Merge remote-tracking branch 'origin/patch_test_dbs' into bcf_parser

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

-1	\N	schema_version	100
+1	\N	schema_version	101
 2	1	assembly.default	NCBI34
 3	1	species.taxonomy_id	9606
 26	1	species.classification	Homo sapiens
@@ -112,3 +112,5 @@
 179	\N	patch	patch_98_99_a.sql|schema_version
 180	\N	patch	patch_99_100_a.sql|schema_version
 181	\N	patch	patch_99_100_b.sql|alter_externaldb_type_notnull
+182	\N	patch	patch_99_100_c.sql|alter_mapping_session_assembly_length
+183	\N	patch	patch_100_101_a.sql|schema_version

modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt

-1	\N	schema_version	100
+1	\N	schema_version	101
 2	1	assembly.default	NCBI34
 33	1	species.classification	Chordata
 32	1	species.classification	Vertebrata
@@ -112,3 +112,5 @@
 161	\N	patch	patch_98_99_a.sql|schema_version
 162	\N	patch	patch_99_100_a.sql|schema_version
 163	\N	patch	patch_99_100_b.sql|alter_externaldb_type_notnull
+164	\N	patch	patch_99_100_c.sql|alter_mapping_session_assembly_length
+165	\N	patch	patch_100_101_a.sql|schema_version

modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt

-1	\N	schema_version	100
+1	\N	schema_version	101
 2014	1	species.classification	Haplorrhini
 40	1	assembly.default	GRCh37
 41	1	assembly.date	2009-02
@@ -117,3 +117,5 @@
 2124	\N	patch	patch_98_99_a.sql|schema_version
 2125	\N	patch	patch_99_100_a.sql|schema_version
 2126	\N	patch	patch_99_100_b.sql|alter_externaldb_type_notnull
+2127	\N	patch	patch_99_100_c.sql|alter_mapping_session_assembly_length
+2128	\N	patch	patch_100_101_a.sql|schema_version

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

@@ -49,3 +49,5 @@
 49	\N	patch	patch_98_99_d.sql|add key data_source_attrib
 50	\N	patch	patch_98_99_e.sql|Fix attrib ids in table variation_citation
 51	\N	patch	patch_99_100_a.sql|schema version
+52	\N	patch	patch_99_100_b.sql|add frequency to structural variation
+53	\N	patch	patch_99_100_c.sql|add class_attrib_id column to phenotype

modules/t/test-genome-DBs/homo_sapiens/variation/phenotype.txt

-1	\N	phenotype	\N
-2	\N	phenotype2	\N
+1	\N	phenotype	\N	\N
+2	\N	phenotype2	\N	\N

modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation_feature.txt

-1	469283	\N	30253000	\N	\N	30254000	\N	1	1	nsv12345	1	1	208	\N	0	0	\N	\N	1
-2	469283	\N	30255000	\N	\N	30256000	\N	1	2	nsv67890	1	1	208	\N	0	1	\N	\N	1
-3	469283	\N	30257000	\N	\N	30258000	\N	1	3	nsv09876	1	1	114	\N	0	0	\N	\N	
+1	469283	\N	30253000	\N	\N	30254000	\N	1	1	nsv12345	1	1	208	\N	0	0	\N	\N	1	\N	\N
+2	469283	\N	30255000	\N	\N	30256000	\N	1	2	nsv67890	1	1	208	\N	0	1	\N	\N	1	\N	\N
+3	469283	\N	30257000	\N	\N	30258000	\N	1	3	nsv09876	1	1	114	\N	0	0	\N	\N		\N	\N

