MG-RAST · teharrison · Feb 3, 2015 · Jan 23, 2015 · Jan 23, 2015 · Jan 26, 2015
diff --git a/src/MGRAST/lib/Auth.pm b/src/MGRAST/lib/Auth.pm
@@ -22,31 +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 => $us, name => "shock_pref_node" });
+            if (scalar(@$prefs)) {
+              my $nodeid = $prefs->[0]->{value};
+              my $response = undef;
+              my $json = new JSON;
+              $json = $json->utf8();
+              $json->max_size(0);
+              $json->allow_nonref;
+              my $agent = LWP::UserAgent->new;
+              eval {
+                my @args = ('Authorization', "mgrast ".$pref->[0]->{value});
+                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/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]));

diff --git 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/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)';

diff --git 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/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 {
@@ -239,13 +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;	
+	        $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 );
            }