Xref table overhaul. Uniqueness enforced, coupled with insert-then-query...

Xref table overhaul. Uniqueness enforced, coupled with insert-then-query execution order in DBEntryAdaptor.

Data patching is slow.

modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm

@@ -132,7 +132,7 @@ sub fetch_by_dbID {
                            -type                => $type,
                            -secondary_db_name   => $secondary_db_name,
                            -secondary_db_table  => $secondary_db_table,
-			   -description         => $description
+			               -description         => $description
           );
 
 
@@ -623,7 +623,7 @@ sub fetch_by_db_accession {
 
 =head2 store
 
-  Arg [1]    : Bio::EnsEMBL::DBEntry $exObj
+  Arg [1]    : Bio::EnsEMBL::DBEntry $dbEntry
                The DBEntry (xref) to be stored
   Arg [2]    : Int $ensID
                The dbID of an EnsEMBL object to associate with this external
@@ -648,7 +648,7 @@ sub fetch_by_db_accession {
 =cut
 
 sub store {
-  my ( $self, $exObj, $ensID, $ensType, $ignore_release ) = @_;
+  my ( $self, $dbEntry, $ensID, $ensType, $ignore_release ) = @_;
 
   my $dbJustInserted;
 
@@ -658,7 +658,6 @@ sub store {
   #
   my $ensembl_id;
 
