Commit e4d7240a authored by Marek Szuba's avatar Marek Szuba Committed by Magali Ruffier
Browse files

Apply missing MySQL test-database patches from 90 to 93

parent 71dab88b
1 \N schema_type variation
2 \N schema_version 90
2 \N schema_version 93
3 \N patch patch_84_85_a.sql|schema version
4 \N patch patch_84_85_b.sql|create sample_synonym
5 \N patch patch_84_85_c.sql|drop column moltype from variation_synonym
......@@ -22,3 +22,12 @@
22 \N patch patch_89_90_b.sql|add start_retained_variant to consequence_types in variation_feature and transcript_variation
23 \N patch patch_89_90_c.sql|remove regulatory and TFBS consequences from consequence_types in transcript_variation
24 \N patch patch_90_91_b.sql|extend the characters supported in the publication.authors column
25 \N patch patch_90_91_a.sql|schema version
26 \N patch patch_90_91_c.sql|Add new column zygosity in the table structural_variation_sample
27 \N patch patch_91_92_a.sql|schema version
28 \N patch patch_91_92_b.sql|Add index on feature_stable_id in regulatory_feature_variation and motif_feature_variation
29 \N patch patch_91_92_c.sql|Change the column zygosity in the table structural_variation_sample
30 \N patch patch_91_92_d.sql|create table to store names of submitters to ClinVar etc
31 \N patch patch_92_93_a.sql|schema version
32 \N patch patch_92_93_b.sql|Extend phenotype_ontology_accession mapped_by_attrib predefined set
33 \N patch patch_92_93_c.sql|Add new evidence attribs to the variation and variation_feature tables
......@@ -168,7 +168,7 @@ 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=25 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=34 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......@@ -193,7 +193,8 @@ CREATE TABLE `motif_feature_variation` (
PRIMARY KEY (`motif_feature_variation_id`),
KEY `variation_feature_idx` (`variation_feature_id`),
KEY `consequence_type_idx` (`consequence_types`),
KEY `somatic_feature_idx` (`feature_stable_id`,`somatic`)
KEY `somatic_feature_idx` (`feature_stable_id`,`somatic`),
KEY `feature_stable_idx` (`feature_stable_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `phenotype` (
......@@ -238,7 +239,7 @@ CREATE TABLE `phenotype_feature_attrib` (
CREATE TABLE `phenotype_ontology_accession` (
`phenotype_id` int(11) unsigned NOT NULL,
`accession` varchar(255) NOT NULL,
`mapped_by_attrib` set('437','438','439','440','441','442','443','444') DEFAULT NULL,
`mapped_by_attrib` set('437','438','439','440','441','442','443','444','588','589','590','591','592','593','594') DEFAULT NULL,
`mapping_type` enum('is','involves') DEFAULT NULL,
PRIMARY KEY (`phenotype_id`,`accession`),
KEY `accession_idx` (`accession`)
......@@ -338,7 +339,8 @@ CREATE TABLE `regulatory_feature_variation` (
PRIMARY KEY (`regulatory_feature_variation_id`),
KEY `variation_feature_idx` (`variation_feature_id`),
KEY `consequence_type_idx` (`consequence_types`),
KEY `somatic_feature_idx` (`feature_stable_id`,`somatic`)
KEY `somatic_feature_idx` (`feature_stable_id`,`somatic`),
KEY `feature_stable_idx` (`feature_stable_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `sample` (
......@@ -465,6 +467,7 @@ CREATE TABLE `structural_variation_sample` (
`structural_variation_sample_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`structural_variation_id` int(10) unsigned NOT NULL,
`sample_id` int(10) unsigned DEFAULT NULL,
`zygosity` tinyint(1) DEFAULT NULL,
PRIMARY KEY (`structural_variation_sample_id`),
KEY `structural_variation_idx` (`structural_variation_id`),
KEY `sample_idx` (`sample_id`)
......@@ -483,6 +486,12 @@ CREATE TABLE `study` (
KEY `external_reference_idx` (`external_reference`)
) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
CREATE TABLE `submitter` (
`submitter_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`description` varchar(255) DEFAULT NULL,
PRIMARY KEY (`submitter_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `submitter_handle` (
`handle_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`handle` varchar(25) DEFAULT NULL,
......@@ -556,7 +565,7 @@ CREATE TABLE `variation` (
`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') DEFAULT NULL,
`evidence_attribs` set('367','368','369','370','371','372','418','421','573','585') DEFAULT NULL,
`display` int(1) DEFAULT '1',
PRIMARY KEY (`variation_id`),
UNIQUE KEY `name` (`name`),
......@@ -597,7 +606,7 @@ CREATE TABLE `variation_feature` (
`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') 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',
PRIMARY KEY (`variation_feature_id`),
......
