diff --git a/.aspell-api-exceptions.pws b/.aspell-api-exceptions.pws
index efa354665f5f6c8bc53784d8acf9e6b591a02141..8589d9cecd52eebe140cd1b92130ef8ba2669f65 100644
--- a/.aspell-api-exceptions.pws
+++ b/.aspell-api-exceptions.pws
@@ -116,6 +116,7 @@ coeruleus
commentId
commonName
compartmentId
+compartmentOrder
complexId
compulyeast
connectedToLdap
diff --git a/CHANGELOG b/CHANGELOG
index f27a7bc28207ddf045d46d604301709bb912c1cf..987325ebd9551cf3e48918e885a10a027902f73b 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,10 +1,17 @@
-minerva (18.0.8) stable; urgency=medium
+minerva (18.1.0) stable; urgency=medium
+ * Small improvement: SBGN-ML import/export is processing notes (#2192)
+ * Small improvement: SBGN-ML import/export is processing compartmentOrder
+ (#2193)
+ * Small improvement: support for links that should be opened immediately
+ (#2189)
* Bug fix: don't create duplicated refresh jobs (#2165)
* Bug fix: performance issues with caching suggested query list for chemicals
(#2168)
* Bug fix: information about species pathway/compartment has not been
separated. This caused to export the model into incorrect SBML - species are
separated using compartment (#2169)
+ * Bug fix: exporting model should provide deterministic output for species and
+ compartments (#2187)
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 19 Dec 2024 13:00:00 +0200
diff --git a/CellDesigner-plugin/pom.xml b/CellDesigner-plugin/pom.xml
index 6001e2e64aaad4a6d8e1f7932556ba447f4d56cb..f196ae52a36c970a3631fb0002fc2b31edfdb5ed 100644
--- a/CellDesigner-plugin/pom.xml
+++ b/CellDesigner-plugin/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</parent>
<artifactId>CellDesigner-plugin</artifactId>
<!-- dependency from the MapViewer model -->
@@ -50,19 +50,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>commons</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
diff --git a/annotation/pom.xml b/annotation/pom.xml
index 6d781a5ea28a476db2e05f951c16418793fc96c8..4f120e85c46f44f56dacae1e61f22a2a7d040615 100644
--- a/annotation/pom.xml
+++ b/annotation/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</parent>
<artifactId>annotation</artifactId>
<name>Annotation module</name>
@@ -19,7 +19,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<!-- dependency from the MapViewer dao -->
@@ -27,7 +27,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<!-- dependency from the MapViewer cell designer parser (we need access
@@ -35,13 +35,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<!-- Log4J2 -->
diff --git a/commons/pom.xml b/commons/pom.xml
index 07b9b977cb78b46b3e9d8e16b1c1601f98781d41..4fc21cf7cf6d475e8356d5f772c698eb8827f86b 100644
--- a/commons/pom.xml
+++ b/commons/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</parent>
<artifactId>commons</artifactId>
<name>Mapviewer commons</name>
diff --git a/converter-CellDesigner/pom.xml b/converter-CellDesigner/pom.xml
index 86b9f56d15043eae1a3e04c7d3aab7e40bb42ed6..7d84518701bdae3e7a0dcde533b7cc70bfe100a2 100644
--- a/converter-CellDesigner/pom.xml
+++ b/converter-CellDesigner/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</parent>
<artifactId>converter-CellDesigner</artifactId>
<name>CellDesigner converter</name>
@@ -17,13 +17,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<!-- Log4J2 -->
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
index dff6f97af0094312578fb5c09a6d4bf02c6a7b62..d0bceeb60ee61462bcc2f7d95e989360a4834256 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
@@ -715,7 +715,7 @@ public class CellDesignerXmlParser extends Converter {
final List<Gene> genes = new ArrayList<>();
final List<Rna> rnas = new ArrayList<>();
final List<AntisenseRna> antisenseRnas = new ArrayList<>();
- for (final Element element : model.getElements()) {
+ for (final Element element : model.getSortedElements()) {
if (element instanceof Protein) {
proteins.add((Protein) element);
} else if (element instanceof Gene) {
diff --git a/converter-SBGNML/pom.xml b/converter-SBGNML/pom.xml
index ab9af58bd45ec28cb539468291298145177867f4..1d56b0ac8303c7f32a48e0b3689fdc27434c65dc 100644
--- a/converter-SBGNML/pom.xml
+++ b/converter-SBGNML/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</parent>
<artifactId>converter-SBGNML</artifactId>
@@ -20,26 +20,26 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
index 321f5d8a44ac4e06591d0722efaae71b4fec1682..151f2ced9724130804a01b5767ca3e8d29f3075f 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
@@ -6,7 +6,7 @@ import lcsb.mapviewer.common.geometry.ColorParser;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.graphics.bioentity.reaction.ReactionConverter;
-import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
+import lcsb.mapviewer.converter.model.sbgnml.parser.NotesConverter;
import lcsb.mapviewer.model.LogMarker;
import lcsb.mapviewer.model.ProjectLogEntryType;
import lcsb.mapviewer.model.graphics.ArrowType;
@@ -168,6 +168,8 @@ public class SbgnmlXmlExporter {
private final ColorParser colorParser = new ColorParser();
+ private final NotesConverter notesConverter = new NotesConverter();
+
private final XmlAnnotationParser xap = new XmlAnnotationParser(new ArrayList<>(), true);
private final java.util.Map<Element, String> exportElementIds = new HashMap<>();
@@ -211,7 +213,7 @@ public class SbgnmlXmlExporter {
final Sbgn sbgnData = new Sbgn();
- for (final Element element : model.getElements()) {
+ for (final Element element : model.getSortedElements()) {
if (element instanceof Species) {
if (((Species) element).getComplex() == null) {
final Glyph newGlyph = elementToGlyph(element);
@@ -253,25 +255,7 @@ public class SbgnmlXmlExporter {
throw new ConverterException("Problem with providing render information");
}
- try {
- final StringBuilder notes = new StringBuilder();
- notes.append("<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>");
- if (model.getNotes() != null) {
- notes.append(new CommonXmlParser().getNotesXmlContent(model.getNotes()));
- }
- notes.append("</body></html>");
-
- final DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
- dbf.setNamespaceAware(true);
- final DocumentBuilder db;
- db = dbf.newDocumentBuilder();
- final Document doc = db.parse(new ByteArrayInputStream(notes.toString().getBytes()));
-
- map.setNotes(new SBGNBase.Notes());
- map.getNotes().getAny().add((org.w3c.dom.Element) (doc.getFirstChild()));
- } catch (final Exception e) {
- logger.warn("Problem with processing notes");
- }
+ map.setNotes(notesConverter.createNotesNode(model.getNotes()));
sbgnData.getMap().add(map);
return sbgnData;
@@ -289,6 +273,10 @@ public class SbgnmlXmlExporter {
newGlyph.setId(elementId);
newGlyph.setClazz(getGlyphClazzFromElement(element).getClazz());
newGlyph.setLabel(getGlyphLabelFromAlias(element));
+ newGlyph.setNotes(notesConverter.createNotesNode(element.getNotes()));
+ if (element.getZ() != null) {
+ newGlyph.setCompartmentOrder(element.getZ().floatValue());
+ }
final Bbox bbox = new Bbox();
bbox.setX(element.getX().floatValue());
@@ -449,7 +437,7 @@ public class SbgnmlXmlExporter {
glyph.setClazz(GlyphClazz.STATE_VARIABLE.getClazz());
final Glyph.State state = new Glyph.State();
- if (structuralState.getName().indexOf("@") >= 0) {
+ if (structuralState.getName().contains("@")) {
state.setValue(structuralState.getName().substring(0, structuralState.getName().indexOf("@")));
state.setVariable(structuralState.getName().substring(structuralState.getName().indexOf("@") + 1));
} else {
@@ -685,14 +673,14 @@ public class SbgnmlXmlExporter {
}
if (species instanceof TruncatedProtein) {
- if (!uoiText.equals("")) {
+ if (!uoiText.isEmpty()) {
uoiText = uoiText.concat("; ");
}
uoiText = uoiText.concat("ct:truncatedProtein");
}
if ((species.getStateLabel() != null) && (species.getStatePrefix() != null)) {
- if (!uoiText.equals("")) {
+ if (!uoiText.isEmpty()) {
uoiText = uoiText.concat("; ");
}
if (!species.getStatePrefix().equals("free input")) {
@@ -703,26 +691,26 @@ public class SbgnmlXmlExporter {
if (!uoiText.contains("ct:")) {
if (species instanceof Rna) {
- if (!uoiText.equals("")) {
+ if (!uoiText.isEmpty()) {
uoiText = uoiText.concat("; ");
}
uoiText = uoiText.concat("ct:RNA");
}
if (species instanceof AntisenseRna) {
- if (!uoiText.equals("")) {
+ if (!uoiText.isEmpty()) {
uoiText = uoiText.concat("; ");
}
uoiText = uoiText.concat("ct:antisenseRNA");
}
if (species instanceof Gene) {
- if (!uoiText.equals("")) {
+ if (!uoiText.isEmpty()) {
uoiText = uoiText.concat("; ");
}
uoiText = uoiText.concat("ct:gene");
}
}
- if (!uoiText.equals("")) {
+ if (!uoiText.isEmpty()) {
uoiGlyph = new Glyph();
uoiGlyph.setClazz(GlyphClazz.UNIT_OF_INFORMATION.getClazz());
uoiGlyph.setId(species.getElementId().concat("uoi"));
@@ -1031,7 +1019,7 @@ public class SbgnmlXmlExporter {
*
* @param reaction the reaction to extract arcs from
* @param glyphList list of all glyphs in the map; used only for parsing operators
- * @return set of all arcs used in the reaction
+ * @return list of all arcs used in the reaction
*/
private List<Arc> getArcsFromReaction(final Reaction reaction, final List<Glyph> glyphList) {
final List<Arc> arcList = new ArrayList<>();
@@ -1179,13 +1167,13 @@ public class SbgnmlXmlExporter {
final DoubleComparator doubleComparator = new DoubleComparator();
for (int i = 1; i < arcPoints.size() - 1; i++) {
final Point2D nextPoint = arcPoints.get(i);
- if ((doubleComparator.compare(nextPoint.getX(), new Double(start.getX())) == 0)
- && (doubleComparator.compare(nextPoint.getY(), new Double(start.getY())) == 0)) {
+ if ((doubleComparator.compare(nextPoint.getX(), (double) start.getX()) == 0)
+ && (doubleComparator.compare(nextPoint.getY(), (double) start.getY()) == 0)) {
arc.getNext().clear();
continue;
}
- if ((doubleComparator.compare(nextPoint.getX(), new Double(end.getX())) == 0)
- && (doubleComparator.compare(nextPoint.getY(), new Double(end.getY())) == 0)) {
+ if ((doubleComparator.compare(nextPoint.getX(), (double) end.getX()) == 0)
+ && (doubleComparator.compare(nextPoint.getY(), (double) end.getY()) == 0)) {
break;
}
final Next next = new Next();
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
index fbeac9272faf24244a4e9bd629a81bb6b78beff5..6e5728d44676d05f5b77857e814edb9125603865 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
@@ -1,38 +1,12 @@
package lcsb.mapviewer.converter.model.sbgnml;
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-
-import org.apache.commons.io.FilenameUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.sbgn.GlyphClazz;
-import org.sbgn.RenderUtil;
-import org.sbgn.SbgnUtil;
-import org.sbgn.bindings.Arc;
-import org.sbgn.bindings.Arc.End;
-import org.sbgn.bindings.Arc.Next;
-import org.sbgn.bindings.Arc.Start;
-import org.sbgn.bindings.Bbox;
-import org.sbgn.bindings.Glyph;
-import org.sbgn.bindings.Map;
-import org.sbgn.bindings.RenderInformation;
-import org.sbgn.bindings.Sbgn;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.ZIndexPopulator;
import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.sbgnml.parser.ElementParser;
+import lcsb.mapviewer.converter.model.sbgnml.parser.NotesConverter;
import lcsb.mapviewer.converter.model.sbgnml.parser.ReactionParser;
import lcsb.mapviewer.converter.model.sbgnml.parser.RenderParser;
import lcsb.mapviewer.converter.model.sbgnml.structures.Process;
@@ -48,24 +22,43 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.sbgn.GlyphClazz;
+import org.sbgn.RenderUtil;
+import org.sbgn.SbgnUtil;
+import org.sbgn.bindings.Arc;
+import org.sbgn.bindings.Arc.End;
+import org.sbgn.bindings.Arc.Next;
+import org.sbgn.bindings.Arc.Start;
+import org.sbgn.bindings.Bbox;
+import org.sbgn.bindings.Glyph;
+import org.sbgn.bindings.Map;
+import org.sbgn.bindings.RenderInformation;
+import org.sbgn.bindings.Sbgn;
+import org.w3c.dom.Node;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
/**
* This class is a parser for SBGN-ML files.
