diff --git a/.gitignore b/.gitignore
index 9af5ee22fdd68c1c25e98614ab516bf4d384d577..4402aa11bc399c03400c4427c669b93ebb2637ce 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,7 +3,6 @@ src/caoscrawler.egg-info/
__pycache__
.tox
TAGS
-src/.coverage
build/
*~
.pdbrc
@@ -14,3 +13,7 @@ provenance.yml
*.tar.gz
*.sql
/integrationtests/test-profile/custom/other/cert/
+src/doc/_apidoc/
+start_caosdb_docker.sh
+src/doc/_apidoc
+/dist/
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b5bc53fed1b069f3a6f665a188aa8bdcd7252570..30a8cd8fe4c08fd3fe0f3f98aaa56b83cb623086 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -152,11 +152,11 @@ inttest:
- CAOSDB_TAG=$CAOSDB_TAG docker-compose up -d
# Store versions of CaosDB parts
- - docker exec -u 0 -t docker_caosdb-server_1 cat /opt/caosdb/git/caosdb_pylib_commit > hash_pylib
- - docker exec -u 0 -t docker_caosdb-server_1 cat /opt/caosdb/git/caosdb_webui_commit > hash_webui
- - docker exec -u 0 -t docker_caosdb-server_1 cat /opt/caosdb/git/caosdb_server_commit > hash_server
- - docker exec -u 0 -t docker_caosdb-server_1 cat /opt/caosdb/git/caosdb_mysqlbackend_commit > hash_mysql
- - docker exec -u 0 -t docker_caosdb-server_1 cat /opt/caosdb/git/caosdb_proto_commit > hash_proto
+ - docker exec -u 0 -t docker-caosdb-server-1 cat /opt/caosdb/git/caosdb_pylib_commit > hash_pylib
+ - docker exec -u 0 -t docker-caosdb-server-1 cat /opt/caosdb/git/caosdb_webui_commit > hash_webui
+ - docker exec -u 0 -t docker-caosdb-server-1 cat /opt/caosdb/git/caosdb_server_commit > hash_server
+ - docker exec -u 0 -t docker-caosdb-server-1 cat /opt/caosdb/git/caosdb_mysqlbackend_commit > hash_mysql
+ - docker exec -u 0 -t docker-caosdb-server-1 cat /opt/caosdb/git/caosdb_proto_commit > hash_proto
- cat hash_server
- cat hash_proto
- cat hash_mysql
@@ -167,8 +167,8 @@ inttest:
- /bin/sh ./run.sh
# Save logs
- - docker logs docker_caosdb-server_1 &> ../caosdb_log.txt
- - docker logs docker_sqldb_1 &> ../mariadb_log.txt
+ - docker logs docker-caosdb-server-1 &> ../caosdb_log.txt
+ - docker logs docker-sqldb-1 &> ../mariadb_log.txt
- cd ..
# Stop the server
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2db8e113fefdefeeaa4817ec61292feff86dc832..6fd18cee55ad484fa54aa527b997fd757fbedde0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,7 +5,30 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
-## [Unreleased]
+## [Unreleased] ##
+
+### Added ###
+
+### Changed ###
+
+- `_AbstractDictElementConverter` uses `re.DOTALL` for `match_value`
+
+### Deprecated ###
+
+### Removed ###
+
+### Fixed ###
+
+* [#31](https://gitlab.com/caosdb/caosdb-crawler/-/issues/31) Identified cache:
+ Hash is the same for Records without IDs
+* [#30](https://gitlab.com/caosdb/caosdb-crawler/-/issues/30)
+* [#23](https://gitlab.com/caosdb/caosdb-crawler/-/issues/23) Crawler may
+ overwrite and delete existing data in case of manually added properties
+
+### Security ###
+
+## [0.1.0] - 2022-10-11
+(Florian Spreckelsen)
### Added
@@ -13,19 +36,23 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
* Added new converters for tables: CSVTableConverter and XLSXTableConverter
* Possibility to authorize updates as in the old crawler
* Allow authorization of inserts
+* Allow splitting cfoods into multiple yaml documents
+* Implemented macros
+* Converters can now filter the list of children
+* You can now crawl data with name conflicts: `synchronize(unique_names=False)`
### Changed
-* Renamed module from `newcrawler` to `caoscrawler`
-
-### Deprecated
-
-### Removed
+* MAINT: Renamed module from `newcrawler` to `caoscrawler`
+* MAINT: Removed global converters from `crawl.py`
### Fixed
* FIX: #12
+* FIX: #14
* FIX: Variables are now also replaced when the value is given as a list.
-+ FIX: #35 Parent cannot be set from value
-
-### Security
+* FIX: #35 Parent cannot be set from value
+* [#6](https://gitlab.com/caosdb/caosdb-crawler/-/issues/6): Fixed many type
+ hints to be compatible to python 3.8
+* [#9](https://gitlab.com/caosdb/caosdb-crawler/-/issues/9): Sclaras of types
+ different than string can now be given in cfood definitions
diff --git a/README.md b/README.md
index 8576e5c969556005fdeb346ef2cdfadf1b7fc266..b97fc8775ba334c03c5c0a42238e9f396301e6b3 100644
--- a/README.md
+++ b/README.md
@@ -38,9 +38,9 @@ The original authors of this package are:
# License
-Copyright (C) 2021 Research Group Biomedical Physics, Max Planck Institute for
+Copyright (C) 2021-2022 Research Group Biomedical Physics, Max Planck Institute for
Dynamics and Self-Organization Göttingen.
-Copyright (C) 2021 IndiScale GmbH
+Copyright (C) 2021-2022 IndiScale GmbH
All files in this repository are licensed under a [GNU Affero General Public
License](LICENCE) (version 3 or later).
diff --git a/RELEASE_GUIDELINES.md b/RELEASE_GUIDELINES.md
new file mode 100644
index 0000000000000000000000000000000000000000..d6bc2c9ae41b8032a5567f786eb060d7b67d2cc5
--- /dev/null
+++ b/RELEASE_GUIDELINES.md
@@ -0,0 +1,47 @@
+# Release Guidelines for the CaosDB Python Client Library
+
+This document specifies release guidelines in addition to the general release
+guidelines of the CaosDB Project
+([RELEASE_GUIDELINES.md](https://gitlab.com/caosdb/caosdb/blob/dev/RELEASE_GUIDELINES.md))
+
+## General Prerequisites
+
+* All tests are passing.
+* FEATURES.md is up-to-date and a public API is being declared in that document.
+* CHANGELOG.md is up-to-date.
+* dependencies in `setup.cfg` are up-to-date.
+
+## Steps
+
+1. Create a release branch from the dev branch. This prevents further changes
+ to the code base and a never ending release process. Naming: `release-<VERSION>`
+
+2. Update CHANGELOG.md
+
+3. Check all general prerequisites.
+
+4. Update the version:
+ - `version` variables in `src/doc/conf.py`
+ - Version in [setup.cfg](./setup.cfg): Check the `MAJOR`, `MINOR`, `MICRO`, `PRE` variables and set
+ `ISRELEASED` to `True`. Use the possibility to issue pre-release versions for testing.
+
+5. Merge the release branch into the main branch.
+
+6. Tag the latest commit of the main branch with `v<VERSION>`.
+
+7. Delete the release branch.
+
+8. Remove possibly existing `./dist` directory with old release.
+
+9. Publish the release by executing `./release.sh` with uploads the caosdb
+ module to the Python Package Index [pypi.org](https://pypi.org).
+
+10. Merge the main branch back into the dev branch.
+
+11. After the merge of main to dev, start a new development version by
+ increasing at least the micro version in [setup.cfg](./setup.cfg) and
+ preparing CHANGELOG.md.
+
+12. Create releases on gitlab.com and gitlab.indiscale.com that contain (at
+ least) the most recent section of the CHANGELOG as the description and link
+ to the PyPi package.
diff --git a/integrationtests/basic_example/test_basic.py b/integrationtests/basic_example/test_basic.py
index b24a1c658cfc9e23ca0ba2de266161864cb6b66c..571720ab1dafd0384672a55ec5c6e8a8aeffb605 100755
--- a/integrationtests/basic_example/test_basic.py
+++ b/integrationtests/basic_example/test_basic.py
@@ -108,7 +108,7 @@ def crawler_extended(ident):
cr = Crawler(debug=True, identifiableAdapter=ident)
crawl_standard_test_directory(cr, cfood="scifolder_extended.yml")
# correct paths for current working directory
- file_list = [r for r in cr.target_data if r.role == "File"]
+ file_list = [r for r in cr.crawled_data if r.role == "File"]
for f in file_list:
f.file = rfp("..", "..", "unittests", "test_directories", f.file)
return cr
@@ -160,7 +160,7 @@ def test_insertion(clear_database, usemodel, ident, crawler):
# Do a second run on the same data, there should a new insert:
cr = Crawler(debug=True, identifiableAdapter=ident)
crawl_standard_test_directory(cr, "example_insert")
- assert len(cr.target_data) == 3
+ assert len(cr.crawled_data) == 3
ins, ups = cr.synchronize()
assert len(ins) == 1
assert len(ups) == 0
@@ -168,7 +168,7 @@ def test_insertion(clear_database, usemodel, ident, crawler):
# Do it again to check whether nothing is changed:
cr = Crawler(debug=True, identifiableAdapter=ident)
crawl_standard_test_directory(cr, "example_insert")
- assert len(cr.target_data) == 3
+ assert len(cr.crawled_data) == 3
ins, ups = cr.synchronize()
assert len(ins) == 0
assert len(ups) == 0
@@ -180,7 +180,7 @@ def test_insert_auth(clear_database, usemodel, ident, crawler):
# Do a second run on the same data, there should a new insert:
cr = Crawler(debug=True, identifiableAdapter=ident, securityMode=SecurityMode.RETRIEVE)
crawl_standard_test_directory(cr, "example_insert")
- assert len(cr.target_data) == 3
+ assert len(cr.crawled_data) == 3
ins, ups = cr.synchronize()
assert len(ins) == 1
assert not ins[0].is_valid()
@@ -190,7 +190,7 @@ def test_insert_auth(clear_database, usemodel, ident, crawler):
# Do it again to check whether nothing is changed:
cr = Crawler(debug=True, identifiableAdapter=ident)
crawl_standard_test_directory(cr, "example_insert")
- assert len(cr.target_data) == 3
+ assert len(cr.crawled_data) == 3
ins, ups = cr.synchronize()
assert len(ins) == 0
assert len(ups) == 0
@@ -205,9 +205,9 @@ def test_insertion_and_update(clear_database, usemodel, ident, crawler):
cr = Crawler(debug=True, identifiableAdapter=ident)
crawl_standard_test_directory(cr, "example_overwrite_1")
- # print(cr.target_data)
+ # print(cr.crawled_data)
# cr.save_debug_data(rfp("provenance.yml"))
- assert len(cr.target_data) == 3
+ assert len(cr.crawled_data) == 3
ins, ups = cr.synchronize()
assert len(ins) == 0
assert len(ups) == 1
@@ -222,7 +222,7 @@ def test_identifiable_update(clear_database, usemodel, ident, crawler):
crawl_standard_test_directory(cr)
# Test the addition of a single property:
- l = cr.target_data
+ l = cr.crawled_data
for record in l:
if (record.parents[0].name == "Measurement" and
record.get_property("date").value == "2020-01-03"):
@@ -238,7 +238,7 @@ def test_identifiable_update(clear_database, usemodel, ident, crawler):
# Test the change within one property:
cr = Crawler(debug=True, identifiableAdapter=ident)
crawl_standard_test_directory(cr)
- l = cr.target_data
+ l = cr.crawled_data
for record in l:
if (record.parents[0].name == "Measurement" and
record.get_property("date").value == "2020-01-03"):
@@ -252,7 +252,7 @@ def test_identifiable_update(clear_database, usemodel, ident, crawler):
# Changing the date should result in a new insertion:
cr = Crawler(debug=True, identifiableAdapter=ident)
crawl_standard_test_directory(cr)
- l = cr.target_data
+ l = cr.crawled_data
for record in l:
if (record.parents[0].name == "Measurement" and
record.get_property("date").value == "2020-01-03"):
@@ -269,7 +269,7 @@ def test_file_insertion_dry(clear_database, usemodel, ident):
crawler_extended = Crawler(debug=True, identifiableAdapter=ident)
crawl_standard_test_directory(
crawler_extended, cfood="scifolder_extended.yml")
- file_list = [r for r in crawler_extended.target_data if r.role == "File"]
+ file_list = [r for r in crawler_extended.crawled_data if r.role == "File"]
assert len(file_list) == 11
for f in file_list:
@@ -305,7 +305,7 @@ def test_file_update(clear_database, usemodel, ident, crawler_extended):
cr = Crawler(debug=True, identifiableAdapter=ident)
crawl_standard_test_directory(cr, cfood="scifolder_extended.yml")
- file_list = [r for r in cr.target_data if r.role == "File"]
+ file_list = [r for r in cr.crawled_data if r.role == "File"]
for f in file_list:
f.file = rfp("..", "..", "unittests", "test_directories", f.file)
ins2, ups2 = cr.synchronize(commit_changes=True)
@@ -320,7 +320,7 @@ def test_file_update(clear_database, usemodel, ident, crawler_extended):
cr2 = Crawler(debug=True, identifiableAdapter=ident)
crawl_standard_test_directory(cr2, cfood="scifolder_extended2.yml")
- file_list = [r for r in cr2.target_data if r.role == "File"]
+ file_list = [r for r in cr2.crawled_data if r.role == "File"]
for f in file_list:
f.file = rfp("..", "..", "unittests", "test_directories", f.file)
ins3, ups3 = cr2.synchronize(commit_changes=True)
diff --git a/integrationtests/test-profile/custom/other/restore/caosdb.2022-01-20T08:27:49.631552786+00:00.dump.sql b/integrationtests/test-profile/custom/other/restore/caosdb.2022-01-20T08:27:49.631552786+00:00.dump.sql
deleted file mode 100644
index c527a0040a469b5f48cbd50c786fe9ff24d545d5..0000000000000000000000000000000000000000
--- a/integrationtests/test-profile/custom/other/restore/caosdb.2022-01-20T08:27:49.631552786+00:00.dump.sql
+++ /dev/null
@@ -1,5716 +0,0 @@
--- MariaDB dump 10.19 Distrib 10.5.12-MariaDB, for debian-linux-gnu (x86_64)
---
--- Host: sqldb Database: caosdb
--- ------------------------------------------------------
--- Server version 10.5.11-MariaDB-1:10.5.11+maria~focal
-
-/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
-/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
-/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
-/*!40101 SET NAMES utf8 */;
-/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
-/*!40103 SET TIME_ZONE='+00:00' */;
-/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */;
-/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */;
-/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */;
-/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
-
---
--- Table structure for table `archive_collection_type`
---
-
-DROP TABLE IF EXISTS `archive_collection_type`;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `archive_collection_type` (
- `domain_id` int(10) unsigned NOT NULL,
- `entity_id` int(10) unsigned NOT NULL,
- `property_id` int(10) unsigned NOT NULL,
- `collection` varchar(255) COLLATE utf8_unicode_ci NOT NULL,
- `_iversion` int(10) unsigned NOT NULL,
- UNIQUE KEY `archive_collection_type-d-e-p-v` (`domain_id`,`entity_id`,`property_id`,`_iversion`),
- KEY `domain_id` (`domain_id`,`entity_id`,`_iversion`),
- KEY `domain_id_2` (`domain_id`,`_iversion`),
- KEY `entity_id` (`entity_id`),
- KEY `property_id` (`property_id`),
- CONSTRAINT `archive_collection_type_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
- CONSTRAINT `archive_collection_type_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
- CONSTRAINT `archive_collection_type_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
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--- Dumping data for table `archive_collection_type`
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- `nanos` int(10) unsigned NOT NULL DEFAULT 0,
- `realm` varbinary(255) NOT NULL,
- KEY `entity_id` (`entity_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
---
--- Dumping data for table `transaction_log`
---
-
-LOCK TABLES `transaction_log` WRITE;
-/*!40000 ALTER TABLE `transaction_log` DISABLE KEYS */;
-INSERT INTO `transaction_log` VALUES ('Insert',100,'admin',1642667277,464000000,'PAM'),('Insert',101,'admin',1642667277,464000000,'PAM'),('Insert',102,'admin',1642667277,633000000,'PAM');
-/*!40000 ALTER TABLE `transaction_log` ENABLE KEYS */;
-UNLOCK TABLES;
-
---
--- Table structure for table `transactions`
---
-
-DROP TABLE IF EXISTS `transactions`;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `transactions` (
- `srid` varbinary(255) NOT NULL,
- `username` varbinary(255) NOT NULL,
- `realm` varbinary(255) NOT NULL,
- `seconds` bigint(20) unsigned NOT NULL,
- `nanos` int(10) unsigned NOT NULL,
- PRIMARY KEY (`srid`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
---
--- Dumping data for table `transactions`
---
-
-LOCK TABLES `transactions` WRITE;
-/*!40000 ALTER TABLE `transactions` DISABLE KEYS */;
-INSERT INTO `transactions` VALUES ('41dd8224-1e1a-4ad9-9d37-bad5841cb2a2','admin','PAM',1642667277,464000000),('c2deb139-70f3-4ba6-bbef-40ae2e33ec7d','admin','PAM',1642667277,633000000),('cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e','administration','CaosDB',0,0);
-/*!40000 ALTER TABLE `transactions` ENABLE KEYS */;
-UNLOCK TABLES;
-
---
--- Table structure for table `units_lin_con`
---
-
-DROP TABLE IF EXISTS `units_lin_con`;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `units_lin_con` (
- `signature_from` bigint(20) NOT NULL,
- `signature_to` bigint(20) NOT NULL,
- `a` decimal(65,30) NOT NULL,
- `b_dividend` int(11) NOT NULL,
- `b_divisor` int(11) NOT NULL,
- `c` decimal(65,30) NOT NULL,
- PRIMARY KEY (`signature_from`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
---
--- Dumping data for table `units_lin_con`
---
-
-LOCK TABLES `units_lin_con` WRITE;
-/*!40000 ALTER TABLE `units_lin_con` DISABLE KEYS */;
-/*!40000 ALTER TABLE `units_lin_con` ENABLE KEYS */;
-UNLOCK TABLES;
-
---
--- Table structure for table `user_info`
---
-
-DROP TABLE IF EXISTS `user_info`;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `user_info` (
- `realm` varbinary(255) NOT NULL,
- `name` varbinary(255) NOT NULL,
- `email` varbinary(255) DEFAULT NULL,
- `status` enum('ACTIVE','INACTIVE') COLLATE utf8_unicode_ci NOT NULL DEFAULT 'INACTIVE',
- `entity` int(10) unsigned DEFAULT NULL,
- PRIMARY KEY (`realm`,`name`),
- KEY `subject_entity` (`entity`),
- CONSTRAINT `subjects_ibfk_1` FOREIGN KEY (`entity`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
---
--- Dumping data for table `user_info`
---
-
-LOCK TABLES `user_info` WRITE;
-/*!40000 ALTER TABLE `user_info` DISABLE KEYS */;
-/*!40000 ALTER TABLE `user_info` ENABLE KEYS */;
-UNLOCK TABLES;
-
---
--- Table structure for table `user_roles`
---
-
-DROP TABLE IF EXISTS `user_roles`;
-/*!40101 SET @saved_cs_client = @@character_set_client */;
-/*!40101 SET character_set_client = utf8 */;
-CREATE TABLE `user_roles` (
- `realm` varbinary(255) NOT NULL,
- `user` varbinary(255) NOT NULL,
- `role` varbinary(255) NOT NULL,
- PRIMARY KEY (`realm`,`user`,`role`),
- KEY `user_roles_ibfk_1` (`role`),
- CONSTRAINT `user_roles_ibfk_1` FOREIGN KEY (`role`) REFERENCES `roles` (`name`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
-/*!40101 SET character_set_client = @saved_cs_client */;
-
---
--- Dumping data for table `user_roles`
---
-
-LOCK TABLES `user_roles` WRITE;
-/*!40000 ALTER TABLE `user_roles` DISABLE KEYS */;
-/*!40000 ALTER TABLE `user_roles` ENABLE KEYS */;
-UNLOCK TABLES;
-
---
--- Dumping routines for database 'caosdb'
---
-/*!50003 DROP FUNCTION IF EXISTS `CaosDBVersion` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` FUNCTION `CaosDBVersion`() RETURNS varchar(255) CHARSET utf8 COLLATE utf8_unicode_ci
- DETERMINISTIC
-RETURN 'v5.0.0' ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP FUNCTION IF EXISTS `constructDateTimeWhereClauseForColumn` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` FUNCTION `constructDateTimeWhereClauseForColumn`(seconds_col VARCHAR(255), nanos_col VARCHAR(255), vDateTimeSecLow VARCHAR(255), vDateTimeNSLow VARCHAR(255), vDateTimeSecUpp VARCHAR(255), vDateTimeNSUpp VARCHAR(255), operator CHAR(4)) RETURNS varchar(20000) CHARSET utf8 COLLATE utf8_unicode_ci
- DETERMINISTIC
-BEGIN
-
- DECLARE isInterval BOOLEAN DEFAULT vDateTimeSecUpp IS NOT NULL or vDateTimeNSUpp IS NOT NULL;
- DECLARE operator_prefix CHAR(1) DEFAULT LEFT(operator,1);
-
- IF isInterval THEN
- IF operator = '=' THEN
- RETURN " 0=1";
- ELSEIF operator = '!=' THEN
- RETURN " 0=1";
- ELSEIF operator = '>' or operator = '<=' THEN
- RETURN CONCAT(" ", seconds_col, operator_prefix, vDateTimeSecUpp);
- ELSEIF operator = '<' or operator = '>=' THEN
- RETURN CONCAT(" ", seconds_col, operator_prefix, vDateTimeSecLow);
- ELSEIF operator = "(" THEN
- RETURN CONCAT(" ", seconds_col, ">=", vDateTimeSecLow, " AND ",seconds_col, "<", vDateTimeSecUpp);
- ELSEIF operator = "!(" THEN
- RETURN CONCAT(" ", seconds_col, "<", vDateTimeSecLow, " OR ", seconds_col, ">=", vDateTimeSecUpp);
- END IF;
- ELSE
- IF operator = '=' THEN
- RETURN CONCAT(" ",
- seconds_col,
- "=", vDateTimeSecLow, IF(vDateTimeNSLow IS NULL, CONCAT(' AND ', nanos_col, ' IS NULL'), CONCAT(' AND ',
- nanos_col,
- '=', vDateTimeNSLow)));
- ELSEIF operator = '!=' THEN
- RETURN CONCAT(" ",
- seconds_col,
- "!=", vDateTimeSecLow, IF(vDateTimeNSLow IS NULL, '', CONCAT(' OR ',
- nanos_col,
- '!=', vDateTimeNSLow)));
- ELSEIF operator = '>' or operator = '<' THEN
- RETURN CONCAT(" ",
- seconds_col, operator, vDateTimeSecLow, IF(vDateTimeNSLow IS NULL, '', CONCAT(' OR (',seconds_col,'=', vDateTimeSecLow, ' AND ',nanos_col, operator, vDateTimeNSLow, ')')));
- ELSEIF operator = '>=' or operator = '<=' THEN
- RETURN CONCAT(
- " ", seconds_col, operator, vDateTimeSecLow,
- IF(vDateTimeNSLow IS NULL,
- '',
- CONCAT(
- ' AND (', seconds_col, operator_prefix, vDateTimeSecLow,
- ' OR ', nanos_col, operator, vDateTimeNSLow,
- ' OR ', nanos_col, ' IS NULL)')));
- ELSEIF operator = "(" THEN
- RETURN IF(vDateTimeNSLow IS NULL,CONCAT(" ",seconds_col,"=", vDateTimeSecLow),CONCAT(" ",seconds_col,"=",vDateTimeSecLow," AND ",nanos_col,"=",vDateTimeNSLow));
- ELSEIF operator = "!(" THEN
- RETURN IF(vDateTimeNSLow IS NULL,CONCAT(" ",seconds_col,"!=",vDateTimeSecLow, ""),CONCAT(" ",seconds_col,"!=",vDateTimeSecLow," OR ",nanos_col, " IS NULL OR ", nanos_col, "!=",vDateTimeNSLow));
- END IF;
- END IF;
- return ' 0=1';
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP FUNCTION IF EXISTS `convert_unit` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` FUNCTION `convert_unit`(unit_sig BIGINT, value DECIMAL(65,30)) RETURNS decimal(65,30)
- DETERMINISTIC
-BEGIN
- DECLARE ret DECIMAL(65,30) DEFAULT value;
-
- SELECT (((value+a)*b_dividend)/b_divisor+c) INTO ret FROM units_lin_con WHERE signature_from=unit_sig;
- RETURN ret;
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP FUNCTION IF EXISTS `getAggValueWhereClause` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` FUNCTION `getAggValueWhereClause`(entities VARCHAR(255), properties VARCHAR(255)) RETURNS varchar(20000) CHARSET utf8 COLLATE utf8_unicode_ci
- DETERMINISTIC
-BEGIN
- RETURN CONCAT(" EXISTS (SELECT 1 FROM `", entities, "` AS ent WHERE ent.id = subdata.entity_id LIMIT 1)", IF(properties IS NOT NULL AND properties != '', CONCAT(" AND EXISTS (SELECT 1 FROM `", properties, "` as props WHERE props.id = subdata.property_id LIMIT 1)"),''));
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP FUNCTION IF EXISTS `getDateTimeWhereClause` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` FUNCTION `getDateTimeWhereClause`(vDateTime VARCHAR(255), operator CHAR(4)) RETURNS varchar(20000) CHARSET utf8 COLLATE utf8_unicode_ci
- DETERMINISTIC
-BEGIN
- DECLARE sep_loc INTEGER DEFAULT LOCATE('--',vDateTime);
- DECLARE vDateTimeLow VARCHAR(255) DEFAULT IF(sep_loc != 0, SUBSTRING_INDEX(vDateTime, '--',1), vDateTime);
- DECLARE vDateTimeUpp VARCHAR(255) DEFAULT IF(sep_loc != 0, SUBSTRING_INDEX(vDateTime, '--',-1), NULL);
-
- DECLARE vDateTimeSecLow VARCHAR(255) DEFAULT SUBSTRING_INDEX(vDateTimeLow, 'UTC', 1);
- DECLARE vDateTimeNSLow VARCHAR(255) DEFAULT IF(SUBSTRING_INDEX(vDateTimeLow, 'UTC', -1)='',NULL,SUBSTRING_INDEX(vDateTimeLow, 'UTC', -1));
-
- DECLARE vDateTimeSecUpp VARCHAR(255) DEFAULT IF(sep_loc != 0, SUBSTRING_INDEX(vDateTimeUpp, 'UTC', 1), NULL);
- DECLARE vDateTimeNSUpp VARCHAR(255) DEFAULT IF(sep_loc != 0 AND SUBSTRING_INDEX(vDateTimeUpp, 'UTC', -1)!='',SUBSTRING_INDEX(vDateTimeUpp, 'UTC', -1),NULL);
-
-
- RETURN constructDateTimeWhereClauseForColumn("subdata.value", "subdata.value_ns", vDateTimeSecLow, vDateTimeNSLow, vDateTimeSecUpp, vDateTimeNSUpp, operator);
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP FUNCTION IF EXISTS `getDateWhereClause` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` FUNCTION `getDateWhereClause`(vDateTimeDotNotation VARCHAR(255), operator CHAR(4)) RETURNS varchar(20000) CHARSET utf8 COLLATE utf8_unicode_ci
- DETERMINISTIC
-BEGIN
- DECLARE isInterval INTEGER DEFAULT LOCATE('--',vDateTimeDotNotation);
-
- DECLARE vILB VARCHAR(255) DEFAULT IF(isInterval != 0, SUBSTRING_INDEX(vDateTimeDotNotation, '--', 1), vDateTimeDotNotation);
