From 24cb55c7261b723f4d26de2af2311bb7c373254b Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Thu, 6 Feb 2014 16:17:23 -0400
Subject: [PATCH 01/52] wrapped command to avoid errors for uninstalled objects

---
 islandora.drush.inc | 28 +++++++++++++++-------------
 1 file changed, 15 insertions(+), 13 deletions(-)

diff --git a/islandora.drush.inc b/islandora.drush.inc
index acf3994f..4013c9a6 100644
--- a/islandora.drush.inc
+++ b/islandora.drush.inc
@@ -177,23 +177,25 @@ function drush_islandora_solution_pack_install_content_models() {
     $objects_to_add = array();
     foreach ($info['objects'] as $key => $candidate) {
       $object = islandora_object_load($candidate);
-      if (in_array('fedora-system:ContentModel-3.0', $object->models)) {
+      if ($object && in_array('fedora-system:ContentModel-3.0', $object->models)) {
         $objects_to_add[] = $candidate;
       }
     }
-    foreach ($objects_to_add as $object_to_add) {
-      $old_object = islandora_object_load($object_to_add->id);
-      if ($old_object) {
-        $deleted = islandora_delete_object($old_object);
-        if (!$deleted) {
-          drush_log(dt('@object did not delete.', array('@object' => $old_object->id), 'error'));
-          continue;
+    if (count($objects_to_add) > 0) {
+      foreach ($objects_to_add as $object_to_add) {
+        $old_object = islandora_object_load($object_to_add->id);
+        if ($old_object) {
+          $deleted = islandora_delete_object($old_object);
+          if (!$deleted) {
+            drush_log(dt('@object did not delete.', array('@object' => $old_object->id), 'error'));
+            continue;
+          }
+        }
+        $new_object = islandora_add_object($object_to_add);
+        $verb = $deleted ? dt("Replaced") : dt("Added");
+        if ($new_object) {
+          drush_log("$verb " . $object_to_add->id . " - " . $object_to_add->label);
         }
-      }
-      $new_object = islandora_add_object($object_to_add);
-      $verb = $deleted ? dt("Replaced") : dt("Added");
-      if ($new_object) {
-        drush_log("$verb " . $object_to_add->id . " - " . $object_to_add->label);
       }
     }
   }

From 024cf013fd79f1b712ba2a9160e20cc0596756e3 Mon Sep 17 00:00:00 2001
From: Jared Whiklo <jwhiklo@gmail.com>
Date: Fri, 7 Mar 2014 16:14:39 -0600
Subject: [PATCH 02/52] Check for hostname

You can enter the Djatoka URL as a relative path or full hostname. I did hostname and didn't get any errors. But this function assumes it is a path and sticks http(s)://<SERVER NAME> in front which causes you to get a blank Jpeg when downloading the clip.
---
 islandora.module | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/islandora.module b/islandora.module
index 9e7809eb..3c4ce68d 100644
--- a/islandora.module
+++ b/islandora.module
@@ -1540,9 +1540,12 @@ function islandora_entity_property_info() {
  */
 function islandora_download_clip(AbstractObject $object) {
   if (isset($_GET['clip'])) {
-    $is_https = isset($_SERVER['HTTPS']) && strtolower($_SERVER['HTTPS']) == 'on';
-    $http_protocol = $is_https ? 'https' : 'http';
-    $url = $http_protocol . '://' . $_SERVER['HTTP_HOST'] . $_GET['clip'];
+    $url = $_GET['clip'];
+    if (!preg_match('/^https?:\/\//',$url)) {
+      $is_https = isset($_SERVER['HTTPS']) && strtolower($_SERVER['HTTPS']) == 'on';
+      $http_protocol = $is_https ? 'https' : 'http';
+      $url = $http_protocol . '://' . $_SERVER['HTTP_HOST'] . $url;
+    }
     $filename = $object->label;
     header("Content-Disposition: attachment; filename=\"{$filename}.jpg\"");
     header("Content-type: image/jpeg");

From ab437cceb20f156ffc424911a85a1c68e75ab05d Mon Sep 17 00:00:00 2001
From: Jared Whiklo <jared_whiklo@umanitoba.ca>
Date: Mon, 10 Mar 2014 12:59:32 -0500
Subject: [PATCH 03/52] You wouldn't like Travis when he's angry.

---
 islandora.module | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/islandora.module b/islandora.module
index 3c4ce68d..97e339d7 100644
--- a/islandora.module
+++ b/islandora.module
@@ -1541,7 +1541,7 @@ function islandora_entity_property_info() {
 function islandora_download_clip(AbstractObject $object) {
   if (isset($_GET['clip'])) {
     $url = $_GET['clip'];
-    if (!preg_match('/^https?:\/\//',$url)) {
+    if (!preg_match('/^https?:\/\//', $url)) {
       $is_https = isset($_SERVER['HTTPS']) && strtolower($_SERVER['HTTPS']) == 'on';
       $http_protocol = $is_https ? 'https' : 'http';
       $url = $http_protocol . '://' . $_SERVER['HTTP_HOST'] . $url;

From 07d082dc7683b9f84701c41cfc8f99598433fe87 Mon Sep 17 00:00:00 2001
From: Adam Vessey <adam@discoverygarden.ca>
Date: Fri, 23 May 2014 17:26:22 +0000
Subject: [PATCH 04/52] Fix error due to incorrect include.

---
 theme/theme.inc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/theme/theme.inc b/theme/theme.inc
index c81a918d..06fc55b7 100644
--- a/theme/theme.inc
+++ b/theme/theme.inc
@@ -276,7 +276,7 @@ function islandora_preprocess_islandora_objects(array &$variables) {
  */
 function theme_islandora_datastream_download_link(array $vars) {
   $datastream = $vars['datastream'];
-  module_load_include('inc', 'islandora', 'includes/utilities');
+  module_load_include('inc', 'islandora', 'includes/datastream');
 
   $label = t('download');
   return islandora_datastream_access(ISLANDORA_VIEW_OBJECTS, $datastream) ?

From b0ca737cf82ab25ed240a00c8230272fe7486518 Mon Sep 17 00:00:00 2001
From: willtp87 <willtp87@hotmail.com>
Date: Mon, 2 Jun 2014 14:02:22 -0300
Subject: [PATCH 05/52] no need for bin mappings

---
 includes/mime_detect.inc | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/includes/mime_detect.inc b/includes/mime_detect.inc
index c1be1b92..a602ace2 100644
--- a/includes/mime_detect.inc
+++ b/includes/mime_detect.inc
@@ -203,8 +203,6 @@ class MimeDetect {
     "inp" => "chemical/x-gamess-input",
     // GAMESS Output.
     "gam" => "chemical/x-gamess-input",
-    // General output file.
-    "out" => "application/octet-stream",
     // Gaussian Cube.
     "cub" => "chemical/x-gaussian-cube",
     // Gaussian 98/03 Cartesian Input.
@@ -217,8 +215,6 @@ class MimeDetect {
     "dx" => "chemical/x-jcamp-dx",
     // MOPAC Cartesian.
     "mop" => "chemical/x-mopac-input",
-    // General Input File.
-    "in" => "application/octet-stream",
     // Compressed formats:
     // (note: http://svn.cleancode.org/svn/email/trunk/mime.types)
     "tgz" => "application/x-gzip",

From f8e7f8062b65f95fb255058eb19b627e7d066826 Mon Sep 17 00:00:00 2001
From: willtp87 <willtp87@hotmail.com>
Date: Mon, 2 Jun 2014 14:32:58 -0300
Subject: [PATCH 06/52] chem mime fixes

---
 includes/mime_detect.inc | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/includes/mime_detect.inc b/includes/mime_detect.inc
index a602ace2..310aa115 100644
--- a/includes/mime_detect.inc
+++ b/includes/mime_detect.inc
@@ -191,6 +191,8 @@ class MimeDetect {
     "xyz" => "chemical/x-xyz",
     // PDB.
     "pdb" => "chemical/x-pdb",
+    // ChemDraw CDX.
+    'cdx' => 'chemical/x-cdx',
     // ChemDraw 3D.
     "c3d" => "chemical/x-chem3d",
     // ChemDraw file.
@@ -208,7 +210,7 @@ class MimeDetect {
     // Gaussian 98/03 Cartesian Input.
     "gau" => "chemical/x-gaussian-input",
     // Corel Multimedia Manager v6 Album.
-    "gal" => "application/octet-stream",
+    'gal' => 'chemical/x-gaussian',
     // JCAMP Spectroscopic Data Exchange Format.
     "jdx" => "chemical/x-jcamp-dx",
     // OpenDX Grid.

From 7488ec6f1a8e7e31f665f2ced673c99711f887e3 Mon Sep 17 00:00:00 2001
From: willtp87 <willtp87@hotmail.com>
Date: Wed, 4 Jun 2014 15:42:44 -0300
Subject: [PATCH 07/52] better chem mimes

---
 includes/mime_detect.inc | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/includes/mime_detect.inc b/includes/mime_detect.inc
index 310aa115..03ece01f 100644
--- a/includes/mime_detect.inc
+++ b/includes/mime_detect.inc
@@ -204,13 +204,11 @@ class MimeDetect {
     // GAMESS Input.
     "inp" => "chemical/x-gamess-input",
     // GAMESS Output.
-    "gam" => "chemical/x-gamess-input",
+    "gam" => "chemical/x-gamess-output",
     // Gaussian Cube.
     "cub" => "chemical/x-gaussian-cube",
     // Gaussian 98/03 Cartesian Input.
     "gau" => "chemical/x-gaussian-input",
-    // Corel Multimedia Manager v6 Album.
-    'gal' => 'chemical/x-gaussian',
     // JCAMP Spectroscopic Data Exchange Format.
     "jdx" => "chemical/x-jcamp-dx",
     // OpenDX Grid.

From 0b7b08a254d2ef37453c85fdafd074ecbb0b8cfb Mon Sep 17 00:00:00 2001
From: nruest <ruestn@gmail.com>
Date: Fri, 6 Jun 2014 12:06:03 -0400
Subject: [PATCH 08/52] Address ISLANDORA-860

---
 includes/utilities.inc | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/includes/utilities.inc b/includes/utilities.inc
index fd6c1c3e..050921cc 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -445,8 +445,9 @@ function islandora_get_datastreams_requirements_from_content_model(AbstractObjec
 /**
  * Prepare an ingestable object.
  *
- * @param string $namespace
- *   The namespace in which the PID for the new object will be created.
+ * @param string $name_source
+ *   Either a pid or namespace in which the PID for the new object will be
+ *   created.
  * @param string $label
  *   An optional label to apply to the object.
  * @param array $datastreams
@@ -471,10 +472,10 @@ function islandora_get_datastreams_requirements_from_content_model(AbstractObjec
  * @return NewFedoraObject
  *   An ingestable NewFedoraObject.
  */
-function islandora_prepare_new_object($namespace = NULL, $label = NULL, $datastreams = array(), $content_models = array(), $relationships = array()) {
+function islandora_prepare_new_object($name_source = NULL, $label = NULL, $datastreams = array(), $content_models = array(), $relationships = array()) {
   global $user;
   $tuque = islandora_get_tuque_connection();
-  $object = isset($namespace) ? $tuque->repository->constructObject($namespace) : new IslandoraNewFedoraObject(NULL, $tuque->repository);
+  $object = isset($name_source) ? $tuque->repository->constructObject($name_source) : new IslandoraNewFedoraObject(NULL, $tuque->repository);
   $object->owner = isset($user->name) ? $user->name : $object->owner;
   $object->label = isset($label) ? $label : $object->label;
   foreach ($content_models as $content_model) {

From ab434c379a9df3aaf090900ce5792d2f57a1690e Mon Sep 17 00:00:00 2001
From: Adam Vessey <adam@discoverygarden.ca>
Date: Thu, 12 Jun 2014 12:58:26 +0000
Subject: [PATCH 09/52] Attempt to get use the new drush release.

---
 tests/scripts/travis_setup.sh | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/tests/scripts/travis_setup.sh b/tests/scripts/travis_setup.sh
index 66061c72..8cee24dd 100755
--- a/tests/scripts/travis_setup.sh
+++ b/tests/scripts/travis_setup.sh
@@ -18,19 +18,11 @@ pear upgrade --force pear
 pear channel-discover pear.drush.org
 
 # "prefer-source" required due to SSL shenanigans on the Travis boxes...
-composer global require --prefer-source 'squizlabs/php_codesniffer=*' 'sebastian/phpcpd=*'
+composer global require --prefer-source 'squizlabs/php_codesniffer=*' 'sebastian/phpcpd=*' 'drush/drush:6.3.0'
 # Because we can't add to the PATH here and this file is used in many repos,
 # let's just throw symlinks in.
 find $HOME/.composer/vendor/bin -executable \! -type d -exec sudo ln -s {}  /usr/local/sbin/ \;
 
-# Install Drush
-git clone https://github.com/drush-ops/drush.git
-pushd drush
-git checkout 5.9.0
-chmod +x drush
-popd
-sudo ln -s $HOME/drush/drush /usr/local/sbin
-
 phpenv rehash
 drush dl --yes drupal
 cd drupal-*

From fe615ea78ed247ec66176f8728349a01814afd1c Mon Sep 17 00:00:00 2001
From: Jordan Dukart <jordan@discoverygarden.ca>
Date: Thu, 26 Jun 2014 14:34:37 +0000
Subject: [PATCH 10/52] Change how the print works.

