refactor scatter_plot

utils/scatter_plot_plugin/Dockerfile → utils/plotting/scatter_plot_tool/Dockerfile

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

utils/plotting/scatter_plot_tool/build-docker.sh

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

utils/scatter_plot_plugin/ict.yml → utils/plotting/scatter_plot_tool/ict.yml

@@ -1,12 +1,12 @@
 specVersion: "0.1.0"
 name: scatter_plot
 version: 0.1.0
-container: scatter-plot-plugin
+container: scatter-plot-tool
 entrypoint:
 title: scatter_plot
 description: Generate a scatter plot
-author: Data Scientist
-contact: [email protected]
+author: Brandon Walker, Nazanin Donyapour
+contact: [email protected], [email protected]
 repository:
 documentation:
 citation:

utils/scatter_plot_plugin/pyproject.toml → utils/plotting/scatter_plot_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"
 matplotlib = "3.8.4"
 
 [tool.poetry.group.dev.dependencies]

utils/scatter_plot_plugin/scatter_plot.cwl → utils/plotting/scatter_plot_tool/scatter_plot_0@1@0.cwl

@@ -12,33 +12,39 @@ baseCommand: ["python", "-m", "polus.mm.utils.scatter_plot"]
 
 hints:
   DockerRequirement:
-    dockerPull: mrbrandonwalker/scatter_plot
+    dockerPull: polusai/scatter-plot-tool@sha256:00a025a1bc943207d8c938af07deb763f6ae1a3a67e94316ea64302427f1de8f
 
 inputs:
 
   xs:
     type:
       type: array
       items: float
-      inputBinding:
-        position: 2
-        prefix: --xs
+    inputBinding:
+      position: 2
+      prefix: --xs
+    doc: |-
+      X-axis array of data
 
   ys:
     type:
       type: array
       items: float
-      inputBinding:
-        position: 3
-        prefix: --ys
+    inputBinding:
+      position: 3
+      prefix: --ys
+    doc: |-
+      Y-axis array of data
 
   ys2:
     type:
       type: array
       items: float
-      inputBinding:
-        position: 4
-        prefix: --ys2
+    inputBinding:
+      position: 4
+      prefix: --ys2
+    doc: |-
+      Alternative Y-axis array of data
 
   output_png_path:
     label: Path to the output png file

utils/plotting/scatter_plot_tool/src/polus/mm/utils/scatter_plot/__main__.py

@@ -0,0 +1,59 @@
+"""parse arguments and call scatter_plot."""
+import argparse
+import logging
+from os import environ
+
+from polus.mm.utils.scatter_plot.scatter_plot import scatter_plot
+
+logging.basicConfig(
+    format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s",
+    datefmt="%d-%b-%y %H:%M:%S",
+)
+POLUS_LOG = getattr(logging, environ.get("POLUS_LOG", "INFO"))
+logger = logging.getLogger("polus.mm.utils.scatter_plot.")
+logger.setLevel(POLUS_LOG)
+
+
+def main(xs: list, ys: list, ys2: list, output_png_path: str) -> None:
+    """scatter_plot."""
+    logger.info(f"xs: {xs}")
+    logger.info(f"ys: {ys}")
+    logger.info(f"ys2: {ys2}")
+    logger.info(f"output_png_path: {output_png_path}")
+
+    scatter_plot(xs=xs, ys=ys, ys2=ys2, output_png_path=output_png_path)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="scatter_plot")
+    parser.add_argument(
+        "--xs",
+        type=float,
+        nargs="+",
+        required=True,
+        help="List of x values",
+    )
+    parser.add_argument(
+        "--ys",
+        type=float,
+        nargs="+",
+        required=True,
+        help="List of y values",
+    )
+    parser.add_argument(
+        "--ys2",
+        type=float,
+        nargs="+",
+        help="Optional second list of y values",
+    )
+    parser.add_argument(
+        "--output_png_path",
+        type=str,
+        required=True,
+        help="Path to the output \
+              png file",
+    )
+
+    args = parser.parse_args()
+
+    main(xs=args.xs, ys=args.ys, ys2=args.ys2, output_png_path=args.output_png_path)

utils/plotting/scatter_plot_tool/tests/test_scatter_plot.py

@@ -0,0 +1,37 @@
+"""Tests for scatter_plot."""
+from pathlib import Path
+
+from polus.mm.utils.scatter_plot.scatter_plot import scatter_plot
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_scatter_plot() -> None:
+    """Test scatter_plot."""
+    scatter_plot([1, 2, 3], [1, 2, 3], [], "test.png")
+    assert Path("test.png").exists()
+
+
+def test_duplicate() -> None:
+    """Test scatter plot CWL."""
+    cwl_file_str = "scatter_plot_0@[email protected]"
+    cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str)
+
+    scatter_plot = Step(clt_path=cwl_file)
+    scatter_plot.xs = [1, 2, 3]
+    scatter_plot.ys = [1, 2, 3]
+    scatter_plot.ys2 = [1, 2, 3]
+    scatter_plot.output_png_path = "test.png"
+
+    steps = [scatter_plot]
+    filename = "scatter_plot"
+    viz = Workflow(steps, filename)
+
+    viz.run()
+
+    outdir = Path("outdir")
+    files = list(outdir.rglob("test.png"))
+
+    assert (
+        files
+    ), f"The file 'test.png' does not exist in any subdirectory of '{outdir}'."