Merge remote-tracking branch 'webwork2-dev/ww2.5.1.1' into ww2.5.1.1

Grabbing bugfixes from webwork2-dev/ww2.5.1.1

.gitignore

@@ -10,4 +10,6 @@ logs/*
 conf/*.conf
 conf/*.apache2-config
 htdocs/site_info.txt
+bin/wwapache2ctl
+webwork2.komodoproject
 #courses.dist/*

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 "$libraryRoot/VERSION") {
-  include("$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 = (
@@ -422,6 +416,10 @@ sub pgfiles {
 	my ($edition, $textauthor, $textsection, $textproblem, $tagged);
 	%textinfo=();
 	my @textproblems = (-1);
+  if ($name =~ /swf$/) {
+      my $applet_file = basename($name);
+      symlink($name,$ce->{webworkDirs}->{htdocs}."/applets/".$applet_file);
+    }
 	if ($name =~ /pg$/) {
 		$pgfile = basename($name);
 		$pgpath = dirname($name);

bin/change_user_id

@@ -0,0 +1,111 @@
+#!/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;
+use File::Copy;
+use File::Basename;
+
+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};
+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 $_;
+}

bin/check_modules.pl

@@ -1,5 +1,5 @@
-#!/usr/bin/perl
-
+#!/usr/bin/env perl
+#
 use strict;
 use warnings;
 
@@ -84,6 +84,7 @@
 	Socket
 	SQL::Abstract
 	String::ShellQuote
+	Text::CSV
 	Text::Wrap
 	Tie::IxHash
 	Time::HiRes

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.

conf/authen_LTI.conf.dist

@@ -23,6 +23,23 @@ $authen{user_module} = [
 #module but the sequence includes an internal authentication
 #system, e.g., Basic_TheLastOption, then the following line
 #must be uncommented for use by WeBWorK::Logout.
+# If it is uncommented and the value = 1,
+# then, if the authentication sequence reaches 
+# Basic_TheLastOption, then WeBWorK::Login
+# will display a screen directing the user
+# back to an external authentication system.
+# On the other hand, if the value = 0 or
+# the line is commented out, then WeBWorK::Login
+# will display the traditional passwork login screen.
+# Upon logging out, if the line is not commented out
+# and the value = 1, then the Logout screen will NOT
+# show a "Login Again" button and will display
+# a message directing the user to go to the
+# external authentication system.
+# On the other hand, if the line is commented out
+# or if the value = 0, then the Logout screen WILL
+# display a "Login Again" button that will take
+# the user to a pasword login screen.
 
 #$external_auth=1;
 

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";
@@ -275,6 +275,7 @@ $courseDirs{templates}   = "$courseDirs{root}/templates";
 
 # Location of course achievement files.
 $courseDirs{achievements}   = "$courseDirs{templates}/achievements";
+$courseDirs{achievements_html} = "$courseDirs{html}/achievements"; #contains badge icons
 $courseURLs{achievements}   = "$courseURLs{html}/achievements";
 
 # Location of course-specific macro files.
@@ -937,9 +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

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;
 }
 

lib/WeBWorK/AchievementEvaluator.pm

@@ -28,7 +28,7 @@ use WeBWorK::CGI;
 use WeBWorK::Utils qw(before after readFile sortAchievements);
 
 use Safe;
-use Storable qw(freeze thaw);
+use Storable qw(nfreeze thaw);
 
 sub checkForAchievements {
 
@@ -225,15 +225,15 @@ sub checkForAchievements {
 	    $achievementPoints += $points;
 	}    
 
-	#update counter, freeze localData and store
+	#update counter, nfreeze localData and store
 	$userAchievement->counter($counter);
-	$userAchievement->frozen_hash(freeze($localData));	
+	$userAchievement->frozen_hash(nfreeze($localData));	
 	$db->putUserAchievement($userAchievement);
 
     }  #end for loop
 
-    #freeze globalData and store
-    $globalUserAchievement->frozen_hash(freeze($globalData));
+    #nfreeze globalData and store
+    $globalUserAchievement->frozen_hash(nfreeze($globalData));
     $db->putGlobalUserAchievement($globalUserAchievement);
 
     return $cheevoMessage;