linkml 1.9.4rc1__py3-none-any.whl → 1.9.5__py3-none-any.whl

linkml/linter/config/datamodel/config.yaml

@@ -37,32 +37,17 @@ classes:
       Each attribute of this class represents a rule that can be enabled and possibly
       configured by a configuration file.
     attributes:
+      canonical_prefixes:
+        range: CanonicalPrefixesConfig
+        description: >-
+          Enforce canonical prefixes by verifying that the mappings defined in the `prefixes`
+          slot agree with those provided by the [prefixmaps](https://github.com/linkml/prefixmaps)
+          package. Not auto-fixable.
       no_empty_title:
         range: NoEmptyTitleConfig
         description: >-
           Disallow empty titles on schema elements. Autofix will transform the element's
           name into a title.
-      permissible_values_format:
-        range: PermissibleValuesFormatRuleConfig
-        description: >-
-          Enforce consistent formatting of enum permissible values. This rule may conflict
-          with the standard_naming rule. Not auto-fixable.
-      tree_root_class:
-        range: TreeRootClassRuleConfig
-        description: >-
-          Require a single class with `tree_root: true` and optionally verify that class's
-          name. Autofix will create a new class with `tree_root: true`, a name based on
-          the rule configuration, and slots for existing classes.
-      recommended:
-        range: RecommendedRuleConfig
-        description: >-
-          Require any slot in the metamodel with `recommended: true` (e.g. description)
-          to be provided. Not auto-fixable.
-      no_xsd_int_type:
-        range: RuleConfig
-        description: >-
-          Disallow use of `uri: xsd:int` in type definitions. Autofix will change the
-          uri to xsd:integer.
       no_invalid_slot_usage:
         range: RuleConfig
         description: >-
@@ -78,6 +63,29 @@ classes:
         description: >-
           Disallow the use of ranges in slot specifications if any of the ranges used
           do not refer to an existing type, class, or enum. Not auto-fixable.
+      no_xsd_int_type:
+        range: RuleConfig
+        description: >-
+          Disallow use of `uri: xsd:int` in type definitions. Autofix will change the
+          uri to xsd:integer.
+      one_identifier_per_class:
+        range: RuleConfig
+        description: >-
+          Ensure that there is only one slot with the `identifier` attribute set to True per class.
+      one_key_per_class:
+        range: RuleConfig
+        description: >-
+          Ensure that there is only one slot with the `key` attribute set to True per class.
+      permissible_values_format:
+        range: PermissibleValuesFormatRuleConfig
+        description: >-
+          Enforce consistent formatting of enum permissible values. This rule may conflict
+          with the standard_naming rule. Not auto-fixable.
+      recommended:
+        range: RecommendedRuleConfig
+        description: >-
+          Require any slot in the metamodel with `recommended: true` (e.g. description)
+          to be provided. Not auto-fixable.
       root_type_checks:
         range: RuleConfig
         description: >-
@@ -90,12 +98,12 @@ classes:
           CamelCase for enums, snake_case (default) or UPPER_SNAKE for permissible_values
           (see permissible_values_upper_case option). This rule may conflict with the
           permissible_values_format rule. Not auto-fixable.
-      canonical_prefixes:
-        range: CanonicalPrefixesConfig
+      tree_root_class:
+        range: TreeRootClassRuleConfig
         description: >-
-          Enforce canonical prefixes by verifying that the mappings defined in the `prefixes`
-          slot agree with those provided by the [prefixmaps](https://github.com/linkml/prefixmaps)
-          package. Not auto-fixable.
+          Require a single class with `tree_root: true` and optionally verify that class's
+          name. Autofix will create a new class with `tree_root: true`, a name based on
+          the rule configuration, and slots for existing classes.
 
   RuleConfig:
     description: >-

linkml/linter/config/default.yaml

@@ -22,6 +22,10 @@ rules:
     level: disabled
   no_undeclared_ranges:
     level: disabled
+  one_identifier_per_class:
+    level: disabled
+  one_key_per_class:
+    level: disabled
   root_type_checks:
     level: disabled
   standard_naming:

linkml/linter/config/recommended.yaml

@@ -9,6 +9,10 @@ rules:
     level: error
   no_undeclared_ranges:
     level: error
+  one_identifier_per_class:
+    level: error
+  one_key_per_class:
+    level: error
   root_type_checks:
     level: error
   standard_naming:

linkml/linter/linter.py

@@ -45,8 +45,7 @@ def get_metamodel_validator() -> Validator:
     meta_json_gen = JsonSchemaGenerator(LOCAL_METAMODEL_YAML_FILE, not_closed=False)
     meta_json_schema = meta_json_gen.generate()
     validator_cls = jsonschema.validators.validator_for(meta_json_schema, default=jsonschema.Draft7Validator)
-    validator = validator_cls(meta_json_schema, format_checker=validator_cls.FORMAT_CHECKER)
-    return validator
+    return validator_cls(meta_json_schema, format_checker=validator_cls.FORMAT_CHECKER)
 
 
 def merge_configs(original: dict, other: dict):

linkml/linter/rules.py

@@ -319,6 +319,43 @@ class RootTypeChecks(LinterRule):
                 yield LinterProblem(f"Root type '{t}' is missing the required 'uri' attribute")
 
