pybioos 0.0.15__py3-none-any.whl → 0.0.17__py3-none-any.whl

bioos/__about__.py

@@ -1,4 +1,4 @@
 # coding:utf-8
 
 # Package version
-__version__ = "0.0.15"
+__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

@@ -4,12 +4,25 @@ import logging
 import os
 import re
 import time
+from typing import Dict, Any
 
 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 = {}, []
+    for col in cols:
+        base = col.split(".")[-1]
+        if base not in seen:
+            seen[base] = 0
+            out.append(base)
+        else:
+            seen[base] += 1
+            out.append(f"{base}_{seen[base]}")   # fastq → fastq_1 → fastq_2
+    return out
 
 def recognize_files_from_input_json(workflow_input_json: dict) -> dict:
     putative_files = {}
@@ -168,6 +181,9 @@ class Bioos_workflow:
                     force_reupload: bool = False):
         if not os.path.isfile(input_json_file):
             raise ParameterError('Input_json_file is not found.')
+        #给每一个data_model加一个uuid，保证不重复
+        if data_model_name == "dm":
+            data_model_name = f"dm_{int(time.time())}"
 
         input_json = json.load(open(input_json_file))
         self.logger.info("Load json input successfully.")
@@ -231,7 +247,8 @@ class Bioos_workflow:
             df[id_col] = [f"tmp_{x}" for x in list(range(len(df)))]
             df = df.reindex(columns=columns)
             columns = [key.split(".")[-1] for key in df.columns.to_list()]
-            df.columns = pd.Index(columns)
+            #df.columns = pd.Index(columns)
+            df.columns = pd.Index(uniquify_columns(df.columns.to_list()))
 
             # write data models
             self.ws.data_models.write({data_model_name: df.applymap(str)},
@@ -243,6 +260,7 @@ class Bioos_workflow:
             for key, _ in unupdate_dict.items():
                 unupdate_dict[key] = f'this.{key.split(".")[-1]}'
 
+
             self.params_submit["inputs"] = json.dumps(unupdate_dict)
             self.params_submit["data_model_name"] = data_model_name
             self.params_submit["row_ids"] = df[id_col].to_list()
@@ -254,7 +272,7 @@ class Bioos_workflow:
         self.logger.info("Build params dict successfully.")
         return self.params_submit
 
-    def postprocess(self, download=False):
+    def postprocess(self, download=False,download_dir="."):
         # 假设全部执行完毕
         #  对运行完成的目录进行下载
         # 证实bioos包只能对文件的list进行下载，不支持文件夹
@@ -268,9 +286,10 @@ class Bioos_workflow:
 
                     files.append(file)
 
-        if download:
+        if download and files:
+            os.makedirs(download_dir, exist_ok=True)
             try:
-                self.ws.files.download(files, ".", flatten=False)
+                self.ws.files.download(files, download_dir, flatten=False)
             except Exception as e:
                 print(f'Some file can not download. \n {e}')
 
@@ -305,7 +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,
@@ -357,6 +376,11 @@ def bioos_workflow():
         "--download_results",
         action='store_true',
         help="Download the submission run result files to local current path.")
+    parser.add_argument(
+        "--download_dir",
+        type=str,
+        default=".",
+        help="本地保存下载结果的目录（默认当前目录）")
 
     parsed_args = parser.parse_args()
 
@@ -395,5 +419,5 @@ def bioos_workflow():
         print(bw.runs)
 
         bw.logger.info("Start to postprocess.")
-        bw.postprocess(download=parsed_args.download_results)
+        bw.postprocess(download=parsed_args.download_results,download_dir = parsed_args.download_dir)
         bw.logger.info("Postprocess finished.")

