Merge branch 'feature-minify' into 'develop'

新增模型代码混淆功能

See merge request bge/bge-python-sdk!5

Author: zhanglei3

.coverage

@@ -1,4 +1,3 @@
-
 [run]
 branch = True
-omit = tests/*
+omit = tests/*,*management*,*__main__.py*,setup.py

.coveragerc

@@ -0,0 +1,128 @@
+# [0.3.0](https://gitlab.omgut.com/bge/bge-python-sdk/compare/v0.2.4...v0.3.0) (2022-04-22)
+
+
+### Bug Fixes
+
+* 修复模型配置命令不输入模型编号无法进入下一步的问题 ([e942e02](https://gitlab.omgut.com/bge/bge-python-sdk/commit/e942e0271c25bb6cba5170c40ead5a6000702cf5))
+* 专业级变异接口regions参数验证 ([56ab2c8](https://gitlab.omgut.com/bge/bge-python-sdk/commit/56ab2c812e6b7cf78534ba91884952081c57e3fb))
+* regions参数改为列表传入 ([023554a](https://gitlab.omgut.com/bge/bge-python-sdk/commit/023554acdf471d45a9800753ab2f2e78addf5ed8))
+
+
+### Features
+
+* 更新 SDK 版本号至 v0.3.0 ([4cd68eb](https://gitlab.omgut.com/bge/bge-python-sdk/commit/4cd68eb6a85e33636934d73024133c948704df1b))
+* 新增命令行打印输出命令运行时间戳 ([d9b2638](https://gitlab.omgut.com/bge/bge-python-sdk/commit/d9b263808748a5d57b3771d208bc6c7e53c9af39))
+* 新增模型代码混淆功能至模型发布命令 ([1383072](https://gitlab.omgut.com/bge/bge-python-sdk/commit/13830724f0ecdbcc392a38ea7877a0a53c863c56))
+* 新增专业级变异接口 ([b753be0](https://gitlab.omgut.com/bge/bge-python-sdk/commit/b753be0b57f86d3e74431cbee226430ff6113c5d))
+* 增加模型代码混淆功能并使用 rich 增强命令行工具 ([44d83c6](https://gitlab.omgut.com/bge/bge-python-sdk/commit/44d83c6f71d6a3e511b5dc9f46790da2d9745ff8))
+* **command:** 增加 bge config list 命令 ([be7e542](https://gitlab.omgut.com/bge/bge-python-sdk/commit/be7e5428efee38026f83acd1d2f33c94b9761c54))
+
+
+
+## [0.2.8](https://gitlab.omgut.com/bge/bge-python-sdk/compare/v0.2.4...v0.2.8) (2022-04-18)
+
+
+### Bug Fixes
+
+* 更新自定义命令顺序 ([df04fcb](https://gitlab.omgut.com/bge/bge-python-sdk/commit/df04fcb773f004f6a399bb1cedfaf3d2cfa9f546))
+* 强制转 biosample_id 为大写,修复 get_taxon_abundance 返回 Model 对象 ([010d831](https://gitlab.omgut.com/bge/bge-python-sdk/commit/010d8313c997fcdb02de295373d8c5df08efcff1))
+* 删除命令中 biosample_id 调用的 upper 方法 ([b43799d](https://gitlab.omgut.com/bge/bge-python-sdk/commit/b43799dccde09f39901d0fbe15f2ddb041cda707))
+* 修复 py2 和 py3 对可变参数与关键字参数的位置格式问题 ([b9820b2](https://gitlab.omgut.com/bge/bge-python-sdk/commit/b9820b233e988b680eabd2ea77fbf4dba98476c7))
+* 修复 python3.7 中 argparser 要求 add_subparsers 要明确指定 required 参数的问题 ([c5a7f32](https://gitlab.omgut.com/bge/bge-python-sdk/commit/c5a7f320ce9ec60baa65e6ed67259292b7b1cf51))
+* 修复安装包时由于依赖造成包安装报错的问题 ([85f4625](https://gitlab.omgut.com/bge/bge-python-sdk/commit/85f462576dae64b696f4f8c95315cc2a98cf69bb))
+* 修复参数为 None 时提示无 upper 的错误 ([8c78a2d](https://gitlab.omgut.com/bge/bge-python-sdk/commit/8c78a2d7e6e37b5146c3f3497862d972298aefc6))
+* 修复模型配置命令不输入模型编号无法进入下一步的问题 ([e942e02](https://gitlab.omgut.com/bge/bge-python-sdk/commit/e942e0271c25bb6cba5170c40ead5a6000702cf5))
+* 修改 get_user 方法默认使用 /profile 接口 ([0acde99](https://gitlab.omgut.com/bge/bge-python-sdk/commit/0acde99603c56b882916520d9c89786535f174e8))
