idmtools-models 0.0.0.dev0__py3-none-any.whl → 0.0.2__py3-none-any.whl

idmtools_models/r/json_r_task.py

@@ -0,0 +1,155 @@
+"""idmtools jsonr task.
+
+Copyright 2021, Bill & Melinda Gates Foundation. All rights reserved.
+"""
+from dataclasses import dataclass, field
+from typing import Optional, List, Type, Union, TYPE_CHECKING
+from idmtools.assets import AssetCollection
+from idmtools.entities.iworkflow_item import IWorkflowItem
+from idmtools.entities.simulation import Simulation
+from idmtools.registry.task_specification import TaskSpecification
+from idmtools_models.json_configured_task import JSONConfiguredTask
+from idmtools_models.r.r_task import RTask
+if TYPE_CHECKING:  # pragma: no cover
+    from idmtools.entities.iplatform import IPlatform
+
+
+@dataclass
+class JSONConfiguredRTask(JSONConfiguredTask, RTask):
+    """
+    JSONConfiguredRTask combines JSONConfiguredTask and RTask.
+
+    Notes:
+        - TODO Add example references here
+
+    See Also:
+        :class:`idmtools_models.json_configured_task.JSONConfiguredTask`
+        :class:`idmtools_models.r.r_task.RTask`
+    """
+    configfile_argument: Optional[str] = field(default="--config", metadata={"md": True})
+
+    def __post_init__(self):
+        """Constructor."""
+        JSONConfiguredTask.__post_init__(self)
+        RTask.__post_init__(self)
+
+    def gather_common_assets(self):
+        """
+        Return the common assets for a JSON Configured Task.
+
+        Returns:
+            Assets
+        """
+        return RTask.gather_common_assets(self)
+
+    def gather_transient_assets(self) -> AssetCollection:
+        """
+        Get Transient assets. This should general be the config.json.
+
+        Returns:
+            Transient assets
+        """
+        return JSONConfiguredTask.gather_transient_assets(self)
+
+    def reload_from_simulation(self, simulation: Simulation, **kwargs):
+        """
+        Reload task details from a simulation. Used in some fetch operations.
+
+        Args:
+            simulation: Simulation that is parent item
+            **kwargs:
+
+        Returns:
+            None
+        """
+        JSONConfiguredTask.reload_from_simulation(self, simulation, **kwargs)
+        RTask.reload_from_simulation(self, simulation, **kwargs)
+
+    def pre_creation(self, parent: Union[Simulation, IWorkflowItem], platform: 'IPlatform'):
+        """
+        Pre-creation event.
+
+        Proxy calls to JSONConfiguredTask and RTask
+
+        Args:
+            parent: Parent item
+            platform: Platform item is being created on
+
+        Returns:
+            None
+        """
+        RTask.pre_creation(self, parent, platform)
+        JSONConfiguredTask.pre_creation(self, parent, platform)
+
+    def post_creation(self, parent: Union[Simulation, IWorkflowItem], platform: 'IPlatform'):
+        """
+        Post-creation of task.
+
+        Proxy calls to JSONConfiguredTask and RTask
+
+        Args:
+            parent: Parent item
+            platform: Platform we are executing on
+
+        Returns:
+            None
+        """
+        JSONConfiguredTask.post_creation(self, parent, platform)
+        RTask.post_creation(self, parent, platform)
+
+
+class JSONConfiguredRTaskSpecification(TaskSpecification):
+    """
+    JSONConfiguredRTaskSpecification provides the plugin info for JSONConfiguredRTask.
+    """
+
+    def get(self, configuration: dict) -> JSONConfiguredRTask:
+        """
+        Get instance of JSONConfiguredRTaskSpecification with configuration provided.
+
+        Args:
+            configuration: Configuration for object
+
+        Returns:
+            JSONConfiguredRTaskSpecification with configuration
+        """
+        return JSONConfiguredRTask(**configuration)
+
+    def get_description(self) -> str:
+        """
+        Get description of plugin.
+
+        Returns:
+            Description of plugin
+        """
+        return "Defines a R script that has a single JSON config file"
+
+    def get_example_urls(self) -> List[str]:
+        """
+        Get Examples for JSONConfiguredRTask.
+
+        Returns:
+            List of Urls that point to examples for JSONConfiguredRTask
+        """
+        from idmtools_models import __version__
+        examples = [f'examples/{example}' for example in ['r_model']]
+        return [self.get_version_url(f'v{__version__}', x) for x in examples]
+
+    def get_type(self) -> Type[JSONConfiguredRTask]:
+        """
+        Get Type for Plugin.
+
+        Returns:
+            JSONConfiguredRTask
+        """
+        return JSONConfiguredRTask
+
+    def get_version(self) -> str:
+        """
+        Returns the version of the plugin.
+
+        Returns:
+            Plugin Version
+        """
+        from idmtools_models import __version__
+        return __version__

