dnastack-client-library 3.1.145__py3-none-any.whl → 3.1.160__py3-none-any.whl

dnastack/cli/commands/auth/commands.py

@@ -158,5 +158,5 @@ class AuthCommandHandler:
         auth_manager.events.on('no-refresh-token', handle_no_refresh_token)
         auth_manager.events.on('refresh-skipped', handle_refresh_skipped)
 
-        auth_manager.initiate_authentications(endpoint_ids, force_refresh, revoke_existing)
+        auth_manager.initiate_authentications(endpoint_ids, force_refresh, revoke_existing, allow_token_exchange=False)
 

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/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/client/workbench/samples/models.py

@@ -26,7 +26,6 @@ class Sample(BaseModel):
     id: str
     created_at: Optional[datetime]
     last_updated_at: Optional[datetime]
-    files: Optional[List[SampleFile]]
 
 
 class SampleListResponse(PaginatedResource):

dnastack/common/auth_manager.py

@@ -10,6 +10,7 @@ from dnastack.common.tracing import Span
 from dnastack.context.models import Context
 from dnastack.http.authenticators.abstract import Authenticator, AuthStateStatus, AuthState
 from dnastack.http.authenticators.factory import HttpAuthenticatorFactory
+from dnastack.http.authenticators.oauth2_adapter.models import GRANT_TYPE_TOKEN_EXCHANGE
 
 
 class ExtendedAuthState(AuthState):
@@ -127,7 +128,8 @@ class AuthManager:
     def initiate_authentications(self,
                                  endpoint_ids: List[str] = None,
                                  force_refresh: bool = False,
-                                 revoke_existing: bool = False):
+                                 revoke_existing: bool = False,
+                                 allow_token_exchange: bool = False):
         trace = Span(origin=self)
 
         authenticators = self.get_authenticators(endpoint_ids)
@@ -137,6 +139,11 @@ class AuthManager:
 
         for authenticator in authenticators:
             state = authenticator.get_state()
+            if not allow_token_exchange and state.auth_info.get('grant_type') == GRANT_TYPE_TOKEN_EXCHANGE:
+                self._logger.debug(f'Skipping token exchange authenticator {authenticator.session_id} (allow_token_exchange=False)')
+                index += 1
+                continue
+            
             basic_event_info = dict(session_id=authenticator.session_id,
                                     state=state,
                                     index=index,

dnastack/constants.py

@@ -1,5 +1,5 @@
 import os
 
-__version__ = "v3.1.145"
+__version__ = "v3.1.160"
 
 LOCAL_STORAGE_DIRECTORY = os.path.join(os.path.expanduser("~"), '.dnastack')

dnastack/context/manager.py

@@ -336,7 +336,7 @@ class BaseContextManager:
             for event_type in self.__propagated_auth_event_types:
                 self.events.relay_from(auth_manager.events, event_type)
 
-            auth_manager.initiate_authentications()
+            auth_manager.initiate_authentications(allow_token_exchange=platform_credentials)
             del auth_manager
 
         # Then, return the repository.

dnastack/http/authenticators/oauth2_adapter/token_exchange.py

@@ -47,7 +47,7 @@ class TokenExchangeAdapter(OAuth2Adapter):
         if context_subject_token:
             return context_subject_token
 
-        audience = self._auth_info.audience or self._auth_info.resource_url
+        audience = self._auth_info.audience or self._auth_info.client_id or self._auth_info.resource_url
         token = self._fetch_cloud_identity_token(audience, trace_context)
         if token:
             return token

