refactor array indices

utils/array-indices-plugin/ict.yml → utils/post-process/array-subset/array-indices-tool/ict.yml

@@ -1,12 +1,12 @@
 specVersion: "0.1.0"
 name: array_indices
 version: 0.1.0
-container: array-indices-plugin
+container: array-indices-tool
 entrypoint:
 title: array_indices
 description: return a subset from a array based on input indices
-author: Data Scientist
-contact: [email protected]
+author: Brandon Walker, Nazanin Donyapour
+contact: [email protected], [email protected]
 repository:
 documentation:
 citation:

utils/array-indices-plugin/pyproject.toml → utils/post-process/array-subset/array-indices-tool/pyproject.toml

@@ -8,8 +8,7 @@ readme = "README.md"
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
 typer = "^0.7.0"
-cwl-utils = "0.33"
-cwltool = "3.1.20240404144621"
+sophios = "0.1.1"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"

utils/post-process/array-subset/array-indices-tool/tests/test_array_indices.py

@@ -0,0 +1,26 @@
+"""Tests for array_indices."""
+from pathlib import Path
+
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_array_indices() -> None:
+    """Test array_indices."""
+    # Define paths and input properties
+    cwl_file_str = "array_indices_0@[email protected]"
+    cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str)
+    input_props = {"input_indices": [1, 3], "input_array": [1, 2, 3, 4, 5]}
+
+    # Create the CWL step
+    array_indices_step = Step(clt_path=cwl_file)
+    array_indices_step.input_indices = input_props["input_indices"]
+    array_indices_step.input_array = input_props["input_array"]
+
+    # Create the workflow and run it
+    steps = [array_indices_step]
+    filename = "array_indices_workflow"
+    workflow = Workflow(steps, filename)
+    workflow.run()
+
+    # cant process the output since no way to grab stdout