From 5aefe46f85709cd5218a5f139616dc925f57b90c Mon Sep 17 00:00:00 2001
From: Adam Vessey <adam@discoverygarden.ca>
Date: Tue, 24 Apr 2012 14:19:47 -0300
Subject: [PATCH 1/9] Use wrapping modify_datastream wrapper in replace
 datastream callback.

---
 fedora_repository.module | 45 +++++++++++++++++-----------------------
 1 file changed, 19 insertions(+), 26 deletions(-)

diff --git a/fedora_repository.module b/fedora_repository.module
index e83d91f5..208e028e 100644
--- a/fedora_repository.module
+++ b/fedora_repository.module
@@ -646,27 +646,27 @@ function fedora_repository_replace_stream_form(&$form_state, $pid, $dsId, $dsLab
  * @return type 
  */
 function fedora_repository_replace_stream_form_validate($form, &$form_state) {
-// If a file was uploaded, process it.
+  // If a file was uploaded, process it.
   if (isset($_FILES['files']) && is_uploaded_file($_FILES['files']['tmp_name']['file'])) {
 
-// attempt to save the uploaded file
+    // attempt to save the uploaded file
     $file = file_save_upload('file', array(), file_directory_path());
 
-// set error is file was not uploaded
+    // set error is file was not uploaded
     if (!$file) {
       form_set_error('file', 'Error uploading file.');
       return;
     }
-
-    $doc = new DOMDocument();
-    module_load_include('inc', 'Fedora_Repository', 'MimeClass');
+    
+    module_load_include('inc', 'fedora_repository', 'MimeClass');
     $mime = new MimeClass();
-    if ($mime->getType($file->filepath) == 'text/xml' && !$doc->load($file->filepath)) {
+    
+    if ($mime->getType($file->filepath) == 'text/xml' && !DOMDocument::load($file->filepath)) {
       form_set_error('file', 'Invalid XML format.');
       return;
     }
 
-// set files to form_state, to process when form is submitted
+    // set files to form_state, to process when form is submitted
     $form_state['values']['file'] = $file;
   }
 }
@@ -683,39 +683,32 @@ function fedora_repository_replace_stream_form_submit($form, &$form_state) {
   $pid = $form_state['values']['pid'];
   $dsid = $form_state['values']['dsId'];
   $dsLabel = $form_state['values']['dsLabel'];
-// Remove the original file extension from the label and add the new one
+  
+  // Remove the original file extension from the label and add the new one
   $indexOfDot = strrpos($dsLabel, '.'); //use strrpos to get the last dot
   if ($indexOfDot !== FALSE) {
     $dsLabel = substr($dsLabel, 0, $indexOfDot);
     $dsLabel .= substr($file->filename, strrpos($file->filename, '.')); // Add the file extention to the end of the label.;
   }
-  module_load_include('inc', 'Fedora_Repository', 'MimeClass');
-  module_load_include('inc', 'fedora_repository', 'api/fedora_item');
 
-  $file_basename = basename($file->filepath);
-  $file_directory = dirname($file->filepath);
-  $streamUrl = $base_url . '/' . $file_directory . '/' . urlencode($file_basename);
+  $streamUrl = url($file->filepath, array(
+    'absolute' => TRUE,
+  ));
 
   /* -----------------------------------------------------------------
    * TODO: need a better way to get mimetypes
    */
+  module_load_include('inc', 'fedora_repository', 'MimeClass');
   $mimetype = new MimeClass();
   $dformat = $mimetype->getType($file->filepath);
 
+  module_load_include('inc', 'fedora_repository', 'api/fedora_item');
   $item = new Fedora_Item($pid);
-  $info = $item->get_datastream_info($dsid);
-
-  if($info->datastream->controlGroup == 'M') {
-    $item->modify_datastream_by_reference($streamUrl, $dsid, $dsLabel, $dformat);
-  } elseif ($info->datastream->controlGroup == 'X') {
-    if($dformat == 'text/xml') {
-      $item->modify_datastream_by_value(file_get_contents($file->filepath), $dsid, $dsLabel, $dformat);
-    }
-    else {
-      drupal_set_message('File must be of mimetype text/xml in order to replace inline XML datastream.', 'error');
-    }
+  
+  if(in_array($info->datastream->controlGroup, array('M', 'X'))) {
+    $item->modify_datastream($streamUrl, $dsid, $dsLabel, $dformat);
   } else {
-    drupal_set_message('Cannot replace Redirect or Managed Datastream.', 'error');
+    drupal_set_message(t('Cannot replace Redirect or Managed Datastream.'), 'error');
   }
 
   $form_state['redirect'] = 'fedora/repository/' . $pid;

From fa77552e57052ace01abef279e0a8cf3946083e2 Mon Sep 17 00:00:00 2001
From: Adam Vessey <adam@discoverygarden.ca>
Date: Wed, 25 Apr 2012 09:22:14 -0300
Subject: [PATCH 2/9] Get the extension without exploding.

---
 MimeClass.inc | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/MimeClass.inc b/MimeClass.inc
index 42c11e37..b2950f6e 100644
--- a/MimeClass.inc
+++ b/MimeClass.inc
@@ -231,9 +231,7 @@ class MimeClass {
    * @return type 
    */
   public function get_mimetype($filename, $debug = FALSE) {
-
-    $file_name_and_extension = explode('.', $filename);
-    $ext = strtolower(array_pop($file_name_and_extension));
+    $ext = strtolower(substr($filename, strrpos($filename, '.') + 1));
 
     if (!empty($this->private_mime_types[$ext])) {
       if (TRUE === $debug)

From 01ac63a3d98c996614f925e6f810098fe7e36117 Mon Sep 17 00:00:00 2001
From: Adam Vessey <adam@discoverygarden.ca>
Date: Wed, 25 Apr 2012 10:05:45 -0300
Subject: [PATCH 3/9] Allow the addition of Redirect and External datastreams.

