dnastack-client-library 3.1.174__py3-none-any.whl → 3.1.178__py3-none-any.whl

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

@@ -7,17 +7,17 @@ from click import style, Group
 
 from dnastack.cli.commands.workbench.runs.utils import UnableToFindParameterError, NoDefaultEngineError
 from dnastack.cli.commands.utils import MAX_RESULTS_ARG, PAGINATION_PAGE_ARG, PAGINATION_PAGE_SIZE_ARG
-from dnastack.cli.commands.workbench.utils import get_ewes_client, NAMESPACE_ARG, create_sort_arg
+from dnastack.cli.commands.workbench.utils import get_ewes_client, NAMESPACE_ARG, create_sort_arg, \
+    parse_to_datetime_iso_format
 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
 from dnastack.client.workbench.ewes.models import ExtendedRunListOptions, ExtendedRunRequest, \
     BatchRunRequest, \
-    MinimalExtendedRunWithOutputs, MinimalExtendedRunWithInputs, State, \
-    ExecutionEngineListOptions
+    MinimalExtendedRunWithOutputs, MinimalExtendedRunWithInputs, ExecutionEngineListOptions, SimpleSample
+from dnastack.client.workbench.common.models import State
 from dnastack.client.workbench.ewes.models import LogType
-from dnastack.client.workbench.samples.models import Sample
 from dnastack.common.json_argument_parser import JsonLike, parse_and_merge_arguments, merge, merge_param_json_data
 from dnastack.common.tracing import Span
 
@@ -78,6 +78,17 @@ def init_runs_commands(group: Group):
                 help='Filter runs by one or more tags. Tags can be specified as a KV pair, inlined JSON, or as a json file preceded by the "@" symbol.',
                 type=JsonLike,
             ),
+            ArgumentSpec(
+                name='samples',
+                arg_names=['--sample'],
+                help='Filter runs by one or more sample IDs. Can be specified multiple times',
+                multiple=True,
+            ),
+            ArgumentSpec(
+                name='storage_account_id',
+                arg_names=['--storage-account'],
+                help='Filter runs by the storage account ID. This will return runs that have outputs stored in the specified storage account.',
+            ),
             NAMESPACE_ARG,
             CONTEXT_ARG,
             SINGLE_ENDPOINT_ID_ARG,
@@ -96,21 +107,15 @@ def init_runs_commands(group: Group):
                   engine: Optional[str],
                   search: Optional[str],
                   tags: JsonLike,
-                  states):
+                  samples: Optional[List[str]] = None,
+                  storage_account_id: Optional[str] = None,
+                  states: Optional[List[State]] = None):
         """
         List workflow runs
 
         docs: https://docs.omics.ai/products/command-line-interface/reference/workbench/runs-list
         """
 
-        def parse_to_datetime_iso_format(date: str, start_of_day: bool = False, end_of_day: bool = False) -> str:
-            if (date is not None) and ("T" not in date):
-                if start_of_day:
-                    return f'{date}T00:00:00.000Z'
-                if end_of_day:
-                    return f'{date}T23:59:59.999Z'
-            return date
-
         order_direction = None
         if order:
             order_and_direction = order.split()
@@ -134,12 +139,13 @@ def init_runs_commands(group: Group):
             until=parse_to_datetime_iso_format(date=submitted_until, end_of_day=True),
             engine_id=engine,
             search=search,
+            sample_ids=samples,
+            storage_account_id=storage_account_id,
             tag=tags
         )
         runs_list = client.list_runs(list_options, max_results)
         show_iterator(output_format=OutputFormat.JSON, iterator=runs_list)
 
-
     @formatted_command(
         group=group,
         name='describe',
@@ -209,7 +215,6 @@ def init_runs_commands(group: Group):
                 ) for described_run in described_runs]
         click.echo(to_json(normalize(described_runs)))
 
-
     @formatted_command(
         group=group,
         name='cancel',
@@ -242,7 +247,6 @@ def init_runs_commands(group: Group):
         result = client.cancel_runs(run_id)
         click.echo(to_json(normalize(result)))
 
-
     @formatted_command(
         group=group,
         name='delete',
@@ -285,7 +289,6 @@ def init_runs_commands(group: Group):
         result = client.delete_runs(run_id)
         click.echo(to_json(normalize(result)))
 
-
     @formatted_command(
         group=group,
         name='logs',
@@ -385,13 +388,13 @@ def init_runs_commands(group: Group):
             return
 
         if task_id:
-            write_logs(client.stream_task_logs(run_id_or_log_url, task_id, log_type, max_bytes=max_bytes, offset=offset),
-                       output_writer)
+            write_logs(
+                client.stream_task_logs(run_id_or_log_url, task_id, log_type, max_bytes=max_bytes, offset=offset),
+                output_writer)
         else:
             write_logs(client.stream_run_logs(run_id_or_log_url, log_type, max_bytes=max_bytes, offset=offset),
                        output_writer)
 
