--- loncom/interface/londocs.pm	2005/06/09 20:41:38	1.184
+++ loncom/interface/londocs.pm	2005/12/22 20:23:39	1.215
@@ -1,7 +1,7 @@
 # The LearningOnline Network
 # Documents
 #
-# $Id: londocs.pm,v 1.184 2005/06/09 20:41:38 www Exp $
+# $Id: londocs.pm,v 1.215 2005/12/22 20:23:39 albertel Exp $
 #
 # Copyright Michigan State University Board of Trustees
 #
@@ -166,7 +166,10 @@ sub dumpcourse {
 	$crs=~s/\_/\//g;
 	foreach (keys %replacehash) {
 	    my $newfilename=$title.'/'.$replacehash{$_};
+	    $newfilename=~s/\.(\w+)$//;
+	    my $ext=$1;
 	    $newfilename=&clean($newfilename);
+	    $newfilename.='.'.$ext;
 	    my @dirs=split(/\//,$newfilename);
 	    my $path='/home/'.$ca.'/public_html';
 	    my $makepath=$path;
@@ -249,11 +252,10 @@ sub dumpcourse {
 # ------------------------------------------------------ Generate "export" button
 
 sub exportbutton {
-    return '';
     return '</td><td bgcolor="#DDDDCC">'.
             '<input type="submit" name="exportcourse" value="'.
             &mt('Export Course to IMS').'" />'.
-            &Apache::loncommon::help_open_topic('Docs_Export_Course_Docs');
+    &Apache::loncommon::help_open_topic('Docs_Export_Course_Docs');
 }
 
 sub exportcourse {
@@ -491,10 +493,21 @@ sub create_ims_store {
 ' identifier="MANIFEST-'.$env{'request.course.id'}.'-'.$now.'"'.
 '  xsi:schemaLocation="http://www.imsglobal.org/xsd/imscp_v1p1imscp_v1p1.xsd'.
 '  http://www.imsglobal.org/xsd/imsmd_v1p2 imsmd_v1p2p2.xsd">'."\n".
+'  <metadata>
+    <schema></schema>
+    <imsmd:lom>
+      <imsmd:general>
+        <imsmd:identifier>'.$env{'request.course.id'}.'</imsmd:identifier>
+        <imsmd:title>
+          <imsmd:langstring xml:lang="en">'.$env{'course.'.$env{'request.course.id'}.'.description'}.'</imsmd:langstring>
+        </imsmd:title>
+      </imsmd:general>
+    </imsmd:lom>
+  </metadata>'."\n".
 '  <organizations default="ORG-'.$env{'request.course.id'}.'-'.$now.'">'."\n".
 '    <organization identifier="ORG-'.$env{'request.course.id'}.'-'.$now.'"'.
 ' structure="hierarchical">'."\n".
-'      <title>'.$env{'request.'.$env{'request.course.id'}.'.description'}.'</title>'
+'      <title>'.$env{'course.'.$env{'request.course.id'}.'.description'}.'</title>'
     } else {
         $$outcome .= 'An error occurred opening the IMS manifest file.<br />'
 ;
@@ -542,7 +555,6 @@ sub build_package {
     $count = 0;
     my $imsresources;
     my $pkgdepth;
-    my $included = 0;
     while ($curRes = $it->next()) {
         if ($curRes == $it->BEGIN_MAP()) {
             $prevdepth = $depth;
@@ -565,10 +577,13 @@ sub build_package {
                 unless ($curRes->is_sequence()) {
                     $resourceref = 'identifierref="RES-'.$env{'request.course.id'}.'-'.$count.'"';
                 }
-                if (($depth <= $prevdepth) && ($count > 1) && ($included)) {
-                    print $ims_manifest "\n".'  </item>'."\n";
+                my $step = $prevdepth - $depth;
+                if (($step >= 0) && ($count > 1)) {
+                    while ($step >= 0) {
+                        print $ims_manifest "\n".'  </item>'."\n";
+                        $step --;
+                    }
                 }
-                $included = 1;
                 $prevdepth = $depth;
 
                 my $itementry =
@@ -610,8 +625,6 @@ sub build_package {
                     }
                 }
                 $pkgdepth = $depth;
-            } else {
-                $included = 0;
             }
         }
     }
@@ -646,7 +659,6 @@ sub process_content {
     my ($count,$curRes,$cdom,$cnum,$symb,$content_file,$href,$copyresult,$tempexport) = @_;
     my $content_type;
     my $message;
-# find where user is author or co-author
     my @uploads = ();
     if ($curRes->is_sequence()) {
         $content_type = 'sequence';
@@ -679,7 +691,7 @@ sub process_content {
         if ($contents) {
             $$content_file = &store_template($contents,$tempexport,$count,$content_type);
         }
-    } elsif ($symb =~ m-lib/templates/examupload\.problem-m) {
+    } elsif ($symb =~ m-lib/templates/examupload\.problem$-) {
         $content_type = 'examupload';
     } elsif ($symb =~ m-adm/(\w+)/(\w+)/(\d+)/bulletinboard$-) {
         $content_type = 'bulletinboard';
@@ -700,6 +712,7 @@ sub process_content {
         if ($2 eq $env{'user.domain'} && $3 eq $env{'user.name'})  {
             $canedit= 1;
         }
+# only include problem code where current user is author
         if ($canedit) {
             $$content_file = &replicate_content($cdom,$cnum,$tempexport,$symb,$count,\$message,$href,'resource');
         } else {
@@ -748,11 +761,13 @@ sub replicate_content {
         if ($copiedfile = Apache::File->new('>'.$destination)) {
             my $content;
             if ($caller eq 'resource') {
-                $content = &Apache::lonnet::getfile('/home/httpd/html/res/'.$url);
+                my $respath =  $Apache::lonnet::perlvar{'lonDocRoot'}.'/res';
+                my $filepath = &Apache::lonnet::filelocation($respath,$url);
+                $content = &Apache::lonnet::getfile($filepath);
                 if ($content eq -1) {
                     $$message = 'Could not copy file '.$filename;
                 } else {
-                    &extract_media($content,$count,$tempexport,$href,'resource');
+                    &extract_media($url,$cdom,$cnum,\$content,$count,$tempexport,$href,$message,'resource');
                     $repstatus = 'ok';
                 }
             } elsif ($caller eq 'uploaded' || $caller eq 'templateupload') {
@@ -760,10 +775,10 @@ sub replicate_content {
                 $repstatus = &Apache::lonnet::getuploaded('GET',$url,$cdom,$cnum,\$content,$rtncode);
                 if ($repstatus eq 'ok') {
                     if ($url =~ /\.html?$/i) {
-                        &extract_media(\$content,$count,$tempexport,$href,'uploaded');
+                        &extract_media($url,$cdom,$cnum,\$content,$count,$tempexport,$href,$message,'uploaded');
                     }
                 } else {
-                    $$message = 'Could not render '.$url.' server message - '.$rtncode;
+                    $$message = 'Could not render '.$url.' server message - '.$rtncode."<br />\n";
                 }
             } elsif ($caller eq 'noedit') {
 # Need to render the resource without the LON-CAPA Internal header and the Post discussion footer, and then set $content equal to this. 
@@ -775,23 +790,85 @@ sub replicate_content {
             }
             close($copiedfile);
         } else {
-            $$message = 'Could not open destination file for '.$filename."\n";
+            $$message = 'Could not open destination file for '.$filename."<br />\n";
         }
     } else {
-        $$message = 'Could not determine name of file for '.$symb."\n";
+        $$message = 'Could not determine name of file for '.$symb."<br />\n";
     }
     if ($repstatus eq 'ok') {
-        $content_name = $count.'/'.$filename;
+        $content_name = 'resources/'.$count.'/'.$filename;
     }
     return $content_name;
 }
 
