pybiolib 1.1.1995__py3-none-any.whl → 1.1.2003__py3-none-any.whl

biolib/_internal/data_record/remote_storage_endpoint.py

@@ -1,23 +1,34 @@
+import os
 from datetime import datetime, timedelta
+from urllib.parse import urlparse
 
 from biolib.api import client as api_client
 from biolib.biolib_api_client.lfs_types import LargeFileSystemVersion
 from biolib.biolib_binary_format.utils import RemoteEndpoint
 from biolib.biolib_logging import logger
+from biolib.typing_utils import Optional
 
 
 class DataRecordRemoteStorageEndpoint(RemoteEndpoint):
     def __init__(self, resource_version_uuid: str):
         self._resource_version_uuid: str = resource_version_uuid
-        self._expires_at = None
-        self._presigned_url = None
+        self._expires_at: Optional[datetime] = None
+        self._presigned_url: Optional[str] = None
 
-    def get_remote_url(self):
-        if not self._presigned_url or datetime.utcnow() > self._expires_at:
+    def get_remote_url(self) -> str:
+        if not self._presigned_url or not self._expires_at or datetime.utcnow() > self._expires_at:
             lfs_version: LargeFileSystemVersion = api_client.get(
                 path=f'/lfs/versions/{self._resource_version_uuid}/',
             ).json()
-            self._presigned_url = lfs_version['presigned_download_url']
+
+            app_caller_proxy_job_storage_base_url = os.getenv('BIOLIB_CLOUD_JOB_STORAGE_BASE_URL', '')
+            if app_caller_proxy_job_storage_base_url:
+                # Done to hit App Caller Proxy when downloading from inside an app
+                parsed_url = urlparse(lfs_version['presigned_download_url'])
+                self._presigned_url = f'{app_caller_proxy_job_storage_base_url}{parsed_url.path}?{parsed_url.query}'
+            else:
+                self._presigned_url = lfs_version['presigned_download_url']
+
             self._expires_at = datetime.utcnow() + timedelta(minutes=8)
             logger.debug(
                 f'DataRecord "{self._resource_version_uuid}" fetched presigned URL '

biolib/compute_node/job_worker/executors/docker_executor.py

@@ -356,6 +356,7 @@ class DockerExecutor:
                 cloud_job = self._options['cloud_job']
                 create_container_args['mem_limit'] = f'{cloud_job["reserved_memory_in_bytes"]}b'
                 create_container_args['nano_cpus'] = cloud_job['reserved_cpu_in_nano_shares']
+                create_container_args['pids_limit'] = 10_000
 
                 biolib_identity_user_email: Optional[str] = cloud_job.get('biolib_identity_user_email')
                 if biolib_identity_user_email:

{pybiolib-1.1.1995.dist-info → pybiolib-1.1.2003.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1995
+Version: 1.1.2003
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.1995.dist-info → pybiolib-1.1.2003.dist-info}/RECORD

@@ -4,7 +4,7 @@ biolib/__init__.py,sha256=nfZvVkrHZLvjvvlAvFzhvem9NMfqgmw8NWaCH9HGzew,4045
 biolib/_internal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/_internal/data_record/__init__.py,sha256=1Bk303i3rFet9veS56fIsrBYtT5X3n9vcsYMA6T6c5o,36
 biolib/_internal/data_record/data_record.py,sha256=ctijrrZ-LfUxtwzS8PEVa1VBuBLVWEhmo2yHcEDkC0A,7178
-biolib/_internal/data_record/remote_storage_endpoint.py,sha256=LPq8Lr5FhKF9_o5K-bUdT7TeLe5XFUD0AAeTkNEVZug,1133
+biolib/_internal/data_record/remote_storage_endpoint.py,sha256=hILu0TmFx-ZyDYbWPC4QEPogP0RRVEqwgJc8OEHYp50,1742
 biolib/_internal/fuse_mount/__init__.py,sha256=B_tM6RM2dBw-vbpoHJC4X3tOAaN1H2RDvqYJOw3xFwg,55
 biolib/_internal/fuse_mount/experiment_fuse_mount.py,sha256=08aUdEq_bvqLBft_gSLjOClKDy5sBnMts1RfJf7AP_U,7012
 biolib/_internal/http_client.py,sha256=DdooXei93JKGYGV4aQmzue_oFzvHkozg2UCxgk9dfDM,5081
@@ -63,7 +63,7 @@ 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=Lo7qgOm6uolNyH7QIuLqTY_6RLyPYeAlOk9HzC82U-s,27332
+biolib/compute_node/job_worker/executors/docker_executor.py,sha256=81ltJvSDpCPBgbffnSQF-fiRpk_94sWZWJRcP0IW_5k,27393
 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
@@ -109,8 +109,8 @@ 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-1.1.1995.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.1995.dist-info/METADATA,sha256=DAKK-AVJu-iyW_SwhKYCOsgPLzJjoOV6C1eIZlaThkE,1508
-pybiolib-1.1.1995.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pybiolib-1.1.1995.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.1995.dist-info/RECORD,,
+pybiolib-1.1.2003.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.2003.dist-info/METADATA,sha256=OllzY7bgzHEQu23N9rHAK3GyFKRCycBbpcwD3q0Xjq8,1508
+pybiolib-1.1.2003.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.1.2003.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.2003.dist-info/RECORD,,