From 7c496e093f43027810a9bdf1d2a38e0a60201e58 Mon Sep 17 00:00:00 2001
From: Daniel <daniel@harvey>
Date: Wed, 12 Aug 2020 16:29:26 +0200
Subject: [PATCH] DOC, STY: Added documentation, also some formatting.
---
doc/table_structure.md | 64 +++++++++++++++++
.../fix_unversioned.sql | 8 ++-
.../patch20200710-3.0.0-rc2/versioning.sql | 9 +--
procedures/deleteEntityProperties.sql | 5 +-
procedures/deleteIsaCache.sql | 3 +-
procedures/entityVersioning.sql | 69 ++++++++++---------
procedures/insertEntity.sql | 6 ++
procedures/insertEntityProperty.sql | 3 +
procedures/retrieveEntity.sql | 33 +++++++--
procedures/retrieveEntityOverrides.sql | 7 +-
procedures/retrieveEntityParents.sql | 14 ++--
procedures/retrieveEntityProperties.sql | 3 +
procedures/updateEntity.sql | 23 +++----
tests/test_0_setup.sql | 22 ++++++
tests/test_entity_versioning.sql | 59 ++++++++++++----
tests/test_insert_update_delete.sql | 5 --
tests/test_reference_values.sql | 33 ++++++---
17 files changed, 269 insertions(+), 97 deletions(-)
diff --git a/doc/table_structure.md b/doc/table_structure.md
index 3ec27dc..59958f5 100644
--- a/doc/table_structure.md
+++ b/doc/table_structure.md
@@ -56,6 +56,20 @@ These tables share (generally) the same set of columns:
- `pidx` :: The property index, becomes nonzero when a property occurs more than
once in an entity.
+### `name_data` ###
+
+This table is used to name RecordTypoes, Records, Properties etc. The column `property_id` has the
+value 20, because that is the entity ID for names:
+
+```sql
+> SELECT * FROM entities WHERE id=20;
++----+-------------------+----------+------+
+| id | description | role | acl |
++----+-------------------+----------+------+
+| 20 | Name of an entity | PROPERTY | 0 |
++----+-------------------+----------+------+
+```
+
## data_type ##
The type of properties is stored here. The columns are:
- `domain_id` :: Property identitification, same as for plain data?
@@ -71,6 +85,56 @@ The type of properties is stored here. The columns are:
- `hash` :: Hash of the file contents, as binary. **TODO** Which algorithm?
- `checked_timestamp` :: Timestamp when last checked?
+## `feature_config` ##
++-------------------+---------+
+| _key | _value |
++-------------------+---------+
+| ENTITY_VERSIONING | ENABLED |
++-------------------+---------+
+
+A key-value store for features. Use the `is_feature_config` procedure to check for the status of
+specific features.
+
+## Versioning tables ##
+
+There are a few extra tables for implementing versioning. Also there is a special column
+`value_iversion` in the `reference_data` table which stores the version of the referenced entity at
+the time of the version. If `value_iversion` is NULL, no specific version is stored.
+
+### transactions ###
+
+Replacement for `transaction_log`, holds ID, user and time of transaction:
+
+- `srid` :: Server request ID, used to identify transactions
+- `username` :: User name
+- `realm` :: Realm for which the user name is valid
+- `seconds` :: Time of transaction: seconds
+- `nanos` :: Time of transaction: sub-second time resolution
+
+### `entity_version` ###
+
+Versioning info for entities:
+
+- `entity_id` :: persistent ID of the entity
+- `hash` :: Hash, for future use.
+- `version` :: External version string, may be globally unique. Should be used by API calls.
+- `_iversion` :: Version ID for this entity for internal use, typically an incremental counter,
+ starting with 1
+- `_ipparent` :: Primary parent ID (internal) for this version, i.e. predecessor
+- `srid` :: Server request / transaction ID which created this version
+
+### `archive_foo_data` ###
+
+Older (i.e. not current) data value, from previous versions of an entity.
+- `domain_id` :: Same as in `foo_data`.
+- `entity_id` :: Same as in `foo_data`.
+- `property_id` :: Same as in `foo_data`.
+- `value` :: The value at the given version.
+- `status` :: The value at the given version.
+- `pidx` :: Same as in `foo_data`.
+- `_iversion` :: Version index of this version.
+- ... :: Data type specific columns may also be there.
