bge-python-sdk 1.0.0__tar.gz → 2.0.0__tar.gz

{bge-python-sdk-1.0.0 → bge_python_sdk-2.0.0}/LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021 teambge
+Copyright (c) 2026 teambge
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

bge_python_sdk-2.0.0/MANIFEST.in

@@ -0,0 +1,10 @@
+include README.md
+include LICENSE
+include pytest.ini
+recursive-include completions *
+include bgesdk/py.typed
+
+# 排除编译产物
+global-exclude *.pyc
+global-exclude *.pyo
+recursive-exclude * __pycache__

{bge-python-sdk-1.0.0/bge_python_sdk.egg-info → bge_python_sdk-2.0.0}/PKG-INFO

@@ -1,14 +1,12 @@
 Metadata-Version: 2.1
 Name: bge-python-sdk
-Version: 1.0.0
+Version: 2.0.0
 Summary: 可用于调用 BGE 开放平台的相关接口。
-Home-page: https://github.com/teambge/bge-python-sdk
-Author: leafcoder,xiangji1204
-Author-email: leafcoder@gmail.com,xiangji1204@genomics.cn
-Maintainer: leafcoder
-Maintainer-email: leafcoder@gmail.com
+Author-email: leafcoder <leafcoder@gmail.com>, xiangji1204 <xiangji1204@genomics.cn>
+Maintainer-email: leafcoder <leafcoder@gmail.com>
 License: MIT
-Keywords: bge-python-sdk bge bgesdk sdk
+Project-URL: Homepage, https://github.com/teambge/bge-python-sdk
+Keywords: bge-python-sdk,bge,bgesdk,sdk
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
 Classifier: License :: OSI Approved :: MIT License
@@ -18,8 +16,6 @@ Classifier: Operating System :: Microsoft :: Windows :: Windows 10
 Classifier: Operating System :: POSIX :: Linux
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
@@ -29,24 +25,23 @@ Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Software Development :: Libraries
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Classifier: Topic :: Utilities
-Requires-Python: >=3.6.3
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: aliyun-python-sdk-core
-Requires-Dist: six
-Requires-Dist: certifi
-Requires-Dist: chardet
-Requires-Dist: idna
-Requires-Dist: requests
-Requires-Dist: urllib3
-Requires-Dist: oss2
-Requires-Dist: docker
-Requires-Dist: pimento
-Requires-Dist: qprompt
-Requires-Dist: requests_toolbelt
-Requires-Dist: validator.py
-Requires-Dist: python-minifier
-Requires-Dist: rich
+Requires-Dist: requests>=2.25.0
+Requires-Dist: oss2>=2.15.0
+Requires-Dist: requests_toolbelt>=1.0.0
+Requires-Dist: aliyun-python-sdk-core>=2.13.0
+Requires-Dist: rich>=10.0.0
+Requires-Dist: rich_argparse>=1.4.0
+Requires-Dist: argcomplete>=2.0.0
+Requires-Dist: python-minifier>=2.4.0
+Requires-Dist: qprompt>=0.16.0
+Requires-Dist: cython>=0.29.0
+Provides-Extra: test
+Requires-Dist: pytest>=7.0; extra == "test"
+Requires-Dist: pytest-cov>=4.0; extra == "test"
+Requires-Dist: requests-mock>=1.9.0; extra == "test"
 
 
 <div align="center">
@@ -115,7 +110,7 @@ $ make install
 再或者
 
 ```shell
-$ python setup.py install
+$ pip install .
 ```
 
 # SDK 文档

{bge-python-sdk-1.0.0 → bge_python_sdk-2.0.0}/README.md

@@ -65,7 +65,7 @@ $ make install
 再或者
 
 ```shell
-$ python setup.py install
+$ pip install .
 ```
 
