pybioos 0.0.17__py3-none-any.whl → 0.0.18__py3-none-any.whl

bioos/__about__.py

@@ -1,4 +1,4 @@
 # coding:utf-8
 
 # Package version
-__version__ = "0.0.17"
+__version__ = "0.0.18"

bioos/bioos.py

@@ -1,7 +1,7 @@
 from pandas import DataFrame
 from volcengine.const.Const import REGION_CN_NORTH1
 
-from bioos.config import Config
+from bioos.config import Config,DEFAULT_ENDPOINT
 from bioos.resource.utility import UtilityResource
 from bioos.resource.workspaces import Workspace
 
@@ -22,7 +22,7 @@ def status() -> Config.LoginInfo:
 
 def login(access_key: str,
           secret_key: str,
-          endpoint: str = None,
+          endpoint: str = DEFAULT_ENDPOINT,
           region: str = REGION_CN_NORTH1) -> bool:
     """Login to the given endpoint using specified account and password.
 
@@ -73,6 +73,28 @@ def list_workspaces() -> DataFrame:
     }).get("Items"))
 
 
+def create_workspace(name: str, description: str) -> dict:
+    """Creates a new workspace in the login environment.
+
+    *Example*:
+    ::
+
+        bioos.create_workspace(name="My Workspace", description="This is my new workspace")
+
+    :param name: Name of the workspace to create
+    :type name: str
+    :param description: Description of the workspace
+    :type description: str
+    :return: Creation result containing workspace information
+    :rtype: dict
+    """
+    params = {
+        "Name": name,
+        "Description": description
+    }
+    return Config.service().create_workspace(params)
+
+
 def workspace(id_: str) -> Workspace:  # 这里是workspace的入口
     """Returns the workspace for the given name .
 

bioos/bioos_workflow.py

@@ -178,7 +178,8 @@ class Bioos_workflow:
                     data_model_name: str = "dm",
                     submission_desc: str = "Submit by pybioos",
                     call_caching: bool = True,
-                    force_reupload: bool = False):
+                    force_reupload: bool = False,
+                    mount_tos: 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
@@ -229,6 +230,7 @@ class Bioos_workflow:
             "outputs": "{}",
             "submission_desc": submission_desc,
             "call_caching": call_caching,
+            "mount_tos": mount_tos,
         }
 
         # if the input json is a batch or singleton submission
@@ -363,6 +365,12 @@ def bioos_workflow():
                         action='store_true',
                         help="Force reupolad tos existed files.")
 
+    parser.add_argument(
+        "--mount_tos",
+        action='store_true',
+        help="是否挂载tos",
+        default=False)
+
     parser.add_argument(
         "--monitor",
         action='store_true',
@@ -394,7 +402,8 @@ def bioos_workflow():
                    data_model_name=parsed_args.data_model_name,
                    submission_desc=parsed_args.submission_desc,
                    call_caching=parsed_args.call_caching,
-                   force_reupload=parsed_args.force_reupload)
+                   force_reupload=parsed_args.force_reupload,
+                   mount_tos=parsed_args.mount_tos)
     bw.submit_workflow_bioosapi()
 
     # moniter

bioos/resource/workflows.py

@@ -795,7 +795,8 @@ class Workflow(metaclass=SingletonType):
                call_caching: bool,
                submission_name_suffix: str = "",
                row_ids: List[str] = [],
-               data_model_name: str = '') -> List[Run]:
+               data_model_name: str = '',
+               mount_tos: bool = False) -> List[Run]:
         """Submit an existed workflow.
 
         *Example*:
@@ -846,6 +847,7 @@ class Workflow(metaclass=SingletonType):
             'Inputs': inputs,
             'ExposedOptions': {
                 "ReadFromCache": call_caching,
+                "MountTOS": mount_tos,
                 # TODO this may change in the future
                 "ExecutionRootDir": f"s3://{self.bucket}"
             },

bioos/resource/workspaces.py

@@ -121,3 +121,8 @@ class Workspace(metaclass=SingletonType):
         if not self._bucket:
             self._bucket = self.basic_info.get("s3_bucket")
         return Workflow(name, self._id, self._bucket)
+
+    def bind_cluster(self, cluster_id: str, type_: str = "workflow") -> dict:
+        """把当前 Workspace 绑定到指定集群"""
+        params = {"ClusterID": cluster_id, "Type": type_, "ID": self._id}
+        return Config.service().bind_cluster_to_workspace(params)

