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Commit d55d2389 authored by tpylak's avatar tpylak
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LMS-2562 thumbnails pyramide: db changes 

SVN: 23326
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screening/source/sql/imaging/postgresql/017/schema-017.sql 0 → 100644
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/* ---------------------------------------------------------------------- */
/* 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'));
CREATE DOMAIN CHANNEL_COLOR AS VARCHAR(20) CHECK (VALUE IN ('BLUE', 'GREEN', 'RED', 'RED_GREEN', 'RED_BLUE', 'GREEN_BLUE'));
CREATE DOMAIN BOOLEAN_CHAR AS BOOLEAN DEFAULT FALSE;
/* ---------------------------------------------------------------------- */
/* Tables */
/* ---------------------------------------------------------------------- */
CREATE TABLE EXPERIMENTS (
ID BIGSERIAL NOT NULL,
PERM_ID CODE NOT NULL,
IMAGE_TRANSFORMER_FACTORY BYTEA,
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,
-- position in the container, one-based
X INTEGER,
Y INTEGER,
CONT_ID TECH_ID NOT NULL,
PRIMARY KEY (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);
-- allows to select one spot of the container quicker
CREATE INDEX SPOTS_COORDS_IDX ON SPOTS(CONT_ID, X, Y);
CREATE TABLE ANALYSIS_DATA_SETS (
ID BIGSERIAL NOT NULL,
PERM_ID CODE NOT NULL,
CONT_ID TECH_ID,
PRIMARY KEY (ID),
UNIQUE (PERM_ID),
CONSTRAINT FK_ANALYSIS_DATA_SET_1 FOREIGN KEY (CONT_ID) REFERENCES CONTAINERS (ID) ON DELETE CASCADE ON UPDATE CASCADE
);
CREATE INDEX ANALYSIS_DATA_SETS_CONT_IDX ON ANALYSIS_DATA_SETS(CONT_ID);
CREATE TABLE IMAGE_DATA_SETS (
ID BIGSERIAL NOT NULL,
PERM_ID CODE NOT NULL,
---- image dataset specific fields (should be refactored)
FIELDS_WIDTH INTEGER,
FIELDS_HEIGHT INTEGER,
-- transformation for merged channels on the dataset level, overrides experiment level transformation
IMAGE_TRANSFORMER_FACTORY BYTEA,
-- a redundant information if there are timepoint or depth stack data for any spots in this dataset
IS_MULTIDIMENSIONAL BOOLEAN_CHAR NOT NULL,
-- Which image library should be used to read the image?
-- If not specified, some heuristics are used, but it is slower and does not try with all the available libraries.
IMAGE_LIBRARY_NAME NAME,
-- Which reader in the library should be used? Valid only if the library name is specified.
-- Should be specified when library name is specified.
IMAGE_LIBRARY_READER_NAME NAME,
---- END image dataset specific fields
CONT_ID TECH_ID,
PRIMARY KEY (ID),
UNIQUE (PERM_ID),
CONSTRAINT FK_IMAGE_DATA_SET_1 FOREIGN KEY (CONT_ID) REFERENCES CONTAINERS (ID) ON DELETE CASCADE ON UPDATE CASCADE
);
CREATE INDEX IMAGE_DATA_SETS_CONT_IDX ON IMAGE_DATA_SETS(CONT_ID);
CREATE TABLE IMAGE_ZOOM_LEVELS (
ID BIGSERIAL NOT NULL,
IS_ORIGINAL BOOLEAN_CHAR NOT NULL,
CONTAINER_DATASET_ID TECH_ID NOT NULL,
-- Perm id of the 'physical' dataset which contains all images with this zoom.
-- Physical datasets are not stored in "image_data_sets" table, but we need the reference to them
-- when we delete or archive one zoom level.
PHYSICAL_DATASET_PERM_ID TEXT NOT NULL,
PRIMARY KEY (ID),
UNIQUE (PHYSICAL_DATASET_PERM_ID),
CONSTRAINT FK_IMAGE_ZOOM_LEVELS_1 FOREIGN KEY (CONTAINER_DATASET_ID) REFERENCES IMAGE_DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE
);
CREATE INDEX IMAGE_ZOOM_LEVELS_PHYS_DS_IDX ON IMAGE_ZOOM_LEVELS (PHYSICAL_DATASET_PERM_ID);
CREATE INDEX IMAGE_ZOOM_LEVELS_CONT_FK_IDX ON IMAGE_ZOOM_LEVELS (CONTAINER_DATASET_ID);
CREATE TABLE CHANNELS (
ID BIGSERIAL NOT NULL,
CODE NAME NOT NULL,
LABEL NAME NOT NULL,
DESCRIPTION DESCRIPTION,
WAVELENGTH INTEGER,
-- RGB color components specify the color in which channel should be displayed
RED_CC INTEGER NOT NULL,
GREEN_CC INTEGER NOT NULL,
BLUE_CC INTEGER NOT NULL,
DS_ID TECH_ID,
EXP_ID TECH_ID,
PRIMARY KEY (ID),
CONSTRAINT FK_CHANNELS_1 FOREIGN KEY (DS_ID) REFERENCES IMAGE_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(CODE, DS_ID),
CONSTRAINT CHANNELS_UK_2 UNIQUE(CODE, EXP_ID)
);
CREATE INDEX CHANNELS_DS_IDX ON CHANNELS(DS_ID);
CREATE TABLE IMAGE_TRANSFORMATIONS (
ID BIGSERIAL NOT NULL,
CODE NAME NOT NULL,
LABEL NAME NOT NULL,
DESCRIPTION character varying(1000),
IMAGE_TRANSFORMER_FACTORY BYTEA NOT NULL,
-- For now there can be only one transformation for each channel which is editable by Image Viewer,
-- but when GUI will support more then this column will become really useful.
