FIX problems after merge of name_data changes from dev

README_SETUP.md

@@ -36,6 +36,40 @@
   be lost afterwards.** And no, there is *no* additional prompt to ask if you
   are sure.  If you `make drop-...`, you *actually* delete the database.
 
+## Versioning
+
+The versioning feature is still experimental. Therefore it is possible to turn
+if on and off with a patch file and a special property.
+
+### Procedures and Functions
+
+The procedures which need to behave differently if the versioning is on or off
+check the return value of `is_feature_config("ENTITY_VERSIONING", "ENABLED")`.
+The `is_feature_config` function checks the `feature_config` table, which is
+a key-value store.
+
+Turn off versioning: Run `UPDATE feature_config SET _value = "DISABLED" WHERE
+_key = "ENTITY_VERSIONING";` on your database.
+
+Turn on versioning again: Run `UPDATE feature_config SET _value = "ENABLED"
+WHERE _key = "ENTITY_VERSIONING";` on your database.
+
+### Data
+
+When the versioning patch is installed, the versioning is turned on by default
+and all old entities become versioned entities with their current version as
+the oldest known version. That is, they all need an entry in the
+`entity_version` table. These entries are generated by the `_fix_unversioned`
+procedure.
+
+If you want to turn off the versioning for the time being you can just turn it
+off for the procedures as described above. You should also empty the
+`entity_version` table because the `_fix_unversioned` procedure is only
+designed to cope with entities which do not have any versioning information at
+all. The already recorded versioning information is of course lost then! If you
+switch on the versioning at a some point in the future, the history begins anew
+with the then current version of the stored entities.
+
 ## Unit tests
 
 * We use [MyTAP-1.0](https://hepabolu.github.io/mytap/) for unit tests.

patches/patch20200426-3.0.0/fix_unversioned.sql → patches/patch20200710-3.0.0-rc2/fix_unversioned.sql

@@ -106,7 +106,3 @@ END;
 //
 
 delimiter ;
-
-CALL _fix_unversioned();
-
-DROP PROCEDURE _fix_unversioned;

patches/patch20200426-3.0.0/patch.sh → patches/patch20200710-3.0.0-rc2/patch.sh

@@ -22,9 +22,9 @@
 # ** end header
 #
 # new entity_version table
-# Update mysql schema to version v3.0.0
-NEW_VERSION="v3.0.0"
-OLD_VERSION="v2.1.2"
+# Update mysql schema to version v3.0.0-rc2
+NEW_VERSION="v3.0.0-rc2"
+OLD_VERSION="v3.0.0-rc1"
 
 if [ -z "$UTILSPATH" ]; then
  UTILSPATH="../utils"
@@ -38,7 +38,10 @@ check_version $OLD_VERSION
 
 mysql_execute_file $PATCH_DIR/feature_config.sql
 mysql_execute_file $PATCH_DIR/versioning.sql
+
 mysql_execute_file $PATCH_DIR/fix_unversioned.sql
+mysql_execute "CALL _fix_unversioned()"
+mysql_execute "DROP PROCEDURE _fix_unversioned"
 
 
 update_version $NEW_VERSION

patches/patch20200426-3.0.0/versioning.sql → patches/patch20200710-3.0.0-rc2/versioning.sql

@@ -282,7 +282,6 @@ CREATE TABLE archive_files (
 
 CREATE TABLE archive_entities (
     id INT UNSIGNED NOT NULL,
-    name VARCHAR(255) DEFAULT NULL,
     description TEXT DEFAULT NULL,
     role ENUM('RECORDTYPE','RECORD','FILE','DOMAIN',
         'PROPERTY','DATATYPE','ROLE','QUERYTEMPLATE') NOT NULL,