 sub extract_media {
-    my ($content,$count,$tempexport,$href,$caller) = @_;
-# @$href will contain path to any embedded resources in the content.
-# For LON-CAPA problems this would be images. applets etc. 
-# For uploaded HTML files this would be images etc.
-# paths will be in the form $count/res/$file, and urls in the $content will be rewritten with the new paths. 
+    my ($url,$cdom,$cnum,$content,$count,$tempexport,$href,$message,$caller) = @_;
+    my ($dirpath,$container);
+    my %allfiles = ();
+    my %codebase = ();
+    if ($url =~ m-(.*/)([^/]+)$-) {
+        $dirpath = $1;
+        $container = $2;
+    } else {
+        $dirpath = $url;
+        $container = '';
+    }
+    &Apache::lonnet::extract_embedded_items(undef,undef,\%allfiles,\%codebase,$content);
+    foreach my $embed_file (keys(%allfiles)) {
+        my $filename;
+        if ($embed_file =~ m#([^/]+)$#) {
+            $filename = $1;
+        } else {
+            $filename = $embed_file;
+        }
+        my $newname = 'res/'.$filename;
+        my ($rtncode,$embed_content,$repstatus);
+        my $embed_url;
+        if ($embed_file =~ m-^/-) {
+            $embed_url = $embed_file;           # points to absolute path
+        } else {
+            if ($embed_file =~ m-https?://-) {
+                next;                           # points to url
+            } else {
+                $embed_url = $dirpath.$embed_file;  # points to relative path
+            }
+        }
+        if ($caller eq 'resource') {
+            my $respath =  $Apache::lonnet::perlvar{'lonDocRoot'}.'/res';  
+            my $embed_path = &Apache::lonnet::filelocation($respath,$embed_url); 
+            $embed_content = &Apache::lonnet::getfile($embed_path);
+            unless ($embed_content eq -1) {
+                $repstatus = 'ok';
+            }
+        } elsif ($caller eq 'uploaded') {
+            
+            $repstatus = &Apache::lonnet::getuploaded('GET',$embed_url,$cdom,$cnum,\$embed_content,$rtncode);
+        }
+        if ($repstatus eq 'ok') {
+            my $destination = $tempexport.'/resources/'.$count.'/res';
+            if (!-e "$destination") {
+                mkdir($destination,0755);
+            }
+            $destination .= '/'.$filename;
+            my $copiedfile;
+            if ($copiedfile = Apache::File->new('>'.$destination)) {
+                print $copiedfile $embed_content;
+                push @{$href}, 'resources/'.$count.'/res/'.$filename;
+                my $attrib_regexp = '';
+                if (@{$allfiles{$embed_file}} > 1) {
+                    $attrib_regexp = join('|',@{$allfiles{$embed_file}});
+                } else {
+                    $attrib_regexp = $allfiles{$embed_file}[0];
+                }
+                $$content =~ s#($attrib_regexp\s*=\s*['"]?)\Q$embed_file\E(['"]?)#$1$newname$2#gi;
+                if ($caller eq 'resource' && $container =~ /\.(problem|library)$/) {
+                    $$content =~ s#\Q$embed_file\E#$newname#gi;
+                }
+            }
+        } else {
+            $$message .= 'replication of embedded file - '.$embed_file.' in '.$url.' failed, reason -'.$rtncode."<br />\n";
+        }
+    }
     return;
 }
 
@@ -812,9 +889,9 @@ sub store_template {
                 close($storetemplate);
             }
             if ($content_type eq 'external') {
-                return $count.'/'.$content_type.'.html';
+                return 'resources/'.$count.'/'.$content_type.'.html';
             } else {
-                return $count.'/'.$content_type.'.xml';
+                return 'resources/'.$count.'/'.$content_type.'.xml';
             }
         }
     }
@@ -840,8 +917,7 @@ sub group_import {
                             '<resource id="2" src="" type="finish"></resource>'."\n".
                             '</map>';
             $env{'form.output'}=$newmapstr;
-            my $home=&Apache::lonnet::homeserver($coursenum,$coursedom);
-            my $result=&Apache::lonnet::finishuserfileupload($coursenum,$coursedom,$home,
+            my $result=&Apache::lonnet::finishuserfileupload($coursenum,$coursedom,
                                                 'output',$1.$2);
             if ($result != m|^/uploaded/|) {
                 $errtext.='Map not saved: A network error occured when trying to save the new map. ';
@@ -904,7 +980,7 @@ sub breadcrumbs {
 }
 
 sub editor {
-    my ($r,$coursenum,$coursedom,$folder,$allowed)=@_;
+    my ($r,$coursenum,$coursedom,$folder,$allowed,$upload_output)=@_;
     my $errtext='';
     my $fatal=0;
     my $container='sequence';
@@ -1032,56 +1108,17 @@ sub editor {
 		}
 
