From fb4717660ec9c80db60a349134c844f46cc2e4bf Mon Sep 17 00:00:00 2001
From: Brandon Duane Walker <walkerbd@UPDATEME.HOSTNAME.COM>
Date: Tue, 21 May 2024 13:46:26 -0400
Subject: [PATCH] rename, use docker hash

---
 .../.bumpversion.cfg                          |  0
 .../rename-residues-mol-tool}/.dockerignore   |  0
 .../rename-residues-mol-tool}/.gitignore      |  0
 .../rename-residues-mol-tool}/CHANGELOG.md    |  0
 .../rename-residues-mol-tool}/Dockerfile      |  2 +-
 .../rename-residues-mol-tool}/README.md       |  0
 .../rename-residues-mol-tool}/VERSION         |  0
 .../rename-residues-mol-tool/build-docker.sh  |  4 ++
 .../rename-residues-mol-tool}/ict.yml         |  2 +-
 .../rename-residues-mol-tool}/pyproject.toml  |  3 +-
 .../rename_residues_mol_0@1@0.cwl}            |  2 +-
 .../mm/utils/rename_residues_mol/__init__.py  |  0
 .../mm/utils/rename_residues_mol/__main__.py  |  0
 .../rename_residues_mol.py                    |  0
 .../tests/5umx_ligand.mol2                    |  0
 .../tests/__init__.py                         |  0
 .../tests/test_rename_residues_mol.py         | 44 +++++++++++++++++++
 .../build-docker.sh                           |  4 --
 .../tests/test_rename_residues_mol.py         | 38 ----------------
 19 files changed, 52 insertions(+), 47 deletions(-)
 rename utils/{rename-residues-mol-plugin => pre-process/structure-changes/rename-residues-mol-tool}/.bumpversion.cfg (100%)
 rename utils/{rename-residues-mol-plugin => pre-process/structure-changes/rename-residues-mol-tool}/.dockerignore (100%)
 rename utils/{rename-residues-mol-plugin => pre-process/structure-changes/rename-residues-mol-tool}/.gitignore (100%)
 rename utils/{rename-residues-mol-plugin => pre-process/structure-changes/rename-residues-mol-tool}/CHANGELOG.md (100%)
 rename utils/{rename-residues-mol-plugin => pre-process/structure-changes/rename-residues-mol-tool}/Dockerfile (84%)
 rename utils/{rename-residues-mol-plugin => pre-process/structure-changes/rename-residues-mol-tool}/README.md (100%)
 rename utils/{rename-residues-mol-plugin => pre-process/structure-changes/rename-residues-mol-tool}/VERSION (100%)
 create mode 100755 utils/pre-process/structure-changes/rename-residues-mol-tool/build-docker.sh
 rename utils/{rename-residues-mol-plugin => pre-process/structure-changes/rename-residues-mol-tool}/ict.yml (96%)
 rename utils/{rename-residues-mol-plugin => pre-process/structure-changes/rename-residues-mol-tool}/pyproject.toml (92%)
 rename utils/{rename-residues-mol-plugin/rename_residues_mol.cwl => pre-process/structure-changes/rename-residues-mol-tool/rename_residues_mol_0@1@0.cwl} (88%)
 rename utils/{rename-residues-mol-plugin => pre-process/structure-changes/rename-residues-mol-tool}/src/polus/mm/utils/rename_residues_mol/__init__.py (100%)
 rename utils/{rename-residues-mol-plugin => pre-process/structure-changes/rename-residues-mol-tool}/src/polus/mm/utils/rename_residues_mol/__main__.py (100%)
 rename utils/{rename-residues-mol-plugin => pre-process/structure-changes/rename-residues-mol-tool}/src/polus/mm/utils/rename_residues_mol/rename_residues_mol.py (100%)
 rename utils/{rename-residues-mol-plugin => pre-process/structure-changes/rename-residues-mol-tool}/tests/5umx_ligand.mol2 (100%)
 rename utils/{rename-residues-mol-plugin => pre-process/structure-changes/rename-residues-mol-tool}/tests/__init__.py (100%)
 create mode 100644 utils/pre-process/structure-changes/rename-residues-mol-tool/tests/test_rename_residues_mol.py
 delete mode 100755 utils/rename-residues-mol-plugin/build-docker.sh
 delete mode 100644 utils/rename-residues-mol-plugin/tests/test_rename_residues_mol.py

diff --git a/utils/rename-residues-mol-plugin/.bumpversion.cfg b/utils/pre-process/structure-changes/rename-residues-mol-tool/.bumpversion.cfg
similarity index 100%
