From d9f3aca29b1a5dad715038baf114d788638b96a7 Mon Sep 17 00:00:00 2001
From: apizer <apizer@math.rochester.edu>
Date: Fri, 12 Oct 2012 15:18:21 -0500
Subject: [PATCH 01/19] Move course tmp files from the course directory to
 WeBWorK's tmp directory.

Changed the default location of all WeBWorK tmp files to
.../webwork2/htdocs/tmp.  We only had to change where course tmp files
are put.  Thhey now go to .../webwork2/htdocs/tmp/course_name/
So .../webwork2/htdocs/tmp is set up in exactly the same way we
suggest people set up /var/www/wwtmp.  There is no real reason now
for people to have to set up /var/www/wwtmp.
---
 conf/defaults.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/defaults.config b/conf/defaults.config
index 8529016d28..50e174eb70 100644
--- a/conf/defaults.config
+++ b/conf/defaults.config
@@ -261,8 +261,8 @@ $courseDirs{html_images} = "$courseDirs{html}/images";
 
 # Location of web-accessible, course-specific temporary files, like static and
 # dynamically-generated PG graphics.
-$courseDirs{html_temp}   = "$courseDirs{html}/tmp";
-$courseURLs{html_temp}   = "$courseURLs{html}/tmp";
+$courseDirs{html_temp}   = "$webworkDirs{htdocs_temp}/$courseName";
+$courseURLs{html_temp}   = "$webworkURLs{htdocs_temp}/$courseName";
 
 # Location of course-specific logs, like the transaction log.
 $courseDirs{logs}        = "$courseDirs{root}/logs";

From f38350c2a62f92144c02be813183e400aefd6440 Mon Sep 17 00:00:00 2001
From: Jason Aubrey <aubreyja@gmail.com>
Date: Wed, 24 Oct 2012 15:33:07 -0500
Subject: [PATCH 02/19] removed errant submodule references

---
 htdocs/themes/math2/codemirror2 | 1 -
 htdocs/themes/ubc/codemirror2   | 1 -
 2 files changed, 2 deletions(-)
 delete mode 160000 htdocs/themes/math2/codemirror2
 delete mode 160000 htdocs/themes/ubc/codemirror2

diff --git a/htdocs/themes/math2/codemirror2 b/htdocs/themes/math2/codemirror2
deleted file mode 160000
index 73edae2aaa..0000000000
--- a/htdocs/themes/math2/codemirror2
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 73edae2aaabf867f45119804b7816a339762414e
diff --git a/htdocs/themes/ubc/codemirror2 b/htdocs/themes/ubc/codemirror2
deleted file mode 160000
index 73edae2aaa..0000000000
--- a/htdocs/themes/ubc/codemirror2
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 73edae2aaabf867f45119804b7816a339762414e

From 198edbf52e140e3f6f37c1e381a1753222d01059 Mon Sep 17 00:00:00 2001
From: Jason Aubrey <aubreyja@gmail.com>
Date: Wed, 24 Oct 2012 16:05:59 -0500
Subject: [PATCH 03/19] Removed errant submodule references

---
 htdocs/themes/math2/codemirror2 | 1 -
 htdocs/themes/ubc/codemirror2   | 1 -
 2 files changed, 2 deletions(-)
 delete mode 160000 htdocs/themes/math2/codemirror2
 delete mode 160000 htdocs/themes/ubc/codemirror2

diff --git a/htdocs/themes/math2/codemirror2 b/htdocs/themes/math2/codemirror2
deleted file mode 160000
index 73edae2aaa..0000000000
--- a/htdocs/themes/math2/codemirror2
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 73edae2aaabf867f45119804b7816a339762414e
diff --git a/htdocs/themes/ubc/codemirror2 b/htdocs/themes/ubc/codemirror2
deleted file mode 160000
index 73edae2aaa..0000000000
--- a/htdocs/themes/ubc/codemirror2
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 73edae2aaabf867f45119804b7816a339762414e

From c1ceb3755941e70af505477469eeffbc39a7510c Mon Sep 17 00:00:00 2001
From: Jason Aubrey <aubreyja@gmail.com>
Date: Fri, 12 Oct 2012 13:05:58 -0500
Subject: [PATCH 04/19] Fixed OPL-update to use libraryVersion from \$ce 
 rather than a VERSION file Changed cherry-picked from webwork2/master
 4663e15316233ec81d56ff75ca7113d5ded9ca1b

---
 bin/OPL-update | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/bin/OPL-update b/bin/OPL-update
index d8a0aedb01..ea022d4d9a 100755
--- a/bin/OPL-update
+++ b/bin/OPL-update
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 # This is the script formerly known as loadDB2, and then known as NPL-update.  
 
