From 53d10bab9c94b6c3fc94e0e341f32a925cd2a4b4 Mon Sep 17 00:00:00 2001 From: Natalie Willhoft <70575561+nwillhoft@users.noreply.github.com> Date: Tue, 28 Jan 2025 23:04:28 +0000 Subject: [PATCH] Patch test dbs to 115 (#676) --- t/test-genome-DBs/ancestral_sequences/core/meta.txt | 3 ++- t/test-genome-DBs/ancestral_sequences/core/table.sql | 2 +- t/test-genome-DBs/gallus_gallus/core/meta.txt | 3 ++- t/test-genome-DBs/gallus_gallus/core/table.sql | 2 +- t/test-genome-DBs/homo_sapiens/core/meta.txt | 3 ++- t/test-genome-DBs/homo_sapiens/core/table.sql | 2 +- t/test-genome-DBs/homo_sapiens/funcgen/meta.txt | 3 ++- t/test-genome-DBs/homo_sapiens/funcgen/table.sql | 2 +- t/test-genome-DBs/homo_sapiens/variation/meta.txt | 3 ++- t/test-genome-DBs/homo_sapiens/variation/table.sql | 2 +- t/test-genome-DBs/homology/compara/meta.txt | 3 ++- t/test-genome-DBs/homology/compara/table.sql | 2 +- t/test-genome-DBs/meleagris_gallopavo/core/meta.txt | 3 ++- t/test-genome-DBs/meleagris_gallopavo/core/table.sql | 2 +- t/test-genome-DBs/multi/compara/meta.txt | 3 ++- t/test-genome-DBs/multi/compara/table.sql | 2 +- t/test-genome-DBs/multi/ontology/meta.txt | 3 ++- t/test-genome-DBs/multi/ontology/table.sql | 2 +- t/test-genome-DBs/taeniopygia_guttata/core/meta.txt | 3 ++- t/test-genome-DBs/taeniopygia_guttata/core/table.sql | 2 +- 20 files changed, 30 insertions(+), 20 deletions(-) diff --git a/t/test-genome-DBs/ancestral_sequences/core/meta.txt b/t/test-genome-DBs/ancestral_sequences/core/meta.txt index 8965108a..d73dee12 100644 --- a/t/test-genome-DBs/ancestral_sequences/core/meta.txt +++ b/t/test-genome-DBs/ancestral_sequences/core/meta.txt @@ -1,5 +1,5 @@ 1 \N schema_type core -2 \N schema_version 114 +2 \N schema_version 115 3 \N patch patch_77_78_a.sql|schema_version 4 \N patch patch_77_78_b.sql|source_column_increase 5 \N patch patch_77_78_c.sql|Change unmapped_reason_id from smallint to int @@ -86,3 +86,4 @@ 885 \N patch patch_112_113_a.sql|schema_version 886 \N patch patch_112_113_b.sql|Ensure meta_value is not null 887 \N patch patch_113_114_a.sql|schema_version +888 \N patch patch_114_115_a.sql|schema_version diff --git a/t/test-genome-DBs/ancestral_sequences/core/table.sql b/t/test-genome-DBs/ancestral_sequences/core/table.sql index 15211d3f..0263882b 100755 --- a/t/test-genome-DBs/ancestral_sequences/core/table.sql +++ b/t/test-genome-DBs/ancestral_sequences/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=888 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; +) ENGINE=MyISAM AUTO_INCREMENT=889 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; CREATE TABLE `meta_coord` ( `table_name` varchar(40) NOT NULL, diff --git a/t/test-genome-DBs/gallus_gallus/core/meta.txt b/t/test-genome-DBs/gallus_gallus/core/meta.txt index 2f042e4e..aa82f5a0 100644 --- a/t/test-genome-DBs/gallus_gallus/core/meta.txt +++ b/t/test-genome-DBs/gallus_gallus/core/meta.txt @@ -1,5 +1,5 @@ 1 \N schema_type core -2 \N schema_version 114 +2 \N schema_version 115 3 \N patch patch_65_66_a.sql|schema_version 4 \N patch patch_65_66_b.sql|fix_external_db_id 5 \N patch patch_65_66_c.sql|reorder_unmapped_obj_index @@ -203,3 +203,4 @@ 454 \N patch patch_112_113_a.sql|schema_version 455 \N patch patch_112_113_b.sql|Ensure meta_value is not null 456 \N patch patch_113_114_a.sql|schema_version +457 \N patch patch_114_115_a.sql|schema_version diff --git a/t/test-genome-DBs/gallus_gallus/core/table.sql b/t/test-genome-DBs/gallus_gallus/core/table.sql