glyphs are assigned to elements having glyph property

converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java

@@ -17,7 +17,10 @@ import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
 import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
 import lcsb.mapviewer.converter.zip.ZipEntryFile;
 import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.layout.graphics.Glyph;
 import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.species.Element;
 
 public class ProjectFactory {
 
@@ -75,6 +78,9 @@ public class ProjectFactory {
         project
             .addOverviewImages(parser.parseOverviewLinks(models, imageEntries, params.getVisualizationDir(), zipFile));
       }
+      if (project.getGlyphs().size() > 0) {
+        assignGlyphsToElements(project);
+      }
       return project;
     } catch (IOException e) {
       throw new InvalidArgumentException(e);
@@ -82,4 +88,44 @@ public class ProjectFactory {
       throw new InvalidInputDataExecption("Invalid coordinates file. " + e.getMessage(), e);
     }
   }
+
+  private void assignGlyphsToElements(Project project) throws InvalidGlyphFile {
+    for (ModelData model : project.getModels()) {
+      for (Element element : model.getElements()) {
+        Glyph glyph = extractGlyph(project, element.getNotes());
+        if (glyph != null) {
+          element.setNotes(removeGlyph(element.getNotes()));
+          element.setGlyph(glyph);
+        }
+      }
+    }
+  }
+
+  String removeGlyph(String notes) {
+    String lines[] = notes.split("[\n\r]+");
+    StringBuilder result = new StringBuilder("");
+    for (String line : lines) {
+      if (!line.startsWith("Glyph:")) {
+        result.append(line + "\n");
+      }
+    }
+    return result.toString();
+  }
+
+  Glyph extractGlyph(Project project, String notes) throws InvalidGlyphFile {
+    String lines[] = notes.split("[\n\r]+");
+    for (String line : lines) {
+      if (line.startsWith("Glyph:")) {
+        String glyphString = line.replace("Glyph:", "").trim().toLowerCase();
+        for (Glyph glyph : project.getGlyphs()) {
+          if (glyph.getFile().getOriginalFileName().toLowerCase().equalsIgnoreCase(glyphString)) {
+            return glyph;
+          }
+        }
+        throw new InvalidGlyphFile("Glyph file doesn't exist: " + glyphString);
+      }
+    }
+    return null;
+  }
+
 }

converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java

@@ -8,8 +8,6 @@ import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
 import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.InputStream;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipFile;
 
@@ -19,133 +17,21 @@ import org.junit.Before;
 import org.junit.Test;
 import org.mockito.Mockito;
 
-import lcsb.mapviewer.common.MimeType;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.InvalidClassException;
 import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
 import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
-import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.layout.Layout;
 import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
 import lcsb.mapviewer.model.map.model.SubmodelType;
-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.type.TransportReaction;
-import lcsb.mapviewer.model.map.species.Complex;
 import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.Species;
 
 public class ComplexZipConverterTest {
 
   @SuppressWarnings("unused")
   private static Logger logger = Logger.getLogger(ComplexZipConverterTest.class);
 
