pybiolib 1.1.1739__py3-none-any.whl → 1.1.1745__py3-none-any.whl

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
 

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

biolib/utils/seq_util.py

@@ -1,5 +1,5 @@
 import re
-from io import BufferedReader
+from io import BufferedIOBase
 from biolib.typing_utils import List, Optional, Dict, Union
 
 allowed_sequence_chars = set("ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789-_.")
@@ -33,7 +33,7 @@ class SeqUtilRecord:
 class SeqUtil:
     @staticmethod
     def parse_fasta(
-        input_file: Union[str, BufferedReader] = None,
+        input_file: Union[str, BufferedIOBase] = None,
         default_header: Optional[str] = None,
         allow_any_sequence_characters: bool = False,
         allow_empty_sequence: bool = False,
@@ -43,14 +43,14 @@ class SeqUtil:
             if file_name:
                 input_file = file_name
             else:
-                raise ValueError("input_file must be a file name (str) or a BufferedReader object")
+                raise ValueError("input_file must be a file name (str) or a BufferedIOBase object")
         if isinstance(input_file, str):
             with open(input_file, 'r') as file_handle:
                 data = file_handle.read().strip()
-        elif isinstance(input_file, BufferedReader):
+        elif isinstance(input_file, BufferedIOBase):
             data = input_file.read().decode('utf-8')
         else:
-            raise ValueError("input_file must be a file name (str) or a BufferedReader object")
+            raise ValueError("input_file must be a file name (str) or a BufferedIOBase object")
         if not data:
             return []
 

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-1.1.1739.dist-info → pybiolib-1.1.1745.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1739
+Version: 1.1.1745
 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-1.1.1739.dist-info → pybiolib-1.1.1745.dist-info}/RECORD

@@ -12,9 +12,9 @@ biolib/app/search_apps.py,sha256=CIanvDebNpMtWck0w4IoR_tRZ6LpSWC8DPxXW2e6Ww4,149
 biolib/biolib_api_client/__init__.py,sha256=E5EMa19wJoblwSdQPYrxc_BtIeRsAuO0L_jQweWw-Yk,182
 biolib/biolib_api_client/api_client.py,sha256=oaLqTb208TLRVW4-h_va734TrVDRD3kLpFJ93cwQTxk,7130
 biolib/biolib_api_client/app_types.py,sha256=vEjkpMwaMfz8MxBBZQfWCkxqT7NXxWocB_Oe9WHjJ_g,2425
-biolib/biolib_api_client/auth.py,sha256=BAXtic6DdaA2QjoDVglnO3PFPoBETQbSraTpIwsZbFc,1267
+biolib/biolib_api_client/auth.py,sha256=kjm0ZHnH3I8so3su2sZbBxNHYp-ZUdrZ5lwQ0K36RSw,949
 biolib/biolib_api_client/biolib_account_api.py,sha256=sHng5jDvSktv6tOLKU8wJRieidY2kLxRU8hI_6ZauXE,210
-biolib/biolib_api_client/biolib_app_api.py,sha256=pr52ARrDeB5ioEA7NAjMdmBYb9V2FPy0_URCwdCRZ0A,4397
+biolib/biolib_api_client/biolib_app_api.py,sha256=vPFoONWh-i-Bg7pm_x50EQqbN9qQFLgNDTkkWKqDUTY,4248
 biolib/biolib_api_client/biolib_job_api.py,sha256=IpFahcRzm7GNy8DJ-XHYe-x7r4Voba8o22IXw5puHn8,6782
 biolib/biolib_api_client/biolib_large_file_system_api.py,sha256=p8QhvQ0aI0NJgyRm7duqDVtPx0zrVaSLKS22ocOafFQ,1038
 biolib/biolib_api_client/common_types.py,sha256=RH-1KNHqUF-EkTpfPOSTt5Mq1GPdfju_cqXDesscO1I,123
@@ -99,10 +99,10 @@ biolib/utils/__init__.py,sha256=AuBhxgZV8-3LWPnewhhYw4isQhPmVs-k55umk8t-r7U,5535
 biolib/utils/app_uri.py,sha256=hOFsTQfA7QbyQyg9ItGdD8VDWBJw0vYMqzLdSiJXmqQ,1857
 biolib/utils/cache_state.py,sha256=BFrZlV4XZIueIFzAFiPidX4hmwADKY5Y5ZuqlerF5l0,3060
 biolib/utils/multipart_uploader.py,sha256=XvGP1I8tQuKhAH-QugPRoEsCi9qvbRk-DVBs5PNwwJo,8452
-biolib/utils/seq_util.py,sha256=P63c1V_T0WU8pbsU4Ib9noxZm2JsvRdgF5WbIsFBEPo,4879
-biolib/utils/zip/remote_zip.py,sha256=NCdUnVbGCv7SfXCI-yVU-is_OnyWmLAnVpIdSvo-W4k,23500
-pybiolib-1.1.1739.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.1739.dist-info/METADATA,sha256=hdjqj_FEqAZbBICI8vKEg1UvGdHyult6DbiMYQ0i1H0,1543
-pybiolib-1.1.1739.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-pybiolib-1.1.1739.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.1739.dist-info/RECORD,,
+biolib/utils/seq_util.py,sha256=3BGUppEaR8asFBxktHCrIW0cMmF23b06PsbDQOoeCDQ,4879
+biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
+pybiolib-1.1.1745.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.1745.dist-info/METADATA,sha256=9o0h8mS0eI03dktYDVNCm_Qjf2JR8EleLReIN1owqgQ,1508
+pybiolib-1.1.1745.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
+pybiolib-1.1.1745.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.1745.dist-info/RECORD,,