diff --git a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
index eefd44b8791b4c3e4a4142c891115de78e94cb28..7c8a5614e878b04ce342d07652280202eb2475bb 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
@@ -3,7 +3,6 @@ package lcsb.mapviewer.common;
import java.awt.Color;
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
-import java.io.FileInputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
@@ -414,7 +413,8 @@ final public class XmlParser {
TransformerFactory factory = TransformerFactory.newInstance();
// Use the factory to create a template containing the xsl file
- Templates template = factory.newTemplates(new StreamSource(ClassLoader.getSystemResourceAsStream("to_lowercase.xsl")));
+ Templates template = factory
+ .newTemplates(new StreamSource(ClassLoader.getSystemResourceAsStream("to_lowercase.xsl")));
// Use the template to create a transformer
Transformer xformer = template.newTransformer();
@@ -428,7 +428,7 @@ final public class XmlParser {
// to the output file
xformer.transform(source, result);
return output.toString("UTF-8");
- } catch (Exception e ) {
+ } catch (Exception e) {
throw new InvalidStateException("Problem with translating input xml", e);
}
}
diff --git a/converter-CellDesigner/pom.xml b/converter-CellDesigner/pom.xml
index 1a8111a55708a201ce456361729bda161fdc808e..641ecc14e374496def655b697e6db0f339b751ee 100644
--- a/converter-CellDesigner/pom.xml
+++ b/converter-CellDesigner/pom.xml
@@ -26,12 +26,6 @@
<version>1.0</version>
</dependency>
- <dependency>
- <groupId>com.googlecode.ez-vcard</groupId>
- <artifactId>ez-vcard</artifactId>
- <version>${ez-vcard.version}</version>
- </dependency>
-
<!-- Log4J -->
<dependency>
<groupId>log4j</groupId>
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 2c0d2e35236f4f13838a0df6097a7f928bf160c0..e25ffdbe72a718117c4db66db0ccd1d3de1a7a94 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
@@ -362,6 +362,9 @@ public class CellDesignerXmlParser extends Converter {
} else if (node.getNodeName().equalsIgnoreCase("rdf:RDF")) {
XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
model.addMiriamData(xmlAnnotationParser.parseRdfNode(node));
+ model.addAuthors(xmlAnnotationParser.getAuthorsFromRdf(node));
+ model.setCreationDate(xmlAnnotationParser.getCreateDateFromRdf(node));
+ model.addModificationDates(xmlAnnotationParser.getModificationDatesFromRdf(node));
} else {
throw new InvalidXmlSchemaException("Unknown element of annotation: " + node.getNodeName());
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
index 4913b32ddb347dea70b0dbc49f41708767ae3f4f..3bd124a15a06835e66a5142163be4c28242fbd61 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
@@ -104,6 +104,21 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
}
}
+ @Test
+ public void testParseVcard() throws Exception {
+ try {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/model_with_vcard.xml"));
+ assertEquals("There is one author defined", 1, model.getAuthors().size());
+ assertNotNull("Author data cannot be null", model.getAuthors().get(0));
+ assertEquals("Modification date is not defined", 1, model.getModificationDates().size());
+ assertNotNull("Creation date is not defined", model.getCreationDate());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testOpenFromInvalidFile() throws Exception {
try {
diff --git a/converter-CellDesigner/testFiles/model_with_vcard.xml b/converter-CellDesigner/testFiles/model_with_vcard.xml
new file mode 100644
index 0000000000000000000000000000000000000000..95201e411c46367fccf146f4fca6dc1e64042d5a
--- /dev/null
+++ b/converter-CellDesigner/testFiles/model_with_vcard.xml
@@ -0,0 +1,75 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases/>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins/>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#untitled">
