update tests to check new patterns

tests/data/expected_json_schema.json

@@ -1,47 +1,52 @@
 {
+  "$schema": "http://json-schema.org/draft-07/schema",
   "title": "Test",
   "type": "object",
   "properties": {
     "name": {
-      "title": "Name",
-      "type": "string",
-      "term": "schema:hello"
+      "title": "name",
+      "term": "schema:hello",
+      "type": "string"
     },
     "number": {
-      "title": "Number",
-      "type": "number",
-      "term": "schema:one"
+      "title": "number",
+      "term": "schema:one",
+      "type": "number"
     },
     "test2": {
-      "title": "Test2",
+      "term": "schema:something",
       "type": "array",
       "items": {
         "$ref": "#/definitions/Test2"
-      },
-      "term": "schema:something"
+      }
+    },
+    "ontology": {
+      "title": "ontology",
+      "type": "string",
+      "enum": [
+        "https://www.evidenceontology.org/term/",
+        "https://amigo.geneontology.org/amigo/term/",
+        "http://semanticscience.org/resource/"
+      ]
     }
   },
   "definitions": {
     "Test2": {
       "title": "Test2",
       "type": "object",
       "properties": {
-        "title": "Test2",
-        "type": "object",
-        "properties": {
-          "names": {
-            "title": "Names",
-            "type": "array",
-            "items": {
-              "type": "string"
-            },
-            "term": "schema:hello"
-          },
-          "number": {
-            "title": "Number",
-            "type": "number",
-            "term": "schema:one"
+        "names": {
+          "title": "names",
+          "term": "schema:hello",
+          "type": "array",
+          "items": {
+            "type": "string"
           }
+        },
+        "number": {
+          "title": "number",
+          "term": "schema:one",
+          "type": "number"
         }
       }
     }

tests/data/expected_python_dc.py

@@ -3,6 +3,7 @@
 from dataclasses import dataclass, field
 from dataclasses_json import config, dataclass_json
 from typing import List, Optional
+from enum import Enum
 from uuid import uuid4
 
 
@@ -12,6 +13,7 @@ class Test:
     name: str
     number: Optional[float] = None
     test2: List[Test2] = field(default_factory=list)
+    ontology: Optional[Ontology] = None
 
     # JSON-LD fields
     id: str = field(
@@ -34,7 +36,28 @@ class Test:
             "test2": "schema:something",
         }
     )
+
+
+
+    def add_to_test2(
+        self,
+        names: List[str],
+        number: Optional[float],
+        **kwargs,
+    ):
+        params = {
+
+            "names": names, 
+            "number": number
+        }
+
+        self.test2.append(
+            Test2(**params)
+        )
 
+        return self.test2[-1]
+
+
 @dataclass_json
 @dataclass
 class Test2:
@@ -60,4 +83,11 @@ class Test2:
             "names": "schema:hello",
             "number": "schema:one",
         }
-    )
+    )
+
+
+
+class Ontology(Enum):
+    ECO = "https://www.evidenceontology.org/term/"
+    GO = "https://amigo.geneontology.org/amigo/term/"
+    SIO = "http://semanticscience.org/resource/"

tests/data/expected_python_sdrdm.py

@@ -34,6 +34,12 @@ class Test(
             json_schema_extra=dict(term = "schema:something",)
         )
 
+    ontology: Optional[Ontology] = element(
+            default=None,
+            tag="ontology",
+            json_schema_extra=dict()
+        )
+
     _repo: str = PrivateAttr(default="https://www.github.com/my/repo/")
 
 
@@ -71,4 +77,11 @@ class Test2(
             json_schema_extra=dict(term = "schema:one",)
         )
 
-    _repo: str = PrivateAttr(default="https://www.github.com/my/repo/")
+    _repo: str = PrivateAttr(default="https://www.github.com/my/repo/")
+
+
+
+class Ontology(Enum):
+    ECO = "https://www.evidenceontology.org/term/"
+    GO = "https://amigo.geneontology.org/amigo/term/"
+    SIO = "http://semanticscience.org/resource/"

tests/data/expected_sdrdm_schema.json

@@ -41,10 +41,22 @@
             "is_attr": false,
             "name": "SomeTest2"
           }
+        },
+        {
+          "name": "ontology",
+          "multiple": false,
+          "dtypes": ["Ontology"],
+          "docstring": "",
+          "options": [],
+          "term": null,
+          "required": false,
+          "xml": {
+            "is_attr": false,
+            "name": "ontology"
+          }
         }
       ],
-      "docstring": "",
-      "object_type": "Object"
+      "docstring": ""
     },
     {
       "name": "Test2",
@@ -76,8 +88,17 @@
           }
         }
       ],
-      "docstring": "",
-      "object_type": "Object"
+      "docstring": ""
+    }
+  ],
+  "enums": [
+    {
+      "name": "Ontology",
+      "mappings": {
+        "ECO": "https://www.evidenceontology.org/term/",
+        "GO": "https://amigo.geneontology.org/amigo/term/",
+        "SIO": "http://semanticscience.org/resource/"
+      }
     }
   ],
   "config": {

tests/data/expected_shacl.ttl

@@ -27,7 +27,7 @@ tst:TestShape
         sh:node md:Test2Shape ;
         sh:minCount 0 ;
 
