dnastack-client-library 3.1.211__py3-none-any.whl → 3.1.213__py3-none-any.whl

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

@@ -1,6 +1,7 @@
 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.samples import samples_command_group
 from dnastack.cli.commands.workbench.runs.tasks import tasks_command_group
 from dnastack.cli.core.group import formatted_group
 
@@ -16,3 +17,4 @@ init_runs_commands(runs_command_group)
 runs_command_group.add_command(tasks_command_group)
 runs_command_group.add_command(events_command_group)
 runs_command_group.add_command(hooks_command_group)
+runs_command_group.add_command(samples_command_group)

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

@@ -0,0 +1,10 @@
+from dnastack.cli.commands.workbench.runs.samples.commands import init_samples_commands
+from dnastack.cli.core.group import formatted_group
+
+
+@formatted_group('samples')
+def samples_command_group():
+    """Manage the samples associated with a run"""
+
+
+init_samples_commands(samples_command_group)

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

@@ -0,0 +1,123 @@
+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, CONTEXT_ARG, SINGLE_ENDPOINT_ID_ARG
+from dnastack.cli.helpers.exporter import to_json, normalize
+from dnastack.client.workbench.ewes.models import SimpleSample
+
+
+def init_samples_commands(group):
+
+    @formatted_command(
+        group=group,
+        name='add',
+        specs=[
+            ArgumentSpec(
+                name='run_id',
+                arg_names=['--run-id'],
+                help='The ID of the run to add samples to',
+                required=True,
+            ),
+            ArgumentSpec(
+                name='samples',
+                arg_names=['--sample'],
+                help='Sample ID to add to the run. Can be specified multiple times.',
+                as_option=True,
+                multiple=True,
+                required=True,
+            ),
+            ArgumentSpec(
+                name='storage_account_id',
+                arg_names=['--storage-account'],
+                help='The storage account ID to associate with the samples.',
+            ),
+            NAMESPACE_ARG,
+            CONTEXT_ARG,
+            SINGLE_ENDPOINT_ID_ARG,
+        ]
+    )
+    def add_samples(context: Optional[str] = None,
+                    endpoint_id: Optional[str] = None,
+                    namespace: Optional[str] = None,
+                    run_id: str = None,
+                    samples: tuple = (),
+                    storage_account_id: Optional[str] = None):
+        """Add samples to a run. Existing samples are preserved."""
+        client = get_ewes_client(context_name=context, endpoint_id=endpoint_id, namespace=namespace)
+        run = client.get_run(run_id)
+        existing = run.request.samples if run.request and run.request.samples else []
+
+        existing_ids = {s.id for s in existing}
+        new_samples = list(existing)
+        for sample_id in samples:
+            if sample_id not in existing_ids:
+                new_samples.append(SimpleSample(id=sample_id, storage_account_id=storage_account_id))
+
+        result = client.update_run_samples(run_id, new_samples)
+        click.echo(to_json(normalize(result)))
+
+    @formatted_command(
+        group=group,
+        name='remove',
+        specs=[
+            ArgumentSpec(
+                name='run_id',
+                arg_names=['--run-id'],
+                help='The ID of the run to remove samples from',
+                required=True,
+            ),
+            ArgumentSpec(
+                name='samples',
+                arg_names=['--sample'],
+                help='Sample ID to remove from the run. Can be specified multiple times.',
+                as_option=True,
+                multiple=True,
+                required=True,
+            ),
+            NAMESPACE_ARG,
+            CONTEXT_ARG,
+            SINGLE_ENDPOINT_ID_ARG,
+        ]
+    )
+    def remove_samples(context: Optional[str] = None,
+                       endpoint_id: Optional[str] = None,
+                       namespace: Optional[str] = None,
+                       run_id: str = None,
+                       samples: tuple = ()):
+        """Remove samples from a run."""
+        client = get_ewes_client(context_name=context, endpoint_id=endpoint_id, namespace=namespace)
+        run = client.get_run(run_id)
+        existing = run.request.samples if run.request and run.request.samples else []
+
+        remove_ids = set(samples)
+        remaining = [s for s in existing if s.id not in remove_ids]
+
+        result = client.update_run_samples(run_id, remaining)
+        click.echo(to_json(normalize(result)))
+
+    @formatted_command(
+        group=group,
+        name='clear',
+        specs=[
+            ArgumentSpec(
+                name='run_id',
+                arg_names=['--run-id'],
+                help='The ID of the run to clear all samples from',
+                required=True,
+            ),
+            NAMESPACE_ARG,
+            CONTEXT_ARG,
+            SINGLE_ENDPOINT_ID_ARG,
+        ]
+    )
+    def clear_samples(context: Optional[str] = None,
+                      endpoint_id: Optional[str] = None,
+                      namespace: Optional[str] = None,
+                      run_id: str = None):
+        """Remove all samples from a run."""
+        client = get_ewes_client(context_name=context, endpoint_id=endpoint_id, namespace=namespace)
+        result = client.update_run_samples(run_id, [])
+        click.echo(to_json(normalize(result)))

