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marcoooomarcoooo
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Updating test dbs to latest schema
1 parent 0e94337 commit f733cb2

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+25
-16
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12 files changed

+25
-16
lines changed

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

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
1 \N schema_type core
2-
2 \N schema_version 107
2+
2 \N schema_version 108
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3 \N patch patch_88_89_a.sql|schema_version
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4 1 schema.load_started 2017-05-08 19:14:41
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5 1 schema.load_started 2017-05-08 19:14:45
@@ -193,3 +193,4 @@
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565 \N patch patch_105_106_a.sql|schema_version
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566 \N patch patch_106_107_a.sql|schema_version
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567 \N patch patch_106_107_b.sql|Added index for seq_region_mapping
196+
568 \N patch patch_107_108_a.sql|schema_version

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -490,7 +490,7 @@ CREATE TABLE `meta` (
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PRIMARY KEY (`meta_id`),
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UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
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KEY `species_value_idx` (`species_id`,`meta_value`)
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) ENGINE=MyISAM AUTO_INCREMENT=568 DEFAULT CHARSET=latin1 CHECKSUM=1;
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) ENGINE=MyISAM AUTO_INCREMENT=569 DEFAULT CHARSET=latin1 CHECKSUM=1;
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CREATE TABLE `meta_coord` (
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`table_name` varchar(40) NOT NULL,

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

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
1 \N schema_type core
2-
2 \N schema_version 107
2+
2 \N schema_version 108
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3 \N patch patch_76_77_a.sql|schema_version
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4 1 assembly.mapping chromosome:BDGP6|contig:BDGP6
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5 1 assembly.mapping contig:BDGP6|chunk:BDGP6
@@ -147,3 +147,4 @@
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237 \N patch patch_105_106_a.sql|schema_version
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238 \N patch patch_106_107_a.sql|schema_version
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239 \N patch patch_106_107_b.sql|Added index for seq_region_mapping
150+
240 \N patch patch_107_108_a.sql|schema_version

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -490,7 +490,7 @@ CREATE TABLE `meta` (
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PRIMARY KEY (`meta_id`),
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UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
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KEY `species_value_idx` (`species_id`,`meta_value`)
493-
) ENGINE=MyISAM AUTO_INCREMENT=240 DEFAULT CHARSET=latin1 CHECKSUM=1;
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) ENGINE=MyISAM AUTO_INCREMENT=241 DEFAULT CHARSET=latin1 CHECKSUM=1;
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CREATE TABLE `meta_coord` (
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`table_name` varchar(40) NOT NULL,

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

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
1 \N schema_type core
2-
2 \N schema_version 107
2+
2 \N schema_version 108
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3 \N patch patch_73_74_a.sql|schema_version
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4 \N patch patch_73_74_b.sql|remove_dnac
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5 \N patch patch_73_74_c.sql|remove_unconventional_transcript_association
@@ -194,3 +194,4 @@
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5893 \N patch patch_105_106_a.sql|schema_version
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5894 \N patch patch_106_107_a.sql|schema_version
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5895 \N patch patch_106_107_b.sql|Added index for seq_region_mapping
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5896 \N patch patch_107_108_a.sql|schema_version

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -490,7 +490,7 @@ CREATE TABLE `meta` (
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PRIMARY KEY (`meta_id`),
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UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
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KEY `species_value_idx` (`species_id`,`meta_value`)
493-
) ENGINE=MyISAM AUTO_INCREMENT=5896 DEFAULT CHARSET=latin1;
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) ENGINE=MyISAM AUTO_INCREMENT=5897 DEFAULT CHARSET=latin1;
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CREATE TABLE `meta_coord` (
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`table_name` varchar(40) NOT NULL,

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

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
1 1 schema_type funcgen
2-
2 \N schema_version 107
2+
2 \N schema_version 108
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3 \N patch patch_87_88_a.sql|schema_version
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4 \N patch patch_87_88_b.sql|seq_region_name_255
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5 \N patch patch_87_88_c.sql|sample_regulatory_feature_id field for regulatory build
@@ -140,3 +140,4 @@
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140 \N patch patch_104_105_b.sql|New indices
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141 \N patch patch_105_106_a.sql|schema_version
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142 \N patch patch_106_107_a.sql|schema_version
143+
143 \N patch patch_107_108_a.sql|schema_version

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -382,7 +382,7 @@ CREATE TABLE `meta` (
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PRIMARY KEY (`meta_id`),
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UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
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KEY `species_value_idx` (`species_id`,`meta_value`)
385-
) ENGINE=MyISAM AUTO_INCREMENT=143 DEFAULT CHARSET=latin1;
385+
) ENGINE=MyISAM AUTO_INCREMENT=144 DEFAULT CHARSET=latin1;
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CREATE TABLE `meta_coord` (
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`table_name` varchar(40) NOT NULL,

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

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
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1 \N schema_type variation
2-
2 \N schema_version 107
2+
2 \N schema_version 108
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3 1 species.production_name homo_sapiens
44
4 \N patch patch_94_95_a.sql|schema version
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5 \N patch patch_94_95_b.sql|create table to store allele synonyms
@@ -30,3 +30,6 @@
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47 \N patch patch_105_106_a.sql|schema version
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48 \N patch patch_106_107_a.sql|schema version
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49 \N patch patch_106_107_b.sql|consequences update
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50 \N patch patch_106_107_c.sql|remove regulatory and TFBS consequences from consequence_types in transcript_variation
34+
51 \N patch patch_107_108_a.sql|schema version
35+
52 \N patch patch_107_108_b.sql|fix SAS population description

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -186,7 +186,7 @@ CREATE TABLE `meta` (
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PRIMARY KEY (`meta_id`),
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UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
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KEY `species_value_idx` (`species_id`,`meta_value`)
189-
) ENGINE=MyISAM AUTO_INCREMENT=50 DEFAULT CHARSET=latin1;
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) ENGINE=MyISAM AUTO_INCREMENT=53 DEFAULT CHARSET=latin1;
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CREATE TABLE `meta_coord` (
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`table_name` varchar(40) NOT NULL,
@@ -544,7 +544,7 @@ CREATE TABLE `transcript_variation` (
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`feature_stable_id` varchar(128) DEFAULT NULL,
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`allele_string` text,
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`somatic` tinyint(1) NOT NULL DEFAULT '0',
547-
`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','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_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,
547+
`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,
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`cds_start` int(11) unsigned DEFAULT NULL,
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`cds_end` int(11) unsigned DEFAULT NULL,
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`cdna_start` int(11) unsigned DEFAULT NULL,

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