add latest patches

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

@@ -94,3 +94,4 @@
 40	1	species.taxonomy_id	1217737
 31	1	species.url	Bacillus_thuringiensis
 55	1	transcriptbuild.level	toplevel
+97	\N	patch	patch_83_84_e.sql|nullable_versions

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

@@ -159,4 +159,4 @@
 162032	469283	31222465	31222583	1	1	0	1	1	ENSE00001109601	1	2004-12-06 12:00:00	2004-12-06 12:00:00
 162033	965899	10060	10405	1	0	0	1	1	ENSE00001109603	1	2004-12-06 12:00:00	2004-12-06 12:00:00
 162034	469290	1	6	1	0	0	1	1	ENSE00000111111	1	2014-12-11 14:00:00	2014-12-11 14:00:00
-162035	469290	5	9	1	0	0	1	1	ENSE00000111112	1	2014-12-11 14:00:00	2014-12-11 14:00:00
\ No newline at end of file
+162035	469290	5	9	1	0	0	1	1	ENSE00000111112	1	2014-12-11 14:00:00	2014-12-11 14:00:00

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

@@ -18,4 +18,4 @@
 18273	protein_coding	1282	469283	31166507	31196939	1	97759	ensembl	KNOWN	MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 1 (APC-BINDING PROTEIN EB1). [Source:SWISSPROT;Acc:Q15691]	1	21738	ENSG00000101367	1	2004-12-06 12:00:00	2004-12-06 12:00:00
 18274	protein_coding	1282	469283	31210077	31225346	1	0	ensembl	NOVEL	\N	1	21739	ENSG00000167097	1	2004-12-06 12:00:00	2004-12-06 12:00:00
 18275	protein_coding	1282	965899	10060	10405	1	0	ensembl	NOVEL	\N	1	21740	ENSG00000355555	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18276	protein_coding	1282	469290	1	150	1	\N	ensembl	NOVEL	weird	1	21741	ENSG00000111111	1	2014-12-11 14:00:00	2014-12-11 14:00:00
\ No newline at end of file
+18276	protein_coding	1282	469290	1	150	1	\N	ensembl	NOVEL	weird	1	21741	ENSG00000111111	1	2014-12-11 14:00:00	2014-12-11 14:00:00

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

@@ -73,3 +73,4 @@
 133	\N	patch	patch_83_84_b.sql|xref.version_default
 134	\N	patch	patch_83_84_c.sql|protein_feature_unique
 135	\N	patch	patch_83_84_d.sql|longer_synonym
+136	\N	patch	patch_83_84_e.sql|nullable_versions

modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Dec 11 17:18:34 2015
+-- Created on Fri May  6 15:44:14 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -270,7 +270,7 @@ CREATE TABLE exon (
   is_current tinyint NOT NULL DEFAULT 1,
   is_constitutive tinyint NOT NULL DEFAULT 0,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -328,7 +328,7 @@ CREATE TABLE gene (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_transcript_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -584,7 +584,7 @@ CREATE UNIQUE INDEX c02 ON misc_set (code);
 CREATE TABLE object_xref (
   object_xref_id integer NOT NULL,
   ensembl_id integer NOT NULL DEFAULT 0,
-  ensembl_object_type enum NOT NULL,
+  ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
   linkage_annotation varchar(255),
   analysis_id smallint NOT NULL
@@ -615,7 +615,7 @@ CREATE TABLE operon (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -633,7 +633,7 @@ CREATE TABLE operon_transcript (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -856,7 +856,7 @@ CREATE TABLE transcript (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_translation_id integer,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -907,7 +907,7 @@ CREATE TABLE translation (
   seq_end integer NOT NULL,
   end_exon_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -936,7 +936,8 @@ CREATE TABLE unmapped_object (
   query_score double precision,
   target_score double precision,
   ensembl_id integer DEFAULT 0,
-  ensembl_object_type enum DEFAULT 'RawContig'
+  ensembl_object_type enum DEFAULT 'RawContig',
+  parent varchar(255)
 );
 
 --
@@ -953,7 +954,7 @@ CREATE TABLE unmapped_reason (
 --
 CREATE TABLE xref (
   xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  external_db_id integer NOT NULL DEFAULT 0,
+  external_db_id integer NOT NULL,
   dbprimary_acc varchar(512) NOT NULL,
   display_label varchar(512) NOT NULL,
   version varchar(10),

modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt

@@ -73,3 +73,4 @@
 122	\N	patch	patch_83_84_b.sql|xref.version_default
 123	\N	patch	patch_83_84_c.sql|protein_feature_unique
 124	\N	patch	patch_83_84_d.sql|longer_synonym
+125	\N	patch	patch_83_84_e.sql|nullable_versions

modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Dec 11 17:18:45 2015
+-- Created on Fri May  6 15:44:32 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -270,7 +270,7 @@ CREATE TABLE exon (
   is_current tinyint NOT NULL DEFAULT 1,
   is_constitutive tinyint NOT NULL DEFAULT 0,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -328,7 +328,7 @@ CREATE TABLE gene (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_transcript_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -615,7 +615,7 @@ CREATE TABLE operon (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -633,7 +633,7 @@ CREATE TABLE operon_transcript (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -856,7 +856,7 @@ CREATE TABLE transcript (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_translation_id integer,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -907,7 +907,7 @@ CREATE TABLE translation (
   seq_end integer NOT NULL,
   end_exon_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );

modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt

@@ -78,3 +78,4 @@
 2085	\N	patch	patch_83_84_b.sql|xref.version_default
 2086	\N	patch	patch_83_84_c.sql|protein_feature_unique
 2087	\N	patch	patch_83_84_d.sql|longer_synonym
+2088	\N	patch	patch_83_84_e.sql|nullable_versions

modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt

 1	\N	schema_type	variation
-2	\N	schema_version	84
+2	\N	schema_version	85
 3	\N	patch	patch_83_84_a.sql|schema version
+4	\N	patch	patch_84_85_a.sql|schema version
+5	\N	patch	patch_84_85_b.sql|create sample_synonym
+6	\N	patch	patch_84_85_c.sql|drop column moltype from variation_synonym
+7	\N	patch	patch_85_86_d.sql|Making attrib_id auto_increment
+8	\N	patch	patch_85_86_e.sql|drop the table tagged_variation_feature