From 2784a19a160288e334e017ef4f671e94ae3a127f Mon Sep 17 00:00:00 2001
From: Ben Woodhead <bwoodhead@upei.ca>
Date: Mon, 8 Aug 2011 16:13:07 -0300
Subject: [PATCH] Added doc tags

---
 plugins/CollectionFormBuilder.inc      |  32 +-
 plugins/CreateCollection.inc           |  30 +-
 plugins/DarwinCore.inc                 |  59 +-
 plugins/DemoFormBuilder.inc            |  32 +-
 plugins/DocumentConverter.inc          |  32 +-
 plugins/Exiftool.inc                   | 101 +--
 plugins/Ffmpeg.inc                     |  37 +-
 plugins/Flv.inc                        | 109 ++--
 plugins/FlvFormBuilder.inc             |  24 +-
 plugins/FormBuilder.inc                | 199 +++---
 plugins/ImageManipulation.inc          |  81 ++-
 plugins/ModsFormBuilder.inc            | 863 +++++++++++++------------
 plugins/PersonalCollectionClass.inc    |  82 ++-
 plugins/QtFormBuilder.php              | 143 ++--
 plugins/Refworks.inc                   | 151 +++--
 plugins/ShowDemoStreamsInFieldSets.inc |  22 +-
 plugins/ShowStreamsInFieldSets.inc     | 111 +++-
 plugins/fedoraObject.inc               |  33 +-
 plugins/herbarium.inc                  |  83 ++-
 plugins/map_viewer.inc                 |  29 +-
 plugins/qt_viewer.inc                  | 140 ++--
 plugins/slide_viewer.inc               |  34 +-
 plugins/tagging_form.inc               |  44 +-
 23 files changed, 1550 insertions(+), 921 deletions(-)

diff --git a/plugins/CollectionFormBuilder.inc b/plugins/CollectionFormBuilder.inc
index 6c5e33b6..26dbda26 100644
--- a/plugins/CollectionFormBuilder.inc
+++ b/plugins/CollectionFormBuilder.inc
@@ -1,37 +1,52 @@
 <?php
+
 // $Id$
 
+/**
+ * @file
+ * Collection Form Builder
+ */
+
 module_load_include('inc', 'fedora_repository', 'plugins/FormBuilder');
-/*
- * Created on 19-Feb-08
- *
- *
+
+/**
  * implements methods from content model ingest form xml
  * builds a dc metadata form
  */
 class CollectionFormBuilder extends FormBuilder {
+
+  /**
+   * Constructor
+   */
   function CollectionFormBuilder() {
     module_load_include('inc', 'CollectionFormBuilder', '');
     drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
   }
 
+  /**
+   * Create Fedora Datastream
+   * @global type $base_url
+   * @param type $form_values
+   * @param type $dom
+   * @param type $rootElement 
+   */
   function createFedoraDataStreams($form_values, &$dom, &$rootElement) {
     module_load_include('inc', 'fedora_repository', 'MimeClass');
     global $base_url;
 
     $mimetype = new MimeClass();
     $server = NULL;
-    $file=$form_values['ingest-file-location'];
+    $file = $form_values['ingest-file-location'];
     $dformat = $mimetype->getType($file);
-    $fileUrl = $base_url . '/'. drupal_urlencode($file);
+    $fileUrl = $base_url . '/' . drupal_urlencode($file);
     $beginIndex = strrpos($fileUrl, '/');
     $dtitle = substr($fileUrl, $beginIndex + 1);
-    $dtitle =  substr($dtitle, 0, strpos($dtitle, "."));
+    $dtitle = substr($dtitle, 0, strpos($dtitle, "."));
     $ds1 = $dom->createElement("foxml:datastream");
     $ds1->setAttribute("ID", "COLLECTION_POLICY"); //set the ID
     $ds1->setAttribute("STATE", "A");
     $ds1->setAttribute("CONTROL_GROUP", "M");
-    $ds1v= $dom->createElement("foxml:datastreamVersion");
+    $ds1v = $dom->createElement("foxml:datastreamVersion");
     $ds1v->setAttribute("ID", "COLLECTION_POLICY.0");
     $ds1v->setAttribute("MIMETYPE", "$dformat");
     $ds1v->setAttribute("LABEL", "$dtitle");
@@ -42,4 +57,5 @@ class CollectionFormBuilder extends FormBuilder {
     $ds1v->appendChild($ds1content);
     $rootElement->appendChild($ds1);
   }
+
 }
diff --git a/plugins/CreateCollection.inc b/plugins/CreateCollection.inc
index 0c185705..cec55648 100644
--- a/plugins/CreateCollection.inc
+++ b/plugins/CreateCollection.inc
@@ -1,22 +1,34 @@
 <?php
+
 // $Id$
 
-/*
- *
- *
- * This Class implements the methods defined in the STANDARD_IMAGE content model
+/**
+ * @file
+ * Create Collection Class
  */
 
+/**
+ * This Class implements the methods defined in the STANDARD_IMAGE content model
+ */
 class CreateCollection {
-  function CreateCollection() {
-
 
+  /**
+   * Constructor
+   */
+  function CreateCollection() {
+    
   }
-  
+
+  /**
+   * ingest collection policy ???
+   * @param type $parameterArray
+   * @param type $dsid
+   * @param type $file
+   * @param type $file_ext
+   * @return type 
+   */
   function ingestCollectionPolicy($parameterArray = NULL, $dsid, $file, $file_ext = NULL) {
     return TRUE; //nothing needed here as we are not transforming any files
   }
 
-
-
 }
diff --git a/plugins/DarwinCore.inc b/plugins/DarwinCore.inc
index 7b9d1fb9..9bbb8de3 100644
--- a/plugins/DarwinCore.inc
+++ b/plugins/DarwinCore.inc
@@ -2,13 +2,25 @@
 
 // $Id$
 
+/**
+ * @file
+ * Darwin Core class
+ */
+
+/**
+ * Darwin Core ???
+ */
 class DarwinCore {
 
+  /**
+   * Constructor
+   * @param type $item 
+   */
   function __construct($item = NULL) {
     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
     if (!empty($item)) {
       $this->owner = $item;
-      if ( array_key_exists('DARWIN_CORE', $item->get_datastreams_list_as_array())) {
+      if (array_key_exists('DARWIN_CORE', $item->get_datastreams_list_as_array())) {
         $dwc = $item->get_datastream_dissemination('DARWIN_CORE');
         if (!empty($dwc)) {
           $this->darwinCoreXML = $dwc;
@@ -17,10 +29,15 @@ class DarwinCore {
     }
   }
 
+  /**
+   * Build Drupal Form
+   * @param type $form
+   * @return int 
+   */
   public function buildDrupalForm($form = array()) {
-        
+
     $dwc_xml = $this->darwinCoreXML;
-        
+
     $dwc = DOMDocument::loadXML($dwc_xml);
 
     $form['dc:type'] = array(
@@ -162,17 +179,22 @@ class DarwinCore {
     $date = $dwc->getElementsByTagNameNS('http://rs.tdwg.org/dwc/terms/', 'eventDate')->item(0)->nodeValue;
     $format = 'Y-m-d H:i:s';
     $form['dwceventDate'] = array(
-       '#type' => 'date_popup', // types 'date_text' and 'date_timezone' are also supported. See .inc file.
-       '#title' => 'select a date',
-       '#default_value' => $date,
-       '#date_format' => $format,
-       '#date_label_position' => 'within', // See other available attributes and what they do in date_api_elements.inc
-       '#date_increment' => 15, // Optional, used by the date_select and date_popup elements to increment minutes and seconds.
+      '#type' => 'date_popup', // types 'date_text' and 'date_timezone' are also supported. See .inc file.
+      '#title' => 'select a date',
+      '#default_value' => $date,
+      '#date_format' => $format,
+      '#date_label_position' => 'within', // See other available attributes and what they do in date_api_elements.inc
+      '#date_increment' => 15, // Optional, used by the date_select and date_popup elements to increment minutes and seconds.
       '#description' => '',
     );
     return $form;
   }
 
+  /**
+   * Handle Form ??
+   * @global type $user
+   * @param type $form_values 
+   */
   public function handleForm($form_values) {
     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
     global $user;
@@ -208,12 +230,20 @@ class DarwinCore {
     $this->darwinCoreXML = $dwc->saveXML();
   }
 
+  /**
+   * asXML ??
+   * @return type 
+   */
   public function asXML() {
     return $this->darwinCoreXML;
   }
 
+  /**
+   * asHTML ??
+   * @return type 
+   */
   public function asHTML() {
-    $path=drupal_get_path('module', 'Fedora_Repository');
+    $path = drupal_get_path('module', 'Fedora_Repository');
     module_load_include('inc', 'fedora_repository', 'ObjectHelper');
     module_load_include('inc', 'fedora_repository', 'CollectionClass');
 
@@ -226,8 +256,7 @@ class DarwinCore {
 
     try {
       $proc = new XsltProcessor();
-    }
-    catch (Exception $e) {
+    } catch (Exception $e) {
       drupal_set_message(t("!e", array('!e' => $e->getMessage())), 'error');
       return " ";
     }
@@ -238,7 +267,7 @@ class DarwinCore {
     $input->loadXML(trim($xmlstr));
     $xsl = $proc->importStylesheet($xsl);
     $newdom = $proc->transformToDoc($input);
-    $content=$newdom->saveXML();
+    $content = $newdom->saveXML();
 
     return $content;
   }
@@ -256,9 +285,7 @@ class DarwinCore {
       'MachineObservation' => 'MachineObservation',
       'NomenclaturalChecklist' => 'NomenclaturalChecklist',
     ),
-    
   );
-
   public $dwcFields = array(
     'dc:type',
     'dc:language',
@@ -283,8 +310,6 @@ class DarwinCore {
     'dwc:eventDate',
     'dwc:eventTime',
   );
-
-
   public $darwinCoreXML = '
 <SimpleDarwinRecordSet xmlns="http://rs.tdwg.org/dwc/xsd/simpledarwincore/" xmlns:dc="http://purl.org/dc/terms/" xmlns:dwc="http://rs.tdwg.org/dwc/terms/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://rs.tdwg.org/dwc/xsd/simpledarwincore/ http://rs.tdwg.org/dwc/xsd/tdwg_dwc_simple.xsd">
   <SimpleDarwinRecord>
diff --git a/plugins/DemoFormBuilder.inc b/plugins/DemoFormBuilder.inc
index 913d8005..9b4219db 100644
--- a/plugins/DemoFormBuilder.inc
+++ b/plugins/DemoFormBuilder.inc
@@ -1,31 +1,44 @@
 <?php
+
 // $Id$
 
+/**
+ * @file
+ * 
+ */
 module_load_include('inc', 'fedora_repository', 'plugins/FormBuilder');
-/*
- * Created on 19-Feb-08
- *
- *
+
+/**
  * implements methods from content model ingest form xml
  * builds a dc metadata form
  */
 class DemoFormBuilder extends FormBuilder {
+
+  /**
+   * Constructor
+   */
   function DemoFormBuilder() {
     module_load_include('inc', 'fedora_repository', 'plugins/FormBuilder');
     drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
   }
 
-  //Override this so we can specify the datastream id of FULL_SIZE  should make this easier
+  /**
+   * Override this so we can specify the datastream id of FULL_SIZE  should make this easier
+   * @global type $base_url
+   * @param type $form_values
+   * @param type $dom
+   * @param type $rootElement 
+   */
   function createFedoraDataStreams($form_values, &$dom, &$rootElement) {
     module_load_include('inc', 'fedora_repository', 'MimeClass');
     global $base_url;
     $mimetype = new MimeClass();
     $server = NULL;
-    $file=$form_values['ingest-file-location'];
+    $file = $form_values['ingest-file-location'];
 
     if (!empty($file)) {
       $dformat = $mimetype->getType($file);
-      $fileUrl = $base_url .'/'. drupal_urlencode($file);
+      $fileUrl = $base_url . '/' . drupal_urlencode($file);
       $beginIndex = strrpos($fileUrl, '/');
       $dtitle = substr($fileUrl, $beginIndex + 1);
       $dtitle = urldecode($dtitle);
@@ -50,7 +63,7 @@ class DemoFormBuilder extends FormBuilder {
       foreach ($_SESSION['fedora_ingest_files'] as $dsid => $createdFile) {
         $createdFile = strstr($createdFile, $file);
         $dformat = $mimetype->getType($createdFile);
-        $fileUrl = $base_url .'/'. drupal_urlencode( $createdFile );
+        $fileUrl = $base_url . '/' . drupal_urlencode($createdFile);
         $beginIndex = strrpos($fileUrl, '/');
         $dtitle = substr($fileUrl, $beginIndex + 1);
         $dtitle = urldecode($dtitle);
@@ -60,7 +73,7 @@ class DemoFormBuilder extends FormBuilder {
         $ds1->setAttribute("ID", "$dsid");
         $ds1->setAttribute("STATE", "A");
         $ds1->setAttribute("CONTROL_GROUP", "M");
-        $ds1v= $dom->createElement("foxml:datastreamVersion");
+        $ds1v = $dom->createElement("foxml:datastreamVersion");
         $ds1v->setAttribute("ID", "$dsid.0");
         $ds1v->setAttribute("MIMETYPE", "$dformat");
         $ds1v->setAttribute("LABEL", "$dtitle");
@@ -73,5 +86,6 @@ class DemoFormBuilder extends FormBuilder {
       }
     }
   }
+
 }
 
diff --git a/plugins/DocumentConverter.inc b/plugins/DocumentConverter.inc
index 3aafb49f..5628cb16 100644
--- a/plugins/DocumentConverter.inc
+++ b/plugins/DocumentConverter.inc
@@ -3,20 +3,35 @@
 // $Id$
 
 /**
- *
+ * @file
+ * Document Converter Class
+ */
+
+/**
  * This class implements document (doc, odt, pdf, etc.) conversion for a generic
  * multi-format document collection.
  */
-
 class DocumentConverter {
 
   private $converter_service_url = "http://localhost:8080/converter/service";
 
+  /**
+   * Constructor
+   * @param type $converter_url 
+   */
   public function __construct($converter_url = NULL) {
     if (!empty($converter_url))
       $this->converter_service_url = $converter_url;
   }
 
+  /**
+   * Convert ???
+   * @param type $parameterArray
+   * @param type $dsid
+   * @param type $file
+   * @param type $output_ext
+   * @return string 
+   */
   function convert($parameterArray = NULL, $dsid, $file, $output_ext) {
     module_load_include('inc', 'fedora_repository', 'MimeClass');
 
@@ -32,7 +47,7 @@ class DocumentConverter {
     $outputType = $helper->get_mimetype($output_ext);
     $inputData = file_get_contents($file);
 
-    $outputFile = $file ."_". $dsid .".". $output_ext;
+    $outputFile = $file . "_" . $dsid . "." . $output_ext;
 
     #debug:
     #drupal_set_message("inputType: $inputType", 'status');
@@ -40,8 +55,8 @@ class DocumentConverter {
     #drupal_set_message("outputFile: $outputFile", 'status');
 
     $ch = curl_init($this->converter_service_url);
-    curl_setopt($ch, CURLOPT_HTTPHEADER, array( "Content-Type: $inputType", "Accept: $outputType" ) );
-    curl_setopt($ch, CURLOPT_POST, 1 );
+    curl_setopt($ch, CURLOPT_HTTPHEADER, array("Content-Type: $inputType", "Accept: $outputType"));
+    curl_setopt($ch, CURLOPT_POST, 1);
     curl_setopt($ch, CURLOPT_TIMEOUT, 120); // times out after 2 minutes 
     curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1); // return into a variable 
     curl_setopt($ch, CURLOPT_POSTFIELDS, $inputData); // add POST fields 
@@ -52,23 +67,24 @@ class DocumentConverter {
 
     $code = curl_getinfo($ch, CURLINFO_HTTP_CODE);
 
-    if (200 == $code) { 
+    if (200 == $code) {
 
       $returnValue = file_put_contents($outputFile, $data);
       if ($returnValue > 0) {
         drupal_set_message("Conversion successful.", 'status');
         $_SESSION['fedora_ingest_files']["$dsid"] = $outputFile;
         return $outputFile;
-      } 
+      }
       else {
         return $returnValue; // a.k.a. FALSE.
       }
-    } 
+    }
     else {
       drupal_set_message("Conversion Failed. Webservice returned $code.", 'status');
       return FALSE;
     }
   }
+
 }
 
 /*
diff --git a/plugins/Exiftool.inc b/plugins/Exiftool.inc
index ec6d7ad0..81cc46ef 100644
--- a/plugins/Exiftool.inc
+++ b/plugins/Exiftool.inc
@@ -1,17 +1,24 @@
 <?php
+
 // $Id$
 
-/*
- *
- *
- * This Class implements the methods defined in the STANDARD_IMAGE content model
+/**
+ * @file
+ * Exiftool
  */
 
+/**
+ * This Class implements the methods defined in the STANDARD_IMAGE content model
+ */
 class Exiftool {
 
   private $pid = NULL;
   private $item = NULL;
 
+  /**
+   * Constructor
+   * @param type $pid 
+   */
   function __construct($pid) {
     //drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
     $this->pid = $pid;
@@ -19,49 +26,61 @@ class Exiftool {
     $this->item = new Fedora_Item($this->pid);
   }
 
+  /**
+   * extract metadata ??
+   * @param type $parameterArray
+   * @param type $dsid
+   * @param type $file
+   * @param type $file_ext
+   * @return type 
+   */
   function extractMetadata($parameterArray, $dsid, $file, $file_ext) {
     $system = getenv('System');
-    $file_suffix = '_'. $dsid . '.xml';
-    $returnValue=TRUE;
-    $output=array();
+    $file_suffix = '_' . $dsid . '.xml';
+    $returnValue = TRUE;
+    $output = array();
     exec('exiftool -X ' . escapeshellarg($file) . '', $output);
-    file_put_contents($file.$file_suffix, implode("\n", $output));
+    file_put_contents($file . $file_suffix, implode("\n", $output));
     $_SESSION['fedora_ingest_files']["$dsid"] = $file . $file_suffix;
     return TRUE;
   }
-  
-  function displayMetadata() { 
-    $output='';
-		$exif = $this->item->get_datastream_dissemination('EXIF'); 
-		if (trim($exif) != '')  {
-	    $exifDom = DOMDocument::loadXML($this->item->get_datastream_dissemination('EXIF'));
-  	  if ($exifDom != NULL) {
-	      $description = $exifDom->getElementsByTagNameNS('http://www.w3.org/1999/02/22-rdf-syntax-ns#','Description');
-  	    if ($description->length > 0) { 
-					$description=$description->item(0);
-					$output .= '<div class="fedora_technical_metadata"><ul>';
-					for ($i=0;$i<$description->childNodes->length;$i++){ 
-					  $name=$description->childNodes->item($i)->nodeName;
-				  	$value=$description->childNodes->item($i)->nodeValue;
-		  			if ($name != '#text'  && !preg_match('/^System\:.*$/',$name) && trim($value) != '') { 
-					    list($type,$name) = preg_split('/\:/',$name);
-				  	  $name = trim(preg_replace('/(?<!^)([A-Z][a-z]|(?<=[a-z])[A-Z])/'," $1", $name));
-	    				$output .= '<li><b>'.$name. '</b>:  '. $value .' </li>';
-					  }
-					}
-					$output.='</ul></div>';
-	
-					$fieldset = array(
-					  '#title' => t("!text", array('!text' => 'Technical Metadata')),
-				  	'#collapsible' => TRUE,
-					  '#collapsed' => TRUE,
-					  '#value' => $output
-					);
-					$output  = theme('fieldset', $fieldset);
-	      }
-  	  }
-	  }
+
+  /**
+   * display metadata ???
+   * @return type 
+   */
+  function displayMetadata() {
+    $output = '';
+    $exif = $this->item->get_datastream_dissemination('EXIF');
+    if (trim($exif) != '') {
+      $exifDom = DOMDocument::loadXML($this->item->get_datastream_dissemination('EXIF'));
+      if ($exifDom != NULL) {
+        $description = $exifDom->getElementsByTagNameNS('http://www.w3.org/1999/02/22-rdf-syntax-ns#', 'Description');
+        if ($description->length > 0) {
+          $description = $description->item(0);
+          $output .= '<div class="fedora_technical_metadata"><ul>';
+          for ($i = 0; $i < $description->childNodes->length; $i++) {
+            $name = $description->childNodes->item($i)->nodeName;
+            $value = $description->childNodes->item($i)->nodeValue;
+            if ($name != '#text' && !preg_match('/^System\:.*$/', $name) && trim($value) != '') {
+              list($type, $name) = preg_split('/\:/', $name);
+              $name = trim(preg_replace('/(?<!^)([A-Z][a-z]|(?<=[a-z])[A-Z])/', " $1", $name));
+              $output .= '<li><b>' . $name . '</b>:  ' . $value . ' </li>';
+            }
+          }
+          $output.='</ul></div>';
+
+          $fieldset = array(
+            '#title' => t("!text", array('!text' => 'Technical Metadata')),
+            '#collapsible' => TRUE,
+            '#collapsed' => TRUE,
+            '#value' => $output
+          );
+          $output = theme('fieldset', $fieldset);
+        }
+      }
+    }
     return $output;
   }
-  
+
 }
diff --git a/plugins/Ffmpeg.inc b/plugins/Ffmpeg.inc
index f2faedac..90436808 100644
--- a/plugins/Ffmpeg.inc
+++ b/plugins/Ffmpeg.inc
@@ -1,26 +1,44 @@
 <?php
+
 // $Id$
 
