pybioos 0.0.13__py3-none-any.whl → 0.0.15__py3-none-any.whl

bioos/__about__.py

@@ -1,4 +1,4 @@
 # coding:utf-8
 
 # Package version
-__version__ = "0.0.13"
+__version__ = "0.0.15"

bioos/bioos_workflow.py

@@ -277,8 +277,13 @@ class Bioos_workflow:
             self.logger.info("Download finish.")
 
     def submit_workflow_bioosapi(self):
+        """Submit workflow using Bio-OS API"""
         self.runs = self.wf.submit(**self.params_submit)
-        self.logger.info("Submit workflow run successfully.")
+        submission_id = self.runs[0].submission
+        run_id = self.runs[0].id
+        self.logger.info(
+            f"Submit workflow run successfully. Submission ID: {submission_id}, Run ID: {run_id}"
+        )
         return self.runs
 
     def monitor_workflow(self):

bioos/bw_import.py

@@ -145,7 +145,7 @@ def bioos_workflow_import():
             else:
                 # 如果没有设置monitor参数，直接退出
                 logger.info(
-                    f"Workflow {args.workflow_name} submitted successfully, {result}"
+                    f"Workflow {args.workflow_name} is still validating, {result}, please wait and check the status later."
                 )
                 sys.exit(0)
 

bioos/bw_import_status_check.py

@@ -0,0 +1,91 @@
+#!/usr/bin/env python3
+# coding: utf-8
+
+import argparse
+import logging
+import sys
+
+from bioos import bioos
+from bioos.config import Config
+from bioos.resource.workflows import WorkflowResource
+
+
+def get_logger():
+    """Setup logger"""
+    logger = logging.getLogger('bw_import_status_check')
+    if not logger.handlers:
+        handler = logging.StreamHandler()
+        formatter = logging.Formatter(
+            '%(asctime)s - %(levelname)s - %(message)s')
+        handler.setFormatter(formatter)
+        logger.addHandler(handler)
+        logger.setLevel(logging.INFO)
+    return logger
+
+
+def bioos_workflow_status_check():
+    """Command line entry point for checking workflow validation status"""
+    parser = argparse.ArgumentParser(
+        description='Bio-OS Workflow Import Status Check Tool',
+        formatter_class=argparse.RawDescriptionHelpFormatter)
+
+    # 必需参数
+    parser.add_argument(
+        '--ak',
+        required=True,
+        help='Access key for your Bio-OS instance platform account')
+    parser.add_argument(
+        '--sk',
+        required=True,
+        help='Secret key for your Bio-OS instance platform account')
+    parser.add_argument('--workspace_name',
+                        required=True,
+                        help='Target workspace name')
+    parser.add_argument('--workflow_id',
+                        required=True,
+                        help='ID of the workflow to check')
+
+    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")
+
+        # 获取workspace ID
+        workspaces = bioos.list_workspaces()
+        workspace_info = workspaces.query(f"Name=='{args.workspace_name}'")
+        if workspace_info.empty:
+            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)
+
+        # 获取工作流状态
+        df = workflow_resource.list()
+        workflow_info = df[df.ID == args.workflow_id]
+
+        if len(workflow_info) == 1:
+            status = workflow_info.iloc[0]["Status"]["Phase"]
+            message = workflow_info.iloc[0]["Status"].get("Message", "")
+
+            # 打印状态信息
+            print(f"Status: {status}")
+            if message:
+                print(f"Message: {message}")
+
+        else:
+            logger.error(f"Workflow with ID {args.workflow_id} not found")
+            sys.exit(1)
+
+    except Exception as e:
+        logger.error(f"Error: {str(e)}")
+        sys.exit(1)
+
+
+if __name__ == '__main__':
+    bioos_workflow_status_check()