IS_EDITABLE BOOLEAN_CHAR NOT NULL,
-- The default choice to present the image.
-- If not present a 'hard-coded' default transformation will become available.
IS_DEFAULT BOOLEAN_CHAR NOT NULL DEFAULT 'F',
CHANNEL_ID TECH_ID NOT NULL,
PRIMARY KEY (ID),
CONSTRAINT FK_IMAGE_TRANSFORMATIONS_CHANNEL FOREIGN KEY (CHANNEL_ID) REFERENCES CHANNELS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
CONSTRAINT IMAGE_TRANSFORMATIONS_UK_1 UNIQUE(CODE, CHANNEL_ID)
);
CREATE INDEX IMAGE_TRANSFORMATIONS_CHANNELS_IDX ON IMAGE_TRANSFORMATIONS(CHANNEL_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,
SERIES_NUMBER INTEGER,
-- For all channel stacks of a well (HCS) or image dataset (microscopy) there should be exactly
-- one record with is_representative = true
is_representative BOOLEAN_CHAR NOT NULL DEFAULT 'F',
DS_ID TECH_ID NOT NULL,
SPOT_ID TECH_ID,
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 IMAGE_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 IMAGES (
ID BIGSERIAL NOT NULL,
PATH FILE_PATH NOT NULL,
IMAGE_ID CODE,
COLOR COLOR_COMPONENT,
PRIMARY KEY (ID)
);
CREATE TABLE ACQUIRED_IMAGES (
ID BIGSERIAL NOT NULL,
IMG_ID TECH_ID,
THUMBNAIL_ID TECH_ID,
IMAGE_TRANSFORMER_FACTORY BYTEA,
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,
CONSTRAINT FK_IMAGES_IMG_OR_THUMB_ARC_CK CHECK (IMG_ID IS NOT NULL OR THUMBNAIL_ID IS NOT NULL)
);
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 EVENTS (
LAST_SEEN_DELETION_EVENT_ID TECH_ID NOT NULL
);
/* ---------------------------------------------------------------------- */
/* FEATURE VECTORS */
/* ---------------------------------------------------------------------- */
CREATE TABLE FEATURE_DEFS (
ID BIGSERIAL NOT NULL,
CODE NAME NOT NULL,
LABEL NAME NOT NULL,
DESCRIPTION DESCRIPTION,
DS_ID TECH_ID NOT NULL,
PRIMARY KEY (ID),
CONSTRAINT FK_FEATURE_DEFS_1 FOREIGN KEY (DS_ID) REFERENCES ANALYSIS_DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
CONSTRAINT FEATURE_DEFS_UK_1 UNIQUE(CODE, DS_ID)
);
CREATE INDEX FEATURE_DEFS_DS_IDX ON FEATURE_DEFS(DS_ID);
CREATE TABLE FEATURE_VOCABULARY_TERMS (
ID BIGSERIAL NOT NULL,
CODE NAME NOT NULL,
SEQUENCE_NUMBER INTEGER NOT NULL,
FD_ID TECH_ID NOT NULL,
PRIMARY KEY (ID),
CONSTRAINT FK_FEATURE_VOCABULARY_TERMS_1 FOREIGN KEY (FD_ID) REFERENCES FEATURE_DEFS (ID) ON DELETE CASCADE ON UPDATE CASCADE
);
CREATE INDEX FEATURE_VOCABULARY_TERMS_FD_IDX ON FEATURE_VOCABULARY_TERMS(FD_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.
-- Contains floats which can be NaN.
-- It is never a case that the whole matrix contains NaN - in such a case we save nothing.
-- If feature definition has some connected vocabulary terms then the matrix
-- stores FEATURE_VOCABULARY_TERMS.SEQUENCE_NUMBER of the terms (should be casted from float to int).
-- If the term is null the Float.NaN is stored.
VALUES BYTEA NOT NULL,
FD_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
-- This constaint does not make any sense. Leave it out for now.
