Merge pull request #798 from IanCa/develop

Add support for loading multiple library schemas with the same prefix

hed/errors/exceptions.py

@@ -40,6 +40,7 @@ class HedExceptions:
     HED_SCHEMA_NODE_NAME_INVALID = 'HED_SCHEMA_NODE_NAME_INVALID'
 
     SCHEMA_DUPLICATE_PREFIX = 'schemaDuplicatePrefix'
+    SCHEMA_DUPLICATE_LIBRARY = "SCHEMA_LIBRARY_INVALID"
     BAD_COLUMN_NAMES = 'BAD_COLUMN_NAMES'
 
 

hed/schema/hed_schema.py

@@ -59,10 +59,19 @@ def library(self):
 
         Returns:
             str: Library name if any.
-
         """
         return self.header_attributes.get(constants.LIBRARY_ATTRIBUTE, "")
 
+    def can_save(self):
+        """ Returns if it's legal to save this schema.
+
+            You cannot save schemas loaded as merged from multiple library schemas.
+
+        Returns:
+            bool: True if this can be saved
+        """
+        return not self.library or "," not in self.library
+
     @property
     def with_standard(self):
         """ The version of the base schema this is extended from, if it exists..
@@ -738,10 +747,14 @@ def _get_attributes_for_section(self, key_class):
     def _add_tag_to_dict(self, long_tag_name, new_entry, key_class):
         # Add the InLibrary attribute to any library schemas as they are loaded
         # These are later removed when they are saved out, if saving unmerged
-        if self.library and (not self.with_standard or (not self.merged and self.with_standard)):
-            # only add it if not already present - This is a rare case
-            if not new_entry.has_attribute(HedKey.InLibrary):
-                new_entry._set_attribute_value(HedKey.InLibrary, self.library)
+        # if self.library and (not self.with_standard or (not self.merged and self.with_standard)):
+        #     # only add it if not already present - This is a rare case
+        #     Todo ian: I think this should be moved up one level for parity with the other loading changes
+        #         .library will be updated to potentially be a list
+        #         Cannot save schema if .library is a list
+        #
+        #     if not new_entry.has_attribute(HedKey.InLibrary):
+        #         new_entry._set_attribute_value(HedKey.InLibrary, self.library)
 
         section = self._sections[key_class]
         return section._add_to_dict(long_tag_name, new_entry)

hed/schema/hed_schema_io.py

@@ -10,18 +10,21 @@
 from hed.schema.schema_io import schema_util
 from hed.schema.hed_schema_group import HedSchemaGroup
 from hed.schema.schema_validation_util import validate_version_string
+from collections import defaultdict
 
 
-MAX_MEMORY_CACHE = 20
+MAX_MEMORY_CACHE = 40
 
 
-def from_string(schema_string, schema_format=".xml", schema_namespace=None):
+def from_string(schema_string, schema_format=".xml", schema_namespace=None, schema=None):
     """ Create a schema from the given string.
 
     Parameters:
         schema_string (str):         An XML or mediawiki file as a single long string.
         schema_format (str):         The schema format of the source schema string.
         schema_namespace (str, None):  The name_prefix all tags in this schema will accept.
+        schema(HedSchema or None): A hed schema to merge this new file into
+                                   It must be a with-standard schema with the same value.
 
     Returns:
         (HedSchema):  The loaded schema.
@@ -39,9 +42,9 @@ def from_string(schema_string, schema_format=".xml", schema_namespace=None):
                            filename=schema_string)
 
     if schema_format.endswith(".xml"):
-        hed_schema = SchemaLoaderXML.load(schema_as_string=schema_string)
+        hed_schema = SchemaLoaderXML.load(schema_as_string=schema_string, schema=schema)
     elif schema_format.endswith(".mediawiki"):
-        hed_schema = SchemaLoaderWiki.load(schema_as_string=schema_string)
+        hed_schema = SchemaLoaderWiki.load(schema_as_string=schema_string, schema=schema)
     else:
         raise HedFileError(HedExceptions.INVALID_EXTENSION, "Unknown schema extension", filename=schema_format)
 
@@ -51,12 +54,14 @@ def from_string(schema_string, schema_format=".xml", schema_namespace=None):
     return hed_schema
 
 
-def load_schema(hed_path=None, schema_namespace=None):
+def load_schema(hed_path=None, schema_namespace=None, schema=None):
     """ Load a schema from the given file or URL path.
 
