From ae94a7824458b7f3c1957740fc764978dd477b44 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 29 Jan 2018 12:27:52 +0100
Subject: [PATCH] parser of sbml function
---
.../celldesigner/CellDesignerXmlParser.java | 1225 +++++++++--------
.../function/FunctionCollectionXmlParser.java | 24 +
.../function/FunctionXmlParser.java | 44 +
.../celldesigner/ComplexParserTests.java | 692 +++++-----
.../function/FunctionXmlParserTest.java | 49 +
converter-CellDesigner/testFiles/function.xml | 70 +
.../testFiles/function/invalid_definition.xml | 2 +
.../testFiles/function/invalid_math.xml | 4 +
.../testFiles/function/simple.xml | 17 +
9 files changed, 1184 insertions(+), 943 deletions(-)
create mode 100644 converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionCollectionXmlParser.java
create mode 100644 converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParser.java
create mode 100644 converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParserTest.java
create mode 100644 converter-CellDesigner/testFiles/function.xml
create mode 100644 converter-CellDesigner/testFiles/function/invalid_definition.xml
create mode 100644 converter-CellDesigner/testFiles/function/invalid_math.xml
create mode 100644 converter-CellDesigner/testFiles/function/simple.xml
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 296e2bd330..05794c33d6 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
@@ -9,6 +9,7 @@ import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
+import java.util.Set;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.lang3.StringEscapeUtils;
@@ -28,6 +29,7 @@ import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.alias.AliasCollectionXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.compartment.CompartmentCollectionXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.function.FunctionCollectionXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionCollectionXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.reaction.UnknownReactionClassException;
import lcsb.mapviewer.converter.model.celldesigner.species.InternalModelSpeciesData;
@@ -37,6 +39,7 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.SbmlFunction;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
@@ -73,609 +76,621 @@ import lcsb.mapviewer.model.map.species.Species;
*/
public class CellDesignerXmlParser extends XmlParser implements IConverter {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(CellDesignerXmlParser.class.getName());
-
- /**
- * CellDesigner parser for layers.
- */
- private LayerXmlParser layerParser = new LayerXmlParser();
-
- /**
- * CellDesigner parser for compartments collections.
- */
- private CompartmentCollectionXmlParser compartmentCollectionXmlParser;
-
- /**
- * CellDesigner parser for species collections.
- */
- private SpeciesCollectionXmlParser speciesSbmlParser;
-
- /**
- * CellDesigner parser for alias collections.
- */
- private AliasCollectionXmlParser aliasCollectionParser;
-
- /**
- * Annotation parser.
- */
- private RestAnnotationParser rap = new RestAnnotationParser();
-
- @Override
- public Model createModel(ConverterParams params) throws InvalidInputDataExecption {
- CellDesignerElementCollection elements = new CellDesignerElementCollection();
-
- Model model = new ModelFullIndexed(null);
-
- if (params.getFilename() != null) {
- model.setName(FilenameUtils.getBaseName(params.getFilename()));
- }
- speciesSbmlParser = new SpeciesCollectionXmlParser(elements);
- aliasCollectionParser = new AliasCollectionXmlParser(elements, model);
- compartmentCollectionXmlParser = new CompartmentCollectionXmlParser(elements);
-
- DOMParser parser = new DOMParser();
- try {
- parser.parse(params.getSource());
- } catch (IOException e) {
- throw new InvalidInputDataExecption("IO Problem with a file: " + params.getSource().getSystemId(), e);
- }
- Document doc = parser.getDocument();
- try {
-
- // Get the document's root XML node
- NodeList root = doc.getChildNodes();
-
- // Navigate down the hierarchy to get to the CEO node
- Node sbmlNode = getNode("SBML", root);
- if (sbmlNode == null) {
- throw new InvalidInputDataExecption("No SBML node");
- }
-
- Node modelNode = getNode("model", sbmlNode.getChildNodes());
- if (modelNode == null) {
- throw new InvalidInputDataExecption("No model node in SBML");
- }
- // we ignore metaid - it's useless and obstruct data model
- // model.setMetaId(getNodeAttr("metaId", modelNode));
- model.setIdModel(getNodeAttr("id", modelNode));
-
- Node compartmentNode = getNode("listOfCompartments", modelNode.getChildNodes());
- if (compartmentNode != null) {
- List<CellDesignerCompartment> compartments = compartmentCollectionXmlParser.parseXmlCompartmentCollection(compartmentNode);
- elements.addElements(compartments);
- }
-
- InternalModelSpeciesData modelData = new InternalModelSpeciesData();
-
- Node speciesNode = getNode("listOfSpecies", modelNode.getChildNodes());
- if (speciesNode != null) {
- List<Pair<String, ? extends CellDesignerSpecies<?>>> species = speciesSbmlParser.parseSbmlSpeciesCollection(speciesNode);
- modelData.updateSpecies(species);
- }
- Node reactionsNode = null;
-
- NodeList nodes = modelNode.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")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("listOfSpecies")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("listOfReactions")) {
- reactionsNode = node;
- } else if (node.getNodeName().equalsIgnoreCase("listOfCompartments")) {
- // we already parsed compartemnts
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("notes")) {
- String notes = rap.getNotes(node);
- if (notes != null) {
- notes = StringEscapeUtils.unescapeHtml4(notes);
- }
- model.setNotes(notes);
- } else if (node.getNodeName().equalsIgnoreCase("listOfUnitDefinitions")) {
- continue; // we can ignore unit definitions
- } else {
- throw new InvalidInputDataExecption("Unknown element of model: " + node.getNodeName());
- }
- }
- }
-
- Node annotationNode = getNode("annotation", modelNode.getChildNodes());
- if (annotationNode == null) {
- throw new InvalidInputDataExecption("No annotation node in SBML/model");
- }
-
- parseAnnotation(model, annotationNode, modelData, elements);
-
- if (speciesNode != null) {
- List<Pair<String, ? extends CellDesignerSpecies<?>>> species = speciesSbmlParser.parseSbmlSpeciesCollection(speciesNode);
- modelData.updateSpecies(species);
- }
-
- if (reactionsNode != null) {
- ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements, params.isSbgnFormat());
- List<Reaction> reactions = reactionCollectionXmlParser.parseXmlReactionCollection(reactionsNode);
- model.addReactions(reactions);
- }
-
- if (params.isSizeAutoAdjust()) {
- Rectangle2D bound = getModelBound(model);
- double width = bound.getWidth() + 2 * (Math.max(0, bound.getX()));
- double height = bound.getHeight() + 2 * (Math.max(0, bound.getY()));
-
- model.setWidth(width);
- model.setHeight(height);
- }
- } catch (InvalidXmlSchemaException e) {
- throw new InvalidInputDataExecption(e);
- } catch (UnknownReactionClassException e) {
- String type = e.getReactionType();
- String reactionId = e.getReactionId();
- String newType = null;
- if ("CATALYSIS".equalsIgnoreCase(type)) {
- newType = "positive influence";
- } else if ("INHIBITION".equalsIgnoreCase(type)) {
- newType = "negative influence";
- } else if ("UNKNOWN_CATALYSIS".equalsIgnoreCase(type)) {
- newType = "unknown positive influence";
- } else if ("UNKNOWN_INHIBITION".equalsIgnoreCase(type)) {
- newType = "unknown negative influence";
- } else if ("PHYSICAL_STIMULATION".equalsIgnoreCase(type)) {
- newType = "reduced physical stimulation";
- } else if ("MODULATION".equalsIgnoreCase(type)) {
- newType = "reduced modulation";
- } else if ("TRIGGER".equalsIgnoreCase(type)) {
- newType = "reduced trigger";
- } else {
- throw new InvalidInputDataExecption(e);
- }
- throw new InvalidInputDataExecption(
- "Reaction type \"" + type + "\" is inappropriate for reaction " + reactionId + ". Suggested type: " + newType
- + " in the \"Reduced\" notation of CellDesigner.",
- e);
- } catch (CellDesignerParserException e) {
- throw new InvalidInputDataExecption(e);
- }
-
- return model;
- }
-
- /**
- * Computes bound of the model.
