provide inof about modifier type

CHANGELOG

 minerva (16.1.0~alpha.0) stable; urgency=medium
+  * Small improvement: API provides information about modifier type (#1085)
   * Bug fix: api endpoints were exposed without 'api' prefix
   * Bug fix: anonymous user could upload file using API
   * Bug fix: when passing JSON in patch/post methods contentType was not

model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNode.java

 package lcsb.mapviewer.model.map.reaction;
 
-import javax.persistence.*;
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.ManyToOne;
+
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
 
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.modelutils.map.ElementUtils;
+import lcsb.mapviewer.modelutils.serializer.model.map.reaction.ReactionNodeSerializer;
 
 /**
  * One of two known types of nodes in the {@link Reaction}. It defines input or
@@ -22,6 +27,7 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
  */
 @Entity
 @DiscriminatorValue("GENERIC_REACTION_NODE")
+@JsonSerialize(using = ReactionNodeSerializer.class)
 public abstract class ReactionNode extends AbstractNode {
 
   /**

model/src/main/java/lcsb/mapviewer/modelutils/serializer/model/map/reaction/ReactionNodeSerializer.java

+package lcsb.mapviewer.modelutils.serializer.model.map.reaction;
+
+import java.io.IOException;
+
+import com.fasterxml.jackson.core.JsonGenerator;
+import com.fasterxml.jackson.databind.JsonSerializer;
+import com.fasterxml.jackson.databind.SerializerProvider;
+
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+
+public class ReactionNodeSerializer extends JsonSerializer<ReactionNode> {
+
+  @Override
+  public void serialize(final ReactionNode node, final JsonGenerator gen,
+      final SerializerProvider serializers)
+      throws IOException {
+    gen.writeStartObject();
+    gen.writeNumberField("aliasId", node.getElement().getId());
+    gen.writeObjectField("stoichiometry", node.getStoichiometry());
+    gen.writeStringField("type", node.getClass().getSimpleName());
+    gen.writeEndObject();
+  }
+
+}
\ No newline at end of file

rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java

@@ -36,7 +36,6 @@ import lcsb.mapviewer.model.map.reaction.NodeOperator;
 import lcsb.mapviewer.model.map.reaction.Product;
 import lcsb.mapviewer.model.map.reaction.Reactant;
 import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
 import lcsb.mapviewer.modelutils.serializer.MathMLSerializer;
 import lcsb.mapviewer.services.QueryException;
 import lcsb.mapviewer.services.interfaces.IReactionService;
@@ -113,27 +112,15 @@ public class ReactionsController extends BaseController {
           value = pt.getPointOnLine(centerLine.getP1(), centerLine.getP2(), 0.5);
           break;
         case "products": {
-          List<Map<String, Object>> ids = new ArrayList<>();
-          for (Product product : reaction.getProducts()) {
-            ids.add(createReactionNode(product));
-          }
-          value = ids;
+          value = reaction.getProducts();
           break;
         }
         case "reactants": {
-          List<Map<String, Object>> ids = new ArrayList<>();
-          for (Reactant reactant : reaction.getReactants()) {
-            ids.add(createReactionNode(reactant));
-          }
-          value = ids;
+          value = reaction.getReactants();
           break;
         }
         case "modifiers": {
-          List<Map<String, Object>> ids = new ArrayList<>();
-          for (Modifier modifier : reaction.getModifiers()) {
-            ids.add(createReactionNode(modifier));
-          }
-          value = ids;
+          value = reaction.getModifiers();
           break;
         }
         case "type":
@@ -233,13 +220,6 @@ public class ReactionsController extends BaseController {
     return result;
   }
 
