From a3bc098cc1809172e670ff4e1c05f28e32217d7f Mon Sep 17 00:00:00 2001
From: Naama Menda <nm249@cornell.edu>
Date: Sun, 17 Apr 2011 15:29:41 -0400
Subject: [PATCH] any user with db permissions should be able to call
 $metadata->store

---
 lib/CXGN/Chado/Stock.pm         | 14 +++++++++++---
 lib/CXGN/Metadata/Metadbdata.pm | 13 +++++++------
 2 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/lib/CXGN/Chado/Stock.pm b/lib/CXGN/Chado/Stock.pm
index 7b5326e..48a1886 100644
--- a/lib/CXGN/Chado/Stock.pm
+++ b/lib/CXGN/Chado/Stock.pm
@@ -422,10 +422,18 @@ sub associate_allele {
     my $metadata = CXGN::Metadata::Metadbdata->new($metadata_schema);
     $metadata->set_create_person_id($sp_person_id);
     my $metadata_id = $metadata->store()->get_metadata_id();
-    #store the image_id - stock_id link
-    my $q = "INSERT INTO phenome.stock_image (stock_id, image_id, metadata_id) VALUES (?,?,?) RETURNING stock_image_id";
+    #check if the allele is already linked
+    my $ids =  $self->get_schema->storage->dbh->selectcol_arrayref
+        ( "SELECT stock_allele_id FROM phenome.stock_allele WHERE stock_id = ? AND allele_id = ?",
+          undef,
+          $self->get_stock_id,
+          $allele_id
+        );
+    if ($ids) { warn "Allele $allele_id is already linked with stock " . $self->get_stock_id ; }
+#store the allele_id - stock_id link
+    my $q = "INSERT INTO phenome.stock_allele (stock_id, allele_id, metadata_id) VALUES (?,?,?) RETURNING stock_allele_id";
     my $sth  = $self->get_schema->storage->dbh->prepare($q);
-    $sth->execute($self->stock_id, $allele_id, $metadata_id);
+    $sth->execute($self->get_stock_id, $allele_id, $metadata_id);
     my ($id) =  $sth->fetchrow_array;
     return $id;
 }
diff --git a/lib/CXGN/Metadata/Metadbdata.pm b/lib/CXGN/Metadata/Metadbdata.pm
index 8611fe8..e19ed08 100644
--- a/lib/CXGN/Metadata/Metadbdata.pm
+++ b/lib/CXGN/Metadata/Metadbdata.pm
@@ -1310,9 +1310,10 @@ sub store {
                      ->dbh()
                      ->selectrow_array("SELECT current_user");
 
-    if ($user ne 'postgres') {
-	croak("USER ACCESS ERROR: Only postgres user can store data.\n");
-    }
+    # should be open for any user with db permissions
+    #if  ($user ne 'postgres') {
+    #croak("USER ACCESS ERROR: Only postgres user can store data.\n");
+    #}
 
 
     my $metadata_row = $self->get_mdmetadata_row();
@@ -1376,13 +1377,13 @@ sub new_data_store {
     my $creation_user = $self->get_object_creation_user();
 
     my $statement = "SELECT sp_person_id FROM sgn_people.sp_person WHERE username=?";
-    my $creation_user_id = $self->get_schema()
+    my $creation_user_id = $self->get_create_person_id || $self->get_schema()
         ->storage()
         ->dbh()
         ->selectrow_array($statement, undef, ($creation_user));
 
-    unless (defined $creation_user) {
-	my $error = "STORE ERROR: None creation user was supplied to CXGN::Metadata::Metadbdata object.\n";
+    unless (defined $creation_user || defined $creation_user_id ) {
+	my $error = "STORE ERROR: No creation user nor id was supplied to CXGN::Metadata::Metadbdata object.\n";
 	$error .= " This parameter is a mandatory parameter for store functions\n";
 	croak($error);
     }
-- 
2.11.4.GIT