rename from utils/rename-residues-mol-plugin/.bumpversion.cfg
rename to utils/pre-process/structure-changes/rename-residues-mol-tool/.bumpversion.cfg
diff --git a/utils/rename-residues-mol-plugin/.dockerignore b/utils/pre-process/structure-changes/rename-residues-mol-tool/.dockerignore
similarity index 100%
rename from utils/rename-residues-mol-plugin/.dockerignore
rename to utils/pre-process/structure-changes/rename-residues-mol-tool/.dockerignore
diff --git a/utils/rename-residues-mol-plugin/.gitignore b/utils/pre-process/structure-changes/rename-residues-mol-tool/.gitignore
similarity index 100%
rename from utils/rename-residues-mol-plugin/.gitignore
rename to utils/pre-process/structure-changes/rename-residues-mol-tool/.gitignore
diff --git a/utils/rename-residues-mol-plugin/CHANGELOG.md b/utils/pre-process/structure-changes/rename-residues-mol-tool/CHANGELOG.md
similarity index 100%
rename from utils/rename-residues-mol-plugin/CHANGELOG.md
rename to utils/pre-process/structure-changes/rename-residues-mol-tool/CHANGELOG.md
diff --git a/utils/rename-residues-mol-plugin/Dockerfile b/utils/pre-process/structure-changes/rename-residues-mol-tool/Dockerfile
similarity index 84%
rename from utils/rename-residues-mol-plugin/Dockerfile
rename to utils/pre-process/structure-changes/rename-residues-mol-tool/Dockerfile
index 3683352e..6aaf49c1 100644
--- a/utils/rename-residues-mol-plugin/Dockerfile
+++ b/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"
diff --git a/utils/rename-residues-mol-plugin/README.md b/utils/pre-process/structure-changes/rename-residues-mol-tool/README.md
similarity index 100%
rename from utils/rename-residues-mol-plugin/README.md
rename to utils/pre-process/structure-changes/rename-residues-mol-tool/README.md
diff --git a/utils/rename-residues-mol-plugin/VERSION b/utils/pre-process/structure-changes/rename-residues-mol-tool/VERSION
similarity index 100%
rename from utils/rename-residues-mol-plugin/VERSION
rename to utils/pre-process/structure-changes/rename-residues-mol-tool/VERSION
diff --git a/utils/pre-process/structure-changes/rename-residues-mol-tool/build-docker.sh b/utils/pre-process/structure-changes/rename-residues-mol-tool/build-docker.sh
new file mode 100755
index 00000000..3f8a4d5f
--- /dev/null
+++ b/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}
diff --git a/utils/rename-residues-mol-plugin/ict.yml b/utils/pre-process/structure-changes/rename-residues-mol-tool/ict.yml
similarity index 96%
rename from utils/rename-residues-mol-plugin/ict.yml
rename to utils/pre-process/structure-changes/rename-residues-mol-tool/ict.yml
index cfb4969c..70280e48 100644
--- a/utils/rename-residues-mol-plugin/ict.yml
+++ b/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
diff --git a/utils/rename-residues-mol-plugin/pyproject.toml b/utils/pre-process/structure-changes/rename-residues-mol-tool/pyproject.toml
similarity index 92%
rename from utils/rename-residues-mol-plugin/pyproject.toml
rename to utils/pre-process/structure-changes/rename-residues-mol-tool/pyproject.toml
index d78e61e0..8fd48a3f 100644
--- a/utils/rename-residues-mol-plugin/pyproject.toml
+++ b/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"
diff --git a/utils/rename-residues-mol-plugin/rename_residues_mol.cwl b/utils/pre-process/structure-changes/rename-residues-mol-tool/rename_residues_mol_0@1@0.cwl
similarity index 88%
rename from utils/rename-residues-mol-plugin/rename_residues_mol.cwl
rename to utils/pre-process/structure-changes/rename-residues-mol-tool/rename_residues_mol_0@1@0.cwl
index c59e6242..315072fe 100644
--- a/utils/rename-residues-mol-plugin/rename_residues_mol.cwl
+++ b/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:
 
