refactor pdb-plugin

utils/pdb-plugin/ict.yml → utils/pre-process/data-download/pdb-tool/ict.yml

@@ -2,13 +2,13 @@ specVersion: 0.1.0
 entrypoint: pdb
 name: 'labshare/download-pdb-file'
 version: 0.1.0
-container: polusai/pdb-plugin:0.1.0
+container: polusai/pdb-tool:0.1.0
 title: Download PDB file
 description: Download PDB file
-author: [Nazanin Donyapour]
+author: Brandon Walker, Nazanin Donyapour
 repository: https://github.com/labshare/mmtools
 documentation: https://ncats.nih.gov/preclinical/core/informatics
-contact: "Nazanin.Donyapour@axleinfo.com"
+contact: brandon.walker@axleinfo.com, [email protected]
 inputs:
 - name: filter
   required: true

utils/pdb-plugin/pyproject.toml → utils/pre-process/data-download/pdb-tool/pyproject.toml

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

utils/pre-process/data-download/pdb-tool/tests/test_pdb.py

@@ -0,0 +1,39 @@
+"""Tests for pdb."""
+import json
+from pathlib import Path
+
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_pdb() -> None:
+    """Test pdb CWL."""
+    # Define file paths
+    cwl_file_str = "pdb_0@[email protected]"
+    cwl_file = Path(__file__).resolve().parent / Path(cwl_file_str)
+    input_yaml_path = Path("pdb.yml")
+
+    # Define configuration
+    config = {"pdb_code": "1e3g", "filter": False}
+    config_json = json.dumps(config)
+
+    # Create CWLWorkflow and configure it
+    pdb_step = Step(clt_path=cwl_file)
+    pdb_step.config = config_json
+    pdb_step.input_yaml_path = input_yaml_path
+
+    # Create Workflow
+    steps = [pdb_step]
+    workflow_name = "pdb_workflow"
+    workflow = Workflow(steps, workflow_name)
+
+    # Run Workflow
+    workflow.run()
+
+    # Check if output file exists
+    outdir = Path(".")
+    files = list(outdir.rglob("system.pdb"))
+
+    assert (
+        files
+    ), f"The file 'system.pdb' does not exist in any subdirectory of '{outdir}'."