- *
- * @param model
- * object for which computaion is done
- * @return bound of the model
- */
- Rectangle2D getModelBound(Model model) {
- double maxX = 0;
- double maxY = 0;
- double minX = model.getWidth();
- double minY = model.getHeight();
- for (Element alias : model.getElements()) {
- maxX = Math.max(maxX, alias.getWidth() + alias.getX());
- maxY = Math.max(maxY, alias.getHeight() + alias.getY());
-
- minX = Math.min(minX, alias.getX());
- minY = Math.min(minY, alias.getY());
-
- }
-
- for (Reaction reaction : model.getReactions()) {
- for (Line2D line : reaction.getLines()) {
- maxX = Math.max(maxX, line.getX1());
- maxX = Math.max(maxX, line.getX2());
- maxY = Math.max(maxY, line.getY1());
- maxY = Math.max(maxY, line.getY2());
-
- minX = Math.min(minX, line.getX1());
- minX = Math.min(minX, line.getX2());
- minY = Math.min(minY, line.getY1());
- minY = Math.min(minY, line.getY2());
- }
- }
-
- for (Layer layer : model.getLayers()) {
- for (PolylineData lline : layer.getLines()) {
- for (Line2D line : lline.getLines()) {
- maxX = Math.max(maxX, line.getX1());
- maxX = Math.max(maxX, line.getX2());
- maxY = Math.max(maxY, line.getY1());
- maxY = Math.max(maxY, line.getY2());
-
- minX = Math.min(minX, line.getX1());
- minX = Math.min(minX, line.getX2());
- minY = Math.min(minY, line.getY1());
- minY = Math.min(minY, line.getY2());
- }
- }
- for (LayerRect rect : layer.getRectangles()) {
- maxX = Math.max(maxX, rect.getX());
- maxX = Math.max(maxX, rect.getX() + rect.getWidth());
- maxY = Math.max(maxY, rect.getY());
- maxY = Math.max(maxY, rect.getY() + rect.getHeight());
-
- minX = Math.min(minX, rect.getX());
- minX = Math.min(minX, rect.getX() + rect.getWidth());
- minY = Math.min(minY, rect.getY());
- minY = Math.min(minY, rect.getY() + rect.getHeight());
- }
- for (LayerOval oval : layer.getOvals()) {
- maxX = Math.max(maxX, oval.getX());
- maxX = Math.max(maxX, oval.getX() + oval.getWidth());
- maxY = Math.max(maxY, oval.getY());
- maxY = Math.max(maxY, oval.getY() + oval.getHeight());
-
- minX = Math.min(minX, oval.getX());
- minX = Math.min(minX, oval.getX() + oval.getWidth());
- minY = Math.min(minY, oval.getY());
- minY = Math.min(minY, oval.getY() + oval.getHeight());
- }
- for (LayerText text : layer.getTexts()) {
- maxX = Math.max(maxX, text.getX());
- maxX = Math.max(maxX, text.getX() + text.getWidth());
- maxY = Math.max(maxY, text.getY());
- maxY = Math.max(maxY, text.getY() + text.getHeight());
-
- minX = Math.min(minX, text.getX());
- minX = Math.min(minX, text.getX() + text.getWidth());
- minY = Math.min(minY, text.getY());
- minY = Math.min(minY, text.getY() + text.getHeight());
- }
- }
-
- Rectangle2D result = new Rectangle2D.Double(minX, minY, maxX - minX, maxY - minY);
- return result;
- }
-
- /**
- * Parse annotation part of CellDesigner xml.
- *
- * @param model
- * model that is parsed (and will be updated)
- * @param modelData
- * object conmtaining infoirmation about species during CellDesigner
- * parsing
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- * @param annotationNode
- * xml node to parse
- * @throws InvalidXmlSchemaException
- * thrown when xmlString is invalid
- */
- private void parseAnnotation(Model model, Node annotationNode, InternalModelSpeciesData modelData, CellDesignerElementCollection elements)
- throws InvalidXmlSchemaException {
- SpeciesCollectionXmlParser parser = new SpeciesCollectionXmlParser(elements);
-
- Node extensionNode = getNode("celldesigner:extension", annotationNode.getChildNodes());
- if (extensionNode == null) {
- throw new InvalidXmlSchemaException("No celldesigner:extension node in SBML/model/annotation");
- }
-
- NodeList nodes = extensionNode.getChildNodes();
- Node includedSpecies = null;
- Node listofSpeciesAlias = null;
- Node listOfComplexSpeciesAlias = null;
- Node listOfComparmentAlias = null;
- Node listOfProteins = null;
- Node listOfGenes = null;
- Node listOfRnas = null;
- Node listOfGroups = null;
- Node listOfAntisenseRnas = null;
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:modelVersion")) {
- // we ignore map version (there is no use for us)
- // model.setVersion(getNodeValue(node));
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:modelDisplay")) {
- model.setWidth(getNodeAttr("sizeX", node));
- model.setHeight(getNodeAttr("sizeY", node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfSpeciesAliases")) {
- listofSpeciesAlias = node;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfComplexSpeciesAliases")) {
- listOfComplexSpeciesAlias = node;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfProteins")) {
- listOfProteins = node;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfGenes")) {
- listOfGenes = node;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfRNAs")) {
- listOfRnas = node;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfAntisenseRNAs")) {
- listOfAntisenseRnas = node;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfIncludedSpecies")) {
- includedSpecies = node;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfCompartmentAliases")) {
- listOfComparmentAlias = node;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfLayers")) {
- model.addLayers(layerParser.parseLayers(node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfGroups")) {
- listOfGroups = node;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfBlockDiagrams")) {
- layerParser.parseBlocks(model, node);
- } else {
- throw new InvalidXmlSchemaException("Unknown element of annotation: " + node.getNodeName());
- }
- }
- }
-
- if (listOfComparmentAlias != null) {
- List<Compartment> aliases = aliasCollectionParser.parseXmlCompartmentAliasCollection(listOfComparmentAlias);
- for (Element alias : aliases) {
- rap.processNotes(alias);
- model.addElement(alias);
- }
- }
-
- if (includedSpecies != null) {
- List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseIncludedSpeciesCollection(includedSpecies);
- modelData.updateSpecies(species);
- }
-
- if (listOfProteins != null) {
- List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseXmlProteinCollection(listOfProteins);
- modelData.updateSpecies(species);
- }
- if (listOfGenes != null) {
- List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseXmlGeneCollection(listOfGenes);
- modelData.updateSpecies(species);
- }
- if (listOfRnas != null) {
- List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseXmlRnaCollection(listOfRnas);
- modelData.updateSpecies(species);
- }
- if (listOfAntisenseRnas != null) {
- List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseXmlAntisenseRnaCollection(listOfAntisenseRnas);
- modelData.updateSpecies(species);
- }
-
- for (CellDesignerSpecies<?> species : modelData.getAll()) {
- if (!species.getElementId().equals("")) {
- elements.addElement(species);
- } else {
- logger.warn(
- "Species (class: " + species.getClass().getName() + ", name: " + species.getName()
- + ") exists in CD file, but is never instantiated. It's CellDesigner file problem.");
- }
- }
-
- if (listOfComplexSpeciesAlias != null) {
- List<Complex> aliases = aliasCollectionParser.parseXmlComplexAliasCollection(listOfComplexSpeciesAlias);
- for (Element alias : aliases) {
- rap.processNotes(alias);
- model.addElement(alias);
- }
- }
-
- if (listofSpeciesAlias != null) {
- List<Species> aliases = aliasCollectionParser.parseXmlSpeciesAliasCollection(listofSpeciesAlias);
- for (Element alias : aliases) {
- rap.processNotes(alias);
- model.addElement(alias);
- }
- }
-
- if (includedSpecies != null) {
- parseAnnotationAliasesConnections(model, getNode("celldesigner:listOfSpeciesAliases", nodes));
- parseAnnotationComplexAliasesConnections(model, getNode("celldesigner:listOfComplexSpeciesAliases", nodes));
- }
-
- if (listOfGroups != null) {
- layerParser.parseGroups(model, listOfGroups);
- }
-
- }
-
- /**
- * Parses celldesigner:listOfComplexSpeciesAliases node for annotation part of
- * the CellDEsigner format.
- *
- * @param model
- * model that is parsed
- * @param aliasNode
- * node to parse
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- void parseAnnotationComplexAliasesConnections(Model model, Node aliasNode) throws InvalidXmlSchemaException {
- NodeList nodes = aliasNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:complexSpeciesAlias")) {
- String aliasId = getNodeAttr("id", node);
- String complexId = getNodeAttr("complexSpeciesAlias", node);
- Complex alias = model.getElementByElementId(aliasId);
- if (alias == null) {
- throw new InvalidXmlSchemaException("Alias does not exist " + aliasId);
- }
- Complex parentComplex = model.getElementByElementId(complexId);
- if (parentComplex != null) {
- parentComplex.addSpecies(alias);
- alias.setComplex(parentComplex);
- }
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfComplexSpeciesAliases: " + node.getNodeName());
- }
- }
- }
-
- }
-
- /**
- * Parses celldesigner:listOfSpeciesAliases node for annotation part of the
- * CellDesigner format.