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/resource/workflows.py

@@ -3,7 +3,7 @@ import os
 import zipfile
 from datetime import datetime
 from io import BytesIO
-from typing import List
+from typing import List, Dict, Optional, Any
 
 import pandas as pd
 from cachetools import TTLCache, cached
@@ -548,17 +548,62 @@ class WorkflowResource(metaclass=SingletonType):
 
 
 class Workflow(metaclass=SingletonType):
+    """Represents a workflow in Bio-OS.
+    
+    This class encapsulates all the information and operations related to a workflow,
+    including its metadata, inputs, outputs, and execution capabilities.
+    """
 
     def __init__(self,
                  name: str,
                  workspace_id: str,
                  bucket: str,
                  check: bool = False):
+        """Initialize a workflow instance.
+        
+        Args:
+            name: The name of the workflow
+            workspace_id: The ID of the workspace containing this workflow
+            bucket: The S3 bucket associated with this workflow
+            check: Whether to check the workflow existence immediately
+        """
         self.name = name
         self.workspace_id = workspace_id
         self.bucket = bucket
+        self._description: str = ""
+        self._create_time: int = 0
+        self._update_time: int = 0
+        self._language: str = "WDL"
+        self._source: str = ""
+        self._tag: str = ""
+        self._token: Optional[str] = None
+        self._main_workflow_path: str = ""
+        self._status: Dict[str, Optional[str]] = {"Phase": "", "Message": None}
+        self._inputs: List[Dict[str, Any]] = []
+        self._outputs: List[Dict[str, Any]] = []
+        self._owner_name: str = ""
+        self._graph: str = ""
+        self._source_type: str = ""
+        
         if check:
-            self.id
+            self.sync()
+
+    def __repr__(self):
+        """Return a string representation of the workflow."""
+        info_dict = dict_str({
+            "id": self.id,
+            "name": self.name,
+            "description": self.description,
+            "language": self.language,
+            "source": self.source,
+            "tag": self.tag,
+            "main_workflow_path": self.main_workflow_path,
+            "status": self.status,
+            "owner_name": self.owner_name,
+            "create_time": self.create_time,
+            "update_time": self.update_time
+        })
+        return f"WorkflowInfo:\n{info_dict}"
 
     @property
     @cached(cache=TTLCache(maxsize=100, ttl=1))
@@ -574,6 +619,140 @@ class Workflow(metaclass=SingletonType):
             raise ParameterError("name")
         return res["ID"].iloc[0]
 
