From b17491ff8c2d4ce88d3cd87c7a6a75e48acbf06e Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Mon, 14 Feb 2011 10:12:22 +0000
Subject: [PATCH] LMS-2044 HCS: Change Data Set Types
SVN: 19929
---
.../migration/migration-065-066.sql | 101 ++++--
.../dist/admin/empty-screening-database.sql | 292 ++++++------------
screening/dist/etc/service.properties | 10 +-
screening/dist/server/web-client.properties | 8 +-
.../server/DssServiceRpcScreening.java | 2 +-
.../application/ClientPluginFactory.java | 8 +-
.../logic/FeatureVectorDatasetLoader.java | 8 +-
...Loader.java => HCSImageDatasetLoader.java} | 18 +-
.../server/logic/ScreeningApiImpl.java | 6 +-
.../server/logic/ScreeningUtils.java | 30 +-
.../shared/basic/dto/ScreeningConstants.java | 54 +++-
11 files changed, 245 insertions(+), 292 deletions(-)
rename screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/{ImageDatasetLoader.java => HCSImageDatasetLoader.java} (89%)
diff --git a/openbis/source/sql/postgresql/migration/migration-065-066.sql b/openbis/source/sql/postgresql/migration/migration-065-066.sql
index 54b7e88e5bc..3d95d3cfa11 100644
--- a/openbis/source/sql/postgresql/migration/migration-065-066.sql
+++ b/openbis/source/sql/postgresql/migration/migration-065-066.sql
@@ -1,40 +1,83 @@
-- Migration from 065 to 066
-ALTER TABLE EXTERNAL_DATA ADD COLUMN SHARE_ID CODE;
-ALTER TABLE EXTERNAL_DATA ADD COLUMN SIZE ORDINAL_INT;
-
-----------------------------------------------------------------------------------------------------
--- Redo part of migration from 056 to 057
---
--- Introduction of a new data type - XML, was done in migration but data.sql wasn't updated.
--- Add the XML data type it if it doesn't exist.
-----------------------------------------------------------------------------------------------------
-
-CREATE OR REPLACE FUNCTION insert_xml_data_type_if_not_exists() RETURNS void AS $$
+--------------------------------------------------------------------------------------
+--------------------------------------------------------------------------------------
+-- This is a screening specific migration. Nothing will be performed on openBIS databases
+-- which are not screening specific.
+--
+-- This migration for each existing connection between oligo well, oligo material and gene material
+-- creates a direct connection between the well and the gene.
+--------------------------------------------------------------------------------------
+--------------------------------------------------------------------------------------
+
+CREATE OR REPLACE FUNCTION INSERT_DATASET_TYPE_IF_NOT_PRESENT(new_code text, new_description text) RETURNS void AS $$
DECLARE
exists bool;
BEGIN
- SELECT true INTO exists
- FROM data_types WHERE code = 'XML';
-
- IF exists IS NULL then
- -- XML data type doesn't exist - insert it
- INSERT INTO data_types (id, code, description)
- VALUES (nextval('data_type_id_seq'), 'XML', 'XML document');
- END IF;
+
+ select true into exists from data_set_types where code = new_code;
+
+ if exists IS NOT NULL then
+ return;
+ end if;
+
+ insert into data_set_types(
+ id,
+ code, description,
+ dbin_id)
+ values(
+ nextval('data_set_type_id_seq'),
+ new_code,
+ new_description,
+ (select id from database_instances where is_original_source = 'T')
+ );
+
END;
$$ LANGUAGE 'plpgsql';
+CREATE OR REPLACE FUNCTION CREATE_HCS_DATASET_TYPES() RETURNS void AS $$
+DECLARE
+ hcs_image_dataset_exists bool;
+BEGIN
+
+ select true
+ into hcs_image_dataset_exists
+ from data_set_types
+ where code = 'HCS_IMAGE';
+
+ if hcs_image_dataset_exists IS NULL then
+ -- skip migration if there is not HCS_IMAGE dataset type
+ return;
+ end if;
+
+ PERFORM INSERT_DATASET_TYPE_IF_NOT_PRESENT(
+ 'HCS_IMAGE_RAW',
+ 'Raw High Content Screening Images');
+ PERFORM INSERT_DATASET_TYPE_IF_NOT_PRESENT(
+ 'HCS_IMAGE_OVERVIEW',
+ 'Overview High Content Screening Images. Generated from raw images.');
+ PERFORM INSERT_DATASET_TYPE_IF_NOT_PRESENT(
+ 'HCS_IMAGE_SEGMENTATION',
+ 'HCS Segmentation Images (overlays)');
+ PERFORM INSERT_DATASET_TYPE_IF_NOT_PRESENT(
+ 'HCS_ANALYSIS_WELL_FEATURES',
+ 'HCS image analysis well feature vectors.');
+ PERFORM INSERT_DATASET_TYPE_IF_NOT_PRESENT(
+ 'HCS_ANALYSIS_CELL_SEGMENTATION',
+ 'HCS image analysis cell segmentation');
+ PERFORM INSERT_DATASET_TYPE_IF_NOT_PRESENT(
+ 'HCS_ANALYSIS_CELL_FEATURES',
+ 'HCS image analysis cell feature vectors');
+ PERFORM INSERT_DATASET_TYPE_IF_NOT_PRESENT(
+ 'HCS_ANALYSIS_CELL_CLASS',
+ 'HCS image analysis cell classification');
-SELECT insert_xml_data_type_if_not_exists();
-DROP FUNCTION insert_xml_data_type_if_not_exists();
+END;
+$$ LANGUAGE 'plpgsql';
-----------------------------------------------------------------------------------------------------
--- Redo part of migration from 063 to 064
---
--- Domain SCRIPT_TYPE created in migration has different values than the one in domain.sql.
--- Alter the domain.
-----------------------------------------------------------------------------------------------------
+select CREATE_HCS_DATASET_TYPES();
+drop function CREATE_HCS_DATASET_TYPES();
+drop function INSERT_DATASET_TYPE_IF_NOT_PRESENT(text, text);
-ALTER DOMAIN script_type DROP CONSTRAINT script_type_check;
-ALTER DOMAIN script_type ADD CONSTRAINT script_type_check CHECK (VALUE IN ('DYNAMIC_PROPERTY', 'MANAGED_PROPERTY'));
+--------------------------------------------------------------------------------------
+--------------------------------------------------------------------------------------=======
diff --git a/screening/dist/admin/empty-screening-database.sql b/screening/dist/admin/empty-screening-database.sql
index c7f058df97a..6e693f45c2a 100644
--- a/screening/dist/admin/empty-screening-database.sql
+++ b/screening/dist/admin/empty-screening-database.sql
@@ -2030,38 +2030,6 @@ CREATE SEQUENCE stpt_id_seq
SELECT pg_catalog.setval('stpt_id_seq', 101, true);
---
--- Data for Name: attachment_contents; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY attachment_contents (id, value) FROM stdin;
-\.
-
-
---
--- Data for Name: attachments; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY attachments (id, expe_id, samp_id, proj_id, exac_id, file_name, registration_timestamp, version, pers_id_registerer, title, description) FROM stdin;
-\.
-
-
---
--- Data for Name: authorization_group_persons; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY authorization_group_persons (ag_id, pers_id) FROM stdin;
-\.
-
-
---
--- Data for Name: authorization_groups; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY authorization_groups (id, dbin_id, code, description, registration_timestamp, pers_id_registerer, modification_timestamp) FROM stdin;
-\.
-
-
--
-- Data for Name: controlled_vocabularies; Type: TABLE DATA; Schema: public; Owner: -
--
@@ -2088,78 +2056,12 @@ COPY controlled_vocabulary_terms (id, code, registration_timestamp, covo_id, per
8 MD_IMAGEXPRESS_MICRO_2 2009-11-29 23:55:18.978884+01 3 1 \N \N 3
\.
-
---
--- Data for Name: data; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY data (id, code, dsty_id, dast_id, expe_id, data_producer_code, production_timestamp, samp_id, registration_timestamp, is_placeholder, is_valid, modification_timestamp, is_derived, pers_id_registerer) FROM stdin;
-\.
-
-
---
--- Data for Name: data_set_properties; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY data_set_properties (id, ds_id, dstpt_id, value, cvte_id, mate_prop_id, pers_id_registerer, registration_timestamp, modification_timestamp) FROM stdin;
-\.
-
-
---
--- Data for Name: data_set_relationships; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY data_set_relationships (data_id_parent, data_id_child) FROM stdin;
-\.
-
-
---
--- Data for Name: data_set_type_property_types; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY data_set_type_property_types (id, dsty_id, prty_id, is_mandatory, is_managed_internally, pers_id_registerer, registration_timestamp, ordinal, section, is_dynamic, script_id) FROM stdin;
-\.
-
-
---
--- Data for Name: data_set_types; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY data_set_types (id, code, description, dbin_id, modification_timestamp, main_ds_pattern, main_ds_path) FROM stdin;
-1 UNKNOWN Unknown 1 2010-05-10 17:57:14.310868+02 \N \N
-3 HCS_IMAGE_ANALYSIS_DATA Data derived from analysis of HCS images 1 2009-11-27 16:02:26.451046+01 \N \N
-2 HCS_IMAGE HCS raw images acquired by microscopes 1 2009-11-27 16:02:26.451046+01 \N \N
-4 HCS_ANALYSIS_PER_GENE Image analysis data aggregated per gene. 1 2009-12-16 16:59:50.743029+01 \N \N
-\.
-
-
---
--- Data for Name: data_store_service_data_set_types; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY data_store_service_data_set_types (data_store_service_id, data_set_type_id) FROM stdin;
-\.
-
-
---
--- Data for Name: data_store_services; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY data_store_services (id, key, label, kind, data_store_id, reporting_plugin_type) FROM stdin;
-1 plate-image-analysis-graph Show Image Analysis Graphs QUERIES 2 \N
-2 default-plate-image-analysis-merger Image Analysis QUERIES 2 \N
-3 plate-image-params-reporter Plate Image Parameters QUERIES 2 \N
-4 plate-image-reporter Plate Images QUERIES 2 \N
-\.
-
-
--
-- Data for Name: data_stores; Type: TABLE DATA; Schema: public; Owner: -
--
COPY data_stores (id, dbin_id, code, download_url, remote_url, session_token, registration_timestamp, modification_timestamp, is_archiver_configured) FROM stdin;
1 1 STANDARD 2010-05-10 17:57:14.310868+02 2010-05-10 17:57:14.310868+02 f
-2 1 DSS-SCREENING http://localhost:8444 http://127.0.0.1:8444 100510175726468-BD82EA5E05B7DFF336D9297C7EB52A2B 2010-05-10 17:57:26.870909+02 2010-05-10 17:57:27.073+02 f
\.
@@ -2189,35 +2091,104 @@ COPY database_instances (id, code, uuid, is_original_source, registration_timest
1 DEMO 678243C3-BD97-42E4-B04B-34DA0C43564D t 2010-05-10 17:57:14.310868+02
\.
-
--
--- Data for Name: database_version_logs; Type: TABLE DATA; Schema: public; Owner: -
+-- Data for Name: data_set_types; Type: TABLE DATA; Schema: public; Owner: -
--
-COPY database_version_logs (db_version, module_name, run_status, run_status_timestamp, module_code, run_exception) FROM stdin;
-051 ./sql/postgresql/051/domains-051.sql SUCCESS 2010-05-10 17:57:09.674 -- Creating domains\\012\\012CREATE DOMAIN AUTHORIZATION_ROLE AS VARCHAR(40) CHECK (VALUE IN ('ADMIN', 'POWER_USER', 'USER', 'OBSERVER', 'ETL_SERVER'));\\012CREATE DOMAIN BOOLEAN_CHAR AS BOOLEAN DEFAULT FALSE;\\012CREATE DOMAIN BOOLEAN_CHAR_OR_UNKNOWN AS CHAR(1) DEFAULT 'U' CHECK (VALUE IN ('F', 'T', 'U'));\\012CREATE DOMAIN CODE AS VARCHAR(60);\\012CREATE DOMAIN COLUMN_LABEL AS VARCHAR(128);\\012CREATE DOMAIN DATA_STORE_SERVICE_KIND AS VARCHAR(40) CHECK (VALUE IN ('PROCESSING', 'QUERIES'));\\012CREATE DOMAIN EVENT_TYPE AS VARCHAR(40) CHECK (VALUE IN ('DELETION', 'INVALIDATION', 'MOVEMENT'));\\012CREATE DOMAIN FILE AS BYTEA;\\012CREATE DOMAIN FILE_NAME AS VARCHAR(100);\\012CREATE DOMAIN GENERIC_VALUE AS VARCHAR(1024);\\012CREATE DOMAIN OBJECT_NAME AS VARCHAR(50);\\012CREATE DOMAIN REAL_VALUE AS REAL;\\012CREATE DOMAIN TECH_ID AS BIGINT;\\012CREATE DOMAIN TIME_STAMP AS TIMESTAMP WITH TIME ZONE;\\012CREATE DOMAIN TIME_STAMP_DFL AS TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP;\\012CREATE DOMAIN USER_ID AS VARCHAR(50);\\012CREATE DOMAIN TITLE_100 AS VARCHAR(100);\\012CREATE DOMAIN GRID_EXPRESSION AS VARCHAR(2000);\\012CREATE DOMAIN GRID_ID AS VARCHAR(200);\\012CREATE DOMAIN ORDINAL_INT AS BIGINT CHECK (VALUE > 0);\\012CREATE DOMAIN DESCRIPTION_2000 AS VARCHAR(2000);\\012CREATE DOMAIN ARCHIVING_STATUS AS VARCHAR(100) CHECK (VALUE IN ('LOCKED', 'AVAILABLE', 'ARCHIVED', 'ARCHIVE_PENDING', 'UNARCHIVE_PENDING'));\\012 \N
-051 ./sql/generic/051/schema-051.sql SUCCESS 2010-05-10 17:57:13.172 -- D:\\\\DDL\\\\postgresql\\\\schema-023.sql\\012--\\012-- Generated for ANSI SQL92 on Fri Jul 04 15:13:22 2008 by Server Generator 10.1.2.6.18\\012------------------------------------------------------------------------------------\\012--\\012-- Post-Generation Modifications:\\012--\\012-- 1. Changed domain FILE from BIT(32000) to BYTEA\\012-- 2. Changed domain TECH_ID from NUMERIC(20) to BIGINT\\012-- 3. Changed domain BOOLEAN_CHAR from CHAR(1) DEFAULT F to BOOLEAN DEFAULT FALSE\\012-- 4. Removed the check constraints to handle boolean values in Oracle for the\\012-- tables MATERIAL_TYPE_PROPERTY_TYPES, EXPERIMENT_TYPE_PROPERTY_TYPES and\\012-- SAMPLE_TYPE_PROPERTY_TYPES (AVCON_%)\\012-- 5. Added the ON DELETE CASCADE qualifier to the foreign keys MAPR_MTPT_FK,\\012-- EXPR_ETPT_FK and SAPR_STPT_FK\\012-- 6. Add the check constraint directly on the domain BOOLEAN_CHAR_OR_UNKNOWN\\012-- CREATE DOMAIN BOOLEAN_CHAR_OR_UNKNOWN AS CHAR(1) CHECK (VALUE in ('F', 'T', 'U')) DEFAULT 'U';\\012-- 7. Add the WITH TIMEZONE qualifier to the domain TIME_STAMP\\012-- CREATE DOMAIN TIME_STAMP AS TIMESTAMP WITH TIME ZONE;\\012-- 8. Add the WITH TIMEZONE and NOT NULL qualifiers to the domain TIME_STAMP_DFL\\012-- CREATE DOMAIN TIME_STAMP_DFL AS TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP;\\012-- 9. Extend the domain EVENT_TYPE by adding the CHECK constraint\\012-- CREATE DOMAIN EVENT_TYPE AS VARCHAR(40) CHECK (VALUE in ('DELETION', 'INVALIDATION', 'MOVEMENT'));\\012-- 10. Extend the domain AUTHORIZATION_ROLE by adding the CHECK constraint\\012-- CREATE DOMAIN AUTHORIZATION_ROLE as VARCHAR(40) CHECK (VALUE IN ('ADMIN', 'POWER_USER', 'USER', 'OBSERVER', 'ETL_SERVER'));\\012-- 11. Added the Sequence and Index sections\\012-- 12. Added DATABASE_INSTANCES.GLOBAL_CODE column for UUID\\012-- 13. DATABASE_INSTANCES.GLOBAL_CODE renamed to DATABASE_INSTANCES.UUID\\012-- 14. OBSERVABLE_TYPES renamed to DATA_SET_TYPES\\012-- 15. OBSERVABLE_TYPE_ID_SEQ renamed to DATA_SET_TYPE_ID_SEQ\\012-- 16. DATA.OBTY_ID renamed to DATA.DSTY_ID;\\012-- 17. some others - the source model should be updated to make these Post-Generation Modifications minimal \\012------------------------------------------------------------------------------------\\012\\012-- Creating tables\\012\\012CREATE TABLE CONTROLLED_VOCABULARIES (ID TECH_ID NOT NULL,CODE CODE NOT NULL,DESCRIPTION DESCRIPTION_2000,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP,PERS_ID_REGISTERER TECH_ID NOT NULL,IS_MANAGED_INTERNALLY BOOLEAN_CHAR NOT NULL DEFAULT 'F',IS_INTERNAL_NAMESPACE BOOLEAN_CHAR NOT NULL DEFAULT 'F',DBIN_ID TECH_ID NOT NULL, MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP, IS_CHOSEN_FROM_LIST BOOLEAN_CHAR NOT NULL DEFAULT TRUE, SOURCE_URI CHARACTER VARYING(250));\\012CREATE TABLE CONTROLLED_VOCABULARY_TERMS (ID TECH_ID NOT NULL,CODE OBJECT_NAME NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP,COVO_ID TECH_ID NOT NULL,PERS_ID_REGISTERER TECH_ID NOT NULL,LABEL COLUMN_LABEL, DESCRIPTION DESCRIPTION_2000, ORDINAL ORDINAL_INT NOT NULL);\\012CREATE TABLE DATA (ID TECH_ID NOT NULL,CODE CODE,DSTY_ID TECH_ID NOT NULL,DAST_ID TECH_ID NOT NULL,EXPE_ID TECH_ID NOT NULL,DATA_PRODUCER_CODE CODE,PRODUCTION_TIMESTAMP TIME_STAMP,SAMP_ID TECH_ID,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP,IS_PLACEHOLDER BOOLEAN_CHAR DEFAULT 'F',IS_VALID BOOLEAN_CHAR DEFAULT 'T', MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP, IS_DERIVED BOOLEAN_CHAR NOT NULL);\\012CREATE TABLE DATABASE_INSTANCES (ID TECH_ID NOT NULL,CODE CODE NOT NULL,UUID CODE NOT NULL,IS_ORIGINAL_SOURCE BOOLEAN_CHAR NOT NULL DEFAULT 'F',REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP);\\012CREATE TABLE DATA_SET_RELATIONSHIPS (DATA_ID_PARENT TECH_ID NOT NULL,DATA_ID_CHILD TECH_ID NOT NULL);\\012CREATE TABLE DATA_STORES (ID TECH_ID NOT NULL,DBIN_ID TECH_ID NOT NULL,CODE CODE NOT NULL,DOWNLOAD_URL VARCHAR(1024) NOT NULL,REMOTE_URL VARCHAR(250) NOT NULL,SESSION_TOKEN VARCHAR(50) NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP,MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP, IS_ARCHIVER_CONFIGURED BOOLEAN_CHAR NOT NULL DEFAULT 'F');\\012CREATE TABLE DATA_STORE_SERVICES (ID TECH_ID NOT NULL, KEY VARCHAR(256) NOT NULL, LABEL VARCHAR(256) NOT NULL, KIND DATA_STORE_SERVICE_KIND NOT NULL, DATA_STORE_ID TECH_ID NOT NULL);\\012CREATE TABLE DATA_STORE_SERVICE_DATA_SET_TYPES (DATA_STORE_SERVICE_ID TECH_ID NOT NULL, DATA_SET_TYPE_ID TECH_ID NOT NULL);\\012CREATE TABLE DATA_TYPES (ID TECH_ID NOT NULL,CODE CODE NOT NULL,DESCRIPTION DESCRIPTION_2000 NOT NULL);\\012CREATE TABLE EVENTS (ID TECH_ID NOT NULL,EVENT_TYPE EVENT_TYPE NOT NULL,DESCRIPTION DESCRIPTION_2000,REASON DESCRIPTION_2000,PERS_ID_REGISTERER TECH_ID NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP, entity_type VARCHAR(80) NOT NULL, identifier VARCHAR(250) NOT NULL);\\012CREATE TABLE EXPERIMENTS (ID TECH_ID NOT NULL,PERM_ID CODE NOT NULL,CODE CODE NOT NULL,EXTY_ID TECH_ID NOT NULL,MATE_ID_STUDY_OBJECT TECH_ID,PERS_ID_REGISTERER TECH_ID NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP, MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP, PROJ_ID TECH_ID NOT NULL,INVA_ID TECH_ID,IS_PUBLIC BOOLEAN_CHAR NOT NULL DEFAULT 'F');\\012CREATE TABLE ATTACHMENTS (ID TECH_ID NOT NULL,EXPE_ID TECH_ID,SAMP_ID TECH_ID,PROJ_ID TECH_ID,EXAC_ID TECH_ID NOT NULL,FILE_NAME FILE_NAME NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP,VERSION INTEGER NOT NULL,PERS_ID_REGISTERER TECH_ID NOT NULL, title TITLE_100, description DESCRIPTION_2000);\\012CREATE TABLE ATTACHMENT_CONTENTS (ID TECH_ID NOT NULL,VALUE FILE NOT NULL);\\012CREATE TABLE EXPERIMENT_PROPERTIES (ID TECH_ID NOT NULL,EXPE_ID TECH_ID NOT NULL,ETPT_ID TECH_ID NOT NULL,VALUE GENERIC_VALUE,CVTE_ID TECH_ID, MATE_PROP_ID TECH_ID, PERS_ID_REGISTERER TECH_ID NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP, MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP);\\012CREATE TABLE EXPERIMENT_TYPES (ID TECH_ID NOT NULL,CODE CODE NOT NULL,DESCRIPTION DESCRIPTION_2000,DBIN_ID TECH_ID NOT NULL, MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP);\\012CREATE TABLE EXPERIMENT_TYPE_PROPERTY_TYPES (ID TECH_ID NOT NULL,EXTY_ID TECH_ID NOT NULL,PRTY_ID