diff --git a/CHANGELOG b/CHANGELOG
index 180fa045336cffa4d3adfab04e0c6de15a08dd2f..0bb8da966a4b3917e0e276515a42b8578ad4fa57 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,9 +1,59 @@
minerva (12.3.0~alpha.0) unstable; urgency=low
- * Feature: annotators are more flexible - you can define set of input and outputs used by
+ * Feature: annotators are more flexible - you can define set of input and outputs used by
annotator (#617)
* Small improvement: added current username next to logout button in admin panel (#660)
* Small improvement: New comment dialog does not contain content of previous comment dialog (#680)
+minerva (12.2.0~beta.2) unstable; urgency=medium
+ * Bug fix: order of the overlays is defined explicitly also for general
+ overlays (#684)
+ * Bug fix: files are saved in proper folder (#694, #670)
+ * Bug fix: removing comments in a project asked for confirmation twice after
+ edit project dialog for specific project was opened; closed and opened
+ again (#697)
+ * Bug fix: clicking on compartment border inside pathway should return
+ compartment, not a pathway (#324)
+ * Bug fix: clicking outside of the element sometimes resulted with the
+ invalid element highlighted (#324)
+ * Bug fix: parent compartment/pathway use proper type name in left panel
+ (#324)
+ * Bug fix: editing/removing project requires Map Management privilege (#681)
+ * Bug fix: when removeAllListeners is called list of registered listeners is
+ cleaned (#687)
+ * Bug fix: when plugin is removed the html elements associated with it are
+ removed as well (#686)
+ * Bug fix: when creating new user default privileges are set properly (#692)
+ * Bug fix: import from SBML issue - reaction with product and modifier being
+ the same element caused exception (#703)
+ * Bug fix: plugin can be added after plugin has been removed in admin plugin
+ panel (#686)
+ * Bug fix: too many annotations (>=100) caused misaligning in the left panel
+ (#708)
+ * Bug fix: text was outside the popup window (#711)
+ * Bug fix: custom semantic zooming contains multiple overlays checkbox was
+ disabled (#715)
+ * Bug fix: export to svg contains viewBox info (#716)
+ * Bug fix: import from sbml with layout could crash when two elements
+ occupied the exact same position (#717)
+ * Bug fix: overlays added via API couldn't be visualized after refresh (#718)
+ * Bug fix: Safari sometimes cached server responses and used wrong data, for
+ example in admin panel configuration tab (#719)
+ * Bug fix: description of transcription site is centered (#720)
+ * Bug fix: selecting too few parameters in export doesn't throw reportable
+ error (#721)
+ * Bug fix: changes in selected checkbox in add project dialog block UI (#722)
+ * Bug fix: providing invalid overlay id in url could break minerva (#726)
+ * Bug fix: removing project that doesn't exist doesn't cause 500 error (#723)
+ * Bug fix: Editing project with images and submaps could cause a problem
+ (#725)
+ * Bug fix: opening map with invalid id shows proper error message (#724)
+ * Bug fix: Fixing an issue where search panel was not properly resized on
+ expansion (#682)
+ * Small improvement: highlighting table rows in admin panel uses better
+ contrast color (#706)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Wed, 20 Feb 2019 14:00:00 +0200
+
minerva (12.2.0~beta.1) unstable; urgency=medium
* Small improvement: list of publication can be filtered by submap (#614)
* Small improvement: report bug utility shows confirmation dialog on success
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
index d5d6ceeda4ef964d18e8fd32b51dcad732e232ef..5bfc3deb6f3345a5df47b492bdc92ccf0e3eb984 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
@@ -633,32 +633,6 @@ public abstract class ElementAnnotator extends CachableInterface {
return "";
}
- /**
- * Provides description for {@link ElementAnnotator} and {@link MiriamType} pair
- * to be used in the frontend.
- *
- * @param mt
- * {@link MiriamType} annotated by this annotator.
- * @return the description
- */
- public String getDescription(MiriamType mt) {
- return "";
- }
-
- /**
- * Provides description for {@link ElementAnnotator}, {@link MiriamType} and
- * {@link MiriamRelationType} triplet to be used in the frontend.
- *
- * @param mt
- * {@link MiriamType} annotated by this annotator
- * @param relationType
- * {@link MiriamRelationType} annotated by this annotator.
- * @return the description
- */
- public String getDescription(MiriamType mt, MiriamRelationType relationType) {
- return "";
- }
-
/**
* Returns list with definitions of the parameters available for this annotator.
*
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/SvgImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/SvgImageGenerator.java
index 6a1aa4f2037cc2e0993a67682f495f6e7ac32326..41cc790acb4dfaaf9270fe540a6dba7fe388a690 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/SvgImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/SvgImageGenerator.java
@@ -1,17 +1,20 @@
package lcsb.mapviewer.converter.graphics;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
import org.apache.batik.dom.GenericDOMImplementation;
import org.apache.batik.svggen.SVGGraphics2D;
import org.apache.batik.svggen.SVGGraphics2DIOException;
import org.w3c.dom.DOMImplementation;
import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.common.exception.NotImplementedException;
/**
* This class implements SVG generator for the image object.This class uses
@@ -21,6 +24,11 @@ import org.w3c.dom.Document;
*
*/
public class SvgImageGenerator extends AbstractImageGenerator {
+
+ /**
+ * Root dom element. We need it to be able to provide viewBox.
+ */
+ private Element root;
@Override
protected void createImageObject(final double width, final double height) {
@@ -32,14 +40,17 @@ public class SvgImageGenerator extends AbstractImageGenerator {
String svgNS = "http://www.w3.org/2000/svg";
Document document = domImpl.createDocument(svgNS, "svg", null);
- // Create an instance of the SVG Generator.
- setGraphics(new SVGGraphics2D(document));
+ // Create an instance of the SVG Generator.
+ SVGGraphics2D graphics =new SVGGraphics2D(document);
+ root = graphics.getRoot();
+ root.setAttributeNS(null, "viewBox", "0 0 "+(int)width+" "+(int)height);
+ setGraphics(graphics);
}
@Override
- public void saveToFileImplementation(final String fileName) throws SVGGraphics2DIOException {
- ((SVGGraphics2D) getGraphics()).stream(fileName);
+ public void saveToFileImplementation(final String fileName) throws IOException {
+ saveToOutputStreamImplementation(new FileOutputStream(fileName));
}
/**
@@ -63,8 +74,9 @@ public class SvgImageGenerator extends AbstractImageGenerator {
@Override
public void saveToOutputStreamImplementation(OutputStream os) throws IOException {
- ((SVGGraphics2D) getGraphics()).stream(new OutputStreamWriter(os));
-
+ //for some reason if you remove this line either viewbox is not define or content is not there
+ ((SVGGraphics2D) getGraphics()).getRoot(root);
+ ((SVGGraphics2D) getGraphics()).stream(root, new OutputStreamWriter(os));
}
@Override
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
index 158269f20afe6240174ce7a288180331f9906d68..980ac89b8315020b225cf2080019aa219c482a3b 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
@@ -699,7 +699,9 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
y = transcriptionSite.getPosition().getY() - DEFAULT_MODIFICATION_DIAMETER - DEFAULT_SPECIES_FONT_SIZE / 2;
if (transcriptionSite.getName() != null && !transcriptionSite.getName().isEmpty()) {
- drawText(new Point2D.Double(x, y), transcriptionSite.getName(), graphics, true, false);
+ Point2D centerTextPoint = new Point2D.Double(
+ transcriptionSite.getPosition().getX() + transcriptionSite.getWidth() / 2, y);
+ drawText(centerTextPoint, transcriptionSite.getName(), graphics, true, false);
}
}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java
index b0a0d88529eda0deb86d53648ff20b75b1d97a53..3d6271639f56196f983535047b0ef02315498a18 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java
@@ -19,6 +19,7 @@ import lcsb.mapviewer.converter.graphics.placefinder.AllPlaceFinderTest;
MapGeneratorTest.class,
NormalImageGeneratorTest.class,
PdfImageGeneratorTest.class,
+ SvgImageGeneratorTest.class
})
public class AllGraphicsTests {
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/SvgImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/SvgImageGeneratorTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..ffd2eec03dba74dee023562c8cff26b94e0d0800
--- /dev/null
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/SvgImageGeneratorTest.java
@@ -0,0 +1,58 @@
+package lcsb.mapviewer.converter.graphics;
+
+import static org.junit.Assert.assertTrue;
+
+import java.io.ByteArrayOutputStream;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
+
+public class SvgImageGeneratorTest extends GraphicsTestFunctions {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSaveToFile() throws Exception {
+ try {
+ Model model = createCompartmentModel();
+
+ SvgImageGenerator sig = new SvgImageGenerator(new AbstractImageGenerator.Params().model(model));
+
+ ByteArrayOutputStream output = new ByteArrayOutputStream();
+ sig.saveToOutputStream(output);
+
+ assertTrue(output.toString().contains("viewBox"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model createCompartmentModel() {
+ Model model = new ModelFullIndexed(null);
+ model.setWidth(526);
+ model.setHeight(346);
+ Complex alias = new Complex("1");
+ alias.setName("a");
+ alias.setX(300);
+ alias.setY(90);
+ alias.setWidth(100);
+ alias.setHeight(50);
+ model.addElement(alias);
+
+ return model;
+ }
+
+}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index 27f45b5e512edf20fd5f678a701b2c47d631c3e3..2f47b556f3e0ecbb3691a40a1e821f20042ed767 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -156,7 +156,7 @@ public class SbmlParser extends Converter {
if (element instanceof Complex && element != species) {
Complex complex = (Complex) element;
if (complex.getWidth() != 0 || complex.getHeight() != 0) {
- if (complex.contains(species)) {
+ if (complex.contains(species) && complex.getSize() > species.getSize()) {
if (result == null) {
result = complex;
} else if (result.getSize() > complex.getSize()) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
index bf6aac35adaa11a56cd4726e487d216883d42858..9c865296714fb03cdd9e4886dd24646da93ff96b 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
@@ -133,6 +133,9 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
nodeClass = node.getClass();
} else if (node.getClass().isAssignableFrom(nodeClass)) {
minervaNode = node;
+ } else if (nodeClass.isAssignableFrom(node.getClass())) {
+ minervaNode = node;
+ nodeClass = node.getClass();
}
}
}
@@ -391,9 +394,10 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
case SUBSTRATE:
nodeClass = Reactant.class;
break;
- case UNDEFINED:
case MODIFIER:
- nodeClass = null;
+ nodeClass = Modifier.class;
+ break;
+ case UNDEFINED:
break;
}
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
index 1e2ecd69f2fe52546509453e9edc7ed2e6dbebf2..519b78264a8169f32302bb865802822dc58f8cc4 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
@@ -6,7 +6,9 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import java.io.FileNotFoundException;
+import java.util.HashSet;
import java.util.List;
+import java.util.Set;
import org.apache.log4j.Logger;
import org.apache.log4j.spi.LoggingEvent;
@@ -14,6 +16,7 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
@@ -21,6 +24,7 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
@@ -203,4 +207,37 @@ public class SbmlParserTest {
assertEquals(1, getWarnings().size());
}
+ @Test
+ public void testCyclicComplexes() throws Exception {
+ try {
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/cyclic_complex.xml"));
+
+ new CreateHierarchyCommand(model, 8, 80).execute();
+
