dnastack-client-library 3.1.159__py3-none-any.whl → 3.1.162__py3-none-any.whl

dnastack/cli/commands/workbench/runs/commands.py

@@ -473,6 +473,13 @@ def init_runs_commands(group: Group):
                 help='If specified, the command will print the request without actually submitting the workflow.',
                 type=bool,
             ),
+            ArgumentSpec(
+                name='run_requests',
+                arg_names=['--run-request'],
+                help='Optional way to specify a complete run request for one or more runs. ',
+                type=JsonLike,
+                multiple=True
+            ),
             ArgumentSpec(
                 name='sample_ids',
                 arg_names=['--samples'],
@@ -496,6 +503,7 @@ def init_runs_commands(group: Group):
                      workflow_params: JsonLike,
                      input_overrides,
                      dry_run: bool,
+                     run_requests: JsonLike,
                      sample_ids: Optional[str]):
         """
         Submit one or more workflows for execution
@@ -579,6 +587,12 @@ def init_runs_commands(group: Group):
             samples=parse_samples()
         )
 
+        for run_request in run_requests:
+            parsed_value = run_request.parsed_value() if run_request else None
+            parsed_run_request  = ExtendedRunRequest(**parsed_value)
+            batch_request.run_requests.append(parsed_run_request)
+
+
         for workflow_param in workflow_params:
             run_request = ExtendedRunRequest(
                 workflow_params=workflow_param.parsed_value() if workflow_param else None

dnastack/client/explorer/client.py

@@ -91,11 +91,9 @@ class ExplorerClient(BaseServiceClient):
                         f"Not authorized to access question '{question_id}'"
                     )
                 elif status_code == 404:
-                    raise ClientError(f"Question '{question_id}' not found")
+                    raise ClientError(e.response, e.trace, f"Question '{question_id}' not found")
                 else:
-                    raise ClientError(
-                        f"Failed to retrieve question '{question_id}': {e.response.text}"
-                    )
+                    raise ClientError(e.response, e.trace, f"Failed to retrieve question '{question_id}'")
 
     def ask_federated_question(
         self,
@@ -179,9 +177,8 @@ class FederatedQuestionListResultLoader(ResultLoader):
                         "Not authorized to list federated questions"
                     )
                 else:
-                    raise ClientError(
-                        f"Failed to load federated questions: {e.response.text}"
-                    )
+                    
+                    raise ClientError(e.response, e.trace, "Failed to load federated questions")
 
 
 class FederatedQuestionQueryResultLoader(ResultLoader):
@@ -247,10 +244,8 @@ class FederatedQuestionQueryResultLoader(ResultLoader):
                         "Not authorized to ask federated questions"
                     )
                 elif status_code == 400:
-                    raise ClientError(
-                        f"Invalid question parameters: {e.response.text}"
-                    )
+                    
+                    raise ClientError(e.response, e.trace, "Invalid question parameters")
                 else:
-                    raise ClientError(
-                        f"Failed to execute federated question: {e.response.text}"
-                    )
+                    
+                    raise ClientError(e.response, e.trace, "Failed to execute federated question")

dnastack/client/workbench/ewes/models.py

@@ -86,6 +86,8 @@ class Log(BaseModel):
     exit_code: Optional[int]
     state: Optional[State]
 
+class RunDependency(BaseModel):
+    run_id: str
 
 class ExtendedRunRequest(BaseModel):
     workflow_url: Optional[str]
@@ -99,6 +101,7 @@ class ExtendedRunRequest(BaseModel):
     submitted_by: Optional[str]
     workflow_params: Optional[Dict]
     workflow_engine_parameters: Optional[Dict]
+    dependencies: Optional[Dict[str, RunDependency]]
     tags: Optional[Dict]
 
 
@@ -124,6 +127,8 @@ class RunEvent(BaseModel):
     created_at: datetime
     metadata: RunEventMetadata
 
+class ExtendedRunEvents(BaseModel):
+    events: Optional[List[RunEvent]]
 
 class ExtendedRun(BaseModel):
     run_id: str
@@ -136,12 +141,11 @@ class ExtendedRun(BaseModel):
     task_logs: Optional[List[Log]]
     task_logs_url: Optional[str]
     outputs: Optional[Dict]
-
-
-class ExtendedRunEvents(BaseModel):
+    dependencies: Optional[Dict[str, RunDependency]]
     events: Optional[List[RunEvent]]
 
