diff --git a/modules/t/test-genome-DBs/circ/core/associated_group.txt b/modules/t/test-genome-DBs/circ/core/associated_group.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/modules/t/test-genome-DBs/circ/core/associated_xref.txt b/modules/t/test-genome-DBs/circ/core/associated_xref.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/modules/t/test-genome-DBs/circ/core/meta.txt b/modules/t/test-genome-DBs/circ/core/meta.txt index 5255a9360b95ebca80c1d226c6582f9fee887d5c..07b26570637bcffad84b748e6a030749f14d4829 100644 --- a/modules/t/test-genome-DBs/circ/core/meta.txt +++ b/modules/t/test-genome-DBs/circ/core/meta.txt @@ -1,4 +1,4 @@ -1 \N schema_version 71 +1 \N schema_version 72 2 1 assembly.default NCBI34 33 1 species.classification Chordata 32 1 species.classification Vertebrata @@ -32,3 +32,5 @@ 81 \N patch patch_69_70_e.sql|protein_feature_hit_description 82 \N patch patch_70_71_a.sql|schema_version 83 \N patch patch_70_71_b.sql|mapping_set_index +84 \N patch patch_71_72_a.sql|schema_version +85 \N patch patch_71_72_b.sql|associated_xref diff --git a/modules/t/test-genome-DBs/circ/core/table.sql b/modules/t/test-genome-DBs/circ/core/table.sql index b2f67ffe5117d32fcc3e0e4399f3db1db4353bc8..b694723385f784f6002eea34f93e3ad5b7e3b10b 100644 --- a/modules/t/test-genome-DBs/circ/core/table.sql +++ b/modules/t/test-genome-DBs/circ/core/table.sql @@ -63,6 +63,28 @@ CREATE TABLE `assembly_exception` ( KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`) ) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1; +CREATE TABLE `associated_group` ( + `associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT, + `description` varchar(128) DEFAULT NULL, + PRIMARY KEY (`associated_group_id`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; + +CREATE TABLE `associated_xref` ( + `associated_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT, + `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0', + `xref_id` int(10) unsigned NOT NULL DEFAULT '0', + `source_xref_id` int(10) unsigned DEFAULT NULL, + `condition_type` varchar(128) DEFAULT NULL, + `associated_group_id` int(10) unsigned DEFAULT NULL, + `rank` int(10) unsigned DEFAULT '0', + PRIMARY KEY (`associated_xref_id`), + UNIQUE KEY `object_associated_source_type_idx` (`object_xref_id`,`xref_id`,`source_xref_id`,`condition_type`,`associated_group_id`), + KEY `associated_source_idx` (`source_xref_id`), + KEY `associated_object_idx` (`object_xref_id`), + KEY `associated_idx` (`xref_id`), + KEY `associated_group_idx` (`associated_group_id`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; + CREATE TABLE `attrib_type` ( `attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT, `code` varchar(15) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '', @@ -425,7 +447,7 @@ 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=84 DEFAULT CHARSET=latin1; +) ENGINE=MyISAM AUTO_INCREMENT=86 DEFAULT CHARSET=latin1; CREATE TABLE `meta_coord` ( `table_name` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '', diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/associated_group.txt b/modules/t/test-genome-DBs/homo_sapiens/core/associated_group.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/associated_xref.txt b/modules/t/test-genome-DBs/homo_sapiens/core/associated_xref.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt index 2e7573efd9ff92b62cceabdcc336b35625158c3f..7def1fec549280298e804de1a3bd4d37b19f90c1 100644 --- a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt +++ b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt @@ -1,4 +1,4 @@ -1 \N schema_version 71 +1 \N schema_version 72 2 1 assembly.default NCBI34 33 1 species.classification Chordata 32 1 species.classification Vertebrata @@ -32,3 +32,5 @@ 77 \N schema_type core 78 \N patch patch_70_71_a.sql|schema_version 79 \N patch patch_70_71_b.sql|mapping_set_index +80 \N patch patch_71_72_a.sql|schema_version +81 \N patch patch_71_72_b.sql|associated_xref diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql index 1de6263fdd229f6bd9a92a436c339c784df96b5e..41ed34a52ff823df2ef0d6f900959a3ed97bab80 100644 --- a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql +++ b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql @@ -63,6 +63,28 @@ CREATE TABLE `assembly_exception` ( KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`) ) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin; +CREATE