---
 islandora.module | 50 ++++++++++++++++++++++++++++++++++++------------
 js/add_print.js  | 18 -----------------
 2 files changed, 38 insertions(+), 30 deletions(-)
 delete mode 100644 js/add_print.js

diff --git a/islandora.module b/islandora.module
index ff077212..0cc2153a 100644
--- a/islandora.module
+++ b/islandora.module
@@ -142,9 +142,11 @@ function islandora_menu() {
     'access arguments' => array(ISLANDORA_VIEW_OBJECTS, 2),
   );
   $items['islandora/object/%islandora_object/print_object'] = array(
+    'title' => 'Print Object',
+    'weight' => 20,
     'page callback' => 'islandora_printer_object',
     'page arguments' => array(2),
-    'type' => MENU_NORMAL_ITEM,
+    'type' => MENU_LOCAL_TASK,
     'access callback' => 'islandora_object_access',
     'access arguments' => array(ISLANDORA_VIEW_OBJECTS, 2),
   );
@@ -182,6 +184,7 @@ function islandora_menu() {
         ISLANDORA_INGEST,
       ), 2),
   );
+  $islandora_path = drupal_get_path('module', 'islandora');
   $items['islandora/object/%islandora_object/manage/overview'] = array(
     'title' => 'Overview',
     'type' => MENU_DEFAULT_LOCAL_TASK,
@@ -1024,17 +1027,6 @@ function islandora_view_object(AbstractObject $object) {
   module_load_include('inc', 'islandora', 'includes/breadcrumb');
   module_load_include('inc', 'islandora', 'includes/utilities');
 
-  // Add the print button via JavaScript.
-  $path = drupal_get_path('module', 'islandora');
-  drupal_add_js(array(
-    'islandora' => array(
-      'print_img' => $path . '/images/print-icon.png'),
-      ), array(
-        'type' => 'setting'));
-
-  drupal_add_js(array('islandora' => array('print_link' => 'islandora/object/' . $object->id . '/print_object')), array('type' => 'setting'));
-  drupal_add_js($path . '/js/add_print.js');
-
   drupal_set_title($object->label);
   drupal_set_breadcrumb(islandora_get_breadcrumbs($object));
 
@@ -1913,3 +1905,37 @@ function islandora_find_package($package_name) {
   }
   return $found && user_access('administer site configuration');
 }
+
+/**
+ * Implements hook_menu_local_tasks_alter().
+ */
+function islandora_menu_local_tasks_alter(&$data, $router_item, $root_path) {
+  if (strpos($root_path, 'islandora/object/%') === 0) {
+    if (isset($data['tabs'][0]['output'])) {
+      foreach ($data['tabs'][0]['output'] as $key => &$tab) {
+        if ($tab['#link']['path'] == 'islandora/object/%/print_object') {
+          if ($root_path == 'islandora/object/%') {
+            $islandora_path = drupal_get_path('module', 'islandora');
+            $tab['#theme'] = 'link';
+            $tab['#text'] = theme('image', array(
+              'path' => "$islandora_path/images/print-icon.png",
+              'alt' => t('Print Object'),
+              'attributes' => array(
+                'id' => 'print_btn',
+              ),
+            ));
+            $tab['#path'] = "{$router_item['href']}/print_object";
+            $tab['#options'] = array(
+              'attributes' => array(),
+              'html' => TRUE,
+            );
+          }
+          else {
+            unset($data['tabs'][0]['output'][$key]);
+            break;
+          }
+        }
+      }
+    }
+  }
+}
\ No newline at end of file
diff --git a/js/add_print.js b/js/add_print.js
deleted file mode 100644
index 0059ed88..00000000
--- a/js/add_print.js
+++ /dev/null
@@ -1,18 +0,0 @@
-/**
- * @file
-* JavaScript file responsable for the print button behaviour.
-* 
-* The print button is added automatically to every view, as metadata
-* can be printed from every object.
-*
-*/
-(function ($) {
-  $(document).ready(function() {
-    $('.tabs .primary').append('<img id="print_btn" title="Print" src="' + Drupal.settings.basePath + Drupal.settings.islandora.print_img + '"></img>');
-    $('#print_btn').css("cursor","pointer");
-    $('#print_btn').click(function() {
-      window.location=Drupal.settings.basePath + Drupal.settings.islandora.print_link;
-    });
-  });
-})(jQuery);
- 

From 09aaf345142a412345b3d3c7b21d1dcdb45b8eac Mon Sep 17 00:00:00 2001
From: Jordan Dukart <jordan@discoverygarden.ca>
Date: Thu, 26 Jun 2014 15:57:02 +0000
Subject: [PATCH 11/52] Newline.

---
 islandora.module | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/islandora.module b/islandora.module
index 0cc2153a..31ea4e65 100644
--- a/islandora.module
+++ b/islandora.module
@@ -1938,4 +1938,4 @@ function islandora_menu_local_tasks_alter(&$data, $router_item, $root_path) {
       }
     }
   }
-}
\ No newline at end of file
+}

From 58a65f77454b4e0c8730d3484323b5a3be09e939 Mon Sep 17 00:00:00 2001
From: willtp87 <willtp87@hotmail.com>
Date: Thu, 26 Jun 2014 15:17:44 -0300
Subject: [PATCH 12/52] stray include removal

---
 theme/theme.inc | 1 -
 1 file changed, 1 deletion(-)

diff --git a/theme/theme.inc b/theme/theme.inc
index 06fc55b7..884025b4 100644
--- a/theme/theme.inc
+++ b/theme/theme.inc
@@ -203,7 +203,6 @@ function theme_islandora_object_print(array &$variables) {
  * Implements hook_preprocess_theme().
  */
 function islandora_preprocess_islandora_objects(array &$variables) {
-  module_load_include('inc', 'islandora_paged_content', 'includes/utilities');
   $display = (empty($_GET['display'])) ? 'grid' : $_GET['display'];
   $grid_display = $display == 'grid';
   $list_display = !$grid_display;

From 0fb4a6d7b6ab6b41a8dd413efd53c541f44d40f0 Mon Sep 17 00:00:00 2001
From: willtp87 <willtp87@hotmail.com>
Date: Sat, 28 Jun 2014 22:36:11 +0000
Subject: [PATCH 13/52] removing deprecated function
 islandora_datastream_get_delete_link

---
 includes/datastream.inc | 18 ------------------
 1 file changed, 18 deletions(-)

diff --git a/includes/datastream.inc b/includes/datastream.inc
index ba2872c2..fde9ab47 100644
--- a/includes/datastream.inc
+++ b/includes/datastream.inc
@@ -290,24 +290,6 @@ function islandora_datastream_get_url(AbstractDatastream $datastream, $type = 'd
   }
 }
 
-/**
- * Gets the delete link.
- *
- * @param AbstractDatastream $datastream
- *   The datastream to generated the url to.
- *
- * @return string
- *   Markup containing the link to the confirm form to delete the datastream.
- */
-function islandora_datastream_get_delete_link(AbstractDatastream $datastream) {
-  $message = islandora_deprecated('7.x-1.2', 'Use the "islandora_datastream_delete_link" theme implementation.');
-  trigger_error(filter_xss($message), E_USER_DEPRECATED);
-
-  return theme('islandora_datastream_delete_link', array(
-    'datastream' => $datastream,
-  ));
-}
-
 /**
  * Gets the edit link.
  *

From bba12090fd8b6c9ed6911b6ee1c391dfac1dd98c Mon Sep 17 00:00:00 2001
From: willtp87 <willtp87@hotmail.com>
Date: Sat, 28 Jun 2014 23:00:09 +0000
Subject: [PATCH 14/52] removing deprecated function
 islandora_datastream_edit_get_link

---
 includes/datastream.inc | 18 ------------------
 1 file changed, 18 deletions(-)

diff --git a/includes/datastream.inc b/includes/datastream.inc
index fde9ab47..a082a013 100644
--- a/includes/datastream.inc
+++ b/includes/datastream.inc
@@ -290,24 +290,6 @@ function islandora_datastream_get_url(AbstractDatastream $datastream, $type = 'd
   }
 }
 
-/**
- * Gets the edit link.
- *
- * @param AbstractDatastream $datastream
- *   The datastream to generated the url to.
- *
- * @return string
- *   Markup containing the link to edit the datastream.
- */
-function islandora_datastream_edit_get_link(AbstractDatastream $datastream) {
-  $message = islandora_deprecated('7.x-1.2', 'Use the "islandora_datastream_edit_link" theme implementation.');
-  trigger_error(filter_xss($message), E_USER_DEPRECATED);
-
-  return theme('islandora_datastream_edit_link', array(
-    'datastream' => $datastream,
-  ));
-}
-
 /**
  * Display the edit datastream page.
  *

From 17057c267646e97b42db383afc6585863a625bce Mon Sep 17 00:00:00 2001
From: willtp87 <willtp87@hotmail.com>
Date: Sat, 28 Jun 2014 23:17:03 +0000
Subject: [PATCH 15/52] removing deprecated function
 islandora_datastream_get_download_link

---
 includes/datastream.inc | 19 -------------------
 1 file changed, 19 deletions(-)

diff --git a/includes/datastream.inc b/includes/datastream.inc
index a082a013..94b819d7 100644
--- a/includes/datastream.inc
+++ b/includes/datastream.inc
@@ -337,25 +337,6 @@ function islandora_edit_datastream_registry_render(array $edit_registry) {
   );
 }
 
-/**
- * Get markup for a download link.
- *
- * @param AbstractDatastream $datastream
- *   The datastream for which to generate a link.
- *
- * @return string
- *   Either the link markup if the user has access or an empty string if the
- *   user is not allowed to see the given datastream.
- */
-function islandora_datastream_get_download_link(AbstractDatastream $datastream) {
-  $message = islandora_deprecated('7.x-1.2', 'Use the "islandora_datastream_download_link" theme implementation.');
-  trigger_error(filter_xss($message), E_USER_DEPRECATED);
-
-  return theme('islandora_datastream_download_link', array(
-    'datastream' => $datastream,
-  ));
-}
-
 /**
  * Get markup for a view link.
  *

From ddd9642d829386ee3a53d8dc4df94b9fb9f669a5 Mon Sep 17 00:00:00 2001
From: willtp87 <willtp87@hotmail.com>
Date: Mon, 30 Jun 2014 00:32:22 +0000
Subject: [PATCH 16/52] removing deprecated function
 islandora_datastream_get_view_link

---
 includes/datastream.inc | 19 -------------------
 1 file changed, 19 deletions(-)

diff --git a/includes/datastream.inc b/includes/datastream.inc
index 94b819d7..42d9ed96 100644
--- a/includes/datastream.inc
+++ b/includes/datastream.inc
@@ -337,25 +337,6 @@ function islandora_edit_datastream_registry_render(array $edit_registry) {
   );
 }
 
-/**
- * Get markup for a view link.
- *
- * @param AbstractDatastream $datastream
- *   The datastream for which to generate a link.
- *
- * @return string
- *   Either the link markup if the user has access or a string containing the
- *   datastream ID if the user is not allowed to see the given datastream.
- */
-function islandora_datastream_get_view_link(AbstractDatastream $datastream) {
-  $message = islandora_deprecated('7.x-1.2', 'Use the "islandora_datastream_view_link" theme implementation.');
-  trigger_error(filter_xss($message), E_USER_DEPRECATED);
-
-  return theme('islandora_datastream_view_link', array(
-    'datastream' => $datastream,
-  ));
-}
-
 /**
  * Set the headers for the chunking of our content.
  *

From 9014acf085ebcb21245fe1d585477c75870249bc Mon Sep 17 00:00:00 2001
From: willtp87 <willtp87@hotmail.com>
Date: Mon, 30 Jun 2014 17:28:54 +0000
Subject: [PATCH 17/52] better xsl handling

---
 includes/mime_detect.inc | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/includes/mime_detect.inc b/includes/mime_detect.inc
index 03ece01f..8aae5393 100644
--- a/includes/mime_detect.inc
+++ b/includes/mime_detect.inc
@@ -132,7 +132,8 @@ class MimeDetect {
     'wbxml' => 'application/vnd.wap.wbxml',
     'xht' => 'application/xhtml+xml',
     'xhtml' => 'application/xhtml+xml',
-    'xsl' => 'text/xml',
+    'xsl' => 'text/xsl',
+    'xslt' => 'text/xsl',
     'xml' => 'text/xml',
     'csv' => 'text/csv',
     'tsv' => 'text/tab-separated-values',