-
   if ( defined($ensID) ) {
     if ( $ensID =~ /^\d+$/ ) {
       $ensembl_id = $ensID;
@@ -683,222 +682,59 @@ sub store {
       throw("Invalid dbID passed to DBEntryAdaptor->store()");
     }
   }
-
-  #
-  # Check for the existance of the external_db, throw if it does not exist
-  #
-
-  my ($dbRef, $release_clause);
-
-  if ( !$ignore_release ) {
-
-	if(defined $exObj->release()){
-	  $release_clause = " AND db_release = ?";
-	}
-	else{
-	  $release_clause = " AND db_release is NULL";
-	}
-
-
-    my $sth = $self->prepare( "
-     SELECT external_db_id
-       FROM external_db
-      WHERE db_name    = ?
-        $release_clause" );
-
-    $sth->bind_param( 1, $exObj->dbname(),  SQL_VARCHAR );
-    $sth->bind_param( 2, $exObj->release(), SQL_VARCHAR ) if defined $exObj->release();
-    $sth->execute();
-
-    ($dbRef) = $sth->fetchrow_array();
-	$sth->finish();
-
-    if ( !$dbRef ) {
-      throw(
-             sprintf( "external_db [%s] release [%s] does not exist",
-                      $exObj->dbname(), $exObj->release() ) );
-    }
-  } else {
-
-    my $sth = $self->prepare( "
-     SELECT external_db_id
-       FROM external_db
-      WHERE db_name = ? " );
-
-    $sth->bind_param( 1, $exObj->dbname(), SQL_VARCHAR );
-
-    $sth->execute();
-
-    ($dbRef) = $sth->fetchrow_array();
-
-    if ( !$dbRef ) {
-      throw(
-          sprintf( "external_db [%s] does not exist", $exObj->dbname() )
-      );
-    }
-  }
-
-  #
-  # Check for the existance of the external reference, add it if not present
-  #
-
-  my $sql =  "SELECT xref_id FROM xref
-                WHERE external_db_id = ?
-                  AND dbprimary_acc  = ?
-                  AND version        = ?";
-
-  if(defined $exObj->info_type){
-    $sql .= " AND  info_type      = ?";
-  }
-  else{
-    $sql .= " AND info_type is null";
-  }
-
-  if(defined $exObj->info_text){
-    $sql .= " AND  info_text      = ?";
-  }
-  else{
-    $sql .= " AND info_text is null";
-  }
-
-  my $sth = $self->prepare($sql);
-
-  $sth->bind_param(1,$dbRef,SQL_INTEGER);
-  $sth->bind_param(2,$exObj->primary_id,SQL_VARCHAR);
-  $sth->bind_param(3,$exObj->version,SQL_VARCHAR);
-
-  my $i = 4;
-  if(defined $exObj->info_type){
-    $sth->bind_param($i++,$exObj->info_type,SQL_VARCHAR);
-  }
-  if(defined $exObj->info_text){
-    $sth->bind_param($i++,$exObj->info_text,SQL_VARCHAR);
-  }
-  $sth->execute();
-
-  my ($dbX) = $sth->fetchrow_array();
-
-  $sth->finish();
-  if(!$dbX) {
-    if(!$exObj->primary_id()) {
-      throw("DBEntry cannot be stored without a primary_id attribute.");
-    }
-
-    #
-    # store the new xref
-    #
-    $sth = $self->prepare( "
-       INSERT ignore INTO xref
-       SET dbprimary_acc = ?,
-           display_label = ?,
-           version = ?,
-           description = ?,
-           external_db_id = ?,
-           info_type = ?,
-           info_text = ?");
-    $sth->bind_param(1, $exObj->primary_id,SQL_VARCHAR);
-    $sth->bind_param(2, $exObj->display_id,SQL_VARCHAR);
-    $sth->bind_param(3, $exObj->version,SQL_VARCHAR);
-    $sth->bind_param(4, $exObj->description,SQL_VARCHAR);
-    $sth->bind_param(5, $dbRef,SQL_INTEGER);
-    $sth->bind_param(6, $exObj->info_type, SQL_VARCHAR);
-    $sth->bind_param(7, $exObj->info_text, SQL_VARCHAR);
-
-    $sth->execute();
-
-    $dbX = $sth->{'mysql_insertid'};
-    $exObj->dbID($dbX);
-    $sth->finish();
-    #
-    # store the synonyms for the new xref
-    #
-    my $synonym_check_sth = $self->prepare(
-              "SELECT xref_id, synonym
-               FROM external_synonym
-               WHERE xref_id = ?
-               AND synonym = ?");
-
-    my $synonym_store_sth = $self->prepare(
-        "INSERT ignore INTO external_synonym
-         SET xref_id = ?, synonym = ?");
-
-    my $synonyms = $exObj->get_all_synonyms();
-    foreach my $syn ( @$synonyms ) {
-	$synonym_check_sth->bind_param(1,$dbX,SQL_INTEGER);
-	$synonym_check_sth->bind_param(2,$syn,SQL_VARCHAR);
-	$synonym_check_sth->execute();
-      my ($dbSyn) = $synonym_check_sth->fetchrow_array();
-	$synonym_store_sth->bind_param(1,$dbX,SQL_INTEGER);
-	$synonym_store_sth->bind_param(2,$syn,SQL_VARCHAR);
-	$synonym_store_sth->execute() if(!$dbSyn);
+  
+  
+  
+    # Ensure external_db contains a record of the intended xref source
+    my $dbRef;
+    $dbRef = $self->_check_external_db($dbEntry,$ignore_release);
+
+    # Attempt to insert DBEntry
+    my $xref_id = $self->_store_or_fetch_xref($dbEntry,$dbRef);
+    $dbEntry->dbID($xref_id); #keeps DBEntry in sync with database
+    ### Attempt to create an object->xref mapping
+    if ($ensembl_id) {$self->_store_object_xref_mapping($ensembl_id,$dbEntry,$ensType)};
+    
+    return $xref_id;
+}
+    
+sub _store_object_xref_mapping {
+    my $self = shift;
+    my $ensembl_id = shift;
+    my $dbEntry = shift;
+    my $ensembl_type = shift;
+    
+    if (not defined ($ensembl_type)) { warning("No Ensembl data type provided for new xref");}
+    
+    my $analysis_id;
+    if ( $dbEntry->analysis() ) {
+        $analysis_id = $self->db()->get_AnalysisAdaptor->store( $dbEntry->analysis() );
+    } else {
+        $analysis_id = 0; ## This used to be undef, but uniqueness in mysql requires a value
     }
-    $synonym_check_sth->finish();
-    $synonym_store_sth->finish();
-  } elsif (! defined( $exObj->dbID() ) ) {
-    $exObj->dbID($dbX);
-  }
-
-  if ( defined($ensembl_id) ) {
-    #
-    # check if the object mapping was already stored
-    #
-    $sth = $self->prepare(
-      qq(
-SELECT  xref_id
-FROM    object_xref
-WHERE   xref_id = ?
-  AND   ensembl_object_type = ?
-  AND   ensembl_id = ?
-  AND   (   linkage_annotation = ?
-  OR        linkage_annotation IS NULL  )) );
-
-    $sth->bind_param( 1, $dbX,                         SQL_INTEGER );
-    $sth->bind_param( 2, $ensType,                     SQL_VARCHAR );
