fixed slq migration files

persist/src/db/10.0.3/fix_db_20161005.sql

@@ -12,7 +12,7 @@ update element_table set alias_type_db ='Right square Compartment' where alias_t
 update element_table set alias_type_db ='Square Compartment' where alias_type_db = 'Square Compartment Alias';
 update element_table set alias_type_db ='Top square Compartment' where alias_type_db = 'Top square Compartment Alias';
 
-alter table node_table drop column element_iddb;
+alter table node_table drop column if exists element_iddb;
 alter table node_table rename alias_iddb to element_iddb;
 
 update element_table set alias_type_db ='Complex' where alias_type_db = 'Complex Species Alias';

persist/src/db/11.0.0/fix_db_20170714.sql

 -- some sequences had too low values
-DO $$ 
+DO ' 
 DECLARE 
 	rec 	RECORD;
 	size 	INT;
 BEGIN
 	FOR rec IN SELECT * FROM information_schema.sequences LOOP
-		/*RAISE NOTICE 'SELECT MAX(iddb)+1 FROM %', REPLACE(rec.sequence_name, '_iddb_seq', '');*/
-		EXECUTE format('SELECT COUNT(1) FROM information_schema.tables WHERE table_name = ''%s''', REPLACE(rec.sequence_name, '_iddb_seq', '')) INTO size;
+		EXECUTE format(''SELECT COUNT(1) FROM information_schema.tables WHERE table_name = ''''%s'''''', REPLACE(rec.sequence_name, ''_iddb_seq'', '''')) INTO size;
 		IF  size = 1 THEN
-			EXECUTE format('SELECT setval(''%s'', (SELECT MAX(iddb)+1 FROM %I))', rec.sequence_name, REPLACE(rec.sequence_name, '_iddb_seq', ''));		
+			EXECUTE format(''SELECT setval(''''%s'''', (SELECT MAX(iddb)+1 FROM %I))'', rec.sequence_name, REPLACE(rec.sequence_name, ''_iddb_seq'', ''''));		
 		END IF;
-		EXECUTE format('SELECT COUNT(1) FROM information_schema.tables WHERE table_name = ''%s''', REPLACE(rec.sequence_name, '_iddb_seq', '_table')) INTO size;
+		EXECUTE format(''SELECT COUNT(1) FROM information_schema.tables WHERE table_name = ''''%s'''''', REPLACE(rec.sequence_name, ''_iddb_seq'', ''_table'')) INTO size;
 		IF  size = 1 THEN
-			EXECUTE format('SELECT setval(''%s'', (SELECT MAX(iddb)+1 FROM %I))', rec.sequence_name, REPLACE(rec.sequence_name, '_iddb_seq', '_table'));
+			EXECUTE format(''SELECT setval(''''%s'''', (SELECT MAX(iddb)+1 FROM %I))'', rec.sequence_name, REPLACE(rec.sequence_name, ''_iddb_seq'', ''_table''));
 		END IF;
 	END LOOP;
-END $$;
+END ';
\ No newline at end of file

persist/src/db/7/fix_db_20140516.sql

@@ -51,7 +51,7 @@ delete from cacheentry;
 ALTER TABLE cacheentry ALTER COLUMN iddb SET DEFAULT nextval('cacheentry_iddb_seq'::regclass);
 
 --recreate search index
-drop index query_index;
+drop index if exists query_index;
 CREATE INDEX query_index
   ON cachequery
   USING btree

persist/src/db/7/fix_db_20141027.sql

@@ -2,7 +2,7 @@
 update cache_type set iddb = 0 where classname='lcsb.mapviewer.reactome.utils.ReactomeConnector';
 update cache_type set iddb = 1 where classname='lcsb.mapviewer.annotation.services.AnnotationRestService';
 update cache_type set iddb = 2 where classname='lcsb.mapviewer.annotation.services.ChEMBLParser';
-update cache_type set iddb = 3 where classname='lcsb.mapviewer.annotation.services.PubmedBackend';
+update cache_type set iddb = 3 where classname='lcsb.mapviewer.annotation.services.PubmedParser';
 update cache_type set iddb = 4 where classname='lcsb.mapviewer.annotation.services.DrugbankHTMLParser';
 update cache_type set iddb = 5 where classname='lcsb.mapviewer.annotation.services.IdConverter';
 update cache_type set iddb = 6 where classname='lcsb.mapviewer.annotation.cache.MockCacheInterface';