make some OMERO model object text properties of unbounded length

components/dsl/src/ome/dsl/SaxReader.java

@@ -1,7 +1,7 @@
 /*
 * ome.dsl.SaxReader
 *
-*   Copyright 2006 University of Dundee. All rights reserved.
+*   Copyright 2006-2016 University of Dundee. All rights reserved.
 *   Use is subject to license terms supplied in LICENSE.txt
 */
 
@@ -268,7 +268,7 @@ public List<SemanticType> process() {
             if (named != null && named.booleanValue()) {
                 Properties p = new Properties();
                 p.setProperty("name", "name");
-                p.setProperty("type", "string");
+                p.setProperty("type", "text");
                 RequiredField r = new RequiredField(namedOrDescribed, p);
                 namedOrDescribed.getProperties().add(r);
             }

components/model/resources/mappings/acquisition.ome.xml

@@ -104,7 +104,7 @@
 			<optional name="mtime" type="timestamp"/>
 			<optional name="ctime" type="timestamp"/>
 			<optional name="hasher" type="ome.model.enums.ChecksumAlgorithm"/>
-			<optional name="hash" type="string"/>
+			<optional name="hash" type="text"/>
 			<optional name="mimetype" type="string"/>
 			<zeromany name="filesetEntries" type="ome.model.fs.FilesetEntry" inverse="originalFile"/>
 			<!--
@@ -191,14 +191,14 @@
 			<optional name="green" type="int"/>
 			<optional name="blue" type="int"/>
 			<optional name="alpha" type="int"/>
-			<optional name="lookupTable" type="string"/>
+			<optional name="lookupTable" type="text"/>
 			<manyone name="logicalChannel" type="ome.model.core.LogicalChannel" inverse="channels"/>
 			<manyone name="pixels" type="ome.model.core.Pixels" ordered="true"/>
 		</properties>
 	</type>
 	<type id="ome.model.core.LogicalChannel">
 		<properties>
-			<optional name="name" type="string"/>
+			<optional name="name" type="text"/>
 			<optional name="pinHoleSize" type="ome.model.units.Length"/>
 			<optional name="illumination" type="ome.model.enums.Illumination"/>
 			<!-- Note: illumination is called IlluminationType in model-->

components/model/resources/mappings/annotations.ome.xml

@@ -2,8 +2,6 @@
 <!--
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 #
-# $Id$
-#
 # Copyright 2008-2014 Glencoe Software, Inc. All rights reserved.
 # Use is subject to license terms supplied in LICENSE.txt
 #
@@ -13,8 +11,8 @@
 <!-- Structured Annotations -->
 	<abstract id="ome.model.annotations.Annotation" discriminator="/" annotated="true">
 		<properties>
-			<optional name="ns" type="string"/>
-			<optional name="name" type="string"/>
+			<optional name="ns" type="text"/>
+			<optional name="name" type="text"/>
 			<optional name="description" type="text"/>
 		</properties>
 	</abstract>

components/model/resources/mappings/containers.ome.xml

@@ -2,7 +2,7 @@
 <!--
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # 
-# Copyright 2006-2015 University of Dundee. All rights reserved.
+# Copyright 2006-2016 University of Dundee. All rights reserved.
 # Use is subject to license terms supplied in LICENSE.txt
 #
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

components/model/resources/mappings/display.ome.xml

@@ -31,7 +31,7 @@
 			<required name="defaultT" type="int"/>
 			<required name="model" type="ome.model.enums.RenderingModel"/>
 			<onemany name="waveRendering" type="ome.model.display.ChannelBinding" inverse="renderingDef" ordered="true"/>
-			<optional name="name" type="string"/>
+			<optional name="name" type="text"/>
 			<optional name="compression" type="double"/>
 			<required name="quantization" type="ome.model.display.QuantumDef"/>
 			<zeromany name="projections" type="ome.model.display.ProjectionDef" inverse="renderingDef" ordered="true"/>

