linkml 1.6.8__py3-none-any.whl → 1.6.9__py3-none-any.whl

linkml/generators/docgen/class.md.jinja2

@@ -33,6 +33,10 @@ URI: {{ gen.uri_link(element) }}
 ```{{ gen.mermaid_directive() }}
 {{ gen.mermaid_diagram([element.name]) }}
 ```
+{% elif diagram_type == "plantuml_class_diagram" %}
+```puml
+{{ gen.mermaid_diagram([element.name]) }}
+```
 {% else %}
 {% include "class_diagram.md.jinja2" %}
 {% endif %}

linkml/generators/docgen/class_diagram.md.jinja2

@@ -13,7 +13,7 @@
       {% for s in schemaview.class_induced_slots(element.name)|sort(attribute='name') -%}
         {{ gen.name(element) }} : {{gen.name(s)}}
         {% if s.range not in gen.all_type_object_names() %}
-          {{ gen.name(element) }} --|> {{ s.range }} : {{ gen.name(s) }}
+          {{ gen.name(element) }} --> {{ s.range }} : {{ gen.name(s) }}
         {% endif %}
       {% endfor %}
 ```
@@ -27,7 +27,7 @@
       {% for s in schemaview.class_induced_slots(element.name)|sort(attribute='name') -%}
         {{ gen.name(element) }} : {{gen.name(s)}}
         {% if s.range not in gen.all_type_object_names() %}
-          {{ gen.name(element) }} --|> {{ s.range }} : {{ gen.name(s) }}
+          {{ gen.name(element) }} --> {{ s.range }} : {{ gen.name(s) }}
         {% endif %}
       {% endfor %}
 ```
@@ -41,7 +41,7 @@
       {% for s in schemaview.class_induced_slots(element.name)|sort(attribute='name') -%}
         {{ gen.name(element) }} : {{gen.name(s)}}
         {% if s.range not in gen.all_type_object_names() %}
-          {{ gen.name(element) }} --|> {{ s.range }} : {{ gen.name(s) }}
+          {{ gen.name(element) }} --> {{ s.range }} : {{ gen.name(s) }}
         {% endif %}
       {% endfor %}
 ```
@@ -52,7 +52,7 @@
       {% for s in schemaview.class_induced_slots(element.name)|sort(attribute='name') -%}
         {{ gen.name(element) }} : {{gen.name(s)}}
         {% if s.range not in gen.all_type_object_names() %}
-          {{ gen.name(element) }} --|> {{ s.range }} : {{ gen.name(s) }}
+          {{ gen.name(element) }} --> {{ s.range }} : {{ gen.name(s) }}
         {% endif %}
       {% endfor %}
 ```

linkml/generators/docgen.py

@@ -28,6 +28,7 @@ from linkml_runtime.utils.schemaview import SchemaView
 
 from linkml._version import __version__
 from linkml.generators.erdiagramgen import ERDiagramGenerator
+from linkml.generators.plantumlgen import PlantumlGenerator
 from linkml.utils.generator import Generator, shared_arguments
 from linkml.workspaces.example_runner import ExampleRunner
 
@@ -38,7 +39,8 @@ class MarkdownDialect(Enum):
 
 
 class DiagramType(Enum):
-    uml_class_diagram = "uml_class_diagram"
+    mermaid_class_diagram = "mermaid_class_diagram"
+    plantuml_class_diagram = "plantuml_class_diagram"
     er_diagram = "er_diagram"
 
 
@@ -593,8 +595,13 @@ class DocGenerator(Generator):
                 return erdgen.serialize_classes(class_names, follow_references=True, max_hops=2)
             else:
                 return erdgen.serialize()
-        elif self.diagram_type.value == DiagramType.uml_class_diagram.value:
+        elif self.diagram_type.value == DiagramType.mermaid_class_diagram.value:
             self.logger.info("This is currently handled in the jinja templates")
+        elif self.diagram_type.value == DiagramType.plantuml_class_diagram.value:
+            plantumlgen = PlantumlGenerator(self.schema)
+            plantuml_diagram = plantumlgen.serialize(classes=class_names)
+            self.logger.debug(f"Created PlantUML diagram for class: {class_names}")
+            return plantuml_diagram
         else:
             raise NotImplementedError(f"Diagram type {self.diagram_type} not implemented")
 

linkml/generators/shexgen.py

@@ -2,6 +2,7 @@
 
 """
 import os
+import urllib.parse as urlparse
 from dataclasses import dataclass, field
 from typing import List, Optional, Union
 
