linkml 1.8.2__py3-none-any.whl → 1.8.4__py3-none-any.whl

linkml/utils/execute_tutorial.py

@@ -10,6 +10,8 @@ import click
 
 from linkml._version import __version__
 
+logger = logging.getLogger(__name__)
+
 re_decl = re.compile(r"^(\S+):$")
 re_start_yaml = re.compile(r"^```(\w+)$")
 re_end_yaml = re.compile(r"^```$")
@@ -46,17 +48,17 @@ def execute_blocks(directory: str, blocks: List[Block]) -> List[str]:
     :return: errors
     """
     Path(directory).mkdir(parents=True, exist_ok=True)
-    logging.info(f"Executing in: {directory}")
+    logger.info(f"Executing in: {directory}")
     last_block = None
     errs = []
 
     def err(e):
         errs.append(e)
-        logging.error(e)
+        logger.error(e)
 
     for block in blocks:
         write_lines(block.prior_lines)
-        logging.info(f"# Block: {block.category} {block.title}")
+        logger.info(f"# Block: {block.category} {block.title}")
         if block.is_file_block():
             path = PurePath(directory, block.title)
             with open(path, "w", encoding="UTF-8") as stream:
@@ -73,44 +75,44 @@ def execute_blocks(directory: str, blocks: List[Block]) -> List[str]:
                 if len(outpath) > 1:
                     raise Exception(f"Maximum 1 token after > in {block.content}. Got: {outpath}")
                 outpath = str(Path(directory, *outpath))
-                logging.info(f"OUTPATH = {outpath}")
+                logger.info(f"OUTPATH = {outpath}")
             else:
                 outpath = None
-            logging.info(f"Executing: {cmd}")
+            logger.info(f"Executing: {cmd}")
             r = subprocess.run(cmd, cwd=directory, capture_output=True)
             block.output = r.stdout.decode("utf-8")
             if outpath:
                 with open(outpath, "w", encoding="UTF-8") as stream:
-                    logging.info(f"WRITING {len(block.output)} TO = {outpath}")
+                    logger.info(f"WRITING {len(block.output)} TO = {outpath}")
                     stream.write(block.output)
             block.error = r.stderr.decode("utf-8")
-            logging.info(f"OUT [sample] = {block.output[0:30]}")
+            logger.info(f"OUT [sample] = {block.output[0:30]}")
             if block.expected_fail:
                 if r.returncode == 0:
                     err(f"Command unexpectedly succeeded: {cmd}")
                 else:
-                    logging.info("Failed as expected")
+                    logger.info("Failed as expected")
                 if block.error:
-                    logging.info(f"ERR [sample] = ...{block.error[-200:]}")
+                    logger.info(f"ERR [sample] = ...{block.error[-200:]}")
             else:
                 if block.error:
-                    logging.info(f"ERR = {block.error}")
+                    logger.info(f"ERR = {block.error}")
                 if r.returncode != 0:
                     err(f"Command failed: {cmd}")
                 else:
-                    logging.info("Success!")
+                    logger.info("Success!")
         elif block.is_stdout():
             if "compare_rdf" in block.annotations:
-                logging.warning("SKIPPING RDF COMPARISON. TODO: https://github.com/linkml/linkml/issues/427")
+                logger.warning("SKIPPING RDF COMPARISON. TODO: https://github.com/linkml/linkml/issues/427")
             elif last_block.output:
                 if last_block.output.strip() != block.content.strip():
                     err(f"Mismatch: {str(last_block.output)} != {block.content}")
                 else:
-                    logging.info("Hurray! Contents match!")
+                    logger.info("Hurray! Contents match!")
             else:
-                logging.info("No comparison performed")
+                logger.info("No comparison performed")
         else:
-            logging.warning(f"Ignoring block: {block}")
+            logger.warning(f"Ignoring block: {block}")
         last_block = block
     return errs
 
