when parsing miriam uri info about bioentity is provided to logger

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractAction.java

@@ -88,7 +88,7 @@ public class CopyPasteAbstractAction {
    */
   protected String getCopyString(String annotationString, String notesString) throws InvalidXmlSchemaException {
     XmlAnnotationParser xap = new XmlAnnotationParser();
-    Set<MiriamData> set = xap.parse(annotationString);
+    Set<MiriamData> set = xap.parse(annotationString, null);
     StringBuilder result = new StringBuilder();
     for (MiriamData md : set) {
       result.append(serialize(md) + "\n");

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

@@ -395,7 +395,7 @@ public class CellDesignerXmlParser extends Converter {
   private void processModelRdfNode(Model model, Node node) throws InvalidXmlSchemaException {
     XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser(
         CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
-    model.addMiriamData(xmlAnnotationParser.parseRdfNode(node));
+    model.addMiriamData(xmlAnnotationParser.parseRdfNode(node, null));
     model.addAuthors(xmlAnnotationParser.getAuthorsFromRdf(node));
     model.setCreationDate(xmlAnnotationParser.getCreateDateFromRdf(node));
     model.addModificationDates(xmlAnnotationParser.getModificationDatesFromRdf(node));

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

@@ -885,7 +885,8 @@ public class RestAnnotationParser {
     Matcher nodeMatcher = rdfNodePattern.matcher(notes);
     if (nodeMatcher.find()) {
       String rdfString = "<rdf:RDF" + nodeMatcher.group(1) + "</rdf:RDF>";
-      element.addMiriamData(xmlAnnotationParser.parse(rdfString));
+      element.addMiriamData(
+          xmlAnnotationParser.parse(rdfString, new LogMarker(ProjectLogEntryType.PARSING_ISSUE, element)));
 
       notes = notes.substring(0, nodeMatcher.start() - "<rdf:RDF".length())
           + notes.substring(nodeMatcher.end() + "</rdf:RDF>".length());

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java

@@ -15,6 +15,8 @@ import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationPars
 import lcsb.mapviewer.converter.model.celldesigner.species.AbstractElementXmlParser;
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
 
@@ -144,7 +146,9 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerC
       Node node = annotationNodes.item(y);
       if (node.getNodeType() == Node.ELEMENT_NODE) {
         if (node.getNodeName().equalsIgnoreCase("rdf:RDF")) {
-          compartment.addMiriamData(xmlAnnotationParser.parseRdfNode(node));
+          compartment.addMiriamData(xmlAnnotationParser.parseRdfNode(node, 
+              new LogMarker(ProjectLogEntryType.PARSING_ISSUE, compartment.getClass().getSimpleName(), 
+                  compartment.getElementId(), "")));
         } else if (node.getNodeName().equalsIgnoreCase("celldesigner:extension")) {
           parseExtensionNode(compartment, node);
         } else if (node.getNodeName().equalsIgnoreCase("celldesigner:name")) {

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java

@@ -19,6 +19,8 @@ import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesigner
 import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.*;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.*;
 import lcsb.mapviewer.converter.model.celldesigner.types.*;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.graphics.*;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
@@ -313,7 +315,8 @@ public class ReactionFromXml {
           try {
             XmlAnnotationParser xmlParser = new XmlAnnotationParser(
                 CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
-            result.addMiriamData(xmlParser.parseRdfNode(node));
+            result.addMiriamData(xmlParser.parseRdfNode(node, new LogMarker(ProjectLogEntryType.PARSING_ISSUE,
+                result.getClass().getSimpleName(), result.getElementId(), model.getName())));
           } catch (InvalidXmlSchemaException e) {
             throw new ReactionParserException("Problem with parsing RDF", result, e);
           }

