Merge pull request #104 from KnowledgeCaptureAndDiscovery/Issues#98&#27

Issues#98&#27

Author: dgarijo

examples/pplan/config.yaml

@@ -11,11 +11,12 @@ openapi:
     version: v1.0.0
   externalDocs:
     description: P-Plan
-    url: https://w3id.org/okn/o/sdm
+    url: http://purl.org/net/p-plan
 
 firebase:
   key: "test"
 
+#endpoint not used for this example.
 endpoint:
   url: http://endpoint.mint.isi.edu/example
   prefix: https://w3id.org/okn/i/example

src/main/java/edu/isi/oba/Mapper.java

@@ -6,25 +6,23 @@
 import io.swagger.v3.oas.models.media.StringSchema;
 import io.swagger.v3.oas.models.media.XML;
 import org.semanticweb.owlapi.apibinding.OWLManager;
-import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat;
 import org.semanticweb.owlapi.model.*;
 
 import static edu.isi.oba.Oba.logger;
 
 import java.io.File;
 import java.io.IOException;
-import java.io.InputStream;
 import java.nio.file.Files;
 import java.nio.file.StandardCopyOption;
 import java.util.*;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import java.util.stream.Collectors;
-import org.semanticweb.owlapi.formats.TurtleDocumentFormat;
 
 class Mapper {
     public static final String DEFAULT_DIR_QUERY = "_default_";
-    public final Map<IRI, String> schemaNames = new HashMap<>();
+    public final Map<IRI, String> schemaNames = new HashMap<>(); //URI-names of the schemas
+    public final Map<IRI, String> schemaDescriptions = new HashMap<>(); //URI-description of the schemas
     public Map<String, Schema> schemas = new HashMap<>();
     final Paths paths = new Paths();
     List<String> selected_paths;
@@ -61,6 +59,7 @@ public Mapper(YamlConfig config_data) throws OWLOntologyCreationException {
         for (OWLOntology ontology : ontologies) {
             Set<OWLClass> classes = ontology.getClassesInSignature();
             setSchemaNames(classes);
+            setSchemaDrescriptions(classes,ontology);
         }
         if (config_data.getClasses() != null)
             this.selected_classes = filter_classes();
@@ -158,7 +157,7 @@ private List<OWLClass> add_owlclass_to_openapi(Query query, Path pathGenerator,
         List<OWLClass> ref = new ArrayList<>();
         String classPrefixIRI = cls.getIRI().getNamespace();
         if (defaultOntologyPrefixIRI.equals(classPrefixIRI)) {
-            MapperSchema mapperSchema = getMapperSchema(query, ontology, cls);
+            MapperSchema mapperSchema = getMapperSchema(query, ontology, cls, this.schemaDescriptions.get(cls.getIRI()));
 
             for (OWLClass ref_class : mapperSchema.getProperties_range()) {
                 if (this.mapped_classes.contains(ref_class)){
@@ -167,7 +166,7 @@ private List<OWLClass> add_owlclass_to_openapi(Query query, Path pathGenerator,
                     for (OWLOntology temp_ontology : this.ontologies) {
                         if ( follow_references ) {
                             this.mapped_classes.add(ref_class);
-                            getMapperSchema(query, temp_ontology, ref_class);
+                            getMapperSchema(query, temp_ontology, ref_class,this.schemaDescriptions.get(ref_class.getIRI()));
                             OWLDocumentFormat format = ontology.getFormat();
                             //String temp_defaultOntologyPrefixIRI = ((RDFXMLDocumentFormat) format).getDefaultPrefix();
                             String temp_defaultOntologyPrefixIRI = format.asPrefixOWLDocumentFormat().getDefaultPrefix();
@@ -184,9 +183,9 @@ private List<OWLClass> add_owlclass_to_openapi(Query query, Path pathGenerator,
         return ref;
     }
 
-    private MapperSchema getMapperSchema(Query query, OWLOntology ontology, OWLClass cls) {
+    private MapperSchema getMapperSchema(Query query, OWLOntology ontology, OWLClass cls, String cls_description) {
         //Convert from OWL Class to OpenAPI Schema.
-        MapperSchema mapperSchema = new MapperSchema(this.ontologies, cls, schemaNames, ontology, follow_references);
+        MapperSchema mapperSchema = new MapperSchema(this.ontologies, cls, cls_description, schemaNames, ontology, follow_references);
         //Write queries
         query.write_readme(mapperSchema.name);
         //Create the OpenAPI schema
@@ -207,21 +206,37 @@ private void setSchemaNames(Set<OWLClass> classes) {
             schemaNames.put(cls.getIRI(), cls.getIRI().getShortForm());
         }
     }
+    
+    /**
+     * Given a set of classes from an ontology, this method initializes
+     * schemaDescriptions with the definitions used to describe an ontology (if provided)
+     * @param classes the classes you want the description for
+     * @param ontology the ontology from where we will extract the descriptions
+     */
+    private void setSchemaDrescriptions(Set<OWLClass> classes,OWLOntology ontology){
+       for (OWLClass cls : classes) {
+           System.out.println(cls);
+           schemaDescriptions.put(cls.getIRI(), ObaUtils.getDescription(cls, ontology));
+       }
+    }
 
