dnastack-client-library 3.1.179__py3-none-any.whl → 3.1.205__py3-none-any.whl

dnastack/client/workbench/ewes/models.py

@@ -21,197 +21,260 @@ class LogType(str, CaseInsensitiveEnum):
 
 
 class WesServiceInfo(Service):
-    workflow_type_versions: Optional[Dict]
-    supported_wes_versions: Optional[List[str]]
-    supported_filesystem_protocols: Optional[List[str]]
-    workflow_engine_versions: Optional[Dict]
-    default_workflow_engine_parameters: Optional[List[Dict]]
-    system_state_counts: Optional[Dict]
-    auth_instructions_url: Optional[str]
-    tags: Optional[Dict]
+    workflow_type_versions: Optional[Dict] = None
+    supported_wes_versions: Optional[List[str]] = None
+    supported_filesystem_protocols: Optional[List[str]] = None
+    workflow_engine_versions: Optional[Dict] = None
+    default_workflow_engine_parameters: Optional[List[Dict]] = None
+    system_state_counts: Optional[Dict] = None
+    auth_instructions_url: Optional[str] = None
+    tags: Optional[Dict] = None
 
 class SimpleSample(BaseModel):
     id: str
-    storage_account_id: Optional[str]
+    storage_account_id: Optional[str] = None
 
 
+class Hook(BaseModel):
+    id: Optional[str] = None
+    type: Optional[str] = None
+    result_data: Optional[Dict] = None
+    config: Optional[Dict] = None
+    state: Optional[str] = None
+    created_at: Optional[datetime] = None
+    started_at: Optional[datetime] = None
+    finished_at: Optional[datetime] = None
+    updated_at: Optional[datetime] = None
+
 class ExtendedRunStatus(BaseModel):
     run_id: str
-    external_id: Optional[str]
+    external_id: Optional[str] = None
     state: State
     start_time: datetime
-    end_time: Optional[datetime]
-    submitted_by: Optional[str]
-    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]
-    workflow_params: Optional[Dict]
-    tags: Optional[Dict]
-    workflow_engine_parameters: Optional[Dict]
-    samples: Optional[List[SimpleSample]]
+    end_time: Optional[datetime] = None
+    submitted_by: Optional[str] = None
+    workflow_id: Optional[str] = None
+    workflow_version_id: Optional[str] = None
+    workflow_url: Optional[str] = None
+    workflow_name: Optional[str] = None
+    workflow_version: Optional[str] = None
+    workflow_authors: Optional[List[str]] = None
+    workflow_type: Optional[str] = None
+    workflow_type_version: Optional[str] = None
+    workflow_params: Optional[Dict] = None
+    tags: Optional[Dict] = None
+    workflow_engine_parameters: Optional[Dict] = None
+    samples: Optional[List[SimpleSample]] = None
+    hooks: Optional[List[Hook]] = None
 
 
 class Log(BaseModel):
-    task_id: Optional[str]
+    task_id: Optional[str] = None
     name: str
-    pretty_name: Optional[str]
-    cmd: Optional[Any]
-    start_time: Optional[datetime]
-    end_time: Optional[datetime]
-    stdout: Optional[str]
-    stderr: Optional[str]
-    exit_code: Optional[int]
-    state: Optional[State]
+    pretty_name: Optional[str] = None
+    cmd: Optional[Any] = None
+    start_time: Optional[datetime] = None
+    end_time: Optional[datetime] = None
+    stdout: Optional[str] = None
+    stderr: Optional[str] = None
+    exit_code: Optional[int] = None
+    state: Optional[State] = None
 
 class RunDependency(BaseModel):
     run_id: str
 
 class ExtendedRunRequest(BaseModel):
-    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]
-    workflow_id: Optional[str]
-    workflow_version_id: Optional[str]
-    submitted_by: Optional[str]
-    workflow_params: Optional[Dict]
-    workflow_engine_parameters: Optional[Dict]
-    dependencies: Optional[List[RunDependency]]
-    tags: Optional[Dict]
-    samples: Optional[List[SimpleSample]]
-
-
-class EventType(str, Enum):
-    PREPROCESSING = "PREPROCESSING"
-    RUN_SUBMITTED = "RUN_SUBMITTED"
-    RUN_SUBMITTED_TO_ENGINE = "RUN_SUBMITTED_TO_ENGINE"
-    ERROR_OCCURRED = "ERROR_OCCURRED"
-    ENGINE_STATUS_UPDATE = "ENGINE_STATUS_UPDATE"
-    STATE_TRANSITION = "STATE_TRANSITION"
-    EVENT_METADATA = "EventMetadata"
+    workflow_url: Optional[str] = None
+    workflow_name: Optional[str] = None
+    workflow_version: Optional[str] = None
+    workflow_authors: Optional[List[str]] = None
+    workflow_type: Optional[str] = None
+    workflow_type_version: Optional[str] = None
+    workflow_id: Optional[str] = None
+    workflow_version_id: Optional[str] = None
+    submitted_by: Optional[str] = None
+    workflow_params: Optional[Dict] = None
+    workflow_engine_parameters: Optional[Dict] = None
+    dependencies: Optional[List[RunDependency]] = None
+    tags: Optional[Dict] = None
+    samples: Optional[List[SimpleSample]] = None
+    hooks: Optional[List[Hook]] = None
+
 
