bge-python-sdk 0.6.0__tar.gz → 0.6.2__tar.gz

bge-python-sdk-0.6.2/PKG-INFO

@@ -0,0 +1,182 @@
+Metadata-Version: 2.1
+Name: bge-python-sdk
+Version: 0.6.2
+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
+License: MIT
+Keywords: bge-python-sdk bge bgesdk sdk
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: Chinese (Simplified)
+Classifier: Operating System :: OS Independent
+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
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Topic :: Utilities
+Requires-Python: >=3.6.3
+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
+
+
+<div align="center">
+
+# BGE 开放平台 SDK - Python 版
+
+
+<p>
+    <!-- Place this tag where you want the button to render. -->
+    <a class="github-button" href="https://github.com/teambge/bge-python-sdk/subscription" data-color-scheme="no-preference: light; light: light; dark: dark;" data-show-count="true" aria-label="Watch teambge/bge-python-sdk on GitHub">
+        <img alt="GitHub forks" src="https://img.shields.io/github/watchers/teambge/bge-python-sdk?style=social">
+    </a>
+    <a class="github-button" href="https://github.com/teambge/bge-python-sdk" data-color-scheme="no-preference: light; light: light; dark: dark;" data-show-count="true" aria-label="Star teambge/bge-python-sdk on GitHub">
+        <img alt="GitHub forks" src="https://img.shields.io/github/stars/teambge/bge-python-sdk?style=social">
+    </a>
+    <a class="github-button" href="https://github.com/teambge/bge-python-sdk/fork" data-color-scheme="no-preference: light; light: light; dark: dark;" data-show-count="true" aria-label="Fork teambge/bge-python-sdk on GitHub">
+        <img alt="GitHub forks" src="https://img.shields.io/github/forks/teambge/bge-python-sdk?style=social">
+    </a>
+</p>
+
+<p>
+    <img src="https://img.shields.io/github/v/release/teambge/bge-python-sdk" data-origin="https://img.shields.io/github/v/release/teambge/bge-python-sdk" alt="GitHub release (latest by date)">
+    <img src="https://img.shields.io/github/languages/top/teambge/bge-python-sdk" data-origin="https://img.shields.io/github/languages/top/teambge/bge-python-sdk" alt="GitHub top language">
+    <img src="https://img.shields.io/github/languages/code-size/teambge/bge-python-sdk" data-origin="https://img.shields.io/github/languages/code-size/teambge/bge-python-sdk" alt="GitHub code size in bytes">
+    <img src="https://img.shields.io/github/commit-activity/w/teambge/bge-python-sdk" data-origin="https://img.shields.io/github/commit-activity/w/teambge/bge-python-sdk" alt="GitHub commit activity">
+    <img src="https://static.pepy.tech/personalized-badge/bge-python-sdk?period=total&units=international_system&left_color=grey&right_color=blue&left_text=Downloads" data-origin="https://static.pepy.tech/personalized-badge/bge-python-sdk?period=total&units=international_system&left_color=grey&right_color=blue&left_text=Downloads" alt="PyPI - Downloads">
+</p>
+
+<pre>
+    ____  ____________   ______  __________  ______  _   __   _____ ____  __ __
+   / __ )/ ____/ ____/  / __ \ \/ /_  __/ / / / __ \/ | / /  / ___// __ \/ //_/
+  / __  / / __/ __/    / /_/ /\  / / / / /_/ / / / /  |/ /   \__ \/ / / / ,<   
+ / /_/ / /_/ / /___   / ____/ / / / / / __  / /_/ / /|  /   ___/ / /_/ / /| |  
+/_____/\____/_____/  /_/     /_/ /_/ /_/ /_/\____/_/ |_/   /____/_____/_/ |_| 
+</pre>
+
+</div>
+
+BGE 开放平台 是一个跨越多级数据的（多）组学数据平台，开发者在获得用户授权后，将可以通过开放平台提供的 API 访问关联用户的（多）组学数据，甚至写入数据。
+
+基于开放平台 API，开发者可避免重复开发采样、提取、测序和生信分析等繁复的流程，直接使用清洁的结构化数据。
+
+开发者可以通过开放平台提供的 API 创建极具创意性的（多）组学应用，如：
+
+* 包含药物代谢或药物服用建议的应用
+* 包含体检数据和营养代谢基因的餐饮应用
+* 包含肠道菌群数据和痛风相关基因的痛风管理应用
+* 基于祖源成分的社交网络应用，等等
+
+BGE 开放平台 API 基于 OAuth 2.0 开发，并使用 SSL/TLS 加密传输，确保用户数据正确无误地授权，并安全地传输到第三方应用，确保用户数据不会被未经授权的应用获得。
+
+# 安装
+
+推荐使用 pip 进行安装。
+
+```shell
+$ pip install -U bge-python-sdk
+```
+
+或者
+
+```shell
+$ make install
+```
+
+再或者
+
+```shell
+$ python setup.py install
+```
+
+# SDK 文档
+
+更加详细的 SDK 文档请查看 [SDK Documents](https://api.bge.genomics.cn/doc/#/sdk/README)。
+
+# 快速开始
+
+BGE 开放平台支持 OAuth2 的两种模式，分别是用户授权模式、客户端模式。
+
+详情请参考开放平台文档 [https://api.bge.genomics.cn/doc](https://api.bge.genomics.cn/doc) 。
+
+## ENDPOINTS
+
+BGE 开放平台提供了如下可用的 `endpoint`。
+
+| endpoint                    | 解释                                                        |
+| --------------------------- | ----------------------------------------------------------- |
+| https://api.bge.genomics.cn | **线上环境** 主域名地址                                     |
+| https://api.bge.omgut.com   | **线上环境** 副域名地址，主域名地址不可用时可替换此域名地址 |
+
+## 授权码模式
+
+```python
+from bgesdk import OAuth2, API
+
+code = '???????'  # 用户确认授权后平台返回的授权码
+client_id = 'demo'
+client_secret = 'demo'
+redirect_uri = 'http://test.cn'
+oauth2 = OAuth2(
+    client_id, client_secret,
+    endpoint='https://api.bge.genomics.cn', max_retries=3, timeout=16,
+    verbose=False)
+token = oauth2.exchange_authorization_code(code, redirect_uri)
+
+api = oauth2.get_api(token.access_token)
+print(api.get_user())
+
+api = API(token.access_token)
+print(api.get_user())
+```
+
+## 客户端模式
+
+```python
+from bgesdk import OAuth2, API
+
+client_id = 'demo'
+client_secret = 'demo'
+oauth2 = OAuth2(
+    client_id, client_secret,
+    endpoint='https://api.bge.genomics.cn', max_retries=3, timeout=16,
+    verbose=False)
+token = oauth2.get_credentials_token()
+
+api = oauth2.get_api(token.access_token)
+print(api.get_variants('E-B1243433', 'rs333'))
+
+api = API(token.access_token)
+print(api.get_variants('E-B1243433', 'rs333'))
+```
+
+# Contributors
+
+* xiangji1204's [github](https://github.com/xiangji1204)
+* leafcoder(leafcoder@gmail.com)'s [github](https://github.com/leafcoder)