@@ -201,20 +203,20 @@ def cli(inputs, directory):
     logging.basicConfig(level=logging.INFO)
     errs = []
     for input in inputs:
-        logging.info(f"INPUT={input}")
+        logger.info(f"INPUT={input}")
         blocks = parse_file_to_blocks(input)
         print(f"## {len(blocks)} Blocks")
         localdir = Path(input).stem
         subdir = PurePath(directory, localdir)
         input_errs = execute_blocks(str(subdir), blocks)
         if len(input_errs) > 0:
-            logging.error(f"TUTORIAL {input} FAILURES: {len(input_errs)}")
+            logger.error(f"TUTORIAL {input} FAILURES: {len(input_errs)}")
         errs += input_errs
-    logging.info(f"Errors = {len(errs)}")
+    logger.info(f"Errors = {len(errs)}")
     if len(errs) > 0:
-        logging.error(f"Encountered {len(errs)} Errors")
+        logger.error(f"Encountered {len(errs)} Errors")
         for err in errs:
-            logging.error(f"Error: {err}")
+            logger.error(f"Error: {err}")
         sys.exit(1)
 
 

linkml/utils/generator.py

@@ -54,6 +54,8 @@ from linkml.utils.mergeutils import alias_root
 from linkml.utils.schemaloader import SchemaLoader
 from linkml.utils.typereferences import References
 
+logger = logging.getLogger(__name__)
+
 
 @lru_cache
 def _resolved_metamodel(mergeimports):
@@ -61,7 +63,7 @@ def _resolved_metamodel(mergeimports):
         raise AssertionError(f"{LOCAL_METAMODEL_YAML_FILE} not found")
 
     base_dir = str(Path(str(LOCAL_METAMODEL_YAML_FILE)).parent)
-    logging.debug(f"BASE={base_dir}")
+    logger.debug(f"BASE={base_dir}")
     metamodel = SchemaLoader(
         LOCAL_METAMODEL_YAML_FILE,
         importmap={"linkml": base_dir},
@@ -179,7 +181,7 @@ class Generator(metaclass=abc.ABCMeta):
 
     def __post_init__(self) -> None:
         if not self.logger:
-            self.logger = logging.getLogger()
+            self.logger = logger
         if self.log_level is not None:
             self.logger.setLevel(self.log_level)
         if self.format is None:
@@ -203,7 +205,7 @@ class Generator(metaclass=abc.ABCMeta):
         if self.uses_schemaloader:
             self._initialize_using_schemaloader(schema)
         else:
-            logging.info(f"Using SchemaView with im={self.importmap} // base_dir={self.base_dir}")
+            self.logger.info(f"Using SchemaView with im={self.importmap} // base_dir={self.base_dir}")
             self.schemaview = SchemaView(schema, importmap=self.importmap, base_dir=self.base_dir)
             if self.include:
                 if isinstance(self.include, (str, Path)):
@@ -840,7 +842,7 @@ class Generator(metaclass=abc.ABCMeta):
             if ":" not in mapping or len(mapping.split(":")) != 2:
                 raise ValueError(f"Definition {defn.name} - unrecognized mapping: {mapping}")
             ns = mapping.split(":")[0]
-            logging.debug(f"Adding {ns} from {mapping} // {defn}")
+            self.logger.debug(f"Adding {ns} from {mapping} // {defn}")
             if ns:
                 self.add_prefix(ns)
 

linkml/utils/mergeutils.py

@@ -18,6 +18,8 @@ from linkml_runtime.utils.namespaces import Namespaces
 from linkml_runtime.utils.yamlutils import extended_str
 from rdflib import URIRef
 
+logger = logging.getLogger(__name__)
+
 
 def merge_schemas(
     target: SchemaDefinition,
@@ -72,7 +74,7 @@ def merge_namespaces(target: SchemaDefinition, mergee: SchemaDefinition, namespa
             # We cannot resolve this to an absolute path, so we have to assume that
             # this prefix is already defined correctly in the target
             if prefix.prefix_prefix not in namespaces:
-                logging.info(
+                logger.info(
                     "Adding an unadjusted relative prefix for %s from %s, "
                     + "as the prefix is not yet defined, even as we cannot adjust it relative to the final file. "
                     + "If it cannot be resolved, add the prefix definition to the input schema!",
@@ -85,7 +87,7 @@ def merge_namespaces(target: SchemaDefinition, mergee: SchemaDefinition, namespa
                     prefix.prefix_prefix in target.prefixes
                     and target.prefixes[prefix.prefix_prefix].prefix_reference != prefix.prefix_reference
                 ):
-                    logging.info(
+                    logger.info(
                         "Ignoring different relative prefix for %s from %s, "
                         + "as we cannot adjust it relative to the final file. "
                         + "Assuming the first found location is correct: %s!",

