Extension to patch to remove null entries from the xref table. Has added...

Extension to patch to remove null entries from the xref table. Has added implications with updating object_xref. If this patch succeeded then this is not an issue for you

sql/patch_67_68_b.sql

@@ -5,16 +5,49 @@
 # Description:
 #   Remove null values from xref and object_xref tables. See also DBEntryAdaptor thread safety changes
 
+# Remove duplicate nulls in xref table
 
-ALTER TABLE xref MODIFY info_type enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','COORDINATE_OVERLAP','CHECKSUM') DEFAULT 'NONE';
+# Need to find the duplicates first and select the lowest xref_id as our "canonical" xref_id
 
-UPDATE xref SET info_type='NONE' WHERE info_type is NULL;
+create temporary table xref_dups
+select `dbprimary_acc`,`external_db_id`,`info_type`,`info_text`, min(xref_id) as xref_id, count(*) as c
+from xref
+group by `dbprimary_acc`,`external_db_id`,`info_type`,`info_text`
+having c > 1;
 
-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;
+# Mark all other duplicate xrefs and flag their new canonical ID
+
+create temporary table xref_MFD
+select x.xref_id, xd.xref_id AS canonical_xref_id
+from xref x join `xref_dups` xd on ( 
+  x.`dbprimary_acc` = xd.`dbprimary_acc` 
+  and x.`external_db_id` = xd.`external_db_id` 
+  and (x.`info_type` = xd.`info_type` || (x.`info_type` IS NULL and xd.`info_type` IS NULL))
+  and (x.`info_text` = xd.`info_text` || (x.`info_text` IS NULL and xd.`info_text` IS NULL))
+  and xd.`xref_id` <> x.`xref_id`
+);
+
+# Delete the duplicates
+
+DELETE FROM xref USING xref JOIN xref_MFD WHERE xref.xref_id = xref_MFD.xref_id;
+
+# Update object_xref xref_ids to the canonical ones
 
+UPDATE object_xref ox join xref_MFD xmfd using (xref_id) set ox.xref_id = xmfd.canonical_xref_id;
+
+# Apply info_text update and set not null constraint
 UPDATE xref SET info_text='' WHERE info_text is NULL;
+
 ALTER TABLE xref MODIFY info_text varchar(255) DEFAULT '' NOT NULL;
 
+# Apply none type, update NULL to NONE and then apply not null constraint
+
+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;
+
 # Remove duplicate nulls in object_xref table
 
 create temporary table object_xref_dups
@@ -35,7 +68,6 @@ from object_xref ox join `object_xref_dups` oxd on (
 );
 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;