updated tests and options

java/buildSrc/src/main/groovy/brapi.schema-tools.java-conventions.gradle

@@ -3,7 +3,7 @@ plugins {
 }
 
 group = 'org.brapi'
-version = '0.11.0-SNAPSHOT'
+version = '0.12.0-SNAPSHOT'
 sourceCompatibility = JavaVersion.VERSION_21
 targetCompatibility = JavaVersion.VERSION_21
 

java/core/src/main/java/org/brapi/schematools/core/openapi/options/PropertiesOptions.java

@@ -69,6 +69,15 @@ public List<BrAPIObjectProperty> getLinkPropertiesFor(BrAPIObjectType brAPIObjec
         return linkProperties ;
     }
 
+    /**
+     * Gets the id parameter name for a type
+     * @param type The BrAPI type
+     * @return the id parameter name for a type
+     */
+    public String getIdPropertyNameFor(String type) {
+        return id.getPropertyNameFor(type) ;
+    }
+
     /**
      * Gets the id parameter name for a type
      * @param type The BrAPI type

java/core/src/main/java/org/brapi/schematools/core/utils/ConfigurationUtils.java

@@ -16,8 +16,7 @@ public class ConfigurationUtils {
     private static final ObjectMapper mapper = new ObjectMapper(new YAMLFactory());
 
     /**
-     * Load the configurations from a file in YAML or Json. The file may have missing
-     * (defined) values, in these cases the default values are loaded.
+     * Load the configurations from a file in YAML or Json.
      * @param configurationsFile The path to the configuration file in YAML or Json.
      * @param configurationClass The configuration class.
      * @param <T> the class of the configuration
@@ -45,8 +44,7 @@ public static <T> T load(String classPath, Class<T> configurationClass) throws I
     }
 
     /**
-     * Load the configurations from an input stream in YAML or Json. The configuration file may have missing
-     * (defined) values, in these cases the default values are loaded.
+     * Load the configurations from an input stream in YAML or Json.
      * @param inputStream The input stream in YAML or Json
      * @param configurationClass The configuration class.
      * @param <T> the class of the configuration

java/core/src/test/java/org/brapi/schematools/core/graphql/options/GraphQLGeneratorOptionsTest.java

@@ -47,6 +47,22 @@ void loadYaml() {
         checkOptions(options);
     }
 
+    @Test
+    void overwrite() {
+        GraphQLGeneratorOptions options = null;
+        try {
+            options = GraphQLGeneratorOptions.load(Path.of(ClassLoader.getSystemResource("graphql-overwrite-options.yaml").toURI()));
+        } catch (IOException | URISyntaxException e) {
+            e.printStackTrace();
+            fail(e.getMessage());
+        }
+
+        checkOptions(options);
+
+        assertEquals("attributeDbId", options.getIds().getIDFieldFor("GermplasmAttribute")) ;
+        assertEquals("attributeDbId", options.getIds().getIDFieldFor("CultivarAttribute")) ;
+    }
+
     private void checkOptions(GraphQLGeneratorOptions options) {
         assertNotNull(options);
 

java/core/src/test/java/org/brapi/schematools/core/openapi/options/OpenAPIGeneratorOptionsTest.java

@@ -53,171 +53,19 @@ void loadYaml() {
     }
 
     @Test
-    void isGeneratingSingleGet() {
-    }
-
-    @Test
-    void isGeneratingListGet() {
-    }
-
-    @Test
-    void isGeneratingSearch() {
-    }
-
-    @Test
-    void isGeneratingPost() {
-    }
-
-    @Test
-    void isGeneratingPut() {
-    }
-
-    @Test
-    void isGeneratingDelete() {
-    }
-
-    @Test
-    void isGeneratingEndpoint() {
-    }
-
-    @Test
-    void isGeneratingEndpointWithId() {
-    }
-
-    @Test
-    void isGeneratingSearchEndpoint() {
-    }
-
-    @Test
-    void isGeneratingSingleGetEndpointFor() {
-    }
-
-    @Test
-    void isGeneratingListGetEndpointFor() {
-    }
-
-    @Test
-    void isGeneratingPostEndpointFor() {
-    }
-
-    @Test
-    void isGeneratingPutEndpointFor() {
-    }
-
-    @Test
-    void isGeneratingDeleteEndpointFor() {
-    }
-
-    @Test
-    void isGeneratingSearchEndpointFor() {
-    }
-
-    @Test
-    void isGeneratingEndpointFor() {
-    }
-
-    @Test
-    void isGeneratingEndpointNameWithIdFor() {
-    }
-
-    @Test
-    void isGeneratingNewRequestFor() {
-    }
-
-    @Test
-    void getNewRequestNameFor() {
-    }
-
-    @Test
-    void isGeneratingListResponseFor() {
-    }
-
-    @Test
-    void getSingleResponseNameFor() {
-    }
-
-    @Test
-    void getListResponseNameFor() {
-    }
-
-    @Test
-    void isGeneratingSearchRequestFor() {
-    }
-
-    @Test
-    void getSearchRequestNameFor() {
-    }
-
-    @Test
-    void getPluralFor() {
-    }
-
-    @Test
-    void getSingularForProperty() {
-    }
-
-    @Test
-    void isSeparatingByModule() {
-    }
-
-    @Test
-    void getSingleGet() {
-    }
-
-    @Test
-    void getListGet() {
-    }
-
-    @Test
-    void getPost() {
-    }
-
-    @Test
-    void getPut() {
-    }
-
-    @Test
-    void getDelete() {
-    }
-
-    @Test
-    void getSearch() {
-    }
-
-    @Test
-    void getIds() {
-    }
-
-    @Test
-    void isCreatingNewRequest() {
-    }
-
-    @Test
-    void getCreatingNewRequestFor() {
-    }
-
-    @Test
-    void getNewRequestNameFormat() {
-    }
-
-    @Test
-    void getSingleResponseNameFormat() {
-    }
-
-    @Test
-    void getListResponseNameFormat() {
-    }
-
-    @Test
-    void getSearchRequestNameFormat() {
-    }
+    void overwrite() {
+        OpenAPIGeneratorOptions options = null;
+        try {
+            options = OpenAPIGeneratorOptions.load(Path.of(ClassLoader.getSystemResource("openapi-overwrite-options.yaml").toURI()));
+        } catch (IOException | URISyntaxException e) {
+            e.printStackTrace();
+            fail(e.getMessage());
+        }
 
