diff --git a/lib/galaxy/tool_util/parser/util.py b/lib/galaxy/tool_util/parser/util.py index 41c25186c14..b2cdfd2bac3 100644 --- a/lib/galaxy/tool_util/parser/util.py +++ b/lib/galaxy/tool_util/parser/util.py @@ -1,5 +1,7 @@ from collections import OrderedDict +DEFAULT_DELTA = "10000" + def is_dict(item): return isinstance(item, dict) or isinstance(item, OrderedDict) diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py index f38301762e0..110524b4659 100644 --- a/lib/galaxy/tool_util/parser/xml.py +++ b/lib/galaxy/tool_util/parser/xml.py @@ -9,6 +9,7 @@ from math import isinf import packaging.version from galaxy.tool_util.deps import requirements +from galaxy.tool_util.parser.util import DEFAULT_DELTA from galaxy.util import string_as_bool, xml_text, xml_to_string from .interface import ( InputSource, @@ -612,7 +613,7 @@ def __parse_test_attributes(output_elem, attrib, parse_elements=False, parse_dis # Number of lines to allow to vary in logs (for dates, etc) attributes['lines_diff'] = int(attrib.pop('lines_diff', '0')) # Allow a file size to vary if sim_size compare - attributes['delta'] = int(attrib.pop('delta', '10000')) + attributes['delta'] = int(attrib.pop('delta', DEFAULT_DELTA)) attributes['sort'] = string_as_bool(attrib.pop('sort', False)) attributes['decompress'] = string_as_bool(attrib.pop('decompress', False)) extra_files = [] diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py index c271a9a1cc6..4ee12798997 100644 --- a/lib/galaxy/tool_util/parser/yaml.py +++ b/lib/galaxy/tool_util/parser/yaml.py @@ -3,6 +3,7 @@ from collections import OrderedDict import packaging.version from galaxy.tool_util.deps import requirements +from galaxy.tool_util.parser.util import DEFAULT_DELTA from .interface import ( InputSource, PageSource, @@ -218,7 +219,7 @@ def _parse_test(i, test_dict): defaults = { 'compare': 'diff', 'lines_diff': 0, - 'delta': 1000, + 'delta': int(DEFAULT_DELTA), 'sort': False, } # TODO diff --git a/lib/galaxy/tool_util/verify/__init__.py b/lib/galaxy/tool_util/verify/__init__.py index 0a2a554da0d..966f13f9060 100644 --- a/lib/galaxy/tool_util/verify/__init__.py +++ b/lib/galaxy/tool_util/verify/__init__.py @@ -16,6 +16,7 @@ try: except ImportError: pysam = None +from galaxy.tool_util.parser.util import DEFAULT_DELTA from galaxy.util import unicodify from galaxy.util.compression_utils import get_fileobj from .asserts import verify_assertions @@ -131,7 +132,7 @@ def verify( elif compare == 're_match_multiline': files_re_match_multiline(local_name, temp_name, attributes=attributes) elif compare == 'sim_size': - delta = attributes.get('delta', '100') + delta = int(attributes.get('delta', DEFAULT_DELTA)) s1 = len(output_content) s2 = os.path.getsize(local_name) if abs(s1 - s2) > int(delta): diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd index 6ae0e3e102c..a812c6dc04d 100644 --- a/lib/galaxy/tool_util/xsd/galaxy.xsd +++ b/lib/galaxy/tool_util/xsd/galaxy.xsd @@ -1314,7 +1314,7 @@ When this attribute is true and ``compare`` is set to ``diff``, try to decompres - If ``compare`` is set to ``sim_size``, this is the number of bytes different allowed. + If ``compare`` is set to ``sim_size``, this is the number of bytes different allowed (default 10000).