- *
- * @author Michał Kuźma
*
+ * @author Michał Kuźma
*/
public class SbgnmlXmlParser {
/**
* Default class logger.
*/
- private Logger logger = LogManager.getLogger();
+ private final Logger logger = LogManager.getLogger();
/**
* List of all arcs that should be translated as activity flow reactions.
*/
- private List<Arc> activityFlowArcs = new ArrayList<>();
+ private final List<Arc> activityFlowArcs = new ArrayList<>();
private Model model;
@@ -77,17 +70,15 @@ public class SbgnmlXmlParser {
private ReactionParser reactionParser;
+ private final NotesConverter notesConverter = new NotesConverter();
+
/**
* Method used to create a model from SBGN-ML file.
*
- * @param filename
- * The filename of the input file.
- * @param inputSbgnmlFile
- * the input file.
- *
+ * @param filename The filename of the input file.
+ * @param inputSbgnmlFile the input file.
* @return valid model parsed from the file
- * @throws InvalidInputDataExecption
- * thrown when input file is invalid
+ * @throws InvalidInputDataExecption thrown when input file is invalid
*/
public Model createModel(final String filename, final File inputSbgnmlFile) throws InvalidInputDataExecption {
@@ -126,23 +117,7 @@ public class SbgnmlXmlParser {
elementParser = new ElementParser(renderParser, model);
reactionParser = new ReactionParser(renderParser, model);
- RestAnnotationParser rap = new RestAnnotationParser();
-
- if (map.getNotes() != null && map.getNotes().getAny().size() > 0) {
- try {
- String notes = "<notes>" + XmlParser.nodeToString(map.getNotes().getAny().get(0).getParentNode(), true)
- + "</notes>";
- DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
- dbf.setNamespaceAware(true);
- DocumentBuilder db;
- db = dbf.newDocumentBuilder();
- Document doc = db.parse(new ByteArrayInputStream(notes.getBytes()));
-
- model.setNotes(rap.getNotes(doc.getFirstChild()));
- } catch (final Exception e) {
- logger.warn("Problem with extracting map notes", e);
- }
- }
+ model.setNotes(notesConverter.parseNotes(map.getNotes()));
elementParser.adjustSizeOfElements(map);
@@ -225,11 +200,9 @@ public class SbgnmlXmlParser {
/**
* Method used to compute height and width of the model.
- *
- * @param map
- * Map parsed from SBGN-ML file
- * @param model
- * Model to be updated
+ *
+ * @param map Map parsed from SBGN-ML file
+ * @param model Model to be updated
*/
private void setModelSize(final Map map, final Model model) {
if (map.getBbox() != null) {
@@ -351,11 +324,9 @@ public class SbgnmlXmlParser {
/**
* Finds a compartment where element should be located (base on the
* coordinates).
- *
- * @param child
- * {@link Element} for which we want to find compartment
- * @param model
- * {@link Model} where we look for a compartment
+ *
+ * @param child {@link Element} for which we want to find compartment
+ * @param model {@link Model} where we look for a compartment
* @return parent {@link Compartment}
*/
private Compartment findParentCompartment(final Element child, final Model model) {
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ElementParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ElementParser.java
index 20aa6fdb5e4691a4715c6b2cb1d7981f54f22333..9c96a1fc768ee3c90ed83ea697a38e9bb7a12c62 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ElementParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ElementParser.java
@@ -72,6 +72,8 @@ public class ElementParser extends GlyphParser {
private final Model model;
+ private final NotesConverter notesConverter = new NotesConverter();
+
public ElementParser(final RenderParser renderParser, final Model model) {
this.renderParser = renderParser;
this.model = model;
@@ -179,6 +181,10 @@ public class ElementParser extends GlyphParser {
compartment.setFillColor(COMPARTMENT_COLOR);
compartment.setBorderColor(COMPARTMENT_COLOR);
+ if (glyph.getCompartmentOrder() != null) {
+ compartment.setZ(Math.round(glyph.getCompartmentOrder()));
+ }
+
if (glyph.getLabel() != null && glyph.getLabel().getBbox() != null) {
compartment.setNameX(glyph.getLabel().getBbox().getX());
compartment.setNameY(glyph.getLabel().getBbox().getY());
@@ -246,6 +252,11 @@ public class ElementParser extends GlyphParser {
element.setName("");
}
+ element.setNotes(notesConverter.parseNotes(g.getNotes()));
+ if (g.getCompartmentOrder() != null) {
+ element.setZ(Math.round(g.getCompartmentOrder()));
+ }
+
if (element instanceof Species) {
final Species newSpecies = (Species) element;
// Add species to parent complex if there is one
@@ -448,8 +459,6 @@ public class ElementParser extends GlyphParser {
* Method used to parse state variable.
*
* @param stateVariable unit of information glyph from sbgn-ml file
- * @throws Exception Exception is thrown if state variable is parsed for species other
- * than Protein
*/
private Residue stateVariableToResidue(final Glyph stateVariable) {
if (stateVariable.getState() != null && (stateVariable.getState().getVariable() == null
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/NotesConverter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/NotesConverter.java
new file mode 100644
index 0000000000000000000000000000000000000000..4db5742a0d245cab88137dbd7cc21491f6429335
--- /dev/null
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/NotesConverter.java
@@ -0,0 +1,62 @@
+package lcsb.mapviewer.converter.model.sbgnml.parser;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.sbgn.bindings.SBGNBase;
+import org.w3c.dom.Document;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import java.io.ByteArrayInputStream;
+
+public class NotesConverter {
+
+ private final Logger logger = LogManager.getLogger();
+
+ private final RestAnnotationParser rap = new RestAnnotationParser();
+
+ public SBGNBase.Notes createNotesNode(final String notes) {
+ SBGNBase.Notes result = new SBGNBase.Notes();
+ try {
+ final StringBuilder notesXml = new StringBuilder();
+ notesXml.append("<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>");
+ if (notes != null) {
+ notesXml.append(new CommonXmlParser().getNotesXmlContent(notes));
+ }
+ notesXml.append("</body></html>");
+
+ final DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
+ dbf.setNamespaceAware(true);
+ final DocumentBuilder db;
+ db = dbf.newDocumentBuilder();
+ final Document doc = db.parse(new ByteArrayInputStream(notesXml.toString().getBytes()));
+
+ result.getAny().add((org.w3c.dom.Element) (doc.getFirstChild()));
+ } catch (final Exception e) {
+ logger.warn("Problem with processing notes");
+ }
+ return result;
+ }
+
+ public String parseNotes(final SBGNBase.Notes notesNode) {
+ if (notesNode != null && !notesNode.getAny().isEmpty()) {
+ try {
+ String notes = "<notes>" + XmlParser.nodeToString(notesNode.getAny().get(0).getParentNode(), true)
+ + "</notes>";
+ DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
+ dbf.setNamespaceAware(true);
+ DocumentBuilder db;
+ db = dbf.newDocumentBuilder();
+ Document doc = db.parse(new ByteArrayInputStream(notes.getBytes()));
+
+ return rap.getNotes(doc.getFirstChild());
+ } catch (final Exception e) {
+ logger.warn("Problem with extracting map notes", e);
+ }
+ }
+ return "";
+ }
+}
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlTestFunctions.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlTestFunctions.java
index be2f8bb72001771afb63b3f6f5ff7ff598d31385..5f38baf0e8e31e2be6d4a8d59ecc2b81d39651fe 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlTestFunctions.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlTestFunctions.java
@@ -1,20 +1,5 @@
package lcsb.mapviewer.converter.model.sbgnml;
-import java.awt.Color;
-import java.awt.Desktop;
-import java.awt.geom.Point2D;
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.nio.charset.StandardCharsets;
-import java.nio.file.Files;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.junit.Rule;
-import org.sbgn.GlyphClazz;
-import org.sbgn.bindings.Bbox;
-import org.sbgn.bindings.Glyph;
-
import lcsb.mapviewer.common.tests.TestUtils;
import lcsb.mapviewer.common.tests.UnitTestFailedWatcher;
import lcsb.mapviewer.converter.Converter;
@@ -28,6 +13,8 @@ import lcsb.mapviewer.model.graphics.HorizontalAlign;
import lcsb.mapviewer.model.graphics.VerticalAlign;
import lcsb.mapviewer.model.map.Drawable;
import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Drug;
@@ -35,23 +22,36 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.StructuralState;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.Rule;
+import org.sbgn.GlyphClazz;
+import org.sbgn.bindings.Bbox;
+import org.sbgn.bindings.Glyph;
+
+import java.awt.Color;
+import java.awt.Desktop;
+import java.awt.geom.Point2D;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
public class SbgnmlTestFunctions extends TestUtils {
protected static Logger logger = LogManager.getLogger();
-
+ private static int counter = 0;
+ private final Converter sbgnmlConverter = new SbgnmlXmlConverter();
@Rule
public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
- private static int counter = 0;
-
protected void showImage(final Model model) throws Exception {
String dir = Files.createTempDirectory("sbml-temp-images-dir").toFile().getAbsolutePath();
AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().height(model.getHeight())
.width(model.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model);
NormalImageGenerator nig = new PngImageGenerator(params);
- String pathWithouExtension = dir + "/" + model.getName();
- String pngFilePath = pathWithouExtension.concat(".png");
+ String pathWithoutExtension = dir + "/" + model.getName();
+ String pngFilePath = pathWithoutExtension.concat(".png");
nig.saveToFile(pngFilePath);
Desktop.getDesktop().open(new File(pngFilePath));
}
@@ -74,6 +74,15 @@ public class SbgnmlTestFunctions extends TestUtils {
return protein;
}
+ protected Compartment createCompartment() {
+ SquareCompartment compartment = new SquareCompartment("id" + (counter++));
+ assignLayout(compartment);
+ compartment.setNameHorizontalAlign(HorizontalAlign.LEFT);
+ compartment.setNameVerticalAlign(VerticalAlign.TOP);
+
+ return compartment;
+ }
+
protected Drug createDrug() {
Drug drug = new Drug("id" + (counter++));
assignLayout(drug);
@@ -114,8 +123,6 @@ public class SbgnmlTestFunctions extends TestUtils {
return structuralState;
}
- private Converter sbgnmlConverter = new SbgnmlXmlConverter();
-
protected Model serializeAndCleanOverSbgn(final Model model) throws InconsistentModelException, ConverterException, InvalidInputDataExecption {
String sbgn = sbgnmlConverter.model2String(model);
// logger.debug(sbgn);
@@ -125,10 +132,14 @@ public class SbgnmlTestFunctions extends TestUtils {
model2.setIdModel(model.getIdModel());
model2.setName(model.getName());
for (final Drawable d : model.getDrawables()) {
- d.setZ(null);
+ if (!(d instanceof Element)) {
+ d.setZ(null);
+ }
}
for (final Drawable d : model2.getDrawables()) {
- d.setZ(null);
+ if (!(d instanceof Element)) {
+ d.setZ(null);
+ }
}
for (final Species e : model.getSpeciesList()) {
e.setInitialAmount(null);
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
index 6db64a2a48370df28d1727e259fd2de15baec58c..bcd816d33ff55997e44fdca3975f1632689ffb36 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
@@ -1,22 +1,9 @@
package lcsb.mapviewer.converter.model.sbgnml;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Point2D;
-import java.io.File;
-import java.io.PrintWriter;
-
-import org.junit.Test;
-import org.sbgn.ArcClazz;
-import org.sbgn.GlyphClazz;
-import org.sbgn.SbgnUtil;
-
import lcsb.mapviewer.common.geometry.PointTransformation;
import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -29,6 +16,19 @@ import lcsb.mapviewer.model.map.species.Drug;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.modelutils.map.ElementUtils;
+import org.junit.Test;
+import org.sbgn.ArcClazz;
+import org.sbgn.GlyphClazz;
+import org.sbgn.SbgnUtil;
+
+import java.awt.geom.Point2D;
+import java.io.File;
+import java.io.PrintWriter;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions {
@@ -68,7 +68,7 @@ public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions {
private static Reaction createReaction(final Class<? extends Reaction> clazz) throws Exception {