bioos/service/BioOsService.py

@@ -47,6 +47,11 @@ class BioOsService(Service):
                 'Action': 'ListWorkspaces',
                 'Version': '2021-03-04'
             }, {}, {}),
+            'CreateWorkspace':
+            ApiInfo('POST', '/', {
+                'Action': 'CreateWorkspace',
+                'Version': '2021-03-04'
+            }, {}, {}),
             'CreateDataModel':
             ApiInfo('POST', '/', {
                 'Action': 'CreateDataModel',
@@ -127,12 +132,19 @@ class BioOsService(Service):
                 'Action': 'DeleteWorkflow',
                 'Version': '2021-03-04'
             }, {}, {}),
+            'BindClusterToWorkspace':
+            ApiInfo('POST', '/', {
+                'Action': 'BindClusterToWorkspace',
+                'Version': '2021-03-04'
+            }, {}, {}),
         }
         return api_info
 
     def list_workspaces(self, params):  # 以下各方法的params需要在外部使用时构建
         return self.__request('ListWorkspaces', params)
 
+    def create_workspace(self, params):
+        return self.__request('CreateWorkspace', params)
     def create_data_model(self, params):
         return self.__request('CreateDataModel', params)
 
@@ -181,6 +193,9 @@ class BioOsService(Service):
     def delete_workflow(self, params):
         return self.__request("DeleteWorkflow", params)
 
+    def bind_cluster_to_workspace(self, params):
+        return self.__request("BindClusterToWorkspace", params)
+
     def __request(self, action, params):
         res = self.json(
             action, dict(),

{pybioos-0.0.17.dist-info → pybioos-0.0.18.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybioos
-Version: 0.0.17
+Version: 0.0.18
 Summary: BioOS SDK for Python
 Home-page: https://github.com/GBA-BI/pybioos
 Author: Jilong Liu

{pybioos-0.0.17.dist-info → pybioos-0.0.18.dist-info}/RECORD

@@ -1,7 +1,7 @@
-bioos/__about__.py,sha256=FvqUBfyX_OkxcuTYr1_lcBcEd13i1ew8F8tEpRfcor8,57
+bioos/__about__.py,sha256=YQNxIWM75-mGePypUWLizOs5j9z-3m-wmI5X1hBjL0g,57
 bioos/__init__.py,sha256=4GZKi13lDTD25YBkGakhZyEQZWTER_OWQMNPoH_UM2c,22
-bioos/bioos.py,sha256=yhaWaJMwP23fMtid2mNWUetGwDUbUtCKwugXt27OLTs,2600
-bioos/bioos_workflow.py,sha256=LRzYxuNnbF3R7urrMRjMRwR2hGDmH_4kP52D2Gger8k,15259
+bioos/bioos.py,sha256=fFnbtwOyF5U3N_D41jXPYB2H4xKBsI931nS-qBUFW70,3231
+bioos/bioos_workflow.py,sha256=s_5lEFclHf3ZAtmIPRYcizQU5sEsc-Zm6FGP89_wL8g,15525
 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
@@ -18,9 +18,9 @@ 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=RZkREd7EzyRqk3gP09HSzeuI3i7Cn7VMhqjp4jj_cjg,29418
-bioos/resource/workspaces.py,sha256=Gmr8y_sjK7TQbhMhQ_7rxqR1KFcwU72I95YYCFrrLBQ,3995
-bioos/service/BioOsService.py,sha256=HuYUEwomHCLpA1MYgVqGyWAQWHM-_BHB-jmy9VsOlnQ,6724
+bioos/resource/workflows.py,sha256=OZ1RRedls4wirri_Ts5dP9IX0XqJA2pwA-_UxORrc-M,29497
+bioos/resource/workspaces.py,sha256=HZCdMzfpSZMm6x9cHDuAXCv-CTCoaVjfQ6EGz-Rek1g,4269
+bioos/service/BioOsService.py,sha256=yXUo6PKaMv8V-SleIwedKtV8aTC3dhESWH2lxL7jY7A,7299
 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
@@ -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-0.0.17.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-0.0.18.dist-info/LICENSE,sha256=cPkGXsgfPgEhIns7Lt3Avxx0Uy-VbdsoP8jvNGuj3cE,1063
+pybioos-0.0.18.dist-info/METADATA,sha256=XJyGrHDGUm0WmQ4hGLx4l59ImW38IpFplODIlLHZCPI,830
+pybioos-0.0.18.dist-info/WHEEL,sha256=OqRkF0eY5GHssMorFjlbTIq072vpHpF60fIQA6lS9xA,92
+pybioos-0.0.18.dist-info/entry_points.txt,sha256=Sc5H0_X7r03Mef4Qd70bebqgdIbVAxLU7nV7qP7cKD4,328
+pybioos-0.0.18.dist-info/top_level.txt,sha256=llpzydkKVDSaWZgz3bsTUsQmhoQpc_JcRJg2-H-5a2U,6
+pybioos-0.0.18.dist-info/RECORD,,