Merge branch 'develop' of github.com:MG-RAST/MG-RAST into develop

MG-RAST · Jan 8, 2013 · 624bce6 · 624bce6
2 parents 69c7a97 + 0e44334
commit 624bce6
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Showing 4 changed files with 10 additions and 10 deletions.
diff --git a/src/MGRAST/lib/resources2/abundanceprofile.pm b/src/MGRAST/lib/resources2/abundanceprofile.pm
@@ -114,7 +114,7 @@ sub instance {
     $job = $job->[0];
 
     # check rights
-    unless ($job->{public} || exists($self->rights->{$id})) {
+    unless ($job->{public} || exists($self->rights->{$id}) || ($self->user && $self->user->has_right(undef, 'view', 'metagenome', '*'))) {
         $self->return_data( {"ERROR" => "insufficient permissions to view this data"}, 401 );
     }
 

diff --git a/src/MGRAST/lib/resources2/m5nr.pm b/src/MGRAST/lib/resources2/m5nr.pm
@@ -142,7 +142,7 @@ sub static {
             $self->return_data({"ERROR" => "invalid min_level for m5nr/ontology: ".$min_lvl." - valid types are [".join(", ", @ont_hier)."]"}, 500);
         }
         if ($pname && ($min_lvl ne 'level1')) {
-            @$data = $mgdb->get_hierarchy_slice('ontology', $source, $pname, $min_lvl);
+            $data = $mgdb->get_hierarchy_slice('ontology', $source, $pname, $min_lvl);
         } else {
             @$data = values %{ $mgdb->get_hierarchy('ontology', $source, undef, undef, $min_lvl) };
         }
@@ -155,7 +155,7 @@ sub static {
             $self->return_data({"ERROR" => "invalid min_level for m5nr/taxonomy: ".$min_lvl." - valid types are [".join(", ", @tax_hier)."]"}, 500);
         }
         if ($pname && ($min_lvl ne 'tax_domain')) {
-            @$data = $mgdb->get_hierarchy_slice('organism', undef, $pname, $min_lvl);
+            $data = $mgdb->get_hierarchy_slice('organism', undef, $pname, $min_lvl);
         } else {
             @$data = values %{ $mgdb->get_hierarchy('organism', undef, undef, undef, $min_lvl) };
         }

diff --git a/src/MGRAST/lib/resources2/matrix.pm b/src/MGRAST/lib/resources2/matrix.pm
@@ -340,7 +340,7 @@ sub prepare_data {
         push @$brows, { id => $rid, metadata => $rmd };
     }
     my $mddb = MGRAST::Metadata->new();
-    my $meta = $mddb->get_jobs_metadata_fast([keys %$col_ids], 1);
+    my $meta = $mddb->get_jobs_metadata_fast($data, 1);
     my $name = $mgdb->_name_map();
     foreach my $cid (sort {$col_ids->{$a} <=> $col_ids->{$b}} keys %$col_ids) {
         my $cmd = exists($meta->{$cid}) ? $meta->{$cid} : undef;

diff --git a/src/MGRAST/lib/resources2/metagenome.pm b/src/MGRAST/lib/resources2/metagenome.pm
@@ -23,12 +23,12 @@ sub new {
                             "library"  => [ 'reference library', 'reference to the related library object' ],
                             "sample"   => [ 'reference sample', 'reference to the related sample object' ],
                             "project"  => [ 'reference project', 'reference to the project object' ],
-                            "metadata" => [ 'hash',    'key value pairs describing metadata' ],
-                            "created"  => [ 'date',    'time the object was first created' ],
+                            "metadata" => [ 'hash', 'key value pairs describing metadata' ],
+                            "created"  => [ 'date', 'time the object was first created' ],
                             "version"  => [ 'integer', 'version of the object' ],
-                            "url"      => [ 'uri',     'resource location of this object instance' ],
-                            "status"   => ['cv', [['public', 'object is public'],
-           										  ['private', 'object is private']]],
+                            "url"      => [ 'uri', 'resource location of this object instance' ],
+                            "status"   => [ 'cv', [ ['public', 'object is public'],
+						    ['private', 'object is private'] ] ],
                             "sequence_type" => [ 'string', 'sequencing type' ]
                           };
     return $self;
@@ -119,7 +119,7 @@ sub instance {
     $job = $job->[0];
 
     # check rights
-    unless ($job->{public} || exists($self->rights->{$id})) {
+    unless ($job->{public} || exists($self->rights->{$id}) || ($self->user && $self->user->has_right(undef, 'view', 'metagenome', '*'))) {
         $self->return_data( {"ERROR" => "insufficient permissions to view this data"}, 401 );
     }