 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[
+    id: Optional[str] = None
+    storage_account_id: Optional[str] = None
+
+
+# Base metadata class for unknown event types
+class UnknownEventMetadata(BaseModel):
+    """Fallback metadata for unknown event types from the server."""
+    event_type: str
+    message: Optional[str] = None
+
+    # Allow arbitrary fields for unknown event types (Pydantic v1)
+    class Config:
+        extra = 'allow'
+
+
+class RunSubmittedMetadata(BaseModel):
+    event_type: Literal["RUN_SUBMITTED"]
+    message: Optional[str] = None
+    start_time: Optional[str] = None
+    submitted_by: Optional[str] = None
+    state: Optional[State] = None
+    workflow_id: Optional[str] = None
+    workflow_version_id: Optional[str] = None
+    workflow_url: Optional[str] = None
+    workflow_name: Optional[str] = None
+    workflow_version: Optional[str] = None
+    workflow_authors: Optional[List[str]] = None
+    workflow_type: Optional[str] = None
+    workflow_type_version: Optional[str] = None
+    tags: Optional[dict[str, str]] = None
+    sample_ids: Optional[List[SampleId]] = None
+
+
+class PreprocessingMetadata(BaseModel):
+    event_type: Literal["PREPROCESSING"]
+    message: Optional[str] = None
+    outcome: Optional[str] = None
+
+
+class ErrorOccurredMetadata(BaseModel):
+    event_type: Literal["ERROR_OCCURRED"]
+    message: Optional[str] = None
+    errors: Optional[List[str]] = None
+
+
+class StateTransitionMetadata(BaseModel):
+    event_type: Literal["STATE_TRANSITION"]
+    message: Optional[str] = None
+    end_time: Optional[str] = None
+    old_state: Optional[State] = None
+    new_state: Optional[State] = None
+    errors: Optional[List[str]] = None
+
+
+class EngineStatusUpdateMetadata(BaseModel):
+    event_type: Literal["ENGINE_STATUS_UPDATE"]
+    message: Optional[str] = None
+
+
+class RunSubmittedToEngineMetadata(BaseModel):
+    event_type: Literal["RUN_SUBMITTED_TO_ENGINE"]
+    message: Optional[str] = None
+    external_id: Optional[str] = None
+
+
+# Custom validator to handle unknown event types gracefully
+def parse_event_metadata(data: Dict[str, Any]) -> Union[
     RunSubmittedMetadata,
     PreprocessingMetadata,
     ErrorOccurredMetadata,
     StateTransitionMetadata,
     EngineStatusUpdateMetadata,
     RunSubmittedToEngineMetadata,
-    RunEventMetadata
-]
+    UnknownEventMetadata
+]:
+    """Parse event metadata, falling back to UnknownEventMetadata for unknown types."""
+    if not isinstance(data, dict):
+        raise ValueError("metadata must be a dict")
+
+    event_type = data.get('event_type')
+    if not event_type:
+        raise ValueError("event_type is required in metadata")
+
+    # Try to parse as known types
+    type_mapping = {
+        "RUN_SUBMITTED": RunSubmittedMetadata,
+        "PREPROCESSING": PreprocessingMetadata,
+        "ERROR_OCCURRED": ErrorOccurredMetadata,
+        "STATE_TRANSITION": StateTransitionMetadata,
+        "ENGINE_STATUS_UPDATE": EngineStatusUpdateMetadata,
+        "RUN_SUBMITTED_TO_ENGINE": RunSubmittedToEngineMetadata,
+    }
+
+    metadata_class = type_mapping.get(event_type)
+    if metadata_class:
+        return metadata_class(**data)
+    else:
+        # Unknown event type - use fallback
+        return UnknownEventMetadata(**data)
+
 