From 9ea9eeed6001f7423b5f489acaac97c7627f5dd6 Mon Sep 17 00:00:00 2001
From: willtp87 <willtp87@hotmail.com>
Date: Mon, 30 Jun 2014 18:45:34 +0000
Subject: [PATCH 18/52] datastream replacing mimes more accurate

---
 includes/datastream.version.inc | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/includes/datastream.version.inc b/includes/datastream.version.inc
index f245830c..515094bd 100644
--- a/includes/datastream.version.inc
+++ b/includes/datastream.version.inc
@@ -280,17 +280,16 @@ function islandora_datastream_version_replace_form($form, &$form_state, Abstract
   $form_state['object_id'] = $object->id;
   $form_state['dsid'] = $datastream->id;
   $form_state['object'] = $object;
-  $extensions = islandora_get_object_extensions($object);
+  $datastream_mime_map = islandora_get_object_extensions($object);
   $mime_detect = new MimeDetect();
   $ext = array();
-  if (isset($extensions[$datastream->id])) {
-    foreach ($extensions[$datastream->id]['mime'] as $key => $value) {
-      $str = $mime_detect->getExtension($value);
-      array_push($ext, $str);
+  if (isset($datastream_mime_map[$datastream->id])) {
+    foreach ($datastream_mime_map[$datastream->id]['mime'] as $key => $value) {
+      $extensions = $mime_detect->getValidExtensions($value);
+      $ext = array_merge($ext, $extensions);
     }
   }
-  $comma = count($ext) > 1 ? "," : "";
-  $ext = array(implode($comma, $ext));
+
   $upload_size = min((int) ini_get('post_max_size'), (int) ini_get('upload_max_filesize'));
   return array(
     'dsid_fieldset' => array(

From 2a127bb1533eb7fb48151667776407607bc49018 Mon Sep 17 00:00:00 2001
From: nruest <ruestn@gmail.com>
Date: Wed, 2 Jul 2014 23:08:38 -0400
Subject: [PATCH 19/52] I suppose we should have warc in here if we have a web
 archive solution pack.

---
 includes/mime_detect.inc | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/includes/mime_detect.inc b/includes/mime_detect.inc
index 8aae5393..74b87fd6 100644
--- a/includes/mime_detect.inc
+++ b/includes/mime_detect.inc
@@ -225,6 +225,8 @@ class MimeDetect {
     "zip" => "application/x-zip",
     // others:
     'bin' => 'application/octet-stream',
+    // Web Archives:
+    "warc" => "application/warc",
   );
   protected $protectedFileExtensions;
   protected $extensionExceptions = array(

From 022842a0a04271676cd69df2e8a631dbb830e12b Mon Sep 17 00:00:00 2001
From: Adam Vessey <adam@discoverygarden.ca>
Date: Thu, 3 Jul 2014 17:21:24 +0000
Subject: [PATCH 20/52] Move hooks calls a little higher.

Where they were in the API, modifications triggering other modifications were
causing old data to be used, so the second (and later) modifications would fail
due to "locking"... We now allow modifications to complete to the point where they
update the lastModifiedDate on instances of Tuque objects before invoking our hooks.
---
 includes/tuque_wrapper.inc | 92 +++++++++++++++++++++++---------------
 1 file changed, 57 insertions(+), 35 deletions(-)

diff --git a/includes/tuque_wrapper.inc b/includes/tuque_wrapper.inc
index 573d7c62..33881193 100644
--- a/includes/tuque_wrapper.inc
+++ b/includes/tuque_wrapper.inc
@@ -173,6 +173,30 @@ class IslandoraFedoraObject extends FedoraObject {
       throw $e;
     }
   }
+
+  /**
+   * Inherits.
+   *
+   * Calls parent and invokes object modified and deleted(/purged) hooks.
+   *
+   * @see FedoraObject::modifyObject()
+   */
+  protected function modifyObject($params) {
+    try {
+      parent::modifyObject($params);
+      islandora_invoke_object_hooks(ISLANDORA_OBJECT_MODIFIED_HOOK, $this->models, $this);
+      if ($this->state == 'D') {
+        islandora_invoke_object_hooks(ISLANDORA_OBJECT_PURGED_HOOK, $this->models, $this->id);
+      }
+    }
+    catch (Exception $e) {
+      watchdog('islandora', 'Failed to modify object: @pid</br>code: @code<br/>message: @msg', array(
+          '@pid' => $this->id,
+          '@code' => $e->getCode(),
+          '@msg' => $e->getMessage()), WATCHDOG_ERROR);
+      throw $e;
+    }
+  }
 }
 
 class IslandoraRepositoryConnection extends RepositoryConnection {}
@@ -219,25 +243,10 @@ class IslandoraFedoraApiM extends FedoraApiM {
     if (isset($params['lastModifiedDate'])) {
       $params['lastModifiedDate'] = (string) $object[$dsid]->createdDate;
     }
-    try {
-      if ($context['block']) {
-        throw new Exception('Modify Datastream was blocked.');
-      }
-      $ret = parent::modifyDatastream($pid, $dsid, $params);
-      islandora_invoke_datastream_hooks(ISLANDORA_DATASTREAM_MODIFIED_HOOK, $object->models, $dsid, $object, $datastream);
-      if (isset($params['dsState']) && $params['dsState'] == 'D') {
-        islandora_invoke_datastream_hooks(ISLANDORA_DATASTREAM_PURGED_HOOK, $object->models, $dsid, $object, $dsid);
-      }
-      return $ret;
-    }
-    catch (Exception $e) {
-      watchdog('islandora', 'Failed to modify datastream @dsid from @pid</br>code: @code<br/>message: @msg', array(
-          '@pid' => $pid,
-          '@dsid' => $dsid,
-          '@code' => $e->getCode(),
-          '@msg' => $e->getMessage()), WATCHDOG_ERROR);
-      throw $e;
+    if ($context['block']) {
+      throw new Exception('Modify Datastream was blocked.');
     }
+    return parent::modifyDatastream($pid, $dsid, $params);
   }
 
   /**
@@ -254,24 +263,10 @@ class IslandoraFedoraApiM extends FedoraApiM {
     );
     islandora_alter_object($object, $context);
     $params = $context['params'];
-    try {
-      if ($context['block']) {
-        throw new Exception('Modify Object was blocked.');
-      }
-      $ret = parent::modifyObject($pid, $params);
-      islandora_invoke_object_hooks(ISLANDORA_OBJECT_MODIFIED_HOOK, $object->models, $object);
-      if (isset($params['state']) && $params['state'] == 'D') {
-        islandora_invoke_object_hooks(ISLANDORA_OBJECT_PURGED_HOOK, $object->models, $object->id);
-      }
-      return $ret;
-    }
-    catch (Exception $e) {
-      watchdog('islandora', 'Failed to modify object: @pid</br>code: @code<br/>message: @msg', array(
-          '@pid' => $pid,
-          '@code' => $e->getCode(),
-          '@msg' => $e->getMessage()), WATCHDOG_ERROR);
-      throw $e;
+    if ($context['block']) {
+      throw new Exception('Modify Object was blocked.');
     }
+    return parent::modifyObject($pid, $params);
   }
 
   /**
@@ -377,6 +372,33 @@ class IslandoraNewFedoraDatastream extends NewFedoraDatastream {
 class IslandoraFedoraDatastream extends FedoraDatastream {
   protected $fedoraRelsIntClass = 'IslandoraFedoraRelsInt';
   protected $fedoraDatastreamVersionClass = 'IslandoraFedoraDatastreamVersion';
+
+  /**
+   * Inherits.
+   *
+   * Calls parent and invokes modified and purged hooks.
+   *
+   * @see FedoraDatastream::modifyDatastream()
+   */
+  protected function modifyDatastream(array $args) {
+    try {
+      parent::modifyDatastream($args);
+      // XXX: Reload datastream from parent.
+      $datastream = $this->parent[$this->id];
+      islandora_invoke_datastream_hooks(ISLANDORA_DATASTREAM_MODIFIED_HOOK, $this->parent->models, $this->id, $this->parent, $datastream);
+      if ($datastream->state == 'D') {
+        islandora_invoke_datastream_hooks(ISLANDORA_DATASTREAM_PURGED_HOOK, $this->parent->models, $this->id, $this->parent, $this->id);
+      }
+    }
+    catch (Exception $e) {
+      watchdog('islandora', 'Failed to modify datastream @dsid from @pid</br>code: @code<br/>message: @msg', array(
+          '@pid' => $this->parent->id,
+          '@dsid' => $this->id,
+          '@code' => $e->getCode(),
+          '@msg' => $e->getMessage()), WATCHDOG_ERROR);
+      throw $e;
+    }
+  }
 }
 
 class IslandoraFedoraDatastreamVersion extends FedoraDatastreamVersion {

From 2712214b81e3a9eb15163cb7a7b0ee0329eb61a3 Mon Sep 17 00:00:00 2001
From: vagrant <vagrant@dgi-vagrant-i7latest.16794.i7latest.dgicloud.com>
Date: Sun, 6 Jul 2014 19:10:04 +0000
Subject: [PATCH 21/52] Removing deprecated function
 islandor_get_comp_ds_mappings.

---
 includes/utilities.inc | 48 ------------------------------------------
 1 file changed, 48 deletions(-)

diff --git a/includes/utilities.inc b/includes/utilities.inc
index 050921cc..d0fffa94 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -649,54 +649,6 @@ function islandora_system_settings_form_default_value($name, $default_value, arr
   return isset($form_state['values'][$name]) ? $form_state['values'][$name] : variable_get($name, $default_value);
 }
 
-/**
- * Returns basic information about DS-COMPOSITE-MODEL.
- *
- * @deprecated
- *   The pre-existing--and more flexible--
- *   islandora_get_datastreams_requirements_from_content_model() should be
- *   preferred, as it addresses the case where a stream can be allowed to have
- *   one of a set of mimetypes (this functions appears to only return the last
- *   declared mimetype for a given datastream).
- *
- * @param string $pid
- *   The PID of content model containing DS_COMP stream.
- *
- * @return array
- *   An associative array mapping datastream IDs to an associative array
- *   representing the parsed DS-COMPOSITE-MODEL of the form:
- *   - DSID: A string containing the datastream ID.
- *     - "mimetype": A string containing the last mimetype declared for the
- *       given datastream ID.
- *     - "optional": An optional boolean indicating that the given datastream
- *       is optional.
- */
-function islandora_get_comp_ds_mappings($pid) {
-  $message = islandora_deprecated('7.x-1.2', t('Refactor to use the more flexible islandora_get_datastreams_requirements_from_content_model().'));
-  trigger_error(filter_xss($message), E_USER_DEPRECATED);
-
-  $cm_object = islandora_object_load($pid);
-  if (!isset($cm_object) || !isset($cm_object['DS-COMPOSITE-MODEL'])) {
-    return FALSE;
-  }
-  $datastream = $cm_object['DS-COMPOSITE-MODEL'];
-  $ds_comp_stream = $datastream->content;
-  $sxml = new SimpleXMLElement($ds_comp_stream);
-  $mappings = array();
-  foreach ($sxml->dsTypeModel as $ds) {
-    $dsid = (string) $ds['ID'];
-    $optional = (string) $ds['optional'];
-    foreach ($ds->form as $form) {
-      $mime = (string) $form['MIME'];
-      if ($optional) {
-        $mappings[$dsid]['optional'] = $optional;
-      }
-      $mappings[$dsid]['mimetype'] = $mime;
-    }
-  }
-  return $mappings;
-}
-
 /**
  * Checks that the given/current account has all the given permissions.
  *

From 29978b7a1ef3cbed8e63a0479b8bd1e556a3edfe Mon Sep 17 00:00:00 2001
From: Adam Vessey <adam@discoverygarden.ca>
Date: Tue, 8 Jul 2014 20:39:51 +0000
Subject: [PATCH 22/52] Resolve issue with recursing. Curse you, PHP!

