--- loncom/interface/loncommon.pm	2017/07/10 12:48:41	1.1284
+++ loncom/interface/loncommon.pm	2017/09/28 19:04:37	1.1295
@@ -1,7 +1,7 @@
 # The LearningOnline Network with CAPA
 # a pile of common routines
 #
-# $Id: loncommon.pm,v 1.1284 2017/07/10 12:48:41 raeburn Exp $
+# $Id: loncommon.pm,v 1.1295 2017/09/28 19:04:37 raeburn Exp $
 #
 # Copyright Michigan State University Board of Trustees
 #
@@ -84,6 +84,8 @@ use Crypt::DES;
 use DynaLoader; # for Crypt::DES version
 use MIME::Lite;
 use MIME::Types;
+use File::Copy();
+use File::Path::Tiny();
 
 # ---------------------------------------------- Designs
 use vars qw(%defaultdesign);
@@ -2477,10 +2479,24 @@ sub create_text_file {
 # ------------------------------------------
 
 sub domain_select {
-    my ($name,$value,$multiple)=@_;
+    my ($name,$value,$multiple,$incdoms,$excdoms)=@_;
+    my @possdoms;
+    if (ref($incdoms) eq 'ARRAY') {
+        @possdoms = @{$incdoms};
+    } else {
+        @possdoms = &Apache::lonnet::all_domains();
+    }
+
     my %domains=map { 
 	$_ => $_.' '. &Apache::lonnet::domain($_,'description') 
-    } &Apache::lonnet::all_domains();
+    } @possdoms;
+
+    if ((ref($excdoms) eq 'ARRAY') && (@{$excdoms} > 0)) {
+        foreach my $dom (@{$excdoms}) {
+            delete($domains{$dom});
+        }
+    }
+
     if ($multiple) {
 	$domains{''}=&mt('Any domain');
 	$domains{'select_form_order'} = [sort {lc($a) cmp lc($b) } (keys(%domains))];
@@ -6452,6 +6468,11 @@ td.LC_menubuttons_text {
   background: $tabbg;
 }
 
+td.LC_zero_height {
+  line-height: 0; 
+  cellpadding: 0;
+}
+
 table.LC_data_table {
   border: 1px solid #000000;
   border-collapse: separate;
@@ -6773,6 +6794,12 @@ td.LC_parm_overview_restrictions  {
   border-collapse: collapse;
 }
 
+span.LC_parm_recursive,
+td.LC_parm_recursive {
+  font-weight: bold;
+  font-size: smaller;
+}
+
 table.LC_parm_overview_restrictions td {
   border-width: 1px 4px 1px 4px;
   border-style: solid;
@@ -7128,6 +7155,7 @@ table.LC_data_table tr > td.LC_docs_entr
   color: #440055;  
 }
 
+.LC_domprefs_email,
 .LC_docs_alias_name,
 .LC_docs_reinit_warn,
 .LC_docs_ext_edit {
@@ -10125,7 +10153,16 @@ sub user_picker {
         $allow_blank = 0;
         $domform = &select_dom_form($currdom,'srchdomain',$allow_blank,1,undef,[$currdom]);
     } else {
-        $domform = &select_dom_form($currdom,'srchdomain',$allow_blank,1);
+        my $defdom = $env{'request.role.domain'};
+        my ($trusted,$untrusted);
+        if (($context eq 'requestcrs') || ($context eq 'course')) {
+            ($trusted,$untrusted) = &Apache::lonnet::trusted_domains('enroll',$defdom);
+        } elsif ($context eq 'author') {
+            ($trusted,$untrusted) = &Apache::lonnet::trusted_domains('othcoau',$defdom);
+        } elsif ($context eq 'domain') {
+            ($trusted,$untrusted) = &Apache::lonnet::trusted_domains('domroles',$defdom);
+        }
+        $domform = &select_dom_form($currdom,'srchdomain',$allow_blank,1,undef,$trusted,$untrusted);
     }
     my $srchinsel = ' <select name="srchin">';
 
