Revert test files to expected schema version.

t/test-genome-DBs/collection/core/meta.txt

@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	108
+2	\N	schema_version	106
 3	\N	patch	patch_88_89_a.sql|schema_version
 4	1	schema.load_started	2017-05-08 19:14:41
 5	1	schema.load_started	2017-05-08 19:14:45
@@ -191,6 +191,3 @@
 563	\N	patch	patch_103_104_a.sql|schema_version
 564	\N	patch	patch_104_105_a.sql|schema_version
 565	\N	patch	patch_105_106_a.sql|schema_version
-566	\N	patch	patch_106_107_a.sql|schema_version
-567	\N	patch	patch_106_107_b.sql|Added index for seq_region_mapping
-568	\N	patch	patch_107_108_a.sql|schema_version

t/test-genome-DBs/collection/core/table.sql

@@ -490,7 +490,7 @@ 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=569 DEFAULT CHARSET=latin1 CHECKSUM=1;
+) ENGINE=MyISAM AUTO_INCREMENT=566 DEFAULT CHARSET=latin1 CHECKSUM=1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
@@ -776,7 +776,6 @@ CREATE TABLE `seq_region_mapping` (
   `external_seq_region_id` int(10) unsigned NOT NULL,
   `internal_seq_region_id` int(10) unsigned NOT NULL,
   `mapping_set_id` int(10) unsigned NOT NULL,
-  UNIQUE KEY `seq_region_mapping_uindex` (`external_seq_region_id`,`internal_seq_region_id`,`mapping_set_id`),
   KEY `mapping_set_idx` (`mapping_set_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 CHECKSUM=1;
 

t/test-genome-DBs/drosophila_melanogaster/core/meta.txt

@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	108
+2	\N	schema_version	106
 3	\N	patch	patch_76_77_a.sql|schema_version
 4	1	assembly.mapping	chromosome:BDGP6|contig:BDGP6
 5	1	assembly.mapping	contig:BDGP6|chunk:BDGP6
@@ -145,6 +145,3 @@
 235	\N	patch	patch_103_104_a.sql|schema_version
 236	\N	patch	patch_104_105_a.sql|schema_version
 237	\N	patch	patch_105_106_a.sql|schema_version
-238	\N	patch	patch_106_107_a.sql|schema_version
-239	\N	patch	patch_106_107_b.sql|Added index for seq_region_mapping
-240	\N	patch	patch_107_108_a.sql|schema_version

t/test-genome-DBs/drosophila_melanogaster/core/table.sql

@@ -490,7 +490,7 @@ 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=241 DEFAULT CHARSET=latin1 CHECKSUM=1;
+) ENGINE=MyISAM AUTO_INCREMENT=238 DEFAULT CHARSET=latin1 CHECKSUM=1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
@@ -776,7 +776,6 @@ CREATE TABLE `seq_region_mapping` (
   `external_seq_region_id` int(10) unsigned NOT NULL,
   `internal_seq_region_id` int(10) unsigned NOT NULL,
   `mapping_set_id` int(10) unsigned NOT NULL,
-  UNIQUE KEY `seq_region_mapping_uindex` (`external_seq_region_id`,`internal_seq_region_id`,`mapping_set_id`),
   KEY `mapping_set_idx` (`mapping_set_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 CHECKSUM=1;
 

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

@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	108
+2	\N	schema_version	106
 3	\N	patch	patch_73_74_a.sql|schema_version
 4	\N	patch	patch_73_74_b.sql|remove_dnac
 5	\N	patch	patch_73_74_c.sql|remove_unconventional_transcript_association
@@ -192,6 +192,3 @@
 5891	\N	patch	patch_103_104_a.sql|schema_version
 5892	\N	patch	patch_104_105_a.sql|schema_version
 5893	\N	patch	patch_105_106_a.sql|schema_version
-5894	\N	patch	patch_106_107_a.sql|schema_version
-5895	\N	patch	patch_106_107_b.sql|Added index for seq_region_mapping
-5896	\N	patch	patch_107_108_a.sql|schema_version