@@ -84,6 +84,7 @@ my $dbh = DBI->connect(
 my $passwd = $ce->{database_password};
 my $user = $ce->{database_username};
 my $libraryRoot = $ce->{problemLibrary}->{root};
+my $libraryVersion = $ce->{problemLibrary}->{version};
 my $verbose = 0;
 my $cnt2 = 0;
 
@@ -98,21 +99,14 @@ sub dbug {
 ##Figure out which set of tables to use
 
 my %tables;
-if( -e "$libraryRoot/VERSION") {
-  require("$libraryRoot/VERSION");
-  if($OPL_VERSION eq '2.5.0') {
+if($libraryVersion eq '2.5') {
 	%tables = %OPLtables;
 	my $lib = 'OPL';
-	print "Got OPLtables!\n";
-  } else {
-	%tables = %NPLtables;
-	my $lib = 'NPL';
-	print "Got NPLtables! (1)\n";
-  }
+	warn "Library version is $libraryVersion; using OPLtables!\n";
 } else {
 	%tables = %NPLtables;
 	my $lib = 'NPL';
-	print "Got NPLtables! (2)\n";
+	print "Library version is $libraryVersion; NPLtables! \n";
 }
 
 @create_tables = (

From 0d0535ce0c2aff7abcc5fafcd9112f7374e0c850 Mon Sep 17 00:00:00 2001
From: Jason Aubrey <aubreyja@gmail.com>
Date: Wed, 24 Oct 2012 17:06:49 -0500
Subject: [PATCH 05/19] CONFIG-README directions out of date and superceeded by
 directions in README"

---
 conf/CONFIG-README | 37 -------------------------------------
 1 file changed, 37 deletions(-)
 delete mode 100644 conf/CONFIG-README

diff --git a/conf/CONFIG-README b/conf/CONFIG-README
deleted file mode 100644
index 47258870c7..0000000000
--- a/conf/CONFIG-README
+++ /dev/null
@@ -1,37 +0,0 @@
-
-FIRST TIME RECONFIGURATION
-
-RENAME global.conf to global.save in order to make sure that the global.conf.dist is read.
-Otherwise the global.conf file will be read instead of global.conf.dist. prelocal.conf and postlocal.conf
-and the behavior will be the same as with the old system.
-
-COPY prelocal.conf.dist to prelocal.conf.
-COPY postlocal.conf.dist to postlocal.conf.
-
-MODIFY prelocal.conf using the data from your global.conf file.  
-In particular you will need to fill in the server name, the 
-password for the database and any modifications you have made as to the 
-location of the temporary files directory. Notice that the location of the temporary files directory
-is used to define several other related subdirectories, so this modification needs to be made
-in prelocal.conf BEFORE the standard global.conf.dist file is read.
-
-
-INSPECT and possibly modify postlocal.conf to add any further local modifications that you had
-made to your global.conf file.
-
-Use the prelocal.conf and postlocal.conf files to make modifications.  
-
-The prelocal.conf file is read before the global.conf.dist file is processed. Non-local variables in this file
-are then available for use in global.conf.dist.
-
-The postlocal.conf file is read after the global.conf.dist file is processed and will overright configurations in global.conf.dist
-
-This new  configuration system should greatly simplify the process of 
-updating webwork2 since it is less likely
-that one will need to modify the config files when upgrading.  Default configurations or permissions for 
-new features will be defined in global.conf.dist and will allow automatic upgrades.  
-
-Overrides for these new features can be added later to postlocal.conf
-
-
-

From c6a5871db0ec8883fa75e6eed1b0b6a90422c42e Mon Sep 17 00:00:00 2001
From: Jason Aubrey <aubreyja@gmail.com>
Date: Sun, 4 Nov 2012 12:06:15 -0600
Subject: [PATCH 06/19] Added wwapache2ctl and webwork2.komodoproject to
 .gitignore (the last is a project file generated by an IDE I'm trying out).

---
 .gitignore | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.gitignore b/.gitignore
index 50679cec15..d384242114 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,4 +10,6 @@ logs/*
 conf/*.conf
 conf/*.apache2-config
 htdocs/site_info.txt
+bin/wwapache2ctl
+webwork2.komodoproject
 #courses.dist/*

From 1051ffe217297daf4651d2a178c864981b326510 Mon Sep 17 00:00:00 2001
From: Jason Aubrey <aubreyja@gmail.com>
Date: Sun, 4 Nov 2012 12:13:16 -0600
Subject: [PATCH 07/19] Sometimes users change user_id's. Given a course_id, an
 existing user_id in that course, and a different user_id, this script will
 (a) create a user for the new user_id if the account doesn't exist and (b)
 will also copy all existing data in the database associated with the old
 user_id to the new user_id. TODO: Currently copies all user set and problem
 data, but does not yet copy achievment data. We also want it to modify
 answer_log data so that the new user_id gets the same past answers.

---
 bin/change_user_id | 107 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 107 insertions(+)
 create mode 100644 bin/change_user_id