linkml/utils/schema_fixer.py

@@ -94,7 +94,7 @@ class SchemaFixer:
         tree_roots = [c for c in sv.all_classes().values() if c.tree_root]
         if len(tree_roots) > 0:
             if force:
-                logging.info("Forcing addition of containers")
+                logger.info("Forcing addition of containers")
             else:
                 raise ValueError(f"Schema already has containers: {tree_roots}")
         container = ClassDefinition(class_name, tree_root=True)
@@ -228,7 +228,7 @@ class SchemaFixer:
             # slots within that are redundant
             slot_usage_keys = list(cls.slot_usage.keys())
             for slot_usage_key in slot_usage_keys:
-                logging.debug(f"TESTING: {class_name}.{slot_usage_key}")
+                logger.debug(f"TESTING: {class_name}.{slot_usage_key}")
                 slot_usage_value = cls.slot_usage[slot_usage_key]
                 # perform a deletion test: what can be retrieved by inference
                 del cls.slot_usage[slot_usage_key]
@@ -236,7 +236,7 @@ class SchemaFixer:
                 try:
                     induced_slot = sv.induced_slot(slot_usage_key, class_name)
                 except ValueError:
-                    logging.warning(f"slot_usage with no slot: {slot_usage_key}")
+                    logger.warning(f"slot_usage with no slot: {slot_usage_key}")
                     continue
                 # restore value
                 cls.slot_usage[slot_usage_key] = slot_usage_value
@@ -258,7 +258,7 @@ class SchemaFixer:
                         continue
                     induced_v = getattr(induced_slot, metaslot_name, None)
                     if v is not None and v != [] and v != {} and v == induced_v:
-                        logging.info(f"REDUNDANT: {class_name}.{slot_usage_key}[{metaslot_name}] = {v}")
+                        logger.info(f"REDUNDANT: {class_name}.{slot_usage_key}[{metaslot_name}] = {v}")
                         to_delete.append(metaslot_name)
                 for metaslot_name in to_delete:
                     del slot_usage_value[metaslot_name]
@@ -302,7 +302,7 @@ class SchemaFixer:
                 if len(vals_strs) == 1:
                     harmonized_slot[k] = vals.pop()
                 elif len(vals_strs) > 1:
-                    logging.info(f"Variable values in {slot_name}.{k}: {vals_strs}")
+                    logger.info(f"Variable values in {slot_name}.{k}: {vals_strs}")
             new_slots[str(slot_name)] = harmonized_slot
         return new_slots
 

linkml/utils/schemaloader.py

@@ -29,6 +29,8 @@ from linkml.utils.mergeutils import merge_classes, merge_schemas, merge_slots, s
 from linkml.utils.rawloader import load_raw_schema
 from linkml.utils.schemasynopsis import SchemaSynopsis
 
+lgr = logging.getLogger(__name__)
+
 
 class SchemaLoader:
     def __init__(
@@ -57,7 +59,7 @@ class SchemaLoader:
         :param source_file_date: modification of source file
         :param source_file_size: size of source file
         """
-        self.logger = logger if logger is not None else logging.getLogger(self.__class__.__name__)
+        self.logger = logger if logger is not None else lgr
         if isinstance(data, SchemaDefinition):
             self.schema = data
         else:
@@ -176,7 +178,7 @@ class SchemaLoader:
                     # mangled names are overwritten if a schema with attributes is passed in
                     # TODO: handle this in a more graceful way
                     #  see https://github.com/linkml/linkml/issues/872
-                    logging.warning(
+                    self.logger.warning(
                         f'Class: "{cls.name}" attribute "{attribute.name}" - '
                         f"mangled name: {mangled_slot_name} already exists",
                     )
@@ -770,7 +772,7 @@ class SchemaLoader:
             if slotname in self.schema.slots:
                 base_slot = self.schema.slots[slotname]
             else:
-                logging.error(f"slot_usage for undefined slot: {slotname}")
+                self.logger.error(f"slot_usage for undefined slot: {slotname}")
                 base_slot = None
             parent_slot = self.schema.slots.get(slot_usage.is_a)
             # Follow the ancestry of the class to get the most proximal parent

linkml/utils/sqlutils.py

@@ -40,6 +40,8 @@ from linkml.utils.datautils import (
     infer_root_class,
 )
 
