diff --git a/admin/islandora.admin.inc b/admin/islandora.admin.inc
index d82b8ef7..49de312c 100644
--- a/admin/islandora.admin.inc
+++ b/admin/islandora.admin.inc
@@ -1,11 +1,14 @@
 <?php
 
 /**
- * @file islandora.admin.inc
- * Create admin form
- * @return array 
+ * @file
+ * islandora.admin.inc: This file contains the general islandora admin form and callback functions.
  */
 
+/**
+ * Create admin form
+ * @return array
+ */
 function islandora_repository_admin($form, &$form_state) {
   module_load_include('inc', 'islandora', 'includes/tuque');
   module_load_include('inc', 'islandora', 'includes/utilities');
@@ -17,7 +20,7 @@ function islandora_repository_admin($form, &$form_state) {
 
   $form = array();
 
-  if(isset($form_state['values']['islandora_base_url'])) {
+  if (isset($form_state['values']['islandora_base_url'])) {
     $url = $form_state['values']['islandora_base_url'];
   }
   else {
@@ -33,7 +36,7 @@ function islandora_repository_admin($form, &$form_state) {
     $info = FALSE;
   }
 
-  if($info) {
+  if ($info) {
     try {
       $dc = $connection->api->m->getDatastream('fedora-system:ContentModel-3.0', 'DC');
     }
@@ -41,9 +44,9 @@ function islandora_repository_admin($form, &$form_state) {
       $dc = FALSE;
     }
   }
-  
-  if($info) {
-    if($dc) {
+
+  if ($info) {
+    if ($dc) {
       $confirmation_message = '<img src="' . url('misc/watchdog-ok.png') . '"/>'
         . t('Successfully connected to Fedora Server (Version !version).', array('!version' => $info['repositoryVersion']));
     }
@@ -77,7 +80,7 @@ function islandora_repository_admin($form, &$form_state) {
     '#type' => 'textfield',
     '#title' => t('Fedora base URL'),
     '#default_value' => variable_get('islandora_base_url', 'http://localhost:8080/fedora'),
-    '#description' => t('The URL to use for REST connections <br>' . $confirmation_message),
+    '#description' => t('The URL to use for REST connections <br />' . $confirmation_message),
     '#required' => TRUE,
     '#ajax' => array(
       'callback' => 'islandora_update_url_div',
@@ -121,20 +124,20 @@ function islandora_repository_admin($form, &$form_state) {
       'progress' => array('type' => 'throbber'),
     ),
   );
-  
-  if(isset($form_state['values']['islandora_namespace_restriction_enforced'])) {
+
+  if (isset($form_state['values']['islandora_namespace_restriction_enforced'])) {
     $namespaces = $form_state['values']['islandora_namespace_restriction_enforced'];
   }
   else {
     $namespaces = variable_get('islandora_namespace_restriction_enforced', FALSE);
   }
 
-  if($namespaces) {
+  if ($namespaces) {
     $form['islandora_tabs']['islandora_namespace']['wrapper']['islandora_pids_allowed'] = array(
       '#type' => 'textfield',
       '#title' => t('PID namespaces allowed in this Drupal install'),
       '#default_value' => variable_get('islandora_pids_allowed', 'default: demo: changeme: ilives: islandora-book: books: newspapers: '),
-      '#description' => t('A space separated list of PID namespaces that users are permitted to access from this Drupal installation. <br /> This could be more than a simple namespace ie demo:mydemos. <br> islandora: is reserved and is always allowed.'),
+      '#description' => t('A space separated list of PID namespaces that users are permitted to access from this Drupal installation. <br /> This could be more than a simple namespace ie demo:mydemos. <br /> islandora: is reserved and is always allowed.'),
       '#weight' => 0,
     );
   }
@@ -158,6 +161,6 @@ function islandora_update_url_div($form, $form_state) {
 function islandora_update_namespace_div($form, $form_state) {
   unset($form_state['submit_handlers']);
   $form_state['rebuild'] = TRUE;
-  
+
   return $form['islandora_tabs']['islandora_namespace']['wrapper'];
 }
\ No newline at end of file
diff --git a/includes/breadcrumb.inc b/includes/breadcrumb.inc
index 3c725b7a..d1cacdbe 100644
--- a/includes/breadcrumb.inc
+++ b/includes/breadcrumb.inc
@@ -1,11 +1,16 @@
 <?php
 
+/**
+ * @file
+ * This file contains functions to create breadcrumbs on Islandora object pages.
+ */
+
 function islandora_get_breadcrumbs($object) {
   $breadcrumbs = array();
 
   islandora_get_breadcrumbs_recursive($object->id, $breadcrumbs, $object->repository);
-  
-  if(isset($breadcrumbs[0])) {
+
+  if (isset($breadcrumbs[0])) {
     unset($breadcrumbs[0]);
   }
 
@@ -69,8 +74,8 @@ function islandora_get_breadcrumbs_recursive($pid, &$breadcrumbs, $repository) {
       islandora_get_breadcrumbs_recursive($parent, $breadcrumbs, $repository);
     }
     else {
-      $breadcrumbs[] = '...'; //Add an non-link, as we don't know how to get back to the root.
-      islandora_get_breadcrumbs_recursive($root, $breadcrumbs, $repository); //And render the last two links and break (on the next pass).
+      $breadcrumbs[] = '...'; // Add an non-link, as we don't know how to get back to the root.
+      islandora_get_breadcrumbs_recursive($root, $breadcrumbs, $repository); // And render the last two links and break (on the next pass).
     }
   }
 }
\ No newline at end of file
diff --git a/includes/datastream.inc b/includes/datastream.inc
index 6a2e8724..fea8747c 100644
--- a/includes/datastream.inc
+++ b/includes/datastream.inc
@@ -1,26 +1,28 @@
 <?php
 