{dnastack_client_library-3.1.145.dist-info → dnastack_client_library-3.1.160.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dnastack-client-library
-Version: 3.1.145
+Version: 3.1.160
 Summary: DNAstack's GA4GH library and CLI
 Author-email: DNAstack <devs@dnastack.com>
 License: Apache License, Version 2.0
@@ -27,6 +27,15 @@ Requires-Dist: kotoba
 Requires-Dist: imagination>=3.3.1
 Requires-Dist: requests-toolbelt<1,>=0.9.1
 Requires-Dist: httpie>=3.2.1
+Requires-Dist: beautifulsoup4>=4.10.0
+Requires-Dist: flask~=2.1
+Requires-Dist: google-cloud-secret-manager
+Requires-Dist: google-crc32c
+Requires-Dist: pandas
+Requires-Dist: python-dotenv
+Requires-Dist: pip>=21.3.1
+Requires-Dist: packaging>=21.3
+Requires-Dist: selenium>=4.1.0
 Provides-Extra: test
 Requires-Dist: selenium>=3.141.0; extra == "test"
 Requires-Dist: pyjwt>=2.1.0; extra == "test"

{dnastack_client_library-3.1.145.dist-info → dnastack_client_library-3.1.160.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=9HWP6mq4zFzR5KcChCWx0_tG3OvN3GT_mjqi3CwAck4,114
+dnastack/constants.py,sha256=gddQdVRGL-wmdJ9LGIac_q3bwrCV5rzW-isACUNjOJI,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
@@ -31,7 +31,7 @@ dnastack/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/cli/commands/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/cli/commands/utils.py,sha256=ZwKTyyvqBTrt27cF9wF6SglE01t7NkHWLMjXegi_6iA,574
 dnastack/cli/commands/auth/__init__.py,sha256=SGnt7w8ccS1ED6EQzBq4PaH3kqoLuXC4wrFMa7P_Vg4,313
-dnastack/cli/commands/auth/commands.py,sha256=RhLvCIwjg3fRbRKSVqYqEFlSaGwp2hJqYByZlMMBkJM,6470
+dnastack/cli/commands/auth/commands.py,sha256=FIQLegV5h6T2IP-fh4xcp7aItC4OkKSOHIlFCBQK1bw,6498
 dnastack/cli/commands/auth/event_handlers.py,sha256=g6FPChlBZZr7M6hejGWT6Z3THNZr7AtbV0S5PJEtU_o,3627
 dnastack/cli/commands/collections/__init__.py,sha256=hrsjIkOvqOnYUN4xwoSB3iTCLrbX6qG-XeafVzoGleI,535
 dnastack/cli/commands/collections/commands.py,sha256=yawGsTZfgkTYvyCIyRaup9mEQOrr_nfE7Cj6lPcEaIk,8978
@@ -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
@@ -138,10 +138,10 @@ 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=qGR--2b-Z71PlNXZt8Sg5LbrDNICFV54l3IWetwCTw8,1504
+dnastack/client/workbench/samples/models.py,sha256=g_04aDltLVRVCstOGkINqJNo1XSKB2aXWwnMfDEhC0Y,1466
 dnastack/client/workbench/storage/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/client/workbench/storage/client.py,sha256=uMr0mtwMj07TKhS2_IHIKoF-JkrEUiFdGpijVHP-vb4,4080
 dnastack/client/workbench/storage/models.py,sha256=S5P1m-blJH5x4glmIcu1KTDoJEjt8Qfp-lEeBW9I7PI,2219
@@ -153,7 +153,7 @@ dnastack/client/workbench/workflow/client.py,sha256=ZbQAzJ1DPoPcMGkJEKSyV37pEpSk
 dnastack/client/workbench/workflow/models.py,sha256=xokiS_Kyet3zbyB8i5Z3Uq3wmvcgPMkTQ2WGWhFrexw,4481
