Miscellaneous Utility Functions

Ensure that value is a list.

Source code in biocypher/biocypher/_misc.py

def to_list(value: Any) -> list:
    """Ensure that ``value`` is a list."""
    if isinstance(value, LIST_LIKE):
        value = list(value)

    else:
        value = [value]

    return value

Return iterables, except strings, wrap simple types into tuple.

Source code in biocypher/biocypher/_misc.py

def ensure_iterable(value: Any) -> Iterable:
    """Return iterables, except strings, wrap simple types into tuple."""
    return value if isinstance(value, LIST_LIKE) else (value,)

Create a visualisation of the inheritance tree using treelib.

Source code in biocypher/biocypher/_misc.py

def create_tree_visualisation(inheritance_graph: dict | nx.Graph) -> Tree:
    """Create a visualisation of the inheritance tree using treelib."""
    inheritance_tree = _get_inheritance_tree(inheritance_graph)
    classes, root = _find_root_node(inheritance_tree)

    tree = Tree()
    tree.create_node(root, root)
    while classes:
        for child in classes:
            parent = inheritance_tree[child]
            if parent in tree.nodes.keys() or parent == root:
                tree.create_node(child, child, parent=parent)

        for node in tree.nodes.keys():
            if node in classes:
                classes.remove(node)

    return tree

Source code in biocypher/biocypher/_misc.py

def from_pascal(s: str, sep: str = " ") -> str:
    underscored = underscore_pattern.sub(sep, s)
    lowercased = lowercase_pattern.sub(
        lambda match: match.group(0).lower(),
        underscored,
    )
    return lowercased

Convert PascalCase to sentence case.

---

s: Input string in PascalCase

---

string in sentence case form

Source code in biocypher/biocypher/_misc.py

def pascalcase_to_sentencecase(s: str) -> str:
    """Convert PascalCase to sentence case.

    Args:
    ----
        s: Input string in PascalCase

    Returns:
    -------
        string in sentence case form

    """
    return from_pascal(s, sep=" ")

Convert snake_case to sentence case.

---

s: Input string in snake_case

---

string in sentence case form

Source code in biocypher/biocypher/_misc.py

def snakecase_to_sentencecase(s: str) -> str:
    """Convert snake_case to sentence case.

    Args:
    ----
        s: Input string in snake_case

    Returns:
    -------
        string in sentence case form

    """
    return " ".join(word.lower() for word in s.split("_"))

Convert sentence case to snake_case.

---

s: Input string in sentence case

---

string in snake_case form

Source code in biocypher/biocypher/_misc.py

def sentencecase_to_snakecase(s: str) -> str:
    """Convert sentence case to snake_case.

    Args:
    ----
        s: Input string in sentence case

    Returns:
    -------
        string in snake_case form

    """
    return "_".join(s.lower().split())

Convert sentence case to PascalCase.

---

s: Input string in sentence case
sep: Separator for the words in the input string

---

string in PascalCase form

Source code in biocypher/biocypher/_misc.py

def sentencecase_to_pascalcase(s: str, sep: str = r"\s") -> str:
    """Convert sentence case to PascalCase.

    Args:
    ----
        s: Input string in sentence case
        sep: Separator for the words in the input string

    Returns:
    -------
        string in PascalCase form

    """
    return re.sub(
        r"(?:^|[" + sep + "])([a-zA-Z])",
        lambda match: match.group(1).upper(),
        s,
    )