- *
- * @param model
- * model that is parsed
- * @param aliasNode
- * node to parse
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- void parseAnnotationAliasesConnections(Model model, Node aliasNode) throws InvalidXmlSchemaException {
- NodeList nodes = aliasNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:speciesAlias")) {
- String aliasId = getNodeAttr("id", node);
- String complexId = getNodeAttr("complexSpeciesAlias", node);
- Element alias = model.getElementByElementId(aliasId);
- if (alias == null) {
- throw new InvalidXmlSchemaException("Alias does not exist " + aliasId);
- } else if (alias instanceof Species) {
- Species species = ((Species) alias);
- Complex complex = model.getElementByElementId(complexId);
- if (complex != null) {
- species.setComplex(complex);
- complex.addSpecies(species);
- }
- }
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfSpeciesAliases: " + node.getNodeName());
- }
- }
- }
- }
-
- /**
- * Transforms model into CellDesigner xml.
- *
- * @param model
- * model that should be transformed
- * @return CellDesigner xml string for the model
- * @throws InconsistentModelException
- * thrown when then model is invalid
- */
- public String toXml(Model model) throws InconsistentModelException {
- CellDesignerElementCollection elements = new CellDesignerElementCollection();
-
- SpeciesCollectionXmlParser speciesCollectionXmlParser = new SpeciesCollectionXmlParser(elements);
- ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements, false);
- aliasCollectionParser = new AliasCollectionXmlParser(elements, model);
-
- StringBuilder result = new StringBuilder();
- result.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
- result.append(
- "<sbml xmlns=\"http://www.sbml.org/sbml/level2/version4\" "
- + "xmlns:celldesigner=\"http://www.sbml.org/2001/ns/celldesigner\" level=\"2\" version=\"4\">\n");
- // metaid is a strang cell designer id, usually it's model id and as far as
- // we can tell it's not used at all
- result.append("<model metaid=\"" + model.getIdModel() + "\" id=\"" + model.getIdModel() + "\">\n");
-
- if (model.getNotes() != null) {
- result.append("<notes>");
- result.append(escapeXml(model.getNotes()));
- result.append("</notes>");
- }
-
- result.append(annotationToXml(model, elements));
-
- compartmentCollectionXmlParser = new CompartmentCollectionXmlParser(elements);
-
- result.append(compartmentCollectionXmlParser.toXml(model.getCompartments()));
-
- result.append(speciesCollectionXmlParser.speciesCollectionToSbmlString(model.getSpeciesList()));
-
- result.append(reactionCollectionXmlParser.reactionCollectionToXmlString(model.getReactions()));
-
- result.append("</model>");
- result.append("</sbml>");
- return result.toString();
- }
-
- /**
- * Generates xml node that should be in annotation part of the model.
- *
- * @param model
- * model to transform
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- * @return annotation xml string for the model
- */
- private String annotationToXml(Model model, CellDesignerElementCollection elements) {
- SpeciesCollectionXmlParser speciesCollectionXmlParser = new SpeciesCollectionXmlParser(elements);
-
- StringBuilder result = new StringBuilder();
- result.append("<annotation>\n");
- result.append("<celldesigner:extension>\n");
- result.append("<celldesigner:modelVersion>4.0</celldesigner:modelVersion>\n");
- result.append("<celldesigner:modelDisplay sizeX=\"" + model.getWidth().intValue() + "\" sizeY=\"" + model.getHeight().intValue() + "\"/>\n");
-
- result.append(speciesCollectionXmlParser.speciesCollectionToXmlIncludedString(model.getSpeciesList()));
-
- result.append(aliasCollectionParser.compartmentAliasCollectionToXmlString(model.getCompartments()));
- result.append(aliasCollectionParser.complexAliasCollectionToXmlString(model.getComplexList()));
- result.append(aliasCollectionParser.speciesAliasCollectionToXmlString(model.getNotComplexSpeciesList()));
-
- List<Protein> proteins = new ArrayList<>();
- List<Gene> genes = new ArrayList<>();
- List<Rna> rnas = new ArrayList<>();
- List<AntisenseRna> antisenseRnas = new ArrayList<>();
- for (Element element : model.getElements()) {
- if (element instanceof Protein) {
- proteins.add((Protein) element);
- } else if (element instanceof Gene) {
- genes.add((Gene) element);
- } else if (element instanceof AntisenseRna) {
- antisenseRnas.add((AntisenseRna) element);
- } else if (element instanceof Rna) {
- rnas.add((Rna) element);
- }
- }
-
- result.append(speciesCollectionXmlParser.proteinCollectionToXmlString(proteins));
- result.append(speciesCollectionXmlParser.geneCollectionToXmlString(genes));
- result.append(speciesCollectionXmlParser.rnaCollectionToXmlString(rnas));
- result.append(speciesCollectionXmlParser.antisenseRnaCollectionToXmlString(antisenseRnas));
- result.append(layerParser.layerCollectionToXml(model.getLayers()));
-
- result.append("</celldesigner:extension>\n");
- result.append("</annotation>\n");
- return result.toString();
- }
-
- @Override
- public InputStream exportModelToInputStream(Model model) throws InconsistentModelException {
- String exportedString = toXml(model);
- InputStream inputStream = new ByteArrayInputStream(exportedString.getBytes());
- return inputStream;
- }
-
- @Override
- public File exportModelToFile(Model model, String filePath) throws InconsistentModelException, IOException {
- File file = new File(filePath);
- String exportedString = toXml(model);
- FileWriter fileWriter = new FileWriter(file);
- fileWriter.write(exportedString);
- fileWriter.flush();
- fileWriter.close();
-
- return file;
- }
-
- @Override
- public String getCommonName() {
- return "CellDesigner SBML";
- }
-
- @Override
- public MimeType getMimeType() {
- return MimeType.SBML;
- }
-
- @Override
- public String getFileExtension() {
- return "xml";
- }
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(CellDesignerXmlParser.class.getName());
+
+ /**
+ * CellDesigner parser for layers.
+ */
+ private LayerXmlParser layerParser = new LayerXmlParser();
+
+ /**
+ * CellDesigner parser for compartments collections.
+ */
+ private CompartmentCollectionXmlParser compartmentCollectionXmlParser;
+
+ /**
+ * CellDesigner parser for species collections.
+ */
+ private SpeciesCollectionXmlParser speciesSbmlParser;
+
+ /**
+ * CellDesigner parser for alias collections.
+ */
+ private AliasCollectionXmlParser aliasCollectionParser;
+
+ /**
+ * Annotation parser.