---
 fedora_repository.module | 80 ++++++++++++++++++++------------------
 formClass.inc            | 83 +++++++++++++++++++++++++++++-----------
 2 files changed, 104 insertions(+), 59 deletions(-)

diff --git a/fedora_repository.module b/fedora_repository.module
index 208e028e..940d1585 100644
--- a/fedora_repository.module
+++ b/fedora_repository.module
@@ -377,37 +377,25 @@ function add_stream_form_submit($form, &$form_state) {
     $form_state['rebuild'] = TRUE;
     return;
   }
-  module_load_include('inc', 'fedora_repository', 'MimeClass');
+  
   module_load_include('inc', 'fedora_repository', 'ObjectHelper');
   module_load_include('inc', 'fedora_repository', 'api/fedora_item');
   $pathToModule = drupal_get_path('module', 'fedora_repository');
 
-  $file = $form_state['values']['add-stream-file-location'];
-
   $pid = $form_state['values']['pid'];
   $dsid = $form_state['values']['stream_id'];
   $dsLabel = $form_state['values']['stream_label'] . substr($file, strrpos($file, '.')); // Add the file extention to the end of the label.;
-  $file_basename = basename($file);
-  $file_directory = dirname($file);
-  $streamUrl = $base_url . '/' . $file_directory . '/' . drupal_urlencode($file_basename);
 
-  /* -----------------------------------------------------------------
-   * need a better way to get mimetypes
-   */
-  $mimetype = new MimeClass();
-  $dformat = $mimetype->getType($file);
-  $controlGroup = "M";
-  if ($dformat == 'text/xml') {
-    $controlGroup = 'X';
-  }
   try {
     $item = new Fedora_Item($pid);
-    $item->add_datastream_from_url($streamUrl, $dsid, $dsLabel, $dformat, $controlGroup);
+    $item->add_datastream_from_url($form_state['storage']['stream_url'], $dsid, $dsLabel, $form_state['storage']['ds_mimetype'], $form_state['values']['control_group']);
 
-    $object_helper = new ObjectHelper();
-    $object_helper->get_and_do_datastream_rules($pid, $dsid, $file);
+    if ($file = $form_state['values']['add-stream-file-location']) {
+      $object_helper = new ObjectHelper();
+      $object_helper->get_and_do_datastream_rules($pid, $dsid, $file);
 
-    file_delete($file);
+      file_delete($file);
+    }
   } catch (exception $e) {
     drupal_set_message(t('@message', array('@message' => check_plain($e->getMessage()))), 'error');
     return;
@@ -434,6 +422,7 @@ function add_stream_form(&$form_state, $pid) {
  * @return type 
  */
 function add_stream_form_validate($form, &$form_state) {
+  module_load_include('inc', 'fedora_repository', 'MimeClass');
   if ($form_state['clicked_button']['#value'] == 'OK') {
     $form_state['rebuild'] = TRUE;
     return;
@@ -444,15 +433,15 @@ function add_stream_form_validate($form, &$form_state) {
     form_set_error('', t('Data stream ID cannot be more than 64 characters.'));
     return FALSE;
   }
-  if (!(preg_match("/^[a-zA-Z]/", $dsid))) {
-    form_set_error('', t("Data stream ID (@dsid) has to start with a letter.", array('@dsid' => check_plain($dsid))));
+  elseif (!(preg_match("/^[a-zA-Z]/", $dsid))) {
+    form_set_error('', t("Data stream ID (@dsid) has to start with a letter.", array('@dsid' => $dsid)));
     return FALSE;
   }
-  if (strlen($dsLabel) > 64) {
+  elseif (strlen($dsLabel) > 64) {
     form_set_error('', t('Data stream Label cannot be more than 64 characters.'));
     return FALSE;
   }
-  if (strpos($dsLabel, '/')) {
+  elseif (strpos($dsLabel, '/') !== FALSE) {
     form_set_error('', t('Data stream Label cannot contain a "/".'));
     return FALSE;
   }
@@ -462,12 +451,30 @@ function add_stream_form_validate($form, &$form_state) {
 //    'file_validate_size' => array(30 * 1024),
   );
 
-  $fileObject = file_save_upload('add-stream-file-location', $validators);
-
-// Move the uploaded file to Drupal's files directory.
-  file_move($fileObject->filepath, 0, 'FILE_EXISTS_RENAME');
-  $form_state['values']['add-stream-file-location'] = $fileObject->filepath;
-// TODO: Add error checking here.
+  $mimetype = new MimeClass();
+  $controlGroup = $form_state['values']['control_group'];
+  if (in_array($controlGroup, array('X', 'M')) && ($fileObject = file_save_upload('add-stream-file-location', $validators)) !== 0) {
+    // Move the uploaded file to Drupal's files directory.
+    file_move($fileObject->filepath, 0, 'FILE_EXISTS_RENAME');
+    $form_state['values']['add-stream-file-location'] = $fileObject->filepath;
+    $form_state['storage']['ds_mimetype'] = $mimetype->getType($fileObject->filepath);
+    
+    $file_basename = basename($fileObject->filepath);
+    $file_directory = dirname($fileObject->filepath);
+    
+    $form_state['storage']['stream_url'] = url($file_directory . '/' . drupal_urlencode($file_basename), array(
+      'absolute' => TRUE,
+    ));
+  }
+  elseif (in_array($controlGroup, array('M', 'R', 'E')) && ($ref = $form_state['values']['ds_reference'])) {
+    $form_state['storage']['ds_mimetype'] = $mimetype->getType($ref);
+    $form_state['storage']['stream_url'] = $form_state['values']['ds_reference'];
+  }
+  else {
+    form_set_error('', t('No file given when "X" or "M", or no reference given when "M", "R" or "E".'));
+  }
+  
+  // TODO: Add error checking here.
   $form_state['rebuild'] = FALSE;
 }
 
