Merge 6c3e5de into c4f6b2e

Ensembl · Mar 28, 2019 · ce67d50 · ce67d50
2 parents c4f6b2e + 6c3e5de
commit ce67d50
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Showing 15 changed files with 194 additions and 55 deletions.
diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/ControlledAnalysis.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/ControlledAnalysis.pm
@@ -71,12 +71,12 @@ sub tests {
       ad.logic_name,
       ad.display_label,
       ad.description,
-      (ad.default_displayable IS NOT NULL),
+      (ad.displayable IS NOT NULL),
       ad.db_version,
       wd.data
     FROM
       analysis_description ad LEFT OUTER JOIN
-      web_data wd ON ad.default_web_data_id = wd.web_data_id
+      web_data wd USING (web_data_id)
     WHERE 
       ad.is_current = 1
   /;

diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/ExonBounds.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/ExonBounds.pm
@@ -41,7 +41,7 @@ sub tests {
 
   my $aa = $self->dba->get_adaptor('Attribute');
   my $attrib = $aa->fetch_by_code('trans_spliced');
-  my $attrib_type_id = $attrib->[0];
+  my $attrib_type_id = $attrib->[0] || 0;
 
   my $exon_transcript_sql = qq/
       exon e INNER JOIN

diff --git a/lib/Bio/EnsEMBL/DataCheck/Manager.pm b/lib/Bio/EnsEMBL/DataCheck/Manager.pm
@@ -183,7 +183,7 @@ sub load_config {
 
     if (!defined $self->output_file) {
       if (defined $config{'output_file'} && exists $config{'output_file'}) {
-        $self->history_file($config{'output_file'});
+        $self->output_file($config{'output_file'});
       }
     }
   }

diff --git a/t/test-genome-DBs/collection/core/meta.txt b/t/test-genome-DBs/collection/core/meta.txt
@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	96
+2	\N	schema_version	97
 3	\N	patch	patch_88_89_a.sql|schema_version
 4	1	schema.load_started	2017-05-08 19:14:41
 5	1	schema.load_started	2017-05-08 19:14:45
@@ -175,3 +175,8 @@
 547	\N	patch	patch_94_95_a.sql|schema_version
 548	\N	patch	patch_94_95_b.sql|vertebrate_division_rename
 549	\N	patch	patch_95_96_a.sql|schema_version
+550	\N	patch	patch_96_97_a.sql|schema_version
+551	\N	patch	patch_96_97_b.sql|biotype_so_term
+552	\N	patch	patch_96_97_c.sql|rnaproduct_tables
+553	\N	patch	patch_96_97_d.sql|add_object_type_rnaproduct
+554	\N	patch	patch_96_97_e.sql|add_stable_id_event_type_rnaproduct
diff --git a/t/test-genome-DBs/collection/core/table.sql b/t/test-genome-DBs/collection/core/table.sql
@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
   `description` text,
   `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;
@@ -489,7 +490,7 @@ 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=550 DEFAULT CHARSET=latin1 CHECKSUM=1;
+) ENGINE=MyISAM AUTO_INCREMENT=555 DEFAULT CHARSET=latin1 CHECKSUM=1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
@@ -538,7 +539,7 @@ CREATE TABLE `misc_set` (
 CREATE TABLE `object_xref` (
   `object_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `ensembl_id` int(10) unsigned NOT NULL,
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker') NOT NULL,
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker','RNAProduct') NOT NULL,
   `xref_id` int(10) unsigned NOT NULL,
   `linkage_annotation` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned DEFAULT NULL,
@@ -715,6 +716,42 @@ CREATE TABLE `repeat_feature` (
   KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80 CHECKSUM=1;
 