-
     @formatted_command(
         group=group,
         name='submit',
@@ -480,10 +483,24 @@ def init_runs_commands(group: Group):
                 type=JsonLike,
                 multiple=True
             ),
+            ArgumentSpec(
+                name="samples",
+                arg_names=['--sample'],
+                help='An optional flag that accepts a Sample IDs to use in the given workflow. '
+                     'If not specified, the workflow will be submitted without any samples. '
+                     'Can be specified multiple times',
+                multiple=True
+            ),
             ArgumentSpec(
                 name='sample_ids',
                 arg_names=['--samples'],
-                help='An optional flag that accepts a comma separated list of Sample IDs to use in the given workflow.',
+                help='An optional flag that accepts a comma separated list of Sample IDs to use in the given workflow. '
+                     'This flag is deprecated, use --sample instead. '
+            ),
+            ArgumentSpec(
+                name='storage_account_id',
+                arg_names=['--storage-account'],
+                help='The storage account ID to restrict sample files to when submitting the workflow. ',
             ),
             NAMESPACE_ARG,
             CONTEXT_ARG,
@@ -504,7 +521,9 @@ def init_runs_commands(group: Group):
                      input_overrides,
                      dry_run: bool,
                      run_requests: JsonLike,
-                     sample_ids: Optional[str]):
+                     sample_ids: Optional[str], # deprecated, use --samples instead
+                     samples: Optional[List[str]] = None,
+                     storage_account_id: Optional[str] = None):
         """
         Submit one or more workflows for execution
 
@@ -523,12 +542,14 @@ def init_runs_commands(group: Group):
 
         # Validation check for --version without --workflow
         if version and not workflow:
-            click.echo(style("Error: You must specify --workflow when using --version.", fg='red'), err=True, color=True)
+            click.echo(style("Error: You must specify --workflow when using --version.", fg='red'), err=True,
+                       color=True)
             exit(1)
 
         # Validation check for --workflow without --version
         if workflow and not version:
-            click.echo(style("Error: You must specify --version when using --workflow.", fg='red'), err=True, color=True)
+            click.echo(style("Error: You must specify --version when using --workflow.", fg='red'), err=True,
+                       color=True)
             exit(1)
 
         # Combine workflow and version if both are provided
@@ -538,11 +559,14 @@ def init_runs_commands(group: Group):
         ewes_client = get_ewes_client(context_name=context, endpoint_id=endpoint_id, namespace=namespace)
 
         def parse_samples():
-            if not sample_ids:
+            if samples:
+                sample_list = samples
+            elif sample_ids:
+                sample_list = sample_ids.split(',')
+            else:
                 return None
 
-            sample_list = sample_ids.split(',')
-            return [Sample(id=sample_id) for sample_id in sample_list]
+            return [SimpleSample(id=sample_id, storage_account_id=storage_account_id) for sample_id in sample_list]
 
         def get_default_engine_id():
             list_options = ExecutionEngineListOptions()
@@ -568,7 +592,8 @@ def init_runs_commands(group: Group):
                         param_preset = ewes_client.get_engine_param_preset(engine_id, param_id)
                         merge(param_presets, param_preset.preset_values)
                     except Exception as e:
-                        raise UnableToFindParameterError(f"Unable to find engine parameter preset with id {param_id}. {e}")
+                        raise UnableToFindParameterError(
+                            f"Unable to find engine parameter preset with id {param_id}. {e}")
 
             default_workflow_engine_parameters = param_presets
         else:
@@ -589,10 +614,9 @@ def init_runs_commands(group: Group):
 
         for run_request in run_requests:
             parsed_value = run_request.parsed_value() if run_request else None
-            parsed_run_request  = ExtendedRunRequest(**parsed_value)
+            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
@@ -615,4 +639,3 @@ def init_runs_commands(group: Group):
         else:
             minimal_batch = ewes_client.submit_batch(batch_request)
             click.echo(to_json(normalize(minimal_batch)))
-

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

@@ -1,14 +1,17 @@
-from typing import Optional
+from typing import Optional, List
 
 import click
 from click import Group
 
-from dnastack.cli.commands.workbench.utils import get_samples_client, NAMESPACE_ARG
+from dnastack.cli.commands.workbench.utils import get_samples_client, NAMESPACE_ARG, parse_to_datetime_iso_format
 from dnastack.cli.core.command import formatted_command
+from dnastack.cli.commands.utils import MAX_RESULTS_ARG, PAGINATION_PAGE_ARG, PAGINATION_PAGE_SIZE_ARG
 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
-from dnastack.client.workbench.samples.models import SampleListOptions
+from dnastack.client.workbench.common.models import State
+from dnastack.client.workbench.samples.models import SampleListOptions, Sex, PerspectiveType
+from dnastack.client.workbench.storage.models import PlatformType
 