+ */
+ private RestAnnotationParser rap = new RestAnnotationParser();
+
+ @Override
+ public Model createModel(ConverterParams params) throws InvalidInputDataExecption {
+ CellDesignerElementCollection elements = new CellDesignerElementCollection();
+ FunctionCollectionXmlParser functionParser = new FunctionCollectionXmlParser();
+
+ Model model = new ModelFullIndexed(null);
+
+ if (params.getFilename() != null) {
+ model.setName(FilenameUtils.getBaseName(params.getFilename()));
+ }
+ speciesSbmlParser = new SpeciesCollectionXmlParser(elements);
+ aliasCollectionParser = new AliasCollectionXmlParser(elements, model);
+ compartmentCollectionXmlParser = new CompartmentCollectionXmlParser(elements);
+
+ DOMParser parser = new DOMParser();
+ try {
+ parser.parse(params.getSource());
+ } catch (IOException e) {
+ throw new InvalidInputDataExecption("IO Problem with a file: " + params.getSource().getSystemId(), e);
+ }
+ Document doc = parser.getDocument();
+ try {
+
+ // Get the document's root XML node
+ NodeList root = doc.getChildNodes();
+
+ // Navigate down the hierarchy to get to the CEO node
+ Node sbmlNode = getNode("SBML", root);
+ if (sbmlNode == null) {
+ throw new InvalidInputDataExecption("No SBML node");
+ }
+
+ Node modelNode = getNode("model", sbmlNode.getChildNodes());
+ if (modelNode == null) {
+ throw new InvalidInputDataExecption("No model node in SBML");
+ }
+ // we ignore metaid - it's useless and obstruct data model
+ // model.setMetaId(getNodeAttr("metaId", modelNode));
+ model.setIdModel(getNodeAttr("id", modelNode));
+
+ Node compartmentNode = getNode("listOfCompartments", modelNode.getChildNodes());
+ if (compartmentNode != null) {
+ List<CellDesignerCompartment> compartments = compartmentCollectionXmlParser
+ .parseXmlCompartmentCollection(compartmentNode);
+ elements.addElements(compartments);
+ }
+
+ InternalModelSpeciesData modelData = new InternalModelSpeciesData();
+
+ Node speciesNode = getNode("listOfSpecies", modelNode.getChildNodes());
+ if (speciesNode != null) {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = speciesSbmlParser
+ .parseSbmlSpeciesCollection(speciesNode);
+ modelData.updateSpecies(species);
+ }
+ Node reactionsNode = null;
+ Node functionsNode = null;
+
+ NodeList nodes = modelNode.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")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("listOfSpecies")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("listOfReactions")) {
+ reactionsNode = node;
+ } else if (node.getNodeName().equalsIgnoreCase("listOfCompartments")) {
+ // we already parsed compartments
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("notes")) {
+ String notes = rap.getNotes(node);
+ if (notes != null) {
+ notes = StringEscapeUtils.unescapeHtml4(notes);
+ }
+ model.setNotes(notes);
+ } else if (node.getNodeName().equalsIgnoreCase("listOfUnitDefinitions")) {
+ continue; // we can ignore unit definitions
+ } else if (node.getNodeName().equalsIgnoreCase("listOfFunctionDefinitions")) {
+ functionsNode = node;
+ } else {
+ throw new InvalidInputDataExecption("Unknown element of model: " + node.getNodeName());
+ }
+ }
+ }
+
+ Node annotationNode = getNode("annotation", modelNode.getChildNodes());
+ if (annotationNode == null) {
+ throw new InvalidInputDataExecption("No annotation node in SBML/model");
+ }
+
+ parseAnnotation(model, annotationNode, modelData, elements);
+
+ if (speciesNode != null) {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = speciesSbmlParser
+ .parseSbmlSpeciesCollection(speciesNode);
+ modelData.updateSpecies(species);
+ }
+ if (functionsNode!=null) {
+ model.addFunctions(functionParser.parseXmlFunctionCollection(functionsNode));
+ }
+
+ if (reactionsNode != null) {
+ ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements,
+ params.isSbgnFormat());
+ List<Reaction> reactions = reactionCollectionXmlParser.parseXmlReactionCollection(reactionsNode);
+ model.addReactions(reactions);
+ }
+
+ if (params.isSizeAutoAdjust()) {
+ Rectangle2D bound = getModelBound(model);
+ double width = bound.getWidth() + 2 * (Math.max(0, bound.getX()));
+ double height = bound.getHeight() + 2 * (Math.max(0, bound.getY()));
+
+ model.setWidth(width);
+ model.setHeight(height);
+ }
+ } catch (InvalidXmlSchemaException e) {
+ throw new InvalidInputDataExecption(e);
+ } catch (UnknownReactionClassException e) {
+ String type = e.getReactionType();
+ String reactionId = e.getReactionId();
+ String newType = null;
+ if ("CATALYSIS".equalsIgnoreCase(type)) {
+ newType = "positive influence";
+ } else if ("INHIBITION".equalsIgnoreCase(type)) {
+ newType = "negative influence";
+ } else if ("UNKNOWN_CATALYSIS".equalsIgnoreCase(type)) {
+ newType = "unknown positive influence";
+ } else if ("UNKNOWN_INHIBITION".equalsIgnoreCase(type)) {
+ newType = "unknown negative influence";
+ } else if ("PHYSICAL_STIMULATION".equalsIgnoreCase(type)) {
+ newType = "reduced physical stimulation";
+ } else if ("MODULATION".equalsIgnoreCase(type)) {
+ newType = "reduced modulation";
+ } else if ("TRIGGER".equalsIgnoreCase(type)) {
+ newType = "reduced trigger";
+ } else {
+ throw new InvalidInputDataExecption(e);
+ }
+ throw new InvalidInputDataExecption("Reaction type \"" + type + "\" is inappropriate for reaction " + reactionId
+ + ". Suggested type: " + newType + " in the \"Reduced\" notation of CellDesigner.", e);
+ } catch (CellDesignerParserException e) {
+ throw new InvalidInputDataExecption(e);
+ }
+
+ return model;
+ }
+
+ /**
+ * Computes bound of the model.
+ *
+ * @param model
+ * object for which computaion is done
+ * @return bound of the model
+ */
+ Rectangle2D getModelBound(Model model) {
+ double maxX = 0;
+ double maxY = 0;
+ double minX = model.getWidth();
+ double minY = model.getHeight();
+ for (Element alias : model.getElements()) {
+ maxX = Math.max(maxX, alias.getWidth() + alias.getX());
+ maxY = Math.max(maxY, alias.getHeight() + alias.getY());
+
+ minX = Math.min(minX, alias.getX());
+ minY = Math.min(minY, alias.getY());
+
+ }
+
+ for (Reaction reaction : model.getReactions()) {
+ for (Line2D line : reaction.getLines()) {
+ maxX = Math.max(maxX, line.getX1());
+ maxX = Math.max(maxX, line.getX2());
+ maxY = Math.max(maxY, line.getY1());
+ maxY = Math.max(maxY, line.getY2());
+
+ minX = Math.min(minX, line.getX1());
+ minX = Math.min(minX, line.getX2());
+ minY = Math.min(minY, line.getY1());
+ minY = Math.min(minY, line.getY2());
+ }
+ }
+
+ for (Layer layer : model.getLayers()) {
+ for (PolylineData lline : layer.getLines()) {
+ for (Line2D line : lline.getLines()) {
+ maxX = Math.max(maxX, line.getX1());
+ maxX = Math.max(maxX, line.getX2());
+ maxY = Math.max(maxY, line.getY1());
+ maxY = Math.max(maxY, line.getY2());
+
+ minX = Math.min(minX, line.getX1());
+ minX = Math.min(minX, line.getX2());
+ minY = Math.min(minY, line.getY1());
+ minY = Math.min(minY, line.getY2());
+ }
+ }
+ for (LayerRect rect : layer.getRectangles()) {
+ maxX = Math.max(maxX, rect.getX());
+ maxX = Math.max(maxX, rect.getX() + rect.getWidth());
+ maxY = Math.max(maxY, rect.getY());
+ maxY = Math.max(maxY, rect.getY() + rect.getHeight());
+
+ minX = Math.min(minX, rect.getX());
+ minX = Math.min(minX, rect.getX() + rect.getWidth());
+ minY = Math.min(minY, rect.getY());
+ minY = Math.min(minY, rect.getY() + rect.getHeight());
+ }
+ for (LayerOval oval : layer.getOvals()) {
+ maxX = Math.max(maxX, oval.getX());
+ maxX = Math.max(maxX, oval.getX() + oval.getWidth());
+ maxY = Math.max(maxY, oval.getY());
+ maxY = Math.max(maxY, oval.getY() + oval.getHeight());
+
+ minX = Math.min(minX, oval.getX());
+ minX = Math.min(minX, oval.getX() + oval.getWidth());
+ minY = Math.min(minY, oval.getY());
+ minY = Math.min(minY, oval.getY() + oval.getHeight());
+ }
+ for (LayerText text : layer.getTexts()) {
+ maxX = Math.max(maxX, text.getX());
+ maxX = Math.max(maxX, text.getX() + text.getWidth());
+ maxY = Math.max(maxY, text.getY());
+ maxY = Math.max(maxY, text.getY() + text.getHeight());
+
+ minX = Math.min(minX, text.getX());
+ minX = Math.min(minX, text.getX() + text.getWidth());
+ minY = Math.min(minY, text.getY());
+ minY = Math.min(minY, text.getY() + text.getHeight());
+ }
+ }
+
+ Rectangle2D result = new Rectangle2D.Double(minX, minY, maxX - minX, maxY - minY);
+ return result;
+ }
+
+ /**
+ * Parse annotation part of CellDesigner xml.