procedures/getFile.sql

-/*
- * ** 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
- *
- * 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
- */
-#-- getFile(ID);
-#-- 
-#-- 
-#-- FileID,
-#-- FilePath,
-#-- FileSize,
-#-- FileHash,
-#-- FileDescription,
-#-- FileCreated,
-#-- FileCreator,
-#-- FileGenerator,
-#-- FileOwner,
-#-- FilePermission,
-#-- FileChecksum
-
-Drop Procedure if exists db_2_0.getFile;
-Delimiter //
-Create Procedure db_2_0.getFile (in FileID INT)
-BEGIN 
-
-Select name, description, role into @name, @description, @role from entities where id=FileID LIMIT 1;
-
-IF @role = 'file' Then
-		Select path, hash, size into @FilePath, @FileHash, @FileSize from files where file_id=FileID LIMIT 1;
-		Select timestamp, user_id, user_agent into @FileCreated, @FileCreator, @FileGenerator from history where entity_id=FileID AND event='insertion' LIMIT 1;
-
-Select 
-FileID as FileID,
-@FilePath as FilePath,
-@FileSize as FileSize,
-@FileHash as FileHash,
-@FileDescription as FileDescription,
-@FileCreated as FileCreated,
-@FileCreator as FileCreator,
-@FileGenerator as FileGenerator,
-NULL	as FileOwner,
-NULL as FilePermission,
-NULL as FileChecksum;
-
-END IF;
-
-END;
-//
-delimiter ;

procedures/registerSubdomain.sql

@@ -38,8 +38,8 @@ BEGIN
     SELECT COUNT(id) INTO ED FROM entities WHERE Role='DOMAIN' AND id!=0;
 
     WHILE ED < amount DO
-        INSERT INTO entities (name, description, role, acl) VALUES
-            (NULL, "Multipurpose subdomain", 'DOMAIN', 0);
+        INSERT INTO entities (description, role, acl) VALUES
+            (NULL, 'DOMAIN', 0);
         SET ED = ED + 1;
     END WHILE;
 

procedures/retrieveEntity.sql

@@ -93,10 +93,19 @@ retrieveEntityBody: BEGIN
                 LIMIT 1;
 
             Select
-                (SELECT Name FROM entities WHERE id=DatatypeID) AS Datatype,
+                ( SELECT value FROM
+                    ( SELECT value FROM name_data
+                        WHERE domain_id = 0
+                        AND entity_ID = DatatypeID
+                        AND property_id = 20
+                        UNION SELECT DatatypeID AS value
+                    ) AS tmp LIMIT 1 ) AS Datatype,
                 CollectionName AS Collection,
                 EntityID AS EntityID,
-                e.name AS EntityName,
+                ( SELECT value FROM archive_name_data
+                    WHERE domain_id = 0
+                    AND entity_ID = EntityID
+                    AND property_id = 20 LIMIT 1) AS EntityName,
                 e.description AS EntityDesc,
                 e.role AS EntityRole,
                 FileSize AS FileSize,
@@ -118,40 +127,46 @@ retrieveEntityBody: BEGIN
     END IF;
 
     Select path, size, hex(hash)
-        into FilePath, FileSize, FileHash
-        from files
-        where file_id = EntityID
+        INTO FilePath, FileSize, FileHash
+        FROM files
+        WHERE file_id = EntityID
         LIMIT 1;
 
-    Select datatype into DatatypeID
-        from data_type
-        where domain_id=0
-        and entity_id=0
-        and property_id=EntityID
+    Select datatype INTO DatatypeID
+        FROM data_type
+        WHERE domain_id=0
+        AND entity_id=0
+        AND property_id=EntityID
         LIMIT 1;
 
-    SELECT collection into CollectionName
-        from collection_type
-        where domain_id=0
-        and entity_id=0
-        and property_id=EntityID
+    SELECT collection INTO CollectionName
+        FROM collection_type
+        WHERE domain_id=0
+        AND entity_id=0
+        AND property_id=EntityID
         LIMIT 1;
 
     Select
-        (Select name from entities where id=DatatypeID) as Datatype,
-        CollectionName as Collection,
-        EntityID as EntityID,
-        e.name as EntityName,
-        e.description as EntityDesc,
-        e.role as EntityRole,
-        FileSize as FileSize,
-        FilePath as FilePath,
-        FileHash as FileHash,
-        (SELECT acl FROM entity_acl as a WHERE a.id = e.acl) as ACL,
-        Version as Version,
-        VersionSeconds as VersionSeconds,
-        VersionNanos as VersionNanos
-    from entities e where id = EntityID LIMIT 1;
+        ( SELECT value FROM name_data
+            WHERE domain_id = 0
+            AND entity_ID = DatatypeID
+            AND property_id = 20 LIMIT 1 ) AS Datatype,
+        CollectionName AS Collection,
+        EntityID AS EntityID,
+        ( SELECT value FROM name_data
+            WHERE domain_id = 0
+            AND entity_ID = EntityID
+            AND property_id = 20 LIMIT 1) AS EntityName,
+        e.description AS EntityDesc,
+        e.role AS EntityRole,
+        FileSize AS FileSize,
+        FilePath AS FilePath,
+        FileHash AS FileHash,
+        (SELECT acl FROM entity_acl AS a WHERE a.id = e.acl) AS ACL,
+        Version AS Version,
+        VersionSeconds AS VersionSeconds,
+        VersionNanos AS VersionNanos
+    FROM entities e WHERE id = EntityID LIMIT 1;
 END;
 //
 

