Merge pull request #877 from IanCa/dev_deprecated

Update deprecatedFrom validation and tests

hed/errors/error_types.py

@@ -127,7 +127,10 @@ class SchemaWarnings:
 class SchemaAttributeErrors:
     SCHEMA_ATTRIBUTE_INVALID = 'SCHEMA_ATTRIBUTE_INVALID'
     SCHEMA_ATTRIBUTE_VALUE_INVALID = 'SCHEMA_ATTRIBUTE_VALUE_INVALID'
+    SCHEMA_DEPRECATION_ERROR = 'SCHEMA_DEPRECATION_ERROR'
     SCHEMA_DEPRECATED_INVALID = "SCHEMA_DEPRECATED_INVALID"
+    SCHEMA_CHILD_OF_DEPRECATED = "SCHEMA_CHILD_OF_DEPRECATED"
+    SCHEMA_ATTRIBUTE_VALUE_DEPRECATED = "SCHEMA_ATTRIBUTE_VALUE_DEPRECATED"
     SCHEMA_SUGGESTED_TAG_INVALID = "SCHEMA_SUGGESTED_TAG_INVALID"
 
     SCHEMA_UNIT_CLASS_INVALID = "SCHEMA_UNIT_CLASS_INVALID"
@@ -136,7 +139,7 @@ class SchemaAttributeErrors:
     SCHEMA_IN_LIBRARY_INVALID = "SCHEMA_IN_LIBRARY_INVALID"
 
     SCHEMA_DEFAULT_UNITS_INVALID = "SCHEMA_DEFAULT_UNITS_INVALID"
-    SCHEMA_CHILD_OF_DEPRECATED = "SCHEMA_CHILD_OF_DEPRECATED"
+    SCHEMA_DEFAULT_UNITS_DEPRECATED = "SCHEMA_DEFAULT_UNITS_DEPRECATED"
     SCHEMA_CONVERSION_FACTOR_NOT_POSITIVE = "SCHEMA_CONVERSION_FACTOR_NOT_POSITIVE"
 
 

hed/errors/schema_error_messages.py

@@ -49,17 +49,24 @@ def schema_warning_non_placeholder_class(tag_name, invalid_attribute_name):
 
 
 @hed_error(SchemaAttributeErrors.SCHEMA_DEPRECATED_INVALID,
-           actual_code=SchemaAttributeErrors.SCHEMA_ATTRIBUTE_VALUE_INVALID)
+           actual_code=SchemaAttributeErrors.SCHEMA_DEPRECATION_ERROR)
 def schema_error_SCHEMA_DEPRECATED_INVALID(tag_name, invalid_deprecated_version):
     return f"'{tag_name}' has invalid or unknown value in attribute deprecatedFrom: '{invalid_deprecated_version}'."
 
 
 @hed_error(SchemaAttributeErrors.SCHEMA_CHILD_OF_DEPRECATED,
-           actual_code=SchemaAttributeErrors.SCHEMA_ATTRIBUTE_VALUE_INVALID)
+           actual_code=SchemaAttributeErrors.SCHEMA_DEPRECATION_ERROR)
 def schema_error_SCHEMA_CHILD_OF_DEPRECATED(deprecated_tag, non_deprecated_child):
     return f"Deprecated tag '{deprecated_tag}' has a child that is not deprecated: '{non_deprecated_child}'."
 
 
+@hed_error(SchemaAttributeErrors.SCHEMA_ATTRIBUTE_VALUE_DEPRECATED,
+           actual_code=SchemaAttributeErrors.SCHEMA_DEPRECATION_ERROR)
+def schema_error_SCHEMA_ATTRIBUTE_VALUE_DEPRECATED(tag, deprecated_suggestion, attribute_name):
+    return (f"Tag '{tag}' {attribute_name} uses '{deprecated_suggestion}' which has been deprecated "
+            f"and an alternative method of tagging should be used.")
+
+
 @hed_error(SchemaAttributeErrors.SCHEMA_SUGGESTED_TAG_INVALID,
            actual_code=SchemaAttributeErrors.SCHEMA_ATTRIBUTE_VALUE_INVALID)
 def schema_error_SCHEMA_SUGGESTED_TAG_INVALID(suggestedTag, invalidSuggestedTag, attribute_name):
@@ -85,6 +92,12 @@ def schema_error_SCHEMA_DEFAULT_UNITS_INVALID(tag, bad_unit, valid_units):
     return f"Tag '{tag}' has an invalid defaultUnit '{bad_unit}'.  Valid units are: '{valid_units}'."
 