 
+class OnePerClass(LinterRule):
+    """Ensures that there is only one slot with the specified attribute per class."""
+
+    id = "one_per_class"
+
+    def _check(self, schema_view: SchemaView, attr_name: str) -> Iterable[LinterProblem]:
+        for cn in schema_view.all_classes():
+            slots_with_attr = [
+                slot
+                for slot in schema_view.class_induced_slots(cn)
+                if hasattr(slot, attr_name) and getattr(slot, attr_name)
+            ]
+            if len(slots_with_attr) > 1:
+                naughty_slots = ", ".join(sorted([slot.name for slot in slots_with_attr]))
+                yield LinterProblem(f"Class '{cn}' has more than one '{attr_name}' slot: {naughty_slots}")
+
+
+class OneIdentifierPerClass(OnePerClass):
+    """Ensure that there is only one slot with the `identifier` attribute set to True per class."""
+
+    id = "one_identifier_per_class"
+
+    def check(self, schema_view: SchemaView, fix: bool = False) -> Iterable[LinterProblem]:
+        """Run the one_identifier_per_class check."""
+        return self._check(schema_view, "identifier")
+
+
+class OneKeyPerClass(OnePerClass):
+    """Ensure that there is only one slot with the `key` attribute set to True per class."""
+
+    id = "one_key_per_class"
+
+    def check(self, schema_view: SchemaView, fix: bool = False) -> Iterable[LinterProblem]:
+        """Run the one_key_per_class check."""
+        return self._check(schema_view, "key")
+
+
 class StandardNamingRule(LinterRule):
     id = "standard_naming"
 

linkml/utils/schema_builder.py

@@ -193,6 +193,8 @@ class SchemaBuilder:
                 if isinstance(pv, str):
                     pv = PermissibleValue(text=pv)
                     enum_def.permissible_values[pv.text] = pv
+                else:
+                    enum_def.permissible_values[pv.text] = pv
         return self
 
     def add_prefix(self, prefix: str, url: str, replace_if_present=False) -> "SchemaBuilder":

linkml/utils/schemaloader.py

@@ -401,10 +401,83 @@ class SchemaLoader:
             # Inline any class definitions that don't have identifiers.  Note that keys ARE inlined
             if slot.range in self.schema.classes:
                 range_class = self.schema.classes[cast(ClassDefinitionName, slot.range)]
-                if slot.inlined_as_list or not any(
+                range_has_identifier = any(
                     [self.schema.slots[s].identifier or self.schema.slots[s].key for s in range_class.slots]
-                ):
-                    slot.inlined = True
+                )
+                # the inference and validation of class inlining is quite complex
+                # slot.inlined and slot.inlined_as_list can have three different values:
+                # True, False or None (if nothing specified in the schema)
+                # range_has_identifier can only be True or False
+                if range_has_identifier is True:
+                    if slot.inlined is False:
+                        if slot.inlined_as_list is True:
+                            slot.inlined = True
+                            # TODO: do not override a given value, but raise an exception
+                            self.logger.warning(
+                                f"Slot '{slot.name}': 'inlining' as list requested. "
+                                + "Overriding inconsistent `inlined: False`!!"
+                            )
+                        elif slot.inlined_as_list is False:
+                            self.logger.warning(
+                                f"Slot '{slot.name}': Specifying a value for 'inlined_as_list' does not "
+                                + "make any sense for non-inlined classes."
+                            )
+                    elif slot.inlined is None:
+                        if slot.inlined_as_list is True:
+                            slot.inlined = True
+                            self.logger.info(
+                                f"Slot '{slot.name}': A value for 'inlined_as_list' specified, but no 'inlined' "
+                                + "specification. `inlined: True` has been automatically set!"
+                            )
+                        elif slot.inlined_as_list is False:
+                            # TODO: decide if `inlined` should be set or not and implement accordingly
+                            self.logger.warning(
+                                f"Slot '{slot.name}': A value for 'inlined_as_list' specified, but no "
+                                + "'inlined' specification."
+                            )
+                    elif slot.inlined is True:
+                        if slot.inlined_as_list is None:
+                            slot.inlined_as_list = False
+                            self.logger.info(
+                                f"Slot '{slot.name}': A class with identifiers ({range_class.name}) will be "
+                                + "'inlined' as a dictionary. `inlined_as_list: False` has been set!"
+                            )
+                else:
+                    if slot.inlined is True:
+                        if slot.inlined_as_list is False:
+                            self.logger.warning(
+                                f"Slot '{slot.name}': A class without identifiers ({range_class.name}) cannot be "
+                                + "'inlined' as a dictionary."
+                            )
+                        elif slot.inlined_as_list is None:
+                            slot.inlined_as_list = True
+                            self.logger.info(
+                                f"Slot '{slot.name}': A class without identifiers ({range_class.name}) will not be "
+                                + "typically 'inlined' as a dictionary. `inlined_as_list: True` has been set!"
+                            )
+                    elif slot.inlined is False:
+                        slot.inlined = True
+                        self.logger.info(
+                            f"Slot '{slot.name}': A class without identifiers ({range_class.name}) MUST be "
+                            + "'inlined', but non-inlined specified. `inlined: True` has been automatically set!"
+                        )
+                    else:
+                        slot.inlined = True
+                        self.logger.info(
+                            f"Slot '{slot.name}': A class without identifiers ({range_class.name}) MUST be "
+                            + "inlined, but nothing specified. `inlined: True` has been automatically set!"
+                        )
+                        if slot.inlined_as_list is False:
+                            self.logger.warning(
+                                f"Slot '{slot.name}': A class without identifiers ({range_class.name}) cannot be "
+                                + "'inlined' as a dictionary."
+                            )
+                        elif slot.inlined_as_list is None:
+                            slot.inlined_as_list = True
+                            self.logger.info(
+                                f"Slot '{slot.name}': A class without identifiers ({range_class.name}) will not be "
+                                + "typically 'inlined' as a dictionary. `inlined_as_list: True` has been set!"
+                            )
 
             if slot.slot_uri is not None:
                 slot.mappings.insert(0, slot.slot_uri)

{linkml-1.9.4rc1.dist-info → linkml-1.9.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: linkml
-Version: 1.9.4rc1
+Version: 1.9.5
 Summary: Linked Open Data Modeling Language
 Author: Deepak Unni
 Author-email: Chris Mungall <cjmungall@lbl.gov>, Sierra Moxon <smoxon@lbl.gov>, Harold Solbrig <solbrig@jhu.edu>, Sujay Patil <spatil@lbl.gov>, Harshad Hegde <hhegde@lbl.gov>, Mark Andrew Miller <MAM@lbl.gov>, Gaurav Vaidya <gaurav@renci.org>, Kevin Schaper <kevin@tislab.org>
@@ -27,7 +27,7 @@ Requires-Dist: isodate>=0.6.0
 Requires-Dist: jinja2>=3.1.0
 Requires-Dist: jsonasobj2<2.0.0,>=1.0.3
 Requires-Dist: jsonschema[format]>=4.0.0
-Requires-Dist: linkml-runtime<2.0.0,>=1.9.4
+Requires-Dist: linkml-runtime<2.0.0,>=1.9.5
 Requires-Dist: openpyxl
 Requires-Dist: parse
 Requires-Dist: prefixcommons>=0.1.7