+
## TODO ##
- entity_acl
diff --git a/patches/patch20200710-3.0.0-rc2/fix_unversioned.sql b/patches/patch20200710-3.0.0-rc2/fix_unversioned.sql
index 329706a..b3017b6 100644
--- a/patches/patch20200710-3.0.0-rc2/fix_unversioned.sql
+++ b/patches/patch20200710-3.0.0-rc2/fix_unversioned.sql
@@ -49,6 +49,8 @@ BEGIN
INSERT IGNORE INTO transactions (srid, username, realm, seconds, nanos)
SELECT tmp.srid, tmp.username, tmp.realm, tmp.seconds, tmp.nanos FROM (
SELECT
+ -- SRID needs to be invented in this case, because original server request ID is
+ -- not known (any more).
SHA2(CONCAT(username, realm, seconds, nanos), 512) AS srid,
username AS username,
realm AS realm,
@@ -57,15 +59,15 @@ BEGIN
FROM transaction_log
WHERE entity_id = unversioned_id
UNION SELECT
- -- this is for the standard entities (id<100)
+ -- this is the fallback for the standard entities (id<100)
SHA2("", 512) AS srid,
"administration" As username,
"CaosDB" AS realm,
0 as seconds,
0 as nanos
- ) AS tmp ORDER BY tmp.seconds DESC, tmp.nanos DESC LIMIT 1;
+ ) AS tmp ORDER BY tmp.seconds DESC, tmp.nanos DESC LIMIT 1; -- only latest transaction
- -- insert single version into entity_version
+ -- insert single (latest) version into entity_version
INSERT INTO entity_version (entity_id, hash, version, _iversion,
_ipparent, srid)
SELECT tmp.entity_id, tmp.hash, tmp.version, tmp._iversion,
diff --git a/patches/patch20200710-3.0.0-rc2/versioning.sql b/patches/patch20200710-3.0.0-rc2/versioning.sql
index 2be9925..9f29897 100644
--- a/patches/patch20200710-3.0.0-rc2/versioning.sql
+++ b/patches/patch20200710-3.0.0-rc2/versioning.sql
@@ -51,9 +51,9 @@ CREATE TABLE transactions (
CREATE TABLE entity_version (
entity_id INT UNSIGNED NOT NULL,
hash VARBINARY(255) DEFAULT NULL,
- version VARBINARY(255) NOT NULL,
- _iversion INT UNSIGNED NOT NULL,
- _ipparent INT UNSIGNED NULL,
+ version VARBINARY(255) NOT NULL, -- external version identifier, may be globally unique
+ _iversion INT UNSIGNED NOT NULL, -- internal version ID, typically an incremental counter
+ _ipparent INT UNSIGNED NULL, -- (internal) ID of the primary parent, i.e. of the predecessor
srid VARBINARY(255) NOT NULL,
PRIMARY KEY (`entity_id`, `_iversion`),
FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
@@ -72,7 +72,8 @@ CREATE TABLE archive_isa (
child_iversion INT UNSIGNED NOT NULL,
parent INT UNSIGNED NOT NULL,
FOREIGN KEY (`parent`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
- FOREIGN KEY (`child`, `child_iversion`) REFERENCES `entity_version` (`entity_id`, `_iversion`) ON DELETE CASCADE
+ FOREIGN KEY (`child`, `child_iversion`) REFERENCES `entity_version`
+ (`entity_id`, `_iversion`) ON DELETE CASCADE
) ENGINE=InnoDB;
CREATE TABLE archive_reference_data (
diff --git a/procedures/deleteEntityProperties.sql b/procedures/deleteEntityProperties.sql
index 1da3fef..2075696 100644
--- a/procedures/deleteEntityProperties.sql
+++ b/procedures/deleteEntityProperties.sql
@@ -4,6 +4,8 @@
*
* 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
@@ -31,10 +33,11 @@ BEGIN
CALL deleteIsa(EntityID);
IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
- SELECT max(e._iversion) INTO IVersion
+ SELECT max(e._iversion) INTO IVersion -- What's the latest version?
FROM entity_version AS e
WHERE e.entity_id = EntityID;
+ -- Copy the rows from *_data to archive_*_data ---------------------
INSERT INTO archive_reference_data (domain_id, entity_id,
property_id, value, value_iversion, status, pidx, _iversion)
SELECT domain_id, entity_id, property_id, value, value_iversion,
diff --git a/procedures/deleteIsaCache.sql b/procedures/deleteIsaCache.sql
index 1c0ab90..f37c3fc 100644
--- a/procedures/deleteIsaCache.sql
+++ b/procedures/deleteIsaCache.sql
@@ -5,6 +5,7 @@
* 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
@@ -48,7 +49,7 @@ BEGIN
FROM entity_version
WHERE entity_id = EntityID;
- -- move to archive_isa before deleting
+ -- move to archive_isa before deleting (only direct child-parent relations)
INSERT INTO archive_isa (child, child_iversion, parent)
SELECT e.child, IVersion AS child_iversion, e.parent
FROM isa_cache AS e
diff --git a/procedures/entityVersioning.sql b/procedures/entityVersioning.sql
index da0decb..b009d3f 100644
--- a/procedures/entityVersioning.sql
+++ b/procedures/entityVersioning.sql
@@ -18,26 +18,28 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-
-DROP PROCEDURE IF EXISTS db_2_0.insert_single_child_version;
delimiter //
+DROP PROCEDURE IF EXISTS db_2_0.insert_single_child_version //
+
/**
* Creates a new version record in the `entity_version` table.