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

@@ -38,24 +38,24 @@ CREATE TABLE `associate_study` (
 
 CREATE TABLE `attrib` (
   `attrib_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
-  `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+  `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
   `value` text NOT NULL,
   PRIMARY KEY (`attrib_id`),
   UNIQUE KEY `type_val_idx` (`attrib_type_id`,`value`(80))
 ) ENGINE=MyISAM AUTO_INCREMENT=422 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `attrib_set` (
-  `attrib_set_id` int(11) unsigned NOT NULL DEFAULT 0,
-  `attrib_id` int(11) unsigned NOT NULL DEFAULT 0,
+  `attrib_set_id` int(11) unsigned NOT NULL DEFAULT '0',
+  `attrib_id` int(11) unsigned NOT NULL DEFAULT '0',
   UNIQUE KEY `set_idx` (`attrib_set_id`,`attrib_id`),
   KEY `attrib_idx` (`attrib_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `attrib_type` (
-  `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+  `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
   `code` varchar(20) NOT NULL DEFAULT '',
   `name` varchar(255) NOT NULL DEFAULT '',
-  `description` text DEFAULT NULL,
+  `description` text,
   PRIMARY KEY (`attrib_type_id`),
   UNIQUE KEY `code_idx` (`code`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -66,7 +66,7 @@ CREATE TABLE `compressed_genotype_region` (
   `seq_region_start` int(11) NOT NULL,
   `seq_region_end` int(11) NOT NULL,
   `seq_region_strand` tinyint(4) NOT NULL,
-  `genotypes` blob DEFAULT NULL,
+  `genotypes` blob,
   KEY `pos_idx` (`seq_region_id`,`seq_region_start`),
   KEY `sample_idx` (`sample_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -74,14 +74,14 @@ CREATE TABLE `compressed_genotype_region` (
 CREATE TABLE `compressed_genotype_var` (
   `variation_id` int(11) unsigned NOT NULL,
   `subsnp_id` int(11) unsigned DEFAULT NULL,
-  `genotypes` blob DEFAULT NULL,
+  `genotypes` blob,
   KEY `variation_idx` (`variation_id`),
   KEY `subsnp_idx` (`subsnp_id`)
 ) 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,
@@ -151,11 +151,11 @@ CREATE TABLE `genotype_code` (
 CREATE TABLE `individual` (
   `individual_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `name` varchar(255) DEFAULT NULL,
-  `description` text DEFAULT NULL,
+  `description` text,
   `gender` enum('Male','Female','Unknown') NOT NULL DEFAULT 'Unknown',
   `father_individual_id` int(10) unsigned DEFAULT NULL,
   `mother_individual_id` int(10) unsigned DEFAULT NULL,
-  `individual_type_id` int(10) unsigned NOT NULL DEFAULT 0,
+  `individual_type_id` int(10) unsigned NOT NULL DEFAULT '0',
   PRIMARY KEY (`individual_id`),
   KEY `father_individual_idx` (`father_individual_id`),
   KEY `mother_individual_idx` (`mother_individual_id`)
@@ -174,19 +174,19 @@ CREATE TABLE `individual_synonym` (
 CREATE TABLE `individual_type` (
   `individual_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `name` varchar(255) NOT NULL,
-  `description` text DEFAULT NULL,
+  `description` text,
   PRIMARY KEY (`individual_type_id`)
 ) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta` (
   `meta_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `species_id` int(10) unsigned DEFAULT 1,
+  `species_id` int(10) unsigned DEFAULT '1',
   `meta_key` varchar(40) NOT NULL,
   `meta_value` varchar(255) NOT NULL,
   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=52 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=54 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
@@ -200,14 +200,14 @@ CREATE TABLE `motif_feature_variation` (
   `variation_feature_id` int(11) unsigned NOT NULL,
   `feature_stable_id` varchar(128) DEFAULT NULL,
   `motif_feature_id` int(11) unsigned NOT NULL,
-  `allele_string` text DEFAULT NULL,
-  `somatic` tinyint(1) NOT NULL DEFAULT 0,
+  `allele_string` text,
+  `somatic` tinyint(1) NOT NULL DEFAULT '0',
   `consequence_types` set('TF_binding_site_variant','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation') DEFAULT NULL,
   `binding_matrix_stable_id` varchar(60) DEFAULT NULL,
   `motif_start` int(11) unsigned DEFAULT NULL,
   `motif_end` int(11) unsigned DEFAULT NULL,
   `motif_score_delta` float DEFAULT NULL,
-  `in_informative_position` tinyint(1) NOT NULL DEFAULT 0,
+  `in_informative_position` tinyint(1) NOT NULL DEFAULT '0',
   PRIMARY KEY (`motif_feature_variation_id`),
   KEY `variation_feature_idx` (`variation_feature_id`),
   KEY `consequence_type_idx` (`consequence_types`),
@@ -220,6 +220,7 @@ CREATE TABLE `phenotype` (
   `stable_id` varchar(255) DEFAULT NULL,
   `name` varchar(50) DEFAULT NULL,
