diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerParserException.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerParserException.java
index 3009ac1a3a426b88498723d37f3d71e7d4d0662d..fa08dbc952962ac9215b98fb2ba3491aebcd91e8 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerParserException.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerParserException.java
@@ -1,57 +1,69 @@
package lcsb.mapviewer.converter.model.celldesigner;
/**
- * Exception that shold be thrown when the parser encouter problem with
- * cellDesigner file.
+ * Exception that should be thrown when the parser encounter problem with
+ * CellDesigner file.
*
* @author Piotr Gawron
*
*/
public abstract class CellDesignerParserException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor - initializes instance variable to unknown.
- */
-
- public CellDesignerParserException() {
- super(); // call superclass constructor
- }
-
- /**
- * Constructor receives some kind of message.
- *
- * @param err
- * message associated with exception
- */
-
- public CellDesignerParserException(final String err) {
- super(err);
- }
-
- /**
- * Constructor receives some kind of message and parent exception.
- *
- * @param err
- * message associated with exception
- * @param throwable
- * parent exception
- */
- public CellDesignerParserException(final String err, final Throwable throwable) {
- super(err, throwable);
- }
-
- /**
- * Public constructor with parent exception that was catched.
- *
- * @param e
- * parent exception
- */
-
- public CellDesignerParserException(final Throwable e) {
- super(e);
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor - initializes instance variable to unknown.
+ */
+
+ public CellDesignerParserException() {
+ super(); // call superclass constructor
+ }
+
+ /**
+ * Constructor receives some kind of message.
+ *
+ * @param err
+ * message associated with exception
+ */
+
+ public CellDesignerParserException(final String err) {
+ super(err);
+ }
+
+ /**
+ * Constructor receives some kind of message and parent exception.
+ *
+ * @param err
+ * message associated with exception
+ * @param throwable
+ * parent exception
+ */
+ public CellDesignerParserException(final String err, final Throwable throwable) {
+ super(err, throwable);
+ }
+
+ /**
+ * Public constructor with parent exception that was caught.
+ *
+ * @param e
+ * parent exception
+ */
+
+ public CellDesignerParserException(final Throwable e) {
+ super(e);
+ }
+
+ public String getMessageWithContext() {
+ String message;
+ if (this.getCause() != null) {
+ message = this.getCause().getMessage();
+ } else {
+ message = this.getMessage();
+ }
+ return getMessageContext() + " " + message;
+ }
+
+ public abstract String getMessageContext();
}
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 a22d3705a50c6340d8ac074a519ef3f6e13b35d4..44ebeb6677f5790802ad14a6a6298cb5e8d13496 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
@@ -243,7 +243,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
} catch (InvalidXmlSchemaException e) {
throw new InvalidInputDataExecption(e);
} catch (CellDesignerParserException e) {
- throw new InvalidInputDataExecption(e);
+ throw new InvalidInputDataExecption(e.getMessageWithContext(), e);
}
return model;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java
index 6057b82fe7b620fa880501edd10447a1b1e1f97f..f5ef296f76ac9ed0284442f3b203432d0ad8562c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java
@@ -27,82 +27,85 @@ import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
*/
public class CompartmentCollectionXmlParser extends XmlParser {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(CompartmentCollectionXmlParser.class.getName());
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(CompartmentCollectionXmlParser.class.getName());
- /**
- * CellDesigner xml parser for single compartment.
- */
- private CompartmentXmlParser compartmentParser;
+ /**
+ * CellDesigner xml parser for single compartment.
+ */
+ private CompartmentXmlParser compartmentParser;
- /**
- * Collection of {@link CellDesignerElement cell designer elements} parsed
- * from xml.
- */
- private CellDesignerElementCollection elements;
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed from
+ * xml.
+ */
+ private CellDesignerElementCollection elements;
- /**
- * Default constructor.
- *
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- */
- public CompartmentCollectionXmlParser(CellDesignerElementCollection elements) {
- this.elements = elements;
- compartmentParser = new CompartmentXmlParser(elements);
- }
+ /**
+ * Default constructor.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
+ public CompartmentCollectionXmlParser(CellDesignerElementCollection elements) {
+ this.elements = elements;
+ compartmentParser = new CompartmentXmlParser(elements);
+ }
- /**
- * Parse CellDEsigner xml node with collection of compartments.