 	    }
-# upload a file, if present
-           if (($env{'form.uploaddoc.filename'}) &&
-               ($env{'form.cmd'}=~/^upload_(\w+)/)) {
-	    if ( ($folder=~/^$1/) || ($1 eq 'default') ) {
-            	my $destination = 'docs/';
-            	if ($folder eq 'default') {
-            	    $destination .= 'default/';
-                } elsif ($folder =~ /^default_(\d+)$/) {
-                    $destination .=  $1.'/';
-                }
-# this is for a course, not a user, so set coursedoc flag
-# probably the only place in the system where this should be "1"
-
-              my $newidx=&Apache::lonratedt::getresidx();
-              $destination .= $newidx;
-	      my $url=&Apache::lonnet::userfileupload('uploaddoc',1,$destination);
-
-              my $ext='false';
-              if ($url=~/^http\:\/\//) { $ext='true'; }
-              $url=~s/\:/\&colon;/g;
-	      my $comment=$env{'form.comment'};
-              $comment=~s/\</\&lt\;/g;
-              $comment=~s/\>/\&gt\;/g;
-              $comment=~s/\:/\&colon;/g;
-              if ($folder=~/^supplemental/) {
-		  $comment=time.'___&&&___'.$env{'user.name'}.'___&&&___'.
-		      $env{'user.domain'}.'___&&&___'.$comment;
-              }
-              $Apache::lonratedt::resources[$newidx]=
-                  $comment.':'.$url.':'.$ext.':normal:res';
-              $Apache::lonratedt::order[$#Apache::lonratedt::order+1]=
-                                                              $newidx;       
-
-	      ($errtext,$fatal)=&storemap($coursenum,$coursedom,$folder.'.'.$container);
-	      if ($fatal) {
-		  $r->print('<p><font color="red">'.$errtext.'</font></p>');
-		  return;
-	      }
-	     }
-            }
+            $r->print($upload_output);
 	    if ($env{'form.cmd'}) {
                 my ($cmd,$idx)=split(/\_/,$env{'form.cmd'});
                 if ($cmd eq 'del') {
 		    my (undef,$url)=split(':',$Apache::lonratedt::resources[$Apache::lonratedt::order[$idx]]);
-		    if ($url=~m|/+uploaded/\Q$coursedom\E/\Q$coursenum\E/|) {
-			unless ($url=~/\.(page|sequence|problem|exam|quiz|assess|survey|form|library)$/) {
-			    &Apache::lonnet::removeuploadedurl($url);
-			}
+		    if (($url=~m|/+uploaded/\Q$coursedom\E/\Q$coursenum\E/|) &&
+			($url!~/\.(page|sequence|problem|exam|quiz|assess|survey|form|library|task)$/)) {
+			&Apache::lonnet::removeuploadedurl($url);
+		    } else {
+			&Apache::lonratedt::makezombie($Apache::lonratedt::order[$idx]);
 		    }
-		    &Apache::lonratedt::makezombie($Apache::lonratedt::order[$idx]);
 		    for (my $i=$idx;$i<$#Apache::lonratedt::order;$i++) {
                         $Apache::lonratedt::order[$i]=
                           $Apache::lonratedt::order[$i+1];
@@ -1178,6 +1215,8 @@ sub editor {
         $r->print('<table>');
         foreach (@Apache::lonratedt::order) {
            my ($name,$url)=split(/\:/,$Apache::lonratedt::resources[$_]);
+	   $name=&Apache::lonratsrv::qtescape($name);
+	   $url=&Apache::lonratsrv::qtescape($url);
            unless ($name) {  $name=(split(/\//,$url))[-1]; }
            unless ($name) { $idx++; next; }
            $r->print(&entryline($idx,$name,$url,$folder,$allowed,$_,$coursenum));
@@ -1214,6 +1253,135 @@ FOLDERINFO
     }
 }
 