@@ -680,6 +687,11 @@ function fedora_repository_replace_stream_form_validate($form, &$form_state) {
 function fedora_repository_replace_stream_form_submit($form, &$form_state) {
   global $base_url;
   $file = $form_state['values']['file'];
+  
+  if ($file !== NULL) {
+    $file = $form_state['values']['reference'];
+  }
+  
   $pid = $form_state['values']['pid'];
   $dsid = $form_state['values']['dsId'];
   $dsLabel = $form_state['values']['dsLabel'];
@@ -702,14 +714,9 @@ function fedora_repository_replace_stream_form_submit($form, &$form_state) {
   $mimetype = new MimeClass();
   $dformat = $mimetype->getType($file->filepath);
 
-  module_load_include('inc', 'fedora_repository', 'api/fedora_item');
   $item = new Fedora_Item($pid);
   
-  if(in_array($info->datastream->controlGroup, array('M', 'X'))) {
-    $item->modify_datastream($streamUrl, $dsid, $dsLabel, $dformat);
-  } else {
-    drupal_set_message(t('Cannot replace Redirect or Managed Datastream.'), 'error');
-  }
+  $item->modify_datastream($streamUrl, $dsid, $dsLabel, $dformat);
 
   $form_state['redirect'] = 'fedora/repository/' . $pid;
 }
@@ -1052,7 +1059,6 @@ function fedora_repository_urlencode_string($str) {
  * @return type 
  */
 function fedora_object_as_attachment($pid, $dsId, $label=NULL, $version=NULL) {
-  global $user;
   module_load_include('inc', 'fedora_repository', 'ObjectHelper');
 
   if ($pid == NULL || $dsId == NULL) {
@@ -1061,7 +1067,7 @@ function fedora_object_as_attachment($pid, $dsId, $label=NULL, $version=NULL) {
   }
 
   $objectHelper = new ObjectHelper();
-  $objectHelper->makeObject($pid, $dsId, 1, $label, FALSE, $version);
+  $objectHelper->makeObject($pid, $dsId, TRUE, $label, FALSE, $version);
 }
 
 /**
diff --git a/formClass.inc b/formClass.inc
index 713f1fcb..db90798c 100644
--- a/formClass.inc
+++ b/formClass.inc
@@ -656,17 +656,21 @@ class formClass {
       }
     }
 
-    $form['add_datastream_label'] = array(
-      '#value' => t('<br /><h3>Add Datastream:</h3>'),
-      '#weight' => -10,
+    $form['fieldset'] = array(
+      '#type' => 'fieldset',
+      '#title' => t('Add datastream'),
     );
+    //$form['add_datastream_label'] = array(
+    //  '#value' => t('<br /><h3>Add Datastream:</h3>'),
+    //  '#weight' => -10,
+    //);
 
-    $form['pid'] = array(
+    $form['fieldset']['pid'] = array(
       '#type' => 'hidden',
       '#value' => "$pid"
     );
 
-    $form['stream_label'] = array(
+    $form['fieldset']['stream_label'] = array(
       '#title' => 'Datastream Label',
       '#required' => 'TRUE',
       '#description' => t('A Human readable label'),
@@ -674,35 +678,37 @@ class formClass {
     );
 
     $form['#attributes']['enctype'] = 'multipart/form-data';
-    $form['add-stream-file-location'] = array(
+    $form['fieldset']['add-stream-file-location'] = array(
       '#type' => 'file',
       '#title' => t('Upload Document'),
       '#size' => 48,
       // '#required'=>'TRUE',
-      '#description' => t('The file to upload.')
+      '#description' => t('The file to upload. (Only for Managed and Inline)')
+    );
+    $form['fieldset']['ds_reference'] = array(
+      '#type' => 'textfield',
+      '#title' => t('Datastream reference'),
+      '#size' => 48,
+      '#description' => t('A URL reference to resolve for the contents of the datastream.  (Required for External and Redirect, but will still work for Managed and Inline.)'),
     );
     $form['#redirect'] = "fedora/repository/$pid/";
-    $form['submit'] = array(
+    $form['fieldset']['submit'] = array(
       '#type' => 'submit',
       '#value' => t('Add Datastream')
     );
 
