Commit f2c97b6a authored by Marek Szuba's avatar Marek Szuba
Browse files

Manually patch the test databases from 90 to 98

parent 791ebe25
This source diff could not be displayed because it is too large. You can view the blob instead.
1 \N schema_version 90
1 \N schema_version 98
2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens
......@@ -89,3 +89,24 @@
156 \N patch patch_89_90_a.sql|schema_version
157 \N patch patch_89_90_b.sql|remove_status
158 \N patch patch_89_90_c.sql|pf_hit_name_case_sensitive
159 \N patch patch_90_91_a.sql|schema_version
160 \N patch patch_90_91_b.sql|align_type
161 \N patch patch_90_91_c.sql|protein_align_type
162 \N patch patch_90_91_d.sql|remove_external_data
163 \N patch patch_91_92_a.sql|schema_version
164 \N patch patch_91_92_b.sql|add_cigar_line_align_type
165 \N patch patch_92_93_a.sql|schema_version
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_b.sql|nullable_ox_analysis
170 \N patch patch_93_94_c.sql|default_aln_type
171 \N patch patch_94_95_a.sql|schema_version
172 \N patch patch_94_95_b.sql|vertebrate_division_rename
173 \N patch patch_95_96_a.sql|schema_version
174 \N patch patch_96_97_a.sql|schema_version
175 \N patch patch_96_97_b.sql|biotype_so_term
176 \N patch patch_96_97_c.sql|rnaproduct_tables
177 \N patch patch_96_97_d.sql|add_object_type_rnaproduct
178 \N patch patch_96_97_e.sql|add_stable_id_event_type_rnaproduct
179 \N patch patch_97_98_a.sql|schema_version
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149839 21722 Translation 102408 119 0
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190803 21731 Translation 128324 119 0
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500 21735 Translation 332 119 \N
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502 21735 Translation 334 119 \N
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104881 21737 Translation 72100 119 \N
104882 21737 Translation 72101 119 \N
130254 21734 Translation 89323 119 \N
130255 21734 Translation 89324 119 \N
130256 21734 Translation 89325 119 \N
130257 21733 Translation 89326 119 \N
130258 21733 Translation 89324 119 \N
130259 21733 Translation 89327 119 \N
142713 21738 Translation 97756 119 \N
142714 21738 Translation 97757 119 \N
142715 21738 Translation 97758 119 \N
142716 21738 Translation 97759 119 \N
149839 21722 Translation 102408 119 \N
149840 21722 Translation 102409 119 \N
149841 21722 Translation 102410 119 \N
149842 21722 Translation 34986 119 \N
149843 21722 Translation 994 119 \N
149844 21720 Translation 102411 119 \N
149845 21720 Translation 102409 119 \N
149846 21720 Translation 102412 119 \N
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151214 21738 Translation 103295 119 \N
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151217 21738 Translation 15954 119 \N
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151219 21738 Translation 2617 119 \N
151220 21738 Translation 18952 119 \N
151221 21738 Translation 50 119 \N
151222 21738 Translation 891 119 \N
151223 21738 Translation 51 119 \N
151224 21738 Translation 269 119 \N
179285 21724 Translation 120576 119 \N
179286 21724 Translation 120577 119 \N
179287 21724 Translation 120578 119 \N
179288 21724 Translation 120579 119 \N
179289 21724 Translation 120580 119 \N
179290 21724 Translation 120581 119 \N
179291 21724 Translation 120582 119 \N
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179294 21724 Translation 1166 119 \N
179295 21724 Translation 793 119 \N
179296 21724 Translation 438 119 \N
190803 21731 Translation 128324 119 \N
190804 21731 Translation 128325 119 \N
190805 21731 Translation 128326 119 \N
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191217 21728 Translation 28816 119 \N
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191222 21728 Translation 54393 119 \N
191223 21728 Translation 612 119 \N
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191225 21728 Translation 128347 119 \N
191226 21728 Translation 673 119 \N
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191240 21725 Translation 128605 119 \N
191241 21725 Translation 28816 119 \N
191242 21725 Translation 128606 119 \N
191243 21725 Translation 128607 119 \N
191244 21725 Translation 315 119 \N
191245 21725 Translation 3908 119 \N
191246 21725 Translation 143 119 \N
229061 21717 Translation 152191 119 \N
229062 21717 Translation 102409 119 \N
229063 21717 Translation 152192 119 \N
229064 21717 Translation 6990 119 \N
229065 21717 Translation 614 119 \N
229073 21716 Translation 152200 119 \N
229074 21716 Translation 102409 119 \N
229075 21716 Translation 152201 119 \N
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229273 21732 Translation 152329 119 \N
229274 21732 Translation 89324 119 \N
229275 21732 Translation 152330 119 \N
238768 21723 Translation 158504 119 \N
238769 21723 Translation 158505 119 \N
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238771 21723 Translation 158507 119 \N
238772 21723 Translation 158508 119 \N
238773 21723 Translation 158509 119 \N
238774 21723 Translation 158510 119 \N
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238791 21723 Translation 257 119 \N
238792 21723 Translation 258 119 \N
238793 21723 Translation 259 119 \N
238794 21723 Translation 612 119 \N
238795 21723 Translation 260 119 \N
238796 21723 Translation 994 119 \N
238797 21723 Translation 5371 119 \N
251369 21723 Translation 166799 119 \N
251370 21723 Translation 166800 119 \N
253531 21736 Translation 168321 119 \N
253532 21736 Translation 168322 119 \N
253533 21736 Translation 168323 119 \N
253534 21736 Translation 168324 119 \N
253682 21727 Translation 168444 119 \N
253683 21727 Translation 168445 119 \N
253684 21727 Translation 168446 119 \N
This source diff could not be displayed because it is too large. You can view the blob instead.