     Parameters:
         hed_path (str or None): A filepath or url to open a schema from.
         schema_namespace (str or None): The name_prefix all tags in this schema will accept.
+        schema(HedSchema or None): A hed schema to merge this new file into
+                                   It must be a with-standard schema with the same value.
 
     Returns:
         HedSchema: The loaded schema.
@@ -77,9 +82,9 @@ def load_schema(hed_path=None, schema_namespace=None):
         file_as_string = schema_util.url_to_string(hed_path)
         hed_schema = from_string(file_as_string, schema_format=os.path.splitext(hed_path.lower())[1])
     elif hed_path.lower().endswith(".xml"):
-        hed_schema = SchemaLoaderXML.load(hed_path)
+        hed_schema = SchemaLoaderXML.load(hed_path, schema=schema)
     elif hed_path.lower().endswith(".mediawiki"):
-        hed_schema = SchemaLoaderWiki.load(hed_path)
+        hed_schema = SchemaLoaderWiki.load(hed_path, schema=schema)
     else:
         raise HedFileError(HedExceptions.INVALID_EXTENSION, "Unknown schema extension", filename=hed_path)
 
@@ -111,7 +116,11 @@ def _load_schema_version(xml_version=None, xml_folder=None):
     """ Return specified version or latest if not specified.
 
     Parameters:
-        xml_version (str): HED version format string. Expected format: '[schema_namespace:][library_name_]X.Y.Z'.
+        xml_version (str): HED version format string. Expected format: '[schema_namespace:][library_name_][X.Y.Z]'
+                                Further versions can be added comma separated after the version number/library name.
+                                e.g. "lib:library,otherlibrary" will load "library" and "otherlibrary" into "lib:"
+                                The schema namespace must be the same and not repeated if loading multiple merged schemas.
+
         xml_folder (str): Path to a folder containing schema.
 
     Returns:
@@ -124,10 +133,44 @@ def _load_schema_version(xml_version=None, xml_folder=None):
         - The prefix is invalid
     """
     schema_namespace = ""
-    library_name = None
     if xml_version:
         if ":" in xml_version:
             schema_namespace, _, xml_version = xml_version.partition(":")
+
+    if xml_version:
+        xml_versions = xml_version.split(",")
+    # Add a blank entry if we have no xml version
+    else:
+        xml_versions = [""]
+
+    first_schema = _load_schema_version_sub(schema_namespace, xml_versions[0], xml_folder=xml_folder)
+    for version in xml_versions[1:]:
+        _load_schema_version_sub(schema_namespace, version, xml_folder=xml_folder, schema=first_schema)
+    return first_schema
+
+
+def _load_schema_version_sub(schema_namespace="", xml_version=None, xml_folder=None, schema=None):
+    """ Return specified version or latest if not specified.
+
+    Parameters:
+        xml_version (str): HED version format string. Expected format: '[schema_namespace:][library_name_][X.Y.Z]'
+
+        xml_folder (str): Path to a folder containing schema.
+        schema(HedSchema or None): A hed schema to merge this new file into
+                                   It must be a with-standard schema with the same value.
+
+    Returns:
+        HedSchema: The requested HedSchema object.
+
+    :raises HedFileError:
+        - The xml_version is not valid.
+        - The specified version cannot be found or loaded
+        - Other fatal errors loading the schema (These are unlikely if you are not editing them locally)
+        - The prefix is invalid
+    """
+    library_name = None
+
+    if xml_version:
         if "_" in xml_version:
             library_name, _, xml_version = xml_version.rpartition("_")
         elif validate_version_string(xml_version):
@@ -138,7 +181,7 @@ def _load_schema_version(xml_version=None, xml_folder=None):
         if not final_hed_xml_file:
             hed_cache.cache_local_versions(xml_folder)
             final_hed_xml_file = hed_cache.get_hed_version_path(xml_version, library_name, xml_folder)
-        hed_schema = load_schema(final_hed_xml_file)
+        hed_schema = load_schema(final_hed_xml_file, schema=schema)
     except HedFileError as e:
         if e.code == HedExceptions.FILE_NOT_FOUND:
             hed_cache.cache_xml_versions(cache_folder=xml_folder)
@@ -147,7 +190,7 @@ def _load_schema_version(xml_version=None, xml_folder=None):
                 raise HedFileError(HedExceptions.FILE_NOT_FOUND,
                                    f"HED version '{xml_version}' not found in cache: {hed_cache.get_cache_directory()}",
                                    filename=xml_folder)
-            hed_schema = load_schema(final_hed_xml_file)
+            hed_schema = load_schema(final_hed_xml_file, schema=schema)
         else:
             raise e
 
