Fixing UD-569. Adding preprocessor to replace comma with whitespace in

all Solr search managers.
Fixing UD-558. Trim the error message if it is over 2000 when saving it
to database.

src/main/java/org/ndexbio/common/models/dao/postgresql/NetworkDAO.java

@@ -30,11 +30,7 @@
  */
 package org.ndexbio.common.models.dao.postgresql;
 
-import java.io.File;
 import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Paths;
-import java.nio.file.StandardCopyOption;
 import java.security.SecureRandom;
 import java.sql.Array;
 import java.sql.PreparedStatement;
@@ -57,7 +53,6 @@
 
 import javax.xml.bind.DatatypeConverter;
 
-import org.apache.commons.io.FileUtils;
 import org.apache.solr.client.solrj.SolrServerException;
 import org.apache.solr.common.SolrDocument;
 import org.apache.solr.common.SolrDocumentList;
@@ -79,7 +74,6 @@
 import org.ndexbio.model.object.network.NetworkIndexLevel;
 import org.ndexbio.model.object.network.NetworkSummary;
 import org.ndexbio.model.object.network.VisibilityType;
-import org.ndexbio.rest.Configuration;
 
 import com.fasterxml.jackson.core.JsonParseException;
 import com.fasterxml.jackson.core.JsonProcessingException;
@@ -1705,15 +1699,18 @@ public int revokeUserPrivilege(UUID networkUUID, UUID userUUID) throws SQLExcept
     }
 
     /**
-     * Becareful when using this function, it commit the db connection of the current DAO object.
+     * Be careful when using this function, it commit the db connection of the current DAO object.
      * 
      * @param networkId
-     * @param ErrorMessage
+     * @param errorMessage
      */
-    public void setErrorMessage(UUID networkId, String ErrorMessage) {
+    public void setErrorMessage(UUID networkId, String errorMessage) {
     	String sql = "update network set error = ? where \"UUID\" = ? and is_deleted=false";
+
+    	String trimedMsg = ( errorMessage.length()>2000) ?
+    			(errorMessage.substring(0, 1996) + "...") : errorMessage ;
     	try ( PreparedStatement pst = db.prepareStatement(sql)) {
-    		pst.setString(1, ErrorMessage);
+    		pst.setString(1, trimedMsg);
     		pst.setObject(2, networkId);
     		int i = pst.executeUpdate();
     		if ( i !=1)

src/main/java/org/ndexbio/common/solr/GroupIndexManager.java

@@ -47,6 +47,7 @@
 import org.apache.solr.common.SolrInputDocument;
 import org.apache.solr.common.util.NamedList;
 import org.ndexbio.model.exceptions.NdexException;
+import org.ndexbio.model.tools.SearchUtilities;
 import org.ndexbio.rest.Configuration;
 
 public class GroupIndexManager implements AutoCloseable{
@@ -101,7 +102,7 @@ public SolrDocumentList searchGroups (String searchTerms, int limit, int offset)
 
 		SolrQuery solrQuery = new SolrQuery();	
 
-		solrQuery.setQuery(searchTerms).setFields(UUID);
+		solrQuery.setQuery(SearchUtilities.preprocessSearchTerm(searchTerms)).setFields(UUID);
 		if ( searchTerms.equalsIgnoreCase("*:*"))
 			solrQuery.setSort(UUID, ORDER.desc);
 		if ( offset >=0)

src/main/java/org/ndexbio/common/solr/NetworkGlobalIndexManager.java

@@ -58,6 +58,7 @@
 import org.apache.solr.common.SolrInputDocument;
 import org.apache.solr.common.util.NamedList;
 import org.ndexbio.common.NdexClasses;
+import org.ndexbio.model.tools.SearchUtilities;
 import org.ndexbio.model.tools.TermUtilities;
 import org.ndexbio.common.util.Util;
 import org.ndexbio.cxio.aspects.datamodels.ATTRIBUTE_DATA_TYPE;
@@ -239,7 +240,7 @@ else if ( permission == Permissions.READ) {
 			solrQuery.setSort(MODIFICATION_TIME, ORDER.desc);
 
 //		solrQuery.setQuery( searchTerms ).setFields(UUID);
-		solrQuery.setQuery("( " + searchTerms + " ) AND _val_:\"div(" + NDEX_SCORE+ ",10)\"" ).setFields(UUID);
+		solrQuery.setQuery("( " + SearchUtilities.preprocessSearchTerm(searchTerms) + " ) AND _val_:\"div(" + NDEX_SCORE+ ",10)\"" ).setFields(UUID);
     	solrQuery.set("defType", "edismax");
 		solrQuery.set("qf","uuid^20 name^10 description^5 labels^6 owner^2 networkType^4 organism^3 disease^3 tissue^3 author^2 methods nodeName represents alias rights^0.6 rightsHolder^0.6");
 		if ( offset >=0)

src/main/java/org/ndexbio/common/solr/SingleNetworkSolrIdxManager.java

@@ -61,6 +61,7 @@
 import org.ndexbio.cxio.core.AspectIterator;
 import org.ndexbio.model.cx.FunctionTermElement;
 import org.ndexbio.model.exceptions.NdexException;
+import org.ndexbio.model.tools.SearchUtilities;
 import org.ndexbio.rest.Configuration;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
@@ -99,7 +100,7 @@ public SolrDocumentList getNodeIdsByQuery(String query, int limit) throws SolrSe
 
 		SolrQuery solrQuery = new SolrQuery();
 
-		solrQuery.setQuery(query).setFields(ID);
+		solrQuery.setQuery(SearchUtilities.preprocessSearchTerm(query)).setFields(ID);
     	solrQuery.set("defType", "edismax");
 		solrQuery.set("qf", NAME + " " + REPRESENTS + " " + ALIAS);
 		solrQuery.setStart(0);

src/main/java/org/ndexbio/common/solr/UserIndexManager.java

@@ -47,6 +47,7 @@
 import org.apache.solr.common.SolrInputDocument;
 import org.apache.solr.common.util.NamedList;
 import org.ndexbio.model.exceptions.NdexException;
+import org.ndexbio.model.tools.SearchUtilities;
 import org.ndexbio.rest.Configuration;
 
 public class UserIndexManager implements AutoCloseable{
@@ -109,7 +110,7 @@ public SolrDocumentList searchUsers (String searchTerms, int limit, int offset)
 
 		SolrQuery solrQuery = new SolrQuery();	
 
-		solrQuery.setQuery(searchTerms).setFields(UUID);
+		solrQuery.setQuery(SearchUtilities.preprocessSearchTerm(searchTerms)).setFields(UUID);
 		if ( searchTerms.equalsIgnoreCase("*:*"))
 			solrQuery.setSort(UUID, ORDER.desc);
 		if ( offset >=0)