-
- DECLARE vEUB VARCHAR(255) DEFAULT IF(isInterval != 0, SUBSTRING_INDEX(vDateTimeDotNotation, '--', -1), NULL);
- DECLARE vILB_Date INTEGER DEFAULT SUBSTRING_INDEX(vILB, '.', 1);
- DECLARE vEUB_Date INTEGER DEFAULT SUBSTRING_INDEX(vEUB, '.', 1);
-
- DECLARE hasTime INTEGER DEFAULT LOCATE('.NULL.NULL',vILB);
-
- DECLARE dom INTEGER DEFAULT vILB_Date % 100;
-
- DECLARE mon INTEGER DEFAULT ((vILB_Date % 10000) - dom) / 100;
-
- DECLARE yea INTEGER DEFAULT (vILB_Date - (vILB_Date % 10000)) / 10000;
-
- IF operator = '=' and hasTime != 0 THEN
- RETURN CONCAT(" subdata.value=", vILB_Date);
- ELSEIF operator = "!=" and hasTime != 0 THEN
- IF mon != 0 and dom != 0 THEN
- RETURN CONCAT(" subdata.value!=", vILB_Date, " and subdata.value%100!=0");
- ELSEIF mon != 0 THEN
- RETURN CONCAT(" subdata.value!=", vILB_Date, " and subdata.value%100=0 and subdata.value%10000!=0");
- ELSE
- RETURN CONCAT(" subdata.value!=", vILB_Date, " and subdata.value%10000=0");
- END IF;
- ELSEIF operator = "(" and hasTime != 0 THEN
- IF mon != 0 and dom != 0 THEN
- RETURN CONCAT(" subdata.value=", vILB_Date);
- ELSEIF mon != 0 THEN
- RETURN CONCAT(" subdata.value=",vILB_Date," OR (subdata.value>", vILB_Date, " and subdata.value<", vEUB_Date, " and subdata.value%10000!=0)");
- ELSE
- RETURN CONCAT(" subdata.value=",vILB_Date," OR (subdata.value>", vILB_Date, " and subdata.value<", vEUB_Date,")");
- END IF;
- ELSEIF operator = "!(" THEN
- IF hasTime = 0 THEN
- RETURN " 0=0";
- END IF;
- IF mon != 0 and dom != 0 THEN
- RETURN CONCAT(" subdata.value!=",vILB_Date);
- ELSEIF mon != 0 THEN
- RETURN CONCAT(" (subdata.value!=",vILB_Date, " AND subdata.value%100=0) OR ((subdata.value<", vILB_Date, " or subdata.value>", vEUB_Date, ") and subdata.value%100!=0)");
- ELSE
- RETURN CONCAT(" (subdata.value!=",vILB_Date, " AND subdata.value%10000=0) OR ((subdata.value<", vILB_Date, " or subdata.value>=", vEUB_Date, ") and subdata.value%10000!=0)");
- END IF;
- ELSEIF operator = "<" THEN
- IF mon != 0 and dom != 0 THEN
- RETURN CONCAT(" subdata.value<", vILB_Date, " and (subdata.value%100!=0 or (subdata.value<", yea*10000+mon*100, " and subdata.value%10000!=0) or (subdata.value<", yea*10000, " and subdata.value%10000=0))");
- ELSEIF mon != 0 THEN
- RETURN CONCAT(" subdata.value<", vILB_Date, " and (subdata.value%10000!=0 or (subdata.value<", yea*10000, "))");
- ELSE
- RETURN CONCAT(" subdata.value<", vILB_Date);
- END IF;
- ELSEIF operator = ">" THEN
- IF mon != 0 and dom != 0 THEN
- RETURN CONCAT(" subdata.value>", vILB_Date);
- ELSEIF mon != 0 THEN
- RETURN CONCAT(" subdata.value>=",vEUB_Date);
- ELSE
- RETURN CONCAT(" subdata.value>=",vEUB_Date);
- END IF;
- ELSEIF operator = "<=" THEN
- IF mon != 0 and dom != 0 THEN
-
- RETURN CONCAT(" subdata.value<=", vILB_Date,
- " or (subdata.value<=", yea*10000 + mon*100, " and subdata.value%100=0)");
- ELSEIF mon != 0 THEN
-
- RETURN CONCAT(" subdata.value<", vEUB_Date);
- ELSE
-
- RETURN CONCAT(" subdata.value<", vEUB_Date);
- END IF;
- ELSEIF operator = ">=" THEN
- IF mon != 0 and dom != 0 THEN
-
- RETURN CONCAT(" subdata.value>=", vILB_Date,
- " or (subdata.value>=", yea*10000 + mon*100, " and subdata.value%100=0)",
- " or (subdata.value>=", yea*10000, " and subdata.value%10000=0)");
- ELSEIF mon != 0 THEN
-
- RETURN CONCAT(" subdata.value>=", yea*10000 + mon*100,
- " or (subdata.value>=", yea*10000, " and subdata.value%10000=0)");
- ELSE
-
- RETURN CONCAT(" subdata.value>=", yea*10000);
- END IF;
- END IF;
-
- return ' 0=1';
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP FUNCTION IF EXISTS `getDoubleWhereClause` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` FUNCTION `getDoubleWhereClause`(value DOUBLE, unit_sig BIGINT, valueStdUnit DECIMAL(65,30), stdUnit_sig BIGINT, o CHAR(4)) RETURNS varchar(20000) CHARSET utf8 COLLATE utf8_unicode_ci
- DETERMINISTIC
-BEGIN
- RETURN IF(unit_sig IS NULL AND value IS NOT NULL,
- CONCAT('subdata.value ', o, ' \'', value, '\''),
- CONCAT(
- IF(value IS NULL, '',
- CONCAT('(subdata.unit_sig=', unit_sig, ' AND subdata.value ', o, ' \'', value, '\') OR ')),
- IF(unit_sig = stdUnit_sig,'',CONCAT('(subdata.unit_sig=', stdUnit_sig,' AND subdata.value ', o, ' \'', valueStdUnit, '\') OR ')),'(standard_unit(subdata.unit_sig)=', stdUnit_sig,' AND convert_unit(subdata.unit_sig,subdata.value) ', o, ' ', valueStdUnit, ')'));
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP FUNCTION IF EXISTS `get_head_relative` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` FUNCTION `get_head_relative`(EntityID INT UNSIGNED,
- Offset INT UNSIGNED) RETURNS varbinary(255)
- READS SQL DATA
-BEGIN
-
-
-
-
- RETURN (
- SELECT e.version
- FROM entity_version AS e
- WHERE e.entity_id = EntityID
- ORDER BY e._iversion DESC
- LIMIT 1 OFFSET Offset
- );
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP FUNCTION IF EXISTS `get_head_version` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` FUNCTION `get_head_version`(EntityID INT UNSIGNED) RETURNS varbinary(255)
- READS SQL DATA
-BEGIN
- RETURN get_head_relative(EntityID, 0);
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP FUNCTION IF EXISTS `get_iversion` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` FUNCTION `get_iversion`(EntityID INT UNSIGNED,
- Version VARBINARY(255)) RETURNS int(10) unsigned
- READS SQL DATA
-BEGIN
- RETURN (
- SELECT e._iversion
- FROM entity_version AS e
- WHERE e.entity_id = EntityID
- AND e.version = Version
- );
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP FUNCTION IF EXISTS `get_primary_parent_version` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` FUNCTION `get_primary_parent_version`(EntityID INT UNSIGNED,
- Version VARBINARY(255)) RETURNS varbinary(255)
- 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)
- WHERE e.entity_id = EntityID
- AND e.version = Version
- );
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP FUNCTION IF EXISTS `get_version_timestamp` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` FUNCTION `get_version_timestamp`(EntityID INT UNSIGNED,
- Version VARBINARY(255)) RETURNS varchar(255) CHARSET utf8 COLLATE utf8_unicode_ci
- 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 )
- WHERE e.entity_id = EntityID
- AND e.version = Version
- );
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP FUNCTION IF EXISTS `is_feature_config` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` FUNCTION `is_feature_config`(_Key VARCHAR(255),
- Expected VARCHAR(255)) RETURNS tinyint(1)
- READS SQL DATA
-BEGIN
- RETURN (
- SELECT f._value = Expected FROM feature_config as f WHERE f._key = _Key
- );
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP FUNCTION IF EXISTS `makeStmt` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` FUNCTION `makeStmt`(sourceSet VARCHAR(255), targetSet VARCHAR(255), data VARCHAR(20000),
- properties VARCHAR(20000), versioned BOOLEAN) RETURNS varchar(20000) CHARSET utf8 COLLATE utf8_unicode_ci
- NO SQL
-BEGIN
- IF sourceSet = "entities" AND versioned THEN
- RETURN CONCAT('INSERT IGNORE INTO `',
- targetSet,
- '` (id, _iversion) SELECT entity_id, _iversion FROM ',
- data,
- IF(properties IS NULL, '',
- CONCAT(' AS data JOIN `', properties, '` AS prop ON (data.property_id = prop.id) WHERE ',
- 'data.entity_id = prop.id2 OR prop.id2 = 0')));
- END IF;
- RETURN CONCAT(
- IF(targetSet IS NULL,
- CONCAT('DELETE FROM `',sourceSet,'` WHERE NOT EXISTS (SELECT 1 FROM '),
- CONCAT('INSERT IGNORE INTO `',targetSet,'` (id) SELECT id FROM `',sourceSet,'` ',
- 'WHERE EXISTS (SELECT 1 FROM ')),
- IF(properties IS NULL,
- CONCAT(data,' as data WHERE '),
- CONCAT('`',properties,'` as prop JOIN ',data,' as data ON (data.property_id=prop.id) WHERE ',
- '(data.entity_id=prop.id2 OR prop.id2=0) AND ')),
- 'data.entity_id=`', sourceSet, '`.`id` LIMIT 1)'
- );
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP FUNCTION IF EXISTS `ms` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` FUNCTION `ms`(ps bigint(20) unsigned ) RETURNS double
-return TRUNCATE(ps/1000000000,3) ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP FUNCTION IF EXISTS `standard_unit` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` FUNCTION `standard_unit`(unit_sig BIGINT) RETURNS bigint(20)
- DETERMINISTIC
-BEGIN
- DECLARE ret BIGINT DEFAULT unit_sig;
-
- SELECT signature_to INTO ret FROM units_lin_con WHERE signature_from=unit_sig;
- RETURN ret;
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP FUNCTION IF EXISTS `_get_head_iversion` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` FUNCTION `_get_head_iversion`(EntityID INT UNSIGNED) RETURNS int(10) unsigned
- READS SQL DATA
-BEGIN
-
-
-
-
- RETURN (
- SELECT e._iversion
- FROM entity_version AS e
- WHERE e.entity_id = EntityID
- ORDER BY e._iversion DESC
- LIMIT 1
- );
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP FUNCTION IF EXISTS `_get_version` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` FUNCTION `_get_version`(EntityID INT UNSIGNED,
- IVersion INT UNSIGNED) RETURNS varbinary(255)
- READS SQL DATA
-BEGIN
- RETURN (
- SELECT version FROM entity_version
- WHERE entity_id = EntityID
- AND _iversion = IVersion
- );
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `applyBackReference` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `applyBackReference`(in sourceSet VARCHAR(255), targetSet VARCHAR(255),
- in propertiesTable VARCHAR(255), in entitiesTable VARCHAR(255), in subQuery BOOLEAN,
- in versioned BOOLEAN)
-BEGIN
- DECLARE newTableName VARCHAR(255) DEFAULT NULL;
-
-
- IF subQuery IS TRUE THEN
- call registerTempTableName(newTableName);
-
- SET @createBackRefSubQueryTableStr = CONCAT('CREATE TEMPORARY TABLE `',newTableName,'` ( entity_id INT UNSIGNED NOT NULL, id INT UNSIGNED NOT NULL, CONSTRAINT `',newTableName,'PK` PRIMARY KEY (id, entity_id))');
-
- PREPARE createBackRefSubQueryTable FROM @createBackRefSubQueryTableStr;
- EXECUTE createBackRefSubQueryTable;
- DEALLOCATE PREPARE createBackRefSubQueryTable;
-
- SET @backRefSubResultSetStmtStr = CONCAT('INSERT IGNORE INTO `',
- newTableName,
- '` (id,entity_id) SELECT entity_id AS id, value AS entity_id FROM `reference_data` AS data ',
- 'WHERE EXISTS (SELECT 1 FROM `',
- sourceSet,
- '` AS source WHERE source.id=data.value LIMIT 1)',
- IF(propertiesTable IS NULL,
- '',
- CONCAT(' AND EXISTS (SELECT 1 FROM `',
- propertiesTable,
- '` AS p WHERE p.id=data.property_id LIMIT 1)')),
- IF(entitiesTable IS NULL,
- '',
- CONCAT(' AND EXISTS (SELECT 1 FROM `',
- entitiesTable,
- '` AS e WHERE e.id=data.entity_id LIMIT 1)'))
- );
-
- PREPARE backRefSubResultSetStmt FROM @backRefSubResultSetStmtStr;
- EXECUTE backRefSubResultSetStmt;
- DEALLOCATE PREPARE backRefSubResultSetStmt;
-
- SELECT newTableName as list;
- ELSE
- IF versioned THEN
- IF sourceSet = "entities" THEN
-
- SET @stmtBackRefStr = CONCAT('INSERT IGNORE INTO `',
- targetSet,
- '` (id, _iversion) SELECT source.id, _get_head_iversion(source.id)',
-
- ' FROM entities AS source WHERE EXISTS (',
- 'SELECT 1 FROM `reference_data` AS data WHERE data.value=source.id AND (',
- 'data.value_iversion IS NULL OR data.value_iversion=_get_head_iversion(source.id))',
- IF(entitiesTable IS NULL,
- '',
- CONCAT(' AND EXISTS (SELECT 1 FROM `',
- entitiesTable,
- '` AS e WHERE e.id=data.entity_id LIMIT 1)')),
- IF(propertiesTable IS NULL,
- '',
- CONCAT(' AND EXISTS (SELECT 1 FROM `',
- propertiesTable,
- '` AS p WHERE p.id=data.property_id LIMIT 1)')),
- ') UNION ALL ',
-
- 'SELECT source.id, source._iversion FROM archive_entities AS source WHERE EXISTS (',
- 'SELECT 1 FROM `reference_data` AS data WHERE data.value=source.id AND ',
- '(data.value_iversion IS NULL OR data.value_iversion=source._iversion)',
- IF(entitiesTable IS NULL,
- '',
- CONCAT(' AND EXISTS (SELECT 1 FROM `',
- entitiesTable,
- '` AS e WHERE e.id=data.entity_id LIMIT 1)')),
- IF(propertiesTable IS NULL,
- '',
- CONCAT(' AND EXISTS (SELECT 1 FROM `',
- propertiesTable,
- '` AS p WHERE p.id=data.property_id LIMIT 1)')),
-
- ')');
- ELSEIF targetSet IS NULL OR sourceSet = targetSet THEN
- SET @stmtBackRefStr = CONCAT('DELETE FROM `',
- sourceSet,
- '` WHERE NOT EXISTS (SELECT 1 FROM `reference_data` AS data WHERE data.value=`',
- sourceSet,
- '`.`id` AND ( data.value_iversion IS NULL OR data.value_iversion=`',
- sourceSet,
- '`._iversion)',
- IF(entitiesTable IS NULL,
- '',
- CONCAT(' AND EXISTS (SELECT 1 FROM `',
- entitiesTable,
- '` AS e WHERE e.id=data.entity_id LIMIT 1)')),
- IF(propertiesTable IS NULL,
- '',
- CONCAT(' AND EXISTS (SELECT 1 FROM `',
- propertiesTable,
- '` AS p WHERE p.id=data.property_id LIMIT 1)')),
- ')');
- ELSE
- SET @stmtBackRefStr = CONCAT('INSERT IGNORE INTO `',
- targetSet,
- '` (id, _iversion) SELECT source.id, source._iversion FROM `',
- sourceSet,
- '` AS source WHERE EXISTS (',
- 'SELECT 1 FROM `reference_data` AS data WHERE data.value=source.id AND',
- ' (data.value_iversion IS NULL OR data.value_iversion=source._iversion)',
- IF(entitiesTable IS NULL,
- '',
- CONCAT(' AND EXISTS (SELECT 1 FROM `',
- entitiesTable,
- '` AS e WHERE e.id=data.entity_id LIMIT 1)')),
- IF(propertiesTable IS NULL,
- '',
- CONCAT(' AND EXISTS (SELECT 1 FROM `',
- propertiesTable,
- '` AS p WHERE p.id=data.property_id LIMIT 1)')),
-
- ')');
- END IF;
- ELSE
-
- IF targetSet IS NULL OR sourceSet = targetSet THEN
-
- SET @stmtBackRefStr = CONCAT('DELETE FROM `',
- sourceSet,
- '` WHERE NOT EXISTS (SELECT 1 FROM `reference_data` AS data WHERE data.value=`',
- sourceSet,
- '`.`id`',
- IF(entitiesTable IS NULL,
- '',
- CONCAT('
- AND EXISTS (SELECT 1 FROM `',
- entitiesTable,
- '` AS e WHERE e.id=data.entity_id LIMIT 1)')),
- IF(propertiesTable IS NULL,
- '',
- CONCAT('
- AND EXISTS (SELECT 1 FROM `',
- propertiesTable,
- '` AS p WHERE p.id=data.property_id LIMIT 1)')),
- ')');
- ELSE
-
- SET @stmtBackRefStr = CONCAT('INSERT IGNORE INTO `',
- targetSet,
- '` (id) SELECT id FROM `',
- sourceSet,
- '` AS source WHERE EXISTS (SELECT 1 FROM `reference_data` AS data WHERE data.value=source.id',
- IF(entitiesTable IS NULL,
- '',
- CONCAT(' AND EXISTS (SELECT 1 FROM `',
- entitiesTable,
- '` AS e WHERE e.id=data.entity_id LIMIT 1)')),
- IF(propertiesTable IS NULL,
- '',
- CONCAT(' AND EXISTS (SELECT 1 FROM `',
- propertiesTable,
- '` AS p WHERE p.id=data.property_id LIMIT 1)')),
- ')');
- END IF;
- END IF;
-
- PREPARE stmtBackRef FROM @stmtBackRefStr;
- EXECUTE stmtBackRef;
- DEALLOCATE PREPARE stmtBackRef;
- END IF;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `applyIDFilter` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `applyIDFilter`(in sourceSet VARCHAR(255), in targetSet VARCHAR(255),
- in o CHAR(2), in vInt BIGINT, in agg CHAR(3), in versioned BOOLEAN)
-IDFILTER_LABEL: BEGIN
-DECLARE data VARCHAR(20000) DEFAULT NULL;
-DECLARE aggVal VARCHAR(255) DEFAULT NULL;
-
-
-IF agg IS NOT NULL THEN
- IF versioned THEN
-
- SELECT 1 FROM id_agg_with_versioning_not_implemented;
- END IF;
- SET @stmtIDAggValStr = CONCAT(
- "SELECT ",
- agg,
- "(id) INTO @sAggVal FROM `",
- sourceSet,
- "`");
- PREPARE stmtIDAggVal FROM @stmtIDAggValStr;
- EXECUTE stmtIDAggVal;
- DEALLOCATE PREPARE stmtIDAggVal;
- SET aggVal = @sAggVal;
-END IF;
-
-
-IF targetSet IS NULL OR targetSet = sourceSet THEN
- SET data = CONCAT(
- "DELETE FROM `",
- sourceSet,
- "` WHERE ",
- IF(o IS NULL OR vInt IS NULL,
- "1=1",
- CONCAT("NOT id",
- o,
- vInt)),
- IF(aggVal IS NULL,
- "",
- CONCAT(" AND id!=",
- aggVal)));
-ELSEIF versioned AND sourceSet = "entities" THEN
-
-
- SET data = CONCAT(
- "INSERT IGNORE INTO `",
- targetSet,
- '` (id, _iversion) SELECT id, _get_head_iversion(id) FROM `entities` WHERE ',
- IF(o IS NULL OR vInt IS NULL,
- "1=1",
- CONCAT("id",
- o,
- vInt)),
- IF(aggVal IS NULL,
- "",
- CONCAT(" AND id=",
- aggVal)),
- ' UNION SELECT id, _iversion FROM `archive_entities` WHERE ',
- IF(o IS NULL OR vInt IS NULL,
- "1=1",
- CONCAT("id",
- o,
- vInt)),
- IF(aggVal IS NULL,
- "",
- CONCAT(" AND id=",
- aggVal)));
-
-
-ELSE
- SET data = CONCAT(
- "INSERT IGNORE INTO `",
- targetSet,
- IF(versioned,
- '` (id, _iversion) SELECT data.id, data._iversion FROM `',
- '` (id) SELECT data.id FROM `'),
- sourceSet,
- "` AS data WHERE ",
- IF(o IS NULL OR vInt IS NULL,
- "1=1",
- CONCAT("data.id",
- o,
- vInt)),
- IF(aggVal IS NULL,
- "",
- CONCAT(" AND data.id=",
- aggVal)));
-END IF;
-
-Set @stmtIDFilterStr = data;
-PREPARE stmtIDFilter FROM @stmtIDFilterStr;
-EXECUTE stmtIDFilter;
-DEALLOCATE PREPARE stmtIDFilter;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `applyPOV` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `applyPOV`(in sourceSet VARCHAR(255),
- in targetSet VARCHAR(255),
- in propertiesTable VARCHAR(255),
- in refIdsTable VARCHAR(255),
- in o CHAR(4),
- in vText VARCHAR(255),
- in vInt INT,
- in vDouble DOUBLE,
- in unit_sig BIGINT,
- in vDoubleStdUnit DOUBLE,
- in stdUnit_sig BIGINT,
- in vDateTime VARCHAR(255),
- in vDateTimeDotNotation VARCHAR(255),
- in agg CHAR(3),
- in pname VARCHAR(255),
- in versioned BOOLEAN)
-POV_LABEL: BEGIN
- DECLARE data TEXT DEFAULT NULL;
- DECLARE sTextData VARCHAR(20000) DEFAULT NULL;
- DECLARE sNameData VARCHAR(20000) DEFAULT NULL;
- DECLARE sEnumData VARCHAR(20000) DEFAULT NULL;
- DECLARE sIntData VARCHAR(20000) DEFAULT NULL;
- DECLARE sDoubleData VARCHAR(20000) DEFAULT NULL;
- DECLARE sDatetimeData VARCHAR(20000) DEFAULT NULL;
- DECLARE sNullData VARCHAR(20000) DEFAULT NULL;
- DECLARE sDateData VARCHAR(20000) DEFAULT NULL;
- DECLARE sRefData VARCHAR(20000) DEFAULT NULL;
- DECLARE aggValue VARCHAR(255) DEFAULT NULL;
- DECLARE aggValueWhereClause VARCHAR(20000) DEFAULT NULL;
- DECLARE distinctUnits INT DEFAULT 0;
- DECLARE usedStdUnit BIGINT DEFAULT NULL;
- DECLARE keepTabl VARCHAR(255) DEFAULT NULL;
- DECLARE existence_op VARCHAR(255) DEFAULT "EXISTS";
-
- IF o = '->' THEN
-
- call applyRefPOV(sourceSet,targetSet, propertiesTable, refIdsTable, versioned);
- LEAVE POV_LABEL;
- ELSEIF o = '0' THEN
-
-
- SET vText = NULL;
- SET sTextData = 'SELECT domain_id, entity_id, property_id FROM `null_data` AS subdata';
-
-
-
- ELSEIF o = '!0' THEN
-
-
- SET vText = NULL;
-
- SET sTextData = CONCAT(
- 'SELECT DISTINCT domain_id, entity_id, property_id FROM `text_data` AS subdata ',
- 'WHERE subdata.value IS NOT NULL UNION ALL ',
- 'SELECT DISTINCT domain_id, entity_id, property_id FROM `name_data` AS subdata ',
- 'WHERE subdata.value IS NOT NULL UNION ALL ',
- 'SELECT DISTINCT domain_id, entity_id, property_id FROM `enum_data` AS subdata ',
- 'WHERE subdata.value IS NOT NULL UNION ALL ',
- 'SELECT DISTINCT domain_id, entity_id, property_id FROM `integer_data` AS subdata ',
- 'WHERE subdata.value IS NOT NULL UNION ALL ',
- 'SELECT DISTINCT domain_id, entity_id, property_id FROM `double_data` AS subdata ',
- 'WHERE subdata.value IS NOT NULL UNION ALL ',
- 'SELECT DISTINCT domain_id, entity_id, property_id FROM `date_data` AS subdata ',
- 'WHERE subdata.value IS NOT NULL UNION ALL ',
- 'SELECT DISTINCT domain_id, entity_id, property_id FROM `datetime_data` AS subdata ',
- 'WHERE subdata.value IS NOT NULL UNION ALL ',
- 'SELECT DISTINCT domain_id, entity_id, property_id FROM `reference_data` AS subdata ',
- 'WHERE subdata.value IS NOT NULL');
-
- ELSEIF o = "(" or o = "!(" THEN
- IF versioned THEN
- SET sTextData = IF(vText IS NULL,
- CONCAT(
- ' SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id) ',
- 'AS _iversion, property_id FROM `date_data` UNION ALL ',
- 'SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_date_data`'),
- IF(vDateTimeDotNotation IS NULL, NULL,
- CONCAT(' SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id) ',
- 'AS _iversion, property_id FROM `date_data` AS subdata WHERE ',
- getDateWhereClause(vDateTimeDotNotation, o), ' UNION ALL ',
- 'SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_date_data` ',
- 'AS subdata WHERE ', getDateWhereClause(vDateTimeDotNotation, o))));
- SET sDatetimeData = IF(vText IS NULL, ' UNION ALL SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id) AS _iversion, property_id FROM `datetime_data` UNION ALL SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_datetime_data`',
- IF(vDateTime IS NULL, NULL,
- CONCAT(' UNION ALL SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id) AS _iversion, property_id FROM `datetime_data` AS subdata WHERE ', getDateTimeWhereClause(vDateTime, o), ' UNION ALL SELECT DISTINCT domain_id, entity_id,_iversion, property_id FROM `archive_datetime_data` AS subdata WHERE ', getDateTimeWhereClause(vDateTime, o))));
- ELSE
- SET sTextData = IF(vText IS NULL,
- ' SELECT DISTINCT domain_id, entity_id, property_id FROM `date_data`',
- IF(vDateTimeDotNotation IS NULL, NULL,
- CONCAT(' SELECT DISTINCT domain_id, entity_id, property_id FROM `date_data` AS subdata WHERE ',
- getDateWhereClause(vDateTimeDotNotation, o))));
- SET sDatetimeData = IF(vText IS NULL,
- ' UNION ALL SELECT DISTINCT domain_id, entity_id, property_id FROM `datetime_data`',
- IF(vDateTime IS NULL, NULL,
- CONCAT(' UNION ALL SELECT DISTINCT domain_id, entity_id, property_id FROM `datetime_data` ',
- 'AS subdata WHERE ', getDateTimeWhereClause(vDateTime, o))));
- END IF;
- SET vText = NULL;
- ELSEIF agg IS NOT NULL THEN
- IF versioned THEN
- SELECT 1 FROM versioned_agg_pov_filter_not_implemented;
- END IF;
-
-
-
- SET aggValueWhereClause = CONCAT(getDoubleWhereClause(vDouble, unit_sig, vDoubleStdUnit, stdUnit_sig, o), ' AND ');
- SET aggValueWhereClause = CONCAT(IF(aggValueWhereClause IS NULL, '', aggValueWhereClause), getAggValueWhereClause(sourceSet, propertiesTable));
-
-
- SET @aggValueStmtStr = CONCAT('SELECT ',agg,'(subdata.value), ', agg, '(convert_unit(subdata.unit_sig,subdata.value)), COUNT(DISTINCT standard_unit(subdata.unit_sig)), max(standard_unit(subdata.unit_sig)) INTO @sAggValue, @sAggValueConvert, @distinctUnits, @StdUnitSig FROM (SELECT entity_id, property_id, value, unit_sig FROM `integer_data` UNION ALL SELECT entity_id, property_id, value, unit_sig FROM `double_data`) AS subdata WHERE ', aggValueWhereClause);
-
-
- PREPARE stmtAggValueStmt FROM @aggValueStmtStr;
- EXECUTE stmtAggValueStmt;
- DEALLOCATE PREPARE stmtAggValueStmt;
-
- SET distinctUnits = @distinctUnits;
- SET aggValue = @sAggValue;
-
-
- IF distinctUnits = 1 THEN
- SET aggValue = @sAggValueConvert;
- SET usedStdUnit = @StdUnitSig;
- ELSE
- call raiseWarning(CONCAT("The filter POV(",IF(pname IS NULL, 'NULL', pname),",",IF(o IS NULL, 'NULL', o),",",IF(vText IS NULL, 'NULL', vText),") with the aggregate function '", agg, "' could not match the values against each other with their units. The values had different base units. Only their numric value had been taken into account." ));
- END IF;
-
- IF aggValue IS NULL THEN
- SET sTextData = 'SELECT NULL as domain_id, NULL as entity_id, NULL as property_id';
- ELSE
- SET sTextData = '';
- SET sIntData = CONCAT(' UNION ALL SELECT DISTINCT domain_id, entity_id, property_id FROM `integer_data` as subdata WHERE ', getDoubleWhereClause(aggValue, usedStdUnit, aggValue, usedStdUnit, '='));
- SET sDoubleData = CONCAT(' SELECT DISTINCT domain_id, entity_id, property_id FROM `double_data` as subdata WHERE ', getDoubleWhereClause(aggValue, usedStdUnit, aggValue, usedStdUnit, '='));
- END IF;
-
- SET vText = NULL;
- ELSE
-
- IF versioned THEN
- SET sTextData = IF(vText IS NULL,
- 'SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id) AS _iversion, property_id FROM `text_data` UNION ALL SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_text_data` ',
- CONCAT(
- 'SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id) AS _iversion, property_id ',
- 'FROM `text_data` AS subdata WHERE subdata.value ', o,' ? ',
- 'UNION ALL SELECT DISTINCT domain_id, entity_id, _iversion, property_id ',
- 'FROM `archive_text_data` AS subdata WHERE subdata.value ', o, '?'