diff --git a/bin/change_user_id b/bin/change_user_id
new file mode 100644
index 0000000000..7bbd6c1ccf
--- /dev/null
+++ b/bin/change_user_id
@@ -0,0 +1,107 @@
+#!/usr/bin/env perl
+#
+#Sometimes a webwork user id changes.  This script transfers the webwork data for the old user_id to the new user_id
+# Update database tables
+#user
+#permission
+#password
+#key
+#set_user
+#problem_user
+#set_locations_user
+#global_achievement_user
+#achievement_user
+#
+# Update answer_log
+
+use strict;
+use warnings;
+
+BEGIN {
+	die "WEBWORK_ROOT not found in environment.\n"
+		unless exists $ENV{WEBWORK_ROOT};
+}
+
+use lib "$ENV{WEBWORK_ROOT}/lib";
+use WeBWorK::CourseEnvironment;
+use WeBWorK::DB;
+use WeBWorK::Utils qw(runtime_use readFile cryptPassword);
+use Data::Dumper;
+
+if((scalar(@ARGV) != 3)) {
+  print "\nSyntax is: change_user_id course_id old_user_id new_user_id";
+  print "\n    (e.g.  newpassword MAT_123 jjones jsmith\n\n";
+  exit();
+}
+
+my $courseID = shift;
+my $old_user_id = shift;
+my $new_user_id = shift;
+
+my $ce = WeBWorK::CourseEnvironment->new({
+	webwork_dir => $ENV{WEBWORK_ROOT},
+	courseName => $courseID
+});
+
+my $db = new WeBWorK::DB($ce->{dbLayout});
+die "Error: $old_user_id does not exist!" unless $db->existsUser($old_user_id);
+
+unless($db->existsUser($new_user_id)) {
+    my $user = $db->getUser($old_user_id);
+    $user->{user_id}=$new_user_id; 
+    $user->{comment} = $user->{comment}."Record created from $old_user_id record";
+    $db->addUser($user);
+}
+
+unless($db->existsPassword($new_user_id)) {
+    my $password = $db->getPassword($old_user_id);
+    $password->{user_id} = $new_user_id;
+    $db->addPassword($password);
+}
+
+unless($db->existsPermissionLevel($new_user_id)) {
+    my $permission = $db->getPermissionLevel($old_user_id);
+    $permission->{user_id} = $new_user_id;
+    $db->addPermissionLevel($permission);
+}
+    
+
+my @old_user_sets = $db->listUserSets($old_user_id);
+foreach(@old_user_sets) {
+    my $set_id = $_;
+    my $new_set = $db->newUserSet;
+    $new_set->user_id($new_user_id);
+    $new_set->set_id($set_id);
+    eval{$db->addUserSet($new_set)};
+    my $old_set = $db->getUserSet($old_user_id,$set_id);
+    foreach(keys %$old_set) {
+        next if /user_id|set_id/;
+        $new_set->$_($old_set->$_);
+    }
+    
+    $db->putUserSet($new_set) unless $db->existsUserSet($new_user_id,$set_id); 
+    my @global_problems = grep { defined $_} $db->getAllGlobalProblems($set_id);
+    foreach(@global_problems) {
+        if($db->existsUserProblem($old_user_id,$set_id,$_->{problem_id})) {
+            my $old_user_problem = $db->getUserProblem($old_user_id,$set_id,$_->{problem_id});
+            my $new_user_problem = $db->newUserProblem;
+            $new_user_problem->user_id($new_user_id);
+            $new_user_problem->set_id($set_id);
+            $new_user_problem->problem_id($_->{problem_id});
+            $db->addUserProblem($new_user_problem) unless $db->existsUserProblem($new_user_id,$set_id,$_->{problem_id});
+            foreach(keys %$old_user_problem) {
+                next if /(user_id|set_id|problem_id)/;
+                $new_user_problem->$_($old_user_problem->$_);
+            }
+            $db->putUserProblem($new_user_problem);
+        }
+    }
+}
+
+my $answer_log = $ce->{courseFiles}->{logs}->{answer_log};
+open(my $fh,">>",$answer_log);
+foreach(<$fh>) {
+    s/$//
+}
+   
+    

From d63615088c284e7c11301d137b4ba7afda36d677 Mon Sep 17 00:00:00 2001
From: "Davide P. Cervone" <dpvc@union.edu>
Date: Sun, 4 Nov 2012 14:48:20 -0500
Subject: [PATCH 08/19] Add a cleanup routine to PG so that MathObjects that
 are part of the output or answer checkers are freed (in order to prevent
 errors about missing packages).

---
 lib/WeBWorK.pm                          |  5 -----
 lib/WeBWorK/ContentGenerator/Problem.pm |  7 +++++++
 lib/WeBWorK/PG.pm                       | 13 +++++++++++++
 3 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/lib/WeBWorK.pm b/lib/WeBWorK.pm
index d7fc724447..759b8e540e 100644
--- a/lib/WeBWorK.pm
+++ b/lib/WeBWorK.pm
@@ -377,11 +377,6 @@ sub dispatch($) {
 	writeTimingLogEntry($ce, "[".$r->uri."]", sprintf("runTime = %.3f sec", $cg_duration)." ".$ce->{dbLayoutName}, "");
 	
 	debug("returning result: " . (defined $result ? $result : "UNDEF") . "\n");
-	    #@LimitedPolynomial::BOP::ISA; #FIXME this  is needed to zero out 
-	    #@LimitedPolynomial::UOP::ISA;
-	    #\@LimitedPolynomial::BOP::ISA and prevent error messages of the form 
-	    #[Sat May 15 14:23:08 2010] [warn] [client 127.0.0.1] [/webwork2/gage_course/test_set/6/] 
-	    #Can't locate package LimitedPolynomial::BOP for @LimitedPolynomial::BOP::add::ISA at /opt/webwork/webwork2/lib/Apache/WeBWorK.pm line 115., referer: http://localhost/webwork2/gage_course/test_set/6/ no one knows why
 	return $result;
 }
 
diff --git a/lib/WeBWorK/ContentGenerator/Problem.pm b/lib/WeBWorK/ContentGenerator/Problem.pm
index cefd5ca099..4e541a6598 100644
--- a/lib/WeBWorK/ContentGenerator/Problem.pm
+++ b/lib/WeBWorK/ContentGenerator/Problem.pm
@@ -472,6 +472,13 @@ sub previewCorrectAnswer {
 # Template escape implementations
 ################################################################################
 
