From 28b4645e67903e90296f8a75b826c42d0b6d8840 Mon Sep 17 00:00:00 2001
From: Tobias Paczian <paczian@mcs.anl.gov>
Date: Fri, 23 Jan 2015 04:59:43 -0600
Subject: [PATCH 01/15] added private option to project resource

---
 src/MGRAST/lib/resources/project.pm | 21 ++++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/src/MGRAST/lib/resources/project.pm b/src/MGRAST/lib/resources/project.pm
index cd060c15..32153a65 100644
--- a/src/MGRAST/lib/resources/project.pm
+++ b/src/MGRAST/lib/resources/project.pm
@@ -192,8 +192,27 @@ sub query {
     if ($limit == 0) {
         $limit = 18446744073709551615;
     }
+
+    # check if we just want the private projects
+    if ($self->cgi->param('private')) {
+      unless ($self->user) {
+	$self->return_data({"ERROR" => "private option requires authentication"}, 400);
+      }
+      my $ids = [];
+      if ($self->cgi->param('edit')) {
+	$ids = $self->user->has_right_to(undef, 'edit', 'project');
+      } else {
+	$ids = $self->user->has_right_to(undef, 'view', 'project');
+      }
+      if (scalar(@$ids) && $ids->[0] eq '*') {
+	shift @$ids;
+      }
+      my $list = join(",", @$ids);
+      $total = scalar(@$ids);
+      $projects = $master->Project->get_objects( {$order => [undef, "id IN ($list) ORDER BY $order LIMIT $limit OFFSET $offset"]} );
+    }
     # get all items the user has access to
-    if (exists $self->rights->{'*'}) {
+    elsif (exists $self->rights->{'*'}) {
         $total    = $master->Project->count_all();
         $projects = $master->Project->get_objects( {$order => [undef, "_id IS NOT NULL ORDER BY $order LIMIT $limit OFFSET $offset"]} );
     } else {

From aefa4b05f17e5ab40ac5c74d21319307919ba347 Mon Sep 17 00:00:00 2001
From: Tobias Paczian <paczian@mcs.anl.gov>
Date: Fri, 23 Jan 2015 08:23:10 -0600
Subject: [PATCH 02/15] added shock preferences

---
 src/MGRAST/lib/resources/user.pm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/src/MGRAST/lib/resources/user.pm b/src/MGRAST/lib/resources/user.pm
index f107ba83..603dbe9b 100644
--- a/src/MGRAST/lib/resources/user.pm
+++ b/src/MGRAST/lib/resources/user.pm
@@ -267,6 +267,25 @@ sub instance {
     if (defined $self->{cgi}->param('comment')) {
       $user->comment(uri_unescape($self->{cgi}->param('comment')));
     }
+
+    # preferences were passed
+    if (defined $rest->[1] && $rest->[1] eq "preferences") {
+      my $prefs = { 'type' => 'preference', 'app' => 'MGRAST', 'id' => 'mgu'.$self->user->_id, "pref" => $self->json->decode($self->cgi->param('prefs')) };
+      
+      # check if we already have a preferences node
+      my $shockprefs = $self->get_shock_query({'type' => 'preference', 'app' => 'MGRAST', 'id' => 'mgu'.$self->user->_id}, $self->mgrast_token);
+      
+      # we do, update the node
+      my $retval = {};
+      if (scalar(@$shockprefs)) {
+	$retval = $self->update_shock_node($shockprefs->[0]->{id}, $prefs, $self->mgrast_token);
+      }
+      # we don't, create a new node
+      else {
+	$retval = $self->set_shock_node("preferences", undef, $prefs, $self->mgrast_token);
+      }
+      $self->return_data( {"OK" => $retval}, 200 );
+    }
   }
 
   # check if this is a user deletion
@@ -403,6 +422,11 @@ sub instance {
     my $prefs = $master->Preferences->get_objects({ user => $user });
     $user->{preferences} = [];
     @{$user->{preferences}} = map { { name => $_->{name}, value => $_->{value} } } @$prefs;
+
+    my $shockprefs = $self->get_shock_query({'type' => 'preference', 'app' => 'MGRAST', 'id' => 'mgu'.$self->user->_id}, $self->mgrast_token);
+    if (scalar(@$shockprefs)) {
+      push(@{$user->{preferences}}, { name => 'shock', value => $shockprefs->[0]->{attributes}->{pref} } );
+    }
   }
   # get the users rights
   elsif ($verb eq 'rights') {

From 77b5135f9eb11fa1ac0170be2c779778af42aa8c Mon Sep 17 00:00:00 2001
From: Tobias Paczian <paczian@mcs.anl.gov>
Date: Mon, 26 Jan 2015 06:01:54 -0600
Subject: [PATCH 03/15] enabled SHOCK preferences object

---
 src/MGRAST/lib/Auth.pm           | 27 +++++++++++++++++++++++++
 src/MGRAST/lib/resources/user.pm | 34 ++++++++++++++++++++------------
 2 files changed, 48 insertions(+), 13 deletions(-)

diff --git a/src/MGRAST/lib/Auth.pm b/src/MGRAST/lib/Auth.pm
index a7c8432c..8956aeaf 100644
--- a/src/MGRAST/lib/Auth.pm
+++ b/src/MGRAST/lib/Auth.pm
@@ -2,6 +2,7 @@ package Auth;
 
 use JSON;
 use CGI;
+use LWP::UserAgent;
 
 sub authenticate {
   my ($key) = @_;
@@ -35,6 +36,32 @@ sub authenticate {
 	  my $verbose = "";
 	  if ($cgi->param('verbosity') && $cgi->param('verbosity') eq 'verbose') {
 	    $verbose = ', "login": "'.$us->{login}.'", "firstname": "'.$us->{firstname}.'", "lastname": "'.$us->{lastname}.'", "email": "'.$us->{email}.'"';
+
+	    # SHOCK preferences
+	    my $prefs = $master->Preferences->get_objects({ user => $user, name => "shock_pref_node" });
+	    if (scalar(@$prefs)) {
+	      my $nodeid = $prefs->[0]->{value};
+	      my $response = undef;
+	      eval {
+		my $json = new JSON;
+		my $agent = LWP::UserAgent->new;
+		my @args = ('Authorization', "OAuth ".$pref->[0]->value);
+		my $get = $agent->get($Conf::shock_url.'/node/'.$nodeid, @args);
+		$response = $json->decode( $get->content );
+	      };
+	      if ($@ || (! ref($response))) {
+		return undef;
+	      } elsif (exists($response->{error}) && $response->{error}) {
+		print $cgi->header(-type => 'application/json',
+				   -status => 500,
+				   -charset => 'UTF-8',
+				   -Access_Control_Allow_Origin => '*' );
+		print $json->encode({"ERROR" => "Unable to GET node $id from Shock: ".$response->{error}[0]}, $response->{status} );
+		exit;
+	      } else {
+		$verbose.=', "preferences": "'.$self-$response->{data}->{attributes}.'"';
+	      }
+	    }
 	  }
           print $cgi->header(-type => 'application/json',
                              -status => 200,
diff --git a/src/MGRAST/lib/resources/user.pm b/src/MGRAST/lib/resources/user.pm
index 603dbe9b..fc431293 100644
--- a/src/MGRAST/lib/resources/user.pm
+++ b/src/MGRAST/lib/resources/user.pm
@@ -272,19 +272,17 @@ sub instance {
     if (defined $rest->[1] && $rest->[1] eq "preferences") {
       my $prefs = { 'type' => 'preference', 'app' => 'MGRAST', 'id' => 'mgu'.$self->user->_id, "pref" => $self->json->decode($self->cgi->param('prefs')) };
       
