pybiolib 1.2.1151__py3-none-any.whl → 1.2.1162__py3-none-any.whl

biolib/_internal/auth_utils.py

@@ -0,0 +1,27 @@
+from typing import Dict
+
+from biolib._internal.http_client import HttpClient
+from biolib.biolib_logging import logger
+
+
+def exchange_username_password_for_tokens(username: str, password: str, base_url: str) -> Dict[str, str]:
+    try:
+        response = HttpClient.request(
+            method='POST',
+            url=f'{base_url}/api/user/token/',
+            data={'username': username, 'password': password},
+        )
+    except Exception as exception:
+        logger.error('Sign in with username/password failed')
+        raise exception
+
+    try:
+        response_dict = response.json()
+    except Exception as error:
+        logger.error('Could not decode response from server as JSON')
+        raise Exception(response.text) from error
+
+    if 'access' not in response_dict or 'refresh' not in response_dict:
+        raise Exception('Invalid response: missing access or refresh token')
+
+    return {'access': response_dict['access'], 'refresh': response_dict['refresh']}

biolib/_session/session.py

@@ -1,6 +1,7 @@
 from biolib import utils
 from biolib._internal.types import Optional
 from biolib.api.client import ApiClient, ApiClientInitDict
+from biolib._internal.auth_utils import exchange_username_password_for_tokens
 from biolib.app import BioLibApp
 
 
@@ -9,14 +10,39 @@ class Session:
         self._api = ApiClient(_init_dict=_init_dict)
 
     @staticmethod
-    def get_session(refresh_token: str, base_url: Optional[str] = None, client_type: Optional[str] = None) -> 'Session':
-        return Session(
-            _init_dict=ApiClientInitDict(
-                refresh_token=refresh_token,
-                base_url=base_url or utils.load_base_url_from_env(),
-                client_type=client_type,
+    def get_session(
+        refresh_token: Optional[str] = None, 
+        base_url: Optional[str] = None, 
+        client_type: Optional[str] = None,
+        username: Optional[str] = None,
+        password: Optional[str] = None
+    ) -> 'Session':
+        if refresh_token and (username or password):
+            raise ValueError("Cannot specify both refresh_token and username/password authentication")
+        
+        if (username and not password) or (password and not username):
+            raise ValueError("Both username and password must be provided for username/password authentication")
+        
+        if not refresh_token and not (username and password):
+            raise ValueError("Must provide either refresh_token or username/password for authentication")
+
+        base_url_resolved = base_url or utils.load_base_url_from_env()
+        
+        if username and password:
+            tokens = exchange_username_password_for_tokens(
+                username,
+                password,
+                base_url_resolved,
             )
+            refresh_token = tokens['refresh']
+
+        init_dict = ApiClientInitDict(
+            refresh_token=str(refresh_token),
+            base_url=base_url_resolved,
+            client_type=client_type,
         )
+            
+        return Session(_init_dict=init_dict)
 
     def load(self, uri: str, suppress_version_warning: bool = False) -> BioLibApp:
         r"""Load a BioLib application by its URI or website URL.

biolib/biolib_api_client/biolib_app_api.py

@@ -57,6 +57,22 @@ def _get_git_branch_name() -> str:
         return ''
 
 
+def _get_git_commit_hash() -> str:
+    try:
+        github_actions_commit_hash = os.getenv('GITHUB_SHA')
+        if github_actions_commit_hash:
+            return github_actions_commit_hash
+
+        gitlab_ci_commit_hash = os.getenv('CI_COMMIT_SHA')
+        if gitlab_ci_commit_hash:
+            return gitlab_ci_commit_hash
+
+        result = subprocess.run(['git', 'rev-parse', 'HEAD'], check=True, stdout=subprocess.PIPE, text=True)
+        return result.stdout.strip()
+    except BaseException:
+        return ''
+
+
 def _get_git_repository_url() -> str:
     try:
         result = subprocess.run(['git', 'remote', 'get-url', 'origin'], check=True, stdout=subprocess.PIPE, text=True)
@@ -125,6 +141,7 @@ class BiolibAppApi:
                 'state': 'published',
                 'app_version_id_to_copy_images_from': app_version_id_to_copy_images_from,
                 'git_branch_name': _get_git_branch_name(),
+                'git_commit_hash': _get_git_commit_hash(),
                 'git_repository_url': _get_git_repository_url(),
             }
             if semantic_version:

biolib/sdk/__init__.py

@@ -12,8 +12,20 @@ from biolib.app import BioLibApp as _BioLibApp
 Runtime = _Runtime
 
