[draft/sketch] Direct entrypoint

bfabric/src/bfabric/experimental/workunit_definition.py

@@ -26,7 +26,7 @@ class WorkunitExecutionDefinition(BaseModel):
     """Input dataset (for dataset-flow applications)"""
 
     resources: list[int] = []
-    """Input resources (for resource-flow applications"""
+    """Input resources (for resource-flow applications)"""
 
     @model_validator(mode="after")
     def either_dataset_or_resources(self) -> WorkunitExecutionDefinition:

bfabric_app_runner/pyproject.toml

@@ -58,12 +58,12 @@ reinstall-package = ["bfabric", "bfabric_scripts", "bfabric_app_runner"]
 
 [tool.black]
 line-length = 120
-target-version = ["py311"]
+target-version = ["py312"]
 
 [tool.ruff]
 line-length = 120
 indent-width = 4
-target-version = "py311"
+target-version = "py312"
 
 extend-exclude = [
     "examples/template"

bfabric_app_runner/src/bfabric_app_runner/cli/__main__.py

@@ -30,7 +30,7 @@
     cmd_action_run_all,
     cmd_action_dispatch,
 )
-from bfabric_app_runner.cli.cmd_prepare import cmd_prepare_workunit
+from bfabric_app_runner.cli.cmd_prepare import cmd_prepare_workunit, cmd_prepare_local_workunit
 from bfabric_app_runner.cli.cmd_run import cmd_run_workunit
 from bfabric_app_runner.cli.inputs import cmd_inputs_prepare, cmd_inputs_clean, cmd_inputs_list, cmd_inputs_check
 from bfabric_app_runner.cli.outputs import cmd_outputs_register, cmd_outputs_register_single_file
@@ -87,6 +87,7 @@
 
 cmd_prepare = cyclopts.App(name="prepare", help="Prepare a workunit for execution.")
 cmd_prepare.command(cmd_prepare_workunit, name="workunit")
+cmd_prepare.command(cmd_prepare_local_workunit, name="local-workunit")
 cmd_prepare.group = groups["Running Apps"]
 app.command(cmd_prepare)
 

bfabric_app_runner/src/bfabric_app_runner/cli/cmd_prepare.py

@@ -4,18 +4,22 @@
 import yaml
 
 from bfabric import Bfabric
-from bfabric.experimental.workunit_definition import WorkunitDefinition
+from bfabric.experimental.workunit_definition import WorkunitDefinition, WorkunitExecutionDefinition
 from bfabric.utils.cli_integration import use_client
 from bfabric_app_runner.actions.config_file import ActionConfig
+from bfabric_app_runner.prepare.local_workunit_definition import LocalWorkunitExecutionDefinition
 from bfabric_app_runner.prepare.makefile_template import render_makefile
 from bfabric_app_runner.specs.app.app_spec import AppSpec
 
 
-def _update_app_version(workunit_definition: WorkunitDefinition, application_version: str) -> WorkunitDefinition:
+def _update_app_version[T: (
+    WorkunitExecutionDefinition,
+    LocalWorkunitExecutionDefinition,
+)](workunit_execution_definition: T, application_version: str) -> T:
     # TODO if this is useful consider moving it to the WorkunitDefinition class
-    workunit_definition = copy.deepcopy(workunit_definition)
-    workunit_definition.execution.raw_parameters["application_version"] = application_version
-    return workunit_definition
+    workunit_execution_definition = copy.deepcopy(workunit_execution_definition)
+    workunit_execution_definition.raw_parameters["application_version"] = application_version
+    return workunit_execution_definition
 
 
 @use_client
@@ -46,8 +50,8 @@ def cmd_prepare_workunit(
 
     workunit_definition = WorkunitDefinition.from_ref(workunit_ref, client=client)
     if force_app_version:
-        workunit_definition = _update_app_version(
-            workunit_definition=workunit_definition, application_version=force_app_version
+        workunit_definition.execution = _update_app_version(
+            workunit_execution_definition=workunit_definition.execution, application_version=force_app_version
         )
 
     # Resolve the app version early, following the pattern used by other commands
@@ -76,6 +80,51 @@ def cmd_prepare_workunit(
     )
 
