class SchemaAdapter():
"""
Manage a biothings_schema.Schema instance.
Provide native type custom format schema class lists.
"""
def __init__(self, doc=None):
contexts = ESSchema.gather_field('@context')
self._schema = SchemaParser(doc, contexts)
self._classes_defs = self._schema.list_all_defined_classes()
self._classes_refs = self._schema.list_all_referenced_classes()
def __getattr__(self, attr):
return getattr(self._schema, attr)
def get_class_defs(self):
# get only classes defined in this schema
# each {} will have a field ref: false
return list(self._get_class_defs().values())
def get_class_refs(self):
# get only classes referenced outside this schema
# each {} will have a field ref: true
return list(self._get_class_refs().values())
def get_classes(self):
# get all classes and label them if they are referenced
defs = self._get_class_defs()
refs = self._get_class_refs()
ans = {}
ans.update(defs)
ans.update(refs)
return list(ans.values())
@staticmethod
def _get_class_info(schema_class):
ans = {} # biothings_schema.SchemaClass -> { ... }
schema_class = SchemaClassWrapper(schema_class)
for key in ('name', 'uri', 'prefix', 'label', 'description',
'parent_classes', 'properties', 'validation'):
try:
ans[key] = getattr(schema_class, key)
except AttributeError:
pass
logging.info(ans['name'])
return ans
def _get_class_defs(self):
ans = {}
for schema_class in self._classes_defs:
if schema_class.name not in ans:
_schema_class = self._get_class_info(schema_class)
_schema_class['ref'] = False
ans[schema_class.name] = _schema_class
return ans
def _get_class_refs(self):
ans = {}
for schema_class in self._classes_refs:
if schema_class.name not in ans:
_schema_class = self._get_class_info(schema_class)
_schema_class['ref'] = True
ans[schema_class.name] = _schema_class
return ans
class SchemaAdapter():
"""
Manage a biothings_schema.Schema instance.
Provide native type custom format schema class lists.
"""
def __init__(self, doc=None, **kwargs):
contexts = ESSchema.gather_field('@context')
self._schema = SchemaParser(schema=doc, context=contexts, **kwargs)
self._classes_defs = self._schema.list_all_defined_classes()
self._classes_refs = self._schema.list_all_referenced_classes()
def __getattr__(self, attr):
return getattr(self._schema, attr)
def get_class_defs(self):
"""get only classes defined in this schema
each {} will have a field ref: false"""
return list(self._get_class_defs().values())
def get_class_refs(self):
"""get only classes referenced outside this schema
each {} will have a field ref: true"""
return list(self._get_class_refs().values())
def get_classes(self, include_ref=True):
"""get all classes and label them if they are referenced
if include_ref is False, only "defined" classes are included.
"""
defs = self._get_class_defs()
ans = {}
ans.update(defs)
if include_ref:
refs = self._get_class_refs()
ans.update(refs)
return list(ans.values())
@staticmethod
def _get_class_info(schema_class):
ans = {} # biothings_schema.SchemaClass -> { ... }
schema_class = SchemaClassWrapper(schema_class)
for key in ('name', 'uri', 'prefix', 'label', 'description',
'parent_classes', 'properties', 'validation'):
try:
ans[key] = getattr(schema_class, key)
except AttributeError:
pass
logging.info(ans['name'])
return ans
def _get_class_defs(self):
ans = {}
for schema_class in self._classes_defs:
if schema_class.name not in ans:
_schema_class = self._get_class_info(schema_class)
_schema_class['ref'] = False
ans[schema_class.name] = _schema_class
return ans
def _get_class_refs(self):
ans = {}
for schema_class in self._classes_refs:
if schema_class.name not in ans:
_schema_class = self._get_class_info(schema_class)
_schema_class['ref'] = True
ans[schema_class.name] = _schema_class
return ans
def has_validation_error(self):
"""return True if there is at least one validation error."""
for err in self._schema.validator.validation_errors:
if not err.warning:
return True
return False
def get_validation_errors(self):
"""return validation errors as a list of dictionaries"""
return [
err.to_dict() for err in self._schema.validator.validation_errors
]