idmtools_models/r/r_task.py

@@ -0,0 +1,146 @@
+"""idmtools rtask.
+
+Copyright 2021, Bill & Melinda Gates Foundation. All rights reserved.
+"""
+import os
+from dataclasses import field, dataclass
+from logging import getLogger, DEBUG
+from typing import Type, Union, TYPE_CHECKING
+from idmtools.assets import Asset, AssetCollection
+from idmtools.core.docker_task import DockerTask
+from idmtools.entities import CommandLine
+from idmtools.entities.iworkflow_item import IWorkflowItem
+from idmtools.entities.simulation import Simulation
+from idmtools.registry.task_specification import TaskSpecification
+
+logger = getLogger(__name__)
+
+if TYPE_CHECKING:  # pragma: no cover
+    from idmtools.entities.iplatform import IPlatform
+
+
+@dataclass
+class RTask(DockerTask):
+    """
+    Defines an RTask for idmtools. Currently only useful for local platform.
+
+    Notes:
+        - TODO rework this to be non-docker
+    """
+    script_path: str = field(default=None, metadata={"md": True})
+    r_path: str = field(default='Rscript', metadata={"md": True})
+
+    def __post_init__(self):
+        """Constructor."""
+        super().__post_init__()
+        cmd_str = f'{self.r_path} ./Assets/{os.path.basename(self.script_path)}'
+        if logger.isEnabledFor(DEBUG):
+            logger.info('Setting command line to %s', cmd_str)
+        self.command = CommandLine.from_string(cmd_str)
+
+    def reload_from_simulation(self, simulation: Simulation, **kwargs):
+        """
+        Reload RTask from a simulation. Used when fetching an simulation to do a recreation.
+
+        Args:
+            simulation: Simulation object containing our metadata to rebuild task
+            **kwargs:
+
+        Returns:
+            None
+        """
+        logger.debug("Reload from simulation")
+        # check experiment level assets for items
+        if simulation.parent.assets:
+            new_assets = AssetCollection()
+            for _i, asset in enumerate(simulation.parent.assets.assets):
+                if asset.filename != self.script_path and asset.absolute_path != self.script_path:
+                    new_assets.add_asset(asset)
+            simulation.parent.assets = new_assets
+
+    def gather_common_assets(self) -> AssetCollection:
+        """
+        Gather R Assets.
+
+        Returns:
+            Common assets
+        """
+        super().gather_common_assets()
+        if logger.isEnabledFor(DEBUG):
+            logger.info('Adding Common asset from %s', self.script_path)
+        self.common_assets.add_or_replace_asset(Asset(absolute_path=self.script_path))
+        return self.common_assets
+
+    def gather_transient_assets(self) -> AssetCollection:
+        """
+        Gather transient assets. Generally this is the simulation level assets.
+
+        Returns:
+            Transient assets(Simulation level Assets)
+        """
+        return self.transient_assets
+
+    def pre_creation(self, parent: Union[Simulation, IWorkflowItem], platform: 'IPlatform'):
+        """
+        Called before creation of parent.
+
+        Args:
+            parent: Parent
+            platform: Platform R Task is executing on
+
+        Returns:
+            None
+
+        Raise:
+            ValueError if script name is not provided
+        """
+        if self.script_path is None:
+            raise ValueError("Script name is required")
+
+        self.command = CommandLine.from_string(f'{self.r_path} {platform.join_path(platform.common_asset_path, os.path.basename(self.script_path))}')
+
+
+class RTaskSpecification(TaskSpecification):
+    """
+    RTaskSpecification defines plugin specification for RTask.
+    """
+
+    def get(self, configuration: dict) -> RTask:
+        """
+        Get instance of RTask.
+
+        Args:
+            configuration: configuration for task
+
+        Returns:
+            RTask with configuration
+        """
+        return RTask(**configuration)
+
+    def get_description(self) -> str:
+        """
+        Returns the Description of the plugin.
+
+        Returns:
+            Plugin Description
+        """
+        return "Defines a R script command"
+
+    def get_type(self) -> Type[RTask]:
+        """
+        Get Type for Plugin.
+
+        Returns:
+            RTask
+        """
+        return RTask
+
+    def get_version(self) -> str:
+        """
+        Returns the version of the plugin.
+
+        Returns:
+            Plugin Version
+        """
+        from idmtools_models import __version__
+        return __version__