-    $sth->bind_param( 3, $ensembl_id,                  SQL_INTEGER );
-    $sth->bind_param( 4, $exObj->linkage_annotation(), SQL_VARCHAR );
-
+    
+    my $sth = $self->prepare(qq(
+        INSERT IGNORE INTO object_xref
+          SET   xref_id = ?,
+                ensembl_object_type = ?,
+                ensembl_id = ?,
+                linkage_annotation = ?,
+                analysis_id = ? ) 
+        );
+    $sth->bind_param( 1, $dbEntry->dbID(),              SQL_INTEGER );
+    $sth->bind_param( 2, $ensembl_type,                 SQL_VARCHAR );
+    $sth->bind_param( 3, $ensembl_id,                   SQL_INTEGER );
+    $sth->bind_param( 4, $dbEntry->linkage_annotation(),SQL_VARCHAR );
+    $sth->bind_param( 5, $analysis_id,                  SQL_INTEGER );
     $sth->execute();
-
-    my ($tst) = $sth->fetchrow_array();
-
     $sth->finish();
-
-    if ( !$tst ) {
-      #
-      # Store the reference to the internal ensembl object
-      #
-      my $analysis_id;
-      if ( $exObj->analysis() ) {
-        $analysis_id =
-          $self->db()->get_AnalysisAdaptor->store( $exObj->analysis() );
-      } else {
-        $analysis_id = undef;
-      }
-
-      $sth = $self->prepare(
-        qq(
-INSERT INTO object_xref
-  SET   xref_id = ?,
-        ensembl_object_type = ?,
-        ensembl_id = ?,
-        linkage_annotation = ?,
-        analysis_id = ? ) );
-
-      $sth->bind_param( 1, $dbX,                         SQL_INTEGER );
-      $sth->bind_param( 2, $ensType,                     SQL_VARCHAR );
-      $sth->bind_param( 3, $ensembl_id,                  SQL_INTEGER );
-      $sth->bind_param( 4, $exObj->linkage_annotation(), SQL_VARCHAR );
-      $sth->bind_param( 5, $analysis_id,                 SQL_INTEGER );
-
-      $sth->execute();
-      $exObj->adaptor($self);
-      my $Xidt = $sth->{'mysql_insertid'};
-
-      #
-      # If this is an IdentityXref need to store in that table too
-      # If its OntologyXref add the linkage type to ontology_xref table
-      #
-      if ( $exObj->isa('Bio::EnsEMBL::IdentityXref') ) {
+    my $object_xref_id = $self->last_insert_id();
+    
+    $dbEntry->adaptor($self); # hand Adaptor to dbEntry for future use with OntologyXrefs
+    
+    if ($object_xref_id) {
+        #no existing object_xref, therefore 
+        if ( $dbEntry->isa('Bio::EnsEMBL::IdentityXref') ) {
         $sth = $self->prepare( "
              INSERT ignore INTO identity_xref
              SET object_xref_id = ?,
@@ -911,43 +747,170 @@ INSERT INTO object_xref
              cigar_line = ?,
              score = ?,
              evalue = ?" );
-        $sth->bind_param( 1, $Xidt,                    SQL_INTEGER );
-        $sth->bind_param( 2, $exObj->xref_identity,    SQL_INTEGER );
-        $sth->bind_param( 3, $exObj->ensembl_identity, SQL_INTEGER );
-        $sth->bind_param( 4, $exObj->xref_start,       SQL_INTEGER );
-        $sth->bind_param( 5, $exObj->xref_end,         SQL_INTEGER );
-        $sth->bind_param( 6, $exObj->ensembl_start,    SQL_INTEGER );
-        $sth->bind_param( 7, $exObj->ensembl_end,      SQL_INTEGER );
-        $sth->bind_param( 8,  $exObj->cigar_line, SQL_LONGVARCHAR );
-        $sth->bind_param( 9,  $exObj->score,      SQL_DOUBLE );
-        $sth->bind_param( 10, $exObj->evalue,     SQL_DOUBLE );
+        $sth->bind_param( 1, $object_xref_id,            SQL_INTEGER );
+        $sth->bind_param( 2, $dbEntry->xref_identity,    SQL_INTEGER );
+        $sth->bind_param( 3, $dbEntry->ensembl_identity, SQL_INTEGER );
+        $sth->bind_param( 4, $dbEntry->xref_start,       SQL_INTEGER );
+        $sth->bind_param( 5, $dbEntry->xref_end,         SQL_INTEGER );
+        $sth->bind_param( 6, $dbEntry->ensembl_start,    SQL_INTEGER );
+        $sth->bind_param( 7, $dbEntry->ensembl_end,      SQL_INTEGER );
+        $sth->bind_param( 8,  $dbEntry->cigar_line,  SQL_LONGVARCHAR );
+        $sth->bind_param( 9,  $dbEntry->score,            SQL_DOUBLE );
+        $sth->bind_param( 10, $dbEntry->evalue,           SQL_DOUBLE );
         $sth->execute();
-      } elsif ( $exObj->isa('Bio::EnsEMBL::OntologyXref') ) {
+      } elsif ( $dbEntry->isa('Bio::EnsEMBL::OntologyXref') ) {
         $sth = $self->prepare( "
              INSERT ignore INTO ontology_xref
                 SET object_xref_id = ?,
                     source_xref_id = ?,
                     linkage_type = ? " );
-        foreach my $info ( @{ $exObj->get_all_linkage_info() } ) {
-          my ( $lt, $sourceXref ) = @{$info};
-          my $sourceXid = undef;
-          if ($sourceXref) {
-            $sourceXref->is_stored( $self->dbc )
-              || $self->store($sourceXref);
-            $sourceXid = $sourceXref->dbID;
-          }
-          $sth->bind_param( 1, $Xidt,      SQL_INTEGER );
-          $sth->bind_param( 2, $sourceXid, SQL_INTEGER );
-          $sth->bind_param( 3, $lt,        SQL_VARCHAR );
-          $sth->execute();
-        }
-      }
-    } ## end if ( !$tst )
-  } ## end if ( defined($ensembl_id...))
+        foreach my $info ( @{ $dbEntry->get_all_linkage_info() } ) {
+            my ( $linkage_type, $sourceXref ) = @{$info};
+            my $sourceXid = undef;
+            if ($sourceXref) {
+              $sourceXref->is_stored( $self->dbc ) || $self->store($sourceXref);
+              $sourceXid = $sourceXref->dbID;
+            }
+            $sth->bind_param( 1, $object_xref_id, SQL_INTEGER );
+            $sth->bind_param( 2, $sourceXid, SQL_INTEGER );
+            $sth->bind_param( 3, $linkage_type,  SQL_VARCHAR );
+            $sth->execute();
+        } #end foreach
+      } #end elsif
+    } # end if ($object_xref_id)
+    return $object_xref_id;
+}
+
+=head2 _check_external_db 
+
+  Arg [1]    : DBEntry object
+  Arg [2]    : Ignore version flag
+  Description: Looks for a record of the given external database
+  Exceptions : Throws on missing external database entry
+  Returntype : Int 
 