     if (!empty($unused_dsids)) {
-      $dsidsForForm = array();
-      foreach ($unused_dsids as $dsid) {
-        $dsidsForForm[$dsid] = $dsid;
-      }
-      $form['stream_id'] = array(
+      $form['fieldset']['stream_id'] = array(
         '#type' => 'select',
         '#title' => t('Datastream ID'),
         '#default_value' => variable_get('feed_item_length', 'teaser'),
-        '#weight' => '-1',
+        '#weight' => -1,
         '#description' => t('Datastream IDs defined by the content model.'),
+        '#options' => array_combine($unused_dsids, $unused_dsids),
       );
-      $form['stream_id']['#options'] = array_combine($unused_dsids, $unused_dsids);
     }
     else {
-      $form['stream_id'] = array(
+      $form['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.'),
@@ -710,6 +716,18 @@ class formClass {
         '#weight' => -1,
       );
     }
+    $form['fieldset']['control_group'] = array(
+      '#type' => 'select',
+      '#title' => t('Control group'),
+      '#options' => array(
+        'X' => t('Inline XML'),
+        'M' => t('Managed datastream'),
+        'E' => t('Externally Referenced/managed datastream'),
+        'R' => t('Redirect datastream'),
+      ),
+      '#description' => t('The manner in which the datastream will be stored.  "Inline XML" must be XML and will be placed directly into the FOXML for the object.  "Managed" datastreams are made to live on the filesystem as discrete files in the Fedora data directory.  Both "Redirect" and "External" streams are URL references; the difference being the redirect stream instruct clients to perform an HTTP redirect, such that the data does not pass though Fedora (useful for streaming). External streams are mediated (by which I mean loaded and streamed from) the Fedora server.'),
+      '#weight' => 0,
+    );
     return $form;
   }
 
@@ -836,12 +854,33 @@ class formClass {
     $form = array();
 
     $form['#attributes']['enctype'] = 'multipart/form-data';
-    $form['file'] = array(
-      '#type' => 'file',
-      '#title' => t('Upload Document'),
-      '#description' => t('The file to upload.')
-    );
-
+    
+    module_load_include('inc', 'fedora_repository', 'api/fedora_item');
+    $item = new Fedora_Item($pid);
+    $info = $item->get_datastream_info($dsId);
+    $control_group = $info->datastream->controlGroup;
+    if (in_array($control_group, array('M', 'X'))) {
+      $form['file'] = array(
+        '#type' => 'file',
+        '#title' => t('Upload Document'),
+        '#description' => t('A file with which to replace the contents of this datastream.'),
+      );
+    }
+    if ($control_group != 'X') {
+      $form['reference'] = array(
+        '#type' => 'textfield',
+        '#title' => t('Reference to object'),
+        '#description' => t('A URL the datastream will be updated to reference.'),
+      );
+    }
+    if ($control_group == 'M') {
+      $form['note'] = array(
+        '#type' => 'item',
+        '#title' => t('NOTE'),
+        '#value' => t('If both a file and a reference are given, the file will be given preference.'),
+      );
+    }
+    
     $form['pid'] = array(
       '#type' => 'value',
       '#value' => $pid,

From 8cfdc902ab4aed96ce89377b9947af994c241e9c Mon Sep 17 00:00:00 2001
From: Adam Vessey <adam@discoverygarden.ca>
Date: Wed, 25 Apr 2012 10:32:26 -0300
Subject: [PATCH 4/9] Fix issue with downloading versioned datastreams.

Had to do with migration to use of newer REST API; it takes the version
parameter differently, as a query parameter instead of a position in the
URL.
---
 ObjectHelper.inc         | 14 +++++++++-----
 fedora_repository.module |  3 ---
 2 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/ObjectHelper.inc b/ObjectHelper.inc
index e866f62f..c83c5eb8 100644
--- a/ObjectHelper.inc
+++ b/ObjectHelper.inc
@@ -72,7 +72,6 @@ class ObjectHelper {
       return ' ';
     }
 
-
     if (variable_get('fedora_object_restrict_datastreams', FALSE) == TRUE) {
       if (($cm = ContentModel::loadFromObject($pid)) == FALSE) {
         drupal_set_message(t("You do not have access to objects without an Islandora Content Model."), 'error');
@@ -91,7 +90,6 @@ class ObjectHelper {
     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
     $item = new Fedora_Item($pid);
 
-
     if (isset($item->datastreams[$dsID])) {
       $mimeType = $item->datastreams[$dsID]['MIMEType'];
       if ($label == NULL) {
@@ -123,8 +121,14 @@ class ObjectHelper {
         $mimeType = 'image/jpeg';
       }
       $url = variable_get('fedora_base_url', 'http://localhost:8080/fedora') . '/objects/' . $pid . '/datastreams/' . $dsID . '/content';
+      $query_options = array();
       if ($version) {
-        $url .= '/' . $version; //drupal_urlencode($version);
+        $query_options['asOfDateTime'] = $version; //drupal_urlencode($version);
+      }
+      if ($query_options) {
+        $url = url($url, array(
+          'query' => $query_options,
+        ));
       }
       $ch = curl_init();
       $user_agent = "Mozilla/4.0 pp(compatible; MSIE 5.01; Windows NT 5.0)";
@@ -184,7 +188,6 @@ class ObjectHelper {
         $curl_out = curl_exec($ch);
         if ($curl_out !== FALSE) {
           $info = curl_getinfo($ch, CURLINFO_EFFECTIVE_URL);
-          //dd($info, 'effective URL');
           if ($url !== $info) { //Handle redirect streams (the final URL is not the same as the Fedora URL)
           