-/*
- *
- *
- * This Class implements the methods defined in the STANDARD_QT content model
+/**
+ * @file
+ * Ffmpeg wrapper class
  */
 
+/**
+ * FFMpeg wrapper class for generating movie thumbnails
+ * 
+ * This Class implements the methods defined in the STANDARD_QT content model
+ */
 class Ffmpeg {
+
+  /**
+   * Default constructor
+   */
   function Ffmpeg() {
+    
   }
 
+  /**
+   * Extract a thumbnail from the movie
+   * @param type $parameterArray
+   * @param type $dsid
+   * @param type $file
+   * @param type $file_ext
+   * @return type 
+   */
   function extract_thumbnail($parameterArray, $dsid, $file, $file_ext) {
-    $defaults = array('ss' => '00:00:10', 's' => null); 
+    $defaults = array('ss' => '00:00:10', 's' => null);
     $params = array_merge($defaults, $parameterArray);
     $system = getenv('System');
-    $file_suffix = '_'. $dsid . '.' . $file_ext;
-    $returnValue=TRUE;
-    $output=array();
+    $file_suffix = '_' . $dsid . '.' . $file_ext;
+    $returnValue = TRUE;
+    $output = array();
     $size = '';
 
-    if($params['s'] != null) {
+    if ($params['s'] != null) {
       $size = ' -s ' . escapeshellarg($params['s']);
     }
     exec('ffmpeg -i ' . escapeshellarg($file) . ' -r 1 -ss ' . escapeshellarg($params['ss']) . ' ' . $size . ' -t 1 ' . escapeshellarg($file . $file_suffix));
@@ -32,4 +50,5 @@ class Ffmpeg {
     $_SESSION['fedora_ingest_files']["$dsid"] = $file . $file_suffix;
     return TRUE;
   }
+
 }
diff --git a/plugins/Flv.inc b/plugins/Flv.inc
index 4b16fe7d..4345428f 100644
--- a/plugins/Flv.inc
+++ b/plugins/Flv.inc
@@ -1,18 +1,31 @@
 <?php
+
 // $Id$
 
-/*
- * Created on 19-Feb-08
- *
- *
+/**
+ * @file
+ * Form Builder class
+ */
+
+/**
  * implements method from content model ingest form xml
  */
 class FormBuilder {
+
+  /**
+   * Constructor
+   */
   function FormBuilder() {
     module_load_include('inc', 'Flv', '');
     drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
   }
 
+  /**
+   * Create QDC Stream ???
+   * @param type $form_values
+   * @param type $dom
+   * @param type $rootElement 
+   */
   function createQDCStream($form_values, &$dom, &$rootElement) {
     $datastream = $dom->createElement("foxml:datastream");
     $datastream->setAttribute("ID", "QDC");
@@ -33,7 +46,7 @@ class FormBuilder {
     $oai->setAttribute('xmlns:xsi', "http://www.w3.org/2001/XMLSchema-instance");
     $content->appendChild($oai);
     //dc elements
-    $previousElement=NULL; //used in case we have to nest elements for qualified dublin core
+    $previousElement = NULL; //used in case we have to nest elements for qualified dublin core
     foreach ($form_values as $key => $value) {
       $index = strrpos($key, '-');
       if ($index > 01) {
@@ -42,7 +55,7 @@ class FormBuilder {
 
       $test = substr($key, 0, 2);
 
-      if ($test=='dc'||$test=='ap') {//don't try to process other form values
+      if ($test == 'dc' || $test == 'ap') {//don't try to process other form values
         try {
           if (!strcmp(substr($key, 0, 4), 'app_')) {
             $key = substr($key, 4);
@@ -52,8 +65,7 @@ class FormBuilder {
             $previousElement = $dom->createElement($key, $value);
             $oai->appendChild($previousElement);
           }
-        }
-        catch (exception $e) {
+        } catch (exception $e) {
           drupal_set_message(t("!e", array('!e' => $e->getMessage())), 'error');
           continue;
         }
@@ -62,10 +74,15 @@ class FormBuilder {
     }
   }
 
+  /**
+   * Handle QDC Form ???
+   * @param type $form_values
+   * @return type 
+   */
   function handleQDCForm($form_values) {
     $dom = new DomDocument("1.0", "UTF-8");
     $dom->formatOutput = TRUE;
-    $pid=$form_values['pid'];
+    $pid = $form_values['pid'];
     $rootElement = $dom->createElement("foxml:digitalObject");
     $rootElement->setAttribute('PID', "$pid");
     $rootElement->setAttribute('xmlns:foxml', "info:fedora/fedora-system:def/foxml#");
@@ -87,13 +104,13 @@ class FormBuilder {
 
     try {
       $soapHelper = new ConnectionHelper();
-      $client=$soapHelper->getSoapClient(variable_get('fedora_soap_manage_url', 'http://localhost:8080/fedora/services/management?wsdl'));
+      $client = $soapHelper->getSoapClient(variable_get('fedora_soap_manage_url', 'http://localhost:8080/fedora/services/management?wsdl'));
 
       if ($client == NULL) {
         drupal_set_message(t('Error getting SOAP client.'), 'error');
         return;
       }
-      $object=$client->__soapCall('ingest', array($params));
+      $object = $client->__soapCall('ingest', array($params));
       $deleteFiles = $form_values['delete_file']; //remove files from drupal file system
 
       if ($deleteFiles > 0) {
@@ -102,20 +119,25 @@ class FormBuilder {
         }
         unlink($form_values['fullpath']);
       }
-    } 
-    catch (exception $e) {
+    } catch (exception $e) {
       drupal_set_message(t('Error ingesting object: !e', array('!e' => $e->getMessage())), 'error');
       return;
     }
   }
 
+  /**
+   * Create Fedora DataStream
+   * @param type $form_values
+   * @param type $dom
+   * @param type $rootElement 
+   */
   function createFedoraDataStreams($form_values, &$dom, &$rootElement) {
     module_load_include('inc', 'fedora_repository', 'MimeClass');
     $mimetype = new MimeClass();
     $server = NULL;
-    $file=$form_values['ingest-file-location'];
+    $file = $form_values['ingest-file-location'];
     $dformat = $mimetype->getType($file);
-    $fileUrl = 'http://'. $_SERVER['HTTP_HOST'] . $file;
+    $fileUrl = 'http://' . $_SERVER['HTTP_HOST'] . $file;
     $beginIndex = strrpos($fileUrl, '/');
     $dtitle = substr($fileUrl, $beginIndex + 1);
     $dtitle = substr($dtitle, 0, strpos($dtitle, "."));
@@ -123,7 +145,7 @@ class FormBuilder {
     $ds1->setAttribute("ID", "OBJ");
     $ds1->setAttribute("STATE", "A");
     $ds1->setAttribute("CONTROL_GROUP", "M");
-    $ds1v= $dom->createElement("foxml:datastreamVersion");
+    $ds1v = $dom->createElement("foxml:datastreamVersion");
     $ds1v->setAttribute("ID", "OBJ.0");
     $ds1v->setAttribute("MIMETYPE", "$dformat");
     $ds1v->setAttribute("LABEL", "$dtitle");
@@ -137,16 +159,16 @@ class FormBuilder {
     foreach ($_SESSION['fedora_ingest_files'] as $dsid => $createdFile) {
       $createdFile = strstr($createdFile, $file);
       $dformat = $mimetype->getType($createdFile);
-      $fileUrl = 'http://'. $_SERVER['HTTP_HOST'] . $createdFile;
+      $fileUrl = 'http://' . $_SERVER['HTTP_HOST'] . $createdFile;
       $beginIndex = strrpos($fileUrl, '/');
       $dtitle = substr($fileUrl, $beginIndex + 1);
-      $dtitle =  substr($dtitle, 0, strpos($dtitle, "."));
-      $dtitle = $dtitle . '_'. $dsid;
+      $dtitle = substr($dtitle, 0, strpos($dtitle, "."));
+      $dtitle = $dtitle . '_' . $dsid;
       $ds1 = $dom->createElement("foxml:datastream");
       $ds1->setAttribute("ID", "$dsid");
       $ds1->setAttribute("STATE", "A");
       $ds1->setAttribute("CONTROL_GROUP", "M");
-      $ds1v= $dom->createElement("foxml:datastreamVersion");
+      $ds1v = $dom->createElement("foxml:datastreamVersion");
       $ds1v->setAttribute("ID", "$dsid.0");
       $ds1v->setAttribute("MIMETYPE", "$dformat");
       $ds1v->setAttribute("LABEL", "$dtitle");
@@ -158,9 +180,12 @@ class FormBuilder {
       $rootElement->appendChild($ds1);
     }
   }
-  
+
   /**
    * creates the RELS-EXT for the foxml
+   * @param type $form_values
+   * @param type $dom
+   * @param type $rootElement 
    */
   function createRelationShips($form_values, &$dom, &$rootElement) {
     $drdf = $dom->createElement("foxml:datastream");
@@ -190,14 +215,16 @@ class FormBuilder {
     $rdf->appendChild($rdfdesc);
     $rdfdesc->appendChild($member);
     $rootElement->appendChild($drdf);
-
   }
-  
+
   /**
    * creates the standard foxml properties
+   * @param type $form_values
+   * @param type $dom
+   * @param type $rootElement 
    */
   function createStandardFedoraStuff($form_values, &$dom, &$rootElement) {
-    /*foxml object properties section */
+    /* foxml object properties section */
     $objproperties = $dom->createElement("foxml:objectProperties");
     $prop1 = $dom->createElement("foxml:property");
     $prop1->setAttribute("NAME", "http://www.w3.org/1999/02/22-rdf-syntax-ns#type");
@@ -222,11 +249,17 @@ class FormBuilder {
     $rootElement->appendChild($objproperties);
   }
 
-
+  /**
+   * Build QDC Form
+   * @param type $form
+   * @param type $ingest_form_definition
+   * @param type $form_values
+   * @return type 
+   */
   function buildQDCForm(&$form, $ingest_form_definition, &$form_values) {
     $form['indicator2'] = array(
-        '#type' => 'fieldset',
-        '#title' => t('Ingest Digital Object Step #2')
+      '#type' => 'fieldset',
+      '#title' => t('Ingest Digital Object Step #2')
     );
     foreach ($ingest_form_definition->form_elements->element as $element) {
       $name = strip_tags($element->name->asXML());
@@ -234,7 +267,7 @@ class FormBuilder {
       $required = strip_tags($element->required->asXML());
       $required = strtolower($required);
       if ($required != 'TRUE') {
-        $required='0';
+        $required = '0';
       }
 
       $description = strip_tags($element->description->asXML());
@@ -247,20 +280,19 @@ class FormBuilder {
           $options["$field"] = $value;
         }
         $form['indicator2']["$name"] = array(
-            '#title' => $title,
-            '#required' => $required,
-            '#description' => $description,
-            '#type' => $type,
-            '#options' => $options,
+          '#title' => $title,
+          '#required' => $required,
+          '#description' => $description,
+          '#type' => $type,
+          '#options' => $options,
         );
-
       }
       else {
         $form['indicator2']["$name"] = array(
-            '#title' => $title,
-            '#required' => $required,
-            '#description' => $description,
-            '#type' => $type
+          '#title' => $title,
+          '#required' => $required,
+          '#description' => $description,
+          '#type' => $type
         );
       }
     }
@@ -269,3 +301,4 @@ class FormBuilder {
   }
 
 }
+
diff --git a/plugins/FlvFormBuilder.inc b/plugins/FlvFormBuilder.inc
index 37b0e0d2..7f929fdd 100644
--- a/plugins/FlvFormBuilder.inc
+++ b/plugins/FlvFormBuilder.inc
@@ -1,20 +1,33 @@
 <?php
+
 // $Id$
 
+/**
+ * @file
+ * FLVFormBuilder
+ */
 module_load_include('inc', 'fedora_repository', 'plugins/FormBuilder');
 
-/*
+/**
  * implements methods from content model ingest form xml
  * builds a dc metadata form
  */
 class FlvFormBuilder extends FormBuilder {
+
+  /**
+   * Constructor
+   */
   function FlvFormBuilder() {
     module_load_include('inc', 'fedora_repository', 'plugins/FormBuilder');
     drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
   }
 
-  /*
+  /**
    * method overrides method in FormBuilder.  We changed the dsid from OBJ to FLV and added the TN datastream
+   * @global type $base_url
+   * @param type $form_values
+   * @param type $dom
+   * @param type $rootElement 
    */
   function createFedoraDataStreams($form_values, &$dom, &$rootElement) {
     module_load_include('inc', 'fedora_repository', 'MimeClass');
@@ -24,7 +37,7 @@ class FlvFormBuilder extends FormBuilder {
     $file = $form_values['ingest-file-location'];
     $dformat = $mimetype->getType($file);
     //$fileUrl = 'http://'.$_SERVER['HTTP_HOST'].$file;
-    $fileUrl = $base_url .'/'. drupal_urlencode($file);
+    $fileUrl = $base_url . '/' . drupal_urlencode($file);
     $beginIndex = strrpos($fileUrl, '/');
     $dtitle = substr($fileUrl, $beginIndex + 1);
     $dtitle = substr($dtitle, 0, strpos($dtitle, "."));
@@ -32,7 +45,7 @@ class FlvFormBuilder extends FormBuilder {
     $ds1->setAttribute("ID", "FLV");
     $ds1->setAttribute("STATE", "A");
     $ds1->setAttribute("CONTROL_GROUP", "M");
-    $ds1v= $dom->createElement("foxml:datastreamVersion");
+    $ds1v = $dom->createElement("foxml:datastreamVersion");
     $ds1v->setAttribute("ID", "FLV.0");
     $ds1v->setAttribute("MIMETYPE", "$dformat");
     $ds1v->setAttribute("LABEL", "$dtitle");
@@ -44,7 +57,7 @@ class FlvFormBuilder extends FormBuilder {
     $rootElement->appendChild($ds1);
 
     $createdFile = drupal_get_path('module', 'Fedora_Repository') . '/images/flashThumb.jpg';
-    $fileUrl = $base_url .'/'. drupal_urlencode($createdFile); //'http://'.$_SERVER['HTTP_HOST'].'/'.$createdFile;
+    $fileUrl = $base_url . '/' . drupal_urlencode($createdFile); //'http://'.$_SERVER['HTTP_HOST'].'/'.$createdFile;
     $ds1 = $dom->createElement("foxml:datastream");
     $ds1->setAttribute("ID", "TN");
     $ds1->setAttribute("STATE", "A");
@@ -60,5 +73,6 @@ class FlvFormBuilder extends FormBuilder {
     $ds1v->appendChild($ds1content);
     $rootElement->appendChild($ds1);
   }
+
 }
 
diff --git a/plugins/FormBuilder.inc b/plugins/FormBuilder.inc
index 4fd3fa7d..075e0dfb 100644
--- a/plugins/FormBuilder.inc
+++ b/plugins/FormBuilder.inc
@@ -2,19 +2,31 @@
 
 // $Id$
 
-/*
- * Created on 19-Feb-08
- *
- *
+/**
+ * @file
+ * FormBuilder class
+ */
+
+/**
  * implements methods from content model ingest form xml
  * builds a dc metadata form
-*/
+ */
 class FormBuilder {
+
+  /**
+   * Constructor
+   */
   function FormBuilder() {
     module_load_include('inc', 'FormBuilder', '');
     drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
   }
 
+  /**
+   * Create QDC Stream ??
+   * @param type $form_values
+   * @param type $dom
+   * @param type $rootElement 
+   */
   function createQDCStream($form_values, &$dom, &$rootElement) {
     $datastream = $dom->createElement("foxml:datastream");
     $datastream->setAttribute("ID", "DC");
@@ -35,7 +47,7 @@ class FormBuilder {
     $oai->setAttribute('xmlns:xsi', "http://www.w3.org/2001/XMLSchema-instance");
     $content->appendChild($oai);
     //dc elements
-    $previousElement=NULL;//used in case we have to nest elements for qualified dublin core
+    $previousElement = NULL; //used in case we have to nest elements for qualified dublin core
     foreach ($form_values as $key => $value) {
       $key = str_replace('_', ':', $key);
       $index = strrpos($key, '-');
@@ -55,18 +67,22 @@ class FormBuilder {
             $previousElement = $dom->createElement($key, $value);
             $oai->appendChild($previousElement);
           }
-        }
-        catch (exception $e) {
+        } catch (exception $e) {
           drupal_set_message(t("!e", array('!e' => $e->getMessage())), 'error');
           continue;
         }
       }
       $rootElement->appendChild($datastream);
     }
-
   }
 
-  //create the security Policy
+  /**
+   * Create the security policy
+   * @param type $collectionPid
+   * @param type $dom
+   * @param type $rootElement
+   * @return type 
+   */
   function createPolicy($collectionPid, &$dom, &$rootElement) {
     module_load_include('inc', 'fedora_repository', 'ObjectHelper');
     $objectHelper = new ObjectHelper();
@@ -78,8 +94,7 @@ class FormBuilder {
     }
     try {
       $xml = new SimpleXMLElement($policyStreamDoc);
-    }
-    catch (Exception $e) {
+    } catch (Exception $e) {
       watchdog(t("Fedora_Repository"), t("Problem getting security policy."), NULL, WATCHDOG_ERROR);
       drupal_set_message(t('Problem getting security policy: !e', array('!e' => $e->getMessage())), 'error');
       return FALSE;
@@ -91,7 +106,7 @@ class FormBuilder {
       return FALSE;
     }
     $dom->importNode($policyElement, TRUE);
-    $value=$policyElement->appendXML($policyStreamDoc);
+    $value = $policyElement->appendXML($policyStreamDoc);
     if (!$value) {
       drupal_set_message(t('Error creating security policy stream.'));
       watchdog(t("Fedora_Repository"), t("Error creating security policy stream, could not parse collection policy template file."), NULL, WATCHDOG_NOTICE);
@@ -114,14 +129,18 @@ class FormBuilder {
     return TRUE;
   }
 
-
+  /**
+   * Handle QDC Form ??
+   * @param type $form_values
+   * @return type 
+   */
   function handleQDCForm($form_values) {
     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
     module_load_include('inc', 'fedora_repository', 'CollectionPolicy');
-    
+
     $dom = new DomDocument("1.0", "UTF-8");
     $dom->formatOutput = TRUE;
-    $pid=$form_values['pid'];
+    $pid = $form_values['pid'];
     $rootElement = $dom->createElement("foxml:digitalObject");
     $rootElement->setAttribute('VERSION', '1.1');
     $rootElement->setAttribute('PID', "$pid");
@@ -134,13 +153,13 @@ class FormBuilder {
     // Create relationships
     $this->createRelationShips($form_values, $dom, $rootElement);
     $collectionPid = $form_values['collection_pid'];
-        
+
     if (($cp = CollectionPolicy::LoadFromCollection($collectionPid)) !== FALSE) {
-      $collectionName = trim($cp->getName()); 
+      $collectionName = trim($cp->getName());
       if (trim($collectionName) != '') {
         $form_values['dc_relation'] = $collectionName;
       }
-    }    
+    }
     // Create dublin core
     $this->createQDCStream($form_values, $dom, $rootElement);
 
@@ -150,43 +169,49 @@ class FormBuilder {
     $this->createPolicy($collectionPid, &$dom, &$rootElement);
 
     try {
-      
+
       $object = Fedora_Item::ingest_from_FOXML($dom);
       if (!empty($object->pid)) {
         // drupal_set_message("Item ". l($object->pid, 'fedora/repository/'. $object->pid) . " created successfully.", "status");
-        drupal_set_message(t("Item !pid created successfully.", array('!pid' => l($object->pid, 'fedora/repository/'. $object->pid))), "status");
+        drupal_set_message(t("Item !pid created successfully.", array('!pid' => l($object->pid, 'fedora/repository/' . $object->pid))), "status");
       }
-      if (!empty( $_SESSION['fedora_ingest_files'])) {
+      if (!empty($_SESSION['fedora_ingest_files'])) {
         foreach ($_SESSION['fedora_ingest_files'] as $dsid => $createdFile) {
           file_delete($createdFile);
         }
       }
       file_delete($form_values['ingest-file-location']);
-    }
-    catch (exception $e) {
+    } catch (exception $e) {
       drupal_set_message(t('Error ingesting object: !e', array('!e' => $e->getMessage())), 'error');
       watchdog(t("Fedora_Repository"), t("Error ingesting object: !e", array('!e' => $e->getMessage())), NULL, WATCHDOG_ERROR);
       return;
     }
   }
 
