pybiolib 1.1.1769__py3-none-any.whl → 1.1.1777__py3-none-any.whl

biolib/compute_node/remote_host_proxy.py

@@ -167,7 +167,7 @@ class RemoteHostProxy:
 
             if utils.IS_RUNNING_IN_CLOUD:
                 config = CloudUtils.get_webserver_config()
-                s3_results_bucket_name = config['s3_general_storage_bucket_name']  # pylint: disable=unsubscriptable-object
+                s3_results_bucket_name = config['s3_general_storage_bucket_name']
                 s3_results_base_url = f'https://{s3_results_bucket_name}.s3.amazonaws.com'
             else:
                 if base_url in ('https://biolib.com', 'https://staging-elb.biolib.com'):
@@ -207,6 +207,12 @@ http {{
         default    "";
     }}
 
+    map $request_method $bearer_token_on_post_and_get {{
+        POST       "{bearer_token}";
+        GET        "{bearer_token}";
+        default    "";
+    }}
+
     server {{
         listen       80;
         resolver 127.0.0.11 valid=30s;
@@ -283,7 +289,7 @@ http {{
 
         location /api/lfs/ {{
             proxy_pass               {base_url}/api/lfs/;
-            proxy_set_header         authorization {'$bearer_token_on_post' if self._can_push_data_record_for_user else '""'};
+            proxy_set_header         authorization {'$bearer_token_on_post_and_get' if self._can_push_data_record_for_user else '""'};
             proxy_set_header         cookie "";
             proxy_ssl_server_name    on;
         }}

biolib/lfs/utils.py

@@ -13,7 +13,7 @@ from biolib.app import BioLibApp
 from biolib.biolib_api_client.biolib_account_api import BiolibAccountApi
 from biolib.biolib_api_client.biolib_large_file_system_api import BiolibLargeFileSystemApi
 from biolib.biolib_api_client import BiolibApiClient
-from biolib.biolib_api_client.lfs_types import LargeFileSystem
+from biolib.biolib_api_client.lfs_types import LargeFileSystem, LargeFileSystemVersion
 from biolib.biolib_logging import logger
 from biolib.biolib_errors import BioLibError
 from biolib.typing_utils import List, Tuple, Iterator, Optional
@@ -111,7 +111,7 @@ def create_large_file_system(lfs_uri: str) -> None:
             path='/lfs/',
             data={
                 'account_handle': uri_parsed['account_handle_normalized'],
-                'name': uri_parsed['app_name_normalized'],
+                'name': uri_parsed['app_name'],
             },
         )
         lfs: LargeFileSystem = response.json()
@@ -132,8 +132,6 @@ def push_large_file_system(lfs_uri: str, input_dir: str, chunk_size_in_mb: Optio
     if os.path.realpath(input_dir) == '/':
         raise BioLibError('Pushing your root directory is not possible')
 
-    lfs_resource = BioLibApp(lfs_uri)
-
     original_working_dir = os.getcwd()
     os.chdir(input_dir)
     files_to_zip, data_size_in_bytes = get_files_and_size_of_directory(directory=os.getcwd())
@@ -155,9 +153,15 @@ def push_large_file_system(lfs_uri: str, input_dir: str, chunk_size_in_mb: Optio
     data_size_in_mb = round(data_size_in_bytes / 10 ** 6)
     print(f'Zipping {len(files_to_zip)} files, in total ~{data_size_in_mb}mb of data')
 
-    lfs_resource_version = BiolibLargeFileSystemApi.create_version(resource_uuid=lfs_resource.uuid)
-    lfs_resource_version_uuid = lfs_resource_version['uuid']
+    runtime_job_data = _RuntimeJobData.get()
+    if runtime_job_data:
+        response = api.client.post(path='/lfs/versions/', data={'resource_uri': lfs_uri})
+        lfs_resource_version: LargeFileSystemVersion = response.json()
+    else:
+        lfs_resource = BioLibApp(lfs_uri)
+        lfs_resource_version = BiolibLargeFileSystemApi.create_version(resource_uuid=lfs_resource.uuid)
 
+    lfs_resource_version_uuid = lfs_resource_version['uuid']
     iterable_zip_stream = get_iterable_zip_stream(files=files_to_zip, chunk_size=chunk_size_in_bytes)
 
     multipart_uploader = utils.MultiPartUploader(

biolib/utils/app_uri.py

@@ -13,6 +13,7 @@ class SemanticVersion(TypedDict):
 class AppUriParsed(TypedDict):
     account_handle_normalized: str
     app_name_normalized: str
+    app_name: str
     resource_name_prefix: Optional[str]
     version: Optional[SemanticVersion]
 
@@ -42,6 +43,7 @@ def parse_app_uri(uri: str) -> AppUriParsed:
         resource_name_prefix=resource_name_prefix.lower() if resource_name_prefix is not None else 'biolib.com',
         account_handle_normalized=account_handle_normalized,
         app_name_normalized=app_name_normalized,
+        app_name=app_name if app_name is not None else account_handle_normalized,
         version=None if not matches.group('version') else SemanticVersion(
             major=int(matches.group('major')),
             minor=int(matches.group('minor')),

