pybiolib 1.1.1741__tar.gz → 1.1.1747__tar.gz

{pybiolib-1.1.1741 → pybiolib-1.1.1747}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1741
+Version: 1.1.1747
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT
@@ -25,7 +25,6 @@ Requires-Dist: flask (>=2.0.1) ; extra == "compute-node"
 Requires-Dist: gunicorn (>=20.1.0) ; extra == "compute-node"
 Requires-Dist: importlib-metadata (>=1.6.1)
 Requires-Dist: pyyaml (>=5.3.1)
-Requires-Dist: requests (>=2.25.1)
 Requires-Dist: rich (>=12.4.4)
 Requires-Dist: typing_extensions (>=3.10.0) ; python_version < "3.8"
 Description-Content-Type: text/markdown

{pybiolib-1.1.1741 → pybiolib-1.1.1747}/biolib/biolib_api_client/auth.py

@@ -1,20 +1,8 @@
-from requests.auth import AuthBase  # type: ignore
-
 from biolib import api
 from biolib.biolib_api_client.api_client import UserTokens
 from biolib.typing_utils import TypedDict, Literal
 
 
-class BearerAuth(AuthBase):
-    def __init__(self, access_token=None):
-        self.access_token = access_token
-
-    def __call__(self, req):
-        if self.access_token:
-            req.headers['Authorization'] = 'Bearer ' + self.access_token
-        return req
-
-
 class AuthChallengeCreate(TypedDict):
     token: str
 

{pybiolib-1.1.1741 → pybiolib-1.1.1747}/biolib/biolib_api_client/biolib_app_api.py

@@ -4,14 +4,14 @@ import re
 import os
 import subprocess
 
-from requests.exceptions import HTTPError
-
 import biolib.api
 from biolib import biolib_errors
+from biolib._internal.http_client import HttpError
 from biolib.typing_utils import Optional
 from biolib.biolib_api_client import AppGetResponse
 from biolib.biolib_logging import logger
 
+
 def encode_multipart(data, files):
     boundary = f'----------{random.randint(0, 1000000000)}'
     line_array = []
@@ -76,13 +76,10 @@ class BiolibAppApi:
             app_response: AppGetResponse = response.json()
             return app_response
 
-        except HTTPError as error:
-            if error.response.status_code == 404:
+        except HttpError as error:
+            if error.code == 404:
                 raise biolib_errors.NotFound(f'Application {uri} not found.') from None
 
-            if error.response.status_code == 400:
-                raise biolib_errors.BioLibError(error.response.content.decode()) from None
-
             raise error
 
     @staticmethod

{pybiolib-1.1.1741 → pybiolib-1.1.1747}/biolib/compute_node/cloud_utils/cloud_utils.py

@@ -68,7 +68,7 @@ class CloudUtils:
         return CloudUtils._webserver_config
 
     @staticmethod
-    def deregister() -> None:
+    def deregister(error: Optional[str] = None) -> None:
         if utils.IS_RUNNING_IN_CLOUD:
             config = CloudUtils.get_webserver_config()
             try:
@@ -78,6 +78,7 @@ class CloudUtils:
                     data={
                         'auth_token': config['compute_node_info']['auth_token'],
                         'public_id': config['compute_node_info']['public_id'],
+                        'error': error,
                     },
                 )
             except BaseException as error:

{pybiolib-1.1.1741 → pybiolib-1.1.1747}/biolib/compute_node/webserver/worker_thread.py

@@ -199,7 +199,7 @@ class WorkerThread(threading.Thread):
                 logger_no_user_data.error(f'Job {self._job_uuid} worker process did not exit within 10 seconds')
                 if utils.IS_RUNNING_IN_CLOUD:
                     logger_no_user_data.error('Deregistering compute node...')
-                    CloudUtils.deregister()
+                    CloudUtils.deregister(error='job_cleanup_timed_out')
                     deregistered_due_to_error = True
 
         # Delete result as error occurred
@@ -249,7 +249,7 @@ class WorkerThread(threading.Thread):
 
         if utils.IS_RUNNING_IN_CLOUD:
             if deregistered_due_to_error:
-                CloudUtils.shutdown() # shutdown now
+                CloudUtils.shutdown()  # shutdown now
             else:
                 webserver_utils.update_auto_shutdown_time()
 

{pybiolib-1.1.1741 → pybiolib-1.1.1747}/biolib/utils/zip/remote_zip.py

@@ -9,14 +9,15 @@ https://github.com/uktrade/stream-unzip
 import io
 import zipfile
 
-import requests
-
 from functools import partial
 from struct import Struct
 import zlib
 
 __all__ = ['RemoteIOError', 'RemoteZip']
 
+from biolib._internal.http_client import HttpClient
+
+
 class RemoteZipError(Exception):
     pass
 
@@ -152,8 +153,7 @@ class RemoteIO(io.IOBase):
 
 
 class RemoteZip(zipfile.ZipFile):
-    def __init__(self, url, initial_buffer_size=64*1024, **kwargs):
-        self.kwargs = kwargs
+    def __init__(self, url, initial_buffer_size=64*1024):
         self.url = url
 
         rio = RemoteIO(self.fetch_fun, initial_buffer_size)
@@ -191,22 +191,14 @@ class RemoteZip(zipfile.ZipFile):
             return "bytes=%s%s" % (range_min, '' if range_min < 0 else '-')
         return "bytes=%s-%s" % (range_min, range_max)
 
-    @staticmethod
-    def request(url, range_header, kwargs):
-        kwargs['headers'] = headers = dict(kwargs.get('headers', {}))
-        headers['Range'] = range_header
-        res = requests.get(url, stream=True, **kwargs)
-        res.raise_for_status()
-        if 'Content-Range' not in res.headers:
-            raise RangeNotSupported("The server doesn't support range requests")
-        return res.raw, res.headers
-
     def fetch_fun(self, data_range, stream=False):
         range_header = self.make_header(*data_range)
-        kwargs = dict(self.kwargs)
         try:
-            res, headers = self.request(self.url, range_header, kwargs)
-            return self.make_buffer(res, headers['Content-Range'], stream=stream)
+            response = HttpClient.request(url=self.url, headers={'Range': range_header})
+            if 'Content-Range' not in response.headers:
+                raise RangeNotSupported("The server doesn't support range requests")
+
+            return self.make_buffer(io.BytesIO(response.content), response.headers['Content-Range'], stream=False)
         except IOError as e:
             raise RemoteIOError(str(e))
 

{pybiolib-1.1.1741 → pybiolib-1.1.1747}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.1.1741"
+version = "1.1.1747"
 description = "BioLib Python Client"
 readme = "README.md"
 license = "MIT"
@@ -31,7 +31,6 @@ docker = ">=5.0.3"
 importlib-metadata = ">=1.6.1"
 python = "^3.6.3"
 pyyaml = ">=5.3.1"
-requests = ">=2.25.1"
 rich = ">=12.4.4"
 typing_extensions = { version = ">=3.10.0", python = "<3.8" }
 
@@ -50,7 +49,6 @@ pytest-timeout = "^2.1.0"
 types-click = "==7.1.8"
 types-Flask = "==1.1.1"
 types-PyYAML = "==5.4.3"
-types-requests = "==2.25.0"
 types-termcolor = "==0.1.1"
 
 [build-system]