Merge branch '550-export-to-sbgn-does-not-export-compartments-and-some-reactions' into 'master'

Resolve "Export to SBGN does not export compartments and some reactions"

Closes #550

See merge request !512

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java

@@ -351,7 +351,6 @@ public class RestAnnotationParser extends XmlParser {
     }
 
     if (notes.indexOf("</head>") >= 0) {
-      logger.debug("Y");
       notes = notes.substring(notes.indexOf("</head>") + "</head>".length());
     }
     notes = notes.replace("xmlns=\"http://www.w3.org/1999/xhtml\"", "");

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java

@@ -3,13 +3,25 @@
  */
 package lcsb.mapviewer.converter.model.sbgnml;
 
+import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.FileInputStream;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.OutputStream;
+import java.nio.charset.StandardCharsets;
 
 import javax.xml.bind.JAXBException;
 
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringEscapeUtils;
+import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
+import org.sbgn.SbgnUtil;
+import org.sbgn.bindings.Sbgn;
+
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
 import lcsb.mapviewer.common.MimeType;
 import lcsb.mapviewer.converter.ConverterException;
 import lcsb.mapviewer.converter.ConverterParams;
@@ -18,67 +30,95 @@ import lcsb.mapviewer.converter.InvalidInputDataExecption;
 import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.model.Model;
 
-import org.sbgn.SbgnUtil;
-import org.sbgn.bindings.Sbgn;
-
 /**
  * @author Michał Kuźma
  *
  */
 public class SbgnmlXmlConverter implements IConverter {
+  Logger logger = Logger.getLogger(SbgnmlXmlConverter.class);
+
+  @Override
+  public Model createModel(ConverterParams params) throws InvalidInputDataExecption {
+    SbgnmlXmlParser parser = new SbgnmlXmlParser();
+    return parser.createModel(params);
+  }
+
+  @Override
+  public InputStream exportModelToInputStream(Model model) throws InconsistentModelException, ConverterException {
+    EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+    Sbgn exportedData;
+    StringBuilder notes = new StringBuilder("");
+    try {
+      Logger.getRootLogger().addAppender(appender);
+      SbgnmlXmlExporter exporter = new SbgnmlXmlExporter();
+      exportedData = exporter.toSbgnml(model);
+      if (!appender.getWarnings().isEmpty()) {
+        for (LoggingEvent event : appender.getWarnings()) {
+          if (event.getMessage() instanceof String) {
+            notes.append("\n" + ((String) event.getMessage()));
+          }
+        }
+      }
+    } finally {
+      Logger.getRootLogger().removeAppender(appender);
+    }
+    try {
+      File tempFile = File.createTempFile("sbgnmlExportTempFile", ".tmp");
+      InputStream result;
+      SbgnUtil.writeToFile(exportedData, tempFile);
+      try (FileInputStream inputStream = new FileInputStream(tempFile)) {
+        String xml = IOUtils.toString(inputStream, "UTF-8");
+        if (notes.length() > 0) {
+          int position = xml.indexOf("<map language");
+          if (position < 0) {
+            throw new ConverterException("problematic output sbgn. Cannot find map tag");
+          }
+          String notesNode = "<notes><html:body xmlns:html=\"http://www.w3.org/1999/xhtml\">" +
+              StringEscapeUtils.escapeXml(notes.toString()) + "\n</html:body></notes> ";
+          xml = xml.substring(0, position) + notesNode + xml.substring(position, xml.length());
+        }
+        result = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+      }
+      return result;
+    } catch (IOException e) {
+      throw new ConverterException(e);
+    } catch (JAXBException e) {
+      throw new ConverterException(e);
+    }
+  }
 
-	@Override
-	public Model createModel(ConverterParams params) throws InvalidInputDataExecption {
-		SbgnmlXmlParser parser = new SbgnmlXmlParser();
-		return parser.createModel(params);
-	}
+  @Override
+  public File exportModelToFile(Model model, String filePath) throws InconsistentModelException, ConverterException {
+    InputStream inputStream = exportModelToInputStream(model);
 
-	@Override
-	public InputStream exportModelToInputStream(Model model) throws InconsistentModelException, ConverterException {
-		SbgnmlXmlExporter exporter = new SbgnmlXmlExporter();
-		Sbgn exportedData = exporter.toSbgnml(model);
-		File tempFile;
-		try {
-			tempFile = File.createTempFile("sbgnmlExportTempFile", ".tmp");
-			SbgnUtil.writeToFile(exportedData, tempFile);
-			InputStream result = new FileInputStream(tempFile);
-			return result;
-		} catch (IOException e) {
-			throw new ConverterException(e);
-		} catch (JAXBException e) {
-			throw new ConverterException(e);
-		}
-	}
+    try {
+      File exportedFile = new File(filePath);
+      if (exportedFile.getParentFile() != null) {
+        exportedFile.getParentFile().mkdirs();
+      }
+      OutputStream outputStream = new FileOutputStream(exportedFile);
+      IOUtils.copy(inputStream, outputStream);
+      outputStream.close();
 