- *
- * @param compartmentsNode
- * xml node to parse
- * @return list of compartments obtained from xml node
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- public List<CellDesignerCompartment> parseXmlCompartmentCollection(Node compartmentsNode) throws InvalidXmlSchemaException {
- List<CellDesignerCompartment> result = new ArrayList<CellDesignerCompartment>();
- NodeList nodes = compartmentsNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("compartment")) {
- Pair<String, CellDesignerCompartment> compartmentPair = compartmentParser.parseXmlElement(node);
- result.add(compartmentPair.getRight());
- } else {
- throw new InvalidXmlSchemaException("Unknown element of model/listOfCompartments: " + node.getNodeName());
- }
- }
- }
- return result;
- }
+ /**
+ * Parse CellDEsigner xml node with collection of compartments.
+ *
+ * @param compartmentsNode
+ * xml node to parse
+ * @return list of compartments obtained from xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ * @throws CompartmentParserException
+ * thrown when there is a problem with parsing a compartment
+ */
+ public List<CellDesignerCompartment> parseXmlCompartmentCollection(Node compartmentsNode)
+ throws InvalidXmlSchemaException, CompartmentParserException {
+ List<CellDesignerCompartment> result = new ArrayList<>();
+ NodeList nodes = compartmentsNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("compartment")) {
+ Pair<String, CellDesignerCompartment> compartmentPair = compartmentParser.parseXmlElement(node);
+ result.add(compartmentPair.getRight());
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of model/listOfCompartments: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
- /**
- * Creates CellDesigner xml string from set of compartments.
- *
- * @param collection
- * collection of compartments to be transformed into xml
- * @return xml representation of the compartments
- */
- public String toXml(Collection<Compartment> collection) {
- StringBuilder result = new StringBuilder();
- result.append("<listOfCompartments>\n");
- Set<String> addedIds = new HashSet<>();
- for (Compartment compartment : collection) {
- String sbmlId = elements.getElementId(compartment);
- if (!addedIds.contains(sbmlId) && !(compartment instanceof PathwayCompartment)) {
- addedIds.add(sbmlId);
- result.append(compartmentParser.toXml(compartment));
- }
- }
- Compartment defaultCompartment = new Compartment("default");
- result.append(compartmentParser.toXml(defaultCompartment));
- result.append("</listOfCompartments>\n");
- return result.toString();
- }
+ /**
+ * Creates CellDesigner xml string from set of compartments.
+ *
+ * @param collection
+ * collection of compartments to be transformed into xml
+ * @return xml representation of the compartments
+ */
+ public String toXml(Collection<Compartment> collection) {
+ StringBuilder result = new StringBuilder();
+ result.append("<listOfCompartments>\n");
+ Set<String> addedIds = new HashSet<>();
+ for (Compartment compartment : collection) {
+ String sbmlId = elements.getElementId(compartment);
+ if (!addedIds.contains(sbmlId) && !(compartment instanceof PathwayCompartment)) {
+ addedIds.add(sbmlId);
+ result.append(compartmentParser.toXml(compartment));
+ }
+ }
+ Compartment defaultCompartment = new Compartment("default");
+ result.append(compartmentParser.toXml(defaultCompartment));
+ result.append("</listOfCompartments>\n");
+ return result.toString();
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserException.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserException.java
new file mode 100644
index 0000000000000000000000000000000000000000..6e8afa1fb25d0e6dd23bad6caa74ee82533cba76
--- /dev/null
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserException.java
@@ -0,0 +1,126 @@
+package lcsb.mapviewer.converter.model.celldesigner.compartment;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerParserException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+
+/**
+ * Exception thrown when problem with parsing {@link Compartment} is
+ * encountered.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CompartmentParserException extends CellDesignerParserException {
+ Logger logger = Logger.getLogger(CompartmentParserException.class);
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Identifier of compartment that was a reason for this exception.
