ENSCORESW-2377: make analysis_id nullable in object_xref

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Apr 24 11:41:38 2018
+-- Created on Wed Apr 25 09:28:02 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -617,7 +617,7 @@ CREATE TABLE object_xref (
   ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
   linkage_annotation varchar(255),
-  analysis_id smallint NOT NULL
+  analysis_id smallint
 );
 
 CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);

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

@@ -120,3 +120,4 @@
 120	\N	patch	patch_92_93_b.sql|biotype_table
 121	\N	patch	patch_92_93_c.sql|collate_index_interpro
 122	\N	patch	patch_93_94_a.sql|schema_version
+123	\N	patch	patch_93_94_c.sql|nullable_ox_analysis

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

@@ -489,7 +489,7 @@ 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=123 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=124 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -541,7 +541,7 @@ CREATE TABLE `object_xref` (
   `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
   `xref_id` int(10) unsigned NOT NULL,
   `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
-  `analysis_id` smallint(5) unsigned NOT NULL,
+  `analysis_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`object_xref_id`),
   UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
   KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Apr 24 11:41:49 2018
+-- Created on Wed Apr 25 09:28:13 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -617,7 +617,7 @@ CREATE TABLE object_xref (
   ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
   linkage_annotation varchar(255),
-  analysis_id smallint NOT NULL
+  analysis_id smallint
 );
 
 CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);

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

@@ -99,3 +99,4 @@
 166	\N	patch	patch_92_93_b.sql|biotype_table
 167	\N	patch	patch_92_93_c.sql|collate_index_interpro
 168	\N	patch	patch_93_94_a.sql|schema_version
+169	\N	patch	patch_93_94_c.sql|nullable_ox_analysis

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

@@ -489,7 +489,7 @@ 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=169 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=170 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -541,7 +541,7 @@ CREATE TABLE `object_xref` (
   `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
   `xref_id` int(10) unsigned NOT NULL,
   `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
-  `analysis_id` smallint(5) unsigned NOT NULL,
+  `analysis_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`object_xref_id`),
   UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
   KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Apr 24 11:42:00 2018
+-- Created on Wed Apr 25 09:28:23 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -617,7 +617,7 @@ CREATE TABLE object_xref (
   ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
   linkage_annotation varchar(255),
-  analysis_id smallint NOT NULL
+  analysis_id smallint
 );
 
 CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);

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

@@ -99,3 +99,4 @@
 148	\N	patch	patch_92_93_b.sql|biotype_table
 149	\N	patch	patch_92_93_c.sql|collate_index_interpro
 150	\N	patch	patch_93_94_a.sql|schema_version
+151	\N	patch	patch_93_94_c.sql|nullable_ox_analysis

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

@@ -489,7 +489,7 @@ 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=151 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=152 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -541,7 +541,7 @@ CREATE TABLE `object_xref` (
   `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
   `xref_id` int(10) unsigned NOT NULL,
   `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
-  `analysis_id` smallint(5) unsigned NOT NULL,
+  `analysis_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`object_xref_id`),
   UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
   KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Apr 24 11:42:12 2018
+-- Created on Wed Apr 25 09:28:34 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -617,7 +617,7 @@ CREATE TABLE object_xref (
   ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
   linkage_annotation varchar(255),
-  analysis_id smallint NOT NULL
+  analysis_id smallint
 );
 
 CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);

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

@@ -104,3 +104,4 @@
 2111	\N	patch	patch_92_93_b.sql|biotype_table
 2112	\N	patch	patch_92_93_c.sql|collate_index_interpro
 2113	\N	patch	patch_93_94_a.sql|schema_version
+2114	\N	patch	patch_93_94_c.sql|nullable_ox_analysis

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

@@ -489,7 +489,7 @@ 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=2114 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2115 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -541,7 +541,7 @@ CREATE TABLE `object_xref` (
   `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
   `xref_id` int(10) unsigned NOT NULL,
   `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
-  `analysis_id` smallint(5) unsigned NOT NULL,
+  `analysis_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`object_xref_id`),
   UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
   KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),

modules/t/test-genome-DBs/mapping/core/SQLite/table.sql

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Apr 24 11:42:24 2018
+-- Created on Wed Apr 25 09:28:44 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -617,7 +617,7 @@ CREATE TABLE object_xref (
   ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
   linkage_annotation varchar(255),
-  analysis_id smallint NOT NULL
+  analysis_id smallint
 );
 
 CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);

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

@@ -60,3 +60,4 @@
 153	\N	patch	patch_92_93_b.sql|biotype_table
 154	\N	patch	patch_92_93_c.sql|collate_index_interpro
 155	\N	patch	patch_93_94_a.sql|schema_version
+156	\N	patch	patch_93_94_c.sql|nullable_ox_analysis

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

@@ -489,7 +489,7 @@ 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=156 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=157 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -541,7 +541,7 @@ CREATE TABLE `object_xref` (
   `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
   `xref_id` int(10) unsigned NOT NULL,
   `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
-  `analysis_id` smallint(5) unsigned NOT NULL,
+  `analysis_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`object_xref_id`),
   UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
   KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),

modules/t/test-genome-DBs/multi/compara/SQLite/table.sql

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Apr 24 11:42:33 2018
+-- Created on Wed Apr 25 09:28:53 2018
 -- 
 
 BEGIN TRANSACTION;

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Apr 24 11:42:43 2018
+-- Created on Wed Apr 25 09:29:04 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -617,7 +617,7 @@ CREATE TABLE object_xref (
   ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
   linkage_annotation varchar(255),
-  analysis_id smallint NOT NULL
+  analysis_id smallint
 );
 
 CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);

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

@@ -177,3 +177,4 @@
 1689	\N	patch	patch_92_93_b.sql|biotype_table
 1690	\N	patch	patch_92_93_c.sql|collate_index_interpro
 1691	\N	patch	patch_93_94_a.sql|schema_version
+1692	\N	patch	patch_93_94_c.sql|nullable_ox_analysis

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

@@ -489,7 +489,7 @@ 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=1692 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=1693 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -541,7 +541,7 @@ CREATE TABLE `object_xref` (
   `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
   `xref_id` int(10) unsigned NOT NULL,
   `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
-  `analysis_id` smallint(5) unsigned NOT NULL,
+  `analysis_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`object_xref_id`),
   UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
   KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),