Merge pull request IQSS#7 from IQSS/master

new code3

scripts/api/data/metadatablocks/citation.tsv

@@ -93,8 +93,8 @@
 	contributorType	Supervisor	13											
 	contributorType	Work Package Leader	14											
 	contributorType	Other	15											
-	authorIdentifierScheme	ISNI	0											
-	authorIdentifierScheme	ORCID	1											
+	authorIdentifierScheme	ORCID	0											
+	authorIdentifierScheme	ISNI	1											
 	language	Abkhaz	0											
 	language	Afar	1											
 	language	Afrikaans	2											
@@ -279,4 +279,4 @@
 	language	Yoruba	181											
 	language	Zhuang, Chuang	182											
 	language	Zulu	183											
-	language	Not applicable	184											
+	language	Not applicable	184											

src/main/java/edu/harvard/iq/dataverse/Template.java

@@ -7,6 +7,7 @@
 import java.util.Comparator;
 import java.util.Date;
 import java.util.HashMap;
+import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 import javax.persistence.CascadeType;
@@ -18,6 +19,7 @@
 import javax.persistence.Temporal;
 import javax.persistence.TemporalType;
 import javax.persistence.Transient;
+import javax.validation.constraints.Size;
 import org.hibernate.validator.constraints.NotBlank;
 
 /**
@@ -47,6 +49,7 @@ public Long getId() {
     }
 
     @NotBlank(message = "Please enter a name.")
+    @Size(max = 255, message = "Name must be at most 255 characters.")
     private String name;
 
     public String getName() {
@@ -276,6 +279,24 @@ public void setDatasetFields(List<DatasetField> datasetFields) {
         this.datasetFields = datasetFields;
     }
 
+    public List<DatasetField> getFlatDatasetFields() {
+        return getFlatDatasetFields(getDatasetFields());
+    }
+
+    private List<DatasetField> getFlatDatasetFields(List<DatasetField> dsfList) {
+        List<DatasetField> retList = new LinkedList();
+        for (DatasetField dsf : dsfList) {
+            retList.add(dsf);
+            if (dsf.getDatasetFieldType().isCompound()) {
+                for (DatasetFieldCompoundValue compoundValue : dsf.getDatasetFieldCompoundValues()) {
+                    retList.addAll(getFlatDatasetFields(compoundValue.getChildDatasetFields()));
+                }
+
+            }
+        }
+        return retList;
+    }
+
     @Override
      public int hashCode() {
         int hash = 0;

src/main/java/edu/harvard/iq/dataverse/TemplatePage.java

@@ -6,13 +6,18 @@
 import edu.harvard.iq.dataverse.engine.command.impl.UpdateDateverseTemplateCommand;
 import java.sql.Timestamp;
 import java.util.Date;
+import java.util.Set;
 import javax.ejb.EJB;
 import javax.ejb.EJBException;
 import javax.faces.application.FacesMessage;
 import javax.faces.context.FacesContext;
 import javax.faces.view.ViewScoped;
 import javax.inject.Inject;
 import javax.inject.Named;
+import javax.validation.ConstraintViolation;
+import javax.validation.Validation;
+import javax.validation.Validator;
+import javax.validation.ValidatorFactory;
 
 /**
  *
@@ -110,6 +115,34 @@ public void edit(TemplatePage.EditMode editMode) {
     }
 
     public String save() {
+
+                boolean dontSave = false;
+        ValidatorFactory factory = Validation.buildDefaultValidatorFactory();
+        Validator validator = factory.getValidator();
+        for (DatasetField dsf : template.getFlatDatasetFields()) {
+            dsf.setValidationMessage(null); // clear out any existing validation message
+            Set<ConstraintViolation<DatasetField>> constraintViolations = validator.validate(dsf);
+            for (ConstraintViolation<DatasetField> constraintViolation : constraintViolations) {
+                FacesContext.getCurrentInstance().addMessage(null, new FacesMessage(FacesMessage.SEVERITY_ERROR, "Validation Error", constraintViolation.getMessage()));
+                dsf.setValidationMessage(constraintViolation.getMessage());
+                dontSave = true;
+                break; // currently only support one message, so we can break out of the loop after the first constraint violation
+            }
+            for (DatasetFieldValue dsfv : dsf.getDatasetFieldValues()) {
+                dsfv.setValidationMessage(null); // clear out any existing validation message
+                Set<ConstraintViolation<DatasetFieldValue>> constraintViolations2 = validator.validate(dsfv);
+                for (ConstraintViolation<DatasetFieldValue> constraintViolation : constraintViolations2) {
+                    FacesContext.getCurrentInstance().addMessage(null, new FacesMessage(FacesMessage.SEVERITY_ERROR, "Validation Error", constraintViolation.getMessage()));
+                    dsfv.setValidationMessage(constraintViolation.getMessage());
+                    dontSave = true;
+                    break; // currently only support one message, so we can break out of the loop after the first constraint violation                    
+                }
+            }
+        }
+        if (dontSave) {
+            return "";
+        }
+
         Command<Dataverse> cmd;
         try {
             if (editMode == EditMode.CREATE) {