 
 def init_samples_commands(group: Group):
@@ -19,22 +22,180 @@ def init_samples_commands(group: Group):
             NAMESPACE_ARG,
             CONTEXT_ARG,
             SINGLE_ENDPOINT_ID_ARG,
+            MAX_RESULTS_ARG,
+            PAGINATION_PAGE_ARG,
+            PAGINATION_PAGE_SIZE_ARG,
+            ArgumentSpec(
+                name='storage_id',
+                arg_names=['--storage-id'],
+                help='Returns samples associated with the specified storage id.',
+                required=False
+            ),
+            ArgumentSpec(
+                name='platform_type',
+                arg_names=['--platform-type'],
+                help='Returns samples associated with the specified platform type.',
+                required=False,
+                type=PlatformType
+            ),
+            ArgumentSpec(
+                name='instrument_id',
+                arg_names=['--instrument-id'],
+                help='Returns samples associated with the specified instrument',
+                required=False
+            ),
+            ArgumentSpec(
+                name='workflow_id',
+                arg_names=['--workflow'],
+                help="Returns samples that were processed by the specified workflow. "
+                     "If the workflow version is not specified returns all workflow versions. " 
+                     "If the --perspective option is set to 'WORKFLOW', then the workflow-id is required",
+                required=False
+            ),
+            ArgumentSpec(
+                name='workflow_version_id',
+                arg_names=['--workflow-version'],
+                help="Returns samples that were processed by the specified workflow version. "
+                     "If the workflow is not specified returns all workflows. "
+                     "If the --perspective option is set to 'WORKFLOW', then the workflow-version-id is required",
+                required=False
+            ),
+            ArgumentSpec(
+                name='states',
+                arg_names=['--state'],
+                help='Returns samples with workflows in the specified states',
+                required=False,
+                type=State,
+                multiple=True
+            ),
+            ArgumentSpec(
+                name='family_ids',
+                arg_names=['--family-id'],
+                help='Returns samples that are part of the specified families',
+                required=False,
+                multiple=True
+            ),
+            ArgumentSpec(
+                name='sample_ids',
+                arg_names=['--sample'],
+                help='Returns samples with the specified id',
+                required=False,
+                multiple=True
+            ),
+            ArgumentSpec(
+                name='sexes',
+                arg_names=['--sex'],
+                help='Returns samples with the specified sex',
+                required=False,
+                multiple=True
+            ),
+            ArgumentSpec(
+                name='perspective',
+                arg_names=['--perspective'],
+                help='Returns samples from the specified perspective. '
+                     'If not specified, returns samples from the default perspective. '
+                     'If perspective is set to "WORKFLOW", then the workflow-id is required. '
+                     'When the perspective is set to "WORKFLOW", all samples are returned with a flag indicating '
+                     'whether they were processed by the specified workflow or not.',
+                required=False,
+                type=PerspectiveType
+            ),
+            ArgumentSpec(
+                name='search',
+                arg_names=['--search'],
+                help='Searches samples by the specified search term. The search term is matched against sample id',
+                required=False
+            ),
+            ArgumentSpec(
+                name='since',
+                arg_names=['--created-since'],
+                help='Returns samples created after the specified date. '
+                     'The timestamp can be in iso date, or datetime format. '
+                     'e.g.: -t "2022-11-23", -t "2022-11-23T23:59:59.999Z"',
+                required=False
+            ),
+            ArgumentSpec(
+                name='until',
+                arg_names=['--created-until'],
+                help='Returns samples created before the specified date. '
+                     'The timestamp can be in iso date, or datetime format. '
+                     'e.g.: -t "2022-11-23", -t "2022-11-23T23:59:59.999Z"',
+                required=False
+            ),
+            ArgumentSpec(
+                name='analyzed',
+                arg_names=['--analyzed'],
+                help='Returns samples that have been analyzed.',
+                required=False,
+                type=bool
+            ),
+            ArgumentSpec(
+                name='not_analyzed',
+                arg_names=['--not-analyzed'],
+                help='Returns samples that have not been analyzed.',
+                required=False,
+                type=bool
+            )
+
         ]
     )
     def list_samples(context: Optional[str],
                      endpoint_id: Optional[str],
-                     namespace: Optional[str]):
+                     namespace: Optional[str],
+                     max_results: Optional[int] = None,
+                     page: Optional[int] = None,
+                     page_size: Optional[int] = None,
+                     storage_id: Optional[str] = None,
+                     platform_type: Optional[PlatformType] = None,
+                     instrument_id: Optional[str] = None,
+                     workflow_id: Optional[str] = None,
+                     workflow_version_id: Optional[str] = None,
+                     states: Optional[List[State]] = None,
+                     family_ids: Optional[List[str]] = None,
+                     sample_ids: Optional[List[str]] = None,
+                     sexes: Optional[List[Sex]] = None,
+                     perspective: Optional[PerspectiveType] = None,
+                     search: Optional[str] = None,
+                     since: Optional[str] = None,
+                     until: Optional[str] = None,
+                     analyzed: Optional[bool] = None,
+                     not_analyzed: Optional[bool] = None
+                     ):
         """
         List samples
-        docs: https://docs.dnastack.com/docs/samples-list
+        docs: https://docs.omics.ai/products/command-line-interface/reference/workbench/samples-list
         """
 
+        if not states:
+            if analyzed:
+                states = [State.QUEUED, State.INITIALIZING, State.RUNNING, State.COMPLETE]
+            elif not_analyzed:
+                states = [State.NOT_PROCESSED]
+
+        if perspective == PerspectiveType.workflow and not workflow_id:
+            raise click.UsageError('When perspective is set to "WORKFLOW", the workflow-id is required.')
+
         client = get_samples_client(context_name=context, endpoint_id=endpoint_id, namespace=namespace)
-        list_options: SampleListOptions = SampleListOptions()
-        samples_list = client.list_samples(list_options)
+        list_options: SampleListOptions = SampleListOptions(
+            page=page,
+            page_size=page_size,
+            storage_id=storage_id,
+            platform_type=platform_type,
+            instrument_id=instrument_id,
+            workflow_id=workflow_id,
+            workflow_version_id=workflow_version_id,
+            states=states,
+            family_id=family_ids,
+            sample_id=sample_ids,
+            sexes=sexes,
+            perspective=perspective,
+            search=search,
+            since=parse_to_datetime_iso_format(since, start_of_day=True),
+            until=parse_to_datetime_iso_format(until, end_of_day=True)
+        )
+        samples_list = client.list_samples(list_options,max_results)
         show_iterator(output_format=OutputFormat.JSON, iterator=samples_list)
 