+ *
+ * @param model
+ * model that is parsed (and will be updated)
+ * @param modelData
+ * object conmtaining infoirmation about species during CellDesigner
+ * parsing
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ * @param annotationNode
+ * xml node to parse
+ * @throws InvalidXmlSchemaException
+ * thrown when xmlString is invalid
+ */
+ private void parseAnnotation(Model model, Node annotationNode, InternalModelSpeciesData modelData,
+ CellDesignerElementCollection elements) throws InvalidXmlSchemaException {
+ SpeciesCollectionXmlParser parser = new SpeciesCollectionXmlParser(elements);
+
+ Node extensionNode = getNode("celldesigner:extension", annotationNode.getChildNodes());
+ if (extensionNode == null) {
+ throw new InvalidXmlSchemaException("No celldesigner:extension node in SBML/model/annotation");
+ }
+
+ NodeList nodes = extensionNode.getChildNodes();
+ Node includedSpecies = null;
+ Node listofSpeciesAlias = null;
+ Node listOfComplexSpeciesAlias = null;
+ Node listOfComparmentAlias = null;
+ Node listOfProteins = null;
+ Node listOfGenes = null;
+ Node listOfRnas = null;
+ Node listOfGroups = null;
+ Node listOfAntisenseRnas = null;
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:modelVersion")) {
+ // we ignore map version (there is no use for us)
+ // model.setVersion(getNodeValue(node));
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:modelDisplay")) {
+ model.setWidth(getNodeAttr("sizeX", node));
+ model.setHeight(getNodeAttr("sizeY", node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfSpeciesAliases")) {
+ listofSpeciesAlias = node;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfComplexSpeciesAliases")) {
+ listOfComplexSpeciesAlias = node;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfProteins")) {
+ listOfProteins = node;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfGenes")) {
+ listOfGenes = node;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfRNAs")) {
+ listOfRnas = node;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfAntisenseRNAs")) {
+ listOfAntisenseRnas = node;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfIncludedSpecies")) {
+ includedSpecies = node;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfCompartmentAliases")) {
+ listOfComparmentAlias = node;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfLayers")) {
+ model.addLayers(layerParser.parseLayers(node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfGroups")) {
+ listOfGroups = node;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfBlockDiagrams")) {
+ layerParser.parseBlocks(model, node);
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of annotation: " + node.getNodeName());
+ }
+ }
+ }
+
+ if (listOfComparmentAlias != null) {
+ List<Compartment> aliases = aliasCollectionParser.parseXmlCompartmentAliasCollection(listOfComparmentAlias);
+ for (Element alias : aliases) {
+ rap.processNotes(alias);
+ model.addElement(alias);
+ }
+ }
+
+ if (includedSpecies != null) {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser
+ .parseIncludedSpeciesCollection(includedSpecies);
+ modelData.updateSpecies(species);
+ }
+
+ if (listOfProteins != null) {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseXmlProteinCollection(listOfProteins);
+ modelData.updateSpecies(species);
+ }
+ if (listOfGenes != null) {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseXmlGeneCollection(listOfGenes);
+ modelData.updateSpecies(species);
+ }
+ if (listOfRnas != null) {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseXmlRnaCollection(listOfRnas);
+ modelData.updateSpecies(species);
+ }
+ if (listOfAntisenseRnas != null) {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser
+ .parseXmlAntisenseRnaCollection(listOfAntisenseRnas);
+ modelData.updateSpecies(species);
+ }
+
+ for (CellDesignerSpecies<?> species : modelData.getAll()) {
+ if (!species.getElementId().equals("")) {
+ elements.addElement(species);
+ } else {
+ logger.warn("Species (class: " + species.getClass().getName() + ", name: " + species.getName()
+ + ") exists in CD file, but is never instantiated. It's CellDesigner file problem.");
+ }
+ }
+
+ if (listOfComplexSpeciesAlias != null) {
+ List<Complex> aliases = aliasCollectionParser.parseXmlComplexAliasCollection(listOfComplexSpeciesAlias);
+ for (Element alias : aliases) {
+ rap.processNotes(alias);
+ model.addElement(alias);
+ }
+ }
+
+ if (listofSpeciesAlias != null) {
+ List<Species> aliases = aliasCollectionParser.parseXmlSpeciesAliasCollection(listofSpeciesAlias);
+ for (Element alias : aliases) {
+ rap.processNotes(alias);
+ model.addElement(alias);
+ }
+ }
+
+ if (includedSpecies != null) {
+ parseAnnotationAliasesConnections(model, getNode("celldesigner:listOfSpeciesAliases", nodes));
+ parseAnnotationComplexAliasesConnections(model, getNode("celldesigner:listOfComplexSpeciesAliases", nodes));
+ }
+
+ if (listOfGroups != null) {
+ layerParser.parseGroups(model, listOfGroups);
+ }
+
+ }
+
+ /**
+ * Parses celldesigner:listOfComplexSpeciesAliases node for annotation part of
+ * the CellDEsigner format.
+ *
+ * @param model
+ * model that is parsed
+ * @param aliasNode
+ * node to parse
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ void parseAnnotationComplexAliasesConnections(Model model, Node aliasNode) throws InvalidXmlSchemaException {
+ NodeList nodes = aliasNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:complexSpeciesAlias")) {
+ String aliasId = getNodeAttr("id", node);
+ String complexId = getNodeAttr("complexSpeciesAlias", node);
+ Complex alias = model.getElementByElementId(aliasId);
+ if (alias == null) {
+ throw new InvalidXmlSchemaException("Alias does not exist " + aliasId);
+ }
+ Complex parentComplex = model.getElementByElementId(complexId);
+ if (parentComplex != null) {
+ parentComplex.addSpecies(alias);
+ alias.setComplex(parentComplex);
+ }
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of celldesigner:listOfComplexSpeciesAliases: " + node.getNodeName());
+ }
+ }
+ }
+
+ }
+
+ /**
+ * Parses celldesigner:listOfSpeciesAliases node for annotation part of the
+ * CellDesigner format.
+ *
+ * @param model
+ * model that is parsed
+ * @param aliasNode
+ * node to parse
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ void parseAnnotationAliasesConnections(Model model, Node aliasNode) throws InvalidXmlSchemaException {
+ NodeList nodes = aliasNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:speciesAlias")) {
+ String aliasId = getNodeAttr("id", node);
+ String complexId = getNodeAttr("complexSpeciesAlias", node);
+ Element alias = model.getElementByElementId(aliasId);
+ if (alias == null) {
+ throw new InvalidXmlSchemaException("Alias does not exist " + aliasId);
+ } else if (alias instanceof Species) {
+ Species species = ((Species) alias);
+ Complex complex = model.getElementByElementId(complexId);
+ if (complex != null) {
+ species.setComplex(complex);
+ complex.addSpecies(species);
+ }
+ }
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of celldesigner:listOfSpeciesAliases: " + node.getNodeName());
+ }
+ }
+ }
+ }
+
+ /**
+ * Transforms model into CellDesigner xml.
+ *
+ * @param model
+ * model that should be transformed
+ * @return CellDesigner xml string for the model
+ * @throws InconsistentModelException
+ * thrown when then model is invalid
+ */
+ public String toXml(Model model) throws InconsistentModelException {
+ CellDesignerElementCollection elements = new CellDesignerElementCollection();
+
+ SpeciesCollectionXmlParser speciesCollectionXmlParser = new SpeciesCollectionXmlParser(elements);
+ ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements, false);
+ aliasCollectionParser = new AliasCollectionXmlParser(elements, model);
+
+ StringBuilder result = new StringBuilder();
+ result.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
+ result.append("<sbml xmlns=\"http://www.sbml.org/sbml/level2/version4\" "
+ + "xmlns:celldesigner=\"http://www.sbml.org/2001/ns/celldesigner\" level=\"2\" version=\"4\">\n");
+ // metaid is a strang cell designer id, usually it's model id and as far as
+ // we can tell it's not used at all
+ result.append("<model metaid=\"" + model.getIdModel() + "\" id=\"" + model.getIdModel() + "\">\n");
+
+ if (model.getNotes() != null) {
+ result.append("<notes>");
+ result.append(escapeXml(model.getNotes()));
+ result.append("</notes>");
+ }
+
+ result.append(annotationToXml(model, elements));
+
+ compartmentCollectionXmlParser = new CompartmentCollectionXmlParser(elements);
+
+ result.append(compartmentCollectionXmlParser.toXml(model.getCompartments()));
+
+ result.append(speciesCollectionXmlParser.speciesCollectionToSbmlString(model.getSpeciesList()));
+
+ result.append(reactionCollectionXmlParser.reactionCollectionToXmlString(model.getReactions()));
+
+ result.append("</model>");
+ result.append("</sbml>");
+ return result.toString();
+ }
+
+ /**
+ * Generates xml node that should be in annotation part of the model.