+ */
+ private String compartmentId;
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * message thrown
+ * @param compartmentId
+ * {@link #compartmentId}
+ */
+ public CompartmentParserException(String message, String compartmentId) {
+ super(message);
+ this.compartmentId = compartmentId;
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * message thrown
+ * @param compartment
+ * {@link #compartmentId}
+ */
+ public CompartmentParserException(String message, Compartment compartment) {
+ super(message);
+ if (compartment != null) {
+ setCompartmentId(compartment.getElementId());
+ }
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * message thrown
+ * @param compartment
+ * {@link #compartmentId}
+ * @param e
+ * super exception
+ */
+ public CompartmentParserException(String message, Compartment compartment, Exception e) {
+ super(message, e);
+ if (compartment != null) {
+ setCompartmentId(compartment.getElementId());
+ }
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param compartment
+ * {@link #compartmentId}
+ * @param e
+ * super exception
+ */
+ public CompartmentParserException(Compartment compartment, Throwable e) {
+ super(e);
+ if (compartment != null) {
+ setCompartmentId(compartment.getElementId());
+ }
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param compartmentId
+ * {@link #compartmentId}
+ * @param e
+ * super exception
+ */
+ public CompartmentParserException(String compartmentId, Throwable e) {
+ super(e);
+ setCompartmentId(compartmentId);
+ }
+
+ /**
+ * @return the compartmentId
+ * @see #compartmentId
+ */
+ public String getCompartmentId() {
+ return compartmentId;
+ }
+
+ /**
+ * @param compartmentId
+ * the compartmentId to set
+ * @see #compartmentId
+ */
+ public void setCompartmentId(String compartmentId) {
+ this.compartmentId = compartmentId;
+ }
+
+ @Override
+ public String getMessageContext() {
+ if (compartmentId != null) {
+ return "[Compartment: " + compartmentId + "]";
+ }
+ return null;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java
index b284a5ab92e67bfb983bb9ffd3a41c5eb376c89c..0c70794f2e649473e2489129773446899819e28e 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java
@@ -23,149 +23,155 @@ import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
*/
public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerCompartment, Compartment> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CompartmentXmlParser.class.getName());
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CompartmentXmlParser.class.getName());
- /**
- * Parser used to retrieve Miriam data for the element.
- */
- private XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
+ /**
+ * Parser used to retrieve Miriam data for the element.
+ */
+ private XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
- /**
- * Collection of {@link CellDesignerElement cell designer elements} parsed
- * from xml.
- */
- private CellDesignerElementCollection elements;
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed from
+ * xml.
+ */
+ private CellDesignerElementCollection elements;
- /**
- * Xml parser used for processing notes into structurized data.
- */
- private RestAnnotationParser rap = new RestAnnotationParser();
+ /**
+ * Xml parser used for processing notes into structurized data.
+ */
+ private RestAnnotationParser rap = new RestAnnotationParser();
- /**
- * Default constructor.
- *
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- */
- public CompartmentXmlParser(CellDesignerElementCollection elements) {
- this.elements = elements;
- }
+ /**
+ * Default constructor.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
+ public CompartmentXmlParser(CellDesignerElementCollection elements) {
+ this.elements = elements;
+ }
- @Override
- public Pair<String, CellDesignerCompartment> parseXmlElement(Node compartmentNode) throws InvalidXmlSchemaException {
- CellDesignerCompartment compartment = new CellDesignerCompartment();
- // we ignore metaid - it's useless and obstruct data model
- // compartment.setMetaId(getNodeAttr("metaid", compartmentNode));
- compartment.setElementId(getNodeAttr("id", compartmentNode));
- compartment.setName(decodeName(getNodeAttr("name", compartmentNode)));
- NodeList nodes = compartmentNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("annotation")) {
- parseAnnotationNode(compartment, node);
- } else if (node.getNodeName().equalsIgnoreCase("notes")) {
- compartment.setNotes(rap.getNotes(node));
- } else {
- throw new InvalidXmlSchemaException("Unknown element of Compartment: " + node.getNodeName());
- }
- }
- }
- return new Pair<String, CellDesignerCompartment>(compartment.getElementId(), compartment);
- }
+ @Override
+ public Pair<String, CellDesignerCompartment> parseXmlElement(Node compartmentNode) throws CompartmentParserException {
+ CellDesignerCompartment compartment = new CellDesignerCompartment();
+ // we ignore metaid - it's useless and obstruct data model
+ // compartment.setMetaId(getNodeAttr("metaid", compartmentNode));
+ compartment.setElementId(getNodeAttr("id", compartmentNode));
+ compartment.setName(decodeName(getNodeAttr("name", compartmentNode)));
+ try {
+ NodeList nodes = compartmentNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("annotation")) {
+ parseAnnotationNode(compartment, node);
+ } else if (node.getNodeName().equalsIgnoreCase("notes")) {
+ compartment.setNotes(rap.getNotes(node));
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of Compartment: " + node.getNodeName());
+ }
+ }
+ }
+ return new Pair<String, CellDesignerCompartment>(compartment.getElementId(), compartment);
+ } catch (InvalidXmlSchemaException e) {
+ throw new CompartmentParserException(compartment.getElementId(), e);
+ }
+ }
- /**
- * Process annotation part of the xml node.