TECH_ID NOT NULL,IS_MANDATORY BOOLEAN_CHAR NOT NULL DEFAULT 'F',IS_MANAGED_INTERNALLY BOOLEAN_CHAR NOT NULL DEFAULT 'F',PERS_ID_REGISTERER TECH_ID NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP, ORDINAL ORDINAL_INT NOT NULL, SECTION DESCRIPTION_2000);\\012CREATE TABLE EXTERNAL_DATA (DATA_ID TECH_ID NOT NULL,LOCATION VARCHAR(1024) NOT NULL,FFTY_ID TECH_ID NOT NULL,LOTY_ID TECH_ID NOT NULL,CVTE_ID_STOR_FMT TECH_ID NOT NULL,IS_COMPLETE BOOLEAN_CHAR_OR_UNKNOWN NOT NULL DEFAULT 'U',CVTE_ID_STORE TECH_ID, STATUS ARCHIVING_STATUS NOT NULL DEFAULT 'AVAILABLE');\\012CREATE TABLE FILE_FORMAT_TYPES (ID TECH_ID NOT NULL,CODE CODE NOT NULL,DESCRIPTION DESCRIPTION_2000,DBIN_ID TECH_ID NOT NULL);\\012CREATE TABLE GRID_CUSTOM_COLUMNS (ID TECH_ID NOT NULL, DBIN_ID TECH_ID NOT NULL, CODE VARCHAR(200) NOT NULL, LABEL column_label NOT NULL, DESCRIPTION DESCRIPTION_2000,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP, PERS_ID_REGISTERER TECH_ID NOT NULL, MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP, EXPRESSION GRID_EXPRESSION NOT NULL, IS_PUBLIC BOOLEAN NOT NULL, GRID_ID GRID_ID NOT NULL);\\012CREATE TABLE GROUPS (ID TECH_ID NOT NULL,CODE CODE NOT NULL,DBIN_ID TECH_ID NOT NULL,DESCRIPTION DESCRIPTION_2000,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP,PERS_ID_REGISTERER TECH_ID NOT NULL);\\012CREATE TABLE INVALIDATIONS (ID TECH_ID NOT NULL,PERS_ID_REGISTERER TECH_ID NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP,REASON DESCRIPTION_2000);\\012CREATE TABLE LOCATOR_TYPES (ID TECH_ID NOT NULL,CODE CODE NOT NULL,DESCRIPTION DESCRIPTION_2000);\\012CREATE TABLE MATERIALS (ID TECH_ID NOT NULL,CODE CODE NOT NULL,MATY_ID TECH_ID NOT NULL,PERS_ID_REGISTERER TECH_ID NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP, MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP, DBIN_ID TECH_ID NOT NULL);\\012CREATE TABLE MATERIAL_PROPERTIES (ID TECH_ID NOT NULL,MATE_ID TECH_ID NOT NULL,MTPT_ID TECH_ID NOT NULL,VALUE GENERIC_VALUE,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP, MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP, PERS_ID_REGISTERER TECH_ID NOT NULL,CVTE_ID TECH_ID, MATE_PROP_ID TECH_ID);\\012CREATE TABLE MATERIAL_TYPES (ID TECH_ID NOT NULL,CODE CODE NOT NULL,DESCRIPTION DESCRIPTION_2000,DBIN_ID TECH_ID NOT NULL, MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP);\\012CREATE TABLE MATERIAL_TYPE_PROPERTY_TYPES (ID TECH_ID NOT NULL,MATY_ID TECH_ID NOT NULL,PRTY_ID TECH_ID NOT NULL,IS_MANDATORY BOOLEAN_CHAR NOT NULL DEFAULT 'F',IS_MANAGED_INTERNALLY BOOLEAN_CHAR NOT NULL DEFAULT 'F',REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP,PERS_ID_REGISTERER TECH_ID NOT NULL, ORDINAL ORDINAL_INT NOT NULL, SECTION DESCRIPTION_2000);\\012CREATE TABLE DATA_SET_TYPES (ID TECH_ID NOT NULL,CODE CODE NOT NULL,DESCRIPTION DESCRIPTION_2000,DBIN_ID TECH_ID NOT NULL, MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP, MAIN_DS_PATTERN VARCHAR(300), MAIN_DS_PATH VARCHAR(1000));\\012CREATE TABLE PERSONS (ID TECH_ID NOT NULL,FIRST_NAME VARCHAR(30),LAST_NAME VARCHAR(30),USER_ID USER_ID NOT NULL,EMAIL OBJECT_NAME,DBIN_ID TECH_ID NOT NULL,GROU_ID TECH_ID,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP,PERS_ID_REGISTERER TECH_ID, DISPLAY_SETTINGS FILE);\\012CREATE TABLE PROJECTS (ID TECH_ID NOT NULL,CODE CODE NOT NULL,GROU_ID TECH_ID NOT NULL,PERS_ID_LEADER TECH_ID,DESCRIPTION DESCRIPTION_2000,PERS_ID_REGISTERER TECH_ID NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP, MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP);\\012CREATE TABLE PROPERTY_TYPES (ID TECH_ID NOT NULL,CODE CODE NOT NULL,DESCRIPTION DESCRIPTION_2000 NOT NULL,LABEL COLUMN_LABEL NOT NULL,DATY_ID TECH_ID NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP,PERS_ID_REGISTERER TECH_ID NOT NULL,COVO_ID TECH_ID,IS_MANAGED_INTERNALLY BOOLEAN_CHAR NOT NULL DEFAULT 'F',IS_INTERNAL_NAMESPACE BOOLEAN_CHAR NOT NULL DEFAULT 'F',DBIN_ID TECH_ID NOT NULL, MATY_PROP_ID TECH_ID);\\012CREATE TABLE ROLE_ASSIGNMENTS (ID TECH_ID NOT NULL,ROLE_CODE AUTHORIZATION_ROLE NOT NULL,GROU_ID TECH_ID,DBIN_ID TECH_ID,PERS_ID_GRANTEE TECH_ID, AG_ID_GRANTEE TECH_ID, PERS_ID_REGISTERER TECH_ID NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP);\\012CREATE TABLE SAMPLES (ID TECH_ID NOT NULL,PERM_ID CODE NOT NULL,CODE CODE NOT NULL,EXPE_ID TECH_ID,SAMP_ID_TOP TECH_ID,SAMP_ID_GENERATED_FROM TECH_ID,SATY_ID TECH_ID NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP,MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP,PERS_ID_REGISTERER TECH_ID NOT NULL,INVA_ID TECH_ID,SAMP_ID_CONTROL_LAYOUT TECH_ID,DBIN_ID TECH_ID,GROU_ID TECH_ID,SAMP_ID_PART_OF TECH_ID);\\012CREATE TABLE SAMPLE_PROPERTIES (ID TECH_ID NOT NULL,SAMP_ID TECH_ID NOT NULL,STPT_ID TECH_ID NOT NULL,VALUE GENERIC_VALUE,CVTE_ID TECH_ID,MATE_PROP_ID TECH_ID,PERS_ID_REGISTERER TECH_ID NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP, MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP);\\012CREATE TABLE SAMPLE_TYPES (ID TECH_ID NOT NULL,CODE CODE NOT NULL,DESCRIPTION DESCRIPTION_2000,DBIN_ID TECH_ID NOT NULL, IS_LISTABLE BOOLEAN_CHAR NOT NULL DEFAULT 'T', GENERATED_FROM_DEPTH INTEGER NOT NULL DEFAULT 0, PART_OF_DEPTH INTEGER NOT NULL DEFAULT 0, MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP, is_auto_generated_code BOOLEAN_CHAR NOT NULL DEFAULT 'F', generated_code_prefix CODE NOT NULL DEFAULT 'S');\\012CREATE TABLE SAMPLE_TYPE_PROPERTY_TYPES (ID TECH_ID NOT NULL,SATY_ID TECH_ID NOT NULL,PRTY_ID TECH_ID NOT NULL,IS_MANDATORY BOOLEAN_CHAR NOT NULL DEFAULT 'F',IS_MANAGED_INTERNALLY BOOLEAN_CHAR NOT NULL DEFAULT 'F',PERS_ID_REGISTERER TECH_ID NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP, IS_DISPLAYED BOOLEAN_CHAR NOT NULL DEFAULT 'T', ORDINAL ORDINAL_INT NOT NULL, SECTION DESCRIPTION_2000);\\012\\012CREATE TABLE DATA_SET_PROPERTIES (ID TECH_ID NOT NULL,DS_ID TECH_ID NOT NULL,DSTPT_ID TECH_ID NOT NULL,VALUE GENERIC_VALUE,CVTE_ID TECH_ID, MATE_PROP_ID TECH_ID, PERS_ID_REGISTERER TECH_ID NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP, MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP);\\012CREATE TABLE DATA_SET_TYPE_PROPERTY_TYPES (ID TECH_ID NOT NULL,DSTY_ID TECH_ID NOT NULL,PRTY_ID TECH_ID NOT NULL,IS_MANDATORY BOOLEAN_CHAR NOT NULL DEFAULT 'F',IS_MANAGED_INTERNALLY BOOLEAN_CHAR NOT NULL DEFAULT 'F',PERS_ID_REGISTERER TECH_ID NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP, ORDINAL ORDINAL_INT NOT NULL, SECTION DESCRIPTION_2000);\\012\\012CREATE TABLE AUTHORIZATION_GROUPS (ID TECH_ID NOT NULL, DBIN_ID TECH_ID NOT NULL, CODE CODE NOT NULL, DESCRIPTION DESCRIPTION_2000,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP, PERS_ID_REGISTERER TECH_ID NOT NULL, MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP);\\012CREATE TABLE AUTHORIZATION_GROUP_PERSONS (AG_ID TECH_ID NOT NULL, PERS_ID TECH_ID NOT NULL);\\012\\012CREATE TABLE FILTERS (ID TECH_ID NOT NULL, DBIN_ID TECH_ID NOT NULL, NAME VARCHAR(200) NOT NULL, DESCRIPTION DESCRIPTION_2000,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP, PERS_ID_REGISTERER TECH_ID NOT NULL, MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP, EXPRESSION VARCHAR(2000) NOT NULL, IS_PUBLIC BOOLEAN NOT NULL, GRID_ID VARCHAR(200) NOT NULL);\\012CREATE TABLE QUERIES (ID TECH_ID NOT NULL, DBIN_ID TECH_ID NOT NULL, NAME VARCHAR(200) NOT NULL, DESCRIPTION DESCRIPTION_2000,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP, PERS_ID_REGISTERER TECH_ID NOT NULL, MODIFICATION_TIMESTAMP TIME_STAMP DEFAULT CURRENT_TIMESTAMP, EXPRESSION VARCHAR(2000) NOT NULL, IS_PUBLIC BOOLEAN NOT NULL);\\012\\012-- Creating sequences\\012\\012CREATE SEQUENCE CONTROLLED_VOCABULARY_ID_SEQ;\\012CREATE SEQUENCE CVTE_ID_SEQ;\\012CREATE SEQUENCE DATABASE_INSTANCE_ID_SEQ;\\012CREATE SEQUENCE DATA_ID_SEQ;\\012CREATE SEQUENCE DATA_SET_RELATIONSHIP_ID_SEQ;\\012CREATE SEQUENCE DATA_STORE_ID_SEQ;\\012CREATE SEQUENCE DATA_STORE_SERVICES_ID_SEQ;\\012CREATE SEQUENCE DATA_TYPE_ID_SEQ;\\012CREATE SEQUENCE ETPT_ID_SEQ;\\012CREATE SEQUENCE EVENT_ID_SEQ;\\012CREATE SEQUENCE ATTACHMENT_ID_SEQ;\\012CREATE SEQUENCE ATTACHMENT_CONTENT_ID_SEQ;\\012CREATE SEQUENCE EXPERIMENT_ID_SEQ;\\012CREATE SEQUENCE EXPERIMENT_PROPERTY_ID_SEQ;\\012CREATE SEQUENCE EXPERIMENT_TYPE_ID_SEQ;\\012CREATE SEQUENCE FILE_FORMAT_TYPE_ID_SEQ;\\012CREATE SEQUENCE GROUP_ID_SEQ;\\012CREATE SEQUENCE INVALIDATION_ID_SEQ;\\012CREATE SEQUENCE LOCATOR_TYPE_ID_SEQ;\\012CREATE SEQUENCE MATERIAL_ID_SEQ;\\012CREATE SEQUENCE MATERIAL_PROPERTY_ID_SEQ;\\012CREATE SEQUENCE MATERIAL_TYPE_ID_SEQ;\\012CREATE SEQUENCE MTPT_ID_SEQ;\\012CREATE SEQUENCE DATA_SET_TYPE_ID_SEQ;\\012CREATE SEQUENCE PERSON_ID_SEQ;\\012CREATE SEQUENCE PROJECT_ID_SEQ;\\012CREATE SEQUENCE PROPERTY_TYPE_ID_SEQ;\\012CREATE SEQUENCE ROLE_ASSIGNMENT_ID_SEQ;\\012CREATE SEQUENCE SAMPLE_ID_SEQ;\\012CREATE SEQUENCE SAMPLE_PROPERTY_ID_SEQ;\\012CREATE SEQUENCE SAMPLE_TYPE_ID_SEQ;\\012CREATE SEQUENCE STPT_ID_SEQ;\\012CREATE SEQUENCE DATA_SET_PROPERTY_ID_SEQ;\\012CREATE SEQUENCE DSTPT_ID_SEQ;\\012CREATE SEQUENCE CODE_SEQ;\\012CREATE SEQUENCE PERM_ID_SEQ;\\012CREATE SEQUENCE AUTHORIZATION_GROUP_ID_SEQ;\\012CREATE SEQUENCE FILTER_ID_SEQ;\\012CREATE SEQUENCE GRID_CUSTOM_COLUMNS_ID_SEQ;\\012CREATE SEQUENCE QUERY_ID_SEQ;\\012\\012-- Creating primary key constraints\\012\\012ALTER TABLE CONTROLLED_VOCABULARIES ADD CONSTRAINT COVO_PK PRIMARY KEY(ID);\\012ALTER TABLE CONTROLLED_VOCABULARY_TERMS ADD CONSTRAINT CVTE_PK PRIMARY KEY(ID);\\012ALTER TABLE DATA ADD CONSTRAINT DATA_PK PRIMARY KEY(ID);\\012ALTER TABLE DATABASE_INSTANCES ADD CONSTRAINT DBIN_PK PRIMARY KEY(ID);\\012ALTER TABLE DATA_STORES ADD CONSTRAINT DAST_PK PRIMARY KEY(ID);\\012ALTER TABLE DATA_STORE_SERVICES ADD CONSTRAINT DSSE_PK PRIMARY KEY(ID);\\012ALTER TABLE DATA_TYPES ADD CONSTRAINT DATY_PK PRIMARY KEY(ID);\\012ALTER TABLE EVENTS ADD CONSTRAINT EVNT_PK PRIMARY KEY(ID);\\012ALTER TABLE EXPERIMENTS ADD CONSTRAINT EXPE_PK PRIMARY KEY(ID);\\012ALTER TABLE ATTACHMENTS ADD CONSTRAINT ATTA_PK PRIMARY KEY(ID);\\012ALTER TABLE ATTACHMENT_CONTENTS ADD CONSTRAINT EXAC_PK PRIMARY KEY(ID);\\012ALTER TABLE EXPERIMENT_PROPERTIES ADD CONSTRAINT EXPR_PK PRIMARY KEY(ID);\\012ALTER TABLE EXPERIMENT_TYPES ADD CONSTRAINT EXTY_PK PRIMARY KEY(ID);\\012ALTER TABLE EXPERIMENT_TYPE_PROPERTY_TYPES ADD CONSTRAINT ETPT_PK PRIMARY KEY(ID);\\012ALTER TABLE EXTERNAL_DATA ADD CONSTRAINT EXDA_PK PRIMARY KEY(DATA_ID);\\012ALTER TABLE FILE_FORMAT_TYPES ADD CONSTRAINT FFTY_PK PRIMARY KEY(ID);\\012ALTER TABLE GROUPS ADD CONSTRAINT GROU_PK PRIMARY KEY(ID);\\012ALTER TABLE INVALIDATIONS ADD CONSTRAINT INVA_PK PRIMARY KEY(ID);\\012ALTER TABLE LOCATOR_TYPES ADD CONSTRAINT LOTY_PK PRIMARY KEY(ID);\\012ALTER TABLE MATERIALS ADD CONSTRAINT MATE_PK PRIMARY KEY(ID);\\012ALTER TABLE MATERIAL_PROPERTIES ADD CONSTRAINT MAPR_PK PRIMARY KEY(ID);\\012ALTER TABLE MATERIAL_TYPES ADD CONSTRAINT MATY_PK PRIMARY KEY(ID);\\012ALTER TABLE MATERIAL_TYPE_PROPERTY_TYPES ADD CONSTRAINT MTPT_PK PRIMARY KEY(ID);\\012ALTER TABLE DATA_SET_TYPES ADD CONSTRAINT DSTY_PK PRIMARY KEY(ID);\\012ALTER TABLE PERSONS ADD CONSTRAINT PERS_PK PRIMARY KEY(ID);\\012ALTER TABLE PROJECTS ADD CONSTRAINT PROJ_PK PRIMARY KEY(ID);\\012ALTER TABLE PROPERTY_TYPES ADD CONSTRAINT PRTY_PK PRIMARY KEY(ID);\\012ALTER TABLE ROLE_ASSIGNMENTS ADD CONSTRAINT ROAS_PK PRIMARY KEY(ID);\\012ALTER TABLE SAMPLES ADD CONSTRAINT SAMP_PK PRIMARY KEY(ID);\\012ALTER TABLE SAMPLE_PROPERTIES ADD CONSTRAINT SAPR_PK PRIMARY KEY(ID);\\012ALTER TABLE SAMPLE_TYPES ADD CONSTRAINT SATY_PK PRIMARY KEY(ID);\\012ALTER TABLE SAMPLE_TYPE_PROPERTY_TYPES ADD CONSTRAINT STPT_PK PRIMARY KEY(ID);\\012ALTER TABLE DATA_SET_TYPE_PROPERTY_TYPES ADD CONSTRAINT DSTPT_PK PRIMARY KEY(ID);\\012ALTER TABLE DATA_SET_PROPERTIES ADD CONSTRAINT DSPR_PK PRIMARY KEY(ID);\\012ALTER TABLE AUTHORIZATION_GROUPS ADD CONSTRAINT AG_PK PRIMARY KEY(ID);\\012ALTER TABLE AUTHORIZATION_GROUP_PERSONS ADD CONSTRAINT AGP_PK PRIMARY KEY(PERS_ID,AG_ID);\\012ALTER TABLE FILTERS ADD CONSTRAINT FILT_PK PRIMARY KEY(ID);\\012ALTER TABLE GRID_CUSTOM_COLUMNS ADD CONSTRAINT GRID_CUSTOM_COLUMNS_PK PRIMARY KEY(ID);\\012ALTER TABLE QUERIES ADD CONSTRAINT QUER_PK PRIMARY KEY(ID);\\012\\012-- Creating unique constraints\\012\\012ALTER TABLE CONTROLLED_VOCABULARIES ADD CONSTRAINT COVO_BK_UK UNIQUE(CODE,IS_INTERNAL_NAMESPACE,DBIN_ID);\\012ALTER TABLE CONTROLLED_VOCABULARY_TERMS ADD CONSTRAINT CVTE_BK_UK UNIQUE(CODE,COVO_ID);\\012ALTER TABLE DATA ADD CONSTRAINT DATA_BK_UK UNIQUE(CODE);\\012ALTER TABLE DATABASE_INSTANCES ADD CONSTRAINT DBIN_BK_UK UNIQUE(CODE);\\012ALTER TABLE DATABASE_INSTANCES ADD CONSTRAINT DBIN_UUID_UK UNIQUE(UUID);\\012ALTER TABLE DATA_SET_RELATIONSHIPS ADD CONSTRAINT DSRE_BK_UK UNIQUE(DATA_ID_CHILD,DATA_ID_PARENT);\\012ALTER TABLE DATA_STORE_SERVICES ADD CONSTRAINT DSSE_BK_UK UNIQUE(KEY, DATA_STORE_ID);\\012ALTER TABLE DATA_STORE_SERVICE_DATA_SET_TYPES ADD CONSTRAINT DSSDST_BK_UK UNIQUE(DATA_STORE_SERVICE_ID, DATA_SET_TYPE_ID);\\012ALTER TABLE DATA_STORES ADD CONSTRAINT DAST_BK_UK UNIQUE(CODE,DBIN_ID);\\012ALTER TABLE DATA_TYPES ADD CONSTRAINT DATY_BK_UK UNIQUE(CODE);\\012ALTER TABLE EXPERIMENTS ADD CONSTRAINT EXPE_BK_UK UNIQUE(CODE,PROJ_ID);\\012ALTER TABLE EXPERIMENTS ADD CONSTRAINT EXPE_PI_UK UNIQUE(PERM_ID);\\012ALTER TABLE EXPERIMENT_PROPERTIES ADD CONSTRAINT EXPR_BK_UK UNIQUE(EXPE_ID,ETPT_ID);\\012ALTER TABLE EXPERIMENT_TYPES ADD CONSTRAINT EXTY_BK_UK UNIQUE(CODE,DBIN_ID);\\012ALTER TABLE EXPERIMENT_TYPE_PROPERTY_TYPES ADD CONSTRAINT ETPT_BK_UK UNIQUE(EXTY_ID,PRTY_ID);\\012ALTER TABLE EXTERNAL_DATA ADD CONSTRAINT EXDA_BK_UK UNIQUE(LOCATION,LOTY_ID);\\012ALTER TABLE FILE_FORMAT_TYPES ADD CONSTRAINT FFTY_BK_UK UNIQUE(CODE,DBIN_ID);\\012ALTER TABLE GROUPS ADD CONSTRAINT GROU_BK_UK UNIQUE(CODE,DBIN_ID);\\012ALTER TABLE LOCATOR_TYPES ADD CONSTRAINT LOTY_BK_UK UNIQUE(CODE);\\012ALTER TABLE MATERIALS ADD CONSTRAINT MATE_BK_UK UNIQUE(CODE,MATY_ID,DBIN_ID);\\012ALTER TABLE MATERIAL_PROPERTIES ADD CONSTRAINT MAPR_BK_UK UNIQUE(MATE_ID,MTPT_ID);\\012ALTER TABLE MATERIAL_TYPES ADD CONSTRAINT MATY_BK_UK UNIQUE(CODE,DBIN_ID);\\012ALTER TABLE MATERIAL_TYPE_PROPERTY_TYPES ADD CONSTRAINT MTPT_BK_UK UNIQUE(MATY_ID,PRTY_ID);\\012ALTER TABLE DATA_SET_TYPES ADD CONSTRAINT DSTY_BK_UK UNIQUE(CODE,DBIN_ID);\\012ALTER TABLE PERSONS ADD CONSTRAINT PERS_BK_UK UNIQUE(DBIN_ID,USER_ID);\\012ALTER TABLE PROJECTS ADD CONSTRAINT PROJ_BK_UK UNIQUE(CODE,GROU_ID);\\012ALTER TABLE PROPERTY_TYPES ADD CONSTRAINT PRTY_BK_UK UNIQUE(CODE,IS_INTERNAL_NAMESPACE,DBIN_ID);\\012ALTER TABLE ROLE_ASSIGNMENTS ADD CONSTRAINT ROAS_PE_GROUP_BK_UK UNIQUE(PERS_ID_GRANTEE,ROLE_CODE,GROU_ID);\\012ALTER TABLE ROLE_ASSIGNMENTS ADD CONSTRAINT ROAS_PE_INSTANCE_BK_UK UNIQUE(PERS_ID_GRANTEE,ROLE_CODE,DBIN_ID);\\012ALTER TABLE ROLE_ASSIGNMENTS ADD CONSTRAINT ROAS_AG_GROUP_BK_UK UNIQUE(AG_ID_GRANTEE,ROLE_CODE,GROU_ID);\\012ALTER TABLE ROLE_ASSIGNMENTS ADD CONSTRAINT ROAS_AG_INSTANCE_BK_UK UNIQUE(AG_ID_GRANTEE,ROLE_CODE,DBIN_ID);\\012ALTER TABLE SAMPLES ADD CONSTRAINT SAMP_PI_UK UNIQUE(PERM_ID);\\012ALTER TABLE SAMPLE_PROPERTIES ADD CONSTRAINT SAPR_BK_UK UNIQUE(SAMP_ID,STPT_ID);\\012ALTER TABLE SAMPLE_TYPES ADD CONSTRAINT SATY_BK_UK UNIQUE(CODE,DBIN_ID);\\012ALTER TABLE SAMPLE_TYPE_PROPERTY_TYPES ADD CONSTRAINT STPT_BK_UK UNIQUE(SATY_ID,PRTY_ID);\\012ALTER TABLE DATA_SET_TYPE_PROPERTY_TYPES ADD CONSTRAINT DSTPT_BK_UK UNIQUE(DSTY_ID,PRTY_ID);\\012ALTER TABLE DATA_SET_PROPERTIES ADD CONSTRAINT DSPR_BK_UK UNIQUE(DS_ID,DSTPT_ID);\\012-- NOTE: following uniqueness constraints for attachments work, because (null != null) in Postgres \\012ALTER TABLE ATTACHMENTS ADD CONSTRAINT ATTA_EXPE_BK_UK UNIQUE(EXPE_ID,FILE_NAME,VERSION);\\012ALTER TABLE ATTACHMENTS ADD CONSTRAINT ATTA_PROJ_BK_UK UNIQUE(PROJ_ID,FILE_NAME,VERSION);\\012ALTER TABLE ATTACHMENTS ADD CONSTRAINT ATTA_SAMP_BK_UK UNIQUE(SAMP_ID,FILE_NAME,VERSION);\\012ALTER TABLE AUTHORIZATION_GROUPS ADD CONSTRAINT AG_BK_UK UNIQUE(CODE,DBIN_ID);\\012ALTER TABLE FILTERS ADD CONSTRAINT FILT_BK_UK UNIQUE(NAME, DBIN_ID, GRID_ID);\\012ALTER TABLE GRID_CUSTOM_COLUMNS ADD CONSTRAINT GRID_CUSTOM_COLUMNS_BK_UK UNIQUE(CODE, DBIN_ID, GRID_ID);\\012ALTER TABLE QUERIES ADD CONSTRAINT QUER_BK_UK UNIQUE(NAME, DBIN_ID);\\012\\012-- Creating foreign key constraints\\012\\012ALTER TABLE CONTROLLED_VOCABULARIES ADD CONSTRAINT COVO_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012ALTER TABLE CONTROLLED_VOCABULARIES ADD CONSTRAINT COVO_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE CONTROLLED_VOCABULARY_TERMS ADD CONSTRAINT CVTE_COVO_FK FOREIGN KEY (COVO_ID) REFERENCES CONTROLLED_VOCABULARIES(ID);\\012ALTER TABLE CONTROLLED_VOCABULARY_TERMS ADD CONSTRAINT CVTE_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE DATA ADD CONSTRAINT DATA_DSTY_FK FOREIGN KEY (DSTY_ID) REFERENCES DATA_SET_TYPES(ID);\\012ALTER TABLE DATA ADD CONSTRAINT DATA_EXPE_FK FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS(ID);\\012ALTER TABLE DATA ADD CONSTRAINT DATA_SAMP_FK FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES(ID);\\012ALTER TABLE DATA ADD CONSTRAINT DATA_DAST_FK FOREIGN KEY (DAST_ID) REFERENCES DATA_STORES(ID);\\012ALTER TABLE DATA_SET_RELATIONSHIPS ADD CONSTRAINT DSRE_DATA_FK_CHILD FOREIGN KEY (DATA_ID_CHILD) REFERENCES DATA(ID);\\012ALTER TABLE DATA_SET_RELATIONSHIPS ADD CONSTRAINT DSRE_DATA_FK_PARENT FOREIGN KEY (DATA_ID_PARENT) REFERENCES DATA(ID);\\012ALTER TABLE DATA_STORES ADD CONSTRAINT DAST_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012ALTER TABLE DATA_STORE_SERVICES ADD CONSTRAINT DSSE_DS_FK FOREIGN KEY (DATA_STORE_ID) REFERENCES DATA_STORES(ID) ON DELETE CASCADE;\\012ALTER TABLE DATA_STORE_SERVICE_DATA_SET_TYPES ADD CONSTRAINT DSSDST_DS_FK FOREIGN KEY (DATA_STORE_SERVICE_ID) REFERENCES DATA_STORE_SERVICES(ID) ON DELETE CASCADE;\\012ALTER TABLE DATA_STORE_SERVICE_DATA_SET_TYPES ADD CONSTRAINT DSSDST_DST_FK FOREIGN KEY (DATA_SET_TYPE_ID) REFERENCES DATA_SET_TYPES(ID) ON DELETE CASCADE;\\012ALTER TABLE EVENTS ADD CONSTRAINT EVNT_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE EXPERIMENTS ADD CONSTRAINT EXPE_EXTY_FK FOREIGN KEY (EXTY_ID) REFERENCES