Merge branch 'devel_13.1.x' into tair-fix

.gitlab-ci.yml

@@ -268,13 +268,9 @@ test_upgrade_debian_package:
      - version=$(echo $debian_file| cut -f2 -d"_")
      - echo "PUT $debian_file /docker/incoming" | sftp -o StrictHostKeyChecking=no user@debian-repo
      - ssh root@debian-repo /usr/local/sbin/reprepro-import
-     - apt-add-repository "deb http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main"
-     - apt-key adv --no-tty --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys EEA14886
      - apt-add-repository "deb http://repo-r3lab.uni.lu/debian/ stable main"
      - apt-key adv --no-tty --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 0xcb185f4e31872412
      - apt-get update
-# auto accept oracle license
-     - echo debconf shared/accepted-oracle-license-v1-1 select true | debconf-set-selections
 #hacky way of installing minerva on docker - by default rc-invoke is preventing services changes on docker
      - mv /usr/sbin/policy-rc.d /usr/sbin/policy-rc.d.backup
      - mv gitlab-ci-policy-rc.d /usr/sbin/policy-rc.d
@@ -315,12 +311,8 @@ test_install_debian_package:
      - debian_file=$(ls debian/*.deb)
      - echo "PUT $debian_file /docker/incoming" | sftp -o StrictHostKeyChecking=no user@debian-repo
      - ssh root@debian-repo /usr/local/sbin/reprepro-import
-     - apt-add-repository "deb http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main"
-     - apt-key adv --no-tty --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys EEA14886
      - apt-add-repository "deb http://debian-repo/ unstable main"
      - apt-get update
-# auto accept oracle license
-     - echo debconf shared/accepted-oracle-license-v1-1 select true | debconf-set-selections
 #hacky way of installing minerva on docker - by default rc-invoke is preventing services changes on docker
      - mv /usr/sbin/policy-rc.d /usr/sbin/policy-rc.d.backup
      - mv gitlab-ci-policy-rc.d /usr/sbin/policy-rc.d

CHANGELOG

 minerva (12.3.1~beta.1) unstable; urgency=low
-  * Bug fix: tair locus identifiers were used improperly - instead of id the 
+  * Bug fix: tair locus identifiers were used improperly - instead of id the
     name was used
 