- ));
- SET sNameData = IF(vText IS NULL, ' UNION ALL SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id) AS _iversion, property_id FROM `name_data` UNION ALL SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_name_data` ', CONCAT(' UNION ALL SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id) AS _iversion, property_id FROM `name_data` AS subdata WHERE subdata.value ', o, ' ? UNION ALL SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_name_data` AS subdata WHERE subdata.value ', o, '?'));
- SET sEnumData = IF(vText IS NULL, ' UNION ALL SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id) AS _iversion, property_id FROM `enum_data` UNION ALL SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_enum_data` ', CONCAT(' UNION ALL SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id) AS _iversion, property_id FROM `enum_data` AS subdata WHERE subdata.value ', o, ' ? UNION ALL SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_enum_data` AS subdata WHERE subdata.value ', o, '?'));
- IF o = "!=" AND refIdsTable IS NOT NULL THEN
- SET existence_op = "NOT EXISTS";
- END IF;
- SET sRefData = IF(vText IS NULL,
- ' UNION ALL SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id) AS _iversion, property_id FROM `reference_data` UNION ALL SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_reference_data`',
- IF(refIdsTable IS NULL,
- NULL,
- CONCAT(' UNION ALL SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id) AS _iversion, property_id FROM `reference_data` AS subdata WHERE ', existence_op, ' (SELECT 1 FROM `', refIdsTable, '` AS refIdsTable WHERE subdata.value=refIdsTable.id LIMIT 1) AND subdata.status != "REPLACEMENT" UNION ALL SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_reference_data` AS subdata WHERE ', existence_op, ' (SELECT 1 FROM `', refIdsTable, '` AS refIdsTable WHERE subdata.value=refIdsTable.id LIMIT 1) AND subdata.status != "REPLACEMENT"')));
- SET sDoubleData = IF(vText IS NULL, ' UNION ALL SELECT DISTINCT subdata.domain_id, subdata.entity_id, _get_head_iversion(subdata.entity_id) AS _iversion, subdata.property_id FROM `double_data` AS subdata UNION ALL SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_double_data` ', IF(vDouble IS NULL, NULL, CONCAT(' UNION ALL SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id), property_id FROM `double_data` AS subdata WHERE ', getDoubleWhereClause(vDouble,unit_sig,vDoubleStdUnit,stdUnit_sig,o), ' UNION ALL SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_double_data` AS subdata WHERE ', getDoubleWhereClause(vDouble, unit_sig, vDoubleStdUnit, stdUnit_sig, o))));
- SET sIntData = IF(vText IS NULL, ' UNION ALL SELECT DISTINCT subdata.domain_id, subdata.entity_id, _get_head_iversion(subdata.entity_id) AS _iversion, subdata.property_id FROM `integer_data` AS subdata UNION ALL SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_integer_data`', IF(vInt IS NULL AND vDoubleStdUnit IS NULL, NULL, CONCAT(' UNION ALL SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id) AS _iversion, property_id FROM `integer_data` AS subdata WHERE ', getDoubleWhereClause(vInt, unit_sig, vDoubleStdUnit, stdUnit_sig, o), ' UNION ALL SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_integer_data` AS subdata WHERE ', getDoubleWhereClause(vInt, unit_sig, vDoubleStdUnit, stdUnit_sig, o))));
- SET sDatetimeData = IF(vText IS NULL,' UNION ALL SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id) AS _iversion, property_id FROM `datetime_data` UNION ALL SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_datetime_data`', IF(vDateTime IS NULL, NULL, CONCAT(' UNION ALL SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id) AS _iversion, property_id FROM `datetime_data` AS subdata WHERE ',getDateTimeWhereClause(vDateTime,o), ' UNION ALL SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_datetime_data` AS subdata WHERE ',getDateTimeWhereClause(vDateTime,o))));
- SET sDateData = IF(vText IS NULL,' UNION ALL SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id) AS _iversion, property_id FROM `date_data` UNION ALL SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_date_data`', IF(vDateTimeDotNotation IS NULL, NULL, CONCAT(' UNION ALL SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id) AS _iversion, property_id FROM `date_data` AS subdata WHERE ', getDateWhereClause(vDateTimeDotNotation,o), ' UNION ALL SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_date_data` AS subdata WHERE ', getDateWhereClause(vDateTimeDotNotation,o))));
- SET sNullData = IF(vText IS NULL, ' UNION ALL SELECT DISTINCT domain_id, entity_id, _get_head_iversion(entity_id) AS _iversion, property_id FROM `null_data` UNION ALL SELECT DISTINCT domain_id, entity_id, _iversion, property_id FROM `archive_null_data`', NULL);
-
- ELSE
- SET sTextData = IF(vText IS NULL, 'SELECT DISTINCT domain_id, entity_id, property_id FROM `text_data`', CONCAT('SELECT DISTINCT domain_id, entity_id, property_id FROM `text_data` AS subdata WHERE subdata.value ',o,' ?'));
- SET sNameData = IF(vText IS NULL, ' UNION ALL SELECT DISTINCT domain_id, entity_id, property_id FROM `name_data`', CONCAT(' UNION ALL SELECT DISTINCT domain_id, entity_id, property_id FROM `name_data` AS subdata WHERE subdata.value ', o, ' ?'));
- SET sEnumData = IF(vText IS NULL, ' UNION ALL SELECT DISTINCT domain_id, entity_id, property_id FROM `enum_data`', CONCAT(' UNION ALL SELECT DISTINCT domain_id, entity_id, property_id FROM `enum_data` AS subdata WHERE subdata.value ', o, ' ?'));
- IF o = "!=" AND refIdsTable IS NOT NULL THEN
- SET existence_op = "NOT EXISTS";
- END IF;
- SET sRefData = IF(vText IS NULL,
- ' UNION ALL SELECT DISTINCT domain_id, entity_id, property_id FROM `reference_data`',
- IF(refIdsTable IS NULL,
- NULL,
- CONCAT(' UNION ALL SELECT DISTINCT domain_id, entity_id, property_id FROM `reference_data` AS subdata WHERE ',existence_op ,' (SELECT 1 FROM `', refIdsTable, '` AS refIdsTable WHERE subdata.value=refIdsTable.id LIMIT 1) AND subdata.status != "REPLACEMENT"')));
- SET sDoubleData = IF(vText IS NULL, ' UNION ALL SELECT DISTINCT subdata.domain_id, subdata.entity_id, subdata.property_id FROM `double_data` AS subdata', IF(vDouble IS NULL, NULL, CONCAT(' UNION ALL SELECT DISTINCT domain_id, entity_id, property_id FROM `double_data` AS subdata WHERE ', getDoubleWhereClause(vDouble,unit_sig,vDoubleStdUnit,stdUnit_sig,o))));
- SET sIntData = IF(vText IS NULL, ' UNION ALL SELECT DISTINCT subdata.domain_id, subdata.entity_id, subdata.property_id FROM `integer_data` AS subdata', IF(vInt IS NULL AND vDoubleStdUnit IS NULL, NULL, CONCAT(' UNION ALL SELECT DISTINCT domain_id, entity_id, property_id FROM `integer_data` AS subdata WHERE ', getDoubleWhereClause(vInt, unit_sig, vDoubleStdUnit, stdUnit_sig, o))));
- SET sDatetimeData = IF(vText IS NULL,' UNION ALL SELECT DISTINCT domain_id, entity_id, property_id FROM `datetime_data`', IF(vDateTime IS NULL, NULL, CONCAT(' UNION ALL SELECT DISTINCT domain_id, entity_id, property_id FROM `datetime_data` AS subdata WHERE ',getDateTimeWhereClause(vDateTime,o))));
- SET sDateData = IF(vText IS NULL,' UNION ALL SELECT DISTINCT domain_id, entity_id, property_id FROM `date_data`', IF(vDateTimeDotNotation IS NULL, NULL, CONCAT(' UNION ALL SELECT DISTINCT domain_id, entity_id, property_id FROM `date_data` AS subdata WHERE ',getDateWhereClause(vDateTimeDotNotation,o))));
- SET sNullData = IF(vText IS NULL, ' UNION ALL SELECT DISTINCT domain_id, entity_id, property_id FROM `null_data`', NULL);
- END IF;
-
- END IF;
-
- SET data = CONCAT('(',sTextData,
- IF(sNameData IS NULL, '', sNameData),
- IF(sEnumData IS NULL, '', sEnumData),
- IF(sDoubleData IS NULL, '', sDoubleData),
- IF(sIntData IS NULL, '', sIntData),
- IF(sDatetimeData IS NULL, '', sDatetimeData),
- IF(sDateData IS NULL, '', sDateData),
- IF(sRefData IS NULL, '', sRefData),
- IF(sNullData IS NULL, '', sNullData),
- ')'
- );
-
-
- call createTmpTable(keepTabl, versioned);
- IF versioned THEN
-
- SET @stmtPOVkeepTblStr = CONCAT(
- 'INSERT IGNORE INTO `', keepTabl, '` (id, _iversion) SELECT entity_id AS id, _iversion FROM ', data,
- ' as data', IF(propertiesTable IS NULL, '', CONCAT(
- ' WHERE EXISTS (Select 1 from `', propertiesTable, '` AS prop ',
- 'WHERE prop.id = data.property_id AND (prop.id2=data.entity_id OR prop.id2=0))')));
-
- IF targetSet IS NOT NULL THEN
- SET @stmtPOVStr = CONCAT('INSERT IGNORE INTO `',
- targetSet,
- '` (id, _iversion) SELECT source.id, source._iversion FROM `',
- keepTabl,
- '` AS source');
- ELSE
-
- SET @stmtPOVStr = CONCAT('DELETE FROM `',
- sourceSet,
- '` WHERE NOT EXISTS (SELECT 1 FROM `',
- keepTabl,
- '` AS data WHERE data.id=`',
- sourceSet,
- '`.`id` AND data._iversion=`',
- sourceSet,
- '`._iversion LIMIT 1)');
-
- END IF;
-
-
- PREPARE stmt3 FROM @stmtPOVStr;
- PREPARE stmtPOVkeepTbl FROM @stmtPOVkeepTblStr;
- IF vText IS NULL THEN
- EXECUTE stmtPOVkeepTbl;
- ELSE
- SET @vText = vText;
- EXECUTE stmtPOVkeepTbl USING @vText, @vText, @vText, @vText, @vText, @vText;
- END IF;
- EXECUTE stmt3;
- DEALLOCATE PREPARE stmt3;
- DEALLOCATE PREPARE stmtPOVkeepTbl;
- ELSE
-
- SET @stmtPOVkeepTblStr = CONCAT('INSERT IGNORE INTO `', keepTabl, '` (id) SELECT DISTINCT entity_id AS id FROM ', data, ' as data', IF(propertiesTable IS NULL, '', CONCAT(' WHERE EXISTS (Select 1 from `', propertiesTable, '` AS prop WHERE prop.id = data.property_id AND (prop.id2=data.entity_id OR prop.id2=0))')));
-
- SET @stmtPOVStr = CONCAT(
- IF(targetSet IS NULL,
- CONCAT('DELETE FROM `',
- sourceSet,
- '` WHERE NOT EXISTS (SELECT 1 FROM `'),
- CONCAT('INSERT IGNORE INTO `',
- targetSet,
- '` (id) SELECT id FROM `',
- sourceSet,
- '` WHERE EXISTS (SELECT 1 FROM `')),
- keepTabl,
- '` AS data WHERE data.id=`',
- sourceSet,
- '`.`id` LIMIT 1)'
- );
-
-
- PREPARE stmt3 FROM @stmtPOVStr;
- PREPARE stmtPOVkeepTbl FROM @stmtPOVkeepTblStr;
- IF vText IS NULL THEN
- EXECUTE stmtPOVkeepTbl;
- ELSE
- SET @vText = vText;
- EXECUTE stmtPOVkeepTbl USING @vText, @vText, @vText;
- END IF;
- EXECUTE stmt3;
- DEALLOCATE PREPARE stmt3;
- DEALLOCATE PREPARE stmtPOVkeepTbl;
- END IF;
-
- SELECT @stmtPOVkeepTblStr as applyPOVStmt1, @stmtPOVStr as applyPOVStmt2, keepTabl as applyPOVIntermediateResultSet;
-
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `applyRefPOV` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `applyRefPOV`(in sourceSet VARCHAR(255), in targetSet VARCHAR(255),
- in properties VARCHAR(255), in refs VARCHAR(255),
- in versioned BOOLEAN)
-BEGIN
- DECLARE data VARCHAR(20000) DEFAULT CONCAT(
- '(SELECT domain_id, entity_id, property_id FROM `reference_data` AS subdata ',
- 'WHERE EXISTS (SELECT 1 FROM `', refs, '` AS refs WHERE subdata.value=refs.id LIMIT 1))');
-
- IF versioned THEN
- SET data = CONCAT(
- '(SELECT domain_id, entity_id, _get_head_iversion(entity_id) AS _iversion, property_id ',
- 'FROM `reference_data` AS subdata WHERE EXISTS (',
- 'SELECT 1 FROM `', refs, '` AS refs WHERE subdata.value=refs.id LIMIT 1) ',
- 'UNION ALL SELECT domain_id, entity_id, _iversion, property_id ',
- 'FROM `archive_reference_data` AS subdata WHERE EXISTS (',
- 'SELECT 1 FROM `', refs, '` AS refs WHERE subdata.value=refs.id LIMIT 1))');
- END IF;
- SET @stmtRefPOVStr = makeStmt(sourceSet,targetSet,data,properties, versioned);
-
- PREPARE stmt4 FROM @stmtRefPOVStr;
- EXECUTE stmt4;
-
- SELECT @stmtRefPOVstr as applyRefPOVStmt;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `applySAT` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `applySAT`(in sourceSet VARCHAR(255), in targetSet VARCHAR(255), in loc MEDIUMTEXT, in op CHAR(5))
-BEGIN
-
- IF targetSet IS NULL OR sourceSet = targetSet THEN
- SET @stmtSATString = CONCAT('DELETE FROM `', sourceSet, '` WHERE id NOT IN (SELECT file_id FROM files WHERE path ', op, ' ?)');
- ELSE
- SET @stmtSATString = CONCAT('INSERT INTO `', targetSet, '` (id) SELECT data.id FROM `',sourceSet,'` as data WHERE EXISTS (SELECT 1 FROM `files` as f WHERE f.file_id=data.id AND f.path ', op, ' ?)');
- END IF;
- PREPARE stmtSAT FROM @stmtSATString;
- SET @loc = loc;
- EXECUTE stmtSAT USING @loc;
- DEALLOCATE PREPARE stmtSAT;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `applyTransactionFilter` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `applyTransactionFilter`(in sourceSet VARCHAR(255), targetSet VARCHAR(255), in transaction VARCHAR(255), in operator_u CHAR(2), in realm VARCHAR(255), in userName VARCHAR(255), in ilb BIGINT, in ilb_nanos INT UNSIGNED, in eub BIGINT, in eub_nanos INT UNSIGNED, in operator_t CHAR(2))
-BEGIN
- DECLARE data TEXT default CONCAT('(SELECT entity_id FROM transaction_log AS t WHERE t.transaction=\'',
- transaction,
- '\'',
- IF(userName IS NOT NULL,
- CONCAT(' AND t.realm', operator_u, '? AND t.username', operator_u, '?'),
- ''
- ),
- IF(ilb IS NOT NULL,
- CONCAT(" AND", constructDateTimeWhereClauseForColumn("t.seconds", "t.nanos", ilb, ilb_nanos, eub, eub_nanos, operator_t)),
- ""
- ),
- ')'
- );
-
- SET @stmtTransactionStr = makeStmt(sourceSet, targetSet, data, NULL, FALSE);
- PREPARE stmtTransactionFilter from @stmtTransactionStr;
- IF userName IS NOT NULL THEN
- SET @userName = userName;
- SET @realm = realm;
- EXECUTE stmtTransactionFilter USING @realm, @userName;
- ELSE
- EXECUTE stmtTransactionFilter;
- END IF;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `calcComplementUnion` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `calcComplementUnion`(in targetSet VARCHAR(255), in subResultSet VARCHAR(255), in universe VARCHAR(255), in versioned BOOLEAN)
-BEGIN
- IF versioned AND universe = "entities" THEN
- SET @stmtComplementUnionStr = CONCAT(
- 'INSERT IGNORE INTO `', targetSet,
- '` SELECT e.id, _get_head_iversion(e.id) FROM entities as e WHERE NOT EXISTS ( SELECT 1 FROM `',
- subResultSet,
- '` AS diff WHERE diff.id=e.id AND diff._iversion = _get_head_iversion(e.id)) UNION ALL SELECT e.id, e._iversion FROM archive_entities AS e WHERE NOT EXISTS ( SELECT 1 FROM `',
- subResultSet,
- '` as diff WHERE e.id = diff.id AND e._iversion = diff._iversion)');
- ELSEIF versioned THEN
- SET @stmtComplementUnionStr = CONCAT(
- 'INSERT IGNORE INTO `', targetSet,
- '` SELECT id FROM `',universe,
- '` AS universe WHERE NOT EXISTS ( SELECT 1 FROM `',
- subResultSet,'`
- AS diff WHERE diff.id=universe.id AND diff._iversion = universe.id_version)');
- ELSE
- SET @stmtComplementUnionStr = CONCAT('INSERT IGNORE INTO `', targetSet, '` SELECT id FROM `',universe, '` AS universe WHERE NOT EXISTS ( SELECT 1 FROM `', subResultSet,'` AS diff WHERE diff.id=universe.id)');
- END IF;
- PREPARE stmtComplementUnion FROM @stmtComplementUnionStr;
- EXECUTE stmtComplementUnion;
- DEALLOCATE PREPARE stmtComplementUnion;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `calcDifference` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `calcDifference`(in resultSetTable VARCHAR(255), in diff VARCHAR(255), in versioned BOOLEAN)
-BEGIN
- IF versioned THEN
- SET @diffStmtStr = CONCAT('DELETE FROM `', resultSetTable, '` WHERE EXISTS ( SELECT 1 FROM `', diff,'` AS diff WHERE diff.id=`',resultSetTable,'`.`id` AND diff._iversion=`', resultSetTable, '`.`_iversion`)');
- ELSE
- SET @diffStmtStr = CONCAT('DELETE FROM `', resultSetTable, '` WHERE EXISTS ( SELECT 1 FROM `', diff,'` AS diff WHERE diff.id=`',resultSetTable,'`.`id`)');
- END IF;
- PREPARE diffStmt FROM @diffStmtStr;
- EXECUTE diffStmt;
- DEALLOCATE PREPARE diffStmt;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `calcIntersection` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `calcIntersection`(in resultSetTable VARCHAR(255), in intersectWith VARCHAR(255), in versioned BOOLEAN)
-BEGIN
- IF versioned THEN
- SET @diffStmtStr = CONCAT('DELETE FROM `',
- resultSetTable,
- '` WHERE NOT EXISTS ( SELECT 1 FROM `',
- intersectWith,
- '` AS diff WHERE diff.id=`',
- resultSetTable,
- '`.`id` AND diff._iversion=`',
- resultSetTable,
- '`.`_iversion`)');
- ELSE
- SET @diffStmtStr = CONCAT('DELETE FROM `', resultSetTable, '` WHERE NOT EXISTS ( SELECT 1 FROM `', intersectWith,'` AS diff WHERE diff.id=`',resultSetTable,'`.`id`)');
- END IF;
- PREPARE diffStmt FROM @diffStmtStr;
- EXECUTE diffStmt;
-
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `calcUnion` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `calcUnion`(in targetSet VARCHAR(255), in sourceSet VARCHAR(255))
-BEGIN
- SET @diffStmtStr = CONCAT('INSERT IGNORE INTO `', targetSet, '` SELECT * FROM `',sourceSet,'`');
- PREPARE diffStmt FROM @diffStmtStr;
- EXECUTE diffStmt;
- DEALLOCATE PREPARE diffStmt;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `cleanUpLinCon` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `cleanUpLinCon`()
-BEGIN
-
- DELETE FROM units_lin_con WHERE NOT EXISTS (SELECT '1' FROM double_data WHERE unit_sig=signature_from) AND NOT EXISTS (SELECT '1' FROM integer_data WHERE unit_sig=signature_from);
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `cleanUpQuery` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `cleanUpQuery`()
-BEGIN
- CREATE TEMPORARY TABLE IF NOT EXISTS warnings (warning TEXT NOT NULL);
- SELECT * from warnings;
-
- SET @pstmtstr = CONCAT('DROP TEMPORARY TABLE IF EXISTS `warnings`',
- IF(@tempTableList IS NULL, '', CONCAT(',',@tempTableList)));
- PREPARE pstmt FROM @pstmtstr;
- EXECUTE pstmt;
-
- SET @tempTableList = NULL;
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `copyTable` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `copyTable`(in fromTable VARCHAR(255), in toTable VARCHAR(255))
-BEGIN
- SET @copyTableStmtStr = CONCAT('INSERT IGNORE INTO `', toTable, '` (id) SELECT id FROM `', fromTable, '`');
- PREPARE copyTableStmt FROM @copyTableStmtStr;
- EXECUTE copyTableStmt;
- DEALLOCATE PREPARE copyTableStmt;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `createTmpTable` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `createTmpTable`(out newTableName VARCHAR(255), in versioned BOOLEAN)
-BEGIN
- call registerTempTableName(newTableName);
-
- IF versioned THEN
- SET @createTableStmtStr = CONCAT('CREATE TEMPORARY TABLE `', newTableName,
- '` ( id INT UNSIGNED, _iversion INT UNSIGNED, PRIMARY KEY (id, _iversion))' );
- ELSE
- SET @createTableStmtStr = CONCAT('CREATE TEMPORARY TABLE `', newTableName,'` ( id INT UNSIGNED PRIMARY KEY)' );
- END IF;
-
- PREPARE createTableStmt FROM @createTableStmtStr;
- EXECUTE createTableStmt;
- DEALLOCATE PREPARE createTableStmt;
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `createTmpTable2` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `createTmpTable2`(out newTableName VARCHAR(255))
-BEGIN
- call registerTempTableName(newTableName);
- SET @createTableStmtStr = CONCAT('CREATE TEMPORARY TABLE `', newTableName,
- '` ( id INT UNSIGNED, id2 INT UNSIGNED, domain INT UNSIGNED, CONSTRAINT `',
- newTableName,'PK` PRIMARY KEY (id,id2,domain) )' );
-
- PREPARE createTableStmt FROM @createTableStmtStr;
- EXECUTE createTableStmt;
- DEALLOCATE PREPARE createTableStmt;
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `deleteEntity` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `deleteEntity`(in EntityID INT UNSIGNED)
-BEGIN
-
-
- DELETE FROM files where file_id=EntityID;
-
-
- DELETE FROM data_type
- WHERE ( domain_id = 0
- AND entity_id = 0
- AND property_id = EntityID )
- OR datatype = EntityID;
- DELETE FROM collection_type
- WHERE domain_id = 0
- AND entity_id = 0
- AND property_id = EntityID;
-
-
- DELETE FROM name_data
- WHERE domain_id = 0
- AND entity_id = EntityID
- AND property_id = 20;
-
- DELETE FROM entities where id=EntityID;
-
-
- DELETE FROM entity_acl
- WHERE NOT EXISTS (
- SELECT 1 FROM entities
- WHERE entities.acl = entity_acl.id LIMIT 1)
- AND NOT EXISTS (
- SELECT 1 FROM archive_entities
- WHERE archive_entities.acl = entity_acl.id LIMIT 1);
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `deleteEntityProperties` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `deleteEntityProperties`(in EntityID INT UNSIGNED)
-BEGIN
- DECLARE IVersion INT UNSIGNED DEFAULT NULL;
-
- CALL deleteIsa(EntityID);
-
- IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
- SELECT max(e._iversion) INTO IVersion
- FROM entity_version AS e
- WHERE e.entity_id = EntityID;
-
-
- 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,
- status, pidx, IVersion AS _iversion
- FROM reference_data
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
-
- INSERT INTO archive_null_data (domain_id, entity_id,
- property_id, status, pidx, _iversion)
- SELECT domain_id, entity_id, property_id, status,
- pidx, IVersion AS _iversion
- FROM null_data
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
-
- INSERT INTO archive_text_data (domain_id, entity_id,
- property_id, value, status, pidx, _iversion)
- SELECT domain_id, entity_id, property_id, value, status,
- pidx, IVersion AS _iversion
- FROM text_data
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
-
- INSERT INTO archive_name_data (domain_id, entity_id,
- property_id, value, status, pidx, _iversion)
- SELECT domain_id, entity_id, property_id, value, status,
- pidx, IVersion AS _iversion
- FROM name_data
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
-
- INSERT INTO archive_enum_data (domain_id, entity_id,
- property_id, value, status, pidx, _iversion)
- SELECT domain_id, entity_id, property_id, value, status,
- pidx, IVersion AS _iversion
- FROM enum_data
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
-
- INSERT INTO archive_integer_data (domain_id, entity_id,
- property_id, value, status, pidx, _iversion, unit_sig)
- SELECT domain_id, entity_id, property_id, value, status,
- pidx, IVersion AS _iversion, unit_sig
- FROM integer_data
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
-
- INSERT INTO archive_double_data (domain_id, entity_id,
- property_id, value, status, pidx, _iversion, unit_sig)
- SELECT domain_id, entity_id, property_id, value, status,
- pidx, IVersion AS _iversion, unit_sig
- FROM double_data
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
-
- INSERT INTO archive_datetime_data (domain_id, entity_id,
- property_id, value, value_ns, status, pidx, _iversion)
- SELECT domain_id, entity_id, property_id, value, value_ns,
- status, pidx, IVersion AS _iversion
- FROM datetime_data
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
-
- INSERT INTO archive_date_data (domain_id, entity_id,
- property_id, value, status, pidx, _iversion)
- SELECT domain_id, entity_id, property_id, value, status,
- pidx, IVersion AS _iversion
- FROM date_data
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
-
- INSERT INTO archive_name_overrides (domain_id, entity_id,
- property_id, name, _iversion)
- SELECT domain_id, entity_id, property_id, name,
- IVersion AS _iversion
- FROM name_overrides
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
-
- INSERT INTO archive_desc_overrides (domain_id, entity_id,
- property_id, description, _iversion)
- SELECT domain_id, entity_id, property_id, description,
- IVersion AS _iversion
- FROM desc_overrides
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
-
- INSERT INTO archive_data_type (domain_id, entity_id,
- property_id, datatype, _iversion)
- SELECT domain_id, entity_id, property_id, datatype,
- IVersion AS _iversion
- FROM data_type
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
-
- INSERT INTO archive_collection_type (domain_id, entity_id,
- property_id, collection, _iversion)
- SELECT domain_id, entity_id, property_id, collection,
- IVersion AS _iversion
- FROM collection_type
- WHERE (domain_id = 0 AND entity_id = EntityID)
- OR domain_id = EntityID;
-
- INSERT INTO archive_query_template_def (id, definition, _iversion)
- SELECT id, definition, IVersion AS _iversion
- FROM query_template_def
- WHERE id = EntityID;
-
- END IF;
-
- DELETE FROM reference_data
- where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
- DELETE FROM null_data
- where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
- DELETE FROM text_data
- where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
- DELETE FROM name_data
- where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
- DELETE FROM enum_data
- where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
- DELETE FROM integer_data
- where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
- DELETE FROM double_data
- where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
- DELETE FROM datetime_data
- where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
- DELETE FROM date_data
- where (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
-
- DELETE FROM name_overrides
- WHERE (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
- DELETE FROM desc_overrides
- WHERE (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
-
- DELETE FROM data_type
- WHERE (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
- DELETE FROM collection_type
- WHERE (domain_id=0 AND entity_id=EntityID) OR domain_id=EntityID;
-
- DELETE FROM query_template_def WHERE id=EntityID;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `deleteIsa` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `deleteIsa`(IN EntityID INT UNSIGNED)
-BEGIN
- DECLARE IVersion INT UNSIGNED DEFAULT NULL;
-
- IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
- SELECT max(_iversion) INTO IVersion
- FROM entity_version
- WHERE entity_id = EntityID;
-
-
- INSERT IGNORE INTO archive_isa (child, child_iversion, parent, direct)
- SELECT e.child, IVersion AS child_iversion, e.parent, rpath = EntityID
- FROM isa_cache AS e
- WHERE e.child = EntityID;
- END IF;
-
- DELETE FROM isa_cache
- WHERE child = EntityID
- OR rpath = EntityID
- OR rpath LIKE concat('%>', EntityID)
- OR rpath LIKE concat('%>', EntityID, '>%');
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `deleteLinCon` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `deleteLinCon`(in sig BIGINT)
-BEGIN
-