components/model/resources/mappings/jobs.ome.xml

@@ -2,8 +2,6 @@
 <!--
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # 
-# $Id$
-# 
 # Copyright 2007-2014 Glencoe Software, Inc. All rights reserved.
 # Use is subject to license terms supplied in LICENSE.txt
 #
@@ -76,8 +74,8 @@
 	<type id="ome.model.jobs.ImportJob" superclass="ome.model.jobs.Job">
 		<!-- Note: ImportJob is not in model-->
 		<properties>
-			<required name="imageName" type="string"/>
-			<required name="imageDescription" type="string"/>
+			<required name="imageName" type="text"/>
+			<required name="imageDescription" type="text"/>
 		</properties>
 	</type>
 	<type id="ome.model.jobs.ScriptJob" superclass="ome.model.jobs.Job">

components/model/resources/mappings/meta.ome.xml

@@ -172,7 +172,7 @@
 
                         <!-- The human-readable text denoting this
                         namespace -->
-			<optional name="displayName" type="string"/>
+			<optional name="displayName" type="text"/>
 
 		</properties>
 	</type>

components/model/resources/mappings/roi.ome.xml

@@ -11,7 +11,7 @@
         <type id="ome.model.roi.Roi" annotated="true" described="true">
                 <properties>
                         <!--optional name="union" type="boolean"/-->
-                        <optional name="name" type="string"/>
+                        <optional name="name" type="text"/>
                         <onemany name="shapes" type="ome.model.roi.Shape" inverse="roi" ordered="true"/>
                         <optional name="image" type="ome.model.core.Image" inverse="rois"/>
                         <optional name="source" type="ome.model.core.OriginalFile"/>

components/model/resources/mappings/screen.ome.xml

@@ -2,9 +2,7 @@
 <!--
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 #
-# $Id$
-#
-# Copyright 2008 University of Dundee. All rights reserved.
+# Copyright 2008-2016 University of Dundee. All rights reserved.
 # Use is subject to license terms supplied in LICENSE.txt
 #
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -16,16 +14,16 @@
 		<properties>
 			<optional name="type" type="string"/>
 			<optional name="protocolIdentifier" type="string"/>
-			<optional name="protocolDescription" type="string"/>
+			<optional name="protocolDescription" type="text"/>
 			<optional name="reagentSetIdentifier" type="string"/>
-			<optional name="reagentSetDescription" type="string"/>
+			<optional name="reagentSetDescription" type="text"/>
 			<child name="plateLinks" type="ome.model.screen.ScreenPlateLink" target="ome.model.screen.Plate"/>
 			<zeromany name="reagents" type="ome.model.screen.Reagent" inverse="screen"/>
 		</properties>
 	</type>
 	<type id="ome.model.screen.PlateAcquisition" described="true" annotated="true">
 		<properties>
-			<optional name="name" type="string"/>
+			<optional name="name" type="text"/>
 			<optional name="startTime" type="timestamp"/>
 			<optional name="endTime" type="timestamp"/>
 			<optional name="maximumFieldCount" type="int"/>
@@ -45,7 +43,7 @@
 			<optional name="rows" type="int"/>
 			<optional name="columns" type="int"/>
 			<!-- end not in model -->
-			<optional name="status" type="string"/>
+			<optional name="status" type="text"/>
 			<optional name="externalIdentifier" type="string"/>
 			<parent name="screenLinks" type="ome.model.screen.ScreenPlateLink" target="ome.model.screen.Screen"/>
 			<zeromany name="wells" type="ome.model.screen.Well" inverse="plate"/>
@@ -67,7 +65,7 @@
                         <!-- end not in model -->
 			<child name="reagentLinks" type="ome.model.screen.WellReagentLink" target="ome.model.screen.Reagent"/>
 			<!-- Note: only one reagent per well in model-->
-			<optional name="externalDescription" type="string"/>
+			<optional name="externalDescription" type="text"/>
 			<optional name="externalIdentifier" type="string"/>
 			<optional name="type" type="string"/>
 			<zeromany name="wellSamples" type="ome.model.screen.WellSample" inverse="well" ordered="true"/>
@@ -88,7 +86,7 @@
 	<type id="ome.model.screen.Reagent" annotated="true" described="true">
 		<!-- Note: Name is optional in model-->
 		<properties>
-			<optional name="name" type="string"/>
+			<optional name="name" type="text"/>
 			<optional name="reagentIdentifier" type="string"/>
 			<manyone name="screen" type="ome.model.screen.Screen" inverse="reagent"/>
 			<parent name="wellLinks" type="ome.model.screen.WellReagentLink" target="ome.model.screen.Well"/>