-      # check if we already have a preferences node
-      my $shockprefs = $self->get_shock_query({'type' => 'preference', 'app' => 'MGRAST', 'id' => 'mgu'.$self->user->_id}, $self->mgrast_token);
-      
-      # we do, update the node
+      my $pref_id = $master->Preferences->get_objects({ user => $user, name => "shock_pref_node" });
+      my $nodeid;
       my $retval = {};
-      if (scalar(@$shockprefs)) {
-	$retval = $self->update_shock_node($shockprefs->[0]->{id}, $prefs, $self->mgrast_token);
-      }
-      # we don't, create a new node
-      else {
+      if (scalar(@$pref_id)) {
+	$nodeid = $pref_id->[0]->{value};
+	$retval = $self->update_shock_node($nodeid, $prefs, $self->mgrast_token);
+      } else {
 	$retval = $self->set_shock_node("preferences", undef, $prefs, $self->mgrast_token);
+	$master->Preferences->create({ user => $user, name => "shock_pref_node", value => $retval->{id} });
       }
-      $self->return_data( {"OK" => $retval}, 200 );
+      $self->return_data( {"OK" => $retval->{attributes}->{pref}}, 200 );
     }
   }
 
@@ -423,9 +421,19 @@ sub instance {
     $user->{preferences} = [];
     @{$user->{preferences}} = map { { name => $_->{name}, value => $_->{value} } } @$prefs;
 
-    my $shockprefs = $self->get_shock_query({'type' => 'preference', 'app' => 'MGRAST', 'id' => 'mgu'.$self->user->_id}, $self->mgrast_token);
-    if (scalar(@$shockprefs)) {
-      push(@{$user->{preferences}}, { name => 'shock', value => $shockprefs->[0]->{attributes}->{pref} } );
+    # check if we already have shock preferences
+    my $nodeid;
+    foreach my $p (@{$user->{preferences}}) {
+      if ($p->{name} eq "shock_pref_node") {
+	$nodeid = $p->{value};
+	last;
+      }
+    }
+    if ($nodeid) {
+      my $shockprefs = $self->get_shock_node($nodeid, $self->mgrast_token);
+      if ($shockprefs) {
+	push(@{$user->{preferences}}, { name => 'shock', value => $shockprefs->{attributes}->{pref} } );
+      }
     }
   }
   # get the users rights

From 5cb8e517b9777f1235b4aeae3056ceb8d62193c3 Mon Sep 17 00:00:00 2001
From: Tobias Paczian <paczian@mcs.anl.gov>
Date: Mon, 26 Jan 2015 08:36:38 -0600
Subject: [PATCH 04/15] removed shock auth from the user preferences until
 shock accepts mg-rast auth

---
 src/MGRAST/lib/Auth.pm           | 82 ++++++++++++++++++--------------
 src/MGRAST/lib/resources/user.pm |  4 +-
 2 files changed, 48 insertions(+), 38 deletions(-)

diff --git a/src/MGRAST/lib/Auth.pm b/src/MGRAST/lib/Auth.pm
index 8956aeaf..57d3760b 100644
--- a/src/MGRAST/lib/Auth.pm
+++ b/src/MGRAST/lib/Auth.pm
@@ -2,7 +2,6 @@ package Auth;
 
 use JSON;
 use CGI;
-use LWP::UserAgent;
 
 sub authenticate {
   my ($key) = @_;
@@ -23,57 +22,68 @@ sub authenticate {
       $key =~ s/^mggo4711//;
 
       use MIME::Base64;
+      use LWP::UserAgent;
+      use Conf;
       my ($u,$p) = split(/\:/, decode_base64($key));
       my $us = $master->User->init( { login => $u } );
       if (ref $us and crypt($p, $us->password) eq $us->password) {
         my $pref = $master->Preferences->get_objects( { name => 'WebServiceKeyTdate', user => $us } );
-        if (scalar(@$pref)) { 
+        if (scalar(@$pref)) {
           if ($pref->[0]->value < time) {
               $pref->[0]->value(time + 1209600);
           }
           $pref = $master->Preferences->get_objects( { name => 'WebServicesKey', user => $us } );
-	  my $cgi = new CGI;
-	  my $verbose = "";
-	  if ($cgi->param('verbosity') && $cgi->param('verbosity') eq 'verbose') {
-	    $verbose = ', "login": "'.$us->{login}.'", "firstname": "'.$us->{firstname}.'", "lastname": "'.$us->{lastname}.'", "email": "'.$us->{email}.'"';
+          my $cgi = new CGI;
+          my $verbose = "";
+          if ($cgi->param('verbosity') && $cgi->param('verbosity') eq 'verbose') {
+            $verbose = ', "login": "'.$us->{login}.'", "firstname": "'.$us->{firstname}.'", "lastname": "'.$us->{lastname}.'", "email": "'.$us->{email}.'"';
 
