[Raisinbread] Added CNV/CPG records for candidates with SNP data (ace…

…s#6900)

Added CNV and CPG records for candidates that already have SNP data. This is necessary so that the CNV and Methylation tabs in the Genomic Browser module can be tested.

    Resolves aces#6881
    Partially resolves aces#6302

raisinbread/RB_files/RB_CNV.sql

@@ -1,5 +1,9 @@
 SET FOREIGN_KEY_CHECKS=0;
 TRUNCATE TABLE `CNV`;
 LOCK TABLES `CNV` WRITE;
+INSERT INTO `CNV` (`CNVID`, `CandID`, `Description`, `Type`, `EventName`, `Common_CNV`, `Characteristics`, `CopyNumChange`, `Inheritance`, `ArrayReport`, `Markers`, `ArrayReportDetail`, `ValidationMethod`, `PlatformID`, `Chromosome`, `Strand`, `EndLoc`, `StartLoc`, `Symbol`, `Name`, `NCBIID`, `OfficialSymbol`, `OfficialName`) VALUES (1,300165,NULL,'gain',NULL,'Y','Unknown',NULL,'unknown','Normal',NULL,NULL,NULL,1,'chr1','+',11007,11008,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `CNV` (`CNVID`, `CandID`, `Description`, `Type`, `EventName`, `Common_CNV`, `Characteristics`, `CopyNumChange`, `Inheritance`, `ArrayReport`, `Markers`, `ArrayReportDetail`, `ValidationMethod`, `PlatformID`, `Chromosome`, `Strand`, `EndLoc`, `StartLoc`, `Symbol`, `Name`, `NCBIID`, `OfficialSymbol`, `OfficialName`) VALUES (2,300165,NULL,'unknown',NULL,'Y','Unknown',NULL,'unknown','Normal',NULL,NULL,NULL,1,'chr1','-',11009,11010,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `CNV` (`CNVID`, `CandID`, `Description`, `Type`, `EventName`, `Common_CNV`, `Characteristics`, `CopyNumChange`, `Inheritance`, `ArrayReport`, `Markers`, `ArrayReportDetail`, `ValidationMethod`, `PlatformID`, `Chromosome`, `Strand`, `EndLoc`, `StartLoc`, `Symbol`, `Name`, `NCBIID`, `OfficialSymbol`, `OfficialName`) VALUES (3,300141,NULL,'unknown',NULL,'Y','Unknown',NULL,'unknown','Normal',NULL,NULL,NULL,1,'chr1','+',11007,11008,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `CNV` (`CNVID`, `CandID`, `Description`, `Type`, `EventName`, `Common_CNV`, `Characteristics`, `CopyNumChange`, `Inheritance`, `ArrayReport`, `Markers`, `ArrayReportDetail`, `ValidationMethod`, `PlatformID`, `Chromosome`, `Strand`, `EndLoc`, `StartLoc`, `Symbol`, `Name`, `NCBIID`, `OfficialSymbol`, `OfficialName`) VALUES (4,300162,NULL,'unknown',NULL,'Y','Unknown',NULL,'unknown','Normal',NULL,NULL,NULL,1,'chr1','+',11007,11008,NULL,NULL,NULL,NULL,NULL);
 UNLOCK TABLES;
 SET FOREIGN_KEY_CHECKS=1;

raisinbread/RB_files/RB_genomic_cpg.sql

@@ -1,5 +1,9 @@
 SET FOREIGN_KEY_CHECKS=0;
 TRUNCATE TABLE `genomic_cpg`;
 LOCK TABLES `genomic_cpg` WRITE;
+INSERT INTO `genomic_cpg` (`sample_label`, `cpg_name`, `beta_value`) VALUES ('sl573847','CPG_573847',1.000);
+INSERT INTO `genomic_cpg` (`sample_label`, `cpg_name`, `beta_value`) VALUES ('sl573848','CPG_573848',1.000);
+INSERT INTO `genomic_cpg` (`sample_label`, `cpg_name`, `beta_value`) VALUES ('sl573851','CPG_573851',1.000);
+INSERT INTO `genomic_cpg` (`sample_label`, `cpg_name`, `beta_value`) VALUES ('sl573852','CPG_573852',1.000);
 UNLOCK TABLES;
 SET FOREIGN_KEY_CHECKS=1;