{linkml-1.9.4rc1.dist-info → linkml-1.9.5.dist-info}/RECORD

@@ -3,53 +3,56 @@ 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/logging.py,sha256=MdVbox1qr6kDUHUCWAmFhV-D6ebs_nn8vVwB8KDQfew,742
-linkml/cli/main.py,sha256=EncEEYMqaSlXj3pOEi8_xqZe12BYPW9IdEMJilGqIkI,5594
+linkml/cli/main.py,sha256=IyLP0yZV4J51rhmw9wdX_4XNKehYlk3L3sBvwv02pXk,5804
+linkml/converter/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+linkml/converter/cli.py,sha256=0xcUXdVPUXZvVuHivUibfVMoCd24oPsjYU1M17H173U,7121
 linkml/generators/PythonGenNotes.md,sha256=SOzZhIBP_O8g46uBTnYy6A7nuP--hh-f_QXEERZRxdk,50822
 linkml/generators/README.md,sha256=fnkmT98lspv8a8FyBLOQsHoBKQaapFGb8H_Stg56dco,4436
-linkml/generators/__init__.py,sha256=AxTltouJeNayg3sJmVM7h4JkCx8NxGa4AV-_awtvfmo,1669
+linkml/generators/__init__.py,sha256=DGSaQ3JOAjI1VwjZQXmU6IPZdAfoBC2ma-N4aRgvGKY,1742
 linkml/generators/csvgen.py,sha256=gPwX5GuwToD2KQF7SrINatqwMYY-54ZsgDTgYH1EM1Y,3242
 linkml/generators/dbmlgen.py,sha256=6TvpdvTEPoprdBHuJpbfIb1Ejwpp20kGNUvW5Av7cpo,5465
-linkml/generators/docgen.py,sha256=Xw1Urg6y6UgYl7jYQWUufC3sV1AgVfUtM6kUUFpC9UU,43316
+linkml/generators/docgen.py,sha256=oB-oN1HFCpVOxBBG__Baka7qOZLR4w_s3vcN5m70xs4,45384
 linkml/generators/dotgen.py,sha256=DR1tC-vZ7Vj-NxEkE-zOPGrwPUIk5Bo2LISsJpS0rUk,5022
-linkml/generators/erdiagramgen.py,sha256=lUHFkiOHiOLvymnKoJ2Erl0SZzXvSnqJzKGfl5K-MyI,12100
+linkml/generators/erdiagramgen.py,sha256=dZ1RfZize7fLEdXSO5DyVAyvC8dIFDCSRrZzyw0hodc,12317
 linkml/generators/excelgen.py,sha256=81x0Ib13ZjLC5WBWsH0aePn8swv_pjZnwV4X-T4q4Jc,7684
 linkml/generators/golanggen.py,sha256=oBXY0gUz2OzI8uKjubUT9WeBJ4TdoOYUqXxNqeEG1gM,5834
 linkml/generators/golrgen.py,sha256=92hswWdusngnGDGD3vpX_iHbIDYRZrRV5xWkpxG7nxw,3448
-linkml/generators/graphqlgen.py,sha256=34qGKjNqz6jJg4b6ClGAA1ffOscSPpeemM3IkifDuRg,3485
+linkml/generators/graphqlgen.py,sha256=I3zWuMOKjZz5KfA-nyJi_RWVfJdDQ8RUccwuXeoTQik,4775
 linkml/generators/javagen.py,sha256=BTAXgvOOvRa3AOfaaiVFyuyaqg4XFR_JbO6_7tT_AnQ,5335
-linkml/generators/jsonldcontextgen.py,sha256=opDZ0q_rc-E8yKeieWZbrMk-np8fheyMVB5jnxmMOz4,8946
+linkml/generators/jsonldcontextgen.py,sha256=JBgfOgjeOBoc0fFlPdKqn-zBeKRs5GopZVH0ltlBU1o,11355
 linkml/generators/jsonldgen.py,sha256=pHSCmZ_qKdzVot_J8XFhPAyYOUYap7Vt6NGigM0-SQ0,7842
-linkml/generators/jsonschemagen.py,sha256=gVfeEzz9izxI231oA48pDc4vTP7rvUUkySmw2T8PNoo,30887
+linkml/generators/jsonschemagen.py,sha256=bGa6nvazlUjCN-G5RbdLaUHoyxEDPfnfuCJ85jrRqfw,31758
 linkml/generators/linkmlgen.py,sha256=j8T7O-_i7JAa87EnHgSqmdeD4RsXOD66MqZU7P-tX2c,4221
 linkml/generators/markdowngen.py,sha256=_4RfmuMNR-m90QdmbG26iFQC_ZSaUBDUWPX_hsqZPLY,35530
-linkml/generators/mermaidclassdiagramgen.py,sha256=9HEcXntK0lL4T2wYpKzeFyTg6rRUt1ZiOVdZgA_l4eg,5145
+linkml/generators/mermaidclassdiagramgen.py,sha256=Zr926xS1K2MqD3K3x9zb9w_ot1T0wyj9U_1ZHZTN2n4,5984
 linkml/generators/namespacegen.py,sha256=C4p9LSwsnDqf6sv-wG5l0VQniWFJ1HA1hRXJBDOg3pM,6467
 linkml/generators/oocodegen.py,sha256=dgcHhpO81qC2Tx-kG_VhZVaoRjOwrcrulIXV8gEU1bY,7808
-linkml/generators/owlgen.py,sha256=HcW5EIohi9YMd6pXH62bAesZrrbBt5H8-4eQ3Eab6ow,58095
-linkml/generators/plantumlgen.py,sha256=S05S13kxDLeKJihZ7BZesuj_8-tQUzsWjL6S478dzQg,15603
+linkml/generators/owlgen.py,sha256=-eCqd0QF_3k0sT6Qjl-uSVGpEGOYtip8wQEfZeovUNo,58581
+linkml/generators/plantumlgen.py,sha256=KUmx25wCcUJrnaOqXJ3EyCx12f9YK2wlrWGOFifKcJc,16053
 linkml/generators/prefixmapgen.py,sha256=X-3K1q5WcSS8TL7rHBOL4qBGBk2Szr7l1_UzRQVvFGA,4246
 linkml/generators/projectgen.py,sha256=qvXIWDfrPYKZT38JCyItQjW1AZofJ4ZyPZeUkscZxOo,9586
 linkml/generators/protogen.py,sha256=a4KUyKj525tuE2YenEJQ_IkbNKnnhVH_N-qTEmMBVY4,2524
 linkml/generators/pythongen.py,sha256=soc3EgUpp1dYwRWx--aVGWo9emCNhj9TvcJsUNunlwE,55847
-linkml/generators/rdfgen.py,sha256=33m01NKAF-AfOLwq_g6I9itle43_u4Ek10mLT8mmuYs,2963
+linkml/generators/rdfgen.py,sha256=X_N_x-EWvcFimsRi7tKnEAKmzOCTM7Z-O5BQgFzYRcY,3458
 linkml/generators/shaclgen.py,sha256=qas_rqhwx7IpnIKAKOtxUTPB7EdhiCcTOLVJQbLOOsk,15277
 linkml/generators/shexgen.py,sha256=fVwrYRifsojiPu6vM1oNwnkSEp4uX-QognHOExJs0cY,9933