+sub process_file_upload {
+    my ($upload_output,$coursenum,$coursedom,$allfiles,$codebase,$uploadcmd) = @_;
+# upload a file, if present
+    my $parseaction;
+   if ($env{'form.parserflag'}) {
+        $parseaction = 'parse';
+    }
+    my $phase_status;
+    my $folder=$env{'form.folder'};
+    if ($folder eq '') {
+        $folder='default';
+    }
+    if ( ($folder=~/^$uploadcmd/) || ($uploadcmd eq 'default') ) {
+        my $errtext='';
+        my $fatal=0;
+        my $container='sequence';
+        if ($env{'form.pagepath'}) {
+            $container='page';
+        }
+        ($errtext,$fatal)=
+              &mapread($coursenum,$coursedom,$folder.'.'.$container);
+        if ($#Apache::lonratedt::order<1) {
+            $Apache::lonratedt::order[0]=1;
+            $Apache::lonratedt::resources[1]='';
+        }
+        if ($fatal) {
+            return 'failed';
+        }
+        my $destination = 'docs/';
+        if ($folder =~ /^supplemental/) {
+            $destination = 'supplemental/';
+        }
+        if (($folder eq 'default') || ($folder eq 'supplemental')) {
+            $destination .= 'default/';
+        } elsif ($folder =~ /^(default|supplemental)_(\d+)$/) {
+            $destination .=  $2.'/';
+        }
+# this is for a course, not a user, so set coursedoc flag
+# probably the only place in the system where this should be "1"
+        my $newidx=&Apache::lonratedt::getresidx();
+        $destination .= $newidx;
+        my $url=&Apache::lonnet::userfileupload('uploaddoc',1,$destination,
+						$parseaction,$allfiles,
+						$codebase);
+        my $ext='false';
+        if ($url=~/^http\:\/\//) { $ext='true'; }
+        $url=~s/\:/\&colon;/g;
+        my $comment=$env{'form.comment'};
+        $comment=~s/\</\&lt\;/g;
+        $comment=~s/\>/\&gt\;/g;
+        $comment=~s/\:/\&colon;/g;
+        if ($folder=~/^supplemental/) {
+              $comment=time.'___&&&___'.$env{'user.name'}.'___&&&___'.
+                  $env{'user.domain'}.'___&&&___'.$comment;
+        }
+
+        $Apache::lonratedt::resources[$newidx]=
+                  $comment.':'.$url.':'.$ext.':normal:res';
+        $Apache::lonratedt::order[$#Apache::lonratedt::order+1]= $newidx;
+        ($errtext,$fatal)=&storemap($coursenum,$coursedom,
+				    $folder.'.'.$container);
+        if ($fatal) {
+            $$upload_output .= '<p><font color="red">'.$errtext.'</font></p>';
+            return 'failed';
+        } else {
+            if ($parseaction eq 'parse') {
+                my $total_embedded = keys(%{$allfiles});
+                if ($total_embedded > 0) {
+                    my $num = 0;
+                    $$upload_output .= 'This file contains embedded multimedia objects, which need to be uploaded to LON-CAPA.<br />
+   <form name="upload_embedded" action="/adm/coursedocs"
+                  method="post" enctype="multipart/form-data">
+   <input type="hidden" name="folderpath" value="'.$env{'form.folderpath'}.'" />   <input type="hidden" name="cmd" value="upload_embedded" />
+   <input type="hidden" name="newidx" value="'.$newidx.'" />
+   <input type="hidden" name="primaryurl" value="'.&Apache::lonnet::escape($url).'" />
+   <input type="hidden" name="phasetwo" value="'.$total_embedded.'" />';
+                    $$upload_output .= '<b>Upload embedded files</b>:<br />
+   <table>';
+                    foreach my $embed_file (keys(%{$allfiles})) {
+                        $$upload_output .= '<tr><td>'.$embed_file.
+          '<input name="embedded_item_'.$num.'" type="file" />
+           <input name="embedded_orig_'.$num.'" type="hidden" value="'.&Apache::lonnet::escape($embed_file).'" />';
+                        my $attrib;
+                        if (@{$$allfiles{$embed_file}} > 1) {
+                            $attrib = join(':',@{$$allfiles{$embed_file}});
+                        } else {
+                            $attrib = $$allfiles{$embed_file}[0];
+                        }
+                        $$upload_output .=
+           '<input name="embedded_attrib_'.$num.'" type="hidden" value="'.$attrib.'" />';
+                        if (exists($$codebase{$embed_file})) {
+                            $$upload_output .= 
+          '<input name="codebase_'.$num.'" type="hidden" value="'.&Apache::lonnet::escape($$codebase{$embed_file}).'" />';
+                        }
+                        $$upload_output .= '</td></tr>';
+                        $num ++;
+                    }
+                    $phase_status = 'phasetwo';
+                    $$upload_output .= '</table><br />
+   <input type ="submit" value="Complete upload" />
+   </form>';
+                } else {
+                    $$upload_output .= 'No embedded items identified<br />';
+                }
+            }
+        }
+    }
+    return $phase_status;
+}
+
+sub process_secondary_uploads {
+    my ($upload_output,$coursedom,$coursenum,$formname,$num,$newidx) = @_;
+    my $folder=$env{'form.folder'};
+    my $destination = 'docs/';
+    if ($folder =~ /^supplemental/) {
+        $destination = 'supplemental/';
+    }
+    if (($folder eq 'default') || ($folder eq 'supplemental')) {
+        $destination .= 'default/';
+    } elsif ($folder =~ /^(default|supplemental)_(\d+)$/) {
+        $destination .=  $1.'/';
+    }
+    $destination .= $newidx;
+    my ($url,$filename);
+    $url=&Apache::lonnet::userfileupload($formname.$num,1,$destination);
+    ($filename) = ($url =~ m-^/uploaded/$coursedom/$coursenum/$destination/(.+)$-);
+    return $filename;
+}
+
 # --------------------------------------------------------------- An entry line
 
 sub entryline {
@@ -1285,7 +1453,24 @@ sub entryline {
                 'ct' => 'Cut',
 		'rn' => 'Rename',
 		'cp' => 'Copy');
+	my $nocopy=0;
+        if ($url=~/\.(page|sequence)$/) {
+	    foreach (&Apache::lonsequence::attemptread(&Apache::lonnet::filelocation('',$url))) {
+		my ($title,$url,$ext,$type)=split(/\:/,$_);
+		if (($url=~/\.(page|sequence)/) && ($type ne 'zombie')) {
+		    $nocopy=1;
+		    last;
+		}
+	    }
+	}
+        my $copylink='&nbsp;';
         if ($env{'form.pagepath'}) {
+           unless ($nocopy) {
+               $copylink=(<<ENDCOPY);
+<a href='javascript:markcopy("$pagepath","$index","$renametitle","page","$pagesymb");'>
+<font size="-2" color="#000099">$lt{'cp'}</font></a></td>
+ENDCOPY
+            }
             $line.=(<<END);
 <form name="entry_$index" action="/adm/coursedocs" method="post">
 <input type="hidden" name="pagepath" value="$env{'form.pagepath'}" />
@@ -1309,10 +1494,15 @@ sub entryline {
 <font size="-2" color="#550044">$lt{'ct'}</font></a>
 <a href='javascript:changename("$pagepath","$index","$renametitle","page","$pagesymb");'>
 <font size="-2" color="#009900">$lt{'rn'}</font></a>
-<a href='javascript:markcopy("$pagepath","$index","$renametitle","page","$pagesymb");'>
-<font size="-2" color="#000099">$lt{'cp'}</font></a></td>
+$copylink
 END
         } else {
+           unless ($nocopy) {
+               $copylink=(<<ENDCOPY);
+<a href='javascript:markcopy("$folderpath","$index","$renametitle","sequence");'>
+<font size="-2" color="#000099">$lt{'cp'}</font></a></td>
+ENDCOPY
+            }
             $line.=(<<END); 
 <form name="entry_$index" action="/adm/coursedocs" method="post">
 <input type="hidden" name="folderpath" value="$env{'form.folderpath'}" />
@@ -1335,8 +1525,7 @@ END
 <font size="-2" color="#550044">$lt{'ct'}</font></a>
 <a href='javascript:changename("$folderpath","$index","$renametitle","sequence");'>
 <font size="-2" color="#009900">$lt{'rn'}</font></a>
-<a href='javascript:markcopy("$folderpath","$index","$renametitle","sequence");'>
-<font size="-2" color="#000099">$lt{'cp'}</font></a></td>
+$copylink
 END
         }
     }
@@ -1366,7 +1555,7 @@ END
 	    &Apache::lonnet::allowuploaded('/adm/coursedoc',$url);
 	}
     }
-    $url=~s/^http\&colon\;\/\//\/adm\/wrapper\/ext\//;
+    $url=~s-^http(\&colon\;|:)//-/adm/wrapper/ext/-;
     if ((!$isfolder) && ($residx) && ($folder!~/supplemental/) && (!$ispage)) {
 	my $symb=&Apache::lonnet::symbclean(
           &Apache::lonnet::declutter('uploaded/'.
@@ -1433,7 +1622,7 @@ END
     }
     $line.='<td bgcolor="#FFFFBB"><a href="'.$url.'"><img src="'.$icon.
 	'" border="0"></a></td>'.
-        "<td bgcolor='#FFFFBB'><a href='$url'>$title</a></td>";
+        "<td bgcolor='#FFFFBB'><a href=\"$url\">$title</a></td>";
     if (($allowed) && ($folder!~/^supplemental/)) {
  	my %lt=&Apache::lonlocal::texthash(
  			      'hd' => 'Hidden',
@@ -1553,6 +1742,24 @@ sub checkonthis {
 