-  return $dbX;
+=cut
+
+sub _check_external_db {
+    my ($self,$db_entry,$ignore) = @_;
+    my ($sql,@bound_params,$sql_helper,$db_name,$db_release);
+    
+    $db_name = $db_entry->dbname();
+    $db_release = $db_entry->release();
+    $sql_helper = $self->dbc->sql_helper;
+    
+    $sql = 'SELECT external_db_id FROM external_db WHERE db_name = ?';
+    push @bound_params,$db_name;
+    unless ($ignore) {
+        if ($db_release) {
+            $sql .= ' AND db_release = ?';
+            push @bound_params,$db_release;
+        } else {
+            $sql .= ' AND db_release is NULL';
+        }
+    }
+    
+    my ($db_id) = @{ $sql_helper->execute_simple(-SQL => $sql, -PARAMS => \@bound_params) };
+    
+    if ($db_id) {
+      return $db_id;
+    }
+    else {
+      throw( sprintf( "external_db [%s] release [%s] does not exist",
+                     $db_name, $db_release)
+      );
+    }
 }
 
+=head2 _store_or_fetch_xref 
+
+    Arg [1]    : DBEntry object
+    Arg [2]    : Database accession for external database
+    Description: Thread-safe method for adding xrefs, or otherwise returning
+                 an xref ID for the inserted or retrieved xref. Also inserts
+                 synonyms for that xref when entire new 
+    Returns    : Int - the DB ID of the xref after insertion 
+=cut
+sub _store_or_fetch_xref {
+    my $self = shift;
+    my $dbEntry = shift;
+    my $dbRef = shift;
+    my $xref_id;
+    
+    my $sth = $self->prepare( "
+       INSERT IGNORE INTO xref
+       SET dbprimary_acc = ?,
+           display_label = ?,
+           version = ?,
+           description = ?,
+           external_db_id = ?,
+           info_type = ?,
+           info_text = ?");
+    $sth->bind_param(1, $dbEntry->primary_id,SQL_VARCHAR);
+    $sth->bind_param(2, $dbEntry->display_id,SQL_VARCHAR);
+    $sth->bind_param(3, $dbEntry->version,SQL_VARCHAR);
+    $sth->bind_param(4, $dbEntry->description,SQL_VARCHAR);
+    $sth->bind_param(5, $dbRef,SQL_INTEGER);
+    $sth->bind_param(6, ($dbEntry->info_type || 'NONE'), SQL_VARCHAR);
+    $sth->bind_param(7, ($dbEntry->info_text || ''), SQL_VARCHAR);
+
+    $sth->execute();
+    $xref_id = $self->last_insert_id('xref_id',undef,'xref');
+    $sth->finish();
+    
+    if ($xref_id) { #insert was successful, store supplementary synonyms
+        # thread safety no longer an issue.
+        my $synonym_check_sth = $self->prepare(
+                  "SELECT xref_id, synonym
+                   FROM external_synonym
+                   WHERE xref_id = ?
+                   AND synonym = ?");
+    
+        my $synonym_store_sth = $self->prepare(
+            "INSERT ignore INTO external_synonym
+             SET xref_id = ?, synonym = ?");
+    
+        my $synonyms = $dbEntry->get_all_synonyms();
+        foreach my $syn ( @$synonyms ) {
+            $synonym_check_sth->bind_param(1,$xref_id,SQL_INTEGER);
+            $synonym_check_sth->bind_param(2,$syn,SQL_VARCHAR);
+            $synonym_check_sth->execute();
+            my ($dbSyn) = $synonym_check_sth->fetchrow_array();
+            $synonym_store_sth->bind_param(1,$xref_id,SQL_INTEGER);
+            $synonym_store_sth->bind_param(2,$syn,SQL_VARCHAR);
+            $synonym_store_sth->execute() if(!$dbSyn);
+        }
+        $synonym_check_sth->finish();
+        $synonym_store_sth->finish();
+        
+    } else { # xref_id already exists, retrieve it
+        my $sql = 'SELECT xref_id FROM xref 
+            WHERE 
+                dbprimary_acc = ?
+            AND display_label = ?
+            AND version = ?
+            AND external_db_id = ?
+            AND info_type = ?
+            AND info_text = ?
+            AND description';
+        if ($dbEntry->description) {$sql .= ' = ?'}
+        else {$sql .= ' is NULL'}
+        
+        $sth = $self->prepare( $sql );
+        $sth->bind_param(1, $dbEntry->primary_id,SQL_VARCHAR);
+        $sth->bind_param(2, $dbEntry->display_id,SQL_VARCHAR);
+        $sth->bind_param(3, $dbEntry->version,SQL_VARCHAR);
+        $sth->bind_param(4, $dbRef,SQL_INTEGER);
+        $sth->bind_param(5, ($dbEntry->info_type || 'NONE'), SQL_VARCHAR);
+        $sth->bind_param(6, ($dbEntry->info_text || ''), SQL_VARCHAR);
+        if ($dbEntry->description) {$sth->bind_param(7, $dbEntry->description,SQL_VARCHAR);}
+        $sth->execute();
+        ($xref_id) = $sth->fetchrow_array();
+        $sth->finish;
+    }
+    
+    return $xref_id;
+}
 
