Merge branch '1132-transcription-site-color' into 'devel_14.0.x'

Resolve "Transcription Site colour is not white black in Empty view"

See merge request !1069

CHANGELOG

@@ -11,6 +11,9 @@ minerva (14.0.9) stable; urgency=medium
   * Bug fix: when data overlay name in zip uploaded zip file is not present the
     name of a file is used as overlay name (#1065)
   * Bug fix: uploading empty data overlay resulted in an error (#1123)
+  * Bug fix: exporting map with glyphs crashed (#1130)
+  * Bug fix: transcription factor on black&white gene are drawn in black
+    (#1132)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 3 Feb 2020 15:00:00 +0200
 

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java

@@ -620,6 +620,9 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
     } else {
       color = Color.BLACK;
     }
+    if (transcriptionSite.getSpecies() != null && transcriptionSite.getSpecies().getColor().equals(Color.WHITE)) {
+      color = Color.BLACK;
+    }
     double y = transcriptionSite.getPosition().getY();
     double x = transcriptionSite.getPosition().getX();
     PolylineData line = new PolylineData();

model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Glyph.java

@@ -69,6 +69,10 @@ public class Glyph implements Serializable {
   public Glyph(Glyph original) {
     // we should reference to the same file
     setFile(original.getFile());
+    if (original.getFile() != null) {
+      // make sure that the content is available
+      original.getFile().getFileContent();
+    }
   }
 
   public UploadedFileEntry getFile() {

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

@@ -16,6 +16,7 @@ import org.junit.runners.Suite.SuiteClasses;
     FileControllerIntegrationTestWithoutTransaction.class,
     FunctionControllerIntegrationTest.class,
     MapControllerIntegrationTest.class,
+    MapControllerIntegrationTestWithoutTransaction.class,
     MiRnaControllerIntegrationTest.class,
     OverlayControllerIntegrationTest.class,
     OverlayControllerIntegrationTestWithoutTransaction.class,

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

@@ -4,6 +4,9 @@ import static org.springframework.test.web.servlet.request.MockMvcRequestBuilder
 import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
 
 import java.awt.geom.Point2D;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
 import java.util.Arrays;
 import java.util.List;
 import java.util.concurrent.*;
@@ -34,6 +37,7 @@ import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.map.Comment;
 import lcsb.mapviewer.model.map.layout.ColorSchemaType;
 import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.graphics.Glyph;
 import lcsb.mapviewer.model.map.model.ModelData;
 import lcsb.mapviewer.model.map.reaction.*;
 import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
@@ -189,6 +193,33 @@ abstract public class ControllerIntegrationTest {
     return user;
   }
 
+  protected Project createProjectWithGlyph(String projectId) throws IOException {
+    User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
+    Project project = new Project(projectId);
+    project.setOwner(admin);
+    UploadedFileEntry  file = createFile(Files.readAllBytes(Paths.get("./src/test/resources/empty.png")), admin);
+    ModelData map = new ModelData();
+    map.setTileSize(256);
+    map.setWidth(100);
+    map.setHeight(100);
+
+    Element element = new GenericProtein("p1");
+    element.setWidth(100.0);
+    element.setHeight(20.0);
+    element.setX(10);
+    element.setX(20);
+    element.setZ(2);
+    Glyph g = new Glyph();
+    g.setFile(file);
+    element.setGlyph(g);
+    map.addElement(element);
+
+    project.addModel(map);
+    project.addGlyph(g);
+    projectDao.add(project);
+    return project;
+  }
+
   protected Project createProject(String projectId) {
     Project project = new Project(projectId);
     project.setOwner(userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN));

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

+package lcsb.mapviewer.web;
+
+import static org.junit.Assert.assertNotNull;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
+
+import java.io.IOException;
+import java.util.function.Supplier;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.*;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.mock.web.MockHttpSession;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.test.web.servlet.RequestBuilder;
+
+import lcsb.mapviewer.converter.graphics.PngImageGenerator;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.services.interfaces.IModelService;
+
+@RunWith(SpringJUnit4ClassRunner.class)
+public class MapControllerIntegrationTestWithoutTransaction extends ControllerIntegrationTest {
+
+  private static final String TEST_PROJECT = "test_project";
+
+  Logger logger = LogManager.getLogger();
+
+  private Project project;
+  private ModelData map;
+
+  @Autowired
+  private IModelService modelService;
+
+  @Before
+  public void setup() throws Exception {
+    callInSeparateThread(new Supplier<Void>() {
+      @Override
+      public Void get() {
+        try {
+          project = createProjectWithGlyph(TEST_PROJECT);
+          map = project.getModels().iterator().next();
+        } catch (IOException e) {
+          e.printStackTrace();
+        }
+        return null;
+      }
+    });
+    assertNotNull(project);
+    modelService.removeModelFromCache(map);
+  }
+
+  @After
+  public void tearDown() throws Exception {
+    removeProjectInSeparateThread(project);
+  }
+
+  @Test
+  public void testDownloadImageWithGlyphs() throws Exception {
+    MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
+
+    //fetch the map (but don't do anything with glyphs)
+    RequestBuilder request2 = get("/projects/" + TEST_PROJECT + "/models/")
+        .session(session);
+
+    mockMvc.perform(request2)
+        .andExpect(status().is2xxSuccessful());
+
+    RequestBuilder request = get("/projects/" + TEST_PROJECT + "/models/" + map.getId() + ":downloadImage?" +
+        "handlerClass=" + PngImageGenerator.class.getCanonicalName())
+            .session(session);
+
+    mockMvc.perform(request)
+        .andExpect(status().is2xxSuccessful());
+  }
+}