SE-170 introducing cascading deletion and new table in datamodel. Version increased to 002

SVN: 13726

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/db/PhosphoNetXDAOFactory.java

@@ -38,7 +38,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQue
 public class PhosphoNetXDAOFactory implements IPhosphoNetXDAOFactory
 {
     /** Current version of the database. */
-    public static final String DATABASE_VERSION = "001";
+    public static final String DATABASE_VERSION = "002";
 
     private static final Logger operationLog =
             LogFactory.getLogger(LogCategory.OPERATION, PhosphoNetXDAOFactory.class);

rtd_phosphonetx/source/sql/postgresql/002/schema-002.sql

+/* ---------------------------------------------------------------------- */
+/* Script generated with: DeZign for Databases v5.2.3                     */
+/* Target DBMS:           PostgreSQL 8                                    */
+/* Project file:          schema.dez                                      */
+/* Project name:                                                          */
+/* Author:                                                                */
+/* Script type:           Database creation script                        */
+/* Created on:            2009-12-07 11:03                                */
+/* Model version:         Version 2009-12-07                              */
+/* ---------------------------------------------------------------------- */
+
+
+/* ---------------------------------------------------------------------- */
+/* Domains                                                                */
+/* ---------------------------------------------------------------------- */
+
+CREATE DOMAIN CHECKSUM AS CHARACTER VARYING(8);
+
+CREATE DOMAIN CODE AS CHARACTER VARYING(40);
+
+CREATE DOMAIN DESCRIPTION AS CHARACTER VARYING(2000);
+
+CREATE DOMAIN INTEGER_NUMBER AS INTEGER;
+
+CREATE DOMAIN REAL_NUMBER AS DOUBLE PRECISION;
+
+CREATE DOMAIN LONG_SEQUENCE AS TEXT;
+
+CREATE DOMAIN SHORT_DESCRIPTION AS CHARACTER VARYING(200);
+
+CREATE DOMAIN TECH_ID AS BIGINT;
+
+CREATE DOMAIN SHORT_SEQUENCE AS CHARACTER VARYING(1000);
+
+CREATE DOMAIN ACCESSION_NUMBER AS CHARACTER VARYING(256);
+
+CREATE DOMAIN SPECTRUM_REFERENCE AS CHARACTER VARYING(100);
+
+/* ---------------------------------------------------------------------- */
+/* Tables                                                                 */
+/* ---------------------------------------------------------------------- */
+
+/* ---------------------------------------------------------------------- */
+/* Add table "EXPERIMENTS"                                                */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE EXPERIMENTS (
+    ID BIGSERIAL  NOT NULL,
+    PERM_ID CODE  NOT NULL,
+    CONSTRAINT PK_EXPERIMENTS PRIMARY KEY (ID),
+    CONSTRAINT TUC_EXPERIMENTS_1 UNIQUE (PERM_ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "DATA_SETS"                                                  */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE DATA_SETS (
+    ID BIGSERIAL  NOT NULL,
+    EXPE_ID TECH_ID  NOT NULL,
+    SAMP_ID TECH_ID,
+    DB_ID TECH_ID  NOT NULL,
+    PERM_ID CODE  NOT NULL,
+    CONSTRAINT PK_DATA_SETS PRIMARY KEY (ID),
+    CONSTRAINT TUC_DATA_SETS_1 UNIQUE (PERM_ID)
+);
+
+CREATE INDEX IX_FK_DATA_SETS_EXPERIMENTS ON DATA_SETS (EXPE_ID);
+
+CREATE INDEX IX_FK_DATA_SETS_SAMPLES ON DATA_SETS (SAMP_ID);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "MODIFICATIONS"                                              */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE MODIFICATIONS (
+    ID BIGSERIAL  NOT NULL,
+    MOPE_ID TECH_ID  NOT NULL,
+    POS INTEGER_NUMBER  NOT NULL,