etc/omero.properties

@@ -44,7 +44,7 @@ omero.db.version=OMERO5.3DEV
 # server that is is being used with. Any changes by
 # developers to the database schema will result in
 # a bump to this value.
-omero.db.patch=12
+omero.db.patch=13
 
 # The string that will be used as the base for LSIDs
 # in all exported OME objects including OME-XML and

sql/psql/OMERO5.3DEV__12/OMERO5.2__0-precheck.sql → sql/psql/OMERO5.3DEV__13/OMERO5.2__0-precheck.sql

@@ -17,7 +17,7 @@
 --
 
 ---
---- OMERO5 readiness check for upgrade from OMERO5.2__0 to OMERO5.3DEV__12.
+--- OMERO5 readiness check for upgrade from OMERO5.2__0 to OMERO5.3DEV__13.
 ---
 
 BEGIN;
@@ -245,6 +245,6 @@ DROP FUNCTION parse_transform(TEXT);
 -- FINISHED
 --
 
-SELECT CHR(10)||CHR(10)||CHR(10)||'YOUR DATABASE IS READY FOR UPGRADE TO VERSION OMERO5.3DEV__12'||CHR(10)||CHR(10)||CHR(10) AS Status;
+SELECT CHR(10)||CHR(10)||CHR(10)||'YOUR DATABASE IS READY FOR UPGRADE TO VERSION OMERO5.3DEV__13'||CHR(10)||CHR(10)||CHR(10) AS Status;
 
 ROLLBACK;

sql/psql/OMERO5.3DEV__12/OMERO5.2__0.sql → sql/psql/OMERO5.3DEV__13/OMERO5.2__0.sql

@@ -17,7 +17,7 @@
 --
 
 ---
---- OMERO5 development release upgrade from OMERO5.2__0 to OMERO5.3DEV__12.
+--- OMERO5 development release upgrade from OMERO5.2__0 to OMERO5.3DEV__13.
 ---
 
 BEGIN;
@@ -95,7 +95,7 @@ DROP FUNCTION db_pretty_version(INTEGER);
 --
 
 INSERT INTO dbpatch (currentVersion, currentPatch, previousVersion, previousPatch)
-             VALUES ('OMERO5.3DEV',  12,           'OMERO5.2',      0);
+             VALUES ('OMERO5.3DEV',  13,           'OMERO5.2',      0);
 
 -- ... up to patch 0:
 
@@ -1976,17 +1976,45 @@ CREATE OR REPLACE FUNCTION filesetjoblink_parent_index_move() RETURNS trigger
 
 DELETE FROM format WHERE id NOT IN (SELECT DISTINCT format FROM image WHERE format IS NOT NULL) AND external_id IS NULL;
 