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java

@@ -17,6 +17,8 @@ import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationPars
 import lcsb.mapviewer.converter.model.celldesigner.structure.*;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SpeciesState;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
 import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
@@ -198,7 +200,8 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
     if (rdfNode != null) {
       XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser(
           CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
-      species.addMiriamData(xmlAnnotationParser.parseRdfNode(rdfNode));
+      species.addMiriamData(xmlAnnotationParser.parseRdfNode(rdfNode, new LogMarker(ProjectLogEntryType.PARSING_ISSUE,
+          species.getClass().getSimpleName(), species.getElementId(), "")));
     }
 
     return result;

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

@@ -984,7 +984,8 @@ public class SbgnmlXmlParser {
           "No rdf node provided in annotation extension");
     } else {
       try {
-        element.addMiriamData(new XmlAnnotationParser().parseRdfNode(rdf));
+        element.addMiriamData(
+            new XmlAnnotationParser().parseRdfNode(rdf, new LogMarker(ProjectLogEntryType.PARSING_ISSUE, element)));
       } catch (InvalidXmlSchemaException e) {
         logger.error(e, e);
       }
@@ -1677,7 +1678,7 @@ public class SbgnmlXmlParser {
         List<Line2D> lines = new ArrayList<>(product.getLine().getLines());
         product.getLine().removeLines();
         Collections.reverse(lines);
-        for (Line2D l: lines) {
+        for (Line2D l : lines) {
           product.getLine().addLine(l.getP2(), l.getP1());
         }
       }

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java

@@ -18,6 +18,8 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
 import lcsb.mapviewer.converter.model.sbml.species.ElementColorEnum;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.compartment.Compartment;
@@ -68,13 +70,13 @@ public class SbmlBioEntityParser {
     this.layout = getSbmlLayout(sbmlModel);
   }
 
-  protected Set<MiriamData> extractMiriamDataFromAnnotation(Annotation annotation) throws InvalidInputDataExecption {
+  protected Set<MiriamData> extractMiriamDataFromAnnotation(Annotation annotation, LogMarker marker) throws InvalidInputDataExecption {
     XmlAnnotationParser parser = new XmlAnnotationParser();
     Set<MiriamData> result = new HashSet<>();
     try {
       Node rdfNode = getRdfNodeFromAnnotation(annotation);
       if (rdfNode != null) {
-        result.addAll(parser.parseRdfNode(rdfNode));
+        result.addAll(parser.parseRdfNode(rdfNode, marker));
       }
     } catch (InvalidXmlSchemaException e) {
       throw new InvalidInputDataExecption(e);
@@ -136,7 +138,7 @@ public class SbmlBioEntityParser {
 
   protected void assignBioEntityData(AbstractNamedSBase sbmlElement, BioEntity result)
       throws InvalidInputDataExecption {
-    result.addMiriamData(extractMiriamDataFromAnnotation(sbmlElement.getAnnotation()));
+    result.addMiriamData(extractMiriamDataFromAnnotation(sbmlElement.getAnnotation(), new LogMarker(ProjectLogEntryType.PARSING_ISSUE, result)));
     result.setName(sbmlElement.getName());
     String notes = NotesUtility.extractNotes(sbmlElement);
     result.setNotes(notes);

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java

@@ -72,7 +72,7 @@ public class SbmlParser extends Converter {
       SbmlParameterParser parameterParser = new SbmlParameterParser(sbmlModel, model);
       SbmlFunctionParser functionParser = new SbmlFunctionParser(sbmlModel, model);
 
-      model.addMiriamData(compartmentParser.extractMiriamDataFromAnnotation(sbmlModel.getAnnotation()));
+      model.addMiriamData(compartmentParser.extractMiriamDataFromAnnotation(sbmlModel.getAnnotation(), null));
       model.addAuthors(compartmentParser.extractAuthorsFromAnnotation(sbmlModel.getAnnotation()));
       model.addModificationDates(compartmentParser.extractModificationDatesFromAnnotation(sbmlModel.getAnnotation()));
       model.setCreationDate(compartmentParser.extractCreationDateFromAnnotation(sbmlModel.getAnnotation()));

converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java

@@ -11,6 +11,8 @@ import org.w3c.dom.*;
 import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.*;
 import lcsb.mapviewer.model.map.model.Author;
 
