From c3bbdb7c72dfc95f13670ecd6bfaa0df4127cc6b Mon Sep 17 00:00:00 2001
From: Chris Fields <cjfields@illinois.edu>
Date: Mon, 12 Sep 2016 22:43:46 -0500
Subject: [PATCH] logic fix for #182

---
 Bio/DB/Taxonomy/entrez.pm | 59 ++++++++++++++++++++++++-----------------------
 t/RemoteDB/Taxonomy.t     | 30 ++++++++++++++++++++++--
 2 files changed, 58 insertions(+), 31 deletions(-)

diff --git a/Bio/DB/Taxonomy/entrez.pm b/Bio/DB/Taxonomy/entrez.pm
index ffc0dac2f..67d255f8f 100644
--- a/Bio/DB/Taxonomy/entrez.pm
+++ b/Bio/DB/Taxonomy/entrez.pm
@@ -321,7 +321,6 @@ sub get_taxon {
         $taxonid = join(',', @uncached);
         
         $p{'id'} = $taxonid;
-        $self->debug("id is $taxonid\n");
 
         my $twig = $self->_run_query($self->_build_url($EntrezFetch, \%p));
         my $root = $twig->root;
@@ -357,35 +356,37 @@ sub get_taxon {
             # requested node, we may as well cache data for the ancestors to
             # reduce the number of accesses to website in future
             my $lineage_ex = $taxon->first_child('LineageEx');
-            my ($ancestor, $lineage_data, @taxa);
-            foreach my $lineage_taxon ($lineage_ex->children) {
-                my $lineage_taxid = $lineage_taxon->first_child_text('TaxId');
-                
-                if (exists $DATA_CACHE->{minimal_info}->{$lineage_taxid} || exists $DATA_CACHE->{full_info}->{$lineage_taxid}) {
-                    $lineage_data = $DATA_CACHE->{minimal_info}->{$lineage_taxid} || $DATA_CACHE->{full_info}->{$lineage_taxid};
-                    next;
-                }
-                else {
-                    $lineage_data = {};
-                }
-                
-                $lineage_data->{id} = $lineage_taxid;
-                $lineage_data->{scientific_name} = $lineage_taxon->first_child_text('ScientificName');
-                $lineage_data->{rank} = $lineage_taxon->first_child_text('Rank');
-                
-                $RELATIONS->{ancestors}->{$lineage_taxid} = $ancestor->{id} if $ancestor;
-                
-                $DATA_CACHE->{minimal_info}->{$lineage_taxid} = $lineage_data;
-            } continue { $ancestor = $lineage_data; unshift(@taxa, $lineage_data); }
-            
-            $RELATIONS->{ancestors}->{$taxid} = $ancestor->{id} if $ancestor;
-            
-            # go through the lineage in reverse so we can remember the children
-            my $child = $data;
-            foreach my $lineage_data (@taxa) {
-                $RELATIONS->{children}->{$lineage_data->{id}}->{$child->{id}} = 1;
-            } continue { $child = $lineage_data; }
+            if (defined $lineage_ex) {
+                my ($ancestor, $lineage_data, @taxa);
+                foreach my $lineage_taxon ($lineage_ex->children) {
+                    my $lineage_taxid = $lineage_taxon->first_child_text('TaxId');
+                    
+                    if (exists $DATA_CACHE->{minimal_info}->{$lineage_taxid} || exists $DATA_CACHE->{full_info}->{$lineage_taxid}) {
+                        $lineage_data = $DATA_CACHE->{minimal_info}->{$lineage_taxid} || $DATA_CACHE->{full_info}->{$lineage_taxid};
+                        next;
+                    }
+                    else {
+                        $lineage_data = {};
+                    }
+                    
+                    $lineage_data->{id} = $lineage_taxid;
+                    $lineage_data->{scientific_name} = $lineage_taxon->first_child_text('ScientificName');
+                    $lineage_data->{rank} = $lineage_taxon->first_child_text('Rank');
+                    
+                    $RELATIONS->{ancestors}->{$lineage_taxid} = $ancestor->{id} if $ancestor;
+                    
+                    $DATA_CACHE->{minimal_info}->{$lineage_taxid} = $lineage_data;
+                } continue { $ancestor = $lineage_data; unshift(@taxa, $lineage_data); }
             
+                $RELATIONS->{ancestors}->{$taxid} = $ancestor->{id} if $ancestor;
+
+                # go through the lineage in reverse so we can remember the children
+                my $child = $data;
+                foreach my $lineage_data (@taxa) {
+                    $RELATIONS->{children}->{$lineage_data->{id}}->{$child->{id}} = 1;
+                } continue { $child = $lineage_data; }
+            }
+
             delete $DATA_CACHE->{minimal_info}->{$taxid};
             $DATA_CACHE->{full_info}->{$taxid} = $data;
             push(@results, $self->_make_taxon($data));
diff --git a/t/RemoteDB/Taxonomy.t b/t/RemoteDB/Taxonomy.t
index f7b5951fa..3a7ddcf65 100644
--- a/t/RemoteDB/Taxonomy.t
+++ b/t/RemoteDB/Taxonomy.t
@@ -8,7 +8,7 @@ BEGIN {
     use Bio::Root::Test;
 
     test_begin(
-        -tests            => 202,
+        -tests            => 214,
         -requires_modules => [qw(DB_File
                                  LWP::UserAgent
                                  XML::Twig )]
@@ -103,7 +103,7 @@ for my $db ($db_entrez, $db_flatfile) {
         is ${$n->name('scientific')}[0], $n->node_name;
 
         my %common_names = map { $_ => 1 } $n->common_names;
-        is keys %common_names, 3, ref($db).": common names";
+        cmp_ok keys %common_names, '>=', 3, ref($db).": common names";
         ok exists $common_names{human};
         ok exists $common_names{man};
 
@@ -446,3 +446,29 @@ ok $node2 = $db_list->get_taxon( -names => [ 'o__Chroococcales', 'g__Microcoleus
 is $node2->scientific_name, $node1->scientific_name;
 is $node2->id, $node1->id;
 is $node2->internal_id, $node1->internal_id;
+
+# tests for #182
+SKIP: {
+    test_skip(-tests => 12, -requires_networking => 1);
+
+    my $db=Bio::DB::Taxonomy->new(-source=>"entrez");
+    
+    my @taxa = qw(viruses Deltavirus unclassified plasmid);
+    
+    for my $taxon (@taxa) {
+        test_taxid($db, $taxon);
+    }
+    
+    sub test_taxid {
+        my ($db, $taxa) = @_;
+        my @taxonids = $db->get_taxonids($taxa);
+        cmp_ok(scalar(@taxonids), '>', 0, "Got IDs returned for $taxa:".join(',', @taxonids));
+        my $taxon; 
+        lives_ok { $taxon = $db->get_taxon(-taxonid => pop @taxonids) } "IDs generates a Bio::Taxonomy::Node";
+        if (defined $taxon) {
+            like( $taxon->scientific_name, qr/$taxa/i, "Name returned matches $taxa");
+        } else {
+            ok(0, "No taxon object returned for $taxa");
+        }
+    }
+}
-- 
2.11.4.GIT