+-- ... up to patch 13:
+
+ALTER TABLE annotation ALTER COLUMN name TYPE TEXT;
+ALTER TABLE annotation ALTER COLUMN ns TYPE TEXT;
+ALTER TABLE channel ALTER COLUMN lookuptable TYPE TEXT;
+ALTER TABLE dataset ALTER COLUMN name TYPE TEXT;
+ALTER TABLE folder ALTER COLUMN name TYPE TEXT;
+ALTER TABLE image ALTER COLUMN name TYPE TEXT;
+ALTER TABLE importjob ALTER COLUMN imagename TYPE TEXT;
+ALTER TABLE importjob ALTER COLUMN imagedescription TYPE TEXT;
+ALTER TABLE logicalchannel ALTER COLUMN name TYPE TEXT;
+ALTER TABLE namespace ALTER COLUMN name TYPE TEXT;
+ALTER TABLE namespace ALTER COLUMN displayname TYPE TEXT;
+ALTER TABLE originalfile ALTER COLUMN name TYPE TEXT;
+ALTER TABLE originalfile ALTER COLUMN hash TYPE TEXT;
+ALTER TABLE plate ALTER COLUMN name TYPE TEXT;
+ALTER TABLE plate ALTER COLUMN status TYPE TEXT;
+ALTER TABLE plateacquisition ALTER COLUMN name TYPE TEXT;
+ALTER TABLE project ALTER COLUMN name TYPE TEXT;
+ALTER TABLE reagent ALTER COLUMN name TYPE TEXT;
+ALTER TABLE renderingdef ALTER COLUMN name TYPE TEXT;
+ALTER TABLE roi ALTER COLUMN name TYPE TEXT;
+ALTER TABLE screen ALTER COLUMN name TYPE TEXT;
+ALTER TABLE screen ALTER COLUMN protocoldescription TYPE TEXT;
+ALTER TABLE screen ALTER COLUMN reagentsetdescription TYPE TEXT;
+ALTER TABLE stagelabel ALTER COLUMN name TYPE TEXT;
+ALTER TABLE well ALTER COLUMN externaldescription TYPE TEXT;
+
 
 --
 -- FINISHED
 --
 
 UPDATE dbpatch SET message = 'Database updated.', finished = clock_timestamp()
     WHERE currentVersion  = 'OMERO5.3DEV' AND
-          currentPatch    = 12            AND
+          currentPatch    = 13            AND
           previousVersion = 'OMERO5.2'    AND
           previousPatch   = 0;
 
-SELECT CHR(10)||CHR(10)||CHR(10)||'YOU HAVE SUCCESSFULLY UPGRADED YOUR DATABASE TO VERSION OMERO5.3DEV__12'||CHR(10)||CHR(10)||CHR(10) AS Status;
+SELECT CHR(10)||CHR(10)||CHR(10)||'YOU HAVE SUCCESSFULLY UPGRADED YOUR DATABASE TO VERSION OMERO5.3DEV__13'||CHR(10)||CHR(10)||CHR(10) AS Status;
 
 COMMIT;

