diff --git a/.docker/Dockerfile b/.docker/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..14ae750aa7f2f0c8262895c9b64a2a7f6e094d0f
--- /dev/null
+++ b/.docker/Dockerfile
@@ -0,0 +1,3 @@
+FROM debian:stretch
+RUN apt-get update && \
+ apt-get install curl -y
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 50d119aae3fbfa99bf3bf8c122b4aa14f4ae0b5d..98008035a95874d678df722819979393f5692f0c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,9 +1,9 @@
#
-# ** 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) 2019 Henrik tom Wörden
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
@@ -18,139 +18,45 @@
# 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
-#
-stages:
- - configure
- - test
- - setup
- - clean
-
-###########################
-# configure
-###########################
-
-configure:mysql55:
- stage: configure
- tags: [ mysql55 ]
- artifacts:
- paths:
- - .config.mysql55
- script:
- - printf "\n\n\n\n\n\n\n\n\n$MYSQL_USER_PASSWORD" > .user_input
- - ./configure < .user_input
- - test -f .config
- - cp .config .config.mysql55
-
-configure:mariadb10.1:
- stage: configure
- tags: [ maria10.1 ]
- artifacts:
- paths:
- - .config.mariadb10.1
- script:
- - printf "\n\n\n\n\ncaosdb-root\n\n\n\n$MYSQL_USER_PASSWORD" > .user_input
- - ./configure < .user_input
- - test -f .config
- - cp .config .config.mariadb10.1
-
-##########################
-# test
-##########################
+variables:
+ CI_REGISTRY_IMAGE: $CI_REGISTRY/caosdb-mysqlbackend-testenv:latest
+ # When using dind, it's wise to use the overlayfs driver for
+ # improved performance.
+ DOCKER_DRIVER: overlay2
-# test the connection
-test:test-connection:mysql55:
- stage: test
- tags: [ mysql55 ]
- dependencies:
- - configure:mysql55
- script:
- - cp .config.mysql55 .config
- - make test-connection
-
-test:test-connection:mariadb10.1:
- stage: test
- tags: [ maria10.1 ]
- dependencies:
- - configure:mariadb10.1
- script:
- - cp .config.mariadb10.1 .config
- - make test-connection
+services:
+ - docker:19.03-dind
-#########################
-# setup
-#########################
-
-# install without patches and drop
-setup:install:mysql55:
- stage: setup
- tags: [ mysql55 ]
- dependencies:
- - configure:mysql55
- script:
- - cp .config.mysql55 .config
- - export $(sed -n '/DATABASE_NAME/p ' .config)
- - make _install
- - make drop-$DATABASE_NAME
-
-setup:install:mariadb10.1:
- stage: setup
- tags: [ maria10.1 ]
- dependencies:
- - configure:mariadb10.1
- script:
- - cp .config.mariadb10.1 .config
- - export $(sed -n '/DATABASE_NAME/p ' .config)
- - make _install
- - make drop-$DATABASE_NAME
-
-# upgrade database with patches and drop
-setup:install_upgrade:mysql55:
- stage: setup
- tags: [ mysql55 ]
- dependencies:
- - configure:mysql55
- script:
- - cp .config.mysql55 .config
- - export $(sed -n '/DATABASE_NAME/p ' .config)
- - make install
- - make drop-$DATABASE_NAME
-
-setup:install_upgrade:mariadb10.1:
- stage: setup
- tags: [ maria10.1 ]
- dependencies:
- - configure:mariadb10.1
- script:
- - cp .config.mariadb10.1 .config
- - export $(sed -n '/DATABASE_NAME/p ' .config)
- - make install
- - make drop-$DATABASE_NAME
-
-###############################
-# cleanup
-###############################
-
-# drop database
-clean:drop:mysql55:
- stage: clean
- when: always
- tags: [ mysql55 ]
- dependencies:
- - configure:mysql55
- script:
- - cp .config.mysql55 .config
- - export $(sed -n '/DATABASE_NAME/p ' .config)
- - if make _exists; then make drop-$DATABASE_NAME ; fi
-
-clean:drop:mariadb10.1:
- stage: clean
- when: always
- tags: [ maria10.1 ]
- dependencies:
- - configure:mariadb10.1
- script:
- - cp .config.mariadb10.1 .config
- - export $(sed -n '/DATABASE_NAME/p ' .config)
- - if make _exists; then make drop-$DATABASE_NAME ; fi
\ No newline at end of file
+image: $CI_REGISTRY_IMAGE
+stages:
+ - setup
+ - deploy
+
+# Trigger building of server image and integration tests
+trigger_build:
+ tags: [ docker ]
+ stage: deploy
+ script:
+ - /usr/bin/curl -X POST
+ -F token=8f29e5eeb7db2123d9c2bb84634da2
+ -F "variables[MYSQLBACKEND]=$CI_COMMIT_REF_NAME"
+ -F "variables[TriggerdBy]=MYSQLBACKEND"
+ -F "variables[TriggerdByHash]=$CI_COMMIT_SHORT_SHA"
+ -F ref=master https://gitlab.indiscale.com/api/v4/projects/14/trigger/pipeline
+
+# Build a docker image in which tests for this repository can run
+build-testenv:
+ tags: [ docker ]
+ image: docker:19.03
+ stage: setup
+ script:
+ - cd .docker
+ - docker login -u testuser -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
+ # use here general latest or specific branch latest...