+logger = logging.getLogger(__name__)
+
 
 @dataclass
 class SQLStore:
@@ -376,7 +378,7 @@ def dump(
 
         inputs = [item for input in inputs for item in glob.glob(input)]
     for input in inputs:
-        logging.info(f"Loading: {input}")
+        logger.info(f"Loading: {input}")
         input_format = _get_format(input, input_format)
         loader = get_loader(input_format)
 

linkml/validator/plugins/pydantic_validation_plugin.py

@@ -37,7 +37,7 @@ class PydanticValidationPlugin(ValidationPlugin):
         """
         pydantic_model = context.pydantic_model(closed=self.closed)
         try:
-            instance = pydantic_model.parse_obj(instance)
+            instance = pydantic_model.model_validate(instance)
         except Exception as e:
             yield ValidationResult(
                 type="Pydantic validation",

linkml/validators/jsonschemavalidator.py

@@ -19,6 +19,8 @@ from linkml.generators.pythongen import PythonGenerator
 from linkml.utils import datautils
 from linkml.utils.datavalidator import DataValidator
 
+logger = logging.getLogger(__name__)
+
 
 class HashableSchemaDefinition(SchemaDefinition):
     def __hash__(self) -> int:
@@ -27,7 +29,7 @@ class HashableSchemaDefinition(SchemaDefinition):
 
 @lru_cache(maxsize=None)
 def _generate_jsonschema(schema, top_class, closed, include_range_class_descendants):
-    logging.debug("Generating JSON Schema")
+    logger.debug("Generating JSON Schema")
     not_closed = not closed
     return JsonSchemaGenerator(
         schema=schema,

linkml/validators/sparqlvalidator.py

@@ -15,6 +15,8 @@ from linkml.reporting import CheckResult, Report
 from linkml.utils.datautils import _get_format, dumpers_loaders, get_dumper
 from linkml.utils.datavalidator import DataValidator
 
+logger = logging.getLogger(__name__)
+
 
 def sparqljson2dict(row: dict):
     return {k: v["value"] for k, v in row.items()}
@@ -55,7 +57,7 @@ class SparqlDataValidator(DataValidator):
                 for row in qres:
                     invalid += row
             except Exception:
-                logging.error(f"FAILED: {qn}")
+                logger.error(f"FAILED: {qn}")
         return invalid
 
     def validate_endpoint(self, url: str, **kwargs):
@@ -65,8 +67,8 @@ class SparqlDataValidator(DataValidator):
         report = Report()
         for qn, q in self.queries.items():
             q += " LIMIT 20"
-            logging.debug(f"QUERY: {qn}")
-            logging.debug(f"{q}")
+            logger.debug(f"QUERY: {qn}")
+            logger.debug(f"{q}")
             sw = SPARQLWrapper(url)
             sw.setQuery(q)
             sw.setReturnFormat(JSON)

linkml/workspaces/example_runner.py

@@ -24,6 +24,8 @@ from linkml._version import __version__
 from linkml.generators.pythongen import PythonGenerator
 from linkml.validator import Validator, _get_default_validator
 
+logger = logging.getLogger(__name__)
+
 
 @dataclass
 class SummaryDocument:
@@ -134,7 +136,7 @@ class ExampleRunner:
             input_examples = glob.glob(os.path.join(str(input_dir), f"*.{fmt}"))
             input_counter_examples = glob.glob(os.path.join(str(counter_example_dir), f"*.{fmt}"))
             if not input_counter_examples:
-                logging.warning(f"No counter examples found in {self.counter_example_input_directory}")
+                logger.warning(f"No counter examples found in {self.counter_example_input_directory}")
             self.process_examples_from_list(input_examples, fmt, False)
             self.process_examples_from_list(input_counter_examples, fmt, True)
 