- *
- * @param compartment
- * object that we create
- * @param xmlNode
- * annotation xml node
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- private void parseAnnotationNode(CellDesignerCompartment compartment, Node xmlNode) throws InvalidXmlSchemaException {
- NodeList annotationNodes = xmlNode.getChildNodes();
- for (int y = 0; y < annotationNodes.getLength(); y++) {
- Node annotationNode = annotationNodes.item(y);
- if (annotationNode.getNodeType() == Node.ELEMENT_NODE) {
- if (annotationNode.getNodeName().equalsIgnoreCase("rdf:RDF")) {
- compartment.addMiriamData(xmlAnnotationParser.parseRdfNode(annotationNode));
- } else if (annotationNode.getNodeName().equalsIgnoreCase("celldesigner:extension")) {
- parseExtensionNode(compartment, annotationNode);
- } else {
- throw new InvalidXmlSchemaException("Unknown element of Compartment/annotation: " + annotationNode.getNodeName());
- }
- }
- }
- }
+ /**
+ * Process annotation part of the xml node.
+ *
+ * @param compartment
+ * object that we create
+ * @param xmlNode
+ * annotation xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ private void parseAnnotationNode(CellDesignerCompartment compartment, Node xmlNode) throws InvalidXmlSchemaException {
+ NodeList annotationNodes = xmlNode.getChildNodes();
+ for (int y = 0; y < annotationNodes.getLength(); y++) {
+ Node annotationNode = annotationNodes.item(y);
+ if (annotationNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (annotationNode.getNodeName().equalsIgnoreCase("rdf:RDF")) {
+ compartment.addMiriamData(xmlAnnotationParser.parseRdfNode(annotationNode));
+ } else if (annotationNode.getNodeName().equalsIgnoreCase("celldesigner:extension")) {
+ parseExtensionNode(compartment, annotationNode);
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown xml tag of compartment->annotation: " + annotationNode.getNodeName());
+ }
+ }
+ }
+ }
- /**
- * Process extension part of the xml node.
- *
- * @param compartment
- * object that we create
- * @param xmlNode
- * annotation xml node
- * @throws InvalidXmlSchemaException
- * thrown when xmlNode is invalid
- */
- private void parseExtensionNode(CellDesignerCompartment compartment, Node xmlNode) throws InvalidXmlSchemaException {
- NodeList annotationNodes = xmlNode.getChildNodes();
- for (int y = 0; y < annotationNodes.getLength(); y++) {
- Node annotationNode = annotationNodes.item(y);
- if (annotationNode.getNodeType() == Node.ELEMENT_NODE) {
- if (annotationNode.getNodeName().equalsIgnoreCase("celldesigner:name")) {
- // ignore it (we already have this name)
- continue;
- } else {
- throw new InvalidXmlSchemaException("Unknown element of Compartment/annotation/extension: " + annotationNode.getNodeName());
- }
- }
- }
- }
+ /**
+ * Process extension part of the xml node.
