Comment out owl related code pending new version

hed/schema/hed_schema.py

@@ -6,8 +6,8 @@
 from hed.schema.schema_io import schema_util
 from hed.schema.schema_io.schema2xml import Schema2XML
 from hed.schema.schema_io.schema2wiki import Schema2Wiki
-from hed.schema.schema_io.schema2owl import Schema2Owl
-from hed.schema.schema_io.owl_constants import ext_to_format
+# from hed.schema.schema_io.schema2owl import Schema2Owl
+# from hed.schema.schema_io.owl_constants import ext_to_format
 from hed.schema.hed_schema_section import (HedSchemaSection, HedSchemaTagSection, HedSchemaUnitClassSection,
                                            HedSchemaUnitSection)
 from hed.errors import ErrorHandler
@@ -246,25 +246,25 @@ def get_as_mediawiki_string(self, save_merged=False):
         output_strings = Schema2Wiki.process_schema(self, save_merged)
         return '\n'.join(output_strings)
 
-    def get_as_owl_string(self, save_merged=False, file_format="owl"):
-        """ Return the schema to a mediawiki string.
-
-        Parameters:
-            save_merged (bool): If True, this will save the schema as a merged schema if it is a "withStandard" schema.
-                                If it is not a "withStandard" schema, this setting has no effect.
-            file_format(str or None): Override format from filename extension.
-                Accepts any value rdflib accepts(We fully support "turtle", "xml"("owl" also accepted) and "json-ld").
-                Other values should work, but aren't as fully supported.
-        Returns:
-            str:  The schema as a string in mediawiki format.
-
-        :raises rdflib.plugin.PluginException:
-            - Invalid format of file_format.  Make sure you use a supported RDF format.
-        """
-        if file_format == "owl":
-            file_format = "xml"
-        rdf_data = Schema2Owl.process_schema(self, save_merged)
-        return rdf_data.serialize(format=file_format)
+    # def get_as_owl_string(self, save_merged=False, file_format="owl"):
+    #     """ Return the schema to a mediawiki string.
+    #
+    #     Parameters:
+    #         save_merged (bool): If True, this will save the schema as a merged schema if it is a "withStandard" schema.
+    #                             If it is not a "withStandard" schema, this setting has no effect.
+    #         file_format(str or None): Override format from filename extension.
+    #             Accepts any value rdflib accepts(We fully support "turtle", "xml"("owl" also accepted) and "json-ld").
+    #             Other values should work, but aren't as fully supported.
+    #     Returns:
+    #         str:  The schema as a string in mediawiki format.
+    #
+    #     :raises rdflib.plugin.PluginException:
+    #         - Invalid format of file_format.  Make sure you use a supported RDF format.
+    #     """
+    #     if file_format == "owl":
+    #         file_format = "xml"
+    #     rdf_data = Schema2Owl.process_schema(self, save_merged)
+    #     return rdf_data.serialize(format=file_format)
 
     def get_as_xml_string(self, save_merged=True):
         """ Return the schema to an XML string.
@@ -298,32 +298,32 @@ def save_as_mediawiki(self, filename, save_merged=False):
                 opened_file.write(string)
                 opened_file.write('\n')
 
-    def save_as_owl(self, filename, save_merged=False, file_format=None):
-        """ Save as json to a file.
-
-        filename: str
-            Save the file here
-        save_merged: bool
-            If True, this will save the schema as a merged schema if it is a "withStandard" schema.
-            If it is not a "withStandard" schema, this setting has no effect.
-        file_format(str or None): Required for owl formatted files other than the following:
-            .ttl: turtle
-            .owl: xml
-            .json-ld: json-ld
-
-        :raises OSError:
-            - File cannot be saved for some reason
-
-        :raises rdflib.plugin.PluginException:
-            - Invalid format of file_format.  Make sure you use a supported RDF format.
-        """
-        ext = os.path.splitext(filename.lower())[1]
-        if ext in ext_to_format and file_format is None:
-            file_format = ext_to_format[ext]
-        if file_format == "owl":
-            file_format = "xml"
-        rdf_data = Schema2Owl.process_schema(self, save_merged)
-        rdf_data.serialize(filename, format=file_format)
+    # def save_as_owl(self, filename, save_merged=False, file_format=None):
+    #     """ Save as json to a file.
+    #
+    #     filename: str
+    #         Save the file here
+    #     save_merged: bool
+    #         If True, this will save the schema as a merged schema if it is a "withStandard" schema.
+    #         If it is not a "withStandard" schema, this setting has no effect.
+    #     file_format(str or None): Required for owl formatted files other than the following:
+    #         .ttl: turtle
+    #         .owl: xml
+    #         .json-ld: json-ld
+    #
+    #     :raises OSError:
+    #         - File cannot be saved for some reason
+    #
+    #     :raises rdflib.plugin.PluginException:
+    #         - Invalid format of file_format.  Make sure you use a supported RDF format.
+    #     """
+    #     ext = os.path.splitext(filename.lower())[1]
+    #     if ext in ext_to_format and file_format is None:
+    #         file_format = ext_to_format[ext]
+    #     if file_format == "owl":
+    #         file_format = "xml"
+    #     rdf_data = Schema2Owl.process_schema(self, save_merged)
+    #     rdf_data.serialize(filename, format=file_format)
 