+  /**
+   * Create Fedora Data stream
+   * @global type $base_url
+   * @param type $form_values
+   * @param type $dom
+   * @param type $rootElement 
+   */
   function createFedoraDataStreams($form_values, &$dom, &$rootElement) {
     module_load_include('inc', 'fedora_repository', 'MimeClass');
     global $base_url;
     $mimetype = new MimeClass();
-    $server=NULL;
-    $file=$form_values['ingest-file-location'];
+    $server = NULL;
+    $file = $form_values['ingest-file-location'];
 
-    if (!empty( $file)) {
+    if (!empty($file)) {
       $dformat = $mimetype->getType($file);
-      
+
       $parts = explode('/', $file);
       foreach ($parts as $n => $part) {
         $parts[$n] = rawurlencode($part);
       }
       $path = implode('/', $parts);
       $fileUrl = $base_url . '/' . $path;
-      
+
       $beginIndex = strrpos($fileUrl, '/');
       $dtitle = substr($fileUrl, $beginIndex + 1);
       $dtitle = urldecode($dtitle);
@@ -194,7 +219,7 @@ class FormBuilder {
       $ds1->setAttribute("ID", "OBJ");
       $ds1->setAttribute("STATE", "A");
       $ds1->setAttribute("CONTROL_GROUP", "M");
-      $ds1v= $dom->createElement("foxml:datastreamVersion");
+      $ds1v = $dom->createElement("foxml:datastreamVersion");
       $rootElement->appendChild($ds1);
 
       $ds1v->setAttribute("ID", "OBJ.0");
@@ -207,27 +232,24 @@ class FormBuilder {
       $ds1v->appendChild($ds1content);
     }
     if (!empty($_SESSION['fedora_ingest_files'])) {
-      
-     
-      
+
       foreach ($_SESSION['fedora_ingest_files'] as $dsid => $createdFile) {
-	
-	
-        if (!empty($file)) { 
-	   $found = strstr($createdFile, $file);
-	   if ($found !== FALSE) {
-	      $createdFile = $found;
-	   }
-	} 
+
+        if (!empty($file)) {
+          $found = strstr($createdFile, $file);
+          if ($found !== FALSE) {
+            $createdFile = $found;
+          }
+        }
 
         $dformat = $mimetype->getType($createdFile);
-	$parts = explode('/', $createdFile);
+        $parts = explode('/', $createdFile);
         foreach ($parts as $n => $part) {
           $parts[$n] = rawurlencode($part);
         }
         $path = implode('/', $parts);
         $fileUrl = $base_url . '/' . $path;
-      
+
         $beginIndex = strrpos($fileUrl, '/');
         $dtitle = substr($fileUrl, $beginIndex + 1);
         $dtitle = urldecode($dtitle);
@@ -236,7 +258,7 @@ class FormBuilder {
         $ds1->setAttribute("ID", "$dsid");
         $ds1->setAttribute("STATE", "A");
         $ds1->setAttribute("CONTROL_GROUP", "M");
-        $ds1v= $dom->createElement("foxml:datastreamVersion");
+        $ds1v = $dom->createElement("foxml:datastreamVersion");
         $ds1v->setAttribute("ID", "$dsid.0");
         $ds1v->setAttribute("MIMETYPE", "$dformat");
         $ds1v->setAttribute("LABEL", "$dtitle");
@@ -250,9 +272,11 @@ class FormBuilder {
     }
   }
 
-  
   /**
    * Creates the RELS-EXT for the foxml
+   * @param type $form_values
+   * @param type $dom
+   * @param type $rootElement 
    */
   function createRelationShips($form_values, &$dom, &$rootElement) {
     $drdf = $dom->createElement("foxml:datastream");
@@ -278,11 +302,11 @@ class FormBuilder {
     if (!isset($relationship)) {
       $relationship = 'isMemberOfCollection';
     }
-    $member = $dom->createElement("fedora:". $relationship);
+    $member = $dom->createElement("fedora:" . $relationship);
     $membr = $form_values['collection_pid'];
     $member->setAttribute("rdf:resource", "info:fedora/$membr");
     $rdfHasModel = $dom->createElement("fedora-model:hasModel");
-    $contentModelPid=$form_values['content_model_pid'];
+    $contentModelPid = $form_values['content_model_pid'];
     $rdfHasModel->setAttribute("rdf:resource", "info:fedora/$contentModelPid");
     $drdf->appendChild($dvrdf);
     $dvrdf->appendChild($dvcontent);
@@ -293,9 +317,11 @@ class FormBuilder {
     $rootElement->appendChild($drdf);
   }
 
-  
   /**
    * Creates the standard foxml properties
+   * @param type $form_values
+   * @param type $dom
+   * @param type $rootElement 
    */
   function createStandardFedoraStuff($form_values, &$dom, &$rootElement) {
     // Foxml object properties section
@@ -315,57 +341,66 @@ class FormBuilder {
     $rootElement->appendChild($objproperties);
   }
 
-
+  /**
+   * Build QDC Form
+   * @param type $form
+   * @param type $elements
+   * @param type $form_values
+   * @return string 
+   */
   function buildQDCForm(&$form, $elements, &$form_values) {
     $form['#multistep'] = TRUE; // used so that it triggers a form rebuild every time.
     $form['indicator2'] = array(
       '#type' => 'fieldset',
       '#title' => t('Ingest digital object step #2'),
     );
-    
+
     foreach ($elements as $element) {
-      
-        if ($element['type'] == 'markup') {
-          $el = array('#value'=> $element['description']);
-        } else {
-          $el = array(
-            '#title' => $element['label'],
-            '#required' => ($element['required'] ? 1 : 0),
-            '#description' => $element['description'],
-            '#type' => $element['type']
-          );
-        }
 
-        $name = explode('][', $element['name']);
-        $elLocation = &$form['indicator2'];
-        while (isset($elLocation[$name[0]]) && ($partial = array_shift($name)) != NULL) {
-         $elLocation = &$elLocation[$partial];
-        }
-			
-			$autocomplete_path = FALSE; 
-			$autocomplete_omit_collection = FALSE;
+      if ($element['type'] == 'markup') {
+        $el = array('#value' => $element['description']);
+      }
+      else {
+        $el = array(
+          '#title' => $element['label'],
+          '#required' => ($element['required'] ? 1 : 0),
+          '#description' => $element['description'],
+          '#type' => $element['type']
+        );
+      }
+
+      $name = explode('][', $element['name']);
+      $elLocation = &$form['indicator2'];
+      while (isset($elLocation[$name[0]]) && ($partial = array_shift($name)) != NULL) {
+        $elLocation = &$elLocation[$partial];
+      }
+
+      $autocomplete_path = FALSE;
+      $autocomplete_omit_collection = FALSE;
       foreach ($element['parameters'] as $key => $val) {
         if ($key == '#autocomplete_path') {
-					$autocomplete_path = $val;
-        } elseif ($key == '#autocomplete_omit_collection') {
-					$autocomplete_omit_collection = TRUE;
-				} else {				
-	        $el[$key]=$val;
-				}
+          $autocomplete_path = $val;
+        }
+        elseif ($key == '#autocomplete_omit_collection') {
+          $autocomplete_omit_collection = TRUE;
+        }
+        else {
+          $el[$key] = $val;
+        }
       }
 
-			if ($autocomplete_path !== FALSE) { 
-				$el['#autocomplete_path'] = $autocomplete_path . (!$autocomplete_omit_collection?'/'.$form_values['storage']['collection_pid']:'/');
-			}     
+      if ($autocomplete_path !== FALSE) {
+        $el['#autocomplete_path'] = $autocomplete_path . (!$autocomplete_omit_collection ? '/' . $form_values['storage']['collection_pid'] : '/');
+      }
 
       if ($element['type'] == 'select' || $element['type'] == 'other_select') {
-        $el['#options']= isset($element['authoritative_list'])?$element['authoritative_list']:array();
+        $el['#options'] = isset($element['authoritative_list']) ? $element['authoritative_list'] : array();
       }
- 
+
       $elLocation[join('][', $name)] = $el;
     }
-    
+
     return $form;
   }
-  
+
 }
diff --git a/plugins/ImageManipulation.inc b/plugins/ImageManipulation.inc
index 9971c367..c9125862 100644
--- a/plugins/ImageManipulation.inc
+++ b/plugins/ImageManipulation.inc
@@ -2,40 +2,54 @@
 
 // $Id$
 
-/*
- *
- *
- * This Class implements the methods defined in the STANDARD_IMAGE content model
+/**
+ * @file
+ * Image Manipulation class
  */
 
+/**
+ * This Class implements the methods defined in the STANDARD_IMAGE content model
+ */
 class ImageManipulation {
 
+  /**
+   * Constructor
+   */
   function ImageManipulation() {
     module_load_include('inc', 'fedora_repository', 'ObjectHelper');
   }
 
+  /**
+   * Create a preview ??
+   * @param type $parameterArray
+   * @param type $dsid
+   * @param type $file
+   * @param type $file_ext
+   * @return string 
+   */
   function createPreview($parameterArray, $dsid, $file, $file_ext) {
     $system = getenv('System');
     $file_suffix = '_' . $dsid . '.' . $file_ext;
-    $width = $parameterArray['width']; 
+    $width = $parameterArray['width'];
 
     if (!isset($parameterArray['height'])) {
-	$height = $width;
-    } else { 
-	$height = $parameterArray['height'];
+      $height = $width;
+    }
+    else {
+      $height = $parameterArray['height'];
     }
 
     $returnValue = TRUE;
     $output = array();
-    
-    $destDir  = dirname($file).'/work';
-    $destFile = $destDir .'/'. basename($file) . $file_suffix;
-    if (!is_dir($destDir)) { 
+
+    $destDir = dirname($file) . '/work';
+    $destFile = $destDir . '/' . basename($file) . $file_suffix;
+    if (!is_dir($destDir)) {
       @mkdir($destDir);
     }
 
     if (!file_exists($destFile)) {
-      exec('convert -resize ' . $width . 'x'.$height.' -quality 85  "' . $file . '"[0] -strip "' .$destFile . '" 2>&1 &', $output, $returnValue);
+      exec('convert -resize ' . $width . 'x' . $height . ' -quality 85  "' . $file . '"[0] -strip "' . $destFile . '" 2>&1 &', $output, $returnValue);
     }
     else
       $returnValue = '0';
@@ -49,6 +63,14 @@ class ImageManipulation {
     }
   }
 
+  /**
+   * Create PNG
+   * @param type $parameterArray
+   * @param type $dsid
+   * @param type $file
+   * @param type $file_ext
+   * @return string 
+   */
   function createPNG($parameterArray = NULL, $dsid, $file, $file_ext) {
     $file_suffix = '_' . $dsid . '.' . $file_ext;
     $returnValue = TRUE;
@@ -69,6 +91,14 @@ class ImageManipulation {
     }
   }
 
+  /**
+   * Create JPEG 2000
+   * @param type $parameterArray
+   * @param type $dsid
+   * @param type $file
+   * @param type $file_ext
+   * @return type 
+   */
   function createJP2($parameterArray = NULL, $dsid, $file, $file_ext) {
     $file_suffix = "_$dsid.$file_ext";
     $return_value = TRUE;
@@ -115,7 +145,14 @@ class ImageManipulation {
     }
   }
 
-  //use imagemapi to manipulate images instead of going directly to imagemagick or whatever
+  /**
+   * use imagemapi to manipulate images instead of going directly to imagemagick or whatever
+   * @param type $parameterArray
+   * @param type $dsid
+   * @param type $file
+   * @param type $file_ext
+   * @return type 
+   */
   function manipulateImage($parameterArray = NULL, $dsid, $file, $file_ext) {
     $height = $parameterArray['height'];
     $width = $parameterArray['width'];
@@ -151,6 +188,14 @@ class ImageManipulation {
     }
   }
 
+  /**
+   * Create Thumbnail from PDF
+   * @param type $parameterArray
+   * @param type $dsid
+   * @param type $file
+   * @param type $file_ext
+   * @return boolean 
+   */
   function createThumbnailFromPDF($parameterArray, $dsid, $file, $file_ext) {
     $height = $parameterArray['height'];
     $width = $parameterArray['width'];
@@ -185,6 +230,14 @@ class ImageManipulation {
     }
   }
 
+  /**
+   * Create Thumbnail
+   * @param type $parameterArray
+   * @param type $dsid
+   * @param type $file
+   * @param type $file_ext
+   * @return boolean 
+   */
   function createThumbnail($parameterArray, $dsid, $file, $file_ext) {
     // var_dump($parameterArray);exit(0);
     $file_suffix = '_' . $dsid . '.' . $file_ext;
diff --git a/plugins/ModsFormBuilder.inc b/plugins/ModsFormBuilder.inc
index 6eb36d1b..b9741dca 100644
--- a/plugins/ModsFormBuilder.inc
+++ b/plugins/ModsFormBuilder.inc
@@ -2,244 +2,268 @@
 
 // $Id$
 
+/**
+ * @file
+ * ModsFormBuilder class
+ */
 module_load_include('inc', 'fedora_repository', 'plugins/FormBuilder');
+
+/**
+ * ModsFormBuilder class ???
+ */
 class ModsFormBuilder extends FormBuilder {
+
   static $MODS_NS = 'http://www.loc.gov/mods/v3';
   protected $cm;
   protected $item;
-  protected $pid; 
-  
- function __construct($pid=null) 
- {
-   parent::__construct();
-   if ($pid !== null)
-   {
-     module_load_include('inc', 'fedora_repository', 'ContentModel');
-     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
-     
-     $this->pid=$pid;
-     $this->cm = ContentModel::loadFromObject($pid);
-     $this->item = new fedora_item($pid);
-   }
- }
-  
- function handleEditMetadataForm(&$form_id, &$form_values, &$soap_client) 
- {
+  protected $pid;
+
+  /**
+   * Constructor
+   * @param type $pid 
+   */
+  function __construct($pid=null) {
+    parent::__construct();
+    if ($pid !== null) {
+      module_load_include('inc', 'fedora_repository', 'ContentModel');
+      module_load_include('inc', 'fedora_repository', 'api/fedora_item');
+
+      $this->pid = $pid;
+      $this->cm = ContentModel::loadFromObject($pid);
+      $this->item = new fedora_item($pid);
+    }
+  }
+
+  /**
+   * Handle Edit Metadata Form ???
+   * @param &$form_id
+   * @param &$form_values
+   * @param &$soap_client
+   */
+  function handleEditMetadataForm(&$form_id, &$form_values, &$soap_client) {
     $dom = new DomDocument("1.0", "UTF-8");
     $dom->formatOutput = TRUE;
-    $mods = $this->modsFromForm($form_values,$dom);
+    $mods = $this->modsFromForm($form_values, $dom);
     $dom->appendChild($mods);
-    
+
     if ($this->item->modify_datastream_by_value($dom->saveXML(), 'MODS', "MODS Record", 'text/xml') !== NULL) {
-        drupal_set_message(t('Successfully updated MODS datastream for object %pid', array('%pid'=>$this->pid)));
-    }
-    drupal_goto('/fedora/repository/'.$this->pid);
- }
-  
- function buildEditMetadataForm()
- {
-     $form['#multistep'] = TRUE; // used so that it triggers a form rebuild every time.
-      $form['indicator2'] = array(
-	'#type' => 'fieldset',
-	'#title' => t('Edit metadata'),
-      );
-  
+      drupal_set_message(t('Successfully updated MODS datastream for object %pid', array('%pid' => $this->pid)));
+    }
+    drupal_goto('/fedora/repository/' . $this->pid);
+  }
+
+  /**
+   * Build Edit Metadata Form
+   * @return array  
+   */
+  function buildEditMetadataForm() {
+    $form['#multistep'] = TRUE; // used so that it triggers a form rebuild every time.
+    $form['indicator2'] = array(
+      '#type' => 'fieldset',
+      '#title' => t('Edit metadata'),
+    );
+
     if ($this->cm !== FALSE && $this->item != NULL) {
-      $form['pid'] = array('#type'=>'hidden','#value'=>$this->pid);
-      
+      $form['pid'] = array('#type' => 'hidden', '#value' => $this->pid);
+
       $elements = $this->cm->getIngestFormElements();
-      $content  = $this->item->get_datastream_dissemination('MODS');
-    
-      if (trim($content) != '') { 
-	$dom = DOMDocument::loadXML($content);
-	$xpath = new DOMXPath($dom);
-	// Register the php: namespace (required)
-	$xpath->registerNamespace("php", "http://php.net/xpath");
-
-	// Register PHP functions (no restrictions)
-	$xpath->registerPHPFunctions();
-	
-	foreach ($elements as $element) {
-
-	  $el = array(
-	    '#title' => $element['label'],
-	    '#required' => ($element['required'] ? 1 : 0),
-	    '#description' => $element['description'],
-	    '#type' => $element['type']
-	  );
-
-	  $includeEl = true;
-	  $elname = explode('][', $element['name']);
-	  $elLocation = &$form['indicator2'];
-	  while (isset($elLocation[$name[0]]) && ($partial = array_shift($elname)) != NULL) {
-	   $elLocation = &$elLocation[$partial];
-	  }
-
-	  foreach ($element['parameters'] as $key => $val) {
-	    switch ($key)  {
-	      case '#autocomplete_path':
-		$val .= '/'. $form_values['storage']['collection_pid'];
-		break;
-		
-	      case '#exclude_from_edit_metadata':
-		$includeEl=FALSE;
-		break;
-		  
-		
-	      case '#edit_metadata_xpath':
-		$nodeList = $xpath->evaluate($val);
+      $content = $this->item->get_datastream_dissemination('MODS');
+
+      if (trim($content) != '') {
+        $dom = DOMDocument::loadXML($content);
+        $xpath = new DOMXPath($dom);
+        // Register the php: namespace (required)
+        $xpath->registerNamespace("php", "http://php.net/xpath");
+
+        // Register PHP functions (no restrictions)
+        $xpath->registerPHPFunctions();
+
+        foreach ($elements as $element) {
+
+          $el = array(
+            '#title' => $element['label'],
+            '#required' => ($element['required'] ? 1 : 0),
+            '#description' => $element['description'],
+            '#type' => $element['type']
+          );
+
+          $includeEl = true;
+          $elname = explode('][', $element['name']);
+          $elLocation = &$form['indicator2'];
+          while (isset($elLocation[$name[0]]) && ($partial = array_shift($elname)) != NULL) {
+            $elLocation = &$elLocation[$partial];
+          }
+
+          foreach ($element['parameters'] as $key => $val) {
+            switch ($key) {
+              case '#autocomplete_path':
+                $val .= '/' . $form_values['storage']['collection_pid'];
+                break;
+
+              case '#exclude_from_edit_metadata':
+                $includeEl = FALSE;
+                break;
+
+
+              case '#edit_metadata_xpath':
+                $nodeList = $xpath->evaluate($val);
 //  		echo $val. ' '.$nodeList->length.' ';
 // 		echo $nodeList->item(0)->nodeValue.' ';
 // 		echo '<br/>';
 