......@@ -28,7 +28,7 @@ CREATE TABLE `analysis` (
`program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`parameters` text COLLATE latin1_bin,
`parameters` text COLLATE latin1_bin DEFAULT NULL,
`module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
......@@ -38,22 +38,22 @@ CREATE TABLE `analysis` (
) ENGINE=MyISAM AUTO_INCREMENT=8412 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
`analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`description` text COLLATE latin1_bin,
`analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
`description` text COLLATE latin1_bin DEFAULT NULL,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`displayable` tinyint(1) NOT NULL DEFAULT '1',
`web_data` text COLLATE latin1_bin,
`displayable` tinyint(1) NOT NULL DEFAULT 1,
`web_data` text COLLATE latin1_bin DEFAULT NULL,
UNIQUE KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly` (
`asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`asm_start` int(10) NOT NULL DEFAULT '0',
`asm_end` int(10) NOT NULL DEFAULT '0',
`cmp_start` int(10) NOT NULL DEFAULT '0',
`cmp_end` int(10) NOT NULL DEFAULT '0',
`ori` tinyint(4) NOT NULL DEFAULT '0',
`asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
`cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
`asm_start` int(10) NOT NULL DEFAULT 0,
`asm_end` int(10) NOT NULL DEFAULT 0,
`cmp_start` int(10) NOT NULL DEFAULT 0,
`cmp_end` int(10) NOT NULL DEFAULT 0,
`ori` tinyint(4) NOT NULL DEFAULT 0,
UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
......@@ -61,14 +61,14 @@ CREATE TABLE `assembly` (
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_region_id` int(11) NOT NULL DEFAULT '0',
`seq_region_start` int(11) NOT NULL DEFAULT '0',
`seq_region_end` int(11) NOT NULL DEFAULT '0',
`seq_region_id` int(11) NOT NULL DEFAULT 0,
`seq_region_start` int(11) NOT NULL DEFAULT 0,
`seq_region_end` int(11) NOT NULL DEFAULT 0,
`exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
`exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
`exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
`exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
`ori` int(11) NOT NULL DEFAULT '0',
`exc_seq_region_id` int(11) NOT NULL DEFAULT 0,
`exc_seq_region_start` int(11) NOT NULL DEFAULT 0,
`exc_seq_region_end` int(11) NOT NULL DEFAULT 0,
`ori` int(11) NOT NULL DEFAULT 0,
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
......@@ -82,12 +82,12 @@ CREATE TABLE `associated_group` (
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',
`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',
`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`),
......@@ -100,14 +100,28 @@ CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`description` text COLLATE latin1_bin,
`description` text COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM AUTO_INCREMENT=392 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `biotype` (
`biotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(64) NOT NULL,
`object_type` enum('gene','transcript') NOT NULL DEFAULT 'gene',
`db_type` set('cdna','core','coreexpressionatlas','coreexpressionest','coreexpressiongnf','funcgen','otherfeatures','rnaseq','variation','vega','presite','sangervega') NOT NULL DEFAULT 'core',
`attrib_type_id` int(11) DEFAULT NULL,
`description` text DEFAULT NULL,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
`so_acc` varchar(64) DEFAULT NULL,
`so_term` varchar(1023) DEFAULT NULL,
PRIMARY KEY (`biotype_id`),
UNIQUE KEY `name_type_idx` (`name`,`object_type`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`species_id` int(10) unsigned NOT NULL DEFAULT '1',
`species_id` int(10) unsigned NOT NULL DEFAULT 1,
`name` varchar(40) NOT NULL,
`version` varchar(255) DEFAULT NULL,
`rank` int(11) NOT NULL,
......@@ -123,9 +137,9 @@ CREATE TABLE `data_file` (
`coord_system_id` int(10) unsigned NOT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
`name` varchar(100) NOT NULL,
`version_lock` tinyint(1) NOT NULL DEFAULT '0',
`absolute` tinyint(1) NOT NULL DEFAULT '0',
`url` text,
`version_lock` tinyint(1) NOT NULL DEFAULT 0,
`absolute` tinyint(1) NOT NULL DEFAULT 0,
`url` text DEFAULT NULL,
`file_type` enum('BAM','BAMCOV','BIGBED','BIGWIG','VCF') DEFAULT NULL,
PRIMARY KEY (`data_file_id`),
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
......@@ -135,11 +149,11 @@ CREATE TABLE `data_file` (
CREATE TABLE `density_feature` (
`density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
`density_type_id` int(11) NOT NULL DEFAULT '0',
`seq_region_id` int(11) NOT NULL DEFAULT '0',
`seq_region_start` int(11) NOT NULL DEFAULT '0',
`seq_region_end` int(11) NOT NULL DEFAULT '0',
`density_value` float NOT NULL DEFAULT '0',
`density_type_id` int(11) NOT NULL DEFAULT 0,
`seq_region_id` int(11) NOT NULL DEFAULT 0,
`seq_region_start` int(11) NOT NULL DEFAULT 0,
`seq_region_end` int(11) NOT NULL DEFAULT 0,
`density_value` float NOT NULL DEFAULT 0,
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
......@@ -147,9 +161,9 @@ CREATE TABLE `density_feature` (
CREATE TABLE `density_type` (
`density_type_id` int(11) NOT NULL AUTO_INCREMENT,
`analysis_id` int(11) NOT NULL DEFAULT '0',
`block_size` int(11) NOT NULL DEFAULT '0',
`region_features` int(11) NOT NULL DEFAULT '0',