- Reaction reaction = clazz.getConstructor(String.class).newInstance(new Object[] { "re" + (counter++) });
+ Reaction reaction = clazz.getConstructor(String.class).newInstance("re" + (counter++));
Ion ion = createIon(counter++);
Ion ion2 = createIon(counter);
@@ -138,6 +138,19 @@ public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions {
assertEquals(0, new ModelComparator().compare(model, model2));
}
+ @Test
+ public void importExportNotes() throws Exception {
+ GenericProtein protein = createProtein();
+ protein.setNotes("hello world");
+ Model model = new ModelFullIndexed(null);
+ model.setWidth(2000);
+ model.setHeight(2000);
+ model.addElement(protein);
+
+ Model model2 = serializeAndCleanOverSbgn(model);
+ assertEquals(0, new ModelComparator().compare(model, model2));
+ }
+
@Test
public void testExportWithWarning() throws Exception {
Converter sbgnmlConverter = new SbgnmlXmlConverter();
@@ -159,4 +172,23 @@ public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions {
assertTrue(SbgnUtil.isValid(tempFile));
}
+ @Test
+ public void importExportZ() throws Exception {
+ GenericProtein protein = createProtein();
+ protein.setZ(3);
+
+ Compartment compartment = createCompartment();
+ compartment.setZ(4);
+ compartment.addElement(protein);
+
+ Model model = new ModelFullIndexed(null);
+ model.setWidth(2000);
+ model.setHeight(2000);
+ model.addElement(protein);
+ model.addElement(compartment);
+
+ Model model2 = serializeAndCleanOverSbgn(model);
+ assertEquals(0, new ModelComparator().compare(model, model2));
+ }
+
}
diff --git a/converter-graphics/pom.xml b/converter-graphics/pom.xml
index b91e1358f054ddd9e7195f4d0b217f3d00db621c..b930fb55b0996679a65c882e6ff86bc040073fdf 100644
--- a/converter-graphics/pom.xml
+++ b/converter-graphics/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</parent>
<artifactId>converter-graphics</artifactId>
<name>MapViewer graphics converter</name>
@@ -18,13 +18,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<!-- Log4J2 -->
diff --git a/converter-sbml/pom.xml b/converter-sbml/pom.xml
index 3d3504367c6360edd74c871edba2d1b787a07b99..dc07a47f36ff66bd91c50cef13f3e4191038ebf7 100644
--- a/converter-sbml/pom.xml
+++ b/converter-sbml/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</parent>
<artifactId>converter-sbml</artifactId>
<name>converter-sbml</name>
@@ -40,22 +40,22 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<!-- Log4J2 -->
@@ -167,7 +167,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
<scope>test</scope>
</dependency>
diff --git a/converter/pom.xml b/converter/pom.xml
index 166b0ab0dd8d01412acf79df838389bca06f6201..2b7328f0f48cea06e1493e7147f0d86443bd4102 100644
--- a/converter/pom.xml
+++ b/converter/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</parent>
<artifactId>converter</artifactId>
@@ -15,7 +15,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>xerces</groupId>
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index b32fd50e3cba1e864ad7dab3708b26c6cb86907c..3c320b72e1dc3aba3ba6ee53c0605dd595d237a1 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
@@ -1,25 +1,5 @@
package lcsb.mapviewer.converter;
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.lang.reflect.Modifier;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipFile;
-
-import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.io.IOUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.TextFileUtils;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidClassException;
@@ -31,6 +11,7 @@ import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
@@ -45,14 +26,32 @@ import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.overlay.DataOverlay;
import lcsb.mapviewer.model.overlay.DataOverlayType;
import lcsb.mapviewer.model.overlay.InvalidDataOverlayException;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.lang.reflect.Modifier;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
/**
* This class allows to create complex {@link Model} that contains submaps. It's
* written in generic way and use {@link Converter} as a class to parse single
* submap.
- *
+ *
* @author Piotr Gawron
- *
*/
public class ComplexZipConverter {
@@ -64,19 +63,19 @@ public class ComplexZipConverter {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
+ private static final String IMMEDIATE_LINK_PREFIX = "IMMEDIATE_LINK:";
/**
* Class used to create single submap from a file.
*/
- private Class<? extends Converter> converterClazz;
+ private final Class<? extends Converter> converterClazz;
/**
* Default constructor. Checks if the class given in the parameter is proper
* {@link Converter} implementation.
- *
- * @param clazz
- * {@link Converter} class used for creation of the single submap
+ *
+ * @param clazz {@link Converter} class used for creation of the single submap
*/
public ComplexZipConverter(final Class<? extends Converter> clazz) {
if (Modifier.isAbstract(clazz.getModifiers())) {
@@ -92,13 +91,11 @@ public class ComplexZipConverter {
/**
* Creates complex {@link Model} that contains submaps.
- *
- * @param params
- * {@link ComplexZipConverterParams object} with information about data
- * from which result is going to be created
+ *
+ * @param params {@link ComplexZipConverterParams object} with information about data
+ * from which result is going to be created
* @return complex {@link Model} created from input data
- * @throws InvalidInputDataExecption
- * thrown when there is a problem with accessing input data
+ * @throws InvalidInputDataExecption thrown when there is a problem with accessing input data
*/
public Model createModel(final ComplexZipConverterParams params) throws InvalidInputDataExecption, ConverterException {
try {
@@ -133,7 +130,7 @@ public class ComplexZipConverter {
} else if (zef instanceof GlyphZipEntryFile) {
continue;
} else if (!isIgnoredFile(entry.getName())) {
- throw new NotImplementedException("Unknwon entry type: " + zef.getClass());
+ throw new NotImplementedException("Unknown entry type: " + zef.getClass());
}
}
}
@@ -156,6 +153,9 @@ public class ComplexZipConverter {
for (final Reaction reaction : mappingModel.getReactions()) {
processReaction(mapping, nameModelMap, result, reaction);
}
+ for (final Species species : mappingModel.getSpeciesList()) {
+ processSpecies(species, nameModelMap);
+ }
}
return result;
} catch (final IOException e) {
@@ -163,6 +163,37 @@ public class ComplexZipConverter {
}
}
+ private void processSpecies(final Species species, final Map<String, Model> nameModelMap) {
+ String notes = species.getNotes();
+ if (notes != null) {
+ String[] lines = notes.split("\n");
+ for (String line : lines) {
+ line = line.trim();
+ if (line.startsWith(IMMEDIATE_LINK_PREFIX)) {
+ String link = line.replace(IMMEDIATE_LINK_PREFIX, "").trim();
+
+ Compartment compartment = species.getCompartment();
+ if (compartment == null) {
+ logger.warn("[SUBMODEL MAPPING] Species {} in mapping file doesn't start inside compartment. Skipped. Link skipped",
+ species.getElementId());
+ } else {
+ String modelName = compartment.getName().toLowerCase();
+ Model model = nameModelMap.get(modelName);
+ if (model == null) {
+ throw new InvalidArgumentException("Mapping file references to " + modelName + " submodel. But such model doesn't exist");
+ }
+ Element elementToChange = model.getElementByElementId(species.getName());
+ if (elementToChange == null) {
+ throw new InvalidArgumentException("Mapping file references to element with alias: " + species.getName()
+ + ". But such element doesn't exist");
+ }
+ elementToChange.setImmediateLink(link);
+ }
+ }
+ }
+ }
+ }
+
protected boolean isIgnoredFile(final String name) {
if (name == null) {
return true;
@@ -170,53 +201,48 @@ public class ComplexZipConverter {
return true;
} else if (name.startsWith(".DS_Store") || name.endsWith(".DS_Store")) {
return true;
- } else if (name.startsWith("__MACOSX")) {
- return true;
+ } else {
+ return name.startsWith("__MACOSX");
}
- return false;
}
/**
* Process a single reaction in mapping file (transforming reaction into
* connection between submodels).
- *
- * @param mapping
- * name of the mapping file
- * @param nameModelMap
- * mapping between file names and models
- * @param topModel
- * top model
- * @param reaction
- * reaction to transform into connection
+ *
+ * @param mapping name of the mapping file
+ * @param nameModelMap mapping between file names and models
+ * @param topModel top model
+ * @param reaction reaction to transform into connection
*/
public void processReaction(final String mapping, final Map<String, Model> nameModelMap, final Model topModel, final Reaction reaction) {
if (reaction.getReactants().size() > 1) {
- logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
- + ") contains too many reactants. Skipped");
+ logger.warn("[SUBMODEL MAPPING] Reaction {} in mapping file ({}) contains too many reactants. Skipped",
+ reaction.getIdReaction(), mapping);
} else if (reaction.getProducts().size() > 1) {
- logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
- + ") contains too many products. Skipped");
- } else if (reaction.getModifiers().size() > 0) {
- logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
- + ") contains modifiers. Skipped");
+ logger.warn("[SUBMODEL MAPPING] Reaction {} in mapping file ({}) contains too many products. Skipped",
+ reaction.getIdReaction(), mapping);
+ } else if (!reaction.getModifiers().isEmpty()) {
+ logger.warn("[SUBMODEL MAPPING] Reaction {} in mapping file ({}) contains modifiers. Skipped",
+ reaction.getIdReaction(), mapping);
} else {
Element fromAlias = reaction.getReactants().get(0).getElement();
Element toAlias = reaction.getProducts().get(0).getElement();
if (!(fromAlias instanceof Species)) {
- logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
- + ") contains doesn't start in species. Skipped");
+ logger.warn("[SUBMODEL MAPPING] Reaction {} in mapping file ({}) contains doesn't start in species. Skipped",
+ reaction.getIdReaction(), mapping);
} else if (!(toAlias instanceof Species)) {
- logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
- + ") contains doesn't end in species. Skipped");
+ logger.warn("[SUBMODEL MAPPING] Reaction {} in mapping file ({}) contains doesn't end in species. Skipped",
+ reaction.getIdReaction(), mapping);
} else {
Complex complexFrom = ((Species) fromAlias).getComplex();
Complex complexTo = ((Species) toAlias).getComplex();
if (complexFrom == null) {
- logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
- + ") contains doesn't start inside complex. Skipped");
+ logger.warn("[SUBMODEL MAPPING] Reaction {} in mapping file ({}) contains doesn't start inside complex. Skipped",
+ reaction.getIdReaction(), mapping);
} else if (complexTo == null && (!(toAlias instanceof Complex))) {
- logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
- + ") contains doesn't end inside complex. Skipped");
+ logger.warn("[SUBMODEL MAPPING] Reaction {} in mapping file ({}) contains doesn't end inside complex. Skipped",
+ reaction.getIdReaction(), mapping);
} else {
if (complexTo == null) {
complexTo = (Complex) toAlias;
@@ -226,11 +252,9 @@ public class ComplexZipConverter {
Model fromModel = nameModelMap.get(fromName);
Model toModel = nameModelMap.get(toName);
if (fromModel == null) {
- throw new InvalidArgumentException(
- "Mapping file references to " + fromName + " submodel. But such model doesn't exist");
+ throw new InvalidArgumentException("Mapping file references to " + fromName + " submodel. But such model doesn't exist");
} else if (toModel == null) {
- throw new InvalidArgumentException(
- "Mapping file references to " + toName + " submodel. But such model doesn't exist");
+ throw new InvalidArgumentException("Mapping file references to " + toName + " submodel. But such model doesn't exist");
}
Element source = fromModel.getElementByElementId(fromAlias.getName());
if (source == null) {
@@ -260,11 +284,9 @@ public class ComplexZipConverter {
/**
* This method validates if information about model and submodels in the params
* are sufficient. If not then appropriate exception will be thrown.