---
 includes/tuque_wrapper.inc        | 76 +++++++++++++++++++++++++++++--
 tests/hooks.test                  |  4 ++
 tests/islandora_hooks_test.module |  8 ++++
 3 files changed, 84 insertions(+), 4 deletions(-)

diff --git a/includes/tuque_wrapper.inc b/includes/tuque_wrapper.inc
index 33881193..348ac60a 100644
--- a/includes/tuque_wrapper.inc
+++ b/includes/tuque_wrapper.inc
@@ -144,6 +144,41 @@ class IslandoraFedoraObject extends FedoraObject {
   protected $fedoraDatastreamClass = 'IslandoraFedoraDatastream';
   protected $fedoraRelsExtClass = 'IslandoraFedoraRelsExt';
 
+  /**
+   * Magical magic, to allow recursive modifications.
+   *
+   * So... Magic functions in PHP are not re-entrant... Meaning that if you
+   * have something which tries to call __set on an object anywhere later in
+   * the callstack after it has already been called, it will not call the
+   * magic method again; instead, it will set the property on the object
+   * proper. Here, we detect the property being set on the object proper, and
+   * restore the magic functionality as long as it keeps getting set...
+   *
+   * Not necessary to try to account for this in Tuque proper, as Tuque itself
+   * does not have a mechanism to trigger modifications resulting from other
+   * modifications.
+   *
+   * @param string $name
+   *   The name of the property being set.
+   * @param mixed $value
+   *   The value to which the property should be set.
+   */
+  public function __set($name, $value) {
+    parent::__set($name, $value);
+
+    // XXX: Due to the structure of the code, we cannot use property_exists()
+    // (because many of the properties are declared in the class, and the magic
+    // triggers due them being NULLed), nor can we use isset() (because it is
+    // implemented as another magic function...).
+    $vars = get_object_vars($this);
+    while (isset($vars[$name])) {
+      $new_value = $this->$name;
+      unset($this->$name);
+      parent::__set($name, $new_value);
+      $vars = get_object_vars($this);
+    }
+  }
+
   /**
    * Ingest the given datastream.
    *
@@ -373,6 +408,41 @@ class IslandoraFedoraDatastream extends FedoraDatastream {
   protected $fedoraRelsIntClass = 'IslandoraFedoraRelsInt';
   protected $fedoraDatastreamVersionClass = 'IslandoraFedoraDatastreamVersion';
 
+  /**
+   * Magical magic, to allow recursive modifications.
+   *
+   * So... Magic functions in PHP are not re-entrant... Meaning that if you
+   * have something which tries to call __set on an object anywhere later in
+   * the callstack after it has already been called, it will not call the
+   * magic method again; instead, it will set the property on the object
+   * proper. Here, we detect the property being set on the object proper, and
+   * restore the magic functionality as long as it keeps getting set...
+   *
+   * Not necessary to try to account for this in Tuque proper, as Tuque itself
+   * does not have a mechanism to trigger modifications resulting from other
+   * modifications.
+   *
+   * @param string $name
+   *   The name of the property being set.
+   * @param mixed $value
+   *   The value to which the property should be set.
+   */
+  public function __set($name, $value) {
+    parent::__set($name, $value);
+
+    // XXX: Due to the structure of the code, we cannot use property_exists()
+    // (because many of the properties are declared in the class, and the magic
+    // triggers due them being NULLed), nor can we use isset() (because it is
+    // implemented as another magic function...).
+    $vars = get_object_vars($this);
+    while (isset($vars[$name])) {
+      $new_value = $this->$name;
+      unset($this->$name);
+      parent::__set($name, $new_value);
+      $vars = get_object_vars($this);
+    }
+  }
+
   /**
    * Inherits.
    *
@@ -383,10 +453,8 @@ class IslandoraFedoraDatastream extends FedoraDatastream {
   protected function modifyDatastream(array $args) {
     try {
       parent::modifyDatastream($args);
-      // XXX: Reload datastream from parent.
-      $datastream = $this->parent[$this->id];
-      islandora_invoke_datastream_hooks(ISLANDORA_DATASTREAM_MODIFIED_HOOK, $this->parent->models, $this->id, $this->parent, $datastream);
-      if ($datastream->state == 'D') {
+      islandora_invoke_datastream_hooks(ISLANDORA_DATASTREAM_MODIFIED_HOOK, $this->parent->models, $this->id, $this->parent, $this);
+      if ($this->state == 'D') {
         islandora_invoke_datastream_hooks(ISLANDORA_DATASTREAM_PURGED_HOOK, $this->parent->models, $this->id, $this->parent, $this->id);
       }
     }
diff --git a/tests/hooks.test b/tests/hooks.test
index d08c537b..b8846c52 100644
--- a/tests/hooks.test
+++ b/tests/hooks.test
@@ -109,9 +109,11 @@ class IslandoraHooksTestCase extends IslandoraWebTestCase {
     $this->repository->ingestObject($object);
     $_SESSION['islandora_hooks']['hook'][ISLANDORA_OBJECT_MODIFIED_HOOK] = FALSE;
     $_SESSION['islandora_hooks']['alter'][ISLANDORA_OBJECT_MODIFIED_HOOK] = FALSE;
+    $_SESSION['islandora_hooks']['iteration'][ISLANDORA_OBJECT_MODIFIED_HOOK] = 0;
     $object->label = "New Label!";
     $this->assert($_SESSION['islandora_hooks']['alter'][ISLANDORA_OBJECT_MODIFIED_HOOK], 'Called "hook_islandora_object_alter" when modifying via set magic functions.');
     $this->assert($_SESSION['islandora_hooks']['hook'][ISLANDORA_OBJECT_MODIFIED_HOOK], 'Called ISLANDORA_OBJECT_MODIFIED_HOOK when modifying via set magic functions.');
+    $this->assertEqual('New Label! + 3', $object->label, 'Re-entered ISLANDORA_OBJECT_MODIFIED_HOOK when modifying via set magic functions.');
 
     // Test blocking the modification.
     try {
@@ -191,10 +193,12 @@ class IslandoraHooksTestCase extends IslandoraWebTestCase {
     $ds = $object->constructDatastream('TEST');
     $object->ingestDatastream($ds);
     $_SESSION['islandora_hooks']['hook'][ISLANDORA_DATASTREAM_MODIFIED_HOOK] = FALSE;
+    $_SESSION['islandora_hooks']['iteration'][ISLANDORA_DATASTREAM_MODIFIED_HOOK] = 0;
     $_SESSION['islandora_hooks']['alter'][ISLANDORA_DATASTREAM_MODIFIED_HOOK] = FALSE;
     $ds->label = "New Label!";
     $this->assert($_SESSION['islandora_hooks']['alter'][ISLANDORA_DATASTREAM_MODIFIED_HOOK], 'Called "hook_islandora_datastream_alter" when modifying via set magic functions.');
     $this->assert($_SESSION['islandora_hooks']['hook'][ISLANDORA_DATASTREAM_MODIFIED_HOOK], 'Called ISLANDORA_DATASTREAM_MODIFIED_HOOK when modifying via set magic functions.');
+    $this->assertEqual('New Label! + 3', $ds->label, 'Re-entered ISLANDORA_DATASTREAM_MODIFIED_HOOK when modifying via set magic functions.');
 
     // Test blocking modifying.
     try {
diff --git a/tests/islandora_hooks_test.module b/tests/islandora_hooks_test.module
index a6b8a5b6..cceb4dbc 100644
--- a/tests/islandora_hooks_test.module
+++ b/tests/islandora_hooks_test.module
@@ -112,6 +112,10 @@ function islandora_hooks_test_islandora_object_ingested(AbstractObject $object)
 function islandora_hooks_test_islandora_object_modified(AbstractObject $object) {
   if ($object->id == 'test:testModifiedObjectHook') {
     $_SESSION['islandora_hooks']['hook'][ISLANDORA_OBJECT_MODIFIED_HOOK] = TRUE;
+    if ($_SESSION['islandora_hooks']['iteration'][ISLANDORA_OBJECT_MODIFIED_HOOK]++ < 3) {
+      $new_label = 'New Label! + ' . $_SESSION['islandora_hooks']['iteration'][ISLANDORA_OBJECT_MODIFIED_HOOK];
+      $object->label = $new_label;
+    }
   }
 }
 
@@ -139,6 +143,10 @@ function islandora_hooks_test_islandora_datastream_ingested(AbstractObject $obje
 function islandora_hooks_test_islandora_datastream_modified(AbstractObject $object, AbstractDatastream $datastream) {
   if ($object->id == 'test:testModifiedDatastreamHook' && $datastream->id == "TEST") {
     $_SESSION['islandora_hooks']['hook'][ISLANDORA_DATASTREAM_MODIFIED_HOOK] = TRUE;
+    if ($_SESSION['islandora_hooks']['iteration'][ISLANDORA_DATASTREAM_MODIFIED_HOOK]++ < 3) {
+      $new_label = 'New Label! + ' . $_SESSION['islandora_hooks']['iteration'][ISLANDORA_DATASTREAM_MODIFIED_HOOK];
+      $datastream->label = $new_label;
+    }
   }
 }
 

From 6133b0973c082d7a4de1ca65a3b2e4d34cbf7cdb Mon Sep 17 00:00:00 2001
From: Jordan Dukart <jordan@discoverygarden.ca>
Date: Wed, 9 Jul 2014 18:45:30 +0000
Subject: [PATCH 23/52] Magic to get around a core Drupal problem.

---
 includes/ingest.form.inc |  6 +++++-
 islandora.module         | 16 ++++++++++++++++
 2 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/includes/ingest.form.inc b/includes/ingest.form.inc
index f7979063..b5a4740d 100644
--- a/includes/ingest.form.inc
+++ b/includes/ingest.form.inc
@@ -706,7 +706,11 @@ function islandora_ingest_form_ingest_button(array &$form_state) {
   $validate_callback = $form_id . '_validate';
   $validate = function_exists($validate_callback) ? array($validate_callback) : NULL;
   $submit_callback = $form_id . '_submit';
-  $submit = function_exists($submit_callback) ? array($submit_callback, 'islandora_ingest_form_submit') : array('islandora_ingest_form_submit');
+  $submit = function_exists($submit_callback) ? array(
+    $submit_callback,
+    'islandora_ingest_form_pre_submit',
+    'islandora_ingest_form_submit',
+  ) : array('islandora_ingest_form_pre_submit', 'islandora_ingest_form_submit');
   return array(
     '#type' => 'submit',
     '#name' => 'ingest',
diff --git a/islandora.module b/islandora.module
index ff077212..2b678b78 100644
--- a/islandora.module
+++ b/islandora.module
@@ -1913,3 +1913,19 @@ function islandora_find_package($package_name) {
   }
   return $found && user_access('administer site configuration');
 }
+
+/**
+ * Helper function for ingest steps and batches.
+ *
+ * When batches within batches are triggered within ingest steps
+ * the submit handler becomes out of scope. When it becomes time to execute the
+ * submit the function cannot be found and fails. This pre-submit is to
+ * get around this problem.
+ *
+ * @see https://www.drupal.org/node/2300367
+ *
+ * @see https://www.drupal.org/node/1300928
+ */
+function islandora_ingest_form_pre_submit($form, &$form_state) {
+  module_load_include('inc', 'islandora', 'includes/ingest.form');
+}

From b7b4717e493240d4d4b2ec00318d6ba4ceaa9e14 Mon Sep 17 00:00:00 2001
From: Jordan Dukart <jordan@discoverygarden.ca>
Date: Thu, 10 Jul 2014 17:24:14 +0000
Subject: [PATCH 24/52] Unused var.

---
 islandora.module | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/islandora.module b/islandora.module
index a626e131..118f7f78 100644
--- a/islandora.module
+++ b/islandora.module
@@ -184,7 +184,6 @@ function islandora_menu() {
         ISLANDORA_INGEST,
       ), 2),
   );
-  $islandora_path = drupal_get_path('module', 'islandora');
   $items['islandora/object/%islandora_object/manage/overview'] = array(
     'title' => 'Overview',
     'type' => MENU_DEFAULT_LOCAL_TASK,
@@ -1922,7 +1921,7 @@ function islandora_ingest_form_pre_submit($form, &$form_state) {
   module_load_include('inc', 'islandora', 'includes/ingest.form');
 }
 
-/* 
+/*
  * Implements hook_menu_local_tasks_alter().
  */
 function islandora_menu_local_tasks_alter(&$data, $router_item, $root_path) {

From d964ea204275b197138af1494c8aabad3a56c3a4 Mon Sep 17 00:00:00 2001
From: Jordan Dukart <jordan@discoverygarden.ca>
Date: Thu, 10 Jul 2014 18:06:59 +0000
Subject: [PATCH 25/52] Appease the Travis gods after a merge conflict fail.

