pybiolib 1.1.1608__tar.gz → 1.1.1629__tar.gz

{pybiolib-1.1.1608 → pybiolib-1.1.1629}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1608
+Version: 1.1.1629
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.1608 → pybiolib-1.1.1629}/biolib/api/__init__.py

@@ -1,5 +1,5 @@
+from biolib._internal.http_client import HttpClient
 from .client import ApiClient as _ApiClient
-from .http_client import HttpClient
 
 _client = _ApiClient()
 client = _client

{pybiolib-1.1.1608 → pybiolib-1.1.1629}/biolib/api/client.py

@@ -2,7 +2,7 @@ from urllib.parse import urljoin, urlencode
 
 from biolib.typing_utils import Dict, Optional, Union
 from biolib.biolib_api_client import BiolibApiClient as DeprecatedApiClient
-from .http_client import HttpResponse, HttpClient
+from biolib._internal.http_client import HttpResponse, HttpClient
 
 OptionalHeaders = Optional[Dict[str, Union[str, None]]]
 

{pybiolib-1.1.1608 → pybiolib-1.1.1629}/biolib/biolib_api_client/api_client.py

@@ -6,7 +6,7 @@ import os
 from datetime import datetime, timezone
 from json.decoder import JSONDecodeError
 
-import requests
+from biolib._internal.http_client import HttpClient
 from biolib.typing_utils import Optional
 from biolib.biolib_errors import BioLibError
 from biolib.biolib_logging import logger, logger_no_user_data
@@ -67,20 +67,19 @@ class _ApiClient:
                 return
 
         # TODO: Implement nicer error handling
-        response = requests.post(
-            url=f'{self.base_url}/api/user/token/refresh/',
-            timeout=5,
-            json={'refresh': self.refresh_token},
-        )
+        try:
+            response = HttpClient.request(method='POST',
+                                        url=f'{self.base_url}/api/user/token/refresh/',
+                                        data={'refresh': self.refresh_token})
+        except Exception as exception:
+            logger.error('Sign in with refresh token failed')
+            raise exception
+
         try:
             response_dict = response.json()
         except JSONDecodeError as error:
             logger.error('Could not decode response from server as JSON:')
             raise BioLibError(response.text) from error
-        if not response.ok:
-            error_message = f'Sign in with refresh token failed: {response_dict.get("detail")}'
-            logger.error(error_message)
-            raise BioLibError(error_message)
 
         self.access_token = response_dict['access']
 
@@ -111,22 +110,21 @@ class _ApiClient:
 
     def sign_in_with_api_token(self, api_token: str) -> None:
         logger_no_user_data.debug('ApiClient: Signing in with BIOLIB_TOKEN...')
-        response = requests.post(
-            url=f'{self.base_url}/api/user/api_tokens/exchange/',
-            json={'token': api_token},
-            timeout=5,
-        )
+        try:
+            response = HttpClient.request(method='POST',
+                                        url=f'{self.base_url}/api/user/api_tokens/exchange/',
+                                        data={'token': api_token})
+        except Exception as exception:
+            logger.error('Sign in with API token failed')
+            raise exception
         try:
             json_response = response.json()
         except JSONDecodeError as error:
             logger.error('Could not decode response from server as JSON')
             raise BioLibError(response.text) from error
-        if not response.ok:
-            logger.error('Sign in with API token failed')
-            raise BioLibError(json_response['detail'])
-        else:
-            self.access_token = json_response['access_token']
-            self.refresh_token = json_response['refresh_token']
+
+        self.access_token = json_response['access_token']
+        self.refresh_token = json_response['refresh_token']
 
     @staticmethod
     def _decode_jwt_without_checking_signature(jwt: str) -> Dict[str, Any]:

{pybiolib-1.1.1608 → pybiolib-1.1.1629}/biolib/biolib_binary_format/utils.py

@@ -1,7 +1,7 @@
 from abc import ABC, abstractmethod
 import io
 
-import biolib.api
+from biolib._internal.http_client import HttpClient
 
 
 class RemoteEndpoint(ABC):
@@ -77,7 +77,7 @@ class RemoteIndexableBuffer(IndexableBuffer):
             return bytes(0)
 
         end = start + length - 1
-        response = biolib.api.HttpClient.request(
+        response = HttpClient.request(
             url=self._endpoint.get_remote_url(),
             headers={'range': f'bytes={start}-{end}'},
         )

