pybioos 0.0.16__py3-none-any.whl → 0.0.17__py3-none-any.whl

bioos/__about__.py

@@ -1,4 +1,4 @@
 # coding:utf-8
 
 # Package version
-__version__ = "0.0.16"
+__version__ = "0.0.17"

bioos/bioos.py

@@ -20,9 +20,9 @@ def status() -> Config.LoginInfo:
     return Config.login_info()
 
 
-def login(endpoint: str,
-          access_key: str,
+def login(access_key: str,
           secret_key: str,
+          endpoint: str = None,
           region: str = REGION_CN_NORTH1) -> bool:
     """Login to the given endpoint using specified account and password.
 
@@ -35,14 +35,16 @@ def login(endpoint: str,
     *Example*:
     ::
 
-        bioos.login(endpoint="https://cloud.xxxxx.xxx.cn",access_key="xxxxxxxx",secret_key="xxxxxxxx")
+        bioos.login(access_key="xxxxxxxx", secret_key="xxxxxxxx")
+        # or specify endpoint explicitly:
+        bioos.login(access_key="xxxxxxxx", secret_key="xxxxxxxx", endpoint="https://cloud.xxxxx.xxx.cn")
 
-    :param endpoint: The environment to be logged in
-    :type endpoint: str
     :param access_key: The specified account's access key
     :type access_key: str
     :param secret_key: Corresponding secret key of the access key
     :type secret_key: str
+    :param endpoint: The environment to be logged in (optional, defaults to Config._endpoint)
+    :type endpoint: str
     :param region: The region to be logged in
     :type region: str
     :return: Login result
@@ -50,7 +52,8 @@ def login(endpoint: str,
     """
     Config.set_access_key(access_key)
     Config.set_secret_key(secret_key)
-    Config.set_endpoint(endpoint)
+    if endpoint is not None:
+        Config.set_endpoint(endpoint)
     Config.set_region(region)
     return Config.login_info().login_status == "Already logged in"
 

bioos/bioos_workflow.py

@@ -10,6 +10,7 @@ import pandas as pd
 
 from bioos import bioos
 from bioos.errors import NotFoundError, ParameterError
+from bioos.config import DEFAULT_ENDPOINT
 
 def uniquify_columns(cols: list[str]) -> list[str]:
     seen, out = {}, []
@@ -323,7 +324,7 @@ def bioos_workflow():
     parser.add_argument("--endpoint",
                         type=str,
                         help="Bio-OS instance platform endpoint",
-                        default="https://bio-top.miracle.ac.cn")
+                        default=DEFAULT_ENDPOINT)
     parser.add_argument(
         "--ak",
         type=str,

bioos/bw_import.py

@@ -1,17 +1,13 @@
 #!/usr/bin/env python3
 # coding: utf-8
-
 import argparse
 import logging
 import os
 import sys
 import time
-
 from bioos import bioos
-from bioos.config import Config
+from bioos.config import Config, DEFAULT_ENDPOINT
 from bioos.resource.workflows import WorkflowResource
-
-
 def get_logger():
     """Setup logger"""
     logger = logging.getLogger('bw_import')
@@ -23,14 +19,11 @@ def get_logger():
         logger.addHandler(handler)
         logger.setLevel(logging.INFO)
     return logger
-
-
 def bioos_workflow_import():
     """Command line entry point"""
     parser = argparse.ArgumentParser(
         description='Bio-OS Workflow Import Tool',
         formatter_class=argparse.RawDescriptionHelpFormatter)
-
     # 必需参数
     parser.add_argument(
         '--ak',
@@ -49,8 +42,10 @@ def bioos_workflow_import():
     parser.add_argument('--workflow_source',
                         required=True,
                         help='Local WDL file path or git repository URL')
-
     # 可选参数
+    parser.add_argument('--endpoint',
+                        help='Bio-OS instance platform endpoint',
+                        default=DEFAULT_ENDPOINT)
     parser.add_argument('--workflow_desc',
                         help='Description for the workflow',
                         default='')
@@ -67,16 +62,13 @@ def bioos_workflow_import():
         type=int,
         default=60,
         help='Time interval in seconds for checking workflow status')
-
     args = parser.parse_args()
     logger = get_logger()
-
     try:
         # 配置Bio-OS
         Config.set_access_key(args.ak)
         Config.set_secret_key(args.sk)
-        Config.set_endpoint("https://bio-top.miracle.ac.cn")
-
+        Config.set_endpoint(args.endpoint)
         # 获取workspace ID
         workspaces = bioos.list_workspaces()
         workspace_info = workspaces.query(f"Name=='{args.workspace_name}'")
@@ -84,10 +76,8 @@ def bioos_workflow_import():
             logger.error(f"Workspace {args.workspace_name} not found")
             sys.exit(1)
         workspace_id = workspace_info["ID"].iloc[0]
-
         # 创建WorkflowResource实例
         workflow_resource = WorkflowResource(workspace_id)
-
         # 导入workflow
         try:
             result = workflow_resource.import_workflow(
@@ -99,19 +89,15 @@ def bioos_workflow_import():
             logger.info(
                 f"Successfully uploaded workflow: {result}, validating..., please wait..."
             )
-
             # 如果设置了monitor参数，则监控工作流状态
             if args.monitor:
                 max_retries = 10  # 最大重试次数
                 retry_count = 0
-
                 while retry_count < max_retries:
                     df = workflow_resource.list()
                     workflow_info = df[df.Name == args.workflow_name]
-
                     if len(workflow_info) == 1:
                         status = workflow_info.iloc[0]["Status"]["Phase"]
-
                         if status == "Succeeded":
                             logger.info(
                                 f"Workflow {args.workflow_name} validated successfully"
@@ -138,7 +124,6 @@ def bioos_workflow_import():
                             f"Workflow {args.workflow_name} not found after import"
                         )
                         sys.exit(1)
-
                 logger.error(
                     f"Workflow validation timeout after {max_retries} retries")
                 sys.exit(1)
@@ -148,15 +133,11 @@ def bioos_workflow_import():
                     f"Workflow {args.workflow_name} is still validating, {result}, please wait and check the status later."
                 )
                 sys.exit(0)
-
         except Exception as e:
             logger.error(f"Failed to import workflow: {str(e)}")
             sys.exit(1)
-
     except Exception as e:
         logger.error(f"Error: {str(e)}")
         sys.exit(1)
-
-
 if __name__ == '__main__':
     bioos_workflow_import()