36 \N schema_version 90
51 \N schema_version 93
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
......@@ -36,3 +36,9 @@
41 \N patch patch_89_90_e.sql|seq_member_projection
42 \N patch patch_89_90_f.sql|gene_member_missing_biotype_groups
43 \N patch patch_90_91_b.sql|gene_member_qc.seq_member_id.unsigned
45 \N patch patch_90_91_a.sql|schema_version
46 \N patch patch_90_91_c.sql|gene_member.biotype_group-index
48 \N patch patch_91_92_a.sql|schema_version
49 \N patch patch_91_92_b.sql|mapping_session_new_type_hmm
50 \N patch patch_91_92_c.sql|gene_tree_root_tag_255
52 \N patch patch_92_93_a.sql|schema_version
......@@ -154,7 +154,9 @@ CREATE TABLE `gene_member` (
KEY `source_name` (`source_name`),
KEY `canonical_member_id` (`canonical_member_id`),
KEY `dnafrag_id_start` (`dnafrag_id`,`dnafrag_start`),
KEY `dnafrag_id_end` (`dnafrag_id`,`dnafrag_end`)
KEY `dnafrag_id_end` (`dnafrag_id`,`dnafrag_end`),
KEY `biotype_dnafrag_id_start_end` (`biotype_group`,`dnafrag_id`,`dnafrag_start`,`dnafrag_end`),
KEY `genome_db_id_biotype` (`genome_db_id`,`biotype_group`)
) ENGINE=MyISAM AUTO_INCREMENT=100281325 DEFAULT CHARSET=latin1 MAX_ROWS=100000000;
CREATE TABLE `gene_member_hom_stats` (
......@@ -272,7 +274,7 @@ CREATE TABLE `gene_tree_root_attr` (
CREATE TABLE `gene_tree_root_tag` (
`root_id` int(10) unsigned NOT NULL,
`tag` varchar(50) NOT NULL,
`tag` varchar(255) DEFAULT NULL,
`value` mediumtext NOT NULL,
KEY `root_id_tag` (`root_id`,`tag`),
KEY `root_id` (`root_id`),
......@@ -409,7 +411,7 @@ CREATE TABLE `homology_member` (
CREATE TABLE `mapping_session` (
`mapping_session_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`type` enum('family','tree') DEFAULT NULL,
`type` enum('family','tree','hmm') DEFAULT NULL,
`when_mapped` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
`rel_from` int(10) unsigned DEFAULT NULL,
`rel_to` int(10) unsigned DEFAULT NULL,
......@@ -434,7 +436,7 @@ 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=44 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=53 DEFAULT CHARSET=latin1;
CREATE TABLE `method_link` (
`method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......