+sub content {
+  my $self = shift;
+  my $result = $self->SUPER::content(@_);
+  $self->{pg}->free if $self->{pg};   # be sure to clean up PG environment when the page is done
+  return $result;
+}
+
 sub pre_header_initialize {
 	my ($self) = @_;
 	my $r = $self->r;
diff --git a/lib/WeBWorK/PG.pm b/lib/WeBWorK/PG.pm
index dffa5107c1..651518ffe2 100644
--- a/lib/WeBWorK/PG.pm
+++ b/lib/WeBWorK/PG.pm
@@ -53,6 +53,19 @@ sub new {
 	return $renderer->new(@_);
 }
 
+sub free {
+	my $self = shift;
+	#
+	#  If certain MathObjects (e.g. LimitedPolynomials) are left in the PG structure, then
+	#  freeing them later can cause "Can't locate package ..." errors in the log during
+	#  perl garbage collection.  So free them here.
+	#
+	$self->{pgcore}{OUTPUT_ARRAY} = [];
+	$self->{answers} = {};
+	undef $self->{translator};
+	foreach (keys %{$self->{pgcore}{PG_ANSWERS_HASH}}) {undef $self->{pgcore}{PG_ANSWERS_HASH}{$_}}
+}
+
 sub defineProblemEnvir {
 	my (
 		$self,

From 26d297985aa745398210a4dd51fc2ca394bfd26f Mon Sep 17 00:00:00 2001
From: Jason Aubrey <aubreyja@gmail.com>
Date: Tue, 6 Nov 2012 09:07:25 -0600
Subject: [PATCH 09/19] I think having the shebang line '/usr/bin/env perl' is
 more portable than /usr/bin/perl. It works on all *nix's and also allows for
 the script to work unmodified when a local administrator changes the perl
 path

---
 bin/check_modules.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bin/check_modules.pl b/bin/check_modules.pl
index fcca289b6b..d0fd873afd 100755
--- a/bin/check_modules.pl
+++ b/bin/check_modules.pl
@@ -1,5 +1,5 @@
-#!/usr/bin/perl
-
+#!/usr/bin/env perl
+#
 use strict;
 use warnings;
 

From e96d5a50d84774170b6018475d28b6aff4d49823 Mon Sep 17 00:00:00 2001
From: Jason Aubrey <aubreyja@gmail.com>
Date: Tue, 6 Nov 2012 11:02:53 -0600
Subject: [PATCH 10/19] Added code to back up existing answer_log and then
 replace old user_id with new user_id

---
 bin/change_user_id | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)
 mode change 100644 => 100755 bin/change_user_id

diff --git a/bin/change_user_id b/bin/change_user_id
old mode 100644
new mode 100755
index 7bbd6c1ccf..3cd0bde055
--- a/bin/change_user_id
+++ b/bin/change_user_id
@@ -16,6 +16,8 @@
 
 use strict;
 use warnings;
+use File::Copy;
+use File::Basename;
 
 BEGIN {
 	die "WEBWORK_ROOT not found in environment.\n"
@@ -99,9 +101,11 @@ foreach(@old_user_sets) {
 }
 
 my $answer_log = $ce->{courseFiles}->{logs}->{answer_log};
-open(my $fh,">>",$answer_log);
-foreach(<$fh>) {
-    s/$//
+my $dirname = dirname($answer_log);
+copy($answer_log,"$dirname/answer_log.bak");
+open(my $in,'<',"$dirname/answer_log.bak") or die "Can't open $dirname/answer_log.bak:$!";
+open(my $out,'>',$answer_log);
+while(<$in>) {
+    s/$old_user_id/$new_user_id/g;
+    print $out $_;
 }
-   
-    

From d42b671eb7e42289d7ea1e76647570d3d48d91cb Mon Sep 17 00:00:00 2001
From: Jason Aubrey <aubreyja@gmail.com>
Date: Tue, 6 Nov 2012 11:03:58 -0600
Subject: [PATCH 11/19] Modified DB.pm to fix issue #68

---
 lib/WeBWorK/DB.pm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/WeBWorK/DB.pm b/lib/WeBWorK/DB.pm
index d118257e79..7e44575519 100644
--- a/lib/WeBWorK/DB.pm
+++ b/lib/WeBWorK/DB.pm
@@ -779,10 +779,10 @@ sub addKey {
 		my ($userID, $proctorID) = ($1, $2);
 		croak "addKey: user $userID not found"
 #			unless $self->{user}->exists($userID);
-			unless $Key -> key eq "nonce" or $self->{user}->exists($Key->user_id);
+			unless $Key -> key eq "nonce" or $self->{user}->exists($userID);
 		croak "addKey: proctor $proctorID not found"
 #			unless $self->{user}->exists($proctorID);
-			unless $Key -> key eq "nonce" or $self->{user}->exists($Key->user_id);
+			unless $Key -> key eq "nonce" or $self->{user}->exists($proctorID);
 	} else {
 		croak "addKey: user ", $Key->user_id, " not found"
 #			unless $self->{user}->exists($Key->user_id);