bioos/bw_import_status_check.py

@@ -6,7 +6,7 @@ import logging
 import sys
 
 from bioos import bioos
-from bioos.config import Config
+from bioos.config import Config, DEFAULT_ENDPOINT
 from bioos.resource.workflows import WorkflowResource
 
 
@@ -44,6 +44,11 @@ def bioos_workflow_status_check():
     parser.add_argument('--workflow_id',
                         required=True,
                         help='ID of the workflow to check')
+    
+    # 可选参数
+    parser.add_argument('--endpoint',
+                        help='Bio-OS instance platform endpoint',
+                        default=DEFAULT_ENDPOINT)
 
     args = parser.parse_args()
     logger = get_logger()
@@ -52,7 +57,7 @@ def bioos_workflow_status_check():
         # 配置Bio-OS
         Config.set_access_key(args.ak)
         Config.set_secret_key(args.sk)
-        Config.set_endpoint("https://bio-top.miracle.ac.cn")
+        Config.set_endpoint(args.endpoint)
 
         # 获取workspace ID
         workspaces = bioos.list_workspaces()

bioos/bw_status_check.py

@@ -6,7 +6,7 @@ import logging
 import sys
 
 from bioos import bioos
-from bioos.config import Config
+from bioos.config import Config, DEFAULT_ENDPOINT
 from bioos.resource.workflows import WorkflowResource
 
 
@@ -44,6 +44,11 @@ def bioos_workflow_status_check():
     parser.add_argument('--submission_id',
                         required=True,
                         help='ID of the submission to check')
+    
+    # 可选参数
+    parser.add_argument('--endpoint',
+                        help='Bio-OS instance platform endpoint',
+                        default=DEFAULT_ENDPOINT)
 
     args = parser.parse_args()
     logger = get_logger()
@@ -52,7 +57,7 @@ def bioos_workflow_status_check():
         # 配置Bio-OS
         Config.set_access_key(args.ak)
         Config.set_secret_key(args.sk)
-        Config.set_endpoint("https://bio-top.miracle.ac.cn")
+        Config.set_endpoint(args.endpoint)
 
         # 获取workspace ID
         workspaces = bioos.list_workspaces()

bioos/config.py

@@ -7,6 +7,9 @@ from bioos.errors import ConfigurationError
 from bioos.log import PyLogger
 from bioos.service.BioOsService import BioOsService
 
+# 默认的 Bio-OS endpoint
+DEFAULT_ENDPOINT = "https://bio-top.miracle.ac.cn"
+
 LOGIN_STATUS = Literal['Already logged in', 'Not logged in']
 