- DELETE FROM units_lin_con WHERE signature_from=sig;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `delete_all_entity_versions` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `delete_all_entity_versions`(
- in EntityID INT UNSIGNED)
-BEGIN
-
- DELETE FROM entity_version WHERE entity_id = EntityID;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `entityACL` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `entityACL`(out ACLID INT UNSIGNED, in ACLSTR VARBINARY(65525))
-BEGIN
- SELECT id INTO ACLID FROM entity_acl as t WHERE t.acl=ACLSTR LIMIT 1;
- IF ACLID IS NULL THEN
- INSERT INTO entity_acl (acl) VALUES (ACLSTR);
- SET ACLID = LAST_INSERT_ID();
- END IF;
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `finishNegationFilter` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `finishNegationFilter`(in resultSetTable VARCHAR(255), in diff VARCHAR(255))
-BEGIN
- call calcDifference(resultSetTable, diff);
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `finishSubProperty` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `finishSubProperty`(in sourceSet VARCHAR(255),in targetSet VARCHAR(255),
- in list VARCHAR(255), in versioned BOOLEAN)
-BEGIN
- DECLARE data VARCHAR(20000) DEFAULT CONCAT('`',list,'`');
- SET @finishSubPropertyStmtStr = makeStmt(sourceSet, targetSet, data, NULL, versioned);
-
- PREPARE finishSubPropertyStmt FROM @finishSubPropertyStmtStr;
- EXECUTE finishSubPropertyStmt;
- DEALLOCATE PREPARE finishSubPropertyStmt;
-
- SELECT @finishSubPropertyStmtStr AS finishSubPropertyStmt;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `getChildren` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `getChildren`(in tableName varchar(255), in versioned BOOLEAN)
-BEGIN
- DECLARE found_children INT UNSIGNED DEFAULT 0;
-
- DROP TEMPORARY TABLE IF EXISTS dependTemp;
- CREATE TEMPORARY TABLE dependTemp (id INT UNSIGNED, _iversion INT UNSIGNED, PRIMARY KEY(id, _iversion));
-
-
- SET @initDepend = CONCAT(
- 'INSERT IGNORE INTO dependTemp (id, _iversion) SELECT i.child, ',
- IF(versioned,
- '_get_head_iversion(i.child)',
- '0'),
- ' FROM isa_cache AS i INNER JOIN `',
- tableName,
- '` AS t ON (i.parent=t.id);');
- PREPARE initDependStmt FROM @initDepend;
-
- EXECUTE initDependStmt;
- SET found_children = found_children + ROW_COUNT();
-
-
-
- IF versioned IS TRUE THEN
- SET @initDepend = CONCAT(
- 'INSERT IGNORE INTO dependTemp (id, _iversion) ',
- 'SELECT i.child, i.child_iversion FROM archive_isa AS i INNER JOIN `',
- tableName,
- '` AS t ON (i.parent=t.id);');
- PREPARE initDependStmt FROM @initDepend;
-
- EXECUTE initDependStmt;
- SET found_children = found_children + ROW_COUNT();
- END IF;
-
-
-
-
- IF found_children != 0 THEN
- SET @transfer = CONCAT(
- 'INSERT IGNORE INTO `',
- tableName,
- IF(versioned,
- '` (id, _iversion) SELECT id, _iversion FROM dependTemp',
- '` (id) SELECT id FROM dependTemp'));
- PREPARE transferstmt FROM @transfer;
- EXECUTE transferstmt;
- DEALLOCATE PREPARE transferstmt;
- END IF;
-
-
- DEALLOCATE PREPARE initDependStmt;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `getDependentEntities` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `getDependentEntities`(in EntityID INT UNSIGNED)
-BEGIN
-
-DROP TEMPORARY TABLE IF EXISTS refering;
-CREATE TEMPORARY TABLE refering (
-id INT UNSIGNED UNIQUE
-);
-
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM reference_data WHERE (value=EntityID OR property_id=EntityID) AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM reference_data WHERE (value=EntityID OR property_id=EntityID) AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0;
-
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM text_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM text_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0;
-
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM enum_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM enum_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0;
-
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM name_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM name_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0;
-
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM integer_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM integer_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0;
-
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM double_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM double_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0;
-
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM datetime_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM datetime_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0;
-
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM date_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM date_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0;
-
-INSERT IGNORE INTO refering (id) SELECT entity_id FROM null_data WHERE property_id=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id FROM null_data WHERE property_id=EntityID AND domain_id!=EntityID AND entity_id!=EntityID AND domain_id!=0;
-
-INSERT IGNORE INTO refering (id) SELECT entity_id from data_type WHERE datatype=EntityID AND domain_id=0 AND entity_id!=EntityID;
-INSERT IGNORE INTO refering (id) SELECT domain_id from data_type WHERE datatype=EntityID;
-
-
-Select id from refering WHERE id!=0 and id!=EntityID;
-
-DROP TEMPORARY TABLE refering;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `getFile` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb4 */ ;
-/*!50003 SET character_set_results = utf8mb4 */ ;
-/*!50003 SET collation_connection = utf8mb4_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `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 ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `getFileIdByPath` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `getFileIdByPath`(in FilePath VARCHAR(255))
-BEGIN
-
-Select file_id as FileID from files where path=FilePath LIMIT 1;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `getRole` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `getRole`(in RoleName VARCHAR(255))
-BEGIN
-
-Select e.id INTO @RoleID from entities e where e.name=RoleName AND e.role=RoleName LIMIT 1;
-
-call retrieveEntity(@RoleID);
-
-
-
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `getRules` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb4 */ ;
-/*!50003 SET character_set_results = utf8mb4 */ ;
-/*!50003 SET collation_connection = utf8mb4_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `getRules`(in DomainID INT UNSIGNED, in EntityID INT UNSIGNED, in TransType VARCHAR(255))
-BEGIN
-
-
-
-
-SELECT rules.transaction, rules.criterion, rules.modus from rules where if(DomainID is null, rules.domain_id=0,rules.domain_id=DomainID) AND if(EntityID is null, rules.entity_id=0,rules.entity_id=EntityID) AND if(TransType is null,true=true,rules.transaction=TransType);
-
-
-
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `get_version_history` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `get_version_history`(
- in EntityID INT UNSIGNED)
-BEGIN
-
- SELECT c.version AS child,
- NULL as parent,
- t.seconds AS child_seconds,
- t.nanos AS child_nanos,
- t.username AS child_username,
- t.realm AS child_realm
- 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
-
-
-
-
-
-
- UNION SELECT c.version AS child,
- p.version AS parent,
- t.seconds AS child_seconds,
- t.nanos AS child_nanos,
- t.username AS child_username,
- t.realm AS child_realm
- 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)
- WHERE p.entity_id = EntityID;
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `initAutoIncrement` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `initAutoIncrement`()
-BEGIN
-
- SELECT @max := MAX(entity_id)+ 1 FROM transaction_log;
- IF @max IS NOT NULL THEN
- SET @stmtStr = CONCAT('ALTER TABLE entities AUTO_INCREMENT=',@max);
- PREPARE stmt FROM @stmtStr;
- EXECUTE stmt;
- DEALLOCATE PREPARE stmt;
- END IF;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `initBackReference` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `initBackReference`(in pid INT UNSIGNED, in pname VARCHAR(255), in entity_id INT UNSIGNED, in ename VARCHAR(255))
-BEGIN
- DECLARE propertiesTable VARCHAR(255) DEFAULT NULL;
- DECLARE entitiesTable VARCHAR(255) DEFAULT NULL;
-
- IF pname IS NOT NULL THEN
-
- call createTmpTable(propertiesTable, FALSE);
- call initSubEntity(pid, pname, propertiesTable);
- END IF;
-
- IF ename IS NOT NULL THEN
-
- call createTmpTable(entitiesTable, FALSE);
- call initSubEntity(entity_id, ename, entitiesTable);
- END IF;
-
- SELECT propertiesTable, entitiesTable;
-
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `initDisjunctionFilter` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `initDisjunctionFilter`(in versioned BOOLEAN)
-BEGIN
- call initEmptyTargetSet(NULL, versioned);
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `initEmptyTargetSet` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `initEmptyTargetSet`(in targetSet VARCHAR(255), in versioned BOOLEAN)
-BEGIN
- DECLARE newTableName VARCHAR(255) DEFAULT targetSet;
- IF targetSet IS NOT NULL THEN
- SET @isNotEmptyVar = NULL;
- SET @isEmptyStmtStr = CONCAT("SELECT 1 INTO @isNotEmptyVar FROM `",targetSet,"` LIMIT 1");
- PREPARE stmtIsNotEmpty FROM @isEmptyStmtStr;
- EXECUTE stmtIsNotEmpty;
- DEALLOCATE PREPARE stmtIsNotEmpty;
- IF @isNotEmptyVar IS NOT NULL THEN
- call createTmpTable(newTableName, versioned);
- END IF;
- ELSE
- call createTmpTable(newTableName, versioned);
- END IF;
- SELECT newTableName AS newTableName;
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `initEntity` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `initEntity`(in eid INT UNSIGNED, in ename VARCHAR(255),
- in enameLike VARCHAR(255), in enameRegexp VARCHAR(255),
- in resultset VARCHAR(255), in versioned BOOLEAN)
-initEntityLabel: BEGIN
- DECLARE select_columns VARCHAR(255) DEFAULT '` (id) SELECT entity_id FROM name_data ';
- SET @initEntityStmtStr = NULL;
-
-
-
- IF versioned IS TRUE THEN
- SET select_columns = '` (id, _iversion) SELECT entity_id, _get_head_iversion(entity_id) FROM name_data ';
- END IF;
- IF ename IS NOT NULL THEN
- SET @initEntityStmtStr = CONCAT(
- 'INSERT IGNORE INTO `',
- resultset,
- select_columns,
- 'WHERE value=?; ');
- SET @query_param = ename;
- ELSEIF enameLike IS NOT NULL THEN
- SET @initEntityStmtStr = CONCAT(
- 'INSERT IGNORE INTO `',
- resultset,
- select_columns,
- 'WHERE value LIKE ?;');
- SET @query_param = enameLike;
- ELSEIF enameRegexp IS NOT NULL THEN
- SET @initEntityStmtStr = CONCAT(
- 'INSERT IGNORE INTO `',
- resultset,
- select_columns,
- 'WHERE value REGEXP ?;');
- SET @query_param = enameRegexp;
- END IF;
-
-
- IF @initEntityStmtStr IS NOT NULL THEN
- PREPARE initEntityStmt FROM @initEntityStmtStr;
- EXECUTE initEntityStmt USING @query_param;
- DEALLOCATE PREPARE initEntityStmt;
- END IF;
-
- IF eid IS NOT NULL THEN
-
- SET @initEntityStmtStr = CONCAT(
- 'INSERT IGNORE INTO `',
- resultset,
- IF(versioned,
- '` (id, _iversion) SELECT id, _get_head_iversion(id) ',
- '` (id) SELECT id '),
- 'FROM entities WHERE id=',eid,';');
- PREPARE initEntityStmt FROM @initEntityStmtStr;
- EXECUTE initEntityStmt;
- DEALLOCATE PREPARE initEntityStmt;
- END IF;
-
-
-
-
- IF versioned IS TRUE THEN
- SET select_columns = '` (id, _iversion) SELECT entity_id, _iversion FROM archive_name_data ';
- IF ename IS NOT NULL THEN
- SET @initEntityStmtStr = CONCAT(
- 'INSERT IGNORE INTO `',
- resultset,
- select_columns,
- 'WHERE value=?; ');
- SET @query_param = ename;
- ELSEIF enameLike IS NOT NULL THEN
- SET @initEntityStmtStr = CONCAT(
- 'INSERT IGNORE INTO `',
- resultset,
- select_columns,
- 'WHERE value LIKE ?;');
- SET @query_param = enameLike;
- ELSEIF enameRegexp IS NOT NULL THEN
- SET @initEntityStmtStr = CONCAT(
- 'INSERT IGNORE INTO `',
- resultset,
- 'WHERE value REGEXP ?;');
- SET @query_param = enameRegexp;
- END IF;
-
-
- IF @initEntityStmtStr IS NOT NULL THEN
- PREPARE initEntityStmt FROM @initEntityStmtStr;
- EXECUTE initEntityStmt USING @query_param;
- DEALLOCATE PREPARE initEntityStmt;
- END IF;
- END IF;
-
-
-
- IF @initEntityStmtStr IS NOT NULL THEN
- call getChildren(resultset, versioned);
- END IF;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `initPOVPropertiesTable` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `initPOVPropertiesTable`(in pid INT UNSIGNED, in pname VARCHAR(255), in sourceSet VARCHAR(255))
-BEGIN
- DECLARE propertiesTable VARCHAR(255) DEFAULT NULL;
- DECLARE replTbl VARCHAR(255) DEFAULT NULL;
- DECLARE ecount INT DEFAULT 0;
- DECLARE t1 BIGINT DEFAULT 0;
- DECLARE t2 BIGINT DEFAULT 0;
- DECLARE t3 BIGINT DEFAULT 0;
- DECLARE t4 BIGINT DEFAULT 0;
- DECLARE t5 BIGINT DEFAULT 0;
- DECLARE t6 BIGINT DEFAULT 0;
-
-
- IF pname is NOT NULL THEN
- SELECT conv( concat( substring(uid,16,3), substring(uid,10,4), substring(uid,1,8)),16,10) div 10000 - (141427 * 24 * 60 * 60 * 1000) as current_mills INTO t1 from (select uuid() uid) as alias;
- call createTmpTable2(propertiesTable);
-
-
- SET @initPOVPropertiesTableStmt1 = CONCAT('INSERT IGNORE INTO `', propertiesTable, '` (id, id2, domain) SELECT property_id, entity_id, domain_id from name_overrides WHERE name = ? UNION ALL SELECT entity_id, domain_id, 0 FROM name_data WHERE value = ?;');
- PREPARE stmt FROM @initPOVPropertiesTableStmt1;
- SET @pname = pname;
- EXECUTE stmt USING @pname, @pname;
- SET ecount = ROW_COUNT();
-
-
- SELECT conv( concat( substring(uid,16,3), substring(uid,10,4), substring(uid,1,8)),16,10) div 10000 - (141427 * 24 * 60 * 60 * 1000) as current_mills INTO t2 from (select uuid() uid) as alias;
- IF pid IS NOT NULL THEN
- SET @initPOVPropertiesTableStmt2 = CONCAT('INSERT IGNORE INTO `', propertiesTable, '` (id, id2, domain) VALUES (?, 0, 0)');
- PREPARE stmt FROM @initPOVPropertiesTableStmt2;
- SET @pid = pid;
- EXECUTE stmt USING @pid;
- SET ecount = ecount + ROW_COUNT();
- END IF;
-
-
- SELECT conv( concat( substring(uid,16,3), substring(uid,10,4), substring(uid,1,8)),16,10) div 10000 - (141427 * 24 * 60 * 60 * 1000) as current_mills INTO t3 from (select uuid() uid) as alias;
- IF ecount > 0 THEN
-
- call getChildren(propertiesTable, False);
- END IF;
-
-
- SELECT conv( concat( substring(uid,16,3), substring(uid,10,4), substring(uid,1,8)),16,10) div 10000 - (141427 * 24 * 60 * 60 * 1000) as current_mills INTO t4 from (select uuid() uid) as alias;
- IF ecount > 0 THEN
- call createTmpTable2(replTbl);
- SET @replTblStmt1 := CONCAT('INSERT IGNORE INTO `',replTbl, '` (id, id2, domain) SELECT r.value as id, r.entity_id as id2, 0 as domain_id FROM reference_data AS r WHERE status="REPLACEMENT" AND domain_id=0 AND EXISTS (SELECT * FROM `', sourceSet, '` AS s WHERE s.id=r.entity_id) AND EXISTS (SELECT * FROM `', propertiesTable, '` AS p WHERE p.domain = 0 AND p.id2=0 AND p.id=r.property_id);');
- PREPARE replStmt1 FROM @replTblStmt1;
- EXECUTE replStmt1;
- DEALLOCATE PREPARE replStmt1;
- SELECT conv( concat( substring(uid,16,3), substring(uid,10,4), substring(uid,1,8)),16,10) div 10000 - (141427 * 24 * 60 * 60 * 1000) as current_mills INTO t5 from (select uuid() uid) as alias;
-
- SET @replTblStmt2 := CONCAT('INSERT IGNORE INTO `', propertiesTable, '` SELECT id, id2, domain FROM `', replTbl, '`;');
- PREPARE replStmt2 FROM @replTblStmt2;
- EXECUTE replStmt2;
- DEALLOCATE PREPARE replStmt2;
- SELECT conv( concat( substring(uid,16,3), substring(uid,10,4), substring(uid,1,8)),16,10) div 10000 - (141427 * 24 * 60 * 60 * 1000) as current_mills INTO t6 from (select uuid() uid) as alias;
- END IF;
- END IF;
- SELECT propertiesTable, t1, t2, t3, t4, t5, t6, @initPOVPropertiesTableStmt1 as initPOVPropertiesTableStmt1, @initPOVPropertiesTableStmt2 as initPOVPropertiesTableStmt2, @replTblStmt1 as replTblStmt1, @replTblStmt2 as replTblStmt2;
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `initPOVRefidsTable` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `initPOVRefidsTable`(in vInt INT UNSIGNED, in vText VARCHAR(255))
-BEGIN
- DECLARE refIdsTable VARCHAR(255) DEFAULT NULL;
-
-
- IF vText IS NOT NULL THEN
-
- call createTmpTable(refIdsTable, FALSE);
- call initSubEntity(vInt, vText, refIdsTable);
-
- END IF;
- SELECT refIdsTable;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `initQuery` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `initQuery`(in versioned BOOLEAN)
-BEGIN
- CREATE TEMPORARY TABLE IF NOT EXISTS warnings (warning TEXT NOT NULL);
-
- call createTmpTable(@resultSet, versioned);
- SELECT @resultSet as tablename;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `initSubEntity` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `initSubEntity`(in e_id INT UNSIGNED, in ename VARCHAR(255), in tableName VARCHAR(255))
-BEGIN
- DECLARE ecount INT DEFAULT 0;
- DECLARE op VARCHAR(255) DEFAULT '=';
-
- IF LOCATE("%", ename) > 0 THEN
- SET op = "LIKE";
- END IF;
-
- SET @stmtStr = CONCAT('INSERT IGNORE INTO `',
- tableName,
- '` (id) SELECT entity_id FROM name_data WHERE value ',
- op,
- ' ? AND domain_id=0;');
-
- PREPARE stmt FROM @stmtStr;
- SET @ename = ename;
- EXECUTE stmt USING @ename;
- SET ecount = ROW_COUNT();
- DEALLOCATE PREPARE stmt;
-
- IF e_id IS NOT NULL THEN
- SET @stmtStr = CONCAT('INSERT IGNORE INTO `', tableName, '` (id) VALUES (', e_id, ')');
- PREPARE stmt FROM @stmtStr;
- EXECUTE stmt;
- SET ecount = ecount + ROW_COUNT();
- DEALLOCATE PREPARE stmt;
- END IF;
-
- IF ecount > 0 THEN
-
- call getChildren(tableName, False);
- END IF;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `initSubProperty` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `initSubProperty`(in sourceSet VARCHAR(255), in propertiesTable VARCHAR(255), in refIdsTable VARCHAR(255))
-BEGIN
-DECLARE newTableName VARCHAR(255) DEFAULT NULL;
- call registerTempTableName(newTableName);
-
- SET @createSubPropertyListTableStr = CONCAT('CREATE TEMPORARY TABLE `', newTableName,'` ( entity_id INT UNSIGNED NOT NULL, id INT UNSIGNED NOT NULL, domain INT UNSIGNED NOT NULL, CONSTRAINT `',newTableName,'PK` PRIMARY KEY (entity_id, id, domain)) ' );
-
- PREPARE createSubPropertyListTable FROM @createSubPropertyListTableStr;
- EXECUTE createSubPropertyListTable;
- DEALLOCATE PREPARE createSubPropertyListTable;
-
- SET @subResultSetStmtStr = CONCAT('INSERT IGNORE INTO `', newTableName, '` (domain, entity_id, id)
- SELECT data1.domain_id as domain, data1.entity_id as entity_id, data1.value as id
- FROM reference_data as data1 JOIN reference_data as data2
- ON (data1.domain_id=0
- AND data1.domain_id=data2.domain_id
- AND data2.entity_id=data1.entity_id
- AND (
- (data1.property_id=data2.value AND data2.status="REPLACEMENT")
- OR
- (data1.property_id!=data2.value AND data2.status!="REPLACEMENT" AND data1.status!="REPLACEMENT" AND data1.property_id=data2.property_id)
- )
- AND EXISTS (SELECT 1 FROM `', sourceSet, '` as source WHERE source.id=data1.entity_id LIMIT 1)',
- IF(propertiesTable IS NULL, '', CONCAT(' AND EXISTS (SELECT 1 FROM `', propertiesTable, '` as props WHERE props.id=data2.property_id LIMIT 1)')),
- IF(refIdsTable IS NULL, '', CONCAT(' AND EXISTS (SELECT 1 FROM `', refIdsTable, '` as refs WHERE refs.id=data1.value LIMIT 1)')),
- ')'
- );
-
-
- PREPARE subResultSetStmt FROM @subResultSetStmtStr;
- EXECUTE subResultSetStmt;
- DEALLOCATE PREPARE subResultSetStmt;
-
- SELECT newTableName as list;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `insertEntity` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `insertEntity`(in EntityName VARCHAR(255), in EntityDesc TEXT, in EntityRole VARCHAR(255), in ACL VARBINARY(65525))
-BEGIN
- DECLARE NewEntityID INT UNSIGNED DEFAULT NULL;
- DECLARE NewACLID INT UNSIGNED DEFAULT NULL;
- DECLARE Hash VARBINARY(255) DEFAULT NULL;
- DECLARE Version VARBINARY(255) DEFAULT NULL;
- DECLARE Transaction VARBINARY(255) DEFAULT NULL;
-
-
-
- call entityACL(NewACLID, ACL);
-
-
- INSERT INTO entities (description, role, acl)
- VALUES (EntityDesc, EntityRole, NewACLID);
-
-
- SET NewEntityID = LAST_INSERT_ID();
-
- IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
-
- SET Transaction = @SRID;
- SET Version = SHA1(UUID());
- CALL insert_single_child_version(NewEntityID, Hash, Version, Null, Transaction);
- END IF;
-
-
-
- IF EntityName IS NOT NULL THEN
- INSERT INTO name_data
- (domain_id, entity_id, property_id, value, status, pidx)
- VALUES (0, NewEntityID, 20, EntityName, "FIX", 0);
- END IF;
-
- SELECT NewEntityID as EntityID, Version as Version;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `insertEntityProperty` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `insertEntityProperty`(
- in DomainID INT UNSIGNED,
- in EntityID INT UNSIGNED,
- in PropertyID INT UNSIGNED,
- in Datatable VARCHAR(255),
- in PropertyValue TEXT,
- in PropertyUnitSig BIGINT,
- in PropertyStatus VARCHAR(255),
- in NameOverride VARCHAR(255),
- in DescOverride TEXT,
- in DatatypeOverride INT UNSIGNED,
- in Collection VARCHAR(255),
- in PropertyIndex INT UNSIGNED)
-BEGIN
- DECLARE ReferenceValueIVersion INT UNSIGNED DEFAULT NULL;
- DECLARE ReferenceValue INT UNSIGNED DEFAULT NULL;
- DECLARE AT_PRESENT INTEGER DEFAULT NULL;
-
- CASE Datatable
- WHEN 'double_data' THEN
- INSERT INTO double_data
- (domain_id, entity_id, property_id, value, unit_sig, status, pidx)
- VALUES
- (DomainID, EntityID, PropertyID, PropertyValue, PropertyUnitSig, PropertyStatus, PropertyIndex);
- WHEN 'integer_data' THEN
- INSERT INTO integer_data
- (domain_id, entity_id, property_id, value, unit_sig, status, pidx)
- VALUES
- (DomainID, EntityID, PropertyID, PropertyValue, PropertyUnitSig, PropertyStatus, PropertyIndex);
- WHEN 'datetime_data' THEN
- INSERT INTO datetime_data
- (domain_id, entity_id, property_id, value, value_ns, status, pidx)
- VALUES
- (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
-
-
- SET AT_PRESENT=LOCATE("@", PropertyValue);
- IF is_feature_config("ENTITY_VERSIONING", "ENABLED") AND AT_PRESENT > 0 THEN
- SET ReferenceValue = SUBSTRING_INDEX(PropertyValue, '@', 1);
- SET ReferenceValueIVersion = get_iversion(ReferenceValue,
- SUBSTRING_INDEX(PropertyValue, '@', -1));
-
- IF ReferenceValueIVersion IS NULL THEN
- SELECT 0 from `ReferenceValueIVersion_WAS_NULL`;
- END IF;
-
- ELSE
- SET ReferenceValue = PropertyValue;
- END IF;
-
- INSERT INTO reference_data
- (domain_id, entity_id, property_id, value, value_iversion, status,
- pidx)
- VALUES
- (DomainID, EntityID, PropertyID, ReferenceValue,
- ReferenceValueIVersion, PropertyStatus, PropertyIndex);
- WHEN 'enum_data' THEN
- INSERT INTO enum_data
- (domain_id, entity_id, property_id, value, status, pidx)
- VALUES
- (DomainID, EntityID, PropertyID, PropertyValue, PropertyStatus, PropertyIndex);
- WHEN 'date_data' THEN
- INSERT INTO date_data
- (domain_id, entity_id, property_id, value, status, pidx)
- VALUES
- (DomainID, EntityID, PropertyID, SUBSTRING_INDEX(PropertyValue, '.', 1), PropertyStatus, PropertyIndex);
- WHEN 'text_data' THEN
- INSERT INTO text_data
- (domain_id, entity_id, property_id, value, status, pidx)
- VALUES
- (DomainID, EntityID, PropertyID, PropertyValue, PropertyStatus, PropertyIndex);
- WHEN 'null_data' THEN
- INSERT INTO null_data
- (domain_id, entity_id, property_id, status, pidx)
- VALUES
- (DomainID, EntityID, PropertyID, PropertyStatus, PropertyIndex);
- WHEN 'name_data' THEN
- INSERT INTO name_data
- (domain_id, entity_id, property_id, value, status, pidx)
- VALUES
- (DomainID, EntityID, PropertyID, PropertyValue, PropertyStatus, PropertyIndex);
-
- ELSE
- SELECT * FROM table_does_not_exist;
- END CASE;
-
- IF DatatypeOverride IS NOT NULL THEN
- call overrideType(DomainID, EntityID, PropertyID, DatatypeOverride);
- IF Collection IS NOT NULL THEN
- INSERT INTO collection_type (domain_id, entity_id, property_id, collection) VALUES (DomainID, EntityID, PropertyID, Collection);
- END IF;
- END IF;
-
- IF NameOverride IS NOT NULL THEN
- call overrideName(DomainID, EntityID, PropertyID, NameOverride);
- END IF;
-
- IF DescOverride IS NOT NULL THEN
- call overrideDesc(DomainID, EntityID, PropertyID, DescOverride);
- END IF;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `insertIsa` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `insertIsa`(IN c INT UNSIGNED, IN p INT UNSIGNED)
-insert_is_a_proc: BEGIN
-
- INSERT INTO isa_cache (child, parent, rpath) VALUES (c, p, c);
-
- IF p = c THEN
-
- LEAVE insert_is_a_proc;
- END IF;
-
-
-
-
-
- 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 AND i.child != i.parent;
-
-
-
- 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 = c AND c = r.child AND l.child != l.parent);
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `insertLinCon` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `insertLinCon`(in signature_from BIGINT, in signature_to BIGINT, in a DECIMAL(65,30), in b_dividend BIGINT, in b_divisor BIGINT, in c DECIMAL(65,30))
-BEGIN
-
- INSERT IGNORE INTO units_lin_con (signature_from, signature_to, a, b_dividend, b_divisor, c) VALUES (signature_from, signature_to, a, b_dividend, b_divisor, c);
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `insertUser` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `insertUser`(in Name VARCHAR(255), in Password VARCHAR(255))
-BEGIN
-
-
-INSERT INTO entities (name, role, acl) VALUES (Name, 'USER', 0);
-
-SET @LAST_UserID = LAST_INSERT_ID();
-
-INSERT INTO passwords VALUES (@LAST_UserID, Password);
-
-Select @LAST_UserID as UserID;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `insert_single_child_version` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `insert_single_child_version`(
- in EntityID INT UNSIGNED,
- in Hash VARBINARY(255),
- in Version VARBINARY(255),
- in Parent VARBINARY(255),
- in Transaction VARBINARY(255))
-BEGIN
- DECLARE newiversion INT UNSIGNED DEFAULT NULL;
- DECLARE newipparent INT UNSIGNED DEFAULT NULL;
-
-