+ - docker pull $CI_REGISTRY_IMAGE || true
+ - docker build
+ --pull
+ --cache-from $CI_REGISTRY_IMAGE
+ -t $CI_REGISTRY_IMAGE .
+ - docker push $CI_REGISTRY_IMAGE
diff --git a/README.md b/README.md
index 92c6a4004870e4a14e6a173fa8e02efe5e39ed36..10fe96d776335d87f870f40a7a98f7d87d98cb6a 100644
--- a/README.md
+++ b/README.md
@@ -14,7 +14,7 @@ setup this code.
# Further Reading
Please refer to the [official gitlab repository of the CaosDB
-project](https://gitlab.gwdg.de/bmp-caosdb/caosdb) for more information.
+project](https://gitlab.com/caosdb/caosdb) for more information.
# License
diff --git a/doc/multipurpose_subdomains.md b/doc/multipurpose_subdomains.md
deleted file mode 100644
index 28001cc48c0c868bd490d0cc4504f2423cc11b62..0000000000000000000000000000000000000000
--- a/doc/multipurpose_subdomains.md
+++ /dev/null
@@ -1,22 +0,0 @@
-# Multipurpose subdomains #
-Multipurpose subdomains are generically used to work with composite
-properties. Currently implemented examples are:
-- Properties with units (if multiple Properties exist)
-- Lists
-- Name overrides
-
-## Example ##
-Let's have a look at this *Record* (simplified XML):
-
-```xml
-<R1>
- <P1 name="Comment">Hello World</P1>
- <P2 name="voltage" unit="V">
- 23
- </P2>
- <P3 comment="list of something">
- V1, V2, V3, V4, ...
- </P3>
-</R1>
-```
-
diff --git a/patches/patch20170825-2.0.30/test.sql b/patches/patch20170825-2.0.30/test.sql
index d303b379fef8348c01d3c4c3ae9e28e601ddc6ab..3b0faefde3447a89f093436d8a9f5b1c2346d4a1 100644
--- a/patches/patch20170825-2.0.30/test.sql
+++ b/patches/patch20170825-2.0.30/test.sql
@@ -22,6 +22,21 @@
*/
SET @@SESSION.max_sp_recursion_depth=25;
+-- Inheritance:
+--
+-- 0
+-- |
+-- 1
+-- |
+-- 2
+-- / \
+-- 3 4
+-- \ /
+-- 5
+-- |
+-- 6
+--
+
SET FOREIGN_KEY_CHECKS = 0;
delete from isa_cache;
-- simple 1->0
@@ -203,7 +218,7 @@ call isSubtype(1,2);
call isSubtype(0,2);
call isSubtype(0,1);
--- remove 2->1
+-- remove 2->1
CREATE TEMPORARY TABLE expected1 SELECT * from isa_cache;
call deleteIsa(2);
select "subtypes:";
@@ -253,7 +268,7 @@ call isSubtype(0,1);
-- and add 2->1 again
call insertIsa(2,1);
-SELECT A.*, B.* FROM isa_cache AS A LEFT JOIN expected1 AS B ON (A.child = B.child AND A.parent=B.parent AND A.rpath=B.rpath) WHERE A.child IS NULL OR B.child IS NULL;
+SELECT A.*, B.* FROM isa_cache AS A LEFT JOIN expected1 AS B ON (A.child = B.child AND A.parent=B.parent AND A.rpath=B.rpath) WHERE A.child IS NULL OR B.child IS NULL;
SELECT A.*, B.* FROM isa_cache AS A RIGHT JOIN expected1 AS B ON (A.child = B.child AND A.parent=B.parent AND A.rpath=B.rpath) WHERE A.child IS NULL OR B.child IS NULL;
-- remove 4->2
@@ -306,7 +321,7 @@ call isSubtype(5,6);
-- and add 4->2 again
call insertIsa(4,2);