EXPERIMENT_TYPES(ID);\\012ALTER TABLE EXPERIMENTS ADD CONSTRAINT EXPE_INVA_FK FOREIGN KEY (INVA_ID) REFERENCES INVALIDATIONS(ID);\\012ALTER TABLE EXPERIMENTS ADD CONSTRAINT EXPE_MATE_FK FOREIGN KEY (MATE_ID_STUDY_OBJECT) REFERENCES MATERIALS(ID);\\012ALTER TABLE EXPERIMENTS ADD CONSTRAINT EXPE_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE EXPERIMENTS ADD CONSTRAINT EXPE_PROJ_FK FOREIGN KEY (PROJ_ID) REFERENCES PROJECTS(ID);\\012ALTER TABLE ATTACHMENTS ADD CONSTRAINT ATTA_EXPE_FK FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS(ID);\\012ALTER TABLE ATTACHMENTS ADD CONSTRAINT ATTA_PROJ_FK FOREIGN KEY (PROJ_ID) REFERENCES PROJECTS(ID);\\012ALTER TABLE ATTACHMENTS ADD CONSTRAINT ATTA_SAMP_FK FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES(ID);\\012ALTER TABLE ATTACHMENTS ADD CONSTRAINT ATTA_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE ATTACHMENTS ADD CONSTRAINT ATTA_CONT_FK FOREIGN KEY (EXAC_ID) REFERENCES ATTACHMENT_CONTENTS(ID);\\012ALTER TABLE EXPERIMENT_PROPERTIES ADD CONSTRAINT EXPR_CVTE_FK FOREIGN KEY (CVTE_ID) REFERENCES CONTROLLED_VOCABULARY_TERMS(ID);\\012ALTER TABLE EXPERIMENT_PROPERTIES ADD CONSTRAINT EXPR_ETPT_FK FOREIGN KEY (ETPT_ID) REFERENCES EXPERIMENT_TYPE_PROPERTY_TYPES(ID) ON DELETE CASCADE;\\012ALTER TABLE EXPERIMENT_PROPERTIES ADD CONSTRAINT EXPR_EXPE_FK FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS(ID);\\012ALTER TABLE EXPERIMENT_PROPERTIES ADD CONSTRAINT EXPR_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE EXPERIMENT_PROPERTIES ADD CONSTRAINT EXPR_MAPR_FK FOREIGN KEY (MATE_PROP_ID) REFERENCES MATERIALS(ID);\\012ALTER TABLE EXPERIMENT_TYPES ADD CONSTRAINT EXTY_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012ALTER TABLE EXPERIMENT_TYPE_PROPERTY_TYPES ADD CONSTRAINT ETPT_EXTY_FK FOREIGN KEY (EXTY_ID) REFERENCES EXPERIMENT_TYPES(ID) ON DELETE CASCADE;\\012ALTER TABLE EXPERIMENT_TYPE_PROPERTY_TYPES ADD CONSTRAINT ETPT_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE EXPERIMENT_TYPE_PROPERTY_TYPES ADD CONSTRAINT ETPT_PRTY_FK FOREIGN KEY (PRTY_ID) REFERENCES PROPERTY_TYPES(ID) ON DELETE CASCADE;\\012ALTER TABLE EXTERNAL_DATA ADD CONSTRAINT EXDA_CVTE_FK FOREIGN KEY (CVTE_ID_STOR_FMT) REFERENCES CONTROLLED_VOCABULARY_TERMS(ID);\\012ALTER TABLE EXTERNAL_DATA ADD CONSTRAINT EXDA_CVTE_STORED_ON_FK FOREIGN KEY (CVTE_ID_STORE) REFERENCES CONTROLLED_VOCABULARY_TERMS(ID);\\012ALTER TABLE EXTERNAL_DATA ADD CONSTRAINT EXDA_DATA_FK FOREIGN KEY (DATA_ID) REFERENCES DATA(ID);\\012ALTER TABLE EXTERNAL_DATA ADD CONSTRAINT EXDA_FFTY_FK FOREIGN KEY (FFTY_ID) REFERENCES FILE_FORMAT_TYPES(ID);\\012ALTER TABLE EXTERNAL_DATA ADD CONSTRAINT EXDA_LOTY_FK FOREIGN KEY (LOTY_ID) REFERENCES LOCATOR_TYPES(ID);\\012ALTER TABLE FILE_FORMAT_TYPES ADD CONSTRAINT FFTY_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012ALTER TABLE GROUPS ADD CONSTRAINT GROU_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012ALTER TABLE GROUPS ADD CONSTRAINT GROU_PERS_FK_REGISTERER FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE INVALIDATIONS ADD CONSTRAINT INVA_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE MATERIALS ADD CONSTRAINT MATE_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012ALTER TABLE MATERIALS ADD CONSTRAINT MATE_MATY_FK FOREIGN KEY (MATY_ID) REFERENCES MATERIAL_TYPES(ID);\\012ALTER TABLE MATERIALS ADD CONSTRAINT MATE_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE MATERIAL_PROPERTIES ADD CONSTRAINT MAPR_CVTE_FK FOREIGN KEY (CVTE_ID) REFERENCES CONTROLLED_VOCABULARY_TERMS(ID);\\012ALTER TABLE MATERIAL_PROPERTIES ADD CONSTRAINT MAPR_MAPR_FK FOREIGN KEY (MATE_PROP_ID) REFERENCES MATERIALS(ID);\\012ALTER TABLE MATERIAL_PROPERTIES ADD CONSTRAINT MAPR_MATE_FK FOREIGN KEY (MATE_ID) REFERENCES MATERIALS(ID);\\012ALTER TABLE MATERIAL_PROPERTIES ADD CONSTRAINT MAPR_MTPT_FK FOREIGN KEY (MTPT_ID) REFERENCES MATERIAL_TYPE_PROPERTY_TYPES(ID) ON DELETE CASCADE;\\012ALTER TABLE MATERIAL_PROPERTIES ADD CONSTRAINT MAPR_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE MATERIAL_TYPES ADD CONSTRAINT MATY_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012ALTER TABLE MATERIAL_TYPE_PROPERTY_TYPES ADD CONSTRAINT MTPT_MATY_FK FOREIGN KEY (MATY_ID) REFERENCES MATERIAL_TYPES(ID) ON DELETE CASCADE;\\012ALTER TABLE MATERIAL_TYPE_PROPERTY_TYPES ADD CONSTRAINT MTPT_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE MATERIAL_TYPE_PROPERTY_TYPES ADD CONSTRAINT MTPT_PRTY_FK FOREIGN KEY (PRTY_ID) REFERENCES PROPERTY_TYPES(ID) ON DELETE CASCADE;\\012ALTER TABLE DATA_SET_TYPES ADD CONSTRAINT DSTY_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012ALTER TABLE PERSONS ADD CONSTRAINT PERS_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012ALTER TABLE PERSONS ADD CONSTRAINT PERS_GROU_FK FOREIGN KEY (GROU_ID) REFERENCES GROUPS(ID);\\012ALTER TABLE PERSONS ADD CONSTRAINT PERS_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE PROJECTS ADD CONSTRAINT PROJ_GROU_FK FOREIGN KEY (GROU_ID) REFERENCES GROUPS(ID);\\012ALTER TABLE PROJECTS ADD CONSTRAINT PROJ_PERS_FK_LEADER FOREIGN KEY (PERS_ID_LEADER) REFERENCES PERSONS(ID);\\012ALTER TABLE PROJECTS ADD CONSTRAINT PROJ_PERS_FK_REGISTERER FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE PROPERTY_TYPES ADD CONSTRAINT PRTY_COVO_FK FOREIGN KEY (COVO_ID) REFERENCES CONTROLLED_VOCABULARIES(ID);\\012ALTER TABLE PROPERTY_TYPES ADD CONSTRAINT PRTY_DATY_FK FOREIGN KEY (DATY_ID) REFERENCES DATA_TYPES(ID);\\012ALTER TABLE PROPERTY_TYPES ADD CONSTRAINT PRTY_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012ALTER TABLE PROPERTY_TYPES ADD CONSTRAINT PRTY_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE PROPERTY_TYPES ADD CONSTRAINT PRTY_MATY_FK FOREIGN KEY (MATY_PROP_ID) REFERENCES MATERIAL_TYPES(ID) ON DELETE CASCADE;\\012ALTER TABLE ROLE_ASSIGNMENTS ADD CONSTRAINT ROAS_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012ALTER TABLE ROLE_ASSIGNMENTS ADD CONSTRAINT ROAS_GROU_FK FOREIGN KEY (GROU_ID) REFERENCES GROUPS(ID);\\012ALTER TABLE ROLE_ASSIGNMENTS ADD CONSTRAINT ROAS_PERS_FK_GRANTEE FOREIGN KEY (PERS_ID_GRANTEE) REFERENCES PERSONS(ID);\\012ALTER TABLE ROLE_ASSIGNMENTS ADD CONSTRAINT ROAS_AG_FK_GRANTEE FOREIGN KEY (AG_ID_GRANTEE) REFERENCES AUTHORIZATION_GROUPS(ID);\\012ALTER TABLE ROLE_ASSIGNMENTS ADD CONSTRAINT ROAS_PERS_FK_REGISTERER FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE SAMPLES ADD CONSTRAINT SAMP_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012ALTER TABLE SAMPLES ADD CONSTRAINT SAMP_GROU_FK FOREIGN KEY (GROU_ID) REFERENCES GROUPS(ID);\\012ALTER TABLE SAMPLES ADD CONSTRAINT SAMP_INVA_FK FOREIGN KEY (INVA_ID) REFERENCES INVALIDATIONS(ID);\\012ALTER TABLE SAMPLES ADD CONSTRAINT SAMP_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE SAMPLES ADD CONSTRAINT SAMP_SAMP_FK_CONTROL_LAYOUT FOREIGN KEY (SAMP_ID_CONTROL_LAYOUT) REFERENCES SAMPLES(ID);\\012ALTER TABLE SAMPLES ADD CONSTRAINT SAMP_SAMP_FK_GENERATED_FROM FOREIGN KEY (SAMP_ID_GENERATED_FROM) REFERENCES SAMPLES(ID);\\012ALTER TABLE SAMPLES ADD CONSTRAINT SAMP_SAMP_FK_PART_OF FOREIGN KEY (SAMP_ID_PART_OF) REFERENCES SAMPLES(ID);\\012ALTER TABLE SAMPLES ADD CONSTRAINT SAMP_SAMP_FK_TOP FOREIGN KEY (SAMP_ID_TOP) REFERENCES SAMPLES(ID);\\012ALTER TABLE SAMPLES ADD CONSTRAINT SAMP_EXPE_FK FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS(ID);\\012ALTER TABLE SAMPLES ADD CONSTRAINT SAMP_SATY_FK FOREIGN KEY (SATY_ID) REFERENCES SAMPLE_TYPES(ID);\\012ALTER TABLE SAMPLE_PROPERTIES ADD CONSTRAINT SAPR_CVTE_FK FOREIGN KEY (CVTE_ID) REFERENCES CONTROLLED_VOCABULARY_TERMS(ID);\\012ALTER TABLE SAMPLE_PROPERTIES ADD CONSTRAINT SAPR_MAPR_FK FOREIGN KEY (MATE_PROP_ID) REFERENCES MATERIALS(ID);\\012ALTER TABLE SAMPLE_PROPERTIES ADD CONSTRAINT SAPR_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE SAMPLE_PROPERTIES ADD CONSTRAINT SAPR_SAMP_FK FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES(ID);\\012ALTER TABLE SAMPLE_PROPERTIES ADD CONSTRAINT SAPR_STPT_FK FOREIGN KEY (STPT_ID) REFERENCES SAMPLE_TYPE_PROPERTY_TYPES(ID) ON DELETE CASCADE;\\012ALTER TABLE SAMPLE_TYPES ADD CONSTRAINT SATY_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012ALTER TABLE SAMPLE_TYPE_PROPERTY_TYPES ADD CONSTRAINT STPT_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE SAMPLE_TYPE_PROPERTY_TYPES ADD CONSTRAINT STPT_PRTY_FK FOREIGN KEY (PRTY_ID) REFERENCES PROPERTY_TYPES(ID) ON DELETE CASCADE;\\012ALTER TABLE SAMPLE_TYPE_PROPERTY_TYPES ADD CONSTRAINT STPT_SATY_FK FOREIGN KEY (SATY_ID) REFERENCES SAMPLE_TYPES(ID) ON DELETE CASCADE;\\012ALTER TABLE DATA_SET_TYPE_PROPERTY_TYPES ADD CONSTRAINT DSTPT_DSTY_FK FOREIGN KEY (DSTY_ID) REFERENCES DATA_SET_TYPES(ID) ON DELETE CASCADE;\\012ALTER TABLE DATA_SET_TYPE_PROPERTY_TYPES ADD CONSTRAINT DSTPT_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE DATA_SET_TYPE_PROPERTY_TYPES ADD CONSTRAINT DSTPT_PRTY_FK FOREIGN KEY (PRTY_ID) REFERENCES PROPERTY_TYPES(ID) ON DELETE CASCADE;\\012ALTER TABLE DATA_SET_PROPERTIES ADD CONSTRAINT DSPR_CVTE_FK FOREIGN KEY (CVTE_ID) REFERENCES CONTROLLED_VOCABULARY_TERMS(ID);\\012ALTER TABLE DATA_SET_PROPERTIES ADD CONSTRAINT DSPR_DSTPT_FK FOREIGN KEY (DSTPT_ID) REFERENCES DATA_SET_TYPE_PROPERTY_TYPES(ID) ON DELETE CASCADE;\\012ALTER TABLE DATA_SET_PROPERTIES ADD CONSTRAINT DSPR_DS_FK FOREIGN KEY (DS_ID) REFERENCES DATA(ID);\\012ALTER TABLE DATA_SET_PROPERTIES ADD CONSTRAINT DSPR_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE DATA_SET_PROPERTIES ADD CONSTRAINT DSPR_MAPR_FK FOREIGN KEY (MATE_PROP_ID) REFERENCES MATERIALS(ID);\\012ALTER TABLE AUTHORIZATION_GROUPS ADD CONSTRAINT AG_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012ALTER TABLE AUTHORIZATION_GROUP_PERSONS ADD CONSTRAINT AGP_AG_FK FOREIGN KEY (AG_ID) REFERENCES AUTHORIZATION_GROUPS(ID);\\012ALTER TABLE AUTHORIZATION_GROUP_PERSONS ADD CONSTRAINT AGP_PERS_FK FOREIGN KEY (PERS_ID) REFERENCES PERSONS(ID);\\012ALTER TABLE AUTHORIZATION_GROUPS ADD CONSTRAINT AG_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012\\012ALTER TABLE FILTERS ADD CONSTRAINT FILT_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE FILTERS ADD CONSTRAINT FILT_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012ALTER TABLE GRID_CUSTOM_COLUMNS ADD CONSTRAINT GRID_CUSTOM_COLUMNS_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE GRID_CUSTOM_COLUMNS ADD CONSTRAINT GRID_CUSTOM_COLUMNS_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012ALTER TABLE QUERIES ADD CONSTRAINT QUER_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012ALTER TABLE QUERIES ADD CONSTRAINT QUER_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012\\012-- Creating check constraints\\012\\012ALTER TABLE EXPERIMENT_PROPERTIES ADD CONSTRAINT EXPR_CK CHECK \\012\\011((VALUE IS NOT NULL AND CVTE_ID IS NULL AND MATE_PROP_ID IS NULL) OR \\012\\011 (VALUE IS NULL AND CVTE_ID IS NOT NULL AND MATE_PROP_ID IS NULL) OR\\012\\011 (VALUE IS NULL AND CVTE_ID IS NULL AND MATE_PROP_ID IS NOT NULL)\\012\\011);\\012ALTER TABLE ROLE_ASSIGNMENTS ADD CONSTRAINT ROAS_DBIN_GROU_ARC_CK CHECK ((DBIN_ID IS NOT NULL AND GROU_ID IS NULL) OR (DBIN_ID IS NULL AND GROU_ID IS NOT NULL));\\012ALTER TABLE ROLE_ASSIGNMENTS ADD CONSTRAINT ROAS_AG_PERS_ARC_CK CHECK ((AG_ID_GRANTEE IS NOT NULL AND PERS_ID_GRANTEE IS NULL) OR (AG_ID_GRANTEE IS NULL AND PERS_ID_GRANTEE IS NOT NULL));\\012\\012ALTER TABLE SAMPLES ADD CONSTRAINT SAMP_DBIN_GROU_ARC_CK CHECK ((DBIN_ID IS NOT NULL AND GROU_ID IS NULL) OR (DBIN_ID IS NULL AND GROU_ID IS NOT NULL));\\012ALTER TABLE SAMPLE_PROPERTIES ADD CONSTRAINT SAPR_CK CHECK \\012\\011((VALUE IS NOT NULL AND CVTE_ID IS NULL AND MATE_PROP_ID IS NULL) OR \\012\\011 (VALUE IS NULL AND CVTE_ID IS NOT NULL AND MATE_PROP_ID IS NULL) OR\\012\\011 (VALUE IS NULL AND CVTE_ID IS NULL AND MATE_PROP_ID IS NOT NULL)\\012\\011);\\012ALTER TABLE MATERIAL_PROPERTIES ADD CONSTRAINT MAPR_CK CHECK \\012\\011((VALUE IS NOT NULL AND CVTE_ID IS NULL AND MATE_PROP_ID IS NULL) OR \\012\\011 (VALUE IS NULL AND CVTE_ID IS NOT NULL AND MATE_PROP_ID IS NULL) OR\\012\\011 (VALUE IS NULL AND CVTE_ID IS NULL AND MATE_PROP_ID IS NOT NULL)\\012\\011);\\012ALTER TABLE DATA_SET_PROPERTIES ADD CONSTRAINT DSPR_CK CHECK \\012\\011((VALUE IS NOT NULL AND CVTE_ID IS NULL AND MATE_PROP_ID IS NULL) OR \\012\\011 (VALUE IS NULL AND CVTE_ID IS NOT NULL AND MATE_PROP_ID IS NULL) OR\\012\\011 (VALUE IS NULL AND CVTE_ID IS NULL AND MATE_PROP_ID IS NOT NULL)\\012\\011);\\012ALTER TABLE ATTACHMENTS ADD CONSTRAINT ATTA_ARC_CK CHECK \\012\\011((EXPE_ID IS NOT NULL AND PROJ_ID IS NULL AND SAMP_ID IS NULL) OR \\012\\011 (EXPE_ID IS NULL AND PROJ_ID IS NOT NULL AND SAMP_ID IS NULL) OR\\012\\011 (EXPE_ID IS NULL AND PROJ_ID IS NULL AND SAMP_ID IS NOT NULL)\\012\\011);\\012ALTER TABLE events ADD CONSTRAINT evnt_et_enum_ck CHECK \\012\\011(entity_type IN ('ATTACHMENT', 'DATASET', 'EXPERIMENT', 'GROUP', 'MATERIAL', 'PROJECT', 'PROPERTY_TYPE', 'SAMPLE', 'VOCABULARY', 'AUTHORIZATION_GROUP')); \\012ALTER TABLE controlled_vocabulary_terms ADD CONSTRAINT cvte_ck CHECK (ordinal > 0);\\012\\012-- Creating indices\\012\\012CREATE INDEX COVO_PERS_FK_I ON CONTROLLED_VOCABULARIES (PERS_ID_REGISTERER);\\012CREATE INDEX CVTE_COVO_FK_I ON CONTROLLED_VOCABULARY_TERMS (COVO_ID);\\012CREATE INDEX CVTE_PERS_FK_I ON CONTROLLED_VOCABULARY_TERMS (PERS_ID_REGISTERER);\\012CREATE INDEX DATA_DSTY_FK_I ON DATA (DSTY_ID);\\012CREATE INDEX DATA_SAMP_FK_I ON DATA (SAMP_ID);\\012CREATE INDEX DATA_EXPE_FK_I ON DATA (EXPE_ID);\\012CREATE INDEX DAST_DBIN_FK_I ON DATA_STORES (DBIN_ID);\\012CREATE INDEX DSRE_DATA_FK_I_CHILD ON DATA_SET_RELATIONSHIPS (DATA_ID_CHILD);\\012CREATE INDEX DSRE_DATA_FK_I_PARENT ON DATA_SET_RELATIONSHIPS (DATA_ID_PARENT);\\012CREATE INDEX DSSE_DS_FK_I ON DATA_STORE_SERVICES (DATA_STORE_ID);\\012CREATE INDEX DSSDST_DS_FK_I ON DATA_STORE_SERVICE_DATA_SET_TYPES (DATA_STORE_SERVICE_ID);\\012CREATE INDEX DSSDST_DST_FK_I ON DATA_STORE_SERVICE_DATA_SET_TYPES (DATA_SET_TYPE_ID);\\012CREATE INDEX ETPT_EXTY_FK_I ON EXPERIMENT_TYPE_PROPERTY_TYPES (EXTY_ID);\\012CREATE INDEX ETPT_PERS_FK_I ON EXPERIMENT_TYPE_PROPERTY_TYPES (PERS_ID_REGISTERER);\\012CREATE INDEX ETPT_PRTY_FK_I ON EXPERIMENT_TYPE_PROPERTY_TYPES (PRTY_ID);\\012CREATE INDEX EVNT_PERS_FK_I ON EVENTS (PERS_ID_REGISTERER);\\012CREATE INDEX ATTA_EXPE_FK_I ON ATTACHMENTS (EXPE_ID);\\012CREATE INDEX ATTA_SAMP_FK_I ON ATTACHMENTS (SAMP_ID);\\012CREATE INDEX ATTA_PROJ_FK_I ON ATTACHMENTS (PROJ_ID);\\012CREATE INDEX ATTA_PERS_FK_I ON ATTACHMENTS (PERS_ID_REGISTERER);\\012CREATE INDEX ATTA_EXAC_FK_I ON ATTACHMENTS (EXAC_ID);\\012CREATE INDEX EXDA_CVTE_FK_I ON EXTERNAL_DATA (CVTE_ID_STOR_FMT);\\012CREATE INDEX EXDA_CVTE_STORED_ON_FK_I ON EXTERNAL_DATA (CVTE_ID_STORE);\\012CREATE INDEX EXDA_FFTY_FK_I ON EXTERNAL_DATA (FFTY_ID);\\012CREATE INDEX EXDA_LOTY_FK_I ON EXTERNAL_DATA (LOTY_ID);\\012CREATE INDEX EXPE_EXTY_FK_I ON EXPERIMENTS (EXTY_ID);\\012CREATE INDEX EXPE_INVA_FK_I ON EXPERIMENTS (INVA_ID);\\012CREATE INDEX EXPE_MATE_FK_I ON EXPERIMENTS (MATE_ID_STUDY_OBJECT);\\012CREATE INDEX EXPE_PERS_FK_I ON EXPERIMENTS (PERS_ID_REGISTERER);\\012CREATE INDEX EXPE_PROJ_FK_I ON EXPERIMENTS (PROJ_ID);\\012CREATE INDEX EXPR_CVTE_FK_I ON EXPERIMENT_PROPERTIES (CVTE_ID);\\012CREATE INDEX EXPR_ETPT_FK_I ON EXPERIMENT_PROPERTIES (ETPT_ID);\\012CREATE INDEX EXPR_EXPE_FK_I ON EXPERIMENT_PROPERTIES (EXPE_ID);\\012CREATE INDEX EXPR_PERS_FK_I ON EXPERIMENT_PROPERTIES (PERS_ID_REGISTERER);\\012CREATE INDEX GROU_DBIN_FK_I ON GROUPS (DBIN_ID);\\012CREATE INDEX GROU_PERS_REGISTERED_BY_FK_I ON GROUPS (PERS_ID_REGISTERER);\\012CREATE INDEX INVA_PERS_FK_I ON INVALIDATIONS (PERS_ID_REGISTERER);\\012CREATE INDEX MAPR_CVTE_FK_I ON MATERIAL_PROPERTIES (CVTE_ID);\\012CREATE INDEX MAPR_MATE_FK_I ON MATERIAL_PROPERTIES (MATE_ID);\\012CREATE INDEX MAPR_MTPT_FK_I ON MATERIAL_PROPERTIES (MTPT_ID);\\012CREATE INDEX MAPR_PERS_FK_I ON MATERIAL_PROPERTIES (PERS_ID_REGISTERER);\\012CREATE INDEX MATE_MATY_FK_I ON MATERIALS (MATY_ID);\\012CREATE INDEX MATE_PERS_FK_I ON MATERIALS (PERS_ID_REGISTERER);\\012CREATE INDEX MTPT_MATY_FK_I ON MATERIAL_TYPE_PROPERTY_TYPES (MATY_ID);\\012CREATE INDEX MTPT_PERS_FK_I ON MATERIAL_TYPE_PROPERTY_TYPES (PERS_ID_REGISTERER);\\012CREATE INDEX MTPT_PRTY_FK_I ON MATERIAL_TYPE_PROPERTY_TYPES (PRTY_ID);\\012CREATE INDEX PERS_GROU_FK_I ON PERSONS (GROU_ID);\\012CREATE INDEX PROJ_GROU_FK_I ON PROJECTS (GROU_ID);\\012CREATE INDEX PROJ_PERS_FK_I_LEADER ON PROJECTS (PERS_ID_LEADER);\\012CREATE INDEX PROJ_PERS_FK_I_REGISTERER ON PROJECTS (PERS_ID_REGISTERER);\\012CREATE INDEX PRTY_COVO_FK_I ON PROPERTY_TYPES (COVO_ID);\\012CREATE INDEX PRTY_DATY_FK_I ON PROPERTY_TYPES (DATY_ID);\\012CREATE INDEX PRTY_PERS_FK_I ON PROPERTY_TYPES (PERS_ID_REGISTERER);\\012CREATE INDEX ROAS_DBIN_FK_I ON ROLE_ASSIGNMENTS (DBIN_ID);\\012CREATE INDEX ROAS_GROU_FK_I ON ROLE_ASSIGNMENTS (GROU_ID);\\012CREATE INDEX ROAS_PERS_FK_I_GRANTEE ON ROLE_ASSIGNMENTS (PERS_ID_GRANTEE);\\012CREATE INDEX ROAS_AG_FK_I_GRANTEE ON ROLE_ASSIGNMENTS (AG_ID_GRANTEE);\\012CREATE INDEX ROAS_PERS_FK_I_REGISTERER ON ROLE_ASSIGNMENTS (PERS_ID_REGISTERER);\\012CREATE INDEX SAMP_INVA_FK_I ON SAMPLES (INVA_ID);\\012CREATE INDEX SAMP_PERS_FK_I ON SAMPLES (PERS_ID_REGISTERER);\\012CREATE INDEX SAMP_SAMP_FK_I_CONTROL_LAYOUT ON SAMPLES (SAMP_ID_CONTROL_LAYOUT);\\012CREATE INDEX SAMP_SAMP_FK_I_GENERATED_FROM ON SAMPLES (SAMP_ID_GENERATED_FROM);\\012CREATE INDEX SAMP_SAMP_FK_I_PART_OF ON SAMPLES (SAMP_ID_PART_OF);\\012CREATE INDEX SAMP_SAMP_FK_I_TOP ON SAMPLES (SAMP_ID_TOP);\\012CREATE INDEX SAMP_EXPE_FK_I ON SAMPLES (EXPE_ID);\\012CREATE INDEX SAMP_CODE_I ON SAMPLES (CODE);\\012CREATE INDEX SAMP_SATY_FK_I ON SAMPLES (SATY_ID);\\012CREATE INDEX SAPR_CVTE_FK_I ON SAMPLE_PROPERTIES (CVTE_ID);\\012CREATE INDEX SAPR_PERS_FK_I ON SAMPLE_PROPERTIES (PERS_ID_REGISTERER);\\012CREATE INDEX SAPR_SAMP_FK_I ON SAMPLE_PROPERTIES (SAMP_ID);\\012CREATE INDEX SAPR_STPT_FK_I ON SAMPLE_PROPERTIES (STPT_ID);\\012CREATE INDEX STPT_PERS_FK_I ON SAMPLE_TYPE_PROPERTY_TYPES (PERS_ID_REGISTERER);\\012CREATE INDEX STPT_PRTY_FK_I ON SAMPLE_TYPE_PROPERTY_TYPES (PRTY_ID);\\012CREATE INDEX STPT_SATY_FK_I ON SAMPLE_TYPE_PROPERTY_TYPES (SATY_ID);\\012CREATE INDEX DSPR_CVTE_FK_I ON DATA_SET_PROPERTIES (CVTE_ID);\\012CREATE INDEX DSPR_DSTPT_FK_I ON DATA_SET_PROPERTIES (DSTPT_ID);\\012CREATE INDEX DSPR_DS_FK_I ON DATA_SET_PROPERTIES (DS_ID);\\012CREATE INDEX DSPR_PERS_FK_I ON DATA_SET_PROPERTIES (PERS_ID_REGISTERER);\\012CREATE INDEX DSTPT_DSTY_FK_I ON DATA_SET_TYPE_PROPERTY_TYPES (DSTY_ID);\\012CREATE INDEX DSTPT_PERS_FK_I ON DATA_SET_TYPE_PROPERTY_TYPES (PERS_ID_REGISTERER);\\012CREATE INDEX DSTPT_PRTY_FK_I ON DATA_SET_TYPE_PROPERTY_TYPES (PRTY_ID);\\012CREATE INDEX FILT_PERS_FK_I ON FILTERS (PERS_ID_REGISTERER);\\012CREATE INDEX FILT_DBIN_FK_I ON FILTERS (DBIN_ID);\\012CREATE INDEX GRID_CUSTOM_COLUMNS_PERS_FK_I ON GRID_CUSTOM_COLUMNS (PERS_ID_REGISTERER);\\012CREATE INDEX GRID_CUSTOM_COLUMNS_DBIN_FK_I ON GRID_CUSTOM_COLUMNS (DBIN_ID);\\012 \N
