dnastack-client-library 3.1.209__py3-none-any.whl → 3.1.211__py3-none-any.whl

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

@@ -1,5 +1,6 @@
 from dnastack.cli.commands.workbench.runs.commands import init_runs_commands
 from dnastack.cli.commands.workbench.runs.events import events_command_group
+from dnastack.cli.commands.workbench.runs.hooks import hooks_command_group
 from dnastack.cli.commands.workbench.runs.tasks import tasks_command_group
 from dnastack.cli.core.group import formatted_group
 
@@ -14,3 +15,4 @@ init_runs_commands(runs_command_group)
 # Register sub-groups
 runs_command_group.add_command(tasks_command_group)
 runs_command_group.add_command(events_command_group)
+runs_command_group.add_command(hooks_command_group)

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

@@ -0,0 +1,10 @@
+from dnastack.cli.commands.workbench.runs.hooks.commands import init_hooks_commands
+from dnastack.cli.core.group import formatted_group
+
+
+@formatted_group('hooks')
+def hooks_command_group():
+    """Interact with a run's hooks"""
+
+# Initialize all commands
+init_hooks_commands(hooks_command_group)

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

@@ -0,0 +1,71 @@
+from typing import Optional
+
+import click
+
+from dnastack.cli.commands.workbench.utils import get_ewes_client, NAMESPACE_ARG
+from dnastack.cli.core.command import formatted_command
+from dnastack.cli.core.command_spec import ArgumentSpec, ArgumentType, CONTEXT_ARG, SINGLE_ENDPOINT_ID_ARG
+from dnastack.cli.helpers.exporter import to_json, normalize
+from dnastack.cli.helpers.iterator_printer import show_iterator, OutputFormat
+
+
+def init_hooks_commands(group):
+
+    @formatted_command(
+        group=group,
+        name='list',
+        specs=[
+            ArgumentSpec(
+                name='run_id',
+                arg_names=['--run-id'],
+                help='Specify the run whose hooks should be listed.',
+                required=True,
+            ),
+            NAMESPACE_ARG,
+            CONTEXT_ARG,
+            SINGLE_ENDPOINT_ID_ARG,
+        ]
+    )
+    def list_hooks(context: Optional[str],
+                   endpoint_id: Optional[str],
+                   namespace: Optional[str],
+                   run_id: str):
+        """
+        List hooks for a run
+        """
+        client = get_ewes_client(context_name=context, endpoint_id=endpoint_id, namespace=namespace)
+        response = client.list_hooks(run_id)
+        show_iterator(output_format=OutputFormat.JSON, iterator=response.hooks or [])
+
+    @formatted_command(
+        group=group,
+        name='describe',
+        specs=[
+            ArgumentSpec(
+                name='hook_id',
+                arg_type=ArgumentType.POSITIONAL,
+                help='The hook ID to describe.',
+                required=True,
+            ),
+            ArgumentSpec(
+                name='run_id',
+                arg_names=['--run-id'],
+                help='Specify the run the hook belongs to.',
+                required=True,
+            ),
+            NAMESPACE_ARG,
+            CONTEXT_ARG,
+            SINGLE_ENDPOINT_ID_ARG,
+        ]
+    )
+    def describe_hook(context: Optional[str],
+                      endpoint_id: Optional[str],
+                      namespace: Optional[str],
+                      run_id: str,
+                      hook_id: str):
+        """
+        Describe a specific hook for a run
+        """
+        client = get_ewes_client(context_name=context, endpoint_id=endpoint_id, namespace=namespace)
+        hook = client.get_hook(run_id, hook_id)
+        click.echo(to_json(normalize(hook)))

dnastack/client/workbench/ewes/client.py

@@ -11,7 +11,8 @@ from dnastack.client.workbench.ewes.models import ExtendedRunEvents, WesServiceI
     BatchRunResponse, BatchRunRequest, ExtendedRunRequest, Log, TaskListOptions, \
     TaskListResponse, LogType, ExecutionEngineListOptions, ExecutionEngineListResponse, ExecutionEngine, \
     EngineParamPreset, EngineParamPresetListOptions, EngineParamPresetListResponse, \
-    EngineHealthCheck, EngineHealthCheckListOptions, EngineHealthCheckListResponse
+    EngineHealthCheck, EngineHealthCheckListOptions, EngineHealthCheckListResponse, \
+    Hook, HookListResponse
 from dnastack.common.tracing import Span
 from dnastack.http.session import HttpSession
 
@@ -280,6 +281,25 @@ class EWesClient(BaseWorkbenchClient):
                                    trace_context=trace)
             return ExtendedRunEvents(**response.json())
 
