From 663589d8fcf05074f772f913753d546a4b4a6136 Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Wed, 10 Apr 2013 11:31:56 -0300
Subject: [PATCH 01/20] added function to create tableselect form item for
 content model selection

---
 includes/utilities.inc | 98 ++++++++++++++++++++++++++++++++++--------
 1 file changed, 81 insertions(+), 17 deletions(-)

diff --git a/includes/utilities.inc b/includes/utilities.inc
index f061f72c..ae7f4b61 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -124,8 +124,7 @@ function islandora_describe_repository($url = NULL) {
     try {
       $info = $connection->api->a->describeRepository();
       return $info;
-    }
-    catch (RepositoryException $e) {
+    } catch (RepositoryException $e) {
       return FALSE;
     }
   }
@@ -204,13 +203,13 @@ function islandora_escape_pid_for_function($pid) {
   // Apparently, case doesn't matter for function calls in PHP, so let's not
   // really worry about changing the case.
   return str_replace(
-    // Any PID characters which are not valid in the name of a PHP function.
-    array(
-      ':',
-      '-',
-    ),
-    '_',
-    $pid
+      // Any PID characters which are not valid in the name of a PHP function.
+      array(
+        ':',
+        '-',
+      ),
+      '_',
+      $pid
   );
 }
 
@@ -281,16 +280,15 @@ function islandora_namespace_accessible($id) {
 function islandora_get_parents_from_rels_ext(FedoraObject $object) {
   try {
     $collections = array_merge(
-      $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOfCollection'),
-      $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOf'));
-  }
-  catch (RepositoryException $e) {
+            $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOfCollection'),
+            $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOf'));
+  } catch (RepositoryException $e) {
     // @todo some logging would be nice, not sure what this throws.
     return array();
   }
   $map = function($o) {
-    return islandora_object_load($o['object']['value']);
-  };
+        return islandora_object_load($o['object']['value']);
+      };
   $collections = array_map($map, $collections);
   return array_filter($collections);
 }
@@ -505,7 +503,7 @@ function islandora_display_repository_inaccessible_message() {
   $text = t('Islandora configuration');
   $link = l($text, 'admin/islandora/configure', array('attributes' => array('title' => $text)));
   $message = t('Could not connect to the repository. Please check the settings on the !link page.',
-             array('!link' => $link));
+          array('!link' => $link));
   drupal_set_message($message, 'error', FALSE);
 }
 
@@ -731,10 +729,76 @@ function islandora_get_content_models($ignore_system_namespace = TRUE) {
     $label = $result['label']['value'];
     $namespace = islandora_get_namespace($content_model);
     $ignore = $ignore_system_namespace && $namespace == 'fedora-system';
-    $ignore |= !islandora_namespace_accessible($namespace);
+    $ignore |= ! islandora_namespace_accessible($namespace);
     if (!$ignore) {
       $content_models[$content_model] = array('pid' => $content_model, 'label' => $label);
     }
   }
   return $content_models;
 }
+
+/**
+ * Returns Drupal tableselect element allowing selection of one or more Content Models
+ * Primarily useful for Admin screens
+ * @param string $variable
+ *   the name of the Drupal variable holding selected content models
+ *   Content models held in this variable will appear at the top of the displyed list
+ * @return array  Drupal form element allowing content model selection
+ */
+
+function islandora_content_model_select_table_form_element($variable) {
+  $connection = islandora_get_tuque_connection();
+  $restricted = variable_get('islandora_namespace_restriction_enforced', FALSE);
+  $allowed_string = variable_get('islandora_pids_allowed', 'default: demo: changeme: islandora:');
+  $namespaces = explode(':', $allowed_string);
+  foreach ($namespaces as $namespace) {
+    if ($namespace) {
+      $allowed[] = trim($namespace);
+    }
+  }
+  $query = 'select $object $title from <#ri>
+          where ($object <fedora-model:label> $title
+          and ($object <fedora-model:hasModel> <info:fedora/fedora-system:ContentModel-3.0>
+          or $object <fedora-rels-ext:isMemberOfCollection> <info:fedora/islandora:ContentModelsCollection>)
+          and $object <fedora-model:state> <info:fedora/fedora-system:def/model#Active>)
+          order by $title';
+
+  $list = $connection->repository->ri->itqlQuery($query, 'unlimited');
+  $other_list = islandora_get_content_models(TRUE);
+  $options = array();
+
+  foreach ($other_list as $pid => $label) {
+    if ($pid) {
+      $item_namespace = explode(':', $pid);
+      if (!$restricted || in_array($item_namespace[0], $allowed)) {
+
+        if (!preg_match('/fedora-system/', $pid)) {
+          $options[$pid] = $label;
+        }
+      }
+    }
+  }
+
+  $selected = variable_get($variable, array(''));
+  foreach ($selected as $cmodel) {
+    $options = array($cmodel => $options[$cmodel]) + $options;
+  }
+  foreach ($options as $key => $value) {
+    $rows[$key] = array(
+      'pid' => $key,
+      'title' => $value,
+    );
+    in_array($key, $selected) ? $defaults[$key] = TRUE : $defaults[$key] = FALSE;
+  }
+  $header = array(
+    'pid' => array('data' => t('PID')),
+    'title' => array('data' => t('Content Model')),
+  );
+//build and return table element
+  return array(
+    '#type' => 'tableselect',
+    '#header' => $header,
+    '#options' => $rows,
+    '#default_value' => $defaults,
+  );
+}
\ No newline at end of file