-051 ./sql/postgresql/051/function-051.sql SUCCESS 2010-05-10 17:57:13.907 -- Creating Functions\\012\\012------------------------------------------------------------------------------------\\012-- Purpose: Create function RENAME_SEQUENCE() that is required for renaming the sequences belonging to tables\\012------------------------------------------------------------------------------------\\012CREATE FUNCTION RENAME_SEQUENCE(OLD_NAME VARCHAR, NEW_NAME VARCHAR) RETURNS INTEGER AS $$\\012DECLARE\\012 CURR_SEQ_VAL INTEGER;\\012BEGIN\\012 SELECT INTO CURR_SEQ_VAL NEXTVAL(OLD_NAME);\\012 EXECUTE 'CREATE SEQUENCE ' || NEW_NAME || ' START WITH ' || CURR_SEQ_VAL;\\012 EXECUTE 'DROP SEQUENCE ' || OLD_NAME;\\012 RETURN CURR_SEQ_VAL;\\012END;\\012$$ LANGUAGE 'plpgsql';\\012\\012\\012------------------------------------------------------------------------------------\\012-- Purpose: Create trigger CONTROLLED_VOCABULARY_CHECK \\012------------------------------------------------------------------------------------\\012\\012CREATE OR REPLACE FUNCTION CONTROLLED_VOCABULARY_CHECK() RETURNS trigger AS $$\\012DECLARE\\012 v_code CODE;\\012BEGIN\\012\\012 select code into v_code from data_types where id = NEW.daty_id;\\012\\012 -- Check if the data is of type "CONTROLLEDVOCABULARY"\\012 if v_code = 'CONTROLLEDVOCABULARY' then\\012 if NEW.covo_id IS NULL then\\012 RAISE EXCEPTION 'Insert/Update of Property Type (Code: %) failed, as its Data Type is CONTROLLEDVOCABULARY, but it is not linked to a Controlled Vocabulary.', NEW.code;\\012 end if;\\012 end if;\\012\\012 RETURN NEW;\\012\\012END;\\012$$ LANGUAGE 'plpgsql';\\012\\012CREATE TRIGGER CONTROLLED_VOCABULARY_CHECK BEFORE INSERT OR UPDATE ON PROPERTY_TYPES\\012 FOR EACH ROW EXECUTE PROCEDURE CONTROLLED_VOCABULARY_CHECK();\\012\\012\\012------------------------------------------------------------------------------------\\012-- Purpose: Create trigger EXTERNAL_DATA_STORAGE_FORMAT_CHECK \\012------------------------------------------------------------------------------------\\012\\012CREATE OR REPLACE FUNCTION EXTERNAL_DATA_STORAGE_FORMAT_CHECK() RETURNS trigger AS $$\\012DECLARE\\012 v_covo_code CODE;\\012 data_code CODE;\\012BEGIN\\012\\012 select code into v_covo_code from controlled_vocabularies\\012 where is_internal_namespace = true and \\012 id = (select covo_id from controlled_vocabulary_terms where id = NEW.cvte_id_stor_fmt);\\012 -- Check if the data storage format is a term of the controlled vocabulary "STORAGE_FORMAT"\\012 if v_covo_code != 'STORAGE_FORMAT' then\\012 select code into data_code from data where id = NEW.data_id; \\012 RAISE EXCEPTION 'Insert/Update of Data (Code: %) failed, as its Storage Format is %, but is required to be STORAGE_FORMAT.', data_code, v_covo_code;\\012 end if;\\012\\012 RETURN NEW;\\012\\012END;\\012$$ LANGUAGE 'plpgsql';\\012\\012CREATE TRIGGER EXTERNAL_DATA_STORAGE_FORMAT_CHECK BEFORE INSERT OR UPDATE ON EXTERNAL_DATA\\012 FOR EACH ROW EXECUTE PROCEDURE EXTERNAL_DATA_STORAGE_FORMAT_CHECK();\\012\\012 \\012------------------------------------------------------------------------------------\\012-- Purpose: Create trigger SAMPLE_CODE_UNIQUENESS_CHECK \\012------------------------------------------------------------------------------------\\012\\012CREATE OR REPLACE FUNCTION SAMPLE_CODE_UNIQUENESS_CHECK() RETURNS trigger AS $$\\012DECLARE\\012 counter INTEGER;\\012BEGIN\\012 LOCK TABLE samples IN EXCLUSIVE MODE;\\012\\011IF (NEW.samp_id_part_of is NULL) THEN\\012\\011\\011IF (NEW.dbin_id is not NULL) THEN\\012\\011\\011\\011SELECT count(*) into counter FROM samples \\012\\011\\011\\011\\011where id != NEW.id and code = NEW.code and samp_id_part_of is NULL and dbin_id = NEW.dbin_id;\\012\\011\\011\\011IF (counter > 0) THEN\\012\\011\\011\\011\\011RAISE EXCEPTION 'Insert/Update of Sample (Code: %) failed because database instance sample with the same code already exists.', NEW.code;\\012\\011\\011\\011END IF;\\012\\011\\011ELSIF (NEW.grou_id is not NULL) THEN\\012\\011\\011\\011SELECT count(*) into counter FROM samples \\012\\011\\011\\011\\011where id != NEW.id and code = NEW.code and samp_id_part_of is NULL and grou_id = NEW.grou_id;\\012\\011\\011\\011IF (counter > 0) THEN\\012\\011\\011\\011\\011RAISE EXCEPTION 'Insert/Update of Sample (Code: %) failed because group sample with the same code already exists.', NEW.code;\\012\\011\\011\\011END IF;\\012\\011\\011END IF;\\012 ELSE\\012\\011\\011IF (NEW.dbin_id is not NULL) THEN\\012\\011\\011\\011SELECT count(*) into counter FROM samples \\012\\011\\011\\011\\011where id != NEW.id and code = NEW.code and samp_id_part_of = NEW.samp_id_part_of and dbin_id = NEW.dbin_id;\\012\\011\\011\\011IF (counter > 0) THEN\\012\\011\\011\\011\\011RAISE EXCEPTION 'Insert/Update of Sample (Code: %) failed because database instance sample with the same code and being the part of the same parent already exists.', NEW.code;\\012\\011\\011\\011END IF;\\012\\011\\011ELSIF (NEW.grou_id is not NULL) THEN\\012\\011\\011\\011SELECT count(*) into counter FROM samples \\012\\011\\011\\011\\011where id != NEW.id and code = NEW.code and samp_id_part_of = NEW.samp_id_part_of and grou_id = NEW.grou_id;\\012\\011\\011\\011IF (counter > 0) THEN\\012\\011\\011\\011\\011RAISE EXCEPTION 'Insert/Update of Sample (Code: %) failed because group sample with the same code and being the part of the same parent already exists.', NEW.code;\\012\\011\\011\\011END IF;\\012\\011\\011END IF;\\012 END IF; \\012 RETURN NEW;\\012END;\\012$$ LANGUAGE 'plpgsql';\\012\\012CREATE TRIGGER SAMPLE_CODE_UNIQUENESS_CHECK BEFORE INSERT OR UPDATE ON SAMPLES\\012 FOR EACH ROW EXECUTE PROCEDURE SAMPLE_CODE_UNIQUENESS_CHECK();\\012 \\012------------------------------------------------------------------------------------\\012-- Purpose: Create trigger MATERIAL/SAMPLE/EXPERIMENT/DATA_SET _PROPERTY_WITH_MATERIAL_DATA_TYPE_CHECK\\012-- It checks that if material property value is assigned to the entity,\\012--\\011\\011\\011\\011\\011\\011then the material type is equal to the one described by property type.\\012------------------------------------------------------------------------------------\\012\\012CREATE OR REPLACE FUNCTION MATERIAL_PROPERTY_WITH_MATERIAL_DATA_TYPE_CHECK() RETURNS trigger AS $$\\012DECLARE\\012 v_type_id CODE;\\012 v_type_id_prop CODE;\\012BEGIN\\012 if NEW.mate_prop_id IS NOT NULL then\\012\\011\\011\\011-- find material type id of the property type \\012\\011\\011\\011select pt.maty_prop_id into v_type_id_prop \\012\\011\\011\\011 from material_type_property_types etpt, property_types pt \\012\\011\\011\\011 where NEW.mtpt_id = etpt.id AND etpt.prty_id = pt.id;\\012\\011\\011\\012\\011\\011\\011if v_type_id_prop IS NOT NULL then\\012\\011\\011\\011\\011-- find material type id of the material which consists the entity's property value\\012\\011\\011\\011\\011select entity.maty_id into v_type_id \\012\\011\\011\\011\\011 from materials entity\\012\\011\\011\\011\\011 where NEW.mate_prop_id = entity.id;\\012\\011\\011\\011\\011if v_type_id != v_type_id_prop then\\012\\011\\011\\011\\011\\011RAISE EXCEPTION 'Insert/Update of property value referencing material (id: %) failed, as referenced material type is different than expected (id %, expected id: %).', \\012\\011\\011\\011\\011\\011\\011\\011 NEW.mate_prop_id, v_type_id, v_type_id_prop;\\012\\011\\011\\011\\011end if;\\012\\011\\011\\011end if;\\012 end if;\\012 RETURN NEW;\\012END;\\012$$ LANGUAGE 'plpgsql';\\012\\012CREATE TRIGGER MATERIAL_PROPERTY_WITH_MATERIAL_DATA_TYPE_CHECK BEFORE INSERT OR UPDATE ON material_properties\\012 FOR EACH ROW EXECUTE PROCEDURE MATERIAL_PROPERTY_WITH_MATERIAL_DATA_TYPE_CHECK();\\012 \\012CREATE OR REPLACE FUNCTION SAMPLE_PROPERTY_WITH_MATERIAL_DATA_TYPE_CHECK() RETURNS trigger AS $$\\012DECLARE\\012 v_type_id CODE;\\012 v_type_id_prop CODE;\\012BEGIN\\012 if NEW.mate_prop_id IS NOT NULL then\\012\\011\\011\\011-- find material type id of the property type \\012\\011\\011\\011select pt.maty_prop_id into v_type_id_prop \\012\\011\\011\\011 from sample_type_property_types etpt, property_types pt \\012\\011\\011\\011 where NEW.stpt_id = etpt.id AND etpt.prty_id = pt.id;\\012\\011\\011\\012\\011\\011\\011if v_type_id_prop IS NOT NULL then\\012\\011\\011\\011\\011-- find material type id of the material which consists the entity's property value\\012\\011\\011\\011\\011select entity.maty_id into v_type_id \\012\\011\\011\\011\\011 from materials entity\\012\\011\\011\\011\\011 where NEW.mate_prop_id = entity.id;\\012\\011\\011\\011\\011if v_type_id != v_type_id_prop then\\012\\011\\011\\011\\011\\011RAISE EXCEPTION 'Insert/Update of property value referencing material (id: %) failed, as referenced material type is different than expected (id %, expected id: %).', \\012\\011\\011\\011\\011\\011\\011\\011\\011\\011\\011\\011\\011 NEW.mate_prop_id, v_type_id, v_type_id_prop;\\012\\011\\011\\011\\011end if;\\012\\011\\011\\011end if;\\012 end if;\\012 RETURN NEW;\\012END;\\012$$ LANGUAGE 'plpgsql';\\012\\012CREATE TRIGGER SAMPLE_PROPERTY_WITH_MATERIAL_DATA_TYPE_CHECK BEFORE INSERT OR UPDATE ON sample_properties\\012 FOR EACH ROW EXECUTE PROCEDURE SAMPLE_PROPERTY_WITH_MATERIAL_DATA_TYPE_CHECK();\\012 \\012CREATE OR REPLACE FUNCTION EXPERIMENT_PROPERTY_WITH_MATERIAL_DATA_TYPE_CHECK() RETURNS trigger AS $$\\012DECLARE\\012 v_type_id CODE;\\012 v_type_id_prop CODE;\\012BEGIN\\012 if NEW.mate_prop_id IS NOT NULL then\\012\\011\\011\\011-- find material type id of the property type \\012\\011\\011\\011select pt.maty_prop_id into v_type_id_prop \\012\\011\\011\\011 from experiment_type_property_types etpt, property_types pt \\012\\011\\011\\011 where NEW.etpt_id = etpt.id AND etpt.prty_id = pt.id;\\012\\011\\011\\012\\011\\011\\011if v_type_id_prop IS NOT NULL then\\012\\011\\011\\011\\011-- find material type id of the material which consists the entity's property value\\012\\011\\011\\011\\011select entity.maty_id into v_type_id \\012\\011\\011\\011\\011 from materials entity\\012\\011\\011\\011\\011 where NEW.mate_prop_id = entity.id;\\012\\011\\011\\011\\011if v_type_id != v_type_id_prop then\\012\\011\\011\\011\\011\\011RAISE EXCEPTION 'Insert/Update of property value referencing material (id: %) failed, as referenced material type is different than expected (id %, expected id: %).', \\012\\011\\011\\011\\011\\011\\011\\011\\011\\011\\011\\011\\011 NEW.mate_prop_id, v_type_id, v_type_id_prop;\\012\\011\\011\\011\\011end if;\\012\\011\\011\\011end if;\\012 end if;\\012 RETURN NEW;\\012END;\\012$$ LANGUAGE 'plpgsql';\\012\\012CREATE TRIGGER EXPERIMENT_PROPERTY_WITH_MATERIAL_DATA_TYPE_CHECK BEFORE INSERT OR UPDATE ON experiment_properties\\012 FOR EACH ROW EXECUTE PROCEDURE EXPERIMENT_PROPERTY_WITH_MATERIAL_DATA_TYPE_CHECK();\\012 \\012 -- data set\\012CREATE OR REPLACE FUNCTION DATA_SET_PROPERTY_WITH_MATERIAL_DATA_TYPE_CHECK() RETURNS trigger AS $$\\012DECLARE\\012 v_type_id CODE;\\012 v_type_id_prop CODE;\\012BEGIN\\012 if NEW.mate_prop_id IS NOT NULL then\\012\\011\\011\\011-- find material type id of the property type \\012\\011\\011\\011select pt.maty_prop_id into v_type_id_prop \\012\\011\\011\\011 from data_set_type_property_types dstpt, property_types pt \\012\\011\\011\\011 where NEW.dstpt_id = dstpt.id AND dstpt.prty_id = pt.id;\\012\\011\\011\\012\\011\\011\\011if v_type_id_prop IS NOT NULL then\\012\\011\\011\\011\\011-- find material type id of the material which consists the entity's property value\\012\\011\\011\\011\\011select entity.maty_id into v_type_id \\012\\011\\011\\011\\011 from materials entity\\012\\011\\011\\011\\011 where NEW.mate_prop_id = entity.id;\\012\\011\\011\\011\\011if v_type_id != v_type_id_prop then\\012\\011\\011\\011\\011\\011RAISE EXCEPTION 'Insert/Update of property value referencing material (id: %) failed, as referenced material type is different than expected (id %, expected id: %).', \\012\\011\\011\\011\\011\\011\\011\\011\\011\\011\\011\\011\\011 NEW.mate_prop_id, v_type_id, v_type_id_prop;\\012\\011\\011\\011\\011end if;\\012\\011\\011\\011end if;\\012 end if;\\012 RETURN NEW;\\012END;\\012$$ LANGUAGE 'plpgsql';\\012\\012CREATE TRIGGER DATA_SET_PROPERTY_WITH_MATERIAL_DATA_TYPE_CHECK BEFORE INSERT OR UPDATE ON data_set_properties\\012 FOR EACH ROW EXECUTE PROCEDURE DATA_SET_PROPERTY_WITH_MATERIAL_DATA_TYPE_CHECK(); \\012 \\012---------------------------------------------------------------------------------------------------\\012-- Purpose: Create DEFERRED triggers:\\012-- * check_dataset_relationships_on_data_table_modification,\\012-- * check_dataset_relationships_on_relationships_table_modification.\\012-- They check that after all modifications of database (just before commit) \\012-- if 'data'/'data_set_relationships' tables are among modified tables \\012-- dataset is not connected with a sample and a parent dataset at the same time.\\012-- This connections are held in two different tables so simple immediate trigger \\012-- with arc check cannot be used and we need two deferred triggers.\\012----------------------------------------------------------------------------------------------------\\012\\012-- trigger for 'data' table\\012\\012CREATE OR REPLACE FUNCTION check_dataset_relationships_on_data_table_modification() RETURNS trigger AS $$\\012DECLARE\\012\\011counter\\011INTEGER;\\012BEGIN\\012\\011-- if there is a connection with a Sample there should not be any connection with a parent Data Set\\012\\011IF (NEW.samp_id IS NOT NULL) THEN\\012\\011\\011-- count number of parents\\012\\011\\011SELECT count(*) INTO counter \\012\\011\\011\\011FROM data_set_relationships \\012\\011\\011\\011WHERE data_id_child = NEW.id;\\012\\011\\011IF (counter > 0) THEN\\012\\011\\011\\011RAISE EXCEPTION 'Insert/Update of Data Set (Code: %) failed because it cannot be connected with a Sample and a parent Data Set at the same time.', NEW.code;\\012\\011\\011END IF;\\012\\011END IF;\\012 RETURN NEW;\\012END;\\012$$ LANGUAGE 'plpgsql';\\012\\012CREATE CONSTRAINT TRIGGER check_dataset_relationships_on_data_table_modification \\012 AFTER INSERT OR UPDATE ON data\\012\\011DEFERRABLE INITIALLY DEFERRED\\012\\011FOR EACH ROW \\012\\011EXECUTE PROCEDURE check_dataset_relationships_on_data_table_modification();\\012\\012-- trigger for 'data_set_relationships'\\012\\012CREATE OR REPLACE FUNCTION check_dataset_relationships_on_relationships_table_modification() RETURNS trigger AS $$\\012DECLARE\\012\\011counter\\011INTEGER;\\012\\011sample_id\\011TECH_ID;\\012\\011data_code\\011CODE;\\012BEGIN\\012\\011-- child will have a parent added so it should not be connected with any sample\\012\\011SELECT samp_id, code INTO sample_id, data_code \\012\\011\\011FROM data \\012\\011\\011WHERE id = NEW.data_id_child;\\012\\011IF (sample_id IS NOT NULL) THEN\\012\\011\\011RAISE EXCEPTION 'Insert/Update of Data Set (Code: %) failed because it cannot be connected to a Sample and to a parent Data Set at the same time.', data_code;\\012\\011END IF;\\012\\011RETURN NEW;\\012END;\\012$$ LANGUAGE 'plpgsql';\\012 \\012CREATE CONSTRAINT TRIGGER check_dataset_relationships_on_relationships_table_modification \\012 AFTER INSERT OR UPDATE ON data_set_relationships\\012\\011DEFERRABLE INITIALLY DEFERRED\\012\\011FOR EACH ROW \\012\\011EXECUTE PROCEDURE check_dataset_relationships_on_relationships_table_modification();\\012 \N