-
     @formatted_command(
         group=group,
         name='describe',
@@ -62,4 +223,3 @@ def init_samples_commands(group: Group):
         client = get_samples_client(context_name=context, endpoint_id=endpoint_id, namespace=namespace)
         described_sample = client.get_sample(sample_id)
         click.echo(to_json(normalize(described_sample)))
-

dnastack/cli/commands/workbench/utils.py

@@ -89,16 +89,10 @@ def get_storage_client(context_name: Optional[str] = None,
         return factory.get(StorageClient, endpoint_id=endpoint_id, context_name=context_name, namespace=namespace)
 
 
-
-
-
-
-
-
-
-
-
-
-
-
-
+def parse_to_datetime_iso_format(date: str, start_of_day: bool = False, end_of_day: bool = False) -> str:
+    if (date is not None) and ("T" not in date):
+        if start_of_day:
+            return f'{date}T00:00:00.000Z'
+        if end_of_day:
+            return f'{date}T23:59:59.999Z'
+    return date

dnastack/cli/commands/workbench/workflows/commands.py

@@ -192,8 +192,9 @@ def init_workflows_commands(group: Group):
             ),
             ArgumentSpec(
                 name='labels',
-                arg_names=['--labels'],
-                help='Comma-separated list of labels for the workflow (e.g., "tag1,tag2,tag3")',
+                arg_names=['--label'],
+                help='Label for the workflow. This flag can be repeated to specify multiple labels (e.g., --label tag1 --label tag2)',
+                multiple=True,
             ),
             NAMESPACE_ARG,
             CONTEXT_ARG,
@@ -209,7 +210,7 @@ def init_workflows_commands(group: Group):
                         organization: Optional[str],
                         entrypoint: str,
                         workflow_file: List[FileOrValue],
-                        labels: Optional[str]):
+                        labels: List[str]):
         """
         Create a new workflow
 
@@ -239,8 +240,8 @@ def init_workflows_commands(group: Group):
             entrypoint = loader.entrypoint
 
         if labels:
-            # Parse and validate labels, but keep as string for WorkflowCreate
-            parsed_labels = [label.strip() for label in labels.split(',') if label.strip()]
+            # Filter out empty labels and strip whitespace
+            parsed_labels = [label.strip() for label in labels if label.strip()]
             if parsed_labels:
                 label_list = ','.join(parsed_labels)
             else:
@@ -334,8 +335,9 @@ def init_workflows_commands(group: Group):
             ),
             ArgumentSpec(
                 name='labels',
-                arg_names=['--labels'],
-                help='A list of labels to apply. This value can be a comma separated list, a file or JSON literal',
+                arg_names=['--label'],
+                help='Label to apply to the workflow. This flag can be repeated to specify multiple labels (e.g., --label tag1 --label tag2)',
+                multiple=True,
             ),
             CONTEXT_ARG,
             SINGLE_ENDPOINT_ID_ARG,
@@ -348,7 +350,7 @@ def init_workflows_commands(group: Group):
                         name: Optional[str],
                         description: FileOrValue,
                         authors: Optional[str],
-                        labels: Optional[str]):
+                        labels: List[str]):
         """
         Update an existing workflow
 

dnastack/cli/commands/workbench/workflows/utils.py

@@ -202,14 +202,12 @@ def _get_replace_patch(path: str, value: str) -> Union[JsonPatch, None]:
     return None
 
 
-def _get_labels_patch(labels: Optional[str]) -> Union[JsonPatch, None]:
-    if labels is None:
+def _get_labels_patch(labels: Optional[List[str]]) -> Union[JsonPatch, None]:
+    if labels is None or len(labels) == 0:
         return None
-    if labels.strip() == "":
-        return JsonPatch(path="/labels", op="remove")
-
+    
     # Clean and validate labels
-    cleaned_labels = [label.strip() for label in labels.split(",") if label.strip()]
+    cleaned_labels = [label.strip() for label in labels if label and label.strip()]
     if not cleaned_labels:
         return JsonPatch(path="/labels", op="remove")
 

dnastack/client/workbench/common/models.py

@@ -0,0 +1,34 @@
+from enum import Enum
+
+
+class State(str, Enum):
+    PREPROCESSING = "PREPROCESSING"
+    UNKNOWN = "UNKNOWN"
+    QUEUED = "QUEUED"
+    INITIALIZING = "INITIALIZING"
+    RUNNING = "RUNNING"
+    PAUSED = "PAUSED"
+    CANCELING = "CANCELING"
+    COMPLETE = "COMPLETE"
+    EXECUTOR_ERROR = "EXECUTOR_ERROR"
+    SYSTEM_ERROR = "SYSTEM_ERROR"
+    CANCELED = "CANCELED"
+    COMPLETE_WITH_ERRORS = "COMPLETE_WITH_ERRORS"
+    PREPROCESSING_ERROR = "PREPROCESSING_ERROR"
+    NOT_PROCESSED = "NOT_PROCESSED"
+
+    def is_error(self) -> bool:
+        return self in [State.COMPLETE_WITH_ERRORS, State.EXECUTOR_ERROR, State.SYSTEM_ERROR]
+
+    def is_terminal(self) -> bool:
+        return self in [State.COMPLETE, State.COMPLETE_WITH_ERRORS, State.CANCELED, State.EXECUTOR_ERROR,
+                        State.SYSTEM_ERROR]
+
+
+class CaseInsensitiveEnum(Enum):
+    @classmethod
+    def _missing_(cls, value):
+        for member in cls:
+            if member.value.lower() == value.lower():
+                return member
+        raise ValueError(f"{value} is not a valid {cls.__name__}")