---
 islandora.module | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/islandora.module b/islandora.module
index 118f7f78..f0bf796b 100644
--- a/islandora.module
+++ b/islandora.module
@@ -1921,7 +1921,7 @@ function islandora_ingest_form_pre_submit($form, &$form_state) {
   module_load_include('inc', 'islandora', 'includes/ingest.form');
 }
 
-/*
+/**
  * Implements hook_menu_local_tasks_alter().
  */
 function islandora_menu_local_tasks_alter(&$data, $router_item, $root_path) {
@@ -1954,4 +1954,3 @@ function islandora_menu_local_tasks_alter(&$data, $router_item, $root_path) {
     }
   }
 }
-

From 29b32e2c073aa8ddd38ef449e7e50b5843c9e0f8 Mon Sep 17 00:00:00 2001
From: willtp87 <willtp87@hotmail.com>
Date: Mon, 14 Jul 2014 13:32:32 +0000
Subject: [PATCH 26/52] not lying about units

---
 includes/utilities.inc | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/includes/utilities.inc b/includes/utilities.inc
index d0fffa94..26633df5 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -30,16 +30,16 @@ function islandora_convert_bytes_to_human_readable($bytes, $precision = 2) {
     return $bytes . ' B';
   }
   elseif (($bytes >= $kilobyte) && ($bytes < $megabyte)) {
-    return round($bytes / $kilobyte, $precision) . ' KB';
+    return round($bytes / $kilobyte, $precision) . ' KiB';
   }
   elseif (($bytes >= $megabyte) && ($bytes < $gigabyte)) {
-    return round($bytes / $megabyte, $precision) . ' MB';
+    return round($bytes / $megabyte, $precision) . ' MiB';
   }
   elseif (($bytes >= $gigabyte) && ($bytes < $terabyte)) {
-    return round($bytes / $gigabyte, $precision) . ' GB';
+    return round($bytes / $gigabyte, $precision) . ' GiB';
   }
   elseif ($bytes >= $terabyte) {
-    return round($bytes / $terabyte, $precision) . ' TB';
+    return round($bytes / $terabyte, $precision) . ' TiB';
   }
   else {
     return $bytes . ' B';

From 6ca6dc4c068954f970f8dc86d75867c2b11b76cc Mon Sep 17 00:00:00 2001
From: Jordan Dukart <jordan@discoverygarden.ca>
Date: Fri, 18 Jul 2014 11:55:44 +0000
Subject: [PATCH 27/52] Make sure our attribute doesn't break markup.

---
 theme/islandora-dublin-core-display.tpl.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/theme/islandora-dublin-core-display.tpl.php b/theme/islandora-dublin-core-display.tpl.php
index 52c80607..4badc619 100644
--- a/theme/islandora-dublin-core-display.tpl.php
+++ b/theme/islandora-dublin-core-display.tpl.php
@@ -20,7 +20,7 @@
     <dl xmlns:dcterms="http://purl.org/dc/terms/" class="islandora-inline-metadata islandora-metadata-fields islandora-object-fields">
       <?php $row_field = 0; ?>
       <?php foreach($dc_array as $key => $value): ?>
-        <dt property="<?php print $value['dcterms']; ?>" content="<?php print filter_xss($value['value']); ?>" class="<?php print $value['class']; ?><?php print $row_field == 0 ? ' first' : ''; ?>">
+        <dt property="<?php print $value['dcterms']; ?>" content="<?php print filter_xss(htmlspecialchars($value['value'], ENT_QUOTES, 'UTF-8')); ?>" class="<?php print $value['class']; ?><?php print $row_field == 0 ? ' first' : ''; ?>">
           <?php print filter_xss($value['label']); ?>
         </dt>
         <dd class="<?php print $value['class']; ?><?php print $row_field == 0 ? ' first' : ''; ?>">

From e65bddc8dc1356d938e86d628971ab804a5cfa6d Mon Sep 17 00:00:00 2001
From: willtp87 <willtp87@hotmail.com>
Date: Sat, 19 Jul 2014 15:51:01 +0000
Subject: [PATCH 28/52] php 5.5 in test matrix

---
 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index 84b226d0..ed29dbcd 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -2,6 +2,7 @@ language: php
 php:
   - 5.3.3
   - 5.4
+  - 5.5
 branches:
   only:
     - /^7.x/

From 369a99712312126d7c97661d67b256b2c9f5a39d Mon Sep 17 00:00:00 2001
From: nruest <ruestn@gmail.com>
Date: Tue, 22 Jul 2014 19:53:05 -0400
Subject: [PATCH 29/52] Add travis #islandora irc notifications

---
 .travis.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 84b226d0..213b8bcd 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -26,3 +26,5 @@ script:
   - drush test-run --uri=http://localhost:8081 Islandora
 after_failure:
   - $ISLANDORA_DIR/tests/scripts/travis_after_failure.sh
+notifications:
+  irc: "irc.freenode.org#islandora"

From 5d1d9a863033e67c554b51f1ed02e303368041f8 Mon Sep 17 00:00:00 2001
From: willtp87 <willtp87@hotmail.com>
Date: Mon, 28 Jul 2014 17:00:13 +0000
Subject: [PATCH 30/52] validator fix

---
 includes/datastream.version.inc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/includes/datastream.version.inc b/includes/datastream.version.inc
index 515094bd..83a94aef 100644
--- a/includes/datastream.version.inc
+++ b/includes/datastream.version.inc
@@ -289,7 +289,7 @@ function islandora_datastream_version_replace_form($form, &$form_state, Abstract
       $ext = array_merge($ext, $extensions);
     }
   }
-
+  $valid_extensions = implode(' ', $ext);
   $upload_size = min((int) ini_get('post_max_size'), (int) ini_get('upload_max_filesize'));
   return array(
     'dsid_fieldset' => array(
@@ -313,7 +313,7 @@ function islandora_datastream_version_replace_form($form, &$form_state, Abstract
         '#description' => t('Select a file to upload.<br/>Files must be less than <strong>@size MB.</strong>', array('@size' => $upload_size)),
         '#upload_location' => 'temporary://',
         '#upload_validators' => array(
-          'file_validate_extensions' => $ext,
+          'file_validate_extensions' => array($valid_extensions),
           // Assume its specified in MB.
           'file_validate_size' => array($upload_size * 1024 * 1024),
         ),

From 80f076f38579d67343719d641ba0f154e354053b Mon Sep 17 00:00:00 2001
From: MorganDawe <mdawe@discoverygarden.ca>
Date: Thu, 31 Jul 2014 16:15:34 +0000
Subject: [PATCH 31/52] Added application/rdf for file extension rng in
 mimedetect.

---
 includes/datastream.inc  | 2 --
 includes/mime_detect.inc | 1 +
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/includes/datastream.inc b/includes/datastream.inc
index ba2872c2..eabb9f94 100644
--- a/includes/datastream.inc
+++ b/includes/datastream.inc
@@ -54,7 +54,6 @@ function islandora_view_datastream(AbstractDatastream $datastream, $download = F
     // Browsers will not append all extensions.
     $mime_detect = new MimeDetect();
     $extension = '.' . $mime_detect->getExtension($datastream->mimetype);
-
     // Prevent adding on a duplicate extension.
     $label = $datastream->label;
     $extension_length = strlen($extension);
@@ -65,7 +64,6 @@ function islandora_view_datastream(AbstractDatastream $datastream, $download = F
     if ($duplicate_extension_position === FALSE) {
       $filename .= $extension;
     }
-
     header("Content-Disposition: attachment; filename=\"$filename\"");
   }
 
diff --git a/includes/mime_detect.inc b/includes/mime_detect.inc
index c1be1b92..93066bf1 100644
--- a/includes/mime_detect.inc
+++ b/includes/mime_detect.inc
@@ -226,6 +226,7 @@ class MimeDetect {
     "tar" => "application/x-tar",
     "gtar" => "application/x-gtar",
     "zip" => "application/x-zip",
+    "rng" => "application/xml",
     // others:
     'bin' => 'application/octet-stream',
   );

From f49f709bad1911f8f7607148116a5dfc4cfd6787 Mon Sep 17 00:00:00 2001
From: Adam Vessey <adam@discoverygarden.ca>
Date: Wed, 20 Aug 2014 16:45:10 -0300
Subject: [PATCH 32/52] Recursive things are exclusively magical.

...  Magically delicious, even.
---
 includes/tuque_wrapper.inc | 46 +++++++++++++++++++++++---------------
 1 file changed, 28 insertions(+), 18 deletions(-)

diff --git a/includes/tuque_wrapper.inc b/includes/tuque_wrapper.inc
index 348ac60a..21a1d0b2 100644
--- a/includes/tuque_wrapper.inc
+++ b/includes/tuque_wrapper.inc
@@ -166,16 +166,21 @@ class IslandoraFedoraObject extends FedoraObject {
   public function __set($name, $value) {
     parent::__set($name, $value);
 
-    // XXX: Due to the structure of the code, we cannot use property_exists()
-    // (because many of the properties are declared in the class, and the magic
-    // triggers due them being NULLed), nor can we use isset() (because it is
-    // implemented as another magic function...).
-    $vars = get_object_vars($this);
-    while (isset($vars[$name])) {
-      $new_value = $this->$name;
-      unset($this->$name);
-      parent::__set($name, $new_value);
+    // Recursion only matters for magic properties... "Plain" properties cannot
+    // call other code in order to start recursing, and in fact we would get
+    // stuck looping with a "plain" property.
+    if ($this->propertyIsMagical($name)) {
+      // XXX: Due to the structure of the code, we cannot use property_exists()
+      // (because many of the properties are declared in the class, and the magic
+      // triggers due them being NULLed), nor can we use isset() (because it is
+      // implemented as another magic function...).
       $vars = get_object_vars($this);
+      while (isset($vars[$name])) {
+        $new_value = $this->$name;
+        unset($this->$name);
+        parent::__set($name, $new_value);
+        $vars = get_object_vars($this);
+      }
     }
   }
 
@@ -430,16 +435,21 @@ class IslandoraFedoraDatastream extends FedoraDatastream {
   public function __set($name, $value) {
     parent::__set($name, $value);
 
-    // XXX: Due to the structure of the code, we cannot use property_exists()
-    // (because many of the properties are declared in the class, and the magic
-    // triggers due them being NULLed), nor can we use isset() (because it is
-    // implemented as another magic function...).
-    $vars = get_object_vars($this);
-    while (isset($vars[$name])) {
-      $new_value = $this->$name;
-      unset($this->$name);
-      parent::__set($name, $new_value);
+    // Recursion only matters for magic properties... "Plain" properties cannot
+    // call other code in order to start recursing, and in fact we would get
+    // stuck looping with a "plain" property.
+    if ($this->propertyIsMagical($name)) {
+      // XXX: Due to the structure of the code, we cannot use property_exists()
+      // (because many of the properties are declared in the class, and the magic
+      // triggers due them being NULLed), nor can we use isset() (because it is
+      // implemented as another magic function...).
       $vars = get_object_vars($this);
+      while (isset($vars[$name])) {
+        $new_value = $this->$name;
+        unset($this->$name);
+        parent::__set($name, $new_value);
+        $vars = get_object_vars($this);
+      }
     }
   }
 

From 862bde2d64aeb47a8d51c32c37f3c963f8c5cefe Mon Sep 17 00:00:00 2001
From: Adam Vessey <adam@discoverygarden.ca>
Date: Thu, 21 Aug 2014 09:31:06 -0300
Subject: [PATCH 33/52] Ermahgerd, lerns ter lerng.

---
 includes/tuque_wrapper.inc | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/includes/tuque_wrapper.inc b/includes/tuque_wrapper.inc
index 21a1d0b2..2f4ea1df 100644
--- a/includes/tuque_wrapper.inc
+++ b/includes/tuque_wrapper.inc
@@ -171,9 +171,9 @@ class IslandoraFedoraObject extends FedoraObject {
     // stuck looping with a "plain" property.
     if ($this->propertyIsMagical($name)) {
       // XXX: Due to the structure of the code, we cannot use property_exists()
-      // (because many of the properties are declared in the class, and the magic
-      // triggers due them being NULLed), nor can we use isset() (because it is
-      // implemented as another magic function...).
+      // (because many of the properties are declared in the class, and the
+      // magic triggers due them being NULLed), nor can we use isset() (because
+      // it is implemented as another magic function...).
       $vars = get_object_vars($this);
       while (isset($vars[$name])) {
         $new_value = $this->$name;
@@ -440,9 +440,9 @@ class IslandoraFedoraDatastream extends FedoraDatastream {
     // stuck looping with a "plain" property.
     if ($this->propertyIsMagical($name)) {
       // XXX: Due to the structure of the code, we cannot use property_exists()
-      // (because many of the properties are declared in the class, and the magic
-      // triggers due them being NULLed), nor can we use isset() (because it is
-      // implemented as another magic function...).
+      // (because many of the properties are declared in the class, and the
+      // magic triggers due them being NULLed), nor can we use isset() (because
+      // it is implemented as another magic function...).
       $vars = get_object_vars($this);
       while (isset($vars[$name])) {
         $new_value = $this->$name;

From 6b69518988bd8803a1d0859acf79daa185df5fa7 Mon Sep 17 00:00:00 2001
From: willtp87 <willtp87@hotmail.com>
Date: Thu, 21 Aug 2014 13:27:39 -0300
Subject: [PATCH 34/52] defer derivatives api

---
 includes/derivatives.inc                 | 39 ++++++++++++++++++++++++
 includes/regenerate_derivatives.form.inc |  2 ++
 islandora.module                         |  8 +++++
 3 files changed, 49 insertions(+)

diff --git a/includes/derivatives.inc b/includes/derivatives.inc
index 72d61235..7248f03f 100644
--- a/includes/derivatives.inc
+++ b/includes/derivatives.inc
@@ -4,6 +4,9 @@
  * Defines functions used when constructing derivatives.
  */
 
