parser of sbml function

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionCollectionXmlParser.java

+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;
+  }
+
+}

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParser.java

+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;
+  }
+
+}

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParserTest.java

+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());
+  }
+
+}

converter-CellDesigner/testFiles/function.xml

+<?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>

converter-CellDesigner/testFiles/function/invalid_definition.xml

+<functionDefinition metaid="function_id" id="function_id" name="Function name">
+</functionDefinition>

converter-CellDesigner/testFiles/function/invalid_math.xml

+<functionDefinition metaid="function_id" id="function_id" name="Function name">
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+</math>
+</functionDefinition>

converter-CellDesigner/testFiles/function/simple.xml

+<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>