*
* Parameters
* ----------
* EntityID
- * The id of the versioned entity.
+ * The ID of the versioned entity.
* Hash
* A hash of the entity. This is currently not implemented properly and only
* there for future use.
* Version
- * The id of the entity version.
+ * The new version ID of the entity, must be produced by the caller. Must be unique for each
+ * EntityID.
* Parent
- * The primary parent version's id.
+ * The version ID of the primary parent (i.e. predecessor). May be NULL; but if given, it must
+ * exist.
* Transaction
- * The id of the transaction which created this entity version (by inserting
+ * The transaction ID which created this entity version (by inserting
* or updating an entity).
*/
CREATE PROCEDURE db_2_0.insert_single_child_version(
@@ -137,7 +139,7 @@ END;
DROP FUNCTION IF EXISTS db_2_0.get_primary_parent_version //
/**
- * Get the version id of the primary parent of a version.
+ * Get the version ID of the primary parent (i.e. predecessor) of a version.
*
* Parameters
* ----------
@@ -158,10 +160,9 @@ READS SQL DATA
BEGIN
RETURN (
SELECT p.version
- FROM entity_version AS e
- INNER JOIN entity_version as p
- ON (e._ipparent = p._iversion
- AND e.entity_id = p.entity_id)
+ FROM entity_version AS e INNER JOIN entity_version AS p
+ ON (e._ipparent = p._iversion
+ AND e.entity_id = p.entity_id)
WHERE e.entity_id = EntityID
AND e.version = Version
);
@@ -184,6 +185,7 @@ DROP FUNCTION IF EXISTS db_2_0.get_version_timestamp //
* Returns
* -------
* The versions' timestamp in <seconds-since-epoch>.<nanoseconds> format.
+ * Note that the dot `.` here is not necessarily a decimal separator.
*/
CREATE FUNCTION db_2_0.get_version_timestamp(
EntityID INT UNSIGNED,
@@ -193,9 +195,8 @@ READS SQL DATA
BEGIN
RETURN (
SELECT concat(t.seconds, '.', t.nanos)
- FROM entity_version AS e
- INNER JOIN transactions AS t
- ON ( e.srid = t.srid )
+ FROM entity_version AS e INNER JOIN transactions AS t
+ ON ( e.srid = t.srid )
WHERE e.entity_id = EntityID
AND e.version = Version
);
@@ -252,9 +253,9 @@ RETURNS VARBINARY(255)
READS SQL DATA
BEGIN
-- This implementation assumes that the distance from the head equals the
- -- difference between the _iversion numbers. This will not be correct anymore,
- -- as soon as branches may split and merge. Then, an tree-walk will be
- -- necessary, traversing the primary parents (_pparent), will be necessary.
+ -- difference between the _iversion numbers. This will not be correct anymore
+ -- as soon as branches may split and merge. Then, a walk over the primary
+ -- parents (_ipparent) will be necessary.
RETURN (
SELECT e.version
FROM entity_version AS e
@@ -297,7 +298,7 @@ END;
DROP PROCEDURE IF EXISTS db_2_0.get_version_history //
/**
- * Select all version information of an entity.
+ * Select version timestamps of an entity.
*
* Parameters
* ----------
@@ -306,18 +307,18 @@ DROP PROCEDURE IF EXISTS db_2_0.get_version_history //
*
* Selects
* -------
- * Tuples (child, parent, child_seconds, child_nanos). child and parent are version ids.
+ * Tuples (child, parent, child_seconds, child_nanos). `child` and `parent` are
+ * version IDs.
*/
CREATE PROCEDURE db_2_0.get_version_history(
in EntityID INT UNSIGNED)
BEGIN
- -- retrieve root(s)
+ -- retrieve root(s) (initial versions)
SELECT c.version AS child,
NULL as parent,
t.seconds AS child_seconds,
t.nanos AS child_nanos
- FROM entity_version AS c
- INNER JOIN transactions as t
+ FROM entity_version AS c INNER JOIN transactions as t
ON ( c.srid = t.srid )
WHERE c.entity_id = EntityID
AND c._ipparent is Null
@@ -326,17 +327,17 @@ BEGIN
-- does not return the root. However, this should be doable in one go with
-- a left join instead of an inner join(?).