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

@@ -490,7 +490,7 @@ 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=5897 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=5894 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
@@ -776,7 +776,6 @@ CREATE TABLE `seq_region_mapping` (
   `external_seq_region_id` int(10) unsigned NOT NULL,
   `internal_seq_region_id` int(10) unsigned NOT NULL,
   `mapping_set_id` int(10) unsigned NOT NULL,
-  UNIQUE KEY `seq_region_mapping_uindex` (`external_seq_region_id`,`internal_seq_region_id`,`mapping_set_id`),
   KEY `mapping_set_idx` (`mapping_set_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 

t/test-genome-DBs/homo_sapiens/funcgen/meta.txt

@@ -1,5 +1,5 @@
 1	1	schema_type	funcgen
-2	\N	schema_version	108
+2	\N	schema_version	106
 3	\N	patch	patch_87_88_a.sql|schema_version
 4	\N	patch	patch_87_88_b.sql|seq_region_name_255
 5	\N	patch	patch_87_88_c.sql|sample_regulatory_feature_id field for regulatory build
@@ -139,5 +139,3 @@
 139	\N	patch	patch_104_105_a.sql|schema_version
 140	\N	patch	patch_104_105_b.sql|New indices
 141	\N	patch	patch_105_106_a.sql|schema_version
-142	\N	patch	patch_106_107_a.sql|schema_version
-143	\N	patch	patch_107_108_a.sql|schema_version

t/test-genome-DBs/homo_sapiens/funcgen/table.sql

@@ -382,7 +382,7 @@ 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=144 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=142 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,

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

@@ -1,5 +1,5 @@
 1	\N	schema_type	variation
-2	\N	schema_version	108
+2	\N	schema_version	106
 3	1	species.production_name	homo_sapiens
 4	\N	patch	patch_94_95_a.sql|schema version
 5	\N	patch	patch_94_95_b.sql|create table to store allele synonyms
@@ -28,8 +28,3 @@
 45	\N	patch	patch_104_105_a.sql|schema version
 46	\N	patch	patch_104_105_b.sql|Increase publication title size
 47	\N	patch	patch_105_106_a.sql|schema version
-48	\N	patch	patch_106_107_a.sql|schema version
-49	\N	patch	patch_106_107_b.sql|consequences update
-50	\N	patch	patch_106_107_c.sql|remove regulatory and TFBS consequences from consequence_types in transcript_variation
-51	\N	patch	patch_107_108_a.sql|schema version
-52	\N	patch	patch_107_108_b.sql|fix SAS population description

t/test-genome-DBs/homo_sapiens/variation/table.sql

@@ -186,7 +186,7 @@ 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=53 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=48 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
@@ -544,7 +544,7 @@ CREATE TABLE `transcript_variation` (
   `feature_stable_id` varchar(128) DEFAULT NULL,
   `allele_string` text,
   `somatic` tinyint(1) NOT NULL DEFAULT '0',
-  `consequence_types` set('splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','feature_elongation','feature_truncation','protein_altering_variant','start_retained_variant','splice_donor_5th_base_variant','splice_donor_region_variant','splice_polypyrimidine_tract_variant') DEFAULT NULL,
+  `consequence_types` set('splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','feature_elongation','feature_truncation','protein_altering_variant','start_retained_variant') DEFAULT NULL,
   `cds_start` int(11) unsigned DEFAULT NULL,
   `cds_end` int(11) unsigned DEFAULT NULL,
   `cdna_start` int(11) unsigned DEFAULT NULL,
@@ -622,7 +622,7 @@ CREATE TABLE `variation_feature` (
   `map_weight` int(11) NOT NULL,
   `flags` set('genotyped') DEFAULT NULL,
   `source_id` int(10) unsigned NOT NULL,
-  `consequence_types` set('intergenic_variant','splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation','feature_elongation','feature_truncation','regulatory_region_variant','TF_binding_site_variant','protein_altering_variant','start_retained_variant','splice_donor_5th_base_variant','splice_donor_region_variant','splice_polypyrimidine_tract_variant') NOT NULL DEFAULT 'intergenic_variant',
+  `consequence_types` set('intergenic_variant','splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation','feature_elongation','feature_truncation','regulatory_region_variant','TF_binding_site_variant','protein_altering_variant','start_retained_variant') NOT NULL DEFAULT 'intergenic_variant',
   `variation_set_id` set('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25','26','27','28','29','30','31','32','33','34','35','36','37','38','39','40','41','42','43','44','45','46','47','48','49','50','51','52','53','54','55','56','57','58','59','60','61','62','63','64') NOT NULL DEFAULT '',
   `class_attrib_id` int(10) unsigned DEFAULT '0',
   `somatic` tinyint(1) NOT NULL DEFAULT '0',

