Merge remote-tracking branch 'origin/master' into migration-script-issues

CHANGELOG

@@ -15,13 +15,22 @@ minerva (16.0.0~alpha.1) stable; urgency=medium
     (#1376)
   * Small improvement: context menu exporting map is more precise about scope
     (#1447)
+  * Small improvement: styling of GENERIC search tab title improved (#1364)
+  * Small improvement: SBML render contains information about species shapes
+    (#1055)
+  * Small improvement: SBML render contains information about modification
+    residues (#1456)
+  * Small improvement: SBML render contains information about structural states
+    (#1456)
+  * Small improvement: SBML render contains process rectangle for reactions
+    (#1457)
   * Bug fix: refreshing page after removing last project on the page redirect to
     proper page (#1051)
   * Bug fix: removing plugin that does not exist anymore does not raise an error
     (#1289)
   * Bug fix: broken overlays crashed minerva upgrade (#1453)
 
- -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 9 Feb 2020 08:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 19 Mar 2021 10:00:00 +0200
 
 minerva (16.0.0~alpha.0) stable; urgency=medium
   * Backward incompatibility: deprecated columns in data overlay table are no

README.md

-[![build status](https://git-r3lab.uni.lu/piotr.gawron/minerva/badges/master/build.svg)](https://git-r3lab.uni.lu/piotr.gawron/minerva/commits/master)
+[![build status](https://git-r3lab.uni.lu/minerva/core/badges/master/pipeline.svg)](https://git-r3lab.uni.lu/minerva/core/badges/master/pipeline.svg)
 [![coverage report](https://git-r3lab.uni.lu/minerva/core/badges/master/coverage.svg)](https://git-r3lab.uni.lu/minerva/core/commits/master)
 
 # For users

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java

@@ -36,7 +36,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
   /**
    * Version of the rest API that is supported by this annotator.
    */
-  static final String SUPPORTED_VERSION = "13.1";
+  static final String SUPPORTED_VERSION = "14.0";
 
   /**
    * Url address of ensembl restful service.

annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotatorTest.java

@@ -171,7 +171,7 @@ public class KeggAnnotatorTest extends AnnotationTestFunctions {
         mdPubmed.add(md);
       }
     }
-    assertEquals("Wrong number of publications extracted from KEGG annotator", 11, mdPubmed.size());
+    assertTrue("Wrong number of publications extracted from KEGG annotator", 11 <= mdPubmed.size());
   }
 
   @Test

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/NotesUtility.java

@@ -27,6 +27,15 @@ public class NotesUtility {
 
   static Logger logger = LogManager.getLogger();
 
+  static {
+    try {
+      // there is a bug in JSBML with initialization
+      new SBMLReader().readNotes(StringTools.toXMLNotesString(""));
+    } catch (XMLStreamException e) {
+      logger.error(e, e);
+    }
+  }
+
   /**
    * Extract notes from SBML node
    * 

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java

@@ -9,15 +9,12 @@ import javax.xml.stream.XMLStreamException;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.sbml.jsbml.Model;
-import org.sbml.jsbml.ext.SBasePlugin;
 import org.sbml.jsbml.ext.layout.*;
 import org.sbml.jsbml.ext.multi.MultiModelPlugin;
 import org.sbml.jsbml.ext.render.*;
 import org.sbml.jsbml.xml.XMLNode;
 
-import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.graphics.ArrowType;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -56,10 +53,13 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
    */
   private Map<String, String> correctedElementId = new HashMap<>();
 
+  private SbmlModelUtils sbmlModelUtils;
+
   public SbmlBioEntityExporter(Model sbmlModel, lcsb.mapviewer.model.map.model.Model minervaModel,
       Collection<SbmlExtension> sbmlExtensions) {
     this.sbmlModel = sbmlModel;
-    this.layout = getLayout(sbmlModel);
+    this.sbmlModelUtils = new SbmlModelUtils(sbmlModel);
+    this.layout = sbmlModelUtils.getLayout();
     this.minervaModel = minervaModel;
     this.sbmlExtensions.addAll(sbmlExtensions);
 
@@ -157,38 +157,10 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
     return (idCounter++) + "";
   }
 