+CREATE TABLE `rnaproduct` (
+  `rnaproduct_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `rnaproduct_type_id` smallint(5) unsigned NOT NULL,
+  `transcript_id` int(10) unsigned NOT NULL,
+  `seq_start` int(10) NOT NULL,
+  `start_exon_id` int(10) unsigned DEFAULT NULL,
+  `seq_end` int(10) NOT NULL,
+  `end_exon_id` int(10) unsigned DEFAULT NULL,
+  `stable_id` varchar(128) DEFAULT NULL,
+  `version` smallint(5) unsigned DEFAULT NULL,
+  `created_date` datetime DEFAULT NULL,
+  `modified_date` datetime DEFAULT NULL,
+  PRIMARY KEY (`rnaproduct_id`),
+  KEY `transcript_idx` (`transcript_id`),
+  KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `rnaproduct_attrib` (
+  `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT '0',
+  `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+  `value` text NOT NULL,
+  UNIQUE KEY `rnaproduct_attribx` (`rnaproduct_id`,`attrib_type_id`,`value`(500)),
+  KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+  KEY `val_only_idx` (`value`(40)),
+  KEY `rnaproduct_idx` (`rnaproduct_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `rnaproduct_type` (
+  `rnaproduct_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+  `code` varchar(20) NOT NULL DEFAULT '',
+  `name` varchar(255) NOT NULL DEFAULT '',
+  `description` text,
+  PRIMARY KEY (`rnaproduct_type_id`),
+  UNIQUE KEY `code_idx` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
 CREATE TABLE `seq_region` (
   `seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `name` varchar(255) NOT NULL,
@@ -773,7 +810,7 @@ CREATE TABLE `stable_id_event` (
   `new_stable_id` varchar(128) DEFAULT NULL,
   `new_version` smallint(6) DEFAULT NULL,
   `mapping_session_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `type` enum('gene','transcript','translation') NOT NULL,
+  `type` enum('gene','transcript','translation','rnaproduct') NOT NULL,
   `score` float NOT NULL DEFAULT '0',
   UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`new_stable_id`,`type`),
   KEY `new_idx` (`new_stable_id`),

diff --git a/t/test-genome-DBs/drosophila_melanogaster/core/meta.txt b/t/test-genome-DBs/drosophila_melanogaster/core/meta.txt
@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	96
+2	\N	schema_version	97
 3	\N	patch	patch_76_77_a.sql|schema_version
 4	1	assembly.mapping	chromosome:BDGP6|contig:BDGP6
 5	1	assembly.mapping	contig:BDGP6|chunk:BDGP6
@@ -129,3 +129,8 @@
 219	\N	patch	patch_94_95_a.sql|schema_version
 220	\N	patch	patch_94_95_b.sql|vertebrate_division_rename
 221	\N	patch	patch_95_96_a.sql|schema_version
+222	\N	patch	patch_96_97_a.sql|schema_version
+223	\N	patch	patch_96_97_b.sql|biotype_so_term
+224	\N	patch	patch_96_97_c.sql|rnaproduct_tables
+225	\N	patch	patch_96_97_d.sql|add_object_type_rnaproduct
+226	\N	patch	patch_96_97_e.sql|add_stable_id_event_type_rnaproduct
diff --git a/t/test-genome-DBs/drosophila_melanogaster/core/table.sql b/t/test-genome-DBs/drosophila_melanogaster/core/table.sql
@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
   `description` text,
   `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;
@@ -489,7 +490,7 @@ 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=222 DEFAULT CHARSET=latin1 CHECKSUM=1;
+) ENGINE=MyISAM AUTO_INCREMENT=227 DEFAULT CHARSET=latin1 CHECKSUM=1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
@@ -538,7 +539,7 @@ CREATE TABLE `misc_set` (
 CREATE TABLE `object_xref` (
   `object_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `ensembl_id` int(10) unsigned NOT NULL,
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker') NOT NULL,
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker','RNAProduct') NOT NULL,
   `xref_id` int(10) unsigned NOT NULL,
   `linkage_annotation` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned DEFAULT NULL,
@@ -715,6 +716,42 @@ CREATE TABLE `repeat_feature` (
   KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM AUTO_INCREMENT=679834 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80 CHECKSUM=1;
 
