diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py index 022631195215..36e1cd60f9ff 100644 --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -664,7 +664,7 @@ def get_chunk(self, trans, dataset: HasFileName, offset: int = 0, ck_size: Optio break offset = bamfile.tell() - bamline = alignment.tostring(bamfile) + bamline = alignment.to_string() # With multiple tags, Galaxy would display each as a separate column # because the 'tostring()' function uses tabs also between tags. # Below code will turn these extra tabs into spaces. diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 20486069aa4b..fc02428c57ea 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -147,11 +147,11 @@ from galaxy.util import ( directory_hash_id, enum_values, + hex_to_lowercase_alphanum, listify, ready_name_for_url, unicodify, unique_id, - hex_to_lowercase_alphanum, ) from galaxy.util.dictifiable import ( dict_for, diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/8a19186a6ee7_add_columns_to_interactivetool_entry_point.py b/lib/galaxy/model/migrations/alembic/versions_gxy/8a19186a6ee7_add_columns_to_interactivetool_entry_point.py index 01d3812bbe04..414a6a2dbd79 100644 --- a/lib/galaxy/model/migrations/alembic/versions_gxy/8a19186a6ee7_add_columns_to_interactivetool_entry_point.py +++ b/lib/galaxy/model/migrations/alembic/versions_gxy/8a19186a6ee7_add_columns_to_interactivetool_entry_point.py @@ -5,7 +5,11 @@ Create Date: 2023-10-05 02:09:32.888292 """ -from sqlalchemy import Column, Text, Boolean +from sqlalchemy import ( + Boolean, + Column, + Text, +) from galaxy.model.migrations.util import ( add_column, diff --git a/lib/galaxy/security/idencoding.py b/lib/galaxy/security/idencoding.py index 7d302e9ef56e..9c0b10ce2a20 100644 --- a/lib/galaxy/security/idencoding.py +++ b/lib/galaxy/security/idencoding.py @@ -11,10 +11,10 @@ import galaxy.exceptions from galaxy.util import ( - smart_str, - unicodify, hex_to_lowercase_alphanum, lowercase_alphanum_to_hex, + smart_str, + unicodify, ) log = logging.getLogger(__name__) diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py index f494f0702021..2db3e454bb22 100644 --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -1890,6 +1890,7 @@ def hex_to_lowercase_alphanum(hex_string: str) -> str: characters a-z and 0-9 """ import numpy as np + return np.base_repr(int(hex_string, 16), 36).lower() @@ -1899,4 +1900,5 @@ def lowercase_alphanum_to_hex(lowercase_alphanum: str) -> str: hexadecimal string """ import numpy as np - return np.base_repr(int(lowercase_alphanum, 36), 16).lower() \ No newline at end of file + + return np.base_repr(int(lowercase_alphanum, 36), 16).lower()