schema-001.sql

/* ---------------------------------------------------------------------- */
/* Domains                                                                */
/* ---------------------------------------------------------------------- */

CREATE DOMAIN TECH_ID AS BIGINT;

CREATE DOMAIN CODE AS VARCHAR(40);

CREATE DOMAIN NAME AS VARCHAR(80);

CREATE DOMAIN DESCRIPTION AS VARCHAR(200);

CREATE DOMAIN FILE_PATH as VARCHAR(1000);

CREATE DOMAIN COLOR_COMPONENT AS VARCHAR(40) CHECK (VALUE IN ('RED', 'GREEN', 'BLUE'));

/* ---------------------------------------------------------------------- */
/* Tables                                                                 */
/* ---------------------------------------------------------------------- */

CREATE TABLE EXPERIMENTS (
  ID BIGSERIAL NOT NULL,
  PERM_ID CODE NOT NULL,

  PRIMARY KEY (ID),
  UNIQUE (PERM_ID)
);

CREATE TABLE CONTAINERS (
  ID BIGSERIAL NOT NULL,
  PERM_ID CODE NOT NULL,

  SPOTS_WIDTH INTEGER,
  SPOTS_HEIGHT INTEGER,
  
  EXPE_ID TECH_ID NOT NULL,

  PRIMARY KEY (ID),
  UNIQUE (PERM_ID),
  CONSTRAINT FK_SAMPLE_1 FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE
);

CREATE INDEX CONTAINERS_EXPE_IDX ON CONTAINERS(EXPE_ID);

CREATE TABLE SPOTS (
  ID BIGSERIAL NOT NULL,
  PERM_ID CODE NOT NULL,
	
	-- position in the container, one-based
  X INTEGER, 
  Y INTEGER, 
  CONT_ID TECH_ID NOT NULL,
  
  PRIMARY KEY (ID),
  UNIQUE (PERM_ID),
  CONSTRAINT FK_SPOT_1 FOREIGN KEY (CONT_ID) REFERENCES CONTAINERS (ID) ON DELETE CASCADE ON UPDATE CASCADE
);

CREATE INDEX SPOTS_CONT_IDX ON SPOTS(CONT_ID);

CREATE TABLE DATA_SETS (
  ID BIGSERIAL NOT NULL,
  PERM_ID CODE NOT NULL,  
  
	FIELDS_WIDTH INTEGER,
	FIELDS_HEIGHT INTEGER,	
  
  CONT_ID TECH_ID NOT NULL,

  PRIMARY KEY (ID),
  UNIQUE (PERM_ID),
  CONSTRAINT FK_DATA_SET_1 FOREIGN KEY (CONT_ID) REFERENCES CONTAINERS (ID) ON DELETE CASCADE ON UPDATE CASCADE
);

CREATE INDEX DATA_SETS_CONT_IDX ON DATA_SETS(CONT_ID);

CREATE TABLE CHANNELS (
    ID BIGSERIAL  NOT NULL,
    
    NAME NAME NOT NULL,
    DESCRIPTION DESCRIPTION,
    WAVELENGTH INTEGER,

    DS_ID TECH_ID,
    EXP_ID TECH_ID,
    
    PRIMARY KEY (ID),
    CONSTRAINT FK_CHANNELS_1 FOREIGN KEY (DS_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
    CONSTRAINT FK_CHANNELS_2 FOREIGN KEY (EXP_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
    CONSTRAINT CHANNELS_DS_EXP_ARC_CK CHECK ((DS_ID IS NOT NULL AND EXP_ID IS NULL) OR (DS_ID IS NULL AND EXP_ID IS NOT NULL)),
    
    CONSTRAINT CHANNELS_UK_1 UNIQUE(NAME, DS_ID),
    CONSTRAINT CHANNELS_UK_2 UNIQUE(NAME, EXP_ID)
);

CREATE INDEX CHANNELS_DS_IDX ON CHANNELS(DS_ID);

CREATE TABLE CHANNEL_STACKS (
    ID BIGSERIAL  NOT NULL,
		
		-- x and y are kind of a two dimensional sequence number, some use case may only use x and leave y alone
		X INTEGER,
		Y INTEGER,
		-- we use the fixed dimension meters here
		Z_in_M REAL,
		-- we use the fixed dimension seconds here
		T_in_SEC REAL,

    DS_ID TECH_ID	NOT NULL,
		SPOT_ID TECH_ID	NOT NULL,

    PRIMARY KEY (ID),
    CONSTRAINT FK_CHANNEL_STACKS_1 FOREIGN KEY (SPOT_ID) REFERENCES SPOTS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
    CONSTRAINT FK_CHANNEL_STACKS_2 FOREIGN KEY (DS_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE
);

