7527 redetect api error

src/main/java/edu/harvard/iq/dataverse/api/Files.java

@@ -48,6 +48,7 @@
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import javax.ejb.EJB;
+import javax.ejb.Stateless;
 import javax.inject.Inject;
 import javax.json.Json;
 import javax.json.JsonReader;
@@ -70,6 +71,7 @@
 import org.glassfish.jersey.media.multipart.FormDataContentDisposition;
 import org.glassfish.jersey.media.multipart.FormDataParam;
 
+@Stateless
 @Path("files")
 public class Files extends AbstractApiBean {
 

src/main/java/edu/harvard/iq/dataverse/engine/command/impl/RedetectFileTypeCommand.java

@@ -62,7 +62,8 @@ public DataFile execute(CommandContext ctxt) throws CommandException {
             }
 
             logger.fine("target file: " + localFile);
-            String newlyDetectedContentType = FileTypeDetection.determineFileType(localFile);
+            String fileName = fileToRedetect.getLatestFileMetadata().getLabel();
+            String newlyDetectedContentType = FileTypeDetection.determineFileType(localFile, fileName);
             fileToRedetect.setContentType(newlyDetectedContentType);
         } catch (IOException ex) {
             throw new CommandException("Exception while attempting to get the bytes of the file during file type redetection: " + ex.getLocalizedMessage(), this);

src/main/java/edu/harvard/iq/dataverse/util/DatasetFieldWalker.java

@@ -15,101 +15,115 @@
 import java.util.logging.Logger;
 
 /**
- * A means of iterating over {@link DatasetField}s, or a collection of them.
- * As these may have a complex structure (compound values, etc), this object 
- * allows processing them via an event stream, similar to SAX parsing of XML.
- * Visiting of the fields is done in display order.
- * 
+ * A means of iterating over {@link DatasetField}s, or a collection of them. As
+ * these may have a complex structure (compound values, etc), this object allows
+ * processing them via an event stream, similar to SAX parsing of XML. Visiting
+ * of the fields is done in display order.
+ *
  * @author michael
  */
 public class DatasetFieldWalker {
 
     private static final Logger logger = Logger.getLogger(DatasetFieldWalker.class.getCanonicalName());
 
     public interface Listener {
-        void startField( DatasetField f );
-        void endField( DatasetField f );
-        void primitiveValue( DatasetFieldValue dsfv );
-        void controledVocabularyValue( ControlledVocabularyValue cvv );
-        void startCompoundValue( DatasetFieldCompoundValue dsfcv );
-        void endCompoundValue( DatasetFieldCompoundValue dsfcv );
+
+        void startField(DatasetField f);
+
+        void endField(DatasetField f);
+
+        void primitiveValue(DatasetFieldValue dsfv);
+
+        void controledVocabularyValue(ControlledVocabularyValue cvv);
+
+        void startCompoundValue(DatasetFieldCompoundValue dsfcv);
+
+        void endCompoundValue(DatasetFieldCompoundValue dsfcv);
     }
-    
+
     /**
      * Convenience method to walk over a field.
+     *
      * @param dsf the field to walk over.
      * @param l the listener to execute on {@code dsf}'s values and structure.
      */
-    public static void walk( DatasetField dsf, Listener l ) {
+    public static void walk(DatasetField dsf, Listener l) {
         DatasetFieldWalker joe = new DatasetFieldWalker(l);
         SettingsServiceBean nullServiceBean = null;
         joe.walk(dsf, nullServiceBean);
     }
 
     /**
-     * Convenience method to walk over a list of fields. Traversal
-     * is done in display order.
+     * Convenience method to walk over a list of fields. Traversal is done in
+     * display order.
+     *
      * @param fields the fields to go over. Does not have to be sorted.
      * @param exclude the fields to skip
      * @param l the listener to execute on each field values and structure.
      */
     public static void walk(List<DatasetField> fields, SettingsServiceBean settingsService, Listener l) {
         DatasetFieldWalker joe = new DatasetFieldWalker(l);
-        for ( DatasetField dsf : sort( fields, DatasetField.DisplayOrder) ) {
+        for (DatasetField dsf : sort(fields, DatasetField.DisplayOrder)) {
             joe.walk(dsf, settingsService);
         }
     }
-    
+
     private Listener l;
-
-
+
     public DatasetFieldWalker(Listener l) {
         this.l = l;
     }
-    
-    public DatasetFieldWalker(){
-        this( null );
+
+    public DatasetFieldWalker() {
+        this(null);
     }
-    
+
     public void walk(DatasetField fld, SettingsServiceBean settingsService) {
         l.startField(fld);
         DatasetFieldType datasetFieldType = fld.getDatasetFieldType();
+        boolean excludeEmailFromExport = settingsService != null 
+                && settingsService.isTrueForKey(SettingsServiceBean.Key.ExcludeEmailFromExport, false);
 
