pybioos 0.0.14__py3-none-any.whl → 0.0.15__py3-none-any.whl

bioos/__about__.py

@@ -1,4 +1,4 @@
 # coding:utf-8
 
 # Package version
-__version__ = "0.0.14"
+__version__ = "0.0.15"

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/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-0.0.14.dist-info → pybioos-0.0.15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybioos
-Version: 0.0.14
+Version: 0.0.15
 Summary: BioOS SDK for Python
 Home-page: https://github.com/GBA-BI/pybioos
 Author: Jilong Liu

{pybioos-0.0.14.dist-info → pybioos-0.0.15.dist-info}/RECORD

@@ -1,4 +1,4 @@
-bioos/__about__.py,sha256=ev5P6FQdPx-W_Hkam384TBq5XWIMHrvDeSBRkz-p7wo,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=BzEPOyAjgdK7Wafbl2b1_qG_VTEdp8xDwKS68tBovjs,14327
@@ -6,7 +6,7 @@ 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
@@ -17,7 +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
@@ -34,9 +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-0.0.14.dist-info/LICENSE,sha256=cPkGXsgfPgEhIns7Lt3Avxx0Uy-VbdsoP8jvNGuj3cE,1063
-pybioos-0.0.14.dist-info/METADATA,sha256=8sh0iBOI-33lr0H0_q6ZOzznns9i46p16siJFcRbnrM,830
-pybioos-0.0.14.dist-info/WHEEL,sha256=OqRkF0eY5GHssMorFjlbTIq072vpHpF60fIQA6lS9xA,92
-pybioos-0.0.14.dist-info/entry_points.txt,sha256=Sc5H0_X7r03Mef4Qd70bebqgdIbVAxLU7nV7qP7cKD4,328
-pybioos-0.0.14.dist-info/top_level.txt,sha256=llpzydkKVDSaWZgz3bsTUsQmhoQpc_JcRJg2-H-5a2U,6
-pybioos-0.0.14.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,,