-  private Layout getLayout(org.sbml.jsbml.Model sbmlModel) {
-    Layout layout = null;
-
-    if (sbmlModel.getExtensionCount() > 0) {
-      for (SBasePlugin plugin : sbmlModel.getExtensionPackages().values()) {
-        if (plugin.getClass().equals(org.sbml.jsbml.ext.layout.LayoutModelPlugin.class)) {
-          LayoutModelPlugin layoutPlugin = (LayoutModelPlugin) plugin;
-          if (layoutPlugin.getLayoutCount() == 0) {
-            logger.warn("Layout plugin available but no layouts defined");
-          } else if (layoutPlugin.getLayoutCount() > 1) {
-            logger.warn(layoutPlugin.getLayoutCount() + " layouts defined. Using first one.");
-            layout = layoutPlugin.getLayout(0);
-          } else {
-            layout = layoutPlugin.getLayout(0);
-          }
-        }
-      }
-    }
-    return layout;
-  }
-
   protected Layout getLayout() {
     return layout;
   }
 
-  protected RenderLayoutPlugin getRenderPlugin() {
-    if (getLayout().getExtensionCount() > 0) {
-      return (RenderLayoutPlugin) getLayout().getExtension("render");
-    }
-    return null;
-  }
-
   protected MultiModelPlugin getMultiPlugin() {
     return (MultiModelPlugin) sbmlModel.getExtension("multi");
   }
@@ -209,208 +181,21 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
     return sbmlGlyphByElementId.get(elementId);
   }
 
-  protected ColorDefinition getColorDefinition(Color color) {
-    RenderLayoutPlugin renderPlugin = getRenderPlugin();
-
-    LocalRenderInformation renderInformation = getRenderInformation(renderPlugin);
-
-    for (ColorDefinition cd : renderInformation.getListOfColorDefinitions()) {
-      if (cd.getValue().equals(color)) {
-        return cd;
-      }
-    }
-    ColorDefinition colorDefinition = new ColorDefinition("color_" + XmlParser.colorToString(color), color);
-
-    renderInformation.addColorDefinition(colorDefinition);
-    return colorDefinition;
-  }
-
-  protected LocalRenderInformation getRenderInformation(RenderLayoutPlugin renderPlugin) {
-    LocalRenderInformation renderInformation = null;
-    for (LocalRenderInformation lri : renderPlugin.getListOfLocalRenderInformation()) {
-      if (lri.getId().equals("minerva_definitions")) {
-        renderInformation = lri;
-      }
-    }
-    if (renderInformation == null) {
-      renderInformation = new LocalRenderInformation("minerva_definitions");
-      renderPlugin.addLocalRenderInformation(renderInformation);
-    }
-    return renderInformation;
-  }
-
   protected void assignStyleToGlyph(AbstractReferenceGlyph speciesGlyph, LocalStyle style) {
     RenderGraphicalObjectPlugin rgop = new RenderGraphicalObjectPlugin(speciesGlyph);
     if (style.getGroup().isSetEndHead()) {
-      LineEnding lineEnding = createLineEndingStyle(style.getGroup().getEndHead());
+      LineEnding lineEnding = sbmlModelUtils.createLineEndingStyle(style.getGroup().getEndHead());
       style.getGroup().setEndHead(lineEnding.getId());
     }
     style.getIDList().add(speciesGlyph.getId());
     speciesGlyph.addExtension(RenderConstants.shortLabel, rgop);
   }
 