 =head2 exists
 

modules/t/test-genome-DBs/homo_sapiens/core/xref.sql

@@ -7,7 +7,6 @@ CREATE TABLE `xref` (
   `description` text collate latin1_bin,
   `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') collate latin1_bin NOT NULL default 'NONE',
   `info_text` varchar(255) collate latin1_bin NOT NULL default '',
-  `priority` int(11) default NULL,
   PRIMARY KEY  (`xref_id`),
   UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`),
   KEY `display_index` (`display_label`)

modules/t/test-genome-DBs/homo_sapiens/core/xref.txt

-614	6	GO:0006464	GO:0006464	1	description	\D	\D	1
-6990	6	GO:0004835	GO:0004835	1	description	\D	\D	1
-102409	2	AL031658	AL031658	1	description	\D	\D	1
-152200	7	Q9BR19	Q9BR19	1	description	\D	\D	1
-152201	3	CAC33959	CAC33959	1	description	\D	\D	1
-152202	5	16118	C20orf125	1	description	\D	\D	1
-152191	7	Q9BR18	Q9BR18	1	description	\D	\D	1
-152192	3	CAC33960	CAC33960	1	description	\D	\D	1
-40088	9	NM_030815	NM_030815	1	description	\D	\D	1
-40089	10	81572	81572	1	description	\D	\D	1
-40090	5	16119	C20orf126	1	description	\D	\D	1
-102414	7	Q9NUG6	Q9NUG6	1	description	\D	\D	1
-102415	3	CAB88101	CAB88101	1	description	\D	\D	1
-102411	7	Q9NUG5	Q9NUG5	1	description	\D	\D	1
-102412	3	CAB88102	CAB88102	1	description	\D	\D	1
-102413	5	16152	C20orf159	1	description	\D	\D	1
-34984	9	NM_080625	NM_080625	1	description	\D	\D	1
-34985	10	140706	140706	1	description	\D	\D	1
-34986	5	16153	C20orf160	1	description	\D	\D	1
-51533	7	Q96MD5	Q96MD5	1	description	\D	\D	1
-51534	2	AK057090	AK057090	1	description	\D	\D	1
-51535	3	BAB71363	BAB71363	1	description	\D	\D	1
-994	6	GO:0007242	GO:0007242	1	description	\D	\D	1
-102408	7	Q9NUG4	Q9NUG4	1	description	\D	\D	1
-102410	3	CAB88103	CAB88103	1	description	\D	\D	1
-257	6	GO:0004674	GO:0004674	1	description	\D	\D	1
-258	6	GO:0004713	GO:0004713	1	description	\D	\D	1
-259	6	GO:0005524	GO:0005524	1	description	\D	\D	1
-260	6	GO:0006468	GO:0006468	1	description	\D	\D	1
-612	6	GO:0016740	GO:0016740	1	description	\D	\D	1
-5371	6	GO:0007498	GO:0007498	1	description	\D	\D	1
-120579	2	AL049539	AL049539	1	description	\D	\D	1
-158504	1	P08631	HCK_HUMAN	1	description	\D	\D	1
-158505	2	M16591	M16591	1	description	\D	\D	1
-158506	3	AAA52643	AAA52643	1	description	\D	\D	1
-158507	2	M16592	M16592	1	description	\D	\D	1
-158508	3	AAA52644	AAA52644	1	description	\D	\D	1
-158509	2	BC014435	BC014435	1	description	\D	\D	1
-158510	3	AAH14435	AAH14435	1	description	\D	\D	1
-158511	2	AK026432	AK026432	1	description	\D	\D	1
-158512	3	BAB15482	BAB15482	1	description	\D	\D	1
-158513	3	CAB75606	CAB75606	1	description	\D	\D	1
-158514	2	X58741	X58741	1	description	\D	\D	1
-158515	3	CAA41565	CAA41565	1	description	\D	\D	1
-158516	2	X58742	X58742	1	description	\D	\D	1
-158517	2	X58743	X58743	1	description	\D	\D	1
-158518	8	2HCK	2HCK	1	description	\D	\D	1
-158519	8	3HCK	3HCK	1	description	\D	\D	1
-158520	8	4HCK	4HCK	1	description	\D	\D	1
-158521	8	5HCK	5HCK	1	description	\D	\D	1
-158522	8	1AD5	1AD5	1	description	\D	\D	1
-158523	8	1BU1	1BU1	1	description	\D	\D	1
-158524	4	142370	142370	1	description	\D	\D	1
-158525	5	4840	HCK	1	description	\D	\D	1
-166799	9	NM_002110	NM_002110	1	description	\D	\D	1
-166800	10	3055	3055	1	description	\D	\D	1
-438	6	GO:0016021	GO:0016021	1	description	\D	\D	1
-793	6	GO:0006810	GO:0006810	1	description	\D	\D	1
-1166	6	GO:0005215	GO:0005215	1	description	\D	\D	1
-37039	9	NM_014742	NM_014742	1	description	\D	\D	1
-37040	10	9777	9777	1	description	\D	\D	1
-120576	1	Q92544	T9S4_HUMAN	1	description	\D	\D	1
-120577	2	D87444	D87444	1	description	\D	\D	1
-120578	3	BAA13385	BAA13385	1	description	\D	\D	1
-120580	3	CAB75607	CAB75607	1	description	\D	\D	1
-120581	2	BC021107	BC021107	1	description	\D	\D	1
-120582	3	AAH21107	AAH21107	1	description	\D	\D	1
-120583	2	BC022850	BC022850	1	description	\D	\D	1
-120584	3	AAH22850	AAH22850	1	description	\D	\D	1
-143	6	GO:0005634	GO:0005634	1	description	\D	\D	1
-315	6	GO:0003677	GO:0003677	1	description	\D	\D	1
-3908	6	GO:0006334	GO:0006334	1	description	\D	\D	1
-28816	2	AL121897	AL121897	1	description	\D	\D	1
-128605	7	Q9H489	Q9H489	1	description	\D	\D	1
-128606	3	CAC16422	CAC16422	1	description	\D	\D	1
-128607	5	16256	TSPYL3	1	description	\D	\D	1
-139	6	GO:0003700	GO:0003700	1	description	\D	\D	1
-141	6	GO:0006355	GO:0006355	1	description	\D	\D	1
-17031	9	NM_002657	NM_002657	1	description	\D	\D	1
-17032	4	604866	604866	1	description	\D	\D	1
-17033	10	5326	5326	1	description	\D	\D	1
-17034	5	9047	PLAGL2	1	description	\D	\D	1
-58594	1	Q9UPG8	PAL2_HUMAN	1	description	\D	\D	1
-58595	2	AF006005	AF006005	1	description	\D	\D	1
-58596	3	AAC34252	AAC34252	1	description	\D	\D	1
-58597	2	D83784	D83784	1	description	\D	\D	1
-58598	3	BAA12113	BAA12113	1	description	\D	\D	1
-58599	3	CAC16423	CAC16423	1	description	\D	\D	1
-168444	7	Q9BW76	Q9BW76	1	description	\D	\D	1
-168445	2	BC000582	BC000582	1	description	\D	\D	1
-168446	3	AAH00582	AAH00582	1	description	\D	\D	1
-673	6	GO:0006493	GO:0006493	1	description	\D	\D	1
-1284	6	GO:0016932	GO:0016932	1	description	\D	\D	1
-19243	6	GO:0030173	GO:0030173	1	description	\D	\D	1
-54393	6	GO:0008417	GO:0008417	1	description	\D	\D	1
-128347	6	GO:0006004	GO:0006004	1	description	\D	\D	1
-128591	7	Q9H488	Q9H488	1	description	\D	\D	1
-128592	2	AF375884	AF375884	1	description	\D	\D	1
-128593	3	AAL09576	AAL09576	1	description	\D	\D	1
-128594	3	CAC16424	CAC16424	1	description	\D	\D	1
-128595	2	D80002	D80002	1	description	\D	\D	1
-128596	3	BAA11497	BAA11497	1	description	\D	\D	1
-128597	5	14988	POFUT1	1	description	\D	\D	1
-20	6	GO:0005875	GO:0005875	1	description	\D	\D	1
-891	6	GO:0007017	GO:0007017	1	description	\D	\D	1
-1444	6	GO:0003777	GO:0003777	1	description	\D	\D	1
-28813	1	O15066	KF3B_HUMAN	1	description	\D	\D	1
-28814	2	AB002357	AB002357	1	description	\D	\D	1
-28815	3	BAA20815	BAA20815	1	description	\D	\D	1
-28817	3	CAC16425	CAC16425	1	description	\D	\D	1
-28818	4	603754	603754	1	description	\D	\D	1
-28819	5	6320	KIF3B	1	description	\D	\D	1
-28820	6	GO:0008574	GO:0008574	1	description	\D	\D	1
-28821	6	GO:0007368	GO:0007368	1	description	\D	\D	1
-28822	6	GO:0008089	GO:0008089	1	description	\D	\D	1