     private void add_path(Path pathGenerator, MapperSchema mapperSchema) {
         String singular_name = "/" + mapperSchema.name.toLowerCase() + "s/{id}";
         String plural_name = "/" + mapperSchema.name.toLowerCase() + "s";
         //Create the plural paths: for example: /models/
-        this.paths.addPathItem(plural_name, pathGenerator.generate_plural(mapperSchema.name));
+        this.paths.addPathItem(plural_name, pathGenerator.generate_plural(mapperSchema.name,
+                mapperSchema.getCls().getIRI().getIRIString()));
         //Create the plural paths: for example: /models/id
-        this.paths.addPathItem(singular_name, pathGenerator.generate_singular(mapperSchema.name));
+        this.paths.addPathItem(singular_name, pathGenerator.generate_singular(mapperSchema.name,
+                mapperSchema.getCls().getIRI().getIRIString()));
     }
 
-    private void add_path_relation(Path pathGenerator, String schema_name, String predicate, String path) {
-        String relation = "/" + schema_name.toLowerCase() + "s/{id}/" + path;
-        this.paths.addPathItem(relation, pathGenerator.generate_plural(schema_name));
-
-    }
+// Method not used
+//    private void add_path_relation(Path pathGenerator, String schema_name, String predicate, String path) {
+//        String relation = "/" + schema_name.toLowerCase() + "s/{id}/" + path;
+//        this.paths.addPathItem(relation, pathGenerator.generate_plural(schema_name));
+//
+//    }
 
     public List<OWLClass> filter_classes() {
         List<String> selected_classes_iri = this.config_data.getClasses();

src/main/java/edu/isi/oba/MapperDataProperty.java

@@ -2,7 +2,6 @@
 
 import io.swagger.v3.oas.models.media.*;
 
-import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import static edu.isi.oba.Oba.logger;
@@ -72,15 +71,17 @@ private String getDataType(String key){
   private static final String BOOLEAN_TYPE = "boolean";
 
   final String name;
+  final String description;
   private List<String> type;
   private Boolean array;
   private Boolean nullable;
 
 
-  public MapperDataProperty(String name, List<String> type, Boolean array, Boolean nullable) {
+  public MapperDataProperty(String name, String description, List<String> type, Boolean array, Boolean nullable) {
     this.dataTypes = new HashMap<>();
     this.setDataTypes();
     this.name = name;
+    this.description = description;
     this.type = type;
     this.array = array;
     this.nullable = nullable;
@@ -93,10 +94,10 @@ public Schema getSchemaByDataProperty(){
     ////}
 
     if (this.type.size() == 0) {
-      return (array) ? arraySchema(new StringSchema(), nullable) : new StringSchema().nullable(nullable);
+      return (array) ? arraySchema(new StringSchema(), nullable) : new StringSchema().nullable(nullable).description(description);
     }
     else if (this.type.size() > 1){
-      return (array) ? arraySchema(new Schema(), nullable) : new Schema().nullable(nullable);
+      return (array) ? arraySchema(new Schema(), nullable) : new Schema().nullable(nullable).description(description);
     }
 
     String schemaType = getDataType(this.type.get(0));
@@ -105,66 +106,69 @@ else if (this.type.size() > 1){
     }
     switch (schemaType) {
       case STRING_TYPE:
-        return (array) ? arraySchema(new StringSchema(), nullable) : new StringSchema().nullable(nullable);
+        return (array) ? arraySchema(new StringSchema(), nullable) : new StringSchema().nullable(nullable).description(description);
       case NUMBER_TYPE:
-        return (array) ? arraySchema(new NumberSchema(), nullable) : new NumberSchema().nullable(nullable);
+        return (array) ? arraySchema(new NumberSchema(), nullable) : new NumberSchema().nullable(nullable).description(description);
       case INTEGER_TYPE:
-        return (array) ? arraySchema(new IntegerSchema(), nullable) : new IntegerSchema().nullable(nullable);
+        return (array) ? arraySchema(new IntegerSchema(), nullable) : new IntegerSchema().nullable(nullable).description(description);
       case BOOLEAN_TYPE:
-        return (array) ? arraySchema(new BooleanSchema(), nullable) : new BooleanSchema().nullable(nullable);
+        return (array) ? arraySchema(new BooleanSchema(), nullable) : new BooleanSchema().nullable(nullable).description(description);
      default:
         logger.warning("datatype mapping failed " + this.type.get(0));
-        return (array) ? arraySchema(new Schema(), nullable) : new Schema().nullable(nullable);
+        return (array) ? arraySchema(new Schema(), nullable) : new Schema().nullable(nullable).description(description);
     }
   }
 