dnastack/client/workbench/ewes/models.py

@@ -1,48 +1,25 @@
 from datetime import datetime
 from enum import Enum
-from typing import Dict, List, Optional, Any
+from typing import Dict, List, Optional, Any, Literal, Union
 
 from pydantic import BaseModel, Field
 
 from dnastack.client.service_registry.models import Service
+from dnastack.client.workbench.common.models import State, CaseInsensitiveEnum
 from dnastack.client.workbench.models import BaseListOptions, PaginatedResource
-from dnastack.client.workbench.samples.models import Sample
 from dnastack.common.json_argument_parser import JSONType
 
 
-class Outcome(str, Enum):
+class Outcome(str, CaseInsensitiveEnum):
     SUCCESS = 'SUCCESS',
     FAILURE = 'FAILURE'
 
 
-class LogType(str, Enum):
+class LogType(str, CaseInsensitiveEnum):
     STDOUT = 'stdout',
     STDERR = 'stderr',
 
 
-class State(str, Enum):
-    PREPROCESSING = "PREPROCESSING"
-    UNKNOWN = "UNKNOWN"
-    QUEUED = "QUEUED"
-    INITIALIZING = "INITIALIZING"
-    RUNNING = "RUNNING"
-    PAUSED = "PAUSED"
-    CANCELING = "CANCELING"
-    COMPLETE = "COMPLETE"
-    EXECUTOR_ERROR = "EXECUTOR_ERROR"
-    SYSTEM_ERROR = "SYSTEM_ERROR"
-    CANCELED = "CANCELED"
-    COMPLETE_WITH_ERRORS = "COMPLETE_WITH_ERRORS"
-    PREPROCESSING_ERROR = "PREPROCESSING_ERROR"
-
-    def is_error(self) -> bool:
-        return self in [State.COMPLETE_WITH_ERRORS, State.EXECUTOR_ERROR, State.SYSTEM_ERROR]
-
-    def is_terminal(self) -> bool:
-        return self in [State.COMPLETE, State.COMPLETE_WITH_ERRORS, State.CANCELED, State.EXECUTOR_ERROR,
-                        State.SYSTEM_ERROR]
-
-
 class WesServiceInfo(Service):
     workflow_type_versions: Optional[Dict]
     supported_wes_versions: Optional[List[str]]
@@ -53,6 +30,10 @@ class WesServiceInfo(Service):
     auth_instructions_url: Optional[str]
     tags: Optional[Dict]
 
+class SimpleSample(BaseModel):
+    id: str
+    storage_account_id: Optional[str]
+
 
 class ExtendedRunStatus(BaseModel):
     run_id: str
@@ -72,6 +53,7 @@ class ExtendedRunStatus(BaseModel):
     workflow_params: Optional[Dict]
     tags: Optional[Dict]
     workflow_engine_parameters: Optional[Dict]
+    samples: Optional[List[SimpleSample]]
 
 
 class Log(BaseModel):
@@ -103,6 +85,7 @@ class ExtendedRunRequest(BaseModel):
     workflow_engine_parameters: Optional[Dict]
     dependencies: Optional[List[RunDependency]]
     tags: Optional[Dict]
+    samples: Optional[List[SimpleSample]]
 
 
 class EventType(str, Enum):
@@ -112,20 +95,74 @@ class EventType(str, Enum):
     ERROR_OCCURRED = "ERROR_OCCURRED"
     ENGINE_STATUS_UPDATE = "ENGINE_STATUS_UPDATE"
     STATE_TRANSITION = "STATE_TRANSITION"
+    EVENT_METADATA = "EventMetadata"
 
+class SampleId(BaseModel):
+    id: Optional[str]
+    storage_account_id: Optional[str]
 
 class RunEventMetadata(BaseModel):
+    event_type: Literal[EventType.EVENT_METADATA]
     message: Optional[str]
+
+
+class RunSubmittedMetadata(RunEventMetadata):
+    event_type: Literal[EventType.RUN_SUBMITTED]
+    start_time: Optional[str]
+    submitted_by: Optional[str]
     state: Optional[State]
+    workflow_id: Optional[str]
+    workflow_version_id: Optional[str]
+    workflow_url: Optional[str]
+    workflow_name: Optional[str]
+    workflow_version: Optional[str]
+    workflow_authors: Optional[List[str]]
+    workflow_type: Optional[str]
+    workflow_type_version: Optional[str]
+    tags: Optional[dict[str, str]]
+    sample_ids: Optional[List[SampleId]]
+
+class PreprocessingMetadata(RunEventMetadata):
+    event_type: Literal[EventType.PREPROCESSING]
+    outcome: Optional[str]
+
+class ErrorOccurredMetadata(RunEventMetadata):
+    event_type: Literal[EventType.ERROR_OCCURRED]
+    errors: Optional[List[str]]
+
+class StateTransitionMetadata(RunEventMetadata):
+    event_type: Literal[EventType.STATE_TRANSITION]
+    end_time: Optional[str]
     old_state: Optional[State]
     new_state: Optional[State]
+    errors: Optional[List[str]]
+
+class EngineStatusUpdateMetadata(RunEventMetadata):
+    event_type: Literal[EventType.ENGINE_STATUS_UPDATE]
+    # Add other fields as you discover them
 