-28823	6	GO:0005873	GO:0005873	1	description	\D	\D	1
-38683	9	NM_004798	NM_004798	1	description	\D	\D	1
-38684	10	9371	9371	1	description	\D	\D	1
-29946	7	Q9UFP8	Q9UFP8	1	description	\D	\D	1
-29947	2	AL117518	AL117518	1	description	\D	\D	1
-29948	3	CAB55975	CAB55975	1	description	\D	\D	1
-128324	7	Q9H466	Q9H466	1	description	\D	\D	1
-128325	2	AL121583	AL121583	1	description	\D	\D	1
-128326	3	CAC00581	CAC00581	1	description	\D	\D	1
-34890	9	NM_080616	NM_080616	1	description	\D	\D	1
-34891	10	140688	140688	1	description	\D	\D	1
-34892	5	16106	C20orf112	1	description	\D	\D	1
-53919	7	Q96MY1	Q96MY1	1	description	\D	\D	1
-53920	2	AK056286	AK056286	1	description	\D	\D	1
-53921	3	BAB71138	BAB71138	1	description	\D	\D	1
-89324	2	AL034550	AL034550	1	description	\D	\D	1
-152329	7	Q9BR34	Q9BR34	1	description	\D	\D	1
-152330	3	CAC33994	CAC33994	1	description	\D	\D	1
-89326	7	Q9NQF6	Q9NQF6	1	description	\D	\D	1
-89327	3	CAC00609	CAC00609	1	description	\D	\D	1
-89323	7	Q9NQF5	Q9NQF5	1	description	\D	\D	1
-89325	3	CAC00610	CAC00610	1	description	\D	\D	1
-332	7	Q9BXE6	Q9BXE6	1	description	\D	\D	1
-333	2	AF336876	AF336876	1	description	\D	\D	1
-334	3	AAK21302	AAK21302	1	description	\D	\D	1
-168321	7	Q9BW53	Q9BW53	1	description	\D	\D	1
-168322	2	BC000628	BC000628	1	description	\D	\D	1
-168323	3	AAH00628	AAH00628	1	description	\D	\D	1
-168324	5	16223	C20orf92	1	description	\D	\D	1
-1043	6	GO:0008372	GO:0008372	1	description	\D	\D	1
-11120	6	GO:0006306	GO:0006306	1	description	\D	\D	1
-15196	6	GO:0003886	GO:0003886	1	description	\D	\D	1
-15947	1	Q9UBC3	DM3B_HUMAN	1	description	\D	\D	1
-15948	2	AF156487	AF156487	1	description	DEPENDENT	test dependent	1
-15949	3	AAD53062	AAD53062	1	description	DEPENDENT	test dependent 2	1
-15950	2	AF156488	AF156488	1	description	SEQUENCE_MATCH	test seq match	1
-15951	3	AAD53063	AAD53063	1	description	INFERRED_PAIR	test infereed pair	1
-15952	2	AF176228	AF176228	1	description	\D	\D	1
-15953	3	AAF04015	AAF04015	1	description	\D	\D	1
-15954	2	AL035071	AL035071	1	description	\D	\D	1
-15955	3	CAB53069	CAB53069	1	description	\D	\D	1
-15956	3	CAB53070	CAB53070	1	description	\D	\D	1
-15957	3	CAB53071	CAB53071	1	description	\D	\D	1
-15958	2	AF129267	AF129267	1	description	\D	\D	1
-15959	3	AAD31432	AAD31432	1	description	\D	\D	1
-15960	2	AF129268	AF129268	1	description	\D	\D	1
-15961	3	AAD31433	AAD31433	1	description	\D	\D	1
-15962	2	AF129269	AF129269	1	description	\D	\D	1
-15963	3	AAD31434	AAD31434	1	description	\D	\D	1
-15964	4	242860	242860	1	description	\D	\D	1
-15965	4	602900	602900	1	description	\D	\D	1
-15966	5	2979	DNMT3B	1	description	\D	\D	1
-15967	6	GO:0008326	GO:0008326	1	description	\D	\D	1
-72100	9	NM_006892	NM_006892	1	description	\D	\D	1
-72101	10	1789	1789	1	description	\D	\D	1
-50	6	GO:0000074	GO:0000074	1	description	\D	\D	1
-51	6	GO:0007048	GO:0007048	1	description	\D	\D	1
-269	6	GO:0008283	GO:0008283	1	description	\D	\D	1
-2617	6	GO:0008017	GO:0008017	1	description	\D	\D	1
-18952	6	GO:0008022	GO:0008022	1	description	\D	\D	1
-97756	9	NM_012325	NM_012325	1	description	\D	\D	1
-97757	4	603108	603108	1	description	\D	\D	1
-97758	10	22919	22919	1	description	\D	\D	1
-97759	5	6890	MAPRE1	1	description	\D	\D	1
-103295	1	Q15691	MAE1_HUMAN	1	description	\D	\D	1
-103296	2	U24166	U24166	1	description	\D	\D	1
-103297	3	AAC09471	AAC09471	1	description	\D	\D	1
-103298	3	CAB53072	CAB53072	1	description	\D	\D	1
-999998	11	IPR000001	IPR000001	1	Test interpro desc1	\D	\D	1
-999999	11	IPR000010	IPR000010	1	Test interpro desc2	\D	\D	1
+614	6	GO:0006464	GO:0006464	1	description	\D	\D
+6990	6	GO:0004835	GO:0004835	1	description	\D	\D
+102409	2	AL031658	AL031658	1	description	\D	\D
+152200	7	Q9BR19	Q9BR19	1	description	\D	\D
+152201	3	CAC33959	CAC33959	1	description	\D	\D
+152202	5	16118	C20orf125	1	description	\D	\D
+152191	7	Q9BR18	Q9BR18	1	description	\D	\D
+152192	3	CAC33960	CAC33960	1	description	\D	\D
+40088	9	NM_030815	NM_030815	1	description	\D	\D
+40089	10	81572	81572	1	description	\D	\D
+40090	5	16119	C20orf126	1	description	\D	\D
+102414	7	Q9NUG6	Q9NUG6	1	description	\D	\D
+102415	3	CAB88101	CAB88101	1	description	\D	\D
+102411	7	Q9NUG5	Q9NUG5	1	description	\D	\D
+102412	3	CAB88102	CAB88102	1	description	\D	\D
+102413	5	16152	C20orf159	1	description	\D	\D
+34984	9	NM_080625	NM_080625	1	description	\D	\D
+34985	10	140706	140706	1	description	\D	\D
+34986	5	16153	C20orf160	1	description	\D	\D
+51533	7	Q96MD5	Q96MD5	1	description	\D	\D
+51534	2	AK057090	AK057090	1	description	\D	\D
+51535	3	BAB71363	BAB71363	1	description	\D	\D
+994	6	GO:0007242	GO:0007242	1	description	\D	\D
+102408	7	Q9NUG4	Q9NUG4	1	description	\D	\D
+102410	3	CAB88103	CAB88103	1	description	\D	\D
+257	6	GO:0004674	GO:0004674	1	description	\D	\D
+258	6	GO:0004713	GO:0004713	1	description	\D	\D
+259	6	GO:0005524	GO:0005524	1	description	\D	\D
+260	6	GO:0006468	GO:0006468	1	description	\D	\D
+612	6	GO:0016740	GO:0016740	1	description	\D	\D
+5371	6	GO:0007498	GO:0007498	1	description	\D	\D
+120579	2	AL049539	AL049539	1	description	\D	\D
+158504	1	P08631	HCK_HUMAN	1	description	\D	\D
+158505	2	M16591	M16591	1	description	\D	\D
+158506	3	AAA52643	AAA52643	1	description	\D	\D
+158507	2	M16592	M16592	1	description	\D	\D
+158508	3	AAA52644	AAA52644	1	description	\D	\D
+158509	2	BC014435	BC014435	1	description	\D	\D
+158510	3	AAH14435	AAH14435	1	description	\D	\D
+158511	2	AK026432	AK026432	1	description	\D	\D
+158512	3	BAB15482	BAB15482	1	description	\D	\D
+158513	3	CAB75606	CAB75606	1	description	\D	\D
+158514	2	X58741	X58741	1	description	\D	\D
+158515	3	CAA41565	CAA41565	1	description	\D	\D
+158516	2	X58742	X58742	1	description	\D	\D
+158517	2	X58743	X58743	1	description	\D	\D
+158518	8	2HCK	2HCK	1	description	\D	\D
+158519	8	3HCK	3HCK	1	description	\D	\D
+158520	8	4HCK	4HCK	1	description	\D	\D
+158521	8	5HCK	5HCK	1	description	\D	\D
+158522	8	1AD5	1AD5	1	description	\D	\D
+158523	8	1BU1	1BU1	1	description	\D	\D
+158524	4	142370	142370	1	description	\D	\D
+158525	5	4840	HCK	1	description	\D	\D
+166799	9	NM_002110	NM_002110	1	description	\D	\D
+166800	10	3055	3055	1	description	\D	\D
+438	6	GO:0016021	GO:0016021	1	description	\D	\D
