From d55d2389cbf9278a2ad6dde8f72877a4a2d5d37e Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Fri, 14 Oct 2011 14:46:16 +0000
Subject: [PATCH] LMS-2562 thumbnails pyramide: db changes
SVN: 23326
---
.../sql/imaging/postgresql/017/schema-017.sql | 375 ++++++++++++++++++
.../migration/migration-016-017.sql | 24 ++
2 files changed, 399 insertions(+)
create mode 100644 screening/source/sql/imaging/postgresql/017/schema-017.sql
create mode 100644 screening/source/sql/imaging/postgresql/migration/migration-016-017.sql
diff --git a/screening/source/sql/imaging/postgresql/017/schema-017.sql b/screening/source/sql/imaging/postgresql/017/schema-017.sql
new file mode 100644
index 00000000000..23b0712b33e
--- /dev/null
+++ b/screening/source/sql/imaging/postgresql/017/schema-017.sql
@@ -0,0 +1,375 @@
+
+/* ---------------------------------------------------------------------- */
+/* 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
diff --git a/screening/source/sql/imaging/postgresql/migration/migration-016-017.sql b/screening/source/sql/imaging/postgresql/migration/migration-016-017.sql
new file mode 100644
index 00000000000..262a76414f3
--- /dev/null
+++ b/screening/source/sql/imaging/postgresql/migration/migration-016-017.sql
@@ -0,0 +1,24 @@
+-- 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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