 /**
- * @file datastream.inc 
+ * @file
+ * This file contains the admin form and callback functions for datastream manipulations.
  */
 
 define('DS_COMP_STREAM', 'DS-COMPOSITE-MODEL');
 /**
+ * Callback function to view or download a datastream.
  *
  * @global object $user
  * @param string $object_id
  * @param string $dsid
- * @return stream 
+ * @return stream
  *  prints datastream to browser
  */
 function islandora_view_datastream($object, $dsid, $method = 'view') {
   // if the object exists but the datastream doesn't
-  if(!isset($object[$dsid])) {
+  if (!isset($object[$dsid])) {
     return drupal_not_found();
   }
 
   header('Content-type: ' . $object[$dsid]->mimetype);
-  if($object[$dsid]->controlGroup == 'M' || $object[$dsid]->controlGroup == 'X') {
+  if ($object[$dsid]->controlGroup == 'M' || $object[$dsid]->controlGroup == 'X') {
     header('Content-length: ' . $object[$dsid]->size);
   }
 
@@ -45,7 +47,7 @@ function islandora_datastream_get_parents($islandora_object) {
   }
   $collections = array_merge($collections1, $collections2);
 
-  foreach($collections as $collection) {
+  foreach ($collections as $collection) {
     try {
       $pid = $collection['object']['value'];
       $object = $repository->getObject($collection['object']['value']);
@@ -55,7 +57,9 @@ function islandora_datastream_get_parents($islandora_object) {
       $parent_collections[$pid]['label'] = $object->label;
       $parent_collections[$pid]['label_link'] = l($parent_collections[$pid]['label'], $parent_collections[$pid]['url']);
     }
-    catch (RepositoryException $e) {}
+    catch (RepositoryException $e) {
+
+    }
   }
 
   return $parent_collections;
@@ -65,13 +69,13 @@ function islandora_datastream_get_parents($islandora_object) {
  *
  * @param array $arr
  *   an array of dsids that are defined by this objects cmodels
- * @param string $ds_comp_stream 
+ * @param string $ds_comp_stream
  *   the dscomposite stream as xml
  */
 function islandora_get_defined_dsids_array(&$arr, $ds_comp_stream) {
   $sxml = new SimpleXMLElement($ds_comp_stream);
   foreach ($sxml->dsTypeModel as $ds) {
-    //$arr[$ds['ID']] 
+    //$arr[$ds['ID']]
     $mimes = array();
     foreach ($ds->form as $form) {
       $mimetype = (string) $form['MIME'];
@@ -88,13 +92,13 @@ function islandora_get_defined_dsids_array(&$arr, $ds_comp_stream) {
  *
  * @global type $user
  * @param string $object_id
- * @return string|array 
+ * @return string|array
  */
 function islandora_get_unused_dsids($object) {
 
   $defined_dsids = array();
 
-  if(!$object) {
+  if (!$object) {
     return $defined_dsids;
   }
 
@@ -124,11 +128,11 @@ function islandora_get_unused_dsids($object) {
  * buids the default add datastream form
  * @param string $object_id
  * @param array $form_state
- * @return array 
+ * @return array
  *  a form ready to be rendered with a call to Drupal render
  */
 function islandora_get_add_datastream_form($object, &$form_state) {
-  $unused_dsids = islandora_get_unused_dsids($object); 
+  $unused_dsids = islandora_get_unused_dsids($object);
   $form = array();
   $form['add_fieldset'] = array(
     '#type' => 'fieldset',
@@ -168,9 +172,9 @@ function islandora_get_add_datastream_form($object, &$form_state) {
   );
 
   if (!empty($unused_dsids)) {
-    $dsidsForForm = array();
+    $dsids_for_form = array();
     foreach ($unused_dsids as $key => $value) {
-      $dsidsForForm[$key] = $key;
+      $dsids_for_form[$key] = $key;
     }
     $form['add_fieldset']['stream_id'] = array(
       '#type' => 'select',
@@ -179,7 +183,7 @@ function islandora_get_add_datastream_form($object, &$form_state) {
       '#weight' => '-1',
       '#description' => t('Datastream IDs defined by the content model.'),
     );
-    $form['add_fieldset']['stream_id']['#options'] = $dsidsForForm;
+    $form['add_fieldset']['stream_id']['#options'] = $dsids_for_form;
   }
   else {
     $form['add_fieldset']['stream_id'] = array(
@@ -201,7 +205,7 @@ function islandora_get_add_datastream_form($object, &$form_state) {
  *   Drupal user
  * @param array $form
  * @param array $form_state
- * @return type 
+ * @return type
  */
 function islandora_add_datastream_form_submit($form, &$form_state) {
   global $base_url;
@@ -212,7 +216,7 @@ function islandora_add_datastream_form_submit($form, &$form_state) {
 
   module_load_include('inc', 'islandora', 'includes/mime.detect');
   $mimetype = new MimeDetect();
-  
+
   $file = $form_state['values']['add-stream-file-location'];
   $file = drupal_realpath($file);
 
@@ -220,11 +224,11 @@ function islandora_add_datastream_form_submit($form, &$form_state) {
   $dsid = $form_state['values']['stream_id'];
   $ds_label = $form_state['values']['stream_label'];
   $dformat = $mimetype->getMimeType($file);
-  $controlGroup = "M";
+  $control_group = "M";
 
   try {
     $fedora_object = islandora_object_load($object_id);
-    $ds = $fedora_object->constructDatastream($dsid, $controlGroup);
+    $ds = $fedora_object->constructDatastream($dsid, $control_group);
     $ds->label = $ds_label;
     $ds->mimetype = $dformat;
     $ds->setContentFromFile($file);
@@ -235,16 +239,16 @@ function islandora_add_datastream_form_submit($form, &$form_state) {
     drupal_set_message(t('@message', array('@message' => check_plain($e->getMessage()))), 'error');
     return;
   }
-  drupal_set_message("Successfully Added Datastream!");
+  drupal_set_message(t("Successfully Added Datastream!"));
   drupal_goto("islandora/object/$object_id");
 }
 
