From c4de0aee2156d10262323bf9a9147d586fcbf370 Mon Sep 17 00:00:00 2001
From: Daniel Berthereau <Daniel.github@Berthereau.net>
Date: Mon, 8 Dec 2014 02:47:02 +0100
Subject: [PATCH 01/15] Avoided a notice when accessing to a public collection
 with a private parent.

---
 views/helpers/CollectionTreeList.php | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/views/helpers/CollectionTreeList.php b/views/helpers/CollectionTreeList.php
index 160f355..729f993 100644
--- a/views/helpers/CollectionTreeList.php
+++ b/views/helpers/CollectionTreeList.php
@@ -1,7 +1,7 @@
 <?php
 /**
  * Collection Tree
- * 
+ *
  * @copyright Copyright 2007-2012 Roy Rosenzweig Center for History and New Media
  * @license http://www.gnu.org/licenses/gpl-3.0.txt GNU GPLv3
  */
@@ -27,14 +27,22 @@ public function collectionTreeList($collectionTree, $linkToCollectionShow = true
         if (!$collectionTree) {
             return;
         }
+
         $collectionTable = get_db()->getTable('Collection');
         $html = '<ul>';
         foreach ($collectionTree as $collection) {
             $html .= '<li>';
-            if ($linkToCollectionShow && !isset($collection['current'])) {
+            // No link to current collection.
+            if ($linkToCollectionShow && !isset($collection['current']) && isset($collection['id'])) {
                 $html .= link_to_collection(null, array(), 'show', $collectionTable->find($collection['id']));
-            } else {
-                $html .= $collection['name'] ? $collection['name'] : __('[Untitled]');
+            }
+            // No link to private parent collection.
+            elseif (!isset($collection['id'])) {
+                $html .= __('[Unavailable]');
+            }
+            // Link to current collection.
+            else {
+                $html .= empty($collection['name']) ? __('[Untitled]') : $collection['name'];
             }
             $html .= $this->collectionTreeList($collection['children'], $linkToCollectionShow);
             $html .= '</li>';

From 0cadbac32287c7324234bd7614def0162449d173 Mon Sep 17 00:00:00 2001
From: Daniel Berthereau <Daniel.github@Berthereau.net>
Date: Mon, 8 Dec 2014 02:47:02 +0100
Subject: [PATCH 02/15] Normalized table uses.

---
 CollectionTreePlugin.php        | 31 +++++++-----
 models/Table/CollectionTree.php | 90 +++++++++++++++++----------------
 2 files changed, 64 insertions(+), 57 deletions(-)

diff --git a/CollectionTreePlugin.php b/CollectionTreePlugin.php
index 921abea..ee63346 100644
--- a/CollectionTreePlugin.php
+++ b/CollectionTreePlugin.php
@@ -160,7 +160,8 @@ public function hookConfig($args)
 
     public function hookBeforeSaveCollection($args)
     {
-        $collectionTree = $this->_db->getTable('CollectionTree')->findByCollectionId($args['record']->id);
+        $collection = $args['record'];
+        $collectionTree = $this->_db->getTable('CollectionTree')->findByCollectionId($collection->id);
         if (!$collectionTree) {
             return;
         }
@@ -169,7 +170,7 @@ public function hookBeforeSaveCollection($args)
         if (isset($args['post']['collection_tree_parent_collection_id'])) {
             $collectionTree->parent_collection_id = $args['post']['collection_tree_parent_collection_id'];
             if (!$collectionTree->isValid()) {
-                $args['record']->addErrorsFrom($collectionTree);
+                $collection->addErrorsFrom($collectionTree);
             }
         }
     }
@@ -179,11 +180,12 @@ public function hookBeforeSaveCollection($args)
      */
     public function hookAfterSaveCollection($args)
     {
-        $collectionTree = $this->_db->getTable('CollectionTree')->findByCollectionId($args['record']->id);
-        
+        $collection = $args['record'];
+        $collectionTree = $this->_db->getTable('CollectionTree')->findByCollectionId($collection->id);
+
         if (!$collectionTree) {
             $collectionTree = new CollectionTree;
-            $collectionTree->collection_id = $args['record']->id;
+            $collectionTree->collection_id = $collection->id;
             $collectionTree->parent_collection_id = 0;
         }
         
@@ -208,16 +210,17 @@ public function hookAfterSaveCollection($args)
      */
     public function hookAfterDeleteCollection($args)
     {
+        $collection = $args['record'];
         $collectionTreeTable = $this->_db->getTable('CollectionTree');
         
         // Delete the relationship with the parent collection.
-        $collectionTree = $collectionTreeTable->findByCollectionId($args['record']->id);
+        $collectionTree = $collectionTreeTable->findByCollectionId($collection->id);
         if ($collectionTree) {
             $collectionTree->delete();
         }
         
         // Move child collections to root level by deleting their relationships.
-        $collectionTrees = $collectionTreeTable->findByParentCollectionId($args['record']->id);
+        $collectionTrees = $collectionTreeTable->findByParentCollectionId($collection->id);
         foreach ($collectionTrees as  $collectionTree) {
             $collectionTree->parent_collection_id = 0;
             $collectionTree->save();
@@ -234,13 +237,14 @@ public function hookCollectionsBrowseSql($args)
             if (!get_option('collection_tree_browse_only_root')) {
                 return;
             }
+            $select = $args['select'];
             $sql = "
             collections.id NOT IN (
-                SELECT ct.collection_id
-                FROM {$this->_db->CollectionTree} ct
-                WHERE ct.parent_collection_id != 0
+                SELECT collection_trees.collection_id
+                FROM {$this->_db->CollectionTree} collection_trees
+                WHERE collection_trees.parent_collection_id != 0
             )";
-            $args['select']->where($sql);
+            $select->where($sql);
         }
     }
 