bioos/bw_status_check.py

@@ -0,0 +1,94 @@
+#!/usr/bin/env python3
+# coding: utf-8
+
+import argparse
+import logging
+import sys
+
+from bioos import bioos
+from bioos.config import Config
+from bioos.resource.workflows import WorkflowResource
+
+
+def get_logger():
+    """Setup logger"""
+    logger = logging.getLogger('bw_status_check')
+    if not logger.handlers:
+        handler = logging.StreamHandler()
+        formatter = logging.Formatter(
+            '%(asctime)s - %(levelname)s - %(message)s')
+        handler.setFormatter(formatter)
+        logger.addHandler(handler)
+        logger.setLevel(logging.INFO)
+    return logger
+
+
+def bioos_workflow_status_check():
+    """Command line entry point for checking workflow run status"""
+    parser = argparse.ArgumentParser(
+        description='Bio-OS Workflow Run Status Check Tool',
+        formatter_class=argparse.RawDescriptionHelpFormatter)
+
+    # 必需参数
+    parser.add_argument(
+        '--ak',
+        required=True,
+        help='Access key for your Bio-OS instance platform account')
+    parser.add_argument(
+        '--sk',
+        required=True,
+        help='Secret key for your Bio-OS instance platform account')
+    parser.add_argument('--workspace_name',
+                        required=True,
+                        help='Target workspace name')
+    parser.add_argument('--submission_id',
+                        required=True,
+                        help='ID of the submission to check')
+
+    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")
+
+        # 获取workspace ID
+        workspaces = bioos.list_workspaces()
+        workspace_info = workspaces.query(f"Name=='{args.workspace_name}'")
+        if workspace_info.empty:
+            logger.error(f"Workspace {args.workspace_name} not found")
+            sys.exit(1)
+        workspace_id = workspace_info["ID"].iloc[0]
+
+        # 获取提交的运行状态
+        resp = Config.service().list_runs({
+            "SubmissionID": args.submission_id,
+            "WorkspaceID": workspace_id
+        })
+
+        if not resp.get("Items"):
+            logger.error(f"No runs found for submission {args.submission_id}")
+            sys.exit(1)
+
+        # 打印所有运行的状态
+        print(f"\nSubmission ID: {args.submission_id}")
+        print("Runs Status:")
+        print("-" * 60)
+        print(f"{'Run ID':<40} {'Status':<10} {'Message'}")
+        print("-" * 60)
+
+        for run in resp.get("Items"):
+            run_id = run.get("ID", "N/A")
+            status = run.get("Status", "Unknown")
+            message = run.get("Message", "")
+            print(f"{run_id:<40} {status:<10} {message}")
+
+    except Exception as e:
+        logger.error(f"Error: {str(e)}")
+        sys.exit(1)
+
+
+if __name__ == '__main__':
+    bioos_workflow_status_check()

bioos/errors.py

@@ -21,7 +21,7 @@ class EnvironmentConfigurationError(ConfigurationError):
 
     def __init__(self, env: str):
         """Initialize the EnvironmentConfigurationError .
-        
+
         :param env: environment name of the configuration
         :type env: str
         """
@@ -51,13 +51,16 @@ class ParameterError(Exception):
     """Exception indicating a required parameter not valid
     """
 
-    def __init__(self, name: str):
+    def __init__(self, name: str, msg: str = None):
         """Initialize the ParameterError .
 
         :param name: name of the parameter
         :type name: str
         """
-        self.message = "parameter '{}' invalid / not found".format(name)
+        self.name = name
+        self.message = f"parameter '{name}' invalid / not found"
+        if msg:
+            self.message += f": {msg}"
         super().__init__(self.message)
 
 