 
+class RunSubmittedToEngineMetadata(RunEventMetadata):
+    event_type: Literal[EventType.RUN_SUBMITTED_TO_ENGINE]
+    external_id: Optional[str]
+
+
+RunEventMetadataUnion = Union[
+    RunSubmittedMetadata,
+    PreprocessingMetadata,
+    ErrorOccurredMetadata,
+    StateTransitionMetadata,
+    EngineStatusUpdateMetadata,
+    RunSubmittedToEngineMetadata,
+    RunEventMetadata
+]
+
 class RunEvent(BaseModel):
     id: str
     event_type: EventType
     created_at: datetime
-    metadata: RunEventMetadata
+    metadata: RunEventMetadataUnion = Field(discriminator='event_type')
+
 
 class ExtendedRunEvents(BaseModel):
     events: Optional[List[RunEvent]]
@@ -174,7 +211,7 @@ class BatchRunRequest(BaseModel):
     default_workflow_engine_parameters: Optional[Dict]
     default_tags: Optional[Dict]
     run_requests: Optional[List[ExtendedRunRequest]]
-    samples: Optional[List[Sample]]
+    samples: Optional[List[SimpleSample]]
 
 
 class BatchRunResponse(BaseModel):
@@ -235,6 +272,8 @@ class ExtendedRunListOptions(BaseListOptions):
     workflow_type: Optional[str]
     workflow_type_version: Optional[str]
     tag: Optional[List[str]]
+    sample_ids: Optional[List[str]]
+    storage_account_id: Optional[str]
 
 
 class TaskListOptions(BaseListOptions):

dnastack/client/workbench/samples/models.py

@@ -3,12 +3,74 @@ from typing import List, Optional, Any
 
 from pydantic import BaseModel
 
+from dnastack.client.workbench.common.models import State, CaseInsensitiveEnum
 from dnastack.client.workbench.models import BaseListOptions, PaginatedResource
 from dnastack.client.workbench.storage.models import PlatformType
 
 
+class OntologyClass(BaseModel):
+    id: str
+    label: Optional[str]
+
+
+class PhenotypicFeature(BaseModel):
+    created_at: Optional[datetime]
+    last_updated_at: Optional[datetime]
+    type: Optional[OntologyClass]
+
+
+class SampleMetrics(BaseModel):
+    file_count: Optional[int]
+    instrument_types: Optional[List[str]]
+
+
+class RunMetadata(BaseModel):
+    run_id: Optional[str]
+    state: Optional[State]
+    start_time: Optional[datetime]
+    end_time: Optional[datetime]
+    updated_time: Optional[datetime]
+    submitted_by: Optional[str]
+    workflow_id: Optional[str]
+    workflow_version_id: Optional[str]
+    workflow_name: Optional[str]
+    workflow_version: Optional[str]
+    last_recorded_event_time: Optional[datetime]
+    tags: Optional[dict[str, str]]
+
+
+class Sex(str, CaseInsensitiveEnum):
+    male = "MALE"
+    female = "FEMALE"
+    unknown_sex = "UNKNOWN_SEX"
+    other_sex = "OTHER_SEX"
+
+
+class AffectedStatus(str, CaseInsensitiveEnum):
+    affected = "AFFECTED"
+    unaffected = "UNAFFECTED"
+    missing = "MISSING"
+
+
+class PerspectiveType(str, CaseInsensitiveEnum):
+    default = "DEFAULT"
+    workflow = "WORKFLOW"
+
+
 class SampleListOptions(BaseListOptions):
-    pass
+    storage_id: Optional[str] = None
+    platform_type: Optional[PlatformType] = None
+    instrument_id: Optional[str] = None
+    workflow_id: Optional[str] = None
+    workflow_version_id: Optional[str] = None
+    states: Optional[List[State]] = None
+    family_id: Optional[List[str]] = None
+    sample_id: Optional[List[str]] = None
+    sexes: Optional[List[Sex]] = None
+    search: Optional[str] = None
+    since: Optional[str] = None
+    until: Optional[str] = None
+    perspective: Optional[PerspectiveType] = None
 
 
 class SampleFile(BaseModel):
@@ -17,15 +79,24 @@ class SampleFile(BaseModel):
     storage_account_id: Optional[str]
     platform_type: Optional[PlatformType]
     instrument_id: Optional[str]
-    region: Optional[str]
     created_at: Optional[datetime]
     last_updated_at: Optional[datetime]
+    size: Optional[int]
 