+    MASS REAL_NUMBER  NOT NULL,
+    CONSTRAINT PK_MODIFICATIONS PRIMARY KEY (ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "PEPTIDES"                                                   */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE PEPTIDES (
+    ID BIGSERIAL  NOT NULL,
+    PROT_ID TECH_ID  NOT NULL,
+    SEQUENCE SHORT_SEQUENCE  NOT NULL,
+    CHARGE INTEGER_NUMBER  NOT NULL,
+    CONSTRAINT PK_PEPTIDES PRIMARY KEY (ID)
+);
+
+CREATE INDEX IX_FK_PEPTIDES_PROTEINS ON PEPTIDES (PROT_ID);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "PROTEINS"                                                   */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE PROTEINS (
+    ID BIGSERIAL  NOT NULL,
+    DASE_ID TECH_ID  NOT NULL,
+    PROBABILITY REAL_NUMBER  NOT NULL,
+    CONSTRAINT PK_PROTEINS PRIMARY KEY (ID)
+);
+
+CREATE INDEX IDX_PROTEINS_1 ON PROTEINS (DASE_ID);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "SAMPLES"                                                    */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE SAMPLES (
+    ID BIGSERIAL  NOT NULL,
+    PERM_ID CODE  NOT NULL,
+    EXPE_ID TECH_ID  NOT NULL,
+    CONSTRAINT PK_SAMPLES PRIMARY KEY (ID),
+    CONSTRAINT TUC_SAMPLES_1 UNIQUE (PERM_ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "SEQUENCES"                                                  */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE SEQUENCES (
+    ID BIGSERIAL  NOT NULL,
+    DB_ID TECH_ID  NOT NULL,
+    PRRE_ID TECH_ID  NOT NULL,
+    AMINO_ACID_SEQUENCE LONG_SEQUENCE  NOT NULL,
+    CHECKSUM CHECKSUM  NOT NULL,
+    CONSTRAINT PK_SEQUENCES PRIMARY KEY (ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "IDENTIFIED_PROTEINS"                                        */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE IDENTIFIED_PROTEINS (
+    ID BIGSERIAL  NOT NULL,
+    PROT_ID TECH_ID  NOT NULL,
+    SEQU_ID TECH_ID  NOT NULL,
+    CONSTRAINT PK_IDENTIFIED_PROTEINS PRIMARY KEY (ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "ABUNDANCES"                                                 */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE ABUNDANCES (
+    ID BIGSERIAL  NOT NULL,
+    PROT_ID TECH_ID  NOT NULL,
+    SAMP_ID TECH_ID  NOT NULL,
+    VALUE REAL_NUMBER  NOT NULL,
+    CONSTRAINT PK_ABUNDANCES PRIMARY KEY (ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "PROBABILITY_FDR_MAPPINGS"                                   */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE PROBABILITY_FDR_MAPPINGS (
+    ID BIGSERIAL  NOT NULL,
+    DASE_ID TECH_ID  NOT NULL,
+    PROBABILITY REAL_NUMBER  NOT NULL,
+    FALSE_DISCOVERY_RATE REAL_NUMBER  NOT NULL,
+    CONSTRAINT PK_PROBABILITY_FDR_MAPPINGS PRIMARY KEY (ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "PROTEIN_REFERENCES"                                         */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE PROTEIN_REFERENCES (
+    ID BIGSERIAL  NOT NULL,
+    ACCESSION_NUMBER ACCESSION_NUMBER  NOT NULL,
+    DESCRIPTION DESCRIPTION,
+    CONSTRAINT PK_PROTEIN_REFERENCES PRIMARY KEY (ID),
+    CONSTRAINT TUC_PROTEIN_REFERENCES_1 UNIQUE (ACCESSION_NUMBER)
+);
+
+CREATE INDEX IDX_PROTEIN_REFERENCES_1 ON PROTEIN_REFERENCES (ACCESSION_NUMBER);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "DATABASES"                                                  */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE DATABASES (
+    ID BIGSERIAL  NOT NULL,
+    NAME_AND_VERSION SHORT_DESCRIPTION  NOT NULL,
+    CONSTRAINT PK_DATABASES PRIMARY KEY (ID),
+    CONSTRAINT TUC_DATABASES_1 UNIQUE (NAME_AND_VERSION)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "MODIFIED_PEPTIDES"                                          */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE MODIFIED_PEPTIDES (