bge-python-sdk-0.6.2/bge_python_sdk.egg-info/PKG-INFO

@@ -0,0 +1,182 @@
+Metadata-Version: 2.1
+Name: bge-python-sdk
+Version: 0.6.2
+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
+License: MIT
+Keywords: bge-python-sdk bge bgesdk sdk
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: Chinese (Simplified)
+Classifier: Operating System :: OS Independent
+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
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Topic :: Utilities
+Requires-Python: >=3.6.3
+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
+
+
+<div align="center">
+
+# BGE 开放平台 SDK - Python 版
+
+
+<p>
+    <!-- Place this tag where you want the button to render. -->
+    <a class="github-button" href="https://github.com/teambge/bge-python-sdk/subscription" data-color-scheme="no-preference: light; light: light; dark: dark;" data-show-count="true" aria-label="Watch teambge/bge-python-sdk on GitHub">
+        <img alt="GitHub forks" src="https://img.shields.io/github/watchers/teambge/bge-python-sdk?style=social">
+    </a>
+    <a class="github-button" href="https://github.com/teambge/bge-python-sdk" data-color-scheme="no-preference: light; light: light; dark: dark;" data-show-count="true" aria-label="Star teambge/bge-python-sdk on GitHub">
+        <img alt="GitHub forks" src="https://img.shields.io/github/stars/teambge/bge-python-sdk?style=social">
+    </a>
+    <a class="github-button" href="https://github.com/teambge/bge-python-sdk/fork" data-color-scheme="no-preference: light; light: light; dark: dark;" data-show-count="true" aria-label="Fork teambge/bge-python-sdk on GitHub">
+        <img alt="GitHub forks" src="https://img.shields.io/github/forks/teambge/bge-python-sdk?style=social">
+    </a>
+</p>
+
+<p>
+    <img src="https://img.shields.io/github/v/release/teambge/bge-python-sdk" data-origin="https://img.shields.io/github/v/release/teambge/bge-python-sdk" alt="GitHub release (latest by date)">
+    <img src="https://img.shields.io/github/languages/top/teambge/bge-python-sdk" data-origin="https://img.shields.io/github/languages/top/teambge/bge-python-sdk" alt="GitHub top language">
+    <img src="https://img.shields.io/github/languages/code-size/teambge/bge-python-sdk" data-origin="https://img.shields.io/github/languages/code-size/teambge/bge-python-sdk" alt="GitHub code size in bytes">
+    <img src="https://img.shields.io/github/commit-activity/w/teambge/bge-python-sdk" data-origin="https://img.shields.io/github/commit-activity/w/teambge/bge-python-sdk" alt="GitHub commit activity">
+    <img src="https://static.pepy.tech/personalized-badge/bge-python-sdk?period=total&units=international_system&left_color=grey&right_color=blue&left_text=Downloads" data-origin="https://static.pepy.tech/personalized-badge/bge-python-sdk?period=total&units=international_system&left_color=grey&right_color=blue&left_text=Downloads" alt="PyPI - Downloads">
+</p>
+
+<pre>
+    ____  ____________   ______  __________  ______  _   __   _____ ____  __ __
+   / __ )/ ____/ ____/  / __ \ \/ /_  __/ / / / __ \/ | / /  / ___// __ \/ //_/
+  / __  / / __/ __/    / /_/ /\  / / / / /_/ / / / /  |/ /   \__ \/ / / / ,<   
+ / /_/ / /_/ / /___   / ____/ / / / / / __  / /_/ / /|  /   ___/ / /_/ / /| |  
+/_____/\____/_____/  /_/     /_/ /_/ /_/ /_/\____/_/ |_/   /____/_____/_/ |_| 
+</pre>
+
+</div>
+
+BGE 开放平台 是一个跨越多级数据的（多）组学数据平台，开发者在获得用户授权后，将可以通过开放平台提供的 API 访问关联用户的（多）组学数据，甚至写入数据。
+
+基于开放平台 API，开发者可避免重复开发采样、提取、测序和生信分析等繁复的流程，直接使用清洁的结构化数据。
+
+开发者可以通过开放平台提供的 API 创建极具创意性的（多）组学应用，如：
+
+* 包含药物代谢或药物服用建议的应用
+* 包含体检数据和营养代谢基因的餐饮应用
+* 包含肠道菌群数据和痛风相关基因的痛风管理应用
+* 基于祖源成分的社交网络应用，等等
+
+BGE 开放平台 API 基于 OAuth 2.0 开发，并使用 SSL/TLS 加密传输，确保用户数据正确无误地授权，并安全地传输到第三方应用，确保用户数据不会被未经授权的应用获得。
+
+# 安装
+
+推荐使用 pip 进行安装。
+
+```shell
+$ pip install -U bge-python-sdk
+```
+
+或者
+
+```shell
+$ make install
+```
+
+再或者
+
+```shell
+$ python setup.py install
+```
+
+# SDK 文档
+
+更加详细的 SDK 文档请查看 [SDK Documents](https://api.bge.genomics.cn/doc/#/sdk/README)。
+
+# 快速开始
+
+BGE 开放平台支持 OAuth2 的两种模式，分别是用户授权模式、客户端模式。
+
+详情请参考开放平台文档 [https://api.bge.genomics.cn/doc](https://api.bge.genomics.cn/doc) 。
+
+## ENDPOINTS
+
+BGE 开放平台提供了如下可用的 `endpoint`。
+
+| endpoint                    | 解释                                                        |
+| --------------------------- | ----------------------------------------------------------- |
+| https://api.bge.genomics.cn | **线上环境** 主域名地址                                     |
+| https://api.bge.omgut.com   | **线上环境** 副域名地址，主域名地址不可用时可替换此域名地址 |
+
+## 授权码模式
+
+```python
+from bgesdk import OAuth2, API
+
+code = '???????'  # 用户确认授权后平台返回的授权码
+client_id = 'demo'
+client_secret = 'demo'
+redirect_uri = 'http://test.cn'
+oauth2 = OAuth2(
+    client_id, client_secret,
+    endpoint='https://api.bge.genomics.cn', max_retries=3, timeout=16,
+    verbose=False)
+token = oauth2.exchange_authorization_code(code, redirect_uri)
+
+api = oauth2.get_api(token.access_token)
+print(api.get_user())
+
+api = API(token.access_token)
+print(api.get_user())
+```
+
+## 客户端模式
+
+```python
+from bgesdk import OAuth2, API
+
+client_id = 'demo'
+client_secret = 'demo'
+oauth2 = OAuth2(
+    client_id, client_secret,
+    endpoint='https://api.bge.genomics.cn', max_retries=3, timeout=16,
+    verbose=False)
+token = oauth2.get_credentials_token()
+
+api = oauth2.get_api(token.access_token)
+print(api.get_variants('E-B1243433', 'rs333'))
+
+api = API(token.access_token)
+print(api.get_variants('E-B1243433', 'rs333'))
+```
+
+# Contributors
+
+* xiangji1204's [github](https://github.com/xiangji1204)
+* leafcoder(leafcoder@gmail.com)'s [github](https://github.com/leafcoder)

