fix: add classes context file (#116)

* fix: create a the file with the classes context and using obasparql 3.4.1

* add docs

docs/features.md

@@ -33,7 +33,10 @@ For each of these paths, OBA generates the SPARQL queries that are necessary to
 
 ### Generating JSON-LD contexts
 
-OBA converts the format of the responses from JSON/LD to plain JSON, which is a widely format used by Web developers. In order to achieve this, OBA requires a file with the context of the ontologies used. The context is used to map simple terms to IRIs. OBA generates these context file automatically.
+OBA converts the format of the responses from JSON/LD to plain JSON, which is a widely format used by Web developers. In order to achieve this, OBA requires two files with the context of the ontologies used. The context is used to map simple terms to IRIs. OBA generates these context file automatically.
+
+!!! note
+    Since OBA 3.3.0, OBA uses two files `context.json` and `context_class.json`. The first file contains all the mappings (classes and properties) and the second file contains the classes mapping. OBAsparql uses the `context.json` for `POST` and `PUT` method and uses the `context_class.json` for `GET` method.
 
 !!! info
     OBA reuses and extends [owl2jsonld](https://github.com/stain/owl2jsonld), developed by [Stain Soiland-Reyes](https://github.com/stain).

examples/modelcatalog/config.yaml

@@ -1,6 +1,6 @@
 ontologies:
-  - https://w3id.org/okn/o/sdm/1.5.0
-  - https://w3id.org/okn/o/sd/1.6.0
+  - https://w3id.org/okn/o/sdm/1.6.0-nm
+  - https://w3id.org/okn/o/sd/1.7.0-nm
 name: modelcatalog
 output_dir: outputs
 openapi:

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

@@ -84,13 +84,18 @@ public static void main(String[] args) throws Exception {
   private static void generate_context(YamlConfig config_data, String destination_dir) {
     List<String> ontologies = config_data.getOntologies();
     JSONObject context_json_object = null;
+    JSONObject context_json_object_class = null;
     try {
-      context_json_object = ObaUtils.generate_context_file(ontologies.toArray(new String[0]));
+      context_json_object = ObaUtils.generate_context_file(ontologies.toArray(new String[0]), false);
+      context_json_object_class = ObaUtils.generate_context_file(ontologies.toArray(new String[0]), true);
     } catch (Exception e) {
       e.printStackTrace();
     }
     String file_path = destination_dir + File.separator + "servers" + File.separator + "context.json";
+    String file_path_class = destination_dir + File.separator + "servers" + File.separator + "context_class.json";
+
     ObaUtils.write_file(file_path, context_json_object.toString(4));
+    ObaUtils.write_file(file_path_class, context_json_object_class.toString(4));
   }
 
   private static void copy_custom_queries(String source, String destination){

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

@@ -226,11 +226,11 @@ public static JSONObject mergeJSONObjects(JSONObject json1, JSONObject json2) {
         return mergedJSON;
     }
 
-    public static JSONObject generate_context_file(String[] ontologies) throws Exception {
+    public static JSONObject generate_context_file(String[] ontologies, Boolean only_classes) throws Exception {
         JSONObject[] jsons = new JSONObject[ontologies.length];
         for (int i = 0; i < ontologies.length; i++) {
             try {
-                jsons[i] = run_owl_jsonld(ontologies[i]);
+                jsons[i] = run_owl_jsonld(ontologies[i], only_classes);
             } catch (IOException e) {
                 e.printStackTrace();
             } catch (InterruptedException e) {
@@ -242,18 +242,28 @@ public static JSONObject generate_context_file(String[] ontologies) throws Excep
 
     /**
      * Method to execute OWL2JSONLD
-     * @param ontology_file file path of the ontology to load 
+     * @param ontology_file file path of the ontology to load
+     * @param only_classes
      * @return JSON object with the context of the ontology
      * @throws Exception 
      */
-    private static JSONObject run_owl_jsonld(String ontology_file) throws Exception {
+    private static JSONObject run_owl_jsonld(String ontology_file, Boolean only_classes) throws Exception {
         ontology_file = new File(ontology_file).toURI().toString();
         String owl2jsonld = "/owl2jsonld-0.3.0-SNAPSHOT-standalone.jar";
         InputStream owl2_jar = ObaUtils.class.getResourceAsStream(owl2jsonld);
         File tempFile = File.createTempFile("oba", "jar");
         copy(owl2_jar,tempFile);
         Runtime rt = Runtime.getRuntime();
-        Process proc = rt.exec(new String[]{"java", "-jar", tempFile.getPath(), ontology_file});
+        String[] cmdarray = new String[0];
+
+        if (only_classes) {
+            cmdarray = new String[]{"java", "-jar", tempFile.getPath(), "-c", ontology_file};
+        }
+        else {
+            cmdarray = new String[]{"java", "-jar", tempFile.getPath(), ontology_file};
+
+        }
+        Process proc = rt.exec(cmdarray);
 
         BufferedReader stdInput = new BufferedReader(new
                 InputStreamReader(proc.getInputStream()));

src/main/resources/servers/python/.openapi-generator/template/requirements.mustache

@@ -1,6 +1,6 @@
 pythonql3==0.9.61
 connexion >= 2.6.0
-obasparql >= 3.3.3
+obasparql >= 3.4.1
 werkzeug==0.16.1
 swagger-ui-bundle >= 0.0.2
 python_dateutil >= 2.6.0

src/main/resources/servers/python/generate-server.sh

@@ -34,6 +34,7 @@ mkdir -p ${PWD}/$SERVER_DIR/contexts/
 echo "Copying query files"
 cp -r ../../queries ${PWD}/$SERVER_DIR/queries
 cp -r ../context.json ${PWD}/$SERVER_DIR/contexts/
+cp -r ../context_class.json ${PWD}/$SERVER_DIR/contexts/
 if [ "$?" == "0" ]; then
         echo -e "${GREEN}SUCCESS${RESET}"
-fi
+fi

src/test/java/edu/isi/oba/ObaUtilsTest.java

@@ -10,12 +10,9 @@
 import java.io.IOException;
 
 import static org.junit.Assert.*;
-import org.semanticweb.owlapi.model.IRI;
+
 import org.semanticweb.owlapi.model.OWLClass;
-import org.semanticweb.owlapi.model.OWLEntity;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
-import org.semanticweb.owlapi.search.EntitySearcher;
-import uk.ac.manchester.cs.owl.owlapi.OWLClassImpl;
 
 public class ObaUtilsTest {
 
@@ -68,7 +65,7 @@ public void run() {
         String[] ontologies = new String[]{"ontology1", "ontology2"};
         JSONObject context = null;
         try {
-            context = ObaUtils.generate_context_file(ontologies);
+            context = ObaUtils.generate_context_file(ontologies, false);
         } catch (Exception e) {
             e.printStackTrace();
         }