-	    # SHOCK preferences
-	    my $prefs = $master->Preferences->get_objects({ user => $user, name => "shock_pref_node" });
-	    if (scalar(@$prefs)) {
-	      my $nodeid = $prefs->[0]->{value};
-	      my $response = undef;
-	      eval {
-		my $json = new JSON;
-		my $agent = LWP::UserAgent->new;
-		my @args = ('Authorization', "OAuth ".$pref->[0]->value);
-		my $get = $agent->get($Conf::shock_url.'/node/'.$nodeid, @args);
-		$response = $json->decode( $get->content );
-	      };
-	      if ($@ || (! ref($response))) {
-		return undef;
-	      } elsif (exists($response->{error}) && $response->{error}) {
-		print $cgi->header(-type => 'application/json',
-				   -status => 500,
-				   -charset => 'UTF-8',
-				   -Access_Control_Allow_Origin => '*' );
-		print $json->encode({"ERROR" => "Unable to GET node $id from Shock: ".$response->{error}[0]}, $response->{status} );
-		exit;
-	      } else {
-		$verbose.=', "preferences": "'.$self-$response->{data}->{attributes}.'"';
-	      }
-	    }
-	  }
+            # SHOCK preferences
+            my $prefs = $master->Preferences->get_objects({ user => $us, name => "shock_pref_node" });
+            if (scalar(@$prefs)) {
+              my $nodeid = $prefs->[0]->{value};
+              my $response = undef;
+              my $json = new JSON;
+              $json = $json->utf8();
+              $json->max_size(0);
+              $json->allow_nonref;
+              my $agent = LWP::UserAgent->new;
+              eval {
+                my @args = ();#('Authorization', "OAuth ".$Conf::mgrast_oauth_token);
+                my $url = $Conf::shock_url.'/node/'.$nodeid;
+                my $get = $agent->get($url, @args);
+                $response = $json->decode( $get->content );
+              };
+              if ($@ || (! ref($response))) {
+                print $cgi->header(-type => 'application/json',
+                                   -status => 500,
+                                   -charset => 'UTF-8',
+                                   -Access_Control_Allow_Origin => '*' );
+                print $json->encode({"ERROR" => "Unable to GET node $nodeid from Shock: ".$response->{error}[0]}, $response->{status} );
+                exit;
+              } elsif (exists($response->{error}) && $response->{error}) {
+                print $cgi->header(-type => 'application/json',
+                                   -status => 500,
+                                   -charset => 'UTF-8',
+                                   -Access_Control_Allow_Origin => '*' );
+                print $json->encode({"ERROR" => "Unable to GET node $nodeid from Shock: ".$response->{error}[0]}, $response->{status} );
+                exit;
+              } else {
+                $verbose.=', "preferences": "'.$json->encode($response->{data}->{attributes}->{pref}).'"';
+              }
+            }
+          }
           print $cgi->header(-type => 'application/json',
                              -status => 200,
-			     -charset => 'UTF-8',
+                             -charset => 'UTF-8',
                              -Access_Control_Allow_Origin => '*' );
           print '{ "token": "'.$pref->[0]->value.'"'.$verbose.' }';
           exit;
         } else {
-	  return (undef, "api access not enabled for this user");
-	}
+          return (undef, "api access not enabled for this user");
+        }
       } else {
-	return (undef, "invalid MG-RAST credentials");
+        return (undef, "invalid MG-RAST credentials");
       }
   }
 
diff --git a/src/MGRAST/lib/resources/user.pm b/src/MGRAST/lib/resources/user.pm
index fc431293..8d069ee4 100644
--- a/src/MGRAST/lib/resources/user.pm
+++ b/src/MGRAST/lib/resources/user.pm
@@ -277,9 +277,9 @@ sub instance {
       my $retval = {};
       if (scalar(@$pref_id)) {
 	$nodeid = $pref_id->[0]->{value};
-	$retval = $self->update_shock_node($nodeid, $prefs, $self->mgrast_token);
+	$retval = $self->update_shock_node($nodeid, $prefs);#, $self->mgrast_token);
       } else {
-	$retval = $self->set_shock_node("preferences", undef, $prefs, $self->mgrast_token);
+	$retval = $self->set_shock_node("preferences", undef, $prefs);#, $self->mgrast_token);
 	$master->Preferences->create({ user => $user, name => "shock_pref_node", value => $retval->{id} });
       }
       $self->return_data( {"OK" => $retval->{attributes}->{pref}}, 200 );

From dc44513a1cfef23d749abd8cc763e8c6cab5335e Mon Sep 17 00:00:00 2001
From: Tobias Paczian <paczian@mcs.anl.gov>
Date: Mon, 26 Jan 2015 08:42:33 -0600
Subject: [PATCH 05/15] fixed quoting bug in auth

---
 src/MGRAST/lib/Auth.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/MGRAST/lib/Auth.pm b/src/MGRAST/lib/Auth.pm
index 57d3760b..bac148ca 100644
--- a/src/MGRAST/lib/Auth.pm
+++ b/src/MGRAST/lib/Auth.pm
@@ -69,7 +69,7 @@ sub authenticate {
                 print $json->encode({"ERROR" => "Unable to GET node $nodeid from Shock: ".$response->{error}[0]}, $response->{status} );
                 exit;
               } else {
-                $verbose.=', "preferences": "'.$json->encode($response->{data}->{attributes}->{pref}).'"';
+                $verbose.=', "preferences": '.$json->encode($response->{data}->{attributes}->{pref});
               }
             }
           }

From 862f7593feadcccac6a749fe47eab4cf79302e40 Mon Sep 17 00:00:00 2001
From: Tobias Paczian <paczian@mcs.anl.gov>
Date: Tue, 27 Jan 2015 04:39:08 -0600
Subject: [PATCH 06/15] fixed grouping calculation