+ for (Species species : model.getSpeciesList()) {
+ Set<Element> parents = new HashSet<>();
+ while (species.getComplex() != null) {
+ assertFalse("Cyclic nesting", parents.contains(species.getComplex()));
+ species= species.getComplex();
+ parents.add(species);
+ }
+
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCyclicComplsexes() throws Exception {
+ try {
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/reaction_with_species_used_twice.xml"));
+ assertEquals(1, model.getReactions().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
}
diff --git a/converter-sbml/testFiles/cyclic_complex.xml b/converter-sbml/testFiles/cyclic_complex.xml
new file mode 100644
index 0000000000000000000000000000000000000000..1bcf87dc149f0e88b0d1e8a89b6ff16dd8401796
--- /dev/null
+++ b/converter-sbml/testFiles/cyclic_complex.xml
@@ -0,0 +1,958 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" level="3" version="1" layout:required="false">
+ <model substanceUnits="mole" timeUnits="second" extentUnits="mole">
+ <listOfUnitDefinitions>
+ <unitDefinition id="per_second">
+ <listOfUnits>
+ <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="comp_0" name="compartment1" constant="false"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species sboTerm="SBO:0000297" id="species_7" name="BasalACh2" compartment="comp_0" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ <species sboTerm="SBO:0000297" id="species_10" name="BasalACh" compartment="comp_0" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ <species sboTerm="SBO:0000297" id="species_8" name="ActiveACh2" compartment="comp_0" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ <species sboTerm="SBO:0000297" id="species_5" name="ActiveACh" compartment="comp_0" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ <species sboTerm="SBO:0000247" id="species_2" name="Basal" compartment="comp_0" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ <species sboTerm="SBO:0000297" id="species_0" name="IntermediateACh" compartment="comp_0" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ <species sboTerm="SBO:0000297" id="species_1" name="IntermediateACh2" compartment="comp_0" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ <species sboTerm="SBO:0000297" id="species_6" name="DesensitisedACh" compartment="comp_0" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ <species sboTerm="SBO:0000247" id="species_4" name="Desensitised" compartment="comp_0" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ <species sboTerm="SBO:0000297" id="species_3" name="DesensitisedACh2" compartment="comp_0" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ <species sboTerm="SBO:0000247" id="species_11" name="Intermediate" compartment="comp_0" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ <species sboTerm="SBO:0000247" id="species_9" name="Active" compartment="comp_0" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction sboTerm="SBO:0000176" id="reaction_glyph_14" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="species_10" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="species_7" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ <reaction sboTerm="SBO:0000176" id="reaction_glyph_0" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="species_7" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="species_8" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ <reaction sboTerm="SBO:0000176" id="reaction_glyph_1" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="species_10" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="species_5" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ <reaction sboTerm="SBO:0000176" id="reaction_glyph_11" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="species_8" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="species_1" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ <reaction sboTerm="SBO:0000176" id="reaction_glyph_3" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="species_5" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="species_8" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ <reaction sboTerm="SBO:0000176" id="reaction_glyph_10" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="species_5" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="species_0" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ <reaction sboTerm="SBO:0000176" id="reaction_glyph_5" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="species_2" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="species_10" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ <reaction sboTerm="SBO:0000176" id="reaction_glyph_2" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="species_0" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="species_1" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ <reaction sboTerm="SBO:0000176" id="reaction_glyph_6" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="species_9" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="species_5" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ <reaction sboTerm="SBO:0000176" id="reaction_glyph_15" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="species_1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="species_3" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ <reaction sboTerm="SBO:0000176" id="reaction_glyph_13" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="species_2" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="species_9" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ <reaction sboTerm="SBO:0000176" id="reaction_glyph_16" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="species_0" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="species_6" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ <reaction sboTerm="SBO:0000176" id="reaction_glyph_9" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="species_4" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="species_6" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ <reaction sboTerm="SBO:0000176" id="reaction_glyph_4" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="species_6" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="species_3" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ <reaction sboTerm="SBO:0000176" id="reaction_glyph_8" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="species_9" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="species_11" constant="false"/>
+ </listOfProducts>
+ </reaction>
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+ <layout:boundingBox layout:id="bb_tg_React15_DL">
+ <layout:position layout:x="337.239206103396" layout:y="61.2084891353298"/>
+ <layout:dimensions layout:width="80" layout:height="40"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="tg_React8_ILL" layout:originOfText="sg_React8_ILL" layout:graphicalObject="sg_React8_ILL">
+ <layout:boundingBox layout:id="bb_tg_React8_ILL">
+ <layout:position layout:x="337.239206103396" layout:y="61.2084891353298"/>
+ <layout:dimensions layout:width="80" layout:height="40"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="tg_React9_A" layout:originOfText="sg_React9_A" layout:graphicalObject="sg_React9_A">
+ <layout:boundingBox layout:id="bb_tg_React9_A">
+ <layout:position layout:x="305.019756063517" layout:y="181.453113676086"/>
+ <layout:dimensions layout:width="80" layout:height="40"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="tg_React9_I" layout:originOfText="sg_React9_I" layout:graphicalObject="sg_React9_I">
+ <layout:boundingBox layout:id="bb_tg_React9_I">
+ <layout:position layout:x="305.019756063517" layout:y="69.8416647540904"/>
+ <layout:dimensions layout:width="80" layout:height="40"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ </layout:listOfTextGlyphs>
+ </layout:layout>
+ </layout:listOfLayouts>
+ </model>
+</sbml>
diff --git a/converter-sbml/testFiles/reaction_with_species_used_twice.xml b/converter-sbml/testFiles/reaction_with_species_used_twice.xml
new file mode 100644
index 0000000000000000000000000000000000000000..312d2da098471077d2b34c09b14c4f7df6606fdb
--- /dev/null
+++ b/converter-sbml/testFiles/reaction_with_species_used_twice.xml
@@ -0,0 +1,125 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" level="3" version="1" layout:required="false">
+ <model substanceUnits="mole" timeUnits="second" extentUnits="mole">
+ <listOfUnitDefinitions>
+ <unitDefinition id="per_second">
+ <listOfUnits>
+ <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="comp_0" name="chl" constant="false"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species sboTerm="SBO:0000247" id="species_9" name="Lysine" compartment="comp_0" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ <species sboTerm="SBO:0000327" id="species_13" name="Aspartate semialdehyde" compartment="comp_0" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ <species sboTerm="SBO:0000252" id="species_1" name="DHDPS1" compartment="comp_0" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction sboTerm="SBO:0000205" id="reaction_glyph_16" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="species_13" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="species_9" constant="false"/>
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference species="species_9"/>
+ <modifierSpeciesReference species="species_1"/>
+ </listOfModifiers>
+ </reaction>
+ </listOfReactions>
+ <layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+ <layout:layout layout:id="predicted_layout">
+ <layout:dimensions layout:width="3003.53089771722" layout:height="1872.10846837268"/>
+ <layout:listOfCompartmentGlyphs>
+ <layout:compartmentGlyph layout:id="cg_comp_0" layout:compartment="comp_0">
+ <layout:boundingBox layout:id="bb_cg_comp_0">
+ <layout:position layout:x="0" layout:y="0"/>
+ <layout:dimensions layout:width="3084" layout:height="1912"/>
+ </layout:boundingBox>
+ </layout:compartmentGlyph>
+ </layout:listOfCompartmentGlyphs>
+ <layout:listOfSpeciesGlyphs>
+ <layout:speciesGlyph layout:id="sg_Lys__sa7661" layout:species="species_9">
+ <layout:boundingBox layout:id="bb_sg_Lys__sa7661">
+ <layout:position layout:x="993.6630278981" layout:y="253.764759320153"/>
+ <layout:dimensions layout:width="80" layout:height="40"/>
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="sg_ASA__sa7670" layout:species="species_13">
+ <layout:boundingBox layout:id="bb_sg_ASA__sa7670">
+ <layout:position layout:x="579.395442443615" layout:y="576.651298580278"/>
+ <layout:dimensions layout:width="80" layout:height="40"/>
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="sg_Vdhdps1_DHDPS1" layout:species="species_1">
+ <layout:boundingBox layout:id="bb_sg_Vdhdps1_DHDPS1">
+ <layout:position layout:x="617.716819753301" layout:y="339.666214868463"/>
+ <layout:dimensions layout:width="80" layout:height="40"/>
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ </layout:listOfSpeciesGlyphs>
+ <layout:listOfReactionGlyphs>
+ <layout:reactionGlyph layout:id="rg_Vdhdps1" layout:reaction="reaction_glyph_16">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
+ <layout:start layout:x="826.529235170857" layout:y="435.208028950216"/>
+ <layout:end layout:x="826.529235170857" layout:y="435.208028950216"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ <layout:listOfSpeciesReferenceGlyphs>
+ <layout:speciesReferenceGlyph layout:id="srg_Lys__sa7661_modifier_2" layout:speciesGlyph="sg_Lys__sa7661" layout:role="modifier">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
+ <layout:start layout:x="1033.6630278981" layout:y="273.764759320153"/>
+ <layout:end layout:x="905.506328076439" layout:y="322.937359825161"/>
+ </layout:curveSegment>
+ <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
+ <layout:start layout:x="905.506328076439" layout:y="322.937359825161"/>
