Merge pull request #9439 from bernt-matthias/topic/sim_size_default

Unify default values used for delta (sim_size)

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)

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 = []

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

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):

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
     </xs:attribute>
     <xs:attribute name="delta" type="xs:integer">
       <xs:annotation>
-        <xs:documentation xml:lang="en">If ``compare`` is set to ``sim_size``, this is the number of bytes different allowed.</xs:documentation>
+        <xs:documentation xml:lang="en">If ``compare`` is set to ``sim_size``, this is the number of bytes different allowed (default 10000).</xs:documentation>
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>