@@ -12559,6 +12596,18 @@ sub decompress_uploaded_file {
 
 sub process_decompression {
     my ($docudom,$docuname,$file,$destination,$dir_root,$hiddenelem) = @_;
+    unless (($dir_root eq '/userfiles') && ($destination =~ m{^(docs|supplemental)/(default|\d+)/\d+$})) {
+        return '<p class="LC_error">'.&mt('Not extracted.').'<br />'.
+               &mt('Unexpected file path.').'</p>'."\n";
+    }
+    unless (($docudom =~ /^$match_domain$/) && ($docuname =~ /^$match_courseid$/)) {
+        return '<p class="LC_error">'.&mt('Not extracted.').'<br />'.
+               &mt('Unexpected course context.').'</p>'."\n";
+    }
+    unless ($file eq &Apache::lonnet::clean_filename($file)) {
+        return '<p class="LC_error">'.&mt('Not extracted.').'<br />'.
+               &mt('Filename contained unexpected characters.').'</p>'."\n";
+    }
     my ($dir,$error,$warning,$output);
     if ($file !~ /\.(zip|tar|bz2|gz|tar.gz|tar.bz2|tgz)$/i) {
         $error = &mt('Filename not a supported archive file type.').
@@ -12593,30 +12642,44 @@ sub process_decompression {
                 }
             }
             my $numskip = scalar(@to_skip);
-            if (($numskip > 0) && 
-                ($numskip == $env{'form.archive_itemcount'})) {
+            my $numoverwrite = scalar(@to_overwrite);
+            if (($numskip) && (!$numoverwrite)) { 
                 $warning = &mt('All items in the archive file already exist, and no overwriting of existing files has been requested.');         
             } elsif ($dir eq '') {
                 $error = &mt('Directory containing archive file unavailable.');
             } elsif (!$error) {
                 my ($decompressed,$display);
-                if ($numskip > 0) {
+                if (($numskip) || ($numoverwrite)) {
                     my $tempdir = time.'_'.$$.int(rand(10000));
                     mkdir("$dir/$tempdir",0755);
-                    system("mv $dir/$file $dir/$tempdir/$file");
-                    ($decompressed,$display) = 
-                        &decompress_uploaded_file($file,"$dir/$tempdir");
-                    foreach my $item (@to_skip) {
-                        if (($item ne '') && ($item !~ /\.\./)) {
-                            if (-f "$dir/$tempdir/$item") { 
-                                unlink("$dir/$tempdir/$item");
-                            } elsif (-d "$dir/$tempdir/$item") {
-                                system("rm -rf $dir/$tempdir/$item");
+                    if (&File::Copy::move("$dir/$file","$dir/$tempdir/$file")) {
+                        ($decompressed,$display) = 
+                            &decompress_uploaded_file($file,"$dir/$tempdir");
+                        foreach my $item (@to_skip) {
+                            if (($item ne '') && ($item !~ /\.\./)) {
+                                if (-f "$dir/$tempdir/$item") { 
+                                    unlink("$dir/$tempdir/$item");
+                                } elsif (-d "$dir/$tempdir/$item") {
+                                    &File::Path::Tiny::rm("$dir/$tempdir/$item");
+                                }
+                            }
+                        }
+                        foreach my $item (@to_overwrite) {
+                            if ((-e "$dir/$tempdir/$item") && (-e "$dir/$item")) {
+                                if (($item ne '') && ($item !~ /\.\./)) {
+                                    if (-f "$dir/$item") {
+                                        unlink("$dir/$item");
+                                    } elsif (-d "$dir/$item") {
+                                        &File::Path::Tiny::rm("$dir/$item");
+                                    }
+                                    &File::Copy::move("$dir/$tempdir/$item","$dir/$item");
+                                }
                             }
                         }
+                        if (&File::Copy::move("$dir/$tempdir/$file","$dir/$file")) {
+                            &File::Path::Tiny::rm("$dir/$tempdir");
+                        }
                     }
-                    system("mv $dir/$tempdir/* $dir");
-                    rmdir("$dir/$tempdir");   
                 } else {
                     ($decompressed,$display) = 
                         &decompress_uploaded_file($file,$dir);
@@ -12634,8 +12697,7 @@ sub process_decompression {
                     if (ref($newdirlistref) eq 'ARRAY') {
                         foreach my $dir_line (@{$newdirlistref}) {
                             my ($item,undef,undef,$testdir)=split(/\&/,$dir_line,5);
-                            unless (($item =~ /^\.+$/) || ($item eq $file) || 
-                                    ((@to_skip > 0) && (grep(/^\Q$item\E$/,@to_skip)))) {