---
 src/MGRAST/lib/WebPage/Analysis.pm | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/MGRAST/lib/WebPage/Analysis.pm b/src/MGRAST/lib/WebPage/Analysis.pm
index ade8a0f4..4f67d646 100644
--- a/src/MGRAST/lib/WebPage/Analysis.pm
+++ b/src/MGRAST/lib/WebPage/Analysis.pm
@@ -600,8 +600,8 @@ sub single_data {
   if ($mg_grp_sel eq 'groups') {
     my $joined_data = {};
     foreach my $row (@$result) {
-      my $id_string = join("|", @$row[1..8]);
       $row->[0] = $collections->{$row->[0]};
+      my $id_string = join("|", @$row[0..8]);
       if (exists($joined_data->{$id_string})) {
 	$row->[10] = sprintf("%.2f", (($joined_data->{$id_string}->[9] * $joined_data->{$id_string}->[10]) + ($row->[9] * $row->[10])) / ($joined_data->{$id_string}->[9] + $row->[9]));
 	$row->[11] = sprintf("%.2f", (($joined_data->{$id_string}->[9] * $joined_data->{$id_string}->[11]) + ($row->[9] * $row->[11])) / ($joined_data->{$id_string}->[9] + $row->[9]));
@@ -715,8 +715,8 @@ sub phylogenetic_data {
   if ($mg_grp_sel eq 'groups') {
     my $joined_data = {};
     foreach my $row (@$result) {
-      my $id_string = join("|", @$row[1..9]);
       $row->[0] = $collections->{$row->[0]};
+      my $id_string = join("|", @$row[0..9]);
       if (exists($joined_data->{$id_string})) {
 	$row->[12] = sprintf("%.2f", (($joined_data->{$id_string}->[10] * $joined_data->{$id_string}->[12]) + ($row->[10] * $row->[12])) / ($joined_data->{$id_string}->[10] + $row->[10]));
 	$row->[13] = sprintf("%.2f", (($joined_data->{$id_string}->[10] * $joined_data->{$id_string}->[13]) + ($row->[10] * $row->[13])) / ($joined_data->{$id_string}->[10] + $row->[10]));
@@ -861,8 +861,8 @@ sub metabolic_data {
   if ($mg_grp_sel eq 'groups') {
     my $joined_data = {};
     foreach my $row (@$all) {
-      my $id_string = join("|", @$row[1..4]);
       $row->[0] = $collections->{$row->[0]};
+      my $id_string = join("|", @$row[0..4]);
       if (exists($joined_data->{$id_string})) {
 	$row->[8] = sprintf("%.2f", (($joined_data->{$id_string}->[6] * $joined_data->{$id_string}->[8]) + ($row->[6] * $row->[8])) / ($joined_data->{$id_string}->[6] + $row->[6]));
 	$row->[9] = sprintf("%.2f", (($joined_data->{$id_string}->[6] * $joined_data->{$id_string}->[9]) + ($row->[6] * $row->[9])) / ($joined_data->{$id_string}->[6] + $row->[6]));
@@ -966,8 +966,8 @@ sub annotation_data {
   if ($mg_grp_sel eq 'groups') {
     my $joined_data = {};
     foreach my $row (@$result) {
-      my $id_string = join("|", @$row[1..2]);
       $row->[0] = $collections->{$row->[0]};
+      my $id_string = join("|", @$row[0..2]);
       if (exists($joined_data->{$id_string})) {
 	$row->[5] = sprintf("%.2f", (($joined_data->{$id_string}->[3] * $joined_data->{$id_string}->[5]) + ($row->[3] * $row->[5])) / ($joined_data->{$id_string}->[3] + $row->[3]));
 	$row->[6] = sprintf("%.2f", (($joined_data->{$id_string}->[3] * $joined_data->{$id_string}->[6]) + ($row->[3] * $row->[6])) / ($joined_data->{$id_string}->[3] + $row->[3]));
@@ -1053,8 +1053,8 @@ sub lca_data {
   if ($mg_grp_sel eq 'groups') {
     my $joined_data = {};
     foreach my $row (@$result) {
-      my $id_string = join("|", @$row[1..8]);
       $row->[0] = $collections->{$row->[0]};
+      my $id_string = join("|", @$row[0..8]);
       if (exists($joined_data->{$id_string})) {
 	$row->[10] = sprintf("%.2f", (($joined_data->{$id_string}->[9] * $joined_data->{$id_string}->[10]) + ($row->[9] * $row->[10])) / ($joined_data->{$id_string}->[9] + $row->[9]));
 	$row->[11] = sprintf("%.2f", (($joined_data->{$id_string}->[9] * $joined_data->{$id_string}->[11]) + ($row->[9] * $row->[11])) / ($joined_data->{$id_string}->[9] + $row->[9]));

From 9fc4f159a0e8552624ad09665f201bfd11ac4d68 Mon Sep 17 00:00:00 2001
From: Jared Bischof <jbischof@gmail.com>
Date: Wed, 28 Jan 2015 11:52:11 -0600
Subject: [PATCH 07/15] Bug fix

---
 src/MGRAST/lib/resources/metagenome.pm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/MGRAST/lib/resources/metagenome.pm b/src/MGRAST/lib/resources/metagenome.pm
index 5f7626cb..ff53393d 100644
--- a/src/MGRAST/lib/resources/metagenome.pm
+++ b/src/MGRAST/lib/resources/metagenome.pm
@@ -305,7 +305,7 @@ sub query {
         if ($self->user->has_star_right('view', 'metagenome')) {
             $solr_query_str .= "(status:private)";
         } else {
-            if (scalar(%{$self->rights}) > 0) {
+            if (scalar(keys %{$self->rights}) > 0) {
                 $solr_query_str .= "(status:private AND (".join(" OR ", map {'id:mgm'.$_} keys %{$self->rights})."))";
             } else {
                 $return_empty_set = 1;
@@ -316,7 +316,7 @@ sub query {
             if ($self->user->has_star_right('view', 'metagenome')) {
                 $solr_query_str .= "(status:*)";
             } else {
-                if (scalar(%{$self->rights}) > 0) {
+                if (scalar(keys %{$self->rights}) > 0) {
                     $solr_query_str .= "((status:public) OR (status:private AND (".join(" OR ", map {'id:mgm'.$_} keys %{$self->rights}).")))";
                 } else {
                     $solr_query_str .= '(status:public)';

From f1c51eacabb88420b193d07549f023516ab9df1e Mon Sep 17 00:00:00 2001
From: Tobias Paczian <paczian@mcs.anl.gov>
Date: Thu, 29 Jan 2015 04:42:50 -0600
Subject: [PATCH 08/15]  added summary verbosity

---
 src/MGRAST/lib/resources/project.pm | 22 ++++++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

diff --git a/src/MGRAST/lib/resources/project.pm b/src/MGRAST/lib/resources/project.pm
index 32153a65..1c69627e 100644
--- a/src/MGRAST/lib/resources/project.pm
+++ b/src/MGRAST/lib/resources/project.pm
@@ -258,14 +258,32 @@ sub prepare_data {
 	        $obj->{samples}   = \@samples;
 	        $obj->{libraries} = \@libraries;
             }
-            if (($self->cgi->param('verbosity') eq 'verbose') || ($self->cgi->param('verbosity') eq 'full')) {
+            if (($self->cgi->param('verbosity') eq 'verbose') || ($self->cgi->param('verbosity') eq 'full') || ($self->cgi->param('verbosity') eq 'summary')) {
 	        my $metadata  = $project->data();
 	        my $desc = $metadata->{project_description} || $metadata->{study_abstract} || " - ";
 	        my $fund = $metadata->{project_funding} || " - ";
 	        $obj->{metadata}       = $metadata;
 	        $obj->{description}    = $desc;
 	        $obj->{funding_source} = $fund;	
-            } elsif ($self->cgi->param('verbosity') ne 'minimal') {
+            } elsif ($self->cgi->param('verbosity') eq 'summary') {
+	      my $jdata = $project->metagenomes_summary();
+	      $obj->{metagenomes} = [];
+	      foreach my $row (@$jdata) {
+		push(@$obj->{metagenomes}, { metagenome_id => $row->[0],
+					     name => $row->[1],
+					     basepairs => $row->[2],
+					     sequences => $row->[3],
+					     biome => $row->[4],
+					     feature => $row->[5],
+					     material => $row->[6],
+					     location => $row->[7],
+					     country => $row->[8],
+					     coordinates => $row->[9],
+					     sequence_type => $row->[10],
+					     sequencing_method => $row->[11] });
+	      }
+	      
+	    } elsif ($self->cgi->param('verbosity') ne 'minimal') {
 	        $self->return_data( {"ERROR" => "invalid value for option verbosity"}, 400 );
             }
         }