- *
- * @param params
- * parameters to validate
- * @param zipFile
- * original {@link ZipFile}
+ *
+ * @param params parameters to validate
+ * @param zipFile original {@link ZipFile}
* @return name of the file containing mapping between submodels
*/
protected String validateSubmodelInformation(final ComplexZipConverterParams params, final ZipFile zipFile) {
@@ -313,22 +335,17 @@ public class ComplexZipConverter {
/**
* Transforms {@link LayoutZipEntryFile} into {@link DataOverlay}.
- *
- * @param zipFile
- * original {@link ZipFile}
- * @param entry
- * entry in a zip file
- * @param params
- * parameters used to make general conversion (we use directory where
- * layout should be stored)
- * @param layoutEntry
- * {@link LayoutZipEntryFile} to transform
+ *
+ * @param zipFile original {@link ZipFile}
+ * @param entry entry in a zip file
+ * @param params parameters used to make general conversion (we use directory where
+ * layout should be stored)
+ * @param layoutEntry {@link LayoutZipEntryFile} to transform
* @return {@link DataOverlay} for a given {@link LayoutZipEntryFile}
- * @throws IOException
- * thrown when there is a problem with accessing {@link ZipFile}
+ * @throws IOException thrown when there is a problem with accessing {@link ZipFile}
*/
public DataOverlay layoutZipEntryFileToLayout(final ComplexZipConverterParams params, final ZipFile zipFile, final ZipEntry entry,
- final LayoutZipEntryFile layoutEntry, final int order) throws IOException, InvalidInputDataExecption {
+ final LayoutZipEntryFile layoutEntry, final int order) throws IOException, InvalidInputDataExecption {
DataOverlay layout = new DataOverlay();
layout.setDescription(layoutEntry.getDescription());
UploadedFileEntry fileEntry = new UploadedFileEntry();
@@ -376,14 +393,11 @@ public class ComplexZipConverter {
/**
* Copy file from zip entry into temporary file.
- *
- * @param zipFile
- * input zip file
- * @param entry
- * entry in the zip file
+ *
+ * @param zipFile input zip file
+ * @param entry entry in the zip file
* @return {@link File} with a copy of data from zip entry
- * @throws IOException
- * thrown when there is a problem with input or output file
+ * @throws IOException thrown when there is a problem with input or output file
*/
protected File saveFileFromZipFile(final ZipFile zipFile, final ZipEntry entry) throws IOException {
InputStream is = zipFile.getInputStream(entry);
@@ -401,17 +415,15 @@ public class ComplexZipConverter {
/**
* Creates instance of {@link Converter} used as a template parameter for this
* class instantiation.
- *
+ *
* @return instance of {@link Converter}
*/
protected Converter createConverterInstance() {
Converter converter;
try {
converter = converterClazz.newInstance();
- } catch (final InstantiationException e) {
- throw new InvalidClassException("Problem with instantation of the class: " + converterClazz, e);
- } catch (final IllegalAccessException e) {
- throw new InvalidClassException("Problem with instantation of the class: " + converterClazz, e);
+ } catch (final InstantiationException | IllegalAccessException e) {
+ throw new InvalidClassException("Problem with instantiation of the class: " + converterClazz, e);
}
return converter;
}
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
index 504c7c05ef9ca53ae319aabef921634de3ac1141..bb16914c1fcbac096fcae43f96ababe675c71b30 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
@@ -1,20 +1,5 @@
package lcsb.mapviewer.converter;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.io.ByteArrayInputStream;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipFile;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidClassException;
import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
@@ -24,6 +9,20 @@ import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.overlay.DataOverlay;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import java.io.ByteArrayInputStream;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
public class ComplexZipConverterTest extends ConverterTestFunctions {
@@ -85,6 +84,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
assertNotNull(al1.getSubmodel());
assertEquals(SubmodelType.DOWNSTREAM_TARGETS, al1.getSubmodel().getType());
assertEquals(s1Model, al1.getSubmodel().getSubmodel().getModel());
+ assertNotNull(al1.getImmediateLink());
Element al2 = model.getElementByElementId("sa2");
assertNull(al2.getSubmodel());
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/MockConverter.java b/converter/src/test/java/lcsb/mapviewer/converter/MockConverter.java
index 3bdba61b86980f3da4e772e32976fede9fad63bc..192a769747572fedd6df7eb6f04d026cbf337027 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/MockConverter.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/MockConverter.java
@@ -1,11 +1,8 @@
package lcsb.mapviewer.converter;
-import java.io.File;
-import java.io.InputStream;
-import java.util.List;
-
import lcsb.mapviewer.common.MimeType;
import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.reaction.Product;
@@ -17,6 +14,10 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Phenotype;
import lcsb.mapviewer.model.map.species.Species;
+import java.io.File;
+import java.io.InputStream;
+import java.util.List;
+
public class MockConverter extends Converter {
protected static Model modelToBeReturned = null;
@@ -82,6 +83,17 @@ public class MockConverter extends Converter {
r3.addReactant(new Reactant(sa7));
r3.addProduct(new Product(ca4));
result.addReaction(r3);
+
+ Species sa8 = new Phenotype("sa8");
+ sa8.setName("sa1");
+ sa8.setNotes("IMMEDIATE_LINK:https://minerva.pages.uni.lu/doc/");
+ result.addElement(sa8);
+
+ Compartment c1 = new Compartment("comp1");
+ c1.setName("main");
+ c1.addElement(sa8);
+ result.addElement(c1);
+
return result;
}
diff --git a/converter/testFiles/complex_model.zip b/converter/testFiles/complex_model.zip
index 2ae7cb3efb7084d6a670d8662a986fcf3f7128de..40cc4e93588a62ae39f833ac8c0c10aff11cfbac 100644
Binary files a/converter/testFiles/complex_model.zip and b/converter/testFiles/complex_model.zip differ
diff --git a/frontend-js/pom.xml b/frontend-js/pom.xml
index 1d13f482779250362688e619ead2ee20d1d2a456..682044db84ea0b1c7939cd3ca7490f533a363a2e 100644
--- a/frontend-js/pom.xml
+++ b/frontend-js/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</parent>
<artifactId>frontend-js</artifactId>
<name>frontend-js</name>
diff --git a/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js b/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
index 68e4d518c999c09233b6f79c6f9204e97250576a..c19b9c9e1231d5f7207622ff130f55a501f8a672 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
@@ -19,6 +19,7 @@ var SearchBioEntityGroup = require('../../map/data/SearchBioEntityGroup');
var logger = require('../../logger');
var Functions = require('../../Functions');
var SearchMapBioEntityGroup = require("../../map/data/SearchMapBioEntityGroup");
+var AbstractDbOverlay = require("../../map/overlay/AbstractDbOverlay");
var QueryType = require("../../map/overlay/AbstractDbOverlay").QueryType;
/**
@@ -72,6 +73,28 @@ function GenericSearchPanel(params) {
}
});
});
+
+ self.getOverlayDb().addListener("onSearch", function (data) {
+ if (data.arg.type === AbstractDbOverlay.QueryType.SEARCH_BY_COORDINATES) {
+ if (data.arg.identifiedElements.length > 0 && data.arg.identifiedElements[0].length > 0) {
+ var identifiedElement = data.arg.identifiedElements[0][0];
+ var model = self.getMap().getSubmapById(identifiedElement.getModelId()).getModel();
+ return model.getByIdentifiedElement(identifiedElement, true).then(function (element) {
+ if (element instanceof Alias) {
+ var link = element.getImmediateLink();
+ if (link != null) {
+ var tab = window.open(link, '_blank');
+ if (tab) {
+ tab.focus();
+ } else {
+ GuiConnector.warn('Browser prevented minerva from opening link: <a href="' + link + '" target="_blank">' + link + '</a>');
+ }
+ }
+ }
+ });
+ }
+ }
+ });
}
GenericSearchPanel.prototype = Object.create(AbstractDbPanel.prototype);
diff --git a/frontend-js/src/main/js/map/data/Alias.js b/frontend-js/src/main/js/map/data/Alias.js
index 9abbc22e119cf957cff57fbca3fa9b458ba91aff..b0bbc8b39c31868f9699d1dbf51d41c6090245ca 100644
--- a/frontend-js/src/main/js/map/data/Alias.js
+++ b/frontend-js/src/main/js/map/data/Alias.js
@@ -56,6 +56,7 @@ Alias.prototype.update = function (javaObject) {
return;
}
this.setDescription(javaObject.getDescription());
+ this.setImmediateLink(javaObject.getImmediateLink());
this.setElementId(javaObject.getElementId());
this.setType(javaObject.getType());
this.setCharge(javaObject.getCharge());
@@ -94,6 +95,7 @@ Alias.prototype.update = function (javaObject) {
return;
}
this.setDescription(javaObject.notes);
+ this.setImmediateLink(javaObject.immediateLink);
this.setElementId(javaObject.elementId);
this.setType(javaObject.type);
this.setCharge(javaObject.charge);
@@ -440,4 +442,21 @@ Alias.prototype.setGlyph = function (glyph) {
this._glyph = glyph;
};
+/**
+ *
+ * @param {string|null} immediateLink
+ */
+Alias.prototype.setImmediateLink = function (immediateLink) {
+ this._immediateLink = immediateLink;
+};
+
+/**
+ *
+ * @returns {string|null}
+ */
+Alias.prototype.getImmediateLink = function () {
+ return this._immediateLink;
+};
+
+
module.exports = Alias;
diff --git a/model-command/pom.xml b/model-command/pom.xml
index 514a83188dea8421d9ac1a5ddc6255533eaa6244..023c9c1f0a0d1b51026c6daaf60d9aa29cd7cf6b 100644
--- a/model-command/pom.xml
+++ b/model-command/pom.xml
@@ -3,7 +3,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</parent>
<artifactId>model-command</artifactId>
<name>Model commands</name>
@@ -16,7 +16,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
@@ -24,7 +24,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<!-- Log4J2-->
diff --git a/model/pom.xml b/model/pom.xml
index f8fc261bbf464cca91d59201a2b72c7b3bd18795..5172f0a04eb9f7c0337ddd6b6b26c9f65647a683 100644
--- a/model/pom.xml
+++ b/model/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</parent>
<artifactId>model</artifactId>
<name>model MapViewer</name>
@@ -15,7 +15,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>commons</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<!-- Java xml serialization -->
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ElementByIdComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ElementByIdComparator.java
new file mode 100644
index 0000000000000000000000000000000000000000..a59f3de08839fd0c05a9b11b5ba0cac761d7a702
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ElementByIdComparator.java
@@ -0,0 +1,18 @@
+package lcsb.mapviewer.model.map.model;
+
+import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.model.map.species.Element;
+
+import java.util.Comparator;
+
+public class ElementByIdComparator implements Comparator<Element> {
+ private final StringComparator comparator = new StringComparator();
+
+ @Override
+ public int compare(final Element o1, final Element o2) {
+ if (comparator.compare(o1.getElementId(), o2.getElementId()) == 0) {
+ return o1.getId() - o2.getId();
+ }
+ return comparator.compare(o1.getElementId(), o2.getElementId());
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
index 0a694e9307b033c47adc5a9a39493d008385082a..b9c683193f3b421dbe0a78938610e3115966f65c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
@@ -1,13 +1,6 @@
package lcsb.mapviewer.model.map.model;
-import java.util.Calendar;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Set;
-
import com.fasterxml.jackson.annotation.JsonIgnore;
-
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.Drawable;
@@ -25,13 +18,18 @@ import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
+import java.util.Calendar;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.List;
+import java.util.Set;
+
/**
* This interface defines functionality that the model container class should
* implement to access data efficiently. It shouldn't be implemented by data
* model.
- *
+ *
* @author Piotr Gawron
- *
*/
public interface Model {
@@ -45,45 +43,38 @@ public interface Model {
/**
* Adds element to the model.
- *
- * @param element
- * element to add
+ *
+ * @param element element to add
*/
void addElement(final Element element);
/**
- *
* @return model width
*/
double getWidth();
/**
* Sets model width.
- *
- * @param width
- * new model width
+ *
+ * @param width new model width
*/
void setWidth(final double width);
/**
* Sets model width.
*
- * @param text
- * new model width
+ * @param text new model width
*/
@JsonIgnore
void setWidth(final String text);
/**
- *
- * @param width
- * new {@link ModelData#width}
+ * @param width new {@link ModelData#width}
*/
@JsonIgnore
void setWidth(final int width);
/**
- *
* @return model height
*/
double getHeight();
@@ -91,24 +82,20 @@ public interface Model {
/**
* Sets model height.
*
- * @param height
- * new model height
+ * @param height new model height
*/
void setHeight(final double height);
/**
* Sets model height.
*
- * @param text
- * new model height
+ * @param text new model height
*/
@JsonIgnore
void setHeight(final String text);
/**
- *
- * @param height
- * new {@link ModelData#height}
+ * @param height new {@link ModelData#height}
*/
@JsonIgnore
void setHeight(final int height);
@@ -121,9 +108,7 @@ public interface Model {
Set<Element> getElements();
/**
- *
- * @param elements
- * new {@link ModelData#elements} collection
+ * @param elements new {@link ModelData#elements} collection
*/
void setElements(final Set<Element> elements);
@@ -131,10 +116,8 @@ public interface Model {
* Returns element with the given element identifier
* ({@link Element#elementId} ).
*
- * @param idElement
- * element identifier
- * @param <T>
- * type of the object to be returned
+ * @param idElement element identifier
+ * @param <T> type of the object to be returned
* @return {@link Element} with the given id
*/
<T extends Element> T getElementByElementId(final String idElement);
@@ -142,8 +125,7 @@ public interface Model {
/**
* Adds reaction to the model.
*
- * @param reaction
- * reaction to add
+ * @param reaction reaction to add
*/
void addReaction(final Reaction reaction);
@@ -162,13 +144,11 @@ public interface Model {
/**
* Adds layer to the model.
*
- * @param layer
- * object to add
+ * @param layer object to add
*/
void addLayer(final Layer layer);
/**
- *
* @return set of layers
*/
Set<Layer> getLayers();
@@ -176,13 +156,11 @@ public interface Model {
/**
* Adds list of elements into model.
*
- * @param elements
- * list of elements
+ * @param elements list of elements
*/
void addElements(final Collection<? extends Element> elements);
/**
- *
* @return short description of the model
*/
String getNotes();
@@ -190,16 +168,14 @@ public interface Model {
/**
* Sets new short description of the model.
*
- * @param notes
- * new short description
+ * @param notes new short description
*/
void setNotes(final String notes);
/**
* Returns reaction with the id given in the parameter.
*
- * @param idReaction
- * reaction identifier ({@link Reaction#idReaction})
+ * @param idReaction reaction identifier ({@link Reaction#idReaction})
* @return reaction with the id given in the parameter
*/
Reaction getReactionByReactionId(final String idReaction);
@@ -207,24 +183,21 @@ public interface Model {
/**
* Adds set of layers to the model.
*
- * @param layers
- * object to add
+ * @param layers object to add
*/
void addLayers(final Collection<Layer> layers);
/**
* Adds {@link ElementGroup} to the model.
*
- * @param elementGroup
- * object to add
+ * @param elementGroup object to add
*/
void addElementGroup(final ElementGroup elementGroup);
/**
* Adds {@link BlockDiagram} to the model.
*
- * @param blockDiagram
- * object to add
+ * @param blockDiagram object to add
*/
void addBlockDiagream(final BlockDiagram blockDiagram);
@@ -235,8 +208,7 @@ public interface Model {
String getIdModel();
/**
- * @param idModel
- * the idModel to set
+ * @param idModel the idModel to set
* @see Model#idModel
*/
void setIdModel(final String idModel);
@@ -248,8 +220,7 @@ public interface Model {
int getTileSize();
/**
- * @param tileSize
- * the tileSize to set
+ * @param tileSize the tileSize to set
* @see ModelData#tileSize
*/
void setTileSize(final int tileSize);
@@ -261,8 +232,7 @@ public interface Model {
int getZoomLevels();
/**
- * @param zoomLevels
- * the zoomLevels to set
+ * @param zoomLevels the zoomLevels to set
* @see ModelData#zoomLevels
*/
void setZoomLevels(final int zoomLevels);
@@ -270,16 +240,14 @@ public interface Model {
/**
* Removes reaction from model.
*
- * @param reaction
- * reaction to remove
+ * @param reaction reaction to remove
*/
void removeReaction(final Reaction reaction);
/**
* Removes {@link Element} from the model.
*
- * @param element
- * element to remove
+ * @param element element to remove
*/
void removeElement(final Element element);
@@ -307,16 +275,14 @@ public interface Model {
/**
* Adds reactions to model.
*
- * @param reactions2
- * list of reaction to add
+ * @param reactions2 list of reaction to add
*/
void addReactions(final List<Reaction> reactions2);
/**
* Returns list of elements with given name.
*
- * @param name
- * name of the element
+ * @param name name of the element
* @return list of elements with given name
*/
List<Element> getElementsByName(final String name);
@@ -324,8 +290,7 @@ public interface Model {
/**
* Returns {@link Element} for given database identifier.
*
- * @param dbId
- * element database identifier ({@link Element#id})
+ * @param dbId element database identifier ({@link Element#id})
* @return {@link Element} for a given id
*/
<T extends Element> T getElementByDbId(final Integer dbId);
@@ -333,8 +298,7 @@ public interface Model {
/**
* Returns {@link Reaction} for given database identifier.
*
- * @param dbId
- * reaction database identifier ({@link Reaction#id})
+ * @param dbId reaction database identifier ({@link Reaction#id})
* @return {@link Reaction} for a given id
*/
Reaction getReactionByDbId(final Integer dbId);
@@ -354,15 +318,12 @@ public interface Model {
List<Element> getElementsSortedBySize();
/**
- *
* @return {@link ModelData#project}
*/
Project getProject();
/**
- *
- * @param project
- * new {@link ModelData#project}
+ * @param project new {@link ModelData#project}
*/
void setProject(final Project project);
@@ -372,7 +333,6 @@ public interface Model {
ModelData getModelData();
/**
- *
* @return {@link ModelData#id}
*/
int getId();
@@ -380,16 +340,14 @@ public interface Model {
/**
* Sets database identifier of the model.
*
- * @param id
- * database identifier
+ * @param id database identifier
*/
void setId(final int id);
/**
* Adds submodel connection.
*
- * @param submodel
- * submodel to add
+ * @param submodel submodel to add
*/
void addSubmodelConnection(final ModelSubmodelConnection submodel);
@@ -410,8 +368,7 @@ public interface Model {
/**
* Sets name of the model.
*
- * @param name
- * name of the model
+ * @param name name of the model
*/
void setName(final String name);
@@ -419,19 +376,17 @@ public interface Model {
* Returns {@link Model submodel} by the {@link ModelData#id database
* identifier} given in the parameter.
*
- * @param idObject
- * the {@link ModelData#id database identifier} that identifies
- * submodel
+ * @param idObject the {@link ModelData#id database identifier} that identifies
+ * submodel
* @return {@link Model submodel} by the {@link ModelData#id database
- * identifier} given in the parameter
+ * identifier} given in the parameter
*/
Model getSubmodelById(final Integer idObject);
/**
* Returns submodel identified by submodel identifier.
*
- * @param identifier
- * identifier of the model
+ * @param identifier identifier of the model
* @return submodel identified by identifier
*/
Model getSubmodelById(final String identifier);
@@ -447,8 +402,7 @@ public interface Model {
/**
* Returns connection to a submodel identified by connection name.
*
- * @param name
- * name of the connection
+ * @param name name of the connection
* @return connection to a submodel identified by connection name
*/
Model getSubmodelByConnectionName(final String name);
@@ -456,8 +410,7 @@ public interface Model {
/**
* Returns connection to a submodel identified by connection identifier.
*
- * @param id
- * id of the connection
+ * @param id id of the connection
* @return connection to a submodel identified by connection identifier
*/
SubmodelConnection getSubmodelConnectionById(final Integer id);
@@ -473,17 +426,16 @@ public interface Model {
* Returns {@link Model submodel} identified by the {@link ModelData#name
* model name}. It returns this 'parent' object when the names matches.
*
- * @param name
- * name of the submodel that should be returned
+ * @param name name of the submodel that should be returned
* @return {@link Model submodel} identified by the {@link ModelData#name
- * model name}
+ * model name}
*/
Model getSubmodelByName(final String name);
/**
* Return list of all {@link BioEntity} in the map. This includes all
* {@link Reaction reactions} and {@link Element elements}.
- *
+ *
* @return list of all {@link BioEntity} in the map
*/
List<BioEntity> getBioEntities();
@@ -532,25 +484,27 @@ public interface Model {
void addMiriamData(final Collection<MiriamData> parseRdfNode);
- public void addAuthor(final Author author);
+ void addAuthor(final Author author);
void addAuthors(final Collection<Author> authorsFromRdf);
- public List<Author> getAuthors();
+ List<Author> getAuthors();
- public Calendar getCreationDate();
+ Calendar getCreationDate();
- public void setCreationDate(final Calendar creationDate);
+ void setCreationDate(final Calendar creationDate);
- public void addModificationDate(final Calendar modificationDate);
+ void addModificationDate(final Calendar modificationDate);
- public List<Calendar> getModificationDates();
+ List<Calendar> getModificationDates();
void addModificationDates(final Collection<Calendar> modificationDatesFromRdf);
- void removeBioEntity(final BioEntity bioEntitiy);
+ void removeBioEntity(final BioEntity bioEntity);
Set<Drawable> getDrawables();
Set<Drawable> getDrawables(boolean onlyVisible);
+
+ Collection<Element> getSortedElements();
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
index 2301de3071c32efbab8e4bdab8b44a885708fb5b..ffa13ff0832c8ee05f30e028ec815bcff95b131e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
@@ -1,18 +1,5 @@
package lcsb.mapviewer.model.map.model;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.BioEntity;
@@ -30,14 +17,25 @@ import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
/**
* This class implements {@link Model} interface. It's is very simple
* implementation containing structures that index the data from
* {@link ModelData} structure and provide access method to this indexed data.
- *
+ *
* @author Piotr Gawron
- *
*/
public class ModelFullIndexed implements Model {
@@ -45,31 +43,31 @@ public class ModelFullIndexed implements Model {
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* Object that map {@link Element#elementId element identifier} into
* {@link Element}.