1 \N schema_type variation
2 \N schema_version 90
2 \N schema_version 93
6 1 species.production_name mus_musculus
15 1 web_config sv_study#Keane 2011 (DGVa study estd118)#Keane 2011#estd118
14 1 web_config set#All failed variants#All failed variants#variation_set_fail_all#failed
......@@ -49,3 +49,12 @@
55 \N patch patch_89_90_b.sql|add start_retained_variant to consequence_types in variation_feature and transcript_variation
56 \N patch patch_89_90_c.sql|remove regulatory and TFBS consequences from consequence_types in transcript_variation
57 \N patch patch_90_91_b.sql|extend the characters supported in the publication.authors column
58 \N patch patch_90_91_a.sql|schema version
59 \N patch patch_90_91_c.sql|Add new column zygosity in the table structural_variation_sample
60 \N patch patch_91_92_a.sql|schema version
61 \N patch patch_91_92_b.sql|Add index on feature_stable_id in regulatory_feature_variation and motif_feature_variation
62 \N patch patch_91_92_c.sql|Change the column zygosity in the table structural_variation_sample
63 \N patch patch_91_92_d.sql|create table to store names of submitters to ClinVar etc
64 \N patch patch_92_93_a.sql|schema version
65 \N patch patch_92_93_b.sql|Extend phenotype_ontology_accession mapped_by_attrib predefined set
66 \N patch patch_92_93_c.sql|Add new evidence attribs to the variation and variation_feature tables
......@@ -168,7 +168,7 @@ 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=58 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=67 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......@@ -193,7 +193,8 @@ CREATE TABLE `motif_feature_variation` (
PRIMARY KEY (`motif_feature_variation_id`),
KEY `variation_feature_idx` (`variation_feature_id`),
KEY `consequence_type_idx` (`consequence_types`),
KEY `somatic_feature_idx` (`feature_stable_id`,`somatic`)
KEY `somatic_feature_idx` (`feature_stable_id`,`somatic`),
KEY `feature_stable_idx` (`feature_stable_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `phenotype` (
......@@ -238,7 +239,7 @@ CREATE TABLE `phenotype_feature_attrib` (
CREATE TABLE `phenotype_ontology_accession` (
`phenotype_id` int(11) unsigned NOT NULL,
`accession` varchar(255) NOT NULL,
`mapped_by_attrib` set('437','438','439','440','441','442','443','444') DEFAULT NULL,
`mapped_by_attrib` set('437','438','439','440','441','442','443','444','588','589','590','591','592','593','594') DEFAULT NULL,
`mapping_type` enum('is','involves') DEFAULT NULL,
PRIMARY KEY (`phenotype_id`,`accession`),
KEY `accession_idx` (`accession`)
......@@ -338,7 +339,8 @@ CREATE TABLE `regulatory_feature_variation` (
PRIMARY KEY (`regulatory_feature_variation_id`),
KEY `variation_feature_idx` (`variation_feature_id`),
KEY `consequence_type_idx` (`consequence_types`),
KEY `somatic_feature_idx` (`feature_stable_id`,`somatic`)
KEY `somatic_feature_idx` (`feature_stable_id`,`somatic`),
KEY `feature_stable_idx` (`feature_stable_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `sample` (
......@@ -465,6 +467,7 @@ CREATE TABLE `structural_variation_sample` (
`structural_variation_sample_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`structural_variation_id` int(10) unsigned NOT NULL,
`sample_id` int(10) unsigned DEFAULT NULL,
`zygosity` tinyint(1) DEFAULT NULL,
PRIMARY KEY (`structural_variation_sample_id`),
KEY `structural_variation_idx` (`structural_variation_id`),
KEY `sample_idx` (`sample_id`)
......@@ -483,6 +486,12 @@ CREATE TABLE `study` (
KEY `external_reference_idx` (`external_reference`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `submitter` (
`submitter_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`description` varchar(255) DEFAULT NULL,
PRIMARY KEY (`submitter_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `submitter_handle` (
`handle_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`handle` varchar(25) DEFAULT NULL,
......@@ -562,7 +571,7 @@ CREATE TABLE `variation` (
`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') DEFAULT NULL,
`evidence_attribs` set('367','368','369','370','371','372','418','421','573','585') DEFAULT NULL,
`display` int(1) DEFAULT '1',
PRIMARY KEY (`variation_id`),
UNIQUE KEY `name` (`name`),
......@@ -603,7 +612,7 @@ CREATE TABLE `variation_feature` (
`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') 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',
PRIMARY KEY (`variation_feature_id`),
......
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