 
+
 class MinimalExtendedRun(BaseModel):
     run_id: Optional[str]
     state: Optional[State]

dnastack/constants.py

@@ -1,5 +1,5 @@
 import os
 
-__version__ = "v3.1.159"
+__version__ = "v3.1.162"
 
 LOCAL_STORAGE_DIRECTORY = os.path.join(os.path.expanduser("~"), '.dnastack')

dnastack/http/session.py

@@ -23,8 +23,8 @@ class AuthenticationError(RuntimeError):
 
 
 class HttpError(RuntimeError):
-    def __init__(self, response: Response, trace_context: Optional[Span] = None):
-        super(HttpError, self).__init__(response, trace_context)
+    def __init__(self, response: Response, trace_context: Optional[Span] = None, message: Optional[str] = None):
+        super(HttpError, self).__init__(response, trace_context, message)
 
     @property
     def response(self) -> Response:
@@ -33,19 +33,26 @@ class HttpError(RuntimeError):
     @property
     def trace(self) -> Span:
         return self.args[1]
+    
+    @property
+    def message(self) -> Optional[str]:
+        return self.args[2] if len(self.args) > 2 else None
 
     def __str__(self):
         response: Response = self.response
 
         error_feedback = f'HTTP {response.status_code}'
 
-        # Prepare the error feedback.
         response_text = response.text.strip()
         if len(response_text) == 0:
             error_feedback = f'{error_feedback} (empty response)'
         else:
             error_feedback = f'{error_feedback}: {response_text}'
 
+        custom_message = self.message
+        if custom_message:
+            error_feedback = f'{custom_message} - {error_feedback}'
+
         trace: Span = self.trace
         if trace:
             error_feedback = f'[{trace.trace_id},{trace.span_id}] {error_feedback}'
@@ -68,6 +75,7 @@ class JsonPatch(BaseModel):
 
 
 class RetryHistoryEntry(BaseModel):
+    url: str
     authenticator_index: int
     with_reauthentication: bool
     with_next_authenticator: bool
@@ -153,7 +161,7 @@ class HttpSession(AbstractContextManager):
                authenticator_index: int = 0,
                retry_history: Optional[List[RetryHistoryEntry]] = None,
                trace_context: Optional[Span] = None,
-               **kwargs) -> Response:
+               **kwargs) -> Response | None | Any:
         trace_context = trace_context or Span(origin=self)
 
         retry_history = retry_history or list()
@@ -317,7 +325,8 @@ class HttpSession(AbstractContextManager):
     def _raise_http_error(self,
                           response: Response,
                           authenticator: Authenticator,
-                          trace_context: Span):
+                          trace_context: Span,
+                          message: Optional[str] = None):
         trace_logger = trace_context.create_span_logger(self.__logger) if trace_context else self.__logger
 
         if isinstance(authenticator, OAuth2Authenticator):
@@ -344,7 +353,7 @@ class HttpSession(AbstractContextManager):
         else:
             trace_logger.error('The authenticator is not available or supported for extracting additional info.')
 
-        raise (ClientError if response.status_code < 500 else ServerError)(response, trace_context=trace_context)
+        raise (ClientError if response.status_code < 500 else ServerError)(response, trace_context=trace_context, message=message)
 
     def __del__(self):
         self.close()

{dnastack_client_library-3.1.159.dist-info → dnastack_client_library-3.1.162.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dnastack-client-library
-Version: 3.1.159
+Version: 3.1.162
 Summary: DNAstack's GA4GH library and CLI
 Author-email: DNAstack <devs@dnastack.com>
 License: Apache License, Version 2.0

{dnastack_client_library-3.1.159.dist-info → dnastack_client_library-3.1.162.dist-info}/RECORD