TABLE `associated_group` ( + `associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT, + `description` varchar(128) DEFAULT NULL, + PRIMARY KEY (`associated_group_id`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; + +CREATE TABLE `associated_xref` ( + `associated_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT, + `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0', + `xref_id` int(10) unsigned NOT NULL DEFAULT '0', + `source_xref_id` int(10) unsigned DEFAULT NULL, + `condition_type` varchar(128) DEFAULT NULL, + `associated_group_id` int(10) unsigned DEFAULT NULL, + `rank` int(10) unsigned DEFAULT '0', + PRIMARY KEY (`associated_xref_id`), + UNIQUE KEY `object_associated_source_type_idx` (`object_xref_id`,`xref_id`,`source_xref_id`,`condition_type`,`associated_group_id`), + KEY `associated_source_idx` (`source_xref_id`), + KEY `associated_object_idx` (`object_xref_id`), + KEY `associated_idx` (`xref_id`), + KEY `associated_group_idx` (`associated_group_id`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; + CREATE TABLE `attrib_type` ( `attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT, `code` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '', @@ -426,7 +448,7 @@ 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=80 DEFAULT CHARSET=latin1; +) ENGINE=MyISAM AUTO_INCREMENT=82 DEFAULT CHARSET=latin1; CREATE TABLE `meta_coord` ( `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '', diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/associated_group.txt b/modules/t/test-genome-DBs/homo_sapiens/empty/associated_group.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/associated_xref.txt b/modules/t/test-genome-DBs/homo_sapiens/empty/associated_xref.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt index 09bfdba9ee49493767ad87232ff60fc77134234d..7744759edf66d58c59eda0bcc62f0a862bc80be0 100644 --- a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt +++ b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt @@ -1,4 +1,4 @@ -1 \N schema_version 71 +1 \N schema_version 72 2 1 assembly.default NCBI34 33 1 species.classification Chordata 32 1 species.classification Vertebrata @@ -32,3 +32,5 @@ 81 \N patch patch_69_70_e.sql|protein_feature_hit_description 82 \N patch patch_70_71_a.sql|schema_version 83 \N patch patch_70_71_b.sql|mapping_set_index +84 \N patch patch_71_72_a.sql|schema_version +85 \N patch patch_71_72_b.sql|associated_xref diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql index d3d1f0f15aef7b85509b4847018f7fea4527fc03..38f23d93215d17f6b6dea4689c9ec0f42d3301f4 100644 --- a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql +++ b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql @@ -63,6 +63,28 @@ CREATE TABLE `assembly_exception` ( KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`) ) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1; +CREATE TABLE `associated_group` ( + `associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT, + `description` varchar(128) DEFAULT NULL, + PRIMARY KEY (`associated_group_id`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; + +CREATE TABLE `associated_xref` ( + `associated_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT, + `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0', + `xref_id` int(10) unsigned NOT NULL DEFAULT '0', + `source_xref_id` int(10) unsigned DEFAULT NULL, + `condition_type` varchar(128) DEFAULT NULL, + `associated_group_id` int(10) unsigned DEFAULT NULL, + `rank` int(10) unsigned DEFAULT '0', + PRIMARY KEY (`associated_xref_id`), + UNIQUE KEY `object_associated_source_type_idx` (`object_xref_id`,`xref_id`,`source_xref_id`,`condition_type`,`associated_group_id`), + KEY `associated_source_idx` (`source_xref_id`), + KEY `associated_object_idx` (`object_xref_id`), + KEY `associated_idx` (`xref_id`), + KEY `associated_group_idx` (`associated_group_id`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; + CREATE TABLE `attrib_type` ( `attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT, `code` varchar(15) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '', @@ -425,7 +447,7 @@ 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=84 DEFAULT CHARSET=latin1; +) ENGINE=MyISAM AUTO_INCREMENT=86 DEFAULT CHARSET=latin1; CREATE TABLE `meta_coord` ( `table_name` varchar(40) CHARACTER SET latin1 COLLATE latin1_bin NOT NULL DEFAULT '',