Fix #723: Manually merge pull request #724 (Catch blank nodes during CSV...

Fix #723: Manually merge pull request #724 (Catch blank nodes during CSV import). Also protect importer against empty source/target ids after trim and add some logging.

modules/DataLaboratoryAPI/src/main/java/org/gephi/datalab/impl/AttributeColumnsControllerImpl.java

@@ -685,7 +685,7 @@ public class AttributeColumnsControllerImpl implements AttributeColumnsControlle
             //Create edges:
             GraphElementsController gec = Lookup.getDefault().lookup(GraphElementsController.class);
             Graph graph = Lookup.getDefault().lookup(GraphController.class).getGraphModel().getGraph();
-            String id = null;
+            String id;
             Edge edge;
             String sourceId, targetId;
             Node source, target;
@@ -694,11 +694,15 @@ public class AttributeColumnsControllerImpl implements AttributeColumnsControlle
             reader = new CsvReader(new FileInputStream(file), separator, charset);
             reader.setTrimWhitespace(false);
             reader.readHeaders();
+            
+            int recordNumber = 0;
             while (reader.readRecord()) {
+                recordNumber++;
                 sourceId = reader.get(sourceColumn);
                 targetId = reader.get(targetColumn);
 
-                if (sourceId == null || sourceId.isEmpty() || targetId == null || targetId.isEmpty()) {
+                if (sourceId == null || sourceId.trim().isEmpty() || targetId == null || targetId.trim().isEmpty()) {
+                    Logger.getLogger("").log(Level.WARNING, "Ignoring record {0} due to empty source and/or target node ids", recordNumber);
                     continue;//No correct source and target ids were provided, ignore row
                 }
 
@@ -791,9 +795,9 @@ public class AttributeColumnsControllerImpl implements AttributeColumnsControlle
                 }
             }
         } catch (FileNotFoundException ex) {
-            Exceptions.printStackTrace(ex);
+            Logger.getLogger("").log(Level.SEVERE, null, ex);
         } catch (IOException ex) {
-            Exceptions.printStackTrace(ex);
+            Logger.getLogger("").log(Level.SEVERE, null, ex);
         } finally {
             if(reader != null){
                 reader.close();

modules/DataLaboratoryPlugin/src/main/java/org/gephi/datalab/plugin/manipulators/general/ui/ImportCSVUIVisualPanel1.java

@@ -50,6 +50,7 @@ import java.lang.reflect.InvocationTargetException;
 import java.nio.charset.Charset;
 import java.util.ArrayList;
 import java.util.HashSet;
+import java.util.LinkedHashSet;
 import java.util.Set;
 import javax.swing.JFileChooser;
 import javax.swing.JOptionPane;
@@ -81,7 +82,8 @@ public class ImportCSVUIVisualPanel1 extends javax.swing.JPanel {
     private int columnCount = 0;
     private boolean hasSourceNodeColumn = false;
     private boolean hasTargetNodeColumn = false;
-    private boolean columnNamesRepeated = false;
+    private boolean hasColumnNamesRepeated = false;
+    private boolean hasRowsMissingSourcesOrTargets = false;
     private ValidationPanel validationPanel;
 
     /** Creates new form ImportCSVUIVisualPanel1 */
@@ -143,7 +145,7 @@ public class ImportCSVUIVisualPanel1 extends javax.swing.JPanel {
                                 prblms.add(getMessage("ImportCSVUIVisualPanel1.validation.no-columns"));
                                 return false;
                             }
-                            if (columnNamesRepeated) {
+                            if (hasColumnNamesRepeated()) {
                                 prblms.add(getMessage("ImportCSVUIVisualPanel1.validation.repeated-columns"));
                                 return false;
                             }
@@ -151,6 +153,12 @@ public class ImportCSVUIVisualPanel1 extends javax.swing.JPanel {
                                 prblms.add(getMessage("ImportCSVUIVisualPanel1.validation.edges.no-source-target-columns"));
                                 return false;
                             }
+                            if (hasRowsMissingSourcesOrTargets()) {
+                                prblms.add(NbBundle.getMessage(ImportCSVUIVisualPanel1.class, 
+                                    "ImportCSVUIVisualPanel1.validation.edges.empty-sources-or-targets"
+                                ));
+                                return false;
+                            }
                             return true;
                         }
                     });
@@ -182,32 +190,55 @@ public class ImportCSVUIVisualPanel1 extends javax.swing.JPanel {
 