From 0010fb8dc59f73398e27740d2ad0e1311c5b9acd Mon Sep 17 00:00:00 2001
From: Paul Vojta <vojta@math.berkeley.edu>
Date: Sun, 9 Dec 2012 11:19:39 -0600
Subject: [PATCH 12/19] CAS authentication module, associated conf file and
 changes to Login.pm and Logout.pm

---
 conf/authen_CAS.conf.dist              |  36 +++++++
 lib/WeBWorK/Authen/CAS.pm              | 136 +++++++++++++++++++++++++
 lib/WeBWorK/ContentGenerator/Login.pm  |  10 ++
 lib/WeBWorK/ContentGenerator/Logout.pm |   3 +
 4 files changed, 185 insertions(+)
 create mode 100644 conf/authen_CAS.conf.dist
 create mode 100644 lib/WeBWorK/Authen/CAS.pm

diff --git a/conf/authen_CAS.conf.dist b/conf/authen_CAS.conf.dist
new file mode 100644
index 0000000000..62417696a1
--- /dev/null
+++ b/conf/authen_CAS.conf.dist
@@ -0,0 +1,36 @@
+#!perl
+
+########################################################################################
+# authen_CAS.conf.dist
+# Copy this file to authen_CAS.conf. Then configure it to match your server's CAS configuration.
+# Then to activate add the following line to localOverrides.conf:
+# include("conf/authen_CAS.conf")
+########################################################################################
+
+# Set CAS as the authentication module to use.
+$authen{user_module} = {
+  "*" => "WeBWorK::Authen::CAS",
+};
+
+$authen{cas_options} = {
+	# Options to pass to the AuthCAS module.
+	# Note that this is (plain) AuthCAS, not Apache::AuthCAS
+	# or Apache2::AuthCAS.
+	# You need at least casUrl and CAFile; others can be set as well.
+	AuthCAS_opts => {
+		# URL of CAS server.  Edit the host below.
+		casURL => '', #e.g. 'https://auth.berkeley.edu/cas',
+
+		# Path of certificate file for CAS server.
+		CAFile => '', #e.g. '/etc/pki/tls/certs/ca-bundle.crt',
+	},
+	# There are no options specific to CAS at this time.  If there were,
+	# though, they would go here.
+
+	# For debugging:
+	#su_from => '8315',
+	su_to => '999999',
+};
+
+
+1; #final line of the file to reassure perl that it was read properly.
diff --git a/lib/WeBWorK/Authen/CAS.pm b/lib/WeBWorK/Authen/CAS.pm
new file mode 100644
index 0000000000..1cc78fea15
--- /dev/null
+++ b/lib/WeBWorK/Authen/CAS.pm
@@ -0,0 +1,136 @@
+################################################################################
+# WeBWorK Online Homework Delivery System
+# Copyright © 2000-2007 The WeBWorK Project, http://openwebwork.sf.net/
+# $CVSHeader: $
+# 
+# This program is free software; you can redistribute it and/or modify it under
+# the terms of either: (a) the GNU General Public License as published by the
+# Free Software Foundation; either version 2, or (at your option) any later
+# version, or (b) the "Artistic License" which comes with this package.
+# 
+# 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 either the GNU General Public License or the
+# Artistic License for more details.
+################################################################################
+
+package WeBWorK::Authen::CAS;
+use base qw/WeBWorK::Authen/;
+
+use strict;
+use warnings;
+use AuthCAS;
+
+use WeBWorK::Debug;
+#$WeBWorK::Debug::Enabled = 1;
+#$WeBWorK::Debug::Logfile = "/opt/webwork/webwork2/logs/cas-debug.log";
+#$WeBWorK::Debug::AllowSubroutineOutput = "get_credentials";
+
+sub get_credentials {
+	my ($self) = @_;
+	my $r = $self->{r};
+	my $ce = $r->ce;
+
+	# if we come in with a user_id, then we've already authenticated
+	#    through the CAS.  So just check the provided user and session key.
+	$self->{external_auth} = 1;
+	if (defined $r->param('key') && defined $r->param('user')) {
+		# These lines were copied from the superclass get_credentials.
+		$self->{session_key} = $r->param('key');
+		$self->{user_id} = $r->param('user');
+		$self->{login_type} = 'normal';
+		$self->{credential_source} = 'params';
+		debug("CAS params user '", $self->{user_id},
+		  "' key '", $self->{session_key}, "'");
+		# Check session key and user here.  Otherwise, a student can
+		#    determine the enrollment status of any other student if
+		#    they know the userid (which is public information at
+		#    Berkeley).  That would be a privacy violation.
+		my $Key = $r->db->getKey($self->{user_id});
+		unless (defined $Key && $Key->key eq $self->{session_key}) {
+			debug('undefined or invalid session key:  $Key->key = ',
+			  defined $Key ? $Key->key : undef, ', user value = ',
+			  $self->{session_key});
+			$self->{error} = "Invalid session key";
+			return 0;
+		}
+		return 1;
+		#debug("falling back to superclass get_credentials");
+		#return $self->SUPER::get_credentials( @_ );
+	} else {
+		#my $cas_url = $ce->{authen}{cas_options}{url};
+		#my $cas_certs = $ce->{authen}{cas_options}{certs};
+		#my $cas = new AuthCAS(casUrl => $cas_url,
+		#    CAFile => $cas_certs);
+		my $cas = new AuthCAS(
+		  %{ $ce->{authen}{cas_options}{AuthCAS_opts} });
+
+		my $service = $ce->{apache_root_url} . $r->location . '/'
+		  . $r->urlpath->arg('courseID') . '/';
+		debug("service = $service");
+		my $ticket = $r->param('ticket') || 0;
+		unless ($ticket) {
+			# there's no ticket, so redirect to get one
+			#
+			my $go_to = $cas->getServerLoginURL($service);
+			#$go_to = 'http://math.berkeley.edu/'; # for debugging
+			debug("no ticket.  Redirecting to $go_to");
+			$self->{redirect} = $go_to;
+			return 0;
+		}
+		# We have a ticket.  Validate it.
+		my $user_id = $cas->validateST($service, $ticket);
+		if (!defined $user_id) {
+			my $err = $cas->get_errors();
+			$err = '<undef>' unless defined $err;
+			$self->{error} = $err;
+			debug("ticket error $err");
+			#return $self->SUPER::get_credentials( @_ );
+			return 0;
+		} else {
+			debug("ticket is good, user is $user_id");
+			if (defined $ce->{authen}{cas_options}{su_from}
+			  && $user_id eq $ce->{authen}{cas_options}{su_from}
+			  && defined $ce->{authen}{cas_options}{su_to}) {
+				$user_id = $ce->{authen}{cas_options}{su_to};
+				debug("hackily changing user to $user_id");
+			}
+			$self->{'user_id'} = $user_id;
+			$self->{r}->param('user', $user_id);
+			$self->{session_key} = undef;
+			$self->{password} = "not\tvalid";
+			$self->{login_type} = 'normal';
+			$self->{credential_source} = 'cas';
+			return 1;
+		}
+	}
+}
+
+# There's no need to provide site_checkPassword, since it's only accessed
+# from checkPassword, which we're replacing.
+
+sub checkPassword {
+	my ( $self, $userID, $clearTextPassword ) = @_;
+	# if we got here, we know we've already successfully authenticated
+	# against the CAS
+	return 1;
+}
+
+# Handle logout by redirecting to the relevant CAS url.
+
+sub logout_user {
+	my ($self) = @_;
+
+	my $ce = $self->{r}->ce;
+
+	# Using AuthCAS::getServerLogoutURL($service) would be overkill,
+	# and (more important) it would send us back here after logging out,
+	# so we'd end up back at the CAS login screen.
+
+	my $go_to = $ce->{authen}{cas_options}{AuthCAS_opts}{casUrl}
+	  . '/logout';
+	debug("logging out.  Redirecting to $go_to");
+	$self->{redirect} = $go_to;
+}
+
+1;
diff --git a/lib/WeBWorK/ContentGenerator/Login.pm b/lib/WeBWorK/ContentGenerator/Login.pm
index 80ea73c2a1..851913e228 100644
--- a/lib/WeBWorK/ContentGenerator/Login.pm
+++ b/lib/WeBWorK/ContentGenerator/Login.pm
@@ -117,6 +117,16 @@ sub links {
 	return( @return);
 }
 
