pybiolib 1.1.1437__py3-none-any.whl → 1.1.1445__py3-none-any.whl

biolib/api/client.py

@@ -56,7 +56,6 @@ class ApiClient:
     ) -> BioLibHTTPResponse:
         url = self._get_absolute_url(path, query_params=params)
         req = urllib.request.Request(url, headers=self._get_headers(headers, authenticate))
-
         retries = 10
         for retry_count in range(retries):
             if retry_count > 0:
@@ -74,12 +73,13 @@ class ApiClient:
 
             except urllib.error.URLError as error:
                 if isinstance(error.reason, socket.timeout):
-                    logger_no_user_data.debug(f'HTTP POST request failed with read timeout for "{path}"')
+                    logger_no_user_data.debug(f'HTTP GET request failed with read timeout for "{path}"')
                 continue
 
         raise Exception(f'HTTP GET request failed after {retries} retries for "{url}"')
 
-    def post(self, path: str, data: Union[Dict, bytes], headers: OptionalHeaders = None) -> BioLibHTTPResponse:
+    def post(self, path: str, data: Optional[Union[Dict, bytes]] = None,
+             headers: OptionalHeaders = None) -> BioLibHTTPResponse:
         retries = 3
         for retry_count in range(retries):
             if retry_count > 0:

biolib/biolib_api_client/auth.py

@@ -1,9 +1,7 @@
-import requests
 from requests.auth import AuthBase  # type: ignore
 
-from biolib.biolib_api_client import BiolibApiClient
+from biolib import api
 from biolib.biolib_api_client.api_client import UserTokens
-from biolib.biolib_errors import BioLibError
 from biolib.typing_utils import TypedDict, Literal
 
 
@@ -33,27 +31,16 @@ class BiolibAuthChallengeApi:
 
     @staticmethod
     def create_auth_challenge() -> AuthChallengeCreate:
-        response = requests.post(
-            url=f'{BiolibApiClient.get().base_url}/api/user/auth_challenges/',
-            timeout=5,
-        )
-
-        if not response.ok:
-            raise BioLibError(response.content.decode())
-
+        response = api._client.post(path='/user/auth_challenges/')  # pylint: disable=protected-access
         response_dict: AuthChallengeCreate = response.json()
         return response_dict
 
     @staticmethod
     def get_auth_challenge_status(token: str) -> AuthChallengeStatus:
-        response = requests.get(
-            url=f'{BiolibApiClient.get().base_url}/api/user/auth_challenges/',
+        response = api._client.get(  # pylint: disable=protected-access
+            path='/user/auth_challenges/',
             headers={'Auth-Challenge-Token': token},
-            timeout=5,
         )
 
-        if not response.ok:
-            raise BioLibError(response.content.decode())
-
         response_dict: AuthChallengeStatus = response.json()
         return response_dict

biolib/jobs/job.py

@@ -1,4 +1,5 @@
 import base64
+import urllib.request
 from datetime import datetime, timedelta
 import sys
 import time
@@ -8,6 +9,7 @@ from urllib.parse import urlparse
 
 import requests
 from biolib import api, utils
+from biolib.api.client import BioLibHTTPResponse
 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
@@ -298,17 +300,20 @@ class Job:
 
     def _print_full_logs(self, node_url: str) -> None:
         try:
-            response = requests.get(f'{node_url}/v1/job/{self._uuid}/status/?logs=full')
-            if not response.ok:
-                raise BioLibError(response.content)
+            req = urllib.request.Request(f'{node_url}/v1/job/{self._uuid}/status/?logs=full')
+            with urllib.request.urlopen(req, timeout=60) as response:
+                biolib_http_response = BioLibHTTPResponse(response)
+                biolib_http_response.raise_for_status()
+                response_json = biolib_http_response.json()
+
         except Exception as error:
             logger.error(f'Could not get full streamed logs due to: {error}')
             raise BioLibError from error
 
-        for status_update in response.json().get('previous_status_updates', []):
+        for status_update in response_json.get('previous_status_updates', []):
             logger.info(f'Cloud: {status_update["log_message"]}')
 
-        self.print_logs_packages(response.json()['streamed_logs_packages_b64'])
+        self.print_logs_packages(response_json['streamed_logs_packages_b64'])
 
     def _get_cloud_job_awaiting_started(self) -> CloudJobStartedDict:
         while True:
@@ -329,10 +334,11 @@ class Job:
     def _get_job_status_from_compute_node(self, compute_node_url):
         for _ in range(15):
             try:
-                response = requests.get(f'{compute_node_url}/v1/job/{self._uuid}/status/')
-                if not response.ok:
-                    raise BioLibError(response.content)
-                return response.json()
+                req = urllib.request.Request(f'{compute_node_url}/v1/job/{self._uuid}/status/')
+                with urllib.request.urlopen(req, timeout=60) as response:
+                    biolib_http_response = BioLibHTTPResponse(response)
+                    biolib_http_response.raise_for_status()
+                    return biolib_http_response.json()
 
             except Exception:  # pylint: disable=broad-except
                 cloud_job = self._get_cloud_job()

{pybiolib-1.1.1437.dist-info → pybiolib-1.1.1445.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1437
+Version: 1.1.1445
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.1437.dist-info → pybiolib-1.1.1445.dist-info}/RECORD