             //Add the parameters passed to Drupal, leaving out the 'q'
@@ -195,7 +198,7 @@ class ObjectHelper {
             }
             
             header('HTTP/1.1 307 Moved Temporarily');
-            header('Location: ' . $info . '?' . http_build_query($query)); //Fedora seems to discard the query portion.
+            header('Location: ' . url($info, array('query' => $query)));
           }
           elseif ((isset($user) && $user->uid != 0) || $forceSoap || isset($_SERVER['HTTPS'])) { //If not anonymous, soap is force or we're using HTTPS
             //Have the webserver mediate the transfer (download and restream)
@@ -211,6 +214,7 @@ class ObjectHelper {
         }
         else {
           //Curl error...
+          watchdog('fedora_repository', 'Curl error.  Info: @info', array('@info' => print_r(curl_getinfo($ch), TRUE)), WATCHDOG_WARNING);
         }   
       }
       curl_close($ch);
diff --git a/fedora_repository.module b/fedora_repository.module
index 940d1585..28dc4e8e 100644
--- a/fedora_repository.module
+++ b/fedora_repository.module
@@ -2272,9 +2272,6 @@ function theme_fedora_repository_solution_packs_list($solution_packs) {
   $header = array();
   $rows = array();
 
-
-
-
   drupal_add_css(drupal_get_path('module', 'update') . '/update.css');
   return $output;
 }

From 7bc755f231380e0b99f472c6877b32a52dd630fa Mon Sep 17 00:00:00 2001
From: Adam Vessey <adam@discoverygarden.ca>
Date: Wed, 25 Apr 2012 11:04:13 -0300
Subject: [PATCH 5/9] Make control group selection optional.

---
 fedora_repository.module | 25 +++++++++++++-------
 formClass.inc            | 50 +++++++++++++++++++++++++---------------
 2 files changed, 49 insertions(+), 26 deletions(-)

diff --git a/fedora_repository.module b/fedora_repository.module
index 28dc4e8e..f14dde6b 100644
--- a/fedora_repository.module
+++ b/fedora_repository.module
@@ -388,7 +388,7 @@ function add_stream_form_submit($form, &$form_state) {
 
   try {
     $item = new Fedora_Item($pid);
-    $item->add_datastream_from_url($form_state['storage']['stream_url'], $dsid, $dsLabel, $form_state['storage']['ds_mimetype'], $form_state['values']['control_group']);
+    $item->add_datastream_from_url($form_state['storage']['stream_url'], $dsid, $dsLabel, $form_state['storage']['ds_mimetype'], $form_state['storage']['control_group']);
 
     if ($file = $form_state['values']['add-stream-file-location']) {
       $object_helper = new ObjectHelper();
@@ -450,14 +450,12 @@ function add_stream_form_validate($form, &$form_state) {
 //    'file_validate_image_resolution' => array('85x85'),
 //    'file_validate_size' => array(30 * 1024),
   );
-
-  $mimetype = new MimeClass();
-  $controlGroup = $form_state['values']['control_group'];
-  if (in_array($controlGroup, array('X', 'M')) && ($fileObject = file_save_upload('add-stream-file-location', $validators)) !== 0) {
+  
+  $controlGroup = $form_state['storage']['control_group'] = $form_state['values']['control_group'];
+  if ((($controlGroup && in_array($controlGroup, array('X', 'M'))) || !$controlGroup) && (($fileObject = file_save_upload('add-stream-file-location', $validators)) !== 0)) {
     // Move the uploaded file to Drupal's files directory.
     file_move($fileObject->filepath, 0, 'FILE_EXISTS_RENAME');
     $form_state['values']['add-stream-file-location'] = $fileObject->filepath;
-    $form_state['storage']['ds_mimetype'] = $mimetype->getType($fileObject->filepath);
     
     $file_basename = basename($fileObject->filepath);
     $file_directory = dirname($fileObject->filepath);
@@ -466,14 +464,25 @@ function add_stream_form_validate($form, &$form_state) {
       'absolute' => TRUE,
     ));
   }
-  elseif (in_array($controlGroup, array('M', 'R', 'E')) && ($ref = $form_state['values']['ds_reference'])) {
-    $form_state['storage']['ds_mimetype'] = $mimetype->getType($ref);
+  elseif ($controlGroup && in_array($controlGroup, array('M', 'R', 'E')) && ($ref = $form_state['values']['ds_reference'])) {
     $form_state['storage']['stream_url'] = $form_state['values']['ds_reference'];
   }
   else {
     form_set_error('', t('No file given when "X" or "M", or no reference given when "M", "R" or "E".'));
   }
   
+  $mimeClass = new MimeClass();
+  $mimetype = $form_state['storage']['ds_mimetype'] = $mimeClass->getType($form_state['storage']['stream_url']);
+  
+  if (!$controlGroup) {
+    if ($mimetype == 'text/xml') {
+      $form_state['storage']['control_group'] = 'X';
+    }
+    else {
+      $form_state['storage']['control_group'] = 'M';
+    }
+  }
+  
   // TODO: Add error checking here.
   $form_state['rebuild'] = FALSE;
 }
diff --git a/formClass.inc b/formClass.inc
index db90798c..a5f9bef6 100644
--- a/formClass.inc
+++ b/formClass.inc
@@ -331,6 +331,13 @@ class formClass {
       '#options' => array(ObjectHelper::$DISPLAY_ALWAYS => t('Always'), ObjectHelper::$DISPLAY_NEVER => t('Never'), ObjectHelper::$DISPLAY_NO_MODEL_OUTPUT => t('Only if no Content Model display output.')),
       '#description' => t('Determines when to display the list of objects when viewing a collection page.'),
     );
+    
+    $form['advanced']['fedora_control_group_control_during_ingest'] = array(
+      '#type' => 'checkbox',
+      '#title' => t('Allow control groups select in datastream ingest'),
+      '#description' => t('Whether or not we should allow the user to select which control group to ingest a stream as, or to follow the old paradigm--to add stream IDed as XML as inline, and everything else as managed.'),
+      '#default_value' => variable_get('fedora_control_group_control_during_ingest', FALSE),
+    );
 