-051 ./sql/postgresql/051/grants-051.sql SUCCESS 2010-05-10 17:57:14.112 -- Granting SELECT privilege to group OPENBIS_READONLY\\012\\012GRANT SELECT ON SEQUENCE attachment_content_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE attachment_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE code_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE controlled_vocabulary_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE cvte_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE data_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE data_set_property_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE data_set_relationship_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE data_set_type_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE data_store_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE DATA_STORE_SERVICES_ID_SEQ TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE data_type_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE database_instance_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE dstpt_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE etpt_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE event_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE experiment_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE experiment_property_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE experiment_type_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE file_format_type_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE group_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE invalidation_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE locator_type_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE material_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE material_property_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE material_type_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE mtpt_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE perm_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE person_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE project_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE property_type_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE role_assignment_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE sample_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE sample_property_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE sample_type_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE stpt_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE authorization_group_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE filter_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON SEQUENCE query_id_seq TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE attachment_contents TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE attachments TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE controlled_vocabularies TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE controlled_vocabulary_terms TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE data TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE data_set_properties TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE data_set_relationships TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE data_set_type_property_types TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE data_set_types TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE data_stores TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE data_types TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE DATA_STORE_SERVICES TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE DATA_STORE_SERVICE_DATA_SET_TYPES TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE database_instances TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE database_version_logs TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE events TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE experiment_properties TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE experiment_type_property_types TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE experiment_types TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE experiments TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE external_data TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE file_format_types TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE groups TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE invalidations TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE locator_types TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE material_properties TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE material_type_property_types TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE material_types TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE materials TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE persons TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE projects TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE property_types TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE role_assignments TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE sample_properties TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE sample_type_property_types TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE sample_types TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE samples TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE authorization_groups TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE authorization_group_persons TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE filters TO GROUP OPENBIS_READONLY;\\012GRANT SELECT ON TABLE queries TO GROUP OPENBIS_READONLY;\\012 \N
-051 ./sql/generic/051/data-051.sql SUCCESS 2010-05-10 17:57:14.533 ----------------------------------------------------------------------------\\012-- Purpose: Insert an initial data set into the table DATABASE_INSTANCES\\012----------------------------------------------------------------------------\\012\\012INSERT INTO database_instances(\\012 id\\012 , code\\012\\011 \\011, uuid\\012 , is_original_source)\\012 VALUES ( nextval('DATABASE_INSTANCE_ID_SEQ')\\012 , 'SYSTEM_DEFAULT'\\012\\011 \\011, 'SYSTEM_DEFAULT'\\012 , 'T');\\012\\012----------------------------------------------------------------------\\012-- Purpose: Insert an initial data set into the table DATA_STORES\\012----------------------------------------------------------------------\\012\\012insert into data_stores\\012(id\\012,code\\012,download_url\\012,remote_url\\012,session_token\\012,dbin_id)\\012values\\012(nextval('DATA_STORE_ID_SEQ')\\012,'STANDARD'\\012,''\\012,''\\012,''\\012,(select id from database_instances where code = 'SYSTEM_DEFAULT')\\012);\\012\\012----------------------------------------------------------------------\\012-- Purpose: Insert an initial data set into the table PERSONS\\012-----------------------------------------------------------------------\\012\\012insert into persons\\012(id\\012,first_name\\012,last_name\\012,user_id\\012,email\\012,dbin_id)\\012values\\012(nextval('PERSON_ID_SEQ')\\012,''\\012,'System User'\\012,'system'\\012,''\\012,(select id from database_instances where code = 'SYSTEM_DEFAULT') );\\012\\012-----------------------------------------------------------------------------------\\012-- Purpose: Create Controlled Vocabulary STORAGE_FORMAT\\012-----------------------------------------------------------------------------------\\012insert into controlled_vocabularies \\012 ( id\\012 , code\\012 , is_internal_namespace \\012 , description\\012 , pers_id_registerer\\012 , is_managed_internally\\012 , dbin_id)\\012values (nextval('CONTROLLED_VOCABULARY_ID_SEQ')\\012 , 'STORAGE_FORMAT'\\012 , true\\012 , 'The on-disk storage format of a data set'\\012 , (select id from persons where user_id ='system')\\012 , true\\012 , (select id from database_instances where code = 'SYSTEM_DEFAULT'));\\012\\012\\012-----------------------------------------------------------------------------------\\012-- Purpose: Create Controlled Vocabulary Terms for STORAGE_FORMAT\\012-----------------------------------------------------------------------------------\\012insert into controlled_vocabulary_terms \\012 ( id\\012 , code\\012 , covo_id \\012 , pers_id_registerer\\012 , ordinal )\\012values (nextval('CVTE_ID_SEQ')\\012 , 'PROPRIETARY'\\012 , (select id from controlled_vocabularies where code = 'STORAGE_FORMAT' and is_internal_namespace = true)\\012 , (select id from persons where user_id ='system')\\012 , 1);\\012\\012insert into controlled_vocabulary_terms \\012 ( id\\012 , code\\012 , covo_id \\012 , pers_id_registerer\\012 , ordinal)\\012values (nextval('CVTE_ID_SEQ')\\012 , 'BDS_DIRECTORY'\\012 , (select id from controlled_vocabularies where code = 'STORAGE_FORMAT' and is_internal_namespace = true)\\012 , (select id from persons where user_id ='system')\\012 , 2);\\012\\012------------------------------------------------------------------\\012-- Purpose: Insert an initial data set into the table DATA_TYPES\\012------------------------------------------------------------------\\012\\012insert into data_types\\012(id\\012,code\\012,description)\\012values \\012(nextval('DATA_TYPE_ID_SEQ')\\012,'VARCHAR'\\012,'Short text'\\012);\\012\\012insert into data_types\\012(id\\012 ,code\\012 ,description)\\012 values \\012 (nextval('DATA_TYPE_ID_SEQ')\\012 ,'MULTILINE_VARCHAR'\\012 ,'Long text'\\012);\\012\\012insert into data_types\\012(id\\012,code\\012,description)\\012values \\012(nextval('DATA_TYPE_ID_SEQ')\\012,'INTEGER'\\012,'Integer number'\\012);\\012\\012insert into data_types\\012(id\\012,code\\012,description)\\012values \\012(nextval('DATA_TYPE_ID_SEQ')\\012,'REAL'\\012,'Real number, i.e. an inexact, variable-precision numeric type'\\012);\\012\\012insert into data_types\\012(id\\012,code\\012,description)\\012values \\012(nextval('DATA_TYPE_ID_SEQ')\\012,'BOOLEAN'\\012,'True or False'\\012);\\012\\012insert into data_types\\012(id\\012,code\\012,description)\\012values \\012(nextval('DATA_TYPE_ID_SEQ')\\012,'TIMESTAMP'\\012,'Both date and time. Format: yyyy-mm-dd hh:mm:ss'\\012);\\012\\012insert into data_types\\012(id\\012 ,code\\012 ,description)\\012 values \\012 (nextval('DATA_TYPE_ID_SEQ')\\012 ,'CONTROLLEDVOCABULARY'\\012 ,'Controlled Vocabulary'\\012);\\012\\012insert into data_types\\012(id\\012 ,code\\012 ,description)\\012 values \\012 (nextval('DATA_TYPE_ID_SEQ')\\012 ,'MATERIAL'\\012 ,'Reference to a material'\\012);\\012\\012insert into data_types\\012(id\\012 ,code\\012 ,description)\\012 values \\012 (nextval('DATA_TYPE_ID_SEQ')\\012 ,'HYPERLINK'\\012 ,'Address of a web page'\\012);\\012\\012----------------------------------------------------------------------\\012-- Purpose: Insert an initial data set into the table PROPERTY_TYPES\\012-----------------------------------------------------------------------\\012\\012insert into property_types\\012(id\\012,code\\012,description\\012,label\\012,daty_id\\012,pers_id_registerer\\012,dbin_id)\\012values \\012(nextval('PROPERTY_TYPE_ID_SEQ')\\012,'DESCRIPTION'\\012,'A Description'\\012,'Description'\\012,(select id from data_types where code ='VARCHAR')\\012,(select id from persons where user_id ='system')\\012,(select id from database_instances where code = 'SYSTEM_DEFAULT')\\012);\\012\\012--------------------------------------------------------------------------\\012-- Purpose: Insert an initial data set into the table DATA_SET_TYPES\\012--------------------------------------------------------------------------\\012\\012insert into data_set_types\\012(id\\012,code\\012,description\\012,dbin_id)\\012values \\012(nextval('DATA_SET_TYPE_ID_SEQ')\\012,'UNKNOWN'\\012,'Unknown'\\012,(select id from database_instances where code = 'SYSTEM_DEFAULT')\\012);\\012\\012-------------------------------------------------------------------------\\012-- Purpose: Insert an initial data set into the table FILE_FORMAT_TYPES\\012-------------------------------------------------------------------------\\012\\012insert into file_format_types\\012(id\\012,code\\012,description\\012,dbin_id)\\012values \\012(nextval('FILE_FORMAT_TYPE_ID_SEQ')\\012,'HDF5'\\012,'Hierarchical Data Format File, version 5'\\012,(select id from database_instances where code = 'SYSTEM_DEFAULT')\\012);\\012\\012insert into file_format_types\\012(id\\012,code\\012,description\\012,dbin_id)\\012values \\012(nextval('FILE_FORMAT_TYPE_ID_SEQ')\\012,'PROPRIETARY'\\012,'Proprietary Format File'\\012,(select id from database_instances where code = 'SYSTEM_DEFAULT')\\012);\\012\\012insert into file_format_types\\012(id\\012,code\\012,description\\012,dbin_id)\\012values \\012(nextval('FILE_FORMAT_TYPE_ID_SEQ')\\012,'SRF'\\012,'Sequence Read Format File'\\012,(select id from database_instances where code = 'SYSTEM_DEFAULT')\\012);\\012\\012insert into file_format_types\\012(id\\012,code\\012,description\\012,dbin_id)\\012values \\012(nextval('FILE_FORMAT_TYPE_ID_SEQ')\\012,'TIFF'\\012,'TIFF File'\\012,(select id from database_instances where code = 'SYSTEM_DEFAULT')\\012);\\012\\012insert into file_format_types\\012(id\\012,code\\012,description\\012,dbin_id)\\012values \\012(nextval('FILE_FORMAT_TYPE_ID_SEQ')\\012,'TSV'\\012,'Tab Separated Values File'\\012,(select id from database_instances where code = 'SYSTEM_DEFAULT')\\012);\\012\\012insert into file_format_types\\012(id\\012,code\\012,description\\012,dbin_id)\\012values \\012(nextval('FILE_FORMAT_TYPE_ID_SEQ')\\012,'XML'\\012,'XML File'\\012,(select id from database_instances where code = 'SYSTEM_DEFAULT')\\012);\\012\\012---------------------------------------------------------------------\\012-- Purpose: Insert an initial data set into the table LOCATOR_TYPES\\012---------------------------------------------------------------------\\012\\012insert into locator_types\\012(id\\012,code\\012,description)\\012values \\012(nextval('LOCATOR_TYPE_ID_SEQ')\\012,'RELATIVE_LOCATION'\\012,'Relative Location'\\012);\\012 \N
-052 ./sql/postgresql/migration/migration-051-052.sql SUCCESS 2010-10-29 13:39:25.352 -- Migration from 051 to 052\\012\\012-- Add QUERY_TYPE column to QUERIES\\012CREATE DOMAIN QUERY_TYPE AS VARCHAR(40) CHECK (VALUE IN ('GENERIC', 'EXPERIMENT', 'SAMPLE', 'DATA_SET', 'MATERIAL'));\\012ALTER TABLE QUERIES ADD COLUMN QUERY_TYPE QUERY_TYPE;\\012UPDATE QUERIES SET QUERY_TYPE = 'GENERIC';\\012ALTER TABLE QUERIES ALTER COLUMN QUERY_TYPE SET NOT NULL; \\012\\012-- add DB_KEY column to QUERIES\\012\\012ALTER TABLE queries ADD COLUMN db_key code NOT NULL DEFAULT '1';\\012 \N
-053 ./sql/postgresql/migration/migration-052-053.sql SUCCESS 2010-10-29 13:39:25.458 -- Migration from 052 to 053\\012\\012-- Change code uniqueness check for samples of specific type.\\012-- If sample_types.is_subcode_unique flag is set to 'true', additional check is performed \\012-- on codes of samples of the type. Subcodes will have to be unique as well.\\012\\012ALTER TABLE sample_types ADD COLUMN is_subcode_unique boolean_char NOT NULL DEFAULT false;\\012\\012CREATE OR REPLACE FUNCTION SAMPLE_SUBCODE_UNIQUENESS_CHECK() RETURNS trigger AS $$\\012DECLARE\\012 counter INTEGER;\\012 unique_subcode BOOLEAN_CHAR;\\012BEGIN\\012 LOCK TABLE samples IN EXCLUSIVE MODE;\\012 \\012 SELECT is_subcode_unique into unique_subcode FROM sample_types WHERE id = NEW.saty_id;\\012 \\012 IF (unique_subcode) THEN\\012 IF (NEW.dbin_id is not NULL) THEN\\012\\011\\011\\011SELECT count(*) into counter FROM samples \\012\\011\\011\\011\\011where id != NEW.id and code = NEW.code and saty_id = NEW.saty_id and dbin_id = NEW.dbin_id;\\012\\011\\011\\011IF (counter > 0) THEN\\012\\011\\011\\011\\011RAISE EXCEPTION 'Insert/Update of Sample (Code: %) failed because database instance sample of the same type with the same subcode already exists.', NEW.code;\\012\\011\\011\\011END IF;\\012\\011\\011ELSIF (NEW.grou_id is not NULL) THEN\\012\\011\\011\\011SELECT count(*) into counter FROM samples \\012\\011\\011\\011\\011where id != NEW.id and code = NEW.code and saty_id = NEW.saty_id and grou_id = NEW.grou_id;\\012\\011\\011\\011IF (counter > 0) THEN\\012\\011\\011\\011\\011RAISE EXCEPTION 'Insert/Update of Sample (Code: %) failed because space sample of the same type with the same subcode already exists.', NEW.code;\\012\\011\\011\\011END IF;\\012\\011\\011END IF;\\012 END IF;\\012 \\012 RETURN NEW;\\012END;\\012$$ LANGUAGE 'plpgsql';\\012\\012CREATE TRIGGER SAMPLE_SUBCODE_UNIQUENESS_CHECK BEFORE INSERT OR UPDATE ON SAMPLES\\012 FOR EACH ROW EXECUTE PROCEDURE SAMPLE_SUBCODE_UNIQUENESS_CHECK();\\012 \\012-- Fixing error messages in old trigger\\012\\012CREATE OR REPLACE FUNCTION SAMPLE_CODE_UNIQUENESS_CHECK() RETURNS trigger AS $$\\012DECLARE\\012 counter INTEGER;\\012BEGIN\\012 LOCK TABLE samples IN EXCLUSIVE MODE;\\012 \\012\\011 IF (NEW.samp_id_part_of is NULL) THEN\\012\\011\\011 IF (NEW.dbin_id is not NULL) THEN\\012\\011\\011\\011 SELECT count(*) into counter FROM samples \\012\\011\\011 where id != NEW.id and code = NEW.code and samp_id_part_of is NULL and dbin_id = NEW.dbin_id;\\012 IF (counter > 0) THEN\\012\\011\\011\\011\\011 RAISE EXCEPTION 'Insert/Update of Sample (Code: %) failed because database instance sample with the same code already exists.', NEW.code;\\012 END IF;\\012\\011\\011 ELSIF (NEW.grou_id is not NULL) THEN\\012\\011\\011\\011 SELECT count(*) into counter FROM samples \\012\\011\\011\\011\\011 where id != NEW.id and code = NEW.code and samp_id_part_of is NULL and grou_id = NEW.grou_id;\\012\\011\\011\\011 IF (counter > 0) THEN\\012\\011\\011\\011\\011 RAISE EXCEPTION 'Insert/Update of Sample (Code: %) failed because space sample with the same code already exists.', NEW.code;\\012\\011\\011\\011 END IF;\\012 END IF;\\012 ELSE\\012\\011\\011 IF (NEW.dbin_id is not NULL) THEN\\012\\011\\011\\011 SELECT count(*) into counter FROM samples \\012\\011\\011\\011\\011 where id != NEW.id and code = NEW.code and samp_id_part_of = NEW.samp_id_part_of and dbin_id = NEW.dbin_id;\\012\\011\\011\\011 IF (counter > 0) THEN\\012\\011\\011\\011\\011 RAISE EXCEPTION 'Insert/Update of Sample (Code: %) failed because database instance sample with the same code and being the part of the same container already exists.', NEW.code;\\012\\011\\011\\011 END IF;\\012\\011\\011 ELSIF (NEW.grou_id is not NULL) THEN\\012\\011\\011\\011 SELECT count(*) into counter FROM samples \\012\\011\\011\\011\\011 where id != NEW.id and code = NEW.code and samp_id_part_of = NEW.samp_id_part_of and grou_id = NEW.grou_id;\\012\\011\\011\\011 IF (counter > 0) THEN\\012\\011\\011\\011\\011 RAISE EXCEPTION 'Insert/Update of Sample (Code: %) failed because space sample with the same code and being the part of the same container already exists.', NEW.code;\\012\\011\\011\\011 END IF;\\012\\011\\011 END IF;\\012 END IF; \\012 \\012 RETURN NEW;\\012END;\\012$$ LANGUAGE 'plpgsql';\\012 \N