+ <layout:end layout:x="826.529235170857" layout:y="435.208028950216"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="srg_Lys__sa7661_product_1" layout:speciesGlyph="sg_Lys__sa7661" layout:role="product">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
+ <layout:start layout:x="826.529235170857" layout:y="435.208028950216"/>
+ <layout:end layout:x="1033.6630278981" layout:y="273.764759320153"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="srg_ASA__sa7670_substrate_1" layout:speciesGlyph="sg_ASA__sa7670" layout:role="substrate">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
+ <layout:start layout:x="826.529235170857" layout:y="435.208028950216"/>
+ <layout:end layout:x="619.395442443615" layout:y="596.651298580278"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="srg_Vdhdps1_DHDPS1_modifier_1" layout:speciesGlyph="sg_Vdhdps1_DHDPS1" layout:role="modifier">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
+ <layout:start layout:x="657.716819753301" layout:y="359.666214868463"/>
+ <layout:end layout:x="817.401465289127" layout:y="431.123446109071"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ </layout:listOfSpeciesReferenceGlyphs>
+ </layout:reactionGlyph>
+ </layout:listOfReactionGlyphs>
+ </layout:layout>
+ </layout:listOfLayouts>
+ </model>
+</sbml>
diff --git a/frontend-js/src/main/css/global.css b/frontend-js/src/main/css/global.css
index 96d4b880bea3ea75bb3c2171c351f94f5e4a6f93..e6ae7e3baaefc2db36fba1de9f8afbc399e94c82 100644
--- a/frontend-js/src/main/css/global.css
+++ b/frontend-js/src/main/css/global.css
@@ -546,16 +546,28 @@ Plugin tabs
overflow: auto;
}
-.minerva-annotation-row-odd {
+.minerva-annotation-row-odd, .minerva-annotation-row-even {
+ height: 26px;
padding: 5px;
+}
+
+.minerva-annotation-row-odd {
background-color: #EAEAEA;
}
.minerva-annotation-row-even {
- padding: 5px;
background-color: #ffffff;
}
+.minerva-annotation-counter {
+ min-width: 28px;
+ float: left;
+}
+
+.minerva-annotation-body {
+ float: left;
+}
+
.minerva-overview-button {
color: #FFFFFF;
height: 36px;
@@ -954,7 +966,7 @@ a.adminLink:hover {
right: .5em;
}
-.popover {
+.minerva-map .popover {
max-width: 800px;
min-width: 390px;
}
@@ -1091,4 +1103,10 @@ input[type=file] {
.minerva-select-annotator-dialog .multi-checkbox-list-selected-entry:hover {
background: #f5f5f5;
cursor: pointer;
-}
\ No newline at end of file
+}
+#minervaAppDiv table.dataTable.hover tbody tr:hover,
+#minervaAppDiv table.dataTable.display tbody tr:hover,
+#minervaAppDiv table.dataTable.display tbody tr:hover > .sorting_1,
+#minervaAppDiv table.dataTable.order-column.stripe tbody tr:hover > .sorting_1 {
+ background-color: #D3D3D3;
+}
diff --git a/frontend-js/src/main/js/GuiConnector.js b/frontend-js/src/main/js/GuiConnector.js
index 608ce9cf5681d04d2bd769e7de31cc612335aa9d..9b5189af4a1bba46bca7ace7be2b5af27a6a5027 100644
--- a/frontend-js/src/main/js/GuiConnector.js
+++ b/frontend-js/src/main/js/GuiConnector.js
@@ -7,7 +7,6 @@ var logger = require('./logger');
var Functions = require('./Functions');
var SecurityError = require('./SecurityError');
var ValidationError = require('./ValidationError');
-var GuiMessageError = require('./gui/GuiMessageError');
/**
* This static global object contains set of functions that returns/set data in
diff --git a/frontend-js/src/main/js/gui/GuiMessageError.js b/frontend-js/src/main/js/gui/GuiMessageError.js
deleted file mode 100644
index 098c45d37b79cd047f9b5070d4770f9f799366e2..0000000000000000000000000000000000000000
--- a/frontend-js/src/main/js/gui/GuiMessageError.js
+++ /dev/null
@@ -1,21 +0,0 @@
-"use strict";
-
-/* exported logger */
-
-var logger = require('../logger');
-
-/**
- *
- * @param {string} message
- * @constructor
- * @extends {Error}
- */
-function GuiMessageError(message) {
- this.message = message;
- this.stack = (new Error(message)).stack;
-}
-
-GuiMessageError.prototype = Object.create(Error.prototype);
-GuiMessageError.prototype.constructor = GuiMessageError;
-
-module.exports = GuiMessageError;
diff --git a/frontend-js/src/main/js/gui/Panel.js b/frontend-js/src/main/js/gui/Panel.js
index 17c65b590bb6ee31015a4cebeab270a120b369e7..d0e8c98d23849c3cfde72903d084784f70077ac9 100644
--- a/frontend-js/src/main/js/gui/Panel.js
+++ b/frontend-js/src/main/js/gui/Panel.js
@@ -43,13 +43,15 @@ function Panel(params) {
}
self.setPanelName(params.panelName);
+ var element = $(self.getElement());
+ element.addClass("minerva-panel");
if (params.scrollable) {
- $(self.getElement()).addClass("pre-scrollable");
+ element.addClass("pre-scrollable");
} else {
- $(self.getElement()).css("overflow-y", "auto");
+ element.css("overflow-y", "auto");
}
- $(self.getElement()).css("position", "relative");
+ element.css("position", "relative");
if (params.helpTip !== undefined) {
self.setHelpTip(params.helpTip);
}
diff --git a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
index 9045e206b85812a4f7bca34bfdae1d205bfb12c0..411134234854650d415c029d0b196b145b2bee3d 100644
--- a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
@@ -293,15 +293,6 @@ AddProjectDialog.prototype.createGeneralTabContent = function () {
help: "Check this checkbox to display each semantic zoom level in the General Overlays"
}));
- $("[name='project-semantic-zooming']", table).change(function () {
- var disable = !$("[name='project-semantic-zooming']", table).is(":checked");
- $("[name='project-semantic-zooming-contains-multiple-overlays']", table).prop("disabled", disable);
- if (disable) {
- $("[name='project-semantic-zooming-contains-multiple-overlays']", table).prop("checked", false);
- }
- });
- $("[name='project-semantic-zooming-contains-multiple-overlays']", table).prop("disabled", !$("[name='project-semantic-zooming']", table).is(":checked"));
-
var saveProjectButton = Functions.createElement({
type: "button",
name: "saveProject",
@@ -797,10 +788,14 @@ AddProjectDialog.prototype.bindProjectUploadPreferences = function (user, type,
var value = user.getPreferences().getProjectUpload()[type];
element.prop('checked', value);
+ GuiConnector.showProcessing();
element.change(function () {
var data = new UserPreferences();
data.getProjectUpload()[type] = element.is(":checked");
- return ServerConnector.updateUserPreferences({user: user, preferences: data}).catch(GuiConnector.alert);
+ return ServerConnector.updateUserPreferences({
+ user: user,
+ preferences: data
+ }).finally(GuiConnector.hideProcessing).catch(GuiConnector.alert);
});
};
@@ -1266,7 +1261,9 @@ AddProjectDialog.prototype.setZipFileContent = function (file) {
guiUtils.hideTab(self, $(".minerva-project-overview-images-tab", self.getElement())[0]);
}
- return self.setZipEntries(entries);
+ return self.setZipEntries(entries).then(function () {
+ self._filename = file.name;
+ });
});
} else {
guiUtils.hideTab(self, $(".minerva-project-overlays-tab", self.getElement())[0]);
diff --git a/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js b/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
index 46e98e86f244812b84a68470aea63f5d0bce1c7b..72f9007e1163463e7ace9ba9cdd194037e8171a8 100644
--- a/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
+++ b/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
@@ -105,6 +105,7 @@ ChooseAnnotatorsDialog.prototype.onChangeParameterValue = function (element, ann
ChooseAnnotatorsDialog.prototype.saveAnnotatorsInfo = function (elementTypes, selectedAnnotators) {
var self = this;
selectedAnnotators = selectedAnnotators.slice();
+ GuiConnector.showProcessing();
return self.getServerConnector().getLoggedUser().then(function (user) {
var elementAnnotators = user.getPreferences()._elementAnnotators;
@@ -115,7 +116,7 @@ ChooseAnnotatorsDialog.prototype.saveAnnotatorsInfo = function (elementTypes, se
user: user,
preferences: user.getPreferences()
});
- }).catch(GuiConnector.alert);
+ }).finally(GuiConnector.hideProcessing).catch(GuiConnector.alert);
};
/**
diff --git a/frontend-js/src/main/js/gui/admin/ChooseValidatorsDialog.js b/frontend-js/src/main/js/gui/admin/ChooseValidatorsDialog.js
index b279827a47eed8b8775c005aae8c5c68c73cc725..29c189bb8484b8c2e6e41ba80ec4348cb9d86725 100644
--- a/frontend-js/src/main/js/gui/admin/ChooseValidatorsDialog.js
+++ b/frontend-js/src/main/js/gui/admin/ChooseValidatorsDialog.js
@@ -160,6 +160,7 @@ ChooseValidatorsDialog.prototype.saveAnnotationsInfo = function (params) {
var requiredAnnotators = params.requiredAnnotators;
var validAnnotators = params.validAnnotators;
var self = this;
+ GuiConnector.showProcessing();
return self.getServerConnector().getLoggedUser().then(function (user) {
var data = new UserPreferences();
@@ -179,7 +180,7 @@ ChooseValidatorsDialog.prototype.saveAnnotationsInfo = function (params) {
user: user,
preferences: data
});
- }).catch(GuiConnector.alert);
+ }).finally(GuiConnector.hideProcessing).catch(GuiConnector.alert);
};
@@ -241,10 +242,11 @@ ChooseValidatorsDialog.prototype.createValidAnnotationsDualListBox = function (u
var elementAnnotators = {};
elementAnnotators[elementType.className] = validAnnotations;
data.setElementValidAnnotations(elementAnnotators);
+ GuiConnector.showProcessing();
return self.getServerConnector().updateUserPreferences({
user: user,
preferences: data
- }).catch(GuiConnector.alert);
+ }).finally(GuiConnector.hideProcessing).catch(GuiConnector.alert);
};
checkboxList.addListener("select", function (element) {
@@ -282,7 +284,11 @@ ChooseValidatorsDialog.prototype.createVerifyAnnotationsDualListBox = function (
"annotation-list": requiredAnnotationsData.list
};
data.setElementRequiredAnnotations(elementRequiredAnnotations);
- return self.getServerConnector().updateUserPreferences({user: user, preferences: data}).catch(GuiConnector.alert);
+ GuiConnector.showProcessing();
+ return self.getServerConnector().updateUserPreferences({
+ user: user,
+ preferences: data
+ }).finally(GuiConnector.hideProcessing).catch(GuiConnector.alert);
}
});
checkbox.checked = requiredAnnotationsData.requiredAtLeastOnce;
@@ -343,7 +349,11 @@ ChooseValidatorsDialog.prototype.createVerifyAnnotationsDualListBox = function (
"annotation-list": requiredAnnotationsData.list
};
data.setElementRequiredAnnotations(elementRequiredAnnotations);
- return self.getServerConnector().updateUserPreferences({user: user, preferences: data}).catch(GuiConnector.alert);
+ GuiConnector.showProcessing();
+ return self.getServerConnector().updateUserPreferences({
+ user: user,
+ preferences: data
+ }).finally(GuiConnector.hideProcessing).catch(GuiConnector.alert);
};
checkboxList.addListener("select", function (element) {
diff --git a/frontend-js/src/main/js/gui/admin/CommentsAdminPanel.js b/frontend-js/src/main/js/gui/admin/CommentsAdminPanel.js
index 432cd9ad99c5186f087f372da9e21c2b3f5c233b..cb021863d262a4846bd5f472ae09cf9dfd0b1f1b 100644
--- a/frontend-js/src/main/js/gui/admin/CommentsAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/CommentsAdminPanel.js
@@ -66,6 +66,25 @@ CommentsAdminPanel.prototype._createGui = function () {
}]
});
+ $("[name='commentsTable']", self.getElement()).on("click", "[name='removeComment']", function () {
+ var button = this;
+ return self.askConfirmRemoval({
+ title: "Why do you want to remove this comment?",
+ input: true
+ }).then(function (param) {
+ if (param.status) {
+ return ServerConnector.removeComment({
+ commentId: $(button).attr("data"),
+ reason: param.reason,
+ projectId: self.getProject().getProjectId()
+ }).then(function () {
+ $(button).after("<span>YES (" + param.reason + ")</span>");
+ button.style.display = "none";
+ });
+ }
+ }).catch(GuiConnector.alert)
+ });
+
};
/**
@@ -93,24 +112,6 @@ CommentsAdminPanel.prototype.refreshComments = function () {
data.push(self.commentToTableRow(comments[i]));
}
dataTable.clear().rows.add(data).draw();
- $("[name='commentsTable']", self.getElement()).on("click", "[name='removeComment']", function () {
- var button = this;
- return self.askConfirmRemoval({
- title: "Why do you want to remove this comment?",
