pivot to yaml structure for tool definitions (#33)

pipeline/tools/loader.py

@@ -0,0 +1,58 @@
+import yaml
+from pathlib import Path
+
+from ..recon.config import tool_paths, defaults
+
+definitions = Path(__file__).parent
+
+
+def join(loader, node):
+    """ yaml tag handler to join a sequence of items into a space-separated string at load time """
+    seq = loader.construct_sequence(node)
+    return " ".join([str(val) for val in seq])
+
+
+def join_empty(loader, node):
+    """ yaml tag handler to join a sequence of items into a single string with no separations """
+    seq = loader.construct_sequence(node)
+    return "".join([str(val) for val in seq])
+
+
+def join_path(loader, node):
+    """ yaml tag handler to join a sequence of items into a filesystem path at load time """
+    seq = loader.construct_sequence(node)
+    return "/".join([str(i) for i in seq])
+
+
+def get_default(loader, node):
+    """ yaml tag handler to access defaults dict at load time """
+    py_str = loader.construct_python_str(node)
+    return py_str.format(**defaults)
+
+
+def get_parent(loader, node):
+    """ yaml tag handler to access tool parents """
+    py_str = loader.construct_python_str(node)
+    return Path(py_str.format(**tool_paths)).parent
+
+
+def get_tool_path(loader, node):
+    """ yaml tag handler to access tool_paths dict at load time """
+    py_str = loader.construct_python_str(node)
+    return py_str.format(**tool_paths)
+
+
+yaml.add_constructor("!join", join)
+yaml.add_constructor("!join_empty", join_empty)
+yaml.add_constructor("!join_path", join_path)
+yaml.add_constructor("!get_default", get_default)
+yaml.add_constructor("!get_tool_path", get_tool_path)
+yaml.add_constructor("!get_parent", get_parent)
+
+
+tools = {}
+for file in definitions.iterdir():
+    if file.name.endswith(".yaml"):
+        config = yaml.full_load(file.read_text())
+        tool_name = str(file.name.replace(".yaml", ""))
+        tools[tool_name] = config