From 1d1e72e1e79c39d9209ceaabfad5d818d4fee4ac Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Thu, 11 Apr 2013 13:44:43 -0300
Subject: [PATCH 02/20] simplified method

---
 includes/utilities.inc | 25 +------------------------
 1 file changed, 1 insertion(+), 24 deletions(-)

diff --git a/includes/utilities.inc b/includes/utilities.inc
index ae7f4b61..4d51c05e 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -745,7 +745,6 @@ function islandora_get_content_models($ignore_system_namespace = TRUE) {
  *   Content models held in this variable will appear at the top of the displyed list
  * @return array  Drupal form element allowing content model selection
  */
-
 function islandora_content_model_select_table_form_element($variable) {
   $connection = islandora_get_tuque_connection();
   $restricted = variable_get('islandora_namespace_restriction_enforced', FALSE);
@@ -756,29 +755,7 @@ function islandora_content_model_select_table_form_element($variable) {
       $allowed[] = trim($namespace);
     }
   }
-  $query = 'select $object $title from <#ri>
-          where ($object <fedora-model:label> $title
-          and ($object <fedora-model:hasModel> <info:fedora/fedora-system:ContentModel-3.0>
-          or $object <fedora-rels-ext:isMemberOfCollection> <info:fedora/islandora:ContentModelsCollection>)
-          and $object <fedora-model:state> <info:fedora/fedora-system:def/model#Active>)
-          order by $title';
-
-  $list = $connection->repository->ri->itqlQuery($query, 'unlimited');
-  $other_list = islandora_get_content_models(TRUE);
-  $options = array();
-
-  foreach ($other_list as $pid => $label) {
-    if ($pid) {
-      $item_namespace = explode(':', $pid);
-      if (!$restricted || in_array($item_namespace[0], $allowed)) {
-
-        if (!preg_match('/fedora-system/', $pid)) {
-          $options[$pid] = $label;
-        }
-      }
-    }
-  }
-
+  $options = islandora_get_content_models(TRUE);
   $selected = variable_get($variable, array(''));
   foreach ($selected as $cmodel) {
     $options = array($cmodel => $options[$cmodel]) + $options;

From 74beb0ca6591a14a6cf2cce57836c961d0506173 Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Thu, 11 Apr 2013 14:48:31 -0300
Subject: [PATCH 03/20] coder changes

---
 includes/utilities.inc | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/includes/utilities.inc b/includes/utilities.inc
index 4d51c05e..a7ec74e0 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -124,7 +124,8 @@ function islandora_describe_repository($url = NULL) {
     try {
       $info = $connection->api->a->describeRepository();
       return $info;
-    } catch (RepositoryException $e) {
+    }
+    catch (RepositoryException $e) {
       return FALSE;
     }
   }
@@ -282,7 +283,8 @@ function islandora_get_parents_from_rels_ext(FedoraObject $object) {
     $collections = array_merge(
             $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOfCollection'),
             $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOf'));
-  } catch (RepositoryException $e) {
+  }
+  catch (RepositoryException $e) {
     // @todo some logging would be nice, not sure what this throws.
     return array();
   }
@@ -398,7 +400,7 @@ function islandora_get_datastreams_requirements_from_content_model(FedoraObject
   $xml = new SimpleXMLElement($object[DS_COMP_STREAM]->content);
   foreach ($xml->dsTypeModel as $ds) {
     $dsid = (string) $ds['ID'];
-    $optional = strtolower((string) $ds['optional']);
+    $optional = drupal_strtolower((string) $ds['optional']);
     $mime = array();
     foreach ($ds->form as $form) {
       $mime[] = (string) $form['MIME'];
@@ -740,12 +742,12 @@ function islandora_get_content_models($ignore_system_namespace = TRUE) {
 /**
  * Returns Drupal tableselect element allowing selection of one or more Content Models
  * Primarily useful for Admin screens
- * @param string $variable
+ * @param string $drupal_variable
  *   the name of the Drupal variable holding selected content models
  *   Content models held in this variable will appear at the top of the displyed list
  * @return array  Drupal form element allowing content model selection
  */
-function islandora_content_model_select_table_form_element($variable) {
+function islandora_content_model_select_table_form_element($drupal_variable) {
   $connection = islandora_get_tuque_connection();
   $restricted = variable_get('islandora_namespace_restriction_enforced', FALSE);
   $allowed_string = variable_get('islandora_pids_allowed', 'default: demo: changeme: islandora:');
@@ -756,7 +758,7 @@ function islandora_content_model_select_table_form_element($variable) {
     }
   }
   $options = islandora_get_content_models(TRUE);
-  $selected = variable_get($variable, array(''));
+  $selected = variable_get($drupal_variable, array(''));
   foreach ($selected as $cmodel) {
     $options = array($cmodel => $options[$cmodel]) + $options;
   }
@@ -772,10 +774,12 @@ function islandora_content_model_select_table_form_element($variable) {
     'title' => array('data' => t('Content Model')),
   );
 //build and return table element
-  return array(
+  $element = array(
     '#type' => 'tableselect',
     '#header' => $header,
     '#options' => $rows,
     '#default_value' => $defaults,
   );
+
+  return $element;
 }
\ No newline at end of file

From 177aaced8685de682dbbc5c71d098e5fc5be1692 Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Thu, 11 Apr 2013 14:55:29 -0300
Subject: [PATCH 04/20] format changes

