refactored rest-api module to use new converter class

commons/src/main/java/lcsb/mapviewer/common/XmlParser.java

@@ -222,7 +222,7 @@ final public class XmlParser {
    * @throws InvalidXmlSchemaException
    *           thrown when there is a problem with xml
    */
-  private static Document getXmlDocumentFromString(final String text, boolean validate) throws InvalidXmlSchemaException {
+  public static Document getXmlDocumentFromString(final String text, boolean validate) throws InvalidXmlSchemaException {
     InputSource is = new InputSource();
     is.setCharacterStream(new StringReader(text));
     try {

rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java

@@ -31,14 +31,11 @@ import lcsb.mapviewer.annotation.services.MiriamConnector;
 import lcsb.mapviewer.annotation.services.PubmedParser;
 import lcsb.mapviewer.annotation.services.PubmedSearchException;
 import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
-import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.comparator.StringComparator;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
-import lcsb.mapviewer.converter.graphics.ImageGenerators;
+import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
 import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
 import lcsb.mapviewer.converter.model.sbml.SbmlParser;
@@ -322,8 +319,8 @@ public abstract class BaseRestImpl {
     this.projectService = projectService;
   }  
   
-  protected IConverter getModelParser(String handlerClass) throws QueryException {
-    for (IConverter converter : getModelConverters()) {
+  protected Converter getModelParser(String handlerClass) throws QueryException {
+    for (Converter converter : getModelConverters()) {
       if (converter.getClass().getCanonicalName().equals(handlerClass)) {
         return converter;
       }
@@ -331,8 +328,8 @@ public abstract class BaseRestImpl {
     throw new QueryException("Unknown handlerClass: " + handlerClass);
   }
 
-  protected List<IConverter> getModelConverters() {
-    List<IConverter> result = new ArrayList<>();
+  protected List<Converter> getModelConverters() {
+    List<Converter> result = new ArrayList<>();
     result.add(new CellDesignerXmlParser());
     result.add(new SbgnmlXmlConverter());
     result.add(new SbmlParser());

rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java

@@ -20,7 +20,7 @@ import lcsb.mapviewer.api.BaseRestImpl;
 import lcsb.mapviewer.api.QueryException;
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
 import lcsb.mapviewer.converter.graphics.ImageGenerators;
 import lcsb.mapviewer.model.graphics.MapCanvasType;
@@ -117,11 +117,11 @@ public class ConfigurationRestImpl extends BaseRestImpl {
 
   public List<Map<String, Object>> getModelFormats(String token) throws SecurityException {
     verifyToken(token);
-    List<IConverter> converters = getModelConverters();
+    List<Converter> converters = getModelConverters();
 
     List<Map<String, Object>> result = new ArrayList<>();
 
-    for (IConverter converter : converters) {
+    for (Converter converter : converters) {
       Map<String, Object> row = new TreeMap<>();
       row.put("name", converter.getCommonName());
       row.put("handler", converter.getClass().getCanonicalName());

rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java

@@ -24,7 +24,7 @@ import lcsb.mapviewer.api.QueryException;
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.converter.ConverterException;
 import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
 import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
 import lcsb.mapviewer.converter.graphics.DrawingException;
@@ -49,8 +49,8 @@ public class ConvertRestImpl extends BaseRestImpl {
 	  ConverterParams params = createConvertParams(input);	  
 	  Model model = getModelParserByNameOrClass(fromFormat).createModel(params);
 	  
-	  IConverter exporter =  getModelParserByNameOrClass(toFormat);
-	  return IOUtils.toString(exporter.exportModelToInputStream(model));
+	  Converter exporter =  getModelParserByNameOrClass(toFormat);
+	  return IOUtils.toString(exporter.model2InputStream(model));
   }
   
   public ByteArrayOutputStream converToImage(String token, String fromFormat, String toFormat, String input,
@@ -82,7 +82,7 @@ public class ConvertRestImpl extends BaseRestImpl {
 	  
 	  	  
 	  List<Object> converters = new ArrayList<>();
-	  for (IConverter converter: getModelConverters()) {
+	  for (Converter converter: getModelConverters()) {
 		  
 		  List<String> names = new ArrayList<>();		  
 		  names.add(removeWhiteSpaces(converter.getCommonName()));
@@ -119,7 +119,7 @@ public class ConvertRestImpl extends BaseRestImpl {
 	  return info;	  
   }
   
-  private IConverter getModelParserByNameOrClass(String id) throws QueryException {
+  private Converter getModelParserByNameOrClass(String id) throws QueryException {
 	  try {
 		  return getModelParserByName(id);
 	  } catch (QueryException e) {
@@ -131,8 +131,8 @@ public class ConvertRestImpl extends BaseRestImpl {
 	  return str.replace(' ', '_');
   }
   
-  private IConverter getModelParserByName(String name) throws QueryException {
-	  for (IConverter converter : getModelConverters()) {
+  private Converter getModelParserByName(String name) throws QueryException {
+	  for (Converter converter : getModelConverters()) {
 		  if (removeWhiteSpaces(converter.getCommonName()).equals(name)) {
 			  return converter;
 		  }

rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java

 package lcsb.mapviewer.api.projects;
 
 import java.awt.geom.Point2D;
-import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.Serializable;
 import java.security.MessageDigest;
@@ -16,7 +15,6 @@ import java.util.Set;
 import java.util.TreeMap;
 
 import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 import org.springframework.util.MultiValueMap;
@@ -31,7 +29,7 @@ import lcsb.mapviewer.api.QueryException;
 import lcsb.mapviewer.api.projects.models.publications.PublicationsRestImpl;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
 import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
 import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
@@ -379,7 +377,7 @@ public class ProjectRestImpl extends BaseRestImpl {
     if (parserClass == null) {
       throw new QueryException("parser is obligatory");
     }
-    IConverter parser = getModelParser(parserClass);
+    Converter parser = getModelParser(parserClass);
 
     List<ZipEntryFile> zipEntries = extractZipEntries(data);
     params.complex(zipEntries.size() > 0);

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

@@ -244,7 +244,7 @@ public class ModelRestImpl extends BaseRestImpl {
     }
 
     Converter parser = getModelParser(handlerClass);
-    InputStream is = parser.exportModelToInputStream(part);
+    InputStream is = parser.model2InputStream(part);
 
     String fileExtension = parser.getFileExtension();