From e0ae1d402602a7279a8e6e874bdd767ca568ca8a Mon Sep 17 00:00:00 2001
From: Tobias Paczian <paczian@mcs.anl.gov>
Date: Thu, 29 Jan 2015 06:06:36 -0600
Subject: [PATCH 09/15] fixed bug in summary verbosity

---
 src/MGRAST/lib/resources/project.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/MGRAST/lib/resources/project.pm b/src/MGRAST/lib/resources/project.pm
index 1c69627e..fe413c13 100644
--- a/src/MGRAST/lib/resources/project.pm
+++ b/src/MGRAST/lib/resources/project.pm
@@ -269,7 +269,7 @@ sub prepare_data {
 	      my $jdata = $project->metagenomes_summary();
 	      $obj->{metagenomes} = [];
 	      foreach my $row (@$jdata) {
-		push(@$obj->{metagenomes}, { metagenome_id => $row->[0],
+		push(@{$obj->{metagenomes}}, { metagenome_id => $row->[0],
 					     name => $row->[1],
 					     basepairs => $row->[2],
 					     sequences => $row->[3],

From 9c50e78b44ac87681a598019aab4f27e48a2beac Mon Sep 17 00:00:00 2001
From: Tobias Paczian <paczian@mcs.anl.gov>
Date: Thu, 29 Jan 2015 06:08:49 -0600
Subject: [PATCH 10/15] fixed another bug in summary verbosity

---
 src/MGRAST/lib/resources/project.pm | 25 +++++++++++++------------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/src/MGRAST/lib/resources/project.pm b/src/MGRAST/lib/resources/project.pm
index fe413c13..f6df4f44 100644
--- a/src/MGRAST/lib/resources/project.pm
+++ b/src/MGRAST/lib/resources/project.pm
@@ -265,22 +265,23 @@ sub prepare_data {
 	        $obj->{metadata}       = $metadata;
 	        $obj->{description}    = $desc;
 	        $obj->{funding_source} = $fund;	
-            } elsif ($self->cgi->param('verbosity') eq 'summary') {
+            }
+	    if ($self->cgi->param('verbosity') eq 'summary') {
 	      my $jdata = $project->metagenomes_summary();
 	      $obj->{metagenomes} = [];
 	      foreach my $row (@$jdata) {
 		push(@{$obj->{metagenomes}}, { metagenome_id => $row->[0],
-					     name => $row->[1],
-					     basepairs => $row->[2],
-					     sequences => $row->[3],
-					     biome => $row->[4],
-					     feature => $row->[5],
-					     material => $row->[6],
-					     location => $row->[7],
-					     country => $row->[8],
-					     coordinates => $row->[9],
-					     sequence_type => $row->[10],
-					     sequencing_method => $row->[11] });
+					       name => $row->[1],
+					       basepairs => $row->[2],
+					       sequences => $row->[3],
+					       biome => $row->[4],
+					       feature => $row->[5],
+					       material => $row->[6],
+					       location => $row->[7],
+					       country => $row->[8],
+					       coordinates => $row->[9],
+					       sequence_type => $row->[10],
+					       sequencing_method => $row->[11] });
 	      }
 	      
 	    } elsif ($self->cgi->param('verbosity') ne 'minimal') {

From 855664809e0f87f7bada898d27408d985e90bfd0 Mon Sep 17 00:00:00 2001
From: Tobias Paczian <paczian@mcs.anl.gov>
Date: Thu, 29 Jan 2015 06:11:04 -0600
Subject: [PATCH 11/15] guess pinky...

---
 src/MGRAST/lib/resources/project.pm | 42 ++++++++++++++---------------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/src/MGRAST/lib/resources/project.pm b/src/MGRAST/lib/resources/project.pm
index f6df4f44..83da18ef 100644
--- a/src/MGRAST/lib/resources/project.pm
+++ b/src/MGRAST/lib/resources/project.pm
@@ -264,27 +264,27 @@ sub prepare_data {
 	        my $fund = $metadata->{project_funding} || " - ";
 	        $obj->{metadata}       = $metadata;
 	        $obj->{description}    = $desc;
-	        $obj->{funding_source} = $fund;	
-            }
-	    if ($self->cgi->param('verbosity') eq 'summary') {
-	      my $jdata = $project->metagenomes_summary();
-	      $obj->{metagenomes} = [];
-	      foreach my $row (@$jdata) {
-		push(@{$obj->{metagenomes}}, { metagenome_id => $row->[0],
-					       name => $row->[1],
-					       basepairs => $row->[2],
-					       sequences => $row->[3],
-					       biome => $row->[4],
-					       feature => $row->[5],
-					       material => $row->[6],
-					       location => $row->[7],
-					       country => $row->[8],
-					       coordinates => $row->[9],
-					       sequence_type => $row->[10],
-					       sequencing_method => $row->[11] });
-	      }
-	      
-	    } elsif ($self->cgi->param('verbosity') ne 'minimal') {
+	        $obj->{funding_source} = $fund;
+		
+		if ($self->cgi->param('verbosity') eq 'summary') {
+		  my $jdata = $project->metagenomes_summary();
+		  $obj->{metagenomes} = [];
+		  foreach my $row (@$jdata) {
+		    push(@{$obj->{metagenomes}}, { metagenome_id => $row->[0],
+						   name => $row->[1],
+						   basepairs => $row->[2],
+						   sequences => $row->[3],
+						   biome => $row->[4],
+						   feature => $row->[5],
+						   material => $row->[6],
+						   location => $row->[7],
+						   country => $row->[8],
+						   coordinates => $row->[9],
+						   sequence_type => $row->[10],
+						   sequencing_method => $row->[11] });
+		  }
+		}
+            } elsif ($self->cgi->param('verbosity') ne 'minimal') {
 	        $self->return_data( {"ERROR" => "invalid value for option verbosity"}, 400 );
             }
         }