index bf64d485..888bed8a 100644 --- a/t/test-genome-DBs/gallus_gallus/core/table.sql +++ b/t/test-genome-DBs/gallus_gallus/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=457 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; +) ENGINE=MyISAM AUTO_INCREMENT=458 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; CREATE TABLE `meta_coord` ( `table_name` varchar(40) NOT NULL, diff --git a/t/test-genome-DBs/homo_sapiens/core/meta.txt b/t/test-genome-DBs/homo_sapiens/core/meta.txt index b09d2bfd..483fefb4 100644 --- a/t/test-genome-DBs/homo_sapiens/core/meta.txt +++ b/t/test-genome-DBs/homo_sapiens/core/meta.txt @@ -1,5 +1,5 @@ 1775 1 xref.timestamp 2012-09-03 21:14:58 -1 \N schema_version 114 +1 \N schema_version 115 2 \N patch patch_52_53_a.sql|schema_version 3 \N patch patch_52_53_b.sql|external_db_type_enum 4 \N patch patch_52_53_c.sql|identity_xref_rename @@ -274,3 +274,4 @@ 1888 \N patch patch_112_113_a.sql|schema_version 1889 \N patch patch_112_113_b.sql|Ensure meta_value is not null 1890 \N patch patch_113_114_a.sql|schema_version +1891 \N patch patch_114_115_a.sql|schema_version diff --git a/t/test-genome-DBs/homo_sapiens/core/table.sql b/t/test-genome-DBs/homo_sapiens/core/table.sql index 2a33102d..18e2723f 100644 --- a/t/test-genome-DBs/homo_sapiens/core/table.sql +++ b/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=1891 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; +) ENGINE=MyISAM AUTO_INCREMENT=1892 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; CREATE TABLE `meta_coord` ( `table_name` varchar(40) NOT NULL, diff --git a/t/test-genome-DBs/homo_sapiens/funcgen/meta.txt b/t/test-genome-DBs/homo_sapiens/funcgen/meta.txt index 4e16b332..c6072d30 100644 --- a/t/test-genome-DBs/homo_sapiens/funcgen/meta.txt +++ b/t/test-genome-DBs/homo_sapiens/funcgen/meta.txt @@ -1,5 +1,5 @@ 1 1 schema_type funcgen -2 \N schema_version 114 +2 \N schema_version 115 3 \N patch patch_88_89_a.sql|schema_version 4 \N patch patch_88_89_b.sql|Created probe_seq table 5 \N patch patch_88_89_c.sql|created probe_feature_transcript table @@ -216,3 +216,4 @@ 791 \N patch patch_112_113_a.sql|schema_version 792 \N patch patch_112_113_b.sql|fix_compatibility_issues 793 \N patch patch_113_114_a.sql|schema_version +794 \N patch patch_114_115_a.sql|schema_version diff --git a/t/test-genome-DBs/homo_sapiens/funcgen/table.sql b/t/test-genome-DBs/homo_sapiens/funcgen/table.sql index 33e4fd40..426d28e5 100644 --- a/t/test-genome-DBs/homo_sapiens/funcgen/table.sql +++ b/t/test-genome-DBs/homo_sapiens/funcgen/table.sql @@ -401,7 +401,7 @@ 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=794 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; +) ENGINE=MyISAM AUTO_INCREMENT=795 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; CREATE TABLE `meta_coord` ( `table_name` varchar(40) NOT NULL, diff --git a/t/test-genome-DBs/homo_sapiens/variation/meta.txt b/t/test-genome-DBs/homo_sapiens/variation/meta.txt index 134d8960..c4b25e1b 100755 --- a/t/test-genome-DBs/homo_sapiens/variation/meta.txt +++ b/t/test-genome-DBs/homo_sapiens/variation/meta.txt @@ -1,5 +1,5 @@ 1 \N schema_type variation -2 \N schema_version 114 +2 \N schema_version 115 3 \N patch patch_73_74_a.sql|schema version 4 \N patch patch_73_74_b.sql|Add doi and UCSC id to publication table 5 \N patch patch_73_74_c.sql|Add clinical_significance to variation_feature table @@ -148,3 +148,4 @@ 148 \N patch patch_112_113_a.sql|schema