@@ -139,7 +140,24 @@ class ShExGenerator(Generator):
             constraint.predicate = self.namespaces.uri_for(slot.slot_uri)
             constraint.min = int(bool(slot.required))
             constraint.max = 1 if not slot.multivalued else -1
-            constraint.valueExpr = self._class_or_type_uri(slot.range)
+            if slot.range in self.schema.enums:
+                # Handle permissible values from enums
+                enum = self.schema.enums[slot.range]
+                values = []
+                for value in enum.permissible_values.values():
+                    if value.meaning:
+                        values.append(self.namespaces.uri_for(value.meaning))
+                    else:
+                        value_uri = f"{self._class_or_type_uri(enum.name)}#{urlparse.quote(value.text)}"
+                        values.append(value_uri)
+                if values:
+                    node_constraint = NodeConstraint(
+                        # id=self._class_or_type_uri(slot.range),
+                        values=values,
+                    )
+                    constraint.valueExpr = node_constraint
+            else:
+                constraint.valueExpr = self._class_or_type_uri(slot.range)
 
     def end_schema(self, output: Optional[str] = None, **_) -> None:
         self.shex.shapes = self.shapes if self.shapes else [Shape()]

linkml/linter/cli.py

@@ -16,7 +16,7 @@ YAML_SUFFIXES = [".yml", ".yaml"]
 DEFAULT_CONFIG_FILES = [".linkmllint.yaml", ".linkmllint.yml"]
 
 
-def get_yaml_files(root: Path) -> Iterable[str]:
+def get_yaml_files(root: Path, accept_dot_files: bool) -> Iterable[str]:
     if root.is_file():
         if root.suffix not in YAML_SUFFIXES:
             raise click.UsageError("SCHEMA must be a YAML file")
@@ -26,6 +26,8 @@ def get_yaml_files(root: Path) -> Iterable[str]:
             for file in files:
                 if file in DEFAULT_CONFIG_FILES:
                     continue
+                if file.startswith(".") and not accept_dot_files:
+                    continue
                 path = Path(dir, file)
                 if path.suffix in YAML_SUFFIXES:
                     yield str(path)
@@ -36,6 +38,7 @@ def get_yaml_files(root: Path) -> Iterable[str]:
     "schema",
     type=click.Path(exists=True, dir_okay=True, file_okay=True, resolve_path=True, path_type=Path),
 )
+@click.option("-a", "--all", is_flag=True, default=False, help="Process files that start with '.'.")
 @click.option(
     "-c",
     "--config",
@@ -82,6 +85,7 @@ def get_yaml_files(root: Path) -> Iterable[str]:
 def main(
     schema: Path,
     fix: bool,
+    all: bool,
     config: str,
     format: str,
     validate: bool,
@@ -124,7 +128,7 @@ def main(
     error_count = 0
     warning_count = 0
     formatter.start_report()
-    for path in get_yaml_files(schema):
+    for path in get_yaml_files(schema, all):
         formatter.start_schema(path)
         report = linter.lint(path, fix=fix, validate_schema=validate, validate_only=validate_only)
         for problem in report:

linkml/utils/datautils.py

@@ -79,14 +79,14 @@ def infer_root_class(sv: SchemaView) -> Optional[ClassDefinitionName]:
         if c.tree_root:
             return c.name
     refs = defaultdict(int)
-    for cn in sv.all_class().keys():
+    for cn in sv.all_classes().keys():
         for sn in sv.class_slots(cn):
             slot = sv.induced_slot(sn, cn)
             r = slot.range
-            if r in sv.all_class():
+            if r in sv.all_classes():
                 for a in sv.class_ancestors(r):
                     refs[a] += 1
-    candidates = [cn for cn in sv.all_class().keys() if cn not in refs]
+    candidates = [cn for cn in sv.all_classes().keys() if cn not in refs]
 
     # throw Exception if unambiguous root cannot be inferred
     if len(candidates) > 1:
@@ -106,7 +106,7 @@ def infer_index_slot(sv: SchemaView, root_class: ClassDefinitionName) -> Optiona
     index_slots = []
     for sn in sv.class_slots(root_class):
         slot = sv.induced_slot(sn, root_class)
-        if slot.multivalued and slot.range in sv.all_class():
+        if slot.multivalued and slot.range in sv.all_classes():
             index_slots.append(sn)
     if len(index_slots) == 1:
         return index_slots[0]

{linkml-1.6.8.dist-info → linkml-1.6.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: linkml
-Version: 1.6.8
+Version: 1.6.9
 Summary: Linked Open Data Modeling Language
 Home-page: https://linkml.io/linkml/
 Keywords: schema,linked data,data modeling,rdf,owl,biolink