+    @property
+    def description(self) -> str:
+        """Get the workflow description."""
+        if not self._description:
+            self.sync()
+        return self._description
+
+    @property
+    def create_time(self) -> int:
+        """Get the workflow creation timestamp."""
+        if not self._create_time:
+            self.sync()
+        return self._create_time
+
+    @property
+    def update_time(self) -> int:
+        """Get the workflow last update timestamp."""
+        if not self._update_time:
+            self.sync()
+        return self._update_time
+
+    @property
+    def language(self) -> str:
+        """Get the workflow language (e.g., WDL)."""
+        if not self._language:
+            self.sync()
+        return self._language
+
+    @property
+    def source(self) -> str:
+        """Get the workflow source location."""
+        if not self._source:
+            self.sync()
+        return self._source
+
+    @property
+    def tag(self) -> str:
+        """Get the workflow version tag."""
+        if not self._tag:
+            self.sync()
+        return self._tag
+
+    @property
+    def token(self) -> Optional[str]:
+        """Get the workflow access token if any."""
+        if not self._token:
+            self.sync()
+        return self._token
+
+    @property
+    def main_workflow_path(self) -> str:
+        """Get the main workflow file path."""
+        if not self._main_workflow_path:
+            self.sync()
+        return self._main_workflow_path
+
+    @property
+    def status(self) -> Dict[str, Optional[str]]:
+        """Get the workflow status information."""
+        if not self._status["Phase"]:
+            self.sync()
+        return self._status
+    @property
+    def inputs(self) -> List[Dict[str, Any]]:
+        """Get the workflow input parameters."""
+        if not self._inputs:
+            self.sync()
+        return self._inputs
+
+    @property
+    def outputs(self) -> List[Dict[str, Any]]:
+        """Get the workflow output parameters."""
+        if not self._outputs:
+            self.sync()
+        return self._outputs
+
+    @property
+    def owner_name(self) -> str:
+        """Get the workflow owner's name."""
+        if not self._owner_name:
+            self.sync()
+        return self._owner_name
+
+    @property
+    def graph(self) -> str:
+        """Get the workflow graph representation."""
+        if not self._graph:
+            self.sync()
+        return self._graph
+
+    @property
+    def source_type(self) -> str:
+        """Get the workflow source type."""
+        if not self._source_type:
+            self.sync()
+        return self._source_type
+
+    @cached(cache=TTLCache(maxsize=100, ttl=1))
+    def sync(self):
+        """Synchronize workflow information with the remote service."""
+        res = WorkflowResource(self.workspace_id). \
+            list().query(f"Name=='{self.name}'")
+        if res.empty:
+            raise ParameterError("name")
+            
+        # Get detailed workflow information
+        params = {
+            'WorkspaceID': self.workspace_id,
+            'Filter': {
+                'IDs': [res["ID"].iloc[0]]
+            }
+        }
+        workflows = Config.service().list_workflows(params).get('Items')
+        if len(workflows) != 1:
+            raise NotFoundError("workflow", self.name)
+            
+        detail = workflows[0]
+        
+        # Update all properties
+        self._description = detail.get("Description", "")
+        self._create_time = detail.get("CreateTime", 0)
+        self._update_time = detail.get("UpdateTime", 0)
+        self._language = detail.get("Language", "WDL")
+        self._source = detail.get("Source", "")
+        self._tag = detail.get("Tag", "")
+        self._token = detail.get("Token")
+        self._main_workflow_path = detail.get("MainWorkflowPath", "")
+        self._status = detail.get("Status", {"Phase": "", "Message": None})
+        self._inputs = detail.get("Inputs", [])
+        self._outputs = detail.get("Outputs", [])
+        self._owner_name = detail.get("OwnerName", "")
+        self._graph = detail.get("Graph", "")
+        self._source_type = detail.get("SourceType", "")
+
     @property
     @cached(cache=TTLCache(maxsize=100, ttl=1))
     def get_cluster(self):
@@ -594,11 +773,14 @@ class Workflow(metaclass=SingletonType):
                 return info['ID']
         raise NotFoundError("cluster", "workflow")
 
-    def query_data_model_id(self, name: str) -> "":
+    def query_data_model_id(self, name: str) -> str:
         """Gets the id of given data_models among those accessible
 
-        :param name:
-        :return:
+        Args:
+            name: The name of the data model
+
+        Returns:
+            str: The ID of the data model, or empty string if not found
         """
         res = DataModelResource(self.workspace_id).list(). \
             query(f"Name=='{name}'")
@@ -682,3 +864,4 @@ class Workflow(metaclass=SingletonType):
         submission_id = Config.service().create_submission(params).get("ID")
 
