pybioos 0.0.15__py3-none-any.whl → 0.0.19__py3-none-any.whl

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-0.0.19.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybioos
-Version: 0.0.15
+Version: 0.0.19
 Summary: BioOS SDK for Python
 Home-page: https://github.com/GBA-BI/pybioos
 Author: Jilong Liu

{pybioos-0.0.15.dist-info → pybioos-0.0.19.dist-info}/RECORD

@@ -1,25 +1,27 @@
-bioos/__about__.py,sha256=zsL_PukbnoBYjoIOAjFEp5bxiw0QpluTLypKg_3j1mw,57
+bioos/__about__.py,sha256=aWkoDtGPtBbAnLeddD1e0dWwgcOhvbjUFTY5JL8fl8k,57
 bioos/__init__.py,sha256=4GZKi13lDTD25YBkGakhZyEQZWTER_OWQMNPoH_UM2c,22
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-bioos/bioos_workflow.py,sha256=BzEPOyAjgdK7Wafbl2b1_qG_VTEdp8xDwKS68tBovjs,14327
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-bioos/config.py,sha256=CvFabYqV1BkFWO8fnr5vBf6xNtNzA8hAEVeEIbvAOm8,4307
+bioos/bioos.py,sha256=fFnbtwOyF5U3N_D41jXPYB2H4xKBsI931nS-qBUFW70,3231
+bioos/bioos_workflow.py,sha256=IhbDVEszcyJ9ivtVGMgI6dOovB18-aRn-kDwPdJSa6I,17709
+bioos/bw_import.py,sha256=kYS4BDbyIXyaFIOCUyOnAzIbLdHvY3l3KLPDVfAnFSM,5829
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 bioos/errors.py,sha256=p0fH6JSMYBjul88lMJ7PPwGNh4SYg62-7VMNuUXWl-E,2540
-bioos/get_submission_logs.py,sha256=jUtT8Vic8h_VOcqrqJsTBSonve64RjbKNAyp0wUtIpg,3934
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 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
 bioos/models/models.py,sha256=HPCLZ4jK2HDth4vrlVHba21CiW6y7y5im1kOjV4adc8,391
-bioos/resource/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
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 bioos/resource/data_models.py,sha256=enKp8yyQI8IbRqe--0Xtyg1XzOwQQPQzoQsx_hNuZ6E,5089
 bioos/resource/files.py,sha256=1HY0IHvq8H843VM2XZIHDdCuXXNcMrlEFhSNqWXmFzE,8456
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 bioos/resource/utility.py,sha256=emY7qVLLLvGmQYlVj-_bLAxU7i1GfQOUybdRkfEDwVA,1300
-bioos/resource/workflows.py,sha256=v2jTAEBhVjp4U-iLaIswYBMkHZ7uQ96dZUE0zvjnrWQ,23426
-bioos/resource/workspaces.py,sha256=Gmr8y_sjK7TQbhMhQ_7rxqR1KFcwU72I95YYCFrrLBQ,3995
-bioos/service/BioOsService.py,sha256=HuYUEwomHCLpA1MYgVqGyWAQWHM-_BHB-jmy9VsOlnQ,6724
+bioos/resource/workflows.py,sha256=k5ZFdce1eHRLJAxz-l_QHEq6J11PUEKWRP6_yW2jR9E,32279
+bioos/resource/workspaces.py,sha256=_oA-Us3nH71RecaSeezhYuVwJDaDucrWbOa9CvzTFGE,9631
+bioos/service/BioOsService.py,sha256=QT848D-JafcZJdCJ_OZsQ8OvPeb4u1hLDtQAVJeEiXk,10513
 bioos/service/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
 bioos/service/api.py,sha256=Khihn187bACEfBcJ-tRS9JO29-VCBsH0-9qq-i5WxkQ,8737
 bioos/service/config.py,sha256=FbBsb6CpcLsQZH7n8uuUbFVhkpqYOEnOe0xGkA7ZrjA,1009
@@ -34,9 +36,9 @@ 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
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