- input: true
- }).then(function (param) {
- if (param.status) {
- return ServerConnector.removeComment({
- commentId: $(button).attr("data"),
- reason: param.reason,
- projectId: self.getProject().getProjectId()
- }).then(function () {
- $(button).after("<span>YES (" + param.reason + ")</span>");
- button.style.display = "none";
- });
- }
- }).catch(GuiConnector.alert)
- });
});
};
@@ -131,10 +132,10 @@ CommentsAdminPanel.prototype.commentToTableRow = function (comment) {
};
var title = null;
if (!comment.isRemoved()) {
- var commentLink = "index.xhtml?id=" + projectId +
- "&x=" + comment.getCoordinates().x +
- "&y=" + comment.getCoordinates().y +
- "&zoom=12" +
+ var commentLink = "index.xhtml?id=" + projectId +
+ "&x=" + comment.getCoordinates().x +
+ "&y=" + comment.getCoordinates().y +
+ "&zoom=12" +
"&comments=on";
title = "<a href='" + commentLink + "' target='" + projectId + "'>" + comment.getTitle() + "</a>";
} else {
@@ -158,12 +159,12 @@ CommentsAdminPanel.prototype.commentToTableRow = function (comment) {
email = "N/A";
}
- return [comment.getId(),
- xss(title),
- xss(author),
- xss(email),
- xss(comment.getContent()),
- remove,
+ return [comment.getId(),
+ xss(title),
+ xss(author),
+ xss(email),
+ xss(comment.getContent()),
+ remove,
toYesNo(comment.isPinned())];
};
diff --git a/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js b/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
index d310210258c9dab50eb9ea9acd6202d6c43d6a89..0ab6f060e07666ae01f051e75ae626ce567c435e 100644
--- a/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
@@ -237,7 +237,7 @@ MapsAdminPanel.prototype.projectToTableRow = function (project, row, user) {
row[4] = status;
var disabled = " disabled ";
- if (user.hasPrivilege(self.getConfiguration().getPrivilegeType(PrivilegeType.ADD_MAP))) {
+ if (user.hasPrivilege(self.getConfiguration().getPrivilegeType(PrivilegeType.PROJECT_MANAGEMENT))) {
disabled = "";
}
row[5] = "<button name='showEditDialog' data='" + project.getProjectId() + "'" + disabled + "><i class='fa fa-edit' style='font-size:17px'></i></button>";
diff --git a/frontend-js/src/main/js/gui/export/ElementExportPanel.js b/frontend-js/src/main/js/gui/export/ElementExportPanel.js
index 5cbc4053b1eed4ea59c88202dda7fcb3ade3fb85..b40080133c3afbcec6d093ab3297d46b0e118357 100644
--- a/frontend-js/src/main/js/gui/export/ElementExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/ElementExportPanel.js
@@ -3,7 +3,7 @@
/* exported logger */
var AbstractExportPanel = require('./AbstractExportPanel');
-var GuiMessageError = require('../GuiMessageError');
+var ValidationError = require('../../ValidationError');
var IdentifiedElement = require('../../map/data/IdentifiedElement');
// noinspection JSUnusedLocalSymbols
@@ -71,7 +71,7 @@ ElementExportPanel.prototype.createResponseString = function () {
var elements = [];
return self.getSelectedTypes().then(function (result) {
if (result.length === 0) {
- return Promise.reject(new GuiMessageError("You must select at least one type"));
+ return Promise.reject(new ValidationError("You must select at least one type"));
}
types = result;
return self.getSelectedIncludedCompartments();
@@ -108,7 +108,7 @@ ElementExportPanel.prototype.createResponseString = function () {
return self.getSelectedColumns();
}).then(function (selectedColumns) {
if (selectedColumns.length === 0) {
- return Promise.reject(new GuiMessageError("You must select at least one column"));
+ return Promise.reject(new ValidationError("You must select at least one column"));
}
var rowPromises = [];
diff --git a/frontend-js/src/main/js/gui/export/NetworkExportPanel.js b/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
index cc5941f29795fe8e83edca8eeb1b1e534ecc4edf..4f84e0ead68ee1c8aa115fb2fb009faa4ccf6f18 100644
--- a/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
@@ -8,7 +8,7 @@ var Promise = require("bluebird");
// noinspection JSUnusedLocalSymbols
var logger = require('../../logger');
var Functions = require('../../Functions');
-var GuiMessageError = require('../GuiMessageError');
+var ValidationError = require('../../ValidationError');
var Alias = require('../../map/data/Alias');
/**
@@ -167,13 +167,13 @@ NetworkExportPanel.prototype.createResponseString = function () {
var reactionTypesDiv = $("[name='reactionTypes']", self.getElement())[0];
return self.getSelectedTypes(elementTypesDiv).then(function (result) {
if (result.length === 0) {
- return Promise.reject(new GuiMessageError("You must select at least one element type"));
+ return Promise.reject(new ValidationError("You must select at least one element type"));
}
elementTypes = result;
return self.getSelectedTypes(reactionTypesDiv);
}).then(function (result) {
if (result.length === 0) {
- return Promise.reject(new GuiMessageError("You must select at least one reaction type"));
+ return Promise.reject(new ValidationError("You must select at least one reaction type"));
}
reactionTypes = result;
return self.getSelectedIncludedCompartments();
@@ -221,7 +221,7 @@ NetworkExportPanel.prototype.createResponseString = function () {
return self.getSelectedColumns();
}).then(function (selectedColumns) {
if (selectedColumns.length === 0) {
- return Promise.reject(new GuiMessageError("You must select at least one column"));
+ return Promise.reject(new ValidationError("You must select at least one column"));
}
var rowPromises = [];
diff --git a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
index 4df361a694d393162ca18c47db1ed84531c3f2d1..fe77c84072e9c6c8377433f09e86a32ea0a92f55 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
+++ b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
@@ -402,21 +402,22 @@ GuiUtils.prototype.createAnnotationList = function (annotations, options) {
} else {
var row = document.createElement("div");
- row.style.height = "26px";
if (j % 2 === 0) {
row.className = "minerva-annotation-row-odd";
} else {
row.className = "minerva-annotation-row-even";
}
- var header = document.createElement("div");
- header.style.width = "28px";
- header.style.float = "left";
- header.innerHTML = "[" + cntAnnotations + "]";
- row.appendChild(header);
+ row.appendChild(Functions.createElement({
+ type: "div",
+ className: "minerva-annotation-counter",
+ content: "[" + cntAnnotations + "]"
+ }));
- var body = document.createElement("div");
- body.style.float = "left";
+ var body = Functions.createElement({
+ type: "div",
+ className: "minerva-annotation-body"
+ });
body.appendChild(link);
row.appendChild(body);
groupContainer.appendChild(row);
@@ -814,7 +815,7 @@ GuiUtils.prototype.createAliasElement = function (params) {
modelId: alias.getModelId()
}), true).then(function (compartment) {
div.appendChild(self.createParamLine({
- label: "Compartment: ", value: compartment.getName(),
+ label: compartment.getType() + ": ", value: compartment.getName(),
className: self._configurationOptionToClassName(ConfigurationType.SHOW_ELEMENT_COMPARTMENT)
}));
})
@@ -1139,6 +1140,23 @@ GuiUtils.prototype.hideTab = function (abstractGuiElement, panel) {
}
};
+/**
+ *
+ * @param {AbstractGuiElement} abstractGuiElement
+ * @param {Panel|HTMLElement} panel
+ */
+GuiUtils.prototype.removeTab = function (abstractGuiElement, panel) {
+ var panelId = getPanelId(panel);
+ var liElement = $("li:has(a[href='#" + panelId + "'])", $(abstractGuiElement.getElement()))[0];
+ var contentElement = $("#" + panelId, $(abstractGuiElement.getElement()))[0];
+ if (liElement !== undefined && contentElement !== undefined) {
+ liElement.parentElement.removeChild(liElement);
+ contentElement.parentElement.removeChild(contentElement);
+ } else {
+ logger.warn("Cannot find tab for panel: " + panel);
+ }
+};
+
/**
*
* @param {AbstractGuiElement} abstractGuiElement
diff --git a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
index eadedffd74d986e72867b839cb675598dfada936..3cfbaf61a480d9a3a938aac318389aefc0dfb5f9 100644
--- a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
@@ -458,6 +458,7 @@ OverlayPanel.prototype.refresh = function (showDefault) {
creator: user.getLogin()
});
}).then(function (customOverlays) {
+ self.getProject().addOrUpdateDataOverlays(customOverlays);
if (!showDefault) {
var id = self.getMap().getBackgroundDataOverlay().getId();
@@ -485,6 +486,22 @@ OverlayPanel.prototype.refresh = function (showDefault) {
var body = document.createElement("tbody");
table.appendChild(body);
+
+ generalOverlays.sort(function (o1, o2) {
+ var val1 = o1.getId();
+ var val2 = o2.getId();
+ if (o1.getOrder() !== o2.getOrder()) {
+ val1 = o1.getOrder();
+ val2 = o2.getOrder();
+ }
+ if (val1 < val2) {
+ return -1;
+ }
+ if (val1 > val2) {
+ return 1;
+ }
+ return 0;
+ });
for (i = 0; i < generalOverlays.length; i++) {
overlay = generalOverlays[i];
body.appendChild(self.createOverlayRow(overlay, selectedOverlay[overlay.getId()], false));
diff --git a/frontend-js/src/main/js/gui/topMenu/TopMenu.js b/frontend-js/src/main/js/gui/topMenu/TopMenu.js
index 9de0a275d327fbb32a9ca04fbb65920886d8958f..7a49e91561726e8c1a722b21bac322d65a364624 100644
--- a/frontend-js/src/main/js/gui/topMenu/TopMenu.js
+++ b/frontend-js/src/main/js/gui/topMenu/TopMenu.js
@@ -181,6 +181,7 @@ TopMenu.prototype.init = function () {
} else {
icon.className = "fa fa-chevron-left";
self.getLeftPanel().show();
+ $(".minerva-panel").each(onresize);
}
self.getMap().getMapCanvas().triggerListeners('resize');
};
diff --git a/frontend-js/src/main/js/map/CustomMap.js b/frontend-js/src/main/js/map/CustomMap.js
index 62c307c332cb806abb5ea24da72ea0d6a8b598e8..4577413f85a47b22333748cb3286cd5424f6b8b0 100644
--- a/frontend-js/src/main/js/map/CustomMap.js
+++ b/frontend-js/src/main/js/map/CustomMap.js
@@ -122,16 +122,14 @@ CustomMap.prototype.init = function () {
return Promise.each(ids, function (overlayId) {
- try {
- return self.openDataOverlay(overlayId);
- } catch (e) {
+ return self.openDataOverlay(overlayId).catch(function (e) {
if (e instanceof SecurityError) {
logger.debug(e.message);
sessionData.setSelectedBackgroundOverlay(self.getProject().getDataOverlays()[0].getId());
} else {
return Promise.reject(e);
}
- }
+ });
});
}).then(function () {
var logo2 = self.getControl(ControlType.LOGO_2_IMG);
@@ -224,7 +222,7 @@ CustomMap.prototype.openDataOverlay = function (param) {
identifier = parseInt(identifier);
if (isNaN(identifier)) {
- throw new Error("invalid id: " + param);
+ return Promise.reject(new Error("invalid id: " + param));
}
var overlayToOpen = null;
@@ -237,7 +235,7 @@ CustomMap.prototype.openDataOverlay = function (param) {
}
if (overlayToOpen === null) {
- throw new SecurityError("You have no privileges for selected overlay");
+ return Promise.reject(new SecurityError("You have no privileges for selected overlay"));
} else {
return overlayToOpen.init().then(function () {
if (overlayToOpen.getInputDataAvailable()) {
@@ -1237,7 +1235,7 @@ CustomMap.prototype.getDistance = function (params) {
var elementWidth = element.getWidth();
var elementHeight = element.getHeight();
return Math.min(
- Functions.distance(p1, new Point(elementX, y)),
+ Functions.distance(p1, new Point(elementX, elementY)),
Functions.distance(p1, new Point(elementX + elementWidth, elementY)),
Functions.distance(p1, new Point(elementX, elementY + elementHeight)),
Functions.distance(p1, new Point(elementX + elementWidth, elementY + elementHeight))
diff --git a/frontend-js/src/main/js/map/data/PluginData.js b/frontend-js/src/main/js/map/data/PluginData.js
index 3f2b82c391aa5834fcbb1165301595e4d3b7f9e3..a2d3c224777835d4ade3a3beaadec1c089343901 100644
--- a/frontend-js/src/main/js/map/data/PluginData.js
+++ b/frontend-js/src/main/js/map/data/PluginData.js
@@ -1,5 +1,7 @@
"use strict";
+var Functions = require('../../Functions');
+
/**
*
* @param {Object} params
@@ -36,11 +38,13 @@ PluginData.prototype.getHash = function () {
/**
*
- * @param {boolean} isPublic