-minerva (12.3.0~alpha.0) unstable; urgency=low
+minerva (13.1.0~alpha.0) unstable; urgency=low
   * Feature: annotators are more flexible - you can define set of input and
     outputs used by annotator (#617)
+  * Feature: changes in admin panel doesn't require saving - they are saved
+    automatically (#676)
+  * Feature: elements can have custom glyphs used for visualization (#487)
+  * Small improvement: all bio entities have z-index associated with them
+    (#487)
   * Small improvement: validation of the organism and disease id on map upload
     added (#618)
   * Small improvement: added current username next to logout button in admin
@@ -12,6 +17,8 @@ minerva (12.3.0~alpha.0) unstable; urgency=low
   * Small improvement: New comment dialog does not contain content of previous
     comment dialog (#680)
   * Small improvement: Left logo is configurable (#731)
+  * Small improvement: list of element types in choose annotator dialog is
+    sorted (#758)
   * Small improvement: Plugin API provides list of overview images (#702)
   * Small improvement: Plugin API allows to show/hide overview images (#702)
   * Small improvement: Plugin API allows to trigger search on the map (#702)
@@ -24,6 +31,8 @@ minerva (12.3.0~alpha.0) unstable; urgency=low
     whitespace, "_" used as separator (#596)
   * Small improvement: list of references in drug panel contains PUBMED prefix
     (#666)
+  * Small improvement: list of projects is auto refreshed every 5 seconds if at
+    least one of the project is uploading/removing (#610)
   * Small improvement: passwords to email account and ldap are not sent over
     API (#732)
   * Small improvement: reactant/product/modifier specific colors are parsed
@@ -33,6 +42,21 @@ minerva (12.3.0~alpha.0) unstable; urgency=low
   * Small improvement: Info tab provides information about model annotations
     and submap tabs provide information about submaps annotations if applicable
     (#591)
+  * Small improvement: uploading sbml file should automatically discover a file
+    type (#784)
+  * Small improvement: when plugin listeners crash the system notifies user
+    about problem with a plugin (#767)
+  * Small improvement: when exporting reaction and elements there is
+    possibility to filter by (sub)map (#615)
+  * Small improvement: during first opening of a map, the zoom level is
+    automatically computed if no default information is provided (#776)
+  * Small improvement: when adding new project columns "Root map", "Mapping
+    file" and "Map type" are merged (#700)
+  * Small improvement: allow admin to disable CORS check (#802)
+  * Small improvement: TransparencyZoomLevelVisibility parameter renamed to
+    SemanticZoomLevelTransparency (#801)
+  * Small improvement: export/import from SBML support z-index in LAYOUT
+    extension
   * Bug fix: progress bar of gene genome mapping upload is refreshing properly
     (#728)
   * Bug fix: when editing project Disease and Organism could not be removed
@@ -41,6 +65,74 @@ minerva (12.3.0~alpha.0) unstable; urgency=low
     "Unknown Inhibition" reactions (#664)
   * Bug fix: "Unknown Catalysis" and "Unknown Inhibition" reaction end is
     slightly separated from target phenotype (#664)
+  * Bug fix: order of genomes in admin panel doesn't change after refreshing
+    list of genomes (#761)
+  * Bug fix: fixing situation when Molart started with variation overlay not
+    having the aa change information
+  * Bug fix: plugin contect element width is adjusted when link to tabs are
+    wrapped in more than one line (#758)
+  * Bug fix: export to CellDesigner preserve font size (#803)
+  * Bug fix: layout data was ignored for some reactions when improting from
+    SBML (#812)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 7 May 2019 15:00:00 +0200
+
+minerva (13.0.0) stable; urgency=medium
+  * Bug fix: Since Oracle Java cannot be installed as debian dependency we use
+    openjdk-8. Due to this dependency minerva can be no longer installed on
+    Ubuntu-14 (#223)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 6 May 2019 18:00:00 +0200
+
+minerva (12.2.3) stable; urgency=medium
+  * Bug fix: sorting of entries in "Edit project->overlays" dialog fixed (#790)
+  * Bug fix: searching of chemicals stopped working due to expired SSL
+    certificate on https://ctdbase.org/
+  * Bug fix: remove button is disabled after starting removing of the data
+    overlay (#791)
+  * Bug fix: search autocomplete hint could be initially hidden (#793)
+  * Bug fix: updating terms of use could crash when list of users was removed
+    in separate tab or by another user (#797)
+  * Bug fix: name of the checkbox in ADD PROJECT window adjusted (#799)
+  * Bug fix: when user didn't have privileges to remove comments the button was
+    active on pages other than page 1 (#792)
+  * Bug fix: export of reaction to SBML didn't work when lines on the map were
+    too short (#805)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 24 Apr 2019 17:00:00 +0200
+
+minerva (12.2.2) stable; urgency=medium
+  * Bug fix: downloading overlays didn't work from admin panel when project
+    with different id than default map was accessed
+  * Bug fix: change of owner of the data overlay in admin panel incorrectly
+    ordered overlays (#777)
+  * Bug fix: chemical search didn't use updated disease identifier, original
+    disease id from project upload was used instead (#779)
+  * Bug fix: user login with special characters (like '@')  could cause
+    problems in admin panel (#780)
+  * Bug fix: removing project without full control in the system (but with
+    enough privileges to remove project) caused "Not enough privileges" error
+    (#778)
+  * Bug fix: export of custom properties (like synonyms) are properly encoded
+    in CellDesigner xml (#785)
+  * Bug fix: notification about not supported version in IE 11 fixed (#783)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 9 Apr 2019 17:00:00 +0200
+
+minerva (12.2.1) stable; urgency=medium
+  * Bug fix: export of reaction colorsi in SBML is properly encoded (COPASI can
+    read colors properly) (#744)
+  * Bug fix: removing active plugin didn't switch plugin tab to the next loaded
+    plugin (#757)
+  * Bug fix: closed submap will not be reopened after page refresh (#763)
+  * Bug fix: comment remove button is disabled for users without proper
+    privileges (#766)
+  * Bug fix: invalid pubmed identifier could break clicking on element
+    containing it (#764, #765, #769)
+  * Bug fix: cache for API queries is explicitly disabled - some queries could
+    be mistakenly cached and the system behaviour might get unstable (#771)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 1 Apr 2019 17:00:00 +0200
 
 minerva (12.2.0) stable; urgency=medium
   * Feature: bug report utility

annotation/src/main/java/lcsb/mapviewer/annotation/cache/ApplicationLevelCache.java