- -- retrieve branches
+ -- retrieve branches (later versions)
UNION SELECT c.version AS child,
p.version AS parent,
t.seconds AS child_seconds,
t.nanos AS child_nanos
FROM entity_version AS p
- INNER JOIN entity_version as c
- INNER JOIN transactions AS t
- ON (c._ipparent = p._iversion
- AND c.entity_id = p.entity_id
- AND t.srid = c.srid)
+ INNER JOIN entity_version as c
+ INNER JOIN transactions AS t
+ ON (c._ipparent = p._iversion
+ AND c.entity_id = p.entity_id
+ AND t.srid = c.srid)
WHERE p.entity_id = EntityID;
END;
//
@@ -368,7 +369,7 @@ CREATE PROCEDURE set_transaction(
nanos INT(10) UNSIGNED)
BEGIN
- SET @SRID = srid;
+ SET @SRID = srid; -- Make the transaction / server request ID globally available.
INSERT INTO transactions (srid, username, realm, seconds, nanos)
VALUES (srid, username, realm, seconds, nanos);
END //
@@ -387,7 +388,8 @@ DROP PROCEDURE IF EXISTS setFileProperties //
* EntityID
* The file's id.
* FilePath
- * Path of the file in the internal file system.
+ * Path of the file in the internal file system. If NULL, an existing file
+ * entity is simply deleted.
* FileSize
* Size of the file in bytes.
* FileHash
@@ -426,10 +428,7 @@ END //
DROP PROCEDURE IF EXISTS retrieveQueryTemplateDef //
/**
- * Insert/Update file properties.
- *
- * If ENTITY_VERSIONING is enabled the old file properties are moved to
- * `archive_files`.
+ * Select a query string from the templates tables.
*
* Parameters
* ----------
@@ -452,11 +451,13 @@ retrieveQueryTemplateDefBody: BEGIN
DECLARE IsHead BOOLEAN DEFAULT TRUE;
IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
+ -- Are we at the head?
IF Version IS NOT NULL THEN
SELECT get_head_version(EntityID) = Version INTO IsHead;
END IF;
IF IsHead IS FALSE THEN
+ -- TODO Use get_iversion(EntityID, Version) instead? Or will that be much slower?
SELECT e._iversion INTO IVersion
FROM entity_version as e
WHERE e.entity_id = EntityID
diff --git a/procedures/insertEntity.sql b/procedures/insertEntity.sql
index 4816edd..50a3997 100644
--- a/procedures/insertEntity.sql
+++ b/procedures/insertEntity.sql
@@ -5,6 +5,7 @@
* 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
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -39,6 +40,11 @@ Currently one of 'RECORDTYPE', 'RECORD', 'FILE', 'DOMAIN', 'PROPERTY',
'DATATYPE', 'ROLE', 'QUERYTEMPLATE'
ACL : VARBINARY(65525)
+
+Select
+======
+
+A tuple (EntityID, Version)
*/
CREATE PROCEDURE db_2_0.insertEntity(in EntityName VARCHAR(255), in EntityDesc TEXT, in EntityRole VARCHAR(255), in ACL VARBINARY(65525))
BEGIN
diff --git a/procedures/insertEntityProperty.sql b/procedures/insertEntityProperty.sql
index 8d7ab63..d208dbc 100644
--- a/procedures/insertEntityProperty.sql
+++ b/procedures/insertEntityProperty.sql
@@ -4,6 +4,8 @@
*
* 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
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -59,6 +61,7 @@ BEGIN
(DomainID, EntityID, PropertyID, SUBSTRING_INDEX(PropertyValue, 'UTC', 1), IF(SUBSTRING_INDEX(PropertyValue, 'UTC', -1)='',NULL,SUBSTRING_INDEX(PropertyValue, 'UTC', -1)), PropertyStatus, PropertyIndex);
WHEN 'reference_data' THEN
+ -- special handling if versioning enabled and specific version of referenced entity is given.