 linkml/generators/sparqlgen.py,sha256=1WjZQFNk3QXMaJhVeztJ1uWg8qojLyGGBdAKSjpVQaI,6176
 linkml/generators/sqlalchemygen.py,sha256=b8vrigGOso66qQrZKlvawRDz-1oDu5LyL-X4F-mkTdc,9053
-linkml/generators/sqltablegen.py,sha256=83j-4ImIZIwz1WTy1fHMGYbP7WjWpN6K0AuNQnXPeXw,18178
+linkml/generators/sqltablegen.py,sha256=BpqE8rTCDrN89usf2-4iijdVOXyWDSNyZlv-DA4KD24,18279
 linkml/generators/sssomgen.py,sha256=zrZy0WL9fF5bk-XAcB-MZYZkhHhqVRHt2rGBUtfqnLY,6891
 linkml/generators/string_template.md,sha256=UMEgU5-JLBEoSpoZ0SKuzcZV6El3vcApm-cvsegsE1c,1780
 linkml/generators/summarygen.py,sha256=abNd39Z-Kn3FX2fjXLeCqvXvFunpqM7UFPimtiCB2p0,3081
 linkml/generators/terminusdbgen.py,sha256=Zizvh_GLBO9LK_X11gUvB_Ip1ttkkfiD4OZBtxjgAG4,4669
 linkml/generators/typescriptgen.py,sha256=wRnZpZ3LEepJRFYHVNP06PX5rPFzIDPglDRxi0Z6Zro,8870
 linkml/generators/yamlgen.py,sha256=PWexYoR3wHRoAUk6zK67fRYjBF6sAmX_iGlOAT0PJq0,1623
+linkml/generators/yarrrmlgen.py,sha256=jEQo6k_w_S3HeYoMm0C5lDDqrXaB_ZMADSJ1i35KCww,5865
 linkml/generators/yumlgen.py,sha256=ZK42N3hJPvvOdztOWCwysARrGVWjg5V4Qx2XcS2Vvgc,13277
 linkml/generators/common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml/generators/common/build.py,sha256=X2QDnybdr5GwDIaXWfwAzIqduqk7_rDReU-7CvcJ2OI,2835
+linkml/generators/common/build.py,sha256=3SxiwOp9bzrt9XVQqgegstGEuiibnG0-4gdlIAiRBtE,2394
 linkml/generators/common/ifabsent_processor.py,sha256=qefNF_rd24DxF4IGAynR9J7zWGH-oMfDULNbFMvZalA,13527
 linkml/generators/common/lifecycle.py,sha256=Rx9q8shhS_e-4Hx_06wOVR1ZW7I3rqNS8_bOM-r9eCw,5541
 linkml/generators/common/naming.py,sha256=KkY3KCTX3DM30VbPjfIS6icEc-IxUNF9hE8GXreDAv4,5081
-linkml/generators/common/template.py,sha256=AmHcTlPnN23H4IvuX70AiTRzd-V16zNFBb7d3cCntFU,3326
+linkml/generators/common/template.py,sha256=-ZuokNyzB8hnHt9t3hJ69ezeRCGiFE7Iy3ufZlmMF4o,15117
 linkml/generators/common/type_designators.py,sha256=ORA9siVxHUXqn3TMuun81m_whqZcX3Zrnn1FDf6dK7c,1931
 linkml/generators/docgen/class.md.jinja2,sha256=2QI-9DpqZ9XJc-g2RwiBa2EkWeDeg4j4HH5cxgE_A3w,4336
 linkml/generators/docgen/class_diagram.md.jinja2,sha256=UCpMYgzbcRsXpb7TnUsCUqIu0yWCEOvPB6o7IOvZFuA,3728
@@ -66,33 +69,73 @@ linkml/generators/javagen/java_record_template.jinja2,sha256=OQZffLSy_xR3FIhQMlt
 linkml/generators/legacy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/generators/panderagen/__init__.py,sha256=Bcthn0rKU6xzQoBU--hfTUJwyOvKjASGICYamEglzcQ,109
 linkml/generators/panderagen/class_generator_mixin.py,sha256=LKdpKb1_pyBN3iyhzsQE_Q9A3S9CnXj0RQUDQw0_Ly4,826
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 linkml/generators/panderagen/enum_generator_mixin.py,sha256=CMILBMjP35L8HHdp7WuO0dAHe9zEVBvN5CBSQlq41_g,708
-linkml/generators/panderagen/panderagen.py,sha256=OxLZrVLzUD5PrmomsC0MYaUM8v0R4djKHDtVr6UjPjQ,6445
-linkml/generators/panderagen/slot_generator_mixin.py,sha256=mDoyptHXiR4TehDmSe3cYX4Mpa1oJUH8apPiJEKycLo,2586
-linkml/generators/panderagen/panderagen_class_based/class.jinja2,sha256=56Pb-6iiGgyfcCT1oE7mD4Rbs637SLgn2wsqH3Eyzwc,686
-linkml/generators/panderagen/panderagen_class_based/enums.jinja2,sha256=7eXfmoz7F6Tb2aYumTwW6UrwrQvqD73oYTi-LbmNCVw,295
+linkml/generators/panderagen/linkml_pandera_validator.py,sha256=lGzngQVtq2QAVhCVBaQhunZBWq-CqHAQMT6_bVwwXmE,7554
+linkml/generators/panderagen/panderagen.py,sha256=U7AJpEIxy_NcyVqAgxWAqlmaYa3jCFD5lxD6qJ4nEtI,7031
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+linkml/generators/panderagen/panderagen_class_based/custom_checks.jinja2,sha256=HwtAHT2cxsne8ACyYlhUUCkAt8cJyE5YUon1jJb0bhE,897
+linkml/generators/panderagen/panderagen_class_based/enums.jinja2,sha256=wgrDEc_rU4GGZkc2e0Fqpt264ftH-jB8kdZ386zc7G4,272
 linkml/generators/panderagen/panderagen_class_based/header.jinja2,sha256=shLPwNAjIPMgR7uoqZWUxo4a_OtV15ywSjYh0m9dIKo,396
-linkml/generators/panderagen/panderagen_class_based/mixins.jinja2,sha256=JCgwGre4FuoEUSbPrg5MRJXZbcx5_3uCt-JuBsG3LRY,955
-linkml/generators/panderagen/panderagen_class_based/pandera.jinja2,sha256=Vlh5tdp7T9gbPst1RR72PdFeboE4Ha0yX5wILXHeZyE,506
