From 7e859e8504813c870147cedf10b8e30fad3e5f8f Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 17 Jan 2019 14:29:11 +0100
Subject: [PATCH] error reporting is a bit more informative
---
.../reaction/ReactionCollectionXmlParser.java | 162 +++++++++---------
1 file changed, 84 insertions(+), 78 deletions(-)
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
index 2f06de27b1..3125c6585a 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
@@ -9,6 +9,7 @@ import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
@@ -17,6 +18,7 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
* Parser used for extracting collections of reaction from CellDesigner xml.
@@ -26,88 +28,92 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
*/
public class ReactionCollectionXmlParser extends XmlParser {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ReactionCollectionXmlParser.class.getName());
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ReactionCollectionXmlParser.class.getName());
- /**
- * Model for which parsing (or transformation to xml) is being done.
- */
- private Model model = null;
+ /**
+ * Model for which parsing (or transformation to xml) is being done.
+ */
+ private Model model = null;
- /**
- * Object used for parsing single reaction.
- */
- private ReactionXmlParser xmlStructureFactory;
+ /**
+ * Object used for parsing single reaction.
+ */
+ private ReactionXmlParser xmlStructureFactory;
- /**
- * Default constructor. Model is required because some nodes require access to
- * other parts of the model.
- *
- * @param sbgn
- * should sbgn standard be used
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- * @param model
- * model that is parsed/transformed into xml
- */
- public ReactionCollectionXmlParser(Model model, CellDesignerElementCollection elements, boolean sbgn) {
- this.model = model;
- xmlStructureFactory = new ReactionXmlParser(elements, sbgn);
- }
+ /**
+ * Default constructor. Model is required because some nodes require access to
+ * other parts of the model.
+ *
+ * @param sbgn
+ * should sbgn standard be used
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ * @param model
+ * model that is parsed/transformed into xml
+ */
+ public ReactionCollectionXmlParser(Model model, CellDesignerElementCollection elements, boolean sbgn) {
+ this.model = model;
+ xmlStructureFactory = new ReactionXmlParser(elements, sbgn);
+ }
- /**
- * Parse CellDesigner xml node with set of reactions into list of
- * {@link Reaction}.
- *
- * @param reactionsNode
- * xml node
- * @return list of reaction taken from xml node
- * @throws CellDesignerParserException
- * thrown when there is a problem with xml node
- * @throws InvalidXmlSchemaException
- * thrown when reactionsNode is invalid xml
- */
- public List<Reaction> parseXmlReactionCollection(Node reactionsNode) throws CellDesignerParserException, InvalidXmlSchemaException {
- List<Reaction> result = new ArrayList<Reaction>();
- NodeList nodes = reactionsNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("reaction")) {
- Reaction reaction = xmlStructureFactory.getReaction(node, model);
- result.add(reaction);
- } else {
- throw new InvalidXmlSchemaException("Unknown element of model/listOfReactions: " + node.getNodeName());
- }
- }
- }
+ /**
+ * Parse CellDesigner xml node with set of reactions into list of
+ * {@link Reaction}.
+ *
+ * @param reactionsNode
+ * xml node
+ * @return list of reaction taken from xml node
+ * @throws CellDesignerParserException
+ * thrown when there is a problem with xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when reactionsNode is invalid xml
+ */
+ public List<Reaction> parseXmlReactionCollection(Node reactionsNode)
+ throws CellDesignerParserException, InvalidXmlSchemaException {
+ List<Reaction> result = new ArrayList<Reaction>();
+ NodeList nodes = reactionsNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("reaction")) {
+ Reaction reaction = xmlStructureFactory.getReaction(node, model);
+ result.add(reaction);
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of model/listOfReactions: " + node.getNodeName());
+ }
+ }
+ }
- return result;
- }
+ return result;
+ }
- /**
- * Transforms set of reactions into CellDesigner xml string.
- *
- * @param collection
- * set of reactions
- * @return CellDesigner xml string representing set of reactions
- * @throws ConverterException
- */
- public String reactionCollectionToXmlString(Collection<Reaction> collection) throws InconsistentModelException {
- String result = "";
- result += "<listOfReactions>\n";
- for (Reaction reaction : collection) {
- try {
- result += xmlStructureFactory.toXml(reaction);
- } catch (SelfReactionException e) {
- logger.warn("Reaction omitted: " + e.getMessage());
- }
- }
- result += "</listOfReactions>\n";
- return result;
- }
+ /**
+ * Transforms set of reactions into CellDesigner xml string.
+ *
+ * @param collection
+ * set of reactions
+ * @return CellDesigner xml string representing set of reactions
+ * @throws ConverterException
+ */
+ public String reactionCollectionToXmlString(Collection<Reaction> collection) throws InconsistentModelException {
+ String result = "";
+ result += "<listOfReactions>\n";
+ for (Reaction reaction : collection) {
+ try {
+ result += xmlStructureFactory.toXml(reaction);
+ } catch (InvalidArgumentException e) {
+ throw new InconsistentModelException(
+ new ElementUtils().getElementTag(reaction) + "Problem with exporting reaction", e);
+ } catch (SelfReactionException e) {
+ logger.warn("Reaction omitted: " + e.getMessage());
+ }
+ }
+ result += "</listOfReactions>\n";
+ return result;
+ }
}
--
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