-054 ./sql/postgresql/migration/migration-053-054.sql SUCCESS 2010-10-29 13:39:25.593 -- Migration from 053 to 054\\012\\012\\012-- Add RELATIONSHIP_TYPES table\\012CREATE TABLE relationship_types (id TECH_ID NOT NULL, code CODE NOT NULL, label COLUMN_LABEL, parent_label COLUMN_LABEL, child_label COLUMN_LABEL, description DESCRIPTION_2000, registration_timestamp TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP, pers_id_registerer TECH_ID NOT NULL, is_managed_internally BOOLEAN_CHAR NOT NULL DEFAULT 'F', is_internal_namespace BOOLEAN_CHAR NOT NULL DEFAULT 'F', dbin_id TECH_ID NOT NULL);\\012\\012-- Add SAMPLE_RELATIONSHIPS table\\012CREATE TABLE sample_relationships (id TECH_ID NOT NULL, sample_id_parent TECH_ID NOT NULL, relationship_id TECH_ID NOT NULL, sample_id_child TECH_ID NOT NULL);\\012\\012-- Add/update constraints\\012ALTER TABLE relationship_types ADD CONSTRAINT rety_pk PRIMARY KEY (id);\\012ALTER TABLE relationship_types ADD CONSTRAINT rety_uk UNIQUE(code,dbin_id);\\012ALTER TABLE sample_relationships ADD CONSTRAINT sare_pk PRIMARY KEY (id);\\012ALTER TABLE sample_relationships ADD CONSTRAINT sare_bk_uk UNIQUE(sample_id_child,sample_id_parent,relationship_id);\\012ALTER TABLE sample_relationships ADD CONSTRAINT sare_data_fk_child FOREIGN KEY (sample_id_child) REFERENCES samples(id) ON DELETE CASCADE;\\012ALTER TABLE sample_relationships ADD CONSTRAINT sare_data_fk_parent FOREIGN KEY (sample_id_parent) REFERENCES samples(id) ON DELETE CASCADE;\\012ALTER TABLE sample_relationships ADD CONSTRAINT sare_data_fk_relationship FOREIGN KEY (relationship_id) REFERENCES relationship_types(id);\\012\\012-- Create index\\012CREATE INDEX sare_data_fk_i_child ON sample_relationships (sample_id_child);\\012CREATE INDEX sare_data_fk_i_parent ON sample_relationships (sample_id_parent);\\012CREATE INDEX sare_data_fk_i_relationship ON sample_relationships (relationship_id);\\012\\012-- Create sequence for RELATIONSHIP_TYPES\\012CREATE SEQUENCE RELATIONSHIP_TYPE_ID_SEQ;\\012CREATE SEQUENCE SAMPLE_RELATIONSHIP_ID_SEQ;\\012\\012-- Create initial relationships\\012insert into relationship_types\\012(id, \\012code, \\012label, \\012parent_label, \\012child_label, \\012description, \\012pers_id_registerer, \\012is_managed_internally, \\012is_internal_namespace, \\012dbin_id) \\012values\\012(\\012nextval('RELATIONSHIP_TYPE_ID_SEQ'),\\012'PARENT_CHILD',\\012'Parent - Child', \\012'Parent', \\012'Child', \\012'Parent - Child relationship', \\012(select id from persons where user_id ='system'), \\012'T', \\012'T', \\012(select id from database_instances where is_original_source = 'T')\\012);\\012\\012insert into relationship_types\\012(id, \\012code, \\012label, \\012parent_label, \\012child_label, \\012description, \\012pers_id_registerer, \\012is_managed_internally, \\012is_internal_namespace, \\012dbin_id) \\012values\\012(\\012nextval('RELATIONSHIP_TYPE_ID_SEQ'),\\012'PLATE_CONTROL_LAYOUT',\\012'Plate - Control Layout', \\012'Plate', \\012'Control Layout', \\012'Plate - Control Layout relationship', \\012(select id from persons where user_id ='system'), \\012'T', \\012'T', \\012(select id from database_instances where is_original_source = 'T')\\012); \\012\\012\\012-- Migrate sample relationships to new schema\\012INSERT INTO sample_relationships (id, sample_id_parent,sample_id_child,relationship_id) (select distinct nextval('SAMPLE_RELATIONSHIP_ID_SEQ') as id, s.SAMP_ID_GENERATED_FROM as parent_id, s.ID as child_id, rt.id as relationship_id from samples s, relationship_types rt WHERE rt.code = 'PARENT_CHILD' and s.SAMP_ID_GENERATED_FROM is not null); \\012INSERT INTO sample_relationships (id, sample_id_parent,sample_id_child,relationship_id) (select distinct nextval('SAMPLE_RELATIONSHIP_ID_SEQ') as id, s.SAMP_ID_CONTROL_LAYOUT as parent_id, s.ID as child_id, rt.id as relationship_id from samples s, relationship_types rt WHERE rt.code = 'PLATE_CONTROL_LAYOUT' and s.SAMP_ID_CONTROL_LAYOUT is not null);\\012\\012-- Drop old sample relations\\012ALTER TABLE SAMPLES DROP COLUMN SAMP_ID_TOP;\\012ALTER TABLE SAMPLES DROP COLUMN SAMP_ID_GENERATED_FROM;\\012ALTER TABLE SAMPLES DROP COLUMN SAMP_ID_CONTROL_LAYOUT;\\012\\012--------------------------------------------------------------------------------------\\012--------------------------------------------------------------------------------------\\012-- This is a screening specific migration. Nothing will be performed on openBIS databases \\012-- which are not screening specific.\\012-- \\012-- This migration for each existing connection between oligo well, oligo material and gene material\\012-- creates a direct connection between the well and the gene. \\012--------------------------------------------------------------------------------------\\012--------------------------------------------------------------------------------------\\012 \\012\\011\\012CREATE OR REPLACE FUNCTION CONNECT_WELLS_WITH_GENES() RETURNS void AS $$\\012DECLARE\\012\\011counter int;\\012\\011oligo_well_exists bool;\\012BEGIN\\012\\011--------------------------------------------------\\012\\011-- create a gene property and assign it to oligo well\\012\\011--------------------------------------------------\\012\\011\\012\\011select true \\012\\011into oligo_well_exists\\012\\011from sample_types \\012\\011where code = 'OLIGO_WELL';\\012\\011\\012\\011if oligo_well_exists IS NULL then \\012\\011\\011-- skip migration if there are no oligo wells\\012\\011\\011return;\\012\\011end if; \\012\\011\\012\\011insert into property_types(\\012\\011\\011id, \\012\\011\\011code, description, label, \\012\\011\\011daty_id,\\012\\011\\011pers_id_registerer,\\012\\011\\011dbin_id,\\012\\011\\011maty_prop_id) \\012\\011values(\\012\\011\\011\\011nextval('PROPERTY_TYPE_ID_SEQ'), \\012\\011\\011\\011'GENE','Inhibited gene','Gene',\\012\\011\\011\\011(select id from data_types where code = 'MATERIAL'), \\012\\011\\011\\011(select id from persons where user_id ='system'), \\012\\011\\011\\011(select id from database_instances where is_original_source = 'T'), \\012\\011\\011\\011(select id from material_types where code = 'GENE')\\012\\011\\011);\\012\\011\\011\\012\\011insert into sample_type_property_types( \\012\\011 id,\\012\\011 saty_id,\\012\\011 prty_id,\\012\\011 is_mandatory,\\012\\011 pers_id_registerer,\\012\\011 ordinal\\012\\011) values(\\012\\011\\011\\011nextval('stpt_id_seq'), \\012\\011\\011\\011(select id from sample_types where code = 'OLIGO_WELL'),\\012\\011\\011\\011(select id from property_types where code = 'GENE'),\\012\\011\\011\\011false,\\012\\011\\011\\011(select id from persons where user_id ='system'),\\012\\011\\011\\011(select max(ordinal)+1 from sample_type_property_types \\012\\011\\011\\011\\011where saty_id = (select id from sample_types where code = 'OLIGO_WELL'))\\012\\011\\011);\\012\\012\\011--------------------------------------------------\\012\\011-- create a gene material property for each oligo well\\012\\011--------------------------------------------------\\012\\011\\011\\012\\011select \\011count(*)\\012\\011into counter\\012\\011from\\012\\011\\011samples well, sample_types well_type, sample_properties well_props, \\012\\011\\011materials well_material, material_properties well_material_props,\\012\\011\\011materials nested_well_material\\012\\011where\\012\\011\\011well_type.code = 'OLIGO_WELL' and\\012\\011\\011-- find 'well_material' assigned to the well\\012\\011\\011well_props.samp_id = well.id and well_material.id = well_props.mate_prop_id and \\012\\011\\011-- additional joins to entity type tables\\012\\011\\011well_type.id = well.saty_id and\\012\\011\\011-- well content material property\\012\\011\\011well_material_props.mate_id = well_material.id and \\012\\011\\011-- material connected to the material in the well (e.g. gene)\\012\\011\\011well_material_props.mate_prop_id = nested_well_material.id and\\012\\011\\011nested_well_material.maty_id = (select id from material_types where code = 'GENE');\\012\\011\\012\\011if counter = 0 then \\012\\011\\011-- skip migration if there are no genes indirectly connected to oligo wells\\012\\011\\011return;\\012\\011end if; \\012\\012\\011insert into sample_properties(id, samp_id, stpt_id, mate_prop_id, pers_id_registerer) (\\012\\011\\011select \\011nextval('sample_property_id_seq') id, \\012\\011\\011\\011well.id samp_id, \\012\\011\\011\\011(select stpt.id from sample_type_property_types stpt, property_types props where stpt.prty_id = props.id and props.code='GENE') stpt_id,\\012\\011\\011\\011nested_well_material.id mate_prop_id,\\012\\011\\011\\011(select id from persons where user_id ='system') pers_id_registerer \\012\\011\\011from\\012\\011\\011\\011samples well, sample_types well_type, sample_properties well_props, \\012\\011\\011\\011materials well_material, material_properties well_material_props,\\012\\011\\011\\011materials nested_well_material\\012\\011\\011where\\012\\011\\011\\011well_type.code = 'OLIGO_WELL' and\\012\\011\\011\\011-- find 'well_material' assigned to the well\\012\\011\\011\\011well_props.samp_id = well.id and well_material.id = well_props.mate_prop_id and \\012\\011\\011\\011-- additional joins to entity type tables\\012\\011\\011\\011well_type.id = well.saty_id and\\012\\011\\011\\011-- well content material property\\012\\011\\011\\011well_material_props.mate_id = well_material.id and \\012\\011\\011\\011-- material connected to the material in the well (e.g. gene)\\012\\011\\011\\011well_material_props.mate_prop_id = nested_well_material.id and\\012\\011\\011\\011nested_well_material.maty_id = (select id from material_types where code = 'GENE')\\012\\011);\\012\\012END;\\012$$ LANGUAGE 'plpgsql';\\012\\012select CONNECT_WELLS_WITH_GENES();\\012drop function CONNECT_WELLS_WITH_GENES();\\012\\012--------------------------------------------------------------------------------------\\012--------------------------------------------------------------------------------------\\012\\012-- drop dataset triggers\\012\\012DROP TRIGGER check_dataset_relationships_on_data_table_modification ON data;\\012DROP FUNCTION check_dataset_relationships_on_data_table_modification();\\012DROP TRIGGER check_dataset_relationships_on_relationships_table_modification ON data_set_relationships;\\012DROP FUNCTION check_dataset_relationships_on_relationships_table_modification();\\012 \\012\\012\\012\\012\\012\\012\\012\\012 \N
-055 ./sql/postgresql/migration/migration-054-055.sql SUCCESS 2010-10-29 13:39:25.602 -- Migration from 054 to 055\\012\\012UPDATE sample_types SET generated_from_depth = 1 WHERE generated_from_depth > 1;\\012 \N
-056 ./sql/postgresql/migration/migration-055-056.sql SUCCESS 2010-10-29 13:39:25.663 -- Migration from 055 to 056\\012\\012--------------------------------------------------------------------------------------\\012--------------------------------------------------------------------------------------\\012-- Screening specific migration. Nothing will be performed on openBIS databases \\012-- which are not screening specific.\\012--------------------------------------------------------------------------------------\\012--------------------------------------------------------------------------------------\\012\\012CREATE OR REPLACE FUNCTION merge_words(text, text) RETURNS text AS $$\\012DECLARE\\012 BEGIN\\012 IF character_length($1) > 0 THEN\\012 RETURN $1 || ' ' || $2;\\012 ELSE\\012 RETURN $2;\\012 END IF;\\012 END;\\012$$ LANGUAGE plpgsql;\\012\\012CREATE AGGREGATE merge_words(text)\\012(\\012 SFUNC = merge_words,\\012 STYPE = text\\012);\\012\\012\\012CREATE OR REPLACE FUNCTION REPLACE_GENE_SYMBOL_BY_GENE_ID() RETURNS void AS $$\\012DECLARE\\012\\011counter int;\\012\\011library_id_assigned_to_gene bool;\\012BEGIN\\012\\011--------------------------------------------------\\012\\011-- create a GENE_SYMBOL property and assign it to GENE\\012\\011--------------------------------------------------\\012\\011\\012\\011select true \\012\\011into library_id_assigned_to_gene \\012\\011from material_type_property_types mtpt, material_types mt, property_types pt \\012\\011where mtpt.maty_id = mt.id and mtpt.prty_id = pt.id \\012\\011\\011and mt.code = 'GENE' and pt.code = 'LIBRARY_ID';\\012\\011\\012\\011if library_id_assigned_to_gene IS NULL then \\012\\011\\011-- skip migration if gene has no library_id property\\012\\011\\011return;\\012\\011end if; \\012\\011\\012\\011\\012\\011select count(*)\\012\\011into counter \\012\\011from \\012\\011\\011(select m.id, count(mp.id) as c \\012\\011\\011\\011from materials m, material_types mt, material_properties mp, material_type_property_types mtpt, property_types pt \\012\\011\\011\\011where m.maty_id = mt.id and mp.mate_id = m.id and mp.mtpt_id = mtpt.id and mtpt.maty_id = mt.id and pt.id = mtpt.prty_id\\012\\011\\011\\011\\011and mt.code = 'GENE' and pt.code = 'LIBRARY_ID' \\012\\011\\011\\011group by m.id) as counter_table \\012\\011where c < 1; \\012\\011\\012\\011if counter > 0 then \\012\\011\\011-- skip migration if there is at least one gene without library_id\\012\\011\\011return;\\012\\011end if;\\012\\011\\012\\011\\012\\011insert into property_types\\012\\011\\011(id\\012\\011\\011,code\\012\\011\\011,description\\012\\011\\011,label\\012\\011\\011,daty_id\\012\\011\\011,pers_id_registerer\\012\\011\\011,dbin_id)\\012\\011values \\012\\011\\011(nextval('PROPERTY_TYPE_ID_SEQ')\\012\\011\\011,'GENE_SYMBOLS'\\012\\011\\011,'Gene symbols'\\012\\011\\011,'Gene symbols'\\012\\011\\011,(select id from data_types where code ='VARCHAR')\\012\\011\\011,(select id from persons where user_id ='system')\\012\\011\\011,(select id from database_instances where is_original_source = 'T')\\012\\011);\\012\\011\\011\\012\\011insert into material_type_property_types( \\012\\011 id,\\012\\011 maty_id,\\012\\011 prty_id,\\012\\011 is_mandatory,\\012\\011 pers_id_registerer,\\012\\011 ordinal\\012\\011) values(\\012\\011\\011\\011nextval('mtpt_id_seq'), \\012\\011\\011\\011(select id from material_types where code = 'GENE'),\\012\\011\\011\\011(select id from property_types where code = 'GENE_SYMBOLS'),\\012\\011\\011\\011false,\\012\\011\\011\\011(select id from persons where user_id ='system'),\\012\\011\\011\\011(select max(ordinal)+1 from material_type_property_types \\012\\011\\011\\011\\011where maty_id = (select id from material_types where code = 'GENE'))\\012\\011\\011);\\012\\012\\011--------------------------------------------------\\012\\011-- create temporary table with all gene migration information\\012\\011--------------------------------------------------\\012\\012\\011create temp table genes \\012\\011(\\012\\011\\011id tech_id,\\012\\011\\011code code,\\012\\011\\011library_id generic_value,\\012\\011\\011gene_codes generic_value,\\012\\011\\011new_id tech_id,\\012\\011\\011library_tech_id tech_id\\011\\011\\012\\011);\\012\\011\\012\\011insert into genes (id, code, library_id, library_tech_id)\\012\\011\\011(select m.id, m.code, mp.value as library_id, mp.id as library_tech_id from materials m, material_properties mp, material_type_property_types mtpt, property_types pt, material_types mt\\012\\011\\011where mp.mate_id = m.id and mp.mtpt_id = mtpt.id and pt.id = mtpt.prty_id and pt.code = 'LIBRARY_ID' and mt.id = m.maty_id and mt.id = mtpt.maty_id and mt.code = 'GENE');\\012\\011\\012\\011update genes set new_id = map.to_id from (select g_from.id as from_id, min(g_to.id) as to_id from genes g_from, genes g_to where g_from.library_id = g_to.library_id group by g_from.id) as map where map.from_id = id;\\011\\012\\011\\012\\011update genes set gene_codes = map.gene_codes from (select g_from.library_id as lib_id, merge_words(distinct g_to.code) as gene_codes from genes g_from, genes g_to where g_from.library_id = g_to.library_id group by g_from.library_id) as map where map.lib_id = library_id;\\011\\012\\012\\011--------------------------------------------------\\012\\011-- update gene references\\012\\011--------------------------------------------------\\012\\012\\011update EXPERIMENTS set MATE_ID_STUDY_OBJECT = genes.new_id from genes where genes.id = MATE_ID_STUDY_OBJECT and not genes.id = genes.new_id;\\012\\011update EXPERIMENT_PROPERTIES set MATE_PROP_ID = genes.new_id from genes where genes.id = MATE_PROP_ID and not genes.id = genes.new_id;\\012\\011update MATERIAL_PROPERTIES set MATE_PROP_ID = genes.new_id from genes where genes.id = MATE_PROP_ID and not genes.id = genes.new_id;\\012\\011update SAMPLE_PROPERTIES set MATE_PROP_ID = genes.new_id from genes where genes.id = MATE_PROP_ID and not genes.id = genes.new_id;\\012\\011update DATA_SET_PROPERTIES set MATE_PROP_ID = genes.new_id from genes where genes.id = MATE_PROP_ID and not genes.id = genes.new_id;\\012\\011\\012\\011delete from material_properties where mate_id in (select id from genes where not genes.id = genes.new_id);\\012\\011delete from MATERIALS where id in (select id from genes where not genes.id = genes.new_id);\\012\\012\\011delete from genes where id in (select id from genes where not genes.id = genes.new_id);\\012\\012\\012\\011--------------------------------------------------\\012\\011-- replace gene code with library_id\\012\\011--------------------------------------------------\\012\\011\\012\\011update materials set code = genes.library_id from genes where materials.id = genes.id ;\\012\\011delete from material_properties where id in (select library_tech_id from genes);\\012\\011\\012\\011--------------------------------------------------\\012\\011-- create a gene symbols property for each gene\\012\\011--------------------------------------------------\\012\\011\\012\\011insert into material_properties\\012\\011\\011(id\\012\\011 , mate_id\\012\\011 , mtpt_id\\012\\011 , "value"\\012\\011 , pers_id_registerer)\\012\\011\\011(select nextval('material_property_id_seq') id\\012\\011 \\011, genes.id mate_id\\012\\011 , (select mtpt.id\\012\\011 \\011\\011from material_type_property_types mtpt, material_types mt, property_types pt\\012\\011 \\011\\011where pt.code = 'GENE_SYMBOLS' and mt.code = 'GENE' and mtpt.prty_id = pt.id\\012\\011 \\011and mtpt.maty_id = mt.id) mtpt_id\\012\\011 , genes.gene_codes "value"\\012\\011 , (select id from persons where user_id = 'system') pers_id_registerer\\012\\011 \\011from genes); \\012\\012\\011--------------------------------------------------\\012\\011-- delete temporary table\\012\\011--------------------------------------------------\\012\\011\\012\\011drop table genes;\\012\\011\\012\\011delete from material_type_property_types where id = \\012\\011\\011(select mtpt.id from material_type_property_types mtpt, material_types mt, property_types pt \\012\\011\\011\\011where pt.id = mtpt.prty_id and mtpt.maty_id = mt.id \\012\\011\\011\\011and pt.code = 'LIBRARY_ID' and mt.code = 'GENE');\\012\\011\\012END;\\012$$ LANGUAGE 'plpgsql';\\012\\012select REPLACE_GENE_SYMBOL_BY_GENE_ID();\\012drop function REPLACE_GENE_SYMBOL_BY_GENE_ID();\\012DROP AGGREGATE merge_words(text);\\012drop function merge_words(text,text);\\012\\012\\012--------------------------------------------------------------------------------------\\012--------------------------------------------------------------------------------------\\012\\012UPDATE sample_types SET code = 'SIRNA_WELL' WHERE code = 'OLIGO_WELL';\\012UPDATE material_types SET code = 'SIRNA' WHERE code = 'OLIGO';\\012UPDATE property_types SET code = 'SIRNA', label = 'siRNA' WHERE code = 'OLIGO';\\012\\012\\012\\012\\012\\012\\012\\012\\012\\012\\012\\012\\012\\012\\012\\012\\012\\012\\012\\012 \N