+ * @param {string|boolean} isPublic
*/
PluginData.prototype.setPublic = function (isPublic) {
if (isPublic === null || isPublic === undefined) {
this._public = false;
+ } else if (Functions.isString(isPublic)) {
+ this._public = (isPublic === "true");
} else {
this._public = isPublic;
}
diff --git a/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js b/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js
index 8f5e46dbf98aebf8616772b197cb3090b97607b6..5f1608fb7887d8c34acdb69ee2c87f43fb7a2136 100644
--- a/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js
@@ -98,28 +98,39 @@ SearchDbOverlay.prototype.getElementsByQuery = function (query) {
/**
*
* @param {Point} coordinates
- * @param {IdentifiedElement} compartment
+ * @param {IdentifiedElement[]} compartments
* @param {number} maxDistance
* @returns {Promise}
* @private
*/
-SearchDbOverlay.prototype._returnCompartmentIfClickOnBorder = function (coordinates, compartment, maxDistance) {
- var model = this.getMap().getSubmapById(compartment.getModelId()).getModel();
-
- return model.getByIdentifiedElement(compartment).then(function (result) {
- var p1 = new Point(result.getX(), result.getY());
- var p2 = new Point(result.getX() + result.getWidth(), result.getY());
- var p3 = new Point(result.getX() + result.getWidth(), result.getY() + result.getHeight());
- var p4 = new Point(result.getX(), result.getY() + result.getHeight());
- var distance = Functions.distance(coordinates, {start: p1, end: p2});
- distance = Math.min(distance, Functions.distance(coordinates, {start: p2, end: p3}));
- distance = Math.min(distance, Functions.distance(coordinates, {start: p3, end: p4}));
- distance = Math.min(distance, Functions.distance(coordinates, {start: p4, end: p1}));
-
- if (maxDistance>distance) {
- return compartment;
- } else {
- return undefined;
+SearchDbOverlay.prototype._returnCompartmentIfClickOnBorder = function (coordinates, compartments, maxDistance) {
+ var promises = [];
+ for (var i = 0; i < compartments.length; i++) {
+ var compartment = compartments[i];
+ var model = this.getMap().getSubmapById(compartment.getModelId()).getModel();
+ promises.push(model.getByIdentifiedElement(compartment).then(function (result) {
+ var p1 = new Point(result.getX(), result.getY());
+ var p2 = new Point(result.getX() + result.getWidth(), result.getY());
+ var p3 = new Point(result.getX() + result.getWidth(), result.getY() + result.getHeight());
+ var p4 = new Point(result.getX(), result.getY() + result.getHeight());
+ var distance = Functions.distance(coordinates, {start: p1, end: p2});
+ distance = Math.min(distance, Functions.distance(coordinates, {start: p2, end: p3}));
+ distance = Math.min(distance, Functions.distance(coordinates, {start: p3, end: p4}));
+ distance = Math.min(distance, Functions.distance(coordinates, {start: p4, end: p1}));
+
+ if (maxDistance > distance) {
+ return new IdentifiedElement(result);
+ } else {
+ return undefined;
+ }
+ })
+ );
+ }
+ return Promise.all(promises).then(function (result) {
+ for (var i = 0; i < result.length; i++) {
+ if (result[i] !== undefined) {
+ return result[i];
+ }
}
});
};
@@ -144,7 +155,7 @@ SearchDbOverlay.prototype._getFirstVisibleParentOrObject = function (identifiedE
//transparent compartments shouldn't be clickable
if (fullElement.getTransparencyLevel() <= zoomLevel && fullElement.getType() === "Compartment") {
var maxDistance = self.computeMaxDistance(model, zoomLevel);
- return self._returnCompartmentIfClickOnBorder(coordinates, identifiedElement, maxDistance);
+ return self._returnCompartmentIfClickOnBorder(coordinates, [identifiedElement], maxDistance);
}
}
return identifiedElement;
@@ -202,18 +213,20 @@ SearchDbOverlay.prototype.findCompartmentByCoordinates = function (coordinates,
return ServerConnector.getClosestElementsByCoordinates({
modelId: model.getId(),
coordinates: coordinates,
- count: 1,
- type: ["Compartment"]
+ count: 10,
+ type: ["Compartment", "Pathway"]
}).then(function (elements) {
- var nestedOverlay = "Pathways and compartments";
if (elements.length === 0) {
return undefined;
} else {
- if (self.getMap().getBackgroundDataOverlay().getName() === nestedOverlay) {
- return self._getFirstVisibleParentOrObject(elements[0], zoom - model.getMinZoom(), coordinates);
- } else {
- return self._returnCompartmentIfClickOnBorder(coordinates, elements[0], maxDistance);
- }
+ return self._returnCompartmentIfClickOnBorder(coordinates, elements, maxDistance).then(function (result) {
+ var nestedOverlay = "Pathways and compartments";
+ if (result === undefined && self.getMap().getBackgroundDataOverlay().getName() === nestedOverlay) {
+ return self._getFirstVisibleParentOrObject(elements[0], zoom - model.getMinZoom(), coordinates);
+ } else {
+ return result;
+ }
+ });
}
});
};
diff --git a/frontend-js/src/main/js/minerva.js b/frontend-js/src/main/js/minerva.js
index 9337a2484105b494ed89eb880d46256fedf52eda..4c3a1d5f827921fc172e7ad8ee02ff9678399a37 100644
--- a/frontend-js/src/main/js/minerva.js
+++ b/frontend-js/src/main/js/minerva.js
@@ -23,12 +23,14 @@ var SelectionContextMenu = require('./gui/SelectionContextMenu');
var GuiConnector = require('./GuiConnector');
var ServerConnector = require('./ServerConnector');
var SecurityError = require('./SecurityError');
+var ValidationError = require('./ValidationError');
var MolArt = require('./map/structure/MolArt');
var Promise = require("bluebird");
var logger = require('./logger');
+var Functions = require('./Functions');
var customMap, leftPanel, topMenu, legend, mapContextMenu, selectionContextMenu;
@@ -63,7 +65,16 @@ function processUrlGetParams(params) {
}
if (GuiConnector.getParams["overlays"] !== undefined) {
- sessionData.setVisibleOverlays(GuiConnector.getParams["overlays"].split(","));
+ var overlays = GuiConnector.getParams["overlays"].split(",");
+ var data = [];
+ for (var i = 0; i < overlays.length; i++) {
+ if (Functions.isInt(parseInt(overlays[i]))) {
+ data.push(overlays[i]);
+ } else {
+ GuiConnector.warn("Invalid overlay id: " + overlays[i]);
+ }
+ }
+ sessionData.setVisibleOverlays(data);
}
if (GuiConnector.getParams["comments"] === "on") {
@@ -479,7 +490,7 @@ function create(params) {
if (project === null) {
var message = "Project with given id doesn't exist.";
message += "<p>Please go to <a href='" + ServerConnector.getServerBaseUrl() + "'>default map</a>";
- return Promise.reject(new Error(message));
+ return Promise.reject(new ValidationError(message));
}
params.setProject(project);
var promise = Promise.resolve();
diff --git a/frontend-js/src/main/js/plugin/MinervaPluginProxy.js b/frontend-js/src/main/js/plugin/MinervaPluginProxy.js
index 32d295284650e715ba1f3d84215684f79e760522..691b8986329af6f7f17f8005aedbfd7f5646745d 100644
--- a/frontend-js/src/main/js/plugin/MinervaPluginProxy.js
+++ b/frontend-js/src/main/js/plugin/MinervaPluginProxy.js
@@ -535,6 +535,7 @@ function createProjectMap(options) {
listenerData.object.removeListener(listenerData.type, listenerWrapper);
removedListeners.push(listenerData.listener);
}
+ listenersData = [];
return removedListeners;
},
getHighlightedBioEntities: function (dbOverlayName) {
diff --git a/frontend-js/src/main/js/plugin/Plugin.js b/frontend-js/src/main/js/plugin/Plugin.js
index 94d44b2662a84803c43b79f6c888d601e66d248d..409d9d68c786c6a3d4c699f794906bad21fd5e82 100644
--- a/frontend-js/src/main/js/plugin/Plugin.js
+++ b/frontend-js/src/main/js/plugin/Plugin.js
@@ -80,7 +80,7 @@ Plugin.prototype.getLoadedPluginData = function () {
/**
*
- * @param minervaPluginProxy
+ * @param {MinervaPluginProxy} minervaPluginProxy
*/
Plugin.prototype.setMinervaPluginProxy = function (minervaPluginProxy) {
this._minervaPluginProxy = minervaPluginProxy;
@@ -88,7 +88,7 @@ Plugin.prototype.setMinervaPluginProxy = function (minervaPluginProxy) {
/**
*
- * @returns {*}
+ * @returns {MinervaPluginProxy}
*/
Plugin.prototype.getMinervaPluginProxy = function () {
return this._minervaPluginProxy;
diff --git a/frontend-js/src/main/js/plugin/PluginManager.js b/frontend-js/src/main/js/plugin/PluginManager.js
index 201c5a8993299c474949b75044e3e3927343c3d6..c1b60b467e964c61ebf6e7a3547630cd62df0a2d 100644
--- a/frontend-js/src/main/js/plugin/PluginManager.js
+++ b/frontend-js/src/main/js/plugin/PluginManager.js
@@ -97,10 +97,7 @@ PluginManager.prototype.addPlugin = function (options) {
serverConnector: self.getServerConnector()
});
plugin.addListener("onUnload", function () {
- self.getGuiUtils().hideTab(self, element);
- if ($("li", self.getElement()).children(':visible').length === 0) {
- $(self.getElement()).hide();
- }
+ self.getGuiUtils().removeTab(self, element);
});
if (!self.isValidUrl(options.url)) {
return Promise.reject(new InvalidArgumentError("url: '" + options.url + "' is invalid"));
@@ -189,6 +186,7 @@ PluginManager.prototype.removePlugin = function (plugin) {
GuiConnector.removeWindowResizeEvent(self._pluginOnResizeHandlers[plugin.getPluginId()]);
return plugin.unload().then(function () {
if (self._plugins.length === 0) {
+ $(self.getElement()).hide();
return self.getMap().getMapCanvas().triggerListeners("resize");
} else {
return self.adjustMinWidth();
diff --git a/frontend-js/src/test/js/gui/admin/AddPluginDialog-test.js b/frontend-js/src/test/js/gui/admin/AddPluginDialog-test.js
index 2275ecb1e0cc75017ba015f8b28a59df1584fea0..6956ab3cbb116a7b14e98b3c198ca7cd519d17fd 100644
--- a/frontend-js/src/test/js/gui/admin/AddPluginDialog-test.js
+++ b/frontend-js/src/test/js/gui/admin/AddPluginDialog-test.js
@@ -5,6 +5,7 @@ require("../../mocha-config");
var AddPluginDialog = require('../../../../main/js/gui/admin/AddPluginDialog');
var ServerConnector = require('../../ServerConnector-mock');
var ValidationError = require('../../../../main/js/ValidationError');
+var PluginData = require('../../../../main/js/map/data/PluginData');
var logger = require('../../logger');
@@ -26,6 +27,12 @@ describe('AddPluginDialog', function () {
serverConnector: ServerConnector
});
};
+ var getPluginsData = ServerConnector.getPluginsData;
+
+ afterEach(function () {
+ ServerConnector.getPluginsData = getPluginsData;
+ });
+
it('init', function () {
helper.loginAsAdmin();
var dialog = createDialog();
@@ -85,8 +92,35 @@ describe('AddPluginDialog', function () {
return dialog.destroy();
});
});
+ it('valid file exists', function () {
+ helper.loginAsAdmin();
+ var dialog = createDialog();
+ ServerConnector.getPluginsData = function () {
+ return Promise.resolve([new PluginData({urls: "./testFiles/plugin/empty.js", isPublic: "true"})]);
+ };
+ return dialog.init().then(function () {
+ $("[name='pluginUrl']").val("./testFiles/plugin/empty.js");
+ return dialog.onValidateClicked();
+ }).then(function () {
+ assert.notOk("error expected");
+ }).catch(function (e) {
+ assert.ok(e instanceof ValidationError);
+ }).finally(function () {
+ return dialog.destroy();
+ });
+ });
+ it('valid file exists as a private plugin', function () {
+ helper.loginAsAdmin();
+ var dialog = createDialog();
+ ServerConnector.getPluginsData = function () {
+ return Promise.resolve([new PluginData({urls: "./testFiles/plugin/empty.js", isPublic: "false"})]);
+ };
+ return dialog.init().then(function () {
+ $("[name='pluginUrl']").val("./testFiles/plugin/empty.js");
+ return dialog.onValidateClicked();
+ }).finally(function () {
+ return dialog.destroy();
+ });
+ });
});
-
-
-})
-;
+});
diff --git a/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js b/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js
index ee2ae9c4c09b824959e0a7cfddc149688882ef35..081fa51d122985ba54ad29e0bee79dac746217d4 100644
--- a/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js
+++ b/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js
@@ -89,6 +89,18 @@ describe('AddProjectDialog', function () {
return dialog.destroy();
});
});
+ it('filename should be the same', function () {
+ var filename = "complex_model_with_submaps.zip";