 /**
- * validates this datastream id against its allowed mimetypes in the dscomposite 
+ * validates this datastream id against its allowed mimetypes in the dscomposite
  * of its content models.
  * @param array $form
  * @param array $form_state
- * @return boolean 
+ * @return boolean
  */
 function islandora_add_datastream_form_validate($form, &$form_state) {
   module_load_include('inc', 'islandora', 'includes/mime.detect');
@@ -254,8 +258,8 @@ function islandora_add_datastream_form_validate($form, &$form_state) {
     return;
   }
   $dsid = $form_state['values']['stream_id'];
-  $dsLabel = $form_state['values']['stream_label'];
-  if (strlen($dsid) > 64) {
+  $ds_label = $form_state['values']['stream_label'];
+  if (drupal_strlen($dsid) > 64) {
     form_set_error('', t('Data stream ID cannot be more than 64 characters.'));
     return FALSE;
   }
@@ -263,11 +267,11 @@ function islandora_add_datastream_form_validate($form, &$form_state) {
     form_set_error('', t("Data stream ID (@dsid) has to start with a letter.", array('@dsid' => check_plain($dsid))));
     return FALSE;
   }
-  if (strlen($dsLabel) > 64) {
+  if (drupal_strlen($ds_label) > 64) {
     form_set_error('', t('Data stream Label cannot be more than 64 characters.'));
     return FALSE;
   }
-  if (strpos($dsLabel, '/')) {
+  if (strpos($ds_label, '/')) {
     form_set_error('', t('Data stream Label cannot contain a "/".'));
     return FALSE;
   }
@@ -275,7 +279,7 @@ function islandora_add_datastream_form_validate($form, &$form_state) {
   $object_id = $form_state['values']['pid'];
   $fedora_object = islandora_object_load($object_id);
 
-  if(isset($fedora_object[$dsid])) {
+  if (isset($fedora_object[$dsid])) {
     form_set_error('', t('Data stream ID already exists in object.'));
     return FALSE;
   }
@@ -283,7 +287,7 @@ function islandora_add_datastream_form_validate($form, &$form_state) {
   $mimetype = new MimeDetect();
   $object = islandora_object_load($form_state['values']['pid']);
   $unused_dsids = islandora_get_unused_dsids($object);
-  if(isset($unused_dsids[$dsid])) {
+  if (isset($unused_dsids[$dsid])) {
     $types_allowed = $unused_dsids[$dsid];
     $arr = array();
     foreach ($types_allowed as $type) {
@@ -295,7 +299,7 @@ function islandora_add_datastream_form_validate($form, &$form_state) {
     // http://api.drupal.org/api/drupal/includes!file.inc/function/file_save_upload/7
     $arr = array();
   }
-  
+
 
   $file = file_save_upload('add-stream-file-location', array('file_validate_extensions' => $arr));
   if ($file) {
@@ -312,7 +316,7 @@ function islandora_add_datastream_form_validate($form, &$form_state) {
  * buids the default add datastream form
  * @param string $object_id
  * @param array $form_state
- * @return array 
+ * @return array
  *  a form ready to be rendered with a call to Drupal render
  */
 function islandora_add_datastream_form($form, &$form_state, $object) {
@@ -356,19 +360,19 @@ function islandora_add_datastream_form($form, &$form_state, $object) {
   );
 
   $unused_dsids = islandora_get_unused_dsids($object);
-  $dsidsForForm = '';
+  $dsids_for_form = '';
   $i = 0;
   foreach ($unused_dsids as $key => $value) {
-    if($i++) {
-      $dsidsForForm .= ", ";
+    if ($i++) {
+      $dsids_for_form .= ", ";
     }
-    $dsidsForForm .= "'$key'";
+    $dsids_for_form .= "'$key'";
   }
 
   $form['add_fieldset']['stream_id'] = array(
     '#title' => 'Datastream ID',
     '#required' => 'TRUE',
-    '#description' => t('An ID for this stream that is unique to this object. Must start with a letter and contain only alphanumeric characters and dashes and underscores. Datastreams that are defined by the content model dont currently exist: <b>' . $dsidsForForm . '</b>.'),
+    '#description' => t('An ID for this stream that is unique to this object. Must start with a letter and contain only alphanumeric characters and dashes and underscores. Datastreams that are defined by the content model dont currently exist: <b>' . $dsids_for_form . '</b>.'),
     '#type' => 'textfield',
     '#weight' => -1,
     '#autocomplete_path' => "islandora/object/$object->id/manage/datastreams/add/autocomplete",
@@ -379,13 +383,13 @@ function islandora_add_datastream_form($form, &$form_state, $object) {
 function islandora_datastream_autocomplete_callback($object, $string = '') {
   $dsids = islandora_get_unused_dsids($object);
   $output = array();
-  foreach($dsids as $id => $ds) {
-    if(trim($string) == '') {
+  foreach ($dsids as $id => $ds) {
+    if (trim($string) == '') {
       $output[$id] = $id;
     }
     else {
       $ret = stripos($id, $string);
-      if($ret !== FALSE) {
+      if ($ret !== FALSE) {
         $output[$id] = $id;
       }
     }
@@ -397,7 +401,7 @@ function islandora_datastream_get_human_readable_size($ds) {
   module_load_include('inc', 'islandora', 'includes/utilities');
 
   // we return - if we don't have a size
-  if($ds->controlGroup == 'M' || $ds->controlGroup == 'X') {
+  if ($ds->controlGroup == 'M' || $ds->controlGroup == 'X') {
     return islandora_convert_bytes_to_human_readable($ds->size);
   }
   else {
@@ -406,7 +410,7 @@ function islandora_datastream_get_human_readable_size($ds) {
 }
 
 function islandora_datastream_get_url($ds, $type = 'download') {
-  if($ds->controlGroup == 'R') {
+  if ($ds->controlGroup == 'R') {
     return $ds->url;
   }
   else {
@@ -417,7 +421,7 @@ function islandora_datastream_get_url($ds, $type = 'download') {
 function islandora_datastream_get_delete_link($ds) {
   $datastreams = module_invoke_all('islandora_undeletable_datastreams', $ds->parent->models);
 