{linkml-1.8.2.dist-info → linkml-1.8.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: linkml
-Version: 1.8.2
+Version: 1.8.4
 Summary: Linked Open Data Modeling Language
 Home-page: https://linkml.io/linkml/
 Keywords: schema,linked data,data modeling,rdf,owl,biolink
@@ -24,6 +24,7 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Provides-Extra: black
+Provides-Extra: numpydantic
 Provides-Extra: shacl
 Provides-Extra: tests
 Requires-Dist: antlr4-python3-runtime (>=4.9.0,<4.10)
@@ -37,6 +38,7 @@ Requires-Dist: jsonasobj2 (>=1.0.3,<2.0.0)
 Requires-Dist: jsonschema[format] (>=4.0.0)
 Requires-Dist: linkml-dataops
 Requires-Dist: linkml-runtime (>=1.8.1,<2.0.0)
+Requires-Dist: numpydantic (>=1.6.1) ; (python_version >= "3.9") and (extra == "numpydantic" or extra == "tests")
 Requires-Dist: openpyxl
 Requires-Dist: parse
 Requires-Dist: prefixcommons (>=0.1.7)

{linkml-1.8.2.dist-info → linkml-1.8.4.dist-info}/RECORD

@@ -2,12 +2,13 @@ linkml/__init__.py,sha256=0REu65rXiOk3F1CYLzq60HiSZ2DfFySfGS6QFljZ01s,3663
 linkml/_version.py,sha256=udxv6OEqcE89DTVMYPtetXYg8IA8Sgc6yW26-6f8C3M,310
 linkml/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/cli/__main__.py,sha256=oPa7Fl2DQP40UivpIWNRr1CgwT2SQM0rhE478155zBY,80
-linkml/cli/main.py,sha256=-VaV8Z6rhadMOIHS9kdeV30NdXsE6jG3kVpvGbkF2wY,5184
+linkml/cli/main.py,sha256=83lyx36tcy95StDRtN7BmwNFCPt4As1wb0wbC3YwHKg,5386
 linkml/generators/PythonGenNotes.md,sha256=wb9BPLLhF6378OKLbwSBAwmniLpwrcT5_bbfCHfLme8,51006
 linkml/generators/README.md,sha256=RMzT8EblC_GEdPy5WyfXHDBXlFI6k6mz3Cx2sdpcyWI,4438
-linkml/generators/__init__.py,sha256=dQ2EUKy_MctEVEzbC3XzEJL5YmYwjYfsa44mG2zKn7g,1517
+linkml/generators/__init__.py,sha256=2qSOnibL6KtzBW3KNqVX1gx1LQttrXlOPbbVDLLV2go,1587
 linkml/generators/common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/generators/common/build.py,sha256=hXf2gf1ox2hiR-D6N-qXt5w5QkISLlo1A-_GurY3yHo,2897
+linkml/generators/common/ifabsent_processor.py,sha256=D8vKZLa15mc_SUyvFsE3NZfWi-c4kawYW6WdGozJLRQ,11275
 linkml/generators/common/lifecycle.py,sha256=UOJXlIyWQkvsn0Dao9_ZDzlamJtiINyVJQ6SRj66L9s,4910
 linkml/generators/common/template.py,sha256=bjcSNiC85MYl9oGhk0ZpqwZpRxxy_NqxG8XBV-TXXDY,3338
 linkml/generators/common/type_designators.py,sha256=lgVcIRJJ-yCvVGeP9U_gQZpm77UmJBQo9Bh3lGJITno,1956
@@ -16,69 +17,71 @@ linkml/generators/docgen/class.md.jinja2,sha256=-JmjYHgYOaaBYd5r-Tr5dkk0CLM_lX0k
 linkml/generators/docgen/class_diagram.md.jinja2,sha256=gzskx4hOpU_s6BqOXdYZ9DwKxuClnsEgDzPurm30PeY,3469
 linkml/generators/docgen/common_metadata.md.jinja2,sha256=gy9J8rghBfKDKimwtHj_XuHY4PJRRYHLXVlBHqWrUzU,1604
 linkml/generators/docgen/enum.md.jinja2,sha256=mXnUrRkleY2bOTEyAZ5c4pcUnqhs6BNa8a-4LVve-eo,1014
-linkml/generators/docgen/index.md.jinja2,sha256=wXUYTmayPLFltC0vbGE_Mf6m3GkkWav7FOEjCvEpHp4,1466