+ *
+ * @param model
+ * model to transform
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ * @return annotation xml string for the model
+ */
+ private String annotationToXml(Model model, CellDesignerElementCollection elements) {
+ SpeciesCollectionXmlParser speciesCollectionXmlParser = new SpeciesCollectionXmlParser(elements);
+
+ StringBuilder result = new StringBuilder();
+ result.append("<annotation>\n");
+ result.append("<celldesigner:extension>\n");
+ result.append("<celldesigner:modelVersion>4.0</celldesigner:modelVersion>\n");
+ result.append("<celldesigner:modelDisplay sizeX=\"" + model.getWidth().intValue() + "\" sizeY=\""
+ + model.getHeight().intValue() + "\"/>\n");
+
+ result.append(speciesCollectionXmlParser.speciesCollectionToXmlIncludedString(model.getSpeciesList()));
+
+ result.append(aliasCollectionParser.compartmentAliasCollectionToXmlString(model.getCompartments()));
+ result.append(aliasCollectionParser.complexAliasCollectionToXmlString(model.getComplexList()));
+ result.append(aliasCollectionParser.speciesAliasCollectionToXmlString(model.getNotComplexSpeciesList()));
+
+ List<Protein> proteins = new ArrayList<>();
+ List<Gene> genes = new ArrayList<>();
+ List<Rna> rnas = new ArrayList<>();
+ List<AntisenseRna> antisenseRnas = new ArrayList<>();
+ for (Element element : model.getElements()) {
+ if (element instanceof Protein) {
+ proteins.add((Protein) element);
+ } else if (element instanceof Gene) {
+ genes.add((Gene) element);
+ } else if (element instanceof AntisenseRna) {
+ antisenseRnas.add((AntisenseRna) element);
+ } else if (element instanceof Rna) {
+ rnas.add((Rna) element);
+ }
+ }
+
+ result.append(speciesCollectionXmlParser.proteinCollectionToXmlString(proteins));
+ result.append(speciesCollectionXmlParser.geneCollectionToXmlString(genes));
+ result.append(speciesCollectionXmlParser.rnaCollectionToXmlString(rnas));
+ result.append(speciesCollectionXmlParser.antisenseRnaCollectionToXmlString(antisenseRnas));
+ result.append(layerParser.layerCollectionToXml(model.getLayers()));
+
+ result.append("</celldesigner:extension>\n");
+ result.append("</annotation>\n");
+ return result.toString();
+ }
+
+ @Override
+ public InputStream exportModelToInputStream(Model model) throws InconsistentModelException {
+ String exportedString = toXml(model);
+ InputStream inputStream = new ByteArrayInputStream(exportedString.getBytes());
+ return inputStream;
+ }
+
+ @Override
+ public File exportModelToFile(Model model, String filePath) throws InconsistentModelException, IOException {
+ File file = new File(filePath);
+ String exportedString = toXml(model);
+ FileWriter fileWriter = new FileWriter(file);
+ fileWriter.write(exportedString);
+ fileWriter.flush();
+ fileWriter.close();
+
+ return file;
+ }
+
+ @Override
+ public String getCommonName() {
+ return "CellDesigner SBML";
+ }
+
+ @Override
+ public MimeType getMimeType() {
+ return MimeType.SBML;
+ }
+
+ @Override
+ public String getFileExtension() {
+ return "xml";
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionCollectionXmlParser.java
new file mode 100644
index 0000000000..ceeaa4963e
--- /dev/null
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionCollectionXmlParser.java
@@ -0,0 +1,24 @@
+package lcsb.mapviewer.converter.model.celldesigner.function;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.model.map.SbmlFunction;
+
+public class FunctionCollectionXmlParser extends XmlParser {
+
+ private FunctionXmlParser functionParser = new FunctionXmlParser();
+
+ public Set<SbmlFunction> parseXmlFunctionCollection(Node functionsNode) throws InvalidXmlSchemaException {
+ Set<SbmlFunction> result = new HashSet<>();
+ for (Node node : super.getNodes("functionDefinition", functionsNode.getChildNodes())) {
+ result.add(functionParser.parseFunction(node));
+ }
+ return result;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParser.java
new file mode 100644
index 0000000000..b25b2829d1
--- /dev/null
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParser.java
@@ -0,0 +1,44 @@
+package lcsb.mapviewer.converter.model.celldesigner.function;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.model.map.SbmlFunction;
+
+public class FunctionXmlParser extends XmlParser {
+ Logger logger = Logger.getLogger(FunctionXmlParser.class);
+
+ public SbmlFunction parseFunction(Node functionNode) throws InvalidXmlSchemaException {
+ String functionId = getNodeAttr("id", functionNode);
+
+ SbmlFunction result = new SbmlFunction(functionId);
+ result.setName(getNodeAttr("name", functionNode));
+ Node mathDefinition = getNode("math", functionNode);
+ if (mathDefinition == null) {
+ throw new InvalidXmlSchemaException("Function " + functionId + " doesn't contain MathML definition (math node)");
+ }
+ result.setDefinition(nodeToString(mathDefinition));
+ result.setArguments(parseArgumentsFromMath(mathDefinition, functionId));
+
+ return result;
+ }
+
+ private List<String> parseArgumentsFromMath(Node mathDefinition, String functionId) throws InvalidXmlSchemaException {
+ List<String> result = new ArrayList<>();
+ Node lambdaDefinition = getNode("lambda", mathDefinition);
+ if (lambdaDefinition == null) {
+ throw new InvalidXmlSchemaException("Function " + functionId + " doesn't contain valid MathML lambda node");
+ }
+ List<Node> variables = super.getNodes("bvar", lambdaDefinition.getChildNodes());
+ for (Node node : variables) {
+ result.add(getNodeValue(getNode("ci", node)).trim());
+ }
+ return result;
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
index ac9d237edf..6484b40970 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
@@ -36,342 +36,358 @@ import lcsb.mapviewer.model.map.species.field.ModificationState;
import lcsb.mapviewer.modelutils.map.ElementUtils;
public class ComplexParserTests extends CellDesignerTestFunctions {
- Logger logger = Logger.getLogger(ComplexParserTests.class);
-
- ElementUtils eu = new ElementUtils();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseCompartmens() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/centeredAnchorInModifier.xml");
-
- assertEquals(0, model.getCompartments().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseBubbles() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/bubbles.xml");
-
- Element species = model.getElementByElementId("sa6");
- assertNotNull(species);
- Protein protein = (Protein) species;
- assertTrue(protein.getModificationResidues().size() > 0);
- assertNotNull(protein.getStructuralState());
- assertFalse(protein.getStructuralState().equals(""));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseCompartmensRelation() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/problematic/elements_in_compartments.xml");
-
- List<Element> aliases = new ArrayList<>();
- aliases.add(model.getElementByElementId("csa3"));
- aliases.add(model.getElementByElementId("csa4"));
- aliases.add(model.getElementByElementId("csa5"));
- aliases.add(model.getElementByElementId("csa6"));
- aliases.add(model.getElementByElementId("sa3"));
- aliases.add(model.getElementByElementId("sa5"));
- aliases.add(model.getElementByElementId("sa6"));
- aliases.add(model.getElementByElementId("sa7"));
- aliases.add(model.getElementByElementId("sa8"));
- aliases.add(model.getElementByElementId("sa9"));
- aliases.add(model.getElementByElementId("sa10"));
- aliases.add(model.getElementByElementId("sa11"));
- aliases.add(model.getElementByElementId("sa12"));
- aliases.add(model.getElementByElementId("sa13"));
- aliases.add(model.getElementByElementId("sa14"));
- aliases.add(model.getElementByElementId("sa15"));
- aliases.add(model.getElementByElementId("sa16"));
- aliases.add(model.getElementByElementId("sa17"));
- aliases.add(model.getElementByElementId("sa18"));
- aliases.add(model.getElementByElementId("sa19"));
- aliases.add(model.getElementByElementId("sa20"));
- for (Element alias : aliases) {
- assertNotNull(eu.getElementTag(alias) + " does not contain info about compartment", alias.getCompartment());
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseProteins() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/problematic/acetyled_protein.xml");
-
- Set<ModificationState> residues = new HashSet<ModificationState>();
- for (Element element : model.getElements()) {
- if (element instanceof Species) {
- Protein p = (Protein) element;
- for (ModificationResidue mr : p.getModificationResidues()) {
- residues.add(mr.getState());
- }
- }
- }
- // we have a protein which is acetylated and not acetylated so two types
- // of residues
- assertEquals(2, residues.size());
-
- assertEquals(ModificationState.ACETYLATED, ((Protein) model.getElementByElementId("sa2")).getModificationResidues().get(0).getState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testNotesComplexesInNested() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/includedSpecies.xml");
- Element species = model.getElementByElementId("sa1");
- assertNotNull(species);
- assertNotNull(species.getNotes());
- assertTrue("Wrong notes: " + species.getNotes(), species.getNotes().contains("hello world"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHypotheticalComplex() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/problematic/hypothetical_complex.xml");