+ var dialog = createDialog();
+ var buf = fs.readFileSync("testFiles/map/" + filename);
+ buf.name = filename;
+ return dialog.init().then(function () {
+ return dialog.setZipFileContent(buf);
+ }).then(function () {
+ assert.equal(filename, dialog.getFilename());
+ return dialog.destroy();
+ });
+ });
it('overlays', function () {
var dialog = createDialog();
var buf = fs.readFileSync("testFiles/map/complex_model_with_overlays.zip");
@@ -131,7 +143,7 @@ describe('AddProjectDialog', function () {
};
var dialog = createDialog();
var projectAdded = false;
- dialog.addListener("onProjectAdd", function(){
+ dialog.addListener("onProjectAdd", function () {
projectAdded = true;
});
diff --git a/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js b/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js
index 65a91982efe8e56d9ee6a180ed2f6908c7b190f6..2ae3767818c37ff3c62881bfefd0c14cc7bff44a 100644
--- a/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js
+++ b/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js
@@ -3,7 +3,7 @@
require("../../mocha-config.js");
var ElementExportPanel = require('../../../../main/js/gui/export/ElementExportPanel');
-var GuiMessageError = require('../../../../main/js/gui/GuiMessageError');
+var ValidationError = require('../../../../main/js/ValidationError');
var MiriamType = require('../../../../main/js/map/data/MiriamType');
var ServerConnector = require('../../ServerConnector-mock');
var logger = require('../../logger');
@@ -197,7 +197,7 @@ describe('ElementExportPanel', function () {
}).then(function () {
return exportObject.createResponseString();
}).then(null, function (error) {
- assert.ok(error instanceof GuiMessageError);
+ assert.ok(error instanceof ValidationError);
});
});
});
diff --git a/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js b/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js
index b3647262a2846b5deb0e7b4868c4dc6b216b181a..1ad333b042c3e591b1b2e305e1e711f81eab30bc 100644
--- a/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js
+++ b/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js
@@ -166,11 +166,14 @@ describe('GuiUtils', function () {
var guiUtils = createGuiUtils(map);
var alias = helper.createAlias(map);
var compartment = helper.createAlias(map);
+ compartment.setName("compartment_name");
+ compartment.setType("XYZ");
+
alias.setCompartmentId(compartment.getId());
- compartment.setName("compartment_name");
return guiUtils.createAliasElement({alias: alias}).then(function (div) {
- assert.ok(div.innerHTML.indexOf("compartment_name") >= 0);
+ assert.ok(div.innerHTML.indexOf(compartment.getName()) >= 0);
+ assert.ok(div.innerHTML.indexOf(compartment.getType()) >= 0);
});
});
diff --git a/frontend-js/src/test/js/map/CustomMap-test.js b/frontend-js/src/test/js/map/CustomMap-test.js
index 3f1508a87d02289b5ec16f50bcfb2fb1fafc64bf..17f110957e8d56789855869f030a5623491a64ee 100644
--- a/frontend-js/src/test/js/map/CustomMap-test.js
+++ b/frontend-js/src/test/js/map/CustomMap-test.js
@@ -70,12 +70,11 @@ describe('CustomMap', function () {
describe("openDataOverlay", function () {
it("for not existing id", function () {
var map = helper.createCustomMap();
- try {
- map.openDataOverlay(-1);
+ return map.openDataOverlay(-1).then(function () {
assert.ok(false);
- } catch (exception) {
+ }).catch(function (exception) {
assert.ok(exception.message.indexOf("You have no privileges") >= 0);
- }
+ });
});
it("for int id", function () {
@@ -1018,4 +1017,84 @@ describe('CustomMap', function () {
return map.getControl(ControlType.LOGO_IMG).onclick()
});
});
+ describe("getDistance", function () {
+ it("inside element", function () {
+ var map = helper.createCustomMap();
+ var alias = helper.createAlias(map);
+ alias.setX(50);
+ alias.setY(60);
+ alias.setWidth(100);
+ alias.setHeight(200);
+ var ie = new IdentifiedElement(alias);
+ return map.getDistance({modelId:map.getId(), coordinates: new Point(100,200), element: ie}).then(function(distance){
+ assert.equal(0, distance);
+ return map.destroy();
+ });
+ });
+ it("to the left", function () {
+ var map = helper.createCustomMap();
+ var alias = helper.createAlias(map);
+ alias.setX(50);
+ alias.setY(60);
+ alias.setWidth(100);
+ alias.setHeight(200);
+ var ie = new IdentifiedElement(alias);
+ return map.getDistance({modelId:map.getId(), coordinates: new Point(1,200), element: ie}).then(function(distance){
+ assert.equal(49, distance);
+ return map.destroy();
+ });
+ });
+ it("to the right", function () {
+ var map = helper.createCustomMap();
+ var alias = helper.createAlias(map);
+ alias.setX(50);
+ alias.setY(60);
+ alias.setWidth(100);
+ alias.setHeight(200);
+ var ie = new IdentifiedElement(alias);
+ return map.getDistance({modelId:map.getId(), coordinates: new Point(161,200), element: ie}).then(function(distance){
+ assert.equal(11, distance);
+ return map.destroy();
+ });
+ });
+ it("to the top", function () {
+ var map = helper.createCustomMap();
+ var alias = helper.createAlias(map);
+ alias.setX(50);
+ alias.setY(60);
+ alias.setWidth(100);
+ alias.setHeight(200);
+ var ie = new IdentifiedElement(alias);
+ return map.getDistance({modelId:map.getId(), coordinates: new Point(100,11), element: ie}).then(function(distance){
+ assert.equal(49, distance);
+ return map.destroy();
+ });
+ });
+ it("to the bottom", function () {
+ var map = helper.createCustomMap();
+ var alias = helper.createAlias(map);
+ alias.setX(50);
+ alias.setY(60);
+ alias.setWidth(100);
+ alias.setHeight(200);
+ var ie = new IdentifiedElement(alias);
+ return map.getDistance({modelId:map.getId(), coordinates: new Point(100,300), element: ie}).then(function(distance){
+ assert.equal(40, distance);
+ return map.destroy();
+ });
+ });
+ it("corner", function () {
+ var map = helper.createCustomMap();
+ var alias = helper.createAlias(map);
+ alias.setX(50);
+ alias.setY(60);
+ alias.setWidth(100);
+ alias.setHeight(200);
+ var ie = new IdentifiedElement(alias);
+ return map.getDistance({modelId:map.getId(), coordinates: new Point(46,57), element: ie}).then(function(distance){
+ assert.equal(5, distance);
+ return map.destroy();
+ });
+ });
+ });
});
diff --git a/frontend-js/src/test/js/minerva-test.js b/frontend-js/src/test/js/minerva-test.js
index b1d38ce2161efa9ddada4df3478ae848da47fc41..9eecc4932fecee98e551462bf7d282bdf3751f4a 100644
--- a/frontend-js/src/test/js/minerva-test.js
+++ b/frontend-js/src/test/js/minerva-test.js
@@ -127,7 +127,7 @@ describe('minerva global', function () {
});
});
- describe('create with overlay', function () {
+ describe('create with layout', function () {
it('background as layout param in URL', function () {
var overlay, project, plugin, map;
return ServerConnectorMock.getProject().then(function (result) {
@@ -191,6 +191,29 @@ describe('minerva global', function () {
});
});
+ describe('create with overlays', function () {
+ it('invalid overlay as param in URL', function () {
+ helper.setUrl("http://test/?overlays=xxx");
+ return ServerConnectorMock.getProject().then(function (project) {
+ var options = helper.createCustomMapOptions(project);
+ return minerva.create(options);
+ }).then(function (result) {
+ assert.equal(1, logger.getWarnings().length);
+ return result.destroy();
+ });
+ });
+ it('valid overlay as param in URL', function () {
+ helper.setUrl("http://test/?overlays=1");
+ return ServerConnectorMock.getProject().then(function (project) {
+ var options = helper.createCustomMapOptions(project);
+ return minerva.create(options);
+ }).then(function (result) {
+ assert.equal(0, logger.getWarnings().length);
+ return result.destroy();
+ });
+ });
+ });
+
it('create restricted map', function () {
var originalFunction = ServerConnectorMock.getProject;
ServerConnectorMock.getProject = function () {
diff --git a/frontend-js/src/test/js/plugin/MinervaPluginProxy-test.js b/frontend-js/src/test/js/plugin/MinervaPluginProxy-test.js
index 3fe725e9187c3368507b6eba9ca1422500601f2e..3edb4540c4f8a39f637a450e1c5561aafb60225a 100644
--- a/frontend-js/src/test/js/plugin/MinervaPluginProxy-test.js
+++ b/frontend-js/src/test/js/plugin/MinervaPluginProxy-test.js
@@ -166,6 +166,23 @@ describe('MinervaPluginProxy', function () {
return map.destroy();
});
});
+ it('call twice', function () {
+ var map = helper.createCustomMap();
+ var proxy = createProxy(map);
+
+ var options = {
+ object: "map",
+ type: "onZoomChanged",
+ callback: function () {
+ }
+ };
+ proxy.project.map.addListener(options);
+ var removedListeners = proxy.project.map.removeAllListeners();
+ assert.equal(1, removedListeners.length);
+ removedListeners = proxy.project.map.removeAllListeners();
+ assert.equal(0, removedListeners.length);
+ return map.destroy();
+ });
it('no listeners', function () {
var map;
return ServerConnector.getProject().then(function (project) {
@@ -688,8 +705,8 @@ describe('MinervaPluginProxy', function () {
helper.createSearchDbOverlay(map);
proxy = createProxy(map);
var overlays = proxy.project.data.getDataOverlays();
- assert.ok(overlays.length>0);
- for (var i=0;i<overlays.length;i++) {
+ assert.ok(overlays.length > 0);
+ for (var i = 0; i < overlays.length; i++) {
assert.ok(overlays[i].getInputDataAvailable());
}
return map.destroy();
diff --git a/frontend-js/src/test/js/plugin/PluginManager-test.js b/frontend-js/src/test/js/plugin/PluginManager-test.js
index e251c7d48b0074f7ad75b41f8103787b4b27147b..b8ff7f823d3d0c7d1a40b8ba183cb32c652d595a 100644
--- a/frontend-js/src/test/js/plugin/PluginManager-test.js
+++ b/frontend-js/src/test/js/plugin/PluginManager-test.js
@@ -122,6 +122,7 @@ describe('PluginManager', function () {
return manager.removePlugin(plugin);
}).then(function () {
assert.equal(0, manager.getPlugins().length);
+ assert.equal(-1, testDiv.innerHTML.indexOf("tab-pane"));
});
});
it('removing non existing plugin', function () {
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/16728/bioEntities.search/coordinates=104.36,182.81&count=1&type=Compartment&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/16728/bioEntities.search/coordinates=104.36,182.81&count=10&type=Compartment,Pathway&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/16728/bioEntities.search/coordinates=104.36,182.81&count=1&type=Compartment&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/16728/bioEntities.search/coordinates=104.36,182.81&count=10&type=Compartment,Pathway&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/empty/models/20638/bioEntities.search/coordinates=553.10,479.18&count=1&type=Compartment&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/empty/models/20638/bioEntities.search/coordinates=553.10,479.18&count=10&type=Compartment,Pathway&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/empty/models/20638/bioEntities.search/coordinates=553.10,479.18&count=1&type=Compartment&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/empty/models/20638/bioEntities.search/coordinates=553.10,479.18&count=10&type=Compartment,Pathway&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=184.79,365.76&count=1&type=Compartment&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=184.79,365.76&count=10&type=Compartment,Pathway&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=184.79,365.76&count=1&type=Compartment&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=184.79,365.76&count=10&type=Compartment,Pathway&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=207.73,479.18&count=1&type=Compartment&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=207.73,479.18&count=10&type=Compartment,Pathway&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=207.73,479.18&count=1&type=Compartment&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=207.73,479.18&count=10&type=Compartment,Pathway&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=316.05,253.61&count=1&type=Compartment&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=316.05,253.61&count=10&type=Compartment,Pathway&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=316.05,253.61&count=1&type=Compartment&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=316.05,253.61&count=10&type=Compartment,Pathway&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=553.10,479.18&count=1&type=Compartment&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=553.10,479.18&count=10&type=Compartment,Pathway&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=553.10,479.18&count=1&type=Compartment&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities.search/coordinates=553.10,479.18&count=10&type=Compartment,Pathway&token=MOCK_TOKEN_ID&