+linkml/generators/docgen/index.md.jinja2,sha256=suXRgJydHrxcMm3quXukaKkThtdzYA9i7BTuMAVKOP0,1502
 linkml/generators/docgen/index.tex.jinja2,sha256=Go_EA-_N4JUpbOYbk3OY11mz5yV70VF2l2sMtgIPWw4,501
 linkml/generators/docgen/schema.md.jinja2,sha256=xlENfnzNRYgPT_0tdqNFxgklVM4Qf5BuzhFVvSMDuxs,70
 linkml/generators/docgen/slot.md.jinja2,sha256=dJHugIv9OPTi3FIn8Iez7CzjQizdXrcn0hcmCmXSgV4,3339
 linkml/generators/docgen/subset.md.jinja2,sha256=EPln_fjlhlkmwEGEp2iPX-9Xm2vVodPZLlRBlYCB_sA,2705
 linkml/generators/docgen/type.md.jinja2,sha256=QmCMJZrFwP33eHkggBVtypbyrxTb-XZn9vHOYojVaYk,635
-linkml/generators/docgen.py,sha256=BbYIL1Bep0La4izwHaYZuTsnbVAv8_zjx3U3r1eHFEQ,36406
+linkml/generators/docgen.py,sha256=SAkqAZxbzHqzKrX3JQpRJr51bdr2gQKs6Bs1h-aVrmI,38711
 linkml/generators/dotgen.py,sha256=vjHveFtKBItHRkowi1I4FHffcn4u4wLpBydYgVxB-vE,5028
 linkml/generators/erdiagramgen.py,sha256=5_VEPvRL0I819wCjk7T5hWffdBPc_qw3XpQdOYpO7uE,11357
 linkml/generators/excelgen.py,sha256=MQRRm1wDbg7auUQH9tGb5aRyrp-e4gjXsY10aoLb9LI,7708
-linkml/generators/golanggen.py,sha256=w3iTcOK69cwCrhE1pZn-PpV59arFZB8uU3ErLFo9i8Y,5803
+linkml/generators/golanggen.py,sha256=Qx1GZRIrKn8jNoO-8fJMjkrwV9ZLwR4NwYBW5kGGp9c,5840
 linkml/generators/golrgen.py,sha256=JB92VDhTuwyaOyxHxB4goIsjZbq4NMf36ESprC3GeBs,3454
 linkml/generators/graphqlgen.py,sha256=-BS-UHPyHqauUgtgcFCO4xSxxogk7BPAQFSXHIrKJT0,2163
 linkml/generators/javagen/example_template.java.jinja2,sha256=ec4CVTv_0zS7V5Y-1E6H4lRraya10gfX7BEMBlu38X4,444
 linkml/generators/javagen/java_record_template.jinja2,sha256=OQZffLSy_xR3FIhQMltvrYyVeut7l2Q-tzK7AOiVmWs,1729
 linkml/generators/javagen.py,sha256=BTAXgvOOvRa3AOfaaiVFyuyaqg4XFR_JbO6_7tT_AnQ,5335
-linkml/generators/jsonldcontextgen.py,sha256=fZ22yjYGLMf_rQYKQSRh3IvMdGVAFhJ0PdQF8d514NI,8689
+linkml/generators/jsonldcontextgen.py,sha256=J-9QF7doco3-hYReiik67PjiaF_UudrFEiVsbnJFCJg,8666
 linkml/generators/jsonldgen.py,sha256=9ru1rb4_u7t_Rp8ILQSmDIsk_evrDL_OeilnQUsu338,7770
-linkml/generators/jsonschemagen.py,sha256=XoA0HJ1XlItogmhr3F8XNnAi1UG6fXeBAKkjme48n7o,30388
+linkml/generators/jsonschemagen.py,sha256=1k00W4I4paKHKZnmcWcMEoAel1VZRHa2rVgcOZW3kZU,30424
 linkml/generators/legacy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/generators/linkmlgen.py,sha256=g1D8B6MBxcG6b9aYCUESp7nDZPmjedCs8rmGm_0GLnE,3484
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 linkml/generators/shexgen.py,sha256=-GFdapDEAUXAjsXdTI7ZlS39YfuvaxfzPkdqUNM19qI,9941
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 linkml/generators/sqlalchemy/__init__.py,sha256=mb9AC1rIFkSiNZhhG0TAk45ol9PjS1XvsrvCjgfVUpQ,249
 linkml/generators/sqlalchemy/sqlalchemy_declarative_template.py,sha256=X_Ws1NUBikMI5HuNgEhl_PIeWM-B-c2B0W9KUBH4QTg,2542