-linkml/generators/panderagen/panderagen_class_based/slots.jinja2,sha256=cy8LKkGNDkNZBoECVOwkvN0MKLj0U_KrgkiOaY317Rc,1416
+linkml/generators/panderagen/panderagen_class_based/pandera.jinja2,sha256=gkON1BzEyIaMl47ZZDqtAYUXErJDNyTY9nSrz-p-Lis,769
+linkml/generators/panderagen/panderagen_class_based/slots.jinja2,sha256=u_pzArB7QFxpfQCro55l22F1c4qwJL0DcBgKbPBs9Mc,1582
+linkml/generators/panderagen/transforms/__init__.py,sha256=lWhHmiw1H5DAaHwEcNIOMCx4F3wG_NM7cIlwJAtfdt8,690
+linkml/generators/panderagen/transforms/collection_dict_model_transform.py,sha256=o1K1JqzIrOKtLfokHYOZ0SZ9dkPpqMVwyzq6jEP8SAw,2580
+linkml/generators/panderagen/transforms/list_dict_model_transform.py,sha256=-Dhb7_rSupAsaitMw0KOo8dK3yo_ZLKlnqXO7HCe_GM,2443
+linkml/generators/panderagen/transforms/model_transform.py,sha256=ZAD7jW1xqe6UU7bWOQ8dV2qs8MrfIR6bQ0GYXLVwlt0,225
+linkml/generators/panderagen/transforms/nested_struct_model_transform.py,sha256=eeJwywRsCVPX9o9ZAor_PPx-yTM0CNE1nX02BmOw9W8,1050
+linkml/generators/panderagen/transforms/simple_dict_model_transform.py,sha256=O2hF4MSCN9i89hzIkDxvkbAJf1zOKPnRQlzjo4ZCjUc,3549
 linkml/generators/pydanticgen/__init__.py,sha256=5SUFNcrh-6MLfMqptR6wPsR2v1Gyrl3wii-yu6kdnQM,700
 linkml/generators/pydanticgen/array.py,sha256=TD3_LStHfGGY1TI7jn_9DeyvLMBmgM4kc0JeOWGzSbs,25803
 linkml/generators/pydanticgen/black.py,sha256=BaJ7b-kMUbIN_cKRT3yCaMEbFwxzj1_U7w4fKQnkL44,723
 linkml/generators/pydanticgen/build.py,sha256=KVRiaJ-o1OuRGyeli8PYDOJPqeSVoKfoibsjffoXeFU,4064
 linkml/generators/pydanticgen/includes.py,sha256=qwC8Lj2enFMLLNbaOlZINra0WSQuI4WS9Bd_ZvgQe1c,476
-linkml/generators/pydanticgen/pydanticgen.py,sha256=tTgegnBae0Y_QfV1BnbRoUw-h5TPdcw_pJImWkF521w,49780
-linkml/generators/pydanticgen/template.py,sha256=QKDjsP3XosdkckMx_lDx7UZsIeIvgk4RdO7wJnDQVG4,24836
-linkml/generators/pydanticgen/templates/attribute.py.jinja,sha256=4s4eUZEqiTxHV2pU8beF761xut4Q-bXwZXF0XBlnXAs,881
-linkml/generators/pydanticgen/templates/base_model.py.jinja,sha256=4wrDfZppqLQqs9NKW0NW_5Q9wJiDOT-P2UKU_d8U07s,407
+linkml/generators/pydanticgen/pydanticgen.py,sha256=6HtWLGVjZsSO_AvBDFI0xt1Xbq03aSerM5ILMwpNgzg,51515
+linkml/generators/pydanticgen/template.py,sha256=fnA8jDTE53h05zA8Rrl6KvHmu3PLYDgqgoeF0HZBPRE,16272
+linkml/generators/pydanticgen/templates/attribute.py.jinja,sha256=A44qNvlszD1FtPGYhh1yHkziBQbw85HP7yiTy486Ca8,928
+linkml/generators/pydanticgen/templates/base_model.py.jinja,sha256=lKxLLCPSvEXQN6nXivBO9T1Vv8AR0YPVcxM1Q4L3PCw,1050
 linkml/generators/pydanticgen/templates/class.py.jinja,sha256=PCkbfRcONxk4ScVHKiGK-6KPjzS94QCKCn262LZ6O_8,691
 linkml/generators/pydanticgen/templates/conditional_import.py.jinja,sha256=r2kb-AOJgqUgU98_tqk2aB4BG1bJFcfV1Ts7TaHTGds,241
 linkml/generators/pydanticgen/templates/enum.py.jinja,sha256=d2j0FbQ4HT-TjspaUkfSHWaHJ50didUBTE8RV9Cj7bo,372
 linkml/generators/pydanticgen/templates/footer.py.jinja,sha256=k764ffh6q-qDJYpTtiUGePOrcw6i81Osrm8mRWs_c2c,156
-linkml/generators/pydanticgen/templates/imports.py.jinja,sha256=3SaYtFofcjCzzJgD6cXZdcLyVVGvzyOcNmskZMfKCyI,1250
+linkml/generators/pydanticgen/templates/imports.py.jinja,sha256=bk21V9ofXAfhT4fFSPodGtzl8OjtewAcHgdMYX-Yvyo,1248
 linkml/generators/pydanticgen/templates/module.py.jinja,sha256=hqZKsJ72yUioBkZAunscVgLSe58OFHf0z6-so_b43U4,526
 linkml/generators/pydanticgen/templates/validator.py.jinja,sha256=oz8XWh4Mt7DRHH0KObKGZWl_WUoR0KzoGMkLOh-NXFU,525
 linkml/generators/python/__init__.py,sha256=NS9fPEuAo0punDplD91F9mcViXMJJv04Q5NkFcKPNvY,40
 linkml/generators/python/python_ifabsent_processor.py,sha256=AqFabuyHCBpPTLO2-XO1uWNh3YcIpc-Na_649o_VmLc,3834
+linkml/generators/rustgen/__init__.py,sha256=2ihCJiuI3AxYo55Sqt4r2wVxn-3Kp6RNgQVQ-SNvaQU,115
+linkml/generators/rustgen/build.py,sha256=vBMcCsDjDM56BzSHFGy0S0Ugv5PusSVBfIWa3chTlbI,1879
+linkml/generators/rustgen/cli.py,sha256=GEQmwxx_yZNcVRA0eUao7Qxgdp8o8NU5GhHq59SQhjQ,2349
+linkml/generators/rustgen/rustgen.py,sha256=OyURn_vvk7OXkG5ivNSBzpMiKJKTIZgGoVdI5bwOEgo,45751
+linkml/generators/rustgen/template.py,sha256=D412jQwfLQy79Z-_jSUUBh6_erTNh95eW4-v7-ed25E,29482