-  private Map<String, Object> createReactionNode(ReactionNode node) {
-    Map<String, Object> result = new TreeMap<>();
-    result.put("aliasId", node.getElement().getId());
-    result.put("stoichiometry", node.getStoichiometry());
-    return result;
-  }
-
   private Map<String, Object> kineticsToMap(SbmlKinetics kinetics) {
     if (kinetics == null) {
       return null;

service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java

@@ -1382,4 +1382,9 @@ public class ProjectService implements IProjectService {
       return new ArrayList<>();
     }
   }
+
+  @Override
+  public void add(Project project) {
+    projectDao.add(project);
+  }
 }

service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java

@@ -124,4 +124,6 @@ public interface IProjectService {
   UploadedFileEntry getFileByProjectId(String projectId);
 
   List<ProjectBackground> getBackgrounds(String projectId, boolean initializeLazy);
+
+  void add(Project project);
 }

web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java

@@ -107,6 +107,7 @@ import lcsb.mapviewer.persist.dao.map.ModelDao;
 import lcsb.mapviewer.persist.dao.user.ResetPasswordTokenDao;
 import lcsb.mapviewer.persist.dao.user.UserDao;
 import lcsb.mapviewer.services.interfaces.IDataOverlayService;
+import lcsb.mapviewer.services.interfaces.IFileService;
 import lcsb.mapviewer.services.interfaces.IProjectService;
 import lcsb.mapviewer.services.interfaces.IUserService;
 import lcsb.mapviewer.web.config.SpringWebConfig;
@@ -161,6 +162,9 @@ abstract public class ControllerIntegrationTest {
   @Autowired
   private UploadedFileEntryDao fileDao;
 
+  @Autowired
+  private IFileService fileService;
+
   @Autowired
   private DataOverlayDao dataOverlayDao;
 
@@ -444,7 +448,7 @@ abstract public class ControllerIntegrationTest {
     background.setCreator(userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN));
     project.addProjectBackground(background);
 
-    projectDao.add(project);
+    projectService.add(project);
     return project;
   }
 
@@ -516,7 +520,7 @@ abstract public class ControllerIntegrationTest {
     file.setOriginalFileName("test_file");
     file.setLength(content.length);
     file.setOwner(user);
-    fileDao.add(file);
+    fileService.add(file);
     return file;
   }
 

web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java

@@ -16,6 +16,8 @@ import static org.springframework.restdocs.request.RequestDocumentation.pathPara
 import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
 import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
 
+import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
 import java.util.function.Supplier;
@@ -30,6 +32,8 @@ import org.junit.runner.RunWith;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
 import org.springframework.mock.web.MockHttpSession;
+import org.springframework.restdocs.payload.FieldDescriptor;
+import org.springframework.restdocs.payload.JsonFieldType;
 import org.springframework.restdocs.payload.ResponseFieldsSnippet;
 import org.springframework.restdocs.request.PathParametersSnippet;
 import org.springframework.restdocs.request.RequestParametersSnippet;
@@ -229,62 +233,85 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
   }
 