+
+    def list_hooks(self, run_id: str, trace: Optional[Span] = None) -> HookListResponse:
+        trace = trace or Span(origin=self)
+        with self.create_http_session() as session:
+            response = session.get(
+                urljoin(self.endpoint.url, f'{self.namespace}/ga4gh/wes/v1/runs/{run_id}/hooks'),
+                trace_context=trace,
+            )
+            return HookListResponse(**response.json())
+
+    def get_hook(self, run_id: str, hook_id: str, trace: Optional[Span] = None) -> Hook:
+        trace = trace or Span(origin=self)
+        with self.create_http_session() as session:
+            response = session.get(
+                urljoin(self.endpoint.url, f'{self.namespace}/ga4gh/wes/v1/runs/{run_id}/hooks/{hook_id}'),
+                trace_context=trace,
+            )
+            return Hook(**response.json())
+
     def list_engines(self,
                      list_options: ExecutionEngineListOptions,
                      max_results: int = None,

dnastack/client/workbench/ewes/models.py

@@ -46,6 +46,12 @@ class Hook(BaseModel):
     finished_at: Optional[datetime] = None
     updated_at: Optional[datetime] = None
 
+
+
+class HookListResponse(BaseModel):
+    hooks: Optional[List[Hook]] = None
+    pagination: Optional[Dict] = None
+
 class ExtendedRunStatus(BaseModel):
     run_id: str
     external_id: Optional[str] = None

dnastack/client/workbench/workflow/models.py

@@ -55,6 +55,7 @@ class WorkflowSource(str, Enum):
     dockstore = "DOCKSTORE"
     custom = "CUSTOM"
     private = "PRIVATE"
+    dnastack = "DNASTACK"
 
 
 class WorkflowFile(BaseModel):

dnastack/constants.py

@@ -1,5 +1,5 @@
 import os
 
-__version__ = "3.1.209"
+__version__ = "3.1.211"
 
 LOCAL_STORAGE_DIRECTORY = os.path.join(os.path.expanduser("~"), '.dnastack')

{dnastack_client_library-3.1.209.dist-info → dnastack_client_library-3.1.211.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dnastack-client-library
-Version: 3.1.209
+Version: 3.1.211
 Summary: DNAstack's GA4GH library and CLI
 Author-email: DNAstack <devs@dnastack.com>
 License: Apache License, Version 2.0

