From 7cad1d6f3d21d291691df4c11b8b3ce4d4d44df4 Mon Sep 17 00:00:00 2001
From: Brandon Duane Walker <walkerbd@UPDATEME.HOSTNAME.COM>
Date: Fri, 31 May 2024 15:40:03 -0400
Subject: [PATCH] Remove cwl_utils

---
 cwl_utils/__init__.py      |   1 -
 cwl_utils/cwl_utilities.py | 104 -------------------------------------
 2 files changed, 105 deletions(-)
 delete mode 100644 cwl_utils/__init__.py
 delete mode 100644 cwl_utils/cwl_utilities.py

diff --git a/cwl_utils/__init__.py b/cwl_utils/__init__.py
deleted file mode 100644
index 676dcf76..00000000
--- a/cwl_utils/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-"""CWL Parsing Utilities."""
diff --git a/cwl_utils/cwl_utilities.py b/cwl_utils/cwl_utilities.py
deleted file mode 100644
index 85463c1e..00000000
--- a/cwl_utils/cwl_utilities.py
+++ /dev/null
@@ -1,104 +0,0 @@
-"""CWL utilities."""
-import subprocess
-from pathlib import Path
-from typing import Any
-
-from ruamel.yaml import YAML
-
-
-def modify_cwl_file(cwl_file: Path, format_dict: dict) -> str:
-    """Modify the CWL file to include the format for the input file.
-
-    If you have multiple file formats then cwltool will result in the error.
-    ref_resolver.py", line 232, in expand_url
-        if url.startswith("_:"):
-    AttributeError: 'CommentedSeq' object has no attribute 'startswith'.
-
-    Args:
-        cwl_file (str): The path to the CWL file.
-        format_dict (Dict): The dictionary of input names to their formats.
-    """
-    modified_cwl_file = f"{str(cwl_file).split('.')[0]}_modified.cwl"
-    # replace format for given input with the provided format
-    yaml = YAML(typ="safe", pure=True)
-    with cwl_file.open(encoding="utf-8") as file:
-        cwl_content = yaml.load(file)
-        inputs = cwl_content.get("inputs", {})
-        for input_name, input_data in inputs.items():
-            if input_name in format_dict:
-                input_data["format"] = format_dict[input_name]["format"]
-                inputs[input_name] = input_data
-        cwl_content["inputs"] = inputs
-    with Path(modified_cwl_file).open("w", encoding="utf-8") as file:
-        yaml.dump(cwl_content, file)
-    return modified_cwl_file
-
-
-def parse_cwl_arguments(cwl_file: Path) -> dict[str, Any]:
-    """Parse the CWL file to get the required inputs.
-
-    Args:
-        cwl_file (Path): The path to the CWL file.
-
-    Returns:
-        Dict[str, Dict]: A dictionary of input names to their properties.
-    """
-    yaml = YAML(typ="safe", pure=True)
-    with cwl_file.open(encoding="utf-8") as file:
-        cwl_content = yaml.load(file)
-    black_list_cwl_types = ["string?", "boolean?", "int?", "float?"]
-    input_to_props: dict[str, Any] = {}
-    inputs = cwl_content.get("inputs", {})
-    for input_name, input_data in inputs.items():
-        default_value = input_data.get("default", "")
-        cwl_type = input_data.get("type", "")
-        if isinstance(cwl_type, dict):
-            the_type = cwl_type["type"]
-            if the_type == "array":
-                items = cwl_type["items"]
-                cwl_type = f"{items}[]"
-        # find inputs that are required
-        if not default_value and cwl_type not in black_list_cwl_types:
-            cwl_format = input_data.get("format", "")
-            if cwl_type == "File" or cwl_type == "File?":
-                # cwltool will complain if passing File? with a File in .yml
-                file_dict = {"class": "File", "path": "", "format": cwl_format}
-                input_to_props[input_name] = file_dict
-            elif cwl_type == "File[]":
-                input_to_props[input_name] = []
-                file_dict = {"class": "File", "path": "", "format": cwl_format}
-                input_to_props[input_name].append(file_dict)
-            elif cwl_type == "string[]" or cwl_type == "float[]" or cwl_type == "int[]":
-                input_to_props[input_name] = []
-            else:
-                input_to_props[input_name] = cwl_type
-
-    return input_to_props
-
-
-def create_input_yaml(input_to_value: dict[str, str], output_yaml: Path) -> None:
-    """Create the input YAML file.
-
-    Args:
-        input_to_value (Dict[str, str]): Dictionary of input names to their values.
-        output_yaml (Path): Path to the output YAML file.
-    """
-    yaml = YAML()
-    with output_yaml.open("w", encoding="utf-8") as file:
-        yaml.dump(input_to_value, file)
-
-
-def call_cwltool(cwl_file: Path, input_yaml_path: Path) -> None:
-    """Call cwltool.
-
-    Args:
-        cwl_file (Path): The path to the CWL file.
-        input_yaml_path (Path): The path to the input YAML file.
-    """
-    command = ["cwltool", "--debug", str(cwl_file), str(input_yaml_path)]
-    completed_process = subprocess.run(
-        command,
-        capture_output=True,
-        text=True,
-    )
-    return completed_process.stdout, completed_process.stderr