*/
- private Map<String, Element> elementByElementId = new HashMap<>();
+ private final Map<String, Element> elementByElementId = new HashMap<>();
/**
* Object that map {@link Element#id element database identifier} into
* {@link Element}.
*/
- private Map<Integer, Element> elementByDbId = new HashMap<>();
+ private final Map<Integer, Element> elementByDbId = new HashMap<>();
/**
* Object that map {@link Reaction#idReaction reaction identifier} into
* {@link Reaction}.
*/
- private Map<String, Reaction> reactionByReactionId = new HashMap<>();
+ private final Map<String, Reaction> reactionByReactionId = new HashMap<>();
/**
* Object that map {@link Reaction#id reaction database identifier} into
* {@link Reaction}.
*/
- private Map<Integer, Reaction> reactionByDbId = new HashMap<>();
+ private final Map<Integer, Reaction> reactionByDbId = new HashMap<>();
/**
* {@link ModelData} object containing "raw" data about the model.
@@ -78,9 +76,8 @@ public class ModelFullIndexed implements Model {
/**
* Default constructor.
- *
- * @param model
- * {@link ModelData} object containing "raw" data about the model
+ *
+ * @param model {@link ModelData} object containing "raw" data about the model
*/
public ModelFullIndexed(final ModelData model) {
if (model == null) {
@@ -202,6 +199,7 @@ public class ModelFullIndexed implements Model {
result.add((Compartment) element);
}
}
+ result.sort(new ElementByIdComparator());
return result;
}
@@ -322,6 +320,7 @@ public class ModelFullIndexed implements Model {
result.add((Species) element);
}
}
+ result.sort(new ElementByIdComparator());
return result;
}
@@ -333,6 +332,7 @@ public class ModelFullIndexed implements Model {
result.add((Species) element);
}
}
+ result.sort(new ElementByIdComparator());
return result;
}
@@ -344,6 +344,7 @@ public class ModelFullIndexed implements Model {
result.add((Complex) element);
}
}
+ result.sort(new ElementByIdComparator());
return result;
}
@@ -700,13 +701,13 @@ public class ModelFullIndexed implements Model {
}
@Override
- public void removeBioEntity(final BioEntity bioEntitiy) {
- if (bioEntitiy instanceof Reaction) {
- removeReaction((Reaction) bioEntitiy);
- } else if (bioEntitiy instanceof Element) {
- removeElement((Element) bioEntitiy);
+ public void removeBioEntity(final BioEntity bioEntity) {
+ if (bioEntity instanceof Reaction) {
+ removeReaction((Reaction) bioEntity);
+ } else if (bioEntity instanceof Element) {
+ removeElement((Element) bioEntity);
} else {
- throw new InvalidArgumentException("Unknown class type:" + bioEntitiy);
+ throw new InvalidArgumentException("Unknown class type:" + bioEntity);
}
}
@@ -731,4 +732,11 @@ public class ModelFullIndexed implements Model {
}
return result;
}
+
+ @Override
+ public Collection<Element> getSortedElements() {
+ List<Element> result = new ArrayList<>(getElements());
+ result.sort(new ElementByIdComparator());
+ return result;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
index 8f06c45f1471fd924cae31d1696bad2370b0902f..55a2f2bb686f9a043efd059ab564fd9a565080ce 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
@@ -311,6 +311,11 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
@JsonProperty(value = "references")
private Set<MiriamData> miriamData = new HashSet<>();
+
+ @JsonProperty(value = "immediateLink")
+ @Column(nullable = true)
+ private String immediateLink;
+
/**
* Constructor that creates a copy of the element given in the parameter.
*
@@ -1141,4 +1146,12 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
public long getEntityVersion() {
throw new NotImplementedException();
}
+
+ public void setImmediateLink(final String immediateLink) {
+ this.immediateLink = immediateLink;
+ }
+
+ public String getImmediateLink() {
+ return immediateLink;
+ }
}
\ No newline at end of file
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
index c2fffd96d1f5f1f0deff454fca5711a2bf2f91aa..e868f83a9385a5a1d23a5975a5a5122eade8be26 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
@@ -1,21 +1,5 @@
package lcsb.mapviewer.model.map.model;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
import lcsb.mapviewer.ModelTestFunctions;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -36,6 +20,21 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.StructuralState;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
public class ModelFullIndexedTest extends ModelTestFunctions {
@@ -543,4 +542,24 @@ public class ModelFullIndexedTest extends ModelTestFunctions {
assertTrue(model.getDrawables().contains(state));
}
+ @Test
+ public void testGetSortedElements() {
+ ModelFullIndexed model = new ModelFullIndexed(null);
+
+ Protein protein1 = new GenericProtein("1");
+ Protein protein2 = new GenericProtein("3");
+ Protein protein3 = new GenericProtein("2");
+ Protein protein4 = new GenericProtein("4");
+
+ model.addElement(protein1);
+
+ assertEquals(protein1, model.getSortedElements().iterator().next());
+ model.addElement(protein2);
+ assertEquals(protein1, model.getSortedElements().iterator().next());
+ model.addElement(protein3);
+ assertEquals(protein1, model.getSortedElements().iterator().next());
+ model.addElement(protein4);
+ assertEquals(protein1, model.getSortedElements().iterator().next());
+ }
+
}
diff --git a/pathvisio/pom.xml b/pathvisio/pom.xml
index ff92c53a0d0166baa33ac29f80770913f3c0c877..3549eb953bf6b638aed3aa88b8549427296c7468 100644
--- a/pathvisio/pom.xml
+++ b/pathvisio/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</parent>
<artifactId>pathvisio</artifactId>
<name>Pathvisio plugin</name>
@@ -77,26 +77,26 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
<scope>test</scope>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<!-- Log4J2 -->
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelToGPML.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelToGPML.java
index 33366ea4f4a148ffb604c598c5de7b9fa98d6a79..7efeeb482288e4cb08877a062b244c6a84e65e50 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelToGPML.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelToGPML.java
@@ -1,23 +1,5 @@
package lcsb.mapviewer.wikipathway.xml;
-import java.awt.Color;
-import java.awt.Polygon;
-import java.awt.Shape;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.text.StringEscapeUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.geometry.ColorParser;
@@ -60,12 +42,28 @@ import lcsb.mapviewer.wikipathway.model.GpmlLineType;
import lcsb.mapviewer.wikipathway.model.InteractionMapping;
import lcsb.mapviewer.wikipathway.model.ShapeMapping;
import lcsb.mapviewer.wikipathway.utils.Geo;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.text.StringEscapeUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.awt.Color;
+import java.awt.Polygon;
+import java.awt.Shape;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
/**
* Class contains methods for ModelToGPML conversion.
- *
+ *
* @author Jan Badura
- *
*/
public class ModelToGPML {
@@ -104,15 +102,15 @@ public class ModelToGPML {
/**
* Parser used to convert from/to xml {@link MiriamData} annotations.
*/
- private ReferenceParser referenceParser;
+ private final ReferenceParser referenceParser;
/**
* Parser used to convert from/to xml (in BioPAX format) {@link MiriamData}
* annotations.
*/
- private BiopaxParser biopaxParser;
+ private final BiopaxParser biopaxParser;
- private ColorParser colorParser = new ColorParser();
+ private final ColorParser colorParser = new ColorParser();
public ModelToGPML(final String mapName) {
referenceParser = new ReferenceParser(mapName);
@@ -121,7 +119,7 @@ public class ModelToGPML {
/**
* Returns new unique identifier for the model.
- *
+ *
* @return new unique identifier for the model
*/
private String getNewId() {
@@ -133,9 +131,8 @@ public class ModelToGPML {
* This function returns GPML Species type based on class. If it can not
* recognize one of (Rna,GeneProduct,Protein,Metabolite) it will throw
* {@link InvalidArgumentException}.
- *
- * @param species
- * species for which GPML type will be returned
+ *
+ * @param species species for which GPML type will be returned
* @return String - type
*/
private String getType(final Species species) {
@@ -171,9 +168,8 @@ public class ModelToGPML {
* Since in pathvisio it is impossible to set the size of group rectangle this
* function calculates new rectangle for complex based on contents of this
* complex.
- *
- * @param alias
- * alias for which rectangle border is calculated
+ *
+ * @param alias alias for which rectangle border is calculated
* @return rectangle border for alias
*/
Shape getShape(final Element alias) {
@@ -237,11 +233,9 @@ public class ModelToGPML {
* This function calculates {@link PolylineData} based on start {@link Reactant}
* and end {@link Product}. If end or start points are to far away from their
* rectangles new points are added.
- *
- * @param start
- * reactant from which polyline starts
- * @param end
- * product where polyline ends
+ *
+ * @param start reactant from which polyline starts
+ * @param end product where polyline ends
* @return {@link PolylineData} between start and end
*/
private PolylineData getPolyline(final Reactant start, final Product end) {
@@ -280,11 +274,9 @@ public class ModelToGPML {
/**
* This function calculates PolylineData based on ReactionNode.
- *
- * @param rn
- * reaction node for which polyline is calculated
- * @param mainLine
- * main line to which polyline is attached
+ *
+ * @param rn reaction node for which polyline is calculated
+ * @param mainLine main line to which polyline is attached
* @return polyline for {@link ReactionNode}
*/
PolylineData getPolyline(final ReactionNode rn, final PolylineData mainLine) {
@@ -328,13 +320,12 @@ public class ModelToGPML {
/**
* This function transform Compartments into Shapes (final Oval or Rectangle)
* from PathVisio.
- *
- * @param model
- * model where compartments are placed
+ *
+ * @param model model where compartments are placed
* @return String that encodes all compartments in GPML format
*/
private String getComparments(final Model model) {
- StringBuilder result = new StringBuilder("");
+ StringBuilder result = new StringBuilder();
for (final Compartment compartment : model.getCompartments()) {
result.append(compartmentToXml(compartment));
}
@@ -342,7 +333,7 @@ public class ModelToGPML {
}
String compartmentToXml(final Compartment ca) {
- StringBuilder comparments = new StringBuilder("");
+ StringBuilder comparments = new StringBuilder();
double x = ca.getCenterX();
double y = ca.getCenterY();
double h = ca.getHeight();
@@ -374,23 +365,18 @@ public class ModelToGPML {
* This function creates Interaction for other product, reactant or modifier
* from main reaction. This is support function for getInteractions(Model
* model).
- *
- * @param rn
- * object representing reactant/product/modifier
- * @param anchId
- * identifier of the anchor where it will be connected
- * @param anchors
- * string builder where anchors are stored (it will be modified to add
- * anchor for this element)
- * @param mainLine
- * line used for connecting this element
+ *
+ * @param rn object representing reactant/product/modifier
+ * @param anchId identifier of the anchor where it will be connected
+ * @param anchors string builder where anchors are stored (it will be modified to add
+ * anchor for this element)
+ * @param mainLine line used for connecting this element
* @return string representing connection of this element to reaction
- * @throws ConverterException
- * thrown when there is a problem with conversion
+ * @throws ConverterException thrown when there is a problem with conversion
*/
private String getInteractionForAnchor(final ReactionNode rn, final String anchId, final StringBuilder anchors, final PolylineData mainLine)
throws ConverterException {
- StringBuilder interaction = new StringBuilder("");
+ StringBuilder interaction = new StringBuilder();
PolylineData line = getPolyline(rn, mainLine);
Point2D ps = line.getStartPoint();
@@ -486,16 +472,14 @@ public class ModelToGPML {
/**
* This function encode Species into DataNodes from GPML format. Empty complexes
* are also transformed into DataNodes.
