add b137 schema changes for the human tables

[dbsnp.git] / schema / human_9606_schema / human_9606_constraint_postgresql.sql

diff --git a/schema/human_9606_schema/human_9606_constraint_postgresql.sql b/schema/human_9606_schema/human_9606_constraint_postgresql.sql
index 92d597308de144e205b928b11b90792595981552..371c73773a372936dbafba58577342ddc86b6aae 100644 (file)
--- a/schema/human_9606_schema/human_9606_constraint_postgresql.sql
+++ b/schema/human_9606_schema/human_9606_constraint_postgresql.sql
@@ -8,6 +8,7 @@ ALTER TABLE BatchStrain ADD CONSTRAINT pk_BatchStrain  PRIMARY KEY  (batch_id,li
 ALTER TABLE BatchValCode ADD CONSTRAINT pk_BatchValCode  PRIMARY KEY  (batch_id);
 ALTER TABLE ClinSigCode ALTER COLUMN create_time SET DEFAULT NOW();
 ALTER TABLE ClinSigCode ALTER COLUMN last_updated_time SET DEFAULT NOW();
+ALTER TABLE ClinSigCode ALTER COLUMN severity_level SET DEFAULT (0);
 ALTER TABLE ClinSigCode ADD CONSTRAINT PK__ClinSigC__357D4CF85DD3445E  PRIMARY KEY  (code);
 ALTER TABLE Contact ADD CONSTRAINT pk_Contact  PRIMARY KEY  (batch_id,handle);
 ALTER TABLE GeneIdToName ADD CONSTRAINT pk_GeneIdToName  PRIMARY KEY  (gene_id);
@@ -15,7 +16,7 @@ ALTER TABLE GtyFreqBySsPop ADD CONSTRAINT pk_GtyFreqBySsPop_b129  PRIMARY KEY  (
 ALTER TABLE IndGrpCode ADD CONSTRAINT pk_IndGrpCode  PRIMARY KEY  (code);
 ALTER TABLE IndivBySource ADD CONSTRAINT pk_IndivBySource  PRIMARY KEY  (src_id,src_ind_id);
 ALTER TABLE Individual ADD CONSTRAINT pk_Individual  PRIMARY KEY  (ind_id);
-ALTER TABLE OmimVarLocusIdSNP ADD CONSTRAINT fk_OmimVarLocusIdSNP_snp_id FOREIGN KEY (snp_id) REFERENCES b134_SNP(snp_id);
+ALTER TABLE OmimVarLocusIdSNP ADD CONSTRAINT fk_OmimVarLocusIdSNP_snp_id FOREIGN KEY (snp_id) REFERENCES b135_SNP(snp_id);
 ALTER TABLE Pedigree ADD CONSTRAINT p_ped_id  PRIMARY KEY  (ped_id);
 ALTER TABLE PedigreeIndividual ADD CONSTRAINT pk_PedigreeIndividual  PRIMARY KEY  (ped_id,ind_id);
 ALTER TABLE PopLine ADD CONSTRAINT pk_PopLine  PRIMARY KEY  (pop_id,line_num);
@@ -24,15 +25,13 @@ ALTER TABLE Population ADD CONSTRAINT pk_Population_pop_id  PRIMARY KEY  (pop_id
 ALTER TABLE SNPAlleleFreq ADD CONSTRAINT pk_SNPAlleleFreq  PRIMARY KEY  (snp_id,allele_id);
 ALTER TABLE SNPAncestralAllele ALTER COLUMN batch_id SET DEFAULT (0);
 ALTER TABLE SNPAncestralAllele ADD CONSTRAINT pk_SNPAncestralAllele  PRIMARY KEY  (snp_id,batch_id);
-ALTER TABLE SNPClinSig ALTER COLUMN upd_time SET DEFAULT NOW();
-ALTER TABLE SNPClinSig ADD CONSTRAINT PK__SNPClinS__430A13A119D3EB23  PRIMARY KEY  (snp_id);
 ALTER TABLE SNPGtyFreq ADD CONSTRAINT pk_SNPGtyFreq  PRIMARY KEY  (snp_id,unigty_id);
 ALTER TABLE SNPHWProb ADD CONSTRAINT pk_SNPHWProb  PRIMARY KEY  (snp_id);
 ALTER TABLE SNPHistory ADD CONSTRAINT pk_SNPHistory  PRIMARY KEY  (snp_id);
-ALTER TABLE SNPSubSNPLink ADD CONSTRAINT fk_SNPSubSNPLink_ss FOREIGN KEY (subsnp_id) REFERENCES SubSNP(subsnp_id);
 ALTER TABLE SNPSuspect ALTER COLUMN upd_time SET DEFAULT NOW();
 ALTER TABLE SNPSuspect ADD CONSTRAINT PK__SNPSuspe__430A13A116D6B790  PRIMARY KEY  (snp_id);
 ALTER TABLE SNPVal ADD CONSTRAINT pk_SNPVal  PRIMARY KEY  (batch_id,snp_id);