src/main/java/edu/harvard/iq/dataverse/dataaccess/TabularSubsetGenerator.java

@@ -562,7 +562,7 @@ private File generateRotatedImage (File tabfile, int varcount, int casecount) th
 
         int MAX_OUTPUT_STREAMS = 32;
         int MAX_BUFFERED_BYTES = 10 * 1024 * 1024; // 10 MB - for now?
-        int MAX_COLUMN_BUFFER = 8192; 
+        int MAX_COLUMN_BUFFER = 8 * 1024; 
 
         // offsetHeader will contain the byte offsets of the individual column 
         // vectors in the final rotated image file
@@ -604,9 +604,18 @@ private File generateRotatedImage (File tabfile, int varcount, int casecount) th
                     tokensize = token.getBytes().length;
                     if (bufferedSizes[varindex]+tokensize > MAX_COLUMN_BUFFER) {
                         // fill the buffer and dump its contents into the temp file:
+                        // (do note that there may be *several* MAX_COLUMN_BUFFERs
+                        // worth of bytes in the token!)
+
+                        int tokenoffset = 0; 
+
                         if (bufferedSizes[varindex] != MAX_COLUMN_BUFFER) {
-                            System.arraycopy(token.getBytes(), 0, bufferedColumns[varindex], bufferedSizes[varindex], MAX_COLUMN_BUFFER-bufferedSizes[varindex]);
-                        }
+                            tokenoffset = MAX_COLUMN_BUFFER-bufferedSizes[varindex];
+                            System.arraycopy(token.getBytes(), 0, bufferedColumns[varindex], bufferedSizes[varindex], tokenoffset);
+                        } // (otherwise the buffer is already full, and we should 
+                          // simply dump it into the temp file, without adding any 
+                          // extra bytes to it)
+
                         File bufferTempFile = columnTempFiles[varindex]; 
                         if (bufferTempFile == null) {
                             bufferTempFile = File.createTempFile("columnBufferFile", "bytes");
@@ -618,18 +627,29 @@ private File generateRotatedImage (File tabfile, int varcount, int casecount) th
                         BufferedOutputStream outputStream = new BufferedOutputStream(new FileOutputStream (bufferTempFile, true));
                         outputStream.write(bufferedColumns[varindex], 0, MAX_COLUMN_BUFFER);
                         cachedfileSizes[varindex] += MAX_COLUMN_BUFFER;
+
+                        // keep writing MAX_COLUMN_BUFFER-size chunks of bytes into 
+                        // the temp file, for as long as there's more than MAX_COLUMN_BUFFER
+                        // bytes left in the token:
+
+                        while (tokensize - tokenoffset > MAX_COLUMN_BUFFER) {
+                            outputStream.write(token.getBytes(), tokenoffset, MAX_COLUMN_BUFFER);
+                            cachedfileSizes[varindex] += MAX_COLUMN_BUFFER;
+                            tokenoffset += MAX_COLUMN_BUFFER;
+                        }
+
                         outputStream.close();
 
                         // buffer the remaining bytes and reset the buffered 
                         // byte counter: 
 
                         System.arraycopy(token.getBytes(), 
-                                MAX_COLUMN_BUFFER-bufferedSizes[varindex],
+                                tokenoffset, 
                                 bufferedColumns[varindex], 
                                 0,
-                                bufferedSizes[varindex] + tokensize - MAX_COLUMN_BUFFER);
+                                tokensize - tokenoffset); 
 
-                        bufferedSizes[varindex] = bufferedSizes[varindex] + tokensize - MAX_COLUMN_BUFFER;
+                        bufferedSizes[varindex] = tokensize - tokenoffset; 
 
                     } else {
                         // continue buffering
@@ -803,7 +823,7 @@ private void reverseRotatedImage (File rotfile, int varcount, int casecount) thr
 
     /**
      * main() method, for testing
-     * usage: java edu.harvard.iq.dataverse.dataaccess.TabularSubsetGenerator testfile.tab varcount casecount
+     * usage: java edu.harvard.iq.dataverse.dataaccess.TabularSubsetGenerator testfile.tab varcount casecount column type
      * make sure the CLASSPATH contains ...
      * 
      */