 linkml/generators/sqlalchemy/sqlalchemy_imperative_template.py,sha256=u4ZpponG1h6XROrOHGOf_0H2e6xL1_s8twAOA-gx94A,1622
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 linkml/generators/sssomgen.py,sha256=zrZy0WL9fF5bk-XAcB-MZYZkhHhqVRHt2rGBUtfqnLY,6891
 linkml/generators/string_template.md,sha256=kRcfic6entgIaJdpSg6GF3jcjC9wbKsCVM6wVT2qipc,1788
 linkml/generators/summarygen.py,sha256=C9r34928QtVMaXTbdch-mRPB5L0jDTGmTnVmtrKrR-0,3083
 linkml/generators/terminusdbgen.py,sha256=ItJ-HTMkkX22Ex1-UjJZmtEtE2fn6UdjAxDtn20RXV8,4713
-linkml/generators/typescriptgen.py,sha256=y8l1A1hAyuiRmXw0CyPXfamBKWpi7ag_lspfr8bnIds,8594
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 linkml/generators/yamlgen.py,sha256=38zdh5T4tObFhCHgbUbKbc0UuFh1TmmsWBkWM9gcvsI,1625
 linkml/generators/yumlgen.py,sha256=Bg1MGlhCCQoswB19mFKh8xB0UcL9MQGHlUrAVGZSWkc,12208
 linkml/linter/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -95,33 +98,33 @@ linkml/linter/formatters/json_formatter.py,sha256=rrOELuETUCFTl1Ewnrus9Rx9hl2g4u
 linkml/linter/formatters/markdown_formatter.py,sha256=sumF2MNJYL5oipLwCftCr3AiaCmVhd9V6di9aYpJ29I,2605
 linkml/linter/formatters/terminal_formatter.py,sha256=xmNwlRieVCssRt3fpnNP5WWw_YXGmaBsbxFoMWufy5M,2085
 linkml/linter/formatters/tsv_formatter.py,sha256=1VW-1Tv16mwhIDpHdExYpJJR3z42K5_XK2C-4mmYYdE,871
-linkml/linter/linter.py,sha256=qfVV-vFT7bUJ2BmmDQteD7Jz8HZ-CNDSvnkyhJ-54H0,5113
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 linkml/linter/rules.py,sha256=Eg_-lIX1KPsCp3PHdPcBiHmSS5qAVZkHbw5LURfkfXk,11481
 linkml/reporting/__init__.py,sha256=Jo0V_nyEcnWhMukMW-bqW9dlbgCfaRlWm3CO-XzgU84,92
 linkml/reporting/model.py,sha256=-10yNfk8wuRC48ZI-akrWvtlJ9a6RYWET2TzlZV3XXo,8622
 linkml/transformers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml/transformers/logical_model_transformer.py,sha256=rPeBYzQdLtcEKPe1kwkOWce4N7HZvFaULDrEGKbB-qI,29838
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 linkml/transformers/model_transformer.py,sha256=tK_MpRDI-q2qfe8KHT6qJHP8ZruKjYx1FcM-Fnjse-E,678
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 linkml/transformers/schema_renamer.py,sha256=DYRbgL9j41M9FdbHYLY3u4YIdDM98laD3cv_lHcgWHQ,5275
 linkml/utils/__init__.py,sha256=Pkyv-Gfb8QoJdInRdJuuUz1Igfe0sT9t8Gv3V_fyTXc,92
 linkml/utils/cli_utils.py,sha256=MdVbox1qr6kDUHUCWAmFhV-D6ebs_nn8vVwB8KDQfew,742
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 linkml/utils/datautils.py,sha256=QlbzwXykh5Fphfe5KxPo6_ekXfniLbHiEGJtLWjUrvY,3742
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 linkml/utils/deprecation.py,sha256=onhB82qjIkKzyUOTO9WDqN6QF3I2cJoyBrbm66vHmgM,8088
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 linkml/utils/helpers.py,sha256=yR8n4zFA5wPcYC7xzRuNF3wO16vG80v6j7DM3qTNmIc,447