---
 includes/utilities.inc | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/includes/utilities.inc b/includes/utilities.inc
index a7ec74e0..ea0fc849 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -204,13 +204,13 @@ function islandora_escape_pid_for_function($pid) {
   // Apparently, case doesn't matter for function calls in PHP, so let's not
   // really worry about changing the case.
   return str_replace(
-      // Any PID characters which are not valid in the name of a PHP function.
-      array(
-        ':',
-        '-',
-      ),
-      '_',
-      $pid
+    // Any PID characters which are not valid in the name of a PHP function.
+    array(
+      ':',
+      '-',
+    ),
+    '_',
+    $pid
   );
 }
 
@@ -281,16 +281,16 @@ function islandora_namespace_accessible($id) {
 function islandora_get_parents_from_rels_ext(FedoraObject $object) {
   try {
     $collections = array_merge(
-            $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOfCollection'),
-            $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOf'));
+      $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOfCollection'),
+      $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOf'));
   }
   catch (RepositoryException $e) {
     // @todo some logging would be nice, not sure what this throws.
     return array();
   }
   $map = function($o) {
-        return islandora_object_load($o['object']['value']);
-      };
+    return islandora_object_load($o['object']['value']);
+  };
   $collections = array_map($map, $collections);
   return array_filter($collections);
 }
@@ -400,7 +400,7 @@ function islandora_get_datastreams_requirements_from_content_model(FedoraObject
   $xml = new SimpleXMLElement($object[DS_COMP_STREAM]->content);
   foreach ($xml->dsTypeModel as $ds) {
     $dsid = (string) $ds['ID'];
-    $optional = drupal_strtolower((string) $ds['optional']);
+    $optional = strtolower((string) $ds['optional']);
     $mime = array();
     foreach ($ds->form as $form) {
       $mime[] = (string) $form['MIME'];
@@ -505,7 +505,7 @@ function islandora_display_repository_inaccessible_message() {
   $text = t('Islandora configuration');
   $link = l($text, 'admin/islandora/configure', array('attributes' => array('title' => $text)));
   $message = t('Could not connect to the repository. Please check the settings on the !link page.',
-          array('!link' => $link));
+             array('!link' => $link));
   drupal_set_message($message, 'error', FALSE);
 }
 
@@ -731,7 +731,7 @@ function islandora_get_content_models($ignore_system_namespace = TRUE) {
     $label = $result['label']['value'];
     $namespace = islandora_get_namespace($content_model);
     $ignore = $ignore_system_namespace && $namespace == 'fedora-system';
-    $ignore |= ! islandora_namespace_accessible($namespace);
+    $ignore |= !islandora_namespace_accessible($namespace);
     if (!$ignore) {
       $content_models[$content_model] = array('pid' => $content_model, 'label' => $label);
     }

From 3b9ae796ef06725459f822b6a7251adfb275ef4d Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Thu, 11 Apr 2013 15:18:05 -0300
Subject: [PATCH 05/20] code sniffer compliant

---
 includes/utilities.inc | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/includes/utilities.inc b/includes/utilities.inc
index ea0fc849..11c65b50 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -740,12 +740,15 @@ function islandora_get_content_models($ignore_system_namespace = TRUE) {
 }
 
 /**
- * Returns Drupal tableselect element allowing selection of one or more Content Models
- * Primarily useful for Admin screens
+ * Returns Drupal tableselect element allowing selection of Content Models.
+ *
  * @param string $drupal_variable
  *   the name of the Drupal variable holding selected content models
- *   Content models held in this variable will appear at the top of the displyed list
- * @return array  Drupal form element allowing content model selection
+ *   Content models held in this variable will appear at the top of
+ *   the displayed list
+ *
+ * @return array
+ *   Drupal form element allowing content model selection
  */
 function islandora_content_model_select_table_form_element($drupal_variable) {
   $connection = islandora_get_tuque_connection();
@@ -773,7 +776,7 @@ function islandora_content_model_select_table_form_element($drupal_variable) {
     'pid' => array('data' => t('PID')),
     'title' => array('data' => t('Content Model')),
   );
-//build and return table element
+  //  Build and return table element.
   $element = array(
     '#type' => 'tableselect',
     '#header' => $header,
@@ -782,4 +785,4 @@ function islandora_content_model_select_table_form_element($drupal_variable) {
   );
 
   return $element;
-}
\ No newline at end of file
+}

From b4b33df1f5eed4f07ef37861e6aeaf6012d7eef9 Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Thu, 11 Apr 2013 15:36:50 -0300
Subject: [PATCH 06/20] removed space, coding standards

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

diff --git a/includes/utilities.inc b/includes/utilities.inc
index 11c65b50..54fe9317 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -776,7 +776,7 @@ function islandora_content_model_select_table_form_element($drupal_variable) {
     'pid' => array('data' => t('PID')),
     'title' => array('data' => t('Content Model')),
   );
-  //  Build and return table element.
+  // Build and return table element.
   $element = array(
     '#type' => 'tableselect',
     '#header' => $header,

From c5d7485153cb44192e0ac45f54364f1ce0cf4ca1 Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Fri, 12 Apr 2013 09:46:29 -0300
Subject: [PATCH 07/20] Converted CM query to sparql to allow for unlabeled
 Content Models