     //Export functionality
     $form['advanced']['module']['export_area'] = array(
@@ -685,12 +692,16 @@ class formClass {
       // '#required'=>'TRUE',
       '#description' => t('The file to upload. (Only for Managed and Inline)')
     );
-    $form['fieldset']['ds_reference'] = array(
-      '#type' => 'textfield',
-      '#title' => t('Datastream reference'),
-      '#size' => 48,
-      '#description' => t('A URL reference to resolve for the contents of the datastream.  (Required for External and Redirect, but will still work for Managed and Inline.)'),
-    );
+    
+    if (variable_get('fedora_control_group_control_during_ingest', FALSE)) {
+      $form['fieldset']['ds_reference'] = array(
+        '#type' => 'textfield',
+        '#title' => t('Datastream reference'),
+        '#size' => 48,
+        '#description' => t('A URL reference to resolve for the contents of the datastream.  (Required for External and Redirect, but will still work for Managed and Inline.)'),
+      );
+    }
+    
     $form['#redirect'] = "fedora/repository/$pid/";
     $form['fieldset']['submit'] = array(
       '#type' => 'submit',
@@ -716,18 +727,21 @@ class formClass {
         '#weight' => -1,
       );
     }
-    $form['fieldset']['control_group'] = array(
-      '#type' => 'select',
-      '#title' => t('Control group'),
-      '#options' => array(
-        'X' => t('Inline XML'),
-        'M' => t('Managed datastream'),
-        'E' => t('Externally Referenced/managed datastream'),
-        'R' => t('Redirect datastream'),
-      ),
-      '#description' => t('The manner in which the datastream will be stored.  "Inline XML" must be XML and will be placed directly into the FOXML for the object.  "Managed" datastreams are made to live on the filesystem as discrete files in the Fedora data directory.  Both "Redirect" and "External" streams are URL references; the difference being the redirect stream instruct clients to perform an HTTP redirect, such that the data does not pass though Fedora (useful for streaming). External streams are mediated (by which I mean loaded and streamed from) the Fedora server.'),
-      '#weight' => 0,
-    );
+    
+    if (variable_get('fedora_control_group_control_during_ingest', FALSE)) {
+      $form['fieldset']['control_group'] = array(
+        '#type' => 'select',
+        '#title' => t('Control group'),
+        '#options' => array(
+          'X' => t('Inline XML'),
+          'M' => t('Managed datastream'),
+          'E' => t('Externally Referenced/managed datastream'),
+          'R' => t('Redirect datastream'),
+        ),
+        '#description' => t('The manner in which the datastream will be stored.  "Inline XML" must be XML and will be placed directly into the FOXML for the object.  "Managed" datastreams are made to live on the filesystem as discrete files in the Fedora data directory.  Both "Redirect" and "External" streams are URL references; the difference being the redirect stream instruct clients to perform an HTTP redirect, such that the data does not pass though Fedora (useful for streaming). External streams are mediated (by which I mean loaded and streamed from) the Fedora server.'),
+        '#weight' => 0,
+      );
+    }
     return $form;
   }
 

From 132248951db9ea383ce3d3c2a2d36a408da83e7a Mon Sep 17 00:00:00 2001
From: Adam Vessey <adam@discoverygarden.ca>
Date: Wed, 25 Apr 2012 12:33:04 -0300
Subject: [PATCH 6/9] Fix error when label contains an extension.

Error intro'd during datastream replace 'improvements'.
---
 fedora_repository.module | 37 ++++++++++++++++---------------------
 1 file changed, 16 insertions(+), 21 deletions(-)

diff --git a/fedora_repository.module b/fedora_repository.module
index f14dde6b..f5e8602e 100644
--- a/fedora_repository.module
+++ b/fedora_repository.module
@@ -674,10 +674,14 @@ function fedora_repository_replace_stream_form_validate($form, &$form_state) {
       return;
     }
     
+    /* -----------------------------------------------------------------
+     * TODO: need a better way to get mimetypes
+     */
     module_load_include('inc', 'fedora_repository', 'MimeClass');
     $mime = new MimeClass();
+    $mimetype = $form_state['storage']['mime_type'] = $mime->getType($file->filepath);
     
-    if ($mime->getType($file->filepath) == 'text/xml' && !DOMDocument::load($file->filepath)) {
+    if ($mimetype == 'text/xml' && !DOMDocument::load($file->filepath)) {
       form_set_error('file', 'Invalid XML format.');
       return;
     }
@@ -694,37 +698,28 @@ function fedora_repository_replace_stream_form_validate($form, &$form_state) {
  * @param array $form_state 
  */
 function fedora_repository_replace_stream_form_submit($form, &$form_state) {
-  global $base_url;
   $file = $form_state['values']['file'];
-  
-  if ($file !== NULL) {
-    $file = $form_state['values']['reference'];
-  }
-  
+
   $pid = $form_state['values']['pid'];
   $dsid = $form_state['values']['dsId'];
   $dsLabel = $form_state['values']['dsLabel'];
   