         return Submission(self.workspace_id, submission_id).runs
+

bioos/workflow_info.py

@@ -0,0 +1,207 @@
+from typing import Dict, Any, List, Optional
+import pandas as pd
+
+from bioos import bioos
+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 = DEFAULT_ENDPOINT):
+        """
+        初始化工作流信息查询类
+
+        Args:
+            ak: Bio-OS 访问密钥
+            sk: Bio-OS 私钥
+            endpoint: Bio-OS API 端点，默认为 https://bio-top.miracle.ac.cn
+        """
+        self.ak = ak
+        self.sk = sk
+        self.endpoint = endpoint
+        # 配置 Bio-OS
+        Config.set_access_key(ak)
+        Config.set_secret_key(sk)
+        Config.set_endpoint(endpoint)
+
+    @staticmethod
+    def _fmt_default(raw: Any) -> str | None:
+        """
+        将 Default 字段格式化成人类可读形式：
+        - None        → None
+        - int/float   → 123 / 1.23
+        - bool        → true / false
+        - 其余字符串  → "value"（保留双引号）
+        """
+        if raw is None:
+            return None
+        if isinstance(raw, (int, float, bool)):
+            return str(raw).lower()  # bool 转成 'true' / 'false'
+        if isinstance(raw, str):
+            lo = raw.lower()
+            # 尝试将字符串视为数字或布尔
+            if lo in {"true", "false"}:
+                return lo
+            try:
+                int(raw);   return raw
+            except ValueError:
+                pass
+            try:
+                float(raw); return raw
+            except ValueError:
+                pass
+            return f"\"{raw}\""
+        return str(raw)
+
+    def get_workspace_id(self, workspace_name: str) -> str:
+        """
+        获取工作区ID
+        Args:
+            workspace_name: 工作区名称
+
+        Returns:
+            str: 工作区ID
+
+        Raises:
+            NotFoundError: 未找到指定工作区
+        """
+        df = bioos.list_workspaces()
+        ser = df[df.Name == workspace_name].ID
+        if len(ser) != 1:
+            raise NotFoundError("Workspace", workspace_name)
+        return ser.to_list()[0]
+
+    def get_workflow(self, workspace_name: str, workflow_name: str):
+        """
+        获取工作流对象
+
+        Args:
+            workspace_name: 工作区名称
+            workflow_name: 工作流名称
+
+        Returns:
+            Workflow: 工作流对象
+        Raises:
+            NotFoundError: 未找到指定工作区或工作流
+        """
+        workspace_id = self.get_workspace_id(workspace_name)
+        ws = bioos.workspace(workspace_id)
+        return ws.workflow(name=workflow_name)
+
+    def list_workflows(self, workspace_name: str) -> List[Dict[str, Any]]:
+        """
+        列出工作区下的所有工作流
+
+        Args:
+            workspace_name: 工作区名称
+
+        Returns:
+            List[Dict[str, Any]]: 工作流列表
+        """
+        workspace_id = self.get_workspace_id(workspace_name)
+        ws = bioos.workspace(workspace_id)
+        return ws.list_workflows()
+
+    def get_workflow_inputs(self, workspace_name: str, workflow_name: str) -> Dict[str, str]:
+        """
+        获取工作流的输入参数模板
+
+        Args:
+            workspace_name: 工作区名称
+            workflow_name: 工作流名称
+
+        Returns:
+            Dict[str, str]: 包含工作流输入参数模板的字典，格式为：
+            {
+                "param_name": "Type (optional, default = value)",  # 对于可选参数
+                "param_name": "Type"                              # 对于必需参数
+            }
+            其中：
+            - Type 为参数类型（如 String, Int, File 等）
+            - optional 表示参数为可选
+            - value 为默认值（数字和布尔值直接显示，字符串加引号）
+        """
+        try:
+            wf = self.get_workflow(workspace_name, workflow_name)
+            result = {}
+            
+            for item in wf.inputs:
+                type_str = item.get("Type", "")
+                optional = item.get("Optional", False)
+                default = self._fmt_default(item.get("Default"))
+
+                if optional:
+                    value = f"{type_str} (optional" + (f", default = {default})" if default is not None else ")")
+                else:
+                    value = type_str
+
+                result[item["Name"]] = value
+
+            return result
+
+        except NotFoundError as e:
+            return {"error": str(e)}
+        except Exception as e:
+            return {"error": str(e)}
+
+    def get_workflow_outputs(self, workspace_name: str, workflow_name: str) -> Dict[str, str]:
+        """
+        获取工作流的输出参数信息
+
+        Args:
+            workspace_name: 工作区名称
+            workflow_name: 工作流名称
+
+        Returns:
+            Dict[str, str]: 包含工作流输出参数的字典
+        """
+        try:
+            wf = self.get_workflow(workspace_name, workflow_name)
+            return {output["Name"]: output["Type"] for output in wf.outputs}
+        except NotFoundError as e:
+            return {"error": str(e)}
+        except Exception as e:
+            return {"error": str(e)}
+
+    def get_workflow_metadata(self, workspace_name: str, workflow_name: str) -> Dict[str, Any]:
+        """
+        获取工作流的元数据信息
+
+        Args:
+            workspace_name: 工作区名称
+            workflow_name: 工作流名称
+
+        Returns:
+            Dict[str, Any]: 包含工作流元数据的字典，包括：
+                - name: 工作流名称
+                - description: 工作流描述
+                - language: 工作流语言
+                - source: 工作流源
+                - tag: 版本标签
+                - status: 工作流状态
+                - owner_name: 所有者
+                - create_time: 创建时间
+                - update_time: 更新时间
+                - main_workflow_path: 主工作流文件路径
+                - source_type: 源类型
+        """
+        try:
+            wf = self.get_workflow(workspace_name, workflow_name)
+            return {
+                "name": wf.name,
+                "description": wf.description,
+                "language": wf.language,
+                "source": wf.source,
+                "tag": wf.tag,
+                "status": wf.status,
+                "owner_name": wf.owner_name,
+                "create_time": wf.create_time,
+                "update_time": wf.update_time,
+                "main_workflow_path": wf.main_workflow_path,
+                "source_type": wf.source_type
+            }
+        except NotFoundError as e:
+            return {"error": str(e)}
+        except Exception as e:
+            return {"error": str(e)} 