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java
index 9faeecc187da386aadfe4587df7189ba150d8edd..2c1fe73421a8c20ce8f7dd4302221fb418b16dda 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java
@@ -60,4 +60,8 @@ public class PathwayCompartment extends Compartment {
}
}
+ @Override
+ public String getStringType() {
+ return "Pathway";
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
index e0d5a159017292f0d8a122f78779f1c97ae08b8b..aaaca22b66b49855f8d19a5ce01736bb59165054 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
@@ -184,13 +184,13 @@ public enum ConfigurationElementType {
ConfigurationElementEditType.TEXT, false, ConfigurationElementTypeGroup.EMAIL_NOTIFICATION),
DEFAULT_VIEW_PROJECT("Default user privilege for: " + PrivilegeType.VIEW_PROJECT.getCommonName(), "true",
- ConfigurationElementEditType.BOOLEAN, true, ConfigurationElementTypeGroup.DEFAULT_USER_PRIVILEGES),
+ ConfigurationElementEditType.BOOLEAN, false, ConfigurationElementTypeGroup.DEFAULT_USER_PRIVILEGES),
DEFAULT_EDIT_COMMENTS_PROJECT("Default user privilege for: " + PrivilegeType.EDIT_COMMENTS_PROJECT.getCommonName(),
- "false", ConfigurationElementEditType.BOOLEAN, true, ConfigurationElementTypeGroup.DEFAULT_USER_PRIVILEGES),
+ "false", ConfigurationElementEditType.BOOLEAN, false, ConfigurationElementTypeGroup.DEFAULT_USER_PRIVILEGES),
DEFAULT_LAYOUT_MANAGEMENT("Default user privilege for: " + PrivilegeType.LAYOUT_MANAGEMENT.getCommonName(), "false",
- ConfigurationElementEditType.BOOLEAN, true, ConfigurationElementTypeGroup.DEFAULT_USER_PRIVILEGES),
+ ConfigurationElementEditType.BOOLEAN, false, ConfigurationElementTypeGroup.DEFAULT_USER_PRIVILEGES),
SHOW_REACTION_TYPE("Show reaction type", "true", ConfigurationElementEditType.BOOLEAN, false,
ConfigurationElementTypeGroup.SEARCH_VISIBLE_PARAMETERS),
@@ -232,7 +232,7 @@ public enum ConfigurationElementType {
ConfigurationElementEditType.STRING, true, ConfigurationElementTypeGroup.LDAP_CONFIGURATION),
DEFAULT_CUSTOM_LAYOUTS("Default user privilege for: " + PrivilegeType.CUSTOM_LAYOUTS.getCommonName(), "0",
- ConfigurationElementEditType.INTEGER, true, ConfigurationElementTypeGroup.DEFAULT_USER_PRIVILEGES),
+ ConfigurationElementEditType.INTEGER, false, ConfigurationElementTypeGroup.DEFAULT_USER_PRIVILEGES),
LDAP_UID("LDAP login (user id)", "uid", ConfigurationElementEditType.STRING, true,
ConfigurationElementTypeGroup.LDAP_CONFIGURATION),
diff --git a/persist/src/main/resources/db/migration/12.2.0~beta.2/V12.2.0.20190221__uploaded_zip_project_file_rename.sql b/persist/src/main/resources/db/migration/12.2.0~beta.2/V12.2.0.20190221__uploaded_zip_project_file_rename.sql
new file mode 100644
index 0000000000000000000000000000000000000000..9125ca61e930c69b49f442e9ebc865bd58d43217
--- /dev/null
+++ b/persist/src/main/resources/db/migration/12.2.0~beta.2/V12.2.0.20190221__uploaded_zip_project_file_rename.sql
@@ -0,0 +1 @@
+update file_entry_table set original_file_name = concat(original_file_name,'.zip') where id in (select file_entry_id from project_table where id in (select project_id from model_data_table where id in (select distinct(parent_model_id) from submodel_connection_table where parent_model_id is not null ))) and not original_file_name like '%zip';
diff --git a/persist/src/main/resources/db/migration/12.2.0~beta.2/V12.2.0.20190222__layout_table_should_not_have_model_id.sql b/persist/src/main/resources/db/migration/12.2.0~beta.2/V12.2.0.20190222__layout_table_should_not_have_model_id.sql
new file mode 100644
index 0000000000000000000000000000000000000000..59c78d4fb1f086ef71629d72ad1b60efc2977227
--- /dev/null
+++ b/persist/src/main/resources/db/migration/12.2.0~beta.2/V12.2.0.20190222__layout_table_should_not_have_model_id.sql
@@ -0,0 +1 @@
+alter table layout_table drop column model_id;
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
index de0b820aa8092cf9556a79cb574c5519c72667b3..44bac7681ebb183629407e94e2bc9f52ac4e89c7 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
@@ -134,24 +134,9 @@ public abstract class BaseRestImpl {
result.put("id", annotation.getId());
if (annotation.getAnnotator() != null) {
- try {
- result.put("annotatorClassName", annotation.getAnnotator().getName());
- result.put("descriptionByType", ((ElementAnnotator) annotation.getAnnotator().getConstructor().newInstance())
- .getDescription(annotation.getDataType()));
- result.put("descriptionByTypeRelation",
- ((ElementAnnotator) annotation.getAnnotator().getConstructor().newInstance())
- .getDescription(annotation.getDataType(), annotation.getRelationType()));
-
- } catch (Exception e) {
- logger.error("Problem with retrieving description from annotator", e);
- result.put("annotatorClassName", "");
- result.put("descriptionByType", "");
- result.put("descriptionByTypeRelation", "");
- }
+ result.put("annotatorClassName", annotation.getAnnotator().getName());
} else {
result.put("annotatorClassName", "");
- result.put("descriptionByType", "");
- result.put("descriptionByTypeRelation", "");
}
return result;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
index 509bdc38d5ca93d16b9955e419ea38ee79d4aafb..2093eee10dcab2859c563657cc31e1890ffb4037 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
@@ -503,6 +503,9 @@ public class ProjectRestImpl extends BaseRestImpl {
public Map<String, Object> removeProject(String token, String projectId, String path)
throws SecurityException, QueryException {
Project project = getProjectService().getProjectByProjectId(projectId, token);
+ if (project == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
if (getConfigurationService().getConfigurationValue(ConfigurationElementType.DEFAULT_MAP)
.equals(project.getProjectId())) {
throw new OperationNotAllowedException("You cannot remove default map");
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
index e8f49bd81b9668101a02ba8d7d831d1af34db5f6..086d8bc3ecd8932cc54d5ce796b807c7d9636d94 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
@@ -154,9 +154,10 @@ public class UserController extends BaseController {
if (auth != null) {
new SecurityContextLogoutHandler().logout(request, response, auth);
}
+ //for some reason spring doesn't invalidate sessionRegistry data on logout
+ userService.logout(token);
Map<String, Object> result = new TreeMap<>();
- result.put("status", "OK");
final Boolean useSecureCookie = false;
final String cookiePath = "/";
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
index 62697f3977247246e7cae238bc4f136804712906..0bcf3cf3dcee4d445b14c2ee2d5821d9b8087db7 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
@@ -15,6 +15,7 @@ import java.util.List;
import java.util.Map;
import org.apache.log4j.Logger;
+import org.junit.Before;
import org.junit.Test;
import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
@@ -50,6 +51,12 @@ public class ProjectRestImplTest extends RestTestFunctions {
@Autowired
ProjectDao projectDao;
+ @Before
+ public void before() {
+ _projectRestImpl.setModelService(modelService);
+ _projectRestImpl.setProjectService(projectService);
+
+ }
@Test
public void testGetModelDataDependencies() throws Exception {
try {
@@ -64,6 +71,16 @@ public class ProjectRestImplTest extends RestTestFunctions {
}
}
+ @Test(expected = ObjectNotFoundException.class)
+ public void testRemoveNonExistentProject() throws Exception {
+ try {
+ _projectRestImpl.removeProject(adminToken, "blabla", null);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test(expected = ObjectNotFoundException.class)
public void testGetInvalidMetaData() throws Exception {
ProjectRestImpl projectRest = createMockProjectRest(null);
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index 7a5b8c0c13ac5c7ab354c8f0fd928699f237cf47..50acecfe1e036ca58799145fb5bdc73749163921 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -652,6 +652,10 @@ public class ProjectService implements IProjectService {
submodelId++;
}
}
+ int order = 0;
+ for (Layout l : project.getLayouts()) {
+ l.setOrderIndex(order++);
+ }
projectDao.update(project);
if (params.isUpdateAnnotations()) {
@@ -683,7 +687,7 @@ public class ProjectService implements IProjectService {
Integer zoomLevels = generator.computeZoomLevels(topModel);
if (zoomLevels > maxZoomLevels) {
throw new InvalidInputDataExecption(
- "Map " + topModel.getName() + " too big. You can change the max size of map in configuration.");
+ "Map " + topModel.getName() + " too big. You can change the max number of map zoom levels in configuration.");
}
topModel.setZoomLevels(zoomLevels);
topModel.setTileSize(MapGenerator.TILE_SIZE);
@@ -1202,9 +1206,8 @@ public class ProjectService implements IProjectService {
Model model = modelService.getLastModelByProjectId(project.getProjectId(), token);
if (model != null) {
// TODO it's a hack to prevent lazy initialization of the project
- project.setModels(model.getProject().getModels());
- project.setLayouts(model.getProject().getLayouts());
- project.setOverviewImages(model.getProject().getOverviewImages());
+ project.getLayouts();
+ project.getOverviewImages();
model.setProject(project);
}
}
diff --git a/web/src/main/java/lcsb/mapviewer/web/bean/utils/ApiAccessControlFilter.java b/web/src/main/java/lcsb/mapviewer/web/bean/utils/ApiAccessControlFilter.java
new file mode 100644
index 0000000000000000000000000000000000000000..1d490fc98a6a2616d541f423891a4a250628782b
--- /dev/null
+++ b/web/src/main/java/lcsb/mapviewer/web/bean/utils/ApiAccessControlFilter.java
@@ -0,0 +1,44 @@
+package lcsb.mapviewer.web.bean.utils;
+
+import java.io.IOException;
+
+import javax.servlet.Filter;
+import javax.servlet.FilterChain;
+import javax.servlet.FilterConfig;
+import javax.servlet.ServletException;
+import javax.servlet.ServletRequest;
+import javax.servlet.ServletResponse;
+import javax.servlet.http.HttpServletResponse;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This filter enables x-frames from another domain if necessary.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ApiAccessControlFilter implements Filter {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ApiAccessControlFilter.class);
+
+ @Override
+ public void init(FilterConfig config) throws ServletException {
+ }
+
+ @Override
+ public void doFilter(ServletRequest req, ServletResponse res, FilterChain chain)
+ throws IOException, ServletException {
+ HttpServletResponse response = (HttpServletResponse) res;
+ response.addHeader("Vary", "*");
+ chain.doFilter(req, response);
+ }
+
+ @Override
+ public void destroy() {
+ }
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/web/bean/utils/StartupBean.java b/web/src/main/java/lcsb/mapviewer/web/bean/utils/StartupBean.java
index 2b16f5cbd3addf9819e7db9ca6253a8f7064c0bd..536011ba9a55409498d1c92008788289e7527a6d 100644
--- a/web/src/main/java/lcsb/mapviewer/web/bean/utils/StartupBean.java
+++ b/web/src/main/java/lcsb/mapviewer/web/bean/utils/StartupBean.java
@@ -6,6 +6,7 @@ import java.io.IOException;
import java.io.InputStream;
import java.util.Properties;
+import javax.annotation.PostConstruct;
import javax.faces.context.FacesContext;
import javax.servlet.ServletContext;
@@ -73,7 +74,7 @@ public class StartupBean {
/**
* Method that process initial script of application.