{bge-python-sdk-0.6.0 → bge-python-sdk-0.6.2}/bge_python_sdk.egg-info/entry_points.txt

@@ -1,3 +1,2 @@
 [console_scripts]
 bge = bgesdk.__main__:main
-

{bge-python-sdk-0.6.0 → bge-python-sdk-0.6.2}/bgesdk/client.py

@@ -633,7 +633,7 @@ class API(object):
         result['result'] = [models.Model(item) for item in result['result']]
         return result
 
-    def get_upload_token(self, **kwargs):
+    def get_upload_token(self, region_id=None, internal=False, **kwargs):
         """获取文件上传授权
         
         获取的授权仅包括当前目录(不含子目录)下的文件读、写权限;
@@ -644,15 +644,21 @@ class API(object):
         timeout = self.timeout
         verbose = self.verbose
         max_retries = self.max_retries
+        data = {}
+        data.update(kwargs)
+        data.update({
+            'region_id': region_id,
+            'internal': internal,
+        })
         request = HTTPRequest(
             self.endpoint, max_retries=max_retries, verbose=verbose)
         request.set_authorization(self.token_type, self.access_token)
-        result = request.post('/sts/token', data=kwargs, timeout=timeout)
+        result = request.post('/sts/token', data=data, timeout=timeout)
         return models.Model(result)
 
     def upload(self, filename, file_or_string, part_size=None,
                multipart_threshold=None, multipart_num_threads=None,
-               cmk_id=None):
+               cmk_id=None, region_id=None, internal=False):
         """上传文件
 
         Args:
@@ -663,11 +669,16 @@ class API(object):
             multipart_num_threads: 分片上传缺省线程数, 默认 4;
             cmk_id (str): 阿里云 KMS 服务用户主密钥 ID,加密上传时提供 CMK ID 即可;
                           提供 cmk_id 后不支持分片上传;
+            region_id(str): 阿里云 OSS 区域编号，默认 oss-cn-shenzhen；
+            internal(bool): 是否使用内部 VPN 域名，默认 False；
 
         Returns:
             object_name: 文件的 OSS 对象名;
         """
-        token = self.get_upload_token()
+        token = self.get_upload_token(
+            region_id=region_id,
+            internal=internal
+        )
         return self._upload(
             token,
             filename,
@@ -680,7 +691,7 @@ class API(object):
 
     def batch_upload(self, files, part_size=None,
                      multipart_threshold=None, multipart_num_threads=None,
-                     cmk_id=None):
+                     cmk_id=None, region_id=None, internal=False):
         """批量上传文件
 