+sub pre_header_initialize {
+	my ($self) = @_;
+	my $authen = $self->r->authen;
+	
+	if ( defined($authen->{redirect}) && $authen->{redirect} ) {
+		$self->reply_with_redirect($authen->{redirect});
+	}
+}
+
+
 sub body {
 	my ($self) = @_;
 	my $r = $self->r;
diff --git a/lib/WeBWorK/ContentGenerator/Logout.pm b/lib/WeBWorK/ContentGenerator/Logout.pm
index 4ea4cde833..643deed077 100644
--- a/lib/WeBWorK/ContentGenerator/Logout.pm
+++ b/lib/WeBWorK/ContentGenerator/Logout.pm
@@ -82,6 +82,9 @@ sub pre_header_initialize {
 	}
 	$self->{keyError} = $keyError;
 
+	# Do any special processing needed by external authentication
+	$authen->logout_user() if $authen->can('logout_user');
+
 	# if we have an authen redirect, all of those errors may be 
 	#    moot, but I think that's unavoidable (-glarose)
 	if ( defined($authen->{redirect}) && $authen->{redirect} ) {

From 3dcb38f6be76026d97ee62b0c1fa98890e05e1f1 Mon Sep 17 00:00:00 2001
From: Paul Vojta <vojta@math.berkeley.edu>
Date: Wed, 2 Jan 2013 14:02:00 -0800
Subject: [PATCH 13/19] Added support for URLs as provided in WWfeedback
 messages