 
 #
+# ----------------------------------------------------------------- List Symbs
+# 
+sub list_symbs {
+   my $r=shift; 
+   my $html=&Apache::lonxml::xmlbegin();
+   $r->print($html.'<head><title>Symb List</title></head>'.
+              &Apache::loncommon::bodytag('Symb List'));
+   my $navmap = Apache::lonnavmaps::navmap->new();
+   $r->print("<pre>\n");
+   foreach my $res ($navmap->retrieveResources()) {
+       $r->print($res->compTitle()."\t".$res->symb()."\n");
+   }
+   $r->print("\n</pre>\n");
+   $r->print('<a href="/adm/coursedocs">'.&mt('Return to DOCS').'</a>');
+}
+
+
+#
 # -------------------------------------------------------------- Verify Content
 # 
 sub verifycontent {
@@ -1584,8 +1791,15 @@ sub verifycontent {
 	     &mt('Return to DOCS').'</a>');
 }
 
+
 # -------------------------------------------------------------- Check Versions
 
+sub devalidateversioncache {
+    my $src=shift;
+    &Apache::lonnet::devalidate_cache_new('courseresversion',$env{'request.course.id'}.'_'.
+					  &Apache::lonnet::clutter($src));
+}
+
 sub checkversions {
     my $r=shift;
     my $html=&Apache::lonxml::xmlbegin();
@@ -1612,6 +1826,7 @@ sub checkversions {
 	foreach (keys %hash) {
 	    if ($_=~/^ids\_(\/res\/.+)$/) {
 		$newsetversions{$1}='mostrecent';
+                &devalidateversioncache($1);
 	    }
 	}
     } elsif ($env{'form.setcurrent'}) {
@@ -1621,6 +1836,7 @@ sub checkversions {
 		my $getvers=&Apache::lonnet::getversion($1);
 		if ($getvers>0) {
 		    $newsetversions{$1}=$getvers;
+		    &devalidateversioncache($1);
 		}
 	    }
 	}
@@ -1631,6 +1847,7 @@ sub checkversions {
 		my $src=$1;
 		if (($env{$_}) && ($env{$_} ne $setversions{$src})) {
 		    $newsetversions{$src}=$env{$_};
+		    &devalidateversioncache($src);
 		}
 	    }
 	}
@@ -1860,22 +2077,22 @@ sub changewarning {
 	if (defined($env{'form.pagepath'})) {
 	    $pathvar='pagepath';
 	    $path=&Apache::lonnet::escape($env{'form.pagepath'});
-	    $path.='&amp;symb='.&Apache::lonnet::escape($env{'form.pagesymb'});
+	    $path.='&amp;pagesymb='.&Apache::lonnet::escape($env{'form.pagesymb'});
 	}
 	$url='/adm/coursedocs?'.$pathvar.'='.$path;
     }
     if (!defined($message)) {
 	$message='Changes will become active for your current session after [_1], or the next time you log in.';
     }
-    $r->print(
-'<script>function reinit(tf) { tf.submit();'.$postexec.' }</script>'. 
-'<form name="reinit" method="post" action="/adm/roles" target="loncapaclient">'.
+    $r->print("\n\n".
+'<script>function reinit(tf) { tf.submit();'.$postexec.' }</script>'."\n". 
+'<form name="reinitform" method="post" action="/adm/roles" target="loncapaclient">'.
 '<input type="hidden" name="orgurl" value="'.$url.
 '" /><input type="hidden" name="selectrole" value="1" /><h3><font color="red">'.
 &mt($message,' <input type="hidden" name="'.
     $env{'request.role'}.'" value="1" /><input type="button" value="'.
     &mt('re-initializing course').'" onClick="reinit(this.form)" />').
-$help{'Caching'}.'</font></h3></form>');
+$help{'Caching'}.'</font></h3></form>'."\n\n");
 }
 
 # ================================================================ Main Handler
@@ -1886,14 +2103,14 @@ sub handler {
     return OK if $r->header_only;
 
 # --------------------------------------------- Initialize help topics for this
-  foreach ('Adding_Course_Doc','Main_Course_Documents',
-           'Adding_External_Resource','Navigate_Content',
-           'Adding_Folders','Docs_Overview', 'Load_Map',
-           'Supplemental','Score_Upload_Form','Adding_Pages',
-           'Importing_LON-CAPA_Resource','Uploading_From_Harddrive',
-	   'Check_Resource_Versions','Verify_Content') {
-      $help{$_}=&Apache::loncommon::help_open_topic('Docs_'.$_);
-  }
+    foreach ('Adding_Course_Doc','Main_Course_Documents',
+	     'Adding_External_Resource','Navigate_Content',
+	     'Adding_Folders','Docs_Overview', 'Load_Map',
+	     'Supplemental','Score_Upload_Form','Adding_Pages',
+	     'Importing_LON-CAPA_Resource','Uploading_From_Harddrive',
+	     'Check_Resource_Versions','Verify_Content') {
+	$help{$_}=&Apache::loncommon::help_open_topic('Docs_'.$_);
+    }
     # Composite help files
     $help{'Syllabus'} = &Apache::loncommon::help_open_topic(
 		    'Docs_About_Syllabus,Docs_Editing_Templated_Pages');
@@ -1907,13 +2124,18 @@ sub handler {
 		  'Docs_About_My_Personal_Info,Docs_Editing_Templated_Pages');
     $help{'Caching'} = &Apache::loncommon::help_open_topic('Caching');
 