   `description` varchar(255) DEFAULT NULL,
+  `class_attrib_id` int(11) DEFAULT NULL,
   PRIMARY KEY (`phenotype_id`),
   UNIQUE KEY `desc_idx` (`description`),
   KEY `name_idx` (`name`),
@@ -233,7 +234,7 @@ CREATE TABLE `phenotype_feature` (
   `study_id` int(11) unsigned DEFAULT NULL,
   `type` enum('Gene','Variation','StructuralVariation','SupportingStructuralVariation','QTL','RegulatoryFeature') DEFAULT NULL,
   `object_id` varchar(255) DEFAULT NULL,
-  `is_significant` tinyint(1) unsigned DEFAULT 1,
+  `is_significant` tinyint(1) unsigned DEFAULT '1',
   `seq_region_id` int(11) unsigned DEFAULT NULL,
   `seq_region_start` int(11) unsigned DEFAULT NULL,
   `seq_region_end` int(11) unsigned DEFAULT NULL,
@@ -267,8 +268,8 @@ CREATE TABLE `population` (
   `population_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `name` varchar(255) DEFAULT NULL,
   `size` int(10) DEFAULT NULL,
-  `description` text DEFAULT NULL,
-  `collection` tinyint(1) DEFAULT 0,
+  `description` text,
+  `collection` tinyint(1) DEFAULT '0',
   `freqs_from_gts` tinyint(1) DEFAULT NULL,
   `display` enum('LD','MARTDISPLAYABLE','UNDISPLAYABLE') DEFAULT 'UNDISPLAYABLE',
   `display_group_id` tinyint(1) DEFAULT NULL,
@@ -310,7 +311,7 @@ CREATE TABLE `population_synonym` (
 CREATE TABLE `protein_function_predictions` (
   `translation_md5_id` int(11) unsigned NOT NULL,
   `analysis_attrib_id` int(11) unsigned NOT NULL,
-  `prediction_matrix` mediumblob DEFAULT NULL,
+  `prediction_matrix` mediumblob,
   PRIMARY KEY (`translation_md5_id`,`analysis_attrib_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
@@ -318,7 +319,7 @@ CREATE TABLE `protein_function_predictions_attrib` (
   `translation_md5_id` int(11) unsigned NOT NULL,
   `analysis_attrib_id` int(11) unsigned NOT NULL,
   `attrib_type_id` int(11) unsigned NOT NULL,
-  `position_values` blob DEFAULT NULL,
+  `position_values` blob,
   PRIMARY KEY (`translation_md5_id`,`analysis_attrib_id`,`attrib_type_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
@@ -350,9 +351,9 @@ CREATE TABLE `regulatory_feature_variation` (
   `regulatory_feature_variation_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
   `variation_feature_id` int(11) unsigned NOT NULL,
   `feature_stable_id` varchar(128) DEFAULT NULL,
-  `feature_type` text DEFAULT NULL,
-  `allele_string` text DEFAULT NULL,
-  `somatic` tinyint(1) NOT NULL DEFAULT 0,
+  `feature_type` text,
+  `allele_string` text,
+  `somatic` tinyint(1) NOT NULL DEFAULT '0',
   `consequence_types` set('regulatory_region_variant','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation') DEFAULT NULL,
   PRIMARY KEY (`regulatory_feature_variation_id`),
   KEY `variation_feature_idx` (`variation_feature_id`),
@@ -365,10 +366,10 @@ CREATE TABLE `sample` (
   `sample_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `individual_id` int(10) unsigned NOT NULL,
   `name` varchar(255) DEFAULT NULL,
-  `description` text DEFAULT NULL,
+  `description` text,
   `study_id` int(10) unsigned DEFAULT NULL,
   `display` enum('REFERENCE','DEFAULT','DISPLAYABLE','UNDISPLAYABLE','LD','MARTDISPLAYABLE') DEFAULT 'UNDISPLAYABLE',
-  `has_coverage` tinyint(1) unsigned NOT NULL DEFAULT 0,
+  `has_coverage` tinyint(1) unsigned NOT NULL DEFAULT '0',
   `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') DEFAULT NULL,
   PRIMARY KEY (`sample_id`),
   KEY `individual_idx` (`individual_id`),
@@ -431,11 +432,11 @@ CREATE TABLE `structural_variation` (
   `alias` varchar(255) DEFAULT NULL,
   `source_id` int(10) unsigned NOT NULL,
   `study_id` int(10) unsigned DEFAULT NULL,
-  `class_attrib_id` int(10) unsigned NOT NULL DEFAULT 0,
+  `class_attrib_id` int(10) unsigned NOT NULL DEFAULT '0',
   `clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
   `validation_status` enum('validated','not validated','high quality') DEFAULT NULL,
-  `is_evidence` tinyint(4) DEFAULT 0,
-  `somatic` tinyint(1) NOT NULL DEFAULT 0,
+  `is_evidence` tinyint(4) DEFAULT '0',
+  `somatic` tinyint(1) NOT NULL DEFAULT '0',
   `copy_number` tinyint(2) DEFAULT NULL,
   PRIMARY KEY (`structural_variation_id`),
   UNIQUE KEY `variation_name` (`variation_name`),
@@ -466,13 +467,15 @@ CREATE TABLE `structural_variation_feature` (
   `variation_name` varchar(255) DEFAULT NULL,
   `source_id` int(10) unsigned NOT NULL,
   `study_id` int(10) unsigned DEFAULT NULL,
-  `class_attrib_id` int(10) unsigned NOT NULL DEFAULT 0,
-  `allele_string` longtext DEFAULT NULL,
-  `is_evidence` tinyint(1) NOT NULL DEFAULT 0,
-  `somatic` tinyint(1) NOT NULL DEFAULT 0,