I had inadvertently provided an older version of CAS.pm when submitting
the original version.  This brings CAS.pm up to date.  The only change
was/is to add support to keep params on the URL being sent to the CAS server
(so that URLs provided by WWfeedback messages work properly).
---
 lib/WeBWorK/Authen/CAS.pm | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/lib/WeBWorK/Authen/CAS.pm b/lib/WeBWorK/Authen/CAS.pm
index 1cc78fea15..a128c0b21e 100644
--- a/lib/WeBWorK/Authen/CAS.pm
+++ b/lib/WeBWorK/Authen/CAS.pm
@@ -65,8 +65,12 @@ sub get_credentials {
 		my $cas = new AuthCAS(
 		  %{ $ce->{authen}{cas_options}{AuthCAS_opts} });
 
-		my $service = $ce->{apache_root_url} . $r->location . '/'
-		  . $r->urlpath->arg('courseID') . '/';
+		my $service = $r->unparsed_uri();
+		# Remove the "ticket=..." parameter that the CAS server added
+		# (Not sure if the second test is really needed.)
+		$service =~ s/[?&]ticket=[^&]*$//
+		  or $service =~ s/([?&])ticket=[^&]*&/$1/;
+		$service = $ce->{apache_root_url} . $service;
 		debug("service = $service");
 		my $ticket = $r->param('ticket') || 0;
 		unless ($ticket) {

From cb0a29158d5b05f311b0142724227e7f5a679f6e Mon Sep 17 00:00:00 2001
From: Paul Vojta <vojta@math.berkeley.edu>
Date: Wed, 2 Jan 2013 14:06:41 -0800
Subject: [PATCH 14/19] Fixed copyright date, and minor code cleanup

---
 lib/WeBWorK/Authen/CAS.pm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/WeBWorK/Authen/CAS.pm b/lib/WeBWorK/Authen/CAS.pm
index a128c0b21e..c3ed38da15 100644
--- a/lib/WeBWorK/Authen/CAS.pm
+++ b/lib/WeBWorK/Authen/CAS.pm
@@ -1,6 +1,6 @@
 ################################################################################
 # WeBWorK Online Homework Delivery System
-# Copyright © 2000-2007 The WeBWorK Project, http://openwebwork.sf.net/
+# Copyright © 2012 The WeBWorK Project, http://openwebwork.sf.net/
 # $CVSHeader: $
 # 
 # This program is free software; you can redistribute it and/or modify it under
@@ -72,8 +72,8 @@ sub get_credentials {
 		  or $service =~ s/([?&])ticket=[^&]*&/$1/;
 		$service = $ce->{apache_root_url} . $service;
 		debug("service = $service");
-		my $ticket = $r->param('ticket') || 0;
-		unless ($ticket) {
+		my $ticket = $r->param('ticket');
+		unless (defined $ticket) {
 			# there's no ticket, so redirect to get one
 			#
 			my $go_to = $cas->getServerLoginURL($service);

From b7afc277a57dd40b00e60de14bc5838e1a3dbf32 Mon Sep 17 00:00:00 2001
From: Jason Aubrey <aubreyja@gmail.com>
Date: Fri, 4 Jan 2013 10:02:13 -0600
Subject: [PATCH 15/19] Fixed typo in authen_CAS.conf.dist

---
 conf/authen_CAS.conf.dist | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/authen_CAS.conf.dist b/conf/authen_CAS.conf.dist
index 62417696a1..60f4c62e60 100644
--- a/conf/authen_CAS.conf.dist
+++ b/conf/authen_CAS.conf.dist
@@ -19,7 +19,7 @@ $authen{cas_options} = {
 	# You need at least casUrl and CAFile; others can be set as well.
 	AuthCAS_opts => {
 		# URL of CAS server.  Edit the host below.
-		casURL => '', #e.g. 'https://auth.berkeley.edu/cas',
+		casUrl => '', #e.g. 'https://auth.berkeley.edu/cas',
 
 		# Path of certificate file for CAS server.
 		CAFile => '', #e.g. '/etc/pki/tls/certs/ca-bundle.crt',

From ba90466c1faf487e431aec43ada56bf0380cc7e0 Mon Sep 17 00:00:00 2001
From: John Hsu <john.hsu@ubc.ca>
Date: Fri, 4 Jan 2013 17:05:27 -0800
Subject: [PATCH 16/19] Enable comma escaping, unicode chars in classlists
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Classlists files as processed by the addcourse script can't deal with users
who, for one reason or another, has a comma in either their first or last
name. Using the Text::CSV module for CSV parsing instead of split() enables
comma escaping values by putting them in double quotes.