raisinbread/RB_files/RB_genomic_cpg_annotation.sql

@@ -1,5 +1,9 @@
 SET FOREIGN_KEY_CHECKS=0;
 TRUNCATE TABLE `genomic_cpg_annotation`;
 LOCK TABLES `genomic_cpg_annotation` WRITE;
+INSERT INTO `genomic_cpg_annotation` (`cpg_name`, `address_id_a`, `probe_seq_a`, `address_id_b`, `probe_seq_b`, `design_type`, `color_channel`, `genome_build`, `probe_snp_10`, `gene_name`, `gene_acc_num`, `gene_group`, `island_loc`, `island_relation`, `fantom_promoter_loc`, `dmr`, `enhancer`, `hmm_island_loc`, `reg_feature_loc`, `reg_feature_group`, `dhs`, `platform_id`, `Chromosome`, `Strand`, `EndLoc`, `StartLoc`) VALUES ('CPG_573847',NULL,NULL,NULL,NULL,NULL,'Red',NULL,NULL,NULL,NULL,NULL,NULL,'island',NULL,'DMR',NULL,NULL,NULL,NULL,NULL,1,'chr1','+',11007,11008);
+INSERT INTO `genomic_cpg_annotation` (`cpg_name`, `address_id_a`, `probe_seq_a`, `address_id_b`, `probe_seq_b`, `design_type`, `color_channel`, `genome_build`, `probe_snp_10`, `gene_name`, `gene_acc_num`, `gene_group`, `island_loc`, `island_relation`, `fantom_promoter_loc`, `dmr`, `enhancer`, `hmm_island_loc`, `reg_feature_loc`, `reg_feature_group`, `dhs`, `platform_id`, `Chromosome`, `Strand`, `EndLoc`, `StartLoc`) VALUES ('CPG_573848',NULL,NULL,NULL,NULL,NULL,'Red',NULL,NULL,NULL,NULL,NULL,NULL,'island',NULL,'DMR',NULL,NULL,NULL,NULL,NULL,1,'chr1','+',11007,11008);
+INSERT INTO `genomic_cpg_annotation` (`cpg_name`, `address_id_a`, `probe_seq_a`, `address_id_b`, `probe_seq_b`, `design_type`, `color_channel`, `genome_build`, `probe_snp_10`, `gene_name`, `gene_acc_num`, `gene_group`, `island_loc`, `island_relation`, `fantom_promoter_loc`, `dmr`, `enhancer`, `hmm_island_loc`, `reg_feature_loc`, `reg_feature_group`, `dhs`, `platform_id`, `Chromosome`, `Strand`, `EndLoc`, `StartLoc`) VALUES ('CPG_573851',NULL,NULL,NULL,NULL,NULL,'Red',NULL,NULL,NULL,NULL,NULL,NULL,'island',NULL,'DMR',NULL,NULL,NULL,NULL,NULL,1,'chr1','+',11007,11008);
+INSERT INTO `genomic_cpg_annotation` (`cpg_name`, `address_id_a`, `probe_seq_a`, `address_id_b`, `probe_seq_b`, `design_type`, `color_channel`, `genome_build`, `probe_snp_10`, `gene_name`, `gene_acc_num`, `gene_group`, `island_loc`, `island_relation`, `fantom_promoter_loc`, `dmr`, `enhancer`, `hmm_island_loc`, `reg_feature_loc`, `reg_feature_group`, `dhs`, `platform_id`, `Chromosome`, `Strand`, `EndLoc`, `StartLoc`) VALUES ('CPG_573852',NULL,NULL,NULL,NULL,NULL,'Red',NULL,NULL,NULL,NULL,NULL,NULL,'island',NULL,'DMR',NULL,NULL,NULL,NULL,NULL,1,'chr1','+',11007,11008);
 UNLOCK TABLES;
 SET FOREIGN_KEY_CHECKS=1;

raisinbread/RB_files/RB_genomic_sample_candidate_rel.sql

@@ -1,5 +1,9 @@
 SET FOREIGN_KEY_CHECKS=0;
 TRUNCATE TABLE `genomic_sample_candidate_rel`;
 LOCK TABLES `genomic_sample_candidate_rel` WRITE;
+INSERT INTO `genomic_sample_candidate_rel` (`sample_label`, `CandID`) VALUES ('sl573852',300139);
+INSERT INTO `genomic_sample_candidate_rel` (`sample_label`, `CandID`) VALUES ('sl573851',300162);
+INSERT INTO `genomic_sample_candidate_rel` (`sample_label`, `CandID`) VALUES ('sl573847',300165);
+INSERT INTO `genomic_sample_candidate_rel` (`sample_label`, `CandID`) VALUES ('sl573848',300165);
 UNLOCK TABLES;
 SET FOREIGN_KEY_CHECKS=1;