         Args:
@@ -689,6 +700,8 @@ class API(object):
             multipart_threshold(num): 上传数据大于或等于该值时分片上传, 默认 100M;
             multipart_num_threads: 分片上传缺省线程数, 默认 4;
             cmk_id (str): 阿里云 KMS 服务用户主密钥 ID,加密上传时提供 CMK ID 即可;
+            region_id(str): 阿里云 OSS 区域编号，默认 oss-cn-shenzhen；
+            internal(bool): 是否使用内部 VPN 域名，默认 False；
 
         Returns:
             object_name: 文件的 OSS 对象名;
@@ -698,7 +711,10 @@ class API(object):
         object_names = []
         if isinstance(files, (list, tuple)):
             files = [files]
-        token = self.get_upload_token()
+        token = self.get_upload_token(
+            region_id=region_id,
+            internal=internal
+        )
         for file_obj in files:
             if not isinstance(file_obj, FileItem):
                 continue
@@ -721,7 +737,7 @@ class API(object):
 
     def upload_dir(self, dirpath, part_size=None,
                    multipart_threshold=None, multipart_num_threads=None,
-                   cmk_id=None):
+                   cmk_id=None, region_id=None, internal=False):
         """上传目录下的文件(不递归上传子文件夹中文件)
 
         仅上传目录中的文件,软链接、符号链接、文件夹均不会上传至平台。
@@ -736,7 +752,10 @@ class API(object):
         Returns:
             object_names: 上传的文件 OSS 对象名列表;
         """
-        token = self.get_upload_token()
+        token = self.get_upload_token(
+            region_id=region_id,
+            internal=internal
+        )
         object_names = []
         for filename in os.listdir(dirpath):
             filepath = join(dirpath, filename)
@@ -871,18 +890,30 @@ class API(object):
         timeout = self.timeout
         try:
             with requests.get(url, stream=True, timeout=timeout) as r:
-                total = int(r.headers['content-length'])
-                for chunk in r.iter_content(chunk_size):
-                    size += len(chunk)
-                    eq_size = int(size * prog_size / total)
-                    equal_s = '=' * eq_size
-                    blank_s = ' ' * (prog_size - eq_size)
-                    progress = '>'.join((equal_s, blank_s))
-                    percent = '%.2f%%' % float(size / total * 100)
-                    sys.stdout.write(
-                        '\r\t%s [%s]' % (percent.rjust(7), progress)
-                    )
-                    fp.write(chunk)
+                total = r.headers.get('content-length')
+                if total is not None:
+                    total = int(total)
+                    for chunk in r.iter_content(chunk_size):
+                        size += len(chunk)
+                        eq_size = int(size * prog_size / total)
+                        equal_s = '=' * eq_size
+                        blank_s = ' ' * (prog_size - eq_size)
+                        progress = '>'.join((equal_s, blank_s))
+                        percent = '%.2f%%' % float(size / total * 100)
+                        sys.stdout.write(
+                            '\r\t%s [%s]' % (percent.rjust(7), progress)
+                        )
+                        sys.stdout.flush()
+                        fp.write(chunk)
+                else:
+                    for chunk in r.iter_content(chunk_size):
+                        size += len(chunk)
+                        sys.stdout.write(
+                            '\r\t已下载文件：%s' % human_byte(size).ljust(7)
+                        )
+                        sys.stdout.flush()
+                        fp.write(chunk)
+                sys.stdout.write('\n')
                 flush_func = getattr(fp, 'flush', None)
                 if flush_func:
                     flush_func()

{bge-python-sdk-0.6.0 → bge-python-sdk-0.6.2}/bgesdk/management/commands/api/commands/aggregate_omics_data.py

@@ -21,7 +21,7 @@ DEFAULT_TOKEN_SECTION = constants.DEFAULT_TOKEN_SECTION
 class Command(BaseCommand):
 
     order = 10
-    help='聚合组学数据（目前仅支持聚合数据流中符合平台设定 JSONPath 规则的数值型数据）。'
+    help = '聚合组学数据（目前仅支持聚合数据流中符合平台设定 JSONPath 规则的数值型数据）。'
 
     def add_arguments(self, parser):
         parser.add_argument(

{bge-python-sdk-0.6.0 → bge-python-sdk-0.6.2}/bgesdk/management/commands/api/commands/download.py

@@ -22,7 +22,7 @@ DEFAULT_TOKEN_SECTION = constants.DEFAULT_TOKEN_SECTION
 class Command(BaseCommand):
 
     order = 13
-    help='下载文件。'
+    help = '下载文件。'
 
     def add_arguments(self, parser):
         parser.add_argument(

{bge-python-sdk-0.6.0 → bge-python-sdk-0.6.2}/bgesdk/management/commands/api/commands/get_data_items.py

@@ -21,7 +21,7 @@ DEFAULT_TOKEN_SECTION = constants.DEFAULT_TOKEN_SECTION
 class Command(BaseCommand):
 
     order = 7
-    help='请求数据项。'
+    help = '请求数据项。'
 
     def add_arguments(self, parser):
         parser.add_argument(

{bge-python-sdk-0.6.0 → bge-python-sdk-0.6.2}/bgesdk/management/commands/api/commands/get_externals.py

