Merge branch '286-sbml-function-visualization' into 'master'

Resolve "sbml function visualization"

Closes #286

See merge request piotr.gawron/minerva!229

frontend-js/testFiles/apiCalls/projects/kinteics_test/models/all/functions/7/token=MOCK_TOKEN_ID&

-{"arguments":["x","y"],"definition":"<math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n<lambda>\n<bvar>\n<ci> x </ci>\n</bvar>\n<bvar>\n<ci> y </ci>\n</bvar>\n<apply>\n<plus/>\n<ci> x </ci>\n<ci> y </ci>\n<cn type=\"integer\"> 2 </cn>\n</apply>\n</lambda>\n\n</math>","functionId":"fun","id":7,"mathMlPresentation":"\n<math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n<mrow>\n<mo>λ</mo>\n<mrow>\n<mo>(</mo>\n<mi> x </mi>\n<mo>,</mo>\n<mi> y </mi>\n<mo>,</mo>\n<mrow>\n<mi> x </mi>\n<mo>+</mo>\n<mi> y </mi>\n<mo>+</mo>\n<mn> 2 </mn>\n</mrow>\n<mo>)</mo>\n</mrow>\n</mrow>\n\n</math>\n","name":"fun"}
\ No newline at end of file
+{"arguments":["x","y"],"definition":"<math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n<lambda>\n<bvar>\n<ci> x </ci>\n</bvar>\n<bvar>\n<ci> y </ci>\n</bvar>\n<apply>\n<plus/>\n<ci> x </ci>\n<ci> y </ci>\n<cn type=\"integer\"> 2 </cn>\n</apply>\n</lambda>\n\n</math>","functionId":"fun","id":7,"mathMlPresentation":"\n<math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n\n\n\n<mrow>\n<mi> x </mi>\n<mo>+</mo>\n<mi> y </mi>\n<mo>+</mo>\n<mn> 2 </mn>\n</mrow>\n\n\n</math>\n","name":"fun"}
\ No newline at end of file

frontend-js/testFiles/apiCalls/projects/sample/miRnas.search/query=hsa-miR-125a-3p&token=MOCK_TOKEN_ID&