-  if ($env{'form.verify'}) {
+# does this user have privileges to modify docs
+    my $allowed=&Apache::lonnet::allowed('mdc',$env{'request.course.id'});
+
+  if ($allowed && $env{'form.verify'}) {
       &verifycontent($r);
-  } elsif ($env{'form.versions'}) {
+  } elsif ($allowed && $env{'form.listsymbs'}) {
+      &list_symbs($r);
+  } elsif ($allowed && $env{'form.versions'}) {
       &checkversions($r);
-  } elsif ($env{'form.dumpcourse'}) {
+  } elsif ($allowed && $env{'form.dumpcourse'}) {
       &dumpcourse($r);
-  } elsif ($env{'form.exportcourse'}) {
+  } elsif ($allowed && $env{'form.exportcourse'}) {
       &exportcourse($r);
   } else {
 # is this a standard course?
@@ -1922,7 +2144,6 @@ sub handler {
     my $forcestandard = 0;
     my $forcesupplement;
     my $script='';
-    my $allowed;
     my $events='';
     my $showdoc=0;
     my $containertag;
@@ -1948,13 +2169,11 @@ sub handler {
     }
     unless ($showdoc) { # got called from remote
        if (($env{'form.folder'}=~/^default_/) || 
-          ($env{'form.folder'} =~ m#^\d+/(pages|sequences)/#)) {
+          ($env{'form.folder'} =~ m:^\d+/(pages|sequences)/:)) {
            $forcestandard = 1;
        } 
        $forcesupplement=($env{'form.folder'}=~/^supplemental_/);
 
-# does this user have privileges to post, etc?
-       $allowed=&Apache::lonnet::allowed('mdc',$env{'request.course.id'});
        if ($allowed) { 
          &Apache::loncommon::get_unprocessed_cgi($ENV{'QUERY_STRING'},['cmd']);
          $script=&Apache::lonratedt::editscript('simple'); 
@@ -2120,7 +2339,7 @@ function removeres(folderpath,index,oldt
 }
 
 function cutres(folderpath,index,oldtitle,container,pagesymb) {
-    if (confirm('WARNING: Cutting a resource makes associated grades and scores inaccessible,\\neven if it is pasted in again elsewhere!\\nCut "'+oldtitle+'"?')) {
+    if (confirm('WARNING: Cutting a resource makes associated grades and scores inaccessible!\\nGrades remain inaccessible if resource is pasted into another folder.\\nCut "'+oldtitle+'"?')) {
 	this.document.forms.renameform.cmd.value='cut_'+index;
 	this.document.forms.renameform.markcopy.value=index;
         if (container == 'sequence') {
@@ -2155,7 +2374,89 @@ ENDNEWSCRIPT
             &Apache::loncommon::bodytag('Course Documents','',$events,
 					'','',$showdoc).
 	    &Apache::loncommon::help_open_menu('','','','',273,'RAT'));
-  unless ($showdoc) {
+  my %allfiles = ();
+  my %codebase = ();
+  my ($upload_result,$upload_output);
+  if ($allowed) {
+      if (($env{'form.uploaddoc.filename'}) &&                                               ($env{'form.cmd'}=~/^upload_(\w+)/)) {
+# Process file upload - phase one - upload and parse primary file.  
+          $upload_result = &process_file_upload(\$upload_output,$coursenum,
+						$coursedom,\%allfiles,
+						\%codebase,$1);
+          if ($upload_result eq 'phasetwo') {
+              $r->print($upload_output);
+          }
+      } elsif ($env{'form.phasetwo'}) {
+          my %newname = ();
+          my %origname = ();
+          my %attribs = ();
+          my $updateflag = 0;
+          my $residx = $env{'form.newidx'};
+          my $primary_url = &Apache::lonnet::unescape($env{'form.primaryurl'});
+# Process file upload - phase two - gather secondary files.
+          for (my $i=0; $i<$env{'form.phasetwo'}; $i++) {
+              if ($env{'form.embedded_item_'.$i.'.filename'}) {
+                  my $javacodebase;
+                  $newname{$i} = &process_secondary_uploads(\$upload_output,$coursedom,$coursenum,'embedded_item_',$i,$residx);
+                  $origname{$i} = &Apache::lonnet::unescape($env{'form.embedded_orig_'.$i});
+                  if (exists($env{'form.embedded_codebase_'.$i})) {
+                      $javacodebase =  &Apache::lonnet::unescape($env{'form.embedded_codebase_'.$i});  
+                      $origname{$i} =~ s#^\Q$javacodebase\E/##; 
+                  }
+                  my @attributes = ();
+                  if ($env{'form.embedded_attrib_'.$i} =~ /:/) {
+                      @attributes = split/:/,$env{'form.embedded_attrib_'.$i};
+                  } else {
+                      @attributes = ($env{'form.embedded_attrib_'.$i});
+                  }
+                  foreach (@attributes) {
+                      push(@{$attribs{$i}},&Apache::lonnet::unescape($_));
+                  }
+                  if ($javacodebase) {
+                      $codebase{$i} = $javacodebase;
+                      $codebase{$i} =~ s#/$##;
+                      $updateflag = 1;
+                  }
+              }
+              unless ($newname{$i} eq $origname{$i}) {
+                  $updateflag = 1;
+              }
+          }
+# Process file upload - phase three - modify primary file
+          if ($updateflag) {
+              my ($content,$rtncode);
+              my $updateflag = 0;
+              my $getstatus = &Apache::lonnet::getuploaded('GET',$primary_url,$coursedom,$coursenum,\$content,\$rtncode);
+              if ($getstatus eq 'ok') {
+                  foreach my $item (keys %newname) {
+                      if ($newname{$item} ne $origname{$item}) {
+                          my $attrib_regexp = '';
+                          if (@{$attribs{$item}} > 1) {
+                              $attrib_regexp = join('|',@{$attribs{$item}});
+                          } else {
+                              $attrib_regexp = $attribs{$item}[0];
+                          }
+                          if ($content =~ m#($attrib_regexp\s*=\s*['"]?)\Q$origname{$item}\E(['"]?)#) {
+                          } 
+                          $content =~ s#($attrib_regexp\s*=\s*['"]?)\Q$origname{$item}\E(['"]?)#$1$newname{$item}$2#gi; 
+                      }
+                      if (exists($codebase{$item})) {
+                          $content =~ s/(codebase\s*=\s*["']?)\Q$codebase{$item}\E(["']?)/$1.$2/i;
+                      }
+                  }
+# Save edited file.
+                  my $saveresult;
+                  my $docuname=$env{'course.'.$env{'request.course.id'}.'.num'};
+                  my $docudom=$env{'course.'.$env{'request.course.id'}.'.domain'};
+                  my $url = &Apache::lonnet::store_edited_file($primary_url,$content,$docudom,$docuname,\$saveresult);
+              } else {
+                  &Apache::lonnet::logthis('retrieval of uploaded file - '.$primary_url.' - for editing, failed: '.$getstatus); 
+              }
+          }
+      }
+  }
+
+  unless ($showdoc ||  $upload_result eq 'phasetwo') {
 # -----------------------------------------------------------------------------
        my %lt=&Apache::lonlocal::texthash(
                 'uplm' => 'Upload a new main course document',
@@ -2169,6 +2470,7 @@ ENDNEWSCRIPT
                 'impo' => 'Import',
                 'selm' => 'Select Map',
                 'load' => 'Load Map',
+                'reco' => 'Recover Deleted Resources',
                 'newf' => 'New Folder',
                 'newp' => 'New Composite Page',
                 'extr' => 'External Resource',
@@ -2183,7 +2485,8 @@ ENDNEWSCRIPT
                 'imsf' => 'Import IMS package',
                 'file' =>  'File',
                 'title' => 'Title',
-                'comment' => 'Comment' 
+                'comment' => 'Comment',
+                'parse' => 'If HTML file, upload embedded images/multimedia files'
 					  );
 # -----------------------------------------------------------------------------
     if ($allowed) {
@@ -2192,6 +2495,7 @@ ENDNEWSCRIPT
        my %lt=&Apache::lonlocal::texthash(
 					 'vc' => 'Verify Content',
 					 'cv' => 'Check/Set Resource Versions',
+					 'ls' => 'List Symbs',
 					  );
 