+linkml/generators/rustgen/templates/Cargo.toml.jinja,sha256=CqHM6DkVLpk9YUD4FJmt4LJLwkEjzGsyUTd1TIAkFqw,1061
+linkml/generators/rustgen/templates/anything.rs.jinja,sha256=WWAO9QkS0kKWkPcW5M6-58X8lyuDpuMpsz_1TEid5ss,5246
+linkml/generators/rustgen/templates/as_key_value.rs.jinja,sha256=dOAWwUy4Ce6jZ-6Uj3cwCGo1-hBdSBsU1eEhUoIHfd8,3181
+linkml/generators/rustgen/templates/class_module.rs.jinja,sha256=HKRA6L74rGLynfvxdLhzuVQK-5s7tWlcpUmUr1NSw5Q,153
+linkml/generators/rustgen/templates/enum.rs.jinja,sha256=YiBvQvjkIKGNv-mtAMCENf7gdM78-d2qOV5uBJXA7Rs,2395
+linkml/generators/rustgen/templates/file.rs.jinja,sha256=UCrDJuZu3q8IX8TW7qhBVmmillJ04iFdQ5XzCSjVGI0,1297
+linkml/generators/rustgen/templates/import.rs.jinja,sha256=fYEG5YYVszjBVp6Gs-pJdgcAoaiHghUQxUg2BA4yyx8,397
+linkml/generators/rustgen/templates/imports.rs.jinja,sha256=2u0cVLBrluxldVnEUJ1ipMJWQGrWidmDP6KbJVyQxi8,158
+linkml/generators/rustgen/templates/lib_shim.rs.jinja,sha256=zY7Cje4tOs7hEPuur5U5BMo8Jc2z4BPDYG2JgFpv__k,1681
+linkml/generators/rustgen/templates/poly.rs.jinja,sha256=CXFmKfNwZMSI2cYXy14vKzv80QGtO86vjTdTf7NZi0U,123
+linkml/generators/rustgen/templates/poly_containers.rs.jinja,sha256=xDZevupLBm0bLjltXc1VzE1tVyAligeOtRZmN6-_puw,12347
+linkml/generators/rustgen/templates/poly_trait.rs.jinja,sha256=Smje9PjD2LZsZ27XVbCcHJeWDU5e1PyNg-zJOAVhf9U,308
+linkml/generators/rustgen/templates/poly_trait_impl.rs.jinja,sha256=u1_DSCB-7vX05_xL34gmIQHKelnexGCQZp_lAXhShyw,95
+linkml/generators/rustgen/templates/poly_trait_impl_orsubtype.rs.jinja,sha256=4GTCjV_1MlUG5O-gN_SD-4UY3RaLvthIYW24sLhXGBs,93
+linkml/generators/rustgen/templates/poly_trait_property.rs.jinja,sha256=tLge1ghiR6lHPUsHDhXIQHPshK7hGkJtXm8hXSiL4-g,428
+linkml/generators/rustgen/templates/poly_trait_property_impl.rs.jinja,sha256=IwJB6vy0ShZgyNvdMo4WUcPmns7qh9gKbDbHfB6KqmU,5196
+linkml/generators/rustgen/templates/poly_trait_property_match.rs.jinja,sha256=qEeKXt1AcEoIpDrbaNkOgyfGs1zgxGtn8SyHo6mgCWA,478
+linkml/generators/rustgen/templates/property.rs.jinja,sha256=7GRXNwEPi1jLttOI27jldcK3H3-tPUVLqvpFr4O_ST4,1350
+linkml/generators/rustgen/templates/pyproject.toml.jinja,sha256=4ViLLeTcLt9wzqe8i80HEypHiU5lGwfzU6IHqzzc1cw,184
+linkml/generators/rustgen/templates/serde_utils.rs.jinja,sha256=PDx0VLooA0sjKGBf_XNxHmiEobGdQMmgW7ew6-Gf5Po,13884
+linkml/generators/rustgen/templates/slot_range_as_union.rs.jinja,sha256=qYeOvojeoPUkUPiRhnX-nurwBfjkIMIeHkIUzEYHu3E,2235
+linkml/generators/rustgen/templates/struct.rs.jinja,sha256=45vGkG8R5OgUVyUWnF40D0sym0FjP46XIDnyzpUItqc,2377
+linkml/generators/rustgen/templates/struct_or_subtype_enum.rs.jinja,sha256=Jpix-C9Hcycg8gyuF_ghHyZAQBH_yKJjpB6P74Yh1mM,3559
+linkml/generators/rustgen/templates/stub_gen.rs.jinja,sha256=3xiRepFCr1vrDUne_4if3Tzil9B4l5lV0x9RRRZeOkU,2093
+linkml/generators/rustgen/templates/stub_utils.rs.jinja,sha256=_FAVspupgJwpdbiSLjvZG0MY6PK5pf-1HibUrTiEf4w,2818
+linkml/generators/rustgen/templates/typealias.rs.jinja,sha256=HQtLzULc-7YaqfVfecYUJBqX7k3PCMEyU9Q8h5-a5vc,413
 linkml/generators/shacl/__init__.py,sha256=KgMOyESGTdKk2Vhx9uuUYgEJPuJQ-iT1vDQVIMoiXCM,58
 linkml/generators/shacl/shacl_data_type.py,sha256=gX3Y2KyTVPwMyef0cJMTEpU9h0oH-H0ThVDORdNW170,1828
 linkml/generators/shacl/shacl_ifabsent_processor.py,sha256=rjxD5OSa7s66ALSj_8CqAqU8oj2NiE4nfOQJ6xCSpjA,4363
@@ -101,14 +144,14 @@ linkml/generators/sqlalchemy/sqlalchemy_declarative_template.py,sha256=X_Ws1NUBi
 linkml/generators/sqlalchemy/sqlalchemy_imperative_template.py,sha256=u4ZpponG1h6XROrOHGOf_0H2e6xL1_s8twAOA-gx94A,1622
 linkml/linter/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/linter/cli.py,sha256=0Bt7-A1zUTJK3rzFj1O-uvLXc0JsO5vkxODvkWOPgT4,4552
-linkml/linter/linter.py,sha256=O7X2i6w-YWKl26FL7WXw9Beh4xkhmYi30PuD_FE3cM8,5187
-linkml/linter/rules.py,sha256=WKTDIA8iQbTOi_hUOEY6AwRY_Xa56AcIJOHQ8oJ0qnc,17342
-linkml/linter/config/default.yaml,sha256=sDKkS9RXhSy7U6YCr5bbzPpCYCvChy6c9PsRd49tJRc,730
-linkml/linter/config/recommended.yaml,sha256=iPvaevOWgNge0ECAQoXE1v78lY_te7i9nyE-xr7pqdc,316
+linkml/linter/linter.py,sha256=wxAopbGgpT19m-FR4vslgCwoVJv9yDS8-zImtWSIwm4,5161