+793	6	GO:0006810	GO:0006810	1	description	\D	\D
+1166	6	GO:0005215	GO:0005215	1	description	\D	\D
+37039	9	NM_014742	NM_014742	1	description	\D	\D
+37040	10	9777	9777	1	description	\D	\D
+120576	1	Q92544	T9S4_HUMAN	1	description	\D	\D
+120577	2	D87444	D87444	1	description	\D	\D
+120578	3	BAA13385	BAA13385	1	description	\D	\D
+120580	3	CAB75607	CAB75607	1	description	\D	\D
+120581	2	BC021107	BC021107	1	description	\D	\D
+120582	3	AAH21107	AAH21107	1	description	\D	\D
+120583	2	BC022850	BC022850	1	description	\D	\D
+120584	3	AAH22850	AAH22850	1	description	\D	\D
+143	6	GO:0005634	GO:0005634	1	description	\D	\D
+315	6	GO:0003677	GO:0003677	1	description	\D	\D
+3908	6	GO:0006334	GO:0006334	1	description	\D	\D
+28816	2	AL121897	AL121897	1	description	\D	\D
+128605	7	Q9H489	Q9H489	1	description	\D	\D
+128606	3	CAC16422	CAC16422	1	description	\D	\D
+128607	5	16256	TSPYL3	1	description	\D	\D
+139	6	GO:0003700	GO:0003700	1	description	\D	\D
+141	6	GO:0006355	GO:0006355	1	description	\D	\D
+17031	9	NM_002657	NM_002657	1	description	\D	\D
+17032	4	604866	604866	1	description	\D	\D
+17033	10	5326	5326	1	description	\D	\D
+17034	5	9047	PLAGL2	1	description	\D	\D
+58594	1	Q9UPG8	PAL2_HUMAN	1	description	\D	\D
+58595	2	AF006005	AF006005	1	description	\D	\D
+58596	3	AAC34252	AAC34252	1	description	\D	\D
+58597	2	D83784	D83784	1	description	\D	\D
+58598	3	BAA12113	BAA12113	1	description	\D	\D
+58599	3	CAC16423	CAC16423	1	description	\D	\D
+168444	7	Q9BW76	Q9BW76	1	description	\D	\D
+168445	2	BC000582	BC000582	1	description	\D	\D
+168446	3	AAH00582	AAH00582	1	description	\D	\D
+673	6	GO:0006493	GO:0006493	1	description	\D	\D
+1284	6	GO:0016932	GO:0016932	1	description	\D	\D
+19243	6	GO:0030173	GO:0030173	1	description	\D	\D
+54393	6	GO:0008417	GO:0008417	1	description	\D	\D
+128347	6	GO:0006004	GO:0006004	1	description	\D	\D
+128591	7	Q9H488	Q9H488	1	description	\D	\D
+128592	2	AF375884	AF375884	1	description	\D	\D
+128593	3	AAL09576	AAL09576	1	description	\D	\D
+128594	3	CAC16424	CAC16424	1	description	\D	\D
+128595	2	D80002	D80002	1	description	\D	\D
+128596	3	BAA11497	BAA11497	1	description	\D	\D
+128597	5	14988	POFUT1	1	description	\D	\D
+20	6	GO:0005875	GO:0005875	1	description	\D	\D
+891	6	GO:0007017	GO:0007017	1	description	\D	\D
+1444	6	GO:0003777	GO:0003777	1	description	\D	\D
+28813	1	O15066	KF3B_HUMAN	1	description	\D	\D
+28814	2	AB002357	AB002357	1	description	\D	\D
+28815	3	BAA20815	BAA20815	1	description	\D	\D
+28817	3	CAC16425	CAC16425	1	description	\D	\D
+28818	4	603754	603754	1	description	\D	\D
+28819	5	6320	KIF3B	1	description	\D	\D
+28820	6	GO:0008574	GO:0008574	1	description	\D	\D
+28821	6	GO:0007368	GO:0007368	1	description	\D	\D
+28822	6	GO:0008089	GO:0008089	1	description	\D	\D
+28823	6	GO:0005873	GO:0005873	1	description	\D	\D
+38683	9	NM_004798	NM_004798	1	description	\D	\D
+38684	10	9371	9371	1	description	\D	\D
+29946	7	Q9UFP8	Q9UFP8	1	description	\D	\D
+29947	2	AL117518	AL117518	1	description	\D	\D
+29948	3	CAB55975	CAB55975	1	description	\D	\D
+128324	7	Q9H466	Q9H466	1	description	\D	\D
+128325	2	AL121583	AL121583	1	description	\D	\D
+128326	3	CAC00581	CAC00581	1	description	\D	\D
+34890	9	NM_080616	NM_080616	1	description	\D	\D
+34891	10	140688	140688	1	description	\D	\D
+34892	5	16106	C20orf112	1	description	\D	\D
+53919	7	Q96MY1	Q96MY1	1	description	\D	\D
+53920	2	AK056286	AK056286	1	description	\D	\D
+53921	3	BAB71138	BAB71138	1	description	\D	\D
+89324	2	AL034550	AL034550	1	description	\D	\D
+152329	7	Q9BR34	Q9BR34	1	description	\D	\D
+152330	3	CAC33994	CAC33994	1	description	\D	\D
+89326	7	Q9NQF6	Q9NQF6	1	description	\D	\D
+89327	3	CAC00609	CAC00609	1	description	\D	\D
+89323	7	Q9NQF5	Q9NQF5	1	description	\D	\D
+89325	3	CAC00610	CAC00610	1	description	\D	\D
+332	7	Q9BXE6	Q9BXE6	1	description	\D	\D
+333	2	AF336876	AF336876	1	description	\D	\D
+334	3	AAK21302	AAK21302	1	description	\D	\D
+168321	7	Q9BW53	Q9BW53	1	description	\D	\D
+168322	2	BC000628	BC000628	1	description	\D	\D
+168323	3	AAH00628	AAH00628	1	description	\D	\D
+168324	5	16223	C20orf92	1	description	\D	\D
+1043	6	GO:0008372	GO:0008372	1	description	\D	\D
+11120	6	GO:0006306	GO:0006306	1	description	\D	\D
+15196	6	GO:0003886	GO:0003886	1	description	\D	\D
+15947	1	Q9UBC3	DM3B_HUMAN	1	description	\D	\D
+15948	2	AF156487	AF156487	1	description	DEPENDENT	test dependent
+15949	3	AAD53062	AAD53062	1	description	DEPENDENT	test dependent 2
+15950	2	AF156488	AF156488	1	description	SEQUENCE_MATCH	test seq match
+15951	3	AAD53063	AAD53063	1	description	INFERRED_PAIR	test inferred pair
+15952	2	AF176228	AF176228	1	description	\D	\D
+15953	3	AAF04015	AAF04015	1	description	\D	\D
+15954	2	AL035071	AL035071	1	description	\D	\D
+15955	3	CAB53069	CAB53069	1	description	\D	\D
+15956	3	CAB53070	CAB53070	1	description	\D	\D
+15957	3	CAB53071	CAB53071	1	description	\D	\D
+15958	2	AF129267	AF129267	1	description	\D	\D
+15959	3	AAD31432	AAD31432	1	description	\D	\D
+15960	2	AF129268	AF129268	1	description	\D	\D
+15961	3	AAD31433	AAD31433	1	description	\D	\D
+15962	2	AF129269	AF129269	1	description	\D	\D
+15963	3	AAD31434	AAD31434	1	description	\D	\D
+15964	4	242860	242860	1	description	\D	\D
+15965	4	602900	602900	1	description	\D	\D
+15966	5	2979	DNMT3B	1	description	\D	\D
+15967	6	GO:0008326	GO:0008326	1	description	\D	\D
+72100	9	NM_006892	NM_006892	1	description	\D	\D
+72101	10	1789	1789	1	description	\D	\D
+50	6	GO:0000074	GO:0000074	1	description	\D	\D
+51	6	GO:0007048	GO:0007048	1	description	\D	\D
+269	6	GO:0008283	GO:0008283	1	description	\D	\D
+2617	6	GO:0008017	GO:0008017	1	description	\D	\D
+18952	6	GO:0008022	GO:0008022	1	description	\D	\D
+97756	9	NM_012325	NM_012325	1	description	\D	\D
+97757	4	603108	603108	1	description	\D	\D
+97758	10	22919	22919	1	description	\D	\D
+97759	5	6890	MAPRE1	1	description	\D	\D
+103295	1	Q15691	MAE1_HUMAN	1	description	\D	\D
+103296	2	U24166	U24166	1	description	\D	\D
+103297	3	AAC09471	AAC09471	1	description	\D	\D
+103298	3	CAB53072	CAB53072	1	description	\D	\D
+999998	11	IPR000001	IPR000001	1	Test interpro desc1	\D	\D
+999999	11	IPR000010	IPR000010	1	Test interpro desc2	\D	\D