+ *
+ * @param compartment
+ * object that we create
+ * @param xmlNode
+ * annotation xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when xmlNode is invalid
+ */
+ private void parseExtensionNode(CellDesignerCompartment compartment, Node xmlNode) throws InvalidXmlSchemaException {
+ NodeList annotationNodes = xmlNode.getChildNodes();
+ for (int y = 0; y < annotationNodes.getLength(); y++) {
+ Node annotationNode = annotationNodes.item(y);
+ if (annotationNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (annotationNode.getNodeName().equalsIgnoreCase("celldesigner:name")) {
+ // ignore it (we already have this name)
+ continue;
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of Compartment/annotation/extension: " + annotationNode.getNodeName());
+ }
+ }
+ }
+ }
- @Override
- public String toXml(Compartment compartment) {
- StringBuilder sb = new StringBuilder("");
- sb.append("<compartment ");
- sb.append("metaid=\"" + elements.getElementId(compartment) + "\" ");
- sb.append("id=\"" + elements.getElementId(compartment) + "\" ");
- sb.append("name=\"" + encodeName(compartment.getName()) + "\" ");
- sb.append("size=\"1\" ");
- sb.append("units=\"volume\" ");
- String parentName = "default";
+ @Override
+ public String toXml(Compartment compartment) {
+ StringBuilder sb = new StringBuilder("");
+ sb.append("<compartment ");
+ sb.append("metaid=\"" + elements.getElementId(compartment) + "\" ");
+ sb.append("id=\"" + elements.getElementId(compartment) + "\" ");
+ sb.append("name=\"" + encodeName(compartment.getName()) + "\" ");
+ sb.append("size=\"1\" ");
+ sb.append("units=\"volume\" ");
+ String parentName = "default";
- if (compartment.getCompartment() != null && !(compartment.getCompartment() instanceof PathwayCompartment)) {
- parentName = elements.getElementId(compartment.getCompartment());
- }
+ if (compartment.getCompartment() != null && !(compartment.getCompartment() instanceof PathwayCompartment)) {
+ parentName = elements.getElementId(compartment.getCompartment());
+ }
- // default is the top level compartment
- if (!compartment.getElementId().equals("default")) {
- sb.append("outside=\"" + parentName + "\" ");
- }
- sb.append(">\n");
- sb.append("<annotation>\n");
- sb.append("<celldesigner:extension>\n");
- sb.append("<celldesigner:name>" + encodeName(compartment.getName()) + "</celldesigner:name>\n");
- sb.append("</celldesigner:extension>\n");
- sb.append(xmlAnnotationParser.dataSetToXmlString(compartment.getMiriamData()));
- sb.append("</annotation>\n");
- sb.append("<notes>");
- sb.append("<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>");
- RestAnnotationParser rap = new RestAnnotationParser();
- sb.append(rap.createAnnotationString(compartment));
- if (compartment.getNotes() != null) {
- sb.append(compartment.getNotes());
- }
- sb.append("</body></html>");
- sb.append("</notes>\n");
- sb.append("</compartment>\n");
- return sb.toString();
- }
+ // default is the top level compartment
+ if (!compartment.getElementId().equals("default")) {
+ sb.append("outside=\"" + parentName + "\" ");
+ }
+ sb.append(">\n");
+ sb.append("<annotation>\n");
+ sb.append("<celldesigner:extension>\n");
+ sb.append("<celldesigner:name>" + encodeName(compartment.getName()) + "</celldesigner:name>\n");
+ sb.append("</celldesigner:extension>\n");
+ sb.append(xmlAnnotationParser.dataSetToXmlString(compartment.getMiriamData()));
+ sb.append("</annotation>\n");
+ sb.append("<notes>");
+ sb.append("<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>");
+ RestAnnotationParser rap = new RestAnnotationParser();
+ sb.append(rap.createAnnotationString(compartment));
+ if (compartment.getNotes() != null) {
+ sb.append(compartment.getNotes());
+ }
+ sb.append("</body></html>");
+ sb.append("</notes>\n");
+ sb.append("</compartment>\n");
+ return sb.toString();
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserException.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserException.java
index 86ed00cd4cd3f3e722d1a58c5bf5a96f7f94f565..0da75c8289fa85a78cd529ab695a5923703d9389 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserException.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserException.java
@@ -12,91 +12,99 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
*/
public class ReactionParserException extends CellDesignerParserException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Identifier of reaction that was a reason for this exception.
- */
- private String reactionId;
+ /**
+ * Identifier of reaction that was a reason for this exception.
+ */
+ private String reactionId;
- /**
- * Default constructor.
- *
- * @param message
- * message thrown
- * @param reactionId
- * {@link #reactionId}
- */
- public ReactionParserException(String message, String reactionId) {
- super(message);
- this.reactionId = reactionId;
- }
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * message thrown
+ * @param reactionId
+ * {@link #reactionId}
+ */
+ public ReactionParserException(String message, String reactionId) {
+ super(message);
+ this.reactionId = reactionId;
+ }
- /**
- * Default constructor.
- *
- * @param message
- * message thrown
- * @param reaction
- * {@link #reactionId}
- */
- public ReactionParserException(String message, Reaction reaction) {
- super(message);
- if (reaction != null) {
- setReactionId(reaction.getIdReaction());
- }
- }
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * message thrown
+ * @param reaction
+ * {@link #reactionId}
+ */
+ public ReactionParserException(String message, Reaction reaction) {
+ super(message);
+ if (reaction != null) {
+ setReactionId(reaction.getIdReaction());
+ }
+ }
- /**
- * Default constructor.