version 149 \N patch patch_112_113_b.sql|Update meta_key length 150 \N patch patch_113_114_a.sql|schema_version +151 \N patch patch_114_115_a.sql|schema_version diff --git a/t/test-genome-DBs/homo_sapiens/variation/table.sql b/t/test-genome-DBs/homo_sapiens/variation/table.sql index 17be1dd0..9d971f63 100755 --- a/t/test-genome-DBs/homo_sapiens/variation/table.sql +++ b/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=151 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; +) ENGINE=MyISAM AUTO_INCREMENT=152 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; CREATE TABLE `meta_coord` ( `table_name` varchar(40) NOT NULL, diff --git a/t/test-genome-DBs/homology/compara/meta.txt b/t/test-genome-DBs/homology/compara/meta.txt index 90512b4e..46a862d9 100644 --- a/t/test-genome-DBs/homology/compara/meta.txt +++ b/t/test-genome-DBs/homology/compara/meta.txt @@ -1,4 +1,4 @@ -128 \N schema_version 114 +130 \N schema_version 115 2 \N schema_type compara 3 \N patch patch_84_85_a.sql|schema_version 4 \N patch patch_84_85_b.sql|gene_tree_root_attr @@ -93,3 +93,4 @@ 126 \N patch patch_112_113_a.sql|schema_version 127 \N patch patch_112_113_b.sql|meta_key_64 129 \N patch patch_113_114_a.sql|schema_version +131 \N patch patch_114_115_a.sql|schema_version diff --git a/t/test-genome-DBs/homology/compara/table.sql b/t/test-genome-DBs/homology/compara/table.sql index 3b93ee62..69067c00 100644 --- a/t/test-genome-DBs/homology/compara/table.sql +++ b/t/test-genome-DBs/homology/compara/table.sql @@ -437,7 +437,7 @@ 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=130 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; +) ENGINE=MyISAM AUTO_INCREMENT=132 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; CREATE TABLE `method_link` ( `method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT, diff --git a/t/test-genome-DBs/meleagris_gallopavo/core/meta.txt b/t/test-genome-DBs/meleagris_gallopavo/core/meta.txt index f840801e..c5316f34 100644 --- a/t/test-genome-DBs/meleagris_gallopavo/core/meta.txt +++ b/t/test-genome-DBs/meleagris_gallopavo/core/meta.txt @@ -1,5 +1,5 @@ 1 \N schema_type core -2 \N schema_version 114 +2 \N schema_version 115 3 \N patch patch_59_60_a.sql|schema_version 4 \N patch patch_59_60_b.sql|rename_go_xref_table 5 \N patch patch_59_60_c.sql|QC_fixes @@ -227,3 +227,4 @@ 1105 \N patch patch_112_113_a.sql|schema_version 1106 \N patch patch_112_113_b.sql|Ensure meta_value is not null 1107 \N patch patch_113_114_a.sql|schema_version +1108 \N patch patch_114_115_a.sql|schema_version diff --git a/t/test-genome-DBs/meleagris_gallopavo/core/table.sql b/t/test-genome-DBs/meleagris_gallopavo/core/table.sql index ef35e545..8447a1da 100644 --- a/t/test-genome-DBs/meleagris_gallopavo/core/table.sql +++ b/t/test-genome-DBs/meleagris_gallopavo/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=1108 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; +) ENGINE=MyISAM AUTO_INCREMENT=1109 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; CREATE TABLE `meta_coord` ( `table_name` varchar(40) NOT NULL, diff --git a/t/test-genome-DBs/multi/compara/meta.txt b/t/test-genome-DBs/multi/compara/meta.txt index e442cc2d..5804a50d 100644 --- a/t/test-genome-DBs/multi/compara/meta.txt +++ b/t/test-genome-DBs/multi/compara/meta.txt @@ -1,4 +1,4 @@ -173 \N schema_version 114 +175 \N schema_version 115 2 \N schema_type compara 3 \N patch patch_71_72_a.sql|schema_version 4 \N patch