+// Relations.
+define('ISLANDORA_DEFER_DERIVATIVES_FLAG', 'deferDerivatives');
+
 /**
  * Decides which derivative function to call and runs it.
  *
@@ -245,3 +248,39 @@ function islandora_filter_derivatives($hooks, $options, AbstractObject $object)
   $hooks = array_filter($hooks, $filter_function);
   return $hooks;
 }
+
+/**
+ * Set the defer derivatives flag on an object.
+ */
+function islandora_set_defer_derivatives_flag(AbstractObject $object) {
+  $object->relationships->add(
+    ISLANDORA_RELS_EXT_URI,
+    ISLANDORA_DEFER_DERIVATIVES_FLAG,
+    'true',
+    RELS_TYPE_PLAIN_LITERAL
+  );
+}
+
+/**
+ * Get the defer derivatives flag on an object.
+ */
+function islandora_get_defer_derivatives_flag(AbstractObject $object) {
+  return $object->relationships->get(
+    ISLANDORA_RELS_EXT_URI,
+    ISLANDORA_DEFER_DERIVATIVES_FLAG,
+    'true',
+    RELS_TYPE_PLAIN_LITERAL
+  );
+}
+
+/**
+ * Remove the defer derivatives flag on an object.
+ */
+function islandora_remove_defer_derivatives_flag(AbstractObject $object) {
+  $object->relationships->remove(
+    ISLANDORA_RELS_EXT_URI,
+    ISLANDORA_DEFER_DERIVATIVES_FLAG,
+    'true',
+    RELS_TYPE_PLAIN_LITERAL
+  );
+}
diff --git a/includes/regenerate_derivatives.form.inc b/includes/regenerate_derivatives.form.inc
index 9a7a097e..437288c9 100644
--- a/includes/regenerate_derivatives.form.inc
+++ b/includes/regenerate_derivatives.form.inc
@@ -95,6 +95,7 @@ function islandora_regenerate_object_derivatives_form_submit(array $form, array
  */
 function islandora_regenerate_object_derivatives_batch(AbstractObject $object) {
   module_load_include('inc', 'islandora', 'includes/derivatives');
+  islandora_remove_defer_derivatives_flag($object);
   return array(
     'title' => t('Regenerating all derivatives for @label', array('@label' => $object->label)),
     'operations' => islandora_do_batch_derivatives($object, array('force' => TRUE)),
@@ -117,6 +118,7 @@ function islandora_regenerate_object_derivatives_batch(AbstractObject $object) {
  */
 function islandora_regenerate_datastream_derivative_batch(AbstractDatastream $datastream) {
   module_load_include('inc', 'islandora', 'includes/derivatives');
+  islandora_remove_defer_derivatives_flag($object);
   return array(
     'title' => t('Regenerating derivatives for the @dsid datastream', array('@dsid' => $datastream->id)),
     'operations' => islandora_do_batch_derivatives($datastream->parent, array(
diff --git a/islandora.module b/islandora.module
index f0bf796b..9c811611 100644
--- a/islandora.module
+++ b/islandora.module
@@ -1719,6 +1719,10 @@ function islandora_islandora_basic_collection_get_query_filters() {
  */
 function islandora_islandora_object_ingested(AbstractObject $object) {
   module_load_include('inc', 'islandora', 'includes/derivatives');
+  // Defer derivatives if necessary.
+  if (islandora_get_defer_derivatives_flag($object)) {
+    return;
+  }
   islandora_run_derivatives($object, NULL);
 }
 
@@ -1730,6 +1734,10 @@ function islandora_islandora_object_ingested(AbstractObject $object) {
  */
 function islandora_islandora_datastream_ingested(AbstractObject $object, AbstractDatastream $datastream) {
   module_load_include('inc', 'islandora', 'includes/derivatives');
+  // Defer derivatives if necessary.
+  if (islandora_get_defer_derivatives_flag($object)) {
+    return;
+  }
   islandora_run_derivatives($object, $datastream->id);
 }
 

From 3850720e65785e101934b054f0a6c4a0e8687474 Mon Sep 17 00:00:00 2001
From: willtp87 <willtp87@hotmail.com>
Date: Thu, 21 Aug 2014 15:30:42 -0300
Subject: [PATCH 35/52] global defer derivatives setting

---
 includes/admin.form.inc |  7 +++++++
 islandora.install       |  1 +
 islandora.module        | 11 +++++++++++
 3 files changed, 19 insertions(+)

diff --git a/includes/admin.form.inc b/includes/admin.form.inc
index 69f09fd2..a1edde0b 100644
--- a/includes/admin.form.inc
+++ b/includes/admin.form.inc
@@ -61,6 +61,13 @@ function islandora_repository_admin(array $form, array &$form_state) {
           '#description' => t('HTTP caching can reduce network traffic, by allowing clients to used cached copies.'),
           '#default_value' => variable_get('islandora_use_datastream_cache_headers', TRUE),
         ),
+        'islandora_defer_derivataves_on_ingest' => array(
+          '#type' => 'checkbox',
+          '#title' => t('Defer derivative generation during ingest'),
+          '#description' => t('Prevent derivatives from running during ingest,
+            useful if derivatives are to be created by an external service.'),
+          '#default_value' => variable_get('islandora_defer_derivataves_on_ingest', FALSE),
+        ),
       ),
       'islandora_namespace' => array(
         '#type' => 'fieldset',
diff --git a/islandora.install b/islandora.install
index f37894e9..8f88dcdd 100644
--- a/islandora.install
+++ b/islandora.install
@@ -46,6 +46,7 @@ function islandora_uninstall() {
   // Add new variables to clean up.
   $variables = array(
     'islandora_ds_replace_exclude_enforced',
+    'islandora_defer_derivataves_on_ingest',
   );
   array_walk($variables, 'variable_del');
 }
diff --git a/islandora.module b/islandora.module
index 9c811611..4691028e 100644
--- a/islandora.module
+++ b/islandora.module
@@ -1962,3 +1962,14 @@ function islandora_menu_local_tasks_alter(&$data, $router_item, $root_path) {
     }
   }
 }
+
+/**
+ * Implements hook_islandora_object_alter().
+ */
+function islandora_islandora_object_alter(AbstractObject $object, array &$context) {
+  // Prevent derivative creation during ingest if var is set.
+  if ($context['action'] == 'ingest' && variable_get('islandora_defer_derivataves_on_ingest', FALSE)) {
+    module_load_include('inc', 'islandora', 'includes/derivatives');
+    islandora_set_defer_derivatives_flag($object);
+  }
+}

From 25b53ba01b8270072fc7cfaeb9d7879e5bf68932 Mon Sep 17 00:00:00 2001
From: willtp87 <willtp87@hotmail.com>
Date: Mon, 25 Aug 2014 10:13:24 -0300
Subject: [PATCH 36/52] copypasta omm nom

---
 includes/regenerate_derivatives.form.inc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/includes/regenerate_derivatives.form.inc b/includes/regenerate_derivatives.form.inc
index 437288c9..1312bec3 100644
--- a/includes/regenerate_derivatives.form.inc
+++ b/includes/regenerate_derivatives.form.inc
@@ -118,7 +118,7 @@ function islandora_regenerate_object_derivatives_batch(AbstractObject $object) {
  */
 function islandora_regenerate_datastream_derivative_batch(AbstractDatastream $datastream) {
   module_load_include('inc', 'islandora', 'includes/derivatives');
-  islandora_remove_defer_derivatives_flag($object);
+  islandora_remove_defer_derivatives_flag($datastream->parent);
   return array(
     'title' => t('Regenerating derivatives for the @dsid datastream', array('@dsid' => $datastream->id)),
     'operations' => islandora_do_batch_derivatives($datastream->parent, array(

From 4dbf46adc9f523bd5cdc8e8de831457161d931a4 Mon Sep 17 00:00:00 2001
From: MorganDawe <mdawe@discoverygarden.ca>
Date: Mon, 25 Aug 2014 15:23:49 -0300
Subject: [PATCH 37/52] Removed rng => application/xml mapping.

---
 includes/mime_detect.inc | 1 -
 1 file changed, 1 deletion(-)

diff --git a/includes/mime_detect.inc b/includes/mime_detect.inc
index 67566743..74b87fd6 100644
--- a/includes/mime_detect.inc
+++ b/includes/mime_detect.inc
@@ -223,7 +223,6 @@ class MimeDetect {
     "tar" => "application/x-tar",
     "gtar" => "application/x-gtar",
     "zip" => "application/x-zip",
-    "rng" => "application/xml",
     // others:
     'bin' => 'application/octet-stream',
     // Web Archives:

From f1de655d9a7294867eeed6b0d9252cbc967182e6 Mon Sep 17 00:00:00 2001
From: MorganDawe <mdawe@discoverygarden.ca>
Date: Mon, 25 Aug 2014 16:25:08 -0300
Subject: [PATCH 38/52] Updated mime detect class.

---
 includes/mime_detect.inc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/includes/mime_detect.inc b/includes/mime_detect.inc
index 74b87fd6..29fcf1e5 100644
--- a/includes/mime_detect.inc
+++ b/includes/mime_detect.inc
@@ -134,7 +134,7 @@ class MimeDetect {
     'xhtml' => 'application/xhtml+xml',
     'xsl' => 'text/xsl',
     'xslt' => 'text/xsl',
-    'xml' => 'text/xml',
+    'xml' => 'application/xml',
     'csv' => 'text/csv',
     'tsv' => 'text/tab-separated-values',
     'txt' => 'text/plain',

From 2b2c5c8601aa62b13d8d926e9d58d24c9d051c7b Mon Sep 17 00:00:00 2001
From: MorganDawe <mdawe@discoverygarden.ca>
Date: Wed, 27 Aug 2014 16:43:53 -0300
Subject: [PATCH 39/52] Updating extestion and mime detection on download to
 use drupals file_g=default_mimetype_mapping() funcitons.

---
 includes/datastream.inc | 4 ++--
 includes/utilities.inc  | 9 +++++++++
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/includes/datastream.inc b/includes/datastream.inc
index edc8ceb1..e31ed254 100644
--- a/includes/datastream.inc
+++ b/includes/datastream.inc
@@ -30,6 +30,7 @@ function islandora_download_datastream(AbstractDatastream $datastream) {
  *   The version of the datastream to display
  */
 function islandora_view_datastream(AbstractDatastream $datastream, $download = FALSE, $version = NULL) {
+  module_load_include('inc', 'islandora', 'includes/utilities');
   // XXX: Certain features of the Devel module rely on the use of "shutdown
   // handlers", such as query logging... The problem is that they might blindly
   // add additional output which will break things if what is actually being
@@ -45,7 +46,6 @@ function islandora_view_datastream(AbstractDatastream $datastream, $download = F
       return drupal_not_found();
     }
   }
-
   header('Content-type: ' . $datastream->mimetype);
   if ($datastream->controlGroup == 'M' || $datastream->controlGroup == 'X') {
     header('Content-length: ' . $datastream->size);
@@ -53,7 +53,7 @@ function islandora_view_datastream(AbstractDatastream $datastream, $download = F
   if ($download) {
     // Browsers will not append all extensions.
     $mime_detect = new MimeDetect();
-    $extension = '.' . $mime_detect->getExtension($datastream->mimetype);
+    $extension = '.' . islandora_get_extension_for_mimetype($datastream->mimetype);//$mime_detect->getExtension($datastream->mimetype);
     // Prevent adding on a duplicate extension.
     $label = $datastream->label;
     $extension_length = strlen($extension);
diff --git a/includes/utilities.inc b/includes/utilities.inc
index 26633df5..4892a4eb 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -46,6 +46,15 @@ function islandora_convert_bytes_to_human_readable($bytes, $precision = 2) {
   }
 }
 
+function islandora_get_extension_for_mimetype($mimetype) {
+  module_load_include('inc', 'file', 'file.mimetypes.inc');
+  dsm($mimetype, "mimetype");
+  $mimetype_mapping = file_default_mimetype_mapping();
+  $extenstion_index = array_search($mimetype, $mimetype_mapping['mimetypes']);
+  $extenstion = array_search($extenstion_index, $mimetype_mapping['extensions']);
+  dsm($extenstion, "extenstion");
+  return $extenstion;
+}
 /**
  * Add a file as managed if is not already.
  *

From 5caf983df8cc8e285f3b6633de5047945b2ba135 Mon Sep 17 00:00:00 2001
From: qadan <daitken@discoverygarden.ca>
Date: Thu, 28 Aug 2014 13:41:52 -0300
Subject: [PATCH 40/52] make the drush webserver logs go somewhere real

---
 tests/scripts/travis_setup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/scripts/travis_setup.sh b/tests/scripts/travis_setup.sh
index 336087ed..70665985 100755
--- a/tests/scripts/travis_setup.sh
+++ b/tests/scripts/travis_setup.sh
@@ -40,7 +40,7 @@ drush si minimal --db-url=mysql://drupal:drupal@localhost/drupal --yes
 sudo chmod a+w sites/default/settings.php
 echo "include_once '$HOME/.composer/vendor/autoload.php';" >> sites/default/settings.php
 sudo chmod a-w sites/default/settings.php
-drush runserver --php-cgi=$HOME/.phpenv/shims/php-cgi localhost:8081 &>/dev/null &
+drush runserver --php-cgi=$HOME/.phpenv/shims/php-cgi localhost:8081 &>/tmp/drush_webserver.log &
 ln -s $ISLANDORA_DIR sites/all/modules/islandora
 mv sites/all/modules/islandora/tests/travis.test_config.ini sites/all/modules/islandora/tests/test_config.ini
 mkdir sites/all/libraries

From 8efd0c23fc0a060e31cd608ef9eb13ff70260a78 Mon Sep 17 00:00:00 2001
From: MorganDawe <mdawe@discoverygarden.ca>
Date: Thu, 28 Aug 2014 15:34:22 -0300
Subject: [PATCH 41/52] Updated file extension logic on ds download.