SET AT_PRESENT=LOCATE("@", PropertyValue);
IF is_feature_config("ENTITY_VERSIONING", "ENABLED") AND AT_PRESENT > 0 THEN
SET ReferenceValue = SUBSTRING_INDEX(PropertyValue, '@', 1);
diff --git a/procedures/retrieveEntity.sql b/procedures/retrieveEntity.sql
index 9451955..e06e6fb 100644
--- a/procedures/retrieveEntity.sql
+++ b/procedures/retrieveEntity.sql
@@ -4,6 +4,8 @@
*
* 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
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -27,7 +29,24 @@ delimiter //
drop procedure if exists db_2_0.retrieveEntity //
-create procedure db_2_0.retrieveEntity(in EntityID INT UNSIGNED, in Version VARBINARY(255))
+/**
+ * Select the content of an entity.
+ *
+ * By default the head is selected, but a specific version may be given.
+ *
+ * Parameters
+ * ----------
+ * EntityID
+ * The entity's id.
+ * Version
+ * The version id. In this procedure only, the version may also be given as
+ * `HEAD` for the latest version or as `HEAD~n`, which retrieves the n-th
+ * ancestor of `HEAD`.
+ *
+ */
+create procedure db_2_0.retrieveEntity(
+ in EntityID INT UNSIGNED,
+ in Version VARBINARY(255))
retrieveEntityBody: BEGIN
DECLARE FilePath VARCHAR(255) DEFAULT NULL;
DECLARE FileSize VARCHAR(255) DEFAULT NULL;
@@ -41,6 +60,7 @@ retrieveEntityBody: BEGIN
IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
+ -- Find out head-ness and version
IF Version IS NULL OR UPPER(Version) = "HEAD" THEN
SET Version = get_head_version(EntityID);
ELSEIF UPPER(LEFT(Version, 5)) = "HEAD~" THEN
@@ -92,7 +112,8 @@ retrieveEntityBody: BEGIN
AND _iversion = IVersion
LIMIT 1;
- Select
+ -- Final select before returning
+ SELECT
( SELECT value FROM
( SELECT value FROM name_data
WHERE domain_id = 0
@@ -110,7 +131,7 @@ retrieveEntityBody: BEGIN
e.role AS EntityRole,
FileSize AS FileSize,
FilePath AS FilePath,
- FileHASh AS FileHASh,
+ FileHash AS FileHash,
(SELECT acl FROM entity_acl AS a WHERE a.id = e.acl) AS ACL,
Version AS Version,
VersionSeconds AS VersionSeconds,
@@ -126,13 +147,13 @@ retrieveEntityBody: BEGIN
END IF;
END IF;
- Select path, size, hex(hash)
+ SELECT path, size, hex(hash)
INTO FilePath, FileSize, FileHash
FROM files
WHERE file_id = EntityID
LIMIT 1;
- Select datatype INTO DatatypeID
+ SELECT datatype INTO DatatypeID
FROM data_type
WHERE domain_id=0
AND entity_id=0
@@ -146,7 +167,7 @@ retrieveEntityBody: BEGIN
AND property_id=EntityID
LIMIT 1;
- Select
+ SELECT
( SELECT value FROM name_data
WHERE domain_id = 0
AND entity_ID = DatatypeID
diff --git a/procedures/retrieveEntityOverrides.sql b/procedures/retrieveEntityOverrides.sql
index 7a929bb..fa43d6b 100644
--- a/procedures/retrieveEntityOverrides.sql
+++ b/procedures/retrieveEntityOverrides.sql
@@ -4,6 +4,8 @@
*
* 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
@@ -54,6 +56,7 @@ retrieveOverridesBody: BEGIN
LEAVE retrieveOverridesBody;
END IF;
+ -- name
SELECT
NULL AS collection_override,
name AS name_override,
@@ -68,6 +71,7 @@ retrieveOverridesBody: BEGIN
UNION ALL
+ -- description
SELECT
NULL AS collection_override,
NULL AS name_override,
@@ -82,6 +86,7 @@ retrieveOverridesBody: BEGIN
UNION ALL
+ -- data type
SELECT
NULL AS collection_override,
NULL AS name_override,
@@ -102,6 +107,7 @@ retrieveOverridesBody: BEGIN
UNION ALL
+ -- collection
SELECT
collection AS collection_override,
NULL AS name_override,
@@ -114,7 +120,6 @@ retrieveOverridesBody: BEGIN
AND entity_id = EntityID
AND _iversion = IVersion;
-
LEAVE retrieveOverridesBody;
END IF;
END IF;