*/
- @EventListener(ApplicationReadyEvent.class)
+ @PostConstruct
public void init() {
loadCustomLog4jProperties();
logger.debug("Application startup script starts");
diff --git a/web/src/main/java/lcsb/mapviewer/web/config/SpringWebConfig.java b/web/src/main/java/lcsb/mapviewer/web/config/SpringWebConfig.java
index 2d829aff04191c94a38102615841660c4c6baaea..b483516ebc6ca3debd6796ebfff8cfb1bde4b852 100644
--- a/web/src/main/java/lcsb/mapviewer/web/config/SpringWebConfig.java
+++ b/web/src/main/java/lcsb/mapviewer/web/config/SpringWebConfig.java
@@ -1,10 +1,13 @@
package lcsb.mapviewer.web.config;
-import lcsb.mapviewer.services.SpringServiceConfig;
import org.springframework.context.annotation.ComponentScan;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
-import org.springframework.web.servlet.config.annotation.*;
+import org.springframework.web.servlet.config.annotation.EnableWebMvc;
+import org.springframework.web.servlet.config.annotation.ResourceHandlerRegistry;
+import org.springframework.web.servlet.config.annotation.WebMvcConfigurerAdapter;
+
+import lcsb.mapviewer.services.SpringServiceConfig;
@Configuration
@EnableWebMvc
diff --git a/web/src/main/java/lcsb/mapviewer/web/config/WebAppInitializer.java b/web/src/main/java/lcsb/mapviewer/web/config/WebAppInitializer.java
index 931e9b49b0741ad8dd2066cecee2618e881ac464..cde1173065dbf35895da25efe6341549c8b720d3 100644
--- a/web/src/main/java/lcsb/mapviewer/web/config/WebAppInitializer.java
+++ b/web/src/main/java/lcsb/mapviewer/web/config/WebAppInitializer.java
@@ -2,12 +2,9 @@ package lcsb.mapviewer.web.config;
import java.io.InputStream;
import java.util.Arrays;
-import java.util.EnumSet;
import java.util.HashSet;
import java.util.Properties;
-import javax.faces.webapp.FacesServlet;
-import javax.servlet.DispatcherType;
import javax.servlet.FilterRegistration;
import javax.servlet.ServletContext;
import javax.servlet.ServletRegistration;
@@ -22,14 +19,13 @@ import org.springframework.web.WebApplicationInitializer;
import org.springframework.web.context.ContextLoaderListener;
import org.springframework.web.context.request.RequestContextListener;
import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
-import org.springframework.web.filter.DelegatingFilterProxy;
import org.springframework.web.servlet.DispatcherServlet;
import lcsb.mapviewer.annotation.SpringAnnotationConfig;
import lcsb.mapviewer.api.SpringRestApiConfig;
import lcsb.mapviewer.persist.SpringPersistConfig;
import lcsb.mapviewer.services.SpringServiceConfig;
-import lcsb.mapviewer.web.bean.utils.CssContentTypeFilter;
+import lcsb.mapviewer.web.bean.utils.ApiAccessControlFilter;
import lcsb.mapviewer.web.bean.utils.JsfAjaxAccessControlAllowFilter;
import lcsb.mapviewer.web.bean.utils.XFrameAccessControlFilter;
@@ -39,18 +35,12 @@ public class WebAppInitializer implements WebApplicationInitializer {
@Override
public void onStartup(ServletContext container) {
- /*
- * ============ ROOT CONTEXT ============
- */
-
AnnotationConfigWebApplicationContext rootContext = new AnnotationConfigWebApplicationContext();
- rootContext.setDisplayName("MapViewer2");
rootContext.register(
SpringAnnotationConfig.class,
SpringPersistConfig.class,
SpringRestApiConfig.class,
- SpringServiceConfig.class,
- SpringWebConfig.class);
+ SpringServiceConfig.class);
container.addListener(new ContextLoaderListener(rootContext));
container.addListener(SessionListener.class);
@@ -79,68 +69,15 @@ public class WebAppInitializer implements WebApplicationInitializer {
logger.error("Problem with loading log4j configuration: " + file);
}
- /*
- * =========== APP CONTEXT ===========
- */
-
- AnnotationConfigWebApplicationContext appContext = new AnnotationConfigWebApplicationContext();
- appContext.setParent(rootContext);
-
- ServletRegistration.Dynamic appDispatcher = container.addServlet("App Servlet", new DispatcherServlet(appContext));
- appDispatcher.setLoadOnStartup(1);
- appDispatcher.addMapping(
- "*.css",
- "*.js",
- "*.gif",
- "*.jpg",
- "*.png",
- "*.pdf",
- "*.ttf",
- "*.svg",
- "*.eot",
- "*.woff",
- "*.woff2",
- "/login",
- "/j_spring_security_logout");
+ AnnotationConfigWebApplicationContext dispatcherContext = new AnnotationConfigWebApplicationContext();
+ dispatcherContext.setParent(rootContext);
+ dispatcherContext.register(SpringWebConfig.class);
- /*
- * ============= FACES CONTEXT =============
- */
-
- AnnotationConfigWebApplicationContext facesContext = new AnnotationConfigWebApplicationContext();
- facesContext.setParent(rootContext);
- ServletRegistration.Dynamic facesDispatcher = container.addServlet("Faces Servlet", new FacesServlet());
- facesDispatcher.setLoadOnStartup(1);
- facesDispatcher.addMapping(
- "*.xhtml",
- "*.jsf",
- "*.faces");
+ ServletRegistration.Dynamic dispatcher =
+ container.addServlet("dispatcher", new DispatcherServlet(dispatcherContext));
+ dispatcher.setLoadOnStartup(1);
+ dispatcher.addMapping("/api/*");
- /*
- * ================ REST API CONTEXT ================
- */
-
- AnnotationConfigWebApplicationContext restApiContext = new AnnotationConfigWebApplicationContext();
- restApiContext.setParent(rootContext);
- restApiContext.register(SpringRestApiConfig.class);
- ServletRegistration.Dynamic restApiDispatcher = container.addServlet("REST API Servlet",
- new DispatcherServlet(restApiContext));
- restApiDispatcher.setLoadOnStartup(1);
- restApiDispatcher.addMapping("/api/*");
-
- /*
- * ================ WEB CONTEXT ================
- */
-
- AnnotationConfigWebApplicationContext webContext = new AnnotationConfigWebApplicationContext();
- webContext.setParent(rootContext);
- webContext.register(SpringWebConfig.class);
- ServletRegistration.Dynamic webDispatcher = container.addServlet("WEB Servlet",
- new DispatcherServlet(webContext));
- webDispatcher.setLoadOnStartup(1);
- webDispatcher.addMapping("/");
-
-
/*
* ======= FILTERS =======
*/
@@ -151,10 +88,6 @@ public class WebAppInitializer implements WebApplicationInitializer {
fileUploadFilterReg.setInitParameter("thresholdSize", "51200");
fileUploadFilterReg.addMappingForServletNames(null, true, "Faces Servlet");
- CssContentTypeFilter cssContentTypeFilter = new CssContentTypeFilter();
- FilterRegistration.Dynamic cssContentTypeFilterReg = container.addFilter("cssContentTypeFix", cssContentTypeFilter);
- cssContentTypeFilterReg.addMappingForUrlPatterns(null, true, "/*");
-
XFrameAccessControlFilter xFrameFilter = new XFrameAccessControlFilter();
FilterRegistration.Dynamic xFrameFilterReg = container.addFilter("xFrameFilter", xFrameFilter);
xFrameFilterReg.addMappingForUrlPatterns(null, true, "/*");
@@ -164,11 +97,10 @@ public class WebAppInitializer implements WebApplicationInitializer {
jsfAjaxAccessControlAllowFilter);
jsfAjaxAccessControlAllowFilterReg.addMappingForUrlPatterns(null, true, "/*");
- DelegatingFilterProxy delegatingFilterProxy = new DelegatingFilterProxy();
- FilterRegistration.Dynamic delegatingFilterProxyReg = container.addFilter("springSecurityFilterChain",
- delegatingFilterProxy);
- delegatingFilterProxyReg.addMappingForUrlPatterns(EnumSet.of(DispatcherType.FORWARD, DispatcherType.REQUEST), false,
- "/*");
+ ApiAccessControlFilter apiFilter = new ApiAccessControlFilter();
+ FilterRegistration.Dynamic apiFilterReg = container.addFilter("apiFilter", apiFilter);
+ apiFilterReg.addMappingForUrlPatterns(null, true, "/api/*");
+
/*
* =============== COOKIE SETTINGS ===============
diff --git a/web/src/main/java/lcsb/mapviewer/web/controler/RootController.java b/web/src/main/java/lcsb/mapviewer/web/controler/RootController.java
deleted file mode 100644
index 92959e5ed0c53bd889b3dbd20fda1e262289b956..0000000000000000000000000000000000000000
--- a/web/src/main/java/lcsb/mapviewer/web/controler/RootController.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package lcsb.mapviewer.web.controler;
-
-import org.apache.log4j.Logger;
-import org.springframework.stereotype.Controller;
-import org.springframework.ui.ModelMap;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.servlet.ModelAndView;
-
-@Controller
-@RequestMapping("/")
-public class RootController {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(RootController.class);
-
- @RequestMapping(value = "/", method = { RequestMethod.GET, RequestMethod.POST })
- public ModelAndView rootPage(ModelMap model) {
- logger.debug("Accessing root page");
- return new ModelAndView("/index.xhtml", model);
- }
-}
\ No newline at end of file
diff --git a/web/src/main/webapp/index.html b/web/src/main/webapp/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..f6119f5330ab13d2b333bde34d4402939b50f9d3
--- /dev/null
+++ b/web/src/main/webapp/index.html
@@ -0,0 +1,10 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+ <meta http-equiv="refresh" content="0; url=index.xhtml" />
+ <p><a href="index.xhtml">Redirect</a></p>
+</head>
+<body>
+
+</body>
+</html>
\ No newline at end of file