+ALTER TABLE SNP_HGVS ADD CONSTRAINT fk_SNP_HGVS FOREIGN KEY (snp_id) REFERENCES b135_SNP(snp_id);
 ALTER TABLE SNP_bitfield ADD CONSTRAINT pk_SNP_bitfield  PRIMARY KEY  (snp_id);
 ALTER TABLE SubPop ALTER COLUMN last_updated_time SET DEFAULT NOW();
 ALTER TABLE SubPop ADD CONSTRAINT fk_SubPop_batch_id FOREIGN KEY (batch_id) REFERENCES Batch(batch_id);
@@ -56,16 +55,17 @@ ALTER TABLE SubSNPSeqPos ADD CONSTRAINT pk_SubSNPSeqPos  PRIMARY KEY  (subsnp_id
 ALTER TABLE SubSNP_top_or_bot ADD CONSTRAINT PK__t_ss_top_or_bot__0D5DFFA8  PRIMARY KEY  (subsnp_id);
 ALTER TABLE SubmittedIndividual ALTER COLUMN ploidy SET DEFAULT 2;
 ALTER TABLE SubmittedIndividual ADD CONSTRAINT pk_SubmittedIndividual  PRIMARY KEY  (pop_id,loc_ind_id_upp);
+ALTER TABLE SuspectReasonCode ALTER COLUMN create_time SET DEFAULT NOW();
+ALTER TABLE SuspectReasonCode ALTER COLUMN last_update_time SET DEFAULT NOW();
+ALTER TABLE SuspectReasonCode ADD CONSTRAINT PK__SuspectR__357D4CF8111DDE3A  PRIMARY KEY  (code);
 ALTER TABLE Synonym ADD CONSTRAINT pk_Synonym  PRIMARY KEY  (subsnp_id,type);
-ALTER TABLE b135_ContigInfo_37_3 ALTER COLUMN last_updated_time SET DEFAULT NOW();
-ALTER TABLE b135_ContigInfo_37_3 ADD CONSTRAINT pk_b135_ContigInfo_37_3  PRIMARY KEY  (contig_gi);
-ALTER TABLE b135_MapLink_37_3 ADD CONSTRAINT fk_b135_MapLink_37_3_rs FOREIGN KEY (snp_id) REFERENCES SNP(snp_id);
-ALTER TABLE b135_SNPChrPosOnRef_37_3 ADD CONSTRAINT fk_b135_SNPChrPosOnRef_37_3_rs FOREIGN KEY (snp_id) REFERENCES SNP(snp_id);
-ALTER TABLE b135_SNPContigLoc_37_3 ADD CONSTRAINT fk_b135_SNPContigLoc_37_3_rs FOREIGN KEY (snp_id) REFERENCES SNP(snp_id);
-ALTER TABLE b135_SNPContigLocusId_37_3 ADD CONSTRAINT fk_b135_SNPContigLocusId_37_3_rs FOREIGN KEY (snp_id) REFERENCES SNP(snp_id);
-ALTER TABLE b135_SNPContigProtein_37_3 ADD CONSTRAINT fk_b135_SNPContigProtein_37_3_rs FOREIGN KEY (snp_id) REFERENCES SNP(snp_id);
-ALTER TABLE b135_SNPMapInfo_37_3 ADD CONSTRAINT fk_b135_SNPMapInfo_37_3_rs FOREIGN KEY (snp_id) REFERENCES SNP(snp_id);
-ALTER TABLE b135_SNPMapLinkProtein_37_3 ADD CONSTRAINT fk_b135_SNPMapLinkProtein_37_3_rs FOREIGN KEY (snp_id) REFERENCES SNP(snp_id);
+ALTER TABLE b137_ContigInfo ALTER COLUMN last_updated_time SET DEFAULT NOW();
+ALTER TABLE b137_ContigInfo ADD CONSTRAINT pk_b137_ContigInfo  PRIMARY KEY  (contig_gi);
+ALTER TABLE b137_MapLink ADD CONSTRAINT fk_b137_MapLink_rs FOREIGN KEY (snp_id) REFERENCES SNP(snp_id);
+ALTER TABLE b137_SNPChrPosOnRef ADD CONSTRAINT fk_b137_SNPChrPosOnRef_rs FOREIGN KEY (snp_id) REFERENCES SNP(snp_id);
+ALTER TABLE b137_SNPContigLoc ADD CONSTRAINT fk_b137_SNPContigLoc_rs FOREIGN KEY (snp_id) REFERENCES SNP(snp_id);
+ALTER TABLE b137_SNPContigLoc ADD CONSTRAINT pk_b137_SNPContigLoc  PRIMARY KEY  (snp_type,snp_id,ctg_id,asn_from);
+ALTER TABLE b137_SNPMapInfo ADD CONSTRAINT fk_b137_SNPMapInfo_rs FOREIGN KEY (snp_id) REFERENCES SNP(snp_id);
 ALTER TABLE dn_IND_batchCount ADD CONSTRAINT pk_dn_IND_batchCount  PRIMARY KEY  (batch_id,pop_id);
 ALTER TABLE dn_PopulationIndGrp ADD CONSTRAINT pk_dn_PopulationIndGrp  PRIMARY KEY  (pop_id);
 ALTER TABLE dn_batchCount ADD CONSTRAINT pk_dn_batchCount  PRIMARY KEY  (batch_id);