{linkml-1.6.8.dist-info → linkml-1.6.9.dist-info}/RECORD

@@ -6,8 +6,8 @@ linkml/generators/__init__.py,sha256=qa22iTeBrcds6ndst_iTPVWLQtBF6NGyhVngBhbhIpc
 linkml/generators/common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/generators/common/type_designators.py,sha256=lgVcIRJJ-yCvVGeP9U_gQZpm77UmJBQo9Bh3lGJITno,1956
 linkml/generators/csvgen.py,sha256=h-Mj-uNrzuETx_G3dW6eFbk1jj0NHSwqbehqR5tA6PM,2955
-linkml/generators/docgen/class.md.jinja2,sha256=05Kbl83ApOMzA7gZeRJjPU7jkZHCIsaKN1BYWNMRTfM,3275
-linkml/generators/docgen/class_diagram.md.jinja2,sha256=ShRhNnIae54Y_4zrfXuIF6BjX8oCHRZJnovE8G1fjOU,2542
+linkml/generators/docgen/class.md.jinja2,sha256=_nQr8ge57ZkX3Hrh-cqPUm8Z7HCnJuuRCgYm0g21mS8,3381
+linkml/generators/docgen/class_diagram.md.jinja2,sha256=lLU_0sQZBttOX5Wiup2oZwrxHuiQtbU9ZgLi66aJvOo,2538
 linkml/generators/docgen/common_metadata.md.jinja2,sha256=zy8Ua3gDtAAq8VA3e3O3ft9W7eJopVZaq5efP8LU_hU,1321
 linkml/generators/docgen/enum.md.jinja2,sha256=mXnUrRkleY2bOTEyAZ5c4pcUnqhs6BNa8a-4LVve-eo,1014
 linkml/generators/docgen/index.md.jinja2,sha256=wXUYTmayPLFltC0vbGE_Mf6m3GkkWav7FOEjCvEpHp4,1466
@@ -16,7 +16,7 @@ linkml/generators/docgen/schema.md.jinja2,sha256=xlENfnzNRYgPT_0tdqNFxgklVM4Qf5B
 linkml/generators/docgen/slot.md.jinja2,sha256=XVd0M4gKx9Q2fONcsUGBRj_bJivyN4P9jhj9IO496jQ,2817
 linkml/generators/docgen/subset.md.jinja2,sha256=fTNIpAkml5RKFbbtLore3IAzFN1cISVsyL1ru2-Z4oA,2665
 linkml/generators/docgen/type.md.jinja2,sha256=QmCMJZrFwP33eHkggBVtypbyrxTb-XZn9vHOYojVaYk,635
-linkml/generators/docgen.py,sha256=zsLzbXN2t9pafQubEnb7QshufMKBMqUWjdLE1OyFyq8,33296
+linkml/generators/docgen.py,sha256=Kwg4ZIXL2e9G-q-_CUoj8Bgnpyyvvh5fKPnseDcTK04,33755
 linkml/generators/dotgen.py,sha256=CnbVY6CO1OMuiYXYnvxgNN2IW1mtOQW-J-QnwZlXkUI,5012
 linkml/generators/erdiagramgen.py,sha256=Gu-_nhLuEPTsYYaoV6tNS1V6cZ2dNJdm6YwxC0VGl7g,10315
 linkml/generators/excelgen.py,sha256=OhVzuQaDESYpAGR8Zv13hiWlDDJA8ugtSZatBJH0hzA,7737
@@ -43,7 +43,7 @@ linkml/generators/pydanticgen.py,sha256=Ak0bpRoQsirnnBd091NiJvMZ-2d0qaQbhxADHy5o
 linkml/generators/pythongen.py,sha256=yGYlRJ4rNm2QQLFDjyuUnqCyKlzz-b3eSOhkSu8aCwI,52491
 linkml/generators/rdfgen.py,sha256=LxzYBaFEkV7rlf54nWv_6H6AGcWMRXwkaeVXq9VYEc8,2693
 linkml/generators/shaclgen.py,sha256=KxNmDZW2ciCuSqUhJ65TxLTjF8jME1FmN5SaWJCuW9k,8662
-linkml/generators/shexgen.py,sha256=Awtn5SyjS-TUcVCwMdT0F7hNO4K8VcSCYBaFru45Mwg,8994
+linkml/generators/shexgen.py,sha256=E-R8jg5Z3JzzsVAIPu6Fs9FtFF7k-I5-5vMwG1jGW2U,9858
 linkml/generators/sparqlgen.py,sha256=xIT4abjYTjPvAjczZ2mkqfap5z8-AImK_jaCvgZyRGs,6120
 linkml/generators/sqlalchemy/__init__.py,sha256=mb9AC1rIFkSiNZhhG0TAk45ol9PjS1XvsrvCjgfVUpQ,249