@@ -292,12 +296,13 @@ public function filterPublicNavigationMain($nav)
      */
     public function filterAdminCollectionsFormTabs($tabs, $args)
     {
+        $collection = $args['collection'];
         $collectionTreeTable = $this->_db->getTable('CollectionTree');
         
         $options = $collectionTreeTable->findPairsForSelectForm();
         $options = array('0' => __('No parent collection')) + $options;
-        
-        $collectionTree = $collectionTreeTable->findByCollectionId($args['collection']->id);
+
+        $collectionTree = $collectionTreeTable->findByCollectionId($collection->id);
         if ($collectionTree) {
             $parentCollectionId = $collectionTree->parent_collection_id;
         } else {
diff --git a/models/Table/CollectionTree.php b/models/Table/CollectionTree.php
index 862c8d4..14a3433 100644
--- a/models/Table/CollectionTree.php
+++ b/models/Table/CollectionTree.php
@@ -44,33 +44,36 @@ class Table_CollectionTree extends Omeka_Db_Table
      */
     public function fetchAssignableParentCollections($collectionId)
     {
-        $db = $this->getDb();
-
         // Must cast null collection ID to 0 to properly bind.
         $collectionId = (int) $collectionId;
 
-        $sql = "
-        SELECT c.*, ct.name
-        FROM {$db->Collection} c
-        LEFT JOIN {$db->CollectionTree} ct
-        ON c.id = ct.collection_id
-        WHERE c.id != ?";
+        $table = $this->_db->getTable('Collection');
+        $alias = $this->getTableAlias();
+        $aliasCollection = $table->getTableAlias();
+
+        // Access rights to collections are automatically managed.
+        $select = $table->getSelect();
+        $select->joinLeft(
+            array($alias => $this->getTableName()),
+            "$aliasCollection.id = $alias.collection_id",
+            array('name'));
+        $select->where("$aliasCollection.id != ?", $collectionId);
 
         // If not a new collection, cache descendant collection IDs and exclude
         // those collections from the result.
         if ($collectionId) {
             $unassignableCollectionIds = $this->getUnassignableCollectionIds();
             if ($unassignableCollectionIds) {
-                $sql .= " AND c.id NOT IN (" . implode(', ', $unassignableCollectionIds) . ")";
+                $select->where("$aliasCollection.id NOT IN (?)", $unassignableCollectionIds);
             }
         }
 
         // Order alphabetically if configured to do so.
         if (get_option('collection_tree_alpha_order')) {
-            $sql .= ' ORDER BY ct.name';
+            $select->order("$alias.name ASC");
         }
 
-        return $db->fetchAll($sql, array((int) $collectionId));
+        return $this->fetchAssoc($select);
     }
 
     /**
@@ -81,15 +84,16 @@ public function fetchAssignableParentCollections($collectionId)
      */
     public function findByCollectionId($collectionId)
     {
-        $db = $this->getDb();
-
-        $sql = "
-        SELECT *
-        FROM {$db->CollectionTree}
-        WHERE collection_id = ?";
+        // Cast to integer to prevent SQL injection.
+        $collectionId = (int) $collectionId;
 
+        $alias = $this->getTableAlias();
+        $select = $this->getSelect();
+        $select->where("$alias.collection_id = ?", $collectionId);
+        $select->limit(1);
+        $select->reset(Zend_Db_Select::ORDER);
         // Child collection IDs are unique, so only fetch one row.
-        return $this->fetchObject($sql, array($collectionId));
+        return $this->fetchObject($select);
     }
 
     /**
@@ -100,14 +104,14 @@ public function findByCollectionId($collectionId)
      */
     public function findByParentCollectionId($parentCollectionId)
     {
-        $db = $this->getDb();
-
-        $sql = "
-        SELECT *
-        FROM {$db->CollectionTree}
-        WHERE parent_collection_id = ?";
-
-        return $this->fetchObjects($sql, array($parentCollectionId));
+        // Cast to integer to prevent SQL injection.
+        $parentCollectionId = (int) $parentCollectionId;
+
+        $alias = $this->getTableAlias();
+        $select = $this->getSelect();
+        $select->where("$alias.parent_collection_id = ?", $parentCollectionId);
+        $select->reset(Zend_Db_Select::ORDER);
+        return $this->fetchObjects($select);
     }
 
     /**
@@ -115,26 +119,23 @@ public function findByParentCollectionId($parentCollectionId)
      */
     public function cacheCollections()
     {
-        $db = $this->getDb();
-        $sql = "
-        SELECT c.*, ct.parent_collection_id, ct.name
-        FROM {$db->Collection} c
-        LEFT JOIN {$db->CollectionTree} ct
-        ON c.id = ct.collection_id";
-
-        // check whether the acl exists -- it doesn't within a background process
-        $acl = get_acl();
-        // Cache only those collections to which the current user has access.
-        if ($acl && ! $acl->isAllowed(current_user(), 'Collections', 'showNotPublic')) {
-            $sql .= ' WHERE c.public = 1';
-        }
+        $table = $this->_db->getTable('Collection');
+        $alias = $this->getTableAlias();
+        $aliasCollection = $table->getTableAlias();
+
+        // Access rights to collections are automatically managed.
+        $select = $table->getSelect();
+        $select->joinLeft(
+            array($alias => $this->getTableName()),
+            "$aliasCollection.id = $alias.collection_id",
+            array('parent_collection_id', 'name'));
 
         // Order alphabetically if configured to do so.
         if (get_option('collection_tree_alpha_order')) {
-            $sql .= ' ORDER BY ct.name';
+            $select->order("$alias.name ASC");
         }
 
-        $this->_collections = $db->fetchAll($sql);
+        $this->_collections = $this->fetchAll($select);
     }
 