-		if (is_string($nodeList)) 
-		{
-		  $el['#default_value']=$nodeList;
-		} else if ($nodeList->length > 1) 
-		{
-		  $el['#default_value'] = array();
-		  foreach ($nodeList as $node)
-		  {
-		    $el['#default_value'][] = $node->nodeValue;
-		  }
-		} else if ($nodeList->length > 0) 
-		{
-		  if ($el['#type'] == 'list') { 
-		    $values=array();
-		    for ($i=0;$i<$nodeList->length;$i++) { 
-		      $values[]=$nodeList->item($i)->nodeValue;
-		    }
-		    $el['#default_value']=join('; ',$values);
-		  } else {
-		    $el['#default_value'] = $nodeList->item(0)->nodeValue;
-		  }
-		}
-		break;
-	    }
-	    
-	    if ($key != '#sticky') {
-	      $el[$key]=$val;
-	    }
-	    
-	  }
-	  
-	  if ($element['type'] == 'people')
-	  {
-
-	    $names = $xpath->evaluate('/mods:mods/mods:name');
-	    $people=array();
-	    foreach ($names as $mname) {
-	      
-	      $type = $mname->getAttribute('type');
-	      $role = $mname->getElementsByTagName('roleTerm')->item(0)->nodeValue;
-	      
-	      $nameParts = $mname->getElementsByTagName('namePart');
-	      foreach ($nameParts as $namePart)
-	      {
-          switch ($namePart->getAttribute('type')) { 
-            case 'given': $given = $namePart->nodeValue; break;
-            case 'family': $family = $namePart->nodeValue; break;
-            case 'termsOfAddress': $title = $namePart->nodeValue; break;
-            case 'date': $date = $namePart->nodeValue; break;
-            default: $name = $namePart->nodeValue; break; 
+                if (is_string($nodeList)) {
+                  $el['#default_value'] = $nodeList;
+                }
+                else if ($nodeList->length > 1) {
+                  $el['#default_value'] = array();
+                  foreach ($nodeList as $node) {
+                    $el['#default_value'][] = $node->nodeValue;
+                  }
+                }
+                else if ($nodeList->length > 0) {
+                  if ($el['#type'] == 'list') {
+                    $values = array();
+                    for ($i = 0; $i < $nodeList->length; $i++) {
+                      $values[] = $nodeList->item($i)->nodeValue;
+                    }
+                    $el['#default_value'] = join('; ', $values);
+                  }
+                  else {
+                    $el['#default_value'] = $nodeList->item(0)->nodeValue;
+                  }
+                }
+                break;
+            }
+
+            if ($key != '#sticky') {
+              $el[$key] = $val;
+            }
           }
-	      }
-	      
-	      $person=array('role'=>$role);
-	      switch ($type)
-	      {
-		case 'personal':
-		  if (isset($given) && isset($family) && !isset($name)) { 
-		      $name = (isset($title)?$title.' ':'').$family.', '.$family;
-		  }
-		  $person['name']=$name;
-		  $person['date']=$date;
-		  break;
-		case 'organization':
-		  $person['organization'] = $name;
-		  break;
-		case 'conference':
-		  $person['conference']=$name;
-		  $person['date']=$date;
-		  break;
-	      }
-	      $people[]=$person;
-	    }
-	    
-	    $names = $xpath->evaluate('/mods:mods/mods:subject/mods:name');
-	    foreach ($names as $mname) {
-	      
-	      $type = $mname->getAttribute('type');
-	      
-	      $nameParts = $mname->getElementsByTagName('namePart');
-	      foreach ($nameParts as $namePart)
-	      {
-		switch ($namePart->getAttribute('type')) { 
-		  case 'given': $given = $namePart->nodeValue; break;
-		  case 'family': $family = $namePart->nodeValue; break;
-		  case 'termsOfAddress': $title = $namePart->nodeValue; break;
-		  case 'date': $date = $namePart->nodeValue; break;
-		  default: $name = $namePart->nodeValue; break; 
-		}
-	      }
-	      
-	      $person=array('subject'=>1);
-	      switch ($type)
-	      {
-		case 'personal':
-		  if (isset($given) && isset($family) && !isset($name)) { 
-		      $name = (isset($title)?$title.' ':'').$family.', '.$family;
-		  }
-		  $person['name']=$name;
-		  $person['date']=$date;
-		  break;
-		case 'organization':
-		  $person['organization'] = $name;
-		  break;
-		case 'conference':
-		  $person['conference']=$name;
-		  $person['date']=$date;
-		  break;
-	      }
-	      $people[]=$person;
-	    }	    
-	    
-	    $el['#default_value'] = $people;
-	    
-	  }
-	    
-	  
-	  if ($element['type'] == 'select' || $element['type'] == 'other_select') {
-	    $el['#options']= isset($element['authoritative_list'])?$element['authoritative_list']:array();
-	  }
-     
-	  if ($includeEl) { 
-	    $elLocation[join('][', $elname)] = $el;
-	  }
-	}
-
-    $form['submit'] = array(
-        '#type' => 'submit',
-        '#submit' => array('fedora_repository_edit_qdc_form_submit'),
-        '#value' => 'Save Metadata'
-    );
-	  
-	return $form;	
 
+          if ($element['type'] == 'people') {
+
+            $names = $xpath->evaluate('/mods:mods/mods:name');
+            $people = array();
+            foreach ($names as $mname) {
+
+              $type = $mname->getAttribute('type');
+              $role = $mname->getElementsByTagName('roleTerm')->item(0)->nodeValue;
+
+              $nameParts = $mname->getElementsByTagName('namePart');
+              foreach ($nameParts as $namePart) {
+                switch ($namePart->getAttribute('type')) {
+                  case 'given': $given = $namePart->nodeValue;
+                    break;
+                  case 'family': $family = $namePart->nodeValue;
+                    break;
+                  case 'termsOfAddress': $title = $namePart->nodeValue;
+                    break;
+                  case 'date': $date = $namePart->nodeValue;
+                    break;
+                  default: $name = $namePart->nodeValue;
+                    break;
+                }
+              }
+
+              $person = array('role' => $role);
+              switch ($type) {
+                case 'personal':
+                  if (isset($given) && isset($family) && !isset($name)) {
+                    $name = (isset($title) ? $title . ' ' : '') . $family . ', ' . $family;
+                  }
+                  $person['name'] = $name;
+                  $person['date'] = $date;
+                  break;
+                case 'organization':
+                  $person['organization'] = $name;
+                  break;
+                case 'conference':
+                  $person['conference'] = $name;
+                  $person['date'] = $date;
+                  break;
+              }
+              $people[] = $person;
+            }
+
+            $names = $xpath->evaluate('/mods:mods/mods:subject/mods:name');
+            foreach ($names as $mname) {
+
+              $type = $mname->getAttribute('type');
+
+              $nameParts = $mname->getElementsByTagName('namePart');
+              foreach ($nameParts as $namePart) {
+                switch ($namePart->getAttribute('type')) {
+                  case 'given': $given = $namePart->nodeValue;
+                    break;
+                  case 'family': $family = $namePart->nodeValue;
+                    break;
+                  case 'termsOfAddress': $title = $namePart->nodeValue;
+                    break;
+                  case 'date': $date = $namePart->nodeValue;
+                    break;
+                  default: $name = $namePart->nodeValue;
+                    break;
+                }
+              }
+
+              $person = array('subject' => 1);
+              switch ($type) {
+                case 'personal':
+                  if (isset($given) && isset($family) && !isset($name)) {
+                    $name = (isset($title) ? $title . ' ' : '') . $family . ', ' . $family;
+                  }
+                  $person['name'] = $name;
+                  $person['date'] = $date;
+                  break;
+                case 'organization':
+                  $person['organization'] = $name;
+                  break;
+                case 'conference':
+                  $person['conference'] = $name;
+                  $person['date'] = $date;
+                  break;
+              }
+              $people[] = $person;
+            }
+
+            $el['#default_value'] = $people;
+          }
+
+
+          if ($element['type'] == 'select' || $element['type'] == 'other_select') {
+            $el['#options'] = isset($element['authoritative_list']) ? $element['authoritative_list'] : array();
+          }
+
+          if ($includeEl) {
+            $elLocation[join('][', $elname)] = $el;
+          }
+        }
+
+        $form['submit'] = array(
+          '#type' => 'submit',
+          '#submit' => array('fedora_repository_edit_qdc_form_submit'),
+          '#value' => 'Save Metadata'
+        );
+
+        return $form;
       }
     }
-    
- }
- 
- function handleModsForm(&$form_values,&$form_state) {
+  }
+
+  /**
+   * Handle Mods Form
+   * @param &$form_values
+   * @param &$form_state
+   */
+  function handleModsForm(&$form_values, &$form_state) {
     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
     module_load_include('inc', 'fedora_repository', 'CollectionPolicy');
-    
-    $form_state['storage']['people']=NULL; //clears out old entities for the next run of the formbuilder. 
-    
+
+    $form_state['storage']['people'] = NULL; //clears out old entities for the next run of the formbuilder. 
+
     $dom = new DomDocument("1.0", "UTF-8");
     $dom->formatOutput = TRUE;
-    $pid=$form_values['pid'];
+    $pid = $form_values['pid'];
     $rootElement = $dom->createElement("foxml:digitalObject");
     $rootElement->setAttribute('VERSION', '1.1');
     $rootElement->setAttribute('PID', "$pid");
@@ -247,24 +271,24 @@ class ModsFormBuilder extends FormBuilder {
     $rootElement->setAttribute('xmlns:xsi', "http://www.w3.org/2001/XMLSchema-instance");
     $rootElement->setAttribute('xsi:schemaLocation', "info:fedora/fedora-system:def/foxml# http://www.fedora.info/definitions/1/0/foxml1-1.xsd");
     $dom->appendChild($rootElement);
-    
+
     // Create standard fedora stuff
     $form_values['dc:title'] = $form_values['mods_title'];
     $this->createStandardFedoraStuff($form_values, $dom, $rootElement);
-    
+
     // Create relationships
     $this->createRelationShips($form_values, $dom, $rootElement);
     $collectionPid = $form_values['collection_pid'];
-        
+
     if (($cp = CollectionPolicy::LoadFromCollection($collectionPid)) !== FALSE) {
-      $collectionName =trim($cp->getName()); 
-      if (trim($collectionName)!='') {
-        $form_values['dc_relation']=$collectionName;
+      $collectionName = trim($cp->getName());
+      if (trim($collectionName) != '') {
+        $form_values['dc_relation'] = $collectionName;
       }
-    }    
+    }
     // Create MODS
     $this->createModsStream($form_values, $dom, $rootElement);
-    $this->createCollectionPolicy($form_values, $dom, $rootElement);    
+    $this->createCollectionPolicy($form_values, $dom, $rootElement);
     $this->createWorkflowStream($form_values, $dom, $rootElement);
 
     if (!empty($form_values['ingest-file-location'])) {
@@ -274,33 +298,37 @@ class ModsFormBuilder extends FormBuilder {
 
 //         header('Content-type: application/xml');
 //         echo $dom->saveXML();  exit();
-   
+
     try {
-        $object = Fedora_Item::ingest_from_FOXML($dom);
-        //for some reason, ingest_from_FOXML does not generate a JMS message
-        //I just modify the workflow DS and it sends a JMS message.  
-        $item = new Fedora_Item($object->pid);
-        $item->modify_datastream_by_value( $item->get_datastream_dissemination('WORKFLOW'), 'WORKFLOW', "Workflow Record", 'text/xml');
-  
-        if (!empty($object->pid)) {
-          drupal_set_message(t("Item !pid created successfully.", array('!pid' => l($object->pid, 'fedora/repository/'. $object->pid))), "status");
-         }
-         if (!empty( $_SESSION['fedora_ingest_files'])) {
-           foreach ($_SESSION['fedora_ingest_files'] as $dsid => $createdFile) {
-            file_delete($createdFile);
-           }
-         }
-         file_delete($form_values['ingest-file-location']);
-    }
-    catch (exception $e) {
+      $object = Fedora_Item::ingest_from_FOXML($dom);
+      //for some reason, ingest_from_FOXML does not generate a JMS message
+      //I just modify the workflow DS and it sends a JMS message.  
+      $item = new Fedora_Item($object->pid);
+      $item->modify_datastream_by_value($item->get_datastream_dissemination('WORKFLOW'), 'WORKFLOW', "Workflow Record", 'text/xml');
+
+      if (!empty($object->pid)) {
+        drupal_set_message(t("Item !pid created successfully.", array('!pid' => l($object->pid, 'fedora/repository/' . $object->pid))), "status");
+      }
+      if (!empty($_SESSION['fedora_ingest_files'])) {
+        foreach ($_SESSION['fedora_ingest_files'] as $dsid => $createdFile) {
+          file_delete($createdFile);
+        }
+      }
+      file_delete($form_values['ingest-file-location']);
+    } catch (exception $e) {
       drupal_set_message(t('Error ingesting object: !e', array('!e' => $e->getMessage())), 'error');
       watchdog(t("Fedora_Repository"), t("Error ingesting object: !e", array('!e' => $e->getMessage())), NULL, WATCHDOG_ERROR);
       return;
     }
-  }  
- 
- 
- function createCollectionPolicy($form_values, &$dom, &$rootElement) {
+  }
+
+  /**
+   * Create Collection Policy ??
+   * @param $form_values
+   * @param &$dom
+   * @param &$rootElement
+   */
+  function createCollectionPolicy($form_values, &$dom, &$rootElement) {
     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
     $model = new fedora_item($form_values['content_model_pid']);
     $ds_list = $model->get_datastreams_list_as_array();
@@ -308,10 +336,10 @@ class ModsFormBuilder extends FormBuilder {
       $cp = $model->get_datastream_dissemination('COLLECTION_POLICY_TMPL');
       $cpDom = DOMDocument::loadXML($cp);
       $cpRootEl = $cpDom->getElementsByTagName('collection_policy');
-      if ($cpRootEl->length >0) {
-        $cpRootEl=$cpRootEl->item(0);
+      if ($cpRootEl->length > 0) {
+        $cpRootEl = $cpRootEl->item(0);
         $newNode = $dom->importNode($cpRootEl, TRUE);
-    
+
         $datastream = $dom->createElement("foxml:datastream");
         $datastream->setAttribute("ID", "COLLECTION_POLICY");
         $datastream->setAttribute("STATE", "A");
@@ -328,7 +356,13 @@ class ModsFormBuilder extends FormBuilder {
       }
     }
   }
- 
+
+  /**
+   * Create Workflow Stream ??
+   * @param $form_values
+   * @param &$dom
+   * @param &$rootElement
+   */
   function createWorkflowStream($form_values, &$dom, &$rootElement) {
     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
     $model = new fedora_item($form_values['content_model_pid']);
@@ -337,10 +371,10 @@ class ModsFormBuilder extends FormBuilder {
       $workflow = $model->get_datastream_dissemination('WORKFLOW_TMPL');
       $workflowDom = DOMDocument::loadXML($workflow);
       $workflowRootEl = $workflowDom->getElementsByTagName('workflow');
-      if ($workflowRootEl->length >0) {
-        $workflowRootEl=$workflowRootEl->item(0);
+      if ($workflowRootEl->length > 0) {
+        $workflowRootEl = $workflowRootEl->item(0);
         $newNode = $dom->importNode($workflowRootEl, TRUE);
-    
+
         $datastream = $dom->createElement("foxml:datastream");
         $datastream->setAttribute("ID", "WORKFLOW");
         $datastream->setAttribute("STATE", "A");
@@ -357,9 +391,15 @@ class ModsFormBuilder extends FormBuilder {
       }
     }
   }
-    
+
+  /**
+   * Create mods Stream ??
+   * @param $form_values
+   * @param &$dom
+   * @param &$rootElement
+   */
   function createModsStream($form_values, &$dom, &$rootElement) {
-    
+
     $datastream = $dom->createElement("foxml:datastream");
     $datastream->setAttribute("ID", "MODS");
     $datastream->setAttribute("STATE", "A");
@@ -371,63 +411,67 @@ class ModsFormBuilder extends FormBuilder {
     $datastream->appendChild($version);
     $content = $dom->createElement("foxml:xmlContent");
     $version->appendChild($content);
-    
-    $mods = $this->modsFromForm($form_values,$dom);
+
+    $mods = $this->modsFromForm($form_values, $dom);
     $content->appendChild($mods);
-    
-    $rootElement->appendChild($datastream);
-  }  
 
+    $rootElement->appendChild($datastream);
+  }
 
-  function modsFromForm(&$form_values,&$dom)
-  {
+  /**
+   * Mods From From ?????
+   * @param type $form_values
+   * @param type $dom
+   * @return type 
+   */
+  function modsFromForm(&$form_values, &$dom) {
 
