Merge pull request #896 from IanCa/develop

Improve schema character validation to match the new spec/utf8 support

hed/errors/error_types.py

@@ -123,6 +123,7 @@ class SchemaWarnings:
     SCHEMA_CHARACTER_INVALID = "SCHEMA_CHARACTER_INVALID"
     SCHEMA_INVALID_CAPITALIZATION = 'invalidCaps'
     SCHEMA_NON_PLACEHOLDER_HAS_CLASS = 'SCHEMA_NON_PLACEHOLDER_HAS_CLASS'
+    SCHEMA_PROLOGUE_CHARACTER_INVALID = "SCHEMA_PROLOGUE_CHARACTER_INVALID"
 
 
 class SchemaAttributeErrors:

hed/errors/schema_error_messages.py

@@ -23,6 +23,13 @@ def schema_error_unknown_attribute(attribute_name, source_tag):
            f"or was used outside of it's defined class."
 
 
+@hed_error(SchemaWarnings.SCHEMA_PROLOGUE_CHARACTER_INVALID, default_severity=ErrorSeverity.WARNING,
+           actual_code=SchemaWarnings.SCHEMA_CHARACTER_INVALID)
+def schema_error_invalid_character_prologue(char_index, source_string, section_name):
+    invalid_char = source_string[char_index]
+    return f"'{section_name}' has invalid character '{invalid_char}' at position {char_index} of string: {source_string}"
+
+
 @hed_error(SchemaWarnings.SCHEMA_INVALID_CHARACTERS_IN_DESC, default_severity=ErrorSeverity.WARNING,
            actual_code=SchemaWarnings.SCHEMA_CHARACTER_INVALID)
 def schema_warning_invalid_chars_desc(desc_string, tag_name, problem_char, char_index):

hed/models/def_expand_gather.py

@@ -155,20 +155,20 @@ def _handle_known_definition(self, def_tag, def_expand_group, def_group):
 
         if def_group_contents:
             if def_group_contents != def_expand_group:
-                self.errors.setdefault(def_tag_name.lower(), []).append(def_expand_group.get_first_group())
+                self.errors.setdefault(def_tag_name.casefold(), []).append(def_expand_group.get_first_group())
             return True
 
         has_extension = "/" in def_tag.extension
         if not has_extension:
             group_tag = def_expand_group.get_first_group()
-            self.def_dict.defs[def_tag_name.lower()] = DefinitionEntry(name=def_tag_name, contents=group_tag,
+            self.def_dict.defs[def_tag_name.casefold()] = DefinitionEntry(name=def_tag_name, contents=group_tag,
                                                                        takes_value=False,
                                                                        source_context=[])
             return True
 
         # this is needed for the cases where we have a definition with errors, but it's not a known definition.
-        if def_tag_name.lower() in self.errors:
-            self.errors.setdefault(f"{def_tag_name.lower()}", []).append(def_expand_group.get_first_group())
+        if def_tag_name.casefold() in self.errors:
+            self.errors.setdefault(f"{def_tag_name.casefold()}", []).append(def_expand_group.get_first_group())
             return True
 
         return False
@@ -181,20 +181,20 @@ def _handle_ambiguous_definition(self, def_tag, def_expand_group):
             def_expand_group (HedGroup): The group containing the def-expand tag.
         """
         def_tag_name = def_tag.extension.split('/')[0]
-        these_defs = self.ambiguous_defs.setdefault(def_tag_name.lower(), AmbiguousDef())
+        these_defs = self.ambiguous_defs.setdefault(def_tag_name.casefold(), AmbiguousDef())
         these_defs.add_def(def_tag, def_expand_group)
 
         try:
             if these_defs.validate():
                 new_contents = these_defs.get_group()
-                self.def_dict.defs[def_tag_name.lower()] = DefinitionEntry(name=def_tag_name, contents=new_contents,
+                self.def_dict.defs[def_tag_name.casefold()] = DefinitionEntry(name=def_tag_name, contents=new_contents,
                                                                            takes_value=True,
                                                                            source_context=[])
-                del self.ambiguous_defs[def_tag_name.lower()]
+                del self.ambiguous_defs[def_tag_name.casefold()]
         except ValueError:
             for ambiguous_def in these_defs.placeholder_defs:
-                self.errors.setdefault(def_tag_name.lower(), []).append(ambiguous_def)
-            del self.ambiguous_defs[def_tag_name.lower()]
+                self.errors.setdefault(def_tag_name.casefold(), []).append(ambiguous_def)
+            del self.ambiguous_defs[def_tag_name.casefold()]
 
         return
 

hed/models/definition_dict.py

@@ -84,7 +84,7 @@ def get(self, def_name):
         Returns:
             DefinitionEntry:  Definition entry for the requested definition.
         """
-        return self.defs.get(def_name.lower())
+        return self.defs.get(def_name.casefold())
 
     def __iter__(self):
         return iter(self.defs)
@@ -144,14 +144,14 @@ def check_for_definitions(self, hed_string_obj, error_handler=None):
                 def_issues += new_def_issues
                 continue
 