+* 专业级变异接口regions参数验证 ([56ab2c8](https://gitlab.omgut.com/bge/bge-python-sdk/commit/56ab2c812e6b7cf78534ba91884952081c57e3fb))
+* regions参数改为列表传入 ([023554a](https://gitlab.omgut.com/bge/bge-python-sdk/commit/023554acdf471d45a9800753ab2f2e78addf5ed8))
+* SDK命令行工具兼容windows系统，代码中print改为sys包输出 ([3cd2824](https://gitlab.omgut.com/bge/bge-python-sdk/commit/3cd2824013b12ccbffbcf24495beb57605044fe2))
+
+
+### Features
+
+* 新增专业级变异接口 ([b753be0](https://gitlab.omgut.com/bge/bge-python-sdk/commit/b753be0b57f86d3e74431cbee226430ff6113c5d))
+
+
+
+## [0.1.5](https://gitlab.omgut.com/bge/bge-python-sdk/compare/v0.1.4...v0.1.5) (2021-09-22)
+
+
+### Features
+
+* 新增批量上传和目录上传接口和命令 ([d14033d](https://gitlab.omgut.com/bge/bge-python-sdk/commit/d14033d983661b304ebacd5a9adbabbd2c1db826))
+
+
+
+## [0.1.4](https://gitlab.omgut.com/bge/bge-python-sdk/compare/v0.1.3...v0.1.4) (2021-09-18)
+
+
+### Bug Fixes
+
+* 更新单元测试 ([fe172c2](https://gitlab.omgut.com/bge/bge-python-sdk/commit/fe172c206f10c9fd85e32e26d2840572d7025f9b))
+* 更新单元测试 OAuth2 的断言信息 ([bda033a](https://gitlab.omgut.com/bge/bge-python-sdk/commit/bda033af2f2c31c3006f6579bd2dfe708ee327e9))
+* 更新日志输出 ([7e50abe](https://gitlab.omgut.com/bge/bge-python-sdk/commit/7e50abeab3dffd3dfe7b65b5bc96c4b1b56e0477))
+* 模型文档预览工具逻辑修改 ([5ba6be5](https://gitlab.omgut.com/bge/bge-python-sdk/commit/5ba6be508242835b76a78b148d261d0de7905100))
+* 删除 token 命令的 --save 参数 ([683a428](https://gitlab.omgut.com/bge/bge-python-sdk/commit/683a4283e5f45bae18ecce3d1fceb5d24ffdeb76))
+* 删除无用参数 ([d7b4853](https://gitlab.omgut.com/bge/bge-python-sdk/commit/d7b4853849719a9bfe15ab026afd2542d38b32db))
+* 删除test.py ([c7a8f80](https://gitlab.omgut.com/bge/bge-python-sdk/commit/c7a8f8017ebad9d5f87d8054fd31cc070f53d31f))
+* 文档上传参数修改 ([59ceedc](https://gitlab.omgut.com/bge/bge-python-sdk/commit/59ceedc34808ebb325d1aa636498b9599e93e1cd))
+* 修复 client.download 中下载文件时 timeout 参数未定义的问题 ([b363659](https://gitlab.omgut.com/bge/bge-python-sdk/commit/b36365975d21317ccfda65e95c5a0ccf75a9eb00))
+* 修复 register_sample 返回对象时出错的问题 ([f848bb4](https://gitlab.omgut.com/bge/bge-python-sdk/commit/f848bb465957b7c8e29501cd2119d083024a5dba))
+* 修复本地测试模型无法 print 打印输出的问题 ([5ee3eb8](https://gitlab.omgut.com/bge/bge-python-sdk/commit/5ee3eb8716ba42007cb032a7db45812f020d8166))
+* 修复创建脚手架时未安装 requests_toolbelt 的问题 ([6f615d2](https://gitlab.omgut.com/bge/bge-python-sdk/commit/6f615d2bd697a5a3ffb71e6e3444a31da9d9084c))
+* 修复命令行工具 bge config 运行中 endpoint 错误的问题 ([2ec09ef](https://gitlab.omgut.com/bge/bge-python-sdk/commit/2ec09efce433f646b816e3f0f3bb207de25ee9c0))
+* 修复模型初始化包含字典的字典时出错的问题 ([83099ca](https://gitlab.omgut.com/bge/bge-python-sdk/commit/83099ca99332b8bbfac8b9c5abf1aa297c018203))
+* 修复模型命令相关脚本中 docker 服务未启动时的错误提示问题 ([55a5045](https://gitlab.omgut.com/bge/bge-python-sdk/commit/55a5045e70218f54469a6e6578384c12c9718be9))