- *
- * @param model
- * model where aliases are placed
+ *
+ * @param model model where aliases are placed
* @return string representing {@link lcsb.mapviewer.wikipathway.model.DataNode
- * data nodes}
- * @throws ConverterException
- * thrown when there is a problem with conversion
+ * data nodes}
+ * @throws ConverterException thrown when there is a problem with conversion
*/
protected String getDataNodes(final Model model) throws ConverterException {
- StringBuilder dataNodes = new StringBuilder("");
+ StringBuilder dataNodes = new StringBuilder();
for (final Species species : model.getNotComplexSpeciesList()) {
if (!(species instanceof Complex) && !(species instanceof Degraded)) {
@@ -657,13 +641,12 @@ public class ModelToGPML {
/**
* This function encode ComplexAliases into Groups from GPML format.
- *
- * @param model
- * model where aliases are placed
+ *
+ * @param model model where aliases are placed
* @return string representing groups in GPML format
*/
protected String getGroups(final Model model) {
- StringBuilder groups = new StringBuilder("");
+ StringBuilder groups = new StringBuilder();
for (final Complex complex : model.getComplexList()) {
if (complex.getElements().size() > 0) {
@@ -685,15 +668,13 @@ public class ModelToGPML {
/**
* This function encode Reactions into Interactions from GPML format.
- *
- * @param model
- * model where reactions are placed
+ *
+ * @param model model where reactions are placed
* @return string with interactions in GPML format
- * @throws ConverterException
- * thrown when there is a problem with conversion
+ * @throws ConverterException thrown when there is a problem with conversion
*/
protected String getInteractions(final Model model) throws ConverterException {
- StringBuilder interactions = new StringBuilder("");
+ StringBuilder interactions = new StringBuilder();
for (final Reaction reaction : model.getReactions()) {
String reactionArrowHead = InteractionMapping.getGpmlInteractionTypeForMinervaReactionClass(reaction.getClass())
@@ -701,8 +682,8 @@ public class ModelToGPML {
String lineStyle = GpmlLineType.getByLineType(reaction.getLine().getType()).getGpmlString();
- StringBuilder anchors = new StringBuilder("");
- StringBuilder tmp = new StringBuilder("");
+ StringBuilder anchors = new StringBuilder();
+ StringBuilder tmp = new StringBuilder();
interactions.append(" <Interaction GraphId=\"" + reaction.getIdReaction() + "\">\n");
if (reaction.getNotes() != null) {
@@ -767,12 +748,12 @@ public class ModelToGPML {
tmp.append(getInteractionForAnchor(modifier, getNewId(), anchors, line));
}
- interactions.append(anchors.toString());
+ interactions.append(anchors);
interactions.append(" </Graphics>\n");
interactions.append(
referenceParser.toXml(reaction.getMiriamData(), new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, reaction)));
interactions.append(" </Interaction>\n");
- interactions.append(tmp.toString());
+ interactions.append(tmp);
}
return interactions.toString();
@@ -780,15 +761,13 @@ public class ModelToGPML {
/**
* This function returns Model in GPML format.
- *
- * @param model
- * model to transform
+ *
+ * @param model model to transform
* @return string in GPML format representing model
- * @throws ConverterException
- * thrown when there is a problem with conversion
+ * @throws ConverterException thrown when there is a problem with conversion
*/
public String getGPML(final Model model) throws ConverterException {
- StringBuilder gpml = new StringBuilder("");
+ StringBuilder gpml = new StringBuilder();
gpml.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
gpml.append("<Pathway xmlns=\"http://pathvisio.org/GPML/2013a\"");
if (model.getName() != null) {
@@ -845,7 +824,7 @@ public class ModelToGPML {
private String getStates(final Model model) throws ConverterException {
StringBuilder result = new StringBuilder();
- for (final Element element : model.getElements()) {
+ for (final Element element : model.getSortedElements()) {
if (element instanceof SpeciesWithModificationResidue) {
for (final ModificationResidue mr : ((SpeciesWithModificationResidue) element).getModificationResidues()) {
result.append(modifictionResidueToState(mr));
@@ -860,7 +839,7 @@ public class ModelToGPML {
}
protected String getShapes(final Model model) throws ConverterException {
- StringBuilder result = new StringBuilder("");
+ StringBuilder result = new StringBuilder();
result.append(getComparments(model));
for (final Species species : model.getNotComplexSpeciesList()) {
diff --git a/persist/pom.xml b/persist/pom.xml
index d648423f8fc46eb16eca081ad11cf5978918b9ea..24678fa8391ffd3ab67ce57fb40b26d08961d182 100644
--- a/persist/pom.xml
+++ b/persist/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</parent>
<artifactId>persist</artifactId>
@@ -26,7 +26,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<!-- Hibernate -->
diff --git a/persist/src/main/resources/db/migration/hsql/18.0.8/V18.0.8.20241213__remove_refresh_jobs.sql b/persist/src/main/resources/db/migration/hsql/18.1.0/V18.0.8.20241213__remove_refresh_jobs.sql
similarity index 100%
rename from persist/src/main/resources/db/migration/hsql/18.0.8/V18.0.8.20241213__remove_refresh_jobs.sql
rename to persist/src/main/resources/db/migration/hsql/18.1.0/V18.0.8.20241213__remove_refresh_jobs.sql
diff --git a/persist/src/main/resources/db/migration/hsql/18.0.8/V18.0.8.20241230.2__set_proper_pathway_and_compartment.sql b/persist/src/main/resources/db/migration/hsql/18.1.0/V18.0.8.20241230.2__set_proper_pathway_and_compartment.sql
similarity index 100%
rename from persist/src/main/resources/db/migration/hsql/18.0.8/V18.0.8.20241230.2__set_proper_pathway_and_compartment.sql
rename to persist/src/main/resources/db/migration/hsql/18.1.0/V18.0.8.20241230.2__set_proper_pathway_and_compartment.sql
diff --git a/persist/src/main/resources/db/migration/hsql/18.0.8/V18.0.8.20241230__add_pathway_to_element.sql b/persist/src/main/resources/db/migration/hsql/18.1.0/V18.0.8.20241230__add_pathway_to_element.sql
similarity index 100%
rename from persist/src/main/resources/db/migration/hsql/18.0.8/V18.0.8.20241230__add_pathway_to_element.sql
rename to persist/src/main/resources/db/migration/hsql/18.1.0/V18.0.8.20241230__add_pathway_to_element.sql
diff --git a/persist/src/main/resources/db/migration/hsql/18.0.8/V18.0.8.20250110__set_proper_pathway_and_compartment.sql b/persist/src/main/resources/db/migration/hsql/18.1.0/V18.0.8.20250110__set_proper_pathway_and_compartment.sql
similarity index 100%
rename from persist/src/main/resources/db/migration/hsql/18.0.8/V18.0.8.20250110__set_proper_pathway_and_compartment.sql
rename to persist/src/main/resources/db/migration/hsql/18.1.0/V18.0.8.20250110__set_proper_pathway_and_compartment.sql
diff --git a/persist/src/main/resources/db/migration/hsql/18.1.0/V18.1.0.20250122__add_immediate_link.sql b/persist/src/main/resources/db/migration/hsql/18.1.0/V18.1.0.20250122__add_immediate_link.sql
new file mode 100644
index 0000000000000000000000000000000000000000..0e3d63ad1584a5f34dd777ed9e0411ff9569c7de
--- /dev/null
+++ b/persist/src/main/resources/db/migration/hsql/18.1.0/V18.1.0.20250122__add_immediate_link.sql
@@ -0,0 +1,2 @@
+alter table element_table
+ add column immediate_link character varying(1024);
diff --git a/persist/src/main/resources/db/migration/postgres/18.0.8/V18.0.8.20241213__remove_refresh_jobs.sql b/persist/src/main/resources/db/migration/postgres/18.1.0/V18.0.8.20241213__remove_refresh_jobs.sql
similarity index 100%
rename from persist/src/main/resources/db/migration/postgres/18.0.8/V18.0.8.20241213__remove_refresh_jobs.sql
rename to persist/src/main/resources/db/migration/postgres/18.1.0/V18.0.8.20241213__remove_refresh_jobs.sql
diff --git a/persist/src/main/resources/db/migration/postgres/18.0.8/V18.0.8.20241230.2__set_proper_pathway_and_compartment.sql b/persist/src/main/resources/db/migration/postgres/18.1.0/V18.0.8.20241230.2__set_proper_pathway_and_compartment.sql
similarity index 100%
rename from persist/src/main/resources/db/migration/postgres/18.0.8/V18.0.8.20241230.2__set_proper_pathway_and_compartment.sql
rename to persist/src/main/resources/db/migration/postgres/18.1.0/V18.0.8.20241230.2__set_proper_pathway_and_compartment.sql
diff --git a/persist/src/main/resources/db/migration/postgres/18.0.8/V18.0.8.20241230__add_pathway_to_element.sql b/persist/src/main/resources/db/migration/postgres/18.1.0/V18.0.8.20241230__add_pathway_to_element.sql
similarity index 100%
rename from persist/src/main/resources/db/migration/postgres/18.0.8/V18.0.8.20241230__add_pathway_to_element.sql
rename to persist/src/main/resources/db/migration/postgres/18.1.0/V18.0.8.20241230__add_pathway_to_element.sql
diff --git a/persist/src/main/resources/db/migration/postgres/18.0.8/V18.0.8.20250110__set_proper_pathway_and_compartment.sql b/persist/src/main/resources/db/migration/postgres/18.1.0/V18.0.8.20250110__set_proper_pathway_and_compartment.sql
similarity index 100%
rename from persist/src/main/resources/db/migration/postgres/18.0.8/V18.0.8.20250110__set_proper_pathway_and_compartment.sql
rename to persist/src/main/resources/db/migration/postgres/18.1.0/V18.0.8.20250110__set_proper_pathway_and_compartment.sql
diff --git a/persist/src/main/resources/db/migration/postgres/18.1.0/V18.1.0.20250122__add_immediate_link.sql b/persist/src/main/resources/db/migration/postgres/18.1.0/V18.1.0.20250122__add_immediate_link.sql
new file mode 100644
index 0000000000000000000000000000000000000000..0e3d63ad1584a5f34dd777ed9e0411ff9569c7de
--- /dev/null
+++ b/persist/src/main/resources/db/migration/postgres/18.1.0/V18.1.0.20250122__add_immediate_link.sql
@@ -0,0 +1,2 @@
+alter table element_table
+ add column immediate_link character varying(1024);
diff --git a/pom.xml b/pom.xml
index a791e54e985f0bd4e321f612cea65907ce21102b..60799bd1b535b763eb2c753bb0f8d60de59a4afc 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,7 @@
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
<packaging>pom</packaging>
<name>parent MapViewer</name>
diff --git a/rest-api/pom.xml b/rest-api/pom.xml
index 2754569a70e17568408aa826e99df2a00ab08c01..35dfb9cb44e0d0fb73e264514a0054c9f097d2b4 100644
--- a/rest-api/pom.xml
+++ b/rest-api/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</parent>
<artifactId>rest-api</artifactId>
<name>rest-api</name>
@@ -19,19 +19,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>service</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>pathvisio</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioentities/elements/ElementsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioentities/elements/ElementsController.java
index fd7befb8ed9ad0ba1b0b9228737b580ff2ee06c3..a7df4e02c53485fcb641729d271459f81df82006 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioentities/elements/ElementsController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioentities/elements/ElementsController.java
@@ -1,23 +1,5 @@
package lcsb.mapviewer.api.projects.models.bioentities.elements;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.security.access.prepost.PreAuthorize;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
-
import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -49,6 +31,23 @@ import lcsb.mapviewer.persist.dao.map.species.ElementProperty;
import lcsb.mapviewer.services.ObjectNotFoundException;
import lcsb.mapviewer.services.interfaces.IElementService;
import lcsb.mapviewer.services.interfaces.IModelService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
@RestController
@RequestMapping(
@@ -58,8 +57,8 @@ import lcsb.mapviewer.services.interfaces.IModelService;
produces = MediaType.APPLICATION_JSON_VALUE)
public class ElementsController extends BaseController {
- private IElementService elementService;
- private IModelService modelService;
+ private final IElementService elementService;
+ private final IModelService modelService;
@Autowired
public ElementsController(final IElementService elementService, final IModelService modelService) {
@@ -68,7 +67,7 @@ public class ElementsController extends BaseController {
}
@PreAuthorize("hasAnyAuthority('IS_ADMIN', 'READ_PROJECT:' + #projectId)")
- @RequestMapping(value = "/", method = { RequestMethod.GET, RequestMethod.POST })
+ @RequestMapping(value = "/", method = {RequestMethod.GET, RequestMethod.POST})
public List<Map<String, Object>> getElements(
final @PathVariable(value = "projectId") String projectId,
final @PathVariable(value = "modelId") String modelId,
@@ -183,6 +182,9 @@ public class ElementsController extends BaseController {