+<dc:creator>
+<rdf:Bag>
+<rdf:li rdf:parseType="Resource">
+<vCard:N rdf:parseType="Resource">
+<vCard:Family>Gawron</vCard:Family>
+<vCard:Given>Piotr</vCard:Given>
+</vCard:N>
+<vCard:EMAIL>piotr.gawron@uni.lu</vCard:EMAIL>
+<vCard:ORG rdf:parseType="Resource">
+<vCard:Orgname>LCSB</vCard:Orgname>
+</vCard:ORG>
+</rdf:li>
+</rdf:Bag>
+</dc:creator>
+<dcterms:created rdf:parseType="Resource">
+<dcterms:W3CDTF>2019-03-26T11:12:52Z</dcterms:W3CDTF>
+</dcterms:created>
+<dcterms:modified rdf:parseType="Resource">
+<dcterms:W3CDTF>2019-03-26T11:12:56Z</dcterms:W3CDTF>
+</dcterms:modified>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+</model>
+</sbml>
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java b/converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java
index e1c24e81fa9ef5484b365ccbdb18c15e1ab91492..95b971649f01b8a3c7c15f3c282cae65f58df57c 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java
@@ -1,11 +1,17 @@
package lcsb.mapviewer.converter.annotation;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Calendar;
import java.util.Collection;
+import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.apache.log4j.Logger;
+import org.w3c.dom.DOMException;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
@@ -16,6 +22,7 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.Author;
/**
* This class allow to parse xml nodes responsible for species annotations in
@@ -68,7 +75,7 @@ public class XmlAnnotationParser {
* @throws InvalidXmlSchemaException
* thrown when there is a problem with xml
*/
- public Set<MiriamData> parseRdfNode(NodeList root) throws InvalidXmlSchemaException {
+ private Set<MiriamData> parseRdfNode(NodeList root) throws InvalidXmlSchemaException {
Node rdf = XmlParser.getNode("rdf:RDF", root);
return parseRdfNode(rdf);
}
@@ -95,6 +102,9 @@ public class XmlAnnotationParser {
MiriamRelationType relationType = MiriamRelationType.getTypeByStringRepresentation(relationTypeString);
if (relationType != null) {
miriamDataSet.addAll(parseMiriamNode(node));
+ } else if (relationTypeString.equals("dc:creator")) {
+ } else if (relationTypeString.equals("dcterms:created")) {
+ } else if (relationTypeString.equals("dcterms:modified")) {
} else {
logger.warn("RDF relation type is not supported: " + relationTypeString);
}
@@ -109,6 +119,112 @@ public class XmlAnnotationParser {
return miriamDataSet;
}
+ public Set<Author> getAuthorsFromRdf(Node rdf) throws InvalidXmlSchemaException {
+ Set<Author> authors = new HashSet<>();
+
+ if (rdf != null) {
+ Node description = XmlParser.getNode("rdf:Description", rdf.getChildNodes());
+ if (description != null) {
+ NodeList list = description.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ String relationTypeString = node.getNodeName();
+ if (relationTypeString.equals("dc:creator")) {
+ Node bag = XmlParser.getNode("rdf:Bag", node.getChildNodes());
+ if (bag == null) {
+ throw new InvalidXmlSchemaException("No rdf:Bag node found");
+ }
+ list = bag.getChildNodes();
+ List<Node> nodes = XmlParser.getNodes("rdf:li", list);
+ for (Node li : nodes) {
+ Author author = parseAuthor(li);
+ authors.add(author);
+ }
+ }
+ }
+ }
+ } else {
+ throw new InvalidXmlSchemaException("rdf:Description node not found");
+ }
+ } else {
+ throw new InvalidXmlSchemaException("rdf:Rdf node not found");
+ }
+ return authors;
+ }
+
+ public Calendar getCreateDateFromRdf(Node rdf) throws InvalidXmlSchemaException {
+ if (rdf != null) {
+ Node description = XmlParser.getNode("rdf:Description", rdf.getChildNodes());
+ if (description != null) {
+ NodeList list = description.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ String relationTypeString = node.getNodeName();
+ if (relationTypeString.equals("dcterms:created")) {
+ Node dateNode = XmlParser.getNode("dcterms:W3CDTF", node);
+ if (dateNode != null) {