     /**
@@ -249,9 +250,10 @@ public function getDescendantTree($collectionId, $cacheDescendantInfo = false, $
             }
 
             // Recurse the child collections, getting their children.
-            $children = $this->getDescendantTree($descendantTree[$i]['id'],
-                                                 $cacheDescendantInfo,
-                                                 $collectionDepth);
+            $children = $this->getDescendantTree(
+                $descendantTree[$i]['id'],
+                $cacheDescendantInfo,
+                $collectionDepth);
 
             // Assign the child collections to the descendant tree.
             if ($children) {

From c9b8ba1d577aaf70f776e5201684f95cb3e562d8 Mon Sep 17 00:00:00 2001
From: Daniel Berthereau <Daniel.github@Berthereau.net>
Date: Mon, 8 Dec 2014 02:47:02 +0100
Subject: [PATCH 03/15] Returned collections as associative arrays with id as
 key.

---
 models/Table/CollectionTree.php | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/models/Table/CollectionTree.php b/models/Table/CollectionTree.php
index 14a3433..617deac 100644
--- a/models/Table/CollectionTree.php
+++ b/models/Table/CollectionTree.php
@@ -148,12 +148,12 @@ public function findPairsForSelectForm($padding = '-')
     {
         $options = array();
 
-        foreach ($this->getRootCollections() as $rootCollection) {
+        foreach ($this->getRootCollections() as $rootCollectionId => $rootCollection) {
 
-            $options[$rootCollection['id']] = $rootCollection['name'] ? $rootCollection['name'] : __('[Untitled]');
+            $options[$rootCollectionId] = $rootCollection['name'] ? $rootCollection['name'] : __('[Untitled]');
 
             $this->_resetCache();
-            $this->getDescendantTree($rootCollection['id'], true);
+            $this->getDescendantTree($rootCollectionId, true);
             foreach ($this->_cache as $collectionId => $collectionDepth) {
                 $collection = $this->getCollection($collectionId);
                 $options[$collectionId] = str_repeat($padding, $collectionDepth) . ' ';
@@ -242,7 +242,7 @@ public function getDescendantTree($collectionId, $cacheDescendantInfo = false, $
         $collectionDepth++;
 
         // Iterate the child collections.
-        $descendantTree = $this->getChildCollections($collectionId);
+        $descendantTree = array_values($this->getChildCollections($collectionId));
         for ($i = 0; $i < count($descendantTree); $i++) {
 
             if ($cacheDescendantInfo) {
@@ -291,7 +291,7 @@ public function getCollection($collectionId)
      * Get the child collections of the specified collection.
      *
      * @param int $collectionId
-     * @return array
+     * @return array Associative array of collections, by id.
      */
     public function getChildCollections($collectionId)
     {
@@ -303,7 +303,7 @@ public function getChildCollections($collectionId)
         $childCollections = array();
         foreach ($this->_collections as $collection) {
             if ($collectionId == $collection['parent_collection_id']) {
-                $childCollections[] = $collection;
+                $childCollections[$collection['id']] = $collection;
             }
         }
         return $childCollections;
@@ -312,7 +312,7 @@ public function getChildCollections($collectionId)
     /**
      * Get all root collections, i.e. those without parent collections.
      *
-     * @return array
+     * @return array Associative array of root collections, by id.
      */
     public function getRootCollections()
     {
@@ -324,7 +324,7 @@ public function getRootCollections()
         $rootCollections = array();
         foreach ($this->_collections as $collection) {
             if (!$collection['parent_collection_id']) {
-                $rootCollections[] = $collection;
+                $rootCollections[$collection['id']] = $collection;
             }
         }
         return $rootCollections;

From 0ab197e7186133e920d69e312561f75d2ca16cc8 Mon Sep 17 00:00:00 2001
From: Daniel Berthereau <Daniel.github@Berthereau.net>
Date: Mon, 8 Dec 2014 02:47:02 +0100
Subject: [PATCH 04/15] Improved cache of collections.

---
 models/Table/CollectionTree.php | 81 ++++++++++++++-------------------
 1 file changed, 34 insertions(+), 47 deletions(-)

diff --git a/models/Table/CollectionTree.php b/models/Table/CollectionTree.php
index 617deac..079565d 100644
--- a/models/Table/CollectionTree.php
+++ b/models/Table/CollectionTree.php
@@ -114,30 +114,6 @@ public function findByParentCollectionId($parentCollectionId)
         return $this->fetchObjects($select);
     }
 
-    /**
-     * Cache collection data.
-     */
-    public function cacheCollections()
-    {
-        $table = $this->_db->getTable('Collection');
-        $alias = $this->getTableAlias();
-        $aliasCollection = $table->getTableAlias();
-
-        // Access rights to collections are automatically managed.
-        $select = $table->getSelect();
-        $select->joinLeft(
-            array($alias => $this->getTableName()),
-            "$aliasCollection.id = $alias.collection_id",
-            array('parent_collection_id', 'name'));
-
-        // Order alphabetically if configured to do so.
-        if (get_option('collection_tree_alpha_order')) {
-            $select->order("$alias.name ASC");
-        }
-
-        $this->_collections = $this->fetchAll($select);
-    }
-
     /**
      * Return the collection tree hierarchy as a one-dimensional array.
      *
@@ -274,17 +250,8 @@ public function getDescendantTree($collectionId, $cacheDescendantInfo = false, $
      */
     public function getCollection($collectionId)
     {
-        // Cache collections in not already.
-        if (!$this->_collections) {
-            $this->cacheCollections();
-        }
-
-        foreach ($this->_collections as $collection) {
-            if ($collectionId == $collection['id']) {
-                return $collection;
-            }
-        }
-        return false;
+        $collections = $this->_getCollections();
+        return isset($collections[$collectionId]) ? $collections[$collectionId] : false;
     }
 