CREATE INDEX CHANNEL_STACKS_DS_IDX ON CHANNEL_STACKS(DS_ID);
CREATE INDEX CHANNEL_STACKS_SPOT_IDX ON CHANNEL_STACKS(SPOT_ID);
CREATE INDEX CHANNEL_STACKS_DIM_IDX ON CHANNEL_STACKS(X, Y, Z_in_M, T_in_SEC);

CREATE TABLE ACQUIRED_IMAGES (
    ID BIGSERIAL  NOT NULL,
   
		IMG_ID   TECH_ID NOT NULL,
		THUMBNAIL_ID  TECH_ID,

    CHANNEL_STACK_ID  TECH_ID NOT NULL,
    CHANNEL_ID  TECH_ID NOT NULL,

    PRIMARY KEY (ID),
    CONSTRAINT FK_IMAGES_1 FOREIGN KEY (CHANNEL_STACK_ID) REFERENCES CHANNEL_STACKS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
    CONSTRAINT FK_IMAGES_2 FOREIGN KEY (CHANNEL_ID) REFERENCES CHANNELS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
    CONSTRAINT FK_IMAGES_3 FOREIGN KEY (IMG_ID) REFERENCES IMAGES (ID) ON DELETE CASCADE ON UPDATE CASCADE,
    CONSTRAINT FK_IMAGES_4 FOREIGN KEY (THUMBNAIL_ID) REFERENCES IMAGES (ID) ON DELETE CASCADE ON UPDATE CASCADE
);

CREATE INDEX IMAGES_CHANNEL_STACK_IDX ON ACQUIRED_IMAGES(CHANNEL_STACK_ID);
CREATE INDEX IMAGES_CHANNEL_IDX ON ACQUIRED_IMAGES(CHANNEL_ID);
CREATE INDEX IMAGES_IMG_IDX ON ACQUIRED_IMAGES(IMG_ID);
CREATE INDEX IMAGES_THUMBNAIL_IDX ON ACQUIRED_IMAGES(THUMBNAIL_ID);

CREATE TABLE IMAGES (
    ID BIGSERIAL  NOT NULL,
   
    PATH	FILE_PATH NOT NULL,
    PAGE	INTEGER,
    COLOR	COLOR_COMPONENT,
    
    PRIMARY KEY (ID)
);

/* ---------------------------------------------------------------------- */
/* FEATURE VECTORS                                                        */
/* ---------------------------------------------------------------------- */ 

/* --- UNUSED YET ---------------------------------------

CREATE TABLE FEATURE_DEFS (
    ID BIGSERIAL  NOT NULL,
    
    NAME NAME NOT NULL,
    DESCRIPTION DESCRIPTION,
    
    DS_ID  TECH_ID NOT NULL,
    
    PRIMARY KEY (ID),
    CONSTRAINT FK_FEATURE_DEFS_1 FOREIGN KEY (DS_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
    CONSTRAINT FEATURE_DEFS_UK_1 UNIQUE(NAME, DS_ID)
);

CREATE INDEX FEATURE_DEFS_DS_IDX ON FEATURE_DEFS(DS_ID);

CREATE TABLE FEATURE_VALUES (
    ID BIGSERIAL  NOT NULL,
		
		-- we use the fixed dimension meters here
		Z_in_M REAL,
		-- we use the fixed dimension seconds here
		T_in_SEC REAL,
		-- serialized 2D matrix with values for each spot
		VALUES BYTEA NOT NULL,
		
		FD_ID  TECH_ID NOT NULL,
		DS_ID  TECH_ID NOT NULL,
		
		PRIMARY KEY (ID),
		CONSTRAINT FK_FEATURE_VALUES_1 FOREIGN KEY (FD_ID) REFERENCES FEATURE_DEFS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
    CONSTRAINT FK_FEATURE_VALUES_2 FOREIGN KEY (DS_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
		CONSTRAINT FEATURE_VALUES_UK_1 UNIQUE(Z_in_M, T_in_SEC)
);

CREATE INDEX FEATURE_VALUES_FD_IDX ON FEATURE_VALUES(FD_ID);
CREATE INDEX FEATURE_VALUES_DS_IDX ON FEATURE_VALUES(DS_ID);
CREATE INDEX FEATURE_VALUES_Z_AND_T_IDX ON FEATURE_VALUES(Z_in_M, T_in_SEC);

  --- END UNUSED YET --------------------------------------- */