-SELECT A.*, B.* FROM isa_cache AS A LEFT JOIN expected1 AS B ON (A.child = B.child AND A.parent=B.parent AND A.rpath=B.rpath) WHERE A.child IS NULL OR B.child IS NULL;
+SELECT A.*, B.* FROM isa_cache AS A LEFT JOIN expected1 AS B ON (A.child = B.child AND A.parent=B.parent AND A.rpath=B.rpath) WHERE A.child IS NULL OR B.child IS NULL;
SELECT A.*, B.* FROM isa_cache AS A RIGHT JOIN expected1 AS B ON (A.child = B.child AND A.parent=B.parent AND A.rpath=B.rpath) WHERE A.child IS NULL OR B.child IS NULL;
-- remove 5->4 and 5->3
@@ -407,7 +422,7 @@ call isSubtype(6,3);
-- and add 5->3 again
call insertIsa(5,3);
-SELECT A.*, B.* FROM isa_cache AS A LEFT JOIN expected1 AS B ON (A.child = B.child AND A.parent=B.parent AND A.rpath=B.rpath) WHERE A.child IS NULL OR B.child IS NULL;
+SELECT A.*, B.* FROM isa_cache AS A LEFT JOIN expected1 AS B ON (A.child = B.child AND A.parent=B.parent AND A.rpath=B.rpath) WHERE A.child IS NULL OR B.child IS NULL;
SELECT A.*, B.* FROM isa_cache AS A RIGHT JOIN expected1 AS B ON (A.child = B.child AND A.parent=B.parent AND A.rpath=B.rpath) WHERE A.child IS NULL OR B.child IS NULL;
-- add cycle 0->3
@@ -428,7 +443,7 @@ call isSubtype(3,2);
-- remove cycle 0->3
call deleteIsa(0);
-SELECT A.*, B.* FROM isa_cache AS A LEFT JOIN expected1 AS B ON (A.child = B.child AND A.parent=B.parent AND A.rpath=B.rpath) WHERE A.child IS NULL OR B.child IS NULL;
+SELECT A.*, B.* FROM isa_cache AS A LEFT JOIN expected1 AS B ON (A.child = B.child AND A.parent=B.parent AND A.rpath=B.rpath) WHERE A.child IS NULL OR B.child IS NULL;
SELECT A.*, B.* FROM isa_cache AS A RIGHT JOIN expected1 AS B ON (A.child = B.child AND A.parent=B.parent AND A.rpath=B.rpath) WHERE A.child IS NULL OR B.child IS NULL;
call deleteIsa(1);
diff --git a/procedures/insertIsaCache.sql b/procedures/insertIsaCache.sql
index 4ff1a46ea6f1c1001cc99840c51b3911bc630323..735ba126a98ee3a050194525a0c437f72f547cdc 100644
--- a/procedures/insertIsaCache.sql
+++ b/procedures/insertIsaCache.sql
@@ -30,11 +30,33 @@ BEGIN
-- foreach supertype of p
-- INSERT (c, supertype, p);
- INSERT IGNORE INTO isa_cache SELECT c AS child, i.parent AS parent, IF(p=i.rpath or i.rpath=parent, p, concat(p, ">", i.rpath)) AS rpath FROM isa_cache AS i WHERE i.child = p;
+ INSERT IGNORE INTO isa_cache SELECT
+ c
+ AS child,
+ i.parent
+ AS parent,
+ IF(p=i.rpath or i.rpath=parent,
+ p,
+ concat(p, ">", i.rpath))
+ AS rpath
+ FROM isa_cache AS i WHERE i.child = p;
-- foreach 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)))) AS rpath FROM isa_cache as l INNER JOIN isa_cache as r ON (l.parent = r.child AND l.parent=c);
+ 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))))
+ AS rpath
+ FROM isa_cache as l
+ INNER JOIN isa_cache as r ON (l.parent = r.child AND l.parent=c);