-  protected LineEnding createLineEndingStyle(String endHead) {
-    String arrowTypeId = endHead.replaceAll("line_ending_", "");
-    LocalRenderInformation renderInformation = getRenderInformation(getRenderPlugin());
-    LineEnding result = renderInformation.getListOfLineEndings().get("line_ending_" + arrowTypeId);
-    if (result != null) {
-      return result;
-    }
-    ArrowType arrowType = ArrowType.valueOf(arrowTypeId);
-    result = new LineEnding();
-    result.setId("line_ending_" + arrowTypeId);
-    result.setGroup(new RenderGroup());
-    renderInformation.getListOfLineEndings().add(result);
-    switch (arrowType) {
-    case FULL:
-      createFullLineEnding(result);
-      break;
-    case BLANK:
-      createBlankLineEnding(result);
-      break;
-    case FULL_CROSSBAR:
-      createFullCrossBarLineEnding(result);
-      break;
-    case BLANK_CROSSBAR:
-      createBlankCrossBarLineEnding(result);
-      break;
-    case CROSSBAR:
-      createCrossBarLineEnding(result);
-      break;
-    case DIAMOND:
-      createDiamondLineEnding(result);
-      break;
-    case OPEN:
-      createOpenLineEnding(result);
-      break;
-    case CIRCLE:
-      createCircleLineEnding(result);
-      break;
-    default:
-      logger.warn("Unknown arrow type: " + arrowType);
-    case NONE:
-      break;
-    }
-
-    return result;
-  }
-
-  private void createCircleLineEnding(LineEnding result) {
-    BoundingBox boundingBox = createBoundingBox(-2, 0, 0, 4, 4);
-    result.getGroup().setFill(getColorDefinition(Color.WHITE).getId());
-    result.setBoundingBox(boundingBox);
-    Ellipse ellipse = new Ellipse();
-    ellipse.setAbsoluteCx(false);
-    ellipse.setAbsoluteCy(false);
-    ellipse.setAbsoluteRx(true);
-    ellipse.setAbsoluteRy(true);
-    ellipse.setCx(0.0);
-    ellipse.setCy(0.0);
-    ellipse.setRx(4.0);
-    ellipse.setRy(4.0);
-    result.getGroup().addElement(ellipse);
-  }
-
-  private void createOpenLineEnding(LineEnding result) {
-    BoundingBox boundingBox = createBoundingBox(-12, -6, 0, 12, 12);
-    result.setBoundingBox(boundingBox);
-    Polygon polygon = new Polygon();
-    polygon.addElement(createRenderPoint(0, 0));
-    polygon.addElement(createRenderPoint(100, 50));
-    polygon.addElement(createRenderPoint(0, 100));
-    polygon.addElement(createRenderPoint(100, 50));
-    result.getGroup().addElement(polygon);
-  }
-
-  private void createDiamondLineEnding(LineEnding result) {
-    BoundingBox boundingBox = createBoundingBox(-18, -6, 0, 18, 12);
-    result.setBoundingBox(boundingBox);
-    result.getGroup().setFill(getColorDefinition(Color.WHITE).getId());
-    Polygon polygon = new Polygon();
-    polygon.addElement(createRenderPoint(50, 0));
-    polygon.addElement(createRenderPoint(100, 50));
-    polygon.addElement(createRenderPoint(50, 100));
-    polygon.addElement(createRenderPoint(0, 50));
-    polygon.addElement(createRenderPoint(50, 0));
-    result.getGroup().addElement(polygon);
-  }
-
-  private void createCrossBarLineEnding(LineEnding result) {
-    BoundingBox boundingBox = createBoundingBox(0, -6, 0, 1, 12);
-    result.setBoundingBox(boundingBox);
-    Polygon crossBar = new Polygon();
-    crossBar.addElement(createRenderPoint(0, 0));
-    crossBar.addElement(createRenderPoint(0, 100));
-    result.getGroup().addElement(crossBar);
-  }
-
-  private void createBlankLineEnding(LineEnding result) {
-    createFullLineEnding(result);
-    result.getGroup().setFill(getColorDefinition(Color.WHITE).getId());
-  }
-
-  private void createFullLineEnding(LineEnding result) {
-    BoundingBox boundingBox = createBoundingBox(-12, -6, 0, 12, 12);
-    result.setBoundingBox(boundingBox);
-    result.getGroup().setFill(getColorDefinition(Color.BLACK).getId());
-    Polygon polygon = new Polygon();
-    polygon.addElement(createRenderPoint(0, 0));
-    polygon.addElement(createRenderPoint(100, 50));
-    polygon.addElement(createRenderPoint(0, 100));
-    polygon.addElement(createRenderPoint(0, 0));
-    result.getGroup().addElement(polygon);
-  }
-
-  private void createBlankCrossBarLineEnding(LineEnding result) {
-    BoundingBox boundingBox = createBoundingBox(-18, -6, 0, 18, 12);
-    result.setBoundingBox(boundingBox);
-    result.getGroup().setFill(getColorDefinition(Color.WHITE).getId());
-    Polygon polygon = new Polygon();
-    polygon.addElement(createRenderPoint(33, 0));
-    polygon.addElement(createRenderPoint(100, 50));
-    polygon.addElement(createRenderPoint(33, 100));
-    polygon.addElement(createRenderPoint(33, 0));
-    result.getGroup().addElement(polygon);
-
-    Polygon crossBar = new Polygon();
-    crossBar.addElement(createRenderPoint(0, 0));
-    crossBar.addElement(createRenderPoint(0, 100));
-    result.getGroup().addElement(crossBar);
-  }
-
-  private void createFullCrossBarLineEnding(LineEnding result) {
-    createBlankCrossBarLineEnding(result);
-    result.getGroup().setFill(getColorDefinition(Color.BLACK).getId());
-  }
-
-  protected RenderPoint createRenderPoint(double percentX, int percentY) {
-    RenderPoint result = new RenderPoint();
-    result.setAbsoluteX(false);
-    result.setX(percentX);
-    result.setAbsoluteY(false);
-    result.setY(percentY);
-    return result;
-  }
-
   protected BoundingBox createBoundingBox(double x, double y, int z, double w, double h) {
-    BoundingBox boundingBox = new BoundingBox();
-
-    boundingBox.setPosition(new Point(x, y, z));
-    Dimensions dimensions = new Dimensions();
-
-    dimensions.setWidth(w);
-    dimensions.setHeight(h);
-    boundingBox.setDimensions(dimensions);
-    return boundingBox;
+    return sbmlModelUtils.createBoundingBox(x, y, z, w, h);
   }
 