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

@@ -1,6 +1,6 @@
 2	\N	schema_type	compara
 3	\N	division	vertebrates
-161	\N	schema_version	108
+155	\N	schema_version	106
 5	\N	patch	patch_70_71_a.sql|other_member_sequence_keys
 6	\N	patch	patch_70_71_b.sql|member_xref
 8	\N	patch	patch_70_71_c.sql|schema_version
@@ -118,7 +118,3 @@
 153	\N	patch	patch_104_105_a.sql|schema_version
 154	\N	patch	patch_104_105_b.sql|genebuild_varchar255
 156	\N	patch	patch_105_106_a.sql|schema_version
-157	\N	patch	patch_105_106_b.sql|clusterset_id_varchar50
-159	\N	patch	patch_106_107_a.sql|schema_version
-160	\N	patch	patch_106_107_b.sql|case_sensitive_stable_id
-162	\N	patch	patch_107_108_a.sql|schema_version

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

@@ -138,7 +138,7 @@ CREATE TABLE `gene_align_member` (
 
 CREATE TABLE `gene_member` (
   `gene_member_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `stable_id` varchar(128) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL,
+  `stable_id` varchar(128) NOT NULL,
   `version` int(10) unsigned DEFAULT '0',
   `source_name` enum('ENSEMBLGENE','EXTERNALGENE') NOT NULL,
   `taxon_id` int(10) unsigned NOT NULL,
@@ -176,7 +176,7 @@ CREATE TABLE `gene_member_hom_stats` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_member_qc` (
-  `gene_member_stable_id` varchar(128) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL,
+  `gene_member_stable_id` varchar(128) NOT NULL,
   `genome_db_id` int(10) unsigned NOT NULL,
   `seq_member_id` int(10) unsigned DEFAULT NULL,
   `n_species` int(11) DEFAULT NULL,
@@ -231,7 +231,7 @@ CREATE TABLE `gene_tree_root` (
   `root_id` int(10) unsigned NOT NULL,
   `member_type` enum('protein','ncrna') NOT NULL,
   `tree_type` enum('clusterset','supertree','tree') NOT NULL,
-  `clusterset_id` varchar(50) NOT NULL DEFAULT 'default',
+  `clusterset_id` varchar(30) NOT NULL DEFAULT 'default',
   `method_link_species_set_id` int(10) unsigned NOT NULL,
   `species_tree_root_id` bigint(20) unsigned DEFAULT NULL,
   `gene_align_id` int(10) unsigned DEFAULT NULL,
@@ -436,7 +436,7 @@ 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=163 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=157 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `method_link` (
   `method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -540,7 +540,7 @@ CREATE TABLE `peptide_align_feature` (
 
 CREATE TABLE `seq_member` (
   `seq_member_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `stable_id` varchar(128) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL,
+  `stable_id` varchar(128) NOT NULL,
   `version` int(10) unsigned DEFAULT '0',
   `source_name` enum('ENSEMBLPEP','ENSEMBLTRANS','Uniprot/SPTREMBL','Uniprot/SWISSPROT','EXTERNALPEP','EXTERNALTRANS','EXTERNALCDS') NOT NULL,
   `taxon_id` int(10) unsigned NOT NULL,