-  public static class MockConverter extends Converter {
-
-    @Override
-    public Model createModel(ConverterParams params) {
-      Model result = new ModelFullIndexed(null);
-
-      Species sa1 = new GenericProtein("sa1");
-      result.addElement(sa1);
-
-      Species sa2 = new GenericProtein("sa2");
-      result.addElement(sa2);
-
-      Species sa3 = new GenericProtein("sa3");
-      result.addElement(sa3);
-
-      Species sa4 = new Phenotype("sa4");
-      result.addElement(sa4);
-
-      Complex ca1 = new Complex("ca1");
-      ca1.setName("main");
-      result.addElement(ca1);
-      Species sa5 = new GenericProtein("sa5");
-      sa5.setName("sa1");
-      result.addElement(sa5);
-      ca1.addSpecies(sa5);
-      Species sa6 = new Phenotype("sa6");
-      sa6.setName("sa4");
-      result.addElement(sa6);
-      ca1.addSpecies(sa6);
-
-      Complex ca2 = new Complex("ca2");
-      ca2.setName("s1");
-      result.addElement(ca2);
-      Species sa7 = new GenericProtein("sa7");
-      sa7.setName("sa1");
-      result.addElement(sa7);
-      ca2.addSpecies(sa7);
-
-      Complex ca3 = new Complex("cs3");
-      ca3.setName("s2");
-      result.addElement(ca3);
-
-      Complex ca4 = new Complex("cs4");
-      ca4.setName("s3");
-      result.addElement(ca4);
-
-      Reaction r1 = new TransportReaction("re1");
-      r1.addReactant(new Reactant(sa5));
-      r1.addProduct(new Product(sa7));
-      result.addReaction(r1);
-
-      Reaction r2 = new TransportReaction("re2");
-      r2.addReactant(new Reactant(sa6));
-      r2.addProduct(new Product(ca3));
-      result.addReaction(r2);
-
-      Reaction r3 = new TransportReaction("re3");
-      r3.addReactant(new Reactant(sa7));
-      r3.addProduct(new Product(ca4));
-      result.addReaction(r3);
-      return result;
-    }
-
-    @Override
-    public String model2String(Model model) throws InconsistentModelException, ConverterException {
-      // TODO Auto-generated method stub
-      return null;
-    }
-
-    @Override
-    public InputStream model2InputStream(Model model) throws InconsistentModelException, ConverterException {
-      // TODO Auto-generated method stub
-      return null;
-    }
-
-    @Override
-    public File model2File(Model model, String filePath) throws InconsistentModelException {
-      // TODO Auto-generated method stub
-      return null;
-    }
-
-    @Override
-    public String getCommonName() {
-      // TODO Auto-generated method stub
-      return null;
-    }
-
-    @Override
-    public MimeType getMimeType() {
-      // TODO Auto-generated method stub
-      return null;
-    }
-
-    @Override
-    public String getFileExtension() {
-      // TODO Auto-generated method stub
-      return null;
-    }
-
-  }
-
   @Before
   public void setUp() throws Exception {
   }

converter/src/test/java/lcsb/mapviewer/converter/MockConverter.java

+package lcsb.mapviewer.converter;
+
+import java.io.File;
+import java.io.InputStream;
+
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+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.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class MockConverter extends Converter {
+
+  public static Model modelToBeReturned = null;
+
+  @Override
+  public Model createModel(ConverterParams params) {
+    if (modelToBeReturned != null) {
+      return modelToBeReturned;
+    }
+    Model result = new ModelFullIndexed(null);
+
+    Species sa1 = new GenericProtein("sa1");
+    result.addElement(sa1);
+
+    Species sa2 = new GenericProtein("sa2");
+    result.addElement(sa2);
+
+    Species sa3 = new GenericProtein("sa3");
+    result.addElement(sa3);
+
+    Species sa4 = new Phenotype("sa4");
+    result.addElement(sa4);
+
+    Complex ca1 = new Complex("ca1");
+    ca1.setName("main");
+    result.addElement(ca1);
+    Species sa5 = new GenericProtein("sa5");
+    sa5.setName("sa1");
+    result.addElement(sa5);
+    ca1.addSpecies(sa5);
+    Species sa6 = new Phenotype("sa6");
+    sa6.setName("sa4");
+    result.addElement(sa6);
+    ca1.addSpecies(sa6);
+
+    Complex ca2 = new Complex("ca2");
+    ca2.setName("s1");
+    result.addElement(ca2);
+    Species sa7 = new GenericProtein("sa7");
+    sa7.setName("sa1");
+    result.addElement(sa7);
+    ca2.addSpecies(sa7);
+
+    Complex ca3 = new Complex("cs3");
+    ca3.setName("s2");
+    result.addElement(ca3);
+
+    Complex ca4 = new Complex("cs4");
+    ca4.setName("s3");
+    result.addElement(ca4);
+
+    Reaction r1 = new TransportReaction("re1");
+    r1.addReactant(new Reactant(sa5));
+    r1.addProduct(new Product(sa7));
+    result.addReaction(r1);
+
+    Reaction r2 = new TransportReaction("re2");
+    r2.addReactant(new Reactant(sa6));
+    r2.addProduct(new Product(ca3));
+    result.addReaction(r2);
+
+    Reaction r3 = new TransportReaction("re3");
+    r3.addReactant(new Reactant(sa7));
+    r3.addProduct(new Product(ca4));
+    result.addReaction(r3);
+    return result;
+  }
+
+  @Override
+  public String model2String(Model model) throws InconsistentModelException, ConverterException {
+    return null;
+  }
+
+  @Override
+  public InputStream model2InputStream(Model model) throws InconsistentModelException, ConverterException {
+    return null;
+  }
+
+  @Override
+  public File model2File(Model model, String filePath) throws InconsistentModelException {
+    return null;
+  }
+
+  @Override
+  public String getCommonName() {
+    return null;
+  }
+
+  @Override
+  public MimeType getMimeType() {
+    return null;
+  }
+
+  @Override
+  public String getFileExtension() {
+    return null;
+  }
+
+}
\ No newline at end of file