Users who have non-ASCII characters in their name gets their name (e.g.:
Frøystein) mangled after going through addcourse. This commit forces Perl
to open the the classlist file with UTF8 encoding. This way the unicode
characters survive intact into the database.
---
 bin/check_modules.pl          |  1 +
 lib/WeBWorK/File/Classlist.pm | 11 ++++++++++-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/bin/check_modules.pl b/bin/check_modules.pl
index d0fd873afd..c1b95fc31e 100755
--- a/bin/check_modules.pl
+++ b/bin/check_modules.pl
@@ -84,6 +84,7 @@
 	Socket
 	SQL::Abstract
 	String::ShellQuote
+	Text::CSV
 	Text::Wrap
 	Tie::IxHash
 	Time::HiRes
diff --git a/lib/WeBWorK/File/Classlist.pm b/lib/WeBWorK/File/Classlist.pm
index cd6312f085..0f28ba7904 100644
--- a/lib/WeBWorK/File/Classlist.pm
+++ b/lib/WeBWorK/File/Classlist.pm
@@ -26,6 +26,7 @@ WeBWorK::File::Classlist - parse and write classlist files.
 use strict;
 use warnings;
 use IO::File;
+use Text::CSV;
 
 our $MIN_FIELDS = 9;
 our $MAX_FIELDS = 11;
@@ -38,10 +39,13 @@ our @EXPORT = qw/parse_classlist write_classlist/;
 sub parse_classlist($) {
 	my ($file) = @_;
 	
+	use open qw( :encoding(UTF-8) :std ); # assume classlist is utf8 encoded
 	my $fh = new IO::File($file, "<")
 		or die "Failed to open classlist '$file' for reading: $!\n";
 	
 	my (@records);
+
+	my $csv = Text::CSV->new({ binary => 1 }); # binary for utf8 compat
 	
 	while (<$fh>) {
 		chomp;
@@ -50,7 +54,12 @@ sub parse_classlist($) {
 		s/^\s*//;
 		s/\s*$//;
 		
-		my @fields = split /\s*,\s*/, $_, -1; # -1 == don't delete empty trailing fields
+		if (!$csv->parse($_)) {
+			warn "Unable to parse line $. of classlist '$file' as CSV.";
+			next;
+		}
+		my @fields = $csv->fields;
+
 		my $fields = @fields;
 		if ($fields < $MIN_FIELDS) {
 			warn "Skipped invalid line $. of classlist '$file': expected at least $MIN_FIELDS fields, got $fields fields.\n";

From 4d6aad603921565740f84b0c805e0ffef3078b28 Mon Sep 17 00:00:00 2001
From: Jason Aubrey <aubreyja@gmail.com>
Date: Fri, 11 Jan 2013 12:23:57 -0800
Subject: [PATCH 17/19] Fixed OPL-update to symlink applets to web accessible
 directory

---
 bin/OPL-update | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/bin/OPL-update b/bin/OPL-update
index ea022d4d9a..6b075d409e 100755
--- a/bin/OPL-update
+++ b/bin/OPL-update
@@ -416,6 +416,10 @@ sub pgfiles {
 	my ($edition, $textauthor, $textsection, $textproblem, $tagged);
 	%textinfo=();
 	my @textproblems = (-1);
+  if ($name =~ /swf$/ {
+      my $applet_file = basename($name);
+      symlink($name,"$webworkDirs{htdocs}/applets/$applet_file");
+    }
 	if ($name =~ /pg$/) {
 		$pgfile = basename($name);
 		$pgpath = dirname($name);

From 64af8b9bfcdf372031fca158ec8fe616072d95be Mon Sep 17 00:00:00 2001
From: Jason Aubrey <aubreyja@gmail.com>
Date: Fri, 11 Jan 2013 15:21:19 -0800
Subject: [PATCH 18/19] OPL-update now symlinks swf applets in the OPL to
 webwork2/htdocs/applets so they can be used in problems easily

---
 bin/OPL-update | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bin/OPL-update b/bin/OPL-update
index 6b075d409e..b55f406195 100755
--- a/bin/OPL-update
+++ b/bin/OPL-update
@@ -416,9 +416,9 @@ sub pgfiles {
 	my ($edition, $textauthor, $textsection, $textproblem, $tagged);
 	%textinfo=();
 	my @textproblems = (-1);
-  if ($name =~ /swf$/ {
+  if ($name =~ /swf$/) {
       my $applet_file = basename($name);
-      symlink($name,"$webworkDirs{htdocs}/applets/$applet_file");
+      symlink($name,$ce->{webworkDirs}->{htdocs}."/applets/".$applet_file);
     }
 	if ($name =~ /pg$/) {
 		$pgfile = basename($name);

From 3e4dbda26711ba887222546eefed088161c4b824 Mon Sep 17 00:00:00 2001
From: "Davide P. Cervone" <dpvc@union.edu>
Date: Thu, 17 Jan 2013 12:44:03 -0500
Subject: [PATCH 19/19] Remove LimitedPolynomials and Inequalities::common from
 the preloaded list (now that the package errors are resolved).  Must put back
 the original contextLimitedPolynomials.pl and contextInequalities.pl as well

---
 conf/defaults.config | 2 --
 1 file changed, 2 deletions(-)

diff --git a/conf/defaults.config b/conf/defaults.config
index 50e174eb70..3afe7dcac6 100644
--- a/conf/defaults.config
+++ b/conf/defaults.config
@@ -938,9 +938,7 @@ ${pg}{modules} = [
 	[qw(Fraction)],
 	[qw(Fun)],
 	[qw(Hermite)],
-	[qw(Inequalities::common)],
 	[qw(Label)],
-	[qw(LimitedPolynomial)],
 	[qw(ChoiceList)],
 	[qw(Match)],
 	[qw(MatrixReal1)], # required by Matrix