@@ -8,7 +8,6 @@ import org.springframework.stereotype.Service;
 import org.w3c.dom.Node;
 
 import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.model.cache.CacheType;
 
 /**

annotation/src/main/java/lcsb/mapviewer/annotation/cache/CachableInterface.java

@@ -7,7 +7,6 @@ import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.w3c.dom.Node;
 
-import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.cache.CacheType;
 import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;

annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java

@@ -70,18 +70,18 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
   /**
    * Home page of ctd database.
    */
-  static final String URL = "https://ctdbase.org/";
+  static final String URL = "http://ctdbase.org/";
 
   /**
    * URL to get a list of chemicals by disease id.
    */
-  public static final String DISEASE_URL = "https://ctdbase.org/detail.go?6578706f7274=1&d-1332398-e=5&view=chem&"
+  public static final String DISEASE_URL = URL + "detail.go?6578706f7274=1&d-1332398-e=5&view=chem&"
       + "type=disease&acc=MESH%3A";
 
   /**
    * URL to get a list of chemicals by gene id.
    */
-  public static final String DISEASE_GENE_URL = "https://ctdbase.org/detail.go?slimTerm=all&6578706f7274=1&qid=3464576&"
+  public static final String DISEASE_GENE_URL = URL + "detail.go?slimTerm=all&6578706f7274=1&qid=3464576&"
       + "d-1332398-e=5&view=disease&type=gene&assnType=curated&acc=";
 
   /**
@@ -404,10 +404,10 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
       }
       if (result != null) {
         MeSH mesh = meshParser.getMeSH(result.getChemicalId());
-        if (mesh!=null) {
-        result.addSynonyms(mesh.getSynonyms());
+        if (mesh != null) {
+          result.addSynonyms(mesh.getSynonyms());
         } else {
-          logger.warn("Problematic mesh id: "+result.getChemicalId());
+          logger.warn("Problematic mesh id: " + result.getChemicalId());
         }
       }
 
@@ -486,7 +486,7 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
         if (entrez == null) {
           invalidHgnc.add(md);
         } else {
-          String query = "https://ctdbase.org/detail.go?type=gene&view=ixn&chemAcc=" + chemID.getResource() + "&acc="
+          String query = URL + "detail.go?type=gene&view=ixn&chemAcc=" + chemID.getResource() + "&acc="
               + entrez.getResource();
           String referencesPage = getWebPageContent(query);
           Matcher matcher = pattern.matcher(referencesPage);
@@ -494,7 +494,7 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
             idx.add(matcher.group(1));
           }
           for (String string : idx) {
-            String query2 = "https://ctdbase.org/detail.go?6578706f7274=1&d-1340579-e=5&type=relationship&ixnId="
+            String query2 = URL + "detail.go?6578706f7274=1&d-1340579-e=5&type=relationship&ixnId="
                 + string;
             String referencesPage2 = getWebPageContent(query2);
             String[] lines = referencesPage2.split("\n");

annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java

@@ -57,7 +57,7 @@ public class PubmedParser extends CachableInterface implements IExternalService
   /**
    * Version of the remote API that is supported by this connecting class.
    */
-  static final String SUPPORTED_VERSION = "6.0.3";
+  static final String SUPPORTED_VERSION = "6.1";
 
   static final String API_URL = "https://www.ebi.ac.uk/europepmc/webservices/rest/";
 

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java

@@ -16,7 +16,6 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerChemical;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
 import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Chemical;

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java

@@ -46,7 +46,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
   /**
    * Version of the rest API that is supported by this annotator.
    */
-  static final String SUPPORTED_VERSION = "9.0";
+  static final String SUPPORTED_VERSION = "10.0";
 
   /**
    * Url address of ensembl restful service.

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java

@@ -9,10 +9,7 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-
-import lcsb.mapviewer.common.XmlParser;
+import org.apache.commons.text.StringEscapeUtils;
 import org.apache.log4j.Logger;
 import org.springframework.stereotype.Service;
 import org.w3c.dom.Node;
@@ -27,6 +24,7 @@ import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
 import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
 import lcsb.mapviewer.annotation.services.IExternalService;
 import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
+import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -266,7 +264,7 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
             Node node = list.item(i);
             if (node.getNodeType() == Node.ELEMENT_NODE) {
               if (node.getNodeName().equals("Gene-ref_syn_E")) {
-                synonyms.add(node.getTextContent());
+				synonyms.add(StringEscapeUtils.unescapeHtml4(node.getTextContent()));
               }
             }
           }

annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java

@@ -156,7 +156,6 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
       assertNotNull(drug);
       assertTrue(drug.getBrandNames().contains("PK-Merz"));
       assertTrue(drug.getBrandNames().contains("Symadine"));
-      assertTrue(drug.getBrandNames().contains("Symmetrel"));
     } catch (Exception e) {
       e.printStackTrace();
       throw e;

annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java

@@ -271,6 +271,23 @@ public class EntrezAnnotatorTest extends AnnotationTestFunctions {
     }
   }
 