                 //Check for repeated column names:
                 Set<String> columnNamesSet = new HashSet<String>();
-                columnNamesRepeated = false;
+                hasColumnNamesRepeated = false;
                 hasSourceNodeColumn = false;
                 hasTargetNodeColumn = false;
+                int sourceColumnIndex = 0, 
+                    targetColumnIndex = 0,
+                    currentColumn = 0;
                 for (String header : headers) {
                     if (header.equalsIgnoreCase("source")) {
                         hasSourceNodeColumn = true;
+                        sourceColumnIndex = currentColumn;
                     }
                     if (header.equalsIgnoreCase("target")) {
                         hasTargetNodeColumn = true;
+                        targetColumnIndex = currentColumn;
                     }
                     if (columnNamesSet.contains(header)) {
-                        columnNamesRepeated = true;
+                        hasColumnNamesRepeated = true;
                         break;
                     }
                     columnNamesSet.add(header);
+                    currentColumn++;
                 }
 
                 ArrayList<String[]> records = new ArrayList<String[]>();
+                hasRowsMissingSourcesOrTargets = false;
+                ImportCSVUIWizardAction.Mode mode = getMode();
                 if (columnCount > 0) {
                     String[] currentRecord;
-                    while (reader.readRecord() && records.size() < MAX_ROWS_PREVIEW) {
-                        currentRecord = new String[reader.getColumnCount()];
+                    
+                    while (reader.readRecord()) {
+                        int recordColumnCount = reader.getColumnCount();
+                        currentRecord = new String[recordColumnCount];
                         for (int i = 0; i < currentRecord.length; i++) {
                             currentRecord[i] = reader.get(i);
                         }
-                        records.add(currentRecord);
+                        
+                        // Search for missing source or target columns for edges table
+                        if(mode == ImportCSVUIWizardAction.Mode.EDGES_TABLE){
+                            if (recordColumnCount < sourceColumnIndex
+                                    || currentRecord[sourceColumnIndex].trim().isEmpty()
+                                    || recordColumnCount < targetColumnIndex
+                                    || currentRecord[targetColumnIndex].trim().isEmpty()) {
+                                hasRowsMissingSourcesOrTargets = true;
+                            }
+                        }
+                        
+                        if (records.size() < MAX_ROWS_PREVIEW) {
+                            records.add(currentRecord);
+                        }
                     }
                 }
                 reader.close();
@@ -265,7 +296,7 @@ public class ImportCSVUIVisualPanel1 extends javax.swing.JPanel {
                 Exceptions.printStackTrace(ex);
             } catch (IOException ex) {
                 JOptionPane.showMessageDialog(this, getMessage("ImportCSVUIVisualPanel1.validation.error"), getMessage("ImportCSVUIVisualPanel1.validation.file-permissions-error"), JOptionPane.ERROR_MESSAGE);
-            }
+            } 
         }
         wizard1.fireChangeEvent();
         pathTextField.setText(pathTextField.getText());//To fire validation panel messages.
@@ -308,8 +339,8 @@ public class ImportCSVUIVisualPanel1 extends javax.swing.JPanel {
         return columnCount;
     }
 
-    public boolean isColumnNamesRepeated() {
-        return columnNamesRepeated;
+    public boolean hasColumnNamesRepeated() {
+        return hasColumnNamesRepeated;
     }
 
     public boolean isValidFile() {
@@ -332,7 +363,11 @@ public class ImportCSVUIVisualPanel1 extends javax.swing.JPanel {
     }
 
     public boolean isCSVValid() {
-        return isValidFile() && hasColumns() && !columnNamesRepeated && areValidColumnsForTable();
+        return isValidFile() && hasColumns() && !hasColumnNamesRepeated && areValidColumnsForTable() &&!hasRowsMissingSourcesOrTargets();
+    }
+
+    public boolean hasRowsMissingSourcesOrTargets() {
+        return hasRowsMissingSourcesOrTargets;
     }
 
     class SeparatorWrapper {

modules/DataLaboratoryPlugin/src/main/resources/org/gephi/datalab/plugin/manipulators/general/ui/Bundle.properties

@@ -50,6 +50,7 @@ ImportCSVUIVisualPanel1.validation.repeated-columns:The file can't have repeated
 ImportCSVUIVisualPanel1.validation.error=Error
 ImportCSVUIVisualPanel1.validation.file-permissions-error=An error happened when reading the file. Make sure the file is not in use and you have permissions.
 ImportCSVUIVisualPanel1.validation.edges.no-source-target-columns=Edges table needs a 'Source' and 'Target' column with nodes ids.
+ImportCSVUIVisualPanel1.validation.edges.empty-sources-or-targets=Found row(s) with empty Source and/or Target columns
 ImportCSVUIVisualPanel2.name=Import settings
 ImportCSVUIVisualPanel2.columnsLabel.text=Imported columns:
 ImportCSVUIVisualPanel2.nodes.description=<html>New columns are created with the specified type.<br />A generated id is assigned if missing.<br />Unless the option 'Force nodes to be created as new ones' is enabled, already existing nodes will be updated.</html>