- *
- * @param message
- * message thrown
- * @param reaction
- * {@link #reactionId}
- * @param e
- * super exception
- */
- public ReactionParserException(String message, Reaction reaction, Exception e) {
- super(message, e);
- if (reaction != null) {
- setReactionId(reaction.getIdReaction());
- }
- }
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * message thrown
+ * @param reaction
+ * {@link #reactionId}
+ * @param e
+ * super exception
+ */
+ public ReactionParserException(String message, Reaction reaction, Exception e) {
+ super(message, e);
+ if (reaction != null) {
+ setReactionId(reaction.getIdReaction());
+ }
+ }
- /**
- * Default constructor.
- *
- * @param reaction
- * {@link #reactionId}
- * @param e
- * super exception
- */
- public ReactionParserException(Reaction reaction, Throwable e) {
- super(e);
- if (reaction != null) {
- setReactionId(reaction.getIdReaction());
- }
- }
+ /**
+ * Default constructor.
+ *
+ * @param reaction
+ * {@link #reactionId}
+ * @param e
+ * super exception
+ */
+ public ReactionParserException(Reaction reaction, Throwable e) {
+ super(e);
+ if (reaction != null) {
+ setReactionId(reaction.getIdReaction());
+ }
+ }
- /**
- * @return the reactionId
- * @see #reactionId
- */
- public String getReactionId() {
- return reactionId;
- }
+ /**
+ * @return the reactionId
+ * @see #reactionId
+ */
+ public String getReactionId() {
+ return reactionId;
+ }
- /**
- * @param reactionId
- * the reactionId to set
- * @see #reactionId
- */
- public void setReactionId(String reactionId) {
- this.reactionId = reactionId;
- }
+ /**
+ * @param reactionId
+ * the reactionId to set
+ * @see #reactionId
+ */
+ public void setReactionId(String reactionId) {
+ this.reactionId = reactionId;
+ }
+
+ @Override
+ public String getMessageContext() {
+ if (reactionId != null) {
+ return "[Reaction: " + reactionId + "]";
+ }
+ return null;
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java
index fcd1d7833f8dbde1ddd24bdb5e766145aa7d3efc..90ba13c3a6b2f031f29fc3629bbfbbabceae3561 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java
@@ -11,7 +11,9 @@ import org.w3c.dom.NodeList;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerParserException;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
+import lcsb.mapviewer.converter.model.celldesigner.compartment.CompartmentParserException;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.species.Element;
@@ -57,8 +59,9 @@ public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>,
* and element parsed from xml node in {@link Pair#right}.
* @throws InvalidXmlSchemaException
* thrown when xml is invalid
+ * @throws CompartmentParserException
*/
- public abstract Pair<String, T> parseXmlElement(Node node) throws InvalidXmlSchemaException;
+ public abstract Pair<String, T> parseXmlElement(Node node) throws InvalidXmlSchemaException, CellDesignerParserException;
/**
* Default constructor.
@@ -132,12 +135,12 @@ public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>,
* and element parsed from xml node in {@link Pair#right}.
* @throws InvalidXmlSchemaException
* thrown when xmlString is invalid
+ * @throws CellDesignerParserException
*/
- public Pair<String, T> parseXmlElement(String xmlString) throws InvalidXmlSchemaException {
+ public Pair<String, T> parseXmlElement(String xmlString) throws InvalidXmlSchemaException, CellDesignerParserException {
Document doc = getXmlDocumentFromString(xmlString);
NodeList root = doc.getChildNodes();
return parseXmlElement(root.item(0));
-
}
/**
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java
index 7f521c9341b93e355b276921906c863e47c6b134..f40328f788cde5be11c89e766430d345490da24e 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java
@@ -28,7 +28,6 @@ import lcsb.mapviewer.converter.model.celldesigner.unit.UnitXmlParserTest;
AllStructureTests.class, //
AllTypesTests.class, //
CellDesignerElementCollectionTest.class, //
- CellDesignerParserExceptionTest.class, //
CellDesignerXmlParserTest.class, //
ComplexParserTests.class, //
InvalidGroupExceptionTest.class, //
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerParserExceptionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerParserExceptionTest.java
deleted file mode 100644
index b586a2cc6624dd9d34d799d880f4db32b71102a4..0000000000000000000000000000000000000000
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerParserExceptionTest.java
+++ /dev/null
@@ -1,52 +0,0 @@
-package lcsb.mapviewer.converter.model.celldesigner;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class CellDesignerParserExceptionTest {
-
- private static class Tmp extends CellDesignerParserException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public Tmp(String string) {
- super(string);
- }
-