- Complex species = (Complex) model.getElementByElementId("csa1");
- assertTrue(species.isHypothetical());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProblematicAcetylation() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/problematic/problematic_acetylation.xml");
- Protein p1 = (Protein) model.getElementByElementId("sa73");
- Protein p2 = (Protein) model.getElementByElementId("sa27");
- assertEquals(ModificationState.ACETYLATED, p1.getModificationResidues().get(0).getState());
- assertFalse(ModificationState.ACETYLATED.equals(p2.getModificationResidues().get(0).getState()));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDuplicateMiriam() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/problematic/duplicated_miriam.xml");
- Protein p1 = (Protein) model.getElementByElementId("sa1");
- Set<String> ids = new HashSet<>();
-
- assertTrue(p1.getMiriamData().size() > 0);
- for (MiriamData md : p1.getMiriamData()) {
- if (md.getDataType().equals(MiriamType.PUBMED)) {
- assertFalse("Protein contains double pubmed annotation for pubmed id: " + md.getResource(), ids.contains(md.getResource()));
- ids.add(md.getResource());
- }
- }
- assertTrue(ids.size() > 0);
- assertEquals(2, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testKappaInDescription() throws Exception {
- try {
- Model model = getModelForFile("testFiles/problematic/kappa_example.xml");
-
- Element species = model.getElementByElementId("sa1");
-
- assertFalse(species.getName().toLowerCase().contains("kappa"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testMissingXmlNodes() throws Exception {
- try {
- Model model = getModelForFile("testFiles/missing_xml_nodes.xml");
-
- assertTrue(((Species) model.getElementByElementId("sa3")).isHypothetical());
- assertTrue(((Species) model.getElementByElementId("sa4")).isHypothetical());
- assertTrue(((Species) model.getElementByElementId("sa5")).isHypothetical());
-
- assertFalse(((Species) model.getElementByElementId("sa12")).isHypothetical());
- assertFalse(((Species) model.getElementByElementId("sa13")).isHypothetical());
- assertFalse(((Species) model.getElementByElementId("sa14")).isHypothetical());
- assertFalse(((Species) model.getElementByElementId("sa15")).isHypothetical());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParsingSpecialCharactersInName() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- model.setIdModel("as");
- model.setWidth(100);
- model.setHeight(100);
- GenericProtein alias = new GenericProtein("aid");
- alias.setName("name & no-name");
- model.addElement(alias);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String string = parser.toXml(model);
-
- InputStream stream = new ByteArrayInputStream(string.getBytes(StandardCharsets.UTF_8));
-
- ConverterParams params = new ConverterParams().inputStream(stream).sizeAutoAdjust(false);
-
- Model model2 = parser.createModel(params);
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParsingEndLineInName() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- model.setIdModel("as");
- model.setWidth(100);
- model.setHeight(100);
- GenericProtein alias = new GenericProtein("aid");
- alias.setName("name\rno-name");
- model.addElement(alias);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String string = parser.toXml(model);
-
- InputStream stream = new ByteArrayInputStream(string.getBytes(StandardCharsets.UTF_8));
-
- ConverterParams params = new ConverterParams().inputStream(stream).sizeAutoAdjust(false);
-
- Model model2 = parser.createModel(params);
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testWarningInParser() throws Exception {
- try {
- getModelForFile("testFiles/problematic/invalid_elements_name.xml");
- assertTrue(getWarnings().size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRnaWithRegion() throws Exception {
- try {
- Model model = getModelForFile("testFiles/rnaWithRegion.xml");
- for (Element species : model.getNotComplexSpeciesList()) {
- Rna rna = (Rna) species;
- assertEquals(1, rna.getRegions().size());
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProtinWithModifications() throws Exception {
- try {
- Model model = getModelForFile("testFiles/proteinWithEverPossibleModification.xml");
- Protein protein = (Protein) model.getElementByElementId("sa1");
- assertEquals(14, protein.getModificationResidues().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAntisenseRnaWithRegion() throws Exception {
- try {
- Model model = getModelForFile("testFiles/antisenseRnaWithRegion.xml");
- for (Species species : model.getNotComplexSpeciesList()) {
- AntisenseRna rna = (AntisenseRna) species;
- assertEquals(1, rna.getRegions().size());
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPhosporylatedProteinToXml() throws Exception {
- try {
- Model model = getModelForFile("testFiles/problematic/phosphorylated_protein.xml");
- model.setName(null);
- CellDesignerXmlParser p = new CellDesignerXmlParser();
- String xml = p.toXml(model);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = p.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- ModelComparator comparator = new ModelComparator();
- assertEquals(0, comparator.compare(model, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Logger logger = Logger.getLogger(ComplexParserTests.class);
+
+ ElementUtils eu = new ElementUtils();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseFunctions() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/function.xml");
+
+ assertEquals(1, model.getFunctions().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseCompartmens() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/centeredAnchorInModifier.xml");
+
+ assertEquals(0, model.getCompartments().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseBubbles() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/bubbles.xml");
+
+ Element species = model.getElementByElementId("sa6");
+ assertNotNull(species);
+ Protein protein = (Protein) species;
+ assertTrue(protein.getModificationResidues().size() > 0);
+ assertNotNull(protein.getStructuralState());
+ assertFalse(protein.getStructuralState().equals(""));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseCompartmensRelation() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/problematic/elements_in_compartments.xml");
+
+ List<Element> aliases = new ArrayList<>();
+ aliases.add(model.getElementByElementId("csa3"));
+ aliases.add(model.getElementByElementId("csa4"));
+ aliases.add(model.getElementByElementId("csa5"));
+ aliases.add(model.getElementByElementId("csa6"));
+ aliases.add(model.getElementByElementId("sa3"));
+ aliases.add(model.getElementByElementId("sa5"));
+ aliases.add(model.getElementByElementId("sa6"));
+ aliases.add(model.getElementByElementId("sa7"));
+ aliases.add(model.getElementByElementId("sa8"));
+ aliases.add(model.getElementByElementId("sa9"));
+ aliases.add(model.getElementByElementId("sa10"));
+ aliases.add(model.getElementByElementId("sa11"));
+ aliases.add(model.getElementByElementId("sa12"));
+ aliases.add(model.getElementByElementId("sa13"));
+ aliases.add(model.getElementByElementId("sa14"));
+ aliases.add(model.getElementByElementId("sa15"));
+ aliases.add(model.getElementByElementId("sa16"));
+ aliases.add(model.getElementByElementId("sa17"));
+ aliases.add(model.getElementByElementId("sa18"));
+ aliases.add(model.getElementByElementId("sa19"));
+ aliases.add(model.getElementByElementId("sa20"));
+ for (Element alias : aliases) {
+ assertNotNull(eu.getElementTag(alias) + " does not contain info about compartment", alias.getCompartment());
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseProteins() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/problematic/acetyled_protein.xml");
+
+ Set<ModificationState> residues = new HashSet<ModificationState>();
+ for (Element element : model.getElements()) {
+ if (element instanceof Species) {
+ Protein p = (Protein) element;
+ for (ModificationResidue mr : p.getModificationResidues()) {
+ residues.add(mr.getState());
+ }
+ }
+ }
+ // we have a protein which is acetylated and not acetylated so two types
+ // of residues
+ assertEquals(2, residues.size());
+
+ assertEquals(ModificationState.ACETYLATED,
+ ((Protein) model.getElementByElementId("sa2")).getModificationResidues().get(0).getState());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testNotesComplexesInNested() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/includedSpecies.xml");
+ Element species = model.getElementByElementId("sa1");
+ assertNotNull(species);
+ assertNotNull(species.getNotes());
+ assertTrue("Wrong notes: " + species.getNotes(), species.getNotes().contains("hello world"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHypotheticalComplex() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/problematic/hypothetical_complex.xml");
+ Complex species = (Complex) model.getElementByElementId("csa1");
+ assertTrue(species.isHypothetical());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProblematicAcetylation() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/problematic/problematic_acetylation.xml");
