glyph data structure created

model/src/main/java/lcsb/mapviewer/model/Project.java

@@ -37,6 +37,7 @@ import lcsb.mapviewer.model.map.OverviewImage;
 import lcsb.mapviewer.model.map.OverviewImageLink;
 import lcsb.mapviewer.model.map.OverviewLink;
 import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.graphics.Glyph;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelData;
 
@@ -182,6 +183,15 @@ public class Project implements Serializable {
   @LazyCollection(LazyCollectionOption.FALSE)
   private List<OverviewImage> overviewImages = new ArrayList<>();
 
+  /**
+   * List of glyph images that can be used to draw elements on maps.
+   */
+  @Cascade({ CascadeType.ALL })
+  @OneToMany(mappedBy = "project", orphanRemoval = true)
+  @OrderBy("id")
+  @LazyCollection(LazyCollectionOption.FALSE)
+  private List<Glyph> glyphs = new ArrayList<>();
+
   /**
    * Default constructor.
    */
@@ -680,4 +690,12 @@ public class Project implements Serializable {
     this.creationDate = creationDate;
   }
 
+  public List<Glyph> getGlyphs() {
+    return glyphs;
+  }
+
+  public void setGlyphs(List<Glyph> glyphs) {
+    this.glyphs = glyphs;
+  }
+
 }

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

+package lcsb.mapviewer.model.map.layout.graphics;
+
+import java.io.Serializable;
+
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToOne;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.map.BioEntity;
+
+/**
+ * This class describes glyph used to represent {@link BioEntity} on the map.
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+@Entity
+public class Glyph implements Serializable {
+
+  /**
+   * 
+   */
+  private static final long serialVersionUID = 1L;
+
+  /**
+   * Default class logger.
+   */
+  @SuppressWarnings("unused")
+  private static Logger logger = Logger.getLogger(Glyph.class);
+
+  /**
+   * Unique database identifier.
+   */
+  @Id
+  @GeneratedValue(strategy = GenerationType.IDENTITY)
+  private int id;
+
+  /**
+   * File that should be used for drawing a glyph.
+   */
+  @Cascade({ CascadeType.SAVE_UPDATE })
+  @OneToOne(fetch = FetchType.LAZY)
+  @JoinColumn(name = "file_entry_id")
+  private UploadedFileEntry file;
+  
+  /**
+   * Project in which this glyph is available.
+   */
+  @ManyToOne(fetch = FetchType.LAZY, optional = false)
+  private Project project;
+
+  public UploadedFileEntry getFile() {
+    return file;
+  }
+
+  public void setFile(UploadedFileEntry file) {
+    this.file = file;
+  }
+
+  public Project getProject() {
+    return project;
+  }
+
+  public void setProject(Project project) {
+    this.project = project;
+  }
+}

model/src/main/java/lcsb/mapviewer/model/map/species/Element.java

@@ -42,6 +42,7 @@ import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.SearchIndex;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
+import lcsb.mapviewer.model.map.layout.graphics.Glyph;
 import lcsb.mapviewer.model.map.layout.graphics.LayerText;
 import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
 import lcsb.mapviewer.model.map.model.Model;
@@ -114,6 +115,13 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
   @ManyToOne(fetch = FetchType.LAZY)
   private ModelData model;
 
+  /**
+   * When defined this represent glyph that should be used for drawing this
+   * element.
+   */
+  @ManyToOne(fetch = FetchType.LAZY)
+  private Glyph glyph;
+
   /**
    * Submodel that is extension of these element.
    */
@@ -1082,4 +1090,12 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
   public void setZ(Integer z) {
     this.z = z;
   }
+
+  public Glyph getGlyph() {
+    return glyph;
+  }
+
+  public void setGlyph(Glyph glyph) {
+    this.glyph = glyph;
+  }
 }
\ No newline at end of file

persist/src/main/resources/db/migration/13.1.0~alpha.0/V13.1.0.20190510__glyph_table.sql

+CREATE SEQUENCE glyph_sequence
+  INCREMENT 1
+  MINVALUE 1
+  MAXVALUE 9223372036854775807
+  START 1
+  CACHE 1;
+
+CREATE TABLE glyph_table
+(
+  id integer NOT NULL DEFAULT nextval('glyph_sequence'::regclass),
+  file_entry_id integer NOT NULL,
+  project_id integer NOT NULL,
+
+  CONSTRAINT glyph_table_pk PRIMARY KEY (id),
+  CONSTRAINT glyph_table_file_entry_fk FOREIGN KEY (file_entry_id)
+      REFERENCES file_entry_table (id) MATCH SIMPLE
+      ON UPDATE NO ACTION ON DELETE NO ACTION,
+  CONSTRAINT glyph_table_project FOREIGN KEY (project_id)
+      REFERENCES project_table (id) MATCH SIMPLE
+      ON UPDATE NO ACTION ON DELETE NO ACTION
+)
+WITH (
+  OIDS=FALSE
+);
+
+alter table element_table add column glyph_id integer;
+alter table element_table add constraint element_table_glyph_fk FOREIGN KEY (glyph_id)
+      REFERENCES glyph_table (id) MATCH SIMPLE
+      ON UPDATE NO ACTION ON DELETE NO ACTION;
+