@@ -21,7 +21,7 @@ DEFAULT_TOKEN_SECTION = constants.DEFAULT_TOKEN_SECTION
 class Command(BaseCommand):
 
     order = 9
-    help='获取套件外部编号对应表。'
+    help = '获取套件外部编号对应表。'
 
     def add_arguments(self, parser):
         parser.add_argument(

{bge-python-sdk-0.6.0 → bge-python-sdk-0.6.2}/bgesdk/management/commands/api/commands/get_range_stream.py

@@ -21,7 +21,7 @@ DEFAULT_TOKEN_SECTION = constants.DEFAULT_TOKEN_SECTION
 class Command(BaseCommand):
 
     order = 8
-    help='请求数据流。'
+    help = '请求数据流。'
 
     def add_arguments(self, parser):
         parser.add_argument(

{bge-python-sdk-0.6.0 → bge-python-sdk-0.6.2}/bgesdk/management/commands/api/commands/get_samples.py

@@ -29,7 +29,7 @@ NOT_PARAM_FIELDS = (
 class Command(BaseCommand):
 
     order = 2
-    help='获取样品信息。'
+    help = '获取样品信息。'
 
     def add_arguments(self, parser):
         parser.add_argument(
@@ -69,7 +69,7 @@ class Command(BaseCommand):
             '--statuses',
             type=str,
             help='数据状态，详情见 BGE 开放平台文档 https://api.bge.genomics.cn/doc/#/ot'
-                'hers/appendix?id=样品状态编码表'
+                 'hers/appendix?id=样品状态编码表'
         )
         parser.add_argument(
             '--require_files',

{bge-python-sdk-0.6.0 → bge-python-sdk-0.6.2}/bgesdk/management/commands/api/commands/get_user.py

@@ -21,7 +21,7 @@ DEFAULT_TOKEN_SECTION = constants.DEFAULT_TOKEN_SECTION
 class Command(BaseCommand):
 
     order = 1
-    help='获取用户信息。'
+    help = '获取用户信息。'
 
     def add_arguments(self, parser):
         parser.add_argument(

{bge-python-sdk-0.6.0 → bge-python-sdk-0.6.2}/bgesdk/management/commands/api/commands/get_variants.py

@@ -21,7 +21,7 @@ DEFAULT_TOKEN_SECTION = constants.DEFAULT_TOKEN_SECTION
 class Command(BaseCommand):
 
     order = 3
-    help='获取变异位点数据。'
+    help = '获取变异位点数据。'
 
     def add_arguments(self, parser):
         parser.add_argument(

{bge-python-sdk-0.6.0 → bge-python-sdk-0.6.2}/bgesdk/management/commands/api/commands/task.py

@@ -21,7 +21,7 @@ DEFAULT_TOKEN_SECTION = constants.DEFAULT_TOKEN_SECTION
 class Command(BaseCommand):
 
     order = 14
-    help='获取 BGE 私有平台任务结果。'
+    help = '获取 BGE 私有平台任务结果。'
 
     def add_arguments(self, parser):
         parser.add_argument(

{bge-python-sdk-0.6.0 → bge-python-sdk-0.6.2}/bgesdk/management/commands/api/commands/upload.py

@@ -22,7 +22,7 @@ DEFAULT_TOKEN_SECTION = constants.DEFAULT_TOKEN_SECTION
 class Command(BaseCommand):
 
     order = 11
-    help='上传文件。'
+    help = '上传文件。'
 
     def add_arguments(self, parser):
         parser.add_argument(
@@ -57,6 +57,16 @@ class Command(BaseCommand):
             '--cmk_id',
             help='阿里云 KMS 服务密钥 ID, 提供时代表使用加密方式上传文件。'
         )
+        parser.add_argument(
+            '-r',
+            '--region_id',
+            help='阿里云 OSS 区域编号，默认 oss-cn-shenzhen。'
+        )
+        parser.add_argument(
+            '--internal',
+            action="store_true",
+            help='是否使用内部 VPC 域名。'
+        )
         parser.add_argument(
             '-t',
             '--access_token',
@@ -82,6 +92,8 @@ class Command(BaseCommand):
         cmk_id = args.cmk_id
         part_size = args.part_size
         multipart_threshold = args.multipart_threshold
+        region_id = args.region_id
+        internal = args.internal
         if not filename:
             filename = posixpath.split(filepath)[1]
         message = '正在上传文件 {}'.format(filepath)
@@ -93,7 +105,9 @@ class Command(BaseCommand):
                     part_size=part_size * 1024 * 1024,
                     multipart_threshold=multipart_threshold * 1024 * 1024,
                     multipart_num_threads=args.multipart_num_threads,
-                    cmk_id=cmk_id
+                    cmk_id=cmk_id,
+                    region_id=region_id,
+                    internal=internal,
                 )
             except APIError as e:
                 output('[red]请求失败：[/red]')

{bge-python-sdk-0.6.0 → bge-python-sdk-0.6.2}/bgesdk/management/commands/api/commands/upload_dir.py