 # SDK 文档

{bge-python-sdk-1.0.0 → bge_python_sdk-2.0.0/bge_python_sdk.egg-info}/PKG-INFO

@@ -1,14 +1,12 @@
 Metadata-Version: 2.1
 Name: bge-python-sdk
-Version: 1.0.0
+Version: 2.0.0
 Summary: 可用于调用 BGE 开放平台的相关接口。
-Home-page: https://github.com/teambge/bge-python-sdk
-Author: leafcoder,xiangji1204
-Author-email: leafcoder@gmail.com,xiangji1204@genomics.cn
-Maintainer: leafcoder
-Maintainer-email: leafcoder@gmail.com
+Author-email: leafcoder <leafcoder@gmail.com>, xiangji1204 <xiangji1204@genomics.cn>
+Maintainer-email: leafcoder <leafcoder@gmail.com>
 License: MIT
-Keywords: bge-python-sdk bge bgesdk sdk
+Project-URL: Homepage, https://github.com/teambge/bge-python-sdk
+Keywords: bge-python-sdk,bge,bgesdk,sdk
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
 Classifier: License :: OSI Approved :: MIT License
@@ -18,8 +16,6 @@ Classifier: Operating System :: Microsoft :: Windows :: Windows 10
 Classifier: Operating System :: POSIX :: Linux
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
@@ -29,24 +25,23 @@ Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Software Development :: Libraries
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Classifier: Topic :: Utilities
-Requires-Python: >=3.6.3
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: aliyun-python-sdk-core
-Requires-Dist: six
-Requires-Dist: certifi
-Requires-Dist: chardet
-Requires-Dist: idna
-Requires-Dist: requests
-Requires-Dist: urllib3
-Requires-Dist: oss2
-Requires-Dist: docker
-Requires-Dist: pimento
-Requires-Dist: qprompt
-Requires-Dist: requests_toolbelt
-Requires-Dist: validator.py
-Requires-Dist: python-minifier
-Requires-Dist: rich
+Requires-Dist: requests>=2.25.0
+Requires-Dist: oss2>=2.15.0
+Requires-Dist: requests_toolbelt>=1.0.0
+Requires-Dist: aliyun-python-sdk-core>=2.13.0
+Requires-Dist: rich>=10.0.0
+Requires-Dist: rich_argparse>=1.4.0
+Requires-Dist: argcomplete>=2.0.0
+Requires-Dist: python-minifier>=2.4.0
+Requires-Dist: qprompt>=0.16.0
+Requires-Dist: cython>=0.29.0
+Provides-Extra: test
+Requires-Dist: pytest>=7.0; extra == "test"
+Requires-Dist: pytest-cov>=4.0; extra == "test"
+Requires-Dist: requests-mock>=1.9.0; extra == "test"
 
 
 <div align="center">
@@ -115,7 +110,7 @@ $ make install
 再或者
 
 ```shell
-$ python setup.py install
+$ pip install .
 ```
 
 # SDK 文档

{bge-python-sdk-1.0.0 → bge_python_sdk-2.0.0}/bge_python_sdk.egg-info/SOURCES.txt

@@ -1,10 +1,8 @@
 LICENSE
 MANIFEST.in
 README.md
+pyproject.toml
 pytest.ini
-requirements.txt
-setup.cfg
-setup.py
 bge_python_sdk.egg-info/PKG-INFO
 bge_python_sdk.egg-info/SOURCES.txt
 bge_python_sdk.egg-info/dependency_links.txt
@@ -19,18 +17,27 @@ bgesdk/error.py
 bgesdk/fs.py
 bgesdk/http.py
 bgesdk/models.py
+bgesdk/py.typed
 bgesdk/utils.py
 bgesdk/version.py
+bgesdk/api/__init__.py
+bgesdk/api/api.py
+bgesdk/api/base.py
+bgesdk/api/file.py
+bgesdk/api/microbiome.py
+bgesdk/api/misc.py
+bgesdk/api/model.py
+bgesdk/api/samples.py
+bgesdk/api/stream.py
+bgesdk/api/variants.py
 bgesdk/management/__init__.py
 bgesdk/management/command.py
 bgesdk/management/constants.py
 bgesdk/management/utils.py
-bgesdk/management/validate.py
 bgesdk/management/commands/__init__.py
 bgesdk/management/commands/config.py
 bgesdk/management/commands/login.py
 bgesdk/management/commands/model.py
-bgesdk/management/commands/model_doc.py
 bgesdk/management/commands/token.py
 bgesdk/management/commands/workon.py
 bgesdk/management/commands/api/__init__.py
@@ -53,15 +60,42 @@ bgesdk/management/commands/api/commands/id_meta.py
 bgesdk/management/commands/api/commands/task.py
 bgesdk/management/commands/api/commands/upload.py
 bgesdk/management/commands/api/commands/upload_dir.py
+bgesdk/management/model_runtime/__init__.py
+bgesdk/management/model_runtime/model_runtime.py
+bgesdk/management/model_runtime/server/model_license.py
+bgesdk/management/model_runtime/server/secure.py
+bgesdk/management/model_runtime/server/setup.py
+bgesdk/management/model_runtime/server/bge_model_server/__init__.py
+bgesdk/management/model_runtime/server/bge_model_server/app/__init__.py
+bgesdk/management/model_runtime/server/bge_model_server/app/__main__.py
+bgesdk/management/model_runtime/server/bge_model_server/app/app_fastapi.py
+bgesdk/management/model_runtime/server/bge_model_server/app/app_tornado.py
+bgesdk/management/model_runtime/server/bge_model_server/app/logging_conf.py
+bgesdk/management/model_runtime/server/build/lib/model_license.py
+bgesdk/management/model_runtime/server/build/lib/secure.py
+bgesdk/management/model_runtime/server/build/lib/bge_model_server/__init__.py
+bgesdk/management/model_runtime/server/build/lib/bge_model_server/app/__init__.py
+bgesdk/management/model_runtime/server/build/lib/bge_model_server/app/__main__.py
+bgesdk/management/model_runtime/server/build/lib/bge_model_server/app/app_fastapi.py
+bgesdk/management/model_runtime/server/build/lib/bge_model_server/app/app_tornado.py
+bgesdk/management/model_runtime/server/build/lib/bge_model_server/app/logging_conf.py
+bgesdk/management/model_runtime/server/wheels/bge_model_server-0.1.0-py3-none-any.whl
+completions/_bge
+completions/bge.bash
 tests/__init__.py
 tests/conftest.py
 tests/test_abundance.py
+tests/test_api_offline.py
+tests/test_api_structure.py
+tests/test_error.py
 tests/test_fs.py
 tests/test_model.py
 tests/test_models.py
+tests/test_models_offline.py
 tests/test_oauth2.py
 tests/test_phenotype.py
 tests/test_samples.py
+tests/test_token.py
 tests/test_user.py
 tests/test_variants.py
 tests/test_wgs.py