-  if(in_array($ds->id, $datastreams)) {
+  if (in_array($ds->id, $datastreams)) {
     return '';
   }
   else {
diff --git a/includes/ingest-menu.inc b/includes/ingest-menu.inc
index 5c1dd9ee..56ae500e 100644
--- a/includes/ingest-menu.inc
+++ b/includes/ingest-menu.inc
@@ -11,13 +11,13 @@
  * @param string $pid
  */
 function islandora_ingest_callback($collection_object) {
-  if(!$collection_object) {
+  if (!$collection_object) {
     return drupal_not_found();
   }
 
   $ingest_registry = module_invoke_all('islandora_ingest_registry', $collection_object);
   $registry_count = count($ingest_registry);
-  
+
   if ($registry_count == 0) {
     // No ingest implementations.
     drupal_set_message(t('There are no ingest methods specified for @name.', array('@name', $collection_object->label)));
@@ -33,7 +33,7 @@ function islandora_ingest_callback($collection_object) {
   }
 }
 
-//@TODO: theme
+// @TODO: theme
 function islandora_ingest_registry_render($ingest_registry) {
   $output = array(
     '#type' => 'markup',
diff --git a/includes/islandora.ingest.inc b/includes/islandora.ingest.inc
index fcc95964..bf33466a 100644
--- a/includes/islandora.ingest.inc
+++ b/includes/islandora.ingest.inc
@@ -1,5 +1,10 @@
 <?php
 
+/**
+ * @file
+ * This file contains ingest callback functions
+ */
+
 function islandora_ingest_get_information(AbstractFedoraObject $collection_object) {
   $models = $collection_object->models;
   $collection_info = module_invoke_all('islandora_ingest_get_information', $models, $collection_object);
@@ -12,7 +17,7 @@ function islandora_ingest_get_object($content_models, $collection_pid, $relation
   global $user;
   $connection = new IslandoraTuque($user);
   $object = $connection->repository->constructObject($namespace);
-  foreach($content_models as $content_model) {
+  foreach ($content_models as $content_model) {
     $object->relationships->add(FEDORA_MODEL_URI, 'hasModel', $content_model['pid']);
   }
   $object->relationships->add(FEDORA_RELS_EXT_URI, $relationship, $collection_pid);
diff --git a/includes/islandora_dublin_core.inc b/includes/islandora_dublin_core.inc
index 41c9bbfa..25580b34 100644
--- a/includes/islandora_dublin_core.inc
+++ b/includes/islandora_dublin_core.inc
@@ -70,7 +70,7 @@ class Dublin_Core {
   /**
    * Serialize this object to XML and return it.
    * @param type $with_preamble
-   * @return type 
+   * @return type
    */
   function as_xml($with_preamble = FALSE) {
     $dc_xml = new DomDocument();
@@ -96,7 +96,7 @@ class Dublin_Core {
    * Create dc from dict ( does nothing )
    */
   static function create_dc_from_dict() {
-    
+
   }
 
   function as_formatted_array() {
@@ -108,9 +108,9 @@ class Dublin_Core {
           if (is_array($values)) {
             $value = '';
             $i = 0;
-            foreach($values as $piece) {
-              if(!empty($piece)) {
-                if($i++) {
+            foreach ($values as $piece) {
+              if (!empty($piece)) {
+                if ($i++) {
                   $value .= ", ";
                 }
                 $value .= $piece;
@@ -121,16 +121,16 @@ class Dublin_Core {
             $value = $values;
           }
           $dc_label = explode(':', $field);
-          $element_label = ucfirst($dc_label[1]);
+          $element_label = drupal_ucfirst($dc_label[1]);
           $dc_array[$field]['label'] = $element_label;
           $dc_array[$field]['value'] = $value;
-          $dc_array[$field]['class'] = strtolower(preg_replace('/[^A-Za-z0-9]/', '-', $field));
+          $dc_array[$field]['class'] = drupal_strtolower(preg_replace('/[^A-Za-z0-9]/', '-', $field));
         }
       }
     }
     return $dc_array;
   }
-  
+
 
   /**
    * Creates a new instance of the class by parsing dc_xml
diff --git a/includes/mime.detect.inc b/includes/mime.detect.inc
index f8878f68..3807c50e 100644
--- a/includes/mime.detect.inc
+++ b/includes/mime.detect.inc
@@ -227,7 +227,7 @@ class MimeDetect {
   public function getMimetype($filename, $debug = FALSE) {
 
     $file_name_and_extension = explode('.', $filename);
-    $ext = strtolower(array_pop($file_name_and_extension));
+    $ext = drupal_strtolower(array_pop($file_name_and_extension));
 
     if (!empty($this->protectedMimeTypes[$ext])) {
       if (TRUE === $debug) {
diff --git a/includes/object_properties.inc b/includes/object_properties.inc
index 2a521f5e..d4f7eeca 100644
--- a/includes/object_properties.inc
+++ b/includes/object_properties.inc
@@ -1,13 +1,20 @@
 <?php
 
 /**
- * may want more validation here the only restrictions i see on
+ * @file
+ * Contains admin form functions for object properties
+ */
+
+/**
+ * Validate function for object properties admin form.
+ *
+ * @TODO: may want more validation here the only restrictions i see on
  * the object label and owner is the foxml schema says they should be
  * an xsd:string there maybe further restrictions such as length but they aren't
  * defined in the schema.
  * @param array $form
  * @param array $form_state
- * @return boolean 
+ * @return boolean
  */
 function islandora_edit_properties_form_validate($form, &$form_state) {
   $islandora_object = islandora_object_load($form_state['values']['pid']);
@@ -18,9 +25,10 @@ function islandora_edit_properties_form_validate($form, &$form_state) {
 }
 