@@ -26,7 +26,7 @@ DEFAULT_TOKEN_SECTION = constants.DEFAULT_TOKEN_SECTION
 class Command(BaseCommand):
 
     order = 12
-    help='上传目录下文件（不递归上传子目录中文件）。'
+    help = '上传目录下文件（不递归上传子目录中文件）。'
 
     def add_arguments(self, parser):
         parser.add_argument(
@@ -56,6 +56,16 @@ class Command(BaseCommand):
             '--cmk_id',
             help='阿里云 KMS 服务密钥 ID，提供时代表使用加密方式上传文件。'
         )
+        parser.add_argument(
+            '-r',
+            '--region_id',
+            help='阿里云 OSS 区域编号，默认 oss-cn-shenzhen。'
+        )
+        parser.add_argument(
+            '--internal',
+            action="store_true",
+            help='是否使用内部 VPC 域名。'
+        )
         parser.add_argument(
             '-t',
             '--access_token',
@@ -77,6 +87,8 @@ class Command(BaseCommand):
         cmk_id = args.cmk_id
         part_size = args.part_size
         multipart_threshold = args.multipart_threshold
+        region_id = args.region_id
+        internal = args.internal
         files = []
         for filename in os.listdir(dirpath):
             filepath = join(dirpath, filename)
@@ -93,7 +105,9 @@ class Command(BaseCommand):
                     part_size=part_size * 1024 * 1024,
                     multipart_threshold=multipart_threshold * 1024 * 1024,
                     multipart_num_threads=args.multipart_num_threads,
-                    cmk_id=cmk_id
+                    cmk_id=cmk_id,
+                    region_id=region_id,
+                    internal=internal,
                 )
             except APIError as e:
                 output('[red]请求失败：[/red]')

{bge-python-sdk-0.6.0 → bge-python-sdk-0.6.2}/bgesdk/version.py

@@ -1,3 +1,3 @@
 #-*- coding: utf-8 -*-
 
-__version__ = '0.6.0'
+__version__ = '0.6.2'

{bge-python-sdk-0.6.0 → bge-python-sdk-0.6.2}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = bge-python-sdk
-version = 0.6.0
+version = 0.6.2
 description = 可用于调用 BGE 开放平台的相关接口。
 long_description = file: README.md
 long_description_content_type = text/markdown

bge-python-sdk-0.6.0/PKG-INFO

@@ -1,167 +0,0 @@
-Metadata-Version: 2.1
-Name: bge-python-sdk
-Version: 0.6.0
-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
-License: MIT
-Description: 
-        <div align="center">
-        
-        # BGE 开放平台 SDK - Python 版
-        
-        
-        <p>
-            <!-- Place this tag where you want the button to render. -->
-            <a class="github-button" href="https://github.com/teambge/bge-python-sdk/subscription" data-color-scheme="no-preference: light; light: light; dark: dark;" data-show-count="true" aria-label="Watch teambge/bge-python-sdk on GitHub">
-                <img alt="GitHub forks" src="https://img.shields.io/github/watchers/teambge/bge-python-sdk?style=social">
-            </a>
-            <a class="github-button" href="https://github.com/teambge/bge-python-sdk" data-color-scheme="no-preference: light; light: light; dark: dark;" data-show-count="true" aria-label="Star teambge/bge-python-sdk on GitHub">
-                <img alt="GitHub forks" src="https://img.shields.io/github/stars/teambge/bge-python-sdk?style=social">
-            </a>
-            <a class="github-button" href="https://github.com/teambge/bge-python-sdk/fork" data-color-scheme="no-preference: light; light: light; dark: dark;" data-show-count="true" aria-label="Fork teambge/bge-python-sdk on GitHub">
-                <img alt="GitHub forks" src="https://img.shields.io/github/forks/teambge/bge-python-sdk?style=social">
-            </a>
-        </p>
-        
-        <p>
-            <img src="https://img.shields.io/github/v/release/teambge/bge-python-sdk" data-origin="https://img.shields.io/github/v/release/teambge/bge-python-sdk" alt="GitHub release (latest by date)">
-            <img src="https://img.shields.io/github/languages/top/teambge/bge-python-sdk" data-origin="https://img.shields.io/github/languages/top/teambge/bge-python-sdk" alt="GitHub top language">
-            <img src="https://img.shields.io/github/languages/code-size/teambge/bge-python-sdk" data-origin="https://img.shields.io/github/languages/code-size/teambge/bge-python-sdk" alt="GitHub code size in bytes">
-            <img src="https://img.shields.io/github/commit-activity/w/teambge/bge-python-sdk" data-origin="https://img.shields.io/github/commit-activity/w/teambge/bge-python-sdk" alt="GitHub commit activity">