-	@Override
-	public File exportModelToFile(Model model, String filePath) throws InconsistentModelException, ConverterException {
-		SbgnmlXmlExporter exporter = new SbgnmlXmlExporter();
-		Sbgn exportedData = exporter.toSbgnml(model);
-		File exportedFile = new File(filePath);
-		if (exportedFile.getParentFile() != null) {
-			exportedFile.getParentFile().mkdirs();
-		}
-		try {
-			SbgnUtil.writeToFile(exportedData, exportedFile);
-		} catch (JAXBException e) {
-			throw new ConverterException(e);
-		}
-		return exportedFile;
-	}
+      return exportedFile;
+    } catch (IOException e) {
+      throw new ConverterException(e);
+    }
+  }
 
-	@Override
-	public String getCommonName() {
-		return "SBGN-ML";
-	}
+  @Override
+  public String getCommonName() {
+    return "SBGN-ML";
+  }
 
-	@Override
-	public MimeType getMimeType() {
-		return MimeType.TEXT;
-	}
+  @Override
+  public MimeType getMimeType() {
+    return MimeType.TEXT;
+  }
 
-	@Override
-	public String getFileExtension() {
-		return "sbgn";
-	}
+  @Override
+  public String getFileExtension() {
+    return "sbgn";
+  }
 
 }

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java

@@ -46,6 +46,7 @@ import lcsb.mapviewer.model.map.reaction.OrOperator;
 import lcsb.mapviewer.model.map.reaction.Product;
 import lcsb.mapviewer.model.map.reaction.Reactant;
 import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
 import lcsb.mapviewer.model.map.reaction.SplitOperator;
 import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
 import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
@@ -160,11 +161,14 @@ public class SbgnmlXmlExporter {
     map.setLanguage(Language.PD.getName());
     Sbgn sbgnData = new Sbgn();
 
-    List<Species> aliases = model.getSpeciesList();
-
-    for (Species a : aliases) {
-      if (a.getComplex() == null) {
-        Glyph newGlyph = aliasToGlyph(a);
+    for (Element element : model.getElements()) {
+      if (element instanceof Species) {
+        if (((Species) element).getComplex() == null) {
+          Glyph newGlyph = aliasToGlyph(element);
+          map.getGlyph().add(newGlyph);
+        }
+      } else if (element instanceof Compartment) {
+        Glyph newGlyph = aliasToGlyph(element);
         map.getGlyph().add(newGlyph);
       }
     }
@@ -177,9 +181,8 @@ public class SbgnmlXmlExporter {
         try {
           map.getArc().add(getArcFromReducedReaction(reaction));
         } catch (InvalidArgumentException e) {
-          logger.warn("Invalid arc type."
-              + " Reduced notation reaction found of type that is not compliant with SBGN-ML format." + " Reaction: "
-              + reaction.getIdReaction());
+          logger.warn(eu.getElementTag(reaction) + "Invalid arc type."
+              + " Reduced notation reaction found of type that is not compliant with SBGN-ML format.");
         }
         continue;
       }
@@ -187,7 +190,6 @@ public class SbgnmlXmlExporter {
     }
 
     sbgnData.setMap(map);
-
     return sbgnData;
   }
 
@@ -707,7 +709,8 @@ public class SbgnmlXmlExporter {
     }
 
     if (reaction.getProducts().get(0).getElement() instanceof Phenotype) {
-      logger.warn("Found Phenotype being a reactant in process. That is discouraged");
+      logger.warn(eu.getElementTag(reaction.getProducts().get(0).getElement())
+          + "Found Phenotype being a reactant in process. That is discouraged");
     }
 
     arc.setSource(sourceTargetMap.get(reaction.getReactants().get(0).getElement().getElementId()));
@@ -801,13 +804,12 @@ public class SbgnmlXmlExporter {
     List<Arc> arcList = new ArrayList<>();
 
     // Parse all nodes except NodeOperators
-    for (AbstractNode node : reaction.getNodes().stream().filter(n -> !(n instanceof NodeOperator))
-        .collect(Collectors.toList())) {
+    for (ReactionNode node : reaction.getReactionNodes()) {
       try {
         arcList.add(getArcFromNode(node, glyphList));
       } catch (InvalidArgumentException ex) {
-        logger.warn("Node skipped in export process, since it is not compliant with SBGN-ML format: "
-            + node.getClass().getName());
+        logger.warn(
+            eu.getElementTag(node) + "Node skipped in export process, since it is not compliant with SBGN-ML format.");
         continue;
       }
     }

