linkml 1.8.3__py3-none-any.whl → 1.8.5__py3-none-any.whl

linkml/generators/graphqlgen.py

@@ -1,11 +1,14 @@
+import logging
 import os
+import re
 from dataclasses import dataclass
 
 import click
-from linkml_runtime.linkml_model.meta import ClassDefinition, SlotDefinition
+from linkml_runtime.linkml_model.meta import ClassDefinition, EnumDefinition, SlotDefinition
 from linkml_runtime.utils.formatutils import camelcase, lcamelcase
 
 from linkml._version import __version__
+from linkml.generators.common.naming import NameCompatibility, NamingProfiles
 from linkml.utils.generator import Generator, shared_arguments
 
 
@@ -19,6 +22,13 @@ class GraphqlGenerator(Generator):
     uses_schemaloader = True
     requires_metamodel = False
 
+    strict_naming: bool = False
+    _permissible_value_valid_characters = re.compile("^[_A-Za-z][_0-9A-Za-z]*?$")
+
+    def __post_init__(self):
+        self.name_compatiblity = NameCompatibility(profile=NamingProfiles.graphql, do_not_fix=self.strict_naming)
+        super().__post_init__()
+
     def visit_schema(self, **kwargs) -> str:
         return self.generate_header()
 
@@ -50,13 +60,35 @@ class GraphqlGenerator(Generator):
             slotrange = slotrange + "!"
         return f"\n    {lcamelcase(aliased_slot_name)}: {slotrange}"
 
+    def visit_enum(self, enum: EnumDefinition):
+        if enum.permissible_values:
+            permissible_values = []
+            for value in enum.permissible_values:
+                permissible_values.append(self.name_compatiblity.compatible(value))
+            values = "\n    ".join(permissible_values)
+            return f"enum {camelcase(enum.name).replace(' ','')}\n  {{\n    {values}\n  }}\n\n"
+        else:
+            logging.warning(
+                f"Enumeration {enum.name} using `reachable_from` instead of `permissible_values` "
+                + "to specify permissible values is not supported yet."
+                + "Enumeration {enum.name} will be silently ignored!!"
+            )
+            return ""
+
 
 @shared_arguments(GraphqlGenerator)
 @click.command(name="graphql")
+@click.option(
+    "--strict-naming",
+    is_flag=True,
+    show_default=True,
+    help="Treat warnings about invalid names or schema elements as errors.",
+)
 @click.version_option(__version__, "-V", "--version")
 def cli(yamlfile, **args):
     """Generate graphql representation of a LinkML model"""
-    print(GraphqlGenerator(yamlfile, **args).serialize(**args))
+    generator = GraphqlGenerator(yamlfile, **args)
+    print(generator.serialize(**args))
 
 
 if __name__ == "__main__":

linkml/generators/jsonschemagen.py

@@ -24,6 +24,8 @@ from linkml._version import __version__
 from linkml.generators.common.type_designators import get_type_designator_value
 from linkml.utils.generator import Generator, shared_arguments
 
+logger = logging.getLogger(__name__)
+
 # Map from underlying python data type to json equivalent
 # Note: The underlying types are a union of any built-in python datatype + any type defined in
 #       linkml-runtime/utils/metamodelcore.py
@@ -222,14 +224,14 @@ class JsonSchemaGenerator(Generator):
 
     def __post_init__(self):
         if self.topClass:
-            logging.warning("topClass is deprecated - use top_class")
+            logger.warning("topClass is deprecated - use top_class")
             self.top_class = self.topClass
 
         super().__post_init__()
 
         if self.top_class:
             if self.schemaview.get_class(self.top_class) is None:
-                logging.warning(f"No class in schema named {self.top_class}")
+                logger.warning(f"No class in schema named {self.top_class}")
 
     def start_schema(self, inline: bool = False) -> JsonSchema:
         self.inline = inline

linkml/generators/owlgen.py

@@ -40,6 +40,8 @@ from linkml import METAMODEL_NAMESPACE_NAME
 from linkml._version import __version__
 from linkml.utils.generator import Generator, shared_arguments
 
+logger = logging.getLogger(__name__)
+
 OWL_TYPE = URIRef  ## RDFS.Literal or OWL.Thing
 
 SWRL = rdflib.Namespace("http://www.w3.org/2003/11/swrl#")
@@ -270,7 +272,7 @@ class OwlSchemaGenerator(Generator):
                     # if isinstance(v, str):
                     #    obj = URIRef(msv.expand_curie(v))
                     # else:
-                    #    logging.debug(f"Skipping {uri} {metaslot_uri} => {v}")
+                    #    logger.debug(f"Skipping {uri} {metaslot_uri} => {v}")
                 else:
                     obj = Literal(v)
                 self.graph.add((uri, metaslot_uri, obj))
@@ -438,7 +440,7 @@ class OwlSchemaGenerator(Generator):
                 if slot:
                     own_slots.append(slot)
                 else:
-                    logging.warning(f"Unknown top-level slot {slot_name}")
+                    logger.warning(f"Unknown top-level slot {slot_name}")
         else:
             own_slots = []
         own_slots.extend(cls.slot_conditions.values())
@@ -503,9 +505,9 @@ class OwlSchemaGenerator(Generator):
             owl_exprs.append(self._complement_of_union_of([self.transform_class_expression(x) for x in cls.none_of]))
         for slot in own_slots:
             if slot.name:
-                owltypes = self.slot_node_owltypes(sv.get_slot(slot.name))
+                owltypes = self.slot_node_owltypes(sv.get_slot(slot.name), owning_class=cls)
             else:
-                owltypes = self.slot_node_owltypes(slot)
+                owltypes = self.slot_node_owltypes(slot, owning_class=cls)
             x = self.transform_class_slot_expression(cls, slot, slot, owltypes)
             if not x:
                 range = sv.schema.default_range
@@ -552,12 +554,28 @@ class OwlSchemaGenerator(Generator):
                     owl_exprs.append(self._some_values_from(slot_uri, has_member_expr))
         return self._intersection_of(owl_exprs)
 
-    def slot_node_owltypes(self, slot: Union[SlotDefinition, AnonymousSlotExpression]) -> Set[URIRef]:
+    def slot_node_owltypes(
+        self,
+        slot: Union[SlotDefinition, AnonymousSlotExpression],
+        owning_class: Optional[Union[ClassDefinition, AnonymousClassExpression]] = None,
+    ) -> Set[URIRef]:
+        """
+        Determine the OWL types of a named slot or slot expression
+
+        The OWL type is either OWL.Thing or RDFS.Datatype
+
+        :param slot:
+        :param owning_class:
+        :return:
+        """
         sv = self.schemaview
         node_types = set()
         if isinstance(slot, SlotDefinition):
-            if slot.range in sv.all_classes():
-                range_class = sv.get_class(slot.range)
+            slot_range = slot.range
+            if isinstance(owning_class, ClassDefinition):
+                slot_range = sv.induced_slot(slot.name, owning_class.name).range
+            if slot_range in sv.all_classes():
+                range_class = sv.get_class(slot_range)
                 if not (range_class and range_class.class_uri == "linkml:Any"):
                     node_types.add(OWL.Thing)
             if slot.range in sv.all_types():
@@ -565,7 +583,7 @@ class OwlSchemaGenerator(Generator):
         for k in ["any_of", "all_of", "exactly_one_of", "none_of"]:
             subslot = getattr(slot, k, None)
             if subslot:
-                node_types.update(self.slot_node_owltypes(subslot))
+                node_types.update(self.slot_node_owltypes(subslot, owning_class=owning_class))
         return node_types
 