---
 includes/mime_detect.inc |  1 -
 includes/utilities.inc   | 29 ++++++++++++++++++++++-------
 islandora.module         |  1 +
 3 files changed, 23 insertions(+), 8 deletions(-)

diff --git a/includes/mime_detect.inc b/includes/mime_detect.inc
index 29fcf1e5..da2c69f3 100644
--- a/includes/mime_detect.inc
+++ b/includes/mime_detect.inc
@@ -134,7 +134,6 @@ class MimeDetect {
     'xhtml' => 'application/xhtml+xml',
     'xsl' => 'text/xsl',
     'xslt' => 'text/xsl',
-    'xml' => 'application/xml',
     'csv' => 'text/csv',
     'tsv' => 'text/tab-separated-values',
     'txt' => 'text/plain',
diff --git a/includes/utilities.inc b/includes/utilities.inc
index 4892a4eb..0612f895 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -46,15 +46,30 @@ function islandora_convert_bytes_to_human_readable($bytes, $precision = 2) {
   }
 }
 
+/**
+ * Retrieve the correct file extension for a give mimetype.
+ *
+ * @param string $mimetype
+ *   The mimetype whose extension is required.
+ *
+ * @return string
+ *   The extension mapped to the given mimetype.
+ */
 function islandora_get_extension_for_mimetype($mimetype) {
-  module_load_include('inc', 'file', 'file.mimetypes.inc');
-  dsm($mimetype, "mimetype");
-  $mimetype_mapping = file_default_mimetype_mapping();
-  $extenstion_index = array_search($mimetype, $mimetype_mapping['mimetypes']);
-  $extenstion = array_search($extenstion_index, $mimetype_mapping['extensions']);
-  dsm($extenstion, "extenstion");
-  return $extenstion;
+  require_once(DRUPAL_ROOT . '/includes/file.mimetypes.inc');
+
+  $mimetype_mapping = file_mimetype_mapping();
+  $extension_index = array_search($mimetype, $mimetype_mapping['mimetypes']);
+  $mime_array_flipped = array_reverse($mimetype_mapping['extensions']);
+  $extension = array_search($extension_index, $mime_array_flipped);
+
+  // We can only have one mapping in drupal for 'xml'.
+  if ($mimetype == "text/xml") {
+    return "xml";
+  }
+  return $extension;
 }
+
 /**
  * Add a file as managed if is not already.
  *
diff --git a/islandora.module b/islandora.module
index b2bb99b8..c930ba5f 100644
--- a/islandora.module
+++ b/islandora.module
@@ -1590,6 +1590,7 @@ function islandora_download_clip(AbstractObject $object) {
 function islandora_file_mimetype_mapping_alter(&$mapping) {
   $mime_detect = new MimeDetect();
   $types = $mime_detect->getMimeTypes();
+
   $diff = array_diff_key($types, $mapping['extensions']);
   foreach ($diff as $ext => $mime) {
     $mapping['mimetypes'][] = $mime;

From 4311be0f0dbde303e402a1e6b6165030734cf86e Mon Sep 17 00:00:00 2001
From: MorganDawe <mdawe@discoverygarden.ca>
Date: Thu, 28 Aug 2014 15:36:49 -0300
Subject: [PATCH 42/52] removed unused code.

---
 includes/datastream.inc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/includes/datastream.inc b/includes/datastream.inc
index e31ed254..5f48211c 100644
--- a/includes/datastream.inc
+++ b/includes/datastream.inc
@@ -53,7 +53,7 @@ function islandora_view_datastream(AbstractDatastream $datastream, $download = F
   if ($download) {
     // Browsers will not append all extensions.
     $mime_detect = new MimeDetect();
-    $extension = '.' . islandora_get_extension_for_mimetype($datastream->mimetype);//$mime_detect->getExtension($datastream->mimetype);
+    $extension = '.' . islandora_get_extension_for_mimetype($datastream->mimetype);
     // Prevent adding on a duplicate extension.
     $label = $datastream->label;
     $extension_length = strlen($extension);

From 212276f6d01b87be1d9a799d835b64d8e0517c7f Mon Sep 17 00:00:00 2001
From: MorganDawe <mdawe@discoverygarden.ca>
Date: Fri, 29 Aug 2014 08:55:21 -0300
Subject: [PATCH 43/52] Corrected small travis issue.

---
 includes/utilities.inc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/includes/utilities.inc b/includes/utilities.inc
index 0612f895..d3d2bbc3 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -56,7 +56,7 @@ function islandora_convert_bytes_to_human_readable($bytes, $precision = 2) {
  *   The extension mapped to the given mimetype.
  */
 function islandora_get_extension_for_mimetype($mimetype) {
-  require_once(DRUPAL_ROOT . '/includes/file.mimetypes.inc');
+  require_once DRUPAL_ROOT . "/includes/file.mimetypes.inc";
 
   $mimetype_mapping = file_mimetype_mapping();
   $extension_index = array_search($mimetype, $mimetype_mapping['mimetypes']);

From d2ecd81ba8ac8999d705184b26399fb992e77159 Mon Sep 17 00:00:00 2001
From: MorganDawe <mdawe@discoverygarden.ca>
Date: Tue, 2 Sep 2014 16:19:42 -0300
Subject: [PATCH 44/52] Code review feedback.

---
 includes/datastream.inc     |  2 +-
 includes/mimetype.utils.inc | 31 +++++++++++++++++++++++++++++++
 includes/utilities.inc      | 24 ------------------------
 3 files changed, 32 insertions(+), 25 deletions(-)
 create mode 100644 includes/mimetype.utils.inc

diff --git a/includes/datastream.inc b/includes/datastream.inc
index 5f48211c..592870b7 100644
--- a/includes/datastream.inc
+++ b/includes/datastream.inc
@@ -30,7 +30,7 @@ function islandora_download_datastream(AbstractDatastream $datastream) {
  *   The version of the datastream to display
  */
 function islandora_view_datastream(AbstractDatastream $datastream, $download = FALSE, $version = NULL) {
-  module_load_include('inc', 'islandora', 'includes/utilities');
+  module_load_include('inc', 'islandora', 'includes/mimetype.utils');
   // XXX: Certain features of the Devel module rely on the use of "shutdown
   // handlers", such as query logging... The problem is that they might blindly
   // add additional output which will break things if what is actually being
diff --git a/includes/mimetype.utils.inc b/includes/mimetype.utils.inc
new file mode 100644
index 00000000..989c55cd
--- /dev/null
+++ b/includes/mimetype.utils.inc
@@ -0,0 +1,31 @@
+<?php
+/**
+ * @file
+ * Mimetype specific utility functions.
+ */
+
+/**
+ * Retrieve the correct file extension for a give mimetype.
+ *
+ * @param string $mimetype
+ *   The mimetype whose extension is required.
+ *
+ * @return string
+ *   The extension mapped to the given mimetype.
+ */
+function islandora_get_extension_for_mimetype($mimetype) {
+  // file.mimetypes.inc is a part of Drupal core, however is not
+  // automatically loaded. Manually require it.
+  require_once DRUPAL_ROOT . "/includes/file.mimetypes.inc";
+
+  $mimetype_mapping = file_mimetype_mapping();
+  $extension_index = array_search($mimetype, $mimetype_mapping['mimetypes']);
+  $mime_array_flipped = array_reverse($mimetype_mapping['extensions']);
+  $extension = array_search($extension_index, $mime_array_flipped);
+
+  // We can only have one mapping in drupal for 'xml'.
+  if ($mimetype == "text/xml") {
+    return "xml";
+  }
+  return $extension;
+}
diff --git a/includes/utilities.inc b/includes/utilities.inc
index d3d2bbc3..26633df5 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -46,30 +46,6 @@ function islandora_convert_bytes_to_human_readable($bytes, $precision = 2) {
   }
 }
 
-/**
- * Retrieve the correct file extension for a give mimetype.
- *
- * @param string $mimetype
- *   The mimetype whose extension is required.
- *
- * @return string
- *   The extension mapped to the given mimetype.
- */
-function islandora_get_extension_for_mimetype($mimetype) {
-  require_once DRUPAL_ROOT . "/includes/file.mimetypes.inc";
-
-  $mimetype_mapping = file_mimetype_mapping();
-  $extension_index = array_search($mimetype, $mimetype_mapping['mimetypes']);
-  $mime_array_flipped = array_reverse($mimetype_mapping['extensions']);
-  $extension = array_search($extension_index, $mime_array_flipped);
-
-  // We can only have one mapping in drupal for 'xml'.
-  if ($mimetype == "text/xml") {
-    return "xml";
-  }
-  return $extension;
-}
-
 /**
  * Add a file as managed if is not already.
  *

From 7bba93d92b702a7aab913ab2bc82d8a2103c59d8 Mon Sep 17 00:00:00 2001
From: willtp87 <willtp87@hotmail.com>
Date: Thu, 4 Sep 2014 10:29:09 -0300
Subject: [PATCH 45/52] typo fix

---
 includes/admin.form.inc | 4 ++--
 islandora.install       | 2 +-
 islandora.module        | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/includes/admin.form.inc b/includes/admin.form.inc
index a1edde0b..42612ea0 100644
--- a/includes/admin.form.inc
+++ b/includes/admin.form.inc
@@ -61,12 +61,12 @@ function islandora_repository_admin(array $form, array &$form_state) {
           '#description' => t('HTTP caching can reduce network traffic, by allowing clients to used cached copies.'),
           '#default_value' => variable_get('islandora_use_datastream_cache_headers', TRUE),
         ),
-        'islandora_defer_derivataves_on_ingest' => array(
+        'islandora_defer_derivatives_on_ingest' => array(
           '#type' => 'checkbox',
           '#title' => t('Defer derivative generation during ingest'),
           '#description' => t('Prevent derivatives from running during ingest,
             useful if derivatives are to be created by an external service.'),
-          '#default_value' => variable_get('islandora_defer_derivataves_on_ingest', FALSE),
+          '#default_value' => variable_get('islandora_defer_derivatives_on_ingest', FALSE),
         ),
       ),
       'islandora_namespace' => array(
diff --git a/islandora.install b/islandora.install
index 8f88dcdd..12c92009 100644
--- a/islandora.install
+++ b/islandora.install
@@ -46,7 +46,7 @@ function islandora_uninstall() {
   // Add new variables to clean up.
   $variables = array(
     'islandora_ds_replace_exclude_enforced',
-    'islandora_defer_derivataves_on_ingest',
+    'islandora_defer_derivatives_on_ingest',
   );
   array_walk($variables, 'variable_del');
 }
diff --git a/islandora.module b/islandora.module
index 3b10d64b..27d0a894 100644
--- a/islandora.module
+++ b/islandora.module
@@ -1965,7 +1965,7 @@ function islandora_menu_local_tasks_alter(&$data, $router_item, $root_path) {
  */
 function islandora_islandora_object_alter(AbstractObject $object, array &$context) {
   // Prevent derivative creation during ingest if var is set.
-  if ($context['action'] == 'ingest' && variable_get('islandora_defer_derivataves_on_ingest', FALSE)) {
+  if ($context['action'] == 'ingest' && variable_get('islandora_defer_derivatives_on_ingest', FALSE)) {
     module_load_include('inc', 'islandora', 'includes/derivatives');
     islandora_set_defer_derivatives_flag($object);
   }

From 087db8b3b05febb2388732cdea816906313998d1 Mon Sep 17 00:00:00 2001
From: lutaylor <luke@discoverygarden.ca>
Date: Fri, 5 Sep 2014 15:06:35 -0300
Subject: [PATCH 46/52] adding reliable install source