     /**
@@ -295,13 +262,9 @@ public function getCollection($collectionId)
      */
     public function getChildCollections($collectionId)
     {
-        // Cache collections if not already.
-        if (!$this->_collections) {
-            $this->cacheCollections();
-        }
-
         $childCollections = array();
-        foreach ($this->_collections as $collection) {
+        $collections = $this->_getCollections();
+        foreach ($collections as $collection) {
             if ($collectionId == $collection['parent_collection_id']) {
                 $childCollections[$collection['id']] = $collection;
             }
@@ -316,13 +279,9 @@ public function getChildCollections($collectionId)
      */
     public function getRootCollections()
     {
-        // Cache collections if not already.
-        if (!$this->_collections) {
-            $this->cacheCollections();
-        }
-
         $rootCollections = array();
-        foreach ($this->_collections as $collection) {
+        $collections = $this->_getCollections();
+        foreach ($collections as $collection) {
             if (!$collection['parent_collection_id']) {
                 $rootCollections[$collection['id']] = $collection;
             }
@@ -348,6 +307,34 @@ public function getUnassignableCollectionIds($collectionId)
         return $unassignableCollections;
     }
 
+    /**
+     * Cache collection data with name and parent id in an associative array.
+     */
+    protected function _getCollections()
+    {
+        if (is_null($this->_collections)) {
+            $table = $this->_db->getTable('Collection');
+            $alias = $this->getTableAlias();
+            $aliasCollection = $table->getTableAlias();
+
+            // Access rights to collections are automatically managed.
+            $select = $table->getSelect();
+            $select->joinLeft(
+                array($alias => $this->getTableName()),
+                "$aliasCollection.id = $alias.collection_id",
+                array('parent_collection_id', 'name'));
+
+            // Order alphabetically if configured to do so.
+            if (get_option('collection_tree_alpha_order')) {
+                $select->order("$alias.name ASC");
+            }
+
+            $this->_collections = $this->fetchAssoc($select);
+        }
+
+        return $this->_collections;
+    }
+
     /**
      * Reset the cache property.
      */

From f1de5a4624f9af9044aa6a500b12baff2e739573 Mon Sep 17 00:00:00 2001
From: Daniel Berthereau <Daniel.github@Berthereau.net>
Date: Mon, 8 Dec 2014 02:47:02 +0100
Subject: [PATCH 05/15] Fixed method findPairsForSelectForm.

---
 models/Table/CollectionTree.php | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/models/Table/CollectionTree.php b/models/Table/CollectionTree.php
index 079565d..4ec7fa6 100644
--- a/models/Table/CollectionTree.php
+++ b/models/Table/CollectionTree.php
@@ -117,10 +117,12 @@ public function findByParentCollectionId($parentCollectionId)
     /**
      * Return the collection tree hierarchy as a one-dimensional array.
      *
+     * @param array $options (optional) Set of parameters for searching/
+     * filtering results.
      * @param string $padding The string representation of the collection depth.
      * @return array
      */
-    public function findPairsForSelectForm($padding = '-')
+    public function findPairsForSelectForm(array $options = array(), $padding = '-')
     {
         $options = array();
 

From df9757b0998b7ea07bc580737b9f97fedf5affdf Mon Sep 17 00:00:00 2001
From: Daniel Berthereau <Daniel.github@Berthereau.net>
Date: Mon, 8 Dec 2014 02:47:02 +0100
Subject: [PATCH 06/15] Added a checkbox to expand advanced search to
 sub-collections.

---
 CollectionTreePlugin.php        | 95 ++++++++++++++++++++++++++++++++-
 models/Table/CollectionTree.php | 22 ++++++++
 2 files changed, 116 insertions(+), 1 deletion(-)

diff --git a/CollectionTreePlugin.php b/CollectionTreePlugin.php
index ee63346..854009b 100644
--- a/CollectionTreePlugin.php
+++ b/CollectionTreePlugin.php
@@ -27,6 +27,9 @@ class CollectionTreePlugin extends Omeka_Plugin_AbstractPlugin
         'after_save_collection',
         'after_delete_collection',
         'collections_browse_sql',
+        'items_browse_sql',
+        'admin_items_search',
+        'public_items_search',
         'admin_collections_show',
         'public_collections_show',
     );
@@ -38,6 +41,7 @@ class CollectionTreePlugin extends Omeka_Plugin_AbstractPlugin
         'admin_navigation_main',
         'public_navigation_main',
         'admin_collections_form_tabs',
+        'items_browse_params',
         'collections_select_options',
     );
 
@@ -248,6 +252,78 @@ public function hookCollectionsBrowseSql($args)
         }
     }
 