+linkml/linter/rules.py,sha256=bVRY3wUIJSTuefd_gVnF2HR7EQRudFWaFnbrAwf4nic,18795
+linkml/linter/config/default.yaml,sha256=B2hyc9xIz0IoncJ4lDMkJ8BmipIzkPWLZHz6xKyREnA,819
+linkml/linter/config/recommended.yaml,sha256=wRY3-gYzfVj7yn4lFOOWFTW3Y3EoLiEFBdX0aWO7Zos,399
 linkml/linter/config/datamodel/.linkmllint.yaml,sha256=40rNhcL35FXQSjlVBMWnyPgplwEUqFT_sJmeZqUzxMw,292
 linkml/linter/config/datamodel/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml/linter/config/datamodel/config.py,sha256=juLR811BlMagvLY_qrT2rbOGqiC3S7PO9MrdvWJHHNU,23821
-linkml/linter/config/datamodel/config.yaml,sha256=z2EFvMXAFL_7hIrBrq_0SK5EQIa14p7VOSGfVUyTtCc,10018
+linkml/linter/config/datamodel/config.py,sha256=4Gr1uY8XXYRU3meAi8D6qlgc3uPlfWwyJMJBOnYTHnw,24772
+linkml/linter/config/datamodel/config.yaml,sha256=jVJJjW_avpGePxu6lEcTO_NNyPYzAG36Ldez8WxZHK0,10368
 linkml/linter/formatters/__init__.py,sha256=lKTbA20yL_TuimKZIBI1DGXgDO7D4QSrJ3zZFCJRwu0,269
 linkml/linter/formatters/formatter.py,sha256=u2DNowT7Nx1rexCMJmghlXklTYb98_Glj5qhnhjTkBc,518
 linkml/linter/formatters/json_formatter.py,sha256=rrOELuETUCFTl1Ewnrus9Rx9hl2g4uucrMfN6yw33iI,767
@@ -124,7 +167,6 @@ linkml/transformers/relmodel_transformer.py,sha256=g3WhT3FyNlxP36lFaJzSh9v9eZweN
 linkml/transformers/rollup_transformer.py,sha256=YP3RyYa0TzfkTrPZ4LnTIedmQWCnneFk3wAT77E1Amc,4549
 linkml/transformers/schema_renamer.py,sha256=DvXsAsxAb8p8RAxR_c74zbn_VRFN1JHCLHcjH9z7qr0,5263
 linkml/utils/__init__.py,sha256=Pkyv-Gfb8QoJdInRdJuuUz1Igfe0sT9t8Gv3V_fyTXc,92
-linkml/utils/converter.py,sha256=0xcUXdVPUXZvVuHivUibfVMoCd24oPsjYU1M17H173U,7121
 linkml/utils/datautils.py,sha256=QlbzwXykh5Fphfe5KxPo6_ekXfniLbHiEGJtLWjUrvY,3742
 linkml/utils/datavalidator.py,sha256=kBdWaVi8IZT1bOwEJgJYx-wZAb_PTBObB9nHpYORfKA,472
 linkml/utils/deprecation.py,sha256=fFd_rUmTJInovuhuHVZf_44fQRve6FyJ43DY2-0XLmA,9781
@@ -135,9 +177,9 @@ linkml/utils/helpers.py,sha256=MomYM4Oof-c1SgyMpjoG0Aob-eaVeF8kXvuzdJiKo_g,3351
 linkml/utils/logictools.py,sha256=dvwuX6DU0PZyxhVr9kphyQFttqZNSbbIRZ7vtTh2gU8,23649
 linkml/utils/mergeutils.py,sha256=uXHuyc13MhATMPaDToSsJlMTXeqQ9AGVEj7uOlcGGLE,10505
 linkml/utils/rawloader.py,sha256=nUB8Gfn8yEVwyo6bx0TtB2mBGkilC-fybi0xvQ73Gks,4417
-linkml/utils/schema_builder.py,sha256=WfTdRnuLUhNj_y_D1uaMCaGXgafUuJkvMyPlW8T11r8,9971
+linkml/utils/schema_builder.py,sha256=dowMWyuo00yjfh0BHCmPiEw12o0tEmj3lXiKVp_VpBU,10055
 linkml/utils/schema_fixer.py,sha256=j9MoPlAd6j8fLC1Mnj_MSojnPlfR_Ml87jQkknjPYjE,16754
-linkml/utils/schemaloader.py,sha256=jc4IL03DSCt2V-POiarUKSh0U8jDzMrrxmXvcwbanIQ,47387
+linkml/utils/schemaloader.py,sha256=0tn6opcJH3njNV6Bkba-8Xsx6fSETyditaAM4v5t2Rg,52070
 linkml/utils/schemasynopsis.py,sha256=0cJZHTIrXTUS6EPvK2YKo7IuvbRQCkWKeRBsyz_zjSo,18441
 linkml/utils/sqlutils.py,sha256=qOnoZvZepo2BcKa3J0Wufhxe4z4ek7SOeHR4O86nlE0,17108
 linkml/utils/typereferences.py,sha256=CcL8ieqFgLq13pvVtYxcJmVy5BzmRpK7VsC0ZVH7mco,2209
@@ -167,8 +209,8 @@ linkml/workspaces/example_runner.py,sha256=EjaAn6vaAKZnFcW5hRopkYBguiaR05aqKbuaM
 linkml/workspaces/datamodel/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/workspaces/datamodel/workspaces.py,sha256=YIGzErECZuMER03h3DcuY3psMb0lDF1Pia_8hreKoTE,14667
 linkml/workspaces/datamodel/workspaces.yaml,sha256=LU0lMJ4W6Tk66r5ECD7OkaVm9kCRfu93yoik1b4gkzQ,4228
-linkml-1.9.4rc1.dist-info/METADATA,sha256=NgqQ9Spo4HP62ByQzFPMlz_xq7mtKW_WK_4eZQKO7ps,3344
-linkml-1.9.4rc1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-linkml-1.9.4rc1.dist-info/entry_points.txt,sha256=BXonQU9A7VqkPV5UA2r0vz0qLdAznpTovTFEI7FGlgE,2336
-linkml-1.9.4rc1.dist-info/licenses/LICENSE,sha256=zsURghk1UIVsx0jaDvEy5QU2UAqecv1vtJozTV8Hwvw,536
-linkml-1.9.4rc1.dist-info/RECORD,,
+linkml-1.9.5.dist-info/METADATA,sha256=eqIaQRCUkqztBU5PVMnm3mhle6_bscQzt7v777M9yRI,3341
+linkml-1.9.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+linkml-1.9.5.dist-info/entry_points.txt,sha256=pxiXrMMc21vHnzIgIUCLNJPySyKeD8rLocgPc2lFOWs,2379
+linkml-1.9.5.dist-info/licenses/LICENSE,sha256=zsURghk1UIVsx0jaDvEy5QU2UAqecv1vtJozTV8Hwvw,536
+linkml-1.9.5.dist-info/RECORD,,