-     ///begin writing MODS
+    ///begin writing MODS
     $mods = $dom->createElement("mods:mods");
     $mods->setAttribute('version', '3.4');
     $mods->setAttribute('xmlns:xlink', "http://www.w3.org/1999/xlink");
     $mods->setAttribute('xmlns:mods', "http://www.loc.gov/mods/v3");
     $mods->setAttribute('xmlns:xsi', "http://www.w3.org/2001/XMLSchema-instance");
     $mods->setAttribute('xsi:schemaLocation', "http://www.loc.gov/mods/v3 http://www.loc.gov/standards/mods/v3/mods-3-0.xsd");
-    
-    
+
+
     if (isset($form_values['mods_title']) && trim($form_values['mods_title']) != '') {
       $titleinfo = $dom->createElement('mods:titleInfo');
-      $title  = $dom->createElement('mods:title', htmlspecialchars($form_values['mods_title']));
+      $title = $dom->createElement('mods:title', htmlspecialchars($form_values['mods_title']));
       $titleinfo->appendChild($title);
       $mods->appendChild($titleinfo);
     }
-    
-    if (isset($form_values['mods_alternative_titles']) && trim($form_values['mods_alternative_titles']) != '') { 
-      $titles=preg_split('/\s+\;\s+/',trim($form_values['mods_alternative_titles']));
+
+    if (isset($form_values['mods_alternative_titles']) && trim($form_values['mods_alternative_titles']) != '') {
+      $titles = preg_split('/\s+\;\s+/', trim($form_values['mods_alternative_titles']));
       foreach ($titles as $t) {
-	 $titleinfo = $dom->createElement('mods:titleInfo'); 
-	 $titleinfo->setAttribute('type','alternative') ; 
-	 $title = $dom->createElement('mods:title',$t);
-	 $titleinfo->appendChild($title);
-	 $mods->appendChild($titleinfo);
+        $titleinfo = $dom->createElement('mods:titleInfo');
+        $titleinfo->setAttribute('type', 'alternative');
+        $title = $dom->createElement('mods:title', $t);
+        $titleinfo->appendChild($title);
+        $mods->appendChild($titleinfo);
       }
     }
-    
-    if (isset($form_values['mods_alternative_title']) && trim($form_values['mods_alternative_title']) != '') { 
-	$titleinfo = $dom->createElement('mods:titleInfo'); 
-	$titleinfo->setAttribute('type','alternative') ; 
-	$title = $dom->createElement('mods:title',trim($form_values['mods_alternative_title']));
-	$titleinfo->appendChild($title);
-	$mods->appendChild($titleinfo);
-    }    
-    
+
+    if (isset($form_values['mods_alternative_title']) && trim($form_values['mods_alternative_title']) != '') {
+      $titleinfo = $dom->createElement('mods:titleInfo');
+      $titleinfo->setAttribute('type', 'alternative');
+      $title = $dom->createElement('mods:title', trim($form_values['mods_alternative_title']));
+      $titleinfo->appendChild($title);
+      $mods->appendChild($titleinfo);
+    }
+
     if (isset($form_values['mods_description']) && trim($form_values['mods_description']) != '') {
-     $abstract = $dom->createElement('mods:abstract', htmlspecialchars(trim($form_values['mods_description'])));
-     $mods->appendChild($abstract);
+      $abstract = $dom->createElement('mods:abstract', htmlspecialchars(trim($form_values['mods_description'])));
+      $mods->appendChild($abstract);
     }
-    
+
     if (isset($form_values['pid']) && trim($form_values['pid']) != '') {
-      $identifier = $dom->createElement('mods:identifier', htmlspecialchars(trim(preg_replace('/\:/','\/',$form_values['pid']))));
+      $identifier = $dom->createElement('mods:identifier', htmlspecialchars(trim(preg_replace('/\:/', '\/', $form_values['pid']))));
       $identifier->setAttribute('type', 'hdl');
       $mods->appendChild($identifier);
     }
-    
+
     if (isset($form_values['collection_pid']) && trim($form_values['collection_pid']) != '') {
       $relatedItem = $dom->createElement('mods:relatedItem');
       $relatedItem->setAttribute('type', 'isMemberOfCollection');
@@ -435,13 +479,13 @@ class ModsFormBuilder extends FormBuilder {
       $relatedItem->appendChild($identifier);
       $mods->appendChild($relatedItem);
     }
-    
+
     if (isset($form_values['mods_identifier']) && trim($form_values['mods_identifier']) != '') {
       $identifier = $dom->createElement('mods:identifier', htmlspecialchars(trim($form_values['mods_identifier'])));
       $identifier->setAttribute('type', 'local');
       $mods->appendChild($identifier);
     }
-    
+
     if (isset($form_values['mods_physicalLocation']) && trim($form_values['mods_physicalLocation']) != '') {
       $location = $dom->createElement('mods:location');
       $physLocation = $dom->createElement('mods:physicalLocation', htmlspecialchars(trim($form_values['mods_physicalLocation'])));
@@ -452,154 +496,152 @@ class ModsFormBuilder extends FormBuilder {
       }
       $mods->appendChild($location);
     }
-     
+
     $originInfo = $dom->createElement('mods:originInfo');
     $addOriginInfo = FALSE;
     if (isset($form_values['mods_pubinfo_place']) && trim($form_values['mods_pubinfo_place']) != '') {
       $place = $dom->createElement('mods:place');
-      $placeTerm=$dom->createElement('mods:placeTerm', htmlspecialchars(trim($form_values['mods_pubinfo_place'])));
+      $placeTerm = $dom->createElement('mods:placeTerm', htmlspecialchars(trim($form_values['mods_pubinfo_place'])));
       $placeTerm->setAttribute('type', 'text');
       $place->appendChild($placeTerm);
       $originInfo->appendChild($place);
       $addOriginInfo = TRUE;
     }
-    
+
     if (isset($form_values['mods_pubinfo_publisher']) && trim($form_values['mods_pubinfo_publisher']) != '') {
       $publisher = $dom->createElement('mods:publisher', htmlspecialchars(trim($form_values['mods_pubinfo_publisher'])));
       $originInfo->appendChild($publisher);
       $addOriginInfo = TRUE;
     }
-    
+
     if (isset($form_values['mods_pubinfo_edition']) && trim($form_values['mods_pubinfo_edition']) != '') {
       $edition = $dom->createElement('mods:edition', htmlspecialchars(trim($form_values['mods_pubinfo_edition'])));
       $originInfo->appendChild($edition);
       $addOriginInfo = TRUE;
     }
-   
-    
+
+
     if (isset($form_values['mods_pubinfo_date']) && trim($form_values['mods_pubinfo_date']) != '' &&
         isset($form_values['mods_pubinfo_dateType']) && trim($form_values['mods_pubinfo_dateType']) != '') {
-       if (in_array($form_values['mods_pubinfo_dateType'], array('issued', 'created', 'copyright', 'captured'))) {
-         $date = $dom->createElement('mods:'. trim($form_values['mods_pubinfo_dateType']) .'Date', htmlspecialchars(trim($form_values['mods_pubinfo_date'])));
-       } 
-       else {
-         //how to handle other types?  otherDate? 
-         $date= $dom->createElement('mods:otherDate', htmlspecialchars(trim($form_values['mods_pubinfo_date'])));
-         $date->setAttribute('type', htmlspecialchars(trim($form_values['mods_pubinfo_dateType'])));
-       }
-       $originInfo->appendChild($date);
-       $addOriginInfo = TRUE;
-    } else {
+      if (in_array($form_values['mods_pubinfo_dateType'], array('issued', 'created', 'copyright', 'captured'))) {
+        $date = $dom->createElement('mods:' . trim($form_values['mods_pubinfo_dateType']) . 'Date', htmlspecialchars(trim($form_values['mods_pubinfo_date'])));
+      }
+      else {
+        //how to handle other types?  otherDate? 
+        $date = $dom->createElement('mods:otherDate', htmlspecialchars(trim($form_values['mods_pubinfo_date'])));
+        $date->setAttribute('type', htmlspecialchars(trim($form_values['mods_pubinfo_dateType'])));
+      }
+      $originInfo->appendChild($date);
+      $addOriginInfo = TRUE;
+    }
+    else {
       if (isset($form_values['mods_createdDate'])) {
-	$date = $dom->createElement('mods:createdDate',htmlspecialchars(trim($form_values['mods_createdDate']))); 
-	$originInfo->appendChild($date);
+        $date = $dom->createElement('mods:createdDate', htmlspecialchars(trim($form_values['mods_createdDate'])));
+        $originInfo->appendChild($date);
         $addOriginInfo = TRUE;
       }
-      
+
       if (isset($form_values['mods_issuedDate'])) {
-	$date = $dom->createElement('mods:issuedDate',htmlspecialchars(trim($form_values['mods_issuedDate']))); 
-	$originInfo->appendChild($date);
+        $date = $dom->createElement('mods:issuedDate', htmlspecialchars(trim($form_values['mods_issuedDate'])));
+        $originInfo->appendChild($date);
         $addOriginInfo = TRUE;
       }
-      
+
       if (isset($form_values['mods_copyrightDate'])) {
-	$date = $dom->createElement('mods:copyrightDate',htmlspecialchars(trim($form_values['mods_copyrightDate']))); 
-	$originInfo->appendChild($date);
+        $date = $dom->createElement('mods:copyrightDate', htmlspecialchars(trim($form_values['mods_copyrightDate'])));
+        $originInfo->appendChild($date);
         $addOriginInfo = TRUE;
       }
-      
+
       if (isset($form_values['mods_capturedDate'])) {
-	$date = $dom->createElement('mods:capturedDate',htmlspecialchars(trim($form_values['mods_capturedDate']))); 
-	$originInfo->appendChild($date);
+        $date = $dom->createElement('mods:capturedDate', htmlspecialchars(trim($form_values['mods_capturedDate'])));
+        $originInfo->appendChild($date);
         $addOriginInfo = TRUE;
       }
-
     }
-    
+
     if (isset($form_values['mods_pubinfo_journalFreq']) && trim($form_values['mods_pubinfo_journalFreq']) != '') {
       $frequency = $dom->createElement('mods:frequency', htmlspecialchars(trim($form_values['mods_pubinfo_journalFreq'])));
       $originInfo->appendChild($frequency);
-      $issuance= $dom->createElement('mods:issuance', 'journal');
+      $issuance = $dom->createElement('mods:issuance', 'journal');
       $originInfo->appendChild($issuance);
       $addOriginInfo = TRUE;
-    } 
+    }
     elseif (isset($form_values['mods_pubinfo_journalFreq'])) {
-      $issuance= $dom->createElement('mods:issuance', 'monographic');
+      $issuance = $dom->createElement('mods:issuance', 'monographic');
       $originInfo->appendChild($issuance);
     }
-    
-    
+
+
     if ($addOriginInfo) {
       $mods->appendChild($originInfo);
     }
-    
+
     if (isset($form_values['mods_note']) && trim($form_values['mods_note']) != '') {
       $note = $dom->createElement('mods:note', htmlspecialchars(trim($form_values['mods_note'])));
       $mods->appendChild($note);
-    }    
-    
+    }
+
     if (isset($form_values['mods_caption']) && trim($form_values['mods_caption']) != '') {
       $note = $dom->createElement('mods:note', htmlspecialchars(trim($form_values['mods_caption'])));
-      $note->setAttribute('type','caption');
+      $note->setAttribute('type', 'caption');
       $mods->appendChild($note);
-    }        
-        
+    }
+
     if (isset($form_values['mods_format']) && trim($form_values['mods_format']) != '') {
       $typeOfResource = $dom->createElement('mods:typeOfResource', htmlspecialchars($form_values['mods_format']));
       $mods->appendChild($typeOfResource);
     }
-    
-    
-    if (isset($form_values['mods_language'])  && trim($form_values['mods_language']) != '')
-    {
+
+
+    if (isset($form_values['mods_language']) && trim($form_values['mods_language']) != '') {
       $languageList = explode(';', htmlspecialchars($form_values['mods_language']));
-      foreach ($languageList as $lang)
-      {
-	$language = $dom->createElement('mods:language'); 
-	$langTerm = $dom->createElement('mods:languageTerm',htmlspecialchars($lang)); 
-	$langTerm->setAttribute('type','text');
-	$language->appendChild($langTerm);
-	$mods->appendChild($language);
+      foreach ($languageList as $lang) {
+        $language = $dom->createElement('mods:language');
+        $langTerm = $dom->createElement('mods:languageTerm', htmlspecialchars($lang));
+        $langTerm->setAttribute('type', 'text');
+        $language->appendChild($langTerm);
+        $mods->appendChild($language);
       }
     }
-        
-    
+
+
     $hasSubject = FALSE;
     $subject = $dom->createElement('mods:subject');
-    
-    
+
+
     // Hierarchical Geographic Subject
     if (isset($form_values['mods_country']) && trim($form_values['mods_country']) != '') {
       $hasSubject = TRUE;
       $geographic = $dom->createElement('mods:hierarchicalGeographic');
-      
-      $country=$dom->createElement('mods:country', htmlspecialchars($form_values['mods_country']));
+
+      $country = $dom->createElement('mods:country', htmlspecialchars($form_values['mods_country']));
       $geographic->appendChild($country);
-      
+
       if (isset($form_values['mods_province']) && trim($form_values['mods_province']) != '') {
-        $province = $dom->createElement('mods:province', htmlspecialchars($form_values['mods_province'])); 
+        $province = $dom->createElement('mods:province', htmlspecialchars($form_values['mods_province']));
         $geographic->appendChild($province);
       }
-      
+
       if (isset($form_values['mods_state']) && trim($form_values['mods_state']) != '') {
-        $state = $dom->createElement('mods:state', htmlspecialchars($form_values['mods_state'])); 
+        $state = $dom->createElement('mods:state', htmlspecialchars($form_values['mods_state']));
         $geographic->appendChild($state);
       }
-      
+
       if (isset($form_values['mods_city']) && trim($form_values['mods_city']) != '') {
-        $city = $dom->createElement('mods:city', htmlspecialchars($form_values['mods_city'])); 
+        $city = $dom->createElement('mods:city', htmlspecialchars($form_values['mods_city']));
         $geographic->appendChild($city);
       }
-      
+
       if (isset($form_values['mods_area']) && trim($form_values['mods_area']) != '') {
-        $state = $dom->createElement('mods:area', htmlspecialchars($form_values['mods_area'])); 
+        $state = $dom->createElement('mods:area', htmlspecialchars($form_values['mods_area']));
         $geographic->appendChild($state);
       }
-      
-      
+
+
       $subject->appendChild($geographic);
     }
-    
+
     if (isset($form_values['mods_date']) && trim($form_values['mods_date']) != '') {
       $hasSubject = TRUE;
       $temporal = $dom->createElement('mods:temporal', htmlspecialchars($form_values['mods_date']));
@@ -608,13 +650,13 @@ class ModsFormBuilder extends FormBuilder {
 
     if (isset($form_values['mods_subjtitle']) && trim($form_values['mods_subjtitle']) != '') {
       $hasSubject = TRUE;
-      $titleInfo= $dom->createElement('mods:titleInfo');
+      $titleInfo = $dom->createElement('mods:titleInfo');
       $title = $dom->createElement('mods:title', htmlspecialchars($form_values['mods_subjtitle']));
       $titleInfo->appendChild($title);
       $subject->appendChild($titleInfo);
-    }    
-    
-    
+    }
+
+
     if (isset($form_values['mods_topics']) && trim($form_values['mods_topics']) != '') {
       $hasSubject = TRUE;
       $topicList = explode(';', htmlspecialchars($form_values['mods_topics']));
@@ -622,102 +664,101 @@ class ModsFormBuilder extends FormBuilder {
       if (isset($form_values['mods_topicAuthority']) && trim($form_values['mods_topicAuthority']) != '') {
         $authority = htmlspecialchars($form_values['mods_topicAuthority']);
       }
-      
+
       foreach ($topicList as $t) {
         $topic = $dom->createElement('mods:topic', $t);
         $topic->setAttribute('authority', $authority);
         $subject->appendChild($topic);
       }
     }
- 
-    
+
+
     if (isset($form_values['mods_cc']['cc']) && $form_values['mods_cc']['cc']['cc_enable']) {
 
-	$commercial = trim($form_values['mods_cc']['cc']['cc_commercial']);
-	$modifications = trim($form_values['mods_cc']['cc']['cc_modifications']);
-	$jurisdiction = trim($form_values['mods_cc']['cc']['cc_jurisdiction']);
-	
-	module_load_include('inc','islandora_form_elements','includes/creative_commons.inc');
-	
-	if (!isset(CreativeCommons::$cc_jurisdiction_vals[$jurisdiction]))
-	    $jurisdiction='';
-	$version = CreativeCommons::$cc_versions[$jurisdiction];
-	
-      $license = 'by'. ($commercial != ''?'-'.$commercial:'') . ($modifications != ''?'-'.$modifications:'') . '/' . $version . '/'.($jurisdiction != ''?$jurisdiction.'/':'') ;
-	
+      $commercial = trim($form_values['mods_cc']['cc']['cc_commercial']);
+      $modifications = trim($form_values['mods_cc']['cc']['cc_modifications']);
+      $jurisdiction = trim($form_values['mods_cc']['cc']['cc_jurisdiction']);
+
+      // Include islandora form elements only if needed ??
+      module_load_include('inc', 'islandora_form_elements', 'includes/creative_commons.inc');
+
+      if (!isset(CreativeCommons::$cc_jurisdiction_vals[$jurisdiction]))
+        $jurisdiction = '';
+      $version = CreativeCommons::$cc_versions[$jurisdiction];
+
+      $license = 'by' . ($commercial != '' ? '-' . $commercial : '') . ($modifications != '' ? '-' . $modifications : '') . '/' . $version . '/' . ($jurisdiction != '' ? $jurisdiction . '/' : '');
+
       $accessCondition = $dom->createElement('mods:accessCondition', htmlspecialchars($license));
       $accessCondition->setAttribute('type', 'Creative Commons License');
       $mods->appendChild($accessCondition);
-	
-	
     }
-    
+
     if (isset($form_values['mods_rights']) && trim($form_values['mods_rights']) != '') {
       $accessCondition = $dom->createElement('mods:accessCondition', htmlspecialchars($form_values['mods_rights']));
       $accessCondition->setAttribute('type', 'restriction on access; use and reproduction');
       $mods->appendChild($accessCondition);
     }
-    
-    if (isset($form_values['mods_people']) &&  isset($form_values['mods_people']['people']) && is_array($form_values['mods_people']['people']) ) {
+
+    if (isset($form_values['mods_people']) && isset($form_values['mods_people']['people']) && is_array($form_values['mods_people']['people'])) {
       foreach ($form_values['mods_people']['people'] as $key => $val) {
         $name = $dom->createElement('mods:name');
-        $appendName=FALSE;
+        $appendName = FALSE;
         if (isset($val['role'])) {
-            $role = $dom->createElement('mods:role');
-            $roleTerm = $dom->createElement('mods:roleTerm', htmlspecialchars(trim($val['role'])));
-            $roleTerm->setAttribute('type', 'text');
-            $roleTerm->setAttribute('authority', 'marcrelator');
-            $role->appendChild($roleTerm);
-            $name->appendChild($role);
+          $role = $dom->createElement('mods:role');
+          $roleTerm = $dom->createElement('mods:roleTerm', htmlspecialchars(trim($val['role'])));
+          $roleTerm->setAttribute('type', 'text');
+          $roleTerm->setAttribute('authority', 'marcrelator');
+          $role->appendChild($roleTerm);
+          $name->appendChild($role);
         }
-      
+
         if (isset($val['organization'])) {
           $name->setAttribute('type', 'organization');
           if (trim($val['organization']) != '') {
-            $namePart=$dom->createElement('mods:namePart', htmlspecialchars(trim($val['organization'])));
+            $namePart = $dom->createElement('mods:namePart', htmlspecialchars(trim($val['organization'])));
             $name->appendChild($namePart);
-            $appendName=TRUE;
+            $appendName = TRUE;
           }
-        } 
+        }
         elseif (isset($val['conference'])) {
           $name->setAttribute('type', 'conference');
           if (trim($val['conference']) != '') {
-            $namePart=$dom->createElement('mods:namePart', htmlspecialchars(trim($val['conference'])));
+            $namePart = $dom->createElement('mods:namePart', htmlspecialchars(trim($val['conference'])));
             $name->appendChild($namePart);
-            $appendName=TRUE;
+            $appendName = TRUE;
           }
-        } 
+        }
         else {
           $name->setAttribute('type', 'personal');
           if (trim($val['name']) != '') {
-            $namePart=$dom->createElement('mods:namePart', htmlspecialchars(trim($val['name'])));
+            $namePart = $dom->createElement('mods:namePart', htmlspecialchars(trim($val['name'])));
             $name->appendChild($namePart);
-            $appendName=TRUE;
-          }   
+            $appendName = TRUE;
+          }
         }
-        
-        if (isset($val['date'])) { 
-          $namePart=$dom->createElement('mods:namePart', htmlspecialchars(trim($val['date'])));
-          $namePart->setAttribute('type','date');
+
+        if (isset($val['date'])) {
+          $namePart = $dom->createElement('mods:namePart', htmlspecialchars(trim($val['date'])));
+          $namePart->setAttribute('type', 'date');
           $name->appendChild($namePart);
         }
-        
+
         if ($appendName) {
-          if (isset($val['subject'])) { 
+          if (isset($val['subject'])) {
             $subject->appendChild($name);
-            $hasSubject=TRUE;
-          } else {
+            $hasSubject = TRUE;
+          }
+          else {
             $mods->appendChild($name);
           }
         }
+      }
+    }
 
-      } 
-    }  
-    
     if ($hasSubject) {
       $mods->appendChild($subject);
     }
-    
+
     return $mods;
   }
 
diff --git a/plugins/PersonalCollectionClass.inc b/plugins/PersonalCollectionClass.inc
index 9644dd71..70d35827 100644
--- a/plugins/PersonalCollectionClass.inc
+++ b/plugins/PersonalCollectionClass.inc
@@ -1,11 +1,31 @@
 <?php
+
 // $Id$
 
+/**
+ * @file
+ * PersonalCollectionClass class
+ */
+
+/**
+ * Personal Collection Class
+ */
 class PersonalCollectionClass {
+
+  /**
+   * Constructor
+   */
   function PersonalCollectionClass() {
     drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
   }
-  
+
+  /**
+   * Create collection
+   * @param type $theUser
+   * @param type $pid
+   * @param type $soapClient
+   * @return type 
+   */
   function createCollection($theUser, $pid, $soapClient) {
     $dom = new DomDocument("1.0", "UTF-8");
     $dom->formatOutput = TRUE;
@@ -23,34 +43,38 @@ class PersonalCollectionClass {
     $value = $this->createPolicyStream($theUser, $dom, $rootElement);
 
     if (!$value) {
-      return FALSE;//error should already be logged.
+      return FALSE; //error should already be logged.
     }
     $this->createCollectionPolicyStream($theUser, $dom, $rootElement);
     try {
       $params = array(
-          'objectXML' => $dom->saveXML(),
-          'format' => "foxml1.0",
-          'logMessage' => "Fedora object ingested",
+        'objectXML' => $dom->saveXML(),
+        'format' => "foxml1.0",
+        'logMessage' => "Fedora object ingested",
       );
 
       $object = $soapClient->__soapCall('ingest', array(
-          $params
-      ));
-
-    }
-    catch (exception $e) {
+            $params
+          ));
+    } catch (exception $e) {
       drupal_set_message(t('Error ingesting personal collection object: !e', array('!e' => $e->getMessage())), 'error');
       return FALSE;
     }
     return TRUE;
   }
 
+  /**
+   * Create Collection Policy Stream ??
+   * @param type $user
+   * @param type $dom
+   * @param type $rootElement
+   * @return type 
+   */
   function createCollectionPolicyStream($user, $dom, $rootElement) {
     $collectionTemplate = file_get_contents(drupal_get_path('module', 'Fedora_Repository') . '/collection_policies/PERSONAL-COLLECTION-POLICY.xml');
     try {
       $xml = new SimpleXMLElement($collectionTemplate);
-    }
-    catch (Exception $e) {
+    } catch (Exception $e) {
       watchdog(t("Fedora_Repository"), t("Problem creating personal collection policy, could not parse collection policy stream."), NULL, WATCHDOG_ERROR);
       drupal_set_message(t('Problem creating personal collection policy, could not parse collection policy stream: !e', array('!e' => $e->getMessage())), 'error');
       return FALSE;
@@ -88,6 +112,13 @@ class PersonalCollectionClass {
     return TRUE;
   }
 
+  /**
+   * Create Policy Stream ??
+   * @param type $user
+   * @param type $dom
+   * @param type $rootElement
+   * @return type 
+   */
   function createPolicyStream($user, $dom, $rootElement) {
     module_load_include('inc', 'fedora_repository', 'SecurityClass');
 
@@ -113,9 +144,15 @@ class PersonalCollectionClass {
     $content->appendChild($policyStream);
     return $this->createChildPolicyStream($dom, $rootElement, $policyStream->cloneNode(TRUE));
   }
-  
-  //right now this is the same as the policy stream for this object, may change
-  //objects in this collection will reference this datastream as their own POLICY stream
+
+  /**
+   * right now this is the same as the policy stream for this object, may change
+   * objects in this collection will reference this datastream as their own POLICY stream ???
+   * @param type $dom
+   * @param type $rootElement
+   * @param type $policyStream
+   * @return type 
+   */
   function createChildPolicyStream($dom, $rootElement, $policyStream) {
     $ds1 = $dom->createElement("foxml:datastream");
 
@@ -135,8 +172,14 @@ class PersonalCollectionClass {
     return TRUE;
   }
 
+  /**
+   * Create standard fedora stuff ??????????????????
+   * @param type $user
+   * @param type $dom
+   * @param type $rootElement 
+   */
   function createStandardFedoraStuff($user, & $dom, & $rootElement) {
-    /*foxml object properties section */
+    /* foxml object properties section */
     $objproperties = $dom->createElement("foxml:objectProperties");
     $prop1 = $dom->createElement("foxml:property");
     $prop1->setAttribute("NAME", "http://www.w3.org/1999/02/22-rdf-syntax-ns#type");
@@ -161,6 +204,13 @@ class PersonalCollectionClass {
     $rootElement->appendChild($objproperties);
   }
 
