refactor filter-array

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

@@ -1,12 +1,12 @@
 specVersion: "0.1.0"
 name: filter_array
 version: 0.1.0
-container: filter-array-plugin
+container: filter-array-tool
 entrypoint:
 title: filter_array
 description: Filter array based on input boolean array
-author: Data Scientist
-contact: [email protected]
+author: Brandon Walker, Nazanin Donyapour
+contact: [email protected], [email protected]
 repository:
 documentation:
 citation:

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

@@ -7,8 +7,7 @@ readme = "README.md"
 
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
-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/filter-array-tool/tests/test_filter_array.py

@@ -0,0 +1,27 @@
+"""Tests for filter_array."""
+from pathlib import Path
+
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_filter_array() -> None:
+    """Test filter_array."""
+    # Define paths and input properties
+    cwl_file_str = "filter_array_0@[email protected]"
+    cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str)
+    input_array = [1, 2, 3]
+    input_bool_array = [False, True, False]
+
+    # Create the CWL step
+    filter_array_step = Step(clt_path=cwl_file)
+    filter_array_step.input_array = input_array
+    filter_array_step.input_bool_array = input_bool_array
+
+    # Create the workflow and run it
+    steps = [filter_array_step]
+    filename = "filter_array_workflow"
+    workflow = Workflow(steps, filename)
+    workflow.run()
+
+    # cant parse stdout