From ec7dad53adfa7c4f10afb5d16942db71f1023aba Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 7 Jun 2019 16:24:45 +0200
Subject: [PATCH] pathways can be drawn using glyphs
---
CHANGELOG | 1 +
.../mapviewer/converter/ProjectFactory.java | 20 ++++++++
.../converter/ProjectFactoryTest.java | 49 +++++++++++++++++++
.../commands/CreateHierarchyCommand.java | 5 +-
.../model/map/layout/graphics/LayerText.java | 19 +++++++
.../V13.1.0.20190607__text_contains_glyph.sql | 5 ++
6 files changed, 97 insertions(+), 2 deletions(-)
create mode 100644 persist/src/main/resources/db/migration/13.1.0~beta.1/V13.1.0.20190607__text_contains_glyph.sql
diff --git a/CHANGELOG b/CHANGELOG
index 484adae3d3..d91c26390c 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -28,6 +28,7 @@ minerva (12.3.1~beta.1) unstable; urgency=low
close button twice (#818)
* Bug fix: empty type for data overlay is allowed (#827)
* Bug fix: genetic variants data overlay was ignoring color parameter (#827)
+ * Bug fix: pathways can be drawn using glyphs (#825)
minerva (13.1.0~beta.0) unstable; urgency=low
* Feature: annotators are more flexible - you can define set of input and
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
index dd5c55cbb8..3b576a5fb2 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
@@ -18,8 +18,11 @@ 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.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.species.Element;
public class ProjectFactory {
@@ -90,7 +93,15 @@ public class ProjectFactory {
}
private void assignGlyphsToElements(Project project) throws InvalidGlyphFile {
+ Set<ModelData> models = new HashSet<>();
+ models.addAll(project.getModels());
+
for (ModelData model : project.getModels()) {
+ for (ModelSubmodelConnection connection : model.getSubmodels()) {
+ models.add(connection.getSubmodel());
+ }
+ }
+ for (ModelData model : models) {
for (Element element : model.getElements()) {
Glyph glyph = extractGlyph(project, element.getNotes());
if (glyph != null) {
@@ -98,6 +109,15 @@ public class ProjectFactory {
element.setGlyph(glyph);
}
}
+ for (Layer layer : model.getLayers()) {
+ for (LayerText text : layer.getTexts()) {
+ Glyph glyph = extractGlyph(project, text.getNotes());
+ if (glyph != null) {
+ text.setNotes(removeGlyph(text.getNotes()));
+ text.setGlyph(glyph);
+ }
+ }
+ }
}
}
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ProjectFactoryTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ProjectFactoryTest.java
index ad6b5dc397..b882d44aa6 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ProjectFactoryTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ProjectFactoryTest.java
@@ -23,6 +23,8 @@ 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.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -211,6 +213,53 @@ public class ProjectFactoryTest extends ConverterTestFunctions {
}
+ @Test
+ public void testParseGlyphsAndPutThemAsTextGlyphs() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ Layer layer = new Layer();
+
+ LayerText text = new LayerText();
+ text.setNotes("Glyph: glyphs/g1.png");
+ layer.addLayerText(text);
+ model.addLayer(layer);
+
+ 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();
+
+ LayerText fetchedProtein = model.getLayers().iterator().next().getTexts().get(0);
+
+ 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;
+ }
+
+ }
+
private GenericProtein createProtein() {
GenericProtein result = new GenericProtein("s" + elementCounter++);
return result;
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
index adb5061425..294b1fb29c 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
@@ -43,11 +43,11 @@ public class CreateHierarchyCommand extends ModelCommand {
private static final double LOG_4 = Math.log(4);
/**
- * Top left corner x coordinate of the text associated with compratment.
+ * Top left corner x coordinate of the text associated with compartment.
*/
private static final double DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
/**
- * Top left corner y coordinate of the text associated with compratment.
+ * Top left corner y coordinate of the text associated with compartment.
*/
private static final double DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
@@ -180,6 +180,7 @@ public class CreateHierarchyCommand extends ModelCommand {
compartment.setName(extractNameFromText(text.getNotes()));
compartment.setNotes(extractNotesFromText(text.getNotes()));
compartment.setZ(text.getZ());
+ compartment.setGlyph(text.getGlyph());
rap.processNotes(compartment);
compartment.setNamePoint(new Point2D.Double(text.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT,
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerText.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerText.java
index d866c3e6e1..ecd49c6f8b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerText.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerText.java
@@ -5,9 +5,11 @@ import java.awt.geom.Rectangle2D;
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.ManyToOne;
import org.apache.log4j.Logger;
@@ -92,6 +94,12 @@ public class LayerText implements Serializable, Drawable {
*/
private Double fontSize = DEFAULT_LAYER_FONT_SIZE;
+ /**
+ * Glyph used for drawing (instead of text).
+ */
+ @ManyToOne(fetch = FetchType.LAZY)
+ private Glyph glyph = null;
+
/**
* Default constructor.
*/
@@ -130,6 +138,9 @@ public class LayerText implements Serializable, Drawable {
height = layerText.getHeight();
notes = layerText.getNotes();
fontSize = layerText.getFontSize();
+ if (layerText.getGlyph() != null) {
+ setGlyph(new Glyph(layerText.getGlyph()));
+ }
}
/**
@@ -377,4 +388,12 @@ public class LayerText implements Serializable, Drawable {
return "x=" + x + ";y=" + y + "; w=" + width + ", h=" + height;
}
+ public Glyph getGlyph() {
+ return glyph;
+ }
+
+ public void setGlyph(Glyph glyph) {
+ this.glyph = glyph;
+ }
+
}
diff --git a/persist/src/main/resources/db/migration/13.1.0~beta.1/V13.1.0.20190607__text_contains_glyph.sql b/persist/src/main/resources/db/migration/13.1.0~beta.1/V13.1.0.20190607__text_contains_glyph.sql
new file mode 100644
index 0000000000..8c1f1ac837
--- /dev/null
+++ b/persist/src/main/resources/db/migration/13.1.0~beta.1/V13.1.0.20190607__text_contains_glyph.sql
@@ -0,0 +1,5 @@
+alter table layer_text_table add column glyph_id integer;
+alter table layer_text_table add constraint layer_text_table_glyph_fk FOREIGN KEY (glyph_id)
+ REFERENCES glyph_table (id) MATCH SIMPLE
+ ON UPDATE NO ACTION ON DELETE NO ACTION;
+
--
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