diff --git a/procedures/retrieveEntityParents.sql b/procedures/retrieveEntityParents.sql
index 6c50e97..16466fc 100644
--- a/procedures/retrieveEntityParents.sql
+++ b/procedures/retrieveEntityParents.sql
@@ -5,6 +5,7 @@
* 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
@@ -80,13 +81,13 @@ retrieveEntityParentsBody: BEGIN
( SELECT value FROM archive_name_data
WHERE domain_id = 0
AND entity_id = ParentID
- AND property_id = 20 ) AS ParentName,
+ AND property_id = 20
+ AND _iversion = IVersion) AS ParentName,
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)
+ FROM archive_isa AS i JOIN entities AS e
+ ON (i.parent = e.id)
WHERE i.child = EntityID
AND i.child_iversion = IVersion;
@@ -103,9 +104,8 @@ retrieveEntityParentsBody: BEGIN
e.description AS ParentDescription,
e.role AS ParentRole,
(SELECT acl FROM entity_acl AS a WHERE a.id = e.acl) AS ACL
- FROM isa_cache AS i
- JOIN entities AS e
- ON (i.parent = e.id)
+ FROM isa_cache AS i JOIN entities AS e
+ ON (i.parent = e.id)
WHERE i.child = EntityID
AND i.rpath = EntityID;
END
diff --git a/procedures/retrieveEntityProperties.sql b/procedures/retrieveEntityProperties.sql
index e149702..3d8eeff 100644
--- a/procedures/retrieveEntityProperties.sql
+++ b/procedures/retrieveEntityProperties.sql
@@ -4,6 +4,8 @@
*
* 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
@@ -140,6 +142,7 @@ retrieveEntityPropertiesBody: BEGIN
SELECT
property_id AS PropertyID,
IF(value_iversion IS NULL, value,
+ -- make it "value@version" if necessary
CONCAT(value, "@", _get_version(value, value_iversion)))
AS PropertyValue,
status AS PropertyStatus,
diff --git a/procedures/updateEntity.sql b/procedures/updateEntity.sql
index 9260c25..226208e 100644
--- a/procedures/updateEntity.sql
+++ b/procedures/updateEntity.sql
@@ -4,6 +4,8 @@
*
* 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
@@ -21,16 +23,16 @@
* ** end header
*/
-
-
-
-
-
-
-
DROP PROCEDURE IF EXISTS db_2_0.updateEntity;
delimiter //
+/*
+ * Update an entity (that is, its metadata like name, description, ...).
+ *
+ * At the moment, the version ID is generated internally.
+ *
+ * Selects the new version identifier for the entity.
+ */
CREATE PROCEDURE db_2_0.updateEntity(
in EntityID INT UNSIGNED,
in EntityName VARCHAR(255),
@@ -54,8 +56,7 @@ BEGIN
FROM entity_version
WHERE entity_id = EntityID;
-
- -- move old data to archive
+ -- move old data to archives
INSERT INTO archive_entities (id, description, role,
acl, _iversion)
SELECT e.id, e.description, e.role, e.acl, OldIVersion
@@ -81,8 +82,6 @@ BEGIN
AND e.property_id = EntityID;
-
-
SET Transaction = @SRID;
SELECT e.version INTO ParentVersion
FROM entity_version as e
@@ -96,7 +95,7 @@ BEGIN
UPDATE entities e
SET e.description = EntityDescription,
e.role=EntityRole,
- e.acl = ACLID
+ e.acl = ACLID
WHERE e.id = EntityID;
-- clean up primary name, because updateEntity might be called without a
diff --git a/tests/test_0_setup.sql b/tests/test_0_setup.sql
index 9b98f5d..4068859 100644
--- a/tests/test_0_setup.sql
+++ b/tests/test_0_setup.sql
@@ -1,3 +1,25 @@
+/**
+ * ** header v3.0
+ * 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/>.
+ *
+ * ** end header
+ */
/**
* Execute an SQL statement and pass if the statement throws an SQLEXCEPTION.
diff --git a/tests/test_entity_versioning.sql b/tests/test_entity_versioning.sql
index 0446dce..0c5147c 100644
--- a/tests/test_entity_versioning.sql
+++ b/tests/test_entity_versioning.sql
@@ -1,3 +1,26 @@
+/**
+ * ** header v3.0
+ * 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/>.
