Loading lib/galaxy/visualization/data_providers/genome.py +9 −1 Original line number Diff line number Diff line Loading @@ -4,6 +4,7 @@ Data providers for genome visualizations. import abc import itertools import logging import math import os import random Loading Loading @@ -44,6 +45,8 @@ 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 log = logging.getLogger(__name__) IntWebParam = Union[str, int] # Loading Loading @@ -234,7 +237,12 @@ class GenomeDataProvider(BaseDataProvider): start, end = int(start), int(end) with self.open_data_file() as data_file: iterator = self.get_iterator(data_file, chrom, start, end, **kwargs) try: data = self.process_data(iterator, start_val, max_vals, start=start, end=end, **kwargs) except ValueError as e: err_msg = f"Could not return data, error was '{e}'" log.warning(err_msg, exc_info=True) raise MessageException(err_msg) return data def get_genome_data(self, chroms_info, **kwargs): Loading Loading
lib/galaxy/visualization/data_providers/genome.py +9 −1 Original line number Diff line number Diff line Loading @@ -4,6 +4,7 @@ Data providers for genome visualizations. import abc import itertools import logging import math import os import random Loading Loading @@ -44,6 +45,8 @@ 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 log = logging.getLogger(__name__) IntWebParam = Union[str, int] # Loading Loading @@ -234,7 +237,12 @@ class GenomeDataProvider(BaseDataProvider): start, end = int(start), int(end) with self.open_data_file() as data_file: iterator = self.get_iterator(data_file, chrom, start, end, **kwargs) try: data = self.process_data(iterator, start_val, max_vals, start=start, end=end, **kwargs) except ValueError as e: err_msg = f"Could not return data, error was '{e}'" log.warning(err_msg, exc_info=True) raise MessageException(err_msg) return data def get_genome_data(self, chroms_info, **kwargs): Loading