---
 tests/scripts/travis_setup.sh | 25 +++++++++++++------------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/tests/scripts/travis_setup.sh b/tests/scripts/travis_setup.sh
index 0b33d4b0..5a8c78ef 100755
--- a/tests/scripts/travis_setup.sh
+++ b/tests/scripts/travis_setup.sh
@@ -1,14 +1,13 @@
 #!/bin/bash
-
 mysql -u root -e 'create database drupal;'
 mysql -u root -e "create database fedora;"
 mysql -u root -e "GRANT ALL PRIVILEGES ON fedora.* To 'fedora'@'localhost' IDENTIFIED BY 'fedora';"
 mysql -u root -e "GRANT ALL PRIVILEGES ON drupal.* To 'drupal'@'localhost' IDENTIFIED BY 'drupal';"
 cd $HOME
 git clone git://github.com/Islandora/tuque.git
-git clone -b $FEDORA_VERSION git://github.com/Islandora/islandora_tomcat.git
+wget http://alpha.library.yorku.ca/islandora_tomcat.$FEDORA_VERSION.tar.gz
+tar xf islandora_tomcat.$FEDORA_VERSION.tar.gz
 cd islandora_tomcat
-git fsck
 export CATALINA_HOME='.'
 export JAVA_OPTS="-Xms1024m -Xmx1024m -XX:MaxPermSize=512m -XX:+CMSClassUnloadingEnabled -Djavax.net.ssl.trustStore=$CATALINA_HOME/fedora/server/truststore -Djavax.net.ssl.trustStorePassword=tomcat"
 ./bin/startup.sh
@@ -18,20 +17,22 @@ pear upgrade --force Console_Getopt
 pear upgrade --force pear
 pear channel-discover pear.drush.org
 
-# "prefer-source" required due to SSL shenanigans on the Travis boxes...
-composer global require --prefer-source 'squizlabs/php_codesniffer=*' 'sebastian/phpcpd=*' 'drush/drush:6.3.0'
-# Because we can't add to the PATH here and this file is used in many repos,
-# let's just throw symlinks in.
-find $HOME/.composer/vendor/bin -executable \! -type d -exec sudo ln -s {}  /usr/local/sbin/ \;
+wget http://alpha.library.yorku.ca/drush-6.3.tar.gz
+tar xf drush-6.3.tar.gz
+sudo mv drush-6.3 /opt/
+sudo ln -s /opt/drush-6.3/drush /usr/bin/drush
+
+wget http://alpha.library.yorku.ca/PHP_CodeSniffer-1.5.4.tgz
+pear install PHP_CodeSniffer-1.5.4.tgz
+
+wget http://alpha.library.yorku.ca/phpcpd.phar
+sudo mv phpcpd.phar /usr/local/bin/phpcpd
+sudo chmod +x /usr/local/bin/phpcpd
 
 phpenv rehash
 drush dl --yes drupal
 cd drupal-*
 drush si minimal --db-url=mysql://drupal:drupal@localhost/drupal --yes
-# Needs to make things from Composer be available (PHP CS, primarily)
-sudo chmod a+w sites/default/settings.php
-echo "include_once '$HOME/.composer/vendor/autoload.php';" >> sites/default/settings.php
-sudo chmod a-w sites/default/settings.php
 drush runserver --php-cgi=$HOME/.phpenv/shims/php-cgi localhost:8081 &>/tmp/drush_webserver.log &
 ln -s $ISLANDORA_DIR sites/all/modules/islandora
 mv sites/all/modules/islandora/tests/travis.test_config.ini sites/all/modules/islandora/tests/test_config.ini

From dcc81b1fcde787c7e6f6b3c695abf61a482e0304 Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Thu, 11 Sep 2014 11:26:32 -0300
Subject: [PATCH 47/52] added islandora xml default for datastrram replacement

---
 includes/datastream.version.inc | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/includes/datastream.version.inc b/includes/datastream.version.inc
index 83a94aef..bd0b8942 100644
--- a/includes/datastream.version.inc
+++ b/includes/datastream.version.inc
@@ -275,6 +275,7 @@ function islandora_get_object_extensions(AbstractObject $object) {
 function islandora_datastream_version_replace_form($form, &$form_state, AbstractDatastream $datastream) {
   module_load_include('inc', 'islandora', 'includes/content_model');
   module_load_include('inc', 'islandora', 'includes/utilities');
+  module_load_include('inc', 'islandora', 'includes/mimetype.utils');
 
   $object = islandora_object_load($datastream->parent->id);
   $form_state['object_id'] = $object->id;
@@ -290,6 +291,7 @@ function islandora_datastream_version_replace_form($form, &$form_state, Abstract
     }
   }
   $valid_extensions = implode(' ', $ext);
+  $valid_extensions .= ' ' . islandora_get_extension_for_mimetype($datastream->mimetype);
   $upload_size = min((int) ini_get('post_max_size'), (int) ini_get('upload_max_filesize'));
   return array(
     'dsid_fieldset' => array(

From b7d20be402298b7fb145acdd2925dab13611f123 Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Fri, 12 Sep 2014 09:39:03 -0300
Subject: [PATCH 48/52] updated mimetype selection

---
 includes/datastream.version.inc | 14 +++++---------
 includes/mimetype.utils.inc     | 33 +++++++++++++++++++++++++++++++--
 2 files changed, 36 insertions(+), 11 deletions(-)

diff --git a/includes/datastream.version.inc b/includes/datastream.version.inc
index bd0b8942..8e7b789c 100644
--- a/includes/datastream.version.inc
+++ b/includes/datastream.version.inc
@@ -282,16 +282,12 @@ function islandora_datastream_version_replace_form($form, &$form_state, Abstract
   $form_state['dsid'] = $datastream->id;
   $form_state['object'] = $object;
   $datastream_mime_map = islandora_get_object_extensions($object);
-  $mime_detect = new MimeDetect();
-  $ext = array();
-  if (isset($datastream_mime_map[$datastream->id])) {
-    foreach ($datastream_mime_map[$datastream->id]['mime'] as $key => $value) {
-      $extensions = $mime_detect->getValidExtensions($value);
-      $ext = array_merge($ext, $extensions);
-    }
+  $mimes = $datastream_mime_map[$datastream->id]['mime'];
+  $drupal_extensions = array();
+  foreach ($mimes as $mime) {
+    $drupal_extensions = array_merge($drupal_extensions, islandora_get_extensions_for_mimetype($mime));
   }
-  $valid_extensions = implode(' ', $ext);
-  $valid_extensions .= ' ' . islandora_get_extension_for_mimetype($datastream->mimetype);
+  $valid_extensions = implode(' ', $drupal_extensions);
   $upload_size = min((int) ini_get('post_max_size'), (int) ini_get('upload_max_filesize'));
   return array(
     'dsid_fieldset' => array(
diff --git a/includes/mimetype.utils.inc b/includes/mimetype.utils.inc
index 989c55cd..a9ca5a6c 100644
--- a/includes/mimetype.utils.inc
+++ b/includes/mimetype.utils.inc
@@ -1,4 +1,5 @@
 <?php
+
 /**
  * @file
  * Mimetype specific utility functions.
@@ -20,8 +21,10 @@ function islandora_get_extension_for_mimetype($mimetype) {
 
   $mimetype_mapping = file_mimetype_mapping();
   $extension_index = array_search($mimetype, $mimetype_mapping['mimetypes']);
-  $mime_array_flipped = array_reverse($mimetype_mapping['extensions']);
-  $extension = array_search($extension_index, $mime_array_flipped);
+  if ($extension_index !== FALSE) {
+    $mime_array_flipped = array_reverse($mimetype_mapping['extensions']);
+    $extension = array_search($extension_index, $mime_array_flipped);
+  }
 
   // We can only have one mapping in drupal for 'xml'.
   if ($mimetype == "text/xml") {
@@ -29,3 +32,29 @@ function islandora_get_extension_for_mimetype($mimetype) {
   }
   return $extension;
 }
+
+/**
+ * Retrieve all file extensions for a give mimetype.
+ *
+ * @param string $mimetype
+ *   The mimetype whose extensions are required.
+ *
+ * @return array
+ *   All known legal extensions.
+ */
+function islandora_get_extensions_for_mimetype($mimetype) {
+  // file.mimetypes.inc is a part of Drupal core, however is not
+  // automatically loaded. Manually require it.
+  require_once DRUPAL_ROOT . "/includes/file.mimetypes.inc";
+  $mimetype_mapping = file_mimetype_mapping();
+  $index = array_search($mimetype, $mimetype_mapping['mimetypes']);
+  $extensions = array();
+  if ($index !== FALSE) {
+    $extensions = array_keys($mimetype_mapping['extensions'], $index);
+  }
+  // We can only have one mapping in drupal for 'xml'.
+  if ($mimetype == "text/xml") {
+    $extensions[] = 'xml';
+  }
+  return $extensions;
+}
\ No newline at end of file

From 3253323765dac9a90ce62b807331b5e1f26d25d4 Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Fri, 12 Sep 2014 09:42:26 -0300
Subject: [PATCH 49/52] updated mimetype selection

---
 includes/datastream.version.inc | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/includes/datastream.version.inc b/includes/datastream.version.inc
index 8e7b789c..be08fb38 100644
--- a/includes/datastream.version.inc
+++ b/includes/datastream.version.inc
@@ -283,11 +283,11 @@ function islandora_datastream_version_replace_form($form, &$form_state, Abstract
   $form_state['object'] = $object;
   $datastream_mime_map = islandora_get_object_extensions($object);
   $mimes = $datastream_mime_map[$datastream->id]['mime'];
-  $drupal_extensions = array();
+  $extensions = array();
   foreach ($mimes as $mime) {
-    $drupal_extensions = array_merge($drupal_extensions, islandora_get_extensions_for_mimetype($mime));
+    $extensions = array_merge($extensions, islandora_get_extensions_for_mimetype($mime));
   }
-  $valid_extensions = implode(' ', $drupal_extensions);
+  $valid_extensions = implode(' ', $extensions);
   $upload_size = min((int) ini_get('post_max_size'), (int) ini_get('upload_max_filesize'));
   return array(
     'dsid_fieldset' => array(

From cc49c28ddd809784861b0cdf6b278f524729875c Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Fri, 12 Sep 2014 10:10:00 -0300
Subject: [PATCH 50/52] coder

---
 includes/mimetype.utils.inc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/includes/mimetype.utils.inc b/includes/mimetype.utils.inc
index a9ca5a6c..3aef6994 100644
--- a/includes/mimetype.utils.inc
+++ b/includes/mimetype.utils.inc
@@ -57,4 +57,4 @@ function islandora_get_extensions_for_mimetype($mimetype) {
     $extensions[] = 'xml';
   }
   return $extensions;
-}
\ No newline at end of file
+}

From 9b49ec7bbfd07c8b661e3f53bbed62325e26ab44 Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Fri, 12 Sep 2014 10:28:41 -0300
Subject: [PATCH 51/52] allwed for existing non-standard mimetype

---
 includes/datastream.version.inc | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/includes/datastream.version.inc b/includes/datastream.version.inc
index be08fb38..e97640d4 100644
--- a/includes/datastream.version.inc
+++ b/includes/datastream.version.inc
@@ -282,7 +282,11 @@ function islandora_datastream_version_replace_form($form, &$form_state, Abstract
   $form_state['dsid'] = $datastream->id;
   $form_state['object'] = $object;
   $datastream_mime_map = islandora_get_object_extensions($object);
+  $current_mime = $datastream->mimetype;
   $mimes = $datastream_mime_map[$datastream->id]['mime'];
+  if (!in_array($current_mime, $mimes)) {
+    $mimes[] = $current_mime;
+  }
   $extensions = array();
   foreach ($mimes as $mime) {
     $extensions = array_merge($extensions, islandora_get_extensions_for_mimetype($mime));

From d47e777adde0c0a58fb9e5d9c76eb27531f131b2 Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Mon, 15 Sep 2014 10:42:11 -0300
Subject: [PATCH 52/52] removed unused variable, added default

---
 includes/datastream.inc     | 1 -
 includes/mimetype.utils.inc | 4 ++--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/includes/datastream.inc b/includes/datastream.inc
index 592870b7..edc0026b 100644
--- a/includes/datastream.inc
+++ b/includes/datastream.inc
@@ -52,7 +52,6 @@ function islandora_view_datastream(AbstractDatastream $datastream, $download = F
   }
   if ($download) {
     // Browsers will not append all extensions.
-    $mime_detect = new MimeDetect();
     $extension = '.' . islandora_get_extension_for_mimetype($datastream->mimetype);
     // Prevent adding on a duplicate extension.
     $label = $datastream->label;
diff --git a/includes/mimetype.utils.inc b/includes/mimetype.utils.inc
index 3aef6994..1a20859d 100644
--- a/includes/mimetype.utils.inc
+++ b/includes/mimetype.utils.inc
@@ -12,13 +12,13 @@
  *   The mimetype whose extension is required.
  *
  * @return string
- *   The extension mapped to the given mimetype.
+ *   The extension mapped to the given mimetype. Defaults to 'bin'.
  */
 function islandora_get_extension_for_mimetype($mimetype) {
   // file.mimetypes.inc is a part of Drupal core, however is not
   // automatically loaded. Manually require it.
   require_once DRUPAL_ROOT . "/includes/file.mimetypes.inc";
-
+  $extension = 'bin';
   $mimetype_mapping = file_mimetype_mapping();
   $extension_index = array_search($mimetype, $mimetype_mapping['mimetypes']);
   if ($extension_index !== FALSE) {