+                            unless (($item =~ /^\.+$/) || ($item eq $file)) {
                                 push(@newitems,$item);
                                 if ($dirptr&$testdir) {
                                     $is_dir{$item} = 1;
@@ -13120,7 +13182,7 @@ END
 sub process_extracted_files {
     my ($context,$docudom,$docuname,$destination,$dir_root,$hiddenelem) = @_;
     my $numitems = $env{'form.archive_count'};
-    return unless ($numitems);
+    return if ((!$numitems) || ($numitems =~ /\D/));
     my @ids=&Apache::lonnet::current_machine_ids();
     my ($prefix,$pathtocheck,$dir,$ishome,$error,$warning,%toplevelitems,%is_dir,
         %folders,%containers,%mapinner,%prompttofetch);
@@ -13133,7 +13195,7 @@ sub process_extracted_files {
     } else {
         $prefix = $Apache::lonnet::perlvar{'lonDocRoot'};
         $pathtocheck = "$dir_root/$docudom/$docuname/$destination";
-        $dir = "$dir_root/$docudom/$docuname";    
+        $dir = "$dir_root/$docudom/$docuname";
     }
     my $currdir = "$dir_root/$destination";
     (my $docstype,$mapinner{'0'}) = ($destination =~ m{^(docs|supplemental)/(\w+)/});
@@ -13222,7 +13284,9 @@ sub process_extracted_files {
                                                         '.'.$containers{$outer},1,1);
                             $newseqid{$i} = $newidx;
                             unless ($errtext) {
-                                $result .=  '<li>'.&mt('Folder: [_1] added to course',$docstitle).'</li>'."\n";
+                                $result .=  '<li>'.&mt('Folder: [_1] added to course',
+                                                       &HTML::Entities::encode($docstitle,'<>&"')).
+                                            '</li>'."\n";
                             }
                         }
                     } else {
@@ -13231,38 +13295,47 @@ sub process_extracted_files {
                             my $url = '/uploaded/'.$docudom.'/'.$docuname.'/'.
                                       $docstype.'/'.$mapinner{$outer}.'/'.$newidx.'/'.
                                       $title;
-                            if (!-e "$prefix$dir/$docstype/$mapinner{$outer}") {
-                                mkdir("$prefix$dir/$docstype/$mapinner{$outer}",0755);
-                            }
-                            if (!-e "$prefix$dir/$docstype/$mapinner{$outer}/$newidx") {
-                                mkdir("$prefix$dir/$docstype/$mapinner{$outer}/$newidx");
-                            }
-                            if (-e "$prefix$dir/$docstype/$mapinner{$outer}/$newidx") {
-                                system("mv $prefix$path $prefix$dir/$docstype/$mapinner{$outer}/$newidx/$title");
-                                $newdest{$i} = "$prefix$dir/$docstype/$mapinner{$outer}/$newidx";
-                                unless ($ishome) {
-                                    my $fetch = "$newdest{$i}/$title";
-                                    $fetch =~ s/^\Q$prefix$dir\E//;
-                                    $prompttofetch{$fetch} = 1;
+                            if (($outer !~ /\D/) && ($mapinner{$outer} !~ /\D/) && ($newidx !~ /\D/)) {
+                                if (!-e "$prefix$dir/$docstype/$mapinner{$outer}") {
+                                    mkdir("$prefix$dir/$docstype/$mapinner{$outer}",0755);
                                 }
-                            }
-                            $LONCAPA::map::resources[$newidx]=
-                                $docstitle.':'.$url.':false:normal:res';
-                            push(@LONCAPA::map::order, $newidx);
-                            my ($outtext,$errtext)=
-                                &LONCAPA::map::storemap('/uploaded/'.$docudom.'/'.
-                                                        $docuname.'/'.$folders{$outer}.
-                                                        '.'.$containers{$outer},1,1);
-                            unless ($errtext) {
-                                if (-e "$prefix$dir/$docstype/$mapinner{$outer}/$newidx/$title") {
-                                    $result .= '<li>'.&mt('File: [_1] added to course',$docstitle).'</li>'."\n";
+                                if (!-e "$prefix$dir/$docstype/$mapinner{$outer}/$newidx") {
+                                    mkdir("$prefix$dir/$docstype/$mapinner{$outer}/$newidx");
                                 }
-                            }
+                                if (-e "$prefix$dir/$docstype/$mapinner{$outer}/$newidx") {
+                                    if (rename("$prefix$path","$prefix$dir/$docstype/$mapinner{$outer}/$newidx/$title")) {
+                                        $newdest{$i} = "$prefix$dir/$docstype/$mapinner{$outer}/$newidx";
+                                        unless ($ishome) {