-[{"id":"hsa-miR-125a-3p","name":"hsa-miR-125a-3p","targets":[{"name":"FYN","references":[{"annotatorClassName":"","article":{"title":"microRNA-125a-3p reduces cell proliferation and migration by targeting Fyn.","authors":["Ninio-Many L"," Grossman H"," Shomron N"," Chuderland D"," Shalgi R."],"journal":"Journal of cell science","year":2013,"link":"http://www.ncbi.nlm.nih.gov/pubmed/23606749","id":"23606749","citationCount":18,"stringAuthors":"Ninio-Many L,  Grossman H,  Shomron N,  Chuderland D,  Shalgi R."},"descriptionByType":"","descriptionByTypeRelation":"","id":0,"link":"http://www.ncbi.nlm.nih.gov/pubmed/23606749","resource":"23606749","type":"PUBMED"}],"targetElements":[],"targetParticipants":[{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":0,"link":"http://www.genenames.org/cgi-bin/gene_symbol_report?match=FYN","resource":"FYN","type":"HGNC_SYMBOL"}]},{"name":"GPC4","references":[{"annotatorClassName":"","article":{"title":"MicroRNA-125a inhibits cell growth by targeting glypican-4.","authors":["Feng C"," Li J"," Ruan J"," Ding K."],"journal":"Glycoconjugate journal","year":2012,"link":"http://www.ncbi.nlm.nih.gov/pubmed/22644326","id":"22644326","citationCount":8,"stringAuthors":"Feng C,  Li J,  Ruan J,  Ding K."},"descriptionByType":"","descriptionByTypeRelation":"","id":0,"link":"http://www.ncbi.nlm.nih.gov/pubmed/22644326","resource":"22644326","type":"PUBMED"}],"targetElements":[],"targetParticipants":[{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":0,"link":"http://www.genenames.org/cgi-bin/gene_symbol_report?match=GPC4","resource":"GPC4","type":"HGNC_SYMBOL"}]},{"name":"RHOA","references":[{"annotatorClassName":"","article":{"title":"MiRNA-125a-3p is a negative regulator of the RhoA-actomyosin pathway in A549 cells.","authors":["Huang B"," Luo W"," Sun L"," Zhang Q"," Jiang L"," Chang J"," Qiu X"," Wang E."],"journal":"International journal of oncology","year":2013,"link":"http://www.ncbi.nlm.nih.gov/pubmed/23525486","id":"23525486","citationCount":8,"stringAuthors":"Huang B,  Luo W,  Sun L,  Zhang Q,  Jiang L,  Chang J,  Qiu X,  Wang E."},"descriptionByType":"","descriptionByTypeRelation":"","id":0,"link":"http://www.ncbi.nlm.nih.gov/pubmed/23525486","resource":"23525486","type":"PUBMED"}],"targetElements":[],"targetParticipants":[{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":0,"link":"http://www.genenames.org/cgi-bin/gene_symbol_report?match=RHOA","resource":"RHOA","type":"HGNC_SYMBOL"}]}]}]
\ No newline at end of file
+[{"id":"hsa-miR-125a-3p","name":"hsa-miR-125a-3p","targets":[{"name":"FYN","references":[{"annotatorClassName":"","article":{"title":"microRNA-125a-3p reduces cell proliferation and migration by targeting Fyn.","authors":["Ninio-Many L"," Grossman H"," Shomron N"," Chuderland D"," Shalgi R."],"journal":"Journal of cell science","year":2013,"link":"http://www.ncbi.nlm.nih.gov/pubmed/23606749","id":"23606749","citationCount":25,"stringAuthors":"Ninio-Many L,  Grossman H,  Shomron N,  Chuderland D,  Shalgi R."},"descriptionByType":"","descriptionByTypeRelation":"","id":0,"link":"http://www.ncbi.nlm.nih.gov/pubmed/23606749","resource":"23606749","type":"PUBMED"}],"targetElements":[],"targetParticipants":[{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":0,"link":"http://www.genenames.org/cgi-bin/gene_symbol_report?match=FYN","resource":"FYN","type":"HGNC_SYMBOL"}]},{"name":"GPC4","references":[{"annotatorClassName":"","article":{"title":"MicroRNA-125a inhibits cell growth by targeting glypican-4.","authors":["Feng C"," Li J"," Ruan J"," Ding K."],"journal":"Glycoconjugate journal","year":2012,"link":"http://www.ncbi.nlm.nih.gov/pubmed/22644326","id":"22644326","citationCount":8,"stringAuthors":"Feng C,  Li J,  Ruan J,  Ding K."},"descriptionByType":"","descriptionByTypeRelation":"","id":0,"link":"http://www.ncbi.nlm.nih.gov/pubmed/22644326","resource":"22644326","type":"PUBMED"}],"targetElements":[],"targetParticipants":[{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":0,"link":"http://www.genenames.org/cgi-bin/gene_symbol_report?match=GPC4","resource":"GPC4","type":"HGNC_SYMBOL"}]},{"name":"RHOA","references":[{"annotatorClassName":"","article":{"title":"MiRNA-125a-3p is a negative regulator of the RhoA-actomyosin pathway in A549 cells.","authors":["Huang B"," Luo W"," Sun L"," Zhang Q"," Jiang L"," Chang J"," Qiu X"," Wang E."],"journal":"International journal of oncology","year":2013,"link":"http://www.ncbi.nlm.nih.gov/pubmed/23525486","id":"23525486","citationCount":8,"stringAuthors":"Huang B,  Luo W,  Sun L,  Zhang Q,  Jiang L,  Chang J,  Qiu X,  Wang E."},"descriptionByType":"","descriptionByTypeRelation":"","id":0,"link":"http://www.ncbi.nlm.nih.gov/pubmed/23525486","resource":"23525486","type":"PUBMED"}],"targetElements":[],"targetParticipants":[{"annotatorClassName":"","descriptionByType":"","descriptionByTypeRelation":"","id":0,"link":"http://www.genenames.org/cgi-bin/gene_symbol_report?match=RHOA","resource":"RHOA","type":"HGNC_SYMBOL"}]}]}]
\ No newline at end of file

rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsRestImpl.java

 package lcsb.mapviewer.api.projects.models.functions;
 
+import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.TreeMap;
 import java.util.List;
 import java.util.Map;
+import java.util.TreeMap;
 
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.Transformer;
 import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+import javax.xml.xpath.XPathExpressionException;
 
+import org.apache.axis.utils.ByteArrayOutputStream;
 import org.apache.log4j.Logger;
 import org.springframework.transaction.annotation.Transactional;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
 