+    /**
+     * Hook for items browse: search in collection's children and selected one.
+     *
+     * @param Omeka_Db_Select $select
+     * @param array $params
+     */
+    public function hookItemsBrowseSql($args)
+    {
+        if (!is_admin_theme()) {
+            $select = $args['select'];
+            $params = $args['params'];
+            if (!empty($params['descendant_or_self'])) {
+                $collection = (integer) $params['descendant_or_self'];
+                $collections = $this->_db->getTable('CollectionTree')
+                    ->getDescendantOrSelfCollections($collection);
+                $collections = array_keys($collections);
+
+                $select->joinInner(
+                    array('collections' => $this->_db->Collection),
+                    'items.collection_id = collections.id',
+                    array());
+
+                // There are descendants.
+                if (count($collections) > 1) {
+                    $select->where('collections.id IN (?)', $collections);
+                }
+                // There is only the collection itself or no collection.
+                else {
+                    $select->where('collections.id = ?', reset($collections));
+                }
+            }
+        }
+    }
+
+    /**
+     * Hook for admin advanced search.
+     *
+     * @return string HTML
+     */
+    public function hookAdminItemsSearch($args)
+    {
+        echo $this->_itemsSearch($args);
+    }
+
+    /**
+     * Hook for public advanced search.
+     *
+     * @return string HTML
+     */
+    public function hookPublicItemsSearch($args)
+    {
+        echo $this->_itemsSearch($args);
+    }
+
+    /**
+     * Append items search checkbox  to the advanced search page.
+     *
+     * @return string HTML
+     */
+    protected function _itemsSearch($args)
+    {
+        $view = $args['view'];
+        $html = '<div id="search-subcollections" class="field">';
+        $html .= $view->formLabel('subcollections', __('Broaden to the sub-collections'));
+        $html .= '<div class="inputs">';
+        $html .= $view->formCheckbox('subcollections', null,
+            array('checked' => false));
+        $html .= '</div>';
+        $html .= '</div>';
+        return $html;
+    }
+
     /**
      * Display the collection's parent collection and child collections.
      */
@@ -255,7 +331,7 @@ public function hookAdminCollectionsShow($args)
     {
         $this->_appendToCollectionsShow($args['collection']);
     }
-    
+
     /**
      * Display the collection's parent collection and child collections.
      */
@@ -315,6 +391,23 @@ public function filterAdminCollectionsFormTabs($tabs, $args)
         return $tabs;
     }
 
+
+    /**
+     * Filter items browse params to broaden the search to subcollections.
+     *
+     * @param array $params
+     * @return array
+     */
+    public function filterItemsBrowseParams($params)
+    {
+        if (!empty($params['collection']) && !empty($params['subcollections'])) {
+            $params['descendant_or_self'] = $params['collection'];
+            $params['collection'] = '';
+        }
+        return $params;
+    }
+
+
     /**
      * Manage search options for collections.
      *
diff --git a/models/Table/CollectionTree.php b/models/Table/CollectionTree.php
index 4ec7fa6..640aaa6 100644
--- a/models/Table/CollectionTree.php
+++ b/models/Table/CollectionTree.php
@@ -274,6 +274,28 @@ public function getChildCollections($collectionId)
         return $childCollections;
     }
 
+    /**
+     * Get the list of descendant collections and the selected one.
+     *
+     * @param int $collectionId
+     * @return array Associative array of collections.
+     */
+    public function getDescendantOrSelfCollections($collectionId)
+    {
+        $collections = array();
+
+        $rootCollection = $this->getCollection($collectionId);
+        if ($rootCollection) {
+            $this->_resetCache();
+            $this->getDescendantTree($collectionId, true);
+            $collections[$collectionId] = $rootCollection;
+            $collections += array_intersect_key($this->_getCollections(), $this->_cache);
+            $this->_resetCache();
+        }
+
+        return $collections;
+    }
+
     /**
      * Get all root collections, i.e. those without parent collections.
      *

From 13d1b48d13e3d508a0db83b06f6ebc37c9db8579 Mon Sep 17 00:00:00 2001
From: Daniel Berthereau <Daniel.github@Berthereau.net>
Date: Mon, 8 Dec 2014 02:47:02 +0100
Subject: [PATCH 07/15] Added an option to expand by default the advanced
 search to subcollections.

---
 CollectionTreePlugin.php                            |  3 ++-
 views/admin/plugins/collection-tree-config-form.php | 12 ++++++++++++
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/CollectionTreePlugin.php b/CollectionTreePlugin.php
index 854009b..ba4ab5c 100644
--- a/CollectionTreePlugin.php
+++ b/CollectionTreePlugin.php
@@ -51,6 +51,7 @@ class CollectionTreePlugin extends Omeka_Plugin_AbstractPlugin
     protected $_options = array(
         'collection_tree_alpha_order' => 0,
         'collection_tree_browse_only_root' => 0,
+        'collection_tree_search_descendant' => 0,
     );
 
     /**
@@ -318,7 +319,7 @@ protected function _itemsSearch($args)
         $html .= $view->formLabel('subcollections', __('Broaden to the sub-collections'));
         $html .= '<div class="inputs">';
         $html .= $view->formCheckbox('subcollections', null,
-            array('checked' => false));
+            array('checked' => (bool) get_option('collection_tree_search_descendant')));
         $html .= '</div>';
         $html .= '</div>';
         return $html;
diff --git a/views/admin/plugins/collection-tree-config-form.php b/views/admin/plugins/collection-tree-config-form.php
index 541b19b..1b2fbfc 100644
--- a/views/admin/plugins/collection-tree-config-form.php
+++ b/views/admin/plugins/collection-tree-config-form.php
@@ -23,3 +23,15 @@
             array('checked' => (bool) get_option('collection_tree_browse_only_root'))); ?>
     </div>
 </div>
+<div class="field">
+    <div class="two columns alpha">
+        <?php echo $this->formLabel('collection_tree_search_descendant', __('Advanced search')); ?>
+    </div>
+    <div class="inputs five columns omega">
+        <p class="explanation"><?php
+            echo __('If checked, the advanced search of items will be expanded by default to all descendant collections of the selected collection.');
+        ?></p>
+        <?php echo $this->formCheckbox('collection_tree_search_descendant', null,
+            array('checked' => (bool) get_option('collection_tree_search_descendant'))); ?>
+    </div>
+</div>

From 2f55d04b9e71e5ef0db93f263577f4a486d36401 Mon Sep 17 00:00:00 2001
From: Daniel Berthereau <Daniel.github@Berthereau.net>
Date: Mon, 8 Dec 2014 02:47:02 +0100
Subject: [PATCH 08/15] Added an option to merge items of subcollections on the
 "Browse collections" page.