+  /**
+   * Create DC Stream ???
+   * @global type $user
+   * @param type $theUser
+   * @param type $dom
+   * @param type $rootElement 
+   */
   function createDCStream($theUser, & $dom, & $rootElement) {
     global $user;
     $datastream = $dom->createElement("foxml:datastream");
diff --git a/plugins/QtFormBuilder.php b/plugins/QtFormBuilder.php
index af66ed31..68c97644 100644
--- a/plugins/QtFormBuilder.php
+++ b/plugins/QtFormBuilder.php
@@ -1,76 +1,86 @@
 <?php
-module_load_include('inc', 'fedora_repository', 'plugins/FormBuilder');
-/*
- *
- *
- *
- * implements methods from content model ingest form xml
- * builds a dc metadata form
- */
- class QtFormBuilder extends FormBuilder{
- 	function QtFormBuilder(){
- 		module_load_include('php', 'Fedora_Repository', 'plugins/FormBuilder');
-                drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
 
- 	}
+// $Id$
 
-/*
- * method overrides method in FormBuilder.  We changed the dsid from OBJ to OBJ and added the TN datastream
+/**
+ * @file
+ * QTFormBuilder class
  */
-		function createFedoraDataStreams($form_values,&$dom, &$rootElement){
-                module_load_include('inc', 'fedora_repository', 'MimeClass');
-                global $base_url;
-                $mimetype = new MimeClass();
-		$server=null;
-		$file=$form_values['ingest-file-location'];
-		$dformat = $mimetype->getType($file);
-		//$fileUrl = 'http://'.$_SERVER['HTTP_HOST'].$file;
-                $fileUrl = $base_url.'/'.drupal_urlencode($file);
-		$beginIndex = strrpos($fileUrl,'/');
-		$dtitle = substr($fileUrl,$beginIndex+1);
-		$dtitle =  substr($dtitle, 0, strpos($dtitle, "."));
-		$ds1 = $dom->createElement("foxml:datastream");
-		$ds1->setAttribute("ID","OBJ");
-		$ds1->setAttribute("STATE","A");
-		$ds1->setAttribute("CONTROL_GROUP","M");
-		$ds1v= $dom->createElement("foxml:datastreamVersion");
-		$ds1v->setAttribute("ID","OBJ.0");
-		$ds1v->setAttribute("MIMETYPE","$dformat");
-		$ds1v->setAttribute("LABEL","$dtitle");
-		$ds1content = $dom->createElement('foxml:contentLocation');
-		$ds1content->setAttribute("REF","$fileUrl");
-		$ds1content->setAttribute("TYPE","URL");
-		$ds1->appendChild($ds1v);
-		$ds1v->appendChild($ds1content);
-		$rootElement->appendChild($ds1);
+module_load_include('inc', 'fedora_repository', 'plugins/FormBuilder');
 
-if(empty($_SESSION['fedora_ingest_files']) || !isset($_SESSION['fedora_ingest_files']['TN'])) { 
-		$createdFile = drupal_get_path('module', 'Fedora_Repository').'/images/qtThumb.jpg';
-		$fileUrl = $base_url.'/'.drupal_urlencode($createdFile);//'http://'.$_SERVER['HTTP_HOST'].'/'.$createdFile;
-		$ds1 = $dom->createElement("foxml:datastream");
-		$ds1->setAttribute("ID","TN");
-		$ds1->setAttribute("STATE","A");
-		$ds1->setAttribute("CONTROL_GROUP","M");
-		$ds1v= $dom->createElement("foxml:datastreamVersion");
-		$ds1v->setAttribute("ID","TN.0");
-		$ds1v->setAttribute("MIMETYPE","image/jpeg");
-		$ds1v->setAttribute("LABEL","Thumbnail");
-		$ds1content = $dom->createElement('foxml:contentLocation');
-		$ds1content->setAttribute("REF","$fileUrl");
-		$ds1content->setAttribute("TYPE","URL");
-		$ds1->appendChild($ds1v);
-		$ds1v->appendChild($ds1content);
-		$rootElement->appendChild($ds1);
-}
+/**
+ * Implements methods from content model ingest form xml
+ *  builds a dc metadata form
+ */
+class QtFormBuilder extends FormBuilder {
+
+  /**
+   * Constructor
+   */
+  function QtFormBuilder() {
+    module_load_include('php', 'Fedora_Repository', 'plugins/FormBuilder');
+    drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
+  }
 
-  if (!empty($_SESSION['fedora_ingest_files'])) {
+  /**
+   * method overrides method in FormBuilder.  We changed the dsid from OBJ to OBJ and added the TN datastream
+   * @global type $base_url
+   * @param type $form_values
+   * @param type $dom
+   * @param type $rootElement 
+   */
+  function createFedoraDataStreams($form_values, &$dom, &$rootElement) {
+    module_load_include('inc', 'fedora_repository', 'MimeClass');
+    global $base_url;
+    $mimetype = new MimeClass();
+    $server = null;
+    $file = $form_values['ingest-file-location'];
+    $dformat = $mimetype->getType($file);
+    //$fileUrl = 'http://'.$_SERVER['HTTP_HOST'].$file;
+    $fileUrl = $base_url . '/' . drupal_urlencode($file);
+    $beginIndex = strrpos($fileUrl, '/');
+    $dtitle = substr($fileUrl, $beginIndex + 1);
+    $dtitle = substr($dtitle, 0, strpos($dtitle, "."));
+    $ds1 = $dom->createElement("foxml:datastream");
+    $ds1->setAttribute("ID", "OBJ");
+    $ds1->setAttribute("STATE", "A");
+    $ds1->setAttribute("CONTROL_GROUP", "M");
+    $ds1v = $dom->createElement("foxml:datastreamVersion");
+    $ds1v->setAttribute("ID", "OBJ.0");
+    $ds1v->setAttribute("MIMETYPE", "$dformat");
+    $ds1v->setAttribute("LABEL", "$dtitle");
+    $ds1content = $dom->createElement('foxml:contentLocation');
+    $ds1content->setAttribute("REF", "$fileUrl");
+    $ds1content->setAttribute("TYPE", "URL");
+    $ds1->appendChild($ds1v);
+    $ds1v->appendChild($ds1content);
+    $rootElement->appendChild($ds1);
 
+    if (empty($_SESSION['fedora_ingest_files']) || !isset($_SESSION['fedora_ingest_files']['TN'])) {
+      $createdFile = drupal_get_path('module', 'Fedora_Repository') . '/images/qtThumb.jpg';
+      $fileUrl = $base_url . '/' . drupal_urlencode($createdFile); //'http://'.$_SERVER['HTTP_HOST'].'/'.$createdFile;
+      $ds1 = $dom->createElement("foxml:datastream");
+      $ds1->setAttribute("ID", "TN");
+      $ds1->setAttribute("STATE", "A");
+      $ds1->setAttribute("CONTROL_GROUP", "M");
+      $ds1v = $dom->createElement("foxml:datastreamVersion");
+      $ds1v->setAttribute("ID", "TN.0");
+      $ds1v->setAttribute("MIMETYPE", "image/jpeg");
+      $ds1v->setAttribute("LABEL", "Thumbnail");
+      $ds1content = $dom->createElement('foxml:contentLocation');
+      $ds1content->setAttribute("REF", "$fileUrl");
+      $ds1content->setAttribute("TYPE", "URL");
+      $ds1->appendChild($ds1v);
+      $ds1v->appendChild($ds1content);
+      $rootElement->appendChild($ds1);
+    }
 
+    if (!empty($_SESSION['fedora_ingest_files'])) {
 
       foreach ($_SESSION['fedora_ingest_files'] as $dsid => $createdFile) {
         $createdFile = strstr($createdFile, $file);
         $dformat = $mimetype->getType($createdFile);
-        $fileUrl = $base_url . '/'. drupal_urlencode($createdFile);
+        $fileUrl = $base_url . '/' . drupal_urlencode($createdFile);
         $beginIndex = strrpos($fileUrl, '/');
         $dtitle = substr($fileUrl, $beginIndex + 1);
         $dtitle = urldecode($dtitle);
@@ -79,7 +89,7 @@ if(empty($_SESSION['fedora_ingest_files']) || !isset($_SESSION['fedora_ingest_fi
         $ds1->setAttribute("ID", "$dsid");
         $ds1->setAttribute("STATE", "A");
         $ds1->setAttribute("CONTROL_GROUP", "M");
-        $ds1v= $dom->createElement("foxml:datastreamVersion");
+        $ds1v = $dom->createElement("foxml:datastreamVersion");
         $ds1v->setAttribute("ID", "$dsid.0");
         $ds1v->setAttribute("MIMETYPE", "$dformat");
         $ds1v->setAttribute("LABEL", "$dtitle");
@@ -91,12 +101,7 @@ if(empty($_SESSION['fedora_ingest_files']) || !isset($_SESSION['fedora_ingest_fi
         $rootElement->appendChild($ds1);
       }
     }
+  }
+}
 
-
-
-	}
-
-
-
- }
 ?>
diff --git a/plugins/Refworks.inc b/plugins/Refworks.inc
index f6e43f95..6fc809e8 100644
--- a/plugins/Refworks.inc
+++ b/plugins/Refworks.inc
@@ -1,6 +1,11 @@
 <?php
+
 // $Id$
 
+/**
+ * @file
+ * Refworks class
+ */
 /*
  * Created on 26-Feb-08
  *
@@ -9,21 +14,35 @@
  */
 module_load_include('inc', 'fedora_repository', 'SecurityClass');
 
+/**
+ * Refworks class ???
+ */
 class Refworks {
+
   private $romeoUrlString = "";
   private $referenceList;
   private $securityHelper;
   private $collectionPolicyStream;
   private $issn = '';
 
+  /**
+   * Constructor
+   */
   function Refworks() {
     $this->romeoUrlString = "http://www.sherpa.ac.uk/romeo/api24.php?issn=";
   }
 
-  function buildForm( &$form, $ingest_form_definition, &$form_values) {
+  /**
+   * Build Form ??
+   * @param type $form
+   * @param type $ingest_form_definition
+   * @param type $form_values
+   * @return type 
+   */
+  function buildForm(&$form, $ingest_form_definition, &$form_values) {
     $form['indicator2'] = array(
-        '#type' => 'fieldset',
-        '#title' => t('Ingest digital object step #2'),
+      '#type' => 'fieldset',
+      '#title' => t('Ingest digital object step #2'),
     );
     foreach ($ingest_form_definition->form_elements->element as $element) {
       $name = strip_tags($element->name->asXML());
@@ -39,11 +58,11 @@ class Refworks {
       $type = strip_tags($element->type->asXML());
 
       $form['indicator2']["$name"] = array(
-          '#title' => $title,
-          '#required' => $required,
-          '#description' => $description,
-          '#prefix' => $prefix,
-          '#type' => $type
+        '#title' => $title,
+        '#required' => $required,
+        '#description' => $description,
+        '#prefix' => $prefix,
+        '#type' => $type
       );
     }
 
@@ -68,21 +87,26 @@ class Refworks {
       //$xml=simplexml_load_string(trim(file_get_contents($file),NULL,TRUE));
       //$dom = dom_import_simplexml($xml);//test to see if it behaves better
       //$xml = new SimpleXMLElement(trim(file_get_contents($file)));
-    }
-    catch (Exception $e) {
+    } catch (Exception $e) {
       drupal_set_message(t('Error processing Refworks file: ') . $e->getMessage());
       return FALSE;
     }
     $this->referenceList = array();
     foreach ($xml->reference as $reference) {
-      array_push( $this->referenceList, $reference );
+      array_push($this->referenceList, $reference);
     }
 
     return $this->referenceList;
   }
-  
-  //create A DC stream with ID of DC
-  function createQDCStream( &$dom, &$rootElement, $reference ) {
+
+  /**
+   * Create a DC stream with ID of DC ???
+   * @param type $dom
+   * @param type $rootElement
+   * @param type $reference
+   * @return type 
+   */
+  function createQDCStream(&$dom, &$rootElement, $reference) {
     $datastream = $dom->createElement("foxml:datastream");
     $datastream->setAttribute("ID", "DC");
     $datastream->setAttribute("STATE", "A");
@@ -126,19 +150,19 @@ class Refworks {
       $oai->appendChild($element);
     }
     foreach ($reference->vo as $value) {
-      $source .= ' Volume: '. $value;
+      $source .= ' Volume: ' . $value;
     }
     foreach ($reference->is as $value) {
-      $source .= ' Issue: '. $value;
+      $source .= ' Issue: ' . $value;
     }
     foreach ($reference->sp as $value) {
-      $source .= ' Start Page: '. $value;
+      $source .= ' Start Page: ' . $value;
     }
     foreach ($reference->op as $value) {
-      $source .= ' Other Pages: '. $value;
+      $source .= ' Other Pages: ' . $value;
     }
     foreach ($reference->ul as $value) {
-      $source .= ' URL: '. $value;
+      $source .= ' URL: ' . $value;
     }
     foreach ($reference->k1 as $value) {
       $element = $dom->createElement('dc:subject', htmlspecialchars($value, ENT_NOQUOTES, 'UTF-8'));
@@ -174,17 +198,17 @@ class Refworks {
       $identifier .= ' ISSN/ISBN: ' . $value;
       //$this->romeoUrlString = $this->romeoUrlString . $value;
       if (!$this->issn == '') {
-        $this->issn=$value;
+        $this->issn = $value;
       }
       else {
-        $this->issn .= ','. $value;
+        $this->issn .= ',' . $value;
       }
     }
     foreach ($reference->ab as $value) {
-      $description = ' abstract: '. $value;
+      $description = ' abstract: ' . $value;
     }
     foreach ($reference->cr as $value) {
-      $description .= ' Cited reference: '. $value;
+      $description .= ' Cited reference: ' . $value;
     }
     $element = $dom->createElement('dc:description', htmlspecialchars($description, ENT_NOQUOTES, 'UTF-8'));
     $oai->appendChild($element);
@@ -196,7 +220,12 @@ class Refworks {
     return $datastream;
   }
 
-  function handleForm( &$form_values ) {
+  /**
+   * Handle Form ??
+   * @param type $form_values
+   * @return type 
+   */
+  function handleForm(&$form_values) {
     $errorMessage = NULL;
     module_load_include('inc', 'fedora_repository', 'CollectionClass');
     module_load_include('inc', 'fedora_repository', 'ContentModel');
@@ -204,10 +233,10 @@ class Refworks {
     $contentModelPid = ContentModel::getPidFromIdentifier($form_values['models']);
     $contentModelDsid = ContentModel::getDSIDFromIdentifier($form_values['models']);
     $collectionHelper = new CollectionClass();
-    $startTime=time();
+    $startTime = time();
     $collection_pid = $form_values['collection_pid'];
 
-    $this->parse_refworks_item( $form_values );
+    $this->parse_refworks_item($form_values);
 
     $this->securityHelper = new SecurityClass();
 
@@ -231,18 +260,18 @@ class Refworks {
       $rootElement->setAttribute('xmlns:xsi', "http://www.w3.org/2001/XMLSchema-instance");
       $rootElement->setAttribute('xsi:schemaLocation', "info:fedora/fedora-system:def/foxml# http://www.fedora.info/definitions/1/0/foxml1-1.xsd");
       $dom->appendChild($rootElement);
-      
+
       //create standard fedora stuff
       $qdc_element = $this->createQDCStream($dom, $rootElement, $reference);
       if (!$qdc_element) {
         drupal_set_message(t('Error creating DC for Refworks'), 'error');
         continue;
       }
-      $item_title='';
+      $item_title = '';
       foreach ($reference->t1 as $value) {
-        $item_title .= ' --- '. $value;
+        $item_title .= ' --- ' . $value;
       }
-      $this->createStandardFedoraStuff($form_values, $dom, $rootElement, $reference );
+      $this->createStandardFedoraStuff($form_values, $dom, $rootElement, $reference);
       $rootElement->appendChild($qdc_element);
       //create relationships
       $this->createRelationShips($form_values, $dom, $rootElement, $pid);
@@ -250,14 +279,14 @@ class Refworks {
 
       $this->createFedoraDataStreams($form_values, $dom, $rootElement, $reference);
 
-      if (!empty ( $this->collectionPolicyStream)) {
+      if (!empty($this->collectionPolicyStream)) {
         $this->create_security_policies($dom, $rootElement, $reference);
       }
 
       $params = array(
-          'objectXML' => $dom->saveXML(), 
-          'format' => 'info:fedora/fedora-system:FOXML-1.1',
-          'logMessage' => "Fedora Object Ingested",
+        'objectXML' => $dom->saveXML(),
+        'format' => 'info:fedora/fedora-system:FOXML-1.1',
+        'logMessage' => "Fedora Object Ingested",
       );
 
       try {
@@ -270,34 +299,36 @@ class Refworks {
           return;
         }
         $object = $client->__soapCall('ingest', array(
-            $params
-        ));
+              $params
+            ));
         watchdog(t("FEDORA_REPOSITORY"), t("Successfully added repository item !pid - !it", array('!pid' => $pid, '!it' => $item_title)), NULL, WATCHDOG_INFO);
         $deleteFiles = $form_values['delete_file']; //remove files from drupal file system
 
         if ($deleteFiles > 0) {
           unlink($form_values['fullpath']);
         }
-      }
-      catch (exception $e) {
+      } catch (exception $e) {
         $errors++;
         $errorMessage = 'yes';
         watchdog(t("FEDORA_REPOSITORY"), t("Error during ingest !it !e", array('!it' => $item_title, '!e' => $e)), NULL, WATCHDOG_ERROR);
-      }     
+      }
       $success++;
     }
     if (isset($errorMessage)) {
-      drupal_set_message(t('Error ingesting one or more records! Check Drupal watchdog logs for more info') , 'error');
+      drupal_set_message(t('Error ingesting one or more records! Check Drupal watchdog logs for more info'), 'error');
     }
     $endTime = time();
-    drupal_set_message(t('Successfull ingest of %success records.  %errors records failed.  Ingest took %seconds seconds',
-      array('%success' => $success-$errors, '%errors' => $errors, '%seconds' => $endTime-$startTime)) , 'info');
+    drupal_set_message(t('Successfull ingest of %success records.  %errors records failed.  Ingest took %seconds seconds', array('%success' => $success - $errors, '%errors' => $errors, '%seconds' => $endTime - $startTime)), 'info');
   }
 
   /**
    * Creates the RELS-EXT for the foxml
+   * @param type $form_values
+   * @param type $dom
+   * @param type $rootElement
+   * @param type $pid 
    */
-  function createRelationShips( $form_values, &$dom, &$rootElement, $pid = NULL ) {
+  function createRelationShips($form_values, &$dom, &$rootElement, $pid = NULL) {
     $drdf = $dom->createElement("foxml:datastream");
     $drdf->setAttribute("ID", "RELS-EXT");
     $drdf->setAttribute("CONTROL_GROUP", "X");
@@ -326,9 +357,13 @@ class Refworks {
     $rdfdesc->appendChild($member);
     $rdfdesc->appendChild($model);
     $rootElement->appendChild($drdf);
-
   }
 
+  /**
+   * Create Romeo Datastream
+   * @param type $dom
+   * @param type $rootElement 
+   */
   function createRomeoDataStream(&$dom, &$rootElement) {
     $ds1 = $dom->createElement("foxml:datastream");
     $ds1->setAttribute("ID", "ROMEO");
@@ -340,7 +375,7 @@ class Refworks {
     $ds1v->setAttribute("LABEL", "ROMEO");
     $ds1content = $dom->createElement('foxml:contentLocation');
     $url = $this->romeoUrlString . $this->issn;
-    $this->issn=''; //clear the issn's for next ingest in case we are doing batch
+    $this->issn = ''; //clear the issn's for next ingest in case we are doing batch
     $ds1content->setAttribute("REF", "$url");
     $ds1content->setAttribute("TYPE", "URL");
     $ds1->appendChild($ds1v);
@@ -348,6 +383,14 @@ class Refworks {
     $rootElement->appendChild($ds1);
   }
 
+  /**
+   * Create Fedora Datastream
+   * @global type $base_url
+   * @param type $form_values
+   * @param type $dom
+   * @param type $rootElement
+   * @param type $reference 
+   */
   function createFedoraDataStreams($form_values, &$dom, &$rootElement, $reference) {
     global $base_url;
     module_load_include('inc', 'fedora_repository', 'MimeClass');
@@ -374,6 +417,10 @@ class Refworks {
 
   /**
    * Creates the standard foxml properties
+   * @param type $form_values
+   * @param type $dom
+   * @param type $rootElement
+   * @param type $reference 
    */
   function createStandardFedoraStuff($form_values, &$dom, &$rootElement, $reference) {
     // Foxml object properties section
@@ -397,10 +444,9 @@ class Refworks {
     $rootElement->appendChild($objproperties);
   }
 