---
 includes/utilities.inc | 75 +++++++++++++++++++++++-------------------
 1 file changed, 42 insertions(+), 33 deletions(-)

diff --git a/includes/utilities.inc b/includes/utilities.inc
index 54fe9317..7e5a339a 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -124,8 +124,7 @@ function islandora_describe_repository($url = NULL) {
     try {
       $info = $connection->api->a->describeRepository();
       return $info;
-    }
-    catch (RepositoryException $e) {
+    } catch (RepositoryException $e) {
       return FALSE;
     }
   }
@@ -204,13 +203,13 @@ function islandora_escape_pid_for_function($pid) {
   // Apparently, case doesn't matter for function calls in PHP, so let's not
   // really worry about changing the case.
   return str_replace(
-    // Any PID characters which are not valid in the name of a PHP function.
-    array(
-      ':',
-      '-',
-    ),
-    '_',
-    $pid
+      // Any PID characters which are not valid in the name of a PHP function.
+      array(
+        ':',
+        '-',
+      ),
+      '_',
+      $pid
   );
 }
 
@@ -281,16 +280,15 @@ function islandora_namespace_accessible($id) {
 function islandora_get_parents_from_rels_ext(FedoraObject $object) {
   try {
     $collections = array_merge(
-      $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOfCollection'),
-      $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOf'));
-  }
-  catch (RepositoryException $e) {
+            $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOfCollection'),
+            $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOf'));
+  } catch (RepositoryException $e) {
     // @todo some logging would be nice, not sure what this throws.
     return array();
   }
   $map = function($o) {
-    return islandora_object_load($o['object']['value']);
-  };
+        return islandora_object_load($o['object']['value']);
+      };
   $collections = array_map($map, $collections);
   return array_filter($collections);
 }
@@ -505,7 +503,7 @@ function islandora_display_repository_inaccessible_message() {
   $text = t('Islandora configuration');
   $link = l($text, 'admin/islandora/configure', array('attributes' => array('title' => $text)));
   $message = t('Could not connect to the repository. Please check the settings on the !link page.',
-             array('!link' => $link));
+          array('!link' => $link));
   drupal_set_message($message, 'error', FALSE);
 }
 
@@ -718,20 +716,23 @@ function islandora_get_allowed_namespaces() {
 function islandora_get_content_models($ignore_system_namespace = TRUE) {
   module_load_include('inc', 'islandora', 'includes/utilities');
   $tuque = islandora_get_tuque_connection();
-  $query = 'select $object $label from <#ri>
-          where ($object <fedora-model:label> $label
-          and ($object <fedora-model:hasModel> <info:fedora/fedora-system:ContentModel-3.0>
-          or $object <fedora-rels-ext:isMemberOfCollection> <info:fedora/islandora:ContentModelsCollection>)
-          and $object <fedora-model:state> <info:fedora/fedora-system:def/model#Active>)
-          order by $label';
+  $query = 'PREFIX fm: <info:fedora/fedora-system:def/model#>
+            SELECT ?object ?label
+            FROM <#ri>
+            WHERE {
+              ?object fm:hasModel <info:fedora/fedora-system:ContentModel-3.0>;
+              OPTIONAL{
+                ?object fm:label ?label
+              }
+             }';
   $content_models = array();
-  $results = $tuque->repository->ri->itqlQuery($query, 'unlimited');
+  $results = $tuque->repository->ri->sparqlQuery($query, 'unlimited');
   foreach ($results as $result) {
     $content_model = $result['object']['value'];
     $label = $result['label']['value'];
     $namespace = islandora_get_namespace($content_model);
     $ignore = $ignore_system_namespace && $namespace == 'fedora-system';
-    $ignore |= !islandora_namespace_accessible($namespace);
+    $ignore |= ! islandora_namespace_accessible($namespace);
     if (!$ignore) {
       $content_models[$content_model] = array('pid' => $content_model, 'label' => $label);
     }
@@ -760,17 +761,25 @@ function islandora_content_model_select_table_form_element($drupal_variable) {
       $allowed[] = trim($namespace);
     }
   }
-  $options = islandora_get_content_models(TRUE);
-  $selected = variable_get($drupal_variable, array(''));
-  foreach ($selected as $cmodel) {
-    $options = array($cmodel => $options[$cmodel]) + $options;
+  $defaults = array();
+  $options = array();
+  $options = $options + islandora_get_content_models(TRUE);
+ 
+  foreach($options as $option){
+    $content_models[$option['pid']] = $option['label'];
   }
-  foreach ($options as $key => $value) {
-    $rows[$key] = array(
-      'pid' => $key,
-      'title' => $value,
+
+  $selected = array_values(variable_get($drupal_variable, array('')));
+  foreach($selected as $selection){
+    $content_models = array($selection => $content_models[$selection]) + $content_models;
+  }
+
+  foreach ($content_models as $pid => $label) {
+    $rows[$pid] = array(
+      'pid' => $pid,
+      'title' => $label,
     );
-    in_array($key, $selected) ? $defaults[$key] = TRUE : $defaults[$key] = FALSE;
+    in_array($pid, $selected) ? $defaults[$pid] = TRUE : $defaults[$pid] = FALSE;
   }
   $header = array(
     'pid' => array('data' => t('PID')),

From cb3e9b083d50a9cf29dce7ba383c7875d4c8be79 Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Fri, 12 Apr 2013 09:59:51 -0300
Subject: [PATCH 08/20] Converted CM query to sparql to allow for unlabeled
 Content Models

---
 includes/utilities.inc | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/includes/utilities.inc b/includes/utilities.inc
index 7e5a339a..cd2cbd86 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -762,8 +762,9 @@ function islandora_content_model_select_table_form_element($drupal_variable) {
     }
   }
   $defaults = array();
-  $options = array();
-  $options = $options + islandora_get_content_models(TRUE);
+  $rows = array();
+  $content_models = array();
+  $options = islandora_get_content_models(TRUE);
  
   foreach($options as $option){
     $content_models[$option['pid']] = $option['label'];
@@ -771,7 +772,9 @@ function islandora_content_model_select_table_form_element($drupal_variable) {
 