+CREATE TABLE `rnaproduct` (
+  `rnaproduct_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `rnaproduct_type_id` smallint(5) unsigned NOT NULL,
+  `transcript_id` int(10) unsigned NOT NULL,
+  `seq_start` int(10) NOT NULL,
+  `start_exon_id` int(10) unsigned DEFAULT NULL,
+  `seq_end` int(10) NOT NULL,
+  `end_exon_id` int(10) unsigned DEFAULT NULL,
+  `stable_id` varchar(128) DEFAULT NULL,
+  `version` smallint(5) unsigned DEFAULT NULL,
+  `created_date` datetime DEFAULT NULL,
+  `modified_date` datetime DEFAULT NULL,
+  PRIMARY KEY (`rnaproduct_id`),
+  KEY `transcript_idx` (`transcript_id`),
+  KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `rnaproduct_attrib` (
+  `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT '0',
+  `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+  `value` text NOT NULL,
+  UNIQUE KEY `rnaproduct_attribx` (`rnaproduct_id`,`attrib_type_id`,`value`(500)),
+  KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+  KEY `val_only_idx` (`value`(40)),
+  KEY `rnaproduct_idx` (`rnaproduct_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `rnaproduct_type` (
+  `rnaproduct_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+  `code` varchar(20) NOT NULL DEFAULT '',
+  `name` varchar(255) NOT NULL DEFAULT '',
+  `description` text,
+  PRIMARY KEY (`rnaproduct_type_id`),
+  UNIQUE KEY `code_idx` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
 CREATE TABLE `seq_region` (
   `seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `name` varchar(255) NOT NULL,
@@ -773,7 +810,7 @@ CREATE TABLE `stable_id_event` (
   `new_stable_id` varchar(128) DEFAULT NULL,
   `new_version` smallint(6) DEFAULT NULL,
   `mapping_session_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `type` enum('gene','transcript','translation') NOT NULL,
+  `type` enum('gene','transcript','translation','rnaproduct') NOT NULL,
   `score` float NOT NULL DEFAULT '0',
   UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`new_stable_id`,`type`),
   KEY `new_idx` (`new_stable_id`),

