From 2471f53aa41812ac9b7e92bc7505aa2536da9633 Mon Sep 17 00:00:00 2001
From: Quazgar <quazgar@posteo.de>
Date: Tue, 7 Apr 2020 14:02:10 +0000
Subject: [PATCH] Fix self-inheritance in cache table
---
patches/utils/patch_header.sh | 17 ++++++-
procedures/deleteEntity.sql | 12 ++++-
procedures/deleteIsaCache.sql | 14 ++++++
procedures/insertEntity.sql | 16 +++++++
procedures/insertIsaCache.sql | 72 ++++++++++++++++++----------
procedures/retrieveEntityParents.sql | 33 +++++++++++--
update_sql_procedures.sh | 16 ++++++-
7 files changed, 145 insertions(+), 35 deletions(-)
diff --git a/patches/utils/patch_header.sh b/patches/utils/patch_header.sh
index fec3997..9fd7d05 100644
--- a/patches/utils/patch_header.sh
+++ b/patches/utils/patch_header.sh
@@ -4,7 +4,8 @@
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-# Copyright 2019 Daniel Hornung
+# Copyright (C) 2019-2020 Daniel Hornung
+# Copyright (C) 2020 IndiScale GmbH <info@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
@@ -101,7 +102,8 @@ while test $# -gt 0; do
esac
done
-source "$ENV_FILE" || true
+[[ -e "$ENV_FILE" ]] && source "$ENV_FILE" \
+ || echo "No ENV_FILE in environment or not found: $ENV_FILE"
if [[ -z "$DATABASE_NAME" && -z "$MYSQL_CONNECTION" ]]
then
@@ -187,6 +189,17 @@ function mysql_execute {
set -e
}
+# Takes a filename with commands instead of command line arguments
+function mysql_execute_file {
+ set +e
+ $CMD_MYSQL $MYSQL_CONNECTION < "$1"
+ ret=${PIPESTATUS[0]}
+ if [ "$ret" -ne 0 ]; then
+ failure "MYSQL ERROR"
+ fi
+ set -e
+}
+
function redo_table {
$CMD_MYSQL $MYSQL_CONNECTION < ${DATABASE_NAME}.${1}.${OLD_VERSION}.dump.sql
}
diff --git a/procedures/deleteEntity.sql b/procedures/deleteEntity.sql
index c83b1d1..0a70f20 100644
--- a/procedures/deleteEntity.sql
+++ b/procedures/deleteEntity.sql
@@ -4,6 +4,7 @@
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -21,11 +22,18 @@
* ** end header
*/
+/* Delete a (sparse) Entity from the database.
+Note that all properties, including is-a relationships of this Entity should
+have been deleted before. This can be done for example with the
+`deleteEntityProperties` procedure.
+Parameters
+==========
-
-
+EntityID : UNSIGNED
+The ID of the Entity.
+*/
DROP PROCEDURE IF EXISTS db_2_0.deleteEntity;
delimiter //
diff --git a/procedures/deleteIsaCache.sql b/procedures/deleteIsaCache.sql
index 57bb651..6713d4a 100644
--- a/procedures/deleteIsaCache.sql
+++ b/procedures/deleteIsaCache.sql
@@ -4,6 +4,7 @@
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -25,6 +26,19 @@ SET GLOBAL log_bin_trust_function_creators = 1;
DROP PROCEDURE IF EXISTS db_2_0.deleteIsa;
DELIMITER //
+/* Delete "is a" relations from the given entity towards ancestors.
+
+Note that relations towards descendants are not deleted (they probably should have been deleted before).
+
+After this procedure, there are no more entries in `isa_cache`, where the
+parameter entity is a child or inside the rpath.
+
+Parameters
+==========
+
+EntityID : UNSIGNED
+Child entity for which all parental relations should be deleted.
+*/
CREATE PROCEDURE db_2_0.deleteIsa(IN EntityID INT UNSIGNED)
BEGIN
diff --git a/procedures/insertEntity.sql b/procedures/insertEntity.sql
index 5b05d36..8e307a8 100644
--- a/procedures/insertEntity.sql
+++ b/procedures/insertEntity.sql
@@ -4,6 +4,7 @@
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -24,6 +25,21 @@
DROP PROCEDURE IF EXISTS db_2_0.insertEntity;
delimiter //
+/* Insert an Entity
+
+Parameters
+==========
+
+EntityName : VARCHAR(255)
+
+EntityDesc : TEXT
+
+EntityRole : VARCHAR(255)
+Currently one of 'RECORDTYPE', 'RECORD', 'FILE', 'DOMAIN', 'PROPERTY',
+'DATATYPE', 'ROLE', 'QUERYTEMPLATE'
+
+ACL : VARBINARY(65525)
+*/
CREATE PROCEDURE db_2_0.insertEntity(in EntityName VARCHAR(255), in EntityDesc TEXT, in EntityRole VARCHAR(255), in ACL VARBINARY(65525))
BEGIN
DECLARE NewEntityID INT UNSIGNED DEFAULT NULL;
diff --git a/procedures/insertIsaCache.sql b/procedures/insertIsaCache.sql
index 735ba12..aacb4cd 100644
--- a/procedures/insertIsaCache.sql
+++ b/procedures/insertIsaCache.sql
@@ -4,6 +4,7 @@
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -23,42 +24,61 @@
DROP PROCEDURE IF EXISTS db_2_0.insertIsa;
DELIMITER //
+/* Insert an "is a" relation
+
+This procedure fills the isa_cache table. All passed entities must be existing
+in entities.id.