From 43a41a6f96a668041f5f436a7a1250a28e7ac689 Mon Sep 17 00:00:00 2001
From: Tobias Paczian <paczian@mcs.anl.gov>
Date: Mon, 2 Feb 2015 07:22:59 -0600
Subject: [PATCH 12/15] fixed shock preferences

---
 src/MGRAST/lib/Auth.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/MGRAST/lib/Auth.pm b/src/MGRAST/lib/Auth.pm
index bac148ca..9bf81d04 100644
--- a/src/MGRAST/lib/Auth.pm
+++ b/src/MGRAST/lib/Auth.pm
@@ -49,7 +49,7 @@ sub authenticate {
               $json->allow_nonref;
               my $agent = LWP::UserAgent->new;
               eval {
-                my @args = ();#('Authorization', "OAuth ".$Conf::mgrast_oauth_token);
+                my @args = ('Authorization', "mgrast ".$pref->[0]->{value});
                 my $url = $Conf::shock_url.'/node/'.$nodeid;
                 my $get = $agent->get($url, @args);
                 $response = $json->decode( $get->content );

From c5bd0d21bb87f69b9e0813db4810664c943451be Mon Sep 17 00:00:00 2001
From: Tobias Paczian <paczian@mcs.anl.gov>
Date: Mon, 2 Feb 2015 09:24:24 -0600
Subject: [PATCH 13/15] udpated to enable optional mg-rast auth

---
 src/MGRAST/lib/resources/resource.pm | 106 ++++++++++++++++++++-------
 src/MGRAST/lib/resources/user.pm     |  10 ++-
 2 files changed, 86 insertions(+), 30 deletions(-)

diff --git a/src/MGRAST/lib/resources/resource.pm b/src/MGRAST/lib/resources/resource.pm
index 5a092a07..ffbb614d 100644
--- a/src/MGRAST/lib/resources/resource.pm
+++ b/src/MGRAST/lib/resources/resource.pm
@@ -547,8 +547,12 @@ sub download_text {
 
 # stream a file from shock to browser
 sub return_shock_file {
-    my ($self, $id, $size, $name, $auth) = @_;
+    my ($self, $id, $size, $name, $auth, $authPrefix) = @_;
         
+    if (! $authPrefix) {
+      $authPrefix = "OAuth";
+    }
+
     my $response = undef;
     # print headers
     print "Content-Type:application/x-download\n";
@@ -560,7 +564,7 @@ sub return_shock_file {
     eval {
         my $url = $Conf::shock_url.'/node/'.$id.'?download_raw';
         my @args = (
-            $auth ? ('Authorization', "OAuth $auth") : (),
+            $auth ? ('Authorization', "$authPrefix $auth") : (),
             ':read_size_hint', 8192,
             ':content_cb', sub{ my ($chunk) = @_; print $chunk; }
         );
@@ -575,12 +579,16 @@ sub return_shock_file {
 
 ## download array of info for metagenome files in shock
 sub get_download_set {
-    my ($self, $mgid, $auth, $seq_only) = @_;
+    my ($self, $mgid, $auth, $seq_only, $authPrefix) = @_;
+
+    if (! $authPrefix) {
+      $authPrefix = "OAuth";
+    }
 
     my %seen = ();
     my %subset = ('preprocess' => 1, 'dereplication' => 1, 'screen' => 1);
     my $stages = [];
-    my $mgdata = $self->get_shock_query({'type' => 'metagenome', 'id' => 'mgm'.$mgid}, $auth);
+    my $mgdata = $self->get_shock_query({'type' => 'metagenome', 'id' => 'mgm'.$mgid}, $auth, $authPrefix);
     @$mgdata = grep { exists($_->{attributes}{stage_id}) && exists($_->{attributes}{data_type}) } @$mgdata;
     @$mgdata = sort { ($a->{attributes}{stage_id} cmp $b->{attributes}{stage_id}) ||
                         ($a->{attributes}{data_type} cmp $b->{attributes}{data_type}) } @$mgdata;
@@ -665,16 +673,20 @@ sub get_download_set {
 
 # add or delete an ACL based on username
 sub edit_shock_acl {
-    my ($self, $id, $auth, $user, $action, $acl) = @_;
+    my ($self, $id, $auth, $user, $action, $acl, $authPrefix) = @_;
     
+    if (! $authPrefix) {
+      $authPrefix = "OAuth";
+    }
+
     my $response = undef;
     my $url = $Conf::shock_url.'/node/'.$id.'/acl/'.$acl.'?users='.$user;
     eval {
         my $tmp = undef;
         if ($action eq 'delete') {
-            $tmp = $self->agent->delete($url, 'Authorization' => "OAuth $auth");
+            $tmp = $self->agent->delete($url, 'Authorization' => "$authPrefix $auth");
         } elsif ($action eq 'put') {
-            $tmp = $self->agent->put($url, 'Authorization' => "OAuth $auth");
+            $tmp = $self->agent->put($url, 'Authorization' => "$authPrefix $auth");
         } else {
             $self->return_data( {"ERROR" => "Invalid Shock ACL action: $action"}, 500 );
         }
@@ -692,8 +704,11 @@ sub edit_shock_acl {
 # create node with optional file and/or attributes
 # file is json struct by default
 sub set_shock_node {
-    my ($self, $name, $file, $attr, $auth, $not_json) = @_;
+    my ($self, $name, $file, $attr, $auth, $not_json, $authPrefix) = @_;
     
+    if (! $authPrefix) {
+      $authPrefix = "OAuth";
+    }
     my $response = undef;
     my $content = {};
     if ($file) {
@@ -705,7 +720,7 @@ sub set_shock_node {
     }
     eval {
         my @args = (
-            $auth ? ('Authorization', "OAuth $auth") : (),
+            $auth ? ('Authorization', "$authPrefix $auth") : (),
             'Content_Type', 'multipart/form-data',
             $content ? ('Content', $content) : ()
         );
@@ -723,13 +738,17 @@ sub set_shock_node {
 
 # set node file_name
 sub update_shock_node_file_name {
-    my ($self, $id, $fname, $auth) = @_;
+    my ($self, $id, $fname, $auth, $authPrefix) = @_;
+
+    if (! $authPrefix) {
+      $authPrefix = "OAuth";
+    }
 
     my $response = undef;
     my $content = {file_name => $fname};
     eval {
         my @args = (
-            $auth ? ('Authorization', "OAuth $auth") : (),
+            $auth ? ('Authorization', "$authPrefix $auth") : (),
             'Content_Type', 'multipart/form-data',
             $content ? ('Content', $content) : ()
         );
@@ -750,13 +769,16 @@ sub update_shock_node_file_name {
 