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java

 package lcsb.mapviewer.converter.model.sbgnml;
 
+import static org.junit.Assert.assertTrue;
+
 import java.io.File;
+import java.io.FileInputStream;
 
+import org.apache.commons.io.IOUtils;
 import org.apache.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
@@ -10,53 +14,97 @@ import org.junit.Test;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.IConverter;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
 
 public class CellDesignerToSbgnTest {
-	Logger logger = Logger.getLogger(CellDesignerToSbgnTest.class);
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testSample() throws Exception {
-		try {
-			IConverter converter = new CellDesignerXmlParser();
-			IConverter converter2 = new SbgnmlXmlConverter();
-
-			Model model;
-			model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/sample.xml"));
-
-			String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
-			converter2.exportModelToFile(model, output);
-			new File(output).delete();
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testSample2() throws Exception {
-		try {
-			IConverter converter = new CellDesignerXmlParser();
-			IConverter converter2 = new SbgnmlXmlConverter();
-
-			Model model;
-			model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/bubbles.xml"));
-
-			String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
-			converter2.exportModelToFile(model, output);
-			new File(output).delete();
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
+  Logger logger = Logger.getLogger(CellDesignerToSbgnTest.class);
+  ElementUtils eu = new ElementUtils();
+
+  @Before
+  public void setUp() throws Exception {
+  }
+
+  @After
+  public void tearDown() throws Exception {
+  }
+
+  @Test
+  public void testSample() throws Exception {
+    try {
+      IConverter converter = new CellDesignerXmlParser();
+      IConverter converter2 = new SbgnmlXmlConverter();
+
+      Model model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/sample.xml"));
+
+      String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
+      converter2.exportModelToFile(model, output);
+
+      try (FileInputStream inputStream = new FileInputStream(output)) {
+        String everything = IOUtils.toString(inputStream, "UTF-8");
+        assertTrue("Warnings are not exported into sbgn", everything.contains("Element type is not supported"));
+      }
+      converter2.createModel(new ConverterParams().filename(output));
+
+      new File(output).delete();
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
+  @Test
+  public void testSample2() throws Exception {
+    try {
+      IConverter converter = new CellDesignerXmlParser();
+      IConverter converter2 = new SbgnmlXmlConverter();
+
+      Model model;
+      model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/bubbles.xml"));
+
+      String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
+      converter2.exportModelToFile(model, output);
+      new File(output).delete();
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testCompartmentsExport() throws Exception {
+    try {
+      IConverter converter = new CellDesignerXmlParser();
+      IConverter converter2 = new SbgnmlXmlConverter();
+
+      Model model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/neuron.xml"));
+
+      String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
+      converter2.exportModelToFile(model, output);
+
+      converter2.createModel(new ConverterParams().filename(output));
+
+      String fileContent;
+      try (FileInputStream inputStream = new FileInputStream(output)) {
+        fileContent = IOUtils.toString(inputStream, "UTF-8");
+      }
+
+      for (Element element : model.getElements()) {
+        if (element instanceof Compartment) {
+          assertTrue(eu.getElementTag(element) + " comparmtent is not exported",
+              fileContent.contains(element.getElementId()));
+        }
+      }
+
+      new File(output).delete();
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
 
 }

converter-SBGNML/testFiles/cellDesigner/sample.xml

@@ -834,64 +834,6 @@ Name: Carney complex, multiple neoplasia and lentiginosis
 Description: RecName: Full=Sodium/calcium exchanger 1; AltName: Full=Na(+)/Ca(2+)-exchange protein 1; Flags: Precursor;
 Previous Symbols:
 Synonyms: CNC, NCX1
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s15">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_066920.1"/></rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:ncbigene:6546"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001106273.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:6546"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:reactome:REACT_20130"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA314"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001106272.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A6546"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001239553.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:hgnc:2141"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001106271.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
 </body>
 </html>
 </notes>

model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java

@@ -14,6 +14,7 @@ import org.reflections.Reflections;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
 import lcsb.mapviewer.model.map.species.Element;
 
 /**
@@ -257,4 +258,8 @@ public final class ElementUtils {
     ElementUtils.reactionClasses = reactionClasses;
   }
 
+  public String getElementTag(ReactionNode node) {
+    return "[" + node.getClass().getSimpleName() + "]" + getElementTag(node.getElement());
+  }
+
 }