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 linkml/utils/logictools.py,sha256=BGtcoqr_Rsu08Ywa6lNiL881uZzQmNWk1p4FEIVKYe0,23641
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 linkml/utils/rawloader.py,sha256=nUB8Gfn8yEVwyo6bx0TtB2mBGkilC-fybi0xvQ73Gks,4417
 linkml/utils/schema_builder.py,sha256=LwaLeo65IQBHcmRD1kIxnjI1idFZyZsgfPACPow1_JY,9983
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 linkml/utils/schemasynopsis.py,sha256=j7sNt6j-E3rmf-1qEo351Kth2kltt6crQV-dxJAGCUE,18414
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 linkml/utils/typereferences.py,sha256=8Yfuz9-HAwOPoJLbIcO_sY9zf32hvPRzGeSOzECfMWA,2232
 linkml/utils/validation.py,sha256=eLw1-d8x3N1V14bSc6H_mJJXo59ryKvvUIBcOJ1dVMw,1438
 linkml/validator/__init__.py,sha256=u0CeorIw50Qqwa60-lIFsJXg-sOdfo90hqvLpyvvwo4,4993
@@ -134,7 +137,7 @@ linkml/validator/loaders/passthrough_loader.py,sha256=fQvBZqzGnpdwpZio4Mbehmsb6e
 linkml/validator/loaders/yaml_loader.py,sha256=ZsMz-oGDkX9oPEOVcKnFRGhU9q0fKoHcL6BLOkCeB4c,914
 linkml/validator/plugins/__init__.py,sha256=0ifiDqpcXVy4X7OJFm7FMYi1-6E06avNIIk9R0c6nD8,693
 linkml/validator/plugins/jsonschema_validation_plugin.py,sha256=c3OjvLR5m83vppsDfkrS9nMXma_ogUxXpZuM_JIUVM4,2634
-linkml/validator/plugins/pydantic_validation_plugin.py,sha256=C-Vp74bz5oqp5V-iuhXW8p0PPDoFY8NCU5x36Ur5Og4,1985
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 linkml/validator/plugins/recommended_slots_plugin.py,sha256=kOdoYQyye47nLA7BjorVmydS84nGpiVy3MoCbPq1Ymo,2308
 linkml/validator/plugins/shacl_validation_plugin.py,sha256=X6h1O54m9P5USvqCvNqELD0YpzXkE6UrmxnV0ukU6E4,3888
 linkml/validator/plugins/validation_plugin.py,sha256=9SMHF8b2bgG9-8351e8bY676e0A4aEBJSXvMjMF5kXg,1548
@@ -142,15 +145,15 @@ linkml/validator/report.py,sha256=LwFpmJ74Cvsi2CuEDhm1a8nn9x1VI3Z98DbkUZVhKMA,89
 linkml/validator/validation_context.py,sha256=Pmccq-LQ9iEeLyZhamp3mKjjtwp4ji1hIe5TT05AUT4,2732
 linkml/validator/validator.py,sha256=BFgfKdu9Nad2dc9XTpmz9daQTj_FTcvo6mBq3e8fhJs,5649
 linkml/validators/__init__.py,sha256=43W3J5NPKhwa3ZFHLRYsJMocwQKWGYCF9Ki9r0ccGbc,202
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-linkml/validators/sparqlvalidator.py,sha256=KU4Vj-B3i_0Fde0Sn89oqkOVxt1UGW3uI4F6YNoJMTQ,4625
+linkml/validators/jsonschemavalidator.py,sha256=zGDPKjr13hXHSH8g1KOzo4PXrfM_TTvpwq_jD03aVUw,8005
+linkml/validators/sparqlvalidator.py,sha256=0iq-oFFLV0Juu6pJskpLOlB7AMZwU3VFvoflzW4ohH8,4660
 linkml/workspaces/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/workspaces/datamodel/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/workspaces/datamodel/workspaces.py,sha256=4HdkqweGNfMPqnB1_Onc9DcTfkhoagTRcqruh08nRoI,14905
 linkml/workspaces/datamodel/workspaces.yaml,sha256=EjVrwPpeRZqJRjuGyyDRxxFzuv55SiLIXPBRUG6HStU,4233
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