 # edit node attributes
 sub update_shock_node {
-    my ($self, $id, $attr, $auth) = @_;
+    my ($self, $id, $attr, $auth, $authPrefix) = @_;
     
+    if (! $authPrefix) {
+      $authPrefix = "OAuth";
+    }
     my $response = undef;
     my $content = {attributes => [undef, "n/a", Content => $self->json->encode($attr)]};
     eval {
         my @args = (
-            $auth ? ('Authorization', "OAuth $auth") : (),
+            $auth ? ('Authorization', "$authPrefix $auth") : (),
             'Content_Type', 'multipart/form-data',
             $content ? ('Content', $content) : ()
         );
@@ -776,11 +798,15 @@ sub update_shock_node {
 
 # get node contents
 sub get_shock_node {
-    my ($self, $id, $auth) = @_;
+    my ($self, $id, $auth, $authPrefix) = @_;
     
+    if (! $authPrefix) {
+      $authPrefix = "OAuth";
+    }
+
     my $response = undef;
     eval {
-        my @args = $auth ? ('Authorization', "OAuth $auth") : ();
+        my @args = $auth ? ('Authorization', "$authPrefix $auth") : ();
         my $get = $self->agent->get($Conf::shock_url.'/node/'.$id, @args);
         $response = $self->json->decode( $get->content );
     };
@@ -795,11 +821,15 @@ sub get_shock_node {
 
 # get the shock preauth url for a file
 sub get_shock_preauth {
-    my ($self, $id, $auth, $fn) = @_;
+    my ($self, $id, $auth, $fn, $authPrefix) = @_;
     
+    if (! $authPrefix) {
+      $authPrefix = "OAuth";
+    }
+
     my $response = undef;
     eval {
-        my @args = $auth ? ('Authorization', "OAuth $auth") : ();
+        my @args = $auth ? ('Authorization', "$authPrefix $auth") : ();
         my $get = $self->agent->get($Conf::shock_url.'/node/'.$id.'?download_url'.($fn ? "&filename=".$fn : ""), @args);
         $response = $self->json->decode( $get->content );
     };
@@ -814,11 +844,15 @@ sub get_shock_preauth {
 
 # write file content to given filepath, else return file content as string
 sub get_shock_file {
-    my ($self, $id, $file, $auth, $index) = @_;
+    my ($self, $id, $file, $auth, $index, $authPrefix) = @_;
     
+    if (! $authPrefix) {
+      $authPrefix = "OAuth";
+    }
+
     my $response = undef;
     my $fhdl = undef;
-    my @args = $auth ? ('Authorization', "OAuth $auth") : ();
+    my @args = $auth ? ('Authorization', "$authPrefix $auth") : ();
     
     if ($file) {
         open($fhdl, ">$file") || return undef;
@@ -840,15 +874,19 @@ sub get_shock_file {
 
 # get list of nodes for query
 sub get_shock_query {
-    my ($self, $params, $auth) = @_;
-    
+    my ($self, $params, $auth, $authPrefix) = @_;
+
+    if (! $authPrefix) {
+      $authPrefix = "OAuth";
+    }    
+
     my $response = undef;
     my $query = '?query&limit=0';
     if ($params && (scalar(keys %$params) > 0)) {
         map { $query .= '&'.$_.'='.$params->{$_} } keys %$params;
     }
     eval {
-        my @args = $auth ? ('Authorization', "OAuth $auth") : ();
+        my @args = $auth ? ('Authorization', "$authPrefix $auth") : ();
         my $get = $self->agent->get($Conf::shock_url.'/node'.$query, @args);
         $response = $self->json->decode( $get->content );
     };
@@ -863,7 +901,11 @@ sub get_shock_query {
 
 # submit job to awe
 sub post_awe_job {
-    my ($self, $workflow, $shock_auth, $awe_auth, $is_string) = @_;
+    my ($self, $workflow, $shock_auth, $awe_auth, $is_string, $authPrefix) = @_;
+
+    if (! $authPrefix) {
+      $authPrefix = "OAuth";
+    }
 
     my $content = undef;
     if ($is_string) {
@@ -876,7 +918,7 @@ sub post_awe_job {
     eval {
         my $post = $self->agent->post($Conf::awe_url.'/job',
                                       'Datatoken', $shock_auth,
-                                      'Authorization', 'OAuth '.$awe_auth,
+                                      'Authorization', "$authPrefix ".$awe_auth,
                                       'Content-Type', 'multipart/form-data',
                                       'Content', $content);
         $response = $self->json->decode( $post->content );
@@ -893,11 +935,15 @@ sub post_awe_job {
 
 # PUT command to perfrom action on a job
 sub awe_job_action {
-    my ($self, $id, $action, $auth) = @_;
+    my ($self, $id, $action, $auth, $authPrefix) = @_;
     
+    if (! $authPrefix) {
+      $authPrefix = "OAuth";
+    }
+
     my $response = undef;
     eval {
-        my @args = $auth ? ('Authorization', "OAuth $auth") : ();
+        my @args = $auth ? ('Authorization', "$authPrefix $auth") : ();
         my $req = POST($Conf::awe_url.'/job/'.$id.'?'.$action, @args);
         $req->method('PUT');
         my $put = $self->agent->request($req);
@@ -912,8 +958,12 @@ sub awe_job_action {
 
 # get list of jobs for query
 sub get_awe_query {
-    my ($self, $params, $auth) = @_;
+    my ($self, $params, $auth, $authPrefix) = @_;
     
+    if (! $authPrefix) {
+      $authPrefix = "OAuth";
+    }
+
     my $response = undef;
     my $query = '?query';
     if ($params && (scalar(keys %$params) > 0)) {
@@ -922,7 +972,7 @@ sub get_awe_query {
         }
     }
     eval {
-        my @args = $auth ? ('Authorization', "OAuth $auth") : ();
+        my @args = $auth ? ('Authorization', "$authPrefix $auth") : ();
         my $get = $self->agent->get($Conf::awe_url.'/job'.$query, @args);
         $response = $self->json->decode( $get->content );
     };
diff --git a/src/MGRAST/lib/resources/user.pm b/src/MGRAST/lib/resources/user.pm
index 8d069ee4..39a94281 100644
--- a/src/MGRAST/lib/resources/user.pm
+++ b/src/MGRAST/lib/resources/user.pm
@@ -270,6 +270,12 @@ sub instance {
 