value = ((Species) element).isBoundaryCondition();
}
break;
+ case "immediatelink":
+ value = element.getImmediateLink();
+ break;
case "constant":
if (element instanceof Species) {
value = ((Species) element).isConstant();
@@ -389,6 +391,7 @@ public class ElementsController extends BaseController {
result.add("other");
result.add("initialConcentration");
result.add("boundaryCondition");
+ result.add("immediateLink");
result.add("constant");
result.add("hypothetical");
result.add("activity");
diff --git a/service/pom.xml b/service/pom.xml
index 3b7309a0d02d1b6f1a48ecb782b211eb2f59e46e..624ca59f523a1215cadee2828f0694ed40ef3423 100644
--- a/service/pom.xml
+++ b/service/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</parent>
<artifactId>service</artifactId>
@@ -19,7 +19,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<!-- dependency from the MapViewer dao -->
@@ -27,47 +27,47 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>annotation</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<!-- dependency from the MapViewer cell designer parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<!-- dependency from the MapViewer SBGN-ML parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-SBGNML</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<!-- dependency from the MapViewer graphics converter -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<!-- dependency from the SBML parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-sbml</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<!-- Log4J2 -->
diff --git a/web/pom.xml b/web/pom.xml
index 6f85acdefcfbc021ce9f1020fe8f3d8dfaf40a04..503ad0060d576cf033c06312e0b8072bbf92179c 100644
--- a/web/pom.xml
+++ b/web/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</parent>
<artifactId>web</artifactId>
<packaging>jar</packaging>
@@ -36,19 +36,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>service</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>rest-api</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>frontend-js</artifactId>
- <version>18.0.8</version>
+ <version>18.1.0</version>
</dependency>
<dependency>
diff --git a/web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java
index bb6f173dce3245cdd6fe3e0997718380a1426013..ae2b7b6c7a0f8bd4864a2b12b152e7cb36842366 100644
--- a/web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java
@@ -1,51 +1,7 @@
package lcsb.mapviewer.web;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
-import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
-import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.patch;
-import static org.springframework.restdocs.payload.PayloadDocumentation.fieldWithPath;
-import static org.springframework.restdocs.payload.PayloadDocumentation.requestFields;
-import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
-import static org.springframework.restdocs.payload.PayloadDocumentation.subsectionWithPath;
-import static org.springframework.restdocs.request.RequestDocumentation.parameterWithName;
-import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
-import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.commons.lang3.StringUtils;
-import org.apache.http.client.entity.UrlEncodedFormEntity;
-import org.apache.http.message.BasicNameValuePair;
-import org.apache.http.util.EntityUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.mock.web.MockHttpSession;
-import org.springframework.restdocs.payload.FieldDescriptor;
-import org.springframework.restdocs.payload.JsonFieldType;
-import org.springframework.restdocs.payload.ResponseFieldsSnippet;
-import org.springframework.restdocs.request.PathParametersSnippet;
-import org.springframework.restdocs.request.RequestParametersSnippet;
-import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
-import org.springframework.test.web.servlet.MvcResult;
-import org.springframework.test.web.servlet.RequestBuilder;
-
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
-
import lcsb.mapviewer.api.projects.models.bioentities.elements.ElementsController;
import lcsb.mapviewer.api.projects.models.bioentities.reactions.ReactionsController;
import lcsb.mapviewer.common.Configuration;
@@ -66,6 +22,49 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
import lcsb.mapviewer.modelutils.serializer.model.map.ElementIdentifierType;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.IUserService;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.http.client.entity.UrlEncodedFormEntity;
+import org.apache.http.message.BasicNameValuePair;
+import org.apache.http.util.EntityUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.mock.web.MockHttpSession;
+import org.springframework.restdocs.payload.FieldDescriptor;
+import org.springframework.restdocs.payload.JsonFieldType;
+import org.springframework.restdocs.payload.ResponseFieldsSnippet;
+import org.springframework.restdocs.request.PathParametersSnippet;
+import org.springframework.restdocs.request.RequestParametersSnippet;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.test.web.servlet.MvcResult;
+import org.springframework.test.web.servlet.RequestBuilder;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
+import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
+import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.patch;
+import static org.springframework.restdocs.payload.PayloadDocumentation.fieldWithPath;
+import static org.springframework.restdocs.payload.PayloadDocumentation.requestFields;
+import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
+import static org.springframework.restdocs.payload.PayloadDocumentation.subsectionWithPath;
+import static org.springframework.restdocs.request.RequestDocumentation.parameterWithName;
+import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
+import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
@RunWith(SpringJUnit4ClassRunner.class)
public class MapControllerIntegrationTest extends ControllerIntegrationTest {
@@ -116,6 +115,10 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
.description("name")
.type("string")
.optional(),
+ fieldWithPath("[].immediateLink")
+ .description("link that should be opened immediately when element is clicked on the map")
+ .type(JsonFieldType.STRING)
+ .optional(),
fieldWithPath("[].modelId")
.description("map identifier")
.type("number")
@@ -514,7 +517,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
RequestBuilder request = get("/minerva/api/projects/*/models/{mapId}/bioEntities:search?coordinates=104.36,182.81",
map.getId())
- .session(session);
+ .session(session);
mockMvc.perform(request)
.andExpect(status().isNotFound());
@@ -810,7 +813,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}:downloadImage?"
+ "handlerClass=" + PngImageGenerator.class.getCanonicalName(), TEST_PROJECT, map.getId())
- .session(session);
+ .session(session);
mockMvc.perform(request)
.andDo(document("projects/project_maps/download_image_simple",
@@ -860,11 +863,11 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
DataOverlay overlay = createOverlay(project, admin, "name\tvalue\nGSTA4\t1");
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}:downloadModel?"
- + "handlerClass={handlerClass}"
- + "&overlayIds={overlayId}", TEST_PROJECT, submap.getId(),
+ + "handlerClass={handlerClass}"
+ + "&overlayIds={overlayId}", TEST_PROJECT, submap.getId(),
CellDesignerXmlParser.class.getCanonicalName(),
overlay.getId())
- .session(session);
+ .session(session);
mockMvc.perform(request)
.andExpect(status().is2xxSuccessful());
@@ -874,7 +877,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
public void testDownloadSubmapModelWithPost() throws Exception {
ModelData submap = getSubmap();
- String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
+ String body = EntityUtils.toString(new UrlEncodedFormEntity(Collections.singletonList(
new BasicNameValuePair("handlerClass", CellDesignerXmlParser.class.getCanonicalName()))));
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}:downloadModel", TEST_PROJECT, submap.getId())
@@ -893,12 +896,12 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN));
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}:downloadImage?"
- + "handlerClass={handlerClass}&overlayIds={ids}",
+ + "handlerClass={handlerClass}&overlayIds={ids}",
TEST_PROJECT,
map.getId(),
PngImageGenerator.class.getCanonicalName(),
overlay.getId())
- .session(session);
+ .session(session);
mockMvc.perform(request)
.andDo(document("projects/project_maps/download_image_data_overlay",
@@ -913,14 +916,14 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
RequestBuilder elementRequest = get("/minerva/api/projects/{projectId}/models/*/bioEntities/elements/",
TEST_PROJECT)
- .session(session);
+ .session(session);
String content = mockMvc.perform(elementRequest).andReturn().getResponse().getContentAsString();
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}:downloadImage?"
- + "handlerClass=" + PdfImageGenerator.class.getCanonicalName()
- + "&polygonString=10000,10000;10001,10000;10000,10001",
+ + "handlerClass=" + PdfImageGenerator.class.getCanonicalName()
+ + "&polygonString=10000,10000;10001,10000;10000,10001",
TEST_PROJECT, map.getId())
- .session(session);
+ .session(session);
mockMvc.perform(request)
.andExpect(status().is2xxSuccessful());
@@ -946,7 +949,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
RequestBuilder request = get("/minerva/api/projects/{projectId}/models/{mapId}:downloadImage?"
+ "handlerClass=" + PdfImageGenerator.class.getCanonicalName()
+ "&polygonString=0,0;100,0;100,100;0,100", TEST_PROJECT, map.getId())
- .session(session);
+ .session(session);
mockMvc.perform(request)
.andDo(document("projects/project_maps/download_image_polygon",
@@ -978,8 +981,8 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
RequestBuilder request = get("/minerva/api/projects/*/models/" + map.getId() + ":downloadImage?"
+ "handlerClass=" + PngImageGenerator.class.getCanonicalName())
- .contentType(MediaType.APPLICATION_FORM_URLENCODED)
- .session(session);
+ .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .session(session);
mockMvc.perform(request)
.andExpect(status().isNotFound());
@@ -992,7 +995,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
RequestBuilder request = get(
"/minerva/api/projects/" + TEST_PROJECT + "/models/" + map.getId() + ":downloadModelWarnings?"
+ "handlerClass=" + SbgnmlXmlConverter.class.getCanonicalName())
- .session(session);
+ .session(session);
String response = mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
@@ -1002,7 +1005,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
});
int elements = ((List<?>) result.get("data")).size();
- assertTrue(elements == 0);
+ assertEquals(0, elements);
}
@Test
@@ -1011,8 +1014,8 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
RequestBuilder request = get("/minerva/api/projects/" + TEST_PROJECT + "/models/" + map.getId() + ":downloadModel?"
+ "handlerClass=" + CellDesignerXmlParser.class.getCanonicalName())
- .accept(MimeType.ZIP.getTextRepresentation() + ";q=0.8")
- .session(session);
+ .accept(MimeType.ZIP.getTextRepresentation() + ";q=0.8")
+ .session(session);
MvcResult result = mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
@@ -1027,8 +1030,8 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
RequestBuilder request = get("/minerva/api/projects/*/models/" + map.getId() + ":downloadModel?"
+ "handlerClass=" + CellDesignerXmlParser.class.getCanonicalName())
- .contentType(MediaType.APPLICATION_FORM_URLENCODED)
- .session(session);
+ .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .session(session);
mockMvc.perform(request)
.andExpect(status().isNotFound());
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java b/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
index 62ad21b1637c23c0a76ceb99b37f52ae8350a251..13293284c354ec1fc344b6bc9ffeb45cc6b82ea9 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
@@ -232,12 +232,16 @@ public class NewApiDocs {
private List<FieldDescriptor> getBioEntitySpecificFields(final String prefix) {
final List<FieldDescriptor> result = new ArrayList<>();
+ result.add(
+ fieldWithPath(prefix + "immediateLink")
+ .description("link that should be opened immediately when element is clicked on the map")
+ .optional()
+ .type(JsonFieldType.STRING));
result.add(
fieldWithPath(prefix + "id")
.description("unique bioEntity identifier")
.type(JsonFieldType.NUMBER));
result.add(
-
fieldWithPath(prefix + "stringType")
.description("type of the bioEntity")
.type(JsonFieldType.STRING));