Check various preconditions in FeatureLocationIndexDataProvider

    GFFReaderWrapper,

    parse_gff_attributes,

)

from galaxy.exceptions import MessageException

from galaxy.model import DatasetInstance

from galaxy.visualization.data_providers.basic import BaseDataProvider

from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and_cigar

        self.converted_dataset = converted_dataset

    def get_data(self, query):

        if self.converted_dataset is None or not self.converted_dataset.is_ok:

            raise MessageException("The dataset is not available or is in an error state.")

        # Init.

        textloc_file = open(self.converted_dataset.get_file_name())

        line_len = int(textloc_file.readline())

        result = []

        with open(self.converted_dataset.get_file_name()) as textloc_file:

            line = textloc_file.readline()

            if not line:

                raise MessageException("The dataset is empty.")

            try:

                line_len = int(line)

            except ValueError:

                raise MessageException(f"Expected an integer at first line, but found: '{line}'")

            if line_len < 1:

                raise MessageException(f"The first line must be a positive integer, but found: {line_len}")

            file_len = os.path.getsize(self.converted_dataset.get_file_name())

            query = query.lower()

            textloc_file.seek(position)

            # At right point in file, generate hits.

        result = []

            while True:

                line = textloc_file.readline()

                if not line.startswith(query):

                    line = line[:-1]

                result.append(line.split()[1:])

        textloc_file.close()

        return result