procedures/retrieveEntityOverrides.sql

@@ -86,8 +86,13 @@ retrieveOverridesBody: BEGIN
                 NULL AS collection_override,
                 NULL AS name_override,
                 NULL AS desc_override,
-                (Select name FROM entities WHERE id=datatype LIMIT 1)
-                    AS type_override,
+                ( SELECT value FROM
+                    ( SELECT value FROM name_data
+                        WHERE domain_id = 0
+                        AND entity_ID = datatypeID
+                        AND property_id = 20
+                        UNION SELECT datatype AS value
+                    ) AS tmp LIMIT 1 ) AS type_override,
                 entity_id,
                 property_id
             FROM archive_data_type
@@ -144,7 +149,10 @@ retrieveOverridesBody: BEGIN
         NULL AS collection_override,
         NULL AS name_override,
         NULL AS desc_override,
-        (Select name FROM entities WHERE id=datatype LIMIT 1) AS type_override,
+        ( SELECT value FROM name_data
+            WHERE domain_id = 0
+            AND entity_ID = datatype
+            AND property_id = 20 LIMIT 1 ) AS type_override,
         entity_id,
         property_id
     FROM data_type

procedures/retrieveEntityParents.sql

@@ -77,7 +77,10 @@ retrieveEntityParentsBody: BEGIN
 
             SELECT
                 i.parent AS ParentID,
-                e.name AS ParentName,
+                ( SELECT value FROM archive_name_data
+                    WHERE domain_id = 0
+                    AND entity_id = ParentID
+                    AND property_id = 20 ) AS ParentName,
                 e.description AS ParentDescription,
                 e.role AS ParentRole,
                 (SELECT acl FROM entity_acl AS a WHERE a.id = e.acl) AS ACL
@@ -93,7 +96,10 @@ retrieveEntityParentsBody: BEGIN
 
     SELECT
         i.parent AS ParentID,
-        e.name AS ParentName,
+        ( SELECT value FROM name_data
+            WHERE domain_id = 0
+            AND entity_id = ParentID
+            AND property_id = 20 ) AS ParentName,
         e.description AS ParentDescription,
         e.role AS ParentRole,
         (SELECT acl FROM entity_acl AS a WHERE a.id = e.acl) AS ACL

procedures/retrieveEntityProperties.sql

@@ -173,6 +173,7 @@ retrieveEntityPropertiesBody: BEGIN
             FROM archive_name_data
             WHERE domain_id = DomainID
             AND entity_id = EntityID
+            AND property_id != 20
             AND _iversion = IVersion;
 
             LEAVE retrieveEntityPropertiesBody;
@@ -286,7 +287,8 @@ retrieveEntityPropertiesBody: BEGIN
         pidx AS PropertyIndex
     FROM name_data
     WHERE domain_id = DomainID
-    AND entity_id = EntityID;
+    AND entity_id = EntityID
+    AND property_id != 20;
 
 
 END;

procedures/updateEntity.sql

@@ -116,7 +116,6 @@ BEGIN
         WHERE domain_id=0 AND entity_id=0 AND property_id=EntityID;
 
     IF Datatype IS NOT NULL THEN
-        INSERT INTO data_type (domain_id, entity_id, property_id, datatype)
         INSERT INTO data_type (domain_id, entity_id, property_id, datatype)
             SELECT 0, 0, EntityID,
                 ( SELECT entity_id FROM name_data WHERE domain_id = 0

tests/test_0_fix_unversioned.sql

+../patches/patch20200710-3.0.0-rc2/fix_unversioned.sql
\ No newline at end of file

tests/test_entity_versioning.sql

@@ -21,10 +21,10 @@ INSERT INTO transactions (srid,seconds,nanos,username,realm) VALUES
 ("SRIDbla", 1234, 2345, "me", "home"),
 ("SRIDblub", 2345, 3465, "me", "home"),
 ("SRIDblieb", 3456, 4576, "you", "home");
-DELETE FROM entities WHERE name="EntityName";
+DELETE FROM entities WHERE id > 99;
 CALL entityACL(@ACLID1, "{acl1}");
 CALL insertEntity("EntityName", "EntityDesc", "RECORDTYPE", "{acl1}");
-SELECT id INTO @EntityID FROM entities WHERE name="EntityName";
+SELECT entity_id INTO @EntityID FROM name_data WHERE value="EntityName";
 