 /**
+ * Submit function for object properties admin form.
  *
  * @param array $form
- * @param array $form_state 
+ * @param array $form_state
  */
 function islandora_edit_properties_form_submit($form, &$form_state) {
   $islandora_object = islandora_object_load($form_state['values']['pid']);
@@ -32,7 +40,7 @@ function islandora_edit_properties_form_submit($form, &$form_state) {
       $islandora_object->owner = $owner;
       drupal_set_message(t('Successfully updated owner %s', array('%s' => $owner)));
     } catch (Exception $e) {
-      form_set_error('object_owner',t('Error updating owner %s', array('%s'=> $e->getMessage())));
+      form_set_error('object_owner', t('Error updating owner %s', array('%s' => $e->getMessage())));
     }
   }
   if (isset($state) && $state != $islandora_object->state) {
@@ -40,7 +48,7 @@ function islandora_edit_properties_form_submit($form, &$form_state) {
       $islandora_object->state = $state;
       drupal_set_message(t('Successfully updated state %s', array('%s' => $state)));
     } catch (Exception $e) {
-      form_set_error('object_state',t('Error updating state %s', array('%s'=> $e->getMessage())));
+      form_set_error('object_state', t('Error updating state %s', array('%s' => $e->getMessage())));
     }
   }
   if (isset($label) && $label != $islandora_object->label) {
@@ -53,18 +61,22 @@ function islandora_edit_properties_form_submit($form, &$form_state) {
   }
 }
 
+/**
+ * Callback function for object properties admin form delete button.
+ */
 function islandora_edit_properties_form_delete($form, &$form_state) {
   $islandora_object = $form_state['values']['pid'];
   drupal_goto("islandora/object/$islandora_object/delete");
 }
 
 /**
+ * Object properties admin form.
  *
  * @param array $form
  * @param array $form_state
  * @param string $object_id
  *   an object id
- * @return array 
+ * @return array
  */
 function islandora_edit_properties_form($form, &$form_state, $object) {
   $form = array();
@@ -111,5 +123,3 @@ function islandora_edit_properties_form($form, &$form_state, $object) {
   );
   return $form;
 }
-
-?>
diff --git a/includes/purge.form.inc b/includes/purge.form.inc
index 28a1854f..62c18ba9 100644
--- a/includes/purge.form.inc
+++ b/includes/purge.form.inc
@@ -1,5 +1,10 @@
 <?php
 
+/**
+ * @file
+ * This file contains the admin (confirmation) form and callback functions to purge an object.
+ */
+
 /**
  * Gives the option of deleting or purging and object.
  *
@@ -154,7 +159,7 @@ function islandora_purge_datastream_submit($form, &$form_state) {
     }
   }
   //notify modules post deletion
-  module_invoke_all('islandora_post_purge_datastream', $object, $datastream_id); 
+  module_invoke_all('islandora_post_purge_datastream', $object, $datastream_id);
   drupal_set_message(t('%d datastream sucessfully purged from Islandora object %o', array('%d' => $datastream_id, '%o' => $object->label)));
   drupal_goto('islandora/object/' . $object->id);
 }
diff --git a/includes/tuque.inc b/includes/tuque.inc
index 597f43fd..7693a703 100644
--- a/includes/tuque.inc
+++ b/includes/tuque.inc
@@ -1,5 +1,10 @@
 <?php
 
+/**
+ * @file
+ * This file contains a class to include the Tuque php library.
+ */
+
 $islandora_module_path = drupal_get_path('module', 'islandora');
 
 //do this until we expost these in a module or library
@@ -54,14 +59,15 @@ class IslandoraTuque {
   public $repository = NULL;
 
   function __construct($user = NULL, $url = NULL) {
-    if(!isset($user)) {
+    if (!isset($user)) {
       global $user;
     }
-    
-    if(!isset($user) || $user->uid == 0){
+
+    if (!isset($user) || $user->uid == 0) {
       $user_string = 'anonymous';
       $pass_string = 'anonymous';
-    } else {
+    }
+    else {
       $user_string = $user->name;
       $pass_string = $user->pass;
     }
@@ -70,7 +76,7 @@ class IslandoraTuque {
       $url = variable_get('islandora_base_url', 'http://localhost:8080/fedora');
     }
 
-    if(self::exists()) {
+    if (self::exists()) {
       $this->connection = new RepositoryConnection($url, $user_string, $pass_string);
       $this->connection->reuseConnection = TRUE;
       $this->api = new FedoraApi($this->connection);
@@ -87,7 +93,7 @@ class IslandoraTuque {
     $islandora_doc_link = l(t('Islandora documentation'), 'https://wiki.duraspace.org/display/ISLANDORA/Islandora');
     $tuque_link = l(t('Tuque Fedora API'), 'http://github.com/islandora/tuque');
     $message = t('Islandora requires the !tuque_url. Please install in /sites/all/libraries/tuque before continuing. See the !islandora_url.', array( '!tuque_url' => $tuque_link, '!islandora_url' => $islandora_doc_link));
-    drupal_set_message($message, 'error', FALSE);
+    drupal_set_message(filter_xss($message), 'error', FALSE);
   }
 }
 
diff --git a/includes/utilities.inc b/includes/utilities.inc
index afcf5f94..d4cb0b40 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -1,39 +1,44 @@
 <?php
 
+/**
+ * @file
+ * Contains islandora utility functions
+ */
+
 /**
  * Convert bytes to human readable format
  *
  * @param integer bytes Size in bytes to convert
  * @return string
  */
-function islandora_convert_bytes_to_human_readable($bytes, $precision = 2)
-{
-    $kilobyte = 1024;
-    $megabyte = $kilobyte * 1024;
-    $gigabyte = $megabyte * 1024;
-    $terabyte = $gigabyte * 1024;
-
-    if (($bytes >= 0) && ($bytes < $kilobyte)) {
-        return $bytes . ' B';
+function islandora_convert_bytes_to_human_readable($bytes, $precision = 2) {
+  $kilobyte = 1024;
+  $megabyte = $kilobyte * 1024;
+  $gigabyte = $megabyte * 1024;
+  $terabyte = $gigabyte * 1024;
 