-            <img src="https://static.pepy.tech/personalized-badge/bge-python-sdk?period=total&units=international_system&left_color=grey&right_color=blue&left_text=Downloads" data-origin="https://static.pepy.tech/personalized-badge/bge-python-sdk?period=total&units=international_system&left_color=grey&right_color=blue&left_text=Downloads" alt="PyPI - Downloads">
-        </p>
-        
-        <pre>
-            ____  ____________   ______  __________  ______  _   __   _____ ____  __ __
-           / __ )/ ____/ ____/  / __ \ \/ /_  __/ / / / __ \/ | / /  / ___// __ \/ //_/
-          / __  / / __/ __/    / /_/ /\  / / / / /_/ / / / /  |/ /   \__ \/ / / / ,<   
-         / /_/ / /_/ / /___   / ____/ / / / / / __  / /_/ / /|  /   ___/ / /_/ / /| |  
-        /_____/\____/_____/  /_/     /_/ /_/ /_/ /_/\____/_/ |_/   /____/_____/_/ |_| 
-        </pre>
-        
-        </div>
-        
-        BGE 开放平台 是一个跨越多级数据的（多）组学数据平台，开发者在获得用户授权后，将可以通过开放平台提供的 API 访问关联用户的（多）组学数据，甚至写入数据。
-        
-        基于开放平台 API，开发者可避免重复开发采样、提取、测序和生信分析等繁复的流程，直接使用清洁的结构化数据。
-        
-        开发者可以通过开放平台提供的 API 创建极具创意性的（多）组学应用，如：
-        
-        * 包含药物代谢或药物服用建议的应用
-        * 包含体检数据和营养代谢基因的餐饮应用
-        * 包含肠道菌群数据和痛风相关基因的痛风管理应用
-        * 基于祖源成分的社交网络应用，等等
-        
-        BGE 开放平台 API 基于 OAuth 2.0 开发，并使用 SSL/TLS 加密传输，确保用户数据正确无误地授权，并安全地传输到第三方应用，确保用户数据不会被未经授权的应用获得。
-        
-        # 安装
-        
-        推荐使用 pip 进行安装。
-        
-        ```shell
-        $ pip install -U bge-python-sdk
-        ```
-        
-        或者
-        
-        ```shell
-        $ make install
-        ```
-        
-        再或者
-        
-        ```shell
-        $ python setup.py install
-        ```
-        
-        # SDK 文档
-        
-        更加详细的 SDK 文档请查看 [SDK Documents](https://api.bge.genomics.cn/doc/#/sdk/README)。
-        
-        # 快速开始
-        
-        BGE 开放平台支持 OAuth2 的两种模式，分别是用户授权模式、客户端模式。
-        
-        详情请参考开放平台文档 [https://api.bge.genomics.cn/doc](https://api.bge.genomics.cn/doc) 。
-        
-        ## ENDPOINTS
-        
-        BGE 开放平台提供了如下可用的 `endpoint`。
-        
-        | endpoint                    | 解释                                                        |
-        | --------------------------- | ----------------------------------------------------------- |
-        | https://api.bge.genomics.cn | **线上环境** 主域名地址                                     |
-        | https://api.bge.omgut.com   | **线上环境** 副域名地址，主域名地址不可用时可替换此域名地址 |
-        
-        ## 授权码模式
-        
-        ```python
-        from bgesdk import OAuth2, API
-        
-        code = '???????'  # 用户确认授权后平台返回的授权码
-        client_id = 'demo'
-        client_secret = 'demo'
-        redirect_uri = 'http://test.cn'
-        oauth2 = OAuth2(
-            client_id, client_secret,
-            endpoint='https://api.bge.genomics.cn', max_retries=3, timeout=16,
-            verbose=False)
-        token = oauth2.exchange_authorization_code(code, redirect_uri)
-        
-        api = oauth2.get_api(token.access_token)
-        print(api.get_user())
-        
-        api = API(token.access_token)
-        print(api.get_user())
-        ```
-        
-        ## 客户端模式
-        
-        ```python
-        from bgesdk import OAuth2, API
-        
-        client_id = 'demo'
-        client_secret = 'demo'
-        oauth2 = OAuth2(
-            client_id, client_secret,
-            endpoint='https://api.bge.genomics.cn', max_retries=3, timeout=16,
-            verbose=False)
-        token = oauth2.get_credentials_token()
-        
-        api = oauth2.get_api(token.access_token)
-        print(api.get_variants('E-B1243433', 'rs333'))
-        
-        api = API(token.access_token)
-        print(api.get_variants('E-B1243433', 'rs333'))
-        ```
-        
-        # Contributors
-        
-        * xiangji1204's [github](https://github.com/xiangji1204)
-        * leafcoder(leafcoder@gmail.com)'s [github](https://github.com/leafcoder)
-        
-Keywords: bge-python-sdk bge bgesdk sdk
-Platform: UNKNOWN
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Intended Audience :: Developers
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Natural Language :: Chinese (Simplified)
-Classifier: Operating System :: OS Independent
-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
-Classifier: Topic :: Software Development :: Libraries
-Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Classifier: Topic :: Utilities
-Requires-Python: >=3.6.3
-Description-Content-Type: text/markdown