{linkml-1.9.4rc1.dist-info → linkml-1.9.5.dist-info}/entry_points.txt

@@ -26,6 +26,7 @@ gen-py-classes = linkml.generators.pythongen:cli
 gen-pydantic = linkml.generators.pydanticgen:cli
 gen-python = linkml.generators.pythongen:cli
 gen-rdf = linkml.generators.rdfgen:cli
+gen-rust = linkml.generators.rustgen.cli:cli
 gen-shacl = linkml.generators.shaclgen:cli
 gen-shex = linkml.generators.shexgen:cli
 gen-sparql = linkml.generators.sparqlgen:cli
@@ -39,7 +40,7 @@ gen-typescript = linkml.generators.typescriptgen:cli
 gen-yaml = linkml.generators.yamlgen:cli
 gen-yuml = linkml.generators.yumlgen:cli
 linkml = linkml.cli.main:linkml
-linkml-convert = linkml.utils.converter:cli
+linkml-convert = linkml.converter.cli:cli
 linkml-jsonschema-validate = linkml.validators.jsonschemavalidator:cli
 linkml-lint = linkml.linter.cli:main
 linkml-run-examples = linkml.workspaces.example_runner:cli

linkml/generators/panderagen/panderagen_class_based/mixins.jinja2

@@ -1,26 +0,0 @@
-{#-
-  Jinja2 Template for a mixin class used by the Linkml/Pandera class-based model
-  Inline generation avoids dependencies on LinkML in the generated code.
-
--#}
-class _LinkmlPanderaValidator:
-
-    @classmethod
-    def generate_polars_schema(cls, object_to_validate) -> dict:
-        """Creates a nested PolaRS schema suitable for loading the object_to_validate.
-        Optional columns that are not present in the data are omitted.
-        This approach is only suitable to enable the test fixtures.
-        """
-        polars_schema = {}
-
-        for column_name, column in cls.to_schema().columns.items():
-            dtype = column.properties["dtype"]
-            required = column.properties["required"]
-
-            if required or column_name in object_to_validate:
-                if dtype.type == pl.Struct:
-                    pass
-                else:
-                    polars_schema[column_name] = dtype.type
-
-        return polars_schema