- IF Parent IS NOT NULL THEN
- SELECT e._iversion INTO newipparent
- FROM entity_version AS e
- WHERE e.entity_id = EntityID
- AND e.version = Parent;
- IF newipparent IS NULL THEN
-
- SELECT concat("This parent does not exists: ", Parent)
- FROM nonexisting;
- END IF;
- END IF;
-
-
-
- SELECT max(e._iversion)+1 INTO newiversion
- FROM entity_version AS e
- WHERE e.entity_id=EntityID;
- IF newiversion IS NULL THEN
- SET newiversion = 1;
- END IF;
-
- INSERT INTO entity_version
- (entity_id, hash, version, _iversion, _ipparent, srid)
- VALUES
- (EntityID, Hash, Version, newiversion, newipparent, Transaction);
-
-
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `intersectTable` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `intersectTable`(in resultSetTable VARCHAR(255), in diff VARCHAR(255))
-BEGIN
- SET @diffStmtStr = CONCAT('DELETE FROM `', resultSetTable, '` WHERE id NOT IN ( SELECT id FROM `', diff,'`)');
- PREPARE diffStmt FROM @diffStmtStr;
- EXECUTE diffStmt;
-
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `isSubtype` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `isSubtype`(in c INT UNSIGNED, in p INT UNSIGNED)
-BEGIN
- DECLARE ret BOOLEAN DEFAULT FALSE;
- SELECT TRUE INTO ret FROM isa_cache AS i WHERE i.child=c AND i.parent=p LIMIT 1;
- SELECT ret as ISA;
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `overrideDesc` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `overrideDesc`(in DomainID INT UNSIGNED, in EntityID INT UNSIGNED, in PropertyID INT UNSIGNED, in Description TEXT)
-BEGIN
- INSERT INTO desc_overrides (domain_id, entity_id, property_id, description) VALUES (DomainID, EntityID, PropertyID, Description);
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `overrideName` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `overrideName`(in DomainID INT UNSIGNED, in EntityID INT UNSIGNED, in PropertyID INT UNSIGNED, in Name VARCHAR(255))
-BEGIN
- INSERT INTO name_overrides (domain_id, entity_id, property_id, name) VALUES (DomainID, EntityID, PropertyID, Name);
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `overrideType` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `overrideType`(in DomainID INT UNSIGNED, in EntityID INT UNSIGNED, in PropertyID INT UNSIGNED, in Datatype INT UNSIGNED)
-BEGIN
- INSERT INTO data_type (domain_id, entity_id, property_id, datatype) VALUES (DomainID, EntityID, PropertyID, Datatype);
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `raiseWarning` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `raiseWarning`(in str VARCHAR(20000))
-BEGIN
- INSERT INTO warnings VALUES (str);
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `registerSubdomain` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `registerSubdomain`(in amount INT UNSIGNED)
-BEGIN
- DECLARE ED INTEGER DEFAULT NULL;
-
- SELECT COUNT(id) INTO ED FROM entities WHERE Role='DOMAIN' AND id!=0;
-
- WHILE ED < amount DO
- INSERT INTO entities (description, role, acl) VALUES
- (NULL, 'DOMAIN', 0);
- SET ED = ED + 1;
- END WHILE;
-
- SELECT id as DomainID FROM entities WHERE Role='DOMAIN' and id!=0;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `registerTempTableName` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `registerTempTableName`(out newTableName VARCHAR(255))
-BEGIN
- SET newTableName = md5(CONCAT(RAND(),CURRENT_TIMESTAMP()));
- SET @tempTableList = IF(@tempTableList IS NULL,
- CONCAT('`',newTableName,'`'),
- CONCAT(@tempTableList, ',`', newTableName, '`')
- );
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `reset_stats` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `reset_stats`()
-BEGIN
- truncate table performance_schema.events_statements_summary_by_digest;
- truncate table performance_schema.events_statements_history_long;
- END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `retrieveDatatype` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `retrieveDatatype`(in DatatypeName VARCHAR(255))
-BEGIN
-
-Select e.id INTO @DatatypeID from entities e where e.name=DatatypeName AND e.role='DATATYPE' LIMIT 1;
-
-call retrieveEntity(@DatatypeID);
-
-
-
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `retrieveEntity` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `retrieveEntity`(
- in EntityID INT UNSIGNED,
- in Version VARBINARY(255))
-retrieveEntityBody: BEGIN
- DECLARE FilePath VARCHAR(255) DEFAULT NULL;
- DECLARE FileSize VARCHAR(255) DEFAULT NULL;
- DECLARE FileHash VARCHAR(255) DEFAULT NULL;
- DECLARE DatatypeID INT UNSIGNED DEFAULT NULL;
- DECLARE CollectionName VARCHAR(255) DEFAULT NULL;
- DECLARE IsHead BOOLEAN DEFAULT TRUE;
- DECLARE IVersion INT UNSIGNED DEFAULT NULL;
-
-
- IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
-
- IF Version IS NULL OR UPPER(Version) = "HEAD" THEN
- SET Version = get_head_version(EntityID);
- ELSEIF UPPER(LEFT(Version, 5)) = "HEAD~" THEN
- SET IsHead = FALSE;
- SET Version = get_head_relative(EntityID, SUBSTR(Version, 6));
- ELSE
- SELECT get_head_version(EntityID) = Version INTO IsHead;
- END IF;
-
- IF IsHead IS FALSE THEN
- SET IVersion=get_iversion(EntityID, Version);
-
- IF IVersion IS NULL THEN
-
- SELECT 0 FROM entities WHERE 0 = 1;
- LEAVE retrieveEntityBody;
- END IF;
-
- SELECT path, size, HEX(hash)
- INTO FilePath, FileSize, FileHash
- FROM archive_files
- WHERE file_id = EntityID
- AND _iversion = IVersion
- LIMIT 1;
-
- SELECT datatype
- INTO DatatypeID
- FROM archive_data_type
- WHERE domain_id = 0
- AND entity_id = 0
- AND property_id = EntityID
- AND _iversion = IVersion
- LIMIT 1;
-
- SELECT collection
- INTO CollectionName
- FROM archive_collection_type
- WHERE domain_id = 0
- AND entity_id = 0
- AND property_id = EntityID
- AND _iversion = IVersion
- LIMIT 1;
-
-
- SELECT
- ( 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,
- ( SELECT value FROM archive_name_data
- WHERE domain_id = 0
- AND entity_ID = EntityID
- AND property_id = 20
- AND _iversion = IVersion
-
- ) 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
- FROM archive_entities AS e
- WHERE e.id = EntityID
- AND e._iversion = IVersion
- LIMIT 1;
-
-
- LEAVE retrieveEntityBody;
-
- END IF;
- END IF;
-
- SELECT path, size, hex(hash)
- 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
- LIMIT 1;
-
- SELECT collection INTO CollectionName
- FROM collection_type
- WHERE domain_id=0
- AND entity_id=0
- AND property_id=EntityID
- LIMIT 1;
-
- SELECT
- ( 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
- FROM entities e WHERE id = EntityID LIMIT 1;
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `retrieveEntityParents` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `retrieveEntityParents`(
- in EntityID INT UNSIGNED,
- in Version VARBINARY(255))
-retrieveEntityParentsBody: BEGIN
-
- DECLARE IVersion INT UNSIGNED DEFAULT NULL;
- DECLARE IsHead BOOLEAN DEFAULT TRUE;
-
- IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
- IF Version IS NOT NULL THEN
- SELECT get_head_version(EntityID) = Version INTO IsHead;
- END IF;
-
- IF IsHead IS FALSE THEN
- SELECT e._iversion INTO IVersion
- FROM entity_version as e
- WHERE e.entity_id = EntityID
- AND e.version = Version;
-
- IF IVersion IS NULL THEN
-
- LEAVE retrieveEntityParentsBody;
- END IF;
-
- SELECT
- i.parent AS ParentID,
- ( 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
- 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.direct IS TRUE
- ;
-
- LEAVE retrieveEntityParentsBody;
- END IF;
- END IF;
-
- SELECT
- i.parent AS ParentID,
- ( 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
- FROM isa_cache AS i JOIN entities AS e
- ON (i.parent = e.id)
- WHERE i.child = EntityID
- AND i.rpath = EntityID;
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `retrieveEntityProperties` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `retrieveEntityProperties`(
- in DomainID INT UNSIGNED,
- in EntityID INT UNSIGNED,
- in Version VARBINARY(255))
-retrieveEntityPropertiesBody: BEGIN
-
- DECLARE IVersion INT UNSIGNED DEFAULT NULL;
- DECLARE IsHead BOOLEAN DEFAULT TRUE;
-
- IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
- IF Version IS NOT NULL THEN
- IF DomainID = 0 THEN
- SELECT get_head_version(EntityID) = Version INTO IsHead;
- ELSE
- SELECT get_head_version(DomainID) = Version INTO IsHead;
- END IF;
-
- END IF;
-
- IF IsHead IS FALSE THEN
- SELECT e._iversion INTO IVersion
- FROM entity_version as e
- WHERE ((e.entity_id = EntityID AND DomainID = 0)
- OR (e.entity_id = DomainID))
- AND e.version = Version;
-
- IF IVersion IS NULL THEN
-
- LEAVE retrieveEntityPropertiesBody;
- END IF;
-
-
- SELECT
- property_id AS PropertyID,
- value AS PropertyValue,
- status AS PropertyStatus,
- pidx AS PropertyIndex
- FROM archive_double_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
- AND _iversion = IVersion
-
- UNION ALL
-
-
- SELECT
- property_id AS PropertyID,
- value AS PropertyValue,
- status AS PropertyStatus,
- pidx AS PropertyIndex
- FROM archive_integer_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
- AND _iversion = IVersion
-
- UNION ALL
-
-
- SELECT
- property_id AS PropertyID,
- CONCAT(value, '.NULL.NULL') AS PropertyValue,
- status AS PropertyStatus,
- pidx AS PropertyIndex
- FROM archive_date_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
- AND _iversion = IVersion
-
- UNION ALL
-
-
- SELECT
- property_id AS PropertyID,
- CONCAT(value, 'UTC', IF(value_ns IS NULL, '', value_ns))
- AS PropertyValue,
- status AS PropertyStatus,
- pidx AS PropertyIndex
- FROM archive_datetime_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
- AND _iversion = IVersion
-
- UNION ALL
-
-
- SELECT
- property_id AS PropertyID,
- value AS PropertyValue,
- status AS PropertyStatus,
- pidx AS PropertyIndex
- FROM archive_text_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
- AND _iversion = IVersion
-
- UNION ALL
-
-
- SELECT
- property_id AS PropertyID,
- value AS PropertyValue,
- status AS PropertyStatus,
- pidx AS PropertyIndex
- FROM archive_enum_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
- AND _iversion = IVersion
-
- UNION ALL
-
-
- SELECT
- property_id AS PropertyID,
- IF(value_iversion IS NULL, value,
-
- CONCAT(value, "@", _get_version(value, value_iversion)))
- AS PropertyValue,
- status AS PropertyStatus,
- pidx AS PropertyIndex
- FROM archive_reference_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
- AND _iversion = IVersion
-
- UNION ALL
-
-
- SELECT
- property_id AS PropertyID,
- NULL AS PropertyValue,
- status AS PropertyStatus,
- pidx AS PropertyIndex
- FROM archive_null_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
- AND _iversion = IVersion
-
- UNION ALL
-
-
- SELECT
- property_id AS PropertyID,
- value AS PropertyValue,
- status AS PropertyStatus,
- pidx AS PropertyIndex
- FROM archive_name_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
- AND property_id != 20
- AND _iversion = IVersion;
-
- LEAVE retrieveEntityPropertiesBody;
- END IF;
- END IF;
-
-
- SELECT
- property_id AS PropertyID,
- value AS PropertyValue,
- status AS PropertyStatus,
- pidx AS PropertyIndex
- FROM double_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
-
- UNION ALL
-
-
- SELECT
- property_id AS PropertyID,
- value AS PropertyValue,
- status AS PropertyStatus,
- pidx AS PropertyIndex
- FROM integer_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
-
- UNION ALL
-
-
- SELECT
- property_id AS PropertyID,
- CONCAT(value, '.NULL.NULL') AS PropertyValue,
- status AS PropertyStatus,
- pidx AS PropertyIndex
- FROM date_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
-
- UNION ALL
-
-
- SELECT
- property_id AS PropertyID,
- CONCAT(value, 'UTC', IF(value_ns IS NULL, '', value_ns))
- AS PropertyValue,
- status AS PropertyStatus,
- pidx AS PropertyIndex
- FROM datetime_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
-
- UNION ALL
-
-
- SELECT
- property_id AS PropertyID,
- value AS PropertyValue,
- status AS PropertyStatus,
- pidx AS PropertyIndex
- FROM text_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
-
- UNION ALL
-
-
- SELECT
- property_id AS PropertyID,
- value AS PropertyValue,
- status AS PropertyStatus,
- pidx AS PropertyIndex
- FROM enum_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
-
- UNION ALL
-
-
- SELECT
- property_id AS PropertyID,
- IF(value_iversion IS NULL, value,
- CONCAT(value, "@", _get_version(value, value_iversion)))
- AS PropertyValue,
- status AS PropertyStatus,
- pidx AS PropertyIndex
- FROM reference_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
-
- UNION ALL
-
-
- SELECT
- property_id AS PropertyID,
- NULL AS PropertyValue,
- status AS PropertyStatus,
- pidx AS PropertyIndex
- FROM null_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
-
- UNION ALL
-
-
- SELECT
- property_id AS PropertyID,
- value AS PropertyValue,
- status AS PropertyStatus,
- pidx AS PropertyIndex
- FROM name_data
- WHERE domain_id = DomainID
- AND entity_id = EntityID
- AND property_id != 20;
-
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `retrieveOverrides` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `retrieveOverrides`(
- in DomainID INT UNSIGNED,
- in EntityID INT UNSIGNED,
- in Version VARBINARY(255))
-retrieveOverridesBody: BEGIN
-
- DECLARE IVersion INT UNSIGNED DEFAULT NULL;
- DECLARE IsHead BOOLEAN DEFAULT TRUE;
-
- IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
- IF Version IS NOT NULL THEN
- IF DomainID = 0 THEN
- SELECT get_head_version(EntityID) = Version INTO IsHead;
- ELSE
- SELECT get_head_version(DomainID) = Version INTO IsHead;
- END IF;
- END IF;
-
- IF IsHead IS FALSE THEN
- SELECT e._iversion INTO IVersion
- FROM entity_version as e
- WHERE ((e.entity_id = EntityID AND DomainID = 0)
- OR (e.entity_id = DomainID))
- AND e.version = Version;
-
- IF IVersion IS NULL THEN
-
- LEAVE retrieveOverridesBody;
- END IF;
-
-
- SELECT
- NULL AS collection_override,
- name AS name_override,
- NULL AS desc_override,
- NULL AS type_override,
- entity_id,
- property_id
- FROM archive_name_overrides
- WHERE domain_id = DomainID
- AND entity_id = EntityID
- AND _iversion = IVersion
-
- UNION ALL
-
-
- SELECT
- NULL AS collection_override,
- NULL AS name_override,
- description AS desc_override,
- NULL AS type_override,
- entity_id,
- property_id
- FROM archive_desc_overrides
- WHERE domain_id = DomainID
- AND entity_id = EntityID
- AND _iversion = IVersion
-
- UNION ALL
-
-
- SELECT
- NULL AS collection_override,
- NULL AS name_override,
- NULL AS desc_override,
- IFNULL((SELECT value FROM name_data
- WHERE domain_id = 0
- AND entity_id = datatype
- AND property_id = 20
- LIMIT 1), datatype) AS type_override,
- entity_id,
- property_id
- FROM archive_data_type
- WHERE domain_id = DomainID
- AND entity_id = EntityID
- AND _iversion = IVersion
-
- UNION ALL
-
-
- SELECT
- collection AS collection_override,
- NULL AS name_override,
- NULL AS desc_override,
- NULL AS type_override,
- entity_id,
- property_id
- FROM archive_collection_type
- WHERE domain_id = DomainID
- AND entity_id = EntityID
- AND _iversion = IVersion;
-
- LEAVE retrieveOverridesBody;
- END IF;
- END IF;
-
- SELECT
- NULL AS collection_override,
- name AS name_override,
- NULL AS desc_override,
- NULL AS type_override,
- entity_id,
- property_id
- FROM name_overrides
- WHERE domain_id = DomainID
- AND entity_id = EntityID
-
- UNION ALL
-
- SELECT
- NULL AS collection_override,
- NULL AS name_override,
- description AS desc_override,
- NULL AS type_override,
- entity_id,
- property_id
- FROM desc_overrides
- WHERE domain_id = DomainID
- AND entity_id = EntityID
-
- UNION ALL
-
- SELECT
- NULL AS collection_override,
- NULL AS name_override,
- NULL AS desc_override,
- IFNULL((SELECT value FROM name_data
- WHERE domain_id = 0
- AND entity_ID = datatype
- AND property_id = 20 LIMIT 1), datatype) AS type_override,
- entity_id,
- property_id
- FROM data_type
- WHERE domain_id = DomainID
- AND entity_id = EntityID
-
- UNION ALL
-
- SELECT
- collection AS collection_override,
- NULL AS name_override,
- NULL AS desc_override,
- NULL AS type_override,
- entity_id,
- property_id
- FROM collection_type
- WHERE domain_id = DomainID
- AND entity_id = EntityID;
-
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `retrieveQueryTemplateDef` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `retrieveQueryTemplateDef`(
- in EntityID INT UNSIGNED,
- in Version VARBINARY(255))
-retrieveQueryTemplateDefBody: BEGIN
-
- DECLARE IVersion INT UNSIGNED DEFAULT NULL;
- DECLARE IsHead BOOLEAN DEFAULT TRUE;
-
- IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
-
- IF Version IS NOT NULL THEN
- SELECT get_head_version(EntityID) = Version INTO IsHead;
- END IF;
-
- IF IsHead IS FALSE THEN
-
- SELECT e._iversion INTO IVersion
- FROM entity_version as e
- WHERE e.entity_id = EntityID
- AND e.version = Version;
-
- IF IVersion IS NULL THEN
-
- LEAVE retrieveQueryTemplateDefBody;
- END IF;
-
- SELECT definition
- FROM archive_query_template_def
- WHERE id = EntityID
- AND _iversion = IVersion;
-
- LEAVE retrieveQueryTemplateDefBody;
- END IF;
- END IF;
-
- SELECT definition
- FROM query_template_def
- WHERE id = EntityID;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `setFileProperties` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `setFileProperties`(
- in EntityID INT UNSIGNED,
- in FilePath TEXT,
- in FileSize BIGINT UNSIGNED,
- in FileHash VARCHAR(255)
-)
-BEGIN
- DECLARE IVersion INT UNSIGNED DEFAULT NULL;
- IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
- SELECT max(e._iversion) INTO IVersion
- FROM entity_version AS e
- WHERE e.entity_id = EntityID;
-
- INSERT INTO archive_files (file_id, path, size, hash,
- _iversion)
- SELECT file_id, path, size, hash, IVersion AS _iversion
- FROM files
- WHERE file_id = EntityID;
- END IF;
-
- DELETE FROM files WHERE file_id = EntityID;
-
- IF FilePath IS NOT NULL THEN
- INSERT INTO files (file_id, path, size, hash)
- VALUES (EntityID, FilePath, FileSize, unhex(FileHash));
- END IF;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `setPassword` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `setPassword`(in EntityID INT UNSIGNED, in NewPassword VARCHAR(255))
-BEGIN
-
-
- DELETE FROM passwords where entity_id=EntityID;
- INSERT INTO passwords (entity_id, password) VALUES (EntityID, NewPassword);
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `set_transaction` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `set_transaction`(
- srid VARBINARY(255),
- username VARCHAR(255),
- realm VARCHAR(255),
- seconds BIGINT UNSIGNED,
- nanos INT(10) UNSIGNED)
-BEGIN
-
- SET @SRID = srid;
- INSERT INTO transactions (srid, username, realm, seconds, nanos)
- VALUES (srid, username, realm, seconds, nanos);
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `showEntityAutoIncr` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `showEntityAutoIncr`()
-BEGIN
-SELECT `AUTO_INCREMENT`
-FROM INFORMATION_SCHEMA.TABLES
-WHERE TABLE_SCHEMA = 'caosdb'
-AND TABLE_NAME = 'entities';
-
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `updateEntity` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `updateEntity`(
- in EntityID INT UNSIGNED,
- in EntityName VARCHAR(255),
- in EntityDescription TEXT,
- in EntityRole VARCHAR(255),
- in Datatype VARCHAR(255),
- in Collection VARCHAR(255),
- in ACL VARBINARY(65525))
-BEGIN
- DECLARE ACLID INT UNSIGNED DEFAULT NULL;
- DECLARE Hash VARBINARY(255) DEFAULT NULL;
- DECLARE Version VARBINARY(255) DEFAULT SHA1(UUID());
- DECLARE ParentVersion VARBINARY(255) DEFAULT NULL;
- DECLARE Transaction VARBINARY(255) DEFAULT NULL;
- DECLARE OldIVersion INT UNSIGNED DEFAULT NULL;
-
- call entityACL(ACLID, ACL);
-
- IF is_feature_config("ENTITY_VERSIONING", "ENABLED") THEN
- SELECT max(_iversion) INTO OldIVersion
- FROM entity_version
- WHERE entity_id = EntityID;
-
-
- INSERT INTO archive_entities (id, description, role,
- acl, _iversion)
- SELECT e.id, e.description, e.role, e.acl, OldIVersion
- FROM entities AS e
- WHERE e.id = EntityID;
-
- INSERT INTO archive_data_type (domain_id, entity_id, property_id,
- datatype, _iversion)
- SELECT e.domain_id, e.entity_id, e.property_id, e.datatype,
- OldIVersion
- FROM data_type AS e
- WHERE e.domain_id = 0
- AND e.entity_id = 0
- AND e.property_id = EntityID;
-
- INSERT INTO archive_collection_type (domain_id, entity_id, property_id,
- collection, _iversion)
- SELECT e.domain_id, e.entity_id, e.property_id, e.collection,
- OldIVersion
- FROM collection_type as e
- WHERE e.domain_id = 0
- AND e.entity_id = 0
- AND e.property_id = EntityID;
-
-
- SET Transaction = @SRID;
- SELECT e.version INTO ParentVersion
- FROM entity_version as e
- WHERE e.entity_id = EntityID
- AND e._iversion = OldIVersion;
- CALL insert_single_child_version(
- EntityID, Hash, Version,
- ParentVersion, Transaction);
- END IF;
-
- UPDATE entities e
- SET e.description = EntityDescription,
- e.role=EntityRole,
- e.acl = ACLID
- WHERE e.id = EntityID;
-
-
-
- DELETE FROM name_data
- WHERE domain_id = 0 AND entity_id = EntityID AND property_id = 20;
- IF EntityName IS NOT NULL THEN
- INSERT INTO name_data
- (domain_id, entity_id, property_id, value, status, pidx)
- VALUES (0, EntityID, 20, EntityName, "FIX", 0);
- END IF;
-
- DELETE FROM data_type
- WHERE domain_id=0 AND entity_id=0 AND property_id=EntityID;
-
- DELETE FROM collection_type
- 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)
- SELECT 0, 0, EntityID,
- ( SELECT entity_id FROM name_data WHERE domain_id = 0
- AND property_id = 20 AND value = Datatype LIMIT 1 );
-
- IF Collection IS NOT NULL THEN
- INSERT INTO collection_type (domain_id, entity_id, property_id,
- collection)
- SELECT 0, 0, EntityID, Collection;
- END IF;
- END IF;
-
- Select Version as Version;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!50003 DROP PROCEDURE IF EXISTS `updateLinCon` */;
-/*!50003 SET @saved_cs_client = @@character_set_client */ ;
-/*!50003 SET @saved_cs_results = @@character_set_results */ ;
-/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8 */ ;
-/*!50003 SET character_set_results = utf8 */ ;
-/*!50003 SET collation_connection = utf8_general_ci */ ;
-/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
-/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
-DELIMITER ;;
-CREATE DEFINER=`caosdb`@`%` PROCEDURE `updateLinCon`(in sig_from BIGINT, in sig_to BIGINT, in new_a DECIMAL(65,30), in new_b_dividend BIGINT, in new_b_divisor BIGINT, in new_c DECIMAL(65,30))
-BEGIN
- UPDATE units_lin_con SET signature_to=sig_to, a=new_a, b_dividend=new_b_dividend, b_divisor=new_b_divisor, c=new_c where signature_from=sig_from;
-
-END ;;
-DELIMITER ;
-/*!50003 SET sql_mode = @saved_sql_mode */ ;
-/*!50003 SET character_set_client = @saved_cs_client */ ;
-/*!50003 SET character_set_results = @saved_cs_results */ ;
-/*!50003 SET collation_connection = @saved_col_connection */ ;
-/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;
-
-/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
-/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */;
-/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */;
-/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
-/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
-/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
-/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
-
--- Dump completed on 2022-01-20 8:27:49
diff --git a/integrationtests/test-profile/custom/other/restore/caosroot.2022-01-20T09271642667269.tar.gz b/integrationtests/test-profile/custom/other/restore/caosroot.2022-01-20T09271642667269.tar.gz
deleted file mode 100644
index 4f6809d8067ecf58fd449567a8339fc3f498e651..0000000000000000000000000000000000000000
Binary files a/integrationtests/test-profile/custom/other/restore/caosroot.2022-01-20T09271642667269.tar.gz and /dev/null differ
diff --git a/integrationtests/test_data/extroot/realworld_example/data/35/03_raw_data/001_dataset1/metadata.json b/integrationtests/test_data/extroot/realworld_example/data/35/03_raw_data/001_dataset1/metadata.json
index 64df90e55eff065b1cc249a634444a72f9fd00d2..9b81cc094bf7d1c35154d8f092a96d5f5fae35c9 100644
--- a/integrationtests/test_data/extroot/realworld_example/data/35/03_raw_data/001_dataset1/metadata.json
+++ b/integrationtests/test_data/extroot/realworld_example/data/35/03_raw_data/001_dataset1/metadata.json
@@ -1,5 +1,5 @@
{
- "title": "Random numbers created on a random autumn day in a random office",
+ "title": "Random numbers created on a random autumn day in a random person's office",
"abstract": "For demonstration purposes we created random numbers on a computer in an office of the CLOUD. This demonstration dataset is used in the DataCloud, a curated cloud storage for scientific data.",
"Event": [
{
diff --git a/integrationtests/test_data/extroot/use_case_simple_presentation/cfood.yml b/integrationtests/test_data/extroot/use_case_simple_presentation/cfood.yml
index 0b17073a823269c9eebbf53df6b9002ac8dbd45f..6495e1828dc56e99459c162f7751951f880ea55c 100644
--- a/integrationtests/test_data/extroot/use_case_simple_presentation/cfood.yml
+++ b/integrationtests/test_data/extroot/use_case_simple_presentation/cfood.yml
@@ -22,7 +22,8 @@ extroot:
records:
mdfile:
- parents: []
+ parents:
+ - mdfile
role: File
path: $DataFile
file: $DataFile
@@ -64,7 +65,8 @@ extroot:
records:
mdfile:
- parents: []
+ parents:
+ - mdfile
role: File
path: $DataFile
file: $DataFile
diff --git a/integrationtests/test_data/extroot/use_case_simple_presentation/model.yml b/integrationtests/test_data/extroot/use_case_simple_presentation/model.yml
index b1dcbd487b56519553a873fdd252c93ce21402a1..bcf041c9586841ef9c61b9aef62574985c2be471 100644
--- a/integrationtests/test_data/extroot/use_case_simple_presentation/model.yml
+++ b/integrationtests/test_data/extroot/use_case_simple_presentation/model.yml
@@ -17,7 +17,6 @@ ScientificActivity:
datatype: TEXT
mdfile:
description: The file storing information about this record.