+  `class_attrib_id` int(10) unsigned NOT NULL DEFAULT '0',
+  `allele_string` longtext,
+  `is_evidence` tinyint(1) NOT NULL DEFAULT '0',
+  `somatic` tinyint(1) NOT NULL DEFAULT '0',
   `breakpoint_order` tinyint(4) DEFAULT NULL,
   `length` int(10) DEFAULT NULL,
   `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 '',
+  `allele_freq` float DEFAULT NULL,
+  `allele_count` int(10) unsigned DEFAULT NULL,
   PRIMARY KEY (`structural_variation_feature_id`),
   KEY `pos_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`),
   KEY `structural_variation_idx` (`structural_variation_id`),
@@ -496,7 +499,7 @@ CREATE TABLE `study` (
   `study_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `source_id` int(10) unsigned NOT NULL,
   `name` varchar(255) DEFAULT NULL,
-  `description` text DEFAULT NULL,
+  `description` text,
   `url` varchar(255) DEFAULT NULL,
   `external_reference` varchar(255) DEFAULT NULL,
   `study_type` varchar(255) DEFAULT NULL,
@@ -539,8 +542,8 @@ CREATE TABLE `transcript_variation` (
   `transcript_variation_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
   `variation_feature_id` int(11) unsigned NOT NULL,
   `feature_stable_id` varchar(128) DEFAULT NULL,
-  `allele_string` text DEFAULT NULL,
-  `somatic` tinyint(1) NOT NULL DEFAULT 0,
+  `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') DEFAULT NULL,
   `cds_start` int(11) unsigned DEFAULT NULL,
   `cds_end` int(11) unsigned DEFAULT NULL,
@@ -549,16 +552,16 @@ CREATE TABLE `transcript_variation` (
   `translation_start` int(11) unsigned DEFAULT NULL,
   `translation_end` int(11) unsigned DEFAULT NULL,
   `distance_to_transcript` int(11) unsigned DEFAULT NULL,
-  `codon_allele_string` text DEFAULT NULL,
-  `pep_allele_string` text DEFAULT NULL,
-  `hgvs_genomic` text DEFAULT NULL,
-  `hgvs_transcript` text DEFAULT NULL,
-  `hgvs_protein` text DEFAULT NULL,
+  `codon_allele_string` text,
+  `pep_allele_string` text,
+  `hgvs_genomic` text,
+  `hgvs_transcript` text,
+  `hgvs_protein` text,
   `polyphen_prediction` enum('unknown','benign','possibly damaging','probably damaging') DEFAULT NULL,
   `polyphen_score` float DEFAULT NULL,
   `sift_prediction` enum('tolerated','deleterious','tolerated - low confidence','deleterious - low confidence') DEFAULT NULL,
   `sift_score` float DEFAULT NULL,
-  `display` int(1) DEFAULT 1,
+  `display` int(1) DEFAULT '1',
   PRIMARY KEY (`transcript_variation_id`),
   KEY `variation_feature_idx` (`variation_feature_id`),
   KEY `consequence_type_idx` (`consequence_types`),
@@ -577,14 +580,14 @@ CREATE TABLE `variation` (
   `source_id` int(10) unsigned NOT NULL,
   `name` varchar(255) DEFAULT NULL,
   `flipped` tinyint(1) unsigned DEFAULT NULL,
-  `class_attrib_id` int(10) unsigned DEFAULT 0,
-  `somatic` tinyint(1) NOT NULL DEFAULT 0,
+  `class_attrib_id` int(10) unsigned DEFAULT '0',
+  `somatic` tinyint(1) NOT NULL DEFAULT '0',
   `minor_allele` varchar(50) DEFAULT NULL,
   `minor_allele_freq` float DEFAULT NULL,
   `minor_allele_count` int(10) unsigned DEFAULT NULL,
   `clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
   `evidence_attribs` set('367','368','369','370','371','372','418','421','573','585') DEFAULT NULL,
-  `display` int(1) DEFAULT 1,
+  `display` int(1) DEFAULT '1',
   PRIMARY KEY (`variation_id`),
   UNIQUE KEY `name` (`name`),
   KEY `source_idx` (`source_id`)
@@ -621,15 +624,15 @@ CREATE TABLE `variation_feature` (
   `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') 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,
+  `class_attrib_id` int(10) unsigned DEFAULT '0',
+  `somatic` tinyint(1) NOT NULL DEFAULT '0',
   `minor_allele` varchar(50) DEFAULT NULL,
   `minor_allele_freq` float DEFAULT NULL,
   `minor_allele_count` int(10) unsigned DEFAULT NULL,
   `alignment_quality` double DEFAULT NULL,
   `evidence_attribs` set('367','368','369','370','371','372','418','421','573','585') DEFAULT NULL,
   `clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
-  `display` int(1) DEFAULT 1,
+  `display` int(1) DEFAULT '1',
   PRIMARY KEY (`variation_feature_id`),
   KEY `pos_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`),
   KEY `variation_idx` (`variation_id`),
@@ -653,7 +656,7 @@ CREATE TABLE `variation_hgvs` (
 CREATE TABLE `variation_set` (
   `variation_set_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `name` varchar(255) DEFAULT NULL,
-  `description` text DEFAULT NULL,
+  `description` text,
   `short_name_attrib_id` int(10) unsigned DEFAULT NULL,
   PRIMARY KEY (`variation_set_id`),
   KEY `name_idx` (`name`)