 
-def get_session(refresh_token: str, base_url: Optional[str] = None, client_type: Optional[str] = None) -> _Session:
-    return _Session.get_session(refresh_token=refresh_token, base_url=base_url, client_type=client_type)
+def get_session(
+    refresh_token: Optional[str] = None,
+    base_url: Optional[str] = None,
+    client_type: Optional[str] = None,
+    username: Optional[str] = None,
+    password: Optional[str] = None,
+) -> _Session:
+    return _Session.get_session(
+        refresh_token=refresh_token,
+        base_url=base_url,
+        client_type=client_type,
+        username=username,
+        password=password,
+    )
 
 
 def push_app_version(uri: str, path: str) -> _BioLibApp:

{pybiolib-1.2.1151.dist-info → pybiolib-1.2.1162.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.1151
+Version: 1.2.1162
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.1151.dist-info → pybiolib-1.2.1162.dist-info}/RECORD

@@ -3,6 +3,7 @@ biolib/_data_record/data_record.py,sha256=BM2WEBnn13reSiAqhBtcV8FLewFWSTcMmFV0bD
 biolib/_internal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/_internal/add_copilot_prompts.py,sha256=wcIdrceFcfKSoEjvM4uNzhKZ0I1-MCFkfNO4duqtGHA,1861
 biolib/_internal/add_gui_files.py,sha256=MrtvkIpe70tVVJYBBsMbRhjsxf55hFzlzn-ea2oinTc,2218
+biolib/_internal/auth_utils.py,sha256=IRNzpgI83iIPVG0vSlPuPri4BRJ_LsIj28M30lrVi5o,978
 biolib/_internal/data_record/__init__.py,sha256=fGdME6JGRU_2VxpJbYpGXYndjN-feUkmKY4fuMyq3cg,76
 biolib/_internal/data_record/data_record.py,sha256=SD3-tKQY2RZv9ZSVNUhd2ISDYV64Fk1Sc642qyf_Vis,4618
 biolib/_internal/data_record/push_data.py,sha256=-L3a_7zZzDCXabBu3O4lWPMAMeBbeRPTrBlEM-_5SCI,2693
@@ -62,7 +63,7 @@ biolib/_internal/types/user.py,sha256=5_hYG0jrdGxynCCWXGaHZCAlVcRKBqMIEA2EBGrnpi
 biolib/_internal/utils/__init__.py,sha256=p5vsIFyu-zYqBgdSMfwW9NC_jk7rXvvCbV4Bzd3As7c,630
 biolib/_internal/utils/multinode.py,sha256=N7kR49xD1PdkMVlxxzRiSYHfgi9MG-kLCwemcY1rojg,8323
 biolib/_runtime/runtime.py,sha256=vRJ0YFSGYVHWULam_fnS2EHmNEm_qkrJXWdsy0n8JDA,5857
-biolib/_session/session.py,sha256=US1Y1jfFIAm86-Lq3C7nCXpZXUJXXBVBkND9djMNYxI,1649
+biolib/_session/session.py,sha256=DgtIQXhPo0iQ8CH64JtDgIYMW77aj9ZagRO5eOSso0k,2690
 biolib/api/__init__.py,sha256=mQ4u8FijqyLzjYMezMUUbbBGNB3iFmkNdjXnWPZ7Jlw,138
 biolib/api/client.py,sha256=2GpKE7QrPgyPdgJgrV7XnZByIJf1n26UCy3aoaHBs1M,7881
 biolib/app/__init__.py,sha256=cdPtcfb_U-bxb9iSL4fCEq2rpD9OjkyY4W-Zw60B0LI,37