+    ID BIGSERIAL  NOT NULL,
+    PEPT_ID TECH_ID  NOT NULL,
+    NTERM_MASS REAL_NUMBER  NOT NULL,
+    CTERM_MASS REAL_NUMBER  NOT NULL,
+    CONSTRAINT PK_MODIFIED_PEPTIDES PRIMARY KEY (ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "SPECTRUM_REFERENCES"                                        */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE SPECTRUM_REFERENCES (
+    ID BIGSERIAL  NOT NULL,
+    PEPT_ID TECH_ID  NOT NULL,
+    REFERENCE SPECTRUM_REFERENCE  NOT NULL,
+    CONSTRAINT PK_SPECTRUM_REFERENCES PRIMARY KEY (ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "MODIFICATION_FRACTIONS"                                     */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE MODIFICATION_FRACTIONS (
+    ID BIGSERIAL  NOT NULL,
+    MODI_ID TECH_ID  NOT NULL,
+    SAMP_ID TECH_ID,
+    FRACTION REAL_NUMBER  NOT NULL,
+    CONSTRAINT PK_MODIFICATION_FRACTIONS PRIMARY KEY (ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "EVENTS"                                                     */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE EVENTS (
+    LAST_SEEN_DELETION_EVENT_ID TECH_ID  NOT NULL
+);
+
+/* ---------------------------------------------------------------------- */
+/* Foreign key constraints                                                */
+/* ---------------------------------------------------------------------- */
+
+ALTER TABLE DATA_SETS ADD CONSTRAINT DA_EX_FK 
+    FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID);
+
+ALTER TABLE DATA_SETS ADD CONSTRAINT DA_SA_FK 
+    FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
+
+ALTER TABLE DATA_SETS ADD CONSTRAINT DATABASES_DATA_SETS 
+    FOREIGN KEY (DB_ID) REFERENCES DATABASES (ID);
+
+ALTER TABLE MODIFICATIONS ADD CONSTRAINT MODIFIED_PEPTIDES_MODIFICATIONS 
+    FOREIGN KEY (MOPE_ID) REFERENCES MODIFIED_PEPTIDES (ID) ON DELETE CASCADE;
+
+ALTER TABLE PEPTIDES ADD CONSTRAINT PE_PR_FK 
+    FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
+
+ALTER TABLE PROTEINS ADD CONSTRAINT DATA_SETS_PROTEINS 
+    FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
+
+ALTER TABLE SEQUENCES ADD CONSTRAINT DATABASES_SEQUENCES 
+    FOREIGN KEY (DB_ID) REFERENCES DATABASES (ID);
+
+ALTER TABLE SEQUENCES ADD CONSTRAINT PROTEIN_REFERENCES_SEQUENCES 
+    FOREIGN KEY (PRRE_ID) REFERENCES PROTEIN_REFERENCES (ID);
+
+ALTER TABLE IDENTIFIED_PROTEINS ADD CONSTRAINT PROTEINS_IDENTIFIED_PROTEINS 
+    FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
+
+ALTER TABLE IDENTIFIED_PROTEINS ADD CONSTRAINT SEQUENCES_IDENTIFIED_PROTEINS 
+    FOREIGN KEY (SEQU_ID) REFERENCES SEQUENCES (ID);
+
+ALTER TABLE ABUNDANCES ADD CONSTRAINT SAMPLES_ABUNDANCES 
+    FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
+
+ALTER TABLE ABUNDANCES ADD CONSTRAINT PROTEINS_ABUNDANCES 
+    FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
+
+ALTER TABLE PROBABILITY_FDR_MAPPINGS ADD CONSTRAINT DATA_SETS_PROBABILITY_FDR_MAPPINGS 
+    FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
+
+ALTER TABLE MODIFIED_PEPTIDES ADD CONSTRAINT PEPTIDES_MODIFIED_PEPTIDES 
+    FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID) ON DELETE CASCADE;
+
+ALTER TABLE SPECTRUM_REFERENCES ADD CONSTRAINT PEPTIDES_SPECTRUM_REFERENCES 
+    FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID) ON DELETE CASCADE;
+
+ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT MODIFICATIONS_MODIFICATION_FRACTIONS 
+    FOREIGN KEY (MODI_ID) REFERENCES MODIFICATIONS (ID) ON DELETE CASCADE;
+
+ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT SAMPLES_MODIFICATION_FRACTIONS 
+    FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);