     def transform_class_slot_expression(
@@ -679,7 +697,7 @@ class OwlSchemaGenerator(Generator):
         if element.equals_string is not None:
             equals_string = element.equals_string
             if is_literal is None:
-                logging.warning(f"ignoring equals_string={equals_string} as unable to tell if literal")
+                logger.warning(f"ignoring equals_string={equals_string} as unable to tell if literal")
             elif is_literal:
                 constraints[XSD.pattern] = equals_string
             else:
@@ -688,7 +706,7 @@ class OwlSchemaGenerator(Generator):
         if element.equals_string_in:
             equals_string_in = element.equals_string_in
             if is_literal is None:
-                logging.warning(f"ignoring equals_string={equals_string_in} as unable to tell if literal")
+                logger.warning(f"ignoring equals_string={equals_string_in} as unable to tell if literal")
             elif is_literal:
                 dt_exprs = [
                     self._datatype_restriction(XSD.string, [self._facet(XSD.pattern, s)]) for s in equals_string_in
@@ -754,7 +772,7 @@ class OwlSchemaGenerator(Generator):
                     if slot_uri == URIRef(att_uri):
                         n += 1
             if n > 1:
-                logging.warning(f"Ambiguous attribute: {slot.name} {slot_uri}")
+                logger.warning(f"Ambiguous attribute: {slot.name} {slot_uri}")
                 return
 
         self.add_metadata(slot, slot_uri)
@@ -845,6 +863,7 @@ class OwlSchemaGenerator(Generator):
                 if not isinstance(v, list):
                     v = [v]
                 impls.extend(v)
+            impls.extend(element.implements)
         for impl in impls:
             if impl.startswith("owl:"):
                 return OWL[impl.split(":")[1]]
@@ -889,7 +908,7 @@ class OwlSchemaGenerator(Generator):
             if pv_owl_type == RDFS.Literal:
                 pv_node = Literal(pv.text)
                 if pv.meaning:
-                    logging.warning(f"Meaning on literal {pv.text} in {e.name} is ignored")
+                    logger.warning(f"Meaning on literal {pv.text} in {e.name} is ignored")
             else:
                 pv_node = self._permissible_value_uri(pv, enum_uri, e)
             pv_uris.append(pv_node)
@@ -950,7 +969,7 @@ class OwlSchemaGenerator(Generator):
     def _add_rule(self, subject: Union[URIRef, BNode], rule: ClassRule, cls: ClassDefinition):
         if not self.use_swrl:
             return
-        logging.warning("SWRL support is experimental and incomplete")
+        logger.warning("SWRL support is experimental and incomplete")
         head = []
         body = []
         for pre in rule.preconditions:
@@ -997,7 +1016,7 @@ class OwlSchemaGenerator(Generator):
                 owltypes.update(x_owltypes)
         owltypes.update(current)
         if len(owltypes) > 1:
-            logging.warning(f"Multiple owl types {owltypes}")
+            logger.warning(f"Multiple owl types {owltypes}")
             # if self.target_profile == OWLProfile.dl:
         return owltypes
 
@@ -1125,7 +1144,7 @@ class OwlSchemaGenerator(Generator):
     ) -> Optional[Union[BNode, URIRef]]:
         graph = self.graph
         if [x for x in exprs if x is None]:
-            logging.warning(f"Null expr in: {exprs} for {predicate} {node}")
+            logger.warning(f"Null expr in: {exprs} for {predicate} {node}")
             exprs = [x for x in exprs if x is not None]
         if len(exprs) == 0:
             return None
@@ -1251,10 +1270,10 @@ class OwlSchemaGenerator(Generator):
             return OWL.ObjectProperty
         is_literal_vals = self.slot_is_literal_map[slot.name]
         if len(is_literal_vals) > 1:
-            logging.warning(f"Ambiguous type for: {slot.name}")
+            logger.warning(f"Ambiguous type for: {slot.name}")
         if range is None:
             if not is_literal_vals:
-                logging.warning(f"Guessing type for {slot.name}")
+                logger.warning(f"Guessing type for {slot.name}")
                 return OWL.ObjectProperty
             if (list(is_literal_vals))[0]:
                 return OWL.DatatypeProperty

linkml/generators/projectgen.py

@@ -26,6 +26,8 @@ from linkml.generators.sqltablegen import SQLTableGenerator
 from linkml.utils.cli_utils import log_level_option
 from linkml.utils.generator import Generator
 