{dnastack_client_library-3.1.209.dist-info → dnastack_client_library-3.1.211.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=Cfd54tZ7BhkWKBRgpXZi0KUD7b5Kxn89WjwHArZw5nc,113
+dnastack/constants.py,sha256=luSsCyuSoskdvEGWRY8zDG3Gt1ncP7S-1MdshbV0_Bs,113
 dnastack/feature_flags.py,sha256=UMNDB07R_ep6Fx3iClhzwOpkWfyYnb418FpoJo50CGs,1411
 dnastack/json_path.py,sha256=TyghhDf7nGQmnsUWBhenU_fKsE_Ez-HLVER6HgH5-hU,2700
 dnastack/omics_cli.py,sha256=ZppKZTHv_XjUUZyRIzSkx0Ug5ODAYrCOTsU0ezCOVrA,3694
@@ -74,11 +74,13 @@ dnastack/cli/commands/workbench/instruments/__init__.py,sha256=ZuRgZxCgqYWkFQdmo
 dnastack/cli/commands/workbench/instruments/commands.py,sha256=MOC1hkZzhwTtcYRk000nUS4uaDpOkSOkx5IWb6nfaBs,2206
 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/__init__.py,sha256=8M_Hd6nikM7YrxOQXbshGCOAxZAfdI9ZPYeajMXsEhg,727
 dnastack/cli/commands/workbench/runs/commands.py,sha256=eosuaLoT-UEebK7nnZqzxrqy1pweXl04bcXVy478MK8,27599
 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
+dnastack/cli/commands/workbench/runs/hooks/__init__.py,sha256=HgaQqV_BIq0F8HaSKOafhlvNwv-8fDdlA9oOUuNffYs,296
+dnastack/cli/commands/workbench/runs/hooks/commands.py,sha256=8elGEH7Rj5sva2Lv580Q2SSpP4k0Tl81jp5xGvYcG-w,2387
 dnastack/cli/commands/workbench/samples/__init__.py,sha256=cRfeKCdHO-0Dq3PFoVcqO7OrQspajIO3h1zNqknKP2U,456
 dnastack/cli/commands/workbench/samples/commands.py,sha256=4o3MwcFib9km23weEOiz_JHGj-BDeWvMO8hItB5W3ng,9521
 dnastack/cli/commands/workbench/samples/files.py,sha256=ihZgHV04fXC8-B0EFZ463SesgI93YSbXXlEtYyaUn8U,3021
@@ -141,8 +143,8 @@ dnastack/client/workbench/models.py,sha256=d0OzcPKePDuyJnOnoScSRQqzHx7SMu_qq1t_b
 dnastack/client/workbench/common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/client/workbench/common/models.py,sha256=cOlwpZGxA23CkjYQ7Uox2-uOA_MwqszHt10OSjXT6AQ,1070
 dnastack/client/workbench/ewes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-dnastack/client/workbench/ewes/client.py,sha256=MZu2roXOECEu79oC2_c8XydAksw3by5wFS-ryzrA53U,15645
-dnastack/client/workbench/ewes/models.py,sha256=bn9qImKDvl4-m8StxUK8Xd6UElqeHZhy9L1pvrvI_Zc,12614
+dnastack/client/workbench/ewes/client.py,sha256=deaG6vCb2r5q7Habfp9QfCVbXQJNjl2GC5dxm_PnDwE,16524
+dnastack/client/workbench/ewes/models.py,sha256=BLG0Jd-8N8r_0yKqb94oZglZ3ymAaS2gdqb0kPcunoY,12729
 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=oExpYx32nunvO2rBUCIZQcU-dUZmLLpSTOAFdKAzk1k,3785
@@ -154,7 +156,7 @@ dnastack/client/workbench/workbench_user_service/client.py,sha256=ZpMOFw5L3NxbC2
 dnastack/client/workbench/workbench_user_service/models.py,sha256=P8WmocouYthi4gnHzNJT2F3iExWTt_2MUnskexN6Rxs,126
 dnastack/client/workbench/workflow/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/client/workbench/workflow/client.py,sha256=UCNGy9SsIOIQuP5AFgFB0WH1ZUvO0ShSaPjrcTN4aMU,22351
-dnastack/client/workbench/workflow/models.py,sha256=QvBMnmb7bqKkwSOUvMOeMJwXoF8X-JW4x8FlY0DDOGw,6018
+dnastack/client/workbench/workflow/models.py,sha256=3xT8kbG8dDmDzc9_0XXIW8tC1U_sC2sg1N4sJ0i3iEk,6044
 dnastack/client/workbench/workflow/utils.py,sha256=Qoo5eENmG8HGKqz-aYiKNzlLgdxHWIcge825b00aSt0,4641
 dnastack/common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/common/auth_manager.py,sha256=22j70VdOEcp1TC2EQps6NkgO8BX70vZdAxsMy6rbY-8,8828
@@ -198,9 +200,9 @@ 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=7UsC8DkStMBx7Bz_xHQNi_J1UO_H4nfHme7oBhokj2I,1339
 dnastack/http/authenticators/oauth2_adapter/token_exchange.py,sha256=nSuAsSKWa_UNqHSbPMOEk4komaFITYAnE04Sk5WOrLc,6332
-dnastack_client_library-3.1.209.dist-info/licenses/LICENSE,sha256=uwybO-wUbQhxkosgjhJlxmYATMy-AzoULFO9FUedE34,11580
-dnastack_client_library-3.1.209.dist-info/METADATA,sha256=wi1ZarZ4hhrHe-Lle2I5OpuE9fDFMUN_2CxB1Lb8z9k,1791
-dnastack_client_library-3.1.209.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-dnastack_client_library-3.1.209.dist-info/entry_points.txt,sha256=Y6OeicsiyGn3-8D-SiV4NiKlJgXfkSqK88kFBR6R1rY,89
-dnastack_client_library-3.1.209.dist-info/top_level.txt,sha256=P2RgRyqJ7hfNy1wLVRoVLJYEppUVkCX3syGK9zBqkt8,9
-dnastack_client_library-3.1.209.dist-info/RECORD,,
+dnastack_client_library-3.1.211.dist-info/licenses/LICENSE,sha256=uwybO-wUbQhxkosgjhJlxmYATMy-AzoULFO9FUedE34,11580
+dnastack_client_library-3.1.211.dist-info/METADATA,sha256=igkuH5IVMlkRQQRU6hhRnj68fD1-xxxut3S-Ljp0p1o,1791
+dnastack_client_library-3.1.211.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+dnastack_client_library-3.1.211.dist-info/entry_points.txt,sha256=Y6OeicsiyGn3-8D-SiV4NiKlJgXfkSqK88kFBR6R1rY,89
+dnastack_client_library-3.1.211.dist-info/top_level.txt,sha256=P2RgRyqJ7hfNy1wLVRoVLJYEppUVkCX3syGK9zBqkt8,9
+dnastack_client_library-3.1.211.dist-info/RECORD,,