+  $streamUrl = ($file !== NULL) ? 
+    url($file->filepath, array('absolute' => TRUE)):
+    url($form_state['values']['reference'], array('absolute' => TRUE));
+    
   // Remove the original file extension from the label and add the new one
-  $indexOfDot = strrpos($dsLabel, '.'); //use strrpos to get the last dot
-  if ($indexOfDot !== FALSE) {
-    $dsLabel = substr($dsLabel, 0, $indexOfDot);
-    $dsLabel .= substr($file->filename, strrpos($file->filename, '.')); // Add the file extention to the end of the label.;
+  // use strrpos to get the last dot
+  if (($indexOfDot = strrpos($dsLabel, '.')) !== FALSE) {
+    $dsLabel = substr($dsLabel, 0, $indexOfDot) .
+      substr($streamUrl, strrpos($streamUrl, '.')); // Add the file extention to the end of the label.
   }
 
-  $streamUrl = url($file->filepath, array(
-    'absolute' => TRUE,
-  ));
+  
 
-  /* -----------------------------------------------------------------
-   * TODO: need a better way to get mimetypes
-   */
-  module_load_include('inc', 'fedora_repository', 'MimeClass');
-  $mimetype = new MimeClass();
-  $dformat = $mimetype->getType($file->filepath);
+  $dformat = $form_state['storage']['mime_type'];
 
   $item = new Fedora_Item($pid);
-  
   $item->modify_datastream($streamUrl, $dsid, $dsLabel, $dformat);
 
   $form_state['redirect'] = 'fedora/repository/' . $pid;

From 5b3fe1ef7627d9b6cf5b326dfdaa70b6b3a0aff5 Mon Sep 17 00:00:00 2001
From: Adam Vessey <adam@discoverygarden.ca>
Date: Thu, 26 Apr 2012 09:48:03 -0300
Subject: [PATCH 7/9] Use Sparql query for breadcrumbs.

---
 ObjectHelper.inc | 52 +++++++++++++++++++++++++++++++-----------------
 1 file changed, 34 insertions(+), 18 deletions(-)

diff --git a/ObjectHelper.inc b/ObjectHelper.inc
index c83c5eb8..1a60784b 100644
--- a/ObjectHelper.inc
+++ b/ObjectHelper.inc
@@ -969,21 +969,33 @@ class ObjectHelper {
       $breadcrumbs[] = l(t('Home'), '<front>');
     }
     else {
-      $query_string = 'select $parentObject $title $content from <#ri>
-                        where (
-                          <info:fedora/' . $pid . '> <fedora-model:label> $title
-                          and $parentObject <fedora-model:hasModel> $content
-                          and (
-                            <info:fedora/' . $pid . '> <fedora-rels-ext:isMemberOfCollection> $parentObject
-                            or <info:fedora/' . $pid . '> <fedora-rels-ext:isMemberOf> $parentObject
-                            or <info:fedora/' . $pid . '> <fedora-rels-ext:isPartOf> $parentObject
-                          )
-                          and $parentObject <fedora-model:state> <info:fedora/fedora-system:def/model#Active>
-                        )
-                        minus $content <mulgara:is> <info:fedora/fedora-system:FedoraObject-3.0>
-                        order by $title desc';
-
-      if (count($results = self::performItqlQuery($query_string)) > 0  && $level > 0) {
+      $sparql_query_string = <<<EOQ
+PREFIX fedora-model: <info:fedora/fedora-system:def/model#>
+PREFIX rels-ext: <info:fedora/fedora-system:def/relations-external#>
+SELECT ?parentObject ?title ?content
+FROM <#ri>
+WHERE {
+  ?this fedora-model:label ?title ;
+        ?relationship ?parentObject .
+  ?parentObject fedora-model:state fedora-model:Active ;
+                fedora-model:hasModel ?content .
+  FILTER(
+    sameTerm(?this, <info:fedora/$pid>) &&
+    (
+      sameTerm(?relationship, rels-ext:isMemberOfCollection) ||
+      sameTerm(?relationship, rels-ext:isMemberOf) ||
+      sameTerm(?relationship, rels-ext:isPartOf)
+    ) &&
+    !sameTerm(?content, <info:fedora/fedora-system:FedoraObject-3.0>)
+  ) .
+}
+ORDER BY DESC(?title)
+EOQ;
+
+      $results = self::performSparqlQuery($sparql_query_string);
+      $next_pid = NULL;
+      
+      if (count($results) > 0  && $level > 0) {
         $parent = $results[0]['parentObject'];
         $this_title = $results[0]['title'];
 
@@ -993,13 +1005,17 @@ class ObjectHelper {
         
         $breadcrumbs[] = l($this_title, "fedora/repository/$pid");
         
-        $level--;
-        $this->getBreadcrumbs($parent, $breadcrumbs);
+        $next_pid = $parent;
       }
       else {
         watchdog('fedora_repository', 'Error generating breadcrumbs for %pid.  Verify there exists relationships back up to %root. (May also be due to a hierarchy deeper than %max_depth).', array('%pid' => $pid, '%root' => $root, '%max_depth' => $max_depth), WATCHDOG_WARNING);
         $breadcrumbs[] = '...'; //Add an non-link, as we don't know how to get back to the root.
-        $this->getBreadcrumbs($root, $breadcrumbs); //And render the last two links and break (on the next pass).
+        $next_pid = $root;  //And cue the last two links to render and break recursion (on the next pass).
+      }
+      
+      if ($next_pid !== NULL) {
+        $level--;
+        $this->getBreadcrumbs($next_pid, $breadcrumbs);
       }
     }
   }

From 3696cab9eac8832e4a9ba09ffc6bfd4ca9338333 Mon Sep 17 00:00:00 2001
From: Adam Vessey <adam@discoverygarden.ca>
Date: Thu, 26 Apr 2012 10:03:45 -0300
Subject: [PATCH 8/9] Generate the download form.