        my $folderpath=$env{'form.folderpath'};
@@ -2226,7 +2530,9 @@ $uploadtag
     <input type="submit" name="versions" value="$lt{'cv'}" />$help{'Check_Resource_Versions'}
 $dumpbut
 $exportbut
-</td></tr></table>
+</td><!-- <td bgcolor="#DDDDCC">
+    <input type="submit" name="listsymbs" value="$lt{'ls'}" />
+</td>--></tr></table>
 </form>
 ENDCOURSEVERIFY
        $r->print(&Apache::loncommon::help_open_topic('Docs_Adding_Course_Doc',
@@ -2250,7 +2556,7 @@ ENDCOURSEVERIFY
            #$postexec='self.close();';
        }
        $hadchanges=0;
-       &editor($r,$coursenum,$coursedom,$folder,$allowed);
+       &editor($r,$coursenum,$coursedom,$folder,$allowed,$upload_output);
        if ($hadchanges) {
 	   &mark_hash_old()
        }
@@ -2259,7 +2565,11 @@ ENDCOURSEVERIFY
                      '.sequence';
        my $pageseq = '/uploaded/'.$coursedom.'/'.$coursenum.'/default_'.time.
                      '.page';
-
+	my $container='sequence';
+	if ($env{'form.pagepath'}) {
+	    $container='page';
+	}
+	my $readfile='/uploaded/'.$coursedom.'/'.$coursenum.'/'.$folder.'.'.$container;
        $r->print(<<ENDFORM);
 <table cellspacing=4 cellpadding=4><tr>
 <th bgcolor="#DDDDDD">$lt{'uplm'}</th>
@@ -2275,6 +2585,14 @@ $lt{'title'}:<br />
 <input type="text" size="50" name="comment">
 $uploadtag
 <input type="hidden" name="cmd" value="upload_default">
+<br />
+<nobr>
+<label>$lt{'parse'}?
+<input type="checkbox" name="parserflag" />
+</label>
+</nobr>
+<br />
+<br />
 <nobr>
 <input type="submit" value="$lt{'upld'}">
  $help{'Uploading_From_Harddrive'}
@@ -2300,6 +2618,10 @@ value="$lt{'selm'}"> <input type="submit
 $help{'Load_Map'}</nobr>
 </p>
 </form>
+<hr />
+<form action="/adm/groupsort" method="post" name="recover">
+<input type="button" name="recovermap" onClick="javascript:groupopen('$readfile',1)" value="$lt{'reco'}" />
+</form>
 ENDFORM
        unless ($env{'form.pagepath'}) {
 	   $r->print(<<ENDFORM);
@@ -2312,7 +2634,7 @@ $uploadtag
 value="$lt{'extr'}" /> $help{'Adding_External_Resource'}
 </nobr>
 </form>
-<form action="/adm/imsimportdocs" method="post" name="ims">
+<br /><form action="/adm/imsimportdocs" method="post" name="ims">
 <input type="hidden" name="folder" value="$folder" />
 <input name="imsimport" type="button" value="$lt{'imsf'}" onClick="javascript:makeims();" />
 </nobr>
@@ -2322,7 +2644,7 @@ ENDFORM
        $r->print('</td><td bgcolor="#DDDDDD">');
        unless ($env{'form.pagepath'}) {
            $r->print(<<ENDFORM);
-<form action="/adm/coursedocs" method="post" name="newfolder">
+<br /><form action="/adm/coursedocs" method="post" name="newfolder">
 <input type="hidden" name="folderpath" value="$env{'form.folderpath'}" />
 <input type=hidden name="importdetail" value="">
 <nobr>
@@ -2331,7 +2653,7 @@ onClick="javascript:makenewfolder(this.f
 value="$lt{'newf'}" />$help{'Adding_Folders'}
 </nobr>
 </form>
-<form action="/adm/coursedocs" method="post" name="newpage">
+<br /><form action="/adm/coursedocs" method="post" name="newpage">
 <input type="hidden" name="folderpath" value="$env{'form.folderpath'}" />
 <input type=hidden name="importdetail" value="">
 <nobr>
@@ -2340,7 +2662,7 @@ onClick="javascript:makenewpage(this.for
 value="$lt{'newp'}" />$help{'Adding_Pages'}
 </nobr>
 </form>
-<form action="/adm/coursedocs" method="post" name="newsyl">
+<br /><form action="/adm/coursedocs" method="post" name="newsyl">
 $uploadtag
 <input type=hidden name="importdetail" 
 value="Syllabus=/public/$coursedom/$coursenum/syllabus">
@@ -2349,7 +2671,7 @@ value="Syllabus=/public/$coursedom/$cour
  $help{'Syllabus'}
 </nobr>
 </form>
-<form action="/adm/coursedocs" method="post" name="newnav">
+<br /><form action="/adm/coursedocs" method="post" name="newnav">
 $uploadtag
 <input type=hidden name="importdetail" 
 value="Navigate Content=/adm/navmaps">
@@ -2358,7 +2680,7 @@ value="Navigate Content=/adm/navmaps">
 $help{'Navigate_Content'}
 </nobr>
 </form>
-<form action="/adm/coursedocs" method="post" name="newsmppg">
+<br /><form action="/adm/coursedocs" method="post" name="newsmppg">
 $uploadtag
 <input type=hidden name="importdetail" value="">
 <nobr>
@@ -2366,7 +2688,7 @@ $uploadtag
 onClick="javascript:makesmppage();" /> $help{'Simple Page'}
 </nobr>
 </form>