diff --git a/t/test-genome-DBs/homo_sapiens/core/meta.txt b/t/test-genome-DBs/homo_sapiens/core/meta.txt
@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	96
+2	\N	schema_version	97
 3	\N	patch	patch_73_74_a.sql|schema_version
 4	\N	patch	patch_73_74_b.sql|remove_dnac
 5	\N	patch	patch_73_74_c.sql|remove_unconventional_transcript_association
@@ -176,3 +176,8 @@
 5871	1	species.classification	Opisthokonta
 5872	1	species.classification	Eukaryota
 5877	\N	patch	patch_95_96_a.sql|schema_version
+5878	\N	patch	patch_96_97_a.sql|schema_version
+5879	\N	patch	patch_96_97_b.sql|biotype_so_term
+5880	\N	patch	patch_96_97_c.sql|rnaproduct_tables
+5881	\N	patch	patch_96_97_d.sql|add_object_type_rnaproduct
+5882	\N	patch	patch_96_97_e.sql|add_stable_id_event_type_rnaproduct
diff --git a/t/test-genome-DBs/homo_sapiens/core/table.sql b/t/test-genome-DBs/homo_sapiens/core/table.sql
@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
   `description` text,
   `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;
@@ -489,7 +490,7 @@ 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=5878 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=5883 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
@@ -538,7 +539,7 @@ CREATE TABLE `misc_set` (
 CREATE TABLE `object_xref` (
   `object_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `ensembl_id` int(10) unsigned NOT NULL,
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker') NOT NULL,
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker','RNAProduct') NOT NULL,
   `xref_id` int(10) unsigned NOT NULL,
   `linkage_annotation` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned DEFAULT NULL,
@@ -715,6 +716,42 @@ CREATE TABLE `repeat_feature` (
   KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM AUTO_INCREMENT=17281504 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 
+CREATE TABLE `rnaproduct` (
+  `rnaproduct_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `rnaproduct_type_id` smallint(5) unsigned NOT NULL,
+  `transcript_id` int(10) unsigned NOT NULL,
+  `seq_start` int(10) NOT NULL,
+  `start_exon_id` int(10) unsigned DEFAULT NULL,
+  `seq_end` int(10) NOT NULL,
+  `end_exon_id` int(10) unsigned DEFAULT NULL,
+  `stable_id` varchar(128) DEFAULT NULL,
+  `version` smallint(5) unsigned DEFAULT NULL,
+  `created_date` datetime DEFAULT NULL,
+  `modified_date` datetime DEFAULT NULL,
+  PRIMARY KEY (`rnaproduct_id`),
+  KEY `transcript_idx` (`transcript_id`),
+  KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `rnaproduct_attrib` (
+  `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT '0',
+  `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+  `value` text NOT NULL,
+  UNIQUE KEY `rnaproduct_attribx` (`rnaproduct_id`,`attrib_type_id`,`value`(500)),
+  KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+  KEY `val_only_idx` (`value`(40)),
+  KEY `rnaproduct_idx` (`rnaproduct_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `rnaproduct_type` (
+  `rnaproduct_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+  `code` varchar(20) NOT NULL DEFAULT '',
+  `name` varchar(255) NOT NULL DEFAULT '',
+  `description` text,
+  PRIMARY KEY (`rnaproduct_type_id`),
+  UNIQUE KEY `code_idx` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
 CREATE TABLE `seq_region` (
   `seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `name` varchar(255) NOT NULL,
@@ -773,7 +810,7 @@ CREATE TABLE `stable_id_event` (
   `new_stable_id` varchar(128) DEFAULT NULL,
   `new_version` smallint(6) DEFAULT NULL,
   `mapping_session_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `type` enum('gene','transcript','translation') NOT NULL,
+  `type` enum('gene','transcript','translation','rnaproduct') NOT NULL,
   `score` float NOT NULL DEFAULT '0',
   UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`new_stable_id`,`type`),
   KEY `new_idx` (`new_stable_id`),

diff --git a/t/test-genome-DBs/homo_sapiens/funcgen/meta.txt b/t/test-genome-DBs/homo_sapiens/funcgen/meta.txt
@@ -1,5 +1,5 @@
 1	1	schema_type	funcgen
-2	\N	schema_version	96
+2	\N	schema_version	97
 3	\N	patch	patch_87_88_a.sql|schema_version
 4	\N	patch	patch_87_88_b.sql|seq_region_name_255
 5	\N	patch	patch_87_88_c.sql|sample_regulatory_feature_id field for regulatory build
@@ -115,3 +115,10 @@
 115	\N	patch	patch_95_96_d.sql|add ReadFile to the enum of the ensembl_object_type
 116	\N	patch	patch_95_96_e.sql|Add description and release_version columns to regulatory_build table
 117	\N	patch	patch_95_96_f.sql|Modify binding_matrix_table
+118	\N	patch	patch_96_97_a.sql|schema_version
+119	\N	patch	patch_96_97_b.sql|Changed to text
+120	\N	patch	patch_96_97_c.sql|Added flag
+121	\N	patch	patch_96_97_d.sql|Fix foreign key data type inconsistencies
+122	\N	patch	patch_96_97_e.sql|Update mirna_target_feature
+123	\N	patch	patch_96_97_f.sql|Add search_terms and full_name columns to epigenome table, rename display_label column to short_name and change description to TEXT
+124	\N	patch	patch_96_97_g.sql|Modify column in regulatory_activity