+* 修复模型运行测试服务器时自动退出的问题 ([e851f22](https://gitlab.omgut.com/bge/bge-python-sdk/commit/e851f220b381fd4c0c53d2e8993847864fc22a12))
+* 修复自定义异常类错误 ([eb56d51](https://gitlab.omgut.com/bge/bge-python-sdk/commit/eb56d51379c8881df349c37ca328a153ea3c09c2))
+* 修改 bge model start 命令不存在 docker 镜像时自动拉取镜像 ([ff71129](https://gitlab.omgut.com/bge/bge-python-sdk/commit/ff711291b31efacaf274c4955778849c13ab5807))
+* 修改 docker 服务未启动时的错误提示 ([6793b05](https://gitlab.omgut.com/bge/bge-python-sdk/commit/6793b05025cab458d1a0e83dcb94fce0cf151d11))
+* 修改 timeout 参数 ([00bcdbb](https://gitlab.omgut.com/bge/bge-python-sdk/commit/00bcdbb0bbd480438615eac91a8d02801ce5e9b8))
+* 修改版本号 ([e9d4ad2](https://gitlab.omgut.com/bge/bge-python-sdk/commit/e9d4ad243050ffbc70606c1581fbf04bdf001fde))
+* 修改版本号 ([cb2e74d](https://gitlab.omgut.com/bge/bge-python-sdk/commit/cb2e74d5ecaa22d971b8202edd3d8a9574d8a726))
+* 修改模型 main.py 模板 ([58f5b8b](https://gitlab.omgut.com/bge/bge-python-sdk/commit/58f5b8b77a88788cb930f859184273ff6b6e2e40))
+* 修改模型依赖包安装命令 ([fcef9e4](https://gitlab.omgut.com/bge/bge-python-sdk/commit/fcef9e4134a112ced96e036954454d4f31a14e97))
+* 修改判断是否已安装docker的逻辑 ([ac6c0af](https://gitlab.omgut.com/bge/bge-python-sdk/commit/ac6c0af9a5fdbaa2880c27439e17987186a3b50e))
+* 修改为不指定具体依赖包版本 ([f67a7b6](https://gitlab.omgut.com/bge/bge-python-sdk/commit/f67a7b68825490597d5e9f459a971f230077b9a2))
+* 直接使用 pytest，避免 tox 提示警告 make 为外部命令 ([1c025f1](https://gitlab.omgut.com/bge/bge-python-sdk/commit/1c025f1c6d6588946eeff1ecfdb48b61482abe56))
+
+
+### Features
+
+* 调整 API 初始化逻辑，去除 OAuth2 依赖 ([f0bbbfb](https://gitlab.omgut.com/bge/bge-python-sdk/commit/f0bbbfbab77b1478dc86c007403ceb7426f041d7))
+* 调整初始化参数等，新增 alive 接口 ([a404ecf](https://gitlab.omgut.com/bge/bge-python-sdk/commit/a404ecf10acaef7a702e876474b443be5bdd285d))
+* 更新版本号到 0.1.1 ([ed7746d](https://gitlab.omgut.com/bge/bge-python-sdk/commit/ed7746d01899990da9a3a82c5cce1e5d067a66f7))
+* 更新模型相关命令 ([572bac4](https://gitlab.omgut.com/bge/bge-python-sdk/commit/572bac4a1bd88d2b7d16477d40d04d41e685a9e4))
+* 获取变异位点与样品数据接口调整，去除问卷相关接口 ([99de9a2](https://gitlab.omgut.com/bge/bge-python-sdk/commit/99de9a2dcd8fadda5e6079b603b29ff2c60271ec))
+* 模型文档发布命令 ([64ae8fa](https://gitlab.omgut.com/bge/bge-python-sdk/commit/64ae8fa4aa6374852efb409a08820101c2b5d97c))
+* 模型文档上传接口 ([d1da6f4](https://gitlab.omgut.com/bge/bge-python-sdk/commit/d1da6f4a11cfea533742f9893121e662bdc1d297))
+* 删除模型 build 命令并限制打包文件上传大小 ([97bc7fd](https://gitlab.omgut.com/bge/bge-python-sdk/commit/97bc7fd9c6ec6b9ff72073d78ab3ebd6cd8de3ca))
+* 升级 SDK 命令行工具 ([5115e67](https://gitlab.omgut.com/bge/bge-python-sdk/commit/5115e67f2f8e1be45738309942bd184f2753b6a3))
+* 升级版本号 ([071f0dd](https://gitlab.omgut.com/bge/bge-python-sdk/commit/071f0dde6237b6d386bcc954a5c10ac4eae99d1b))
+* 添加git忽略文件 ([d1eb89f](https://gitlab.omgut.com/bge/bge-python-sdk/commit/d1eb89f19794511062aaf426fa414fda45b3f976))