     def save_as_xml(self, filename, save_merged=True):
         """ Save as XML to a file.

hed/schema/hed_schema_io.py

@@ -5,15 +5,15 @@
 
 from hed.schema.schema_io.xml2schema import SchemaLoaderXML
 from hed.schema.schema_io.wiki2schema import SchemaLoaderWiki
-from hed.schema.schema_io.owl2schema import SchemaLoaderOWL
+# from hed.schema.schema_io.owl2schema import SchemaLoaderOWL
 from hed.schema import hed_cache
 
 from hed.errors.exceptions import HedFileError, HedExceptions
 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
-from hed.schema.schema_io.owl_constants import ext_to_format
+# from hed.schema.schema_io.owl_constants import ext_to_format
 from urllib.error import URLError
 
 MAX_MEMORY_CACHE = 40
@@ -26,7 +26,6 @@ def from_string(schema_string, schema_format=".xml", schema_namespace=None, sche
         schema_string (str):         An XML, mediawiki or OWL, file as a single long string
         schema_format (str):         The schema format of the source schema string.
             Allowed normal values: .mediawiki, .xml
-            Allowed owl values: xml, owl, pretty-xml, turtle (or any other value rdflib supports)
         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.
@@ -54,9 +53,9 @@ def from_string(schema_string, schema_format=".xml", schema_namespace=None, sche
         hed_schema = SchemaLoaderXML.load(schema_as_string=schema_string, schema=schema, name=name)
     elif schema_format.endswith(".mediawiki"):
         hed_schema = SchemaLoaderWiki.load(schema_as_string=schema_string, schema=schema, name=name)
-    elif schema_format:
-        hed_schema = SchemaLoaderOWL.load(schema_as_string=schema_string, schema=schema, file_format=schema_format,
-                                          name=name)
+    # elif schema_format:
+    #     hed_schema = SchemaLoaderOWL.load(schema_as_string=schema_string, schema=schema, file_format=schema_format,
+    #                                       name=name)
     else:
         raise HedFileError(HedExceptions.INVALID_EXTENSION, f"Unknown schema extension {schema_format}", filename=name)
 
@@ -65,18 +64,14 @@ def from_string(schema_string, schema_format=".xml", schema_namespace=None, sche
     return hed_schema
 
 
-def load_schema(hed_path, schema_namespace=None, schema=None, file_format=None, name=None):
+def load_schema(hed_path, schema_namespace=None, schema=None, name=None):
     """ Load a schema from the given file or URL path.
 
     Parameters:
         hed_path (str): 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.
-        file_format(str or None): Required for owl formatted files other than the following:
-            .ttl: turtle
-            .owl: xml
-            .json-ld: json-ld
         name(str or None): User supplied identifier for this schema
 
     Returns:
@@ -100,10 +95,10 @@ def load_schema(hed_path, schema_namespace=None, schema=None, file_format=None,
         except URLError as e:
             raise HedFileError(HedExceptions.URL_ERROR, str(e), hed_path) from e
         hed_schema = from_string(file_as_string, schema_format=os.path.splitext(hed_path.lower())[1], name=name)
-    elif ext in ext_to_format:
-        hed_schema = SchemaLoaderOWL.load(hed_path, schema=schema, file_format=ext_to_format[ext], name=name)
-    elif file_format:
-        hed_schema = SchemaLoaderOWL.load(hed_path, schema=schema, file_format=file_format, name=name)
+    # elif ext in ext_to_format:
+    #     hed_schema = SchemaLoaderOWL.load(hed_path, schema=schema, file_format=ext_to_format[ext], name=name)
+    # elif file_format:
+    #     hed_schema = SchemaLoaderOWL.load(hed_path, schema=schema, file_format=file_format, name=name)
     elif hed_path.lower().endswith(".xml"):
         hed_schema = SchemaLoaderXML.load(hed_path, schema=schema, name=name)
     elif hed_path.lower().endswith(".mediawiki"):