@@ -66,14 +68,14 @@ public class XmlAnnotationParser {
    * @throws InvalidXmlSchemaException
    *           thrown when there is a problem with xml
    */
-  public Set<MiriamData> parse(String data) throws InvalidXmlSchemaException {
+  public Set<MiriamData> parse(String data, LogMarker marker) throws InvalidXmlSchemaException {
     // start from creating a DOM parser and parse the whole document
     Document doc = XmlParser.getXmlDocumentFromString(data);
 
     NodeList root = doc.getChildNodes();
 
     // process the whole schema
-    return parseRdfNode(root);
+    return parseRdfNode(root, marker);
   }
 
   /**
@@ -85,9 +87,9 @@ public class XmlAnnotationParser {
    * @throws InvalidXmlSchemaException
    *           thrown when there is a problem with xml
    */
-  private Set<MiriamData> parseRdfNode(NodeList root) throws InvalidXmlSchemaException {
+  private Set<MiriamData> parseRdfNode(NodeList root, LogMarker marker) throws InvalidXmlSchemaException {
     Node rdf = XmlParser.getNode("rdf:RDF", root);
-    return parseRdfNode(rdf);
+    return parseRdfNode(rdf, marker);
   }
 
   /**
@@ -99,7 +101,7 @@ public class XmlAnnotationParser {
    * @throws InvalidXmlSchemaException
    *           thrown when there is a problem with xml
    */
-  public Set<MiriamData> parseRdfNode(Node rdf) throws InvalidXmlSchemaException {
+  public Set<MiriamData> parseRdfNode(Node rdf, LogMarker marker) throws InvalidXmlSchemaException {
     Set<MiriamData> miriamDataSet = new HashSet<>();
     if (rdf != null) {
       Node description = XmlParser.getNode("rdf:Description", rdf.getChildNodes());
@@ -111,7 +113,7 @@ public class XmlAnnotationParser {
             String relationTypeString = node.getNodeName();
             MiriamRelationType relationType = MiriamRelationType.getTypeByStringRepresentation(relationTypeString);
             if (relationType != null) {
-              miriamDataSet.addAll(parseMiriamNode(node));
+              miriamDataSet.addAll(parseMiriamNode(node, marker));
             } else if (relationTypeString.equals("dc:creator")) {
             } else if (relationTypeString.equals("dcterms:created")) {
             } else if (relationTypeString.equals("dcterms:modified")) {
@@ -239,7 +241,7 @@ public class XmlAnnotationParser {
    * @throws InvalidXmlSchemaException
    *           thrown when there is a problem with xml
    */
-  public Set<MiriamData> parseMiriamNode(Node node) throws InvalidXmlSchemaException {
+  public Set<MiriamData> parseMiriamNode(Node node, LogMarker logMarker) throws InvalidXmlSchemaException {
     Set<MiriamData> result = new HashSet<>();
     NodeList list = node.getChildNodes();
     String relationTypeString = node.getNodeName();
@@ -259,7 +261,8 @@ public class XmlAnnotationParser {
       try {
         MiriamData md = MiriamType.getMiriamByUri(dataTypeUri);
         if (relationType == null) {
-          logger.warn("Unknown relation type: " + relationTypeString + ". For miriam uri: " + dataTypeUri + ".");
+          logger.warn(logMarker,
+              "Unknown relation type: " + relationTypeString + ". For miriam uri: " + dataTypeUri + ".");
         } else {
           if (!MiriamType.PUBMED.equals(md.getDataType())) {
             md.setRelationType(relationType);
@@ -267,7 +270,7 @@ public class XmlAnnotationParser {
           result.add(md);
         }
       } catch (InvalidArgumentException e) {
-        logger.warn(e.getMessage());
+        logger.warn(logMarker, e.getMessage());
       }
     }
     return result;

converter/src/test/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParserTest.java

