linkml 1.7.8__py3-none-any.whl → 1.7.9__py3-none-any.whl

linkml/generators/csvgen.py

@@ -3,9 +3,9 @@ Generate CSVs
 """
 
 import os
-import sys
 from csv import DictWriter
 from dataclasses import dataclass
+from io import StringIO
 from typing import List, Optional, Set
 
 import click
@@ -42,14 +42,20 @@ class CsvGenerator(Generator):
     writer: Optional[DictWriter] = None
     """Python dictwriter"""
 
+    _str_io: Optional[StringIO] = None
+    """String that the writer outputs to"""
+
     def __post_init__(self):
         super().__post_init__()
+        self._str_io = None
+
         self.generate_header()  # TODO: don't do this in initialization
 
-    def generate_header(self):
-        print(f"# metamodel_version: {self.schema.metamodel_version}")
+    def generate_header(self) -> str:
+        out = f"# metamodel_version: {self.schema.metamodel_version}"
         if self.schema.version:
-            print(f"# version: {self.schema.version}")
+            out = "\n".join([out, f"# version: {self.schema.version}"])
+        return out
 
     def visit_schema(self, classes: List[ClassDefinitionName] = None, **_) -> None:
         # Note: classes comes from the "root" argument
@@ -65,8 +71,9 @@ class CsvGenerator(Generator):
             else:
                 self.closure.update(self.ancestors(self.schema.classes[clsname]))
 
+        self._str_io = StringIO()
         dialect: str = "excel" if self.format == "csv" else "excel-tab"
-        self.writer = DictWriter(sys.stdout, ["id", "mappings", "description"], dialect=dialect)
+        self.writer = DictWriter(self._str_io, ["id", "mappings", "description"], dialect=dialect)
         self.writer.writeheader()
 
     def visit_class(self, cls: ClassDefinition) -> bool:
@@ -83,6 +90,9 @@ class CsvGenerator(Generator):
             return True
         return False
 
+    def end_schema(self, **kwargs) -> str:
+        return self._str_io.getvalue()
+
 
 @shared_arguments(CsvGenerator)
 @click.command()

linkml/generators/docgen/class_diagram.md.jinja2

@@ -1,19 +1,29 @@
+{% macro slot_relationship(element, slot) %}
+    {% set range_element = gen.name(schemaview.get_element(slot.range)) %}
+    {% set relation_label = gen.name(slot) %}
+    {{ gen.name(element) }} --> "{{ gen.cardinality(slot) }}" {{ range_element }} : {{ relation_label }}
+    click {{ range_element }} href "../{{ range_element }}"
+{% endmacro %}
+
 {% if schemaview.class_parents(element.name) and schemaview.class_children(element.name) %}
 ```{{ gen.mermaid_directive() }}
  classDiagram
     class {{ gen.name(element) }}
+    click {{ gen.name(element) }} href "../{{gen.name(element)}}"
       {% for s in schemaview.class_parents(element.name)|sort(attribute='name') -%}
         {{ gen.name(schemaview.get_element(s)) }} <|-- {{ gen.name(element) }}
+        click {{ gen.name(schemaview.get_element(s)) }} href "../{{gen.name(schemaview.get_element(s))}}"
       {% endfor %}
 
       {% for s in schemaview.class_children(element.name)|sort(attribute='name') -%}
         {{ gen.name(element) }} <|-- {{ gen.name(schemaview.get_element(s)) }}
+        click {{ gen.name(schemaview.get_element(s)) }} href "../{{gen.name(schemaview.get_element(s))}}"
       {% endfor %}
       
       {% 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) }}
+          {{ slot_relationship(element, s) }}
         {% endif %}
       {% endfor %}
 ```
@@ -21,13 +31,15 @@
 ```{{ gen.mermaid_directive() }}
  classDiagram
     class {{ gen.name(element) }}
+    click {{ gen.name(element) }} href "../{{gen.name(element)}}"
       {% for s in schemaview.class_parents(element.name)|sort(attribute='name') -%}
         {{ gen.name(schemaview.get_element(s)) }} <|-- {{ gen.name(element) }}
+        click {{ gen.name(schemaview.get_element(s)) }} href "../{{gen.name(schemaview.get_element(s))}}"
       {% endfor %}
       {% 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) }}
+          {{ slot_relationship(element, s) }}
         {% endif %}
       {% endfor %}
 ```
@@ -35,13 +47,15 @@
 ```{{ gen.mermaid_directive() }}
  classDiagram
     class {{ gen.name(element) }}
+    click {{ gen.name(element) }} href "../{{gen.name(element)}}"
       {% for s in schemaview.class_children(element.name)|sort(attribute='name') -%}
         {{ gen.name(element) }} <|-- {{ gen.name(schemaview.get_element(s)) }}
+        click {{ gen.name(schemaview.get_element(s)) }} href "../{{gen.name(schemaview.get_element(s))}}"
       {% endfor %}
       {% 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) }}
+          {{ slot_relationship(element, s) }}
         {% endif %}
       {% endfor %}
 ```
@@ -49,10 +63,11 @@
 ```{{ gen.mermaid_directive() }}
  classDiagram
     class {{ gen.name(element) }}
+    click {{ gen.name(element) }} href "../{{gen.name(element)}}"
       {% 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) }}
+          {{ slot_relationship(element, s) }}
         {% endif %}
       {% endfor %}
 ```