---
 CollectionTreePlugin.php                      | 22 ++++++++++++++++++-
 .../plugins/collection-tree-config-form.php   | 13 +++++++++++
 2 files changed, 34 insertions(+), 1 deletion(-)

diff --git a/CollectionTreePlugin.php b/CollectionTreePlugin.php
index ba4ab5c..ca90e3d 100644
--- a/CollectionTreePlugin.php
+++ b/CollectionTreePlugin.php
@@ -51,6 +51,7 @@ class CollectionTreePlugin extends Omeka_Plugin_AbstractPlugin
     protected $_options = array(
         'collection_tree_alpha_order' => 0,
         'collection_tree_browse_only_root' => 0,
+        'collection_tree_show_subcollections' => 0,
         'collection_tree_search_descendant' => 0,
     );
 
@@ -265,7 +266,18 @@ public function hookItemsBrowseSql($args)
             $select = $args['select'];
             $params = $args['params'];
             if (!empty($params['descendant_or_self'])) {
-                $collection = (integer) $params['descendant_or_self'];
+                // Collection can be an object when not called from search form.
+                if ($params['descendant_or_self'] instanceof Collection) {
+                    $collection = $params['descendant_or_self']->id;
+                }
+                // Else this should be a non empty integer.
+                else {
+                    $collection = (integer) $params['descendant_or_self'];
+                    if (empty($collection)) {
+                        return;
+                    }
+                }
+
                 $collections = $this->_db->getTable('CollectionTree')
                     ->getDescendantOrSelfCollections($collection);
                 $collections = array_keys($collections);
@@ -401,6 +413,14 @@ public function filterAdminCollectionsFormTabs($tabs, $args)
      */
     public function filterItemsBrowseParams($params)
     {
+        // Check if this is a direct query (not from advanced search).
+        if (!is_admin_theme()
+                && !isset($params['subcollections'])
+                && get_option('collection_tree_show_subcollections')
+            ) {
+             $params['subcollections'] = 1;
+        }
+
         if (!empty($params['collection']) && !empty($params['subcollections'])) {
             $params['descendant_or_self'] = $params['collection'];
             $params['collection'] = '';
diff --git a/views/admin/plugins/collection-tree-config-form.php b/views/admin/plugins/collection-tree-config-form.php
index 1b2fbfc..710f24e 100644
--- a/views/admin/plugins/collection-tree-config-form.php
+++ b/views/admin/plugins/collection-tree-config-form.php
@@ -23,6 +23,19 @@
             array('checked' => (bool) get_option('collection_tree_browse_only_root'))); ?>
     </div>
 </div>
+<div class="field">
+    <div class="two columns alpha">
+        <?php echo $this->formLabel('collection_tree_show_subcollections', __('Show collection')); ?>
+    </div>
+    <div class="inputs five columns omega">
+        <p class="explanation"><?php
+            echo __('The "Show collection" page can show items of current collection only, or all items of subcollections.');
+            echo ' ' . __('This is specially useful when root collections are empty and used as main categories.');
+        ?></p>
+        <?php echo $this->formCheckbox('collection_tree_show_subcollections', null,
+            array('checked' => (bool) get_option('collection_tree_show_subcollections'))); ?>
+    </div>
+</div>
 <div class="field">
     <div class="two columns alpha">
         <?php echo $this->formLabel('collection_tree_search_descendant', __('Advanced search')); ?>

From e040bfaf76a22851e5d73ee2bb852ba3119331f1 Mon Sep 17 00:00:00 2001
From: Daniel Berthereau <Daniel.github@Berthereau.net>
Date: Mon, 8 Dec 2014 02:47:02 +0100
Subject: [PATCH 09/15] Added ReadMe.

---
 README.md | 74 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 74 insertions(+)
 create mode 100644 README.md

diff --git a/README.md b/README.md
new file mode 100644
index 0000000..1db8f1a
--- /dev/null
+++ b/README.md
@@ -0,0 +1,74 @@
+Collection Tree (plugin for Omeka)
+==================================
+
+
+Summary
+-------
+
+This plugin for [Omeka] gives administrators the ability to create a
+hierarchical tree of their collections.
+
+
+Installation
+------------
+
+Uncompress files and rename plugin folder "CollectionTree".
+
+Then install it like any other Omeka plugin and follow the config instructions.
+
+
+Warning
+-------
+
+Use it at your own risk.
+
+It's always recommended to backup your files and database so you can roll back
+if needed.
+
+
+Troubleshooting
+---------------
+
+See online issues on [Collection Tree issues] page on GitHub.
+
+
+License
+-------
+
+This plugin is published under [GNU/GPL].
+
+This program is free software; you can redistribute it and/or modify it under
+the terms of the GNU General Public License as published by the Free Software
+Foundation; either version 3 of the License, or (at your option) any later
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+details.
+
+You should have received a copy of the GNU General Public License along with
+this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+
+Contact
+-------
+
+Current maintainers:
+
+* Roy Rosenzweig Center for History and New Media
+
+
+Copyright
+---------
+
+* Copyright Roy Rosenzweig Center for History and New Media, 2007-2013
+* Copyright Daniel Berthereau, 2014 (improvements)
+
+
+[Omeka]: https://omeka.org
+[Collection Tree]: https://github.com/Omeka/plugin-CollectionTree
+[Collection Tree issues]: https://github.com/Omeka/plugin-CollectionTree/issues
+[GNU/GPL]: https://www.gnu.org/licenses/gpl-3.0.html "GNU/GPL v3"
+[Daniel-KM]: https://github.com/Daniel-KM "Daniel Berthereau"

From 23453fdb762622b4d810d846b3f9b31f5fc54905 Mon Sep 17 00:00:00 2001
From: Daniel Berthereau <Daniel.github@Berthereau.net>
Date: Tue, 9 Dec 2014 02:47:02 +0100
Subject: [PATCH 10/15] Fixed params and query to get subcollections.

---
 CollectionTreePlugin.php | 82 +++++++++++++++++++++++-----------------
 1 file changed, 48 insertions(+), 34 deletions(-)

diff --git a/CollectionTreePlugin.php b/CollectionTreePlugin.php
index ca90e3d..14a51db 100644
--- a/CollectionTreePlugin.php
+++ b/CollectionTreePlugin.php
@@ -262,40 +262,43 @@ public function hookCollectionsBrowseSql($args)
      */
     public function hookItemsBrowseSql($args)
     {
-        if (!is_admin_theme()) {
-            $select = $args['select'];
-            $params = $args['params'];
-            if (!empty($params['descendant_or_self'])) {
-                // Collection can be an object when not called from search form.
-                if ($params['descendant_or_self'] instanceof Collection) {
-                    $collection = $params['descendant_or_self']->id;
-                }
-                // Else this should be a non empty integer.
-                else {
-                    $collection = (integer) $params['descendant_or_self'];
-                    if (empty($collection)) {
-                        return;
-                    }
-                }
+        if (is_admin_theme()) {
+            return;
+        }
 
-                $collections = $this->_db->getTable('CollectionTree')
-                    ->getDescendantOrSelfCollections($collection);
-                $collections = array_keys($collections);
+        $params = $args['params'];
+        if (empty($params['descendant_or_self'])) {
+            return;
+        }
 
-                $select->joinInner(
-                    array('collections' => $this->_db->Collection),
-                    'items.collection_id = collections.id',
-                    array());
+        $collection = $params['descendant_or_self'] instanceof Collection
+            // Collection can be an object when not called from search form.
+            ? $params['descendant_or_self']->id
+            // Else this should be an integer.
+            : (integer) $params['descendant_or_self'];
 
-                // There are descendants.
-                if (count($collections) > 1) {
-                    $select->where('collections.id IN (?)', $collections);
-                }
-                // There is only the collection itself or no collection.
-                else {
-                    $select->where('collections.id = ?', reset($collections));
-                }
-            }
+        if (empty($collection)) {
+            return;
+        }
+
+        $select = $args['select'];
+
+        $collections = $this->_db->getTable('CollectionTree')
+            ->getDescendantOrSelfCollections($collection);
+        $collections = array_keys($collections);
+
+        $select->joinInner(
+            array('collection_tree_collections' => $this->_db->Collection),
+            'items.collection_id = collection_tree_collections.id',
+            array());
+
+        // There are descendants.
+        if (count($collections) > 1) {
+            $select->where('collection_tree_collections.id IN (?)', $collections);
+        }
+        // There is only the collection itself or no collection.
+        else {
+            $select->where('collection_tree_collections.id = ?', reset($collections));
         }
     }
 
@@ -421,10 +424,21 @@ public function filterItemsBrowseParams($params)
              $params['subcollections'] = 1;
         }
 
-        if (!empty($params['collection']) && !empty($params['subcollections'])) {
-            $params['descendant_or_self'] = $params['collection'];
-            $params['collection'] = '';
+        if (!empty($params['subcollections'])) {
+            $collection = 0;
+            if (!empty($params['collection_id'])) {
+                $collection = $params['collection_id'];
+                $params['collection_id'] = '';
+            }
+            if (!empty($params['collection'])) {
+                $collection = $params['collection'];
+                $params['collection'] = '';
+            }
+            if ($collection) {
+                $params['descendant_or_self'] = $collection;
+            }
         }
+
         return $params;
     }
 

From b0db83525cf9db4dafa6b26f8f48992f5262fc46 Mon Sep 17 00:00:00 2001
From: Daniel Berthereau <Daniel.github@Berthereau.net>
Date: Mon, 21 Sep 2015 00:00:00 +0200
Subject: [PATCH 11/15] Improved config form.

---
 CollectionTreePlugin.php | 6 ++++--
 plugin.ini               | 4 ++--
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/CollectionTreePlugin.php b/CollectionTreePlugin.php
index 14a51db..11ee5c6 100644
--- a/CollectionTreePlugin.php
+++ b/CollectionTreePlugin.php
@@ -159,8 +159,10 @@ public function hookConfigForm($args)
     public function hookConfig($args)
     {
         $post = $args['post'];
-        foreach ($post as $key => $value) {
-            set_option($key, $value);
+        foreach ($this->_options as $optionKey => $optionValue) {
+            if (isset($post[$optionKey])) {
+                set_option($optionKey, $post[$optionKey]);
+            }
         }
     }
 
diff --git a/plugin.ini b/plugin.ini
index 270a54b..a45ec7b 100644
--- a/plugin.ini
+++ b/plugin.ini
@@ -3,8 +3,8 @@ name="Collection Tree"
 author="Roy Rosenzweig Center for History and New Media"
 description="Gives administrators the ability to create a hierarchical tree of their collections."
 license="GPLv3"
-link="http://omeka.org/codex/Plugins/CollectionTree_2.0"
-support_link="http://omeka.org/forums/forum/plugins"
+link="https://omeka.org/codex/Plugins/CollectionTree_2.0"
+support_link="https://omeka.org/forums/forum/plugins"
 version="2.0.2"
 omeka_minimum_version="2.0"
 omeka_target_version="2.0"

From cc34720e9b2b4c56e00b2d499bc525bca04a36f1 Mon Sep 17 00:00:00 2001
From: John Flatness <john@zerocrates.org>
Date: Wed, 10 Feb 2016 13:33:57 +0100
Subject: [PATCH 12/15] Strict standards fix for findPairsForSelectForm

---
 models/Table/CollectionTree.php | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/models/Table/CollectionTree.php b/models/Table/CollectionTree.php
index 640aaa6..f52624f 100644
--- a/models/Table/CollectionTree.php
+++ b/models/Table/CollectionTree.php
@@ -124,6 +124,12 @@ public function findByParentCollectionId($parentCollectionId)
      */
     public function findPairsForSelectForm(array $options = array(), $padding = '-')
     {
+        if (isset($params['padding'])) {
+            $padding = $params['padding'];
+        } else {
+            $padding = '-';
+        }
+
         $options = array();
 
         foreach ($this->getRootCollections() as $rootCollectionId => $rootCollection) {

From 0d341bc7808a133d5e720abe2fc8a73ae089dec6 Mon Sep 17 00:00:00 2001
From: Jim Safley <jimsafley@gmail.com>
Date: Wed, 21 Dec 2016 16:13:15 -0500
Subject: [PATCH 13/15] Update copy

---
 views/admin/plugins/collection-tree-config-form.php | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/views/admin/plugins/collection-tree-config-form.php b/views/admin/plugins/collection-tree-config-form.php
index 2466d7c..6798c10 100644
--- a/views/admin/plugins/collection-tree-config-form.php
+++ b/views/admin/plugins/collection-tree-config-form.php
@@ -13,7 +13,7 @@
 </div>
 <div class="field">
     <div class="two columns alpha">
-        <?php echo $this->formLabel('collection_tree_browse_only_root', __('Browse root-level')); ?>
+        <?php echo $this->formLabel('collection_tree_browse_only_root', __('Browse root-level collections only')); ?>
     </div>
     <div class="inputs five columns omega">
         <p class="explanation"><?php
@@ -25,12 +25,11 @@
 </div>
 <div class="field">
     <div class="two columns alpha">
-        <?php echo $this->formLabel('collection_tree_show_subcollections', __('Show collection')); ?>
+        <?php echo $this->formLabel('collection_tree_show_subcollections', __('Show subcollection items')); ?>
     </div>
     <div class="inputs five columns omega">
         <p class="explanation"><?php
-            echo __('The "Show collection" page can show items of current collection only, or all items of subcollections.');
-            echo ' ' . __('This is specially useful when root collections are empty and used as main categories.');
+            echo __('On public collection show pages, display items belonging to all subcollections. This is especially useful when root collections are empty and used as main categories.');
         ?></p>
         <?php echo $this->formCheckbox('collection_tree_show_subcollections', null,
             array('checked' => (bool) get_option('collection_tree_show_subcollections'))); ?>
@@ -38,11 +37,11 @@
 </div>
 <div class="field">
     <div class="two columns alpha">
-        <?php echo $this->formLabel('collection_tree_search_descendant', __('Advanced search')); ?>
+        <?php echo $this->formLabel('collection_tree_search_descendant', __('Expand search to subcollection items by default')); ?>
     </div>
     <div class="inputs five columns omega">
         <p class="explanation"><?php
-            echo __('If checked, the advanced search of items will be expanded by default to all descendant collections of the selected collection.');
+            echo __('When searching by collection, expand searching to all subcollections by default.');
         ?></p>
         <?php echo $this->formCheckbox('collection_tree_search_descendant', null,
             array('checked' => (bool) get_option('collection_tree_search_descendant'))); ?>

From fcf0ae1d57fbf7f72daed8a6d42e98127cbc4d30 Mon Sep 17 00:00:00 2001
From: Jim Safley <jimsafley@gmail.com>
Date: Wed, 21 Dec 2016 16:13:29 -0500
Subject: [PATCH 14/15] Filter item browse in admin theme

An earlier commit limited the item browse SQL hook to the public theme. This broke the search on the admin side since filterItemsBrowseParams() removed the collection_id, resulting in a search on all items when searching by collection.
---
 CollectionTreePlugin.php | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/CollectionTreePlugin.php b/CollectionTreePlugin.php
index 11ee5c6..f08430f 100644
--- a/CollectionTreePlugin.php
+++ b/CollectionTreePlugin.php
@@ -264,10 +264,6 @@ public function hookCollectionsBrowseSql($args)
      */
     public function hookItemsBrowseSql($args)
     {
-        if (is_admin_theme()) {
-            return;
-        }
-
         $params = $args['params'];
         if (empty($params['descendant_or_self'])) {
             return;

From 5ac1c48daea84f83f52972e3600b6d8e383d7f55 Mon Sep 17 00:00:00 2001
From: Jim Safley <jimsafley@gmail.com>
Date: Wed, 21 Dec 2016 16:23:18 -0500
Subject: [PATCH 15/15] Use correct markup

---
 CollectionTreePlugin.php | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/CollectionTreePlugin.php b/CollectionTreePlugin.php
index f08430f..8bcfe5c 100644
--- a/CollectionTreePlugin.php
+++ b/CollectionTreePlugin.php
@@ -327,15 +327,14 @@ public function hookPublicItemsSearch($args)
      */
     protected function _itemsSearch($args)
     {
-        $view = $args['view'];
-        $html = '<div id="search-subcollections" class="field">';
-        $html .= $view->formLabel('subcollections', __('Broaden to the sub-collections'));
-        $html .= '<div class="inputs">';
-        $html .= $view->formCheckbox('subcollections', null,
-            array('checked' => (bool) get_option('collection_tree_search_descendant')));
-        $html .= '</div>';
-        $html .= '</div>';
-        return $html;
+        return '<div class="field">
+            <div class="two columns alpha">
+                <label for="public">' . __('Expand to subcollections') . '</label>
+            </div>
+            <div class="five columns omega inputs">
+                ' . $args['view']->formCheckbox('subcollections', null, array('checked' => (bool) get_option('collection_tree_search_descendant'))) . '
+            </div>
+        </div>';
     }
 
     /**