   $selected = array_values(variable_get($drupal_variable, array('')));
   foreach($selected as $selection){
-    $content_models = array($selection => $content_models[$selection]) + $content_models;
+    if(isset($content_models[$selection])){
+      $content_models = array($selection => $content_models[$selection]) + $content_models;
+    }
   }
 
   foreach ($content_models as $pid => $label) {
@@ -791,6 +794,7 @@ function islandora_content_model_select_table_form_element($drupal_variable) {
     '#header' => $header,
     '#options' => $rows,
     '#default_value' => $defaults,
+    '#empty' => t("There are no content models in this Fedora Repository.")
   );
 
   return $element;

From 0731a26e15c303516c08d04d4c739631f7459ccb Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Fri, 12 Apr 2013 10:57:28 -0300
Subject: [PATCH 09/20] Made query more robust

---
 includes/utilities.inc | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/includes/utilities.inc b/includes/utilities.inc
index cd2cbd86..f5922ddc 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -717,14 +717,24 @@ function islandora_get_content_models($ignore_system_namespace = TRUE) {
   module_load_include('inc', 'islandora', 'includes/utilities');
   $tuque = islandora_get_tuque_connection();
   $query = 'PREFIX fm: <info:fedora/fedora-system:def/model#>
+            PREFIX fr: <info:fedora/fedora-system:def/relations-external#>
             SELECT ?object ?label
             FROM <#ri>
             WHERE {
-              ?object fm:hasModel <info:fedora/fedora-system:ContentModel-3.0>;
+              {?object fm:hasModel <info:fedora/fedora-system:ContentModel-3.0>;
+                       fm:state <info:fedora/fedora-system:def/model#Active>
+              OPTIONAL{
+                 ?object fm:label ?label
+              }
+            }
+            UNION
+              {?object fr:isMemberOfCollection <info:fedora/islandora:ContentModelsCollection>;
+                fm:state <info:fedora/fedora-system:def/model#Active>
               OPTIONAL{
                 ?object fm:label ?label
               }
-             }';
+            }
+           }';
   $content_models = array();
   $results = $tuque->repository->ri->sparqlQuery($query, 'unlimited');
   foreach ($results as $result) {
@@ -754,18 +764,11 @@ function islandora_get_content_models($ignore_system_namespace = TRUE) {
 function islandora_content_model_select_table_form_element($drupal_variable) {
   $connection = islandora_get_tuque_connection();
   $restricted = variable_get('islandora_namespace_restriction_enforced', FALSE);
-  $allowed_string = variable_get('islandora_pids_allowed', 'default: demo: changeme: islandora:');
-  $namespaces = explode(':', $allowed_string);
-  foreach ($namespaces as $namespace) {
-    if ($namespace) {
-      $allowed[] = trim($namespace);
-    }
-  }
   $defaults = array();
   $rows = array();
   $content_models = array();
+
   $options = islandora_get_content_models(TRUE);
- 
   foreach($options as $option){
     $content_models[$option['pid']] = $option['label'];
   }

From 273e591f6e33b3da45a202b419876238be193754 Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Fri, 12 Apr 2013 11:01:41 -0300
Subject: [PATCH 10/20] reverted auto-formatting

---
 includes/utilities.inc | 30 ++++++++++++++++--------------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/includes/utilities.inc b/includes/utilities.inc
index f5922ddc..90117d59 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -124,7 +124,8 @@ function islandora_describe_repository($url = NULL) {
     try {
       $info = $connection->api->a->describeRepository();
       return $info;
-    } catch (RepositoryException $e) {
+    }
+    catch (RepositoryException $e) {
       return FALSE;
     }
   }
@@ -203,13 +204,13 @@ function islandora_escape_pid_for_function($pid) {
   // Apparently, case doesn't matter for function calls in PHP, so let's not
   // really worry about changing the case.
   return str_replace(
-      // Any PID characters which are not valid in the name of a PHP function.
-      array(
-        ':',
-        '-',
-      ),
-      '_',
-      $pid
+    // Any PID characters which are not valid in the name of a PHP function.
+    array(
+      ':',
+      '-',
+    ),
+    '_',
+    $pid
   );
 }
 
@@ -280,15 +281,16 @@ function islandora_namespace_accessible($id) {
 function islandora_get_parents_from_rels_ext(FedoraObject $object) {
   try {
     $collections = array_merge(
-            $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOfCollection'),
-            $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOf'));
-  } catch (RepositoryException $e) {
+      $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOfCollection'),
+      $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOf'));
+  }
+  catch (RepositoryException $e) {
     // @todo some logging would be nice, not sure what this throws.
     return array();
   }
   $map = function($o) {
-        return islandora_object_load($o['object']['value']);
-      };
+    return islandora_object_load($o['object']['value']);
+  };
   $collections = array_map($map, $collections);
   return array_filter($collections);
 }
@@ -503,7 +505,7 @@ function islandora_display_repository_inaccessible_message() {
   $text = t('Islandora configuration');
   $link = l($text, 'admin/islandora/configure', array('attributes' => array('title' => $text)));
   $message = t('Could not connect to the repository. Please check the settings on the !link page.',
-          array('!link' => $link));
+             array('!link' => $link));
   drupal_set_message($message, 'error', FALSE);
 }
 