-- 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_Z_AND_T_IDX ON FEATURE_VALUES(Z_in_M, T_in_SEC);
/* ---------------------------------------------------------------------- */
/* FUNCTIONS AND TRIGGERS */
/* ---------------------------------------------------------------------- */
CREATE OR REPLACE FUNCTION DELETE_UNUSED_IMAGES() RETURNS trigger AS $$
BEGIN
delete from images where id = OLD.img_id or id = OLD.thumbnail_id;
RETURN NEW;
END;
$$ LANGUAGE 'plpgsql';
CREATE TRIGGER UNUSED_IMAGES AFTER DELETE ON ACQUIRED_IMAGES
FOR EACH ROW EXECUTE PROCEDURE DELETE_UNUSED_IMAGES();
------------------------------------------------------------------------------------
-- Purpose: Create trigger CHANNEL_STACKS_CHECK which checks if both spot_id and dataset.cont_id
-- are both null or not null.
------------------------------------------------------------------------------------
CREATE OR REPLACE FUNCTION CHANNEL_STACKS_CHECK() RETURNS trigger AS $$
DECLARE
v_cont_id CODE;
BEGIN
select cont_id into v_cont_id from image_data_sets where id = NEW.ds_id;
-- Check that if there is no spot than there is no dataset container as well
if v_cont_id IS NULL then
if NEW.spot_id IS NOT NULL then
RAISE EXCEPTION 'Insert/Update of CHANNEL_STACKS failed, as the dataset container is not set, but spot is (spot id = %).',NEW.spot_id;
end if;
else
if NEW.spot_id IS NULL then
RAISE EXCEPTION 'Insert/Update of CHANNEL_STACKS failed, as the dataset container is set (id = %), but spot is not set.',v_cont_id;
end if;
end if;
RETURN NEW;
END;
$$ LANGUAGE 'plpgsql';
CREATE TRIGGER CHANNEL_STACKS_CHECK BEFORE INSERT OR UPDATE ON CHANNEL_STACKS
FOR EACH ROW EXECUTE PROCEDURE CHANNEL_STACKS_CHECK();
------------------------------------------------------------------------------------
-- Purpose: Create trigger IMAGE_TRANSFORMATIONS_DEFAULT_CHECK which checks
-- if at most one channel's transformation is default
------------------------------------------------------------------------------------
CREATE OR REPLACE FUNCTION IMAGE_TRANSFORMATIONS_DEFAULT_CHECK() RETURNS trigger AS $$
DECLARE
v_is_default boolean;
BEGIN
if NEW.is_default = 'T' then
select is_default into v_is_default from IMAGE_TRANSFORMATIONS
where is_default = 'T'
and channel_id = NEW.channel_id
and id != NEW.id;
if v_is_default is NOT NULL then
RAISE EXCEPTION 'Insert/Update of image transformation (Code: %) failed, as the new record has is_default set to true and there is already a default record defined.', NEW.code;
end if;
end if;
RETURN NEW;
END;
$$ LANGUAGE 'plpgsql';
CREATE TRIGGER IMAGE_TRANSFORMATIONS_DEFAULT_CHECK BEFORE INSERT OR UPDATE ON IMAGE_TRANSFORMATIONS
FOR EACH ROW EXECUTE PROCEDURE IMAGE_TRANSFORMATIONS_DEFAULT_CHECK();
\ No newline at end of file
screening/source/sql/imaging/postgresql/migration/migration-016-017.sql 0 → 100644
+ 24
− 0
View file @ d55d2389
-- Migration from 016 to 017
CREATE TABLE IMAGE_ZOOM_LEVELS (
ID BIGSERIAL NOT NULL,
IS_ORIGINAL BOOLEAN_CHAR NOT NULL,
CONTAINER_DATASET_ID TECH_ID NOT NULL,
-- Perm id of the 'physical' dataset which contains all images with this zoom.
-- Physical datasets are not stored in "image_data_sets" table, but we need the reference to them
-- when we delete or archive one zoom level.
PHYSICAL_DATASET_PERM_ID TEXT NOT NULL,
PRIMARY KEY (ID),
UNIQUE (PHYSICAL_DATASET_PERM_ID),
CONSTRAINT FK_IMAGE_ZOOM_LEVELS_1 FOREIGN KEY (CONTAINER_DATASET_ID) REFERENCES IMAGE_DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE
);
CREATE INDEX IMAGE_ZOOM_LEVELS_PHYS_DS_IDX ON IMAGE_ZOOM_LEVELS (PHYSICAL_DATASET_PERM_ID);
CREATE INDEX IMAGE_ZOOM_LEVELS_CONT_FK_IDX ON IMAGE_ZOOM_LEVELS (CONTAINER_DATASET_ID);
ALTER TABLE ACQUIRED_IMAGES ALTER COLUMN IMG_ID DROP NULL;
ALTER TABLE ACQUIRED_IMAGES ADD CONSTRAINT FK_IMAGES_IMG_OR_THUMB_ARC_CK CHECK (IMG_ID IS NOT NULL OR THUMBNAIL_ID IS NOT NULL);
\ No newline at end of file
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