sql/patch_67_68_b.sql

+# patch_67_68_b.sql
+#
+# Title: 
+#
+# Description:
+#   Remove null values from xref and object_xref tables. See also DBEntryAdaptor thread safety changes
+
+
+ALTER TABLE xref MODIFY info_type enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','COORDINATE_OVERLAP','CHECKSUM') DEFAULT 'NONE';
+
+UPDATE xref SET info_type='NONE' WHERE info_type is NULL;
+
+ALTER TABLE xref MODIFY info_type enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','COORDINATE_OVERLAP','CHECKSUM') DEFAULT 'NONE' NOT NULL;
+
+UPDATE xref SET info_text='' WHERE info_text is NULL;
+ALTER TABLE xref MODIFY info_text varchar(255) DEFAULT '' NOT NULL;
+
+# Remove duplicate nulls in object_xref table
+
+create temporary table object_xref_dups
+select `ensembl_id`, `ensembl_object_type`, `xref_id`, `linkage_annotation`, `analysis_id`, min(object_xref_id) as object_xref_id, count(*) as c
+from object_xref
+group by `ensembl_id`, `ensembl_object_type`, `xref_id`, `linkage_annotation`, `analysis_id`
+having c > 1;
+
+create temporary table object_xref_MFD
+select ox.object_xref_id
+from object_xref ox join `object_xref_dups` oxd on ( 
+	ox.`ensembl_id` = oxd.`ensembl_id` 
+	and ox.ensembl_object_type = oxd.ensembl_object_type 
+	and ox.xref_id = oxd.xref_id
+	and (ox.linkage_annotation = oxd.linkage_annotation || (ox.`linkage_annotation` IS NULL and oxd.`linkage_annotation` IS NULL))
+	and (ox.analysis_id = oxd.analysis_id || (ox.`analysis_id` IS NULL and oxd.`analysis_id` IS NULL))
+	and oxd.`object_xref_id` <> ox.`object_xref_id`
+);
+ALTER TABLE object_xref_MFD ADD INDEX dribbling_simpleton(object_xref_id);
+
+-- DELETE FROM object_xref WHERE object_xref_id = ANY (SELECT object_xref_id FROM object_xref_MFD);
+DELETE FROM object_xref USING object_xref JOIN object_xref_MFD WHERE object_xref.object_xref_id = object_xref_MFD.object_xref_id;
+
+UPDATE object_xref SET analysis_id = 0 WHERE analysis_id is NULL;
+ALTER TABLE object_xref MODIFY analysis_id smallint(5) unsigned DEFAULT 0 NOT NULL;
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+  VALUES (NULL, 'patch', 'patch_67_68_b.sql|xref_uniqueness');