+                                            my $fetch = "$newdest{$i}/$title";
+                                            $fetch =~ s/^\Q$prefix$dir\E//;
+                                            $prompttofetch{$fetch} = 1;
+                                        }
+                                    }
+                                }
+                                $LONCAPA::map::resources[$newidx]=
+                                    $docstitle.':'.$url.':false:normal:res';
+                                push(@LONCAPA::map::order, $newidx);
+                                my ($outtext,$errtext)=
+                                    &LONCAPA::map::storemap('/uploaded/'.$docudom.'/'.
+                                                            $docuname.'/'.$folders{$outer}.
+                                                            '.'.$containers{$outer},1,1);
+                                unless ($errtext) {
+                                    if (-e "$prefix$dir/$docstype/$mapinner{$outer}/$newidx/$title") {
+                                        $result .= '<li>'.&mt('File: [_1] added to course',
+                                                              &HTML::Entities::encode($docstitle,'<>&"')).
+                                                   '</li>'."\n";
+                                    }
+                                }
+                            } else {
+                                $warning .= &mt('Item extracted from archive: [_1] has unexpected path.',
+                                                &HTML::Entities::encode($path,'<>&"')).'<br />';
+                            } 
                         }
                     }
                 }
             } else {
-                $warning .= &mt('Item extracted from archive: [_1] has unexpected path.',$path).'<br />'; 
+                $warning .= &mt('Item extracted from archive: [_1] has unexpected path.',
+                                &HTML::Entities::encode($path,'<>&"')).'<br />'; 
             }
         }
         for (my $i=1; $i<=$numitems; $i++) {
@@ -13323,7 +13396,9 @@ sub process_extracted_files {
                         }
                         if ($fullpath ne '') {
                             if (-e "$prefix$path") {
-                                system("mv $prefix$path $fullpath/$title");
+                                unless (rename("$prefix$path","$fullpath/$title")) {
+                                     $warning .= &mt('Failed to rename dependency').'<br />';
+                                }
                             }
                             if (-e "$fullpath/$title") {
                                 my $showpath;
@@ -13332,21 +13407,26 @@ sub process_extracted_files {
                                 } else {
                                     $showpath = "/$title";
                                 } 
-                                $result .= '<li>'.&mt('[_1] included as a dependency',$showpath).'</li>'."\n";
-                            } 
-                            unless ($ishome) {
-                                my $fetch = "$fullpath/$title";
-                                $fetch =~ s/^\Q$prefix$dir\E//; 
-                                $prompttofetch{$fetch} = 1;
+                                $result .= '<li>'.&mt('[_1] included as a dependency',
+                                                      &HTML::Entities::encode($showpath,'<>&"')).
+                                           '</li>'."\n";
+                                unless ($ishome) {
+                                    my $fetch = "$fullpath/$title";
+                                    $fetch =~ s/^\Q$prefix$dir\E//; 
+                                    $prompttofetch{$fetch} = 1;
+                                }
                             }
                         }
                     }
                 } elsif ($env{'form.archive_'.$referrer{$i}} eq 'discard') {
                     $warning .= &mt('[_1] is a dependency of [_2], which was discarded.',
-                                    $path,$env{'form.archive_content_'.$referrer{$i}}).'<br />';
+                                    &HTML::Entities::encode($path,'<>&"'),
+                                    &HTML::Entities::encode($env{'form.archive_content_'.$referrer{$i}},'<>&"')).
+                                '<br />';
                 }
             } else {
-                $warning .= &mt('Item extracted from archive: [_1] has unexpected path.',$path).'<br />'; 
+                $warning .= &mt('Item extracted from archive: [_1] has unexpected path.',
+                                &HTML::Entities::encode($path)).'<br />'; 
             }
         }
         if (keys(%todelete)) {
@@ -13635,20 +13715,21 @@ sub upfile_store {
 