-057 ./sql/postgresql/migration/migration-056-057.sql SUCCESS 2010-10-29 13:39:25.755 -- Migration from 056 to 057\\012\\012-- Introduction of a new data type - XML.\\012\\012INSERT INTO data_types (id, code, description) VALUES (nextval('data_type_id_seq'), 'XML', 'XML document');\\012\\012-- Property types of XML data type can optionally hold XMLSchema and XSLT. \\012\\012CREATE DOMAIN text_value AS text;\\012\\012ALTER TABLE property_types ADD COLUMN schema text_value;\\012ALTER TABLE property_types ADD COLUMN transformation text_value;\\012\\012-- Remove length restriction for property values - change domain from generic_value to text_value.\\012ALTER TABLE data_set_properties ALTER COLUMN value TYPE text_value;\\012ALTER TABLE experiment_properties ALTER COLUMN value TYPE text_value;\\012ALTER TABLE material_properties ALTER COLUMN value TYPE text_value;\\012ALTER TABLE sample_properties ALTER COLUMN value TYPE text_value;\\012DROP DOMAIN generic_value;\\012 \N
-058 ./sql/postgresql/migration/migration-057-058.sql SUCCESS 2010-10-29 13:39:25.775 -- Migration from 057 to 058\\012\\012ALTER TABLE DATA ADD COLUMN PERS_ID_REGISTERER TECH_ID;\\012ALTER TABLE DATA ADD CONSTRAINT DATA_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012 \N
-059 ./sql/postgresql/migration/migration-058-059.sql SUCCESS 2010-10-29 13:39:25.812 -- Migration from 058 to 059\\012\\012-- Add ENTITY_TYPE_CODE column to QUERIES\\012ALTER TABLE queries ADD COLUMN entity_type_code CODE;\\012\\012------------------------------------------------------------------------------------\\012-- Purpose: Create trigger that checks if entity_type_code specified in a query\\012-- matches a code of an entity of type specified in query_type.\\012------------------------------------------------------------------------------------\\012\\012CREATE OR REPLACE FUNCTION query_entity_type_code_check() RETURNS trigger AS $$\\012DECLARE\\012 counter INTEGER;\\012BEGIN\\012 if (NEW.entity_type_code IS NOT NULL) then\\012 if (NEW.query_type = 'GENERIC') then\\012 RAISE EXCEPTION 'Insert/Update of Query (Name: %) failed because entity_type has to be null for GENERIC queries.', NEW.name;\\012 elsif (NEW.query_type = 'EXPERIMENT') then\\012 SELECT count(*) INTO counter FROM experiment_types WHERE code = NEW.entity_type_code;\\012\\011\\011 elsif (NEW.query_type = 'DATA_SET') then\\012 SELECT count(*) INTO counter FROM data_set_types WHERE code = NEW.entity_type_code;\\012\\011\\011 elsif (NEW.query_type = 'MATERIAL') then\\012 SELECT count(*) INTO counter FROM material_types WHERE code = NEW.entity_type_code;\\012\\011\\011 elsif (NEW.query_type = 'SAMPLE') then\\012 SELECT count(*) INTO counter FROM sample_types WHERE code = NEW.entity_type_code;\\012\\011\\011 end if;\\012\\011\\011 if (counter = 0) then\\012\\011\\011\\011 RAISE EXCEPTION 'Insert/Update of Query (Name: %) failed because % Type (Code: %) does not exist.', NEW.name, NEW.query_type, NEW.entity_type_code;\\012\\011\\011 end if;\\011\\011\\011\\012 end if;\\012 RETURN NEW;\\012END;\\012$$ LANGUAGE 'plpgsql';\\012\\012CREATE TRIGGER query_entity_type_code_check BEFORE INSERT OR UPDATE ON queries\\012 FOR EACH ROW EXECUTE PROCEDURE query_entity_type_code_check();\\012 \\012------------------------------------------------------------------------------------\\012-- Add a new domain to capture the allowed values for ReportingPluginType\\012-- Store the ReportingPluginType on the DATA_STORE_SERVICES table\\012------------------------------------------------------------------------------------\\012CREATE DOMAIN DATA_STORE_SERVICE_REPORTING_PLUGIN_TYPE AS VARCHAR(40) CHECK (VALUE IN ('TABLE_MODEL', 'DSS_LINK'));\\012ALTER TABLE DATA_STORE_SERVICES ADD COLUMN REPORTING_PLUGIN_TYPE DATA_STORE_SERVICE_REPORTING_PLUGIN_TYPE;\\012\\012------------------------------------------------------------------------------------\\012-- Put the sequences query_id_seq and grid_custom_columns in use\\012-- (by mistake, filter_id_seq had been used for queries and grid custom columns)\\012------------------------------------------------------------------------------------\\012SELECT setval('query_id_seq', nextval('filter_id_seq'));\\012SELECT setval('grid_custom_columns_id_seq', currval('filter_id_seq'));\\012 \N
-060 ./sql/postgresql/migration/migration-059-060.sql SUCCESS 2010-10-29 13:39:26.04 -- Migration from 059 to 060\\012\\012------------------------------------------------------------------------------------\\012-- Drop trigger on queries.entity_type_code column to enable storing a regexp there.\\012------------------------------------------------------------------------------------\\012\\012DROP TRIGGER query_entity_type_code_check ON queries;\\012DROP FUNCTION query_entity_type_code_check();\\012\\012------------------------------------------------------------------------------------\\012-- Dynamic properties\\012------------------------------------------------------------------------------------\\012\\012-- Create SCRIPTS table\\012\\012CREATE TABLE SCRIPTS (ID TECH_ID NOT NULL,DBIN_ID TECH_ID NOT NULL,NAME VARCHAR(200) NOT NULL,DESCRIPTION DESCRIPTION_2000,SCRIPT TEXT_VALUE NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP,PERS_ID_REGISTERER TECH_ID NOT NULL);\\012CREATE SEQUENCE SCRIPT_ID_SEQ;\\012ALTER TABLE SCRIPTS ADD CONSTRAINT SCRI_PK PRIMARY KEY(ID);\\012ALTER TABLE SCRIPTS ADD CONSTRAINT SCRI_UK UNIQUE(NAME,DBIN_ID);\\012ALTER TABLE SCRIPTS ADD CONSTRAINT SCRI_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012ALTER TABLE SCRIPTS ADD CONSTRAINT SCRI_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012CREATE INDEX SCRIPT_PERS_FK_I ON SCRIPTS (PERS_ID_REGISTERER);\\012CREATE INDEX SCRIPT_DBIN_FK_I ON SCRIPTS (DBIN_ID);\\012\\012-- Add IS_DYNAMIC column to *_PROPERTY_TYPES tables \\012\\012ALTER TABLE MATERIAL_TYPE_PROPERTY_TYPES ADD COLUMN IS_DYNAMIC BOOLEAN NOT NULL DEFAULT FALSE;\\012ALTER TABLE SAMPLE_TYPE_PROPERTY_TYPES ADD COLUMN IS_DYNAMIC BOOLEAN NOT NULL DEFAULT FALSE;\\012ALTER TABLE EXPERIMENT_TYPE_PROPERTY_TYPES ADD COLUMN IS_DYNAMIC BOOLEAN NOT NULL DEFAULT FALSE;\\012ALTER TABLE DATA_SET_TYPE_PROPERTY_TYPES ADD COLUMN IS_DYNAMIC BOOLEAN NOT NULL DEFAULT FALSE;\\012\\012-- Add SCRIPT_ID column to *_PROPERTY_TYPES tables \\012\\012ALTER TABLE MATERIAL_TYPE_PROPERTY_TYPES ADD COLUMN SCRIPT_ID TECH_ID;\\012ALTER TABLE SAMPLE_TYPE_PROPERTY_TYPES ADD COLUMN SCRIPT_ID TECH_ID;\\012ALTER TABLE EXPERIMENT_TYPE_PROPERTY_TYPES ADD COLUMN SCRIPT_ID TECH_ID;\\012ALTER TABLE DATA_SET_TYPE_PROPERTY_TYPES ADD COLUMN SCRIPT_ID TECH_ID;\\012\\012-- Make SCRIPT_ID reference SCRIPTS\\012\\012ALTER TABLE MATERIAL_TYPE_PROPERTY_TYPES ADD CONSTRAINT MTPT_SCRIPT_FK FOREIGN KEY (SCRIPT_ID) REFERENCES SCRIPTS(ID);\\012ALTER TABLE SAMPLE_TYPE_PROPERTY_TYPES ADD CONSTRAINT STPT_SCRIPT_FK FOREIGN KEY (SCRIPT_ID) REFERENCES SCRIPTS(ID);\\012ALTER TABLE EXPERIMENT_TYPE_PROPERTY_TYPES ADD CONSTRAINT ETPT_SCRIPT_FK FOREIGN KEY (SCRIPT_ID) REFERENCES SCRIPTS(ID);\\012ALTER TABLE DATA_SET_TYPE_PROPERTY_TYPES ADD CONSTRAINT DSTPT_SCRIPT_FK FOREIGN KEY (SCRIPT_ID) REFERENCES SCRIPTS(ID);\\012\\012-- Check SCRIPT_ID is filled when IS_DYNAMIC is TRUE\\012\\012ALTER TABLE MATERIAL_TYPE_PROPERTY_TYPES ADD CONSTRAINT MTPT_CK CHECK ((IS_DYNAMIC IS TRUE AND SCRIPT_ID IS NOT NULL) OR (IS_DYNAMIC IS FALSE AND SCRIPT_ID IS NULL));\\012ALTER TABLE SAMPLE_TYPE_PROPERTY_TYPES ADD CONSTRAINT STPT_CK CHECK ((IS_DYNAMIC IS TRUE AND SCRIPT_ID IS NOT NULL) OR (IS_DYNAMIC IS FALSE AND SCRIPT_ID IS NULL));\\012ALTER TABLE EXPERIMENT_TYPE_PROPERTY_TYPES ADD CONSTRAINT ETPT_CK CHECK ((IS_DYNAMIC IS TRUE AND SCRIPT_ID IS NOT NULL) OR (IS_DYNAMIC IS FALSE AND SCRIPT_ID IS NULL));\\012ALTER TABLE DATA_SET_TYPE_PROPERTY_TYPES ADD CONSTRAINT DSTPT_CK CHECK ((IS_DYNAMIC IS TRUE AND SCRIPT_ID IS NOT NULL) OR (IS_DYNAMIC IS FALSE AND SCRIPT_ID IS NULL));\\012\\012 \N
-\.
-
+insert into data_set_types(
+ id,
+ code, description,
+ dbin_id)
+values(
+ nextval('data_set_type_id_seq'),
+ 'UNKNOWN',
+ 'Unknown',
+ (select id from database_instances where is_original_source = 'T')
+ );
+
+insert into data_set_types(
+ id,
+ code, description,
+ dbin_id)
+values(
+ nextval('data_set_type_id_seq'),
+ 'HCS_IMAGE_RAW',
+ 'Raw High Content Screening Images',
+ (select id from database_instances where is_original_source = 'T')
+ );
+
+insert into data_set_types(
+ id,
+ code, description,
+ dbin_id)
+values(
+ nextval('data_set_type_id_seq'),
+ 'HCS_IMAGE_OVERVIEW',
+ 'Overview High Content Screening Images. Generated from raw images.',
+ (select id from database_instances where is_original_source = 'T')
+ );
+
+insert into data_set_types(
+ id,
+ code, description,
+ dbin_id)
+values(
+ nextval('data_set_type_id_seq'),
+ 'HCS_IMAGE_SEGMENTATION',
+ 'HCS Segmentation Images (overlays).',
+ (select id from database_instances where is_original_source = 'T')
+ );
+
+insert into data_set_types(
+ id,
+ code, description,
+ dbin_id)
+values(
+ nextval('data_set_type_id_seq'),
+ 'HCS_ANALYSIS_WELL_FEATURES',
+ 'HCS image analysis well feature vectors.',
+ (select id from database_instances where is_original_source = 'T')
+ );
+
+insert into data_set_types(
+ id,
+ code, description,
+ dbin_id)
+values(
+ nextval('data_set_type_id_seq'),
+ 'HCS_ANALYSIS_CELL_SEGMENTATION',
+ 'HCS image analysis cell segmentation',
+ (select id from database_instances where is_original_source = 'T')
+ );
+
+insert into data_set_types(
+ id,
+ code, description,
+ dbin_id)
+values(
+ nextval('data_set_type_id_seq'),
+ 'HCS_ANALYSIS_CELL_FEATURES',
+ 'HCS image analysis cell feature vectors',
+ (select id from database_instances where is_original_source = 'T')
+ );
+
+insert into data_set_types(
+ id,
+ code, description,
+ dbin_id)
+values(
+ nextval('data_set_type_id_seq'),
+ 'HCS_ANALYSIS_CELL_CLASS',
+ 'HCS image analysis cell classification',
+ (select id from database_instances where is_original_source = 'T')
+ );
--
--- Data for Name: events; Type: TABLE DATA; Schema: public; Owner: -
+-- Data for Name: database_version_logs; Type: TABLE DATA; Schema: public; Owner: -
--
-COPY events (id, event_type, description, reason, pers_id_registerer, registration_timestamp, entity_type, identifier) FROM stdin;
-1590 DELETION DEMO:/TEST/A [20100511094535163-3] x 3 2010-05-11 09:47:47.333773+02 SAMPLE 20100511094535163-3
+COPY database_version_logs (db_version, module_name, run_status, run_status_timestamp, module_code, run_exception) FROM stdin;
+060 ./sql/postgresql/migration/migration-059-060.sql SUCCESS 2010-10-29 13:39:26.04 -- Migration from 059 to 060\\012\\012------------------------------------------------------------------------------------\\012-- Drop trigger on queries.entity_type_code column to enable storing a regexp there.\\012------------------------------------------------------------------------------------\\012\\012DROP TRIGGER query_entity_type_code_check ON queries;\\012DROP FUNCTION query_entity_type_code_check();\\012\\012------------------------------------------------------------------------------------\\012-- Dynamic properties\\012------------------------------------------------------------------------------------\\012\\012-- Create SCRIPTS table\\012\\012CREATE TABLE SCRIPTS (ID TECH_ID NOT NULL,DBIN_ID TECH_ID NOT NULL,NAME VARCHAR(200) NOT NULL,DESCRIPTION DESCRIPTION_2000,SCRIPT TEXT_VALUE NOT NULL,REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP,PERS_ID_REGISTERER TECH_ID NOT NULL);\\012CREATE SEQUENCE SCRIPT_ID_SEQ;\\012ALTER TABLE SCRIPTS ADD CONSTRAINT SCRI_PK PRIMARY KEY(ID);\\012ALTER TABLE SCRIPTS ADD CONSTRAINT SCRI_UK UNIQUE(NAME,DBIN_ID);\\012ALTER TABLE SCRIPTS ADD CONSTRAINT SCRI_DBIN_FK FOREIGN KEY (DBIN_ID) REFERENCES DATABASE_INSTANCES(ID);\\012ALTER TABLE SCRIPTS ADD CONSTRAINT SCRI_PERS_FK FOREIGN KEY (PERS_ID_REGISTERER) REFERENCES PERSONS(ID);\\012CREATE INDEX SCRIPT_PERS_FK_I ON SCRIPTS (PERS_ID_REGISTERER);\\012CREATE INDEX SCRIPT_DBIN_FK_I ON SCRIPTS (DBIN_ID);\\012\\012-- Add IS_DYNAMIC column to *_PROPERTY_TYPES tables \\012\\012ALTER TABLE MATERIAL_TYPE_PROPERTY_TYPES ADD COLUMN IS_DYNAMIC BOOLEAN NOT NULL DEFAULT FALSE;\\012ALTER TABLE SAMPLE_TYPE_PROPERTY_TYPES ADD COLUMN IS_DYNAMIC BOOLEAN NOT NULL DEFAULT FALSE;\\012ALTER TABLE EXPERIMENT_TYPE_PROPERTY_TYPES ADD COLUMN IS_DYNAMIC BOOLEAN NOT NULL DEFAULT FALSE;\\012ALTER TABLE DATA_SET_TYPE_PROPERTY_TYPES ADD COLUMN IS_DYNAMIC BOOLEAN NOT NULL DEFAULT FALSE;\\012\\012-- Add SCRIPT_ID column to *_PROPERTY_TYPES tables \\012\\012ALTER TABLE MATERIAL_TYPE_PROPERTY_TYPES ADD COLUMN SCRIPT_ID TECH_ID;\\012ALTER TABLE SAMPLE_TYPE_PROPERTY_TYPES ADD COLUMN SCRIPT_ID TECH_ID;\\012ALTER TABLE EXPERIMENT_TYPE_PROPERTY_TYPES ADD COLUMN SCRIPT_ID TECH_ID;\\012ALTER TABLE DATA_SET_TYPE_PROPERTY_TYPES ADD COLUMN SCRIPT_ID TECH_ID;\\012\\012-- Make SCRIPT_ID reference SCRIPTS\\012\\012ALTER TABLE MATERIAL_TYPE_PROPERTY_TYPES ADD CONSTRAINT MTPT_SCRIPT_FK FOREIGN KEY (SCRIPT_ID) REFERENCES SCRIPTS(ID);\\012ALTER TABLE SAMPLE_TYPE_PROPERTY_TYPES ADD CONSTRAINT STPT_SCRIPT_FK FOREIGN KEY (SCRIPT_ID) REFERENCES SCRIPTS(ID);\\012ALTER TABLE EXPERIMENT_TYPE_PROPERTY_TYPES ADD CONSTRAINT ETPT_SCRIPT_FK FOREIGN KEY (SCRIPT_ID) REFERENCES SCRIPTS(ID);\\012ALTER TABLE DATA_SET_TYPE_PROPERTY_TYPES ADD CONSTRAINT DSTPT_SCRIPT_FK FOREIGN KEY (SCRIPT_ID) REFERENCES SCRIPTS(ID);\\012\\012-- Check SCRIPT_ID is filled when IS_DYNAMIC is TRUE\\012\\012ALTER TABLE MATERIAL_TYPE_PROPERTY_TYPES ADD CONSTRAINT MTPT_CK CHECK ((IS_DYNAMIC IS TRUE AND SCRIPT_ID IS NOT NULL) OR (IS_DYNAMIC IS FALSE AND SCRIPT_ID IS NULL));\\012ALTER TABLE SAMPLE_TYPE_PROPERTY_TYPES ADD CONSTRAINT STPT_CK CHECK ((IS_DYNAMIC IS TRUE AND SCRIPT_ID IS NOT NULL) OR (IS_DYNAMIC IS FALSE AND SCRIPT_ID IS NULL));\\012ALTER TABLE EXPERIMENT_TYPE_PROPERTY_TYPES ADD CONSTRAINT ETPT_CK CHECK ((IS_DYNAMIC IS TRUE AND SCRIPT_ID IS NOT NULL) OR (IS_DYNAMIC IS FALSE AND SCRIPT_ID IS NULL));\\012ALTER TABLE DATA_SET_TYPE_PROPERTY_TYPES ADD CONSTRAINT DSTPT_CK CHECK ((IS_DYNAMIC IS TRUE AND SCRIPT_ID IS NOT NULL) OR (IS_DYNAMIC IS FALSE AND SCRIPT_ID IS NULL));\\012\\012 \N
\.
@@ -2260,14 +2231,6 @@ COPY experiments (id, perm_id, code, exty_id, mate_id_study_object, pers_id_regi
\.
---
--- Data for Name: external_data; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY external_data (data_id, location, ffty_id, loty_id, cvte_id_stor_fmt, is_complete, cvte_id_store, status) FROM stdin;
-\.
-
-
--
-- Data for Name: file_format_types; Type: TABLE DATA; Schema: public; Owner: -
--
@@ -2296,14 +2259,6 @@ COPY filters (id, dbin_id, name, description, registration_timestamp, pers_id_re
\.
---
--- Data for Name: grid_custom_columns; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY grid_custom_columns (id, dbin_id, code, label, description, registration_timestamp, pers_id_registerer, modification_timestamp, expression, is_public, grid_id) FROM stdin;
-\.
-
-
--
-- Data for Name: groups; Type: TABLE DATA; Schema: public; Owner: -
--
@@ -2313,14 +2268,6 @@ COPY groups (id, code, dbin_id, description, registration_timestamp, pers_id_reg
\.
---
--- Data for Name: invalidations; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY invalidations (id, pers_id_registerer, registration_timestamp, reason) FROM stdin;
-\.
-
-
--
-- Data for Name: locator_types; Type: TABLE DATA; Schema: public; Owner: -
--
@@ -2330,14 +2277,6 @@ COPY locator_types (id, code, description) FROM stdin;
\.
---
--- Data for Name: material_properties; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY material_properties (id, mate_id, mtpt_id, value, registration_timestamp, modification_timestamp, pers_id_registerer, cvte_id, mate_prop_id) FROM stdin;
-\.
-
-
--
-- Data for Name: material_type_property_types; Type: TABLE DATA; Schema: public; Owner: -
--
@@ -2371,14 +2310,6 @@ COPY material_types (id, code, description, dbin_id, modification_timestamp) FRO
\.
---
--- Data for Name: materials; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY materials (id, code, maty_id, pers_id_registerer, registration_timestamp, modification_timestamp, dbin_id) FROM stdin;
-\.
-
-
--
-- Data for Name: persons; Type: TABLE DATA; Schema: public; Owner: -
--
@@ -2419,14 +2350,6 @@ COPY property_types (id, code, description, label, daty_id, registration_timesta
\.
---
--- Data for Name: queries; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY queries (id, dbin_id, name, description, registration_timestamp, pers_id_registerer, modification_timestamp, expression, is_public, query_type, db_key, entity_type_code) FROM stdin;
-\.
-
-
--
-- Data for Name: relationship_types; Type: TABLE DATA; Schema: public; Owner: -
--
@@ -2446,23 +2369,6 @@ COPY role_assignments (id, role_code, grou_id, dbin_id, pers_id_grantee, ag_id_g
1 ADMIN \N 1 3 \N 1 2010-05-10 17:57:26.252547+02
\.
-
---
--- Data for Name: sample_properties; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY sample_properties (id, samp_id, stpt_id, value, cvte_id, mate_prop_id, pers_id_registerer, registration_timestamp, modification_timestamp) FROM stdin;
-\.
-
-
---
--- Data for Name: sample_relationships; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY sample_relationships (id, sample_id_parent, relationship_id, sample_id_child) FROM stdin;
-\.