modules/t/test-genome-DBs/ontology/ontology/meta.txt

@@ -9,7 +9,7 @@
 10	patch	patch_72_73_b.sql|meta	\N
 12	patch	patch_73_74_a.sql|schema_version	\N
 14	patch	patch_74_75_a.sql|schema_version	\N
-15	schema_version	100	\N
+15	schema_version	101	\N
 16	patch	patch_75_76_a.sql|schema_version	\N
 17	patch	patch_76_77_a.sql|schema_version	\N
 18	patch	patch_77_78_a.sql|schema_version	\N
@@ -43,3 +43,4 @@
 46	patch	patch_97_98_a.sql|schema_version	\N
 47	patch	patch_98_99_a.sql|schema_version	\N
 48	patch	patch_99_100_a.sql|schema_version	\N
+49	patch	patch_100_101_a.sql|schema_version	\N

modules/t/test-genome-DBs/ontology/ontology/table.sql

@@ -141,7 +141,7 @@ 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=49 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+) ENGINE=MyISAM AUTO_INCREMENT=50 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
 
 CREATE TABLE `ontology` (
   `ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -196,13 +196,13 @@ CREATE TABLE `synonym` (
 CREATE TABLE `term` (
   `term_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `ontology_id` int(10) unsigned NOT NULL,
-  `subsets` text COLLATE utf8_unicode_ci DEFAULT NULL,
+  `subsets` text COLLATE utf8_unicode_ci,
   `accession` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
   `name` varchar(255) CHARACTER SET utf8 NOT NULL,
-  `definition` text CHARACTER SET utf8 DEFAULT NULL,
-  `is_root` int(11) NOT NULL DEFAULT 0,
-  `is_obsolete` int(11) NOT NULL DEFAULT 0,
-  `iri` text COLLATE utf8_unicode_ci DEFAULT NULL,
+  `definition` text CHARACTER SET utf8,
+  `is_root` int(11) NOT NULL DEFAULT '0',
+  `is_obsolete` int(11) NOT NULL DEFAULT '0',
+  `iri` text COLLATE utf8_unicode_ci,
   PRIMARY KEY (`term_id`),
   UNIQUE KEY `accession` (`accession`),
   UNIQUE KEY `term_ontology_acc_idx` (`ontology_id`,`accession`),