linkml/generators/docgen.py

@@ -567,23 +567,60 @@ class DocGenerator(Generator):
     @staticmethod
     def cardinality(slot: SlotDefinition) -> str:
         """
-        Render combination of required, multivalued, and recommended as a range, e.g. 0..*
-        :param slot:
-        :return:
+        Render combination of required, multivalued, recommended, and exact_cardinality as a range,
+        according to Mermaid conventions. Considers 'required' and 'multivalued' to set defaults
+        for 'minimum_cardinality' and 'maximum_cardinality'.
+
+        Reference: https://mermaid.js.org/syntax/classDiagram.html#cardinality-multiplicity-on-relations
+
+        The different cardinality options are:
+        - 1 Only 1
+        - 0..1 Zero or One
+        - 1..* One or more
+        - * Many
+        - n n (where n>1)
+        - 0..n zero to n (where n>1)
+        - 1..n one to n (where n>1)
+        :param slot: SlotDefinition
+        :return: cardinality string as used in Mermaid diagrams
         """
-        if slot.required or slot.identifier:
-            min = "1"
-        else:
-            min = "0"
-        if slot.multivalued:
-            max = "*"
+        if slot.exact_cardinality is not None:
+            cardinality = str(slot.exact_cardinality)  # handles 'n' case
         else:
-            max = "1"
+            if slot.required or slot.identifier:
+                min_card = "1"
+            else:
+                min_card = str(slot.minimum_cardinality) if slot.minimum_cardinality is not None else "0"
+
+            if slot.multivalued:
+                max_card = "*"
+            else:
+                max_card = str(slot.maximum_cardinality) if slot.maximum_cardinality is not None else "1"
+
+            if min_card == "0":
+                if max_card == "1":
+                    cardinality = "0..1"  # handles '0..1' case
+                elif max_card == "*":
+                    cardinality = "*"  # handles '*' case
+                else:
+                    cardinality = f"0..{max_card}"  # handles '0..n' case
+            elif min_card == "1":
+                if max_card == "1":
+                    cardinality = "1"  # handles '1' case
+                elif max_card == "*":
+                    cardinality = "1..*"  # handles '1..*' case
+                else:
+                    cardinality = f"1..{max_card}"  # handles '1..n' case
+            else:
+                if max_card == "*":
+                    cardinality = f"{min_card}..*"  # handles 'n..*' case
+                else:
+                    cardinality = f"{min_card}..{max_card}"  # handles 'n..m' case
+
         if slot.recommended:
-            info = " _recommended_"
-        else:
-            info = ""
-        return f"{min}..{max}{info}"
+            cardinality += " _recommended_"
+
+        return cardinality
 
     def mermaid_directive(self) -> str:
         """
@@ -932,6 +969,14 @@ class DocGenerator(Generator):
     "--example-directory",
     help="Folder in which example files are found. These are used to make inline examples",
 )
+@click.option(
+    "-d",
+    "--include",
+    help="""
+Include LinkML Schema outside of imports mechanism.  Helpful in including deprecated classes and slots in a separate
+YAML, and including it when necessary but not by default (e.g. in documentation or for backwards compatibility)
+""",
+)
 @click.version_option(__version__, "-V", "--version")
 @click.command()
 def cli(

linkml/generators/graphqlgen.py

@@ -19,28 +19,26 @@ class GraphqlGenerator(Generator):
     uses_schemaloader = True
     requires_metamodel = False
 
-    def __post_init__(self):
-        super().__post_init__()
-        # TODO: move this
-        self.generate_header()
+    def visit_schema(self, **kwargs) -> str:
+        return self.generate_header()
 