-  private Schema getObjectPropertiesByRef(String ref, boolean array, boolean nullable){
-    Schema object = new ObjectSchema();
-    object.set$ref(ref);
-
-    if (array) {
-      ArraySchema objects = new ArraySchema();
-      objects.setNullable(nullable);
-      objects.setItems(object);
-      return objects;
-    }
-    else {
-      return object;
-    }
-
-
-  }
-  private Schema getComposedSchemaObject(List<String> refs, boolean array, boolean nullable){
-    Schema object = new ObjectSchema();
-    object.setType("object");
-
-    if (array) {
-      ArraySchema objects = new ArraySchema();
-      objects.setNullable(nullable);
-      objects.setItems(object);
-      return objects;
-    }
-    else {
-      return object;
-    }
-
-        /*ComposedSchema composedSchema = new ComposedSchema();
-        List<Schema> items = new ArrayList<>();
-        for (String ref : refs){
-            Schema item = getObjectPropertiesByRef(ref, array, nullable);
-            items.add(item);
-        }
-        composedSchema.setAnyOf(items);
-        return composedSchema;
-        */
-
-  }
+  //Not used
+//  private Schema getObjectPropertiesByRef(String ref, boolean array, boolean nullable){
+//    Schema object = new ObjectSchema();
+//    object.set$ref(ref);
+//
+//    if (array) {
+//      ArraySchema objects = new ArraySchema();
+//      objects.setNullable(nullable);
+//      objects.setItems(object);
+//      return objects;
+//    }
+//    else {
+//      return object;
+//    }
+//
+//
+//  }
+//  not used
+//  private Schema getComposedSchemaObject(List<String> refs, boolean array, boolean nullable){
+//    Schema object = new ObjectSchema();
+//    object.setType("object");
+//
+//    if (array) {
+//      ArraySchema objects = new ArraySchema();
+//      objects.setNullable(nullable);
+//      objects.setItems(object);
+//      return objects;
+//    }
+//    else {
+//      return object;
+//    }
+//
+//        /*ComposedSchema composedSchema = new ComposedSchema();
+//        List<Schema> items = new ArrayList<>();
+//        for (String ref : refs){
+//            Schema item = getObjectPropertiesByRef(ref, array, nullable);
+//            items.add(item);
+//        }
+//        composedSchema.setAnyOf(items);
+//        return composedSchema;
+//        */
+//
+//  }
 
 
 
 
   private ArraySchema arraySchema(Schema base, boolean nullable) {
     ArraySchema array = new ArraySchema();
+    array.setDescription(description);
     array.setNullable(nullable);
     array.setItems(base);
     return array;

src/main/java/edu/isi/oba/MapperObjectProperty.java

@@ -2,25 +2,26 @@
 
 import io.swagger.v3.oas.models.media.*;
 
-import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
 
 class MapperObjectProperty {
   final String name;
+  final String description;
   private List<String> ref;
   private Boolean array;
   private Boolean nullable;
 
-  public MapperObjectProperty(String name, List<String> ref) {
+  public MapperObjectProperty(String name, String description, List<String> ref) {
     this.name = name;
+    this.description = description;
     this.ref = ref;
     this.array = true;
     this.nullable = true;
   }
 
-  public MapperObjectProperty(String name, List<String> ref, Boolean array, Boolean nullable) {
+  public MapperObjectProperty(String name, String description, List<String> ref, Boolean array, Boolean nullable) {
     this.name = name;
+    this.description = description;
     this.ref = ref;
     this.array = array;
     this.nullable = nullable;
@@ -42,9 +43,11 @@ public Schema getSchemaByObjectProperty(){
   private Schema getObjectPropertiesByRef(String ref, boolean array, boolean nullable){
     Schema object = new ObjectSchema();
     object.set$ref(ref);
+    object.setDescription(description);
 
     if (array) {
       ArraySchema objects = new ArraySchema();
+      objects.setDescription(description);
       objects.setNullable(nullable);
       objects.setItems(object);
       return objects;
@@ -58,9 +61,11 @@ private Schema getObjectPropertiesByRef(String ref, boolean array, boolean nulla
   private Schema getComposedSchemaObject(List<String> refs, boolean array, boolean nullable){
     Schema object = new ObjectSchema();
     object.setType("object");
+    object.setDescription(description);
 
     if (array) {
       ArraySchema objects = new ArraySchema();
+      objects.setDescription(description);
       objects.setNullable(nullable);
       objects.setItems(object);
       return objects;