-        if ( datasetFieldType.isControlledVocabulary() ) {
-            for ( ControlledVocabularyValue cvv 
-                    : sort(fld.getControlledVocabularyValues(), ControlledVocabularyValue.DisplayOrder) ) {
+        if (datasetFieldType.isControlledVocabulary()) {
+            for (ControlledVocabularyValue cvv
+                    : sort(fld.getControlledVocabularyValues(), ControlledVocabularyValue.DisplayOrder)) {
                 l.controledVocabularyValue(cvv);
             }
-
-        } else if ( datasetFieldType.isPrimitive() ) {
-            for ( DatasetFieldValue pv : sort(fld.getDatasetFieldValues(), DatasetFieldValue.DisplayOrder) ) {
-                if (settingsService != null && settingsService.isTrueForKey(SettingsServiceBean.Key.ExcludeEmailFromExport, false) && DatasetFieldType.FieldType.EMAIL.equals(pv.getDatasetField().getDatasetFieldType().getFieldType())) {
+
+        } else if (datasetFieldType.isPrimitive()) {
+            for (DatasetFieldValue pv : sort(fld.getDatasetFieldValues(), DatasetFieldValue.DisplayOrder)) {
+                //if (settingsService != null && settingsService.isTrueForKey(SettingsServiceBean.Key.ExcludeEmailFromExport, false) && DatasetFieldType.FieldType.EMAIL.equals(pv.getDatasetField().getDatasetFieldType().getFieldType())) {
+                // Please note that settingsService.isTrueForKey(...) is not free, 
+                // it translates into one named database query on the setting table. 
+                // Not implying that this will solve the EJB rollback issue in #7527
+                // somehow, but it is insane that we were doing that for every primitive 
+                // field in the dataset metadata. -- L.A.
+                if (DatasetFieldType.FieldType.EMAIL.equals(pv.getDatasetField().getDatasetFieldType().getFieldType()) && excludeEmailFromExport) {
                     continue;
                 }
                 l.primitiveValue(pv);
             }
-            
-        } else if ( datasetFieldType.isCompound() ) {
-           for ( DatasetFieldCompoundValue dsfcv : sort( fld.getDatasetFieldCompoundValues(), DatasetFieldCompoundValue.DisplayOrder) ) {
-               l.startCompoundValue(dsfcv);
-               for ( DatasetField dsf : sort(dsfcv.getChildDatasetFields(), DatasetField.DisplayOrder ) ) {
-                   walk(dsf, settingsService);
-               }
-               l.endCompoundValue(dsfcv);
-           }
+
+        } else if (datasetFieldType.isCompound()) {
+            for (DatasetFieldCompoundValue dsfcv : sort(fld.getDatasetFieldCompoundValues(), DatasetFieldCompoundValue.DisplayOrder)) {
+                l.startCompoundValue(dsfcv);
+                for (DatasetField dsf : sort(dsfcv.getChildDatasetFields(), DatasetField.DisplayOrder)) {
+                    walk(dsf, settingsService);
+                }
+                l.endCompoundValue(dsfcv);
+            }
         }
         l.endField(fld);
     }
-
-
+
     public void setL(Listener l) {
         this.l = l;
     }
-    
-    static private <T> Iterable<T> sort( List<T> list, Comparator<T> cmp ) {
+
+    static private <T> Iterable<T> sort(List<T> list, Comparator<T> cmp) {
         ArrayList<T> tbs = new ArrayList<>(list);
         Collections.sort(tbs, cmp);
         return tbs;
     }
-    
+
 }

src/main/java/edu/harvard/iq/dataverse/util/FileTypeDetection.java

@@ -4,9 +4,10 @@
 import java.io.IOException;
 
 public class FileTypeDetection {
-
-    public static String determineFileType(File file) throws IOException {
-        return FileUtil.determineFileType(file, file.getName());
+    // Question: why do we need this utility? - as opposed to just calling the 
+    // static method in FileUtil directly? - L.A. 
+    public static String determineFileType(File file, String fileName) throws IOException {
+        return FileUtil.determineFileType(file, fileName);
     }
 
 }

src/test/java/edu/harvard/iq/dataverse/util/FileTypeDetectionTest.java

@@ -36,7 +36,7 @@ public static void tearDownClass() {
     public void testDetermineFileTypeJupyterNoteboook() throws Exception {
         File file = new File("src/test/java/edu/harvard/iq/dataverse/util/irc-metrics.ipynb");
         // https://jupyter.readthedocs.io/en/latest/reference/mimetype.html
-        assertEquals("application/x-ipynb+json", FileTypeDetection.determineFileType(file));
+        assertEquals("application/x-ipynb+json", FileTypeDetection.determineFileType(file, file.getName()));
     }
 
 }