rename, use docker hash

utils/rename-residues-mol-plugin/Dockerfile → utils/pre-process/structure-changes/rename-residues-mol-tool/Dockerfile

@@ -1,4 +1,4 @@
-# docker build -f Dockerfile -t mrbrandonwalker/rename_residues_mol_tool .
+# docker build -f Dockerfile -t polusai/rename-residues-mol-tool:0.1.0 .
 FROM condaforge/mambaforge
 
 ENV EXEC_DIR="/opt/executables"

utils/pre-process/structure-changes/rename-residues-mol-tool/build-docker.sh

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

utils/rename-residues-mol-plugin/ict.yml → utils/pre-process/structure-changes/rename-residues-mol-tool/ict.yml

@@ -1,7 +1,7 @@
 specVersion: "0.1.0"
 name: rename_residues_mol
 version: 0.1.0
-container: rename-residues-mol-plugin
+container: rename-residues-mol-tool
 entrypoint:
 title: rename_residues_mol
 description: Run a python3 script

utils/rename-residues-mol-plugin/pyproject.toml → utils/pre-process/structure-changes/rename-residues-mol-tool/pyproject.toml

@@ -9,8 +9,7 @@ packages = [{include = "polus", from = "src"}]
 [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/rename-residues-mol-plugin/rename_residues_mol.cwl → utils/pre-process/structure-changes/rename-residues-mol-tool/rename_residues_mol_0@1@0.cwl

@@ -12,7 +12,7 @@ baseCommand: ["python", "-m", "polus.mm.utils.rename_residues_mol"]
 
 hints:
   DockerRequirement:
-    dockerPull: mrbrandonwalker/rename_residues_mol_tool
+    dockerPull: polusai/rename-residues-mol-tool@sha256:6ef6a91b88870bd55e1408efd49828d7be35bdb3656847a943232a52d3cd092a
 
 inputs:
 

utils/pre-process/structure-changes/rename-residues-mol-tool/tests/test_rename_residues_mol.py

@@ -0,0 +1,44 @@
+"""Tests for rename_residues_mol."""
+from pathlib import Path
+
+from polus.mm.utils.rename_residues_mol.rename_residues_mol import rename_residues_mol
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_rename_residues_mol() -> None:
+    """Test rename_residues_mol."""
+    input_mol2_path = "5umx_ligand.mol2"
+    input_mol2_path_path = Path(__file__).resolve().parent / Path(input_mol2_path)
+    output_mol2_path = "output.mol2"
+    rename_residues_mol(input_mol2_path_path, output_mol2_path)
+    assert Path(output_mol2_path).exists()
+
+
+def test_rename_residues_mol_cwl() -> None:
+    """Test rename_residues_mol CWL."""
+    cwl_file_str = "rename_residues_mol_0@[email protected]"
+    cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str)
+
+    # Create a Step instance
+    rename_residues_step = Step(clt_path=cwl_file)
+
+    # Define input paths
+    input_mol2_path = Path(__file__).resolve().parent / "5umx_ligand.mol2"
+    rename_residues_step.input_mol2_path = input_mol2_path
+    rename_residues_step.output_mol2_path = "system.mol2"
+
+    # Create a Workflow instance
+    steps = [rename_residues_step]
+    viz = Workflow(steps, "rename_residues_mol")
+
+    # Run the workflow
+    viz.run()
+
+    # Check if the expected output file exists
+    outdir = Path("outdir")
+    files = list(outdir.rglob("system.mol2"))
+
+    assert (
+        files
+    ), f"The file 'system.mol2' does not exist in any subdirectory of '{outdir}'."