+  @Test
+  public void testAnnotateElementWithEncodedSynonyms() throws Exception {
+    try {
+      Species proteinAlias = new GenericProtein("id");
+      proteinAlias.addMiriamData(new MiriamData(MiriamType.ENTREZ, "834106"));
+      entrezAnnotator.annotateElement(proteinAlias);
+
+      for (String synonym : proteinAlias.getSynonyms()) {
+        assertFalse("Invalid character found in synonym: " + synonym, synonym.contains("&"));
+      }
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testParseEntrezResponse() throws Exception {
     WebPageDownloader downloader = entrezAnnotator.getWebPageDownloader();

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

@@ -8,7 +8,10 @@ import org.apache.log4j.Logger;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 
 public abstract class Comparator<T extends Object> implements java.util.Comparator<T> {
-  Logger logger = Logger.getLogger(Comparator.class);
+  /**
+   * Default class logger.
+   */
+  private static Logger logger = Logger.getLogger(Comparator.class);
   private Class<T> comparatorClazz;
   private boolean exactClassMatch;
   private List<Comparator<? extends T>> subClassComparatorList = new ArrayList<>();

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

@@ -151,6 +151,11 @@ public final class Configuration {
    */
   private static List<String> xFrametDomain = new ArrayList<>();
 
+  /**
+   * Should CORS be disabled.
+   */
+  private static boolean disableCors = false;
+
   /**
    * Directory where tomcat webapp folder is located. Default value is "." because
    * it should be set to proper value when tomcat application is deployed and run.
@@ -438,4 +443,12 @@ public final class Configuration {
     Configuration.sessionLength = sessionLength;
   }
 
+  public static boolean isDisableCors() {
+    return disableCors;
+  }
+
+  public static void setDisableCors(boolean disableCors) {
+    Configuration.disableCors = disableCors;
+  }
+
 }

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

@@ -2,6 +2,7 @@ package lcsb.mapviewer.common;
 
 import java.awt.Color;
 import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
 import java.io.FileReader;
 import java.io.IOException;
 import java.io.InputStream;
@@ -14,13 +15,18 @@ import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Result;
+import javax.xml.transform.Source;
+import javax.xml.transform.Templates;
 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.transform.stream.StreamSource;
 
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.output.ByteArrayOutputStream;
 import org.apache.commons.text.StringEscapeUtils;
 import org.apache.log4j.Logger;
 import org.w3c.dom.Document;
@@ -31,6 +37,7 @@ import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 
 /**
@@ -78,7 +85,8 @@ final public class XmlParser {
   }
 
   /**
-   * private constructor. This class has no state and contains only static utility methods.
+   * private constructor. This class has no state and contains only static utility
+   * methods.
    */
   private XmlParser() {
   }
@@ -222,7 +230,8 @@ final public class XmlParser {
    * @throws InvalidXmlSchemaException
    *           thrown when there is a problem with xml
    */
-  public 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 {
@@ -398,4 +407,30 @@ final public class XmlParser {
     }
     return result;
   }
+
+  public static String lowercaseXmlNames(String inputXml) {
+    try {
+      TransformerFactory factory = TransformerFactory.newInstance();
+
+      // Use the factory to create a template containing the xsl file
+      Templates template = factory
+          .newTemplates(new StreamSource(ClassLoader.getSystemResourceAsStream("to_lowercase.xsl")));
+
+      // Use the template to create a transformer
+      Transformer xformer = template.newTransformer();
+
+      ByteArrayOutputStream output = new ByteArrayOutputStream();
+      // Prepare the input and output files
+      Source source = new StreamSource(new ByteArrayInputStream(inputXml.getBytes()));
+      Result result = new StreamResult(output);
+
+      // Apply the xsl file to the source file and write the result
+      // to the output file
+      xformer.transform(source, result);
+      return output.toString("UTF-8");
+    } catch (Exception e) {
+      throw new InvalidStateException("Problem with translating input xml", e);
+    }
+  }
+
 }

