The YAML parser/renderer is its own validating tool for the language.
Exceptions produced are subclasses of util.GeneralProteinError.
When possible, they provide the line number in the source code.
Errors Checklist
YAML Syntax Error: This is by far the most common error. Invalid YAML can cause preprocessing failures. Validate YAML syntax and directive structure.
Do not forget to add a colon (:) after a key,
when the value is on the following lines.
Incorrect keywords: A Protein keyword is a YAML key that starts a construct.
All keywords must start with a dot (.), e.g. : .if. Any unknown keyword,
or key not starting with a dot will be ignored.
Unquoted Jinja expressions: A Protein file must be a valid YAML file. It means that values
that contain a Jinja expression must be quoted:
❌ Incorrect: message: Hello, {{ name }}!
✅ Correct: message:"Hello, {{ name }}!"
Undefined Variables: A variable used in an expression is not defined in the current context or scope. Ensure all variables are declared within .local or passed correctly.
Duplicate keys: A mapping (dictionary) can have only one key of each type.
If a key is repeated, the parser will raise an error.
If you are using the same key two times or more, it's likely that you should
use a sequence (list) of mappings instead of a mapping.
[This is principle applicable to YAML in general.]
Missing Functions or Modules: Occurs if a referenced function or module is not imported or defined. Verify .module imports and .function definitions.
Argument Mismatches: When calling functions, ensure the number and order of arguments match the .args definition.
Incorrect Expression Syntax: Jinja2 expressions must be properly formatted. Check for missing braces, quotes, or invalid operations.
Debugging Tips
Check error messages carefully for line numbers (in the YAML file) and hints
Use minimal examples to isolate issues
Add Jinja variables that use variables defined in .local to print intermediate values