Version bump to 3.0.0-rc3

patches/patch20201110-3.0.0-rc3/patch.sh

+#!/bin/bash
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2018 Research Group Biomedical Physics,
+# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+# ** end header
+#
+# new entity_version table
+# Update mysql schema to version v3.0.0-rc3
+NEW_VERSION="v3.0.0-rc3"
+OLD_VERSION="v3.0.0-rc2"
+
+if [ -z "$UTILSPATH" ]; then
+ UTILSPATH="../utils"
+fi
+
+. $UTILSPATH/patch_header.sh $*
+
+
+check_version $OLD_VERSION
+
+
+mysql_execute_file $PATCH_DIR/update_archive_isa.sql
+
+
+update_version $NEW_VERSION
+
+success
+

patches/patch20201110-3.0.0-rc3/update_archive_isa.sql

+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ */
+
+-- Create tables for versioning.
+
+ALTER TABLE archive_isa
+    ADD COLUMN `direct` BOOLEAN DEFAULT TRUE;

procedures/deleteIsaCache.sql

@@ -50,10 +50,10 @@ BEGIN
             FROM entity_version
             WHERE entity_id = EntityID;
 
-        -- move to archive_isa before deleting (only direct child-parent relations)
-        INSERT IGNORE INTO archive_isa (child, child_iversion, parent)
+        -- move to archive_isa before deleting
+        INSERT IGNORE INTO archive_isa (child, child_iversion, parent, direct)
             -- TODO copy rpath as well
-            SELECT e.child, IVersion AS child_iversion, e.parent
+            SELECT e.child, IVersion AS child_iversion, e.parent, rpath = EntityID
             FROM isa_cache AS e
             WHERE e.child = EntityID;
     END IF;

procedures/retrieveEntityParents.sql

@@ -78,18 +78,19 @@ retrieveEntityParentsBody: BEGIN
 
             SELECT
                 i.parent AS ParentID,
-                ( SELECT value FROM archive_name_data
+                ( SELECT value FROM name_data
                     WHERE domain_id = 0
                     AND entity_id = ParentID
                     AND property_id = 20
-                    AND _iversion = IVersion) AS ParentName,
+                ) AS ParentName, -- This is not necessarily the name of the parent at the time of IVersion but it is a good guess. Future implementations of the archive_isa table should also store the IVersion of the parents. Only then the historically correct ParentName can be reconstructed.
                 e.description AS ParentDescription,
                 e.role AS ParentRole,
                 (SELECT acl FROM entity_acl AS a WHERE a.id = e.acl) AS ACL
                 FROM archive_isa AS i JOIN entities AS e
                     ON (i.parent = e.id)
                 WHERE i.child = EntityID
-                AND i.child_iversion = IVersion;
+                AND i.child_iversion = IVersion
+                AND i.direct IS TRUE;
 
             LEAVE retrieveEntityParentsBody;
         END IF;

tests/test_autotap.sql

@@ -2539,13 +2539,6 @@ SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','entityACL','N
 SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','entityACL','DEFINER','');
 SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','entityACL','CONTAINS SQL','');
 
--- PROCEDURES _caosdb_schema_unit_tests.finishNegationFilter
-
-SELECT tap.has_procedure('_caosdb_schema_unit_tests','finishNegationFilter','');
-SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','finishNegationFilter','NO','');
-SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','finishNegationFilter','DEFINER','');
-SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','finishNegationFilter','CONTAINS SQL','');
-
 -- PROCEDURES _caosdb_schema_unit_tests.finishSubProperty
 
 SELECT tap.has_procedure('_caosdb_schema_unit_tests','finishSubProperty','');
@@ -2595,27 +2588,6 @@ SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','initBackRefer
 SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','initBackReference','DEFINER','');
 SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','initBackReference','CONTAINS SQL','');
 
--- PROCEDURES _caosdb_schema_unit_tests.initConjunctionFilter
-
-SELECT tap.has_procedure('_caosdb_schema_unit_tests','initConjunctionFilter','');
-SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','initConjunctionFilter','NO','');
-SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','initConjunctionFilter','DEFINER','');
-SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','initConjunctionFilter','CONTAINS SQL','');
-
--- PROCEDURES _caosdb_schema_unit_tests.initDisjunctionFilter
-
-SELECT tap.has_procedure('_caosdb_schema_unit_tests','initDisjunctionFilter','');
-SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','initDisjunctionFilter','NO','');
-SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','initDisjunctionFilter','DEFINER','');
-SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','initDisjunctionFilter','CONTAINS SQL','');
-
--- PROCEDURES _caosdb_schema_unit_tests.initNegationFilter
-
-SELECT tap.has_procedure('_caosdb_schema_unit_tests','initNegationFilter','');
-SELECT tap.procedure_is_deterministic('_caosdb_schema_unit_tests','initNegationFilter','NO','');
-SELECT tap.procedure_security_type_is('_caosdb_schema_unit_tests','initNegationFilter','DEFINER','');
-SELECT tap.procedure_sql_data_access_is('_caosdb_schema_unit_tests','initNegationFilter','CONTAINS SQL','');
-
 -- PROCEDURES _caosdb_schema_unit_tests.initPOVRefidsTable
 
 SELECT tap.has_procedure('_caosdb_schema_unit_tests','initPOVRefidsTable','');