+* 项目重构 ([8e78015](https://gitlab.omgut.com/bge/bge-python-sdk/commit/8e78015776752757a1b3613220e367ed71ad6e9e))
+* 项目重构 ([a088b39](https://gitlab.omgut.com/bge/bge-python-sdk/commit/a088b39d7e64fe622b1f4cfee28f04f340e88f94))
+* 新增 api 命令行工具并重构命令实现方式 ([4d142b8](https://gitlab.omgut.com/bge/bge-python-sdk/commit/4d142b83dbf3cf9cfe99366f4ef07e48f58c68c0))
+* 新增 OAuth2 数据模型，升级 Model 类，支持 json 格式的导入导出 ([740053a](https://gitlab.omgut.com/bge/bge-python-sdk/commit/740053a94dc03a6a205bb91cd8f9d39173db1363))
+* 新增 sdk 打包 ignore 特性,支持定义不希望打包上传的 unix filename patterns ([08a8f46](https://gitlab.omgut.com/bge/bge-python-sdk/commit/08a8f46f9e8c290dd5713bb990aac31dac9e87e7))
+* 新增 SDK 命令行工具 ([d8e8135](https://gitlab.omgut.com/bge/bge-python-sdk/commit/d8e813550a44f963c7a0db59937fefa65fa07d89))
+* 新增 upload 方法直接上传文件 ([859f47a](https://gitlab.omgut.com/bge/bge-python-sdk/commit/859f47a2e63d990c97e62d6b5cff5c188ce73ec4))
+* 新增客户端加密上传文件功能 ([c3a8983](https://gitlab.omgut.com/bge/bge-python-sdk/commit/c3a8983dfd1e416bd58af0378cbf35004c01d32b))
+* 新增模型配置项可选菜单和整数范围限制 ([052dd54](https://gitlab.omgut.com/bge/bge-python-sdk/commit/052dd54d8426425ea22bd5307f7fdf51e295a5ef))
+* 新增模型启动本地测试服务器命令 ([e11eda9](https://gitlab.omgut.com/bge/bge-python-sdk/commit/e11eda947c880d3ebba64a7156cadc4af0081b59))
+* 新增上传 pypi 命令 ([b819ed0](https://gitlab.omgut.com/bge/bge-python-sdk/commit/b819ed078535616c4ddb42b4286d48ca7d587224))
+* 新增上传模型数据集命令和接口，并增加文件上传进度日志 ([c987041](https://gitlab.omgut.com/bge/bge-python-sdk/commit/c9870410527e6da360aefd8a5026bf25bda93b05))
+* 新增授权码模式、用户、任务等命令 ([d21c098](https://gitlab.omgut.com/bge/bge-python-sdk/commit/d21c098d831c4cb13d326994055aff8bccae2875))
+* 新增数据流接口、部署模型、回滚模型接口 ([c78eed4](https://gitlab.omgut.com/bge/bge-python-sdk/commit/c78eed4eb98f7203ce7ff81bab35addfd4d703ea))
+* 新增数据项接口 ([45b4e2f](https://gitlab.omgut.com/bge/bge-python-sdk/commit/45b4e2f64656a9f21b465f0a4db8ff00f73f82f7))
+* 新增数据项接口 ([f91e7ea](https://gitlab.omgut.com/bge/bge-python-sdk/commit/f91e7eab95ce63396f76f124e480c98bdbc2ad3d))
+* 新增文件上传默认增加自定义头部保存上传文件的客户端编号,并新增 introspect 接口 ([94947e2](https://gitlab.omgut.com/bge/bge-python-sdk/commit/94947e2e540fd7bfa1a3cd9b623cd48ff12d6b39))
+* 新增下载文件到 file like object 的方法 ([30e74e7](https://gitlab.omgut.com/bge/bge-python-sdk/commit/30e74e7eaebb48686b3cbbce1d4fa1e25acbb2f8))
+* 修改上传日志为单行覆盖输出 ([86a6e9f](https://gitlab.omgut.com/bge/bge-python-sdk/commit/86a6e9f7b0ba41c15f365c8b0971190e3627778f))
+* 修改上传日志为单行覆盖输出 ([978af20](https://gitlab.omgut.com/bge/bge-python-sdk/commit/978af209bfb6ace017960ab696dbaf6ca07914c6))
+* 异常捕获简化处理 ([bfff596](https://gitlab.omgut.com/bge/bge-python-sdk/commit/bfff596354e638b7a4f02c077468e770aa062cda))
+* Change version ([af97b33](https://gitlab.omgut.com/bge/bge-python-sdk/commit/af97b33c14550696e4c5729494fc22d8908a2133))
+* sdk第一次提交 ([77f7fa5](https://gitlab.omgut.com/bge/bge-python-sdk/commit/77f7fa503f071b0b316e5164b7a1e987264d6e83))
+
+
+