bge_python_sdk-2.0.0/bge_python_sdk.egg-info/requires.txt

@@ -0,0 +1,15 @@
+requests>=2.25.0
+oss2>=2.15.0
+requests_toolbelt>=1.0.0
+aliyun-python-sdk-core>=2.13.0
+rich>=10.0.0
+rich_argparse>=1.4.0
+argcomplete>=2.0.0
+python-minifier>=2.4.0
+qprompt>=0.16.0
+cython>=0.29.0
+
+[test]
+pytest>=7.0
+pytest-cov>=4.0
+requests-mock>=1.9.0

bge_python_sdk-2.0.0/bge_python_sdk.egg-info/top_level.txt

@@ -0,0 +1,6 @@
+bgesdk
+completions
+dist
+docs
+htmlcov
+tests

bge_python_sdk-2.0.0/bgesdk/__init__.py

@@ -0,0 +1,5 @@
+from .client import API, OAuth2, endpoints
+from .fs import FileItem
+from .version import __version__
+
+__all__ = ['API', 'OAuth2', 'endpoints', 'FileItem', '__version__']

bge_python_sdk-2.0.0/bgesdk/__main__.py

@@ -0,0 +1,66 @@
+from . import version
+from .management import commands as commands_package
+from .management.command import CommandError, GroupedRichHelpFormatter
+from .management.utils import discover_commands, output
+
+from typing import Any
+
+import argparse
+import sys
+
+argcomplete: Any = None  # 提供 shell 自动补全（可选依赖），未安装时为 None
+try:
+    import argcomplete  # type: ignore[no-redef]
+except ImportError:
+    pass
+
+try:
+    import readline  # noqa: F401  # 启用交互式历史/补全等副作用
+except ImportError:
+    pass
+
+
+def init_parser():
+    parser = argparse.ArgumentParser(
+        description=(
+            'BGE 开放平台 SDK 命令行工具提供了初始化模型脚手架、部署模型、'
+            '初始化模型文档配置文件、上传图片、部署模型文档等命令。'
+        ),
+        formatter_class=GroupedRichHelpFormatter,
+    )
+    parser.add_argument(
+        '-V',
+        '--version',
+        action='version',
+        help='显示当前 BGE 开放平台 Python SDK 版本号。',
+        version=f'version {version.__version__}',
+    )
+    subparsers = parser.add_subparsers(
+        dest='command', help='SDK 命令行工具可选子命令。', required=False
+    )
+    discover_commands(commands_package, subparsers)
+    return parser
+
+
+def main():
+    parser = init_parser()
+    if argcomplete is not None:
+        argcomplete.autocomplete(parser)
+    if len(sys.argv) < 2:
+        parser.print_help(sys.stderr)
+        sys.exit(1)
+    input_args = sys.argv[1:]
+    args = parser.parse_args(input_args)
+    try:
+        args.method(args)
+    except KeyboardInterrupt:
+        sys.exit(1)
+    except CommandError as exc:
+        sys.exit(exc.code)
+    except Exception as exc:  # noqa: BLE001  统一兜底，避免原始堆栈泄露
+        output(f'[red]命令执行出错：{exc}[/red]')
+        sys.exit(2)
+
+
+if __name__ == '__main__':
+    main()