converter/src/test/java/lcsb/mapviewer/converter/ProjectFactoryTest.java

 package lcsb.mapviewer.converter;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
 
@@ -16,18 +17,22 @@ import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Test;
 
-import lcsb.mapviewer.converter.ComplexZipConverterTest.MockConverter;
 import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
 import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
 import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.OverviewImage;
 import lcsb.mapviewer.model.map.OverviewLink;
 import lcsb.mapviewer.model.map.OverviewModelLink;
+import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.GenericProtein;
 
-public class ProjectFactoryTest {
+public class ProjectFactoryTest extends ConverterTestFunctions {
   Logger logger = Logger.getLogger(ProjectFactoryTest.class);
 
+  int elementCounter = 0;
+
   @AfterClass
   public static void tearDownAfterClass() throws Exception {
   }
@@ -38,6 +43,7 @@ public class ProjectFactoryTest {
 
   @After
   public void tearDown() throws Exception {
+    MockConverter.modelToBeReturned = null;
   }
 
   @Test
@@ -153,7 +159,51 @@ public class ProjectFactoryTest {
       Project project = projectFactory.create(params);
       assertNotNull(project);
       assertEquals(1, project.getGlyphs().size());
-      
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
+  @Test
+  public void testParseGlyphsAndPutThemAsElementGlyphs() throws Exception {
+    try {
+      Model model = new ModelFullIndexed(null);
+      GenericProtein protein = createProtein();
+      protein.setNotes("Glyph: glyphs/g1.png");
+      model.addElement(protein);
+
+      MockConverter.modelToBeReturned = model;
+
+      ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
+      ProjectFactory projectFactory = new ProjectFactory(converter);
+
+      ComplexZipConverterParams params = new ComplexZipConverterParams();
+      params.zipFile(new ZipFile("testFiles/complex_with_glyphs.zip"));
+      params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+
+      ZipFile zipFile = new ZipFile("testFiles/complex_with_glyphs.zip");
+
+      ZipEntryFileFactory factory = new ZipEntryFileFactory();
+      Enumeration<? extends ZipEntry> entries = zipFile.entries();
+      while (entries.hasMoreElements()) {
+        ZipEntry entry = entries.nextElement();
+        if (!entry.isDirectory()) {
+          params.entry(factory.createZipEntryFile(entry, zipFile));
+        }
+      }
+
+      Project project = projectFactory.create(params);
+      assertNotNull(project);
+      model = project.getModels().iterator().next().getModel();
+
+      GenericProtein fetchedProtein = (GenericProtein) model.getElements().iterator().next();
+
+      assertFalse("Glyph field should be removed from notes", fetchedProtein.getNotes().contains("Glyph"));
+      assertNotNull("Glyph in the protein is not defined but should", fetchedProtein.getGlyph());
+
     } catch (Exception e) {
       e.printStackTrace();
       throw e;
@@ -161,4 +211,9 @@ public class ProjectFactoryTest {
 
   }
 
+  private GenericProtein createProtein() {
+    GenericProtein result = new GenericProtein("s" + elementCounter++);
+    return result;
+  }
+
 }