 
@@ -14,7 +17,7 @@ class Config:
     _service: BioOsService = None
     _access_key: str = os.environ.get('VOLC_ACCESSKEY')
     _secret_key: str = os.environ.get('VOLC_SECRETKEY')
-    _endpoint: str = os.environ.get('BIOOS_ENDPOINT')
+    _endpoint: str = os.environ.get('BIOOS_ENDPOINT', DEFAULT_ENDPOINT)
     _region: str = REGION_CN_NORTH1
     Logger = PyLogger()  # 这里是把类赋给了Logger变量
 

bioos/get_submission_logs.py

@@ -7,7 +7,7 @@ import os
 import sys
 
 from bioos import bioos
-from bioos.config import Config
+from bioos.config import Config, DEFAULT_ENDPOINT
 
 
 def get_logger():
@@ -48,6 +48,11 @@ def get_submission_logs():
         '--output_dir',
         default='.',
         help='Local directory to save the logs (default: current directory)')
+    
+    # 可选参数
+    parser.add_argument('--endpoint',
+                        help='Bio-OS instance platform endpoint',
+                        default=DEFAULT_ENDPOINT)
 
     args = parser.parse_args()
     logger = get_logger()
@@ -56,7 +61,7 @@ def get_submission_logs():
         # 配置Bio-OS
         Config.set_access_key(args.ak)
         Config.set_secret_key(args.sk)
-        Config.set_endpoint("https://bio-top.miracle.ac.cn")
+        Config.set_endpoint(args.endpoint)
 
         # 获取workspace ID
         workspaces = bioos.list_workspaces()

bioos/workflow_info.py

@@ -2,14 +2,13 @@ from typing import Dict, Any, List, Optional
 import pandas as pd
 
 from bioos import bioos
-from bioos.config import Config
+from bioos.config import Config, DEFAULT_ENDPOINT
 from bioos.errors import NotFoundError
 
-
 class WorkflowInfo:
     """Bio-OS 工作流信息查询类"""
 
-    def __init__(self, ak: str, sk: str, endpoint: str = "https://bio-top.miracle.ac.cn"):
+    def __init__(self, ak: str, sk: str, endpoint: str = DEFAULT_ENDPOINT):
         """
         初始化工作流信息查询类
 

{pybioos-0.0.16.dist-info → pybioos-0.0.17.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybioos
-Version: 0.0.16
+Version: 0.0.17
 Summary: BioOS SDK for Python
 Home-page: https://github.com/GBA-BI/pybioos
 Author: Jilong Liu
@@ -13,13 +13,15 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Interface Engine/Protocol Translator
 License-File: LICENSE
-Requires-Dist: volcengine >=1.0.61
-Requires-Dist: tabulate >=0.8.10
-Requires-Dist: click >=8.0.0
-Requires-Dist: pandas >=1.3.0
-Requires-Dist: tos ==2.5.6
-Requires-Dist: cachetools >=5.2.0
-Requires-Dist: typing-extensions >=4.4.0
-Requires-Dist: apscheduler >=3.10.4
-Requires-Dist: colorama >=0.4.6
+Requires-Dist: volcengine (>=1.0.61)
+Requires-Dist: tabulate (>=0.8.10)
+Requires-Dist: click (>=8.0.0)
+Requires-Dist: pandas (>=1.3.0)
+Requires-Dist: tos (==2.5.6)
+Requires-Dist: cachetools (>=5.2.0)
+Requires-Dist: typing-extensions (>=4.4.0)
+Requires-Dist: apscheduler (>=3.10.4)
+Requires-Dist: colorama (>=0.4.6)
+
+UNKNOWN
 