diff --git a/utils/rename-residues-mol-plugin/src/polus/mm/utils/rename_residues_mol/__init__.py b/utils/pre-process/structure-changes/rename-residues-mol-tool/src/polus/mm/utils/rename_residues_mol/__init__.py
similarity index 100%
rename from utils/rename-residues-mol-plugin/src/polus/mm/utils/rename_residues_mol/__init__.py
rename to utils/pre-process/structure-changes/rename-residues-mol-tool/src/polus/mm/utils/rename_residues_mol/__init__.py
diff --git a/utils/rename-residues-mol-plugin/src/polus/mm/utils/rename_residues_mol/__main__.py b/utils/pre-process/structure-changes/rename-residues-mol-tool/src/polus/mm/utils/rename_residues_mol/__main__.py
similarity index 100%
rename from utils/rename-residues-mol-plugin/src/polus/mm/utils/rename_residues_mol/__main__.py
rename to utils/pre-process/structure-changes/rename-residues-mol-tool/src/polus/mm/utils/rename_residues_mol/__main__.py
diff --git a/utils/rename-residues-mol-plugin/src/polus/mm/utils/rename_residues_mol/rename_residues_mol.py b/utils/pre-process/structure-changes/rename-residues-mol-tool/src/polus/mm/utils/rename_residues_mol/rename_residues_mol.py
similarity index 100%
rename from utils/rename-residues-mol-plugin/src/polus/mm/utils/rename_residues_mol/rename_residues_mol.py
rename to utils/pre-process/structure-changes/rename-residues-mol-tool/src/polus/mm/utils/rename_residues_mol/rename_residues_mol.py
diff --git a/utils/rename-residues-mol-plugin/tests/5umx_ligand.mol2 b/utils/pre-process/structure-changes/rename-residues-mol-tool/tests/5umx_ligand.mol2
similarity index 100%
rename from utils/rename-residues-mol-plugin/tests/5umx_ligand.mol2
rename to utils/pre-process/structure-changes/rename-residues-mol-tool/tests/5umx_ligand.mol2
diff --git a/utils/rename-residues-mol-plugin/tests/__init__.py b/utils/pre-process/structure-changes/rename-residues-mol-tool/tests/__init__.py
similarity index 100%
rename from utils/rename-residues-mol-plugin/tests/__init__.py
rename to utils/pre-process/structure-changes/rename-residues-mol-tool/tests/__init__.py
diff --git a/utils/pre-process/structure-changes/rename-residues-mol-tool/tests/test_rename_residues_mol.py b/utils/pre-process/structure-changes/rename-residues-mol-tool/tests/test_rename_residues_mol.py
new file mode 100644
index 00000000..a4f27a1b
--- /dev/null
+++ b/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@1@0.cwl"
+    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}'."
diff --git a/utils/rename-residues-mol-plugin/build-docker.sh b/utils/rename-residues-mol-plugin/build-docker.sh
deleted file mode 100755
index 441a3fa9..00000000
--- a/utils/rename-residues-mol-plugin/build-docker.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/bash
-
-version=$(<VERSION)
-docker build . -t polusai/rename-residues-mol-plugin:${version}
diff --git a/utils/rename-residues-mol-plugin/tests/test_rename_residues_mol.py b/utils/rename-residues-mol-plugin/tests/test_rename_residues_mol.py
deleted file mode 100644
index 407655b0..00000000
--- a/utils/rename-residues-mol-plugin/tests/test_rename_residues_mol.py
+++ /dev/null
@@ -1,38 +0,0 @@
-"""Tests for rename_residues_mol."""
-import sys
-from pathlib import Path
-
-from polus.mm.utils.rename_residues_mol.rename_residues_mol import rename_residues_mol
-
-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
-
-
-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.cwl"
-    cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str)
-    input_to_props = parse_cwl_arguments(cwl_file)
-    file_path_str = "5umx_ligand.mol2"
-    file_path = str(Path(__file__).resolve().parent / Path(file_path_str))
-    input_to_props["input_mol2_path"]["path"] = file_path
-
-    input_yaml_path = Path("rename_residues_mol.yml")
-    create_input_yaml(input_to_props, input_yaml_path)
-
-    stdout, stderr = call_cwltool(cwl_file, input_yaml_path)
-    assert Path("system.mol2").exists()