@@ -1,6 +1,6 @@
 dnastack/__init__.py,sha256=mslf7se8vBSK_HkqWTGPdibeVhT4xyKXgzQBV7dEK1M,333
 dnastack/__main__.py,sha256=EKmtIs4TBseQJi-OT_U6LqRyKLiyrGTBuTQg9zE-G2I,4376
-dnastack/constants.py,sha256=Lgz298BXYq_2gOGdhlAdlDkzJjgpA-c6hddW5d5bRuQ,114
+dnastack/constants.py,sha256=6P579Aw9VUw8nJ_eFzwu-eQjSXMo09xI9vmHC62W9wM,114
 dnastack/feature_flags.py,sha256=RK_V_Ovncoe6NeTheAA_frP-kYkZC1fDlTbbup2KYG4,1419
 dnastack/json_path.py,sha256=TyghhDf7nGQmnsUWBhenU_fKsE_Ez-HLVER6HgH5-hU,2700
 dnastack/omics_cli.py,sha256=ZppKZTHv_XjUUZyRIzSkx0Ug5ODAYrCOTsU0ezCOVrA,3694
@@ -75,7 +75,7 @@ dnastack/cli/commands/workbench/instruments/commands.py,sha256=MOC1hkZzhwTtcYRk0
 dnastack/cli/commands/workbench/namespaces/__init__.py,sha256=D4b8BMxuVb7tuQ8ZY-vQracVp-wPv7RrIHhOe9DeAvA,309
 dnastack/cli/commands/workbench/namespaces/commands.py,sha256=36WHG4h6U69_32tnTWvTFRzNtRvTCbF-u0P4U5qsCoc,887
 dnastack/cli/commands/workbench/runs/__init__.py,sha256=krxeV0LGOsgl0yW6e_cynwGJb8PClrWvvt8icHwSHXw,600
-dnastack/cli/commands/workbench/runs/commands.py,sha256=53lohWqeC4_Hv2jghxzErP0HgfxxjnMOZSfRRb9zOIg,25181
+dnastack/cli/commands/workbench/runs/commands.py,sha256=KS1DUMI2uQpX5hMOyFNrFliKsg7hF3uhsS5TEzMj6ro,25761
 dnastack/cli/commands/workbench/runs/events.py,sha256=eJL8zApopJKGumZlDlFGxNbToCgnzKltanbUUeXjUw8,1244
 dnastack/cli/commands/workbench/runs/tasks.py,sha256=aYLgSAAv3XqN36gLw-YeJ4_gQ-csiFp7bF4yLEX1QMw,1719
 dnastack/cli/commands/workbench/runs/utils.py,sha256=5ROpUn9JIG5J6oHNQjDIPUHjLvKOuddYOesDL3PTT24,233
@@ -125,7 +125,7 @@ dnastack/client/datasources/__init__.py,sha256=HxDIHuQX8KMWr3o70ucL3x79pXKaIHbBq
 dnastack/client/datasources/client.py,sha256=jfVzCSKuQJsggbvfJVbftYJ0hd6gAPsBZMgvINOgjRE,4671
 dnastack/client/datasources/model.py,sha256=dV9Sf05ivIq0ubwIIYK3kSv1xJ_TtjxvVp_ddI9aHEk,214
 dnastack/client/explorer/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-dnastack/client/explorer/client.py,sha256=A_C2YN5rLc-KqOBxmYHvLcq1tbRrRwRdfmV8DwcQAuQ,9511
+dnastack/client/explorer/client.py,sha256=_YisPn9jQUSk-O-8E9Vncn_jALLRvu7etYC-1KK3vKY,9416
 dnastack/client/explorer/models.py,sha256=vrltbcb4qAx6z1oGXG8ufw2kZ36dDiwU5QGqOomYp6c,3126
 dnastack/client/service_registry/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/client/service_registry/client.py,sha256=r7D8CnPJLbNkc03g2PYHt880Ba1oPW2d8B0ShP0p4Eo,1131
@@ -138,7 +138,7 @@ dnastack/client/workbench/base_client.py,sha256=KlkSO1c32bKhojfco8NcVBVSY5x_PZAC
 dnastack/client/workbench/models.py,sha256=RBo7wmWMSDkgiFZHaWh2ehKeTM8ERywug1bMGKDOm0k,446
 dnastack/client/workbench/ewes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/client/workbench/ewes/client.py,sha256=yIqjwyyY9q0NrxpTX6LrnlnjavHoa6Fo073O3Lokkaw,15637
-dnastack/client/workbench/ewes/models.py,sha256=wnzthvBjzG_Zq1lyVJBTN5gWgT9gO1sZ0-Q91isy7FA,8214