-    } elseif (($bytes >= $kilobyte) && ($bytes < $megabyte)) {
-        return round($bytes / $kilobyte, $precision) . ' KB';
-
-    } elseif (($bytes >= $megabyte) && ($bytes < $gigabyte)) {
-        return round($bytes / $megabyte, $precision) . ' MB';
-
-    } elseif (($bytes >= $gigabyte) && ($bytes < $terabyte)) {
-        return round($bytes / $gigabyte, $precision) . ' GB';
-
-    } elseif ($bytes >= $terabyte) {
-        return round($bytes / $terabyte, $precision) . ' TB';
-    } else {
-        return $bytes . ' B';
-    }
+  if (($bytes >= 0) && ($bytes < $kilobyte)) {
+    return $bytes . ' B';
+  }
+  elseif (($bytes >= $kilobyte) && ($bytes < $megabyte)) {
+    return round($bytes / $kilobyte, $precision) . ' KB';
+  }
+  elseif (($bytes >= $megabyte) && ($bytes < $gigabyte)) {
+    return round($bytes / $megabyte, $precision) . ' MB';
+  }
+  elseif (($bytes >= $gigabyte) && ($bytes < $terabyte)) {
+    return round($bytes / $gigabyte, $precision) . ' GB';
+  }
+  elseif ($bytes >= $terabyte) {
+    return round($bytes / $terabyte, $precision) . ' TB';
+  }
+  else {
+    return $bytes . ' B';
+  }
 }
 
 function islandora_control_group_to_human_readable($control_group) {
-  switch($control_group) {
+  switch ($control_group) {
     case 'M':
       return '<b>M</b>anaged';
     case 'X':
@@ -54,7 +59,7 @@ function islandora_control_group_to_human_readable($control_group) {
  */
 function islandora_validate_pid($pid) {
   $valid = FALSE;
-  if (strlen(trim($pid)) <= 64 && preg_match('/^([A-Za-z0-9]|-|\.)+:(([A-Za-z0-9])|-|\.|~|_|(%[0-9A-F]{2}))+$/', trim($pid))) {
+  if (drupal_strlen(trim($pid)) <= 64 && preg_match('/^([A-Za-z0-9]|-|\.)+:(([A-Za-z0-9])|-|\.|~|_|(%[0-9A-F]{2}))+$/', trim($pid))) {
     $valid = TRUE;
   }
 
@@ -68,7 +73,7 @@ function islandora_validate_pid($pid) {
  */
 function islandora_validate_dsid($dsid) {
   $valid = FALSE;
-  if (strlen(trim($dsid)) <= 64 && preg_match('/^[a-zA-Z0-9\_\-\.]+$/', trim($dsid))) {
+  if (drupal_strlen(trim($dsid)) <= 64 && preg_match('/^[a-zA-Z0-9\_\-\.]+$/', trim($dsid))) {
     $valid = TRUE;
   }
 
@@ -76,9 +81,9 @@ function islandora_validate_dsid($dsid) {
 }
 
 /* Helper function to describe a Fedora repository.
- * 
+ *
  * Can be used to check if Fedora is available.
- * 
+ *
  * @param $url
  *   A url to a Fedora repository.
  * @return
@@ -86,7 +91,7 @@ function islandora_validate_dsid($dsid) {
  *   or if the url is incorrect.
  */
 function islandora_describe_repository($url) {
-  
+
   $connection = new IslandoraTuque(NULL, $url);
   try {
     $info = $connection->api->a->describeRepository();
diff --git a/islandora.api.php b/islandora.api.php
index 49085b1d..7dcfb87b 100644
--- a/islandora.api.php
+++ b/islandora.api.php
@@ -1,83 +1,89 @@
 <?php
+
+/**
+ * @file
+ * This file lists and documents all available hook functions to manipulate data.
+ */
+
 /**
  * remove a datastream from a repository object
  * @param object $fedora_object
  *  tuque FedoraObject
- * @param string $datastream_id 
+ * @param string $datastream_id
  */
-function hook_islandora_purge_datastream ($fedora_object, $datastream_id){}
+function hook_islandora_purge_datastream($fedora_object, $datastream_id) {}
 
 /**
  *
- * @param type $object 
+ * @param type $object
  *   tuque FedoraObject
  */
-function hook_islandora_purge_object($islandora_object) {} 
+function hook_islandora_purge_object($islandora_object) {}
 
 /**
  * allows modules to add to a repository objects display.  If you implement this
- * hook you should also register your module for view with the get types hook.  
- * 
- * islandora gets all displays back in an array and iterates over them.  the order 
+ * hook you should also register your module for view with the get types hook.
+ *
+ * islandora gets all displays back in an array and iterates over them.  the order
  * they are displayed is based on the order of the key of the array that each
  * module returns.
- * 
- * your module may also want to register a varible that says whether or not it 
+ *
+ * your module may also want to register a varible that says whether or not it
  * should be part of the default display. Modules can also add secondary tabs as
- * a way to add there output to an islandora display.  the basic image module has 
+ * a way to add there output to an islandora display.  the basic image module has
  * samples of both (the secondary tabs examples are commented out)
- * 
+ *
  * @param type $islandora_object
- *   tuque FedoraObject 
+ *   tuque FedoraObject
  */
-function hook_islandora_view_object($islandora_object){}
+function hook_islandora_view_object($islandora_object) {}
 
 /**
  * returns an array listing object types provided by sub modules
  *  Ex.  array($types['islandora:collectionCModel'][ISLANDORA_VIEW_HOOK] = variable_get('islandora_basic_collection_use_for_default_tab', TRUE);
  * $types['islandora:collectionCModel'][ISLANDORA_EDIT_HOOK] = FALSE;
- * 
- * @return array 
+ *
+ * @return array
  */
-function hook_islandora_get_types(){}
+function hook_islandora_get_types() {}
 
 /**
  * allows modules to define an object edit page by cmodel
- * 
+ *
  * your module should return true for ISLANDORA_EDIT_HOOK in its get_types function
- * 
+ *
  * islandora provides a default implementation that should work for most use cases
  * @param string $islandora_object
- * @return string 
- * 
+ * @return string
+ *
  */
-function hook_islandora_edit_object($islandora_object){}
+function hook_islandora_edit_object($islandora_object) {}
 