- datatype: FILE
Experiment:
description: |
diff --git a/integrationtests/test_issues.py b/integrationtests/test_issues.py
new file mode 100644
index 0000000000000000000000000000000000000000..78beb63c55bbce9cb1082345bdb4ccb1f9a3129f
--- /dev/null
+++ b/integrationtests/test_issues.py
@@ -0,0 +1,128 @@
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2022 Indiscale GmbH <info@indiscale.com>
+# 2022 Florian Spreckelsen <f.spreckelsen@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/>.
+#
+from pytest import fixture, mark
+
+import caosdb as db
+
+from caoscrawler.crawl import Crawler
+from caoscrawler.identifiable_adapters import CaosDBIdentifiableAdapter
+from caoscrawler.structure_elements import Dict
+
+
+@fixture
+def clear_database():
+ db.execute_query("FIND ENTITY").delete(raise_exception_on_error=False)
+
+
+def test_issue_23(clear_database):
+ """Test that an update leaves existing properties, that were not found by
+ the crawler, unchanged.
+
+ See issue https://gitlab.com/caosdb/caosdb-crawler/-/issues/23
+
+ """
+
+ # insert a simplistic model an arecord of type TestType with identifying
+ # property and prop_a, but not prop_b.
+ prop_ident = db.Property(name="identifying_prop", datatype=db.TEXT)
+ prop_a = db.Property(name="prop_a", datatype=db.TEXT)
+ prop_b = db.Property(name="prop_b", datatype=db.TEXT)
+ rt = db.RecordType(name="TestType")
+ rec = db.Record(name="TestRec").add_parent(rt)
+ rec.add_property(name="identifying_prop", value="identifier")
+ rec.add_property(name="prop_a", value="something")
+ db.Container().extend([prop_ident, prop_a, prop_b, rt, rec]).insert()
+
+ # set up crawler, first cfood defining a TestType record with
+ # identifying_prop and prop_b, but not prop_a ...
+ crawler_definition = {
+ "DictTest": {
+ "type": "Dict",
+ "match": "(.*)",
+ "records": {
+ "TestType": {}
+ },
+ "subtree": {
+ "identifying_element": {
+ "type": "DictTextElement",
+ "match_name": "ident",
+ "match_value": "(?P<ident_value>.*)",
+ "records": {
+ "TestType": {
+ "identifying_prop": "$ident_value"
+ }
+ }
+ },
+ "other_element": {
+ "type": "DictTextElement",
+ "match_name": "prop_b",
+ "match_value": "(?P<other_value>.*)",
+ "records": {
+ "TestType": {
+ "prop_b": "$other_value"
+ }
+ }
+ }
+ }
+ }
+ }
+
+ # register identifiable for TestType
+ ident = CaosDBIdentifiableAdapter()
+ ident.register_identifiable("TestType", db.RecordType().add_parent(
+ name="TestType").add_property(name="identifying_prop"))
+
+ crawler = Crawler(debug=True, identifiableAdapter=ident)
+ converter_registry = crawler.load_converters(crawler_definition)
+
+ # the dictionary to be crawled...
+ test_dict = {
+ "ident": "identifier",
+ "prop_b": "something_else"
+ }
+
+ records = crawler.start_crawling(
+ Dict("TestDict", test_dict), crawler_definition, converter_registry)
+
+ assert len(records) == 1
+ rec_crawled = records[0]
+ assert rec_crawled.parents[0].name == "TestType"
+ assert rec_crawled.get_property("identifying_prop") is not None
+ assert rec_crawled.get_property("identifying_prop").value == "identifier"
+ assert rec_crawled.get_property("prop_b") is not None
+ assert rec_crawled.get_property("prop_b").value == "something_else"
+ # no interaction with the database yet, so the rrecord shouldn't have a prop_a yet
+ assert rec_crawled.get_property("prop_a") is None
+
+ # synchronize with database and update the record
+ ins, ups = crawler.synchronize()
+ assert len(ins) == 0
+ assert len(ups) == 1
+
+ # retrieve and check that name and properties have been combined correctly
+ rec_retrieved = db.Record(id=rec.id).retrieve()
+ assert rec_retrieved.name == rec.name
+ assert rec_retrieved.get_property(
+ "identifying_prop").value == rec.get_property("identifying_prop").value
+ assert rec_retrieved.get_property(
+ "prop_a").value == rec.get_property("prop_a").value
+ assert rec_retrieved.get_property(
+ "identifying_prop").value == rec_crawled.get_property("identifying_prop").value
+ assert rec_retrieved.get_property(
+ "prop_b").value == rec_crawled.get_property("prop_b").value
diff --git a/integrationtests/test_realworld_example.py b/integrationtests/test_realworld_example.py
index 19a9aca2eaabce59b9570ade9ad7bae6eb43f9b9..7360d9670554a039b879ec337b0ed78763d1d589 100644
--- a/integrationtests/test_realworld_example.py
+++ b/integrationtests/test_realworld_example.py
@@ -83,19 +83,7 @@ def clear_database():
def create_identifiable_adapter():
ident = CaosDBIdentifiableAdapter()
- ident.register_identifiable("license", (
- db.RecordType()
- .add_parent("license")
- .add_property("name")))
- ident.register_identifiable("project_type", (
- db.RecordType()
- .add_parent("project_type")
- .add_property("name")))
- ident.register_identifiable("Person", (
- db.RecordType()
- .add_parent("Person")
- .add_property("full_name")))
-
+ ident.load_from_yaml_definition(os.path.join(DATADIR, "identifiables.yml"))
return ident
@@ -124,7 +112,7 @@ def test_dataset(clear_database, usemodel):
" given_name='Max'", unique=True)
dataset = db.execute_query(f"FIND RECORD Dataset with Dataspace={dataspace.id} AND title="
- "'Random numbers created on a random autumn day in a random office'"
+ "'Random numbers created on a random autumn day in a random person\\'s office'"
"", unique=True)
assert db.execute_query(f"COUNT RECORD with id={dataset.id} AND WHICH REFERENCES Person WITH full_name="
"'Alexa Nozone' AND WHICH REFERENCES Person WITH full_name='Max Schmitt'"
diff --git a/integrationtests/test_use_case_simple_presentation.py b/integrationtests/test_use_case_simple_presentation.py
index bf16ef3be7179372ace7d05d67ffee33890fcc3c..1d611ba4b002aa4c5b31f6f6a2862985c9d4298f 100644
--- a/integrationtests/test_use_case_simple_presentation.py
+++ b/integrationtests/test_use_case_simple_presentation.py
@@ -34,14 +34,15 @@ from caosadvancedtools.loadFiles import loadpath
from caosadvancedtools.models import parser as parser
from caoscrawler.crawl import crawler_main
-
-# TODO(fspreck) Re-eneable once this is part of dev in advancedusertools.
-# from caosadvancedtools.testutils import clear_database, set_test_key
+# TODO: wait for release of this feature in pylib
+# from caosdb.utils.register_tests import clear_database, set_test_key
# set_test_key("10b128cf8a1372f30aa3697466bb55e76974e0c16a599bb44ace88f19c8f61e2")
DATADIR = os.path.join(os.path.dirname(__file__), "test_data",
"extroot", "use_case_simple_presentation")
+# TODO: remove this
+
@pytest.fixture
def clear_database():
diff --git a/release.sh b/release.sh
new file mode 100755
index 0000000000000000000000000000000000000000..1af097f014de6cd9eb3d3e8ba5da34aea0fe1671
--- /dev/null
+++ b/release.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+rm -rf dist/ build/ .eggs/
+python setup.py sdist bdist_wheel
+python -m twine upload -s dist/*
diff --git a/setup.cfg b/setup.cfg
index 9c652aa9ad32757075bd37f0bd5efeadcaa34582..994ba7cacf2fc3cf5ff93a17a23eb5bcec34067f 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
[metadata]
name = caoscrawler
-version = 0.1
+version = 0.1.1
author = Alexander Schlemmer
author_email = alexander.schlemmer@ds.mpg.de
description = A new crawler for caosdb
@@ -10,19 +10,19 @@ long_description_content_type = text/markdown
# project_urls
classifiers =
Programming Language :: Python :: 3
- License :: OSI Approved :: AGPLv3
+ License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)
Operating System :: OS Independent
[options]
package_dir =
= src
packages = find:
-python_requires = >=3.6
+python_requires = >=3.8
install_requires =
importlib-resources
- caosdb
- caosadvancedtools
- yaml-header-tools
+ caosdb > 0.9.0
+ caosadvancedtools >= 0.6.0
+ yaml-header-tools >= 0.2.1
pyyaml
odfpy #make optional
pandas
diff --git a/src/caoscrawler/converters.py b/src/caoscrawler/converters.py
index 48c3c947b0f5480a8d64f3d895c80b455c66bb3a..6f76a1dafc3c41b0cc49bfcf4e3ccc8289115abe 100644
--- a/src/caoscrawler/converters.py
+++ b/src/caoscrawler/converters.py
@@ -35,8 +35,8 @@ from .structure_elements import (StructureElement, Directory, File, Dict, JSONFi
DictIntegerElement, DictBooleanElement,
DictFloatElement, DictDictElement,
TextElement, DictTextElement, DictElement, DictListElement)
-from typing import Optional, Union
-from abc import abstractmethod
+from typing import Dict as Dict_t, List, Optional, Tuple, Union
+from abc import ABCMeta, abstractmethod
from string import Template
import yaml_header_tools
@@ -50,6 +50,23 @@ SPECIAL_PROPERTIES = ("description", "name", "id", "path",
"file", "checksum", "size")
+def _only_max(children_with_keys):
+
+ return [max(children_with_keys, key=lambda x: x[1])[0]]
+
+
+def _only_min(children_with_keys):
+
+ return [min(children_with_keys, key=lambda x: x[1])[0]]
+
+
+# names of functions that can be used to filter children
+FILTER_FUNCTIONS = {
+ "only_max": _only_max,
+ "only_min": _only_min,
+}
+
+
def str_to_bool(x):
if str(x).lower() == "true":
return True
@@ -139,15 +156,21 @@ def handle_value(value: Union[dict, str, list], values: GeneralStore):
propvalue = value
# variables replacement:
- propvalue = [replace_variables(i, values) for i in propvalue]
+ propvalue = list()
+ for element in value:
+ # Do the element-wise replacement only, when its type is string:
+ if type(element) == str:
+ propvalue.append(replace_variables(element, values))
+ else:
+ propvalue.append(element)
return (propvalue, collection_mode)
else:
# value is another simple type
- # collection_mode = "single"
- # propvalue = value["value"]
- # return (propvalue, collection_mode)
- raise RuntimeError()
+ collection_mode = "single"
+ propvalue = value
+ # Return it immediately, otherwise variable substitution would be done and fail:
+ return (propvalue, collection_mode)
propvalue = replace_variables(propvalue, values)
return (propvalue, collection_mode)
@@ -195,15 +218,15 @@ def create_records(values: GeneralStore,
keys_modified.append((name, key))
propvalue, collection_mode = handle_value(value, values)
- if key in SPECIAL_PROPERTIES:
+ if key.lower() in SPECIAL_PROPERTIES:
# e.g. description, name, etc.
# list mode does not work for them
- if key == "path" and not propvalue.startswith(os.path.sep):
+ if key.lower() == "path" and not propvalue.startswith(os.path.sep):
propvalue = os.path.sep + propvalue
# Convert relative to absolute paths:
propvalue = os.path.normpath(propvalue)
- setattr(c_record, key, propvalue)
+ setattr(c_record, key.lower(), propvalue)
else:
if c_record.get_property(key) is None:
@@ -238,7 +261,7 @@ def create_records(values: GeneralStore,
return keys_modified
-class Converter(object):
+class Converter(object, metaclass=ABCMeta):
"""
Converters treat StructureElements contained in the hierarchical sturcture.
"""
@@ -250,7 +273,7 @@ class Converter(object):
self.name = name
# Used to store usage information for debugging:
- self.metadata: dict[str, set[str]] = {
+ self.metadata: Dict_t[str, set[str]] = {
"usage": set()
}
@@ -266,6 +289,10 @@ class Converter(object):
def converter_factory(definition: dict,
name: str,
converter_registry: dict):
+ """creates a Converter instance of the appropriate class.
+
+ The `type` key in the `definition` defines the Converter class which is being used.
+ """
if "type" not in definition:
raise RuntimeError(
@@ -315,12 +342,48 @@ class Converter(object):
records,
self.definition["records"])
+ def filter_children(self, children_with_strings:
+ List[Tuple[StructureElement, str]], expr: str,
+ group: str, rule: str):
+ """Filter children according to regexp `expr` and `rule`."""
+
+ if rule not in FILTER_FUNCTIONS:
+ raise RuntimeError(
+ f"{rule} is not a known filter rule. Only {list(FILTER_FUNCTIONS.keys())} are implemented."
+ )
+
+ to_be_filtered = []
+ unmatched_children = []
+
+ for (child, name) in children_with_strings:
+
+ m = re.match(expr, name)
+ if m is None:
+ unmatched_children.append(child)
+ else:
+ to_be_filtered.append((child, m.groupdict()[group]))
+
+ filtered_children = FILTER_FUNCTIONS[rule](to_be_filtered)
+
+ return filtered_children+unmatched_children
+
@abstractmethod
def typecheck(self, element: StructureElement):
+ """
+ Check whether the current structure element can be converted using
+ this converter.
+ """
pass
@abstractmethod
def match(self, element: StructureElement) -> Optional[dict]:
+ """
+ This method is used to implement detailed checks for matching compatibility
+ of the current structure element with this converter.
+
+ The return value is a dictionary providing possible matched variables from the
+ structure elements information.
+ """
pass
@@ -339,7 +402,15 @@ class DirectoryConverter(Converter):
raise RuntimeError(
"Directory converters can only create children from directories.")
- return self.create_children_from_directory(element)
+ children = self.create_children_from_directory(element)
+
+ if "filter" in self.definition:
+
+ tuple_list = [(c, c.name) for c in children]
+
+ return self.filter_children(tuple_list, **self.definition["filter"])
+
+ return children
def typecheck(self, element: StructureElement):
return isinstance(element, Directory)
@@ -360,7 +431,7 @@ class DirectoryConverter(Converter):
element: A directory (of type Directory) which will be traversed.
"""
- children: list[StructureElement] = []
+ children: List[StructureElement] = []
for name in sorted(os.listdir(element.path)):
path = os.path.join(element.path, name)
@@ -409,7 +480,7 @@ class MarkdownFileConverter(Converter):
header = yaml_header_tools.get_header_from_file(
element.path, clean=False)
- children: list[StructureElement] = []
+ children: List[StructureElement] = []
for name, entry in header.items():
if type(entry) == list:
@@ -463,6 +534,8 @@ class DictConverter(Converter):
children.append(DictBooleanElement(name, value))
elif type(value) == float:
children.append(DictFloatElement(name, value))
+ elif type(value) == type(None):
+ continue
else:
children.append(DictElement(name, value))
warnings.warn(f"The value in the dict for key:{name} has an unknown type. "
@@ -483,6 +556,7 @@ class DictConverter(Converter):
return {}
+# TODO: difference to SimpleFileConverter? Do we need both?
class FileConverter(Converter):
def typecheck(self, element: StructureElement):
return isinstance(element, File)
@@ -514,6 +588,8 @@ class JSONFileConverter(DictConverter):
def create_children(self, generalStore: GeneralStore, element: StructureElement):
if not self.typecheck(element):
raise RuntimeError("A JSON file is needed to create children")
+ # TODO: either add explicit type check for File structure element here,
+ # or add a comment to suppress mypy type warning.
with open(element.path, 'r') as json_file:
json_data = json.load(json_file)
if not isinstance(json_data, dict):
@@ -562,7 +638,7 @@ class _AbstractDictElementConverter(Converter):
m1 = re.match(self.definition["match_name"], element.name)
if m1 is None:
return None
- m2 = re.match(self.definition["match_value"], str(element.value))
+ m2 = re.match(self.definition["match_value"], str(element.value), re.DOTALL)
if m2 is None:
return None
values = dict()
@@ -689,7 +765,8 @@ class TableConverter(Converter):
# The option can often either be a single value or a list of values.
# In the latter case each element of the list will be converted to the defined type.
if isinstance(el, list):
- option_dict[opt_name] = [opt_conversion(el_el) for el_el in el]
+ option_dict[opt_name] = [
+ opt_conversion(el_el) for el_el in el]
else:
option_dict[opt_name] = opt_conversion(el)
return option_dict
diff --git a/src/caoscrawler/crawl.py b/src/caoscrawler/crawl.py
index 1e09d3d8cb0f9d04e7ecd4931eb8a7ea66f2ea96..ad77e678a31a9bd950c89019f38ce58a20d9c2e3 100644
--- a/src/caoscrawler/crawl.py
+++ b/src/caoscrawler/crawl.py
@@ -50,17 +50,22 @@ from .identifiable_adapters import (IdentifiableAdapter,
LocalStorageIdentifiableAdapter,
CaosDBIdentifiableAdapter)
from collections import defaultdict
-from typing import Union, Any, Optional, Type
+from typing import Any, Dict, List, Optional, Type, Union
from caosdb.apiutils import compare_entities, merge_entities
from copy import deepcopy
from jsonschema import validate
-logger = logging.getLogger(__name__)
+from .macros import defmacro_constructor, macro_constructor
+logger = logging.getLogger(__name__)
SPECIAL_PROPERTIES_STRICT = ("description", "name", "id", "path")
SPECIAL_PROPERTIES_NOT_STRICT = ("file", "checksum", "size")
+# Register the macro functions from the submodule:
+yaml.SafeLoader.add_constructor("!defmacro", defmacro_constructor)
+yaml.SafeLoader.add_constructor("!macro", macro_constructor)
+
def check_identical(record1: db.Entity, record2: db.Entity, ignore_id=False):
"""
@@ -108,7 +113,7 @@ def check_identical(record1: db.Entity, record2: db.Entity, ignore_id=False):
return False
for attribute in ("datatype", "importance", "unit"):
# only make an update for those attributes if there is a value difference and
- # the value in the target_data is not None
+ # the value in the crawled_data is not None
if attribute in comp[0]["properties"][key]:
attr_val = comp[0]["properties"][key][attribute]
other_attr_val = (comp[1]["properties"][key][attribute]
@@ -160,7 +165,6 @@ class Crawler(object):
"""
def __init__(self,
- converters: list[Converter] = [],
generalStore: Optional[GeneralStore] = None,
debug: bool = False,
identifiableAdapter: IdentifiableAdapter = None,
@@ -171,15 +175,14 @@ class Crawler(object):
Parameters
----------
- converters : list[Converter]
- The set of converters used for this crawler.
recordStore : GeneralStore
An initial GeneralStore which might store e.g. environment variables.
debug : bool
Create a debugging information tree when set to True.
The debugging information tree is a variable stored in
self.debug_tree. It is a dictionary mapping directory entries
- to a tuple of general stores and record stores which are valid for the directory scope.
+ to a tuple of general stores and record stores which are valid for
+ the directory scope.
Furthermore, it is stored in a second tree named self.debug_copied whether the
objects in debug_tree had been copied from a higher level in the hierarchy
of the structureelements.
@@ -190,10 +193,11 @@ class Crawler(object):
Please use SecurityMode Enum
"""
- # TODO: check if this feature is really needed
- self.global_converters = converters
-
- self.identified_cache = IdentifiedCache()
+ # The following caches store records, where we checked whether they exist on the remote
+ # server. Since, it is important to know whether they exist or not, we store them into two
+ # different caches.
+ self.remote_existing_cache = IdentifiedCache()
+ self.remote_missing_cache = IdentifiedCache()
self.recordStore = RecordStore()
self.securityMode = securityMode
@@ -211,8 +215,8 @@ class Crawler(object):
# order in the tuple:
# 0: generalStore
# 1: recordStore
- self.debug_tree: dict[str, tuple] = dict()
- self.debug_metadata: dict[str, dict] = dict()
+ self.debug_tree: Dict[str, tuple] = dict()
+ self.debug_metadata: Dict[str, dict] = dict()
self.debug_metadata["copied"] = dict()
self.debug_metadata["provenance"] = defaultdict(lambda: dict())
self.debug_metadata["usage"] = defaultdict(lambda: set())
@@ -225,7 +229,29 @@ class Crawler(object):
# Load the cfood from a yaml file:
with open(crawler_definition_path, "r") as f:
- crawler_definition = yaml.safe_load(f)
+ crawler_definitions = list(yaml.safe_load_all(f))
+
+ crawler_definition = self._load_definition_from_yaml_dict(
+ crawler_definitions)
+
+ return self._resolve_validator_paths(crawler_definition, crawler_definition_path)
+
+ def _load_definition_from_yaml_dict(self, crawler_definitions: List[Dict]):
+ """Load crawler definitions from a list of (yaml) dicts `crawler_definitions` which
+ contains either one or two documents.
+
+ Doesn't resolve the validator paths in the cfood definition, so for
+ internal and testing use only.
+
+ """
+ if len(crawler_definitions) == 1:
+ # Simple case, just one document:
+ crawler_definition = crawler_definitions[0]
+ elif len(crawler_definitions) == 2:
+ crawler_definition = crawler_definitions[1]
+ else:
+ raise RuntimeError(
+ "Crawler definition must not contain more than two documents.")