rtd_phosphonetx/source/sql/postgresql/migration/migration-001-002.sql

+CREATE TABLE EVENTS (
+    LAST_SEEN_DELETION_EVENT_ID TECH_ID  NOT NULL
+);
+
+
+ALTER TABLE MODIFICATIONS DROP CONSTRAINT MODIFIED_PEPTIDES_MODIFICATIONS;
+ALTER TABLE MODIFICATIONS ADD CONSTRAINT MODIFIED_PEPTIDES_MODIFICATIONS 
+    FOREIGN KEY (MOPE_ID) REFERENCES MODIFIED_PEPTIDES (ID) ON DELETE CASCADE;
+
+ALTER TABLE PEPTIDES DROP CONSTRAINT PE_PR_FK;
+ALTER TABLE PEPTIDES ADD CONSTRAINT PE_PR_FK 
+    FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
+
+ALTER TABLE PROTEINS DROP CONSTRAINT DATA_SETS_PROTEINS; 
+ALTER TABLE PROTEINS ADD CONSTRAINT DATA_SETS_PROTEINS 
+    FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
+
+ALTER TABLE IDENTIFIED_PROTEINS DROP CONSTRAINT PROTEINS_IDENTIFIED_PROTEINS;
+ALTER TABLE IDENTIFIED_PROTEINS ADD CONSTRAINT PROTEINS_IDENTIFIED_PROTEINS 
+    FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
+    
+ALTER TABLE ABUNDANCES DROP CONSTRAINT PROTEINS_ABUNDANCES;
+ALTER TABLE ABUNDANCES ADD CONSTRAINT PROTEINS_ABUNDANCES 
+    FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
+
+ALTER TABLE PROBABILITY_FDR_MAPPINGS DROP CONSTRAINT DATA_SETS_PROBABILITY_FDR_MAPPINGS;
+ALTER TABLE PROBABILITY_FDR_MAPPINGS ADD CONSTRAINT DATA_SETS_PROBABILITY_FDR_MAPPINGS 
+    FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
+
+ALTER TABLE MODIFIED_PEPTIDES DROP CONSTRAINT PEPTIDES_MODIFIED_PEPTIDES;
+ALTER TABLE MODIFIED_PEPTIDES ADD CONSTRAINT PEPTIDES_MODIFIED_PEPTIDES 
+    FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID) ON DELETE CASCADE;
+
+ALTER TABLE SPECTRUM_REFERENCES DROP CONSTRAINT PEPTIDES_SPECTRUM_REFERENCES;
+ALTER TABLE SPECTRUM_REFERENCES ADD CONSTRAINT PEPTIDES_SPECTRUM_REFERENCES 
+    FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID) ON DELETE CASCADE;
+
+ALTER TABLE MODIFICATION_FRACTIONS DROP CONSTRAINT MODIFICATIONS_MODIFICATION_FRACTIONS;
+ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT MODIFICATIONS_MODIFICATION_FRACTIONS 
+    FOREIGN KEY (MODI_ID) REFERENCES MODIFICATIONS (ID) ON DELETE CASCADE;
+    
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