Patch test databases for RNAPRoduct tests

Apply patch_96_97_{c,d,e}, insert the necessary data into
homo_sapiens/core.

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

 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Feb 12 15:00:19 2019
+-- Created on Mon Mar 18 14:30:07 2019
 -- 
 
 BEGIN TRANSACTION;
@@ -615,7 +615,7 @@ CREATE UNIQUE INDEX "code_idx02" ON "misc_set" ("code");
 CREATE TABLE "object_xref" (
   "object_xref_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   "ensembl_id" integer NOT NULL DEFAULT 0,
-  "ensembl_object_type" enum NOT NULL DEFAULT 'RawContig',
+  "ensembl_object_type" enum NOT NULL,
   "xref_id" integer NOT NULL,
   "linkage_annotation" varchar(255),
   "analysis_id" smallint
@@ -787,6 +787,46 @@ CREATE TABLE "repeat_feature" (
   "score" double precision
 );
 
+--
+-- Table: "rnaproduct"
+--
+CREATE TABLE "rnaproduct" (
+  "rnaproduct_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  "rnaproduct_type_id" smallint NOT NULL,
+  "transcript_id" integer NOT NULL,
+  "seq_start" integer NOT NULL,
+  "start_exon_id" integer,
+  "seq_end" integer NOT NULL,
+  "end_exon_id" integer,
+  "stable_id" varchar(128),
+  "version" smallint,
+  "created_date" datetime,
+  "modified_date" datetime
+);
+
+--
+-- Table: "rnaproduct_attrib"
+--
+CREATE TABLE "rnaproduct_attrib" (
+  "rnaproduct_id" integer NOT NULL DEFAULT 0,
+  "attrib_type_id" smallint NOT NULL DEFAULT 0,
+  "value" text NOT NULL
+);
+
+CREATE UNIQUE INDEX "rnaproduct_attribx" ON "rnaproduct_attrib" ("rnaproduct_id", "attrib_type_id", "value");
+
+--
+-- Table: "rnaproduct_type"
+--
+CREATE TABLE "rnaproduct_type" (
+  "rnaproduct_type_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  "code" varchar(20) NOT NULL DEFAULT '',
+  "name" varchar(255) NOT NULL DEFAULT '',
+  "description" text
+);
+
+CREATE UNIQUE INDEX "code_idx03" ON "rnaproduct_type" ("code");
+
 --
 -- Table: "seq_region"
 --
@@ -854,7 +894,7 @@ CREATE TABLE "stable_id_event" (
   "new_stable_id" varchar(128),
   "new_version" smallint,
   "mapping_session_id" integer NOT NULL DEFAULT 0,
-  "type" enum NOT NULL DEFAULT 'gene',
+  "type" enum NOT NULL,
   "score" float NOT NULL DEFAULT 0
 );
 

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

@@ -19,3 +19,4 @@
 19	karyotype_rank	Rank in the karyotype	For a given seq_region, if it is part of the species karyotype, will indicate its rank
 20	proj_parent_g	projection parent gene	Stable identifier of the parent gene this gene was projected from (projection between different species and/or assemblies).
 21	proj_parent_t	projection parent transcript	Stable identifier of the parent transcript this transcript was projected from (projection between different species and/or assemblies).
+22	mirna_arm	miRNA arm	Hairpin arm from which this miRNA has come from

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

@@ -107,3 +107,6 @@
 174	\N	patch	patch_95_96_a.sql|schema_version
 175	\N	patch	patch_96_97_a.sql|schema_version
 176	\N	patch	patch_96_97_b.sql|biotype_so_term
+177	\N	patch	patch_96_97_c.sql|rnaproduct_tables
+178	\N	patch	patch_96_97_d.sql|add_object_type_rnaproduct
+179	\N	patch	patch_96_97_e.sql|add_stable_id_event_type_rnaproduct

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

@@ -203,3 +203,5 @@
 253682	21727	Translation	168444	119	0
 253683	21727	Translation	168445	119	0
 253684	21727	Translation	168446	119	0
+999998	1	RNAProduct	123456	\N	0
+999999	2	RNAProduct	123457	\N	0

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

+1	2	21717	46	162035	67	162035	ENSM00000000001	1	2018-05-14 12:00:00	2018-05-14 12:00:00
+2	2	21717	7	\N	28	\N	ENSM00000000002	1	2018-05-21 17:00:00	2018-05-21 17:00:00

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

+1	10	Placeholder
+1	22	3
+2	10	Placeholder
+2	22	5

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

+1	generic	generic	Generic mature RNA
+2	miRNA	microRNA	Mature microRNA strand
+3	circRNA	Circular RNA	\N

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

+131538	20	4	64444167
 368744	AL359765.6.1.13780	4	13780
 317101	AL031658.11.1.162976	4	162976
 339816	AL353092.6.1.25010	4	25010

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

@@ -490,7 +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=177 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=180 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -539,7 +539,7 @@ CREATE TABLE `misc_set` (
 CREATE TABLE `object_xref` (
   `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
   `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker','RNAProduct') COLLATE latin1_bin NOT NULL,
   `xref_id` int(10) unsigned NOT NULL,
   `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `analysis_id` smallint(5) unsigned DEFAULT NULL,
@@ -547,7 +547,7 @@ CREATE TABLE `object_xref` (
   UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`),
   KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),
   KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=253694 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=1000000 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `ontology_xref` (
   `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -716,6 +716,42 @@ CREATE TABLE `repeat_feature` (
   KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM AUTO_INCREMENT=922516 DEFAULT CHARSET=latin1 COLLATE=latin1_bin 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 AUTO_INCREMENT=3 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 AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
+
 CREATE TABLE `seq_region` (
   `seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `name` varchar(255) COLLATE latin1_bin NOT NULL,
@@ -774,7 +810,7 @@ CREATE TABLE `stable_id_event` (
   `new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `new_version` smallint(6) DEFAULT NULL,
   `mapping_session_id` int(10) NOT NULL DEFAULT '0',
-  `type` enum('gene','transcript','translation') COLLATE latin1_bin NOT NULL DEFAULT 'gene',
+  `type` enum('gene','transcript','translation','rnaproduct') COLLATE latin1_bin NOT NULL,
   `score` float NOT NULL DEFAULT '0',
   UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
   KEY `new_idx` (`new_stable_id`),

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

@@ -181,5 +181,7 @@
 103296	2	U24166	U24166	1	description		D
 103297	3	AAC09471	AAC09471	1	description		D
 103298	3	CAB53072	CAB53072	1	description		D
+123456	3300	MIMAT0000416	hsa-miR-1-3p	1	description		D
+123457	3300	MIMAT0031892	hsa-miR-1-5p	1	description		D
 999998	11	IPR000001	IPR000001	1	Test interpro desc1		D
 999999	11	IPR000010	IPR000010	1	Test interpro desc2		D