@@ -158,14 +201,14 @@ def _load_schema_version(xml_version=None, xml_folder=None):
 
 
 def load_schema_version(xml_version=None, xml_folder=None):
-    """ Return a HedSchema or HedSchemaGroup extracted from xml_version field.
+    """ Return a HedSchema or HedSchemaGroup extracted from xml_version
 
     Parameters:
         xml_version (str or list or None): List or str specifying which official HED schemas to use.
                                            An empty string returns the latest version
                                            A json str format is also supported,
                                            based on the output of HedSchema.get_formatted_version
-                                           Basic format: '[schema_namespace:][library_name_]X.Y.Z'.
+                                           Basic format: '[schema_namespace:][library_name_][X.Y.Z]'.
         xml_folder (str): Path to a folder containing schema.
 
     Returns:
@@ -185,10 +228,41 @@ def load_schema_version(xml_version=None, xml_folder=None):
         except json.decoder.JSONDecodeError as e:
             raise HedFileError(HedExceptions.CANNOT_PARSE_JSON, str(e), xml_version) from e
     if xml_version and isinstance(xml_version, list):
-        schemas = [_load_schema_version(xml_version=version, xml_folder=xml_folder) for version in xml_version]
+        xml_versions = parse_version_list(xml_version)
+        schemas = [_load_schema_version(xml_version=version, xml_folder=xml_folder) for version in xml_versions.values()]
         if len(schemas) == 1:
             return schemas[0]
 
         return HedSchemaGroup(schemas)
     else:
         return _load_schema_version(xml_version=xml_version, xml_folder=xml_folder)
+
+
+def parse_version_list(xml_version_list):
+    """Takes a list of xml versions and returns a dictionary split by prefix
+
+        e.g. ["score", "testlib"] will return {"": "score, testlib"}
+        e.g. ["score", "testlib", "ol:otherlib"] will return {"": "score, testlib", "ol:": "otherlib"}
+
+    Parameters:
+        xml_version_list (list): List of str specifying which hed schemas to use
+
+    Returns:
+        HedSchema or HedSchemaGroup: The schema or schema group extracted.
+    """
+    out_versions = defaultdict(list)
+    for version in xml_version_list:
+        schema_namespace = ""
+        if version and ":" in version:
+            schema_namespace, _, version = version.partition(":")
+
+        if version is None:
+            version = ""
+        if version in out_versions[schema_namespace]:
+            raise HedFileError(HedExceptions.SCHEMA_DUPLICATE_LIBRARY, f"Attempting to load the same library '{version}' twice: {out_versions[schema_namespace]}",
+                               filename=None)
+        out_versions[schema_namespace].append(version)
+
+    out_versions = {key: ",".join(value) if not key else f"{key}:" + ",".join(value) for key, value in out_versions.items()}
+
+    return out_versions

hed/schema/schema_attribute_validators.py

@@ -208,7 +208,7 @@ def in_library_check(hed_schema, tag_entry, attribute_name):
     issues = []
 
     library = tag_entry.attributes.get(attribute_name, "")
-    if hed_schema.library != library:
+    if library not in hed_schema.library.split(","):
         issues += ErrorHandler.format_error(SchemaAttributeErrors.SCHEMA_IN_LIBRARY_INVALID,
                                             tag_entry.name,
                                             library)

hed/schema/schema_io/base2schema.py

@@ -1,8 +1,10 @@
 import copy
 from hed.errors.exceptions import HedFileError, HedExceptions
 from hed.schema import HedSchema
+from hed.schema.hed_schema_constants import HedKey
 from abc import abstractmethod, ABC
 from hed.schema import schema_validation_util
+from hed.schema import hed_schema_constants
 
 
 class SchemaLoader(ABC):
@@ -12,20 +14,21 @@ class SchemaLoader(ABC):
 
         SchemaLoaderXML(filename) will load just the header_attributes
     """
-    def __init__(self, filename, schema_as_string=None):
+    def __init__(self, filename, schema_as_string=None, schema=None):
         """Loads the given schema from one of the two parameters.
 
