deriva-ml 1.14.0__py3-none-any.whl → 1.14.27__py3-none-any.whl

deriva_ml/execution/execution_configuration.py

@@ -0,0 +1,163 @@
+"""Configuration management for DerivaML executions.
+
+This module provides functionality for configuring and managing execution parameters in DerivaML.
+It includes:
+
+- ExecutionConfiguration class: Core class for execution settings
+- Parameter validation: Handles JSON and file-based parameters
+- Dataset specifications: Manages dataset versions and materialization
+- Asset management: Tracks required input files
+
+The module supports both direct parameter specification and JSON-based configuration files.
+
+Typical usage example:
+    >>> config = ExecutionConfiguration(
+    ...     workflow="analysis_workflow",
+    ...     datasets=[DatasetSpec(rid="1-abc123", version="1.0.0")],
+    ...     parameters={"threshold": 0.5},
+    ...     description="Process sample data"
+    ... )
+    >>> execution = ml.create_execution(config)
+"""
+
+from __future__ import annotations
+
+import json
+import sys
+from pathlib import Path
+from typing import Any
+
+from pydantic import BaseModel, ConfigDict, Field, field_validator
+
+from deriva_ml.core.definitions import RID
+from deriva_ml.dataset.aux_classes import DatasetSpec
+from deriva_ml.execution.workflow import Workflow
+
+
+class ExecutionConfiguration(BaseModel):
+    """Configuration for a DerivaML execution.
+
+    Defines the complete configuration for a computational or manual process in DerivaML,
+    including required datasets, input assets, workflow definition, and parameters.
+
+    Attributes:
+        datasets (list[DatasetSpec]): Dataset specifications, each containing:
+            - rid: Dataset Resource Identifier
+            - version: Version to use
+            - materialize: Whether to extract dataset contents
+        assets (list[RID]): Resource Identifiers of required input assets.
+        workflow (RID | Workflow): Workflow definition or its Resource Identifier.
+        parameters (dict[str, Any] | Path): Execution parameters, either as:
+            - Dictionary of parameter values
+            - Path to JSON file containing parameters
+        description (str): Description of execution purpose (supports Markdown).
+        argv (list[str]): Command line arguments used to start execution.
+
+    Example:
+        >>> config = ExecutionConfiguration(
+        ...     workflow=Workflow.create_workflow("analysis", "python_script"),
+        ...     datasets=[
+        ...         DatasetSpec(rid="1-abc123", version="1.0.0", materialize=True)
+        ...     ],
+        ...     parameters={"threshold": 0.5, "max_iterations": 100},
+        ...     description="Process RNA sequence data"
+        ... )
+    """
+
+    datasets: list[DatasetSpec] = []
+    assets: list[RID] = []
+    workflow: RID | Workflow
+    parameters: dict[str, Any] | Path = {}
+    description: str = ""
+    argv: list[str] = Field(default_factory=lambda: sys.argv)
+
+    model_config = ConfigDict(arbitrary_types_allowed=True)
+
+    @field_validator("parameters", mode="before")
+    @classmethod
+    def validate_parameters(cls, value: Any) -> Any:
+        """Validates and loads execution parameters.
+
+        If value is a file path, loads and parses it as JSON. Otherwise, returns
+        the value as is.
+
+        Args:
+            value: Parameter value to validate, either:
+                - Dictionary of parameters
+                - Path to JSON file
+                - String path to JSON file
+
+        Returns:
+            dict[str, Any]: Validated parameter dictionary.
+
+        Raises:
+            ValueError: If JSON file is invalid or cannot be read.
+            FileNotFoundError: If parameter file doesn't exist.
+
+        Example:
+            >>> config = ExecutionConfiguration(parameters="params.json")
+            >>> print(config.parameters)  # Contents of params.json as dict
+        """
+        if isinstance(value, str) or isinstance(value, Path):
+            with Path(value).open("r") as f:
+                return json.load(f)
+        else:
+            return value
+
+    @field_validator("workflow", mode="before")
+    @classmethod
+    def validate_workflow(cls, value: Any) -> Any:
+        """Validates workflow specification.
+
+        Args:
+            value: Workflow value to validate (RID or Workflow object).
+
+        Returns:
+            RID | Workflow: Validated workflow specification.
+        """
+        return value
+
+    @staticmethod
+    def load_configuration(path: Path) -> ExecutionConfiguration:
+        """Creates an ExecutionConfiguration from a JSON file.
+
+        Loads and parses a JSON configuration file into an ExecutionConfiguration
+        instance. The file should contain a valid configuration specification.
+
+        Args:
+            path: Path to JSON configuration file.
+
+        Returns:
+            ExecutionConfiguration: Loaded configuration instance.
+
+        Raises:
+            ValueError: If JSON file is invalid or missing required fields.
+            FileNotFoundError: If configuration file doesn't exist.
+
+        Example:
+            >>> config = ExecutionConfiguration.load_configuration(Path("config.json"))
+            >>> print(f"Workflow: {config.workflow}")
+            >>> print(f"Datasets: {len(config.datasets)}")
+        """
+        with Path(path).open() as fd:
+            config = json.load(fd)
+        return ExecutionConfiguration.model_validate(config)
+
+    # def download_execution_configuration(
+    #     self, configuration_rid: RID
+    # ) -> ExecutionConfiguration:
+    #     """Create an ExecutionConfiguration object from a catalog RID that points to a JSON representation of that
+    #     configuration in hatrac
+    #
+    #     Args:
+    #         configuration_rid: RID that should be to an asset table that refers to an execution configuration
+    #
+    #     Returns:
+    #         A ExecutionConfiguration object for configured by the parameters in the configuration file.
+    #     """
+    #     AssertionError("Not Implemented")
+    #     configuration = self.retrieve_rid(configuration_rid)
+    #     with NamedTemporaryFile("w+", delete=False, suffix=".json") as dest_file:
+    #         hs = HatracStore("https", self.host_name, self.credential)
+    #         hs.get_obj(path=configuration["URL"], destfilename=dest_file.name)
+    #         return ExecutionConfiguration.load_configuration(Path(dest_file.name))