Merge pull request #9 from EMBL-EBI-GCA/dr_faang_seed

FAANG seeding changes
EMBL-EBI-GCA · Jun 29, 2016 · f8ae446 · f8ae446
2 parents f770110 + b3d0195
commit f8ae446
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Showing 12 changed files with 250 additions and 110 deletions.
diff --git a/modules/ReseqTrack/Attribute.pm b/modules/ReseqTrack/Attribute.pm
@@ -15,12 +15,13 @@ sub new{
   my ($class, @args) = @_;
   my $self = $class->SUPER::new(@args);
 
-  my ($table_name, $other_id, $attribute_name, $attribute_value ) =
-      rearrange([qw(TABLE_NAME OTHER_ID ATTRIBUTE_NAME ATTRIBUTE_VALUE ) ], @args);
+  my ($table_name, $other_id, $attribute_name, $attribute_value, $attribute_units ) =
+      rearrange([qw(TABLE_NAME OTHER_ID ATTRIBUTE_NAME ATTRIBUTE_VALUE ATTRIBUTE_UNITS) ], @args);
   $self->table_name($table_name);
   $self->other_id($other_id);
   $self->attribute_name($attribute_name);
   $self->attribute_value($attribute_value);
+  $self->attribute_units($attribute_units);
   return $self;
 }
 
@@ -69,6 +70,13 @@ sub attribute_value{
   return $self->{attribute_value};
 }
 
+sub attribute_units{
+  my ($self, $arg) = @_;
+  if(defined $arg){
+    $self->{attribute_units} = $arg;
+  }
+  return $self->{attribute_units};
+}
 
 
 

diff --git a/modules/ReseqTrack/DBSQL/AttributeAdaptor.pm b/modules/ReseqTrack/DBSQL/AttributeAdaptor.pm
@@ -21,7 +21,7 @@ sub new {
 
 sub columns{
   return "attribute.attribute_id, attribute.other_id, attribute.table_name, ".
-      "attribute.attribute_name, attribute.attribute_value";
+      "attribute.attribute_name, attribute.attribute_value, attribute.attribute_units";
 }
 
 sub table_name{
@@ -89,7 +89,8 @@ sub store{
   	$attribute->dbID($exists->dbID);
   	$attribute->adaptor($self);
 
-    if($update && $exists->attribute_value ne $attribute->attribute_value){
+    if($update &&
+      ($exists->attribute_value ne $attribute->attribute_value || $exists->attribute_units // '' ne $attribute->attribute_units // '')){
       $attribute->dbID($exists->dbID);
 #      print "existing stats id is " . $exists->dbID . "\n";
 #			print "reassigned stats id is: " . $attribute->dbID . "\n";
@@ -101,12 +102,13 @@ sub store{
 
 
   my $sql = "insert into attribute (other_id, table_name, attribute_name, ".
-      "attribute_value) values(?, ?, ?, ?)";
+      "attribute_value, attribute_units) values(?, ?, ?, ?, ?)";
   my $sth = $self->prepare($sql);
   $sth->bind_param(1, $attribute->other_id);
   $sth->bind_param(2, $attribute->table_name);
   $sth->bind_param(3, $attribute->attribute_name);
   $sth->bind_param(4, $attribute->attribute_value);
+  $sth->bind_param(5, $attribute->attribute_units);
   $sth->execute;
 
   my $dbID = $sth->{'mysql_insertid'};
@@ -125,16 +127,19 @@ sub update{
       ", other_id = ? ".
       ", attribute_name = ? ".
       ", attribute_value = ? ".
+      ", attribute_units = ? ".
       "where attribute_id = ? ";
   my $sth = $self->prepare($sql);
 
   $sth->bind_param(1, $attribute->table_name);
   $sth->bind_param(2, $attribute->other_id);
   $sth->bind_param(3, $attribute->attribute_name);
   $sth->bind_param(4, $attribute->attribute_value);
-  $sth->bind_param(5, $attribute->dbID);  
+  $sth->bind_param(5, $attribute->attribute_units);
+  $sth->bind_param(6, $attribute->dbID);  
   $sth->execute; 
   $sth->finish; 
+
   return $attribute; 
 }
 
@@ -149,6 +154,7 @@ sub object_from_hashref{
     -table_name => $hashref->{table_name},
     -attribute_name => $hashref->{attribute_name},
     -attribute_value => $hashref->{attribute_value},
+    -attribute_units => $hashref->{attribute_units},
       );
   return $attribute;
 }

diff --git a/modules/ReseqTrack/DBSQL/BaseAdaptor.pm b/modules/ReseqTrack/DBSQL/BaseAdaptor.pm
@@ -198,12 +198,12 @@ sub store_attributes{
   my ($self, $object, $update) = @_;
   throw("Can't store attributes for ".$object." that isnt a ReseqTrack::HasHistory ")  unless($object->isa("ReseqTrack::HasHistory"));
   my $attr_a = $self->db->get_AttributeAdaptor();
-  
+
   if($object->attributes){
-    foreach my $statistics(@{$object->attributes}){
-      $statistics->other_id($object->dbID);
-      $statistics->table_name($object->object_table_name);
-      $attr_a->store($statistics, $update);
+    foreach my $attribute(@{$object->attributes}){
+      $attribute->other_id($object->dbID);
+      $attribute->table_name($object->object_table_name);
+      $attr_a->store($attribute, $update);
     }
   }
 }

diff --git a/modules/ReseqTrack/DBSQL/ERA/BaseEraAdaptor.pm b/modules/ReseqTrack/DBSQL/ERA/BaseEraAdaptor.pm
@@ -65,14 +65,15 @@ sub attach_attributes_from_xml {
 
         my $key   = uc( $element->first_child_text('TAG') );
         my $value = $element->first_child_text('VALUE');
+        my $units = $element->first_child_text('UNITS');
 
         for ( $key, $value ) {
           s/^\s+|\s+$//g;
         }
 
         if ($value) {
           push @attributes,
-            create_attribute_for_object( $object, $key, $value );
+            create_attribute_for_object( $object, $key, $value, $units );
         }
        }
     }