CHANGELOG.md

@@ -2,9 +2,11 @@ node {
   stage('SCM') {
     checkout scm
   }
+
   environment {
-    JAVA_HOME = '/usr/lib/jvm/jdk-11'
+    JAVA_HOME = '/usr/lib/jvm/jdk-11.0.2'
   }
+
   stage('SonarQube Analysis') {
     def scannerHome = tool 'SonarScanner';
     withSonarQubeEnv() {

Jenkinsfile

@@ -6,10 +6,9 @@ install:
 	$(PYTHON) setup.py install
 
 # 构建源码包
-build: wheel
+build:
 	$(PYTHON) setup.py bdist_wheel
-	$(PYTHON) setup.py sdist --formats=gztar,zip,bztar,xztar,ztar,tar
-	$(PYTHON) setup.py bdist
+	$(PYTHON) setup.py sdist
 
 # 单元测试
 test:
@@ -25,6 +24,9 @@ upload:
 	pip install twine; \
 	twine upload dist/*
 
+changelog:
+	npm run changelog
+
 clean:
 	rm -rf build \
 		   dist \
@@ -40,6 +42,7 @@ clean:
 		   bgesdk/management/commands/api/commands/*.pyc \
 		   bgesdk/management/commands/api/commands/__pycache__/ \
 		   tests/*.pyc \
-		   tests/__pycache__/
+		   tests/__pycache__/ \
+		   .bge/tmp/*
 
-.PHONY: test upload upload-test build wheel install clean
+.PHONY: test upload upload-test build install changelog clean

