refactor combine structure

utils/combine-structure-plugin/Dockerfile → utils/pre-process/structure-change/combine-structure-tool/Dockerfile

@@ -1,4 +1,4 @@
-# docker build -f Dockerfile -t mrbrandonwalker/combine_structure_tool .
+# docker build -f Dockerfile -t polusai/combine-structure-tool .
 FROM condaforge/mambaforge
 
 ENV EXEC_DIR="/opt/executables"

utils/pre-process/structure-change/combine-structure-tool/build-docker.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/combine-structure-tool:${version}

utils/combine-structure-plugin/combine_structure.cwl → utils/pre-process/structure-change/combine-structure-tool/combine_structure_0@1@0.cwl

@@ -12,7 +12,7 @@ baseCommand: ["conda", "run", "-n", "project_env", "python", "-m", "polus.mm.uti
 
 hints:
   DockerRequirement:
-    dockerPull: mrbrandonwalker/combine_structure_tool
+    dockerPull: polusai/combine-structure-tool@sha256:860eac0403aaadc1d76a46ba1cb47e359f05338af6fc7be47ccb495f86764de0
 
 inputs:
   input_structure1:

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

@@ -1,12 +1,12 @@
 specVersion: "0.1.0"
 name: combine_structure
 version: 0.1.0
-container: combine-structure-plugin
+container: combine-structure-tool
 entrypoint:
 title: combine_structure
 description: A tool that employs RDKit to combine two XYZ structures in a single PDB file.
-author: Data Scientist
-contact: [email protected]
+author: Brandon Walker, Nazanin Donyapour
+contact: [email protected], [email protected]
 repository:
 documentation:
 citation:

utils/combine-structure-plugin/pyproject.toml → utils/pre-process/structure-change/combine-structure-tool/pyproject.toml

@@ -8,6 +8,9 @@ packages = [{include = "polus", from = "src"}]
 
 [tool.poetry.dependencies]
 typer = "^0.7.0"
+python = ">=3.9,<3.12"
+sophios = "0.1.1"
+rdkit = "2024.3.3"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"

utils/combine-structure-plugin/tests/test_combine_structure.py → utils/pre-process/structure-change/combine-structure-tool/tests/test_combine_structure.py

@@ -1,16 +1,9 @@
 """Tests for combine_structure."""
-import sys
 from pathlib import Path
 
 from polus.mm.utils.combine_structure.combine_structure import combine_structure
-
-current_dir = Path(__file__).resolve().parent
-target_dir = current_dir.parent.parent.parent / "cwl_utils"
-sys.path.append(str(target_dir))
-
-from cwl_utilities import call_cwltool  # noqa: E402
-from cwl_utilities import create_input_yaml  # noqa: E402
-from cwl_utilities import parse_cwl_arguments  # noqa: E402
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
 
 
 def test_combine_structure() -> None:
@@ -24,16 +17,25 @@ def test_combine_structure() -> None:
 
 def test_combine_structure_cwl() -> None:
     """Test combine_structure CWL."""
+    # Define paths and input properties
     input_structure1 = Path(__file__).resolve().parent / Path("5umx_protein.xyz")
     input_structure2 = Path(__file__).resolve().parent / Path("5umx_ligand.xyz")
     output_structure_path = "combined_structure.xyz"
-    cwl_file_str = "combine_structure.cwl"
+    cwl_file_str = "combine_structure_0@1@0.cwl"
     cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str)
-    input_to_props = parse_cwl_arguments(cwl_file)
-    input_to_props["input_structure1"]["path"] = str(input_structure1)
-    input_to_props["input_structure2"]["path"] = str(input_structure2)
-    input_yaml_path = Path("combine_structure.yml")
-    create_input_yaml(input_to_props, input_yaml_path)
-    call_cwltool(cwl_file, input_yaml_path)
+
+    # Create the CWL step
+    combine_structure_step = Step(clt_path=cwl_file)
+    combine_structure_step.input_structure1 = str(input_structure1)
+    combine_structure_step.input_structure2 = str(input_structure2)
+    combine_structure_step.output_structure_path = "system.pdb"
+
+    # Create the workflow and run it
+    steps = [combine_structure_step]
+    filename = "combine_structure_workflow"
+    workflow = Workflow(steps, filename)
+    workflow.run()
+
+    # Check for the expected output
     assert Path(output_structure_path).exists()
-    Path(output_structure_path).unlink()
+    Path(output_structure_path).unlink()  # Clean up the output file