`Context.combine` is O(2n^2)

One last little perf thing before i quit for the night.

combine calls add_prefix in a loop: https://github.com/linkml/prefixmaps/blob/82bfdbc1c908fe9fb80c5b5b051e419a389595c3/src/prefixmaps/datamodel/context.py#L158

add_prefix calls prefixes and namespaces https://github.com/linkml/prefixmaps/blob/82bfdbc1c908fe9fb80c5b5b051e419a389595c3/src/prefixmaps/datamodel/context.py#L195-L197

prefixes and namespaces iterate over prefix_expansions https://github.com/linkml/prefixmaps/blob/82bfdbc1c908fe9fb80c5b5b051e419a389595c3/src/prefixmaps/datamodel/context.py#L241

add_prefix appends to prefix_expansions https://github.com/linkml/prefixmaps/blob/82bfdbc1c908fe9fb80c5b5b051e419a389595c3/src/prefixmaps/datamodel/context.py#L207

so for each item in the context, prefix_expansions is iterated twice and then grows.

This makes combining contexts very expensive - 124s for 24 calls (5.2s/call) in the linkml tests. 5.2s/call makes it not great for runtime use :(

Here's a very lazy fix that isn't great but it works - check for duplication only once when adding. it's not pretty bc i didn't want to disrupt the nested if/else in add_prefix, but would be simplified if that was flattened.


@dataclass
class Context:

    _prefixes: Optional[List[str]] = None
    _prefixes_lower: Optional[List[str]] = None
    _namespaces: Optional[List[str]] = None
    _namespaces_lower: Optional[List[str]] = None

    def add_prefix(
        self,
        prefix: PREFIX,
        namespace: NAMESPACE,
        status: StatusType = StatusType.canonical,
        preferred: bool = False,
    ):
        # ...
        prefixes = self.prefixes(lower=True)
        namespaces = self.namespaces(lower=True)
        if prefix.lower() in prefixes:
            if namespace.lower() in namespaces:
                return
                # status = StatusType.multi_alias
            else:
                status = StatusType.prefix_alias
                self._namespaces.append(namespace)
                self._namespaces_lower.append(namespace.lower())
        else:
            self._prefixes.append(prefix)
            self._prefixes_lower.append(prefix.lower())
            if namespace.lower() in namespaces:
                status = StatusType.namespace_alias
            else:
                self._namespaces.append(namespace)
                self._namespaces_lower.append(namespace.lower())
        self.prefix_expansions.append(
            PrefixExpansion(
                context=self.name,
                prefix=prefix,
                namespace=namespace,
                status=status,
            )
        )

    def prefixes(self, lower=False) -> List[str]:
        """
        All unique prefixes in all prefix expansions.

        :param lower: if True, the prefix is normalized to lowercase.
        :return:
        """
        if lower:
            if self._prefixes_lower is None:
                self._prefixes_lower = list({pe.prefix.lower() for pe in self.prefix_expansions})
            return self._prefixes_lower
        else:
            if self._prefixes is None:
                self._prefixes = list({pe.prefix for pe in self.prefix_expansions})
            return self._prefixes

    def namespaces(self, lower=False) -> List[str]:
        """
        All unique namespaces in all prefix expansions

        :param lower: if True, the namespace is normalized to lowercase.
        :return:
        """
        if lower:
            if self._namespaces_lower is None:
                self._namespaces_lower = list({pe.namespace.lower() for pe in self.prefix_expansions})
            return self._namespaces_lower
        else:
            if self._namespaces is None:
                self._namespaces = list({pe.namespace for pe in self.prefix_expansions})
            return self._namespaces

After changes no longer appears in profiling results bc takes no time.

linkml / prefixmaps

`Context.combine` is O(2n^2) #68