@@ -72,7 +73,7 @@ biolib/biolib_api_client/__init__.py,sha256=E5EMa19wJoblwSdQPYrxc_BtIeRsAuO0L_jQ
 biolib/biolib_api_client/api_client.py,sha256=IONzXeFCHl4wuct6fqOC_7NiTv_zFy6ys0hsAtvLzTA,7578
 biolib/biolib_api_client/app_types.py,sha256=P2MbwYZ0VsPUcbcX27lSvVlAYSbkz_IqWTcbxFyuu7I,2477
 biolib/biolib_api_client/auth.py,sha256=kjm0ZHnH3I8so3su2sZbBxNHYp-ZUdrZ5lwQ0K36RSw,949
-biolib/biolib_api_client/biolib_app_api.py,sha256=N8l6tDsLy7CUNZ3z6hoa2vYlQ_g4Y43udLbinigZz-4,5464
+biolib/biolib_api_client/biolib_app_api.py,sha256=slnJVuWtN_Et1PSnjN7mPmYWJvk0Rp-h0rvdrW1R9u8,6041
 biolib/biolib_api_client/biolib_job_api.py,sha256=3Hzv5Os4d377pKrCzg3i7c5xiy9FiqeVssub690GLdA,7423
 biolib/biolib_api_client/common_types.py,sha256=RH-1KNHqUF-EkTpfPOSTt5Mq1GPdfju_cqXDesscO1I,123
 biolib/biolib_api_client/job_types.py,sha256=yBdBwjharbQJuXCi2xKMi0t_r6XxnbWnkchHekTpCJY,1351
@@ -146,7 +147,7 @@ biolib/jobs/job_result.py,sha256=L__GA5dNSDFHoQpAG2xb-tNqp_p4fQl53bAmlcvAt6M,607
 biolib/jobs/types.py,sha256=ezvaoTANsWazK6PmfpYcqezdfjP7MNBEBfqIZGoZhz8,997
 biolib/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/runtime/__init__.py,sha256=MlRepA11n2H-3plB5rzWyyHK2JmP6PiaP3i6x3vt0mg,506
-biolib/sdk/__init__.py,sha256=Z1S5BgpvM87S2o1libtqkYN1CfYUhn_d4ChEJjwdFKM,2356
+biolib/sdk/__init__.py,sha256=ziBjyQQHxix-QlYtxt13UKhxZrRDyj3Zmtu9PMnFbCI,2545
 biolib/tables.py,sha256=MmruV-nJLc3HbLVJBAiDuDCgS2-4oaUkpoCLLUNYbxQ,1173
 biolib/typing_utils.py,sha256=ntzrlyTkUaO2OtccLYzCAGztGdca0WT5fikJUmSkT-Y,148
 biolib/user/__init__.py,sha256=Db5wtxLfFz3ID9TULSSTo77csw9tO6RtxMRvV5cqKEE,39
@@ -157,8 +158,8 @@ biolib/utils/cache_state.py,sha256=u256F37QSRIVwqKlbnCyzAX4EMI-kl6Dwu6qwj-Qmag,3
 biolib/utils/multipart_uploader.py,sha256=XvGP1I8tQuKhAH-QugPRoEsCi9qvbRk-DVBs5PNwwJo,8452
 biolib/utils/seq_util.py,sha256=Ozk0blGtPur_D9MwShD02r_mphyQmgZkx-lOHOwnlIM,6730
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.2.1151.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.1151.dist-info/METADATA,sha256=Bh16IOuD7nJW0zGBpjUyvyjDw1TjVsvFNybYupwZ_Cs,1571
-pybiolib-1.2.1151.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-pybiolib-1.2.1151.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.1151.dist-info/RECORD,,
+pybiolib-1.2.1162.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.1162.dist-info/METADATA,sha256=5OdMqnb943o_dfeM4uEDOjXiDPVStXS5HFFVslX3YRw,1571
+pybiolib-1.2.1162.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+pybiolib-1.2.1162.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.1162.dist-info/RECORD,,