 
+def cmd_prepare_local_workunit(
+    app_spec: Path,
+    work_dir: Path,
+    workunit_ref: Path,
+    *,
+    ssh_user: str | None = None,
+    force_storage: Path | None = None,
+    force_app_version: str | None = None,
+    read_only: bool = False,
+    use_external_runner: bool = False,
+    # TODO these two are a bit weird but required right now (because they correspond to registration and not execution)
+    app_id: int = 0,
+    app_name: str = "local_app",
+) -> None:
+    """Exprimental: Prepares a local workunit for processing."""
+    # TODO this is mostly cmd_prepare_workunit with some changes
+    work_dir.mkdir(parents=True, exist_ok=True)
+    workunit_execution_definition = LocalWorkunitExecutionDefinition.from_yaml(workunit_ref)
+    if force_app_version:
+        workunit_execution_definition = _update_app_version(
+            workunit_execution_definition=workunit_execution_definition, application_version=force_app_version
+        )
+
+    # Resolve the app version early, following the pattern used by other commands
+    app_full_spec = AppSpec.load_yaml(app_yaml=app_spec, app_id=app_id, app_name=app_name)
+
+    workunit_definition_path = work_dir / "workunit_definition.yml"
+    workunit_execution_definition.to_yaml(path=workunit_definition_path)
+    _write_app_env_file(
+        path=work_dir / "app_env.yml",
+        app_ref=app_spec.resolve(),
+        workunit_ref=workunit_definition_path,
+        ssh_user=ssh_user,
+        force_storage=force_storage,
+        read_only=read_only,
+    )
+    # Render the workunit Makefile template
+    render_makefile(
+        path=work_dir / "Makefile",
+        bfabric_app_spec=app_full_spec.bfabric,
+        rename_existing=True,
+        use_external_runner=use_external_runner,
+    )
+
+
 def _write_app_env_file(
     path: Path,
     app_ref: Path,

bfabric_app_runner/src/bfabric_app_runner/prepare/local_workunit_definition.py

@@ -0,0 +1,41 @@
+"""TODO this module is experimental and might be better integrated into different modules later."""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+import yaml
+from pydantic import BaseModel, model_validator
+
+from bfabric_app_runner.specs.inputs_spec import LocalInputSpecType  # noqa: TC001
+
+if TYPE_CHECKING:
+    from pathlib import Path
+
+
+class LocalWorkunitExecutionDefinition(BaseModel):
+    """Experimental definition of a local workunit for local execution.
+
+    This is trying to match the structure of WorkunitExecutionRegistration, but, it's notably not compatible right
+    now due to the WorkunitExecutionDefinition using IDs instead of full objects (and even less so InputSpecs).
+    """
+
+    raw_parameters: dict[str, str | None]
+    """The parameters passed to the workunit, in their raw form, i.e. everything is a string or None."""
+
+    dataset: LocalInputSpecType | None = None
+    """Input dataset (for dataset-flow applications)"""
+
+    resources: list[LocalInputSpecType] = []
+    """Input resources (for resource-flow applications)"""
+
+    @model_validator(mode="after")
+    def _mutually_exclusive(self) -> LocalWorkunitExecutionDefinition:
+        if (self.dataset is None) == (not self.resources):
+            raise ValueError("either dataset or resources must be provided, but not both")
+        return self
+
+    @classmethod
+    def from_yaml(cls, path: Path) -> LocalWorkunitExecutionDefinition:
+        parsed = yaml.safe_load(path.read_text())
+        return cls.model_validate(parsed)

bfabric_app_runner/src/bfabric_app_runner/specs/inputs_spec.py

@@ -17,16 +17,19 @@
 if TYPE_CHECKING:
     from pathlib import Path
 
+LocalInputSpecType = Annotated[
+    FileSpec | StaticYamlSpec | StaticFileSpec,
+    Field(discriminator="type"),
+]
+
 InputSpecType = Annotated[
-    BfabricResourceSpec
-    | FileSpec
+    LocalInputSpecType
+    | BfabricResourceSpec
     | BfabricDatasetSpec
     | BfabricOrderFastaSpec
     | BfabricAnnotationSpec
     | BfabricResourceArchiveSpec
-    | BfabricResourceDatasetSpec
-    | StaticYamlSpec
-    | StaticFileSpec,
+    | BfabricResourceDatasetSpec,
     Field(discriminator="type"),
 ]