From c431a070f32213247a44716af63f248070a0348e Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Fri, 12 Apr 2013 11:18:49 -0300
Subject: [PATCH 11/20] minor formatting changes

---
 includes/utilities.inc | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/includes/utilities.inc b/includes/utilities.inc
index 90117d59..52186681 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -744,7 +744,7 @@ function islandora_get_content_models($ignore_system_namespace = TRUE) {
     $label = $result['label']['value'];
     $namespace = islandora_get_namespace($content_model);
     $ignore = $ignore_system_namespace && $namespace == 'fedora-system';
-    $ignore |= ! islandora_namespace_accessible($namespace);
+    $ignore |= !islandora_namespace_accessible($namespace);
     if (!$ignore) {
       $content_models[$content_model] = array('pid' => $content_model, 'label' => $label);
     }
@@ -771,13 +771,13 @@ function islandora_content_model_select_table_form_element($drupal_variable) {
   $content_models = array();
 
   $options = islandora_get_content_models(TRUE);
-  foreach($options as $option){
+  foreach ($options as $option){
     $content_models[$option['pid']] = $option['label'];
   }
 
   $selected = array_values(variable_get($drupal_variable, array('')));
-  foreach($selected as $selection){
-    if(isset($content_models[$selection])){
+  foreach ($selected as $selection){
+    if (isset($content_models[$selection])){
       $content_models = array($selection => $content_models[$selection]) + $content_models;
     }
   }
@@ -799,7 +799,7 @@ function islandora_content_model_select_table_form_element($drupal_variable) {
     '#header' => $header,
     '#options' => $rows,
     '#default_value' => $defaults,
-    '#empty' => t("There are no content models in this Fedora Repository.")
+    '#empty' => t("There are no content models in this Fedora Repository."),
   );
 
   return $element;

From 37071f0ec084e1f950a4fcb7bebca080676ac611 Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Fri, 12 Apr 2013 11:31:48 -0300
Subject: [PATCH 12/20] minor formatting changes

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

diff --git a/includes/utilities.inc b/includes/utilities.inc
index 52186681..f1d221fc 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -771,13 +771,13 @@ function islandora_content_model_select_table_form_element($drupal_variable) {
   $content_models = array();
 
   $options = islandora_get_content_models(TRUE);
-  foreach ($options as $option){
+  foreach ($options as $option) {
     $content_models[$option['pid']] = $option['label'];
   }
 
   $selected = array_values(variable_get($drupal_variable, array('')));
-  foreach ($selected as $selection){
-    if (isset($content_models[$selection])){
+  foreach ($selected as $selection) {
+    if (isset($content_models[$selection])) {
       $content_models = array($selection => $content_models[$selection]) + $content_models;
     }
   }

From 8f5cf316041f997ddb5be9502668c6ec704342c1 Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Mon, 15 Apr 2013 20:01:16 -0300
Subject: [PATCH 13/20] used constants, removed unused variable

---
 includes/utilities.inc | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/includes/utilities.inc b/includes/utilities.inc
index f1d221fc..df924dce 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -718,8 +718,8 @@ function islandora_get_allowed_namespaces() {
 function islandora_get_content_models($ignore_system_namespace = TRUE) {
   module_load_include('inc', 'islandora', 'includes/utilities');
   $tuque = islandora_get_tuque_connection();
-  $query = 'PREFIX fm: <info:fedora/fedora-system:def/model#>
-            PREFIX fr: <info:fedora/fedora-system:def/relations-external#>
+  $query = "PREFIX fm: <" . FEDORA_MODEL_URI . ">
+            PREFIX fr: <" . FEDORA_RELS_EXT_URI . ">
             SELECT ?object ?label
             FROM <#ri>
             WHERE {
@@ -736,7 +736,7 @@ function islandora_get_content_models($ignore_system_namespace = TRUE) {
                 ?object fm:label ?label
               }
             }
-           }';
+           }";
   $content_models = array();
   $results = $tuque->repository->ri->sparqlQuery($query, 'unlimited');
   foreach ($results as $result) {
@@ -765,7 +765,6 @@ function islandora_get_content_models($ignore_system_namespace = TRUE) {
  */
 function islandora_content_model_select_table_form_element($drupal_variable) {
   $connection = islandora_get_tuque_connection();
-  $restricted = variable_get('islandora_namespace_restriction_enforced', FALSE);
   $defaults = array();
   $rows = array();
   $content_models = array();

From 69ce869b818dcd9bfad37bed2879160755541913 Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Wed, 17 Apr 2013 11:01:08 -0300
Subject: [PATCH 14/20] removed unused variable

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

diff --git a/includes/utilities.inc b/includes/utilities.inc
index df924dce..90676923 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -764,7 +764,6 @@ function islandora_get_content_models($ignore_system_namespace = TRUE) {
  *   Drupal form element allowing content model selection
  */
 function islandora_content_model_select_table_form_element($drupal_variable) {
-  $connection = islandora_get_tuque_connection();
   $defaults = array();
   $rows = array();
   $content_models = array();

From 3da2fdcb9f46dd1ae8ad6485680eb8b610e8e3ae Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Fri, 19 Apr 2013 09:48:45 -0300
Subject: [PATCH 15/20] added default, changed sorting

