Add custom template loader (#388)

Template schemas may now be passed to the `--template` option; pass the
path to the YAML file. The schema may still include imports, like the
`ontogpt` `core` schema, as long as they are present in the `templates`
directory already (or are part of the standard `ontogpt` installation).

src/ontogpt/io/template_loader.py

@@ -4,6 +4,7 @@
 import logging
 from pathlib import Path
 
+from linkml.generators.pydanticgen import PydanticGenerator
 from linkml_runtime import SchemaView
 from linkml_runtime.linkml_model import ClassDefinition
 
@@ -17,24 +18,56 @@ def get_template_details(template: TEMPLATE_NAME) -> ClassDefinition:
  """
  Get the LinkML class, module, and schemaview for a template.
 
+ This may be a template already known to ontogpt or the path
+ to a custom template. It is assumed to be the latter if the
+ template input is a path to a YAML file.
  :param template: template name of the form module.ClassName
  :return: tuple of (LinkML class definition, module, specific
  Python class, schemaview)
  """
- logger.info(f"Loading schema for {template}")
- if "." in template:
- module_name, class_name = template.split(".", 1)
- else:
- module_name = template
+ # Check if template is a path to a YAML file
+ # If so, this is a custom schema and needs python classes
+ if template.endswith(".yaml"):
+ logger.info(f"Loading custom schema from {template}")
+ path_to_template = Path(template)
+
+ # Check if file exists first
+ if not path_to_template.exists():
+ raise FileNotFoundError(f"Template file not found at {template}")
+
+ # Copy the schema to the templates directory
+ # So it will have access to imports like the core schema
+ templates_path = this_path.parent / "templates"
+ new_path_to_template = templates_path / path_to_template.name
+ new_path_to_template.write_text(path_to_template.read_text())
+ module_name = new_path_to_template.stem
+ path_to_module = new_path_to_template.with_suffix(".py")
+
+ sv = SchemaView(new_path_to_template)
+
+ gen = PydanticGenerator(str(new_path_to_template), pydantic_version=2)
+ path_to_module.write_text(gen.serialize())
+
+ mod = importlib.import_module(f"ontogpt.templates.{module_name}")
  class_name = None
- path_to_template = get_template_path(module_name)
- sv = SchemaView(path_to_template)
+
+ else:
+ logger.info(f"Loading schema for {template}")
+ if "." in template:
+ module_name, class_name = template.split(".", 1)
+ else:
+ module_name = template
+ class_name = None
+ path_to_template = get_template_path(module_name)
+ sv = SchemaView(path_to_template)
+ mod = importlib.import_module(f"ontogpt.templates.{module_name}")
+
  if class_name is None:
  roots = [c.name for c in sv.all_classes().values() if c.tree_root]
  if len(roots) != 1:
  raise ValueError(f"Template {template} does not have singular root: {roots}")
  class_name = roots[0]
- mod = importlib.import_module(f"ontogpt.templates.{module_name}")
+
  pyclass = mod.__dict__[class_name]
 
  logger.info(f"Getting class for template {template}")