-
-
--
-- Data for Name: sample_type_property_types; Type: TABLE DATA; Schema: public; Owner: -
--
@@ -2487,22 +2393,6 @@ COPY sample_types (id, code, description, dbin_id, is_listable, generated_from_d
\.
---
--- Data for Name: samples; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY samples (id, perm_id, code, expe_id, saty_id, registration_timestamp, modification_timestamp, pers_id_registerer, inva_id, dbin_id, grou_id, samp_id_part_of) FROM stdin;
-\.
-
-
---
--- Data for Name: scripts; Type: TABLE DATA; Schema: public; Owner: -
---
-
-COPY scripts (id, dbin_id, name, description, script, registration_timestamp, pers_id_registerer) FROM stdin;
-\.
-
-
--
-- Name: ag_bk_uk; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
--
diff --git a/screening/dist/etc/service.properties b/screening/dist/etc/service.properties
index 38db9f1686d..155796734de 100644
--- a/screening/dist/etc/service.properties
+++ b/screening/dist/etc/service.properties
@@ -107,12 +107,12 @@ imaging-db.adminPassword =
reporting-plugins = default-plate-image-analysis, plate-image-analysis-graph
default-plate-image-analysis.label = Image Analysis Results
-default-plate-image-analysis.dataset-types = HCS_IMAGE_ANALYSIS_DATA, HCS_ANALYSIS_PER_GENE
+default-plate-image-analysis.dataset-types = HCS_ANALYSIS_WELL_FEATURES
default-plate-image-analysis.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.ImageAnalysisMergedRowsReportingPlugin
default-plate-image-analysis.properties-file =
plate-image-analysis-graph.label = Image Analysis Graphs
-plate-image-analysis-graph.dataset-types = HCS_IMAGE_ANALYSIS_DATA, HCS_ANALYSIS_PER_GENE
+plate-image-analysis-graph.dataset-types = HCS_ANALYSIS_WELL_FEATURES
plate-image-analysis-graph.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.ImageAnalysisGraphReportingPlugin
plate-image-analysis-graph.servlet-path = datastore_server_graph/
plate-image-analysis-graph.properties-file = etc/tabular-data-graph.properties
@@ -210,7 +210,7 @@ merged-channels-images.data-set-info-extractor.space-code = ${import-space-code}
merged-channels-images.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
merged-channels-images.type-extractor.file-format-type = JPG
merged-channels-images.type-extractor.locator-type = RELATIVE_LOCATION
-merged-channels-images.type-extractor.data-set-type = HCS_IMAGE
+merged-channels-images.type-extractor.data-set-type = HCS_IMAGE_OVERVIEW
merged-channels-images.type-extractor.is-measured = true
# Note: this storage processor is able to process folders compressed with zip as well
@@ -274,7 +274,7 @@ split-channels-images.data-set-info-extractor.space-code = ${import-space-code}
split-channels-images.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
split-channels-images.type-extractor.file-format-type = JPG
split-channels-images.type-extractor.locator-type = RELATIVE_LOCATION
-split-channels-images.type-extractor.data-set-type = HCS_IMAGE
+split-channels-images.type-extractor.data-set-type = HCS_IMAGE_OVERVIEW
split-channels-images.type-extractor.is-measured = true
split-channels-images.storage-processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor
@@ -304,7 +304,7 @@ image-analysis-results.data-set-info-extractor.space-code = ${import-space-code}
image-analysis-results.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
image-analysis-results.type-extractor.file-format-type = CSV
image-analysis-results.type-extractor.locator-type = RELATIVE_LOCATION
-image-analysis-results.type-extractor.data-set-type = HCS_IMAGE_ANALYSIS_DATA
+image-analysis-results.type-extractor.data-set-type = HCS_ANALYSIS_WELL_FEATURES
image-analysis-results.type-extractor.is-measured = false
# The storage processor (IStorageProcessor implementation)
diff --git a/screening/dist/server/web-client.properties b/screening/dist/server/web-client.properties
index fa2a0d8e22e..8f1e6e035a6 100644
--- a/screening/dist/server/web-client.properties
+++ b/screening/dist/server/web-client.properties
@@ -57,23 +57,23 @@ detail-views = plate-or-well-view, image-data-view, image-analysis-data-view, mi
#experiment-view.hide-sections = data-sets-section, attachment-section
plate-or-well-view.view = generic_sample_viewer
-plate-or-well-view.types = PLATE, SIRNA_WELL, CONTROL_WELL
+plate-or-well-view.types = PLATE.*, .*WELL.*
plate-or-well-view.hide-sections = container-sample-section, derived-samples-section, parent-samples-section
image-data-view.view = generic_dataset_viewer
-image-data-view.types = HCS_IMAGE
+image-data-view.types = HCS_IMAGE.*
image-data-view.hide-sections = data-set-parents-section, data-set-children-section, plate-layout-dataset-section
image-data-view.hide-smart-view = false
image-data-view.hide-file-view = true
image-analysis-data-view.view = generic_dataset_viewer
-image-analysis-data-view.types = HCS_IMAGE_ANALYSIS_DATA
+image-analysis-data-view.types = HCS_ANALYSIS_WELL_FEATURES.*
image-analysis-data-view.hide-sections = data-set-parents-section, data-set-children-section
image-analysis-data-view.hide-smart-view = true
image-analysis-data-view.hide-file-view = true
microscopy-dataset-view.view = generic_dataset_viewer
-microscopy-dataset-view.types = MICROSCOPY_IMAGE
+microscopy-dataset-view.types = MICROSCOPY_IMAGE, .*IMG.*
microscopy-dataset-view.hide-sections = data-set-children-section, data-set-parents-section
microscopy-dataset-view.hide-smart-view = false
microscopy-dataset-view.hide-file-view = true
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
index 6494c911cb0..f6458265b55 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
@@ -1003,7 +1003,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
private boolean isImageDataset(ExternalData dataset)
{
String datasetTypeCode = dataset.getDataSetType().getCode();
- return datasetTypeCode.matches(ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PATTERN)
+ return datasetTypeCode.matches(ScreeningConstants.ANY_HCS_IMAGE_DATASET_TYPE_PATTERN)
|| datasetTypeCode
.matches(ScreeningConstants.MICROSCOPY_IMAGE_DATASET_TYPE_PATTERN);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ClientPluginFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ClientPluginFactory.java
index d8d1fae2996..a2973390af2 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ClientPluginFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ClientPluginFactory.java
@@ -107,7 +107,7 @@ public final class ClientPluginFactory extends AbstractClientPluginFactory<Scree
types.add(ScreeningConstants.CONTROL_WELL_SAMPLE_TYPE_PATTERN);
types.add(ScreeningConstants.NON_CONTROL_WELL_SAMPLE_TYPE_PATTERN);
// -- microscopy sample
- types.add(ScreeningConstants.IMAGE_SAMPLE_TYPE_PATTERN);
+ types.add(ScreeningConstants.MICROSCOPY_IMAGE_SAMPLE_TYPE_PATTERN);
} else if (entityKind == EntityKind.MATERIAL)
{
types.add(ScreeningConstants.GENE_PLUGIN_TYPE_CODE);
@@ -121,7 +121,7 @@ public final class ClientPluginFactory extends AbstractClientPluginFactory<Scree
} else if (entityKind == EntityKind.DATA_SET)
{
- types.add(ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PATTERN);
+ types.add(ScreeningConstants.ANY_HCS_IMAGE_DATASET_TYPE_PATTERN);
types.add(ScreeningConstants.MICROSCOPY_IMAGE_DATASET_TYPE_PATTERN);
}
return types;
@@ -246,7 +246,7 @@ public final class ClientPluginFactory extends AbstractClientPluginFactory<Scree
final IEntityInformationHolderWithPermId entity)
{
String datasetTypeCode = entity.getEntityType().getCode();
- if (datasetTypeCode.matches(ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PATTERN))
+ if (datasetTypeCode.matches(ScreeningConstants.ANY_HCS_IMAGE_DATASET_TYPE_PATTERN))
{
return createHCSImageDatasetTabItemFactory(entity);
} else if (datasetTypeCode
@@ -362,7 +362,7 @@ public final class ClientPluginFactory extends AbstractClientPluginFactory<Scree
{
throw new UserFailureException("Cannot browse objects of the "
+ ScreeningConstants.LIBRARY_PLUGIN_TYPE_CODE + " type.");
- } else if (sampleTypeCode.matches(ScreeningConstants.IMAGE_SAMPLE_TYPE_PATTERN))
+ } else if (sampleTypeCode.matches(ScreeningConstants.MICROSCOPY_IMAGE_SAMPLE_TYPE_PATTERN))
{
return createImageSampleViewer(entity, false);
} else
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java
index 622f24bbdd3..cc4381c9cfa 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java
@@ -36,7 +36,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConst
/**
* @author Chandrasekhar Ramakrishnan
*/
-class FeatureVectorDatasetLoader extends ImageDatasetLoader
+class FeatureVectorDatasetLoader extends HCSImageDatasetLoader
{
// TODO 2010-05-27, CR : See PlateDatasetLoader todo comment
@@ -51,7 +51,7 @@ class FeatureVectorDatasetLoader extends ImageDatasetLoader
Collection<? extends PlateIdentifier> plates)
{
super(session, businessObjectFactory, homeSpaceOrNull, plates,
- ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PATTERN,
+ ScreeningConstants.ANY_HCS_IMAGE_DATASET_TYPE_PATTERN,
ScreeningConstants.HCS_IMAGE_ANALYSIS_DATASET_TYPE_PATTERN);
featureVectorDatasetTypeCode = ScreeningConstants.HCS_IMAGE_ANALYSIS_DATASET_TYPE_PATTERN;
}
@@ -113,7 +113,7 @@ class FeatureVectorDatasetLoader extends ImageDatasetLoader
{
featureVectorDatasetSet.put(dataset.getId(), dataset);
} else if (ScreeningUtils.isTypeMatching(dataset,
- ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PATTERN))
+ ScreeningConstants.ANY_HCS_IMAGE_DATASET_TYPE_PATTERN))
{
imageDatasets.add(dataset);
}
@@ -236,7 +236,7 @@ class FeatureVectorDatasetLoader extends ImageDatasetLoader
return new FeatureVectorDatasetReference(externalData.getCode(),
getDataStoreUrlFromDataStore(dataStore), createPlateIdentifier(parentDataset),
createExperimentIdentifier(externalData), extractPlateGeometry(parentDataset),
- externalData.getRegistrationDate(), asImageDataset(parentDataset),
+ externalData.getRegistrationDate(), tryAsImageDataset(parentDataset),
extractProperties(externalData));
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoader.java
similarity index 89%
rename from screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoader.java
index 5dcd63527f0..98810053aa9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoader.java
@@ -29,21 +29,21 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifi
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
/**
- * Utility class for loading image datasets.
+ * Utility class for loading HCS image datasets.
*
* @author Chandrasekhar Ramakrishnan
*/
-class ImageDatasetLoader extends PlateDatasetLoader
+class HCSImageDatasetLoader extends PlateDatasetLoader
{
// TODO 2010-05-27, CR : See PlateDatasetLoader todo comment
- ImageDatasetLoader(Session session, IScreeningBusinessObjectFactory businessObjectFactory,
+ HCSImageDatasetLoader(Session session, IScreeningBusinessObjectFactory businessObjectFactory,
String homeSpaceOrNull, Collection<? extends PlateIdentifier> plates,
String... datasetTypeCodes)
{
super(session, businessObjectFactory, homeSpaceOrNull, plates,
(datasetTypeCodes.length == 0) ? new String[]
- { ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PATTERN } : datasetTypeCodes);
+ { ScreeningConstants.ANY_HCS_IMAGE_DATASET_TYPE_PATTERN } : datasetTypeCodes);
}
/**
@@ -141,7 +141,11 @@ class ImageDatasetLoader extends PlateDatasetLoader
List<ImageDatasetReference> references = new ArrayList<ImageDatasetReference>();
for (ExternalData imageDataset : imageDatasets)
{
- references.add(asImageDataset(imageDataset));
+ ImageDatasetReference reference = tryAsImageDataset(imageDataset);
+ if (reference != null)
+ {
+ references.add(reference);
+ }
}
return references;
}
@@ -157,7 +161,7 @@ class ImageDatasetLoader extends PlateDatasetLoader
}
}
- protected ImageDatasetReference asImageDataset(ExternalData externalData)
+ protected ImageDatasetReference tryAsImageDataset(ExternalData externalData)
{
if (externalData == null || ScreeningUtils.isHcsImageDataset(externalData) == false)
{
@@ -168,6 +172,6 @@ class ImageDatasetLoader extends PlateDatasetLoader
getDataStoreUrlFromDataStore(dataStore), createPlateIdentifier(externalData),
createExperimentIdentifier(externalData), extractPlateGeometry(externalData),
externalData.getRegistrationDate(), extractProperties(externalData),
- asImageDataset(tryGetParent(externalData)));
+ tryAsImageDataset(tryGetParent(externalData)));
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
index 9f68eaad7c8..6bb6e5a375d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
@@ -124,19 +124,19 @@ public class ScreeningApiImpl
public List<ImageDatasetReference> listImageDatasets(List<? extends PlateIdentifier> plates)
{
- return new ImageDatasetLoader(session, businessObjectFactory,
+ return new HCSImageDatasetLoader(session, businessObjectFactory,
session.tryGetHomeGroupCode(), plates).getImageDatasetReferences();
}
public List<ImageDatasetReference> listRawImageDatasets(List<? extends PlateIdentifier> plates)
{
- return new ImageDatasetLoader(session, businessObjectFactory,
+ return new HCSImageDatasetLoader(session, businessObjectFactory,
session.tryGetHomeGroupCode(), plates).getRawImageDatasetReferences();
}
public List<ImageDatasetReference> listSegmentationImageDatasets(List<? extends PlateIdentifier> plates)
{
- return new ImageDatasetLoader(session, businessObjectFactory,
+ return new HCSImageDatasetLoader(session, businessObjectFactory,
session.tryGetHomeGroupCode(), plates).getSegmentationImageDatasetReferences();
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningUtils.java
index a47b4f94216..9dbce47b5ed 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningUtils.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningUtils.java
@@ -72,8 +72,8 @@ public class ScreeningUtils
public static <T extends DataPE> List<T> filterImageOverlayDatasets(Collection<T> datasets)
{
return filterDatasetsByTypePattern(datasets,
- ScreeningConstants.IMAGE_OVERLAY_DATASET_TYPE_PATTERN,
- ScreeningConstants.HCS_SEGMENTATION_IMAGE_DATASET_TYPE_PATTERN);
+ ScreeningConstants.HCS_SEGMENTATION_IMAGE_DATASET_TYPE_PATTERN,
+ ScreeningConstants.MICROSCOPY_SEGMENTATION_IMAGE_DATASET_TYPE_PATTERN);
}
/** excludes overlay image data sets even when they match to the image dataset pattern */
@@ -81,13 +81,13 @@ public class ScreeningUtils
{
List<ExternalDataPE> allDatasets =
filterDatasetsByTypePattern(datasets,
- ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PATTERN,
- ScreeningConstants.MICROSCOPY_IMAGE_DATASET_TYPE_PATTERN);
+ ScreeningConstants.ANY_HCS_IMAGE_DATASET_TYPE_PATTERN,
+ ScreeningConstants.ANY_MICROSCOPY_IMAGE_DATASET_TYPE_PATTERN);
allDatasets =
excludeDatasetsByTypePattern(allDatasets,
- ScreeningConstants.IMAGE_OVERLAY_DATASET_TYPE_PATTERN,
- ScreeningConstants.HCS_SEGMENTATION_IMAGE_DATASET_TYPE_PATTERN);
+ ScreeningConstants.HCS_SEGMENTATION_IMAGE_DATASET_TYPE_PATTERN,
+ ScreeningConstants.MICROSCOPY_SEGMENTATION_IMAGE_DATASET_TYPE_PATTERN);
return allDatasets;
}
@@ -96,12 +96,8 @@ public class ScreeningUtils
{
return excludeDatasetsByTypePattern(datasets,
ScreeningConstants.HCS_IMAGE_ANALYSIS_DATASET_TYPE_PATTERN,
- ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PATTERN,
- ScreeningConstants.HCS_RAW_IMAGE_DATASET_TYPE_PATTERN,
- ScreeningConstants.HCS_RAW_IMAGE_LEGACY_DATASET_TYPE,
- ScreeningConstants.IMAGE_OVERLAY_DATASET_TYPE_PATTERN,
- ScreeningConstants.HCS_SEGMENTATION_IMAGE_DATASET_TYPE_PATTERN,
- ScreeningConstants.MICROSCOPY_IMAGE_DATASET_TYPE_PATTERN);
+ ScreeningConstants.ANY_HCS_IMAGE_DATASET_TYPE_PATTERN,
+ ScreeningConstants.ANY_MICROSCOPY_IMAGE_DATASET_TYPE_PATTERN);
}
private static <T extends DataPE> List<T> excludeDatasetsByTypePattern(List<T> datasets,
@@ -147,13 +143,14 @@ public class ScreeningUtils
return dataset.getDataSetType().getCode().matches(datasetTypeCodePattern);
}
+ /**
+ * true if a dataset contains HCS images. Such a dataset can be a parent of a feature vector
+ * dataset or overlay dataset.
+ */
public static boolean isHcsImageDataset(ExternalData externalData)
{
return isOneOfTypesMatching(externalData,
- ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PATTERN,
- ScreeningConstants.HCS_RAW_IMAGE_DATASET_TYPE_PATTERN,
- ScreeningConstants.HCS_RAW_IMAGE_LEGACY_DATASET_TYPE,
- ScreeningConstants.HCS_SEGMENTATION_IMAGE_DATASET_TYPE_PATTERN);
+ ScreeningConstants.ANY_HCS_IMAGE_DATASET_TYPE_PATTERN);
}
public static boolean isRawHcsImageDataset(ExternalData externalData)
@@ -166,7 +163,6 @@ public class ScreeningUtils
public static boolean isSegmentationHcsImageDataset(ExternalData externalData)
{
return isOneOfTypesMatching(externalData,
- ScreeningConstants.IMAGE_OVERLAY_DATASET_TYPE_PATTERN,
ScreeningConstants.HCS_SEGMENTATION_IMAGE_DATASET_TYPE_PATTERN);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java
index 8d12db8fdf4..7827083b057 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java
@@ -35,35 +35,34 @@ public class ScreeningConstants
// ---- required entity type patterns -----------
- // type of the dataset which stores image analysis data, there should be at most one
- public static final String HCS_IMAGE_ANALYSIS_DATASET_TYPE_PATTERN =
- "HCS_IMAGE_ANALYSIS_DATA|.*HCS_WELL_FV.*";
+ // --- HCS dataset types
- // type of the dataset which stores plate image overlays
- public static final String IMAGE_OVERLAY_DATASET_TYPE_PATTERN = ".*OVERLAY.*";
+ private static final String HCS_IMAGE_DATASET_PREFIX = "HCS_IMAGE";
// type of the dataset which stores plate image overlays
public static final String HCS_SEGMENTATION_IMAGE_DATASET_TYPE_PATTERN =
- "HCS_IMAGE_SEGMENTATION.*";
+ (HCS_IMAGE_DATASET_PREFIX + ".*OVERLAY.*") + "|" // legacy
+ + (HCS_IMAGE_DATASET_PREFIX + "_SEGMENTATION.*");
// Type of the dataset which stores raw plate images.
- public static final String HCS_RAW_IMAGE_DATASET_TYPE_PATTERN = "HCS_IMAGE_RAW.*";
+ public static final String HCS_RAW_IMAGE_DATASET_TYPE_PATTERN = HCS_IMAGE_DATASET_PREFIX
+ + "_RAW.*";
// The plain old legacy type for raw image data sets.
- public static final String HCS_RAW_IMAGE_LEGACY_DATASET_TYPE = "HCS_IMAGE";
-
- // Type of the dataset which stores plate images.
+ public static final String HCS_RAW_IMAGE_LEGACY_DATASET_TYPE = HCS_IMAGE_DATASET_PREFIX;
+
+ // Type of the dataset which stores plate images (raw, overvies or overlays).
// We do not want old analysis data to match to this pattern.
- public static final String HCS_IMAGE_DATASET_TYPE_PATTERN =
- ".*" + HCS_RAW_IMAGE_LEGACY_DATASET_TYPE + "($|[^_].*|_[^A].*|_A[^N].*|_AN[^A].*)";
+ public static final String ANY_HCS_IMAGE_DATASET_TYPE_PATTERN = HCS_IMAGE_DATASET_PREFIX
+ + "($|[^_].*|_[^A].*|_A[^N].*|_AN[^A].*)";
- public static final String HCS_PLATE_SAMPLE_TYPE_PATTERN = ".*PLATE.*";
+ // type of the dataset which stores image analysis data, there should be at most one
+ public static final String HCS_IMAGE_ANALYSIS_DATASET_TYPE_PATTERN = "HCS_IMAGE_ANALYSIS_DATA|" // legacy
+ + "HCS_ANALYSIS_WELL_FEATURES.*";
- // type of the dataset which stores microscopy images
- public static final String MICROSCOPY_IMAGE_DATASET_TYPE_PATTERN = "MICROSCOPY_IMAGE|.*IMG.*";
+ // --- HCS sample types
- // the sample is considered to be a microscopy sample if its type code contains this string
- public static final String IMAGE_SAMPLE_TYPE_PATTERN = ".*IMG.*";
+ public static final String HCS_PLATE_SAMPLE_TYPE_PATTERN = "PLATE.*";
// the non-control well has to have a type code which contains this string
public static final String NON_CONTROL_WELL_SAMPLE_TYPE_PATTERN =
@@ -72,6 +71,27 @@ public class ScreeningConstants
// the well is considered to be a control well if its type code contains this string
public static final String CONTROL_WELL_SAMPLE_TYPE_PATTERN = ".*CONTROL.*";
+ // --- Microscopy
+
+ // --- Microscopy dataset types
+
+ public static final String ANY_MICROSCOPY_IMAGE_DATASET_TYPE_PATTERN = ".*IMG.*";
+
+ // type of the dataset which stores microscopy images
+ public static final String MICROSCOPY_IMAGE_DATASET_TYPE_PATTERN = "MICROSCOPY_IMAGE|"// legacy
+ + ANY_MICROSCOPY_IMAGE_DATASET_TYPE_PATTERN;
+
+ // type of the dataset which stores image overlays
+ public static final String MICROSCOPY_SEGMENTATION_IMAGE_DATASET_TYPE_PATTERN =
+ ANY_MICROSCOPY_IMAGE_DATASET_TYPE_PATTERN + ".*OVERLAY.*|" + // legacy
+ ANY_MICROSCOPY_IMAGE_DATASET_TYPE_PATTERN + ".*SEGMENTATION.*";
+
+ // --- Microscopy sample types
+
+ // the sample is considered to be a microscopy sample if its type code contains this string
+ public static final String MICROSCOPY_IMAGE_SAMPLE_TYPE_PATTERN =
+ ANY_MICROSCOPY_IMAGE_DATASET_TYPE_PATTERN;
+
// ----
// code of plate geometry vocabulary
--
GitLab