-<form action="/adm/coursedocs" method="post" name="newsmpproblem">
+<br /><form action="/adm/coursedocs" method="post" name="newsmpproblem">
 $uploadtag
 <input type=hidden name="importdetail" value="">
 <nobr>
@@ -2374,7 +2696,7 @@ $uploadtag
 onClick="javascript:makesmpproblem();" />$help{'Simple Problem'}
 </nobr>
 </form>
-<form action="/adm/coursedocs" method="post" name="newexamupload">
+<br /><form action="/adm/coursedocs" method="post" name="newexamupload">
 $uploadtag
 <input type=hidden name="importdetail" value="">
 <nobr>
@@ -2383,7 +2705,7 @@ onClick="javascript:makeexamupload();" /
 $help{'Score_Upload_Form'}
 </nobr>
 </form>
-<form action="/adm/coursedocs" method="post" name="newbul">
+<br /><form action="/adm/coursedocs" method="post" name="newbul">
 $uploadtag
 <input type=hidden name="importdetail" value="">
 <nobr>
@@ -2392,7 +2714,7 @@ onClick="javascript:makebulboard();" />
 $help{'Bulletin Board'}
 </nobr>
 </form>
-<form action="/adm/coursedocs" method="post" name="newaboutme">
+<br /><form action="/adm/coursedocs" method="post" name="newaboutme">
 $uploadtag
 <input type=hidden name="importdetail" 
 value="$plainname=/adm/$udom/$uname/aboutme">
@@ -2401,7 +2723,7 @@ value="$plainname=/adm/$udom/$uname/abou
 $help{'My Personal Info'}
 </nobr>
 </form>
-<form action="/adm/coursedocs" method="post" name="newaboutsomeone">
+<br /><form action="/adm/coursedocs" method="post" name="newaboutsomeone">
 $uploadtag
 <input type=hidden name="importdetail" value="">
 <nobr>
@@ -2421,7 +2743,7 @@ $uploadtag
 onClick="javascript:makesmpproblem();" />$help{'Simple Problem'}
 </nobr>
 </form>
-<form action="/adm/coursedocs" method="post" name="newexamupload">
+<br /><form action="/adm/coursedocs" method="post" name="newexamupload">
 $uploadtag
 <input type=hidden name="importdetail" value="">
 <nobr>
@@ -2464,7 +2786,15 @@ ENDBLOCK
 <tr><td bgcolor="#DDDDDD">
 <form action="/adm/coursedocs" method="post" enctype="multipart/form-data">
 <input type="file" name="uploaddoc" size="40">
-<br />$lt{'comment'}:<br />
+<br />
+<br />
+<nobr>
+<label>$lt{'parse'}?
+<input type="checkbox" name="parserflag" />
+</label>
+</nobr>
+<br /><br />
+$lt{'comment'}:<br />
 <textarea cols=50 rows=4 name='comment'>
 </textarea>
 <br />
@@ -2486,7 +2816,7 @@ onClick="javascript:makenewfolder(this.f
 value="$lt{'newf'}" /> $help{'Adding_Folders'}
 </nobr>
 </form>
-<form action="/adm/coursedocs" method="post" name="supnewext">
+<br /><form action="/adm/coursedocs" method="post" name="supnewext">
 <input type="hidden" name="folderpath" value="$env{'form.folderpath'}" />
 <input type=hidden name="importdetail" value="">
 <nobr>
@@ -2495,7 +2825,7 @@ onClick="javascript:makenewext('supnewex
 value="$lt{'extr'}" /> $help{'Adding_External_Resource'}
 </nobr>
 </form>
-<form action="/adm/coursedocs" method="post" name="supnewsyl">
+<br /><form action="/adm/coursedocs" method="post" name="supnewsyl">
 <input type="hidden" name="folderpath" value="$env{'form.folderpath'}" />
 <input type=hidden name="importdetail" 
 value="Syllabus=/public/$coursedom/$coursenum/syllabus">
@@ -2504,7 +2834,7 @@ value="Syllabus=/public/$coursedom/$cour
 $help{'Syllabus'}
 </nobr>
 </form>
-<form action="/adm/coursedocs" method="post" name="subnewaboutme">
+<br /><form action="/adm/coursedocs" method="post" name="subnewaboutme">
 <input type="hidden" name="folderpath" value="$env{'form.folderpath'}" />
 <input type=hidden name="importdetail" 
 value="$plainname=/adm/$udom/$uname/aboutme">
@@ -2523,11 +2853,13 @@ ENDSUPFORM
     }
     $r->print('</table>');
   } else {
+      unless ($upload_result eq 'phasetwo') {
 # -------------------------------------------------------- This is showdoc mode
-      $r->print("<h1>".&mt('Uploaded Document').' - '.
+          $r->print("<h1>".&mt('Uploaded Document').' - '.
 		&Apache::lonnet::gettitle($r->uri).'</h1><p>'.
 &mt('It is recommended that you use an up-to-date virus scanner before handling this file.')."</p><p><table>".
-         &entryline(0,&mt("Click to download or use your browser's Save Link function"),$showdoc).'</table></p>');
+          &entryline(0,&mt("Click to download or use your browser's Save Link function"),$showdoc).'</table></p>');
+      }
   }
  }
  $r->print('</body></html>');