# TODO: at this point this function can already load the cfood schema extensions
# from the crawler definition and add them to the yaml schema that will be
@@ -240,11 +266,16 @@ class Crawler(object):
for key in crawler_definition["Converters"]:
schema["cfood"]["$defs"]["converter"]["properties"]["type"]["enum"].append(
key)
+ if len(crawler_definitions) == 2:
+ if "Converters" in crawler_definitions[0]["metadata"]:
+ for key in crawler_definitions[0]["metadata"]["Converters"]:
+ schema["cfood"]["$defs"]["converter"]["properties"]["type"]["enum"].append(
+ key)
# Validate the cfood schema:
validate(instance=crawler_definition, schema=schema["cfood"])
- return self._resolve_validator_paths(crawler_definition, crawler_definition_path)
+ return crawler_definition
def _resolve_validator_paths(self, definition: dict, definition_path: str):
"""Resolve path to validation files with respect to the file in which
@@ -284,7 +315,7 @@ class Crawler(object):
"""
# Defaults for the converter registry:
- converter_registry: dict[str, dict[str, str]] = {
+ converter_registry: Dict[str, Dict[str, str]] = {
"Directory": {
"converter": "DirectoryConverter",
"package": "caoscrawler.converters"},
@@ -376,9 +407,13 @@ class Crawler(object):
converter_registry)
@staticmethod
- def create_local_converters(crawler_definition: dict,
- converter_registry: dict):
- local_converters = []
+ def initialize_converters(crawler_definition: dict, converter_registry: dict):
+ """
+ takes the cfood as dict (`crawler_definition`) and creates the converter objects that
+ are defined on the highest level. Child Converters will in turn be created during the
+ initialization of the Converters.
+ """
+ converters = []
for key, value in crawler_definition.items():
# Definitions and Converters are reserved keywords
@@ -390,12 +425,12 @@ class Crawler(object):
continue
elif key == "Converters":
continue
- local_converters.append(Converter.converter_factory(
+ converters.append(Converter.converter_factory(
value, key, converter_registry))
- return local_converters
+ return converters
- def start_crawling(self, items: Union[list[StructureElement], StructureElement],
+ def start_crawling(self, items: Union[List[StructureElement], StructureElement],
crawler_definition: dict,
converter_registry: dict):
"""
@@ -412,7 +447,7 @@ class Crawler(object):
Returns
-------
- target_data : list
+ crawled_data : list
the final list with the target state of Records.
"""
@@ -425,20 +460,19 @@ class Crawler(object):
items = [items]
self.run_id = uuid.uuid1()
- local_converters = Crawler.create_local_converters(crawler_definition,
- converter_registry)
+ local_converters = Crawler.initialize_converters(
+ crawler_definition, converter_registry)
# This recursive crawling procedure generates the update list:
- self.target_data: list[db.Record] = []
- self._crawl(items,
- self.global_converters, local_converters, self.generalStore, self.recordStore,
- [], [])
+ self.crawled_data: List[db.Record] = []
+ self._crawl(items, local_converters, self.generalStore,
+ self.recordStore, [], [])
if self.debug:
- self.debug_converters = self.global_converters + local_converters
+ self.debug_converters = local_converters
- return self.target_data
+ return self.crawled_data
- def synchronize(self, commit_changes: bool = True):
+ def synchronize(self, commit_changes: bool = True, unique_names=True):
"""
Carry out the actual synchronization.
"""
@@ -446,34 +480,28 @@ class Crawler(object):
# After the crawling, the actual synchronization with the database, based on the
# update list is carried out:
- return self._synchronize(self.target_data, commit_changes)
+ return self._synchronize(self.crawled_data, commit_changes, unique_names=unique_names)
- def can_be_checked_externally(self, record: db.Record):
+ def has_reference_value_without_id(self, record: db.Record):
"""
- Returns False if there is at least one property in record which:
+ Returns True if there is at least one property in `record` which:
a) is a reference property AND
b) where the value is set to a db.Entity (instead of an ID) AND
- c) where the ID of the value is not set (to an integer)
+ c) where the ID of the value (the db.Entity object in b)) is not set (to an integer)
- Returns True otherwise.
+ Returns False otherwise.
"""
for p in record.properties:
if isinstance(p.value, list):
for el in p.value:
if isinstance(el, db.Entity) and el.id is None:
- return False
- # TODO: please check!
- # I removed the condition "is_reference", because the datatype field
- # that is checked within this function is not always present for references
- # parsed from the file structure. We have to rely on the condition, that
- # if a property value is of type entity, it can be assumed to be a reference.
- # elif (is_reference(p) and isinstance(p.value, db.Entity)
- # and p.value.id is None):
+ return True
elif isinstance(p.value, db.Entity) and p.value.id is None:
- return False
- return True
+ return True
+ return False
- def create_flat_list(self, ent_list: list[db.Entity], flat: list[db.Entity]):
+ @staticmethod
+ def create_flat_list(ent_list: List[db.Entity], flat: List[db.Entity]):
"""
Recursively adds all properties contained in entities from ent_list to
the output list flat. Each element will only be added once to the list.
@@ -489,32 +517,32 @@ class Crawler(object):
if isinstance(el, db.Entity):
if el not in flat:
flat.append(el)
- # TODO: move inside if block?
- self.create_flat_list([el], flat)
+ Crawler.create_flat_list([el], flat)
elif isinstance(p.value, db.Entity):
if p.value not in flat:
flat.append(p.value)
- # TODO: move inside if block?
- self.create_flat_list([p.value], flat)
+ Crawler.create_flat_list([p.value], flat)
- def all_references_are_existing_already(self, record: db.Record):
+ def has_missing_object_in_references(self, record: db.Record):
"""
- returns true if all references either have IDs or were checked remotely and not found (i.e.
- they exist in the local cache)
+ returns False if any property value is a db.Entity object that
+ is contained in the `remote_missing_cache`. If the record has such an object in the
+ reference properties, it means that it references another Entity, where we checked
+ whether it exists remotely and it was not found.
"""
for p in record.properties:
# if (is_reference(p)
# Entity instead of ID and not cached locally
if (isinstance(p.value, list)):
for el in p.value:
- if (isinstance(el, db.Entity) and el.id is None
- and self.get_identified_record_from_local_cache(el) is None):
- return False
- if (isinstance(p.value, db.Entity) and p.value.id is None
- and self.get_identified_record_from_local_cache(p.value) is None):
+ if (isinstance(el, db.Entity)
+ and self.get_from_remote_missing_cache(el) is not None):
+ return True
+ if (isinstance(p.value, db.Entity)
+ and self.get_from_remote_missing_cache(p.value) is not None):
# might be checked when reference is resolved
- return False
- return True
+ return True
+ return False
def replace_references_with_cached(self, record: db.Record):
"""
@@ -527,7 +555,7 @@ class Crawler(object):
lst = []
for el in p.value:
if (isinstance(el, db.Entity) and el.id is None):
- cached = self.get_identified_record_from_local_cache(
+ cached = self.get_from_any_cache(
el)
if cached is None:
raise RuntimeError("Not in cache.")
@@ -542,7 +570,7 @@ class Crawler(object):
lst.append(el)
p.value = lst
if (isinstance(p.value, db.Entity) and p.value.id is None):
- cached = self.get_identified_record_from_local_cache(p.value)
+ cached = self.get_from_any_cache(p.value)
if cached is None:
raise RuntimeError("Not in cache.")
if not check_identical(cached, p.value, True):
@@ -553,7 +581,7 @@ class Crawler(object):
raise RuntimeError("Not identical.")
p.value = cached
- def get_identified_record_from_local_cache(self, record: db.Record):
+ def get_from_remote_missing_cache(self, record: db.Record):
"""
returns the identifiable if an identifiable with the same values already exists locally
(Each identifiable that is not found on the remote server, is 'cached' locally to prevent
@@ -567,12 +595,57 @@ class Crawler(object):
identifiable = record
# return None
- if identifiable in self.identified_cache:
- return self.identified_cache[identifiable]
+ if identifiable in self.remote_missing_cache:
+ return self.remote_missing_cache[identifiable]
else:
return None
- def add_identified_record_to_local_cache(self, record: db.Record):
+ def get_from_any_cache(self, record: db.Record):
+ """
+ returns the identifiable if an identifiable with the same values already exists locally
+ (Each identifiable that is not found on the remote server, is 'cached' locally to prevent
+ that the same identifiable exists twice)
+ """
+ if self.identifiableAdapter is None:
+ raise RuntimeError("Should not happen.")
+ identifiable = self.identifiableAdapter.get_identifiable(record)
+ if identifiable is None:
+ # TODO: check whether the same idea as below works here
+ identifiable = record
+ # return None
+
+ if identifiable in self.remote_existing_cache:
+ return self.remote_existing_cache[identifiable]
+ elif identifiable in self.remote_missing_cache:
+ return self.remote_missing_cache[identifiable]
+ else:
+ return None
+
+ def add_to_remote_missing_cache(self, record: db.Record):
+ """
+ adds the given identifiable to the local cache
+
+ No identifiable with the same values must exist locally.
+ (Each identifiable that is not found on the remote server, is 'cached' locally to prevent
+ that the same identifiable exists twice)
+
+ Return False if there is no identifiable for this record and True otherwise.
+ """
+ self.add_to_cache(record=record, cache=self.remote_missing_cache)
+
+ def add_to_remote_existing_cache(self, record: db.Record):
+ """
+ adds the given identifiable to the local cache
+
+ No identifiable with the same values must exist locally.
+ (Each identifiable that is not found on the remote server, is 'cached' locally to prevent
+ that the same identifiable exists twice)
+
+ Return False if there is no identifiable for this record and True otherwise.
+ """
+ self.add_to_cache(record=record, cache=self.remote_existing_cache)
+
+ def add_to_cache(self, record: db.Record, cache):
"""
adds the given identifiable to the local cache
@@ -597,23 +670,32 @@ class Crawler(object):
# if there is no identifiable, for the cache that is the same
# as if the complete entity is the identifiable:
identifiable = record
- self.identified_cache.add(identifiable=identifiable, record=record)
+ cache.add(identifiable=identifiable, record=record)
- def copy_attributes(self, fro: db.Entity, to: db.Entity):
- """
- Copy all attributes from one entity to another entity.
+ @staticmethod
+ def bend_references_to_new_object(old, new, entities):
+ """ Bend references to the other object
+ Iterate over all entities in `entities` and check the values of all properties of
+ occurances of old Entity and replace them with new Entity
"""
-
- merge_entities(to, fro)
-
- def split_into_inserts_and_updates(self, ent_list: list[db.Entity]):
+ for el in entities:
+ for p in el.properties:
+ if isinstance(p.value, list):
+ for index, val in enumerate(p.value):
+ if val is old:
+ p.value[index] = new
+ else:
+ if p.value is old:
+ p.value = new
+
+ def split_into_inserts_and_updates(self, ent_list: List[db.Entity]):
if self.identifiableAdapter is None:
raise RuntimeError("Should not happen.")
- to_be_inserted: list[db.Entity] = []
- to_be_updated: list[db.Entity] = []
+ to_be_inserted: List[db.Entity] = []
+ to_be_updated: List[db.Entity] = []
flat = list(ent_list)
# assure all entities are direct members TODO Can this be removed at some point?Check only?
- self.create_flat_list(ent_list, flat)
+ Crawler.create_flat_list(ent_list, flat)
# TODO: can the following be removed at some point
for ent in flat:
@@ -632,94 +714,54 @@ class Crawler(object):
if (record.id is not None or record in to_be_inserted):
raise RuntimeError("This should not be reached since treated elements"
"are removed from the list")
- # Check the local cache first for duplicate
- elif self.get_identified_record_from_local_cache(record) is not None:
-
- # This record is a duplicate that can be removed. Make sure we do not lose
- # information
- # Update an (local) identified record that will be inserted
- newrecord = self.get_identified_record_from_local_cache(
- record)
- self.copy_attributes(fro=record, to=newrecord)
- # Bend references to the other object
- # TODO refactor this
- for el in flat + to_be_inserted + to_be_updated:
- for p in el.properties:
- if isinstance(p.value, list):
- for index, val in enumerate(p.value):
- if val is record:
- p.value[index] = newrecord
- else:
- if p.value is record:
- p.value = newrecord
+ # Check whether this record is a duplicate that can be removed
+ elif self.get_from_any_cache(record) is not None:
+ # We merge the two in order to prevent loss of information
+ newrecord = self.get_from_any_cache(record)
+ merge_entities(newrecord, record)
+ Crawler.bend_references_to_new_object(
+ old=record, new=newrecord, entities=flat+to_be_updated+to_be_inserted)
del flat[i]
+ resolved_references = True
- # all references need to be IDs that exist on the remote server
- elif self.can_be_checked_externally(record):
-
- # Check remotely
+ # can we check whether the record(identifiable) exists on the remote server?
+ elif not self.has_reference_value_without_id(
+ self.identifiableAdapter.get_identifiable(record)):
# TODO: remove deepcopy?
- identified_record = self.identifiableAdapter.retrieve_identified_record_for_record(
- deepcopy(record))
+ identified_record = (
+ self.identifiableAdapter.retrieve_identified_record_for_record(
+ deepcopy(record)))
if identified_record is None:
- # identifiable does not exist remotely
+ # identifiable does not exist remotely -> record needs to be inserted
to_be_inserted.append(record)
- self.add_identified_record_to_local_cache(record)
+ self.add_to_remote_missing_cache(record)
del flat[i]
else:
# side effect
record.id = identified_record.id
- # On update every property needs to have an ID.
- # This will be achieved by the function execute_updates_in_list below.
- # For files this is not enough, we also need to copy over
- # checksum and size:
+ # Copy over checksum and size too if it is a file
if isinstance(record, db.File):
record._size = identified_record._size
record._checksum = identified_record._checksum
to_be_updated.append(record)
- # TODO think this through
- self.add_identified_record_to_local_cache(record)
+ self.add_to_remote_existing_cache(record)
del flat[i]
resolved_references = True
- # e.g. references an identifiable that does not exist remotely
- elif self.all_references_are_existing_already(record):
-
- # TODO: (for review)
- # This was the old version, but also for this case the
- # check for identifiables has to be done.
- # to_be_inserted.append(record)
- # self.add_identified_record_to_local_cache(record)
- # del flat[i]
-
- # TODO: (for review)
- # If the following replacement is not done, the cache will
- # be invalid as soon as references are resolved.
- # replace references by versions from cache:
- self.replace_references_with_cached(record)
-
- identified_record = self.identifiableAdapter.retrieve_identified_record_for_record(
- deepcopy(record))
- if identified_record is None:
- # identifiable does not exist remotely
- to_be_inserted.append(record)
- self.add_identified_record_to_local_cache(record)
- del flat[i]
- else:
- # side effect
- record.id = identified_record.id
- # On update every property needs to have an ID.
- # This will be achieved by the function execute_updates_in_list below.
-
- to_be_updated.append(record)
- # TODO think this through
- self.add_identified_record_to_local_cache(record)
- del flat[i]
-
+ # is it impossible to check this record because an identifiable references a
+ # missing record?
+ elif self.has_missing_object_in_references(
+ self.identifiableAdapter.get_identifiable(record)):
+ to_be_inserted.append(record)
+ self.add_to_remote_missing_cache(record)
+ del flat[i]
resolved_references = True
+ for record in flat:
+ self.replace_references_with_cached(record)
+
if len(flat) > 0:
raise RuntimeError(
"Could not resolve all Entity references. Circular Dependency?")
@@ -738,35 +780,124 @@ class Crawler(object):
el.value[index] = val.id
@staticmethod
- def remove_unnecessary_updates(target_data: list[db.Record],
- identified_records: list[db.Record]):
+ def _merge_properties_from_remote(
+ crawled_data: List[db.Record],
+ identified_records: List[db.Record]
+ ):
+ """Merge entity representation that was created by crawling the data with remotely found
+ identified records s.th. new properties and property values are updated correctly but
+ additional properties are not overwritten.
+
+ Parameters
+ ----------
+ crawled_data : list[db.Record]
+ List of the Entities created by the crawler
+ identified_records : list[db.Record]
+ List of identified remote Records
+
+ Returns
+ -------
+ to_be_updated : list[db.Record]
+ List of merged records
"""
- checks whether all relevant attributes (especially Property values) are equal
+ to_be_updated = []
+ for target, identified in zip(crawled_data, identified_records):
+ # Special treatment for name and description in case they have been
+ # set in the server independently from the crawler
+ for attr in ["name", "description"]:
+ if getattr(target, attr) is None:
+ # The crawler didn't find any name or description, i.e., not
+ # an empty one. In this case (and only in this), keep any
+ # existing name or description.
+ setattr(target, attr, getattr(identified, attr))
+
+ # Create a temporary copy since the merge will be conducted in place
+ tmp = deepcopy(identified)
+ # A force merge will overwrite any properties that both the
+ # identified and the crawled record have with the values of the
+ # crawled record while keeping existing properties intact.
+ merge_entities(tmp, target, force=True)
+ to_be_updated.append(tmp)
+
+ return to_be_updated
+
+ @staticmethod
+ def remove_unnecessary_updates(
+ crawled_data: List[db.Record],
+ identified_records: List[db.Record]
+ ):
+ """Compare the Records to be updated with their remote
+ correspondant. Only update if there are actual differences.
- Returns (in future)
+ Returns
-------
update list without unecessary updates
"""
- if len(target_data) != len(identified_records):
+ if len(crawled_data) != len(identified_records):
raise RuntimeError("The lists of updates and of identified records need to be of the "
"same length!")
- # TODO this can now easily be changed to a function without side effect
- for i in reversed(range(len(target_data))):
- identical = check_identical(target_data[i], identified_records[i])
+ actual_updates = []
+ for i in reversed(range(len(crawled_data))):
- if identical:
- del target_data[i]
- continue
- else:
- pass
+ if not check_identical(crawled_data[i], identified_records[i]):
+ actual_updates.append(crawled_data[i])
+
+ return actual_updates
+
+ @staticmethod
+ def execute_parent_updates_in_list(to_be_updated, securityMode, run_id, unique_names):
+ """
+ Execute the updates of changed parents.
+
+ This method is used before the standard inserts and needed
+ because some changes in parents (e.g. of Files) might fail
+ if they are not updated first.
+ """
+ Crawler.set_ids_and_datatype_of_parents_and_properties(to_be_updated)
+ parent_updates = db.Container()
+
+ for record in to_be_updated:
+ old_entity = Crawler._get_entity_by_id(record.id)
+
+ # Check whether the parents have been changed and add them if missing
+ # in the old entity:
+ changes_made = False
+ for parent in record.parents:
+ found = False
+ for old_parent in old_entity.parents:
+ if old_parent.id == parent.id:
+ found = True
+ break
+ if not found:
+ old_entity.add_parent(id=parent.id)
+ changes_made = True
+ if changes_made:
+ parent_updates.append(old_entity)
+ logger.debug("RecordTypes need to be added to the following entities:")
+ logger.debug(parent_updates)
+ if len(parent_updates) > 0:
+ if securityMode.value > SecurityMode.INSERT.value:
+ parent_updates.update(unique=False)
+ elif run_id is not None:
+ update_cache = UpdateCache()
+ update_cache.insert(parent_updates, run_id)
+ logger.info("Some entities need to be updated because they are missing a parent "
+ "RecordType. The update was NOT executed due to the chosen security "
+ "mode. This might lead to a failure of inserts that follow.")
+ logger.info(parent_updates)
@staticmethod
def _get_entity_by_name(name):
return db.Entity(name=name).retrieve()
@staticmethod
- def execute_inserts_in_list(to_be_inserted, securityMode, run_id: int = None):
+ def _get_entity_by_id(id):
+ return db.Entity(id=id).retrieve()
+
+ @staticmethod
+ def execute_inserts_in_list(to_be_inserted, securityMode, run_id: int = None,
+ unique_names=True):
for record in to_be_inserted:
for prop in record.properties:
entity = Crawler._get_entity_by_name(prop.name)
@@ -775,7 +906,7 @@ class Crawler(object):
logger.debug(to_be_inserted)
if len(to_be_inserted) > 0:
if securityMode.value > SecurityMode.RETRIEVE.value:
- db.Container().extend(to_be_inserted).insert()
+ db.Container().extend(to_be_inserted).insert(unique=unique_names)
elif run_id is not None:
update_cache = UpdateCache()
update_cache.insert(to_be_inserted, run_id, insert=True)
@@ -793,22 +924,24 @@ class Crawler(object):
_resolve_datatype(prop, entity)
@staticmethod
- def execute_updates_in_list(to_be_updated, securityMode, run_id: int = None):
+ def execute_updates_in_list(to_be_updated, securityMode, run_id: int = None,
+ unique_names=True):
Crawler.set_ids_and_datatype_of_parents_and_properties(to_be_updated)
logger.debug("UPDATE")
logger.debug(to_be_updated)
if len(to_be_updated) > 0:
if securityMode.value > SecurityMode.INSERT.value:
- db.Container().extend(to_be_updated).update()
+ db.Container().extend(to_be_updated).update(unique=unique_names)
elif run_id is not None:
update_cache = UpdateCache()
update_cache.insert(to_be_updated, run_id)
- def _synchronize(self, target_data: list[db.Record], commit_changes: bool = True):
+ def _synchronize(self, crawled_data: List[db.Record], commit_changes: bool = True,
+ unique_names=True):
"""
This function applies several stages:
- 1) Retrieve identifiables for all records in target_data.
- 2) Compare target_data with existing records.
+ 1) Retrieve identifiables for all records in crawled_data.
+ 2) Compare crawled_data with existing records.
3) Insert and update records based on the set of identified differences.
This function makes use of an IdentifiableAdapter which is used to retrieve
@@ -823,8 +956,7 @@ class Crawler(object):
if self.identifiableAdapter is None:
raise RuntimeError("Should not happen.")
- to_be_inserted, to_be_updated = self.split_into_inserts_and_updates(
- target_data)
+ to_be_inserted, to_be_updated = self.split_into_inserts_and_updates(crawled_data)
# TODO: refactoring of typo
for el in to_be_updated:
@@ -835,14 +967,21 @@ class Crawler(object):
self.identifiableAdapter.retrieve_identified_record_for_record(
record)
for record in to_be_updated]
- # remove unnecessary updates from list by comparing the target records to the existing ones
- self.remove_unnecessary_updates(to_be_updated, identified_records)
+ # Merge with existing data to prevent unwanted overwrites
+ to_be_updated = self._merge_properties_from_remote(to_be_updated,
+ identified_records)
+ # remove unnecessary updates from list by comparing the target records
+ # to the existing ones
+ to_be_updated = self.remove_unnecessary_updates(
+ to_be_updated, identified_records)
if commit_changes:
+ self.execute_parent_updates_in_list(to_be_updated, securityMode=self.securityMode,
+ run_id=self.run_id, unique_names=unique_names)
self.execute_inserts_in_list(
- to_be_inserted, self.securityMode, self.run_id)
+ to_be_inserted, self.securityMode, self.run_id, unique_names=unique_names)
self.execute_updates_in_list(
- to_be_updated, self.securityMode, self.run_id)
+ to_be_updated, self.securityMode, self.run_id, unique_names=unique_names)
update_cache = UpdateCache()
pending_inserts = update_cache.get_inserts(self.run_id)
@@ -882,7 +1021,7 @@ ____________________\n""".format(i + 1, len(pending_changes)) + str(el[3]))
@staticmethod
def debug_build_usage_tree(converter: Converter):
- res: dict[str, dict[str, Any]] = {
+ res: Dict[str, Dict[str, Any]] = {
converter.name: {
"usage": ", ".join(converter.metadata["usage"]),
"subtree": {}
@@ -899,7 +1038,7 @@ ____________________\n""".format(i + 1, len(pending_changes)) + str(el[3]))
return res
def save_debug_data(self, filename: str):
- paths: dict[str, Union[dict, list]] = dict()
+ paths: Dict[str, Union[dict, list]] = dict()
def flatten_debug_info(key):
mod_info = self.debug_metadata[key]
@@ -924,17 +1063,16 @@ ____________________\n""".format(i + 1, len(pending_changes)) + str(el[3]))
with open(filename, "w") as f:
f.write(yaml.dump(paths, sort_keys=False))
- def _crawl(self, items: list[StructureElement],
- global_converters: list[Converter],
- local_converters: list[Converter],
+ def _crawl(self, items: List[StructureElement],
+ local_converters: List[Converter],
generalStore: GeneralStore,
recordStore: RecordStore,
- structure_elements_path: list[str], converters_path: list[str]):
+ structure_elements_path: List[str], converters_path: List[str]):
"""
Crawl a list of StructureElements and apply any matching converters.
items: structure_elements (e.g. files and folders on one level on the hierarchy)
- global_converters and local_converters: globally or locally defined converters for
+ local_converters: locally defined converters for
treating structure elements. A locally defined converter could be
one that is only valid for a specific subtree of the originally
cralwed StructureElement structure.
@@ -942,7 +1080,8 @@ ____________________\n""".format(i + 1, len(pending_changes)) + str(el[3]))
global stores of the Crawler object.
"""
for element in items:
- for converter in global_converters + local_converters:
+ for converter in local_converters:
+
# type is something like "matches files", replace isinstance with "type_matches"
# match function tests regexp for example
if (converter.typecheck(element) and
@@ -968,7 +1107,8 @@ ____________________\n""".format(i + 1, len(pending_changes)) + str(el[3]))
self.debug_tree[str(element)] = (
generalStore_copy.get_storage(), recordStore_copy.get_storage())
self.debug_metadata["copied"][str(element)] = (
- generalStore_copy.get_dict_copied(), recordStore_copy.get_dict_copied())
+ generalStore_copy.get_dict_copied(),
+ recordStore_copy.get_dict_copied())
self.debug_metadata["usage"][str(element)].add(
"/".join(converters_path + [converter.name]))
mod_info = self.debug_metadata["provenance"]
@@ -979,10 +1119,11 @@ ____________________\n""".format(i + 1, len(pending_changes)) + str(el[3]))
record_identifier = record_name + \
"_" + str(internal_id)
converter.metadata["usage"].add(record_identifier)
- mod_info[record_identifier][prop_name] = (structure_elements_path + [element.get_name()],
- converters_path + [converter.name])
+ mod_info[record_identifier][prop_name] = (
+ structure_elements_path + [element.get_name()],
+ converters_path + [converter.name])
- self._crawl(children, global_converters, converter.converters,
+ self._crawl(children, converter.converters,
generalStore_copy, recordStore_copy,
structure_elements_path + [element.get_name()],
converters_path + [converter.name])
@@ -991,7 +1132,7 @@ ____________________\n""".format(i + 1, len(pending_changes)) + str(el[3]))
# to the general update container.
scoped_records = recordStore.get_records_current_scope()
for record in scoped_records:
- self.target_data.append(record)
+ self.crawled_data.append(record)
# TODO: the scoped variables should be cleaned up as soon if the variables
# are no longer in the current scope. This can be implemented as follows,
@@ -1004,7 +1145,7 @@ ____________________\n""".format(i + 1, len(pending_changes)) + str(el[3]))
# del recordStore[name]
# del generalStore[name]
- return self.target_data
+ return self.crawled_data
def crawler_main(crawled_directory_path: str,
@@ -1014,7 +1155,9 @@ def crawler_main(crawled_directory_path: str,
provenance_file: str = None,
dry_run: bool = False,
prefix: str = "",
- securityMode: int = SecurityMode.UPDATE):
+ securityMode: int = SecurityMode.UPDATE,
+ unique_names=True,
+ ):
"""
Parameters
@@ -1035,6 +1178,8 @@ def crawler_main(crawled_directory_path: str,
remove the given prefix from file paths
securityMode : int
securityMode of Crawler
+ unique_names : bool
+ whether or not to update or insert entities inspite of name conflicts
Returns
-------
@@ -1062,10 +1207,13 @@ def crawler_main(crawled_directory_path: str,
"update": updates}))
else:
rtsfinder = dict()
- for elem in crawler.target_data:
+ for elem in crawler.crawled_data:
if isinstance(elem, db.File):
# correct the file path:
# elem.file = os.path.join(args.path, elem.file)
+ if prefix is None:
+ raise RuntimeError(
+ "No prefix set. Prefix must be set if files are used.")
if elem.path.startswith(prefix):
elem.path = elem.path[len(prefix):]
elem.file = None
@@ -1092,7 +1240,7 @@ def crawler_main(crawled_directory_path: str,
raise RuntimeError("Missing RecordTypes: {}".
format(", ".join(notfound)))
- crawler.synchronize(commit_changes=True)
+ crawler.synchronize(commit_changes=True, unique_names=unique_names)
return 0
@@ -1110,6 +1258,7 @@ def parse_args():
help="The subtree of files below the given path will "
"be considered. Use '/' for everything.")
parser.add_argument("-s", "--security-mode", choices=["retrieve", "insert", "update"],
+ default="retrieve",
help="Determines whether entities may only be read from the server, or "
"whether inserts or even updates may be done.")
parser.add_argument("-n", "--dry-run", action="store_true",
@@ -1118,9 +1267,9 @@ def parse_args():
# TODO: load identifiables is a dirty implementation currently
parser.add_argument("-i", "--load-identifiables",
- help="Load identifiables from "
- "the given yaml file.")