-    @Test
-    void builder() {
-    }
+        checkOptions(options);
 
-    @Test
-    void toBuilder() {
+        assertEquals("attributeDbId", options.getProperties().getIdPropertyNameFor("GermplasmAttribute")) ;
+        assertEquals("attributeDbId", options.getProperties().getIdPropertyNameFor("CultivarAttribute")) ;
     }
 
     private void checkOptions(OpenAPIGeneratorOptions options) {

java/core/src/test/resources/graphql-overwrite-options.yaml

@@ -0,0 +1,124 @@
+pluralFor:
+    AlleleMatrix: AlleleMatrix
+ids:
+    useIDType: true
+    nameFormat: "%sDbId"
+    fieldFor:
+        CultivarAttribute: attributeDbId
+        CultivarAttributeValue: attributeValueDbId
+        GermplasmAttribute: attributeDbId
+        GermplasmAttributeValue: attributeValueDbId
+        LocaleAttribute: attributeDbId
+        LocaleAttributeValue: attributeValueDbId
+        ObservationUnitAttribute: attributeDbId
+        ObservationUnitAttributeValue: attributeValueDbId
+        SeedLotAttribute: attributeDbId
+        SeedLotAttributeValue: attributeValueDbId
+input:
+    name: input
+    nameFormat: "%sInput"
+    typeNameFormat: "%sInput"
+queryType:
+    name: Query
+    partitionedByCrop: true
+    singleQuery:
+        generate: true
+        pluralisingName: false
+        nameFormat: "%s"
+        descriptionFormat: Returns a %s object by id
+        generateFor:
+            AlleleMatrix: false
+            Call: false
+            Cross: false
+            Event: false
+            MarkerPosition: false
+            PlannedCross: false
+    listQuery:
+        generate: true
+        pluralisingName: true
+        nameFormat: "%s"
+        descriptionFormat: Returns %s objects
+        responseTypeNameFormat: "%sListResponse"
+        dataFieldName: data
+        pagedDefault: true
+        paged:
+            BreedingMethod: false
+        input:
+            BreedingMethod: false
+            CrossingProject: true
+        generateFor:
+            AlleleMatrix: false
+        pagingInputName: paging
+        pageInputTypeName: PageInput
+        pageTypeName: PageInfo
+        pageFieldName: page
+    searchQuery:
+        generate: true
+        pluralisingName: true
+        nameFormat: "%sSearch"
+        descriptionFormat: Returns %s objects
+        responseTypeNameFormat: "%sResponse"
+        searchIdFieldName: searchResultsDbId
+        generateFor:
+            AlleleMatrix: false
+            BreedingMethod: false
+            Cross: false
+            CrossProject: false
+            Method: false
+            Ontology: false
+            Scale: false
+            Trait: false
+mutationType:
+    name: Mutation
+    createMutation:
+        generate: true
+        pluralisingName: false
+        nameFormat: create%s
+        descriptionFormat: Create a new %s
+        generateFor:
+            AlleleMatrix: false
+            Call: false
+            CallSet: false
+            Cross: false
+            Event: false
+            GenomeMap: false
+            MarkerPosition: false
+            PedigreeNode: false
+            Reference: false
+            Variant: false
+    updateMutation:
+        generate: true
+        pluralisingName: false
+        nameFormat: update%s
+        descriptionFormat: Update the details for an existing %s
+        generateFor:
+            AlleleMatrix: false
+            Call: false
+            CallSet: false
+            Cross: false
+            Event: false
+            GenomeMap: false
+            MarkerPosition: false
+            PedigreeNode: false
+            Reference: false
+            Variant: false
+    deleteMutation:
+        generate: false
+        pluralisingName: true
+        multiple: true
+        nameFormat: delete%s
+        descriptionFormat: Delete existing %s
+        generateFor:
+            AlleleMatrix: false
+            Call: false
+            CallSet: false
+            Event: false
+            GenomeMap: false
+            MarkerPosition: false
+            PedigreeNode: false
+            Reference: false
+            Variant: false
+            VariantSet: false
+mergeOneOfType: true
+mergingOneOfTypeFor:
+    GeoJSONGeometry: false