+ *
+ * ** end header
+ */
+
USE _caosdb_schema_unit_tests;
BEGIN;
CALL tap.no_plan();
@@ -17,7 +40,7 @@ CALL tap.no_plan();
DELETE FROM entity_version;
DELETE FROM transactions;
DELETE FROM feature_config WHERE _key = "ENTITY_VERSIONING";
-INSERT INTO transactions (srid,seconds,nanos,username,realm) VALUES
+INSERT INTO transactions (srid,seconds,nanos,username,realm) VALUES
("SRIDbla", 1234, 2345, "me", "home"),
("SRIDblub", 2345, 3465, "me", "home"),
("SRIDblieb", 3456, 4576, "you", "home");
@@ -37,7 +60,7 @@ SELECT tap.eq(@x, NULL, "no parent for the first version");
-- add a second version
SELECT count(*) INTO @x FROM entity_version;
-SELECT tap.eq(@x, 1, "one version there yet");
+SELECT tap.eq(@x, 1, "one version there already");
CALL insert_single_child_version(@EntityID, "hashblub", "versionblub", "versionbla", "SRIDblub");
SELECT _ipparent INTO @x from entity_version WHERE version="versionblub";
@@ -45,12 +68,15 @@ SELECT tap.eq(@x, 1, "the original entity is the parent");
-- error: parent does not exist
SELECT count(*) INTO @x FROM entity_version;
-SELECT tap.eq(@x, 2, "two version there yet");
+SELECT tap.eq(@x, 2, "two versions there already");
-CALL tap._assert_throws(concat("CALL insert_single_child_version(", @EntityID, ', "hashblieb", "versionblieb", "non-existing-parent", "SRIDBlieb")'), "non existing parent throws");
+CALL tap._assert_throws(
+ concat("CALL insert_single_child_version(",
+ @EntityID, ', "hashblieb", "versionblieb", "non-existing-parent", "SRIDBlieb")'),
+ "non existing parent throws");
SELECT count(*) INTO @x FROM entity_version;
-SELECT tap.eq(@x, 2, "still two version there");
+SELECT tap.eq(@x, 2, "still two versions there");
-- TEST get_primary_parent_version
@@ -196,11 +222,12 @@ SET @TheUser = "TheUser"; -- used to identify the matching entry in transaction_
-- fill transaction_log: one entity with two updates (and one insert) and another entity with insert and delete.
INSERT INTO transaction_log (transaction, entity_id, username, realm, seconds, nanos)
-- the first entry is the one which is be found by _fix_unversioned
- VALUES ("Update", @EntityID, @TheUser, "CaosDB", 23458, 254),
- -- the rest is dummy data
- ("Update", @EntityID, "OtherUser", "CaosDB", 2345, 633), -- not the latest transaction
- ("Insert", @EntityID, "OtherUser", "CaosDB", 245, 633), -- not the latest transaction
- ("Insert", @EntityID + 1, @TheUser, "CaosDB", 2325, 653), -- not the right entity, inserted before our target
+ VALUES
+ ("Update", @EntityID, @TheUser, "CaosDB", 23458, 254),
+ -- the rest is dummy data
+ ("Update", @EntityID, "OtherUser", "CaosDB", 2345, 633), -- not the latest transaction
+ ("Insert", @EntityID, "OtherUser", "CaosDB", 245, 633), -- not the latest transaction
+ ("Insert", @EntityID + 1, @TheUser, "CaosDB", 2325, 653), -- not the right entity, inserted before our target
("Delete", @EntityID + 1, @TheUser, "CaosDB", 232526, 653); -- not the right entity, deleted after our target
@@ -214,12 +241,16 @@ SELECT tap.eq(COUNT(*), 0, "still, no transaction there") FROM transactions;
-- call _fix_unversioned
CALL _fix_unversioned();
-SELECT tap.eq(COUNT(*), @NumOfEntities, "after _fix_unversioned, one entry for our test entity in entity_version") FROM entity_version;
-SELECT tap.eq(COUNT(*), 2, "after _fix_unversioned, one entry for our test entity in transactions, one for the standard entities.") FROM transactions;
+SELECT tap.eq(COUNT(*), @NumOfEntities,
+ "after _fix_unversioned, one entry for our test entity in entity_version")
+ FROM entity_version;
+SELECT tap.eq(COUNT(*), 2,
+ "after _fix_unversioned, one entry for our test entity in transactions, one for the standard entities.")
