Merge pull request #260 from Ensembl/feature/schema_update

update to latest schema

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Wed Apr 25 09:28:53 2018
+-- Created on Tue Jul  3 16:05:34 2018
 -- 
 
 BEGIN TRANSACTION;
@@ -301,7 +301,7 @@ CREATE TABLE gene_tree_root_attr (
 --
 CREATE TABLE gene_tree_root_tag (
   root_id integer NOT NULL,
-  tag varchar(50) NOT NULL,
+  tag varchar(255),
   value mediumtext NOT NULL
 );
 
@@ -408,7 +408,7 @@ CREATE TABLE hmm_profile (
 CREATE TABLE homology (
   homology_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   method_link_species_set_id integer NOT NULL,
-  description enum,
+  description enum NOT NULL,
   is_tree_compliant tinyint NOT NULL DEFAULT 0,
   dn float(10,5),
   ds float(10,5),
@@ -479,7 +479,8 @@ CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_va
 CREATE TABLE method_link (
   method_link_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   type varchar(50) NOT NULL DEFAULT '',
-  class varchar(50) NOT NULL DEFAULT ''
+  class varchar(50) NOT NULL DEFAULT '',
+  display_name varchar(255) NOT NULL DEFAULT ''
 );
 
 CREATE UNIQUE INDEX type02 ON method_link (type);

modules/t/test-genome-DBs/multi/compara/meta.txt

@@ -43,3 +43,5 @@
 50	\N	patch	patch_91_92_c.sql|gene_tree_root_tag_255
 52	\N	patch	patch_92_93_a.sql|schema_version
 54	\N	patch	patch_93_94_a.sql|schema_version
+55	\N	patch	patch_93_94_b.sql|homology_description_not_null
+56	\N	patch	patch_93_94_c.sql|method_link_display_name

modules/t/test-genome-DBs/multi/compara/method_link.txt

-401	PROTEIN_TREES	ProteinTree.protein_tree_node
-201	ENSEMBL_ORTHOLOGUES	Homology.homology
-202	ENSEMBL_PARALOGUES	Homology.homology
-402	NC_TREES	NCTree.nc_tree_node
-101	SYNTENY	SyntenyRegion.synteny
-16	LASTZ_NET	GenomicAlignBlock.pairwise_alignment
+401	PROTEIN_TREES	ProteinTree.protein_tree_node	Protein-trees
+201	ENSEMBL_ORTHOLOGUES	Homology.homology	Orthologues
+202	ENSEMBL_PARALOGUES	Homology.homology	Paralogues
+402	NC_TREES	NCTree.nc_tree_node	ncRNA-trees
+101	SYNTENY	SyntenyRegion.synteny	Synteny
+16	LASTZ_NET	GenomicAlignBlock.pairwise_alignment	LastZ

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

@@ -375,7 +375,7 @@ CREATE TABLE `hmm_profile` (
 CREATE TABLE `homology` (
   `homology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `method_link_species_set_id` int(10) unsigned NOT NULL,
-  `description` enum('ortholog_one2one','ortholog_one2many','ortholog_many2many','within_species_paralog','other_paralog','gene_split','between_species_paralog','alt_allele','homoeolog_one2one','homoeolog_one2many','homoeolog_many2many') DEFAULT NULL,
+  `description` enum('ortholog_one2one','ortholog_one2many','ortholog_many2many','within_species_paralog','other_paralog','gene_split','between_species_paralog','alt_allele','homoeolog_one2one','homoeolog_one2many','homoeolog_many2many') NOT NULL,
   `is_tree_compliant` tinyint(1) NOT NULL DEFAULT '0',
   `dn` float(10,5) DEFAULT NULL,
   `ds` float(10,5) DEFAULT NULL,
@@ -436,12 +436,13 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)),
   KEY `species_value_idx` (`species_id`,`meta_value`(255))
-) ENGINE=MyISAM AUTO_INCREMENT=55 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=57 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `method_link` (
   `method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `type` varchar(50) NOT NULL DEFAULT '',
   `class` varchar(50) NOT NULL DEFAULT '',
+  `display_name` varchar(255) NOT NULL DEFAULT '',
   PRIMARY KEY (`method_link_id`),
   UNIQUE KEY `type` (`type`)
 ) ENGINE=MyISAM AUTO_INCREMENT=403 DEFAULT CHARSET=latin1;