Commit fc66fc2c authored by Piotr Gawron's avatar Piotr Gawron
Browse files

visualization of sbml function removes lambda expression and provides only the function

parent 9596d419
Pipeline #4152 failed with stage
in 59 seconds
{"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
[{"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
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) {
......
......@@ -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 {
......
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 {
}
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"));
}
}
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment