diff -Naru search_original/.cvsignore search/.cvsignore
--- search_original/.cvsignore	1970-01-01 09:00:00.000000000 +0900
+++ search/.cvsignore	2007-12-19 18:20:01.965250000 +0900
@@ -0,0 +1 @@
+delete_log.php
diff -Naru search_original/cron.php search/cron.php
--- search_original/cron.php	2009-01-08 16:30:17.283625000 +0900
+++ search/cron.php	2009-06-08 14:48:01.221404900 +0900
@@ -12,6 +12,28 @@
 *   adds documents created since the last index run
 */
 
+// (Shirai147): Enabling search/cron.php to run at command line (2009/06/05)
+// (Shirai147): Add from here
+    /**
+    * includes and requires
+    */
+    if (!isset($_SERVER['REMOTE_ADDR'])) {
+        if (isset($_SERVER['argv'][0])) {
+            chdir(dirname($_SERVER['argv'][0]));
+        }
+        require_once('../config.php');
+        define('FULLME', 'cron');
+/// emulate normal session
+        $SESSION = new object();
+        $USER = get_admin();      /// Temporarily, to provide environment for this script
+
+/// ignore admins timezone, language and locale - use site deafult instead!
+        $USER->timezone = $CFG->timezone;
+        $USER->lang = '';
+        $USER->theme = '';
+        course_setup(SITEID);
+    }
+// (Shirai147): Add to here
     if (!defined('MOODLE_INTERNAL')) {
         die('Direct access to this script is forbidden.');    ///  It must be included from a Moodle page
     }
diff -Naru search_original/documents/assignment_document.php search/documents/assignment_document.php
--- search_original/documents/assignment_document.php	2009-06-05 09:48:14.138625000 +0900
+++ search/documents/assignment_document.php	2009-06-08 15:13:46.452550500 +0900
@@ -125,6 +125,10 @@
                         case 'upload' : {
                             $submitted->source = 'files';
                             $submitted->data = "{$assignment->course}/moddata/assignment/{$assignment->id}/{$submission->userid}";
+// (Debug011): $submitted->path is not set when the type of the assignment is uploadsingle/upload (2009/06/04)
+// (Debug011): Add from here
+                            $submitted->path = $submitted->data;
+// (Debug011): Add to here
                         }
                         break;
                         case 'offline' : continue; // cannot index, no content in Moodle !!
@@ -132,20 +136,41 @@
                 }
                 if (empty($submitted)) continue; // ignoring
 
-                if ($submitted->source = 'text'){
+// (Debug010): The uploaded files as the assignment aren't made indeies since these files are misstaken for 'test' (2009/06/04)
+// (Debug010): Modified from here
+//              if ($submitted->source = 'text'){
+                if ($submitted->source == 'text'){
+// (Debug010): Modified to here
                     $submission->description = $submitted->data;
                     $submission->description = preg_replace("/<[^>]*>/", '', $submission->description); // stip all tags
                     $documents[] = new AssignmentSearchDocument(get_object_vars($submission), $cm->id, 'submission', $assignment->course, $submission->userid, $context->id);
                     mtrace("finished online submission for {$submission->authors} in assignement {$assignment->name}");
-                } elseif ($submitted->source = 'files'){
+// (Debug010): Modified from here
+//              } elseif ($submitted->source = 'files'){
+                } elseif ($submitted->source == 'files'){
+// (Debug010): Modified to here
+// (Debug011): $submitted->path is not set when the type of the assignment is uploadsingle/upload (2009/06/04)
+// (Debug011): Modified from here
                     $SUBMITTED = opendir($submitted->path);
+                    $SUBMITTED = opendir("{$CFG->dataroot}/{$submitted->path}");
+// (Debug011): Modified to here
                     while($entry = readdir($SUBMITTED)){
                         if (ereg("^\.", $entry)) continue; // exclude hidden and dirs . and .. 
                         $path = "{$submitted->path}/{$entry}";
-                        $documents[] = assignment_get_physical_file($submission, $assignment, $cm, $path, $context_id, $documents);
+// (Debug015): function assignment_get_physical_file() does not have argument $getsingle (2009/06/04)
+// (Debug015): Deleting "$documents[] = ", and adding parameter 'false'
+// (Debug012): $context->id is $context_id (2009/06/04)
+// (Debug012) & (Debug015): Modified from here
+//                      $documents[] = assignment_get_physical_file($submission, $assignment, $cm, $path, $context_id, $documents);
+                        assignment_get_physical_file($submission, $assignment, $cm, $path, $context->id, false, $documents);
+// (Debug012): Modified to here
                         mtrace("finished attachement $path for {$submission->authors} in assignement {$assignment->name}");
                     } 
-                    closedir($submission->path);                            
+// (Debug014): $submission->path is $SUBMITTED (2009/06/04)
+// (Debug014): Modified from here
+//                  closedir($submission->path);                            
+                    closedir($SUBMITTED);
+// (Debug014): Modified to here
                 }
             }
         }
@@ -165,7 +190,11 @@
 * @param documents the array of documents, by ref, where to add the new document.
 * @return a search document when unique or false.
 */
-function assignment_get_physical_file(&$submission, &$assignment, &$cm, $path, $context_id, &$documents = null){
+// (Debug015): function assignment_get_physical_file() does not have argument $getsingle (2009/06/04)
+// (Debug015): Modified from here
+// function assignment_get_physical_file(&$submission, &$assignment, &$cm, $path, $context_id, &$documents = null){
+function assignment_get_physical_file(&$submission, &$assignment, &$cm, $path, $context_id, $getsingle, &$documents = null){
+// (Debug015): Modified to here
     global $CFG;
     
     $fileparts = pathinfo($path);
@@ -185,7 +214,13 @@
     if (file_exists($CFG->dirroot.'/search/documents/physical_'.$ext.'.php')){
         include_once($CFG->dirroot.'/search/documents/physical_'.$ext.'.php');
         $function_name = 'get_text_for_indexing_'.$ext;
-        $submission->description = $function_name(null, $path);
+// (Debug013): First argument of functions get_text_for_indexing_() is 'call by reference' (2009/06/04)
+// (Debug013): Comment out this line
+//      $submission->description = $function_name(null, $path);
+// (Debug013): Add from here
+        $dummyResource = null;
+        $submission->description = $function_name($dummyResource, $path);
+// (Debug013): Add to here
         
         // get authors
         $user = get_record('user', 'id', $submission->userid);
diff -Naru search_original/documents/data_document.php search/documents/data_document.php
--- search_original/documents/data_document.php	2009-06-05 09:48:14.138625000 +0900
+++ search/documents/data_document.php	2009-06-08 15:17:11.719348700 +0900
@@ -46,7 +46,11 @@
         if ($record['userid']){
             $user = get_record('user', 'id', $record['userid']);
         }
-        $doc->author = (isset($user)) ? $user->firstname.' '.$user->lastname : '' ;
+// (Debug005): function fullname() is not used in data module to set the author field (2009/06/03)
+// (Debug005): Modified from here
+//      $doc->author = (isset($user)) ? $user->firstname.' '.$user->lastname : '' ;
+        $doc->author = (isset($user)) ? fullname($user) : '' ;
+// (Debug005): Modified to here
         $doc->contents  = $record['content'];
         $doc->url       = data_make_link($record['dataid'], $record['id']);
         
diff -Naru search_original/documents/forum_document.php search/documents/forum_document.php
--- search_original/documents/forum_document.php	2009-06-05 09:48:14.138625000 +0900
+++ search/documents/forum_document.php	2009-06-08 14:49:54.915797500 +0900
@@ -93,6 +93,13 @@
 
     $coursemodule = get_field('modules', 'id', 'name', 'forum');
     $cm = get_record('course_modules', 'course', $forum->course, 'module', $coursemodule, 'instance', $forum->id);
+// (Shirai136): When the course module does not exist in mdl_course_modules, SQL syntax error will occur (2009/05/29)
+// (Shirai136): Add from here
+    if (empty($cm)) {
+        mtrace("Missing this forum: Course=".$forum->course."/ ForumID=".$forum->id);
+        return $documents;
+    }
+// (Shirai136): Add to here
     $context = get_context_instance(CONTEXT_MODULE, $cm->id);
 
     foreach($posts as $aPost) {
diff -Naru search_original/documents/glossary_document.php search/documents/glossary_document.php
--- search_original/documents/glossary_document.php	2009-05-20 21:10:49.503625000 +0900
+++ search/documents/glossary_document.php	2009-06-08 15:18:56.758828400 +0900
@@ -44,7 +44,11 @@
 
         if ($entry['userid'])
             $user = get_record('user', 'id', $entry['userid']);
-        $doc->author    = ($user ) ? $user->firstname.' '.$user->lastname : '' ;
+// (Debug009): function fullname() is not used in glossary module to set the author field (2009/06/04)
+// (Debug009): Modified from here
+//      $doc->author    = ($user ) ? $user->firstname.' '.$user->lastname : '' ;
+        $doc->author    = ($user ) ? fullname($user) : '' ;
+// (Debug009): Modified to here
         $doc->contents  = strip_tags($entry['definition']);
         $doc->url       = glossary_make_link($entry['id']);
         
@@ -77,7 +81,11 @@
 
         if ($entry['userid'])
             $user = get_record('user', 'id', $entry['userid']);
-        $doc->author    = ($user ) ? $user->firstname.' '.$user->lastname : '' ;
+// (Debug009): function fullname() is not used in glossary module to set the author field (2009/06/04)
+// (Debug009): Modified from here
+//      $doc->author    = ($user ) ? $user->firstname.' '.$user->lastname : '' ;
+        $doc->author    = ($user ) ? fullname($user) : '' ;
+// (Debug009): Modified to here
         $doc->contents  = strip_tags($entry['entrycomment']);
         $doc->url       = glossary_make_link($entry['entryid']);
         
diff -Naru search_original/documents/label_document.php search/documents/label_document.php
--- search_original/documents/label_document.php	2009-06-05 09:48:14.138625000 +0900
+++ search/documents/label_document.php	2009-06-08 14:50:23.476103900 +0900
@@ -88,6 +88,13 @@
 
     $coursemodule = get_field('modules', 'id', 'name', 'label');
     $cm = get_record('course_modules', 'course', $label->course, 'module', $coursemodule, 'instance', $label->id);
+// (Shirai136): When the course module does not exist in mdl_course_modules, SQL syntax error will occur (2009/05/29)
+// (Shirai136): Add from here
+    if (empty($cm)) {
+        mtrace("Missing this label: Course=".$label->course."/ LabelID=".$label->id);
+        return $documents;
+    }
+// (Shirai136): Add to here
     $context = get_context_instance(CONTEXT_MODULE, $cm->id);
 
     $documents[] = new LabelSearchDocument(get_object_vars($label), $context->id);
diff -Naru search_original/documents/physical_doc.php search/documents/physical_doc.php
--- search_original/documents/physical_doc.php	2009-06-05 09:48:14.138625000 +0900
+++ search/documents/physical_doc.php	2009-06-08 14:52:04.218366300 +0900
@@ -30,7 +30,11 @@
     // just call pdftotext over stdout and capture the output
     if (!empty($CFG->block_search_word_to_text_cmd)){
         if (!file_exists("{$moodleroot}{$CFG->block_search_word_to_text_cmd}")){
-            mtrace('Error with MSWord to text converter command : exectutable not found at '.$moodleroot.$CFG->block_search_word_to_text_cmd);
+(Shirai145): Adding path for external converter and modifying "exectuable" -> "executable" (2009/05/30)
+// (Shirai145): Modified from here
+//          mtrace('Error with MSWord to text converter command : exectutable not found at '.$moodleroot.$CFG->block_search_word_to_text_cmd);
+            mtrace('Error with MSWord to text converter command : executable not found at '.$moodleroot.$CFG->block_search_word_to_text_cmd);
+// (Shirai145): Modified to here
         } else {
             if ($directfile == ''){
                 $file = escapeshellarg("{$CFG->dataroot}/{$resource->course}/{$resource->reference}");
diff -Naru search_original/documents/resource_document.php search/documents/resource_document.php
--- search_original/documents/resource_document.php	2009-06-05 09:48:14.138625000 +0900
+++ search/documents/resource_document.php	2009-06-08 15:20:31.283423400 +0900
@@ -100,6 +100,13 @@
         foreach($resources as $aResource){
             $coursemodule = get_field('modules', 'id', 'name', 'resource');
             $cm = get_record('course_modules', 'course', $aResource->course, 'module', $coursemodule, 'instance', $aResource->id);
+// (Shirai136): When the course module does not exist in mdl_course_modules, SQL syntax error will occur (2009/05/29)
+// (Shirai136): Add from here
+            if (empty($cm)) {
+                mtrace("Missing this resource: Course=".$aResource->course."/ ResourceID=".$aResource->id);
+                return $documents;
+            }
+// (Shirai136): Add to here
             $context = get_context_instance(CONTEXT_MODULE, $cm->id);
             $aResource->id = $cm->id;
             $documents[] = new ResourceSearchDocument(get_object_vars($aResource), $context->id);
@@ -258,7 +265,11 @@
         $cm = get_record('course_modules', 'id', $resource->id);
         $context = get_context_instance(CONTEXT_MODULE, $cm->id);
         if ($resource->type == 'file' && @$CFG->block_search_enable_file_indexing){
-            $document = resource_get_physical_file($resource, true, $context->id);
+// (Debug008): The order of arguments $contex->id and true are wrong (exchanged) (2009/06/04)
+// (Debug008): Modified from here
+//          $document = resource_get_physical_file($resource, true, $context->id);
+            $document = resource_get_physical_file($resource, $context->id, true);
+// (Debug008): Modified to here
             if (!$document) mtrace("Warning : this document {$resource->name} will not be indexed");
             return $document;
         } else {
diff -Naru search_original/documents/user_document.php search/documents/user_document.php
--- search_original/documents/user_document.php	2009-06-05 09:48:14.138625000 +0900
+++ search/documents/user_document.php	2009-06-08 15:22:43.945958300 +0900
@@ -270,13 +270,21 @@
         }
     } elseif ($itemtype == 'post') {
         if ($post = get_records('post', 'id', $id)){
+// (Debug006): The return value of get_records() are array() (2009/06/03)
+// (Debug006): Add from here
+            $post = $post[$id];
+// (Debug006): Add to here
             $texts = array();
             $texts[] = $post->subject;
             $texts[] = $post->summary;
             $texts[] = $post->content;
             $post->description = implode(" ", $texts);
             $posthash = get_object_vars($post);
-            return new UserPostSearchDocument($posthash, $user->id, 'post', null);
+// (Debug007): $user->id is $post->userid (2009/06/03)
+// (Debug007): Modified from here
+//          return new UserPostSearchDocument($posthash, $user->id, 'post', null);
+            return new UserPostSearchDocument($posthash, $post->userid, 'post', null);
+// (Debug007): Modified to here
         }
     } elseif ($itemtype == 'attachment' && @$CFG->block_search_enable_file_indexing) {
         if ($post = get_records('post', 'id', $id)){
diff -Naru search_original/documents/wiki_document.php search/documents/wiki_document.php
--- search_original/documents/wiki_document.php	2009-06-05 09:48:14.138625000 +0900
+++ search/documents/wiki_document.php	2009-06-08 14:55:21.343850900 +0900
@@ -169,6 +169,13 @@
     if ($entries){
         $coursemodule = get_field('modules', 'id', 'name', 'wiki');
         $cm = get_record('course_modules', 'course', $wiki->course, 'module', $coursemodule, 'instance', $wiki->id);
+// (Shirai136): When the course module does not exist in mdl_course_modules, SQL syntax error will occur (2009/05/29)
+// (Shirai136): Add from here
+        if (empty($cm)) {
+            mtrace("Missing this wiki: Course=".$wiki->course."/ WikiID=".$wiki->id);
+            return $documents;
+        }
+// (Shirai136): Add to here
         $context = get_context_instance(CONTEXT_MODULE, $cm->id);
         foreach($entries as $entry) {
     
