From a3129c016d6ea25fc4efdbe4dfd456ecece068f5 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 9 Feb 2018 14:28:44 +0100
Subject: [PATCH] sbml function mathML is parsed properly
---
.../model/celldesigner/function/FunctionXmlParser.java | 6 +++---
.../celldesigner/function/FunctionXmlParserTest.java | 1 +
.../converter/model/sbml/SbmlFunctionExporter.java | 3 +--
.../converter/model/sbml/SbmlFunctionParser.java | 4 +++-
.../model/map/kinetics/SbmlFunctionComparator.java | 2 +-
.../api/projects/models/functions/FunctionsRestImpl.java | 9 +++++++++
6 files changed, 18 insertions(+), 7 deletions(-)
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
index 917ca54b97..9031ca2f6a 100644
--- 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
@@ -22,7 +22,9 @@ public class FunctionXmlParser extends XmlParser {
if (mathDefinition == null) {
throw new InvalidXmlSchemaException("Function " + functionId + " doesn't contain MathML definition (math node)");
}
- result.setDefinition(nodeToString(mathDefinition).replace(" xmlns=\"http://www.w3.org/1998/Math/MathML\"", ""));
+ String definition = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
+ + nodeToString(mathDefinition).replace(" xmlns=\"http://www.w3.org/1998/Math/MathML\"", "") + "</math>";
+ result.setDefinition(definition);
result.setArguments(parseArgumentsFromMath(mathDefinition, functionId));
return result;
@@ -47,9 +49,7 @@ public class FunctionXmlParser extends XmlParser {
result.append("id=\"" + fun.getElementId() + "\" ");
result.append("name=\"" + fun.getName() + "\" ");
result.append(">\n");
- result.append("<math xmlns=\"http://www.w3.org/1998/Math/MathML\">");
result.append(fun.getDefinition());
- result.append("</math>\n");
result.append("</functionDefinition>\n");
return result.toString();
}
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
index 34eaac74cb..35cc01fa93 100644
--- 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
@@ -26,6 +26,7 @@ public class FunctionXmlParserTest extends CellDesignerTestFunctions {
assertNotNull(fun);
assertEquals(fun.getFunctionId(), "function_id");
assertEquals(fun.getName(), "Function name");
+ assertTrue("math node is not present", fun.getDefinition().indexOf("math") >= 0);
assertTrue(fun.getDefinition().indexOf("lambda") >= 0);
assertTrue(fun.getDefinition().indexOf("apply") >= 0);
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionExporter.java
index 1ef4edfa9b..d534a4ff11 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionExporter.java
@@ -25,8 +25,7 @@ public class SbmlFunctionExporter {
FunctionDefinition result = new FunctionDefinition();
result.setName(unit.getName());
String definition = unit.getDefinition();
- definition = definition.replace(" xmlns=\"http://www.sbml.org/sbml/level2/version4\"", "");
- definition = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">" + definition + "</math>";
+ definition = definition.replace("lambda xmlns=\"http://www.sbml.org/sbml/level2/version4\"", "lambda");
result.setMath(ASTNode.parseMathML(definition));
result.setId(unit.getFunctionId());
return result;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionParser.java
index c2facb4d7c..cb2550ba4c 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionParser.java
@@ -26,7 +26,9 @@ public class SbmlFunctionParser extends SbmlBioEntityParser {
result.setName(unitDefinition.getName());
Node node = super.getXmlDocumentFromString(unitDefinition.getMath().toMathML());
Node mathDefinition = getNode("math", node);
- result.setDefinition(super.nodeToString(mathDefinition));
+ String definition = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
+ + nodeToString(mathDefinition).replace(" xmlns=\"http://www.w3.org/1998/Math/MathML\"", "") + "</math>";
+ result.setDefinition(definition);
result.setArguments(parseArgumentsFromMath(mathDefinition, result.getFunctionId()));
return result;
} catch (InvalidXmlSchemaException e) {
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparator.java
index 15f90d66f8..03c5f71cd1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparator.java
@@ -26,7 +26,7 @@ public class SbmlFunctionComparator extends Comparator<SbmlFunction> {
return stringComparator.compare(arg0.getName(), arg1.getName());
}
- if (stringComparator.compare(arg0.getDefinition(), arg1.getDefinition()) != 0) {
+ if (stringComparator.compare(arg0.getDefinition(), arg1.getDefinition(), true) != 0) {
logger.debug("definition different");
logger.debug(arg0.getDefinition());
logger.debug(arg1.getDefinition());
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsRestImpl.java
index 975151ba92..aa0214b288 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsRestImpl.java
@@ -1,16 +1,20 @@
package lcsb.mapviewer.api.projects.models.functions;
+import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import javax.xml.transform.TransformerException;
+
import org.apache.log4j.Logger;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.ObjectNotFoundException;
import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.SecurityException;
@@ -44,6 +48,11 @@ public class FunctionsRestImpl extends BaseRestImpl {
result.put("functionId", function.getFunctionId());
result.put("name", function.getName());
result.put("definition", function.getDefinition());
+ try {
+ result.put("mathMlPresentation", super.mathMLToPresentationML(function.getDefinition()));
+ } catch (IOException | InvalidXmlSchemaException | TransformerException e) {
+ logger.error("Problems with transforming kinetics", e);
+ }
result.put("arguments", function.getArguments());
return result;
}
--
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