   private ResponseFieldsSnippet listOfReactionResponseFields() {
-    return responseFields(
+    List<FieldDescriptor> fields = new ArrayList<>(Arrays.asList(
         fieldWithPath("[].id")
             .description("unique element identifier")
-            .type("number")
+            .type(JsonFieldType.NUMBER)
             .optional(),
         fieldWithPath("[].reactionId")
             .description("reaction identifier taken from source file")
-            .type("string")
+            .type(JsonFieldType.STRING)
             .optional(),
         fieldWithPath("[].modelId")
             .description("map identifier")
-            .type("number")
+            .type(JsonFieldType.NUMBER)
             .optional(),
         fieldWithPath("[].type")
             .description("reaction type")
-            .type("string")
+            .type(JsonFieldType.STRING)
             .optional(),
         subsectionWithPath("[].centerPoint")
             .description("center point")
-            .type("point")
+            .type(JsonFieldType.OBJECT)
             .optional(),
         subsectionWithPath("[].lines")
             .description("list of lines used to draw reaction")
-            .type("array<line>")
+            .type(JsonFieldType.ARRAY)
             .optional(),
         fieldWithPath("[].hierarchyVisibilityLevel")
             .description("at what zoom level this element becomes visible in hierarchical view")
-            .type("string")
+            .type(JsonFieldType.STRING)
             .optional(),
         subsectionWithPath("[].references")
             .description("list of references")
-            .type("array<Reference>")
+            .type(JsonFieldType.ARRAY)
             .optional(),
-        subsectionWithPath("[].modifiers")
+        fieldWithPath("[].modifiers")
             .description("list of modifiers")
-            .type("array<object>")
+            .type(JsonFieldType.ARRAY)
             .optional(),
-        subsectionWithPath("[].reactants")
+        fieldWithPath("[].reactants")
             .description("list of reactants")
-            .type("array<object>")
+            .type(JsonFieldType.ARRAY)
             .optional(),
-        subsectionWithPath("[].products")
+        fieldWithPath("[].products")
             .description("list of products")
-            .type("array<object>")
+            .type(JsonFieldType.ARRAY)
             .optional(),
         fieldWithPath("[].notes")
             .description("notes and description")
-            .type("string")
+            .type(JsonFieldType.STRING)
             .optional(),
         fieldWithPath("[].kineticLaw")
             .description("SBML kinetics law")
-            .type("object")
+            .type(JsonFieldType.OBJECT)
             .optional(),
         subsectionWithPath("[].other")
             .description("list of oher properties")
-            .type("object")
+            .type(JsonFieldType.OBJECT)
+            .optional()));
+    fields.addAll(reactionNodeFields("[].reactants[]"));
+    fields.addAll(reactionNodeFields("[].products[]"));
+    fields.addAll(reactionNodeFields("[].modifiers[]"));
+    return responseFields(fields);
+  }
+
+  private List<FieldDescriptor> reactionNodeFields(String prefix) {
+    if (!prefix.endsWith(".") && !prefix.isEmpty()) {
+      prefix = prefix + ".";
+    }
+    return Arrays.asList(
+        fieldWithPath(prefix + "aliasId")
+            .description("element identifier")
+            .type(JsonFieldType.NUMBER)
+            .optional(),
+        fieldWithPath(prefix + "type")
+            .description("type")
+            .type(JsonFieldType.STRING)
+            .optional(),
+        fieldWithPath(prefix + "stoichiometry")
+            .description("element stoichiometry")
+            .type(JsonFieldType.STRING)
             .optional());
   }
 

web/src/test/java/lcsb/mapviewer/web/ReactionControllerIntegrationTest.java

@@ -6,10 +6,11 @@ import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.junit.*;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
 import org.springframework.mock.web.MockHttpSession;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.test.web.servlet.RequestBuilder;
@@ -36,10 +37,8 @@ public class ReactionControllerIntegrationTest extends ControllerIntegrationTest
 
   @Before
   public void setup() {
-    callInSeparateThreadNoReturn(() -> {
-      project = createProject(TEST_PROJECT);
-      anonymous = userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN);
-    });
+    project = createProject(TEST_PROJECT);
+    anonymous = userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN);
   }
 
   @After
@@ -51,8 +50,7 @@ public class ReactionControllerIntegrationTest extends ControllerIntegrationTest
   public void testGetAllReactions() throws Exception {
     userService.grantUserPrivilege(anonymous, PrivilegeType.READ_PROJECT, project.getProjectId());
 
-    RequestBuilder request = get("/api/projects/" + TEST_PROJECT + "/models/*/bioEntities/reactions/")
-        .contentType(MediaType.APPLICATION_FORM_URLENCODED);
+    RequestBuilder request = get("/api/projects/{projectId}/models/*/bioEntities/reactions/", TEST_PROJECT);
 
     String response = mockMvc.perform(request)
         .andExpect(status().is2xxSuccessful())
@@ -70,7 +68,6 @@ public class ReactionControllerIntegrationTest extends ControllerIntegrationTest
     MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
 
     RequestBuilder request = get("/api/projects/*/models/*/bioEntities/reactions/")
-        .contentType(MediaType.APPLICATION_FORM_URLENCODED)
         .session(session);
 
     mockMvc.perform(request)