commons/src/main/java/lcsb/mapviewer/common/comparator/CalendarComparator.java

+package lcsb.mapviewer.common.comparator;
+
+import java.util.Calendar;
+import java.util.Comparator;
+
+/**
+ * Comparator implementation for {@link Calendar} class.
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+public class CalendarComparator implements Comparator<Calendar> {
+
+  @Override
+  public int compare(Calendar arg0, Calendar arg1) {
+    if (arg0 == null) {
+      if (arg1 == null) {
+        return 0;
+      } else {
+        return 1;
+      }
+
+    } else if (arg1 == null) {
+      return -1;
+    }
+    return ((Long) arg0.getTimeInMillis()).compareTo(arg1.getTimeInMillis());
+  }
+
+}

commons/src/main/java/lcsb/mapviewer/common/comparator/IntegerComparator.java

@@ -10,18 +10,18 @@ import java.util.Comparator;
  */
 public class IntegerComparator implements Comparator<Integer> {
 
-	@Override
-	public int compare(Integer arg0, Integer arg1) {
-		if (arg0 == null) {
-			if (arg1 == null) {
-				return 0;
-			} else {
-				return 1;
-			}
-		} else if (arg1 == null) {
-			return -1;
-		}
-		return arg0.compareTo(arg1);
-	}
+  @Override
+  public int compare(Integer arg0, Integer arg1) {
+    if (arg0 == null) {
+      if (arg1 == null) {
+        return 0;
+      } else {
+        return 1;
+      }
+    } else if (arg1 == null) {
+      return -1;
+    }
+    return arg0.compareTo(arg1);
+  }
 
 }

commons/src/main/resources/to_lowercase.xsl

+<?xml version="1.0" encoding="ISO-8859-1"?>
+<xsl:stylesheet version="1.0"
+ xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
+    <xsl:variable
+       name="lcase">abcdefghijklmnopqrstuvwxyz</xsl:variable>
+    <xsl:variable
+       name="ucase">ABCDEFGHIJKLMNOPQRSTUVWXYZ</xsl:variable>
+    
+    <xsl:template match="@*|node()">
+        <xsl:copy>
+            <xsl:apply-templates select="@*|node()"/>
+        </xsl:copy>
+    </xsl:template>
+    <xsl:template match="*">
+        <xsl:element name="{translate(local-name(),$ucase,$lcase)}">
+            <xsl:apply-templates select="@*|node()"/>
+        </xsl:element>
+    </xsl:template>
+    
+</xsl:stylesheet>

commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java

@@ -149,7 +149,7 @@ public class XmlParserTest {
   }
 
   boolean threadSucceded;
-  
+
   @Test
   public void testConcurrencyParse() throws Exception {
     try {
@@ -182,7 +182,6 @@ public class XmlParserTest {
 
   }
 
-
   @Test
   public void testInvalidNodeToString() throws Exception {
     try {
@@ -451,4 +450,19 @@ public class XmlParserTest {
       throw e;
     }
   }
+
+  @Test
+  public void testLowercaseXmlNames() throws Exception {
+    try {
+      String inputXml = "<node><ASD>Test</ASD></node>";
+      String outputXml = XmlParser.lowercaseXmlNames(inputXml);
+
+      assertTrue(outputXml.indexOf("asd") >= 0);
+      assertTrue(outputXml.indexOf("Test") >= 0);
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
 }

converter-CellDesigner/pom.xml

-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 	<parent>

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

@@ -22,6 +22,7 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.ZIndexPopulator;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
 import lcsb.mapviewer.converter.model.celldesigner.alias.AliasCollectionXmlParser;
 import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
@@ -144,7 +145,10 @@ public class CellDesignerXmlParser extends Converter {
       }
       // we ignore metaid - it's useless and obstruct data model
       // model.setMetaId(XmlParser.getNodeAttr("metaId", modelNode));
-      model.setIdModel(XmlParser.getNodeAttr("id", modelNode));
+      String modelId = XmlParser.getNodeAttr("id", modelNode);
+      if (modelId != null && !modelId.isEmpty()) {
+        model.setIdModel(modelId);
+      }
 
       Node compartmentNode = XmlParser.getNode("listOfCompartments", modelNode.getChildNodes());