     # preferences were passed
     if (defined $rest->[1] && $rest->[1] eq "preferences") {
+      my $userToken = $master->Preferences->get_objects({ user => $user, name => "WebServicesKey" });
+      if (scalar(@$userToken)) {
+	$userToken = $userToken->[0]->{value};
+      } else {
+	$self->return_data( {"ERROR" => "insufficient permissions for this user call"}, 401 );
+      }
       my $prefs = { 'type' => 'preference', 'app' => 'MGRAST', 'id' => 'mgu'.$self->user->_id, "pref" => $self->json->decode($self->cgi->param('prefs')) };
       
       my $pref_id = $master->Preferences->get_objects({ user => $user, name => "shock_pref_node" });
@@ -277,9 +283,9 @@ sub instance {
       my $retval = {};
       if (scalar(@$pref_id)) {
 	$nodeid = $pref_id->[0]->{value};
-	$retval = $self->update_shock_node($nodeid, $prefs);#, $self->mgrast_token);
+	$retval = $self->update_shock_node($nodeid, $prefs, $userToken, "mgrast");
       } else {
-	$retval = $self->set_shock_node("preferences", undef, $prefs);#, $self->mgrast_token);
+	$retval = $self->set_shock_node("preferences", undef, $prefs, $userToken, undef, "mgrast");
 	$master->Preferences->create({ user => $user, name => "shock_pref_node", value => $retval->{id} });
       }
       $self->return_data( {"OK" => $retval->{attributes}->{pref}}, 200 );

From 6534e513390bc3d745044635bf6c16ac0daae9be Mon Sep 17 00:00:00 2001
From: Tobias Paczian <paczian@mcs.anl.gov>
Date: Tue, 3 Feb 2015 04:23:53 -0600
Subject: [PATCH 14/15] fixed user preferences retrieval

---
 src/MGRAST/lib/resources/user.pm | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/src/MGRAST/lib/resources/user.pm b/src/MGRAST/lib/resources/user.pm
index 39a94281..a57500ab 100644
--- a/src/MGRAST/lib/resources/user.pm
+++ b/src/MGRAST/lib/resources/user.pm
@@ -436,7 +436,17 @@ sub instance {
       }
     }
     if ($nodeid) {
-      my $shockprefs = $self->get_shock_node($nodeid, $self->mgrast_token);
+      my $userToken;
+      foreach my $p (@$prefs) {
+	if ($p->{name} eq "WebServicesKey") {
+	  $userToken = $p->{value};
+	  last;
+	}
+      }
+      unless ($userToken) {
+	$self->return_data( {"ERROR" => "insufficient permissions for this user call"}, 401 );
+      }
+      my $shockprefs = $self->get_shock_node($nodeid, $userToken, "mgrast");
       if ($shockprefs) {
 	push(@{$user->{preferences}}, { name => 'shock', value => $shockprefs->{attributes}->{pref} } );
       }

From 910a2db67b828b11fd9c993044ae37246d4f0b80 Mon Sep 17 00:00:00 2001
From: Jared Bischof <jbischof@gmail.com>
Date: Tue, 3 Feb 2015 13:09:57 -0600
Subject: [PATCH 15/15] Edited Shock ACL interaction to match new Shock api.

---
 src/MGRAST/lib/resources/job.pm      |  2 +-
 src/MGRAST/lib/resources/notebook.pm |  2 +-
 src/MGRAST/lib/resources/resource.pm | 30 ++++++++++++++++++++++++++++
 3 files changed, 32 insertions(+), 2 deletions(-)

diff --git a/src/MGRAST/lib/resources/job.pm b/src/MGRAST/lib/resources/job.pm
index 27c796c5..bcde0039 100644
--- a/src/MGRAST/lib/resources/job.pm
+++ b/src/MGRAST/lib/resources/job.pm
@@ -362,7 +362,7 @@ sub job_action {
                 my $attr = $n->{attributes};
                 $attr->{status} = 'public';
                 $self->update_shock_node($n->{id}, $attr, $self->mgrast_token);
-                $self->edit_shock_acl($n->{id}, $self->mgrast_token, 'mgrast', 'delete', 'read');
+                $self->edit_shock_public_acl($n->{id}, $self->mgrast_token, 'put', 'read');
             }
             # update db
             $job->public(1);
diff --git a/src/MGRAST/lib/resources/notebook.pm b/src/MGRAST/lib/resources/notebook.pm
index 0b7d4e66..39e52521 100644
--- a/src/MGRAST/lib/resources/notebook.pm
+++ b/src/MGRAST/lib/resources/notebook.pm
@@ -429,7 +429,7 @@ sub shock_post_acl {
         map { $self->edit_shock_acl($id, $self->{nb_token}, $_, 'put', 'read') } @$access;
     } elsif ($self->{nb_token} && $self->{nb_info} && (@$access == 0)) {
         # public
-        $self->edit_shock_acl($id, $self->{nb_token}, $self->{nb_info}{username}, 'delete', 'read');
+        $self->edit_shock_public_acl($id, $self->{nb_token}, 'put', 'read');
     } else {
         # missing config
         print STDERR "Missing notebook config options\n";
diff --git a/src/MGRAST/lib/resources/resource.pm b/src/MGRAST/lib/resources/resource.pm
index ffbb614d..2f2ea913 100644
--- a/src/MGRAST/lib/resources/resource.pm
+++ b/src/MGRAST/lib/resources/resource.pm
@@ -701,6 +701,36 @@ sub edit_shock_acl {
     }
 }
 
+# add or delete public from a node ACL
+sub edit_shock_public_acl {
+    my ($self, $id, $auth, $action, $acl, $authPrefix) = @_;
+
+    if (! $authPrefix) {
+      $authPrefix = "OAuth";
+    }
+
+    my $response = undef;
+    my $url = $Conf::shock_url.'/node/'.$id.'/acl/public_'.$acl;
+    eval {
+        my $tmp = undef;
+        if ($action eq 'delete') {
+            $tmp = $self->agent->delete($url, 'Authorization' => "$authPrefix $auth");
+        } elsif ($action eq 'put') {
+            $tmp = $self->agent->put($url, 'Authorization' => "$authPrefix $auth");
+        } else {
+            $self->return_data( {"ERROR" => "Invalid Shock ACL action: $action"}, 500 );
+        }
+        $response = $self->json->decode( $tmp->content );
+    };
+    if ($@ || (! ref($response))) {
+        return undef;
+    } elsif (exists($response->{error}) && $response->{error}) {
+        $self->return_data( {"ERROR" => "Unable to $action public ACL for '$acl' to node $id in Shock: ".$response->{error}[0]}, $response->{status} );
+    } else {
+        return $response->{data};
+    }
+}
+
 # create node with optional file and/or attributes
 # file is json struct by default
 sub set_shock_node {