---
 includes/utilities.inc | 52 +++++++++++++++++++++++-------------------
 1 file changed, 29 insertions(+), 23 deletions(-)

diff --git a/includes/utilities.inc b/includes/utilities.inc
index 90676923..d1b32d4e 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -204,13 +204,13 @@ function islandora_escape_pid_for_function($pid) {
   // Apparently, case doesn't matter for function calls in PHP, so let's not
   // really worry about changing the case.
   return str_replace(
-    // Any PID characters which are not valid in the name of a PHP function.
-    array(
-      ':',
-      '-',
-    ),
-    '_',
-    $pid
+      // Any PID characters which are not valid in the name of a PHP function.
+      array(
+        ':',
+        '-',
+      ),
+      '_',
+      $pid
   );
 }
 
@@ -281,16 +281,16 @@ function islandora_namespace_accessible($id) {
 function islandora_get_parents_from_rels_ext(FedoraObject $object) {
   try {
     $collections = array_merge(
-      $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOfCollection'),
-      $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOf'));
+            $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOfCollection'),
+            $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOf'));
   }
   catch (RepositoryException $e) {
     // @todo some logging would be nice, not sure what this throws.
     return array();
   }
   $map = function($o) {
-    return islandora_object_load($o['object']['value']);
-  };
+        return islandora_object_load($o['object']['value']);
+      };
   $collections = array_map($map, $collections);
   return array_filter($collections);
 }
@@ -505,7 +505,7 @@ function islandora_display_repository_inaccessible_message() {
   $text = t('Islandora configuration');
   $link = l($text, 'admin/islandora/configure', array('attributes' => array('title' => $text)));
   $message = t('Could not connect to the repository. Please check the settings on the !link page.',
-             array('!link' => $link));
+          array('!link' => $link));
   drupal_set_message($message, 'error', FALSE);
 }
 
@@ -744,7 +744,7 @@ function islandora_get_content_models($ignore_system_namespace = TRUE) {
     $label = $result['label']['value'];
     $namespace = islandora_get_namespace($content_model);
     $ignore = $ignore_system_namespace && $namespace == 'fedora-system';
-    $ignore |= !islandora_namespace_accessible($namespace);
+    $ignore |= ! islandora_namespace_accessible($namespace);
     if (!$ignore) {
       $content_models[$content_model] = array('pid' => $content_model, 'label' => $label);
     }
@@ -759,11 +759,12 @@ function islandora_get_content_models($ignore_system_namespace = TRUE) {
  *   the name of the Drupal variable holding selected content models
  *   Content models held in this variable will appear at the top of
  *   the displayed list
- *
+ * @param array $default_values_array
+ *   default values to display if $drupal_variable is unset
  * @return array
  *   Drupal form element allowing content model selection
  */
-function islandora_content_model_select_table_form_element($drupal_variable) {
+function islandora_content_model_select_table_form_element($drupal_variable, $default_values_array = array('')) {
   $defaults = array();
   $rows = array();
   $content_models = array();
@@ -773,19 +774,24 @@ function islandora_content_model_select_table_form_element($drupal_variable) {
     $content_models[$option['pid']] = $option['label'];
   }
 
-  $selected = array_values(variable_get($drupal_variable, array('')));
-  foreach ($selected as $selection) {
-    if (isset($content_models[$selection])) {
-      $content_models = array($selection => $content_models[$selection]) + $content_models;
-    }
-  }
-
+  $selected = array_values(variable_get($drupal_variable, $default_values_array));
+  $comparator = function ($a, $b) use ($selected) {
+        $a_val = $b_val = 0;
+        if (in_array($a, $selected)) {
+          $a_val = 1;
+        }
+        if (in_array($b, $selected)) {
+          $b_val = 1;
+        }
+        return $a_val = $b_val;
+      };
+  uksort($content_models, $comparator);
   foreach ($content_models as $pid => $label) {
     $rows[$pid] = array(
       'pid' => $pid,
       'title' => $label,
     );
-    in_array($pid, $selected) ? $defaults[$pid] = TRUE : $defaults[$pid] = FALSE;
+    $defaults[$pid] = in_array($pid, $selected);
   }
   $header = array(
     'pid' => array('data' => t('PID')),

From b58fd31f9c179c8c83124c797af2eaf384b8d4eb Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Fri, 19 Apr 2013 11:38:40 -0300
Subject: [PATCH 16/20] formatting, made query more efficient

---
 includes/utilities.inc | 41 +++++++++++++++++++----------------------
 1 file changed, 19 insertions(+), 22 deletions(-)

