that is the output from the patch_test_databases.pl

modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm

@@ -259,15 +259,8 @@ sub store {
 
   $sth->execute();
 
-  if (defined($sth->err)){ # is defined if server sends a message
-    if ($sth->err eq 0){
+  if (defined($sth->err) && $sth->err eq 0){ # is a warning if 0 and defined
       warning('SQL warning : ' . $sth->errstr ."\n");
-    }
-    elsif ($sth->err){ # not an empty string or zero
-      warning('SQL error : ' . $sth->errstr ."\n");
-    }
-    elsif ($sth->err eq ''){ # SQL info messages 
-    }
   }
  
   my $dbID = $self->last_insert_id('protein_feature_id', undef, 'protein_feature');

modules/t/test-genome-DBs/circ/core/meta.txt

@@ -105,3 +105,4 @@
 105	\N	patch	patch_86_87_c.sql|datetime_default_NULL
 106	\N	patch	patch_87_88_a.sql|schema_version
 107	\N	patch	patch_87_88_b.sql|seq_region_name_255
+108	\N	patch	patch_87_88_c.sql|protein_featue_uniqueness

modules/t/test-genome-DBs/circ/core/table.sql

@@ -477,7 +477,7 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=108 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=109 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -664,7 +664,7 @@ CREATE TABLE `protein_feature` (
   `external_data` text COLLATE latin1_bin,
   `hit_description` text COLLATE latin1_bin,
   PRIMARY KEY (`protein_feature_id`),
-  UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
+  UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`,`analysis_id`),
   KEY `translation_idx` (`translation_id`),
   KEY `hitname_idx` (`hit_name`),
   KEY `analysis_idx` (`analysis_id`)

modules/t/test-genome-DBs/mus_musculus/core/meta.txt

@@ -162,3 +162,4 @@
 1674	\N	patch	patch_86_87_c.sql|datetime_default_NULL
 1675	\N	patch	patch_87_88_a.sql|schema_version
 1676	\N	patch	patch_87_88_b.sql|seq_region_name_255
+1677	\N	patch	patch_87_88_c.sql|protein_featue_uniqueness

modules/t/test-genome-DBs/mus_musculus/core/table.sql

@@ -477,7 +477,7 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=1677 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=1678 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -664,7 +664,7 @@ CREATE TABLE `protein_feature` (
   `external_data` text COLLATE latin1_bin,
   `hit_description` text COLLATE latin1_bin,
   PRIMARY KEY (`protein_feature_id`),
-  UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
+  UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`,`analysis_id`),
   KEY `translation_idx` (`translation_id`),
   KEY `hitname_idx` (`hit_name`),
   KEY `analysis_idx` (`analysis_id`)

modules/t/test-genome-DBs/nameless/core/meta.txt

@@ -83,3 +83,4 @@
 137	\N	patch	patch_86_87_c.sql|datetime_default_NULL
 138	\N	patch	patch_87_88_a.sql|schema_version
 139	\N	patch	patch_87_88_b.sql|seq_region_name_255
+140	\N	patch	patch_87_88_c.sql|protein_featue_uniqueness

modules/t/test-genome-DBs/nameless/core/table.sql

@@ -467,7 +467,7 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=140 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=141 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -654,7 +654,7 @@ CREATE TABLE `protein_feature` (
   `external_data` text COLLATE latin1_bin,
   `hit_description` text COLLATE latin1_bin,
   PRIMARY KEY (`protein_feature_id`),
-  UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
+  UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`,`analysis_id`),
   KEY `translation_idx` (`translation_id`),
   KEY `hitname_idx` (`hit_name`),
   KEY `analysis_idx` (`analysis_id`)