+ return getDateFromNode(dateNode);
+ }
+ }
+ }
+ }
+ } else {
+ throw new InvalidXmlSchemaException("rdf:Description node not found");
+ }
+ } else {
+ throw new InvalidXmlSchemaException("rdf:Rdf node not found");
+ }
+ return null;
+ }
+
+ private Calendar getDateFromNode(Node dateNode) {
+ SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd hh:mm:ss");
+ try {
+ Date date = dateFormat.parse(dateNode.getTextContent().replaceAll("[T]", " "));
+ Calendar result = Calendar.getInstance();
+ result.setTime(date);
+ return result;
+ } catch (ParseException | DOMException e) {
+ logger.warn("Problem with parsing date: ", e);
+ }
+ return null;
+ }
+
+ private Author parseAuthor(Node li) {
+ NodeList list = li.getChildNodes();
+ String firstName = null;
+ String lastName = null;
+ String organization = null;
+ String email = null;
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equals("vCard:EMAIL")) {
+ email = node.getNodeValue();
+ } else if (node.getNodeName().equals("vCard:ORG")) {
+ organization = node.getNodeValue();
+ } else if (node.getNodeName().equals("vCard:N")) {
+ Node familyNode = XmlParser.getNode("vCard:Family", node);
+ if (familyNode != null) {
+ lastName = familyNode.getNodeValue();
+ }
+ Node givenNode = XmlParser.getNode("vCard:Given", node);
+ if (givenNode != null) {
+ firstName = givenNode.getNodeValue();
+ }
+ } else {
+ logger.warn("Unknown data node in vcard: " + node.getNodeName());
+ }
+ }
+ }
+ Author author = new Author(firstName, lastName);
+ author.setEmail(email);
+ author.setOrganisation(organization);
+ return author;
+ }
+
/**
* This method converts a xml node into MiriamData object (annotation of a
* species).
@@ -199,4 +315,32 @@ public class XmlAnnotationParser {
return result.toString();
}
+ public List<Calendar> getModificationDatesFromRdf(Node rdf) throws InvalidXmlSchemaException {
+ List<Calendar> result = new ArrayList<>();
+
+ if (rdf != null) {
+ Node description = XmlParser.getNode("rdf:Description", rdf.getChildNodes());
+ if (description != null) {
+ NodeList list = description.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ String relationTypeString = node.getNodeName();
+ if (relationTypeString.equals("dcterms:modified")) {
+ for (Node dateNode : XmlParser.getNodes("dcterms:W3CDTF", node.getChildNodes())) {
+ result.add(getDateFromNode(dateNode));
+ }
+ }
+ }
+ }
+ } else {
+ throw new InvalidXmlSchemaException("rdf:Description node not found");
+ }
+ } else {
+ throw new InvalidXmlSchemaException("rdf:Rdf node not found");
+ }
+
+ return result;
+ }
+
}
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 74557fa936c06412b1778c53f8116d26839ef4d7..ff797ab9e935d907175f2bdfb61b7f81848fa744 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
@@ -549,7 +549,9 @@ public interface Model {
void addMiriamData(Collection<MiriamData> parseRdfNode);
public void addAuthor(Author author);
-
+
+ void addAuthors(Set<Author> authorsFromRdf);
+
public List<Author> getAuthors();
public Calendar getCreationDate();
@@ -560,4 +562,7 @@ public interface Model {
public List<Calendar> getModificationDates();
+ void addModificationDates(List<Calendar> modificationDatesFromRdf);
+
+
}
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 5e9bc0ef741d6adf2cae4621caa15232eb5fb12e..2c9905f430b8469b698a5225d75bf6300276248d 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
@@ -719,4 +719,18 @@ public class ModelFullIndexed implements Model {
public void addAuthor(Author author) {
modelData.addAuthor(author);
}
+
+ @Override
+ public void addAuthors(Set<Author> authors) {
+ for (Author author : authors) {
+ addAuthor(author);
+ }
+ }
+
+ @Override
+ public void addModificationDates(List<Calendar> modificationDates) {
+ for (Calendar calendar : modificationDates) {
+ addModificationDate(calendar);
+ }
+ }
}