bioos/get_submission_logs.py

@@ -0,0 +1,119 @@
+#!/usr/bin/env python3
+# coding: utf-8
+
+import argparse
+import logging
+import os
+import sys
+
+from bioos import bioos
+from bioos.config import Config
+
+
+def get_logger():
+    """Setup logger"""
+    logger = logging.getLogger('get_submission_logs')
+    if not logger.handlers:
+        handler = logging.StreamHandler()
+        formatter = logging.Formatter(
+            '%(asctime)s - %(levelname)s - %(message)s')
+        handler.setFormatter(formatter)
+        logger.addHandler(handler)
+        logger.setLevel(logging.INFO)
+    return logger
+
+
+def get_submission_logs():
+    """Command line entry point for downloading workflow submission logs"""
+    parser = argparse.ArgumentParser(
+        description='Bio-OS Workflow Submission Logs Download Tool',
+        formatter_class=argparse.RawDescriptionHelpFormatter)
+
+    # 必需参数
+    parser.add_argument(
+        '--ak',
+        required=True,
+        help='Access key for your Bio-OS instance platform account')
+    parser.add_argument(
+        '--sk',
+        required=True,
+        help='Secret key for your Bio-OS instance platform account')
+    parser.add_argument('--workspace_name',
+                        required=True,
+                        help='Target workspace name')
+    parser.add_argument('--submission_id',
+                        required=True,
+                        help='ID of the submission to download logs')
+    parser.add_argument(
+        '--output_dir',
+        default='.',
+        help='Local directory to save the logs (default: current directory)')
+
+    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")
+
+        # 获取workspace ID
+        workspaces = bioos.list_workspaces()
+        workspace_info = workspaces.query(f"Name=='{args.workspace_name}'")
+        if workspace_info.empty:
+            logger.error(f"Workspace {args.workspace_name} not found")
+            sys.exit(1)
+        workspace_id = workspace_info["ID"].iloc[0]
+
+        # 获取workspace对象
+        ws = bioos.workspace(workspace_id)
+
+        # 列出所有文件
+        logger.info(f"Listing files for submission {args.submission_id}")
+        files_df = ws.files.list()
+
+        # 过滤出与submission相关的日志文件
+        log_files = []
+        for file in files_df.key:
+            if args.submission_id in file:
+                # 检查是否是日志文件
+                if (file.endswith('.log') or 'stderr' in file
+                        or 'stdout' in file or '/log/' in file):
+                    log_files.append(file)
+
+        if not log_files:
+            logger.error(
+                f"No log files found for submission {args.submission_id}")
+            sys.exit(1)
+
+        logger.info(f"Found {len(log_files)} log files")
+
+        # 创建输出目录
+        output_path = os.path.join(args.output_dir, args.submission_id)
+        os.makedirs(output_path, exist_ok=True)
+
+        # 下载文件
+        logger.info("Downloading log files...")
+        try:
+            ws.files.download(log_files, output_path, flatten=False)
+            logger.info(f"Successfully downloaded log files to {output_path}")
+        except Exception as e:
+            logger.error(f"Error downloading some files: {str(e)}")
+            logger.info("Continuing with successfully downloaded files...")
+
+        # 打印下载的文件列表
+        logger.info("\nDownloaded files:")
+        for root, _, files in os.walk(output_path):
+            for file in files:
+                rel_path = os.path.relpath(os.path.join(root, file),
+                                           output_path)
+                logger.info(f"  {rel_path}")
+
+    except Exception as e:
+        logger.error(f"Error: {str(e)}")
+        sys.exit(1)
+
+
+if __name__ == '__main__':
+    get_submission_logs()

bioos/resource/workflows.py

@@ -417,7 +417,7 @@ class WorkflowResource(metaclass=SingletonType):
             raise ParameterError("name", name)
 
         if language != "WDL":
-            raise ParameterError("language", language)
+            raise ParameterError("language", f"Unsupported language: '{language}'. Only 'WDL' is supported.")
 
         if source.startswith("http://") or source.startswith("https://"):
             params = {
@@ -432,7 +432,50 @@ class WorkflowResource(metaclass=SingletonType):
             }
             if token:
                 params["Token"] = token
-        elif os.path.exists(source):
+            return Config.service().create_workflow(params)
+        elif os.path.isdir(source):
+            # 扫描文件夹中的所有 WDL 文件，并构建相对路径
+            # 用 source 来检验上传的是否是文件夹
+            source_files = []
+            for root, _, files in os.walk(source):
+                for file in files:
+                    if file.endswith('.wdl'):
+                        full_path = os.path.join(root, file)
+                        relative_path = os.path.relpath(full_path, source)  # 获取文件相对于source的相对路径。
+                        source_files.append({
+                            "name": relative_path,  # 使用相对路径
+                            "originFile": open(full_path, "rb").read()
+                        })
+
+            if not source_files:
+                raise ParameterError("source", "No WDL files found in the specified folder")
+
+            # 确保主工作流路径是相对路径
+            if main_workflow_path:
+                if not os.path.exists(main_workflow_path):
+                    raise ParameterError("main_workflow_path", f"Main workflow file {main_workflow_path} not found")
+                main_relative = os.path.relpath(main_workflow_path, source)
+            else:
+                main_relative = None
+
+            zip_base64 = zip_files(source_files, "base64")
+
+            params = {
+                "WorkspaceID": self.workspace_id,
+                "Name": name,
+                "Description": description,
+                "Language": language,
+                "SourceType": "file",
+                "Content": zip_base64,
+            }
+            if main_relative:
+                params["MainWorkflowPath"] = os.path.basename(main_relative)
+            if token:
+                params["Token"] = token
+
+            return Config.service().create_workflow(params)
+        #单文件上传
+        elif os.path.isfile(source) and source.endswith('.wdl'):
             source_files = [{
                 "name": os.path.basename(source),
                 "originFile": open(source, "rb").read()
@@ -450,10 +493,9 @@ class WorkflowResource(metaclass=SingletonType):
                 "Content": zip_base64,
                 "MainWorkflowPath": main_workflow_path,
             }
+            return Config.service().create_workflow(params)
         else:
-            raise ParameterError("source", source)
-
-        return Config.service().create_workflow(params)
+            raise ParameterError("source",f"Workflow source '{source}' does not exist.")
 