-            self.defs[def_tag_name.lower()] = DefinitionEntry(name=def_tag_name, contents=group_tag,
+            self.defs[def_tag_name.casefold()] = DefinitionEntry(name=def_tag_name, contents=group_tag,
                                                               takes_value=def_takes_value,
                                                               source_context=context)
 
         return def_issues
 
     def _strip_value_placeholder(self, def_tag_name):
-        def_takes_value = def_tag_name.lower().endswith("/#")
+        def_takes_value = def_tag_name.endswith("/#")
         if def_takes_value:
             def_tag_name = def_tag_name[:-len("/#")]
         return def_tag_name, def_takes_value
@@ -162,7 +162,7 @@ def _validate_name_and_context(self, def_tag_name, error_handler):
         else:
             context = []
         new_def_issues = []
-        if def_tag_name.lower() in self.defs:
+        if def_tag_name.casefold() in self.defs:
             new_def_issues += ErrorHandler.format_error_with_context(error_handler,
                                                                      DefinitionErrors.DUPLICATE_DEFINITION,
                                                                      def_name=def_tag_name)
@@ -263,7 +263,7 @@ def get_definition_entry(self, def_tag):
         """
         tag_label, _, placeholder = def_tag.extension.partition('/')
 
-        label_tag_lower = tag_label.lower()
+        label_tag_lower = tag_label.casefold()
         def_entry = self.defs.get(label_tag_lower)
         return def_entry
 
@@ -281,7 +281,7 @@ def _get_definition_contents(self, def_tag):
         """
         tag_label, _, placeholder = def_tag.extension.partition('/')
 
-        label_tag_lower = tag_label.lower()
+        label_tag_lower = tag_label.casefold()
         def_entry = self.defs.get(label_tag_lower)
         if def_entry is None:
             # Could raise an error here?

hed/models/df_util.py

@@ -123,22 +123,20 @@ def sort_dataframe_by_onsets(df):
     return df
 
 
-def replace_ref(text, newvalue, column_ref):
+def replace_ref(text, oldvalue, newvalue="n/a"):
     """ Replace column ref in x with y.  If it's n/a, delete extra commas/parentheses.
 
     Parameters:
         text (str): The input string containing the ref enclosed in curly braces.
+        oldvalue (str): The full tag or ref to replace
         newvalue (str): The replacement value for the ref.
-        column_ref (str): The ref to be replaced, without curly braces.
 
     Returns:
         str: The modified string with the ref replaced or removed.
     """
-    # Note: This function could easily be updated to handle non-curly brace values, but it seemed faster this way
-
     # If it's not n/a, we can just replace directly.
     if newvalue != "n/a":
-        return text.replace(f"{{{column_ref}}}", newvalue)
+        return text.replace(oldvalue, newvalue)
 
     def _remover(match):
         p1 = match.group("p1").count("(")
@@ -162,7 +160,7 @@ def _remover(match):
     # c1/c2 contain the comma(and possibly spaces) separating this ref from other tags
     # p1/p2 contain the parentheses directly surrounding the tag
     # All four groups can have spaces.
-    pattern = r'(?P<c1>[\s,]*)(?P<p1>[(\s]*)\{' + column_ref + r'\}(?P<p2>[\s)]*)(?P<c2>[\s,]*)'
+    pattern = r'(?P<c1>[\s,]*)(?P<p1>[(\s]*)' + oldvalue + r'(?P<p2>[\s)]*)(?P<c2>[\s,]*)'
     return re.sub(pattern, _remover, text)
 
 
@@ -192,7 +190,7 @@ def _handle_curly_braces_refs(df, refs, column_names):
             # column_name_brackets = f"{{{replacing_name}}}"
             # df[column_name] = pd.Series(x.replace(column_name_brackets, y) for x, y
             #                             in zip(df[column_name], saved_columns[replacing_name]))
-            new_df[column_name] = pd.Series(replace_ref(x, y, replacing_name) for x, y
+            new_df[column_name] = pd.Series(replace_ref(x, f"{{{replacing_name}}}", y) for x, y
                                             in zip(new_df[column_name], saved_columns[replacing_name]))
     new_df = new_df[remaining_columns]
 
@@ -220,7 +218,7 @@ def split_delay_tags(series, hed_schema, onsets):
         return
     split_df = pd.DataFrame({"onset": onsets, "HED": series, "original_index": series.index})
     delay_strings = [(i, HedString(hed_string, hed_schema)) for (i, hed_string) in series.items() if
-                     "delay/" in hed_string.lower()]
+                     "delay/" in hed_string.casefold()]
     delay_groups = []
     for i, delay_string in delay_strings:
         duration_tags = delay_string.find_top_level_tags({DefTagNames.DELAY_KEY})

hed/models/hed_group.py

@@ -353,6 +353,10 @@ def lower(self):
         """ Convenience function, equivalent to str(self).lower(). """
         return str(self).lower()
 
+    def casefold(self):
+        """ Convenience function, equivalent to str(self).casefold(). """
+        return str(self).casefold()
+
     def get_as_indented(self, tag_attribute="short_tag"):
         """Return the string as a multiline indented format.
 