 =pod
 
-=item * &load_tmp_file($r)
+=item * &load_tmp_file($r,$datatoken)
 
 Load uploaded file from tmp, $r should be the HTTP Request object,
-needs $env{'form.datatoken'},
+$datatoken is the name to assign to the temporary file.
 sets $env{'form.upfile'} to the contents of the file
 
 =cut
 
 sub load_tmp_file {
-    my $r=shift;
+    my ($r,$datatoken) = @_;
+    return if ($datatoken eq '');
     my @studentdata=();
     {
         my $studentfile = $r->dir_config('lonDaemons').
-                              '/tmp/'.$env{'form.datatoken'}.'.tmp';
+                              '/tmp/'.$datatoken.'.tmp';
         if ( open(my $fh,"<$studentfile") ) {
             @studentdata=<$fh>;
             close($fh);
@@ -13657,6 +13738,14 @@ sub load_tmp_file {
     $env{'form.upfile'}=join('',@studentdata);
 }
 
+sub valid_datatoken {
+    my ($datatoken) = @_;
+    if ($datatoken =~ /^$match_username\_$match_domain\_enroll_$match_domain\_$match_courseid\_\d+_\d+$/) {
+        return $datatoken;
+    }
+    return;
+}
+
 =pod
 
 =item * &upfile_record_sep()
@@ -16063,7 +16152,23 @@ sub init_user_environment {
 	    opendir(DIR,$lonids);
 	    while ($filename=readdir(DIR)) {
 		if ($filename=~/^$username\_\d+\_$domain\_$authhost\.id$/) {
-		    unlink($lonids.'/'.$filename);
+                    if ($ENV{'SERVER_PORT'} == 443) {
+                        my $linkedfile;
+                        if (tie(my %oldenv,'GDBM_File',"$lonids/$cookie.id",
+                                &GDBM_READER(),0640)) {
+                            if (exists($oldenv{'user.linkedenv'})) {
+                                $linkedfile = $oldenv{'user.linkedenv'};
+                            }
+                            untie(%oldenv);
+                        }
+                        if (unlink($lonids.'/'.$filename)) {
+                            if ($linkedfile =~ /^[a-f0-9]+_linked\.id$/) {
+                                unlink($lonids.'/'.$linkedfile);
+                            }
+                        }
+                    } else {
+                        unlink($lonids.'/'.$filename);
+                    }
 		}
 	    }
 	    closedir(DIR);
@@ -16189,8 +16294,36 @@ sub init_user_environment {
                                                       $reqauthor{'author'}{'timestamp'};
                 }
             }
+            my ($types,$typename) = &course_types();
+            if (ref($types) eq 'ARRAY') {
+                my @options = ('approval','validate','autolimit');
+                my $optregex = join('|',@options);
+                my (%willtrust,%trustchecked);
+                foreach my $type (@{$types}) {
+                    my $dom_str = $env{'environment.reqcrsotherdom.'.$type};
+                    if ($dom_str ne '') {
+                        my $updatedstr = '';
+                        my @possdomains = split(',',$dom_str);
+                        foreach my $entry (@possdomains) {
+                            my ($extdom,$extopt) = split(':',$entry);
+                            unless ($trustchecked{$extdom}) {
+                                $willtrust{$extdom} = &Apache::lonnet::will_trust('reqcrs',$domain,$extdom);
+                                $trustchecked{$extdom} = 1;
+                            }
+                            if ($willtrust{$extdom}) {
+                                $updatedstr .= $entry.',';
+                            }
+                        }
+                        $updatedstr =~ s/,$//;
+                        if ($updatedstr) {
+                            $userenv{'reqcrsotherdom.'.$type} = $updatedstr;
+                        } else {
+                            delete($userenv{'reqcrsotherdom.'.$type});
+                        }
+                    }
+                }
+            }
         }
-
 	$env{'user.environment'} = "$lonids/$cookie.id";
 
 	if (tie(my %disk_env,'GDBM_File',"$lonids/$cookie.id",