Split get_files into smaller functions

The get_files function does many different things, split it into smaller ones.

    def get_files(
        self, bundle: str = None, tags: List[str] = None, version: int = None
    ) -> Query:
        """Fetches files from the store based on the specified filters.
        Args:
            bundle (str, optional): Name of the bundle to fetch files from.
            tags (List[str], optional): List of tags to filter files by.
            version (int, optional): ID of the version to fetch files from.

        Returns:
            Query: A query that match the specified filters.
        """
        query = self._get_file_query()
        if bundle:
            LOG.info(f"Fetching files from bundle {bundle}")
            query = apply_bundle_filter(
                bundles=query.join(self.File.version, self.Version.bundle),
                filter_functions=[BundleFilters.FILTER_BY_NAME],
                bundle_name=bundle,
            )

        if tags:
            formatted_tags = ",".join(tags)
            LOG.info(f"Fetching files with tags in [{formatted_tags}]")

            query = apply_file_tag_filter(
                files_tags=query.join(File.tags),
                filter_functions=[FileTagFilter.FILTER_FILES_BY_TAGS],
                tags=tags,
            )

        if version:
            LOG.info(f"Fetching files from version {version}")
            query = apply_version_filter(
                versions=query.join(self.File.version),
                filter_functions=[VersionFilters.FILTER_BY_ID],
                version_id=version,
            )

        return query

Clinical-Genomics / housekeeper

Split get_files into smaller functions #106