 dnastack/client/workbench/workflow/utils.py,sha256=Yw9X-Gtu5lYPDCZjimFJMhrib9ELl07YyD4A-L8Y7pE,4661
 dnastack/common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-dnastack/common/auth_manager.py,sha256=N5lVkM94KGSh8Lje6os9v6rQC082vVJiRwe33US517g,8587
+dnastack/common/auth_manager.py,sha256=AFMDIR01AQ2EPNyUZ7RMS8A8FvdRUMEhLtFjTd5Mdqw,9051
 dnastack/common/class_decorator.py,sha256=vu-TytoFW06IZwuTl54oR-YKqftAPeyIGJeqSG3WvO4,2470
 dnastack/common/console.py,sha256=edvhWiXtPPXg508RCcfuWKElpLdRu2A9p1kLhdsTtSw,602
 dnastack/common/environments.py,sha256=VDSSxvtxd60IxAyjgwx9YJuAwWkorhnAMN-XaV087gw,2529
@@ -175,7 +175,7 @@ dnastack/configuration/wrapper.py,sha256=qLmI8bgwTTflym_e0HC85IwdoCuLfazJt_O8mJJ
 dnastack/context/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/context/context_wraper.py,sha256=G88LciVBW5HJkvhi3oYS6RlrH_-l0H2CSYSU8nS33_0,315
 dnastack/context/helper.py,sha256=GOlmi2ddkstSRBo3sG6yB8_2oMFqN1o6yI8Ny-gpkbQ,1475
-dnastack/context/manager.py,sha256=PMIGG34alXjFN6WJTqDpSEAO8jdRagzLs6iamcDlz7g,17354
+dnastack/context/manager.py,sha256=4Z_KhDhIClkUOiT605yi9SwehdqiJwYth4T3G3Lb4rM,17395
 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
@@ -193,10 +193,10 @@ dnastack/http/authenticators/oauth2_adapter/cloud_providers.py,sha256=UHQ-YHHr5i
 dnastack/http/authenticators/oauth2_adapter/device_code_flow.py,sha256=dXI5CyUcsqYg6gf5vDC_3eY6Cc-H1C8W7FeD_24j92A,6750
 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=aLSs0P5lj5LgpqUTzAn0hdbZxseVhqX2qV8KdcjmY6k,6303
-dnastack_client_library-3.1.145.dist-info/licenses/LICENSE,sha256=uwybO-wUbQhxkosgjhJlxmYATMy-AzoULFO9FUedE34,11580
-dnastack_client_library-3.1.145.dist-info/METADATA,sha256=10kJ53EGKrSgDaOEIBGHvQARcwfp488x6WmLMQ_ur6c,1490
-dnastack_client_library-3.1.145.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-dnastack_client_library-3.1.145.dist-info/entry_points.txt,sha256=Y6OeicsiyGn3-8D-SiV4NiKlJgXfkSqK88kFBR6R1rY,89
-dnastack_client_library-3.1.145.dist-info/top_level.txt,sha256=P2RgRyqJ7hfNy1wLVRoVLJYEppUVkCX3syGK9zBqkt8,9
-dnastack_client_library-3.1.145.dist-info/RECORD,,
+dnastack/http/authenticators/oauth2_adapter/token_exchange.py,sha256=nSuAsSKWa_UNqHSbPMOEk4komaFITYAnE04Sk5WOrLc,6332
+dnastack_client_library-3.1.160.dist-info/licenses/LICENSE,sha256=uwybO-wUbQhxkosgjhJlxmYATMy-AzoULFO9FUedE34,11580
+dnastack_client_library-3.1.160.dist-info/METADATA,sha256=MhN44vdROVWBseHG309SvqkHlvKcnT3AEigPkn2iImk,1766
+dnastack_client_library-3.1.160.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+dnastack_client_library-3.1.160.dist-info/entry_points.txt,sha256=Y6OeicsiyGn3-8D-SiV4NiKlJgXfkSqK88kFBR6R1rY,89
+dnastack_client_library-3.1.160.dist-info/top_level.txt,sha256=P2RgRyqJ7hfNy1wLVRoVLJYEppUVkCX3syGK9zBqkt8,9
+dnastack_client_library-3.1.160.dist-info/RECORD,,