-  protected LocalStyle createStyle(T element) {
-    LocalRenderInformation renderInformation = getRenderInformation(getRenderPlugin());
-    LocalStyle style = new LocalStyle();
-    style.setGroup(new RenderGroup());
-    renderInformation.addLocalStyle(style);
-    return style;
-  }
+  protected abstract LocalStyle createStyle(T element);
 
   protected boolean isProvideDefaults() {
     return provideDefaults;
@@ -435,4 +220,18 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
     return result;
   }
 
+  protected ColorDefinition getColorDefinition(Color color) {
+    return sbmlModelUtils.getColorDefinition(color);
+  }
+
+  protected LocalStyle createStyle() {
+    return sbmlModelUtils.createStyle();
+  }
+
+  protected void createAbsolutePoint(Polygon polygon, double x, double y) {
+    RenderPoint p1 = polygon.createRenderPoint();
+    p1.setX(new RelAbsVector(Math.round(x)));
+    p1.setY(new RelAbsVector(Math.round(y)));
+  }
+
 }

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java

@@ -51,11 +51,9 @@ public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.
     textGlyph.setGraphicalObject(speciesGlyph.getId());
 
     if (isExtensionEnabled(SbmlExtension.RENDER)) {
-      LocalRenderInformation renderInformation = getRenderInformation(getRenderPlugin());
-      LocalStyle style = new LocalStyle();
+      LocalStyle style = createStyle();
       style.getIDList().add(textGlyph.getId());
-      RenderGroup group = new RenderGroup();
-      style.setGroup(group);
+      RenderGroup group = style.getGroup();
       group.setVTextAnchor(VTextAnchor.MIDDLE);
       group.setTextAnchor(HTextAnchor.MIDDLE);
       switch (element.getNameHorizontalAlign()) {
@@ -81,7 +79,6 @@ public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.
         break;
       }
       group.setStroke(getColorDefinition(element.getFontColor()).getId());
-      renderInformation.addLocalStyle(style);
     }
     textGlyph.setBoundingBox(createBoundingBox(x, y, element.getZ() + 1, width, height));
 
@@ -89,7 +86,7 @@ public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.
 
   @Override
   protected LocalStyle createStyle(T element) {
-    LocalStyle result = super.createStyle(element);
+    LocalStyle result = createStyle();
     ColorDefinition color = getColorDefinition(element.getFillColor());
     result.getGroup().setFill(color.getId());
     result.getGroup().setFontSize(element.getFontSize().shortValue());

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java

@@ -52,9 +52,10 @@ public class SbmlExporter {
       ByteArrayOutputStream stream = new ByteArrayOutputStream();
       SBMLWriter.write(doc, stream, "minerva", Configuration.getSystemVersion(null));
       return stream.toString("UTF-8")
-          // TODO bug: https://github.com/sbmlteam/jsbml/issues/158
-          .replace("<listOfSpeciesFeatures>", "<multi:listOfSpeciesFeatures>")
-          .replace("</listOfSpeciesFeatures>", "</multi:listOfSpeciesFeatures>");
+          // COPASI does not accept double coordinates
+          .replace(".0\"", "\"")
+          .replace(".0+", "+")
+          .replace(".0%\"", "%\"");
     } catch (UnsupportedEncodingException | XMLStreamException e) {
       throw new InvalidStateException(e);
     }