bge-python-sdk-0.6.0/bge_python_sdk.egg-info/PKG-INFO

@@ -1,167 +0,0 @@
-Metadata-Version: 2.1
-Name: bge-python-sdk
-Version: 0.6.0
-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
-License: MIT
-Description: 
-        <div align="center">
-        
-        # BGE 开放平台 SDK - Python 版
-        
-        
-        <p>
-            <!-- Place this tag where you want the button to render. -->
-            <a class="github-button" href="https://github.com/teambge/bge-python-sdk/subscription" data-color-scheme="no-preference: light; light: light; dark: dark;" data-show-count="true" aria-label="Watch teambge/bge-python-sdk on GitHub">
-                <img alt="GitHub forks" src="https://img.shields.io/github/watchers/teambge/bge-python-sdk?style=social">
-            </a>
-            <a class="github-button" href="https://github.com/teambge/bge-python-sdk" data-color-scheme="no-preference: light; light: light; dark: dark;" data-show-count="true" aria-label="Star teambge/bge-python-sdk on GitHub">
-                <img alt="GitHub forks" src="https://img.shields.io/github/stars/teambge/bge-python-sdk?style=social">
-            </a>
-            <a class="github-button" href="https://github.com/teambge/bge-python-sdk/fork" data-color-scheme="no-preference: light; light: light; dark: dark;" data-show-count="true" aria-label="Fork teambge/bge-python-sdk on GitHub">
-                <img alt="GitHub forks" src="https://img.shields.io/github/forks/teambge/bge-python-sdk?style=social">
-            </a>
-        </p>
-        
-        <p>
-            <img src="https://img.shields.io/github/v/release/teambge/bge-python-sdk" data-origin="https://img.shields.io/github/v/release/teambge/bge-python-sdk" alt="GitHub release (latest by date)">
-            <img src="https://img.shields.io/github/languages/top/teambge/bge-python-sdk" data-origin="https://img.shields.io/github/languages/top/teambge/bge-python-sdk" alt="GitHub top language">
-            <img src="https://img.shields.io/github/languages/code-size/teambge/bge-python-sdk" data-origin="https://img.shields.io/github/languages/code-size/teambge/bge-python-sdk" alt="GitHub code size in bytes">
-            <img src="https://img.shields.io/github/commit-activity/w/teambge/bge-python-sdk" data-origin="https://img.shields.io/github/commit-activity/w/teambge/bge-python-sdk" alt="GitHub commit activity">
-            <img src="https://static.pepy.tech/personalized-badge/bge-python-sdk?period=total&units=international_system&left_color=grey&right_color=blue&left_text=Downloads" data-origin="https://static.pepy.tech/personalized-badge/bge-python-sdk?period=total&units=international_system&left_color=grey&right_color=blue&left_text=Downloads" alt="PyPI - Downloads">
-        </p>
-        
-        <pre>
-            ____  ____________   ______  __________  ______  _   __   _____ ____  __ __
-           / __ )/ ____/ ____/  / __ \ \/ /_  __/ / / / __ \/ | / /  / ___// __ \/ //_/
-          / __  / / __/ __/    / /_/ /\  / / / / /_/ / / / /  |/ /   \__ \/ / / / ,<   
-         / /_/ / /_/ / /___   / ____/ / / / / / __  / /_/ / /|  /   ___/ / /_/ / /| |  
-        /_____/\____/_____/  /_/     /_/ /_/ /_/ /_/\____/_/ |_/   /____/_____/_/ |_| 
-        </pre>
-        
-        </div>
-        
-        BGE 开放平台 是一个跨越多级数据的（多）组学数据平台，开发者在获得用户授权后，将可以通过开放平台提供的 API 访问关联用户的（多）组学数据，甚至写入数据。
-        
-        基于开放平台 API，开发者可避免重复开发采样、提取、测序和生信分析等繁复的流程，直接使用清洁的结构化数据。
-        
-        开发者可以通过开放平台提供的 API 创建极具创意性的（多）组学应用，如：
-        
-        * 包含药物代谢或药物服用建议的应用
-        * 包含体检数据和营养代谢基因的餐饮应用
-        * 包含肠道菌群数据和痛风相关基因的痛风管理应用
-        * 基于祖源成分的社交网络应用，等等
-        
-        BGE 开放平台 API 基于 OAuth 2.0 开发，并使用 SSL/TLS 加密传输，确保用户数据正确无误地授权，并安全地传输到第三方应用，确保用户数据不会被未经授权的应用获得。
-        
-        # 安装
-        
-        推荐使用 pip 进行安装。
-        
-        ```shell
-        $ pip install -U bge-python-sdk
-        ```
-        
-        或者
-        
-        ```shell
-        $ make install
-        ```
-        
-        再或者
-        
-        ```shell
-        $ python setup.py install
-        ```
-        
-        # SDK 文档
-        
-        更加详细的 SDK 文档请查看 [SDK Documents](https://api.bge.genomics.cn/doc/#/sdk/README)。
-        
-        # 快速开始
-        
-        BGE 开放平台支持 OAuth2 的两种模式，分别是用户授权模式、客户端模式。
-        
-        详情请参考开放平台文档 [https://api.bge.genomics.cn/doc](https://api.bge.genomics.cn/doc) 。
-        
-        ## ENDPOINTS
-        
-        BGE 开放平台提供了如下可用的 `endpoint`。
-        
-        | endpoint                    | 解释                                                        |
-        | --------------------------- | ----------------------------------------------------------- |
-        | https://api.bge.genomics.cn | **线上环境** 主域名地址                                     |
-        | https://api.bge.omgut.com   | **线上环境** 副域名地址，主域名地址不可用时可替换此域名地址 |
-        
-        ## 授权码模式
-        
-        ```python
-        from bgesdk import OAuth2, API
-        
-        code = '???????'  # 用户确认授权后平台返回的授权码
-        client_id = 'demo'
-        client_secret = 'demo'
-        redirect_uri = 'http://test.cn'
-        oauth2 = OAuth2(
-            client_id, client_secret,
-            endpoint='https://api.bge.genomics.cn', max_retries=3, timeout=16,
-            verbose=False)
-        token = oauth2.exchange_authorization_code(code, redirect_uri)
-        
-        api = oauth2.get_api(token.access_token)
-        print(api.get_user())
-        
-        api = API(token.access_token)
-        print(api.get_user())
-        ```
-        
-        ## 客户端模式
-        
-        ```python
-        from bgesdk import OAuth2, API
-        
-        client_id = 'demo'
-        client_secret = 'demo'
-        oauth2 = OAuth2(
-            client_id, client_secret,
-            endpoint='https://api.bge.genomics.cn', max_retries=3, timeout=16,
-            verbose=False)
-        token = oauth2.get_credentials_token()
-        
-        api = oauth2.get_api(token.access_token)
-        print(api.get_variants('E-B1243433', 'rs333'))
-        
-        api = API(token.access_token)
-        print(api.get_variants('E-B1243433', 'rs333'))
-        ```
-        
-        # Contributors
-        
-        * xiangji1204's [github](https://github.com/xiangji1204)
-        * leafcoder(leafcoder@gmail.com)'s [github](https://github.com/leafcoder)
-        
-Keywords: bge-python-sdk bge bgesdk sdk
-Platform: UNKNOWN
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Intended Audience :: Developers
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Natural Language :: Chinese (Simplified)
-Classifier: Operating System :: OS Independent
-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
-Classifier: Topic :: Software Development :: Libraries
-Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Classifier: Topic :: Utilities
-Requires-Python: >=3.6.3
-Description-Content-Type: text/markdown