- public Tmp() {
- super();
- }
-
- public Tmp(String string, Exception exception) {
- super(string, exception);
- }
-
- public Tmp(Exception exception) {
- super(exception);
- }
-
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor() {
- assertNotNull(new Tmp());
- assertNotNull(new Tmp("str"));
- assertNotNull(new Tmp("str2", new Exception()));
- assertNotNull(new Tmp(new Exception()));
- }
-
-}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParserTest.java
index abda4fa5533377a45132beebcbefb97e50bfc6c6..674077ea546d3fd9033d55a4cb62bc13a9a001c7 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParserTest.java
@@ -19,7 +19,6 @@ import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
import lcsb.mapviewer.converter.model.celldesigner.species.ProteinXmlParserTest;
@@ -27,122 +26,122 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompart
import lcsb.mapviewer.model.map.compartment.Compartment;
public class CompartmentXmlParserTest extends CellDesignerTestFunctions {
- protected Logger logger = Logger.getLogger(ProteinXmlParserTest.class.getName());
-
- CompartmentXmlParser compartmentParser;
- CellDesignerElementCollection elements;
- String testProteinFile = "testFiles/xmlNodeTestExamples/compartment.xml";
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
- compartmentParser = new CompartmentXmlParser(elements);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseXmlCompartment() {
- try {
- String xmlString = readFile(testProteinFile);
-
- Pair<String, CellDesignerCompartment> result = compartmentParser.parseXmlElement(xmlString);
- CellDesignerCompartment compartment = result.getRight();
- assertNotNull(compartment);
- assertEquals("c1", compartment.getElementId());
- assertEquals(1, compartment.getMiriamData().size());
- assertEquals("c1", compartment.getName());
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unexpected exception occured");
- }
- }
-
- @Test
- public void testToXml() throws Exception {
- try {
- String xmlString = readFile(testProteinFile);
-
- Pair<String, CellDesignerCompartment> result = compartmentParser.parseXmlElement(xmlString);
- CellDesignerCompartment compartment = result.getRight();
- Compartment alias = compartment.createModelElement("id");
- String transformedXml = compartmentParser.toXml(alias);
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("compartment", root.item(0).getNodeName());
-
- Pair<String, CellDesignerCompartment> result2 = compartmentParser.parseXmlElement(compartmentParser.toXml(alias));
- CellDesignerCompartment compartment2 = result2.getRight();
- assertEquals(alias.getMiriamData().size(), compartment2.getMiriamData().size());
- assertEquals(alias.getName(), compartment2.getName());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidCompartment() throws Exception {
- try {
- compartmentParser.parseXmlElement(readFile("testFiles/invalid/compartment.xml"));
- fail("Exception expected");
-
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of Compartment"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidCompartment2() throws Exception {
- try {
- compartmentParser.parseXmlElement(readFile("testFiles/invalid/compartment2.xml"));
- fail("Exception expected");
-
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of Compartment/annotation"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidCompartment3() throws Exception {
- try {
- compartmentParser.parseXmlElement(readFile("testFiles/invalid/compartment3.xml"));
- fail("Exception expected");
-
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of Compartment/annotation/extension"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlWithParent() throws Exception {
- try {
- Compartment child = new Compartment("c_1");
- Compartment parent = new Compartment("p_1");
- child.setCompartment(parent);
-
- String xml = compartmentParser.toXml(child);
- assertTrue(xml.contains(parent.getElementId()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ protected Logger logger = Logger.getLogger(ProteinXmlParserTest.class.getName());
+
+ CompartmentXmlParser compartmentParser;
+ CellDesignerElementCollection elements;
+ String testProteinFile = "testFiles/xmlNodeTestExamples/compartment.xml";
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+ compartmentParser = new CompartmentXmlParser(elements);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseXmlCompartment() {
+ try {
+ String xmlString = readFile(testProteinFile);
+
+ Pair<String, CellDesignerCompartment> result = compartmentParser.parseXmlElement(xmlString);
+ CellDesignerCompartment compartment = result.getRight();
+ assertNotNull(compartment);
+ assertEquals("c1", compartment.getElementId());
+ assertEquals(1, compartment.getMiriamData().size());