-    def generate_header(self):
-        print(f"# metamodel_version: {self.schema.metamodel_version}")
+    def generate_header(self) -> str:
+        out = f"# metamodel_version: {self.schema.metamodel_version}\n"
         if self.schema.version:
-            print(f"# version: {self.schema.version}")
+            out += f"# version: {self.schema.version}\n"
+        return out
 
-    def visit_class(self, cls: ClassDefinition) -> bool:
+    def visit_class(self, cls: ClassDefinition) -> str:
         etype = "interface" if (cls.abstract or cls.mixin) and not cls.mixins else "type"
         mixins = ", ".join([camelcase(mixin) for mixin in cls.mixins])
-        print(f"{etype} {camelcase(cls.name)}" + (f" implements {mixins}" if mixins else ""))
-        print("  {")
-        return True
+        out = f"{etype} {camelcase(cls.name)}" + (f" implements {mixins}" if mixins else "")
+        out = "\n".join([out, "  {"])
+        return out
 
-    def end_class(self, cls: ClassDefinition) -> None:
-        print("  }")
-        print()
+    def end_class(self, cls: ClassDefinition) -> str:
+        return "\n  }\n\n"
 
-    def visit_class_slot(self, cls: ClassDefinition, aliased_slot_name: str, slot: SlotDefinition) -> None:
+    def visit_class_slot(self, cls: ClassDefinition, aliased_slot_name: str, slot: SlotDefinition) -> str:
         slotrange = (
             camelcase(slot.range)
             if slot.range in self.schema.classes or slot.range in self.schema.types or slot.range in self.schema.enums
@@ -50,7 +48,7 @@ class GraphqlGenerator(Generator):
             slotrange = f"[{slotrange}]"
         if slot.required:
             slotrange = slotrange + "!"
-        print(f"    {lcamelcase(aliased_slot_name)}: {slotrange}")
+        return f"\n    {lcamelcase(aliased_slot_name)}: {slotrange}"
 
 
 @shared_arguments(GraphqlGenerator)

linkml/generators/jsonldcontextgen.py

@@ -89,7 +89,7 @@ class ContextGenerator(Generator):
         flatprefixes: Optional[bool] = False,
         model: Optional[bool] = True,
         **_,
-    ) -> None:
+    ) -> str:
         if model is None:
             model = self.model
         context = JsonObj()
@@ -126,8 +126,8 @@ class ContextGenerator(Generator):
         if output:
             with open(output, "w", encoding="UTF-8") as outf:
                 outf.write(as_json(context))
-        else:
-            print(as_json(context))
+
+        return str(as_json(context)) + "\n"
 
     def visit_class(self, cls: ClassDefinition) -> bool:
         class_def = {}

linkml/generators/jsonldgen.py

@@ -151,7 +151,7 @@ class JSONLDGenerator(Generator):
     def visit_subset(self, ss: SubsetDefinition) -> None:
         self._visit(ss)
 
-    def end_schema(self, context: str = None, **_) -> None:
+    def end_schema(self, context: str = None, **_) -> str:
         self._add_type(self.schema)
         base_prefix = self.default_prefix()
 
@@ -186,8 +186,9 @@ class JSONLDGenerator(Generator):
             if base_prefix:
                 self.schema["@context"].append({"@base": base_prefix})
         # json_obj["@id"] = self.schema.id
-        print(as_json(self.schema, indent="  "))
+        out = str(as_json(self.schema, indent="  ")) + "\n"
         self.schema = self.original_schema
+        return out
 
 
 @shared_arguments(JSONLDGenerator)

linkml/generators/jsonschemagen.py

@@ -185,6 +185,7 @@ class JsonSchemaGenerator(Generator):
     indent: int = 4
 
     inline: bool = False
+
     top_class: Optional[Union[ClassDefinitionName, str]] = None  # JSON object is one instance of this
     """Class instantiated by the root node of the document tree"""
 
@@ -662,6 +663,14 @@ disable pretty-printing and return the most compact JSON representation
 Specify from which slot are JSON Schema 'title' annotations generated.
 """,
 )
+@click.option(
+    "-d",
+    "--include",
+    help="""
+Include LinkML Schema outside of imports mechanism.  Helpful in including deprecated classes and slots in a separate
+YAML, and including it when necessary but not by default (e.g. in documentation or for backwards compatibility)
+""",
+)
 @click.version_option(__version__, "-V", "--version")
 def cli(yamlfile, **kwargs):
     """Generate JSON Schema representation of a LinkML model"""