INNER CODE UNIT · Python

_add_edam_ontologies

nf-core/tools · nf_core/modules/lint/__init__.py:575

        def _add_edam_ontologies(section, edam_formats, desc):
            expected_ontologies = []
            current_ontologies = []
            if "pattern" in section:
                pattern = section["pattern"]
                # Check pattern detection and process for different cases
                if re.search(r"{", pattern):
                    for extension in re.split(r",|{|}", pattern):
                        if extension in edam_formats:
                            expected_ontologies.append((edam_formats[extension][0], extension))
                else:
                    if re.search(r"\.\w+$", pattern):
                        extension = pattern.split(".")[-1]
                        if extension in edam_formats:
                            expected_ontologies.append((edam_formats[extension][0], extension))
                # remove duplicated entries
                expected_ontologies = list(dict(expected_ontologies).items())
            if "ontologies" in section:

View source record →