 /**
  * allows modules to alter the fedora object before it is pass through the edit
  * hooks
- * @param type $islandora_object 
+ * @param type $islandora_object
  *   a tugue FedoraObject
  */
-function islandora_islandora_edit_object_alter ($islandora_object){}
+function islandora_islandora_edit_object_alter($islandora_object) {}
 
 
 /**
- * creates and populates a php Fedora object. 
+ * creates and populates a php Fedora object.
  */
-function hook_islandora_preingest_alter(){}
+function hook_islandora_preingest_alter() {}
 
 /**
  * modules can implement this hook to add or remove datastreams after an
- * object has been ingested.  
- * 
- * Each module should check for the newly ingested repository objects content 
- * model to make sure it is a type of object they want to act on.  
- * 
- * @param type $islandora_object 
+ * object has been ingested.
+ *
+ * Each module should check for the newly ingested repository objects content
+ * model to make sure it is a type of object they want to act on.
+ *
+ * @param type $islandora_object
  *   tugue FeodoraObject
  */
-function hook_islandora_postingest($islandora_object){}
+function hook_islandora_postingest($islandora_object) {}
 
 /**
  * Register potential ingest routes. Implementations should return an array containing possible routes.
@@ -96,25 +102,25 @@ function hook_islandora_edit_datastream_registry($islandora_object, $ds_id) {}
 
 /**
  * alter an object before it gets used further down the stack
- * @param type $object 
+ * @param type $object
  *   a tuque FedoraObject
  */
-function hook_islandora_object_alter ($fedora_object){}
+function hook_islandora_object_alter($fedora_object) {}
 
 /**
- * insert or remove rendered elements by implementing this function 
- * in your module 
- * @param type $arr 
+ * insert or remove rendered elements by implementing this function
+ * in your module
+ * @param type $arr
  *   an arr of rendered views
  */
-function hook_islandora_display_alter ($arr){}
+function hook_islandora_display_alter($arr) {}
 
 /**
  *
  * @param type $islandora_object
  *   a tuque FedoraObject
  * @param array $content_models
- * @param string $collection_pid 
+ * @param string $collection_pid
  */
-function hook_islandora_ingest_pre_ingest($islandora_object, $content_models, $collection_pid){}
+function hook_islandora_ingest_pre_ingest($islandora_object, $content_models, $collection_pid) {}
 
diff --git a/islandora.install b/islandora.install
index e69de29b..3fdd0fd7 100644
--- a/islandora.install
+++ b/islandora.install
@@ -0,0 +1,6 @@
+<?php
+
+/**
+ * @file
+ * This file contains all install functions.
+ */
\ No newline at end of file
diff --git a/islandora.module b/islandora.module
index 246b6718..17171ff8 100644
--- a/islandora.module
+++ b/islandora.module
@@ -1,28 +1,28 @@
 <?php
 
 /*
- * @file islandora.module
- * defines paths (drupal menu items) as entry points and acts as a hub for dispatching tasks to other modules.
- * 
- * 
+ * @file
+ *
+ * islandora.module: defines paths (drupal menu items) as entry points and acts as a hub for dispatching tasks to other modules.
+ *
  * This file is part of Islandora.
- * 
+ *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
  * the Free Software Foundation, either version 3 of the License, or
  * (at your option) any later version.
- * 
+ *
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public License
  * along with the program.  If not, see <http ://www.gnu.org/licenses/>.
  */
 
 
-//Permissions
+// Permissions
 define('FEDORA_VIEW', 'view fedora repository');
 define('FEDORA_METADATA_EDIT', 'edit fedora metadata');
 define('FEDORA_ADD_DS', 'add fedora datastreams');
@@ -31,12 +31,12 @@ define('FEDORA_PURGE', 'delete fedora objects and datastreams');
 define('FEDORA_MODIFY_STATE', 'modify fedora state');
 define('FEDORA_MANAGE', 'manage fedora items');
 
-//hooks
+// hooks
 define('ISLANDORA_VIEW_HOOK', 'islandora_view_object');
 define('ISLANDORA_EDIT_HOOK', 'islandora_edit_object');
 
 /**
- * Implementation of hook_menu. 
+ * Implements hook_menu().
  * we need some standard entry points so we can have consistent urls for different Object actions
  */
 function islandora_menu() {
@@ -215,20 +215,20 @@ function islandora_admin_paths() {
  * @param string $op
  * @param string $pid
  *
- *  @return boolean 
+ *  @return boolean
  */
 function islandora_access_callback($object = NULL, $perm = NULL) {
-  if(!$object || !$perm) {
+  if (!$object || !$perm) {
     return FALSE;
   }
 
   $isRestricted = variable_get('islandora_namespace_restriction_enforced', FALSE);
-  
+
   if (!$isRestricted) {
     $namespace_access = TRUE;
   }
   else {
-    $pid_namespace = substr($object->id, 0, strpos($object->id, ':') + 1); //Get the namespace (with colon)
+    $pid_namespace = substr($object->id, 0, strpos($object->id, ':') + 1); // Get the namespace (with colon)
     $allowed_namespaces = explode(" ", variable_get('islandora_pids_allowed', 'default: demo: changeme: islandora: ilives: islandora-book: books: newspapers: '));
     $namespace_access = in_array($pid_namespace, $allowed_namespaces);
   }
@@ -238,7 +238,7 @@ function islandora_access_callback($object = NULL, $perm = NULL) {
 
 /**
  * returns an array listing object types provided by sub modules
- * @return array 
+ * @return array
  */
 function islandora_get_types() {
   return module_invoke_all('islandora_get_types');
@@ -255,10 +255,10 @@ function islandora_init() {
  * that handle this function this module will build a default page.
  * @global object $user
  * @param string $object_id
- * @return string 
+ * @return string
  */
 function islandora_edit_object($object) {
-  if(!$object) {
+  if (!$object) {
     return drupal_not_found();
   }
   drupal_alter('islandora_edit_object', $object);
@@ -274,7 +274,7 @@ function islandora_edit_object($object) {
 /**
  * edit properties form
  * @param type $object_id
- * @return string 
+ * @return string
  */
 function islandora_edit_properties($object_id) {
   $object = islandora_object_load($object_id);
@@ -290,7 +290,7 @@ function islandora_edit_properties($object_id) {
 /**
  * builds a default page for the edit tab
  *
- * @param object $fedora_object 
+ * @param object $fedora_object
  *   A tuque Fedora Object
  */
 function islandora_islandora_edit_object($fedora_object) {
@@ -315,14 +315,14 @@ function islandora_view_default_object() {
  * their modules want to provide a view for.
  * @global object $user
  * @param string $object_id
- * 
- * @return string 
+ *
+ * @return string
  */
 function islandora_view_object($fedora_object = NULL) {
   module_load_include('inc', 'islandora', 'includes/breadcrumb');
   global $user;
 