 
 -- TEST insert_single_child_version
@@ -67,8 +67,9 @@ SELECT count(*) INTO @x FROM entity_version;
 SELECT tap.eq(@x, 0, "no versions there any more");
 
 
--- TEARDOWN clean up a litte
-DELETE FROM entities WHERE name="EntityName";
+-- TEARDOWN clean up
+DELETE FROM name_data WHERE entity_id > 99;
+DELETE FROM entities WHERE id > 99;
 
 -- #####################################################################
 -- TEST the call of insert_single_child_version from within insertEntity
@@ -82,9 +83,9 @@ SELECT tap.eq(@x, 0, "before insertEntity, no versions there");
 -- TEST insertEntity - should produce a version w/o parent
 SET @SRID = "SRIDbla";
 CALL insertEntity("EntityName", "EntityDesc", "RECORDTYPE", "{acl1}");
-SELECT id INTO @EntityID FROM entities WHERE name="EntityName";
+SELECT entity_id INTO @EntityID FROM name_data WHERE value="EntityName";
 CALL insertEntity("ParentName", "ParentDesc", "RECORDTYPE", "{acl1}");
-SELECT id INTO @ParentID FROM entities WHERE name="ParentName";
+SELECT entity_id INTO @ParentID FROM name_data WHERE value="ParentName";
 CALL insertIsa(@EntityID, @ParentID);
 CALL insertEntityProperty(0, @EntityID, 17, "null_data", NULL, NULL,
     "RECOMMENDED", NULL, "DescOverride", NULL, NULL, 0);
@@ -189,7 +190,7 @@ DELETE FROM feature_config WHERE _key = "ENTITY_VERSIONING";
 CALL entityACL(@ACLID1, "{acl1}");
 CALL insertEntity("EntityName", "EntityDesc", "RECORDTYPE", "{acl1}");
 SELECT count(*) INTO @NumOfEntities FROM entities;
-SELECT id INTO @EntityID FROM entities WHERE name="EntityName";
+SELECT entity_id INTO @EntityID FROM name_data WHERE value="EntityName";
 
 SET @TheUser = "TheUser"; -- used to identify the matching entry in transaction_log
 -- fill transaction_log: one entity with two updates (and one insert) and another entity with insert and delete.
@@ -243,8 +244,8 @@ CALL entityACL(@ACLID1, "{acl1}");
 CALL insertEntity("EntityName1", "EntityDesc1", "RECORDTYPE", "{acl1}");
 CALL insertEntity("EntityName2", "EntityDesc2", "RECORDTYPE", "{acl1}");
 SELECT count(*) INTO @NumOfEntities FROM entities;
-SELECT id INTO @EntityID1 FROM entities WHERE name="EntityName1";
-SELECT id INTO @EntityID2 FROM entities WHERE name="EntityName2";
+SELECT entity_id INTO @EntityID1 FROM name_data WHERE value="EntityName1";
+SELECT entity_id INTO @EntityID2 FROM name_data WHERE value="EntityName2";
 
 INSERT INTO transaction_log (transaction, entity_id, username, realm, seconds,
         nanos)

utils/make_db

@@ -56,7 +56,7 @@ function _execute_tests () {
     for tfile in $TESTS ; do
         echo "Running $tfile"
         echo "----- $tfile -----" >> .TEST_RESULTS
-        cat $tfile | $MYSQL_CMD $(get_db_args_nodb) --disable-pager --batch --raw --skip-column-names --unbuffered >> .TEST_RESULTS 2>&1
+        cat $tfile | $MYSQL_CMD -D $UNITTEST_DATABASE $(get_db_args_nodb) --disable-pager --batch --raw --skip-column-names --unbuffered >> .TEST_RESULTS 2>&1
     done;
 
     popd