{pybioos-0.0.15.dist-info → pybioos-0.0.17.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybioos
-Version: 0.0.15
+Version: 0.0.17
 Summary: BioOS SDK for Python
 Home-page: https://github.com/GBA-BI/pybioos
 Author: Jilong Liu

{pybioos-0.0.15.dist-info → pybioos-0.0.17.dist-info}/RECORD

@@ -1,14 +1,15 @@
-bioos/__about__.py,sha256=zsL_PukbnoBYjoIOAjFEp5bxiw0QpluTLypKg_3j1mw,57
+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=BzEPOyAjgdK7Wafbl2b1_qG_VTEdp8xDwKS68tBovjs,14327
-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=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
@@ -17,7 +18,7 @@ bioos/resource/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
 bioos/resource/data_models.py,sha256=enKp8yyQI8IbRqe--0Xtyg1XzOwQQPQzoQsx_hNuZ6E,5089
 bioos/resource/files.py,sha256=1HY0IHvq8H843VM2XZIHDdCuXXNcMrlEFhSNqWXmFzE,8456
 bioos/resource/utility.py,sha256=emY7qVLLLvGmQYlVj-_bLAxU7i1GfQOUybdRkfEDwVA,1300
-bioos/resource/workflows.py,sha256=v2jTAEBhVjp4U-iLaIswYBMkHZ7uQ96dZUE0zvjnrWQ,23426
+bioos/resource/workflows.py,sha256=RZkREd7EzyRqk3gP09HSzeuI3i7Cn7VMhqjp4jj_cjg,29418
 bioos/resource/workspaces.py,sha256=Gmr8y_sjK7TQbhMhQ_7rxqR1KFcwU72I95YYCFrrLBQ,3995
 bioos/service/BioOsService.py,sha256=HuYUEwomHCLpA1MYgVqGyWAQWHM-_BHB-jmy9VsOlnQ,6724
 bioos/service/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
@@ -34,9 +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-0.0.15.dist-info/LICENSE,sha256=cPkGXsgfPgEhIns7Lt3Avxx0Uy-VbdsoP8jvNGuj3cE,1063
-pybioos-0.0.15.dist-info/METADATA,sha256=mtaPib2vulNih35eFfmzWcpz8sdMHOWjZ-IYYwxqHDE,830
-pybioos-0.0.15.dist-info/WHEEL,sha256=OqRkF0eY5GHssMorFjlbTIq072vpHpF60fIQA6lS9xA,92
-pybioos-0.0.15.dist-info/entry_points.txt,sha256=Sc5H0_X7r03Mef4Qd70bebqgdIbVAxLU7nV7qP7cKD4,328
-pybioos-0.0.15.dist-info/top_level.txt,sha256=llpzydkKVDSaWZgz3bsTUsQmhoQpc_JcRJg2-H-5a2U,6
-pybioos-0.0.15.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,,