 
 class Sample(BaseModel):
     id: str
     created_at: Optional[datetime]
     last_updated_at: Optional[datetime]
+    father_id: Optional[str]
+    mother_id: Optional[str]
+    family_id: Optional[str]
+    sex: Optional[str]
+    metrics: Optional[SampleMetrics]
+    phenotypes: Optional[List[PhenotypicFeature]]
+    runs: Optional[List[RunMetadata]]
+    affected_status: Optional[AffectedStatus]
+    has_been_analyzed: Optional[bool]
 
 
 class SampleListResponse(PaginatedResource):

dnastack/client/workbench/storage/models.py

@@ -1,21 +1,12 @@
-from enum import Enum
 from typing import Optional, List, Any, Literal, Union
 
 from pydantic import BaseModel
 
+from dnastack.client.workbench.common.models import CaseInsensitiveEnum
 from dnastack.client.workbench.models import BaseListOptions
 from dnastack.client.workbench.models import PaginatedResource
 
 
-class CaseInsensitiveEnum(Enum):
-    @classmethod
-    def _missing_(cls, value):
-        for member in cls:
-            if member.value.lower() == value.lower():
-                return member
-        raise ValueError(f"{value} is not a valid {cls.__name__}")
-
-
 class Provider(str, CaseInsensitiveEnum):
     aws = "aws"
     gcp = "gcp"
@@ -24,6 +15,7 @@ class Provider(str, CaseInsensitiveEnum):
 
 class PlatformType(str, CaseInsensitiveEnum):
     pacbio = "pacbio"
+    custom = "custom"
 
 
 class AwsStorageAccountCredentials(BaseModel):

dnastack/constants.py

@@ -1,5 +1,5 @@
 import os
 
-__version__ = "v3.1.174"
+__version__ = "v3.1.178"
 
 LOCAL_STORAGE_DIRECTORY = os.path.join(os.path.expanduser("~"), '.dnastack')

{dnastack_client_library-3.1.174.dist-info → dnastack_client_library-3.1.178.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dnastack-client-library
-Version: 3.1.174
+Version: 3.1.178
 Summary: DNAstack's GA4GH library and CLI
 Author-email: DNAstack <devs@dnastack.com>
 License: Apache License, Version 2.0