{pybiolib-1.1.1608 → pybiolib-1.1.1629}/biolib/compute_node/job_worker/executors/docker_executor.py

@@ -1,4 +1,5 @@
 import json
+import subprocess
 import tempfile
 import time
 import tarfile
@@ -490,6 +491,34 @@ class DockerExecutor:
                 self._send_system_exception,
             ) from exception
 
+    def _get_container_upper_dir_path(self) -> Optional[str]:
+        data = self._container.attrs['GraphDriver']['Data']
+        upper_dir: Optional[str] = data['UpperDir'] if data else None
+
+        if not upper_dir and utils.IS_RUNNING_IN_CLOUD:
+            # Get upperdir from containerd ctr CLI
+            result = subprocess.run(
+                args=[
+                    'ctr',
+                    '--namespace', 'moby',
+                    'snapshots',
+                    '--snapshotter', 'nydus',
+                    'mounts',
+                    '/some_arbitrary_path',
+                    str(self._container.id),
+                ],
+                check=False,
+                capture_output=True,
+            )
+            if result.returncode == 0:
+                match = re.search(r'upperdir=([^,]+)', result.stdout.decode('utf-8'))
+                upper_dir = match.group(1) if match else None
+
+        if upper_dir and os.path.exists(upper_dir):
+            return upper_dir
+
+        return None
+
     def _get_changed_files_in_docker_container(self, pre_start_diff: List[Dict]) -> List[FileInContainer]:
         from_mappings = [mapping['from_path'] for mapping in self._options['module']['output_files_mappings']]
         pre_start_diff_paths = [obj['Path'] for obj in pre_start_diff]
@@ -516,11 +545,10 @@ class DockerExecutor:
                     return True
             return False
 
-        data = self._container.attrs['GraphDriver']['Data']
-        overlay_upper_dir_path = data['UpperDir'] if data and os.path.exists(data['UpperDir']) else None
+        overlay_upper_dir_path = self._get_container_upper_dir_path()
         if not overlay_upper_dir_path:
             logger_no_user_data.debug(
-                'Docker Overlay2 UpperDir not available. Falling back to container.get_archive() for file extraction'
+                'Docker UpperDir not available. Falling back to container.get_archive() for file extraction'
             )
 
         logger.debug(f'overlay_upper_dir_path={overlay_upper_dir_path}')

{pybiolib-1.1.1608 → pybiolib-1.1.1629}/biolib/jobs/job.py

@@ -8,6 +8,7 @@ from urllib.parse import urlparse
 
 import requests
 from biolib import api, utils
+from biolib._internal.http_client import HttpClient
 from biolib.biolib_api_client.biolib_job_api import BiolibJobApi
 from biolib.biolib_binary_format import LazyLoadedFile, ModuleOutputV2, ModuleInput, ModuleInputDict
 from biolib.biolib_binary_format.stdout_and_stderr import StdoutAndStderr
@@ -302,7 +303,9 @@ class Job:
 
     def _print_full_logs(self, node_url: str) -> None:
         try:
-            response_json = api.HttpClient.request(url=f'{node_url}/v1/job/{self._uuid}/status/?logs=full').json()
+            response_json = HttpClient.request(
+                url=f'{node_url}/v1/job/{self._uuid}/status/?logs=full'
+            ).json()
         except Exception as error:
             logger.error(f'Could not get full streamed logs due to: {error}')
             raise BioLibError from error
@@ -331,7 +334,9 @@ class Job:
     def _get_job_status_from_compute_node(self, compute_node_url):
         for _ in range(15):
             try:
-                return api.HttpClient.request(url=f'{compute_node_url}/v1/job/{self._uuid}/status/').json()
+                return HttpClient.request(
+                    url=f'{compute_node_url}/v1/job/{self._uuid}/status/'
+                ).json()
             except Exception:  # pylint: disable=broad-except
                 cloud_job = self._get_cloud_job()
                 logger.debug("Failed to get status from compute node, retrying...")

{pybiolib-1.1.1608 → pybiolib-1.1.1629}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.1.1608"
+version = "1.1.1629"
 description = "BioLib Python Client"
 readme = "README.md"
 license = "MIT"