Merging result of refactoring the models

.github/workflows/ci.yaml

@@ -104,7 +104,7 @@ jobs:
         with:
           coverageCommand: coverage xml
           debug: true
-        uses: paambaati/codeclimate-action@v4.0.0
+        uses: paambaati/codeclimate-action@v5.0.0
         env:
           CC_TEST_REPORTER_ID: ${{ secrets.CC_TEST_REPORTER_ID }}
 

docs/source/conf.py

@@ -87,7 +87,7 @@
     'vcs_pageview_mode': '',
     'style_nav_header_background': 'LightSlateGray',
     # Toc options
-    'collapse_navigation': True,
+    'collapse_navigation': False,
     'sticky_navigation': True,
     'navigation_depth': 4,
     'includehidden': True,

docs/source/index.rst

@@ -21,7 +21,7 @@ Note:  this is a work in progress. More information is coming.
    user_guide.rst
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 4
    :caption: HED Python API:
 
    api2.rst

hed/__init__.py

@@ -12,7 +12,7 @@
 
 from hed.schema.hed_schema import HedSchema
 from hed.schema.hed_schema_group import HedSchemaGroup
-from hed.schema.hed_schema_io import get_schema, load_schema, load_schema_version
+from hed.schema.hed_schema_io import load_schema, load_schema_version
 
 
 # from hed import errors, models, schema, tools, validator

hed/errors/__init__.py

@@ -1,4 +1,4 @@
-from .error_reporter import ErrorHandler, get_printable_issue_string, sort_issues
+from .error_reporter import ErrorHandler, get_printable_issue_string, sort_issues, replace_tag_references
 from .error_types import DefinitionErrors, OnsetErrors, SchemaErrors, SchemaWarnings,  SidecarErrors, \
     ValidationErrors, ColumnErrors
 from .error_types import ErrorContext, ErrorSeverity

hed/errors/error_messages.py

@@ -5,8 +5,7 @@
 """
 
 from hed.errors.error_reporter import hed_error, hed_tag_error
-from hed.errors.error_types import ValidationErrors, SchemaErrors, \
-    SidecarErrors, SchemaWarnings, ErrorSeverity, DefinitionErrors, OnsetErrors, ColumnErrors
+from hed.errors.error_types import ValidationErrors, SidecarErrors, ErrorSeverity, DefinitionErrors, OnsetErrors, ColumnErrors
 
 
 @hed_tag_error(ValidationErrors.UNITS_INVALID)
@@ -165,13 +164,13 @@ def val_error_sidecar_key_missing(invalid_key, category_keys):
 
 @hed_tag_error(ValidationErrors.HED_DEF_EXPAND_INVALID, actual_code=ValidationErrors.DEF_EXPAND_INVALID)
 def val_error_bad_def_expand(tag, actual_def, found_def):
-    return f"A data-recording’s Def-expand tag does not match the given definition." + \
+    return f"A data-recording's Def-expand tag does not match the given definition." + \
            f"Tag: '{tag}'.  Actual Def: {actual_def}.  Found Def: {found_def}"
 
 
 @hed_tag_error(ValidationErrors.HED_DEF_UNMATCHED, actual_code=ValidationErrors.DEF_INVALID)
 def val_error_def_unmatched(tag):
-    return f"A data-recording’s Def tag cannot be matched to definition.  Tag: '{tag}'"
+    return f"A data-recording's Def tag cannot be matched to definition.  Tag: '{tag}'"
 
 
 @hed_tag_error(ValidationErrors.HED_DEF_VALUE_MISSING, actual_code=ValidationErrors.DEF_INVALID)
@@ -186,7 +185,7 @@ def val_error_def_value_extra(tag):
 
 @hed_tag_error(ValidationErrors.HED_DEF_EXPAND_UNMATCHED, actual_code=ValidationErrors.DEF_EXPAND_INVALID)
 def val_error_def_expand_unmatched(tag):
-    return f"A data-recording’s Def-expand tag cannot be matched to definition.  Tag: '{tag}'"
+    return f"A data-recording's Def-expand tag cannot be matched to definition.  Tag: '{tag}'"
 
 
 @hed_tag_error(ValidationErrors.HED_DEF_EXPAND_VALUE_MISSING, actual_code=ValidationErrors.DEF_EXPAND_INVALID)
@@ -228,60 +227,11 @@ def val_warning_capitalization(tag):
 
