pybiolib 1.1.2199__py3-none-any.whl → 1.1.2208__py3-none-any.whl

biolib/_internal/data_record/data_record.py

@@ -83,6 +83,8 @@ def verify_schema(specification: SqliteV1DatabaseSchema, actual_schema: SqliteV1
 
 def get_data_record_state_from_uri(uri) -> 'DataRecordVersionInfo':
     app_response: AppGetResponse = api_client.get(path='/app/', params={'uri': uri}).json()
+    if app_response['app']['type'] != 'data-record':
+        raise Exception(f'Resource "{uri}" is not a Data Record')
     return DataRecordVersionInfo(
         resource_uri=app_response['app_version']['app_uri'],
         resource_uuid=app_response['app']['public_id'],

biolib/biolib_api_client/app_types.py

@@ -32,6 +32,7 @@ class App(TypedDict):
     public_id: str
     state: str
     resource_uri: str
+    type: str
 
 
 class AppGetResponse(TypedDict):

biolib/compute_node/job_worker/job_storage.py

@@ -47,8 +47,21 @@ class JobStorage:
         module_output_path = os.path.join(job_temporary_dir, JobStorage.module_output_file_name)
         module_output_size = os.path.getsize(module_output_path)
 
+        # Calculate chunk size based on max chunk count of 10_000, using 9_000 to be on the safe side
+        max_chunk_count = 9_000
+        min_chunk_size_bytes = 50_000_000
+        chunk_size_in_bytes = max(min_chunk_size_bytes, module_output_size // max_chunk_count)
+
+        logger_no_user_data.debug(
+            f'Job "{job_uuid}" uploading result of size {module_output_size} bytes '
+            f'with chunk size of {chunk_size_in_bytes} bytes...'
+        )
+
         with open(module_output_path, mode='rb') as module_output_file:
-            module_output_iterator = get_chunk_iterator_from_file_object(module_output_file)
+            module_output_iterator = get_chunk_iterator_from_file_object(
+                file_object=module_output_file,
+                chunk_size_in_bytes=chunk_size_in_bytes,
+            )
             multipart_uploader = JobStorage._get_module_output_uploader(job_uuid)
             multipart_uploader.upload(
                 payload_iterator=module_output_iterator,

{pybiolib-1.1.2199.dist-info → pybiolib-1.1.2208.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.2199
+Version: 1.1.2208
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.2199.dist-info → pybiolib-1.1.2208.dist-info}/RECORD

@@ -4,7 +4,7 @@ biolib/__init__.py,sha256=_tThyzISH81yS9KXP_X3qEiKXmsIp5XOBcJIODfLVnc,4338
 biolib/_data_record/data_record.py,sha256=CoyYRse5VdUBhQzzPfR9BkytgOsM-IZxkfMX1kyRnPk,12589
 biolib/_internal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/_internal/data_record/__init__.py,sha256=fGdME6JGRU_2VxpJbYpGXYndjN-feUkmKY4fuMyq3cg,76
-biolib/_internal/data_record/data_record.py,sha256=YmaAABR57goDCE8-rKb2j0FPMSbDtRPCm_HhT3mM074,4299
+biolib/_internal/data_record/data_record.py,sha256=g_-jdy5-Zem3dthwxJj2OuQqkDGTyc-iGqN1rtYYD1A,4418
 biolib/_internal/data_record/remote_storage_endpoint.py,sha256=eCptuZ4DMAPnaNCVDvpWXwXGI6Jac9U1N5dqU8Cj95Q,1732
 biolib/_internal/file_utils.py,sha256=4jT6j7bB21c0JNn5BfnyWQib_zt0CVtJ_TiOFOStRcE,2604
 biolib/_internal/fuse_mount/__init__.py,sha256=B_tM6RM2dBw-vbpoHJC4X3tOAaN1H2RDvqYJOw3xFwg,55
@@ -31,7 +31,7 @@ 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=ciNx4ybpyKG5LEf4KQdGEz13r0jTxImyQat4_HDecD0,7373
-biolib/biolib_api_client/app_types.py,sha256=FxSr4UqfnMhLe34p8bm02wsC3g1Jz8iaing5tRKDOQI,2442
+biolib/biolib_api_client/app_types.py,sha256=1sXz9XnLRKNALMglNdTbew7AL6OkcUan0MPdj4xQLis,2456
 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=7bKfav3-12ewXkEUoLdCmbWdebW8148kxfGJW9SsXZI,7125
@@ -80,7 +80,7 @@ biolib/compute_node/job_worker/executors/tars/__init__.py,sha256=47DEQpj8HBSa-_T
 biolib/compute_node/job_worker/executors/types.py,sha256=yP5gG39hr-DLnw9bOE--VHi-1arDbIYiGuV1rlTbbHI,1466
 biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py,sha256=_cvEiZbOwfkv6fYmfrvdi_FVviIEYr_dSClQcOQaUWM,1198
 biolib/compute_node/job_worker/job_max_runtime_timer_thread.py,sha256=K_xgz7IhiIjpLlXRk8sqaMyLoApcidJkgu29sJX0gb8,1174
-biolib/compute_node/job_worker/job_storage.py,sha256=LNkklckDLbYgCHsK5FGrEK75Kw-H4f4JcTCAtuE9His,4035
+biolib/compute_node/job_worker/job_storage.py,sha256=lScHI3ubcHKagSEW243tgbIWXUfbWDHDjEOPMvXxJE8,4603
 biolib/compute_node/job_worker/job_worker.py,sha256=fuWoYJo9HOqLmWl8yeCXh0mhT4ebbkrWac-BVb58khs,28842
 biolib/compute_node/job_worker/large_file_system.py,sha256=XXqRlVtYhs-Ji9zQGIk5KQPXFO_Q5jJH0nnlw4GkeMY,10461
 biolib/compute_node/job_worker/mappings.py,sha256=Z48Kg4nbcOvsT2-9o3RRikBkqflgO4XeaWxTGz-CNvI,2499
@@ -116,8 +116,8 @@ 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=ZQFcaE37B2dtucN2zDjOmdya_X0ITc1zBFZJNQY13XA,5183
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.1.2199.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.2199.dist-info/METADATA,sha256=trNj9xrA58S69VzTCtCLri0Xdbchjqaou0EPizVAlv0,1508
-pybiolib-1.1.2199.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pybiolib-1.1.2199.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.2199.dist-info/RECORD,,
+pybiolib-1.1.2208.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.2208.dist-info/METADATA,sha256=2yI-Ekgvu56nB9gdvkhAlulW1Ww7eh3fgQU8CPaIyJU,1508
+pybiolib-1.1.2208.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.1.2208.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.2208.dist-info/RECORD,,