{pybiolib-1.1.1769.dist-info → pybiolib-1.1.1777.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1769
+Version: 1.1.1777
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.1769.dist-info → pybiolib-1.1.1777.dist-info}/RECORD

@@ -68,7 +68,7 @@ biolib/compute_node/job_worker/large_file_system.py,sha256=XXqRlVtYhs-Ji9zQGIk5K
 biolib/compute_node/job_worker/mappings.py,sha256=Z48Kg4nbcOvsT2-9o3RRikBkqflgO4XeaWxTGz-CNvI,2499
 biolib/compute_node/job_worker/utilization_reporter_thread.py,sha256=7tm5Yk9coqJ9VbEdnO86tSXI0iM0omwIyKENxdxiVXk,8575
 biolib/compute_node/job_worker/utils.py,sha256=wgxcIA8yAhUPdCwyvuuJ0JmreyWmmUoBO33vWtG60xg,1282
-biolib/compute_node/remote_host_proxy.py,sha256=SAp8H-mlNLF5njISF6LTXhSnO9-l5KATiABk-06lS8k,14520
+biolib/compute_node/remote_host_proxy.py,sha256=skBwx6LsMsFfypkxpvL-PqgsjCQbUVTUjlXeKc-VkAw,14648
 biolib/compute_node/socker_listener_thread.py,sha256=T5_UikA3MB9bD5W_dckYLPTgixh72vKUlgbBvj9dbM0,1601
 biolib/compute_node/socket_sender_thread.py,sha256=YgamPHeUm2GjMFGx8qk-99WlZhEs-kAb3q_2O6qByig,971
 biolib/compute_node/utils.py,sha256=M7i_WTyxbFM3Lri9RWZ_8FeQNYrQIWpKGLfp2I55oeY,4677
@@ -87,7 +87,7 @@ biolib/jobs/job_result.py,sha256=8GasUmUXD8SjUYrE2N-HrDx7-AI6TEkFONH8H91t01Q,491
 biolib/jobs/types.py,sha256=4OAvlhOKANzFMrZDd-mhXpEd8RaKcx8sPneZUoWhJ2U,970
 biolib/lfs/__init__.py,sha256=wspftSqe_x7xPMZbeW8mcIBuxbHFCiFI3V4TuZU4nZ4,193
 biolib/lfs/cache.py,sha256=pQS2np21rdJ6I3DpoOutnzPHpLOZgUIS8TMltUJk_k4,2226
-biolib/lfs/utils.py,sha256=YUFZlGABMfuOA0BwZ8JGOd-OKNGQVUElLP_4CHe4zyw,10461
+biolib/lfs/utils.py,sha256=tyCVRJs-7haykck_iND7HQ6dZ3pdxs-uDu96YSCLP4Y,10722
 biolib/runtime/__init__.py,sha256=WyuNnkzj1r-Sx4J-xWzp3US2oo9m5aIuCOYRmjlZ3ug,44
 biolib/runtime/results.py,sha256=OEtDFb5Auiubh6EClT9L_wMzfRpehIfRwj-8MSVDoz4,522
 biolib/sdk/__init__.py,sha256=vqqE2Sf3gLySkaJv8VgWtPRkYMi9hOf66y9Ay2waYVE,1339
@@ -98,13 +98,13 @@ biolib/typing_utils.py,sha256=krMhxB3SedVQA3HXIrC7DBXWpHKWN5JNmXGcSrrysOc,263
 biolib/user/__init__.py,sha256=Db5wtxLfFz3ID9TULSSTo77csw9tO6RtxMRvV5cqKEE,39
 biolib/user/sign_in.py,sha256=CvHBgoYjg5d5CL9etVopns_g1pImgW8mQH3zAjpe1Ik,2061
 biolib/utils/__init__.py,sha256=fwjciJyJicvYyZcVTzfDBgD0SKY13DeXqvTeG4qZIy8,5548
-biolib/utils/app_uri.py,sha256=hOFsTQfA7QbyQyg9ItGdD8VDWBJw0vYMqzLdSiJXmqQ,1857
+biolib/utils/app_uri.py,sha256=qkI5IsnOfnjKPRBds644FMiajeB074svb7GztoHKb04,1957
 biolib/utils/cache_state.py,sha256=GaGPxQ1GfrBL6Mzo_HJPpmZCd_CbUDN_l_C5frQ5Sfs,3092
 biolib/utils/multipart_uploader.py,sha256=XvGP1I8tQuKhAH-QugPRoEsCi9qvbRk-DVBs5PNwwJo,8452
 biolib/utils/seq_util.py,sha256=3BGUppEaR8asFBxktHCrIW0cMmF23b06PsbDQOoeCDQ,4879
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.1.1769.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.1769.dist-info/METADATA,sha256=KXli3IcKBh46aLip_NXxYFBYM6frmXZaid1fZATYEnw,1508
-pybiolib-1.1.1769.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pybiolib-1.1.1769.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.1769.dist-info/RECORD,,
+pybiolib-1.1.1777.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.1777.dist-info/METADATA,sha256=f64jPn9vmTg73YM_JZ_n7XxnCEzAgBqP-WUz4u8E0M4,1508
+pybiolib-1.1.1777.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.1.1777.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.1777.dist-info/RECORD,,