@@ -28,7 +28,7 @@ public class XmlAnnotationParserTest extends ConverterTestFunctions {
 
     String xml = readFile("testFiles/annotation/rdf.xml");
 
-    Set<MiriamData> set = xap.parse(xml);
+    Set<MiriamData> set = xap.parse(xml, null);
     assertEquals(2, set.size());
   }
 
@@ -38,7 +38,7 @@ public class XmlAnnotationParserTest extends ConverterTestFunctions {
 
     String xml = readFile("testFiles/annotation/rdf_has_property.xml");
 
-    Set<MiriamData> set = xap.parse(xml);
+    Set<MiriamData> set = xap.parse(xml, null);
     assertEquals(0, super.getWarnings().size());
     assertEquals(7, set.size());
   }
@@ -49,7 +49,7 @@ public class XmlAnnotationParserTest extends ConverterTestFunctions {
     XmlAnnotationParser parser = new XmlAnnotationParser();
     String xml = parser.miriamDataToXmlString(md);
     assertNotNull(xml);
-    Set<MiriamData> set = parser.parseMiriamNode(super.getNodeFromXmlString(xml));
+    Set<MiriamData> set = parser.parseMiriamNode(super.getNodeFromXmlString(xml), null);
     assertNotNull(set);
     assertEquals(1, set.size());
     MiriamData md1 = set.iterator().next();
@@ -63,7 +63,7 @@ public class XmlAnnotationParserTest extends ConverterTestFunctions {
   public void testParseInvalidRdf() throws Exception {
     XmlAnnotationParser xap = new XmlAnnotationParser();
 
-    xap.parseRdfNode((Node) null);
+    xap.parseRdfNode((Node) null, null);
   }
 
   @Test
@@ -71,7 +71,7 @@ public class XmlAnnotationParserTest extends ConverterTestFunctions {
     XmlAnnotationParser xap = new XmlAnnotationParser();
     String xml = readFile("testFiles/annotation/rdf_with_creator_tag.xml");
 
-    Set<MiriamData> set = xap.parse(xml);
+    Set<MiriamData> set = xap.parse(xml, null);
     assertTrue(set.size() > 0);
   }
 
@@ -81,7 +81,7 @@ public class XmlAnnotationParserTest extends ConverterTestFunctions {
 
     String xml = readFile("testFiles/annotation/invalid_rdf2.xml");
 
-    xap.parse(xml);
+    xap.parse(xml, null);
   }
 
   @Test
@@ -90,7 +90,7 @@ public class XmlAnnotationParserTest extends ConverterTestFunctions {
 
     String xml = readFile("testFiles/annotation/invalid_rdf3.xml");
 
-    xap.parse(xml);
+    xap.parse(xml, null);
 
     assertEquals(1, getWarnings().size());
   }
@@ -101,7 +101,7 @@ public class XmlAnnotationParserTest extends ConverterTestFunctions {
 
     String xml = readFile("testFiles/annotation/invalid_rdf4.xml");
 
-    xap.parse(xml);
+    xap.parse(xml, null);
 
     assertEquals(1, getWarnings().size());
   }
@@ -111,7 +111,7 @@ public class XmlAnnotationParserTest extends ConverterTestFunctions {
     MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "e:f");
     XmlAnnotationParser parser = new XmlAnnotationParser(Arrays.asList(MiriamRelationType.BQ_BIOL_ENCODES));
     String xml = parser.miriamDataToXmlString(md);
-    Set<MiriamData> set = parser.parseMiriamNode(super.getNodeFromXmlString(xml));
+    Set<MiriamData> set = parser.parseMiriamNode(super.getNodeFromXmlString(xml), null);
     assertNotNull(set);
     MiriamData md1 = set.iterator().next();
     assertNotEquals(md.getRelationType(), md1.getRelationType());