-
   /**
    * Read the list of Users from the U1 field and Roles from the U2 field and add elements
-   * to the security policy record for this item, then add the record as the security policy datastream.
+   *  to the security policy record for this item, then add the record as the security policy datastream.
    *
    * @param array $form_values
    * @param DOMDocument $dom
@@ -417,8 +463,8 @@ class Refworks {
     $ds1v->setAttribute("ID", "POLICY.0");
     $ds1v->setAttribute("MIMETYPE", "text/xml");
     $ds1v->setAttribute("LABEL", "POLICY Record");
-    $ds1content = $dom->createElement( "foxml:xmlContent" );
-    
+    $ds1content = $dom->createElement("foxml:xmlContent");
+
     $custom_policy = $this->collectionPolicyStream;
     $allowed_users_and_roles = array();
     $allowed_users_and_roles['users'] = array();
@@ -428,11 +474,11 @@ class Refworks {
         array_push($allowed_users_and_roles['users'], $name);
       }
     }
-    if (empty( $reference->u1)) {
+    if (empty($reference->u1)) {
       // If no "u1" value exists, add the currently logged-in user to the item's security policy.
       array_push($allowed_users_and_roles['users'], $user->name);
     }
-    
+
     foreach ($reference->u2 as $rolelist) {
       foreach (explode(';', strip_tags($rolelist->asXML())) as $role) {
         array_push($allowed_users_and_roles['roles'], $role);
@@ -444,6 +490,7 @@ class Refworks {
     $ds1v->appendChild($ds1content);
 
     $rootElement->appendChild($ds1);
-    $ds1content->appendChild($dom->importNode( dom_import_simplexml($custom_policy_sxe), TRUE));    
+    $ds1content->appendChild($dom->importNode(dom_import_simplexml($custom_policy_sxe), TRUE));
   }
+
 }
diff --git a/plugins/ShowDemoStreamsInFieldSets.inc b/plugins/ShowDemoStreamsInFieldSets.inc
index dd81410f..914c8bc5 100644
--- a/plugins/ShowDemoStreamsInFieldSets.inc
+++ b/plugins/ShowDemoStreamsInFieldSets.inc
@@ -1,18 +1,32 @@
 <?php
+
 // $Id$
 
-/*
- * Created on 17-Apr-08
- *
- *
+/**
+ * @file
+ * ShowDemoStreamsInFieldSets class
+ */
+
+/**
+ * Show Demo Streams in Field Sets ???
  */
 class ShowDemoStreamsInFieldSets {
   private $pid = NULL;
+  
+  /**
+   * Constructor
+   * @param type $pid 
+   */
   function ShowDemoStreamsInFieldSets($pid) {
   //drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
     $this->pid = $pid;
   }
 
+  /**
+   * Show Medium Size ??
+   * @global type $base_url
+   * @return type 
+   */
   function showMediumSize() {
     global $base_url;
     $collection_fieldset = array(
diff --git a/plugins/ShowStreamsInFieldSets.inc b/plugins/ShowStreamsInFieldSets.inc
index d0860ab2..77eada60 100644
--- a/plugins/ShowStreamsInFieldSets.inc
+++ b/plugins/ShowStreamsInFieldSets.inc
@@ -1,15 +1,31 @@
 <?php
+
 // $Id$
 
-/*
- * Created on 17-Apr-08
+/**
+ * @file
+ * ShowStreamsInFieldSets class
+ */
+
+/**
+ * Show Streams In Field Sets ??
  */
 class ShowStreamsInFieldSets {
+
   private $pid = NULL;
+
+  /**
+   * Constructor
+   * @param type $pid 
+   */
   function ShowStreamsInFieldSets($pid) {
     $this->pid = $pid;
   }
 
+  /**
+   * Show the FLV ??
+   * @return type 
+   */
   function showFlv() {
     //FLV is the datastream id
     $path = drupal_get_path('module', 'Fedora_Repository');
@@ -17,11 +33,11 @@ class ShowStreamsInFieldSets {
     $content = "";
     $pathTojs = drupal_get_path('module', 'Fedora_Repository') . '/js/swfobject.js';
     drupal_add_js("$pathTojs");
-    $content .= '<div id="player'. $this->pid . 'FLV"><a href="http://www.macromedia.com/go/getflashplayer">Get the Flash Player</a> to see this player.</div>';
-    drupal_add_js('var s1 = new SWFObject("'. $fullPath . '/flash/flvplayer.swf","single","320","240","7");
+    $content .= '<div id="player' . $this->pid . 'FLV"><a href="http://www.macromedia.com/go/getflashplayer">Get the Flash Player</a> to see this player.</div>';
+    drupal_add_js('var s1 = new SWFObject("' . $fullPath . '/flash/flvplayer.swf","single","320","240","7");
     s1.addParam("allowfullscreen","TRUE");
-    s1.addVariable("file","'. base_path() . 'fedora/repository/'. $this->pid . '/FLV/FLV.flv");
-    s1.write("player'. $this->pid . 'FLV");', 'inline', 'footer');
+    s1.addVariable("file","' . base_path() . 'fedora/repository/' . $this->pid . '/FLV/FLV.flv");
+    s1.write("player' . $this->pid . 'FLV");', 'inline', 'footer');
     $collection_fieldset = array(
       '#title' => t('Flash Video'),
       '#collapsible' => TRUE,
@@ -30,30 +46,42 @@ class ShowStreamsInFieldSets {
     return theme('fieldset', $collection_fieldset);
   }
 
+  /**
+   * Show the TN ??
+   * @global type $base_url
+   * @return type 
+   */
   function showTN() {
     global $base_url;
     $collection_fieldset = array(
       '#title' => '',
       '#attributes' => array(),
       '#collapsible' => FALSE,
-      '#value' => '<a href="'. $base_url . '/fedora/repository/'. $this->pid . '/OBJ/"><img src="'. $base_url . '/fedora/repository/'. $this->pid . '/TN/TN'.'" /></a>',
+      '#value' => '<a href="' . $base_url . '/fedora/repository/' . $this->pid . '/OBJ/"><img src="' . $base_url . '/fedora/repository/' . $this->pid . '/TN/TN' . '" /></a>',
     );
     return theme('fieldset', $collection_fieldset);
   }
 
-
-  // Same as showTN but artinventory stores the image in a dsid of IMAGE instead of OBJ
+  /**
+   * Same as showTN but artinventory stores the image in a dsid of IMAGE instead of OBJ
+   * @global type $base_url
+   * @return type 
+   */
   function showArtInventoryTN() {
     global $base_url;
     $collection_fieldset = array(
       '#collapsible' => FALSE,
-      '#value' => '<a href="'. $base_url . '/fedora/repository/'. $this->pid . '/IMAGE/image.jpg"><img src="'. $base_url . '/fedora/repository/'. $this->pid . '/TN/TN'. '" /></a>',
+      '#value' => '<a href="' . $base_url . '/fedora/repository/' . $this->pid . '/IMAGE/image.jpg"><img src="' . $base_url . '/fedora/repository/' . $this->pid . '/TN/TN' . '" /></a>',
     );
     return theme('fieldset', $collection_fieldset);
   }
 
   /**
    * Embed Google Docs' PDF viewer into the page.
+   * @global type $base_url
+   * @global type $base_path
+   * @global type $user
+   * @return type 
    */
   function showPDFPreview() {
     global $base_url;
@@ -74,21 +102,21 @@ class ShowStreamsInFieldSets {
     $objectHelper = new ObjectHelper();
     $item = new Fedora_Item($this->pid);
     if (key_exists('TN', $item->datastreams)) {
-      $tn_url = $base_url.'/fedora/repository/'.$item->pid.'/TN';
+      $tn_url = $base_url . '/fedora/repository/' . $item->pid . '/TN';
     }
     else {
-      $tn_url = $base_path.drupal_get_path('module', 'fedora_repository').'/images/Crystal_Clear_app_download_manager.png';
+      $tn_url = $base_path . drupal_get_path('module', 'fedora_repository') . '/images/Crystal_Clear_app_download_manager.png';
     }
     $dc_html = $objectHelper->getFormattedDC($item);
-    
-    $dl_link = l('<div  style="float:left; padding: 10px"><img src="'.$tn_url.'"><br />View Document</div>', 'fedora/repository/'.$this->pid.'/OBJ', array('html' => TRUE));
-    
+
+    $dl_link = l('<div  style="float:left; padding: 10px"><img src="' . $tn_url . '"><br />View Document</div>', 'fedora/repository/' . $this->pid . '/OBJ', array('html' => TRUE));
+
     $tabset['first_tab']['tabs']['view'] = array(
       '#type' => 'tabpage',
       '#title' => t('View'),
       '#content' => $dl_link . $dc_html,
     );
-    
+
     if (fedora_repository_access(OBJECTHELPER :: $EDIT_FEDORA_METADATA, $this->pid, $user)) {
       $editform = drupal_get_form('fedora_repository_edit_qdc_form', $this->pid, 'DC');
       $tabset['first_tab']['tabs']['edit'] = array(
@@ -97,23 +125,26 @@ class ShowStreamsInFieldSets {
         '#content' => $editform,
       );
     }
-    
+
     $tabset['second_tab'] = array(
       '#type' => 'tabpage',
       '#title' => t('Read Online'),
-      '#content' => "<iframe src=\"http://docs.google.com/viewer?url=". $base_url . '/fedora/repository/'. 
-        $this->pid . '/OBJ/preview.pdf'. "&embedded=TRUE\" style=\"width:600px; height:500px;\" frameborder=\"0\"></iframe>"
+      '#content' => "<iframe src=\"http://docs.google.com/viewer?url=" . $base_url . '/fedora/repository/' .
+      $this->pid . '/OBJ/preview.pdf' . "&embedded=TRUE\" style=\"width:600px; height:500px;\" frameborder=\"0\"></iframe>"
     );
 
     // Render the tabset.
     return $tabset;
   }
 
-
+  /**
+   * Show QDC ??
+   * @return type 
+   */
   function showQdc() {
     module_load_include('inc', 'fedora_repository', 'ObjectHelper');
     $objectHelper = new ObjectHelper();
-    $content=$objectHelper->getQDC($this->pid);
+    $content = $objectHelper->getQDC($this->pid);
     $collection_fieldset = array(
       '#title' => t('Description'),
       '#collapsible' => TRUE,
@@ -123,29 +154,35 @@ class ShowStreamsInFieldSets {
     return theme('fieldset', $collection_fieldset);
   }
 
+  /**
+   * Show Object Link ??
+   * @global type $base_url
+   * @return type 
+   */
   function showOBJLink() {
     global $base_url;
     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
     $item = new Fedora_Item($this->pid);
     $streams = $item->get_datastreams_list_as_array();
-    return "<a href='". $base_url ."/fedora/repository/". $this->pid ."/OBJ/". $streams['OBJ']['label'] ."'>". $streams['OBJ']['label'] ."</a>";
+    return "<a href='" . $base_url . "/fedora/repository/" . $this->pid . "/OBJ/" . $streams['OBJ']['label'] . "'>" . $streams['OBJ']['label'] . "</a>";
   }
 
-
-
+  /**
+   * Show REF works ??
+   * @return type 
+   */
   function showRefworks() {
-    $path=drupal_get_path('module', 'fedora_repository');
+    $path = drupal_get_path('module', 'fedora_repository');
     module_load_include('inc', 'fedora_repository', 'ObjectHelper');
     $collectionHelper = new CollectionClass();
-    $xmlstr=$collectionHelper->getStream($this->pid, "refworks");
+    $xmlstr = $collectionHelper->getStream($this->pid, "refworks");
     html_entity_decode($xmlstr);
     if ($xmlstr == NULL || strlen($xmlstr) < 5) {
       return " ";
     }
     try {
       $proc = new XsltProcessor();
-    }
-    catch (Exception $e) {
+    } catch (Exception $e) {
       drupal_set_message(t("!e", array('!e' => $e->getMessage())), 'error');
       return " ";
     }
@@ -165,9 +202,14 @@ class ShowStreamsInFieldSets {
     return theme('fieldset', $collection_fieldset);
   }
 
+  /**
+   * Show JP2000
+   * @param type $collapsed
+   * @return type 
+   */
   function showJP2($collapsed = FALSE) {
-    $viewer_url = variable_get('fedora_base_url', '') . '/get/'. $this->pid . '/ilives:viewerSdef/getViewer';
-    $html = '<iframe src="'. $viewer_url . '" frameborder="0" style="width: 100%; height: 400px;">Errors: unable to load viewer</iframe>';
+    $viewer_url = variable_get('fedora_base_url', '') . '/get/' . $this->pid . '/ilives:viewerSdef/getViewer';
+    $html = '<iframe src="' . $viewer_url . '" frameborder="0" style="width: 100%; height: 400px;">Errors: unable to load viewer</iframe>';
     $fieldset = array(
       '#title' => t('Viewer'),
       '#collapsible' => TRUE,
@@ -177,6 +219,11 @@ class ShowStreamsInFieldSets {
     return theme('fieldset', $fieldset);
   }
 
+  /**
+   * Show Romeo ??
+   * @param type $collapsed
+   * @return type 
+   */
   function showRomeo($collapsed = FALSE) {
     $path = drupal_get_path('module', 'Fedora_Repository');
     module_load_include('inc', 'fedora_repository', 'CollectionClass');
@@ -189,8 +236,7 @@ class ShowStreamsInFieldSets {
 
     try {
       $proc = new XsltProcessor();
-    }
-    catch (Exception $e) {
+    } catch (Exception $e) {
       drupal_set_message(t("!e", array('!e' => $e->getMessage())), 'error');
       return;
     }
@@ -210,4 +256,5 @@ class ShowStreamsInFieldSets {
     );
     return theme('fieldset', $collection_fieldset);
   }
+
 }
diff --git a/plugins/fedoraObject.inc b/plugins/fedoraObject.inc
index 3520614c..c5521242 100644
--- a/plugins/fedoraObject.inc
+++ b/plugins/fedoraObject.inc
@@ -1,7 +1,22 @@
 <?php
 
+// $Id$
+
+/**
+ * @file
+ * FedoraObject class
+ */
+
+/**
+ * Fedora Object class ??
+ */
 class FedoraObject {
-  function  __construct($pid = '') {
+
+  /**
+   * Constructor
+   * @param type $pid 
+   */
+  function __construct($pid = '') {
     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
     if (!empty($pid)) {
 
@@ -9,7 +24,12 @@ class FedoraObject {
       $this->item = new Fedora_Item($pid);
     }
   }
-  
+
+  /**
+   * Show Field Sets
+   * @global type $user
+   * @return type 
+   */
   public function showFieldSets() {
     global $user;
     $objectHelper = new ObjectHelper();
@@ -27,16 +47,16 @@ class FedoraObject {
       '#type' => 'tabset',
     );
     $dc_html = $objectHelper->getFormattedDC($this->item);
-    
+
     $ds_list = $objectHelper->get_formatted_datastream_list($this->pid, NULL, $this->item);
-    
+
 
     $tabset['fedora_object_details']['tabset']['view'] = array(
       '#type' => 'tabpage',
       '#title' => t('View'),
       '#content' => $dc_html . $ds_list . $purge_form,
     );
-    
+
     if (fedora_repository_access(OBJECTHELPER :: $EDIT_FEDORA_METADATA, $this->pid, $user)) {
       $editform = drupal_get_form('fedora_repository_edit_qdc_form', $this->pid, 'DC');
       $tabset['fedora_object_details']['tabset']['edit'] = array(
@@ -46,7 +66,8 @@ class FedoraObject {
         '#content' => $editform,
       );
     }
-    
+
     return $tabset;
   }
+
 }
\ No newline at end of file
diff --git a/plugins/herbarium.inc b/plugins/herbarium.inc
index 3af6f8bd..38d6b024 100644
--- a/plugins/herbarium.inc
+++ b/plugins/herbarium.inc
@@ -2,8 +2,17 @@
 
 // $Id$
 
+/**
+ * @file
+ * Herbarium class
+ */
+
+/**
+ * Herbarium ???
+ */
 class Herbarium {
-  function  __construct($pid = '') {
+
+  function __construct($pid = '') {
     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
     if (!empty($pid)) {
       $this->pid = $pid;
@@ -11,15 +20,26 @@ class Herbarium {
     }
   }
 
+  /**
+   * Build a drupal form ??
+   * @param type $form
+   * @param type $form_state
+   * @return type 
+   */
   public function buildDrupalForm($form = array(), $form_state = array()) {
     // We don't need to add anything beyond the standard Darwin Core form so just pass this through
     // If we wanted to we could add other fields.
     module_load_include('inc', 'fedora_repository', 'plugins/DarwinCore');
-    
+
     $dwc = new DarwinCore($this->item);
     return $dwc->buildDrupalForm($form);
   }
 
+  /**
+   * Build edit metadata form
+   * @param type $form
+   * @return type 
+   */
   public function buildEditMetadataForm($form = array()) {
     $form['submit'] = array(
       '#type' => 'submit',
@@ -34,10 +54,17 @@ class Herbarium {
       '#type' => 'hidden',
       '#value' => "DARWIN_CORE",
     );
-    
+
     return $this->buildDrupalForm($form);
   }
 
+  /**
+   * handle edit metadata form ??
+   * @global type $user
+   * @param type $form_id
+   * @param type $form_values
+   * @return type 
+   */
   public function handleEditMetadataForm($form_id, $form_values) {
     /*
      * Process the metadata form
@@ -51,11 +78,15 @@ class Herbarium {
     $dwc = new DarwinCore($this->item);
     $dwc->handleForm($form_values);
     $this->item->purge_datastream('DARWIN_CORE');
-    $this->item->add_datastream_from_string($dwc->darwinCoreXML, 'DARWIN_CORE',
-            'Darwin Core Metadata', 'text/xml', 'X');
+    $this->item->add_datastream_from_string($dwc->darwinCoreXML, 'DARWIN_CORE', 'Darwin Core Metadata', 'text/xml', 'X');
     return TRUE;
   }
 
+  /**
+   * Handle Ingest Form
+   * @global type $user
+   * @param type $form_values 
+   */
   public function handleIngestForm($form_values) {
     /*
      * process the metadata form
@@ -70,51 +101,52 @@ class Herbarium {
     $dwc = new DarwinCore();
     $dwc->handleForm($form_values);
     $label = $form_values['dwc:institutionCode'] . ':'
-            . $form_values['dwc:collectionCode'] . ':'
-            . $form_values['dwc:catalogNumber'];
+        . $form_values['dwc:collectionCode'] . ':'
+        . $form_values['dwc:catalogNumber'];
 
-    $new_item = Fedora_Item::ingest_new_item($form_values['pid'], 'A', $label,
-            $user->name);
+    $new_item = Fedora_Item::ingest_new_item($form_values['pid'], 'A', $label, $user->name);
 
-    $new_item->add_datastream_from_string($dwc->darwinCoreXML, 'DARWIN_CORE',
-            'Darwin Core Metadata', 'text/xml', 'X');
+    $new_item->add_datastream_from_string($dwc->darwinCoreXML, 'DARWIN_CORE', 'Darwin Core Metadata', 'text/xml', 'X');
     $file = $form_values['ingest-file-location'];
 
-    if (!empty( $file)) {
+    if (!empty($file)) {
       $dformat = $mimetype->getType($file);
-      $new_item->add_datastream_from_file($file, 'FULL_SIZE',
-              "$label-full-size", $dformat, 'M');
+      $new_item->add_datastream_from_file($file, 'FULL_SIZE', "$label-full-size", $dformat, 'M');
     }
 
     $new_item->add_relationship('hasModel', $form_values['content_model_pid'], FEDORA_MODEL_URI);
     $new_item->add_relationship(!empty($form_values['relationship']) ? $form_values['relationship'] : 'isMemberOfCollection', $form_values['collection_pid']);
-    
+
     if (!empty($_SESSION['fedora_ingest_files'])) {
       foreach ($_SESSION['fedora_ingest_files'] as $dsid => $created_file) {
         $created_file_format = $mimetype->getType($created_file);
         $created_filename = strstr($created_file, $file);
-        $new_item->add_datastream_from_file($created_file, $dsid,
-                $created_filename, $created_file_format, 'M');
-        
+        $new_item->add_datastream_from_file($created_file, $dsid, $created_filename, $created_file_format, 'M');
       }
     }
   }
 
+  /**
+   * Show Field Sets
+   * @global type $base_url
+   * @global type $user
+   * @return string 
+   */
   public function showFieldSets() {
     module_load_include('inc', 'fedora_repository', 'plugins/tagging_form');
     module_load_include('inc', 'fedora_repository', 'plugins/DarwinCore');
     global $base_url;
 