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlModelUtils.java

+package lcsb.mapviewer.converter.model.sbml;
+
+import java.awt.Color;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.ext.SBasePlugin;
+import org.sbml.jsbml.ext.layout.*;
+import org.sbml.jsbml.ext.render.*;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.model.graphics.ArrowType;
+
+public class SbmlModelUtils {
+
+  private Logger logger = LogManager.getLogger();
+
+  private final Model sbmlModel;
+
+  private Layout layout;
+
+  public SbmlModelUtils(Model model) {
+    this.sbmlModel = model;
+    this.layout = computeLayout();
+  }
+
+  private Layout computeLayout() {
+    Layout layout = null;
+    if (sbmlModel.getExtensionCount() > 0) {
+      for (SBasePlugin plugin : sbmlModel.getExtensionPackages().values()) {
+        if (plugin.getClass().equals(org.sbml.jsbml.ext.layout.LayoutModelPlugin.class)) {
+          LayoutModelPlugin layoutPlugin = (LayoutModelPlugin) plugin;
+          if (layoutPlugin.getLayoutCount() == 0) {
+            logger.warn("Layout plugin available but no layouts defined");
+          } else if (layoutPlugin.getLayoutCount() > 1) {
+            logger.warn(layoutPlugin.getLayoutCount() + " layouts defined. Using first one.");
+            layout = layoutPlugin.getLayout(0);
+          } else {
+            layout = layoutPlugin.getLayout(0);
+          }
+        }
+      }
+    }
+    return layout;
+  }
+
+  public Layout getLayout() {
+    return layout;
+  }
+
+  public RenderLayoutPlugin getRenderPlugin() {
+    if (getLayout().getExtensionCount() > 0) {
+      return (RenderLayoutPlugin) getLayout().getExtension("render");
+    }
+    return null;
+  }
+
+  public ColorDefinition getColorDefinition(Color color) {
+    RenderLayoutPlugin renderPlugin = getRenderPlugin();
+
+    LocalRenderInformation renderInformation = getRenderInformation(renderPlugin);
+
+    for (ColorDefinition cd : renderInformation.getListOfColorDefinitions()) {
+      if (cd.getValue().equals(color)) {
+        return cd;
+      }
+    }
+    ColorDefinition colorDefinition = new ColorDefinition("color_" + XmlParser.colorToString(color), color);
+
+    renderInformation.addColorDefinition(colorDefinition);
+    return colorDefinition;
+  }
+
+  public LocalRenderInformation getRenderInformation() {
+    return getRenderInformation(getRenderPlugin());
+  }
+
+  public LocalRenderInformation getRenderInformation(RenderLayoutPlugin renderPlugin) {
+    LocalRenderInformation renderInformation = null;
+    for (LocalRenderInformation lri : renderPlugin.getListOfLocalRenderInformation()) {
+      if (lri.getId().equals("minerva_definitions")) {
+        renderInformation = lri;
+      }
+    }
+    if (renderInformation == null) {
+      renderInformation = new LocalRenderInformation("minerva_definitions");
+      renderPlugin.addLocalRenderInformation(renderInformation);
+    }
+    return renderInformation;
+  }
+
+  public LocalStyle createStyle() {
+    LocalRenderInformation renderInformation = getRenderInformation(getRenderPlugin());
+    LocalStyle style = new LocalStyle();
+    style.setGroup(new RenderGroup());
+    renderInformation.addLocalStyle(style);
+    return style;
+  }
+
+  protected LineEnding createLineEndingStyle(String endHead) {
+    String arrowTypeId = endHead.replaceAll("line_ending_", "");
+    LocalRenderInformation renderInformation = getRenderInformation();
+    LineEnding result = renderInformation.getListOfLineEndings().get("line_ending_" + arrowTypeId);
+    if (result != null) {
+      return result;
+    }
+    ArrowType arrowType = ArrowType.valueOf(arrowTypeId);
+    result = new LineEnding();
+    result.setId("line_ending_" + arrowTypeId);
+    result.setGroup(new RenderGroup());
+    renderInformation.getListOfLineEndings().add(result);
+    switch (arrowType) {
+    case FULL:
+      createFullLineEnding(result);
+      break;
+    case BLANK:
+      createBlankLineEnding(result);
+      break;
+    case FULL_CROSSBAR:
+      createFullCrossBarLineEnding(result);
+      break;
+    case BLANK_CROSSBAR:
+      createBlankCrossBarLineEnding(result);
+      break;
+    case CROSSBAR:
+      createCrossBarLineEnding(result);
+      break;
+    case DIAMOND:
+      createDiamondLineEnding(result);
+      break;
+    case OPEN:
+      createOpenLineEnding(result);
+      break;
+    case CIRCLE:
+      createCircleLineEnding(result);
+      break;
+    default:
+      logger.warn("Unknown arrow type: " + arrowType);
+    case NONE:
+      break;
+    }
+