 class RunEvent(BaseModel):
     id: str
-    event_type: EventType
+    event_type: str
     created_at: datetime
-    metadata: RunEventMetadataUnion = Field(discriminator='event_type')
+    metadata: Union[
+        RunSubmittedMetadata,
+        PreprocessingMetadata,
+        ErrorOccurredMetadata,
+        StateTransitionMetadata,
+        EngineStatusUpdateMetadata,
+        RunSubmittedToEngineMetadata,
+        UnknownEventMetadata
+    ]
+
+    @classmethod
+    def parse_obj(cls, obj: Any) -> 'RunEvent':
+        """Custom validation to handle unknown event types (Pydantic v1)."""
+        if isinstance(obj, dict):
+            # Parse metadata with our custom function
+            if 'metadata' in obj:
+                obj = {**obj, 'metadata': parse_event_metadata(obj['metadata'])}
+        return super().parse_obj(obj)
 
 
 class ExtendedRunEvents(BaseModel):
-    events: Optional[List[RunEvent]]
+    events: Optional[List[RunEvent]] = None
 
 class ExtendedRun(BaseModel):
     run_id: str
-    external_id: Optional[str]
-    engine_id: Optional[str]
-    request: Optional[ExtendedRunRequest]
-    state: Optional[State]
-    run_log: Optional[Log]
-    errors: Optional[List[str]]
-    task_logs: Optional[List[Log]]
-    task_logs_url: Optional[str]
-    outputs: Optional[Dict]
-    dependencies: Optional[List[RunDependency]]
-    events: Optional[List[RunEvent]]
+    external_id: Optional[str] = None
+    engine_id: Optional[str] = None
+    request: Optional[ExtendedRunRequest] = None
+    state: Optional[State] = None
+    run_log: Optional[Log] = None
+    errors: Optional[List[str]] = None
+    task_logs: Optional[List[Log]] = None
+    task_logs_url: Optional[str] = None
+    outputs: Optional[Dict] = None
+    dependencies: Optional[List[RunDependency]] = None
+    events: Optional[List[RunEvent]] = None
 
 
 
 class MinimalExtendedRun(BaseModel):
-    run_id: Optional[str]
-    state: Optional[State]
-    msg: Optional[str]
-    error_code: Optional[int]
-    timestamp: Optional[str]
-    trace_id: Optional[str]
+    run_id: Optional[str] = None
+    state: Optional[State] = None
+    msg: Optional[str] = None
+    error_code: Optional[int] = None
+    timestamp: Optional[str] = None
+    trace_id: Optional[str] = None
 
 
 class MinimalExtendedRunWithInputs(BaseModel):
     run_id: str
-    inputs: Optional[Dict]
+    inputs: Optional[Dict] = None
 
 
 class MinimalExtendedRunWithOutputs(BaseModel):
     run_id: str
-    outputs: Optional[Dict]
+    outputs: Optional[Dict] = None
 
 
 class BatchRunRequest(BaseModel):
     workflow_url: str
-    workflow_type: Optional[str]
-    workflow_type_version: Optional[str]
-    engine_id: Optional[str]
-    default_workflow_params: Optional[Dict]
-    default_workflow_engine_parameters: Optional[Dict]
-    default_tags: Optional[Dict]
-    run_requests: Optional[List[ExtendedRunRequest]]
-    samples: Optional[List[SimpleSample]]
+    workflow_type: Optional[str] = None
+    workflow_type_version: Optional[str] = None
+    engine_id: Optional[str] = None
+    default_workflow_params: Optional[Dict] = None
+    default_workflow_engine_parameters: Optional[Dict] = None
+    default_tags: Optional[Dict] = None
+    run_requests: Optional[List[ExtendedRunRequest]] = None
+    samples: Optional[List[SimpleSample]] = None
 
 
 class BatchRunResponse(BaseModel):
@@ -220,20 +283,20 @@ class BatchRunResponse(BaseModel):
 
 class RunId(BaseModel):
     run_id: str
-    state: Optional[State]
+    state: Optional[State] = None
 
 
 class WorkbenchApiError(BaseModel):
-    timestamp: Optional[str]
-    msg: Optional[str]
-    error_code: Optional[int]
-    trace_id: Optional[str]
+    timestamp: Optional[str] = None
+    msg: Optional[str] = None
+    error_code: Optional[int] = None
+    trace_id: Optional[str] = None
 
 
 class ActionResult(BaseModel):
     outcome: Outcome
-    data: Optional[Any]
-    exception: Optional[WorkbenchApiError]
+    data: Optional[Any] = None
+    exception: Optional[WorkbenchApiError] = None
 
 
 class BatchActionResult(BaseModel):
@@ -255,25 +318,27 @@ class ExtendedRunListResponse(PaginatedResource):
 