 linkml/generators/sqlalchemy/sqlalchemy_declarative_template.py,sha256=X_Ws1NUBikMI5HuNgEhl_PIeWM-B-c2B0W9KUBH4QTg,2542
@@ -59,7 +59,7 @@ linkml/generators/typescriptgen.py,sha256=VDJ-97jk7zqYx6XlnIcxZmY8mCv885T7D2brKJ
 linkml/generators/yamlgen.py,sha256=bI4ebWe8vebR3xGVgto5TH0ZDej-RlZPTYqJ26BxKpg,1651
 linkml/generators/yumlgen.py,sha256=547atFkqJd9WtL_LdR-tUME9g7lWaFa3yHFvpnX6J1E,12145
 linkml/linter/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml/linter/cli.py,sha256=RpZYyR_Re0E7yh1fifvQVJagi8KvLDaseF3Zgs2E3uw,4254
+linkml/linter/cli.py,sha256=BpQiETcRfQlZsI1-JALyU9wXPgPOm_KE_n11p0iJaC8,4494
 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=4HtqHF2ZiYx0Izm50eUQRvygsm1xSnkc49w0nd9zbGk,16837
@@ -84,7 +84,7 @@ linkml/transformers/schema_renamer.py,sha256=Cr18TyktX64b5iFh5V6R_ILPVzXjbDYVDDZ
 linkml/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml/utils/cli_utils.py,sha256=MdVbox1qr6kDUHUCWAmFhV-D6ebs_nn8vVwB8KDQfew,742
 linkml/utils/converter.py,sha256=rdhCI7Tsjddr3o1rVBfMq5gQubk_GE6fqlBBmyxI5_M,6270
-linkml/utils/datautils.py,sha256=2XWM9LBSVp8v3SwIZECrX3SjDUYzdnP-syjp6YdL89E,3734
+linkml/utils/datautils.py,sha256=QlbzwXykh5Fphfe5KxPo6_ekXfniLbHiEGJtLWjUrvY,3742
 linkml/utils/datavalidator.py,sha256=kBdWaVi8IZT1bOwEJgJYx-wZAb_PTBObB9nHpYORfKA,472
 linkml/utils/execute_tutorial.py,sha256=T4kHTSyz3ItJGEUZxVjR-3yLVKnOr5Ix4NMGE47-IuE,6912
 linkml/utils/generator.py,sha256=WAlP_gfZfAZYNklsh8l4GtiWZ338kjLg7xpQAANgUNg,38217
@@ -124,8 +124,8 @@ linkml/workspaces/datamodel/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMp
 linkml/workspaces/datamodel/workspaces.py,sha256=4HdkqweGNfMPqnB1_Onc9DcTfkhoagTRcqruh08nRoI,14905
 linkml/workspaces/datamodel/workspaces.yaml,sha256=EjVrwPpeRZqJRjuGyyDRxxFzuv55SiLIXPBRUG6HStU,4233
 linkml/workspaces/example_runner.py,sha256=uumXyPZ7xUJSZyRtjDP4TCCxgKSSOfebpufXc0_l0jY,11610
-linkml-1.6.8.dist-info/WHEEL,sha256=vVCvjcmxuUltf8cYhJ0sJMRDLr1XsPuxEId8YDzbyCY,88
-linkml-1.6.8.dist-info/LICENSE,sha256=kORMoywK6j9_iy0UvLR-a80P1Rvc9AOM4gsKlUNZABg,535
-linkml-1.6.8.dist-info/entry_points.txt,sha256=za8r49Z5gcz3rAYTZLbxw5EPZr1rGuxSe1uiRUpf8R0,2143
-linkml-1.6.8.dist-info/METADATA,sha256=AnOhJfXSxtF9U1R0uUcrEIyf21cT4voTXlmC77iI7eM,3446
-linkml-1.6.8.dist-info/RECORD,,
+linkml-1.6.9.dist-info/WHEEL,sha256=vVCvjcmxuUltf8cYhJ0sJMRDLr1XsPuxEId8YDzbyCY,88
+linkml-1.6.9.dist-info/LICENSE,sha256=kORMoywK6j9_iy0UvLR-a80P1Rvc9AOM4gsKlUNZABg,535
+linkml-1.6.9.dist-info/entry_points.txt,sha256=za8r49Z5gcz3rAYTZLbxw5EPZr1rGuxSe1uiRUpf8R0,2143
+linkml-1.6.9.dist-info/METADATA,sha256=KsqVPfLcVUKxAlb-hz4AFdd6Pk5VGUjtmGx3wj5x7U8,3446
+linkml-1.6.9.dist-info/RECORD,,