...  As opposed to spitting out markup for it directly.
---
 ObjectHelper.inc         | 18 +++---------------
 fedora_repository.module | 36 ++++++++++++++++++++++++++++++++++++
 2 files changed, 39 insertions(+), 15 deletions(-)

diff --git a/ObjectHelper.inc b/ObjectHelper.inc
index 1a60784b..aa093839 100644
--- a/ObjectHelper.inc
+++ b/ObjectHelper.inc
@@ -359,7 +359,7 @@ class ObjectHelper {
     $content = '';
     $id = $dataStreamValue->ID;
     $label = $dataStreamValue->label;
-    $label = str_replace("_", " ", $label);
+    //$label = str_replace("_", " ", $label);
     $label_deslashed = preg_replace('/\//i', '${1}_', $label); // Necessary to handle the case of Datastream labels that contain slashes. Ugh.
     $mimeType = $dataStreamValue->MIMEType;
 
@@ -368,20 +368,8 @@ class ObjectHelper {
         'target' => '_blank',
       ),
     ));
-    $action = url("fedora/repository/object_download/$pid/$id/$label_deslashed");
-    $downloadVersion = '<form method="GET" action="' . $action . '"><input type="submit" value="' . t('Download') . '"></form>';
-    if (user_access(ObjectHelper::$EDIT_FEDORA_METADATA)) {
-      $versions = $item->get_datastream_history($id);
-      if (is_array($versions)) {
-        $downloadVersion = '<form method="GET" action="' . $action . '" onsubmit="this.action=\'' . $action . '\' + \'/\'+this.version.value;">';
-        $downloadVersion .= '<input type="submit" value="' . t('Download') . '">';
-        $downloadVersion .= '<select name="version">';
-        foreach ($versions as $version) {
-          $downloadVersion .= '<option>' . $version->createDate . '</option>';
-        }
-        $downloadVersion .= '</select></form>';
-      }
-    }
+    
+    $downloadVersion = drupal_get_form('fedora_repository_download_datastream_form', $pid, $id, $label_deslashed);
 
     return array(
       array(
diff --git a/fedora_repository.module b/fedora_repository.module
index f5e8602e..5b6052b1 100644
--- a/fedora_repository.module
+++ b/fedora_repository.module
@@ -623,6 +623,42 @@ function fedora_repository_purge_stream_form_submit($form, &$form_state) {
   $form_state['redirect'] = $base_url . "/fedora/repository/$pid";
 }
 
+function fedora_repository_download_datastream_form(&$form_state, $pid, $dsid, $label) {
+  $form = array(
+    '#action' => url("fedora/repository/object_download/$pid/$dsid/$label"),
+    'submit' => array(
+      '#type' => 'submit',
+      '#value' => t('Download'),
+    ),
+  );
+  
+  if (user_access(ObjectHelper::$EDIT_FEDORA_METADATA)) {
+    $item = new Fedora_Item($pid);
+    $versions = $item->get_datastream_history($dsid);
+    $version_array = array();
+    if (is_array($versions)) {
+      foreach ($versions as $version) {
+        $version_array[] = $version->createDate;
+      }
+    }
+    else {
+      $version_array[] = $versions->createDate;
+    }
+    
+    if (count($version_array) > 1) {
+      $form['#attributes'] = array(
+        'onsubmit' => 'this.action="' . $form['#action'] . '/" + this.version.value;'
+      );
+      $form['version'] = array(
+        '#type' => 'select',
+        '#options' => array_combine($version_array, $version_array),
+      );
+    }
+  }
+  
+  return $form;
+}
+
 /**
  * fedora repository replace stream
  * @param type $pid

From 08545aa19498bd7bd76e0bca7bcd543f7b1aff59 Mon Sep 17 00:00:00 2001
From: Adam Vessey <adam@discoverygarden.ca>
Date: Thu, 26 Apr 2012 16:07:41 -0300
Subject: [PATCH 9/9] Fix error message.

Was using wrong variable name.
---
 ObjectHelper.inc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ObjectHelper.inc b/ObjectHelper.inc
index aa093839..f8195a11 100644
--- a/ObjectHelper.inc
+++ b/ObjectHelper.inc
@@ -996,7 +996,7 @@ EOQ;
         $next_pid = $parent;
       }
       else {
-        watchdog('fedora_repository', 'Error generating breadcrumbs for %pid.  Verify there exists relationships back up to %root. (May also be due to a hierarchy deeper than %max_depth).', array('%pid' => $pid, '%root' => $root, '%max_depth' => $max_depth), WATCHDOG_WARNING);
+        watchdog('fedora_repository', 'Error generating breadcrumbs for %pid.  Verify there exists relationships back up to %root. (May also be due to a hierarchy deeper than %max_depth).', array('%pid' => $pid, '%root' => $root, '%max_depth' => $max_level), WATCHDOG_WARNING);
         $breadcrumbs[] = '...'; //Add an non-link, as we don't know how to get back to the root.
         $next_pid = $root;  //And cue the last two links to render and break recursion (on the next pass).
       }