+ FROM transactions;
SELECT tap.eq(entity_id, @EntityID, "versioned entity has correct id") FROM entity_version WHERE entity_id > 99;
SELECT tap.ok(srid IS NOT NULL, "srid was generated and user/time matches entries from transaction_log")
- FROM transactions AS t JOIN transaction_log AS l
+ FROM transactions AS t JOIN transaction_log AS l
ON (l.seconds = t.seconds AND l.nanos = t.nanos AND l.username = t.username AND l.realm = t.realm)
WHERE l.entity_id = @EntityID AND l.username = @TheUser;
@@ -249,7 +280,7 @@ SELECT entity_id INTO @EntityID2 FROM name_data WHERE value="EntityName2";
INSERT INTO transaction_log (transaction, entity_id, username, realm, seconds,
nanos)
- -- the first entry is the one which is be found by _fix_unversioned
+ -- the first entry is the one which will be found by _fix_unversioned
VALUES ("INSERT", @EntityID1, "User", "CaosDB", 10000, 250),
("INSERT", @EntityID2, "User", "CaosDB", 10000, 250),
("UPDATE", @EntityID2, "User", "CaosDB", 20000, 250);
diff --git a/tests/test_insert_update_delete.sql b/tests/test_insert_update_delete.sql
index a43e028..a11b05e 100644
--- a/tests/test_insert_update_delete.sql
+++ b/tests/test_insert_update_delete.sql
@@ -29,7 +29,6 @@ SELECT tap.eq(acl, @ACLID1, "correct acl id had been assigned")
-- TEST insertEntityProperty
-
CALL insertEntity("AProperty", "APropDesc", "PROPERTY", "{acl1}");
SELECT entity_id INTO @PropID FROM name_data WHERE value="AProperty";
INSERT INTO data_type (domain_id, entity_id, property_id, datatype) VALUES (0, 0, @PropID, @TextDatatypeID);
@@ -41,7 +40,6 @@ SELECT COUNT(*) INTO @x FROM null_data;
SELECT tap.eq(@x, 1, "One row in null_data table");
-- TEST updateEntity
-
CALL updateEntity(@EntityID, "NewEntityName", "NewEntityDesc", "RECORD", NULL, NULL, "{acl2}");
SELECT tap.eq(COUNT(entity_id), 0, "Old Entity name not present")
@@ -58,20 +56,17 @@ CALL updateEntity(@EntityID, "NewEntityName", "NewEntityDesc", "RECORD", NULL, N
-- TEST deleteEntityProperties
-
CALL deleteEntityProperties(@EntityID);
SELECT COUNT(*) INTO @x FROM null_data;
SELECT tap.eq(@x, 0, "data removed from null_data table");
-- TEST deleteEntity
-
CALL deleteEntity(@EntityID);
CALL deleteEntity(@PropID);
SELECT COUNT(id) INTO @x FROM entities WHERE id>100;
SELECT tap.eq(@x, 0, "entity deleted");
-
-- TESTS END
CALL tap.finish();
diff --git a/tests/test_reference_values.sql b/tests/test_reference_values.sql
index e59c1f1..47b4db4 100644
--- a/tests/test_reference_values.sql
+++ b/tests/test_reference_values.sql
@@ -1,3 +1,26 @@
+/**
+ * ** header v3.0
+ * 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/>.
+ *
+ * ** end header
+ */
+
USE _caosdb_schema_unit_tests;
BEGIN;
@@ -8,10 +31,9 @@ CALL tap.no_plan();
-- #####################################################################
-- SETUP
-
DELETE FROM entity_version;
DELETE FROM transactions;
-INSERT INTO transactions (srid,seconds,nanos,username,realm) VALUES
+INSERT INTO transactions (srid,seconds,nanos,username,realm) VALUES
("SRIDbla", 1234, 2345, "me", "home"),
("SRIDblub", 2345, 3465, "me", "home"),
("SRIDblieb", 3456, 4576, "you", "home");
@@ -22,7 +44,6 @@ SET @Value=50;
-- switch off versioning
DELETE FROM feature_config WHERE _key = "ENTITY_VERSIONING";
-
-- TEST insertEntityProperty without Versioning
CALL insertEntityProperty(0, @EntityID, @PropertyID, "reference_data", @Value,
NULL, "FIX", NULL, NULL, NULL, NULL, 0);
@@ -36,7 +57,6 @@ SELECT tap.eq("FIX", status, "status ok") FROM reference_data;
SELECT tap.eq("0", pidx, "pidx ok") FROM reference_data;
SELECT tap.eq(NULL, value_iversion, "value_iversion ok") FROM reference_data;
-
-- clean up
DELETE FROM reference_data WHERE domain_id=0 AND entity_id=99;
@@ -44,7 +64,6 @@ DELETE FROM reference_data WHERE domain_id=0 AND entity_id=99;
-- TODO TEST insertEntityProperty with Versioning
-- #####################################################################
-
-- switch on versioning
INSERT INTO feature_config (_key, _value) VALUES ("ENTITY_VERSIONING", "ENABLED");
@@ -110,13 +129,9 @@ CALL tap._assert_throws('
NULL, "FIX", NULL, NULL, NULL, NULL, 0)', "non-existing-version id");
-
-
-- #####################################################################
-- TEST retrieveEntityProperty without Versioning
-- #####################################################################
-
-
CALL tap.finish();
ROLLBACK;
--
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