 
 class ExtendedRunListOptions(BaseListOptions):
-    expand: Optional[bool]
-    until: Optional[str]
-    since: Optional[str]
-    search: Optional[str]
-    sort: Optional[str]
-    order: Optional[str] = Field(type=str, deprecated=True, default=None)
-    direction: Optional[str]
-    batch_id: Optional[str]
-    state: Optional[List[State]]
-    engine_id: Optional[str]
-    submitted_by: Optional[str]
-    workflow_name: Optional[str]
-    workflow_version: Optional[str]
-    workflow_url: Optional[str]
-    workflow_type: Optional[str]
-    workflow_type_version: Optional[str]
-    tag: Optional[List[str]]
-    sample_ids: Optional[List[str]]
-    storage_account_id: Optional[str]
+    expand: Optional[bool] = None
+    until: Optional[str] = None
+    since: Optional[str] = None
+    search: Optional[str] = None
+    sort: Optional[str] = None
+    order: Optional[str] = Field(deprecated=True, default=None, json_schema_extra={'type': 'string'})
+    direction: Optional[str] = None
+    batch_id: Optional[str] = None
+    state: Optional[List[State]] = None
+    engine_id: Optional[str] = None
+    submitted_by: Optional[str] = None
+    workflow_name: Optional[str] = None
+    workflow_version: Optional[str] = None
+    workflow_url: Optional[str] = None
+    workflow_type: Optional[str] = None
+    workflow_type_version: Optional[str] = None
+    tag: Optional[List[str]] = None
+    sample_ids: Optional[List[str]] = None
+    storage_account_id: Optional[str] = None
+    show_hidden: Optional[bool] = False
+
 
 
 class TaskListOptions(BaseListOptions):
@@ -294,15 +359,15 @@ class ExecutionEngineProviderType(str, Enum):
 class ExecutionEngine(BaseModel):
     id: str
     name: str
-    description: Optional[str]
+    description: Optional[str] = None
     provider: ExecutionEngineProviderType
-    region: Optional[str]
-    default: Optional[bool]
-    created_at: Optional[datetime]
-    updated_at: Optional[datetime]
-    state: Optional[str]
+    region: Optional[str] = None
+    default: Optional[bool] = None
+    created_at: Optional[datetime] = None
+    updated_at: Optional[datetime] = None
+    state: Optional[str] = None
     health: Optional[str] = Field(default=None, deprecated=True)
-    engine_adapter_configuration: Optional[Dict[str, JSONType]]
+    engine_adapter_configuration: Optional[Dict[str, JSONType]] = None
 
 
 class ExecutionEngineListResponse(PaginatedResource):
@@ -319,12 +384,12 @@ class ExecutionEngineListOptions(BaseListOptions):
 class EngineParamPreset(BaseModel):
     id: str
     name: str
-    default: Optional[bool]
+    default: Optional[bool] = None
     preset_values: Dict[str, object]
     engine_id: str
-    etag: Optional[str]
-    created_at: Optional[datetime]
-    updated_at: Optional[datetime]
+    etag: Optional[str] = None
+    created_at: Optional[datetime] = None
+    updated_at: Optional[datetime] = None
 
 
 class EngineParamPresetListResponse(PaginatedResource):
@@ -349,11 +414,11 @@ class CheckType(str, Enum):
 class Check(BaseModel):
     type: CheckType
     outcome: Outcome
-    error: Optional[str]
+    error: Optional[str] = None
 
 
 class EngineHealthCheck(BaseModel):
-    created_at: Optional[datetime]
+    created_at: Optional[datetime] = None
     outcome: str
     checks: List[Check]
     
@@ -366,6 +431,6 @@ class EngineHealthCheckListResponse(PaginatedResource):
 
 
 class EngineHealthCheckListOptions(BaseListOptions):
-    outcome: Optional[str]
-    check_type: Optional[str]
-    sort: Optional[str]
+    outcome: Optional[str] = None
+    check_type: Optional[str] = None
+    sort: Optional[str] = None

dnastack/client/workbench/models.py

@@ -4,19 +4,19 @@ from pydantic import BaseModel
 
 
 class BaseListOptions(BaseModel):
-    page_token: Optional[str]
-    page: Optional[int]
-    page_size: Optional[int]
+    page_token: Optional[str] = None
+    page: Optional[int] = None
+    page_size: Optional[int] = None
 
 
 class Pagination(BaseModel):
-    next_page_url: Optional[str]
-    total_elements: Optional[int]
+    next_page_url: Optional[str] = None
+    total_elements: Optional[int] = None
 
 
 class PaginatedResource(BaseModel):
-    pagination: Optional[Pagination]
-    next_page_token: Optional[str]
+    pagination: Optional[Pagination] = None
+    next_page_token: Optional[str] = None
 
     def items(self) -> List[Any]:
         pass