sql/psql/OMERO5.3DEV__13/OMERO5.3DEV__12.sql

@@ -0,0 +1,96 @@
+-- Copyright (C) 2012-4 Glencoe Software, Inc. All rights reserved.
+-- Use is subject to license terms supplied in LICENSE.txt
+--
+-- This program is free software; you can redistribute it and/or modify
+-- it under the terms of the GNU General Public License as published by
+-- the Free Software Foundation; either version 2 of the License, or
+-- (at your option) any later version.
+--
+-- This program is distributed in the hope that it will be useful,
+-- but WITHOUT ANY WARRANTY; without even the implied warranty of
+-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+-- GNU General Public License for more details.
+--
+-- You should have received a copy of the GNU General Public License along
+-- with this program; if not, write to the Free Software Foundation, Inc.,
+-- 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+--
+
+---
+--- OMERO5 development release upgrade from OMERO5.3DEV__12 to OMERO5.3DEV__13.
+---
+
+BEGIN;
+
+
+--
+-- check OMERO database version
+--
+
+CREATE OR REPLACE FUNCTION omero_assert_db_version(expected_version VARCHAR, expected_patch INTEGER) RETURNS void AS $$
+
+DECLARE
+    current_version VARCHAR;
+    current_patch INTEGER;
+
+BEGIN
+    SELECT currentversion, currentpatch INTO STRICT current_version, current_patch
+        FROM dbpatch ORDER BY id DESC LIMIT 1;
+
+    IF current_version <> expected_version OR current_patch <> expected_patch THEN
+        RAISE EXCEPTION 'wrong OMERO database version for this upgrade script';
+    END IF;
+
+END;$$ LANGUAGE plpgsql;
+
+SELECT omero_assert_db_version('OMERO5.3DEV', 12);
+DROP FUNCTION omero_assert_db_version(varchar, int);
+
+
+--
+-- Actual upgrade
+--
+
+INSERT INTO dbpatch (currentVersion, currentPatch, previousVersion, previousPatch)
+             VALUES ('OMERO5.3DEV',  13,           'OMERO5.3DEV',   12);
+
+ALTER TABLE annotation ALTER COLUMN name TYPE TEXT;
+ALTER TABLE annotation ALTER COLUMN ns TYPE TEXT;
+ALTER TABLE channel ALTER COLUMN lookuptable TYPE TEXT;
+ALTER TABLE dataset ALTER COLUMN name TYPE TEXT;
+ALTER TABLE folder ALTER COLUMN name TYPE TEXT;
+ALTER TABLE image ALTER COLUMN name TYPE TEXT;
+ALTER TABLE importjob ALTER COLUMN imagename TYPE TEXT;
+ALTER TABLE importjob ALTER COLUMN imagedescription TYPE TEXT;
+ALTER TABLE logicalchannel ALTER COLUMN name TYPE TEXT;
+ALTER TABLE namespace ALTER COLUMN name TYPE TEXT;
+ALTER TABLE namespace ALTER COLUMN displayname TYPE TEXT;
+ALTER TABLE originalfile ALTER COLUMN name TYPE TEXT;
+ALTER TABLE originalfile ALTER COLUMN hash TYPE TEXT;
+ALTER TABLE plate ALTER COLUMN name TYPE TEXT;
+ALTER TABLE plate ALTER COLUMN status TYPE TEXT;
+ALTER TABLE plateacquisition ALTER COLUMN name TYPE TEXT;
+ALTER TABLE project ALTER COLUMN name TYPE TEXT;
+ALTER TABLE reagent ALTER COLUMN name TYPE TEXT;
+ALTER TABLE renderingdef ALTER COLUMN name TYPE TEXT;
+ALTER TABLE roi ALTER COLUMN name TYPE TEXT;
+ALTER TABLE screen ALTER COLUMN name TYPE TEXT;
+ALTER TABLE screen ALTER COLUMN protocoldescription TYPE TEXT;
+ALTER TABLE screen ALTER COLUMN reagentsetdescription TYPE TEXT;
+ALTER TABLE stagelabel ALTER COLUMN name TYPE TEXT;
+ALTER TABLE well ALTER COLUMN externaldescription TYPE TEXT;
+
+
+--
+-- FINISHED
+--
+
+UPDATE dbpatch SET message = 'Database updated.', finished = clock_timestamp()
+    WHERE currentVersion  = 'OMERO5.3DEV' AND
+          currentPatch    = 13            AND
+          previousVersion = 'OMERO5.3DEV' AND
+          previousPatch   = 12;
+
+SELECT CHR(10)||CHR(10)||CHR(10)||'YOU HAVE SUCCESSFULLY UPGRADED YOUR DATABASE TO VERSION OMERO5.3DEV__13'||CHR(10)||CHR(10)||CHR(10) AS Status;
+
+COMMIT;

sql/psql/OMERO5.3DEV__12/psql-footer.sql → sql/psql/OMERO5.3DEV__13/psql-footer.sql

@@ -2042,7 +2042,7 @@ alter table dbpatch alter message set default 'Updating';
 -- running so that if anything goes wrong, we'll have some record.
 --
 insert into dbpatch (currentVersion, currentPatch, previousVersion, previousPatch, message)
-             values ('OMERO5.3DEV',  12,    'OMERO5.3DEV',   0,             'Initializing');
+             values ('OMERO5.3DEV',  13,    'OMERO5.3DEV',   0,             'Initializing');
 
 --
 -- Temporarily make event columns nullable; restored below.
@@ -3162,7 +3162,7 @@ CREATE TRIGGER preserve_folder_tree
 -- Here we have finished initializing this database.
 update dbpatch set message = 'Database ready.', finished = clock_timestamp()
   where currentVersion = 'OMERO5.3DEV' and
-        currentPatch = 12 and
+        currentPatch = 13 and
         previousVersion = 'OMERO5.3DEV' and
         previousPatch = 0;