dnastack/client/workbench/ewes/client.py

@@ -12,7 +12,7 @@ from dnastack.client.workbench.ewes.models import ExtendedRunEvents, WesServiceI
     TaskListResponse, LogType, ExecutionEngineListOptions, ExecutionEngineListResponse, ExecutionEngine, \
     EngineParamPreset, EngineParamPresetListOptions, EngineParamPresetListResponse, \
     EngineHealthCheck, EngineHealthCheckListOptions, EngineHealthCheckListResponse, \
-    Hook, HookListResponse
+    Hook, HookListResponse, SimpleSample, UpdateRunSamplesRequest
 from dnastack.common.tracing import Span
 from dnastack.http.session import HttpSession
 
@@ -300,6 +300,18 @@ class EWesClient(BaseWorkbenchClient):
             )
             return Hook(**response.json())
 
+    def update_run_samples(self, run_id: str, samples: List[SimpleSample], trace: Optional[Span] = None) -> ExtendedRunStatus:
+        trace = trace or Span(origin=self)
+        with self.create_http_session() as session:
+            request = UpdateRunSamplesRequest(samples=samples)
+            response = session.submit(
+                method='put',
+                url=urljoin(self.endpoint.url, f'{self.namespace}/ga4gh/wes/v1/runs/{run_id}/samples'),
+                json=request.model_dump(by_alias=True),
+                trace_context=trace
+            )
+            return ExtendedRunStatus(**response.json())
+
     def list_engines(self,
                      list_options: ExecutionEngineListOptions,
                      max_results: int = None,

dnastack/client/workbench/ewes/models.py

@@ -35,6 +35,10 @@ class SimpleSample(BaseModel):
     storage_account_id: Optional[str] = None
 
 
+class UpdateRunSamplesRequest(BaseModel):
+    samples: List[SimpleSample]
+
+
 class Hook(BaseModel):
     id: Optional[str] = None
     type: Optional[str] = None
@@ -173,6 +177,22 @@ class RunSubmittedToEngineMetadata(BaseModel):
     external_id: Optional[str] = None
 
 
+class SamplesUpdatedMetadata(BaseModel):
+    event_type: Literal["SAMPLES_UPDATED"]
+    message: Optional[str] = None
+    old_sample_ids: Optional[List[SampleId]] = None
+    new_sample_ids: Optional[List[SampleId]] = None
+    state: Optional[State] = None
+    start_time: Optional[str] = None
+    end_time: Optional[str] = None
+    submitted_by: Optional[str] = None
+    workflow_id: Optional[str] = None
+    workflow_version_id: Optional[str] = None
+    workflow_name: Optional[str] = None
+    workflow_version: Optional[str] = None
+    tags: Optional[dict[str, str]] = None
+
+
 # Custom validator to handle unknown event types gracefully
 def parse_event_metadata(data: Dict[str, Any]) -> Union[
     RunSubmittedMetadata,
@@ -181,6 +201,7 @@ def parse_event_metadata(data: Dict[str, Any]) -> Union[
     StateTransitionMetadata,
     EngineStatusUpdateMetadata,
     RunSubmittedToEngineMetadata,
+    SamplesUpdatedMetadata,
     UnknownEventMetadata
 ]:
     """Parse event metadata, falling back to UnknownEventMetadata for unknown types."""
@@ -199,6 +220,7 @@ def parse_event_metadata(data: Dict[str, Any]) -> Union[
         "STATE_TRANSITION": StateTransitionMetadata,
         "ENGINE_STATUS_UPDATE": EngineStatusUpdateMetadata,
         "RUN_SUBMITTED_TO_ENGINE": RunSubmittedToEngineMetadata,
+        "SAMPLES_UPDATED": SamplesUpdatedMetadata,
     }
 
     metadata_class = type_mapping.get(event_type)
@@ -220,6 +242,7 @@ class RunEvent(BaseModel):
         StateTransitionMetadata,
         EngineStatusUpdateMetadata,
         RunSubmittedToEngineMetadata,
+        SamplesUpdatedMetadata,
         UnknownEventMetadata
     ]
 

dnastack/client/workbench/workbench_user_service/models.py

@@ -1,7 +1,9 @@
+from typing import Optional
+
 from pydantic import BaseModel
 
 
 class WorkbenchUser(BaseModel):
     email: str
-    full_name: str
+    full_name: Optional[str] = None
     default_namespace: str

dnastack/constants.py

@@ -1,5 +1,5 @@
 import os
 
-__version__ = "3.1.211"
+__version__ = "3.1.213"
 