 
+@hed_error(SchemaAttributeErrors.SCHEMA_DEFAULT_UNITS_DEPRECATED,
+           actual_code=SchemaAttributeErrors.SCHEMA_DEPRECATION_ERROR)
+def schema_error_SCHEMA_DEFAULT_UNITS_DEPRECATED(unit_class, bad_unit):
+    return f"Unit class '{unit_class}' defaultUnit '{bad_unit}' is deprecated.  Please find an alternative default."
+
+
 @hed_error(SchemaAttributeErrors.SCHEMA_CONVERSION_FACTOR_NOT_POSITIVE,
            actual_code=SchemaAttributeErrors.SCHEMA_ATTRIBUTE_VALUE_INVALID)
 def schema_error_SCHEMA_CONVERSION_FACTOR_NOT_POSITIVE(tag, conversion_factor):

hed/schema/schema_attribute_validators.py

@@ -14,7 +14,7 @@
 from hed.errors.error_types import SchemaWarnings, ValidationErrors, SchemaAttributeErrors
 from hed.errors.error_reporter import ErrorHandler
 from hed.schema.hed_cache import get_hed_versions
-from hed.schema.hed_schema_constants import HedKey, character_types
+from hed.schema.hed_schema_constants import HedKey, character_types, HedSectionKey
 from hed.schema.schema_validation_util import schema_version_for_library
 from semantic_version import Version
 
@@ -39,6 +39,36 @@ def tag_is_placeholder_check(hed_schema, tag_entry, attribute_name):
     return issues
 
 
+def attribute_is_deprecated(hed_schema, tag_entry, attribute_name):
+    """ Check if the attribute is deprecated.
+
+        does not check value.
+
+    Parameters:
+        hed_schema (HedSchema): The schema to use for validation
+        tag_entry (HedSchemaEntry): The schema entry for this tag.
+        attribute_name (str): The name of this attribute
+
+    Returns:
+        list: A list of issues. Each issue is a dictionary.
+    """
+    issues = []
+    # Attributes has to check properties
+    section_key = HedSectionKey.Attributes
+    if tag_entry.section_key == HedSectionKey.Attributes:
+        section_key = HedSectionKey.Properties
+
+    attribute_entry = hed_schema.get_tag_entry(attribute_name, section_key)
+    if (attribute_entry and attribute_entry.has_attribute(HedKey.DeprecatedFrom)
+            and not tag_entry.has_attribute(HedKey.DeprecatedFrom)):
+        issues += ErrorHandler.format_error(SchemaAttributeErrors.SCHEMA_ATTRIBUTE_VALUE_DEPRECATED,
+                                            tag_entry.name,
+                                            attribute_entry.name,
+                                            attribute_name)
+
+    return issues
+
+
 # todo: This needs to be refactored, these next several functions are near identical
 def tag_exists_check(hed_schema, tag_entry, attribute_name):
     """ Check if the list of possible tags exists in the schema.
@@ -56,11 +86,18 @@ def tag_exists_check(hed_schema, tag_entry, attribute_name):
     possible_tags = tag_entry.attributes.get(attribute_name, "")
     split_tags = possible_tags.split(",")
     for org_tag in split_tags:
-        if org_tag and org_tag not in hed_schema.tags:
+        org_entry = hed_schema.tags.get(org_tag)
+        if org_tag and not org_entry:
             issues += ErrorHandler.format_error(SchemaAttributeErrors.SCHEMA_SUGGESTED_TAG_INVALID,
                                                 tag_entry.name,
                                                 org_tag,
                                                 attribute_name)
+        elif (org_entry and org_entry.has_attribute(HedKey.DeprecatedFrom)
+              and not tag_entry.has_attribute(HedKey.DeprecatedFrom)):
+            issues += ErrorHandler.format_error(SchemaAttributeErrors.SCHEMA_ATTRIBUTE_VALUE_DEPRECATED,
+                                                tag_entry.name,
+                                                org_tag,
+                                                attribute_name)
 
