pybiolib 1.1.1995__tar.gz → 1.1.2003__tar.gz

{pybiolib-1.1.1995 → pybiolib-1.1.2003}/PKG-INFO

@@ -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 → pybiolib-1.1.2003}/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 '

{pybiolib-1.1.1995 → pybiolib-1.1.2003}/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 → pybiolib-1.1.2003}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.1.1995"
+version = "1.1.2003"
 description = "BioLib Python Client"
 readme = "README.md"
 license = "MIT"