         Parameters:
             filename(str or None): A valid filepath or None
             schema_as_string(str or None): A full schema as text or None
+            schema(HedSchema or None): A hed schema to merge this new file into
+                                       It must be a with-standard schema with the same value.
         """
         if schema_as_string and filename:
             raise HedFileError(HedExceptions.BAD_PARAMETERS, "Invalid parameters to schema creation.",
                                filename)
-
         self.filename = filename
         self.schema_as_string = schema_as_string
-
+        self.appending_to_schema = False
         try:
             self.input_data = self._open_file()
         except OSError as e:
@@ -34,11 +37,28 @@ def __init__(self, filename, schema_as_string=None):
             raise HedFileError(HedExceptions.FILE_NOT_FOUND, str(e), filename)
         except ValueError as e:
             raise HedFileError(HedExceptions.FILE_NOT_FOUND, str(e), filename)
-
-        self._schema = HedSchema()
-        self._schema.filename = filename
+
+        # self._schema.filename = filename
         hed_attributes = self._get_header_attributes(self.input_data)
         schema_validation_util.validate_attributes(hed_attributes, filename=self.filename)
+
+        withStandard = hed_attributes.get(hed_schema_constants.WITH_STANDARD_ATTRIBUTE, "")
+        self.library = hed_attributes.get(hed_schema_constants.LIBRARY_ATTRIBUTE, "")
+        if not schema:
+            self._schema = HedSchema()
+        else:
+            self._schema = schema
+            self.appending_to_schema = True
+            if not self._schema.with_standard:
+                raise HedFileError(HedExceptions.SCHEMA_DUPLICATE_PREFIX,
+                                   "Trying to load multiple normal schemas as a merged one with the same namespace.  "
+                                   "Ensure schemas have the withStandard header attribute set",
+                                   self.filename)
+            elif withStandard != self._schema.with_standard:
+                raise HedFileError(HedExceptions.BAD_WITH_STANDARD_VERSION,
+                                   "When merging two schemas without a schema namespace, you they must have the same withStandard value.", self.filename)
+            hed_attributes[hed_schema_constants.LIBRARY_ATTRIBUTE] = self._schema.library + f",{self.library}"
+        self._schema.filename = filename
         self._schema.header_attributes = hed_attributes
         self._loading_merged = False
 
@@ -48,16 +68,19 @@ def schema(self):
         return self._schema
 
     @classmethod
-    def load(cls, filename=None, schema_as_string=None):
+    def load(cls, filename=None, schema_as_string=None, schema=None):
         """ Loads and returns the schema, including partnered schema if applicable.
 
         Parameters:
             filename(str or None): A valid filepath or None
             schema_as_string(str or None): A full schema as text or None
+            schema(HedSchema or None): A hed schema to merge this new file into
+                           It must be a with-standard schema with the same value.
+
         Returns:
             schema(HedSchema): The new schema
         """
-        loader = cls(filename, schema_as_string)
+        loader = cls(filename, schema_as_string, schema)
         return loader._load()
 
     def _load(self):
@@ -68,7 +91,7 @@ def _load(self):
         """
         self._loading_merged = True
         # Do a full load of the standard schema if this is a partnered schema
-        if self._schema.with_standard and not self._schema.merged:
+        if not self.appending_to_schema and self._schema.with_standard and not self._schema.merged:
             from hed.schema.hed_schema_io import load_schema_version
             saved_attr = self._schema.header_attributes
             try:
@@ -102,3 +125,14 @@ def _get_header_attributes(self, input_data):
     def _parse_data(self):
         """Puts the input data into the new schema"""
         pass
+
+    def _add_to_dict_base(self, entry, key_class):
+        if not entry.has_attribute(HedKey.InLibrary) and self.appending_to_schema and self._schema.merged:
+            return None
+
+        if self.library and (not self._schema.with_standard or (not self._schema.merged and self._schema.with_standard)):
+            # only add it if not already present - This is a rare case
+            if not entry.has_attribute(HedKey.InLibrary):
+                entry._set_attribute_value(HedKey.InLibrary, self.library)
+
+        return self._schema._add_tag_to_dict(entry.name, entry, key_class)

hed/schema/schema_io/schema2base.py

@@ -1,5 +1,6 @@
 """Baseclass for mediawiki/xml writers"""
 from hed.schema.hed_schema_constants import HedSectionKey, HedKey
+from hed.errors.exceptions import HedFileError, HedExceptions
 
 
 class Schema2Base:
@@ -29,6 +30,10 @@ def process_schema(cls, hed_schema, save_merged=False):
             Varies based on inherited class
 
         """
+        if not hed_schema.can_save():
+            raise HedFileError(HedExceptions.SCHEMA_LIBRARY_INVALID,
+                               "Cannot save a schema merged from multiple library schemas",
+                               hed_schema.filename)
         saver = cls()
         saver._save_lib = False
         saver._save_base = False