bge_python_sdk-2.0.0/bgesdk/api/__init__.py

@@ -0,0 +1,5 @@
+"""按域拆分的 API 子模块包。"""
+
+from .api import API
+
+__all__ = ['API']

bge_python_sdk-2.0.0/bgesdk/api/api.py

@@ -0,0 +1,29 @@
+"""API 客户端聚合层。
+
+按域将能力拆分为多个 Mixin（Samples / Variants / Microbiome / File / Model /
+Stream / Misc），由本模块聚合为 ``API`` 类。对外公开接口与历史 ``client.API``
+保持一致，调用方无需变更（``api.get_samples(...)`` 等照常可用）。
+"""
+
+from .file import FileMixin
+from .microbiome import MicrobiomeMixin
+from .misc import MiscMixin
+from .model import ModelMixin
+from .samples import SamplesMixin
+from .stream import StreamMixin
+from .variants import VariantsMixin
+
+
+class API(
+    SamplesMixin,
+    VariantsMixin,
+    MicrobiomeMixin,
+    FileMixin,
+    ModelMixin,
+    StreamMixin,
+    MiscMixin,
+):
+    """BGE 开放平台接口调用客户端。
+
+    基础设施与账户域由 ``APIBase`` 经各 Mixin 间接继承提供，其余按业务域分散于各 Mixin。
+    """