{dnastack_client_library-3.1.174.dist-info → dnastack_client_library-3.1.178.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=vbKzJJ---CEwR9P2AZ8zLB38xcayn3Rx2YAgVujUQC8,114
+dnastack/constants.py,sha256=AI1IU23sAhHWoNio023xumhXKUt3mTm5_X01kKUlhl8,114
 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
@@ -65,7 +65,7 @@ dnastack/cli/commands/publisher/datasources/__init__.py,sha256=90suC61lfFF1WzIU9
 dnastack/cli/commands/publisher/datasources/commands.py,sha256=nG_h44zWA061J5UZCofNhYGpBY-rJhAQuvPEdaGS8LY,1320
 dnastack/cli/commands/publisher/datasources/utils.py,sha256=DjhT7yYj3NSkE9APvAwUIecVoy-PXcutgZAjyUUdiU0,735
 dnastack/cli/commands/workbench/__init__.py,sha256=H4CGbc31-21mRZqJMtzi2Cg4e_D9a9ibqFjwXQTcXNY,1092
-dnastack/cli/commands/workbench/utils.py,sha256=5r3OPH7sg4tNFgiPM7r3ZoyHMnrg1J7PxOxQhKwT8gA,4349
+dnastack/cli/commands/workbench/utils.py,sha256=vDSJbZUxnqfjq7BaNSPW3hZlu0w40T2xF1Ci6_pnshs,4640
 dnastack/cli/commands/workbench/engines/__init__.py,sha256=qB1rfGXNJ6_N6F5UYXos4hHDwhm8PtlbrCCt_uNhIIw,653
 dnastack/cli/commands/workbench/engines/commands.py,sha256=dHie3J2wDSMDQ9HB9rJQNL3oVyngHk44pKO5nj34mX0,2465
 dnastack/cli/commands/workbench/engines/healthchecks.py,sha256=CEcbEqpAC1NsMRXxfl9Ti2yAekuBAjlB7Moz-IPrkEA,2351
@@ -75,12 +75,12 @@ 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=KS1DUMI2uQpX5hMOyFNrFliKsg7hF3uhsS5TEzMj6ro,25761
+dnastack/cli/commands/workbench/runs/commands.py,sha256=8y3sz2mVB6xfcEdjaB1l3LDkLeOSSruFqaKGDocJSsk,27239
 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/samples/__init__.py,sha256=cRfeKCdHO-0Dq3PFoVcqO7OrQspajIO3h1zNqknKP2U,456
-dnastack/cli/commands/workbench/samples/commands.py,sha256=0h_sihwJZaZPyGV7sEStzhF4HUPNYU2EnjjA32pHkZs,2232
+dnastack/cli/commands/workbench/samples/commands.py,sha256=pMqzdmrjZBCaSdo7gCsg9tcSp6WHrIHZSu8-MlN55yY,9529
 dnastack/cli/commands/workbench/samples/files.py,sha256=ihZgHV04fXC8-B0EFZ463SesgI93YSbXXlEtYyaUn8U,3021
 dnastack/cli/commands/workbench/storage/__init__.py,sha256=gRq4_3dFBA13vAOOKCY4rYMC4Ksr6rypyCCUuzXVn-g,625
 dnastack/cli/commands/workbench/storage/add.py,sha256=GVL7yX8eXOgPar_TVYFQvoFedIG7p-9esT-0l9MDyig,10075
@@ -88,8 +88,8 @@ dnastack/cli/commands/workbench/storage/commands.py,sha256=m_h2hUhTZ24YCreavRjIc
 dnastack/cli/commands/workbench/storage/update.py,sha256=man43AfkFA-9STQiSH4_SuIIgVx8GFH-RRt7ZZbc9ek,10525
 dnastack/cli/commands/workbench/storage/utils.py,sha256=uZPN6rx14y8Wymc2uDOiGj4imSJOWbDWMm1Fmta_pYE,3204
 dnastack/cli/commands/workbench/workflows/__init__.py,sha256=GLUXWR2UD5ZOlvfcUv2o2oz_k7mmPWU8650egt3rDfM,513
-dnastack/cli/commands/workbench/workflows/commands.py,sha256=EHNNx3uN2SpZobw6jc0a-EFC7C4NZpPP4AR7a0wOdv8,15028
-dnastack/cli/commands/workbench/workflows/utils.py,sha256=0k31Gud5E4Vgxkd-Di_7PrcxBwx4FMOg1DSAy2PsZhk,12517
+dnastack/cli/commands/workbench/workflows/commands.py,sha256=opDNFNXHAdNL9pKy7LEdTlmm0HCASOgQ6seD9dd_eTE,15114
+dnastack/cli/commands/workbench/workflows/utils.py,sha256=9cEmJUy5MgrQShygc-PrBvX2AIMbfKsucj1P_mA9Xx0,12463
 dnastack/cli/commands/workbench/workflows/versions/__init__.py,sha256=tiVcCClMNuxmBwJEJQrvm8_t-ytzjOHaILAfAGFCoQY,979
 dnastack/cli/commands/workbench/workflows/versions/commands.py,sha256=fS5YrQcTSbHUig8kDuD3daWatZtXnopUT4eyWuzQT5w,16150
 dnastack/cli/commands/workbench/workflows/versions/defaults.py,sha256=NoDsUpkrFFLzw9J6l3ebdViwt6OaNFrmGxjv3yBFMak,12265
@@ -138,15 +138,17 @@ dnastack/client/service_registry/models.py,sha256=X0vf1sv1f5sZ_7wZMmynjPF57ZrKHZ
 dnastack/client/workbench/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/client/workbench/base_client.py,sha256=KlkSO1c32bKhojfco8NcVBVSY5x_PZACgPI9Q8c7sRE,6808
 dnastack/client/workbench/models.py,sha256=RBo7wmWMSDkgiFZHaWh2ehKeTM8ERywug1bMGKDOm0k,446
+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=yIqjwyyY9q0NrxpTX6LrnlnjavHoa6Fo073O3Lokkaw,15637
-dnastack/client/workbench/ewes/models.py,sha256=3XGVMW2eXlnd84BuluhjvNfKvxVrd06WTdZO6G4Kc7w,8394
+dnastack/client/workbench/ewes/models.py,sha256=UP3GOfzoHDAcCc08f-iLI22Bv_f-VH8bVdpIgu3v8DM,9637
 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
+dnastack/client/workbench/samples/models.py,sha256=pgHOvVwrDmhkPoe4nxv9zwwscFqphvoJUW-27gv4DQM,3512
 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
+dnastack/client/workbench/storage/models.py,sha256=0nhH2zNXyeg1SSh6s3_jOSI-WeersRlicTB2yNvKIgo,2030
 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
@@ -196,9 +198,9 @@ 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-3.1.174.dist-info/licenses/LICENSE,sha256=uwybO-wUbQhxkosgjhJlxmYATMy-AzoULFO9FUedE34,11580
-dnastack_client_library-3.1.174.dist-info/METADATA,sha256=JU8SXKzCq8yUGGEQi9Jw-xFnmNbY1UTTRjpXfOKNoqU,1766
-dnastack_client_library-3.1.174.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-dnastack_client_library-3.1.174.dist-info/entry_points.txt,sha256=Y6OeicsiyGn3-8D-SiV4NiKlJgXfkSqK88kFBR6R1rY,89
-dnastack_client_library-3.1.174.dist-info/top_level.txt,sha256=P2RgRyqJ7hfNy1wLVRoVLJYEppUVkCX3syGK9zBqkt8,9
-dnastack_client_library-3.1.174.dist-info/RECORD,,
+dnastack_client_library-3.1.178.dist-info/licenses/LICENSE,sha256=uwybO-wUbQhxkosgjhJlxmYATMy-AzoULFO9FUedE34,11580
+dnastack_client_library-3.1.178.dist-info/METADATA,sha256=OE5a2KDbMyIzjQ2Ojl4rimVi0n-5lp1Cpt5AuroaLnM,1766
+dnastack_client_library-3.1.178.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+dnastack_client_library-3.1.178.dist-info/entry_points.txt,sha256=Y6OeicsiyGn3-8D-SiV4NiKlJgXfkSqK88kFBR6R1rY,89
+dnastack_client_library-3.1.178.dist-info/top_level.txt,sha256=P2RgRyqJ7hfNy1wLVRoVLJYEppUVkCX3syGK9zBqkt8,9
+dnastack_client_library-3.1.178.dist-info/RECORD,,