diff --git a/includes/utilities.inc b/includes/utilities.inc
index d1b32d4e..5b60df50 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -204,7 +204,7 @@ function islandora_escape_pid_for_function($pid) {
   // Apparently, case doesn't matter for function calls in PHP, so let's not
   // really worry about changing the case.
   return str_replace(
-      // Any PID characters which are not valid in the name of a PHP function.
+ // Any PID characters which are not valid in the name of a PHP function.
       array(
         ':',
         '-',
@@ -281,8 +281,8 @@ function islandora_namespace_accessible($id) {
 function islandora_get_parents_from_rels_ext(FedoraObject $object) {
   try {
     $collections = array_merge(
-            $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOfCollection'),
-            $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOf'));
+      $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOfCollection'),
+      $object->relationships->get(FEDORA_RELS_EXT_URI, 'isMemberOf'));
   }
   catch (RepositoryException $e) {
     // @todo some logging would be nice, not sure what this throws.
@@ -724,17 +724,14 @@ function islandora_get_content_models($ignore_system_namespace = TRUE) {
             FROM <#ri>
             WHERE {
               {?object fm:hasModel <info:fedora/fedora-system:ContentModel-3.0>;
-                       fm:state <info:fedora/fedora-system:def/model#Active>
-              OPTIONAL{
-                 ?object fm:label ?label
+                       fm:state fm:Active
               }
-            }
-            UNION
-              {?object fr:isMemberOfCollection <info:fedora/islandora:ContentModelsCollection>;
-                fm:state <info:fedora/fedora-system:def/model#Active>
-              OPTIONAL{
-                ?object fm:label ?label
+            UNION{
+                ?object fr:isMemberOfCollection <info:fedora/islandora:ContentModelsCollection>;
+                fm:state fm:Active
               }
+            OPTIONAL{
+                 ?object fm:label ?label
             }
            }";
   $content_models = array();
@@ -744,7 +741,7 @@ function islandora_get_content_models($ignore_system_namespace = TRUE) {
     $label = $result['label']['value'];
     $namespace = islandora_get_namespace($content_model);
     $ignore = $ignore_system_namespace && $namespace == 'fedora-system';
-    $ignore |= ! islandora_namespace_accessible($namespace);
+    $ignore |= !islandora_namespace_accessible($namespace);
     if (!$ignore) {
       $content_models[$content_model] = array('pid' => $content_model, 'label' => $label);
     }
@@ -776,15 +773,15 @@ function islandora_content_model_select_table_form_element($drupal_variable, $de
 
   $selected = array_values(variable_get($drupal_variable, $default_values_array));
   $comparator = function ($a, $b) use ($selected) {
-        $a_val = $b_val = 0;
-        if (in_array($a, $selected)) {
-          $a_val = 1;
-        }
-        if (in_array($b, $selected)) {
-          $b_val = 1;
-        }
-        return $a_val = $b_val;
-      };
+    $a_val = $b_val = 0;
+    if (in_array($a, $selected)) {
+      $a_val = 1;
+    }
+    if (in_array($b, $selected)) {
+      $b_val = 1;
+    }
+    return $a_val = $b_val;
+  };
   uksort($content_models, $comparator);
   foreach ($content_models as $pid => $label) {
     $rows[$pid] = array(

From 84aa0c58f4181132b17fecad2108ecbd39e3bfc0 Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Fri, 19 Apr 2013 14:46:11 -0300
Subject: [PATCH 17/20] changed operator

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

diff --git a/includes/utilities.inc b/includes/utilities.inc
index 5b60df50..ca1867d3 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -778,9 +778,9 @@ function islandora_content_model_select_table_form_element($drupal_variable, $de
       $a_val = 1;
     }
     if (in_array($b, $selected)) {
-      $b_val = 1;
+      $b_val - 1;
     }
-    return $a_val = $b_val;
+    return $a_val - $b_val;
   };
   uksort($content_models, $comparator);
   foreach ($content_models as $pid => $label) {

From 553810a133fbb6ed8f05bd78f7ac5d53ac5d9d8e Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Fri, 19 Apr 2013 14:48:29 -0300
Subject: [PATCH 18/20] changed operator

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

diff --git a/includes/utilities.inc b/includes/utilities.inc
index ca1867d3..d40b044a 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -778,9 +778,9 @@ function islandora_content_model_select_table_form_element($drupal_variable, $de
       $a_val = 1;
     }
     if (in_array($b, $selected)) {
-      $b_val - 1;
+      $b_val = 1;
     }
-    return $a_val - $b_val;
+    return $b_val - $a_val;
   };
   uksort($content_models, $comparator);
   foreach ($content_models as $pid => $label) {

From 9496b0e5fda04424717ff201c8921ecedd116607 Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Fri, 19 Apr 2013 17:01:31 -0300
Subject: [PATCH 19/20] formatting

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

diff --git a/includes/utilities.inc b/includes/utilities.inc
index d40b044a..6d20dff5 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -765,7 +765,6 @@ function islandora_content_model_select_table_form_element($drupal_variable, $de
   $defaults = array();
   $rows = array();
   $content_models = array();
-
   $options = islandora_get_content_models(TRUE);
   foreach ($options as $option) {
     $content_models[$option['pid']] = $option['label'];

From f9e406471593e71ae36ef872474ffb96de9036c4 Mon Sep 17 00:00:00 2001
From: Alan Stanley <astanley@upei.ca>
Date: Fri, 19 Apr 2013 17:16:32 -0300
Subject: [PATCH 20/20] coder standards

---
 includes/utilities.inc | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/includes/utilities.inc b/includes/utilities.inc
index b6bb1854..fbc4585a 100644
--- a/includes/utilities.inc
+++ b/includes/utilities.inc
@@ -204,7 +204,7 @@ function islandora_escape_pid_for_function($pid) {
   // Apparently, case doesn't matter for function calls in PHP, so let's not
   // really worry about changing the case.
   return str_replace(
- // Any PID characters which are not valid in the name of a PHP function.
+  // Any PID characters which are not valid in the name of a PHP function.
       array(
         ':',
         '-',
@@ -289,8 +289,8 @@ function islandora_get_parents_from_rels_ext(FedoraObject $object) {
     return array();
   }
   $map = function($o) {
-        return islandora_object_load($o['object']['value']);
-      };
+    return islandora_object_load($o['object']['value']);
+  };
   $collections = array_map($map, $collections);
   return array_filter($collections);
 }
@@ -770,6 +770,7 @@ function islandora_get_content_models($ignore_system_namespace = TRUE) {
  *   the displayed list
  * @param array $default_values_array
  *   default values to display if $drupal_variable is unset
+ *
  * @return array
  *   Drupal form element allowing content model selection
  */