-  if(!$fedora_object) {
+  if (!$fedora_object) {
     return drupal_not_found();
   }
 
@@ -348,10 +348,10 @@ function islandora_view_object($fedora_object = NULL) {
 }
 
 /**
- * the default view hook.  If there are no modules registered to handle this objects cmodels or there are 
+ * the default view hook.  If there are no modules registered to handle this objects cmodels or there are
  * not any cmodels specified this will create a default display.
  * @param string $object_id
- * @return string 
+ * @return string
  */
 function islandora_islandora_view_object($object) {
   $supported_models = islandora_get_types();
@@ -425,17 +425,17 @@ function islandora_permission() {
  * a helper function to get a connection and return an object
  * @global object $user
  * @param string $object_id
- * @return FedoraObject 
+ * @return FedoraObject
  */
 function islandora_object_load($object_id) {
   module_load_include('inc', 'islandora', 'includes/tuque');
   static $islandora_tuque = NULL;
 
-  if(!$islandora_tuque) {
+  if (!$islandora_tuque) {
     $islandora_tuque = new IslandoraTuque();
   }
 
-  if(IslandoraTuque::exists()) {
+  if (IslandoraTuque::exists()) {
     try {
       $fedora_object = $islandora_tuque->repository->getObject($object_id);
     } catch (Exception $e) {
@@ -450,13 +450,13 @@ function islandora_object_load($object_id) {
 }
 
 function islandora_ingest_access_callback($object, $perm) {
-  if(islandora_access_callback($object, $perm) === FALSE) {
+  if (islandora_access_callback($object, $perm) === FALSE) {
     return FALSE;
   }
 
   $ingest_registry = module_invoke_all('islandora_ingest_registry', $object);
 
-  if(count($ingest_registry) > 0) {
+  if (count($ingest_registry) > 0) {
     return TRUE;
   }
   else {
diff --git a/theme/islandora-object-edit.tpl.php b/theme/islandora-object-edit.tpl.php
index 2d88e27e..f0005083 100644
--- a/theme/islandora-object-edit.tpl.php
+++ b/theme/islandora-object-edit.tpl.php
@@ -1,50 +1,24 @@
 <?php
 
-/*
- * islandora-object-edit.tpl.php
- * 
+/**
+ * @file
+ * islandora-object-edit.tpl.php: This is a template for objects that do not have
+ * a module to registered to build their display.
  *
- * 
- * This file is part of Islandora.
- * 
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License
- * along with the program.  If not, see <http ://www.gnu.org/licenses/>.
- */
-?>
-<?php
-
-/* 
- * this is a template for objects that do not have a module to registered to build their display.
- * 
  * islandora_object is a fedora tuque Object
  *    $object->label
  *    $object->id
  * to get the contents of a datastream
- *    $object['dsid']->content 
- * 
+ *    $object['dsid']->content
+ *
  * $dublin_core is a Dublin_Core object
  * which is an array of elements, such as dc.title
  * and each element has an array of values.  dc.title can have none, one or many titles
  * this is the case for all dc elements.
- * 
- * 
- * 
+ *
  */
-
-//dsm($object);
-
-drupal_set_title($islandora_object->label);
-//print($islandora_object->label . ' ' . $islandora_object->id); 
-print (theme_table($variables['datastream_table']));
 ?>
 
+<?php drupal_set_title($islandora_object->label); ?>
+
+<?php print (theme_table($variables['datastream_table'])); ?>
\ No newline at end of file
diff --git a/theme/islandora-object.tpl.php b/theme/islandora-object.tpl.php
index 0dd6a66e..d6efaac3 100644
--- a/theme/islandora-object.tpl.php
+++ b/theme/islandora-object.tpl.php
@@ -1,30 +1,8 @@
 <?php
 
 /*
- * islandora-object.tpl.php
- * 
- *
- * 
- * This file is part of Islandora.
- * 
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License
- * along with the program.  If not, see <http ://www.gnu.org/licenses/>.
- */
-?>
-<?php
-
-/* 
- * this is a template for objects that do not have a module to registered to build their display.
+ * @file
+ * This is a template for objects that do not have a module to registered to build their display.
  * 
  * islandora_object is a fedora tuque Object
  *    $object->label             - The label for this object.
diff --git a/theme/islandora.theme.inc b/theme/islandora.theme.inc
index 821ddf95..b0e79739 100644
--- a/theme/islandora.theme.inc
+++ b/theme/islandora.theme.inc
@@ -1,5 +1,10 @@
 <?php
 
+/**
+ * @file
+ * This file contains all theme and preprocess functions.
+ */
+
 /**
  * preprocess the edit template
  * @global string $base_url
@@ -72,9 +77,11 @@ function islandora_preprocess_islandora_default(&$variables) {
       $datastreams[$id]['mimetype'] = $ds->mimetype;
       $datastreams[$id]['size'] = islandora_datastream_get_human_readable_size($ds);
       $datastreams[$id]['created_date'] = $ds->createdDate->format("Y-m-d");
-      $datastreams[$id]['class'] = strtolower(preg_replace('/[^A-Za-z0-9]/', '-', $id));
+      $datastreams[$id]['class'] = drupal_strtolower(preg_replace('/[^A-Za-z0-9]/', '-', $id));
+    }
+    catch (RepositoryException $e) {
+
     }
-    catch (RepositoryException $e) {}
   }
   $variables['datastreams'] = $datastreams;
   try {