{pybioos-0.0.16.dist-info → pybioos-0.0.17.dist-info}/RECORD

@@ -1,15 +1,15 @@
-bioos/__about__.py,sha256=TRnHZsxI7bVBqxAdnBiKbEhtnboUzdISbOREW1kz-io,56
+bioos/__about__.py,sha256=FvqUBfyX_OkxcuTYr1_lcBcEd13i1ew8F8tEpRfcor8,57
 bioos/__init__.py,sha256=4GZKi13lDTD25YBkGakhZyEQZWTER_OWQMNPoH_UM2c,22
-bioos/bioos.py,sha256=fHzOb1l5wYxw6NVYYZDiFcgk4V28BAgWEc3ev12reWs,2409
-bioos/bioos_workflow.py,sha256=BgooweeFT4O7SyProup2gOVSeXDb3pXWge--PD7J-lE,15232
-bioos/bw_import.py,sha256=lQk_ch_tTz8l4bnWniOzWZ1IxI6ZvKlaASkNMsdDGfA,5697
-bioos/bw_import_status_check.py,sha256=sJuso2SAfZWvPzypnGge25Ayv5PsSGRXqSNNwIhNu-E,2794
-bioos/bw_status_check.py,sha256=FVilkawRA7GD1JXUBeaR28W1DfN9bAzYBIAjqi4JIno,2916
-bioos/config.py,sha256=CvFabYqV1BkFWO8fnr5vBf6xNtNzA8hAEVeEIbvAOm8,4307
+bioos/bioos.py,sha256=yhaWaJMwP23fMtid2mNWUetGwDUbUtCKwugXt27OLTs,2600
+bioos/bioos_workflow.py,sha256=LRzYxuNnbF3R7urrMRjMRwR2hGDmH_4kP52D2Gger8k,15259
+bioos/bw_import.py,sha256=kYS4BDbyIXyaFIOCUyOnAzIbLdHvY3l3KLPDVfAnFSM,5829
+bioos/bw_import_status_check.py,sha256=x9Y_0I8huoC7aBgObuox-0z6foSr99TXQB7jozyQ7Eo,2972
+bioos/bw_status_check.py,sha256=Etj_zp6tS0cj4t-nksUq221pPIWUFS0Lz0q0Uqflpes,3094
+bioos/config.py,sha256=-1qS0uYgV-h3d67LyOuJ3lzDskEytXHI7T65-p8tnhA,4405
 bioos/errors.py,sha256=p0fH6JSMYBjul88lMJ7PPwGNh4SYg62-7VMNuUXWl-E,2540
-bioos/get_submission_logs.py,sha256=jUtT8Vic8h_VOcqrqJsTBSonve64RjbKNAyp0wUtIpg,3934
+bioos/get_submission_logs.py,sha256=e0OlWwMso8bB6u1TepJpRim2L-trxM6x3IdgZSwo7jc,4112
 bioos/log.py,sha256=twiCvf5IgJB7uvzANwBluSlztJN8ZrxbGZUBGlZ0vps,3204
-bioos/workflow_info.py,sha256=bE9h1pE7Co8icS-J5WVHfSAbjef9EtLhpWjbHQcnFfc,6838
+bioos/workflow_info.py,sha256=5PT45Lv-Js84ljZxjb9uNl0Jd5l-LYnXyKHYKrOhcjI,6840
 bioos/internal/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
 bioos/internal/tos.py,sha256=0R6YN2lxjjZsuMfv0yLSkBmz_LqmzQGb8GagnUMc8EY,12264
 bioos/models/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
@@ -35,9 +35,9 @@ bioos/tests/workspaces.py,sha256=LuuRrTs2XqfE5mGQyJNl9RBtuMb4NZHBJFoO8HMZVYQ,522
 bioos/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bioos/utils/common_tools.py,sha256=fgMoE_-qZjgfQtUj_pmCTyYDtbJasyfH4Gm3VQsbgBQ,1651
 bioos/utils/workflows.py,sha256=zRbwTUigoM5V5LFOgzQPm3kwxt5Ogz95OFfefJc6Fjo,133
-pybioos-0.0.16.dist-info/LICENSE,sha256=cPkGXsgfPgEhIns7Lt3Avxx0Uy-VbdsoP8jvNGuj3cE,1063
-pybioos-0.0.16.dist-info/METADATA,sha256=9M9p2P6lr9kiUB1KIQ15MZPIADDBFhw8YD1Zjho1oBk,803
-pybioos-0.0.16.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-pybioos-0.0.16.dist-info/entry_points.txt,sha256=O-8Gg-zLuYcnOYbx1BMqAgEsoEZfKwtM19cUctHuYus,327
-pybioos-0.0.16.dist-info/top_level.txt,sha256=llpzydkKVDSaWZgz3bsTUsQmhoQpc_JcRJg2-H-5a2U,6
-pybioos-0.0.16.dist-info/RECORD,,
+pybioos-0.0.17.dist-info/LICENSE,sha256=cPkGXsgfPgEhIns7Lt3Avxx0Uy-VbdsoP8jvNGuj3cE,1063
+pybioos-0.0.17.dist-info/METADATA,sha256=thfygW7I6xtSkuKrMuzRw00fzmtPRtvFB5yfNIHRoj8,830
+pybioos-0.0.17.dist-info/WHEEL,sha256=OqRkF0eY5GHssMorFjlbTIq072vpHpF60fIQA6lS9xA,92
+pybioos-0.0.17.dist-info/entry_points.txt,sha256=Sc5H0_X7r03Mef4Qd70bebqgdIbVAxLU7nV7qP7cKD4,328
+pybioos-0.0.17.dist-info/top_level.txt,sha256=llpzydkKVDSaWZgz3bsTUsQmhoQpc_JcRJg2-H-5a2U,6
+pybioos-0.0.17.dist-info/RECORD,,

{pybioos-0.0.16.dist-info → pybioos-0.0.17.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: bdist_wheel (0.36.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{pybioos-0.0.16.dist-info → pybioos-0.0.17.dist-info}/entry_points.txt

@@ -4,3 +4,4 @@ bw_import = bioos.bw_import:bioos_workflow_import
 bw_import_status_check = bioos.bw_import_status_check:bioos_workflow_status_check
 bw_status_check = bioos.bw_status_check:bioos_workflow_status_check
 get_submission_logs = bioos.get_submission_logs:get_submission_logs
+