+ assertEquals("c1", compartment.getName());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unexpected exception occured");
+ }
+ }
+
+ @Test
+ public void testToXml() throws Exception {
+ try {
+ String xmlString = readFile(testProteinFile);
+
+ Pair<String, CellDesignerCompartment> result = compartmentParser.parseXmlElement(xmlString);
+ CellDesignerCompartment compartment = result.getRight();
+ Compartment alias = compartment.createModelElement("id");
+ String transformedXml = compartmentParser.toXml(alias);
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("compartment", root.item(0).getNodeName());
+
+ Pair<String, CellDesignerCompartment> result2 = compartmentParser.parseXmlElement(compartmentParser.toXml(alias));
+ CellDesignerCompartment compartment2 = result2.getRight();
+ assertEquals(alias.getMiriamData().size(), compartment2.getMiriamData().size());
+ assertEquals(alias.getName(), compartment2.getName());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidCompartment() throws Exception {
+ try {
+ compartmentParser.parseXmlElement(readFile("testFiles/invalid/compartment.xml"));
+ fail("Exception expected");
+
+ } catch (CompartmentParserException e) {
+ assertTrue(e.getMessage().contains("Unknown element of Compartment"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidCompartment2() throws Exception {
+ try {
+ compartmentParser.parseXmlElement(readFile("testFiles/invalid/compartment2.xml"));
+ fail("Exception expected");
+
+ } catch (CompartmentParserException e) {
+ assertTrue(e.getMessage().contains("Unknown xml tag of compartment"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidCompartment3() throws Exception {
+ try {
+ compartmentParser.parseXmlElement(readFile("testFiles/invalid/compartment3.xml"));
+ fail("Exception expected");
+
+ } catch (CompartmentParserException e) {
+ assertTrue(e.getMessage().contains("Unknown element of Compartment/annotation/extension"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlWithParent() throws Exception {
+ try {
+ Compartment child = new Compartment("c_1");
+ Compartment parent = new Compartment("p_1");
+ child.setCompartment(parent);
+
+ String xml = compartmentParser.toXml(child);
+ assertTrue(xml.contains(parent.getElementId()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/InvalidInputDataExecption.java b/converter/src/main/java/lcsb/mapviewer/converter/InvalidInputDataExecption.java
index ebc92805a166ffd772c6113a65f84b3aaeafa4f4..beb5e030263771059539640016e412157d12235a 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/InvalidInputDataExecption.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/InvalidInputDataExecption.java
@@ -8,61 +8,61 @@ package lcsb.mapviewer.converter;
*/
public class InvalidInputDataExecption extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor with exception message.
- *
- * @param message
- * error message
- */
- public InvalidInputDataExecption(String message) {
- super(message);
- }
+ /**
+ * Default constructor with exception message.
+ *
+ * @param message
+ * error message
+ */
+ public InvalidInputDataExecption(String message) {
+ super(message);
+ }
- /**
- * Default constructor with super exception as a source.
- *
- * @param e
- * super exception
- */
- public InvalidInputDataExecption(Exception e) {
- super(e);
- }
+ /**
+ * Default constructor with super exception as a source.
+ *
+ * @param e
+ * super exception
+ */
+ public InvalidInputDataExecption(Exception e) {
+ super(e);
+ }
- /**
- * Default constructor - initializes instance variable to unknown.
- */
+ /**
+ * Default constructor - initializes instance variable to unknown.
+ */
- public InvalidInputDataExecption() {
- super(); // call superclass constructor
- }
+ public InvalidInputDataExecption() {
+ super(); // call superclass constructor
+ }
- /**
- * Default constructor.
- *
- * @param message
- * exception message
- * @param e
- * super exception
- */
- public InvalidInputDataExecption(String message, Exception e) {
- super(message, e);
- }
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ * @param e
+ * super exception
+ */
+ public InvalidInputDataExecption(String message, Exception e) {
+ super(message, e);
+ }
- /**
- * Default constructor with exception message.
- *
- * @param message
- * error message
- * @param filename
- * name of the file where data is invalid
- */
- public InvalidInputDataExecption(String message, String filename) {
- super("[File \"" + filename + "\"]: " + message.trim());
- }
+ /**
+ * Default constructor with exception message.
+ *
+ * @param message
+ * error message
+ * @param filename
+ * name of the file where data is invalid
+ */
+ public InvalidInputDataExecption(String message, String filename) {
+ super("[File \"" + filename + "\"]: " + message.trim());
+ }
}