     $tabset = array();
-    
+
     global $user;
     $qs = '';
     if ($user->uid != 0) {
-      $qs = '?uid='. base64_encode($user->name . ':'. $user->pass);
+      $qs = '?uid=' . base64_encode($user->name . ':' . $user->pass);
     }
 
-    $viewer_url = variable_get('fedora_base_url', '') . '/get/'. $this->pid . '/ilives:viewerSdef/getViewer'. $qs;
-    $html = '<iframe src="'. $viewer_url . '"  scrolling="no" frameborder="0" style="width: 100%; height: 800px;">Errors: unable to load viewer</iframe>';
+    $viewer_url = variable_get('fedora_base_url', '') . '/get/' . $this->pid . '/ilives:viewerSdef/getViewer' . $qs;
+    $html = '<iframe src="' . $viewer_url . '"  scrolling="no" frameborder="0" style="width: 100%; height: 800px;">Errors: unable to load viewer</iframe>';
     $tabset['second_tab'] = array(
 //     $collection_fieldset = array (
       '#type' => 'tabpage',
@@ -126,8 +158,8 @@ class Herbarium {
       '#type' => 'tabpage',
       '#title' => t('View'),
       // This will be the content of the tab.
-      '#content' => '<a href="'. $base_url . '/fedora/repository/'. $this->pid . '/FULL_JPG/"><img src="'. $base_url . '/fedora/imageapi/'.
-        $this->pid . '/JPG/JPG.jpg'. '" /></a>'. '<p>'. drupal_get_form('fedora_repository_image_tagging_form', $this->pid) . '</p>',
+      '#content' => '<a href="' . $base_url . '/fedora/repository/' . $this->pid . '/FULL_JPG/"><img src="' . $base_url . '/fedora/imageapi/' .
+      $this->pid . '/JPG/JPG.jpg' . '" /></a>' . '<p>' . drupal_get_form('fedora_repository_image_tagging_form', $this->pid) . '</p>',
     );
 
     $dwc = new DarwinCore($this->item);
@@ -138,7 +170,7 @@ class Herbarium {
     $tabset['third_tab']['tabset'] = array(
       '#type' => 'tabset',
     );
-    
+
     $tabset['third_tab']['tabset']['view'] = array(
       '#type' => 'tabpage',
       '#title' => t('Darwin Core'),
@@ -168,4 +200,5 @@ class Herbarium {
     }
     return $tabset;
   }
+
 }
diff --git a/plugins/map_viewer.inc b/plugins/map_viewer.inc
index 0a1bda62..3e9bcfb6 100644
--- a/plugins/map_viewer.inc
+++ b/plugins/map_viewer.inc
@@ -1,13 +1,33 @@
 <?php
+
 // $Id$
 
+/**
+ * @file
+ * ShowMapStreamsInFieldSets class
+ */
+
+/**
+ * Show Map Streams in Field Sets Class ??
+ */
 class ShowMapStreamsInFieldSets {
-  private $pid =NULL;
 
+  private $pid = NULL;
+
+  /**
+   * Constructor
+   * @param type $pid 
+   */
   function ShowMapStreamsInFieldSets($pid) {
     $this->pid = $pid;
   }
 
+  /**
+   * Show JPEG
+   * @global type $base_url
+   * @global type $user
+   * @return type 
+   */
   function showJPG() {
     module_load_include('inc', 'fedora_repository', 'plugins/tagging_form');
     module_load_include('inc', 'fedora_repository', 'plugins/ShowStreamsInFieldSets');
@@ -27,8 +47,8 @@ class ShowMapStreamsInFieldSets {
       $qs = '?uid=' . base64_encode($user->name . ':' . $user->pass);
     }
 
-    $viewer_url = variable_get('fedora_base_url', '') . '/get/'. $this->pid . '/ilives:viewerSdef/getViewer'. $qs;
-    $html = '<iframe src="'. $viewer_url . '"  scrolling="no" frameborder="0" style="width: 100%; height: 800px;">Errors: unable to load viewer</iframe>';
+    $viewer_url = variable_get('fedora_base_url', '') . '/get/' . $this->pid . '/ilives:viewerSdef/getViewer' . $qs;
+    $html = '<iframe src="' . $viewer_url . '"  scrolling="no" frameborder="0" style="width: 100%; height: 800px;">Errors: unable to load viewer</iframe>';
 
     drupal_add_css(path_to_theme() . '/header-viewer.css', 'theme');
     drupal_add_css(drupal_get_path('module', 'fedora_repository') . '/js/iiv/css/jquery-ui/smoothness/jquery-ui-1.7.2.custom.css');
@@ -46,9 +66,10 @@ class ShowMapStreamsInFieldSets {
       '#type' => 'tabpage',
       '#title' => t('Description'),
       '#content' => $item->get_dissemination('islandora:mods2htmlSdef', 'mods2html')
-        . $objectHelper->get_formatted_datastream_list($this->pid, NULL, $item),
+      . $objectHelper->get_formatted_datastream_list($this->pid, NULL, $item),
     );
     // Render the tabset.
     return tabs_render($tabset);
   }
+
 }
diff --git a/plugins/qt_viewer.inc b/plugins/qt_viewer.inc
index 996b12b6..a61a6033 100644
--- a/plugins/qt_viewer.inc
+++ b/plugins/qt_viewer.inc
@@ -1,60 +1,96 @@
 <?php
+
 // $Id$
 
+/**
+ * @file
+ * ShowQTStreamsInFieldSets class
+ */
+
+/**
+ * Show QT Stream in Field Sets
+ */
 class ShowQtStreamsInFieldSets {
-  private $pid =NULL;
 
+  private $pid = NULL;
+
+  /**
+   * Constructor
+   * @param type $pid 
+   */
   function ShowQtStreamsInFieldSets($pid) {
     $this->pid = $pid;
   }
 
+  /**
+   * Returna a new Fedora Object with the QT movie ???
+   * @return fedora_item 
+   */
   function fedoraObject() {
     return new fedora_item($this->pid);
   }
 
+  /**
+   * Tecnical metadata ??
+   * @param type $defaults
+   * @param type $dsid
+   * @return type 
+   */
   function technicalMetadata($defaults = array(), $dsid = 'OBJ_EXIFTOOL') {
     $data = $defaults;
 
     try {
-    $src = ObjectHelper::getStream($this->pid, $dsid);
-
-    $doc = new SimpleXMLElement($src);
-    $doc->registerXPathNamespace('File', 'http://ns.exiftool.ca/File/1.0/');
-    $doc->registerXPathNamespace('Composite', 'http://ns.exiftool.ca/Composite/1.0/');
-    $mime = reset($doc->xpath('//File:MIMEType'));
-    $data['mime'] = $mime;
-    if(strpos($mime, 'audio/') !== false) {
-      $data['width'] = 300;
-      $data['height'] = 0;
-    } else {
-      $size = reset($doc->xpath('//Composite:ImageSize/text()'));
-      list($width, $height) = explode('x', $size);
-      $data['width'] = $width;
-      $data['height'] = $height;
-    }
+      $src = ObjectHelper::getStream($this->pid, $dsid);
+
+      $doc = new SimpleXMLElement($src);
+      $doc->registerXPathNamespace('File', 'http://ns.exiftool.ca/File/1.0/');
+      $doc->registerXPathNamespace('Composite', 'http://ns.exiftool.ca/Composite/1.0/');
+      $mime = reset($doc->xpath('//File:MIMEType'));
+      $data['mime'] = $mime;
+      if (strpos($mime, 'audio/') !== false) {
+        $data['width'] = 300;
+        $data['height'] = 0;
+      }
+      else {
+        $size = reset($doc->xpath('//Composite:ImageSize/text()'));
+        list($width, $height) = explode('x', $size);
+        $data['width'] = $width;
+        $data['height'] = $height;
+      }
 
-    $data['doc'] = $src;
-    } catch(Exception $e) {
-    $data = $defaults;
+      $data['doc'] = $src;
+    } catch (Exception $e) {
+      $data = $defaults;
     }
 
     return $data;
   }
 
+  /**
+   * Get Poster Frame Datastream Information ??
+   * @param type $dsid
+   * @return type 
+   */
   function getPosterFrameDatastreamInfo($dsid = 'FULL_SIZE') {
     $p = ObjectHelper::getDatastreamInfo($this->pid, $dsid);
-    if(empty($p) || $p == ' ' || $p === false) {
+    if (empty($p) || $p == ' ' || $p === false) {
       return false;
     }
     return $p;
   }
 
+  /**
+   * Get Media Datastream Information ??
+   * @param type $dsid
+   * @param type $alt
+   * @return type 
+   */
   function getMediaDatastreamInfo($dsid = 'OBJ', $alt = array('')) {
     $p = ObjectHelper::getDatastreamInfo($this->pid, $dsid);
-    if(empty($p) || $p == ' ' || $p === false) {
-      if(!empty($alt)) {
-       $ds = array_shift($alt);
-       return $this->getMediaDatastreamInfo($ds, $alt);
+    if (empty($p) || $p == ' ' || $p === false) {
+      if (!empty($alt)) {
+        $ds = array_shift($alt);
+        return $this->getMediaDatastreamInfo($ds, $alt);
       }
       return false;
     }
@@ -62,10 +98,19 @@ class ShowQtStreamsInFieldSets {
     return $p;
   }
 
+  /**
+   * Is download enabled. It always returns false. ??? 
+   * @return FALSE 
+   */
   function enableDownload() {
     return false;
   }
 
+  /**
+   * Show the QT ???
+   * @global type $base_url
+   * @return type 
+   */
   function showQt() {
     module_load_include('inc', 'fedora_repository', 'plugins/tagging_form');
     module_load_include('inc', 'fedora_repository', 'plugins/ShowStreamsInFieldSets');
@@ -77,32 +122,32 @@ class ShowQtStreamsInFieldSets {
 
     $pframe = $this->getPosterFrameDatastreamInfo();
     $media = $this->getMediaDatastreamInfo('PROXY', array('OBJ'));
-    if($media === false ) {
+    if ($media === false) {
       return '';
     }
     global $base_url;
     $path = drupal_get_path('module', 'Fedora_Repository');
-    $fullPath=base_path().$path;
-    $content= '';
-    $pathTojs = drupal_get_path('module', 'Fedora_Repository').'/js/AC_Quicktime.js';
+    $fullPath = base_path() . $path;
+    $content = '';
+    $pathTojs = drupal_get_path('module', 'Fedora_Repository') . '/js/AC_Quicktime.js';
     drupal_add_js($pathTojs);
 
-    $divid = 'player'.md5($this->pid).'MOV';
-    $content .= '<div  class="player"  id="' . $divid .'">';
-    if($pframe !== false) {
-      $content .= '<div class="poster" style="cursor: pointer; position: relative; width: ' . $width .'px; min-height: ' . ($height) . 'px;">';
-      $content .= '<img src="' . base_path().'fedora/repository/'.$this->pid.'/'. $pframe->ID . '/poster.jpg' . '" />';
+    $divid = 'player' . md5($this->pid) . 'MOV';
+    $content .= '<div  class="player"  id="' . $divid . '">';
+    if ($pframe !== false) {
+      $content .= '<div class="poster" style="cursor: pointer; position: relative; width: ' . $width . 'px; min-height: ' . ($height) . 'px;">';
+      $content .= '<img src="' . base_path() . 'fedora/repository/' . $this->pid . '/' . $pframe->ID . '/poster.jpg' . '" />';
       $content .= '<div class="play" style="font-size: 128px; color: white; position: absolute; top: 50%; left: 50%; margin-top: -0.085em; margin-left: -0.33em; opacity: 0.9; ">▶</div>';
       $content .= '</div>';
     }
     $content .= '</div>';
-    if($this->enableDownload()) {
-    $url = base_path().'fedora/repository/'.$this->pid.'/OBJ/MOV.mov';
+    if ($this->enableDownload()) {
+      $url = base_path() . 'fedora/repository/' . $this->pid . '/OBJ/MOV.mov';
       $content .= '<a class="download" href="' . $url . '">Download Media File</a>';
     }
-    $src = base_path().'fedora/repository/'.$this->pid.'/' . $media->ID. '/MOV.mov';
-$qtparams = '';
-  $qtparams .= "'autostart', '" . ($pframe !== false ? 'true' : 'false') . "', ";
+    $src = base_path() . 'fedora/repository/' . $this->pid . '/' . $media->ID . '/MOV.mov';
+    $qtparams = '';
+    $qtparams .= "'autostart', '" . ($pframe !== false ? 'true' : 'false') . "', ";
     $init = <<<EOD
      $(function() { 
        src = "$src";
@@ -126,13 +171,14 @@ $qtparams = '';
     });
 EOD;
 
-     drupal_add_js($init, 'inline', 'footer');
+    drupal_add_js($init, 'inline', 'footer');
+
+    $collection_fieldset = array(
+      '#title' => t('Quicktime'),
+      '#collapsible' => TRUE,
+      '#collapsed' => FALSE,
+      '#value' => $content);
+    return theme('fieldset', $collection_fieldset);
+  }
 
-     $collection_fieldset = array(
-       	 '#title' => t('Quicktime'),
-       	 '#collapsible' => TRUE,
-       	 '#collapsed' => FALSE,
-       	 '#value' => $content);
-     return theme('fieldset',$collection_fieldset);
-   }
 }
diff --git a/plugins/slide_viewer.inc b/plugins/slide_viewer.inc
index 30d2eb01..1d23b227 100644
--- a/plugins/slide_viewer.inc
+++ b/plugins/slide_viewer.inc
@@ -1,15 +1,34 @@
 <?php
+
 // $Id$
 
+/**
+ * @file
+ * ShowSlideStreamsInFieldSets class
+ */
+
+/**
+ * ShowSlideStreamInFieldSets ??????
+ */
 class ShowSlideStreamsInFieldSets {
 
   private $pid = NULL;
 
+  /**
+   * Contructor 
+   * @param type $pid 
+   */
   function ShowSlideStreamsInFieldSets($pid) {
     //drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
     $this->pid = $pid;
   }
-  
+
+  /**
+   * Show JPEG
+   * @global type $base_url
+   * @global type $user
+   * @return type 
+   */
   function showJPG() {
     module_load_include('inc', 'fedora_repository', 'plugins/tagging_form');
     module_load_include('inc', 'fedora_repository', 'plugins/ShowStreamsInFieldSets');
@@ -17,14 +36,14 @@ class ShowSlideStreamsInFieldSets {
     global $user;
 
     $tabset = array();
-    
+
     $qs = '';
     if ($user->uid != 0) {
       $qs = '?uid=' . base64_encode($user->name . ':' . $user->pass);
     }
 
-    $viewer_url = variable_get('fedora_base_url', 'http://localhost:8080/fedora') . '/get/'. $this->pid . '/ilives:viewerSdef/getViewer'. $qs;
-    $html = '<iframe src="'. $viewer_url . '" scrolling="no" frameborder="0" style="width: 100%; height: 800px;">Errors: unable to load viewer</iframe>';
+    $viewer_url = variable_get('fedora_base_url', 'http://localhost:8080/fedora') . '/get/' . $this->pid . '/ilives:viewerSdef/getViewer' . $qs;
+    $html = '<iframe src="' . $viewer_url . '" scrolling="no" frameborder="0" style="width: 100%; height: 800px;">Errors: unable to load viewer</iframe>';
 
     drupal_add_css(path_to_theme() . '/header-viewer.css', 'theme');
 
@@ -38,10 +57,11 @@ class ShowSlideStreamsInFieldSets {
       '#type' => 'tabpage',
       '#title' => t('View'),
       // This will be the content of the tab.
-      '#content' => '<img src="'. $base_url .
-        '/fedora/imageapi/'. $this->pid . '/JPG/JPG.jpg'. '" />'. '<p>'. drupal_get_form('fedora_repository_image_tagging_form', $this->pid) . '</p>',
+      '#content' => '<img src="' . $base_url .
+      '/fedora/imageapi/' . $this->pid . '/JPG/JPG.jpg' . '" />' . '<p>' . drupal_get_form('fedora_repository_image_tagging_form', $this->pid) . '</p>',
     );
-    
+
     return $tabset;
   }
+
 }
diff --git a/plugins/tagging_form.inc b/plugins/tagging_form.inc
index 2b374b3c..acc826fd 100644
--- a/plugins/tagging_form.inc
+++ b/plugins/tagging_form.inc
@@ -1,11 +1,21 @@
 <?php
+
 // $Id$
 
-/* 
+/**
+ * @file
+ * Tagging Form???
+ */
+/*
  * To change this template, choose Tools | Templates
  * and open the template in the editor.
  */
 
+/**
+ * Show subject tags ???
+ * @param type $pid
+ * @return string 
+ */
 function _show_subject_tags($pid) {
   module_load_include('inc', 'fedora_repository', 'api/fedora_item');
   module_load_include('inc', 'fedora_repository', 'api/dublin_core');
@@ -15,13 +25,20 @@ function _show_subject_tags($pid) {
   if (!empty($tags->tags)) {
     $output = "<ul>";
     foreach ($tags->tags as $tag) {
-      $output .= "<li title=". $tag['creator'] . '>'. $tag['name'] . '</li> ';
+      $output .= "<li title=" . $tag['creator'] . '>' . $tag['name'] . '</li> ';
     }
     $output .= "</ul>";
   }
   return $output;
 }
 
+/**
+ * Fedora repository image tagging form ????
+ * @global type $base_url
+ * @param type $form_state
+ * @param type $pid
+ * @return type 
+ */
 function fedora_repository_image_tagging_form($form_state, $pid) {
   module_load_include('inc', 'fedora_repository', 'api/fedora_item');
   module_load_include('inc', 'fedora_repository', 'api/dublin_core');
@@ -29,7 +46,7 @@ function fedora_repository_image_tagging_form($form_state, $pid) {
   global $base_url;
 
   if (!empty($form_state['post']['pid'])) {
-      $pid = $form_state['post']['pid'];
+    $pid = $form_state['post']['pid'];
   }
   $obj = new Fedora_Item($pid);
   $form['tags-wrapper'] = array(
@@ -49,8 +66,8 @@ function fedora_repository_image_tagging_form($form_state, $pid) {
       '#prefix' => '<li>',
       '#suffix' => '</li>',
     );
-      $form['tags-wrapper']['tags'][$tag['name']]['tag'] = array(
-      '#prefix' => '<a title="Added by '. $tag['creator'] . '" href="'. $base_url . '/fedora/repository/mnpl_advanced_search/tag:'. $tag['name'] . '">',
+    $form['tags-wrapper']['tags'][$tag['name']]['tag'] = array(
+      '#prefix' => '<a title="Added by ' . $tag['creator'] . '" href="' . $base_url . '/fedora/repository/mnpl_advanced_search/tag:' . $tag['name'] . '">',
       '#value' => $tag['name'],
       '#suffix' => '</a>',
     );
@@ -58,7 +75,7 @@ function fedora_repository_image_tagging_form($form_state, $pid) {
       // Delete button for each existing tag.
       $form['tags-wrapper']['tags'][$tag['name']]['delete'] = array(
         '#type' => 'imagebutton',
-        '#image' => $base_url . '/'. drupal_get_path('module', 'fedora_repository') . '/images/remove_icon.png',
+        '#image' => $base_url . '/' . drupal_get_path('module', 'fedora_repository') . '/images/remove_icon.png',
         '#default_value' => $tag['name'],
         '#title' => t('Delete this tag'),
       );
@@ -84,10 +101,15 @@ function fedora_repository_image_tagging_form($form_state, $pid) {
   if (empty($form_state['pid'])) {
     $form_state['pid'] = $pid;
   }
-  
+
   return $form;
 }
 
+/**
+ * Hook image button process ???
+ * @param type $form
+ * @return string 
+ */
 function hook_imagebutton_process($form) {
   $form['op_x'] = array(
     '#name' => $form['#name'] . '_x',
@@ -98,6 +120,12 @@ function hook_imagebutton_process($form) {
   return $form;
 }
 
+/**
+ * Fedora repository image tagging from submit ???
+ * @global type $user
+ * @param type $form
+ * @param type $form_state 
+ */
 function fedora_repository_image_tagging_form_submit($form, &$form_state) {
   module_load_include('inc', 'fedora_repository', 'api/fedora_item');
   module_load_include('inc', 'fedora_repository', 'api/tagging');
@@ -110,7 +138,7 @@ function fedora_repository_image_tagging_form_submit($form, &$form_state) {
     array_push($tagset->tags, array('name' => $form_state['values']['addtag'], 'creator' => $user->name));
   }
   elseif (!empty($form_state['values']['delete'])) {
-    for ( $i=0; $i < count($tagset->tags); $i++ ) {
+    for ($i = 0; $i < count($tagset->tags); $i++) {
       if ($tagset->tags[$i]['name'] == $form_state['clicked_button']['#value']) {
         unset($tagset->tags[$i]);
       }