TO_START_COMPUTE_CONTAINER.value, self._send_system_exception

biolib/jobs/job.py

@@ -412,6 +412,7 @@ class Job:
         result_prefix: Optional[str] = None,
         timeout: Optional[int] = None,
         notify: bool = False,
+        requested_machine_count: Optional[int] = None,
     ) -> 'Job':
         if len(module_input_serialized) < 500_000:
             _job_dict = BiolibJobApi.create_job_with_data(
@@ -424,6 +425,7 @@ class Job:
                 requested_machine=machine,
                 requested_timeout_seconds=timeout,
                 result_name_prefix=result_prefix,
+                requested_machine_count=requested_machine_count,
             )
             return Job(cast(JobDict, _job_dict))
 
@@ -435,6 +437,7 @@ class Job:
             notify=notify,
             override_command=override_command,
             timeout=timeout,
+            requested_machine_count=requested_machine_count,
         )
         JobStorage.upload_module_input(job=job_dict, module_input_serialized=module_input_serialized)
         cloud_job = BiolibJobApi.create_cloud_job(job_id=job_dict['public_id'], result_name_prefix=result_prefix)

{pybiolib-1.1.2097.dist-info → pybiolib-1.1.2112.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.2097
+Version: 1.1.2112
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.2097.dist-info → pybiolib-1.1.2112.dist-info}/RECORD

@@ -21,14 +21,14 @@ biolib/_runtime/runtime.py,sha256=zy9HrE4X5hBqm8doUHkckyflquSBDSXV3REhT2MQGas,27
 biolib/api/__init__.py,sha256=mQ4u8FijqyLzjYMezMUUbbBGNB3iFmkNdjXnWPZ7Jlw,138
 biolib/api/client.py,sha256=9MD1qI52BnRC_QSydFGjyFquwFw0R9dkDfUrjUouuHQ,3490
 biolib/app/__init__.py,sha256=cdPtcfb_U-bxb9iSL4fCEq2rpD9OjkyY4W-Zw60B0LI,37
-biolib/app/app.py,sha256=8AvPYL1W2wxQ7t7BB2KeVU2WPrm3UL6vVuHPGs8g9L0,8388
+biolib/app/app.py,sha256=P2RwaDAskUHzlciuTJUroqUocRwoyOLT6YbgMyCRRDI,8484
 biolib/app/search_apps.py,sha256=K4a41f5XIWth2BWI7OffASgIsD0ko8elCax8YL2igaY,1470
 biolib/biolib_api_client/__init__.py,sha256=E5EMa19wJoblwSdQPYrxc_BtIeRsAuO0L_jQweWw-Yk,182
 biolib/biolib_api_client/api_client.py,sha256=krlSRmmAwtdMMyN1XzQhh1gihB1ERSIVslWQ-dqI1yU,7188
 biolib/biolib_api_client/app_types.py,sha256=FxSr4UqfnMhLe34p8bm02wsC3g1Jz8iaing5tRKDOQI,2442
 biolib/biolib_api_client/auth.py,sha256=kjm0ZHnH3I8so3su2sZbBxNHYp-ZUdrZ5lwQ0K36RSw,949
 biolib/biolib_api_client/biolib_app_api.py,sha256=DndlVxrNTes6DOaWyMINLGZQCRMWVvR7gwt5HVlyf5Y,4240
-biolib/biolib_api_client/biolib_job_api.py,sha256=IpFahcRzm7GNy8DJ-XHYe-x7r4Voba8o22IXw5puHn8,6782
+biolib/biolib_api_client/biolib_job_api.py,sha256=7bKfav3-12ewXkEUoLdCmbWdebW8148kxfGJW9SsXZI,7125
 biolib/biolib_api_client/common_types.py,sha256=RH-1KNHqUF-EkTpfPOSTt5Mq1GPdfju_cqXDesscO1I,123
 biolib/biolib_api_client/job_types.py,sha256=Dl4NhU2xpgpXV-7YIoDf6WL63SLR5bni55OX8x5539M,1300
 biolib/biolib_api_client/lfs_types.py,sha256=joZWP6-sa5_Ug_6xIp5fHAgEo_bqLE3rbleQocZtDcg,339
@@ -68,7 +68,7 @@ biolib/compute_node/job_worker/cache_state.py,sha256=MwjSRzcJJ_4jybqvBL4xdgnDYSI
 biolib/compute_node/job_worker/cache_types.py,sha256=ajpLy8i09QeQS9dEqTn3T6NVNMY_YsHQkSD5nvIHccQ,818
 biolib/compute_node/job_worker/docker_image_cache.py,sha256=ansHIkJIq_EMW1nZNlW-RRLVVeKWTbzNICYaOHpKiRE,7460
 biolib/compute_node/job_worker/executors/__init__.py,sha256=bW6t1qi3PZTlHM4quaTLa8EI4ALTCk83cqcVJfJfJfE,145
-biolib/compute_node/job_worker/executors/docker_executor.py,sha256=81ltJvSDpCPBgbffnSQF-fiRpk_94sWZWJRcP0IW_5k,27393
+biolib/compute_node/job_worker/executors/docker_executor.py,sha256=2H7GooL0oAifPcbie0unatB4fRoHyqbsr6S91uagc_g,27952
 biolib/compute_node/job_worker/executors/docker_types.py,sha256=VhsU1DKtJjx_BbCkVmiPZPH4ROiL1ygW1Y_s1Kbpa2o,216
 biolib/compute_node/job_worker/executors/tars/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/compute_node/job_worker/executors/types.py,sha256=yP5gG39hr-DLnw9bOE--VHi-1arDbIYiGuV1rlTbbHI,1466
@@ -94,7 +94,7 @@ biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuF
 biolib/experiments/experiment.py,sha256=IMjnokTc9ZEKUjpsM_JnFolh9HsLbjXus_xKBb2ypJ8,7219
 biolib/experiments/types.py,sha256=n9GxdFA7cLMfHvLLqLmZzX31ELeSSkMXFoEEdFsdWGY,171
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
-biolib/jobs/job.py,sha256=npnARoP408SXD2UqyzFRJYdEJsP_gHoBh2xQkNegYqg,18884
+biolib/jobs/job.py,sha256=aJck0zl6QTE-70pkHY9tKDctchdJyA-YaCIozrlqGkA,19065
 biolib/jobs/job_result.py,sha256=rALHiKYNaC9lHi_JJqBob1RubzNLwG9Z386kwRJjd2M,5885
 biolib/jobs/types.py,sha256=qhadtH2KDC2WUOOqPiwke0YgtQY4FtuB71Stekq1k48,970
 biolib/runtime/__init__.py,sha256=Fg2ZIAmUegurLKagpBNfRgLcOwR2VZSmXQpb-ryRwI0,505
@@ -111,8 +111,8 @@ 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=jC5WhH63FTD7SLFJbxQGA2hOt9NTwq9zHl_BEec1Z0c,4907
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.1.2097.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.2097.dist-info/METADATA,sha256=-4wEBR8SXfG_VDlLRZR7UgrlKee5VydzL-L6wMKP17Y,1508
-pybiolib-1.1.2097.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pybiolib-1.1.2097.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.2097.dist-info/RECORD,,
+pybiolib-1.1.2112.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.2112.dist-info/METADATA,sha256=zFj4CxOhsy98RLU_W0SYBRreB85CsOhtcAg6UZ_Af4I,1508
+pybiolib-1.1.2112.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.1.2112.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.2112.dist-info/RECORD,,