Replace old, undistributed CSV parser library with Commons CSV

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaCsv2RdfController.java

@@ -141,7 +141,7 @@ public class JenaCsv2RdfController extends JenaIngestController {
     }
 
 	 public Model doExecuteCsv2Rdf(VitroRequest vreq, FileItem fileStream, String filePath) throws Exception {
-			char[] quoteChars = {'"'};
+			char quoteChar = '"';
 			String namespace = "";
 			String tboxNamespace = vreq.getParameter("tboxNamespace");
 			String typeName = vreq.getParameter("typeName");
@@ -162,7 +162,7 @@ public class JenaCsv2RdfController extends JenaIngestController {
 				separatorChar = '\t';
 			}
 			
-			Csv2Rdf c2r = new Csv2Rdf(separatorChar, quoteChars,namespace,tboxNamespace,typeName);
+			Csv2Rdf c2r = new Csv2Rdf(separatorChar, quoteChar,namespace,tboxNamespace,typeName);
 			
 			InputStream is = null;
 			

api/src/main/java/edu/cornell/mannlib/vitro/webapp/ontology/update/OntologyChangeParser.java

@@ -5,14 +5,16 @@ package edu.cornell.mannlib.vitro.webapp.ontology.update;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
+import java.io.InputStreamReader;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.StringTokenizer;
 
+import org.apache.commons.csv.CSVFormat;
+import org.apache.commons.csv.CSVParser;
+import org.apache.commons.csv.CSVRecord;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.skife.csv.CSVReader;
-import org.skife.csv.SimpleReader;
 
 import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.AtomicChangeType;
 
@@ -35,7 +37,6 @@ public class OntologyChangeParser {
 		
 	/**
 	 * @param diffPath Diff path
-	 * @throws IOException 
 	 */
 	
 	@SuppressWarnings({ "unchecked", "null", "static-access" })
@@ -50,52 +51,53 @@ public class OntologyChangeParser {
 		String destinationURI = null;
 		StringTokenizer stArr = null; 
 		FileInputStream in = new FileInputStream(new File(diffPath));
-		CSVReader readFile = new SimpleReader();
+
-		readFile.setSeperator('\t');
+		CSVParser readFile = new CSVParser(new InputStreamReader(in),
-		
+				CSVFormat.DEFAULT.withRecordSeparator('\t'));
-		List<String[]> rows = readFile.parse(in);
+
-		
+		int rowNum = 0;
-		for(int rowNum = 0; rowNum < rows.size(); rowNum++){
+		for (CSVRecord record : readFile) {
-			
+			rowNum++;
-			String[] cols = rows.get(rowNum);
+			if (record.size() != 5) {
-			if (cols.length != 5) {
+				logger.logError("Invalid PromptDiff data at row " + (rowNum)
-				logger.logError("Invalid PromptDiff data at row " + (rowNum + 1) 
+					   + ". Expected 5 columns; found " + record.size() );
-					   + ". Expected 5 columns; found " + cols.length );
 			} else {
-		
+				String col = null;
 				changeObj = new AtomicOntologyChange();
-				
+
-				if (cols[0] != null && cols[0].length() > 0) {
+				col = record.get(0);
-					changeObj.setSourceURI(cols[0]);
+				if (col != null && col.length() > 0) {
-				}
+					changeObj.setSourceURI(col);
-				
-				if (cols[1] != null && cols[1].length() > 0) {
-					changeObj.setDestinationURI(cols[1]);
 				}
 
-				if (cols[4] != null && cols[4].length() > 0) {
+				col = record.get(1);
-                  changeObj.setNotes(cols[4]);
+				if (col != null && col.length() > 0) {
+					changeObj.setDestinationURI(col);
+				}
+
+				col = record.get(4);
+				if (col != null && col.length() > 0) {
+                  changeObj.setNotes(col);
                 }
 
-				if ("Yes".equals(cols[2])) {
+				if ("Yes".equals(record.get(2))) {
 					changeObj.setAtomicChangeType(AtomicChangeType.RENAME);
-				} else if ("Delete".equals(cols[3])) {
+				} else if ("Delete".equals(record.get(3))) {
 					changeObj.setAtomicChangeType(AtomicChangeType.DELETE); 
-				} else if ("Add".equals(cols[3])) {
+				} else if ("Add".equals(record.get(3))) {
 					changeObj.setAtomicChangeType(AtomicChangeType.ADD);
 				} else {
 					logger.logError("Invalid rename or change type data: '" +
-							cols[2] + " " + cols[3] + "'");
+							record.get(2) + " " + record.get(3) + "'");
 				}
-				
+
-				
 			    log.debug(changeObj);
 				
 				changeObjects.add(changeObj);
-					
 			}
-			
 		}
+
+		readFile.close();
 		
 		if (changeObjects.size() == 0) {
 			logger.log("No ABox updates are required.");

api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/Csv2Rdf.java

@@ -4,14 +4,15 @@ package edu.cornell.mannlib.vitro.webapp.utils;
 
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.InputStreamReader;
 import java.util.List;
 import java.util.Random;
 
 import javax.servlet.http.HttpServletRequest;
 
-import org.skife.csv.CSVReader;
+import org.apache.commons.csv.CSVFormat;
-import org.skife.csv.SimpleReader;
+import org.apache.commons.csv.CSVParser;
-
+import org.apache.commons.csv.CSVRecord;
 import org.apache.jena.datatypes.xsd.XSDDatatype;
 import org.apache.jena.ontology.DatatypeProperty;
 import org.apache.jena.ontology.Individual;
@@ -34,11 +35,11 @@ public class Csv2Rdf {
 	private String individualNameBase;
 	private String propertyNameBase;
 	private char separatorChar;
-    private char[] quoteChars;
+    private char quoteChar;
 	