+
+Parameters
+==========
+
+c : UNSIGNED
+The child entity
+
+p : UNSIGNED
+The parent entity
+*/
CREATE PROCEDURE db_2_0.insertIsa(IN c INT UNSIGNED, IN p INT UNSIGNED)
-BEGIN
+insert_is_a_proc: BEGIN
- INSERT INTO isa_cache (child, parent, rpath) VALUES (c,p,c);
-
- -- foreach supertype of p
+ INSERT INTO isa_cache (child, parent, rpath) VALUES (c, p, c);
+
+ IF p = c THEN
+ -- Any additional entries would be redundant.
+ LEAVE insert_is_a_proc;
+ END IF;
+
+ -- Insert ancestors older than parents:
+ -- for each supertype of p
-- INSERT (c, supertype, p);
INSERT IGNORE INTO isa_cache SELECT
c
- AS child,
+ AS child, -- Current child
i.parent
- AS parent,
- IF(p=i.rpath or i.rpath=parent,
- p,
- concat(p, ">", i.rpath))
+ AS parent, -- Existing supertype
+ IF(p=i.rpath or i.rpath=parent, -- If ancestor=parent or parent = grandparent:
+ p, -- New parent (directly)
+ concat(p, ">", i.rpath)) -- Else "p>super.rpath"
AS rpath
- FROM isa_cache AS i WHERE i.child = p;
-
+ FROM isa_cache AS i WHERE i.child = p; -- Select rows with supertype
- -- foreach subtype of c insert each supertype of p
+ -- Propagate to descendants:
+ -- for each subtype of c: insert each supertype of p
INSERT IGNORE INTO isa_cache SELECT
- l.child,
- r.parent,
- if(l.rpath=l.child and r.rpath=c,
- c,
- concat(if(l.rpath=l.child,
- c,
- concat(l.rpath, '>', c)),
- if(r.rpath=c,
- '',
- concat('>', r.rpath))))
+ l.child, -- Descendant as found in isa_cache
+ r.parent, -- Ancestor as found in isa_cache
+ if(l.rpath=l.child and r.rpath=c, -- if distance=1 for left and right:
+ c, -- rpath = current child
+ concat(if(l.rpath=l.child, -- if dist=1 for descendant:
+ c, -- rpath starts with c
+ concat(l.rpath, '>', c)), -- rpath starts with "desc.rpath > c"
+ if(r.rpath=c, -- if dist=1 for ancestor
+ '', -- rpath is finished
+ concat('>', r.rpath)))) -- rpath continuees with " > ancest.rpath"
AS rpath
- FROM isa_cache as l
- INNER JOIN isa_cache as r ON (l.parent = r.child AND l.parent=c);
-
-
+ FROM
+ isa_cache as l INNER JOIN isa_cache as r
+ ON (l.parent = c AND c = r.child); -- Left: descendants of c, right: ancestors
END;
//
diff --git a/procedures/retrieveEntityParents.sql b/procedures/retrieveEntityParents.sql
index 9b99c36..ffd9f13 100644
--- a/procedures/retrieveEntityParents.sql
+++ b/procedures/retrieveEntityParents.sql
@@ -4,6 +4,7 @@
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -23,8 +24,33 @@
DROP PROCEDURE IF EXISTS db_2_0.retrieveEntityParents;
-delimiter //
+DELIMITER //
+/* Retrieve the parents of an Entity.
+
+Parameters
+==========
+
+EntityID : UNSIGNED
+Child entity for which all parental relations should be deleted.
+
+Returns
+=======
+ParentID : INT UNSIGNED
+ Each parent's ID
+
+ParentName :
+ The parent's name.
+
+ParentDescription :
+ The parent's description.
+
+ParentRole :
+ The parent's Role.
+
+ACL :
+ Access control list something
+*/
CREATE PROCEDURE db_2_0.retrieveEntityParents(in EntityID INT UNSIGNED)
BEGIN
@@ -32,6 +58,7 @@ SELECT parent AS ParentID, name AS ParentName, description AS ParentDescription,
+END
+//
-END//
-delimiter ;
+DELIMITER ;
diff --git a/update_sql_procedures.sh b/update_sql_procedures.sh
index 7b0b457..22f823a 100755
--- a/update_sql_procedures.sh
+++ b/update_sql_procedures.sh
@@ -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>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
@@ -29,11 +30,22 @@ source patches/utils/patch_header.sh
echo -n "updating rules ... "
set -e
-mysql_execute "$(sed s/db_2_0/$DATABASE_NAME/g rules.sql)"
+temp_rules_sql=$(tempfile --suffix=.sql)
+sed s/db_2_0/$DATABASE_NAME/g rules.sql > "$temp_rules_sql"
+mysql_execute_file "$temp_rules_sql"
+# We keep this for debugging purposes...
+# rm "$temp_rules_sql"
+
echo "[OK]"
echo -n "updating procedures ... "
-mysql_execute "$(sed s/db_2_0/$DATABASE_NAME/g procedures/*.sql procedures/query/*.sql)"
+temp_proc_sql=$(tempfile --suffix=.sql)
+sed -e "s/db_2_0/$DATABASE_NAME/g" procedures/*.sql procedures/query/*.sql \
+ > "$temp_proc_sql"
+mysql_execute_file "$temp_proc_sql"
+# We keep this for debugging purposes...
+# rm "$temp_proc_sql"
+
success
--
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