 @hed_tag_error(ValidationErrors.UNITS_MISSING, default_severity=ErrorSeverity.WARNING)
 def val_warning_default_units_used(tag, default_unit):
+    if default_unit is None:
+        return f"No unit specified on - '{tag}'.  Multiple default values exist and cannot be inferred"
     return f"No unit specified. Using '{default_unit}' as the default - '{tag}'"
 
 
-@hed_error(SchemaErrors.HED_SCHEMA_DUPLICATE_NODE)
-def schema_error_hed_duplicate_node(tag, duplicate_tag_list, section):
-    tag_join_delimiter = "\n\t"
-    return f"Duplicate term '{str(tag)}' used {len(duplicate_tag_list)} places in '{section}' section schema as:" + \
-           f"{tag_join_delimiter}{tag_join_delimiter.join(duplicate_tag_list)}"
-
-
-@hed_error(SchemaErrors.HED_SCHEMA_DUPLICATE_FROM_LIBRARY)
-def schema_error_hed_duplicate_node(tag, duplicate_tag_list, section):
-    tag_join_delimiter = "\n\t"
-    return f"Duplicate term '{str(tag)}' was found in the library and in the standard schema in '{section}' section schema as:" + \
-           f"{tag_join_delimiter}{tag_join_delimiter.join(duplicate_tag_list)}"
-
-
-@hed_error(SchemaErrors.SCHEMA_ATTRIBUTE_INVALID)
-def schema_error_unknown_attribute(attribute_name, source_tag):
-    return f"Attribute '{attribute_name}' used by '{source_tag}' was not defined in the schema, " \
-           f"or was used outside of it's defined class."
-
-
-@hed_error(SchemaWarnings.INVALID_CHARACTERS_IN_DESC, default_severity=ErrorSeverity.WARNING,
-           actual_code=SchemaWarnings.HED_SCHEMA_CHARACTER_INVALID)
-def schema_warning_invalid_chars_desc(desc_string, tag_name, problem_char, char_index):
-    return f"Invalid character '{problem_char}' in desc for '{tag_name}' at position {char_index}.  '{desc_string}"
-
-
-@hed_error(SchemaWarnings.INVALID_CHARACTERS_IN_TAG, default_severity=ErrorSeverity.WARNING,
-           actual_code=SchemaWarnings.HED_SCHEMA_CHARACTER_INVALID)
-def schema_warning_invalid_chars_tag(tag_name, problem_char, char_index):
-    return f"Invalid character '{problem_char}' in tag '{tag_name}' at position {char_index}."
-
-
-@hed_error(SchemaWarnings.INVALID_CAPITALIZATION, default_severity=ErrorSeverity.WARNING)
-def schema_warning_invalid_capitalization(tag_name, problem_char, char_index):
-    return "First character must be a capital letter or number.  " + \
-           f"Found character '{problem_char}' in tag '{tag_name}' at position {char_index}."
-
-
-@hed_error(SchemaWarnings.NON_PLACEHOLDER_HAS_CLASS, default_severity=ErrorSeverity.WARNING)
-def schema_warning_non_placeholder_class(tag_name, invalid_attribute_name):
-    return "Only placeholder nodes('#') can have a unit or value class." + \
-           f"Found {invalid_attribute_name} on {tag_name}"
-
-
-@hed_error(SchemaWarnings.INVALID_ATTRIBUTE, default_severity=ErrorSeverity.ERROR)
-def schema_error_invalid_attribute(tag_name, invalid_attribute_name):
-    return f"'{invalid_attribute_name}' should not be present in a loaded schema, found on '{tag_name}'." \
-           f"Something went very wrong."
-
-
-
 @hed_error(SidecarErrors.BLANK_HED_STRING)
 def sidecar_error_blank_hed_string():
     return "No HED string found for Value or Category column."
@@ -389,6 +339,11 @@ def onset_error_offset_before_onset(tag):
     return f"Offset tag '{tag}' does not have a matching onset."
 
 
+@hed_tag_error(OnsetErrors.ONSET_SAME_DEFS_ONE_ROW, actual_code=ValidationErrors.ONSET_OFFSET_INSET_ERROR)
+def onset_error_same_defs_one_row(tag, def_name):
+    return f"'{tag}' uses name '{def_name}', which was already used at this onset time."
+
+
 @hed_tag_error(OnsetErrors.INSET_BEFORE_ONSET, actual_code=ValidationErrors.ONSET_OFFSET_INSET_ERROR)
 def onset_error_inset_before_onset(tag):
     return f"Inset tag '{tag}' does not have a matching onset."