bge_python_sdk-2.0.0/bgesdk/api/base.py

@@ -0,0 +1,210 @@
+"""API 基础设施与账户域方法（基类）。
+
+本模块承载：
+* 服务可用性检查 ``alive`` 与上传进度回调 ``progress_callback``（模块级函数）；
+* ``APIBase``：鉴权、请求创建与账户域（introspect / get_user / get_overview）方法。
+其余按域方法拆分到同级 Mixin 模块，最终由 ``bgesdk.api.api.API`` 聚合。
+"""
+
+from __future__ import annotations
+
+from .. import constants, models
+from ..error import BGEError
+from ..http import HTTPRequest
+from ..utils import human_byte, new_logger
+
+from typing import Any
+
+import sys
+import threading
+
+
+def progress_callback(bytes_consumed: int, total_bytes: int) -> None:
+    sys.stdout.write(
+        '\r文件大小: {}, 上传进度: {}%, 已上传 {}'.format(
+            human_byte(total_bytes, 2),
+            '%.2f' % ((bytes_consumed / total_bytes) * 100),
+            human_byte(bytes_consumed, 2),
+        )
+    )
+    sys.stdout.flush()
+
+
+def alive(self) -> bool:
+    """检查服务可用性
+
+    Returns:
+        布尔型: True 代表可用, False 代表不可用
+    """
+    timeout = self.timeout
+    verbose = self.verbose
+    max_retries = self.max_retries
+    request = HTTPRequest(
+        self.endpoint, max_retries=max_retries, verbose=verbose
+    )
+    try:
+        request.get('/ping', timeout=timeout)
+    except Exception:
+        return False
+    return True
+
+
+class APIBase:
+    """BGE 开放平台接口调用客户端基类（基础设施 + 账户域）。"""
+
+    token_type = 'Bearer'
+    alive = alive
+
+    _token: Any | None
+    _token_leeway: int
+    _token_lock: Any
+
+    def _ensure_access_token(self) -> None:
+        """调用前确保 access_token 有效：自定义 provider 或内置刷新。"""
+        with self._token_lock:
+            if self.token_provider is not None:
+                token = self.token_provider()
+                if token:
+                    self.access_token = token
+                return
+            if self._token is not None and self._token.is_expired(
+                self._token_leeway
+            ):
+                self._token = self._token.refresh()
+                self.access_token = self._token['access_token']
+
+    def __init__(
+        self,
+        access_token: str | models.Model,
+        endpoint: str | None = None,
+        max_retries: int | None = None,
+        timeout: int | None = 18,
+        verbose: bool = False,
+        token_provider: Any | None = None,
+    ) -> None:
+        self.token_provider = token_provider
+        self._token = None
+        self._token_leeway = 60
+        self._token_lock = threading.RLock()
+        if token_provider is None and hasattr(access_token, 'is_expired'):
+            # 传入的是带刷新能力的 token 对象，启用内置自动续期
+            self._token = access_token
+            assert isinstance(access_token, models.Model)
+            access_token = access_token['access_token']
+        self.access_token = access_token
+        if endpoint is None:
+            endpoint = constants.DEFAULT_ENDPOINT
+        self.endpoint = endpoint
+        if max_retries is not None:
+            max_retries = int(max_retries)
+        self.max_retries = max_retries
+        if timeout is not None:
+            timeout = int(timeout)
+        self.timeout = timeout
+        self.verbose = verbose
+        self.logger = new_logger(self.__class__.__name__, verbose=verbose)
+
+    def _create_request(self) -> HTTPRequest:
+        """创建预配置的HTTP请求对象
+
+        Returns:
+            HTTPRequest: 请求对象；
+        """
+        self._ensure_access_token()
+        verbose = self.verbose
+        max_retries = self.max_retries
+        request = HTTPRequest(
+            self.endpoint, max_retries=max_retries, verbose=verbose
+        )
+        request.set_authorization(self.token_type, self.access_token)
+        return request
+
+    def introspect(self) -> models.Model:
+        """验证当前使用的 access_token 有效性
+
+        Returns:
+            Model: Token 元数据；
+        """
+        timeout = self.timeout
+        request = self._create_request()
+        result = request.get(
+            '/oauth2/introspect',
+            params={'token': self.access_token},
+            timeout=timeout,
+        )
+        return models.Model(result)
+
+    def get_user(self, **params: Any) -> models.Model:
+        """获取用户信息
+
+        Returns:
+            Model: 用户数据；
+        """
+        timeout = self.timeout
+        request = self._create_request()
+        result = request.get('/profile', params=params, timeout=timeout)
+        return models.Model(result)
+
+    def get_overview(
+        self,
+        idcard: str | None = None,
+        phone: str | None = None,
+        biosample_id: str | None = None,
+        project_id: str | None = None,
+        external_sample_id: str | None = None,
+        **kwargs: Any,
+    ) -> models.Model:
+        """获取用户数据概览
+
+        Args:
+            idcard (str, 非必填): 身份证；
+            phone (str, 非必填): 手机号；提供了参数 phone，禁止再提供 biosample_id、
+                project_id、external_sample_id；
+            biosample_id (str, 非必填): BGE 样本编号；提供了参数 biosample_id，禁
+                止再提供 phone、project_id、external_sample_id；
+            project_id (str, 非必填): BGE 项目编号；提供了参数 project_id 必须提
+                供 external_sample_id，且 phone 和 biosample_id 必须为空；
+            external_sample_id (str, 非必填): 外部样本编号；提供了参数
+                external_sample_id 必须提供 project_id，且 phone 和
+                biosample_id 必须为空；
+
+        Returns:
+            Model: 用户数据概览；
+        """
+        data: dict = {}
+        data.update(kwargs)
+        if phone and (biosample_id or project_id or external_sample_id):
+            raise BGEError(
+                '若提供了 phone 参数，则禁止同时提供 biosample_id、'
+                'project_id 和 external_sample_id。'
+            )
+        elif biosample_id and (phone or project_id or external_sample_id):
+            raise BGEError(
+                '若提供了 biosample_id 参数，则禁止同时提供 phone、'
+                'project_id 和 external_sample_id。'
+            )
+        else:
+            if (not project_id and external_sample_id) or (
+                project_id and not external_sample_id
+            ):
+                raise BGEError(
+                    'project_id 与 external_sample_id 必须同时提供。'
+                )
+            if project_id and external_sample_id and (phone or biosample_id):
+                raise BGEError(
+                    '提供 external_sample_id 时必须同时提供 project_id，'
+                    '且 phone 与 biosample_id 必须为空。'
+                )
+        data.update(
+            {
+                'idcard': idcard,
+                'phone': phone,
+                'biosample_id': biosample_id,
+                'project_id': project_id,
+                'external_sample_id': external_sample_id,
+            }
+        )
+        timeout = self.timeout
+        request = self._create_request()
+        result = request.post('/user/overview', data=data, timeout=timeout)
+        return models.Model(result)