patch_71_72_b.sql|new member_production_counts table @@ -137,3 +137,4 @@ 171 \N patch patch_112_113_a.sql|schema_version 172 \N patch patch_112_113_b.sql|meta_key_64 174 \N patch patch_113_114_a.sql|schema_version +176 \N patch patch_114_115_a.sql|schema_version diff --git a/t/test-genome-DBs/multi/compara/table.sql b/t/test-genome-DBs/multi/compara/table.sql index 935bd7a1..596b2e59 100644 --- a/t/test-genome-DBs/multi/compara/table.sql +++ b/t/test-genome-DBs/multi/compara/table.sql @@ -437,7 +437,7 @@ 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=175 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; +) ENGINE=MyISAM AUTO_INCREMENT=177 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; CREATE TABLE `method_link` ( `method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT, diff --git a/t/test-genome-DBs/multi/ontology/meta.txt b/t/test-genome-DBs/multi/ontology/meta.txt index 4602ee89..7348c8f2 100644 --- a/t/test-genome-DBs/multi/ontology/meta.txt +++ b/t/test-genome-DBs/multi/ontology/meta.txt @@ -5,7 +5,7 @@ 7 patch patch_71_72_d.sql|patch_version_fix \N 8 patch patch_71_72_e.sql|is_obsolete \N 1 schema_type ontology \N -5 schema_version 114 \N +5 schema_version 115 \N 10 patch patch_72_73_a.sql|schema_version \N 11 patch patch_72_73_b.sql|meta_species \N 13 patch patch_73_74_a.sql|schema_version \N @@ -59,3 +59,4 @@ 62 patch patch_112_113_a.sql|schema_version \N 63 patch patch_112_113_b.sql|Ensure meta_value is not null \N 64 patch patch_113_114_a.sql|schema_version \N +65 patch patch_114_115_a.sql|schema_version \N diff --git a/t/test-genome-DBs/multi/ontology/table.sql b/t/test-genome-DBs/multi/ontology/table.sql index e1d87e6d..6ef6df56 100644 --- a/t/test-genome-DBs/multi/ontology/table.sql +++ b/t/test-genome-DBs/multi/ontology/table.sql @@ -27,7 +27,7 @@ CREATE TABLE `meta` ( `species_id` int(10) unsigned DEFAULT NULL, PRIMARY KEY (`meta_id`), UNIQUE KEY `key_value_idx` (`meta_key`,`meta_value`) -) ENGINE=MyISAM AUTO_INCREMENT=65 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; +) ENGINE=MyISAM AUTO_INCREMENT=66 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; CREATE TABLE `ontology` ( `ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT, diff --git a/t/test-genome-DBs/taeniopygia_guttata/core/meta.txt b/t/test-genome-DBs/taeniopygia_guttata/core/meta.txt index 6cdaf445..f83e5da6 100644 --- a/t/test-genome-DBs/taeniopygia_guttata/core/meta.txt +++ b/t/test-genome-DBs/taeniopygia_guttata/core/meta.txt @@ -1,4 +1,4 @@ -1 \N schema_version 114 +1 \N schema_version 115 2 \N patch patch_50_51_a.sql|schema_version 3 \N patch patch_50_51_b.sql|protein_feature_hit_name 4 \N patch patch_50_51_c.sql|meta_coord_index @@ -271,3 +271,4 @@ 1327 \N patch patch_112_113_a.sql|schema_version 1328 \N patch patch_112_113_b.sql|Ensure meta_value is not null 1329 \N patch patch_113_114_a.sql|schema_version +1330 \N patch patch_114_115_a.sql|schema_version diff --git a/t/test-genome-DBs/taeniopygia_guttata/core/table.sql b/t/test-genome-DBs/taeniopygia_guttata/core/table.sql index 7c0d0a35..8bebe4c1 100644 --- a/t/test-genome-DBs/taeniopygia_guttata/core/table.sql +++ b/t/test-genome-DBs/taeniopygia_guttata/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=1330 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; +) ENGINE=MyISAM AUTO_INCREMENT=1331 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC; CREATE TABLE `meta_coord` ( `table_name` varchar(40) NOT NULL, -- GitLab