@@ -180,7 +187,11 @@
             if (is_array($pages)) {
                 foreach($pages as $page) {
                     if (strlen($page->content) > 0) {
-                        $documents[] = new WikiSearchDocument(get_object_vars($page), $entry->wikiid, $entry->course, $entry->groupid, $page->userid, $context->id);
+// (Shirai140): The course name is not displayed when the search result is wiki (2009/05/29)
+// (Shirai140): Modified from here
+//                      $documents[] = new WikiSearchDocument(get_object_vars($page), $entry->wikiid, $entry->course, $entry->groupid, $page->userid, $context->id);
+                        $documents[] = new WikiSearchDocument(get_object_vars($page), $entry->wikiid, $wiki->course, $entry->groupid, $page->userid, $context->id);
+// (Shirai140): Modified to here
                     } 
                 } 
             } 
@@ -200,6 +211,12 @@
     $entry = get_record('wiki_entries', 'id', $page->wiki);
     $coursemodule = get_field('modules', 'id', 'name', 'wiki');
     $cm = get_record('course_modules', 'course', $entry->course, 'module', $coursemodule, 'instance', $entry->wikiid);
+// (Shirai136): Add from here
+    if (empty($cm)) {
+        mtrace("Missing this wiki: Course=".$entry->course."/ WikiID=".$entry->wikiid);
+        return array();
+    }
+// (Shirai136): Add to here
     $context = get_context_instance(CONTEXT_MODULE, $cm->id);
     return new WikiSearchDocument(get_object_vars($page), $entry->wikiid, $entry->course, $entry->groupid, $page->userid, $context->id);
 }
diff -Naru search_original/indexer.php search/indexer.php
--- search_original/indexer.php	2009-05-20 21:10:49.503625000 +0900
+++ search/indexer.php	2009-06-08 14:49:12.590923300 +0900
@@ -33,6 +33,12 @@
     /**
     * includes and requires
     */
+// (Shirai146): Enabling search/indexer.php to run at command line (2009/06/05)
+// (Shirai146): Add from here
+    if (!isset($_SERVER['REMOTE_ADDR']) && isset($_SERVER['argv'][0])) {
+        chdir(dirname($_SERVER['argv'][0]));
+    }
+// (Shirai146): Add to here
     require_once('../config.php');
     require_once($CFG->dirroot.'/search/lib.php');
 
@@ -42,7 +48,25 @@
 
 /// only administrators can index the moodle installation, because access to all pages is required
 
+// (Shirai146): Add from here
+    if (isset($_SERVER['REMOTE_ADDR'])) {
+// (Shirai146): Add to here
     require_login();
+// (Shirai146): Add from here
+    } else {
+        $_GET['areyousure'] = 'yes';
+        define('FULLME', 'cron');
+/// emulate normal session
+        $SESSION = new object();
+        $USER = get_admin();      /// Temporarily, to provide environment for this script
+
+/// ignore admins timezone, language and locale - use site deafult instead!
+        $USER->timezone = $CFG->timezone;
+        $USER->lang = '';
+        $USER->theme = '';
+        course_setup(SITEID);
+    }
+// (Shirai146): Add to here
     
     if (empty($CFG->enableglobalsearch)) {
         error(get_string('globalsearchdisabled', 'search'));