@@ -442,9 +446,9 @@ def find_tags(self, search_tags, recursive=False, include_groups=2):
             tags = self.get_all_tags()
         else:
             tags = self.tags()
-        search_tags = {tag.lower() for tag in search_tags}
+        search_tags = {tag.casefold() for tag in search_tags}
         for tag in tags:
-            if tag.short_base_tag.lower() in search_tags:
+            if tag.short_base_tag.casefold() in search_tags:
                 found_tags.append((tag, tag._parent))
 
         if include_groups == 0 or include_groups == 1:
@@ -454,7 +458,7 @@ def find_tags(self, search_tags, recursive=False, include_groups=2):
     def find_wildcard_tags(self, search_tags, recursive=False, include_groups=2):
         """ Find the tags and their containing groups.
 
-            This searches tag.short_tag.lower(), with an implicit wildcard on the end.
+            This searches tag.short_tag.casefold(), with an implicit wildcard on the end.
 
             e.g. "Eve" will find Event, but not Sensory-event.
 
@@ -475,11 +479,11 @@ def find_wildcard_tags(self, search_tags, recursive=False, include_groups=2):
         else:
             tags = self.tags()
 
-        search_tags = {search_tag.lower() for search_tag in search_tags}
+        search_tags = {search_tag.casefold() for search_tag in search_tags}
 
         for tag in tags:
             for search_tag in search_tags:
-                if tag.short_tag.lower().startswith(search_tag):
+                if tag.short_tag.casefold().startswith(search_tag):
                     found_tags.append((tag, tag._parent))
                     # We can't find the same tag twice
                     break
@@ -575,7 +579,7 @@ def find_tags_with_term(self, term, recursive=False, include_groups=2):
         else:
             tags = self.tags()
 
-        search_for = term.lower()
+        search_for = term.casefold()
         for tag in tags:
             if search_for in tag.tag_terms:
                 found_tags.append((tag, tag._parent))

hed/models/hed_string.py

@@ -353,11 +353,11 @@ def find_top_level_tags(self, anchor_tags, include_groups=2):
         Returns:
             list: The returned result depends on include_groups.
         """
-        anchor_tags = {tag.lower() for tag in anchor_tags}
+        anchor_tags = {tag.casefold() for tag in anchor_tags}
         top_level_tags = []
         for group in self.groups():
             for tag in group.tags():
-                if tag.short_base_tag.lower() in anchor_tags:
+                if tag.short_base_tag.casefold() in anchor_tags:
                     top_level_tags.append((tag, group))
                     # Only capture a max of 1 per group.  These are implicitly unique.
                     break

hed/models/hed_tag.py

@@ -309,6 +309,10 @@ def lower(self):
         """ Convenience function, equivalent to str(self).lower(). """
         return str(self).lower()
 
+    def casefold(self):
+        """ Convenience function, equivalent to str(self).casefold(). """
+        return str(self).casefold()
+
     def _calculate_to_canonical_forms(self, hed_schema):
         """ Update internal state based on schema.
 
@@ -617,24 +621,24 @@ def replace_placeholder(self, placeholder_value):
     def __hash__(self):
         if self._schema_entry:
             return hash(
-                self._namespace + self._schema_entry.short_tag_name.lower() + self._extension_value.lower())
+                self._namespace + self._schema_entry.short_tag_name.casefold() + self._extension_value.casefold())
         else:
-            return hash(self.lower())
+            return hash(self.casefold())
 
     def __eq__(self, other):
         if self is other:
             return True
 
         if isinstance(other, str):
-            return self.lower() == other.lower()
+            return self.casefold() == other.casefold()
 
         if not isinstance(other, HedTag):
             return False
 
         if self.short_tag == other.short_tag:
             return True
 
-        if self.org_tag.lower() == other.org_tag.lower():
+        if self.org_tag.casefold() == other.org_tag.casefold():
             return True
         return False
 

hed/models/query_handler.py

@@ -44,7 +44,7 @@ def __init__(self, expression_string):
         """
         self.tokens = []
         self.at_token = -1
-        self.tree = self._parse(expression_string.lower())
+        self.tree = self._parse(expression_string.casefold())
         self._org_string = expression_string
 
     def search(self, hed_string_obj):

hed/models/string_util.py

@@ -38,7 +38,7 @@ def split_base_tags(hed_string, base_tags, remove_group=False):
             - The second HedString object contains the tags from hed_string that match the base_tags.
     """
 
-    base_tags = [tag.lower() for tag in base_tags]
+    base_tags = [tag.casefold() for tag in base_tags]
     include_groups = 0
     if remove_group:
         include_groups = 2
@@ -70,7 +70,7 @@ def split_def_tags(hed_string, def_names, remove_group=False):
     include_groups = 0
     if remove_group:
         include_groups = 2
-    wildcard_tags = [f"def/{def_name}".lower() for def_name in def_names]
+    wildcard_tags = [f"def/{def_name}".casefold() for def_name in def_names]
     found_things = hed_string.find_wildcard_tags(wildcard_tags, recursive=True, include_groups=include_groups)
     if remove_group:
         found_things = [tag if isinstance(group, HedString) else group for tag, group in found_things]