@@ -2,14 +2,14 @@ LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
 README.md,sha256=_IH7pxFiqy2bIAmaVeA-iVTyUwWRjMIlfgtUbYTtmls,368
 biolib/__init__.py,sha256=yoQA2fWt8aToFas3sx6UIoFBW7-dd2yf7Nyi5smQl88,3418
 biolib/api/__init__.py,sha256=fhsbqVxDYfQ2NMYKkFW-msplAa1YPllfKEkAtLdD9IM,95
-biolib/api/client.py,sha256=2_z_oGY00_Mt9WjP5i-b6ecJFqrTJ_X3VXJrAQGiZ5U,6251
+biolib/api/client.py,sha256=9z__FvXvwqYgjvesHyZxD8QGD3veAnaEYOZ1WKWsLvo,6279
 biolib/app/__init__.py,sha256=cdPtcfb_U-bxb9iSL4fCEq2rpD9OjkyY4W-Zw60B0LI,37
 biolib/app/app.py,sha256=6V_36uqwiC5ERtv2wU7J3KxbV9dKxMlKugx15ylSsTY,10186
 biolib/app/search_apps.py,sha256=CIanvDebNpMtWck0w4IoR_tRZ6LpSWC8DPxXW2e6Ww4,1495
 biolib/biolib_api_client/__init__.py,sha256=E5EMa19wJoblwSdQPYrxc_BtIeRsAuO0L_jQweWw-Yk,182
 biolib/biolib_api_client/api_client.py,sha256=4H1lFXWTm-MGmgP8wEHWWzLH_YGnCVx1aQJX0H2PFDg,7092
 biolib/biolib_api_client/app_types.py,sha256=vEjkpMwaMfz8MxBBZQfWCkxqT7NXxWocB_Oe9WHjJ_g,2425
-biolib/biolib_api_client/auth.py,sha256=mmfeH1ujDRH3_RodqagYtPAfCbFe4SYtJGuFeJzK-UQ,1668
+biolib/biolib_api_client/auth.py,sha256=eR1DhaijmiL7pKKxNGsHL4g5AZwBqgMrJLpUzoskLDU,1341
 biolib/biolib_api_client/biolib_account_api.py,sha256=2Mc6SbmjBSsz8lF2H3iiaZHEm47LyI0B4rjmvzxKHt4,580
 biolib/biolib_api_client/biolib_app_api.py,sha256=qYUSTyVxCCidNCX7xIQlaQ6vyGLkx1O7PXSxPltlUgA,3793
 biolib/biolib_api_client/biolib_job_api.py,sha256=EBtKdfe8wrU5ZoiZ8KxtBKCwxq4gAuU6zwxN8r4NikA,7860
@@ -76,7 +76,7 @@ biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuF
 biolib/experiments/experiment.py,sha256=xUd3LkV5ztFIjTx_ehBu8e-flvfuQnYimFtPj1upzb0,5942
 biolib/experiments/types.py,sha256=n9GxdFA7cLMfHvLLqLmZzX31ELeSSkMXFoEEdFsdWGY,171
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
-biolib/jobs/job.py,sha256=O2JK59CKgozXKthtakwSHl2ceGSPNtrx7UkvpaktaEI,14912
+biolib/jobs/job.py,sha256=5sGXJ5yJL1ywg-OMMtUIEdvvWXW6MOYntlOOPec5wUg,15290
 biolib/jobs/job_result.py,sha256=8GasUmUXD8SjUYrE2N-HrDx7-AI6TEkFONH8H91t01Q,4913
 biolib/jobs/types.py,sha256=kn4Vc0fDi6jFVcjpcKH6AYFKXkVA_CaRvtmsJoSyr0c,905
 biolib/lfs/__init__.py,sha256=wspftSqe_x7xPMZbeW8mcIBuxbHFCiFI3V4TuZU4nZ4,193
@@ -96,8 +96,8 @@ biolib/utils/cache_state.py,sha256=BFrZlV4XZIueIFzAFiPidX4hmwADKY5Y5ZuqlerF5l0,3
 biolib/utils/multipart_uploader.py,sha256=Bf09MJcIOBwzG8L1i5UeQ2cNcYohxklhhWWAMpnE41I,9671
 biolib/utils/seq_util.py,sha256=QRLYIPg1yM_LF9bFuM-Ow14gTHoG3rOK6CeGHD705qw,2612
 biolib/utils/zip/remote_zip.py,sha256=NCdUnVbGCv7SfXCI-yVU-is_OnyWmLAnVpIdSvo-W4k,23500
-pybiolib-1.1.1437.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.1437.dist-info/METADATA,sha256=lzl9SUdg7ODpQRUJqVxk8ZSRHbcSLUYuc4V47llMdE0,1492
-pybiolib-1.1.1437.dist-info/WHEEL,sha256=d2fvjOD7sXsVzChCqf0Ty0JbHKBaLYwDbGQDwQTnJ50,88
-pybiolib-1.1.1437.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.1437.dist-info/RECORD,,
+pybiolib-1.1.1445.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.1445.dist-info/METADATA,sha256=DRlu0hb5CL798tkSRbozD7W_lKGNr-iRJICvkTBR5s0,1492
+pybiolib-1.1.1445.dist-info/WHEEL,sha256=d2fvjOD7sXsVzChCqf0Ty0JbHKBaLYwDbGQDwQTnJ50,88
+pybiolib-1.1.1445.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.1445.dist-info/RECORD,,