+dnastack/client/workbench/ewes/models.py,sha256=MBSkYxFW8nX9OlzijJxzZ3I7zCUFHM83PXF4zXbnZeY,8404
 dnastack/client/workbench/samples/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/client/workbench/samples/client.py,sha256=2X34SYTjV6n4yZz0q7Kaa4NPWDHRi2ut0uJWL3zXZWA,5901
 dnastack/client/workbench/samples/models.py,sha256=g_04aDltLVRVCstOGkINqJNo1XSKB2aXWwnMfDEhC0Y,1466
@@ -179,7 +179,7 @@ dnastack/context/manager.py,sha256=4Z_KhDhIClkUOiT605yi9SwehdqiJwYth4T3G3Lb4rM,1
 dnastack/context/models.py,sha256=BXSJZSwiopNZ_l2nY8uzofoYebLYwu0BLbirSBIY110,671
 dnastack/http/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/http/client_factory.py,sha256=HdRZpTEnFQcHEdVbdYl7AbCcRUv3K3kVyznIxEWIqvA,650
-dnastack/http/session.py,sha256=R-rsE_TTswlTTlqJW7a6_O-sVMmbrnEMnKBf7m_5I8U,15058
+dnastack/http/session.py,sha256=LAVJW6RzURnHf0lpl3GYQjAzPb9QB9PESOyB7nKesTw,15413
 dnastack/http/session_info.py,sha256=I0m8Z17MCtsWgMCmlzhtOzsXZfUddBAXp0XSOLWfgrM,9366
 dnastack/http/authenticators/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/http/authenticators/abstract.py,sha256=b5zXqSdCasiy6Bz5LYTr7e_p7l4__Mq5shgTV6bBGnk,9241
@@ -194,9 +194,9 @@ dnastack/http/authenticators/oauth2_adapter/device_code_flow.py,sha256=dXI5CyUcs
 dnastack/http/authenticators/oauth2_adapter/factory.py,sha256=ZtNXOklWEim-26ooNoPp3ji_hRg1vf4fHHnY94F0wLI,1087
 dnastack/http/authenticators/oauth2_adapter/models.py,sha256=iY7asrSElyjubInrGV5rJKKZAxJWeq7csnaj-EqMq00,943
 dnastack/http/authenticators/oauth2_adapter/token_exchange.py,sha256=nSuAsSKWa_UNqHSbPMOEk4komaFITYAnE04Sk5WOrLc,6332
-dnastack_client_library-3.1.159.dist-info/licenses/LICENSE,sha256=uwybO-wUbQhxkosgjhJlxmYATMy-AzoULFO9FUedE34,11580
-dnastack_client_library-3.1.159.dist-info/METADATA,sha256=8WpjZzXD8-Zq7hzlzrm953TLgASaQrScgbOPFqKldYg,1766
-dnastack_client_library-3.1.159.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-dnastack_client_library-3.1.159.dist-info/entry_points.txt,sha256=Y6OeicsiyGn3-8D-SiV4NiKlJgXfkSqK88kFBR6R1rY,89
-dnastack_client_library-3.1.159.dist-info/top_level.txt,sha256=P2RgRyqJ7hfNy1wLVRoVLJYEppUVkCX3syGK9zBqkt8,9
-dnastack_client_library-3.1.159.dist-info/RECORD,,
+dnastack_client_library-3.1.162.dist-info/licenses/LICENSE,sha256=uwybO-wUbQhxkosgjhJlxmYATMy-AzoULFO9FUedE34,11580
+dnastack_client_library-3.1.162.dist-info/METADATA,sha256=hE05Y8wAcmuy8xIoXPuktKrh5pqISri-tDkdQ8Guv0s,1766
+dnastack_client_library-3.1.162.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+dnastack_client_library-3.1.162.dist-info/entry_points.txt,sha256=Y6OeicsiyGn3-8D-SiV4NiKlJgXfkSqK88kFBR6R1rY,89
+dnastack_client_library-3.1.162.dist-info/top_level.txt,sha256=P2RgRyqJ7hfNy1wLVRoVLJYEppUVkCX3syGK9zBqkt8,9
+dnastack_client_library-3.1.162.dist-info/RECORD,,