Makefile

@@ -2,8 +2,6 @@
 
 from __future__ import unicode_literals
 
-import json
-
 
 class BGEError(Exception):
     """SDK 错误"""
@@ -13,11 +11,12 @@ class APIError(BGEError):
     """接口错误"""
 
     def __init__(self, code, msg, data=None):
-        self.code = int(code)
+        self.code = code = int(code)
         self.msg = msg
         self.data = data
-        super(APIError, self).__init__({
-            'code': self.code,
-            'msg': self.msg,
-            'data': self.data
-        })
+        self.result = result = {
+            'code': code,
+            'msg': msg,
+            'data': data
+        }
+        super(APIError, self).__init__(result)

bgesdk/error.py

@@ -1,18 +1,17 @@
-import json
 import sys
 
 from bgesdk.client import API
 from bgesdk.error import APIError
 from bgesdk.management import constants
 from bgesdk.management.command import BaseCommand
 from bgesdk.management.utils import (
-    get_active_project,
     config_get,
-    read_config,
-    output
+    get_active_project,
+    output,
+    output_json,
+    read_config
 )
 from bgesdk.models import ModelEncoder
-from bgesdk.version import __version__
 
 
 DEFAULT_OAUTH2_SECTION = constants.DEFAULT_OAUTH2_SECTION
@@ -69,12 +68,6 @@ def add_arguments(self, parser):
             default=100,
             help='聚合时间维度返回数。'
         )
-        parser.add_argument(
-            '--pretty',
-            default=False,
-            action='store_true',
-            help='打印可读性高的 JSON 字符串。'
-        )
         parser.add_argument(
             '-t',
             '--access_token',
@@ -83,7 +76,6 @@ def add_arguments(self, parser):
         )
 
     def handler(self, args):
-        pretty = args.pretty
         access_token = args.access_token
         project = get_active_project()
         oauth2_section = DEFAULT_OAUTH2_SECTION
@@ -104,13 +96,11 @@ def handler(self, args):
                 periods=args.periods
             )
         except APIError as e:
-            output('请求失败：{}'.format(e))
+            output('[red]请求失败：[/red]')
+            output_json(e.result)
             sys.exit(1)
-        if pretty:
-            result = json.dumps(
-                result, ensure_ascii=False, indent=4, cls=ModelEncoder
-            )
-        else:
-            result = json.dumps(result, ensure_ascii=False, cls=ModelEncoder)
-        output('请求成功，返回值：')
-        output(result)
+        output('[green]请求成功：[/green]')
+        output_json(
+            result,
+            cls=ModelEncoder
+        )

bgesdk/management/commands/api/commands/aggregate_omics_data.py

@@ -6,12 +6,13 @@
 from bgesdk.management import constants
 from bgesdk.management.command import BaseCommand
 from bgesdk.management.utils import (
-    get_active_project,
     config_get,
-    read_config,
-    output
+    console,
+    get_active_project,
+    output,
+    output_json,
+    read_config
 )
-from bgesdk.version import __version__
 
 
 DEFAULT_OAUTH2_SECTION = constants.DEFAULT_OAUTH2_SECTION
@@ -79,7 +80,11 @@ def handler(self, args):
         api = API(access_token, endpoint=endpoint, timeout=18.)
         filename = posixpath.split(object_name)[1]
         if filename == '':
-            output('下载失败，object_name 不是文件：{}'.format(repr(object_name)))
+            output(
+                '[red]下载失败，object_name 不是文件：{}[/red]'.format(
+                    repr(object_name)
+                )
+            )
             sys.exit(1)
         if posixpath.exists(filename):
             basename, suffix = posixpath.splitext(filename)
@@ -90,16 +95,19 @@ def handler(self, args):
                 if not posixpath.exists(filename):
                     break
                 i += 1
-        try:
-            with open(filename, mode) as fp:
-                api.download(
-                    object_name,
-                    fp,
-                    region=args.region,
-                    expiration_time=args.expiration_time,
-                    chunk_size=args.chunk_size
-                )
-        except APIError as e:
-            output('\n\n请求失败：{}'.format(e))
-            sys.exit(1)
-        output('\n\n文件下载成功：{}'.format(filename))
+        message = '正在下载 {}'.format(object_name)
+        with console.status(message, spinner='earth'):
+            try:
+                with open(filename, mode) as fp:
+                    api.download(
+                        object_name,
+                        fp,
+                        region=args.region,
+                        expiration_time=args.expiration_time,
+                        chunk_size=args.chunk_size
+                    )
+            except APIError as e:
+                output('[red]请求失败：[/red]')
+                output_json(e.result)
+                sys.exit(1)
+            output('[green]文件下载成功：[/green]{}'.format(filename))