+logger = logging.getLogger(__name__)
+
 PATH_FSTRING = str
 GENERATOR_NAME = str
 ARG_DICT = Dict[str, Any]
@@ -63,14 +65,14 @@ GEN_MAP = {
 
 @lru_cache()
 def get_local_imports(schema_path: str, dir: str):
-    logging.info(f"GETTING IMPORTS = {schema_path}")
+    logger.info(f"GETTING IMPORTS = {schema_path}")
     all_imports = [schema_path]
     with open(schema_path) as stream:
         with open(schema_path) as stream:
             schema = yaml.safe_load(stream)
             for imp in schema.get("imports", []):
                 imp_path = os.path.join(dir, imp) + ".yaml"
-                logging.info(f" IMP={imp} //  path={imp_path}")
+                logger.info(f" IMP={imp} //  path={imp_path}")
                 if os.path.isfile(imp_path):
                     all_imports += get_local_imports(imp_path, dir)
     return all_imports
@@ -105,23 +107,23 @@ class ProjectGenerator:
             all_schemas = [schema_path]
         else:
             all_schemas = get_local_imports(schema_path, os.path.dirname(schema_path))
-        logging.debug(f"ALL_SCHEMAS = {all_schemas}")
+        logger.debug(f"ALL_SCHEMAS = {all_schemas}")
         for gen_name, (gen_cls, gen_path_fmt, default_gen_args) in GEN_MAP.items():
             if config.includes is not None and config.includes != [] and gen_name not in config.includes:
-                logging.info(f"Skipping {gen_name} as not in inclusion list: {config.includes}")
+                logger.info(f"Skipping {gen_name} as not in inclusion list: {config.includes}")
                 continue
             if config.excludes is not None and gen_name in config.excludes:
-                logging.info(f"Skipping {gen_name} as it is in exclusion list")
+                logger.info(f"Skipping {gen_name} as it is in exclusion list")
                 continue
-            logging.info(f"Generating: {gen_name}")
+            logger.info(f"Generating: {gen_name}")
             for local_path in all_schemas:
-                logging.info(f" SCHEMA: {local_path}")
+                logger.info(f" SCHEMA: {local_path}")
                 name = os.path.basename(local_path).replace(".yaml", "")
                 gen_path = gen_path_fmt.format(name=name)
                 gen_path_full = f"{config.directory}/{gen_path}"
                 parts = gen_path_full.split("/")
                 parent_dir = "/".join(parts[0:-1])
-                logging.info(f" PARENT={parent_dir}")
+                logger.info(f" PARENT={parent_dir}")
                 Path(parent_dir).mkdir(parents=True, exist_ok=True)
                 gen_path_full = "/".join(parts)
                 all_gen_args = {
@@ -143,13 +145,13 @@ class ProjectGenerator:
                     if isinstance(v, str):
                         v = v.format(name=name, parent=parent_dir)
                     serialize_args[k] = v
-                logging.info(f" {gen_name} ARGS: {serialize_args}")
+                logger.info(f" {gen_name} ARGS: {serialize_args}")
                 gen_dump = gen.serialize(**serialize_args)
 
                 if gen_name != "excel":
                     if parts[-1] != "":
                         # markdowngen does not write to a file
-                        logging.info(f"  WRITING TO: {gen_path_full}")
+                        logger.info(f"  WRITING TO: {gen_path_full}")
                         with open(gen_path_full, "w", encoding="UTF-8") as stream:
                             stream.write(gen_dump)
                 else:
@@ -249,7 +251,7 @@ def cli(
             project_config.generator_args = yaml.safe_load(generator_arguments)
         except Exception:
             raise Exception("Argument must be a valid YAML blob")
-        logging.info(f"generator args: {project_config.generator_args}")
+        logger.info(f"generator args: {project_config.generator_args}")
     if dir is not None:
         project_config.directory = dir
     project_config.mergeimports = mergeimports