     return issues
 
@@ -70,11 +107,18 @@ def unit_class_exists(hed_schema, tag_entry, attribute_name):
     possible_unit_classes = tag_entry.attributes.get(attribute_name, "")
     split_tags = possible_unit_classes.split(",")
     for org_tag in split_tags:
-        if org_tag and org_tag not in hed_schema.unit_classes:
+        unit_class_entry = hed_schema.unit_classes.get(org_tag)
+        if org_tag and not unit_class_entry:
             issues += ErrorHandler.format_error(SchemaAttributeErrors.SCHEMA_UNIT_CLASS_INVALID,
                                                 tag_entry.name,
                                                 org_tag,
                                                 attribute_name)
+        elif (unit_class_entry and unit_class_entry.has_attribute(HedKey.DeprecatedFrom)
+              and not tag_entry.has_attribute(HedKey.DeprecatedFrom)):
+            issues += ErrorHandler.format_error(SchemaAttributeErrors.SCHEMA_ATTRIBUTE_VALUE_DEPRECATED,
+                                                tag_entry.name,
+                                                org_tag,
+                                                attribute_name)
 
     return issues
 
@@ -83,24 +127,38 @@ def value_class_exists(hed_schema, tag_entry, attribute_name):
     issues = []
     possible_value_classes = tag_entry.attributes.get(attribute_name, "")
     split_tags = possible_value_classes.split(",")
+
     for org_tag in split_tags:
-        if org_tag and org_tag not in hed_schema.value_classes:
+        value_class_entry = hed_schema.value_classes.get(org_tag)
+        if org_tag and not value_class_entry:
             issues += ErrorHandler.format_error(SchemaAttributeErrors.SCHEMA_VALUE_CLASS_INVALID,
                                                 tag_entry.name,
                                                 org_tag,
                                                 attribute_name)
+        elif (value_class_entry and value_class_entry.has_attribute(HedKey.DeprecatedFrom)
+              and not tag_entry.has_attribute(HedKey.DeprecatedFrom)):
+            issues += ErrorHandler.format_error(SchemaAttributeErrors.SCHEMA_ATTRIBUTE_VALUE_DEPRECATED,
+                                                tag_entry.name,
+                                                org_tag,
+                                                attribute_name)
 
     return issues
 
 
 def unit_exists(hed_schema, tag_entry, attribute_name):
     issues = []
-    default_unit = tag_entry.attributes.get(attribute_name, "")
-    if default_unit and default_unit not in tag_entry.derivative_units:
+    unit = tag_entry.attributes.get(attribute_name, "")
+    unit_entry = tag_entry.derivative_units.get(unit)
+    if unit and not unit_entry:
         issues += ErrorHandler.format_error(SchemaAttributeErrors.SCHEMA_DEFAULT_UNITS_INVALID,
                                             tag_entry.name,
-                                            default_unit,
+                                            unit,
                                             tag_entry.units)
+    elif (unit_entry and unit_entry.has_attribute(HedKey.DeprecatedFrom)
+          and not tag_entry.has_attribute(HedKey.DeprecatedFrom)):
+        issues += ErrorHandler.format_error(SchemaAttributeErrors.SCHEMA_DEFAULT_UNITS_DEPRECATED,
+                                            tag_entry.name,
+                                            unit_entry.name)
 
     return issues
 

hed/schema/schema_compliance.py

@@ -86,7 +86,9 @@ def check_attributes(self):
             for tag_entry in self.hed_schema[section_key].values():
                 self.error_handler.push_error_context(ErrorContext.SCHEMA_TAG, tag_entry.name)
                 for attribute_name in tag_entry.attributes:
-                    validators = self.attribute_validators.get(attribute_name, [])
+                    # Always check deprecated
+                    validators = self.attribute_validators.get(attribute_name, []) \
+                                  + [schema_attribute_validators.attribute_is_deprecated]
                     for validator in validators:
                         self.error_handler.push_error_context(ErrorContext.SCHEMA_ATTRIBUTE, attribute_name)
                         new_issues = validator(self.hed_schema, tag_entry, attribute_name)