-    public Csv2Rdf(char[] quoteChars, String namespace, String tboxNamespace, String typeName) {
+    public Csv2Rdf(char quoteChar, String namespace, String tboxNamespace, String typeName) {
     	this.separatorChar = ',';
-		this.quoteChars = quoteChars;
+		this.quoteChar = quoteChar;
 		this.namespace = namespace;
 		this.tboxNamespace = tboxNamespace;
 		this.typeName = typeName;
@@ -46,9 +47,9 @@ public class Csv2Rdf {
 		this.propertyNameBase = individualNameBase+"_";
 	}
     
-	public Csv2Rdf(char separatorChar, char[] quoteChars, String namespace, String tboxNamespace, String typeName) {
+	public Csv2Rdf(char separatorChar, char quoteChar, String namespace, String tboxNamespace, String typeName) {
 		this.separatorChar = separatorChar;
-		this.quoteChars = quoteChars;
+		this.quoteChar = quoteChar;
 		this.namespace = namespace;
 		this.tboxNamespace = tboxNamespace;
 		this.typeName = typeName;
@@ -66,47 +67,48 @@ public class Csv2Rdf {
         ontModel.addSubModel(tboxOntModel);
         OntClass theClass = tboxOntModel.createClass(tboxNamespace+typeName);
 
-		CSVReader cReader = new SimpleReader();
+		URIGenerator uriGen = (wadf != null && destination != null)
-		cReader.setSeperator(separatorChar);
-		cReader.setQuoteCharacters(quoteChars);	
-
-		URIGenerator uriGen = (wadf != null && destination != null) 
 				? new RandomURIGenerator(wadf, destination)
-		        : new SequentialURIGenerator();
+				: new SequentialURIGenerator();
-		
-		List<String[]> fileRows = cReader.parse(fis);
-		
-        String[] columnHeaders = fileRows.get(0);
 
-        DatatypeProperty[] dpArray = new DatatypeProperty[columnHeaders.length];
+		CSVParser cReader = new CSVParser(new InputStreamReader(fis),
+				CSVFormat.DEFAULT.withRecordSeparator(separatorChar)
+								.withQuote(quoteChar));
 
-        for (int i=0; i<columnHeaders.length; i++) {
+		DatatypeProperty[] dpArray = null;
-            dpArray[i] = tboxOntModel.createDatatypeProperty(tboxNamespace+propertyNameBase+columnHeaders[i].replaceAll("\\W",""));
+
-        }
+		for (CSVRecord cRecord : cReader) {
-        Individual ind = null;
+			if (dpArray == null) {
-        for (int row=1; row<fileRows.size(); row++) {    	
+				dpArray = new DatatypeProperty[cRecord.size()];
-        	String uri = uriGen.getNextURI();
+
-        	if(uri!=null)
+				for (int i = 0; i < dpArray.length; i++) {
-        		ind = ontModel.createIndividual(uri,theClass);
+					dpArray[i] = tboxOntModel.createDatatypeProperty(tboxNamespace+propertyNameBase+cRecord.get(i).replaceAll("\\W",""));
-        	else
+				}
-        		ind = ontModel.createIndividual(theClass);
+			} else {
-	        String[] cols = fileRows.get(row);
+				Individual ind = null;
-	        for (int col=0; col<cols.length; col++) {
+				String uri = uriGen.getNextURI();
-				String value = cols[col].trim();
+				if (uri!=null) {
-	            if (value.length()>0) {
+					ind = ontModel.createIndividual(uri, theClass);
-	                ind.addProperty(dpArray[col], value); // no longer using: , XSDDatatype.XSDstring);
+				} else {
-	                // TODO: specification of datatypes for columns
+					ind = ontModel.createIndividual(theClass);
-	            }
+				}
-	        }
+				for (int col = 0; col<cRecord.size() && col < dpArray.length; col++) {
-        }
+					String value = cRecord.get(col).trim();
-        
+					if (value.length()>0) {
+						ind.addProperty(dpArray[col], value); // no longer using: , XSDDatatype.XSDstring);
+						// TODO: specification of datatypes for columns
+					}
+				}
+			}
+		}
+
+		cReader.close();
         ontModel.removeSubModel(tboxOntModel);
 		
 		Model[] resultModels = new Model[2];
 		resultModels[0] = ontModel;
 		resultModels[1] = tboxOntModel;
 		return resultModels;
-		
 	}
 	
 	private interface URIGenerator {

dependencies/pom.xml

@@ -111,6 +111,11 @@
             <artifactId>commons-lang3</artifactId>
             <version>3.4</version>
         </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-csv</artifactId>
+            <version>1.4</version>
+        </dependency>
         <dependency>
             <groupId>commons-logging</groupId>
             <artifactId>commons-logging</artifactId>
@@ -243,12 +248,6 @@
             <version>1.2.1</version>
         </dependency>
 
-        <dependency>
-            <groupId>org.vivoweb.dependencies</groupId>
-            <artifactId>csv</artifactId>
-            <version>1.0</version>
-        </dependency>
-
         <dependency>
             <groupId>javax.json</groupId>
             <artifactId>javax.json-api</artifactId>