 LOCAL_STORAGE_DIRECTORY = os.path.join(os.path.expanduser("~"), '.dnastack')

{dnastack_client_library-3.1.211.dist-info → dnastack_client_library-3.1.213.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dnastack-client-library
-Version: 3.1.211
+Version: 3.1.213
 Summary: DNAstack's GA4GH library and CLI
 Author-email: DNAstack <devs@dnastack.com>
 License: Apache License, Version 2.0

{dnastack_client_library-3.1.211.dist-info → dnastack_client_library-3.1.213.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=luSsCyuSoskdvEGWRY8zDG3Gt1ncP7S-1MdshbV0_Bs,113
+dnastack/constants.py,sha256=b8sniKgFeXepJPRzikcxFUOWeDdagxeJE6sIvbmR1Sc,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
@@ -74,13 +74,15 @@ 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=8M_Hd6nikM7YrxOQXbshGCOAxZAfdI9ZPYeajMXsEhg,727
+dnastack/cli/commands/workbench/runs/__init__.py,sha256=O8RlOTe3edomgPAXV5WqaOI-r-CuKD7Fmg2WESGQhRk,860
 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/runs/samples/__init__.py,sha256=AQISCkkLz1u0CaVX8qzHUzJDo5YNTFMUFQoVEkcbDY8,297
+dnastack/cli/commands/workbench/runs/samples/commands.py,sha256=8MyN0PS9R-dzXPxJKG-df93TXYgm_g55LykJokt8VDM,4585
 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
@@ -143,8 +145,8 @@ 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=deaG6vCb2r5q7Habfp9QfCVbXQJNjl2GC5dxm_PnDwE,16524
-dnastack/client/workbench/ewes/models.py,sha256=BLG0Jd-8N8r_0yKqb94oZglZ3ymAaS2gdqb0kPcunoY,12729
+dnastack/client/workbench/ewes/client.py,sha256=Vh_KYwlUygQO3N_TW9Ye9o5b6XWXqhC-NcOMivpEQB8,17184
+dnastack/client/workbench/ewes/models.py,sha256=t9VyZ5fUikiTv1GGyll1Wt2B2dkQtNh6UsL8FCSRLyY,13494
 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
@@ -153,7 +155,7 @@ dnastack/client/workbench/storage/client.py,sha256=SdvY3ieUjFeBoX0AvdeNjVBx5gM5B
 dnastack/client/workbench/storage/models.py,sha256=O2Z6mlUZU7Xtp6ehXYthEh3qZNvj8DH2FDOW7WM5beA,2198
 dnastack/client/workbench/workbench_user_service/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/client/workbench/workbench_user_service/client.py,sha256=ZpMOFw5L3NxbC2WtKpH3OJ435zEjy0-m4p0WgzQEOB0,1219
-dnastack/client/workbench/workbench_user_service/models.py,sha256=P8WmocouYthi4gnHzNJT2F3iExWTt_2MUnskexN6Rxs,126
+dnastack/client/workbench/workbench_user_service/models.py,sha256=WPiXK9sTzsD6OPJ7zQPRbz0ArsQx7BcAPIEd1qhSU0c,172
 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=3xT8kbG8dDmDzc9_0XXIW8tC1U_sC2sg1N4sJ0i3iEk,6044
@@ -200,9 +202,9 @@ 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-3.1.211.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,,
+dnastack_client_library-3.1.213.dist-info/licenses/LICENSE,sha256=uwybO-wUbQhxkosgjhJlxmYATMy-AzoULFO9FUedE34,11580
+dnastack_client_library-3.1.213.dist-info/METADATA,sha256=ubFSa3FAuDwsq30tgJXLajs1WHYwAqqmE0cTzgyIxIE,1791
+dnastack_client_library-3.1.213.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+dnastack_client_library-3.1.213.dist-info/entry_points.txt,sha256=Y6OeicsiyGn3-8D-SiV4NiKlJgXfkSqK88kFBR6R1rY,89
+dnastack_client_library-3.1.213.dist-info/top_level.txt,sha256=P2RgRyqJ7hfNy1wLVRoVLJYEppUVkCX3syGK9zBqkt8,9
+dnastack_client_library-3.1.213.dist-info/RECORD,,