 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;
@@ -49,15 +62,38 @@ public class FunctionsRestImpl extends BaseRestImpl {
     result.put("name", function.getName());
     result.put("definition", function.getDefinition());
     try {
-      result.put("mathMlPresentation", super.mathMLToPresentationML(function.getDefinition()));
-    } catch (IOException | InvalidXmlSchemaException | TransformerException e) {
+      String definition = extractLambda(function.getDefinition());
+      result.put("mathMlPresentation", super.mathMLToPresentationML(definition));
+    } catch (Exception e) {
       logger.error("Problems with transforming kinetics", e);
     }
     result.put("arguments", function.getArguments());
     return result;
   }
 
-  public List<Map<String, Object>> getFunctions(String projectId, String modelId, String token) throws SecurityException, QueryException {
+  protected String extractLambda(String definition)
+      throws SAXException, IOException, ParserConfigurationException, XPathExpressionException, TransformerException {
+    String result = definition.replaceAll("<lambda>", "").replaceAll("</lambda>", "");
+
+    DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
+    Document document = dbf.newDocumentBuilder().parse(new InputSource(new ByteArrayInputStream(result.getBytes())));
+
+    NodeList nodes = document.getElementsByTagName("bvar");
+    for (int i = nodes.getLength() - 1; i >= 0; i--) {
+      Node e = nodes.item(i);
+      e.getParentNode().removeChild(e);
+    }
+
+    TransformerFactory tf = TransformerFactory.newInstance();
+    Transformer t = tf.newTransformer();
+    ByteArrayOutputStream baos = new ByteArrayOutputStream();
+    t.transform(new DOMSource(document), new StreamResult(baos));
+
+    return baos.toString();
+  }
+
+  public List<Map<String, Object>> getFunctions(String projectId, String modelId, String token)
+      throws SecurityException, QueryException {
     List<Map<String, Object>> result = new ArrayList<>();
     List<Model> models = getModels(projectId, modelId, token);
     for (Model model : models) {

rest-api/src/test/java/lcsb/mapviewer/api/projects/models/AllModelsTests.java

@@ -5,13 +5,15 @@ import org.junit.runners.Suite;
 import org.junit.runners.Suite.SuiteClasses;
 
 import lcsb.mapviewer.api.projects.models.bioEntities.AllBioeEntitiesTests;
+import lcsb.mapviewer.api.projects.models.functions.AllFunctionsTests;
 import lcsb.mapviewer.api.projects.models.publications.AllPublicationsTests;
 
 @RunWith(Suite.class)
 @SuiteClasses({ //
-		AllBioeEntitiesTests.class, //
-		AllPublicationsTests.class, //
-		ModelRestImplTest.class,//
+    AllBioeEntitiesTests.class, //
+    AllFunctionsTests.class, //
+    AllPublicationsTests.class, //
+    ModelRestImplTest.class,//
 })
 public class AllModelsTests {
 

rest-api/src/test/java/lcsb/mapviewer/api/projects/models/functions/AllFunctionsTests.java

+package lcsb.mapviewer.api.projects.models.functions;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ FunctionsRestImplTest.class })
+public class AllFunctionsTests {
+
+}

rest-api/src/test/java/lcsb/mapviewer/api/projects/models/functions/FunctionsRestImplTest.java

+package lcsb.mapviewer.api.projects.models.functions;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.api.RestTestFunctions;
+
+public class FunctionsRestImplTest extends RestTestFunctions {
+  Logger logger = Logger.getLogger(FunctionsRestImplTest.class);
+
+  @Autowired
+  FunctionsRestImpl functionRestImpl;
+
+  @Test
+  public void testExtractLambda() throws Exception{
+    String lambda = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n<lambda>\n<bvar>\n<ci> x </ci>\n</bvar>\n<bvar>\n<ci> y </ci>\n</bvar>\n<apply>\n<plus/>\n<ci> x </ci>\n<ci> y </ci>\n<cn type=\"integer\"> 2 </cn>\n</apply>\n</lambda>\n\n</math>";
+    String definition = functionRestImpl.extractLambda(lambda);
+    assertNotNull(definition);
+    assertFalse(definition.contains("lambda"));
+    assertFalse(definition.contains("bvar"));
+    assertTrue(definition.contains("math"));
+    assertTrue(definition.contains("apply"));
+  }
+
+}