+ Protein p1 = (Protein) model.getElementByElementId("sa73");
+ Protein p2 = (Protein) model.getElementByElementId("sa27");
+ assertEquals(ModificationState.ACETYLATED, p1.getModificationResidues().get(0).getState());
+ assertFalse(ModificationState.ACETYLATED.equals(p2.getModificationResidues().get(0).getState()));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDuplicateMiriam() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/problematic/duplicated_miriam.xml");
+ Protein p1 = (Protein) model.getElementByElementId("sa1");
+ Set<String> ids = new HashSet<>();
+
+ assertTrue(p1.getMiriamData().size() > 0);
+ for (MiriamData md : p1.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.PUBMED)) {
+ assertFalse("Protein contains double pubmed annotation for pubmed id: " + md.getResource(),
+ ids.contains(md.getResource()));
+ ids.add(md.getResource());
+ }
+ }
+ assertTrue(ids.size() > 0);
+ assertEquals(2, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testKappaInDescription() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/problematic/kappa_example.xml");
+
+ Element species = model.getElementByElementId("sa1");
+
+ assertFalse(species.getName().toLowerCase().contains("kappa"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testMissingXmlNodes() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/missing_xml_nodes.xml");
+
+ assertTrue(((Species) model.getElementByElementId("sa3")).isHypothetical());
+ assertTrue(((Species) model.getElementByElementId("sa4")).isHypothetical());
+ assertTrue(((Species) model.getElementByElementId("sa5")).isHypothetical());
+
+ assertFalse(((Species) model.getElementByElementId("sa12")).isHypothetical());
+ assertFalse(((Species) model.getElementByElementId("sa13")).isHypothetical());
+ assertFalse(((Species) model.getElementByElementId("sa14")).isHypothetical());
+ assertFalse(((Species) model.getElementByElementId("sa15")).isHypothetical());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParsingSpecialCharactersInName() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ model.setIdModel("as");
+ model.setWidth(100);
+ model.setHeight(100);
+ GenericProtein alias = new GenericProtein("aid");
+ alias.setName("name & no-name");
+ model.addElement(alias);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String string = parser.toXml(model);
+
+ InputStream stream = new ByteArrayInputStream(string.getBytes(StandardCharsets.UTF_8));
+
+ ConverterParams params = new ConverterParams().inputStream(stream).sizeAutoAdjust(false);
+
+ Model model2 = parser.createModel(params);
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParsingEndLineInName() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ model.setIdModel("as");
+ model.setWidth(100);
+ model.setHeight(100);
+ GenericProtein alias = new GenericProtein("aid");
+ alias.setName("name\rno-name");
+ model.addElement(alias);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String string = parser.toXml(model);
+
+ InputStream stream = new ByteArrayInputStream(string.getBytes(StandardCharsets.UTF_8));
+
+ ConverterParams params = new ConverterParams().inputStream(stream).sizeAutoAdjust(false);
+
+ Model model2 = parser.createModel(params);
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testWarningInParser() throws Exception {
+ try {
+ getModelForFile("testFiles/problematic/invalid_elements_name.xml");
+ assertTrue(getWarnings().size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRnaWithRegion() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/rnaWithRegion.xml");
+ for (Element species : model.getNotComplexSpeciesList()) {
+ Rna rna = (Rna) species;
+ assertEquals(1, rna.getRegions().size());
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProtinWithModifications() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/proteinWithEverPossibleModification.xml");
+ Protein protein = (Protein) model.getElementByElementId("sa1");
+ assertEquals(14, protein.getModificationResidues().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAntisenseRnaWithRegion() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/antisenseRnaWithRegion.xml");
+ for (Species species : model.getNotComplexSpeciesList()) {
+ AntisenseRna rna = (AntisenseRna) species;
+ assertEquals(1, rna.getRegions().size());
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPhosporylatedProteinToXml() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/problematic/phosphorylated_protein.xml");
+ model.setName(null);
+ CellDesignerXmlParser p = new CellDesignerXmlParser();
+ String xml = p.toXml(model);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = p.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ ModelComparator comparator = new ModelComparator();
+ assertEquals(0, comparator.compare(model, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParserTest.java
new file mode 100644
index 0000000000..71af481a35
--- /dev/null
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParserTest.java
@@ -0,0 +1,49 @@
+package lcsb.mapviewer.converter.model.celldesigner.function;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.IOException;
+
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.model.map.SbmlFunction;
+
+public class FunctionXmlParserTest extends CellDesignerTestFunctions {
+
+ FunctionXmlParser parser = new FunctionXmlParser();
+
+ @Test
+ public void testParseBasicData() throws InvalidXmlSchemaException, IOException {
+ SbmlFunction fun = parser
+ .parseFunction(super.getXmlDocumentFromFile("testFiles/function/simple.xml").getFirstChild());
+ assertNotNull(fun);
+ assertEquals(fun.getFunctionId(), "function_id");
+ assertEquals(fun.getName(), "Function name");
+ assertTrue(fun.getDefinition().indexOf("lambda") >= 0);
+ assertTrue(fun.getDefinition().indexOf("apply") >= 0);
+ }
+
+ @Test
+ public void testParseArgumentsData() throws InvalidXmlSchemaException, IOException {
+ SbmlFunction fun = parser
+ .parseFunction(super.getXmlDocumentFromFile("testFiles/function/simple.xml").getFirstChild());
+ assertNotNull(fun);
+ assertEquals(fun.getArguments().size(), 2);
+ assertEquals(fun.getArguments().get(0), "x");
+ }
+
+ @Test(expected = InvalidXmlSchemaException.class)
+ public void testParseInvalidDefinition() throws InvalidXmlSchemaException, IOException {
+ parser.parseFunction(super.getXmlDocumentFromFile("testFiles/function/invalid_definition.xml").getFirstChild());
+ }
+
+ @Test(expected = InvalidXmlSchemaException.class)
+ public void testParseInvalidMathMLNode() throws InvalidXmlSchemaException, IOException {
+ parser.parseFunction(super.getXmlDocumentFromFile("testFiles/function/invalid_math.xml").getFirstChild());
+ }
+
+}
diff --git a/converter-CellDesigner/testFiles/function.xml b/converter-CellDesigner/testFiles/function.xml
new file mode 100644
index 0000000000..acdb36ed9a
--- /dev/null
+++ b/converter-CellDesigner/testFiles/function.xml
@@ -0,0 +1,70 @@
+<?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>
+</annotation>
+<listOfFunctionDefinitions>
+<functionDefinition metaid="function_id" id="function_id" name="Function name">
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<lambda>
+<bvar>
+<ci> x </ci>
+</bvar>
+<bvar>
+<ci> y </ci>
+</bvar>
+<apply>
+<plus/>
+<ci> x </ci>
+<ci> y </ci>
+</apply>
+</lambda>
+</math>
+</functionDefinition>
+</listOfFunctionDefinitions>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00006" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00007" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00008" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+</model>
+</sbml>
diff --git a/converter-CellDesigner/testFiles/function/invalid_definition.xml b/converter-CellDesigner/testFiles/function/invalid_definition.xml
new file mode 100644
index 0000000000..185faad8a7
--- /dev/null
+++ b/converter-CellDesigner/testFiles/function/invalid_definition.xml
@@ -0,0 +1,2 @@
+<functionDefinition metaid="function_id" id="function_id" name="Function name">
+</functionDefinition>
diff --git a/converter-CellDesigner/testFiles/function/invalid_math.xml b/converter-CellDesigner/testFiles/function/invalid_math.xml
new file mode 100644
index 0000000000..81df2b0f89
--- /dev/null
+++ b/converter-CellDesigner/testFiles/function/invalid_math.xml
@@ -0,0 +1,4 @@
+<functionDefinition metaid="function_id" id="function_id" name="Function name">
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+</math>
+</functionDefinition>
diff --git a/converter-CellDesigner/testFiles/function/simple.xml b/converter-CellDesigner/testFiles/function/simple.xml
new file mode 100644
index 0000000000..8f43b43daa
--- /dev/null
+++ b/converter-CellDesigner/testFiles/function/simple.xml
@@ -0,0 +1,17 @@
+<functionDefinition metaid="function_id" id="function_id" name="Function name">
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<lambda>
+<bvar>
+<ci> x </ci>
+</bvar>
+<bvar>
+<ci> y </ci>
+</bvar>
+<apply>
+<plus/>
+<ci> x </ci>
+<ci> y </ci>
+</apply>
+</lambda>
+</math>
+</functionDefinition>
--
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