     def list(self) -> DataFrame:
         """Lists all workflows' information .

{pybioos-0.0.13.dist-info → pybioos-0.0.15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybioos
-Version: 0.0.13
+Version: 0.0.15
 Summary: BioOS SDK for Python
 Home-page: https://github.com/GBA-BI/pybioos
 Author: Jilong Liu

{pybioos-0.0.13.dist-info → pybioos-0.0.15.dist-info}/RECORD

@@ -1,10 +1,13 @@
-bioos/__about__.py,sha256=qoWnBZVGtNFcDVMbr_1oumQPR0jCeSSHSMfjBEQKgTw,57
+bioos/__about__.py,sha256=zsL_PukbnoBYjoIOAjFEp5bxiw0QpluTLypKg_3j1mw,57
 bioos/__init__.py,sha256=4GZKi13lDTD25YBkGakhZyEQZWTER_OWQMNPoH_UM2c,22
 bioos/bioos.py,sha256=fHzOb1l5wYxw6NVYYZDiFcgk4V28BAgWEc3ev12reWs,2409
-bioos/bioos_workflow.py,sha256=LbKxK7Otzj9apJciI3jg_cfh92x9aZGlUyN5ZRAdZeU,14127
-bioos/bw_import.py,sha256=BGH_sxAWMKNebPRUB89iMFRBHA52c7txaq7l1AkLmuU,5659
+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/errors.py,sha256=Lzz2rkjDOTR2X9CnVkmsmqeOgmNqbi46WAxnC6LEGm0,2459
+bioos/errors.py,sha256=p0fH6JSMYBjul88lMJ7PPwGNh4SYg62-7VMNuUXWl-E,2540
+bioos/get_submission_logs.py,sha256=jUtT8Vic8h_VOcqrqJsTBSonve64RjbKNAyp0wUtIpg,3934
 bioos/log.py,sha256=twiCvf5IgJB7uvzANwBluSlztJN8ZrxbGZUBGlZ0vps,3204
 bioos/internal/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
 bioos/internal/tos.py,sha256=0R6YN2lxjjZsuMfv0yLSkBmz_LqmzQGb8GagnUMc8EY,12264
@@ -14,7 +17,7 @@ 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=DUAwq0AE7FZbnb5iJUGEKC5XzGFl_CcJy7Sh0KO-EvM,21387
+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/service/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
@@ -31,9 +34,9 @@ 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-0.0.13.dist-info/LICENSE,sha256=cPkGXsgfPgEhIns7Lt3Avxx0Uy-VbdsoP8jvNGuj3cE,1063
-pybioos-0.0.13.dist-info/METADATA,sha256=-jL5IDsWxBmicw6QXvkWFzGAxIZ4fKh-bnS6lMsAunk,830
-pybioos-0.0.13.dist-info/WHEEL,sha256=OqRkF0eY5GHssMorFjlbTIq072vpHpF60fIQA6lS9xA,92
-pybioos-0.0.13.dist-info/entry_points.txt,sha256=G8eh4umiCimlV9nNNeyA3vqLyG3jfUj8uVNrgvAuhAM,110
-pybioos-0.0.13.dist-info/top_level.txt,sha256=llpzydkKVDSaWZgz3bsTUsQmhoQpc_JcRJg2-H-5a2U,6
-pybioos-0.0.13.dist-info/RECORD,,
+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-0.0.15.dist-info/entry_points.txt

@@ -0,0 +1,7 @@
+[console_scripts]
+bw = bioos.bioos_workflow:bioos_workflow
+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
+

pybioos-0.0.13.dist-info/entry_points.txt

@@ -1,4 +0,0 @@
-[console_scripts]
-bw = bioos.bioos_workflow:bioos_workflow
-bw_import = bioos.bw_import:bioos_workflow_import
-