refactor extract-model

utils/extract-model-plugin/ict.yml → utils/pre-process/structure-change/extract-model-tool/ict.yml

@@ -1,12 +1,12 @@
 specVersion: "0.1.0"
 name: extract_model
 version: 0.1.0
-container: extract-model-plugin
+container: extract-model-tool
 entrypoint:
 title: extract_model
 description: This class is a wrapper of the Structure Checking tool to extract a model from a 3D structure.
-author: Data Scientist
-contact: [email protected]
+author: Brandon Walker, Nazanin Donyapour
+contact: [email protected], [email protected]
 repository:
 documentation:
 citation:

utils/pre-process/structure-change/extract-model-tool/tests/test_extract_model.py

@@ -0,0 +1,34 @@
+"""Tests for extract_model."""
+from pathlib import Path
+
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_extract_model() -> None:
+    """Test extract_model."""
+    # Define paths and input properties
+    cwl_file_str = "extract_model_0@[email protected]"
+    cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str)
+    input_structure_path = Path(__file__).resolve().parent / Path("extract_model.pdb")
+    config = '{"models": [1, 2, 3]}'
+
+    # Create the CWL step
+    extract_model_step = Step(clt_path=cwl_file)
+    extract_model_step.input_structure_path = input_structure_path
+    extract_model_step.output_structure_path = "system.pdb"
+    extract_model_step.config = config
+
+    # Create the workflow and run it
+    steps = [extract_model_step]
+    filename = "extract_model_workflow"
+    workflow = Workflow(steps, filename)
+    workflow.run()
+
+    # Check for the expected output file
+    outdir = Path("outdir")
+    files = list(outdir.rglob("system.pdb"))
+
+    assert (
+        files
+    ), f"The file 'system.pdb' does not exist in any subdirectory of '{outdir}'."