-    ].
+    ];
 
 tst:Test2Shape
     a sh:NodeShape ;

tests/data/expected_shex.shex

@@ -3,11 +3,31 @@ PREFIX tst: <https://www.github.com/my/repo/>
 PREFIX schema: <http://schema.org/>
 
 tst:Test {
-    schema:hello xsd:string;
-    schema:one xsd:double?;
-    schema:something @tst:Test2*;
+    schema:hello xsd:string {
+        shex:annotation [
+            shex:label "name"
+        ]
+    };
+    schema:one xsd:double? {
+        shex:annotation [
+            shex:label "number"
+        ]
+    };
+    schema:something @tst:Test2* {
+        shex:annotation [
+            shex:label "test2"
+        ]
+    };
 }
 tst:Test2 {
-    schema:hello xsd:string*;
-    schema:one xsd:double?;
+    schema:hello xsd:string* {
+        shex:annotation [
+            shex:label "names"
+        ]
+    };
+    schema:one xsd:double? {
+        shex:annotation [
+            shex:label "number"
+        ]
+    };
 }

tests/data/expected_xml_schema.xsd

@@ -8,18 +8,28 @@
     <!-- Test Definition -->
     <xs:complexType name="TestType">
         <xs:sequence>
-            <xs:element name="test2" type="Test2Type"  maxOccurs="unbounded" />
+            <xs:element name="test2" type="Test2Type"  maxOccurs="unbounded"/>
+            <xs:element name="ontology" type="OntologyType" />
         </xs:sequence>
-        <xs:attribute name="name" type="xs:string" use="required" />
-        <xs:attribute name="number" type="xs:float"  />
+        <xs:attribute name="name" type="xs:string" use="required"/>
+        <xs:attribute name="number" type="xs:float" />
     </xs:complexType>
 
     <!-- Test2 Definition -->
     <xs:complexType name="Test2Type">
         <xs:sequence>
-            <xs:element name="names" type="xs:string"  maxOccurs="unbounded" />
+            <xs:element name="names" type="xs:string"  maxOccurs="unbounded"/>
         </xs:sequence>
-        <xs:attribute name="number" type="xs:float"  />
+        <xs:attribute name="number" type="xs:float" />
     </xs:complexType>
 
+    <!-- Enum Ontology Definition -->
+    <xs:simpleType name="OntologyType">
+        <xs:restriction base="xs:string">
+            <xs:enumeration value="https://www.evidenceontology.org/term/"/>
+            <xs:enumeration value="https://amigo.geneontology.org/amigo/term/"/>
+            <xs:enumeration value="http://semanticscience.org/resource/"/>
+        </xs:restriction>
+    </xs:simpleType>
+
 </xs:schema>

tests/data/model.md

@@ -22,6 +22,8 @@ nsmap:
   - Type: Test2[]
   - Term: schema:something
   - XML: SomeTest2
+- ontology
+  - Type: Ontology
 
 ### Test2
 
@@ -33,3 +35,16 @@ nsmap:
   - Type: float
   - Term: schema:one
   - XML: @number
+
+
+## Enumerations
+
+### Ontology
+
+Ontology endpoints for different types of sequences.
+
+```
+GO = "https://amigo.geneontology.org/amigo/term/"
+SIO = "http://semanticscience.org/resource/"
+ECO = "https://www.evidenceontology.org/term/"
+```

tests/integration_tests.rs

@@ -36,7 +36,7 @@ mod tests {
             .find(|o| o.name == "Test2".to_string())
             .unwrap();
 
-        assert_eq!(test1.attributes.len(), 3);
+        assert_eq!(test1.attributes.len(), 4);
         assert_eq!(test2.attributes.len(), 2);
 
         // Check if the attributes are correct
@@ -46,6 +46,7 @@ mod tests {
             "name".to_string(),
             "number".to_string(),
             "test2".to_string(),
+            "ontology".to_string(),
         ];
 
         assert_eq!(test1_attr_names, expected);