-
+ help="Load identifiables from the given yaml file.")
+ parser.add_argument("-u", "--unique-names",
+ help="Insert or updates entities even if name conflicts exist.")
parser.add_argument("-p", "--prefix",
help="Remove the given prefix from the paths "
"of all file objects.")
@@ -1142,16 +1291,17 @@ def main():
logger.setLevel(logging.INFO)
sys.exit(crawler_main(
- args.crawled_directory_path,
- args.cfood_file_name,
- args.load_identifiables,
- args.debug,
- args.provenance,
- args.dry_run,
- args.prefix,
- {"retrieve": SecurityMode.RETRIEVE,
- "insert": SecurityMode.INSERT,
- "update": SecurityMode.UPDATE}[args.security_mode]
+ crawled_directory_path=args.crawled_directory_path,
+ cfood_file_name=args.cfood_file_name,
+ identifiables_definition_file=args.load_identifiables,
+ debug=args.debug,
+ provenance_file=args.provenance,
+ dry_run=args.dry_run,
+ prefix=args.prefix,
+ securityMode={"retrieve": SecurityMode.RETRIEVE,
+ "insert": SecurityMode.INSERT,
+ "update": SecurityMode.UPDATE}[args.security_mode],
+ unique_names=args.unique_names,
))
diff --git a/src/caoscrawler/identifiable_adapters.py b/src/caoscrawler/identifiable_adapters.py
index 0b00cbeaefe42bcf600db735d27c67571ca6a79b..73ce38fb593f321f9f80cc6c06034c7df0f14c76 100644
--- a/src/caoscrawler/identifiable_adapters.py
+++ b/src/caoscrawler/identifiable_adapters.py
@@ -4,8 +4,8 @@
# ** header v3.0
# This file is a part of the CaosDB Project.
#
-# Copyright (C) 2021 Henrik tom Wörden
-# 2021 Alexander Schlemmer
+# Copyright (C) 2021-2022 Henrik tom Wörden
+# 2021-2022 Alexander Schlemmer
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
@@ -52,8 +52,11 @@ def convert_value(value):
return str(value.id)
elif isinstance(value, datetime):
return value.isoformat()
+ elif type(value) == str:
+ # replace single quotes, otherwise they may break the queries
+ return value.replace("\'", "\\'")
else:
- return str(value)
+ return f"{value}"
class IdentifiableAdapter(metaclass=ABCMeta):
@@ -205,18 +208,10 @@ class IdentifiableAdapter(metaclass=ABCMeta):
# TODO: how to handle missing values in identifiables
# raise an exception?
raise NotImplementedError(
- f"RECORD\n{record}\nPROPERTY\n{prop.name}"
+ f"The following record is missing an identifying property:"
+ f"RECORD\n{record}\nIdentifying PROPERTY\n{prop.name}"
)
newval = record_prop.value
- if isinstance(record_prop.value, db.Entity):
- newval = self.resolve_reference(record_prop.value)
- elif isinstance(record_prop.value, list):
- newval = list()
- for element in record_prop.value:
- if isinstance(element, db.Entity):
- newval.append(self.resolve_reference(element))
- else:
- newval.append(element)
record_prop_new = db.Property(name=record_prop.name,
id=record_prop.id,
description=record_prop.description,
@@ -368,16 +363,13 @@ class LocalStorageIdentifiableAdapter(IdentifiableAdapter):
# a) prop_record.value has a registered identifiable:
# in this case, fetch the identifiable and set the value accordingly
if isinstance(prop.value, db.Entity): # lists are not checked here
- registered = self.get_registered_identifiable(prop.value)
+ otherid = prop_record.value
+ if isinstance(prop_record.value, db.Entity):
+ otherid = prop_record.value.id
+ if prop.value.id != otherid:
+ return False
- if registered is None:
- raise NotImplementedError("Non-identifiable references cannot"
- " be used as properties in identifiables.")
-
- raise RuntimeError("The identifiable which is used as property"
- " here has to be inserted first.")
-
- if prop.value != prop_record.value:
+ elif prop.value != prop_record.value:
return False
return True
@@ -387,7 +379,8 @@ class LocalStorageIdentifiableAdapter(IdentifiableAdapter):
if self.check_record(record, identifiable):
candidates.append(record)
if len(candidates) > 1:
- raise RuntimeError("Identifiable was not defined unambigiously.")
+ raise RuntimeError(
+ f"Identifiable was not defined unambigiously. Possible candidates are {candidates}")
if len(candidates) == 0:
return None
return candidates[0]
@@ -469,7 +462,8 @@ class CaosDBIdentifiableAdapter(IdentifiableAdapter):
query_string = self.create_query_for_identifiable(identifiable)
candidates = db.execute_query(query_string)
if len(candidates) > 1:
- raise RuntimeError("Identifiable was not defined unambigiously.")
+ raise RuntimeError(
+ f"Identifiable was not defined unambigiously.\n{query_string}\nReturned the following {candidates}.")
if len(candidates) == 0:
return None
return candidates[0]
diff --git a/src/caoscrawler/identified_cache.py b/src/caoscrawler/identified_cache.py
index 0b9d7a47bdecc4094edb1296f4c04dfa083a2436..b5db8ba04fc813ea8aca0131c6265adab666b2e7 100644
--- a/src/caoscrawler/identified_cache.py
+++ b/src/caoscrawler/identified_cache.py
@@ -23,13 +23,52 @@
# ** end header
#
+
"""
-stores identified records and is able to detect duplicates
+This module is a cache for Records where we checked the existence in a remote server using
+identifiables. If the Record was found, this means that we identified the corresponding Record
+in the remote server and the ID of the local object can be set.
+To prevent querying the server again and again for the same objects, this cache allows storing
+Records that were found on a remote server and those that were not (typically in separate caches).
+The look up in the cache is done using a hash of a string representation.
+
+TODO: We need a general review:
+- How are entities identified with each other?
+- What happens if the identification fails?
+
+Checkout how this was done in the old crawler.
"""
import caosdb as db
from hashlib import sha256
+from datetime import datetime
+
+
+def _value_representation(value):
+ """returns the string representation of property values to be used in the hash function """
+
+ # TODO: (for review)
+ # This expansion of the hash function was introduced recently
+ # to allow the special case of Files as values of properties.
+ # We need to review the completeness of all the cases here, as the cache
+ # is crucial for correct identification of insertion and updates.
+ if value is None:
+ return "None"
+ elif isinstance(value, db.File):
+ return str(value.path)
+ elif isinstance(value, db.Entity):
+ if value.id is not None:
+ return str(value.id)
+ else:
+ return "PyID="+str(id(value))
+ elif isinstance(value, list):
+ return "["+", ".join([_value_representation(el) for el in value])+"]"
+ elif (isinstance(value, str) or isinstance(value, int) or isinstance(value, float)
+ or isinstance(value, datetime)):
+ return str(value)
+ else:
+ raise ValueError(f"Unknown datatype of the value: {value}")
def _create_hashable_string(identifiable: db.Record):
@@ -46,28 +85,11 @@ def _create_hashable_string(identifiable: db.Record):
# sorted([p.name for p in identifiable.parents])
raise RuntimeError("Cache entry can only be generated for entities with 1 parent.")
rec_string = "P<{}>N<{}>".format(identifiable.parents[0].name, identifiable.name)
+ # TODO this structure neglects Properties if multiple exist for the same name
for pname in sorted([p.name for p in identifiable.properties]):
- value = str(identifiable.get_property(pname).value)
-
- # TODO: (for review)
- # This expansion of the hash function was introduced recently
- # to allow the special case of Files as values of properties.
- # We need to review the completeness of all the cases here, as the cache
- # is crucial for correct identification of insertion and updates.
- if isinstance(identifiable.get_property(pname).value, db.File):
- value = str(identifiable.get_property(pname).value.path)
- elif isinstance(identifiable.get_property(pname).value, db.Entity):
- value = str(identifiable.get_property(pname).value.id)
- elif isinstance(identifiable.get_property(pname).value, list):
- tmplist = []
- for val in identifiable.get_property(pname).value:
- if isinstance(val, db.Entity):
- tmplist.append(val.id)
- else:
- tmplist.append(val)
- value = str(tmplist)
-
- rec_string += "{}:".format(pname) + value
+
+ rec_string += ("{}:".format(pname) +
+ _value_representation(identifiable.get_property(pname).value))
return rec_string
diff --git a/src/caoscrawler/macros/__init__.py b/src/caoscrawler/macros/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..0acfb1763039a3bb800bbf0e26d6940b49d045cf
--- /dev/null
+++ b/src/caoscrawler/macros/__init__.py
@@ -0,0 +1 @@
+from .macro_yaml_object import defmacro_constructor, macro_constructor
diff --git a/src/caoscrawler/macros/macro_yaml_object.py b/src/caoscrawler/macros/macro_yaml_object.py
new file mode 100644
index 0000000000000000000000000000000000000000..2849986e6deb5cb2cba9e45516e6ce8e1a93dfa0
--- /dev/null
+++ b/src/caoscrawler/macros/macro_yaml_object.py
@@ -0,0 +1,155 @@
+#!/usr/bin/env python3
+# encoding: utf-8
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2022 Alexander Schlemmer
+#
+# 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
+#
+
+# Function to expand a macro in yaml
+# A. Schlemmer, 05/2022
+
+from dataclasses import dataclass
+from typing import Any, Dict
+from copy import deepcopy
+from string import Template
+
+
+@dataclass
+class MacroDefinition:
+ """
+ Stores a macro definition.
+ name: Name of the macro
+ params: variables and default values to be substituted in keys or values
+ definition: A dictionary that will be substituted including parameters
+ """
+ name: str
+ params: Dict[str, Any]
+ definition: Any
+
+
+# This dictionary stores the macro definitions
+macro_store: Dict[str, MacroDefinition] = dict()
+
+
+def substitute(propvalue, values: dict):
+ """
+ Substitution of variables in strings using the variable substitution
+ library from python's standard library.
+ """
+ propvalue_template = Template(propvalue)
+ return propvalue_template.safe_substitute(**values)
+
+
+def substitute_dict(sourced: Dict[str, Any], values: Dict[str, Any]):
+ """
+ Create a copy of sourced.
+ Afterwards recursively do variable substitution on all keys and values.
+ """
+ d = deepcopy(sourced)
+ # Changes in keys:
+ replace: Dict[str, str] = dict()
+ for k in d:
+ replacement = substitute(k, values)
+ if replacement != k:
+ replace[k] = replacement
+ for k, v in replace.items():
+ d[v] = d[k]
+ del d[k]
+ # Changes in values:
+ for k, v in d.items():
+ if isinstance(v, str):
+ d[k] = substitute(v, values)
+ elif isinstance(v, list):
+ subst_list = list()
+ for i in d[k]:
+ if isinstance(i, str):
+ subst_list.append(substitute(i, values))
+ elif isinstance(i, dict):
+ subst_list.append(substitute_dict(i, values))
+ else:
+ subst_list.append(i)
+ d[k] = subst_list
+ elif isinstance(v, dict):
+ d[k] = substitute_dict(v, values)
+ else:
+ pass
+ return d
+
+
+def defmacro_constructor(loader, node):
+ """
+ Function for registering macros in yaml files.
+
+ It can be registered in pyaml using:
+ yaml.SafeLoader.add_constructor("!defmacro", defmacro_constructor)
+ """
+
+ value = loader.construct_mapping(node, deep=True)
+ params = {}
+ if "params" in value:
+ params = value["params"]
+ macro = MacroDefinition(
+ value["name"], params,
+ value["definition"])
+ macro_store[macro.name] = macro
+ return {}
+
+
+def macro_constructor(loader, node):
+ """
+ Function for substituting macros in yaml files.
+
+ It can be registered in pyaml using:
+ yaml.SafeLoader.add_constructor("!macro", macro_constructor)
+ """
+ res = dict()
+ value = loader.construct_mapping(node, deep=True)
+ for name, params_setter in value.items():
+ if name in macro_store:
+ # If params_setter is a list, run this for every element:
+ if params_setter is not None and isinstance(params_setter, list):
+ for el in params_setter:
+ macro = macro_store[name]
+ params = deepcopy(macro.params)
+ if el is not None:
+ if isinstance(el, dict):
+ params.update(el)
+ else:
+ raise RuntimeError("params type not supported")
+ else:
+ raise RuntimeError("params type must not be None")
+ definition = substitute_dict(macro.definition, params)
+ res.update(definition)
+ else:
+ # This is just a single macro:
+ macro = macro_store[name]
+ params = deepcopy(macro.params)
+ if params_setter is not None:
+ if isinstance(params_setter, dict):
+ params.update(params_setter)
+ else:
+ raise RuntimeError("params type not supported")
+ definition = substitute_dict(macro.definition, params)
+ res.update(definition)
+ else:
+ # If there is no macro with that name, just keep that node:
+ res[name] = params_setter
+
+ return res
diff --git a/src/caoscrawler/structure_elements.py b/src/caoscrawler/structure_elements.py
index 6be653a4758e8c3fb789b22ea655836a3d976c34..01996b4ff3e14a9739857e6e03ceca161300b37e 100644
--- a/src/caoscrawler/structure_elements.py
+++ b/src/caoscrawler/structure_elements.py
@@ -23,12 +23,15 @@
# ** end header
#
+from typing import Dict
+
+
class StructureElement(object):
""" base class for elements in the hierarchical data structure """
def __init__(self, name):
# Used to store usage information for debugging:
- self.metadata: dict[str, set[str]] = {
+ self.metadata: Dict[str, set[str]] = {
"usage": set()
}
diff --git a/src/doc/README_SETUP.md b/src/doc/README_SETUP.md
new file mode 100644
index 0000000000000000000000000000000000000000..b6995c9a2d950ecd1e832d5b49dac9ed88a7e455
--- /dev/null
+++ b/src/doc/README_SETUP.md
@@ -0,0 +1,82 @@
+# Getting started with the CaosDB Crawler #
+
+## Installation ##
+
+### Requirements ###
+
+
+### How to install ###
+
+#### Linux ####
+
+Make sure that Python (at least version 3.8) and pip is installed, using your system tools and
+documentation.
+
+Then open a terminal and continue in the [Generic installation](#generic-installation) section.
+
+#### Windows ####
+
+If a Python distribution is not yet installed, we recommend Anaconda Python, which you can download
+for free from [https://www.anaconda.com](https://www.anaconda.com). The "Anaconda Individual Edition" provides most of all
+packages you will ever need out of the box. If you prefer, you may also install the leaner
+"Miniconda" installer, which allows you to install packages as you need them.
+
+After installation, open an Anaconda prompt from the Windows menu and continue in the [Generic
+installation](#generic-installation) section.
+
+#### MacOS ####
+
+If there is no Python 3 installed yet, there are two main ways to
+obtain it: Either get the binary package from
+[python.org](https://www.python.org/downloads/) or, for advanced
+users, install via [Homebrew](https://brew.sh/). After installation
+from python.org, it is recommended to also update the TLS certificates
+for Python (this requires administrator rights for your user):
+
+```sh
+# Replace this with your Python version number:
+cd /Applications/Python\ 3.9/
+
+# This needs administrator rights:
+sudo ./Install\ Certificates.command
+```
+
+After these steps, you may continue with the [Generic
+installation](#generic-installation).
+
+#### Generic installation ####
+
+---
+
+Obtain the sources from GitLab and install from there (`git` must be installed for
+this option):
+
+```sh
+git clone https://gitlab.com/caosdb/caosdb-crawler
+cd caosdb-crawler
+pip3 install --user .
+```
+
+**Note**: In the near future, this package will also be made available on PyPi.
+
+## Configuration ##
+
+
+
+## Try it out ##
+
+
+
+## Run Unit Tests
+
+## Documentation ##
+
+Build documentation in `src/doc` with `make html`.
+
+### Requirements ###
+
+- `sphinx`
+- `sphinx-autoapi`
+- `recommonmark`
+
+### Troubleshooting ###
diff --git a/src/doc/_apidoc/modules.rst b/src/doc/_apidoc/modules.rst
deleted file mode 100644
index 17f187982981ffbf7bcc857056d10644c2bd422b..0000000000000000000000000000000000000000
--- a/src/doc/_apidoc/modules.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-newcrawler
-==========
-
-.. toctree::
- :maxdepth: 4
-
- newcrawler
diff --git a/src/doc/_apidoc/newcrawler.converters.rst b/src/doc/_apidoc/newcrawler.converters.rst
deleted file mode 100644
index 893391c229b94baeed9a44c57877ed33f37b2f5e..0000000000000000000000000000000000000000
--- a/src/doc/_apidoc/newcrawler.converters.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-newcrawler.converters module
-============================
-
-.. automodule:: newcrawler.converters
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/src/doc/_apidoc/newcrawler.crawl.rst b/src/doc/_apidoc/newcrawler.crawl.rst
deleted file mode 100644
index b00a6ab6498a0482cea3e9faa54d66d66991dc2d..0000000000000000000000000000000000000000
--- a/src/doc/_apidoc/newcrawler.crawl.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-newcrawler.crawl module
-=======================
-
-.. automodule:: newcrawler.crawl
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/src/doc/_apidoc/newcrawler.identifiable_adapters.rst b/src/doc/_apidoc/newcrawler.identifiable_adapters.rst
deleted file mode 100644
index d8926f41b72d2c54931f045d75f9fe59b21e6076..0000000000000000000000000000000000000000
--- a/src/doc/_apidoc/newcrawler.identifiable_adapters.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-newcrawler.identifiable\_adapters module
-========================================
-
-.. automodule:: newcrawler.identifiable_adapters
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/src/doc/_apidoc/newcrawler.identified_cache.rst b/src/doc/_apidoc/newcrawler.identified_cache.rst
deleted file mode 100644
index 6f697362ad44d1fec01f328550dc8667cc889019..0000000000000000000000000000000000000000
--- a/src/doc/_apidoc/newcrawler.identified_cache.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-newcrawler.identified\_cache module
-===================================
-
-.. automodule:: newcrawler.identified_cache
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/src/doc/_apidoc/newcrawler.rst b/src/doc/_apidoc/newcrawler.rst
deleted file mode 100644
index 202444a5efbde248e52d712575ade49f6dd50601..0000000000000000000000000000000000000000
--- a/src/doc/_apidoc/newcrawler.rst
+++ /dev/null
@@ -1,24 +0,0 @@
-newcrawler package
-==================
-
-Submodules
-----------
-
-.. toctree::
- :maxdepth: 4
-
- newcrawler.converters
- newcrawler.crawl
- newcrawler.identifiable_adapters
- newcrawler.identified_cache
- newcrawler.stores
- newcrawler.structure_elements
- newcrawler.utils
-
-Module contents
----------------
-
-.. automodule:: newcrawler
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/src/doc/_apidoc/newcrawler.stores.rst b/src/doc/_apidoc/newcrawler.stores.rst
deleted file mode 100644
index 7d446c1cd45a6bf1c4b6cf1b1d33e9a2a5ad9751..0000000000000000000000000000000000000000
--- a/src/doc/_apidoc/newcrawler.stores.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-newcrawler.stores module
-========================
-
-.. automodule:: newcrawler.stores
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/src/doc/_apidoc/newcrawler.structure_elements.rst b/src/doc/_apidoc/newcrawler.structure_elements.rst
deleted file mode 100644
index 4613e1d58b0ef9c7cc38096aa25270f469836ce5..0000000000000000000000000000000000000000
--- a/src/doc/_apidoc/newcrawler.structure_elements.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-newcrawler.structure\_elements module
-=====================================
-
-.. automodule:: newcrawler.structure_elements
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/src/doc/_apidoc/newcrawler.utils.rst b/src/doc/_apidoc/newcrawler.utils.rst
deleted file mode 100644
index 4df55a234fd85072068e41d1ce7bb3b17fd1a698..0000000000000000000000000000000000000000
--- a/src/doc/_apidoc/newcrawler.utils.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-newcrawler.utils module
-=======================
-
-.. automodule:: newcrawler.utils
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/src/doc/cfood.rst b/src/doc/cfood.rst
new file mode 100644
index 0000000000000000000000000000000000000000..677cadc55709c6c25d16ff547b311102ee78699a
--- /dev/null
+++ b/src/doc/cfood.rst
@@ -0,0 +1,149 @@
+CFood-Definition
+================
+
+The crawler specification is called CFood-definition. It is stored inside a yaml file, or - more precisely - inside of one single or two yaml documents inside a yaml file.
+
+The specification consists of three separate parts:
+#. Metadata and macro definitions
+#. Custom converter registrations
+#. The converter tree specification
+
+In the simplest case, there is just one yaml file with just a single document including at least
+the converter tree specification (see :ref:`example 1<example_1>`). Additionally the custom converter part may be also included in
+this single document (for historical reasons, see :ref:`example 2<example_2>`), but it is recommended to include them in the separate
+document together with the metadata and :doc:`macro<macros>` definitions (see :ref:`below<example_4>`).
+
+If metadata and macro definitions are provided, there **must** be a second document preceeding the
+converter tree specification, including these definitions.
+
+Examples
+++++++++
+
+A single document with a converter tree specification:
+
+.. _example_1:
+.. code-block:: yaml
+
+ extroot:
+ type: Directory
+ match: ^extroot$
+ subtree:
+ DataAnalysis:
+ type: Directory
+ match: DataAnalysis
+ # (...)
+
+
+A single document with a converter tree specification, but also including a custom converters section:
+
+.. _example_2:
+.. code-block:: yaml
+
+ Converters:
+ CustomConverter_1:
+ package: mypackage.converters
+ converter: CustomConverter1
+ CustomConverter_2:
+ package: mypackage.converters
+ converter: CustomConverter2
+
+ extroot:
+ type: Directory
+ match: ^extroot$
+ subtree:
+ DataAnalysis:
+ type: Directory
+ match: DataAnalysis
+ # (...)
+
+
+
+A yaml multi-document, defining metadata and some macros in the first document and declaring
+two custom converters in the second document (**not recommended**, see the recommended version :ref:`below<example_4>`). Please note, that two separate yaml documents can be defined using the ``---`` syntax:
+
+
+.. _example_3:
+.. code-block:: yaml
+
+ ---
+ metadata:
+ name: Datascience CFood
+ description: CFood for data from the local data science work group
+ macros:
+ - !defmacro
+ name: SimulationDatasetFile
+ params:
+ match: null
+ recordtype: null
+ nodename: null
+ definition:
+ # (...)
+ ---
+ Converters:
+ CustomConverter_1:
+ package: mypackage.converters
+ converter: CustomConverter1
+ CustomConverter_2:
+ package: mypackage.converters
+ converter: CustomConverter2
+
+ extroot:
+ type: Directory
+ match: ^extroot$
+ subtree:
+ DataAnalysis:
+ type: Directory
+ match: DataAnalysis
+ # (...)
+
+
+
+The **recommended way** of defining metadata, custom converters, macros and the main cfood specification is shown in the following code example:
+
+
+.. _example_4:
+.. code-block:: yaml
+
+ ---
+ metadata:
+ name: Datascience CFood
+ description: CFood for data from the local data science work group
+ macros:
+ - !defmacro
+ name: SimulationDatasetFile
+ params:
+ match: null
+ recordtype: null
+ nodename: null
+ definition:
+ # (...)
+ Converters:
+ CustomConverter_1:
+ package: mypackage.converters
+ converter: CustomConverter1
+ CustomConverter_2:
+ package: mypackage.converters
+ converter: CustomConverter2
+ ---
+ extroot:
+ type: Directory
+ match: ^extroot$
+ subtree:
+ DataAnalysis:
+ type: Directory
+ match: DataAnalysis
+ # (...)
+
+
+List Mode
+---------
+
+Specifying values of properties can make use of two special characters, in order to automatically
+create lists or multi properties instead of single values:
+
+.. code-block:: yaml
+
+ Experiment1:
+ Measurement: +Measurement <- Element in List (list is cleared before run)
+ *Measurement <- Multi Property (properties are removed before run)
+ Measurement <- Overwrite
diff --git a/src/doc/concepts.rst b/src/doc/concepts.rst
new file mode 100644
index 0000000000000000000000000000000000000000..c0f21cbaa322caddabed8e045f7b6fc4253d2959
--- /dev/null
+++ b/src/doc/concepts.rst
@@ -0,0 +1,119 @@
+Concepts
+))))))))
+
+Structure Elements
+++++++++++++++++++
+
+This hierarchical structure is assumed to be consituted of a tree of
+StructureElements. The tree is created on the fly by so called Converters which
+are defined in a yaml file. The tree of StructureElements is a model
+of the existing data (For example could a tree of Python file objects
+(StructureElements) represent a file tree that exists on some file server).
+
+Relevant sources in:
+src/structure_elements.py
+
+Converters
+++++++++++
+
+Converters treat StructureElements and thereby create the StructureElement that
+are the children of the treated StructureElement. Converters therefore create
+the above named tree. The definition of a Converter also contains what
+Converters shall be used to treat the generated child-StructureElements. The
+definition is therefore a tree itself.
+
+See `:doc:converters<converters>` for details.
+
+
+
+Relevant sources in:
+src/converters.py
+
+
+
+Identifiables
++++++++++++++
+
+Relevant sources in:
+src/identifiable_adapters.py
+
+The Crawler
++++++++++++
+
+The crawler can be considered the main program doing the synchronization in basically two steps:
+#. Based on a yaml-specification scan the file system (or other sources) and create a set of CaosDB Entities that are supposed to be inserted or updated in a CaosDB instance.
+#. Compare the current state of the CaosDB instance with the set of CaosDB Entities created in step 1, taking into account the :ref:`registered identifiables<Identifiables>`. Insert or update entites accordingly.
+
+Relevant sources in:
+src/crawl.py
+
+
+
+Special Cases
+=============
+
+Variable Precedence
++++++++++++++++++++
+
+Let's assume the following situation
+
+.. code-block:: yaml
+
+ description:
+ type: DictTextElement
+ match_value: (?P<description>.*)
+ match_name: description
+
+
+Making use of the $description variable could refer to two different variables created here:
+1. The structure element path.
+2. The value of the matched expression.
+
+The matched expression does take precedence over the structure element path and shadows it.
+
+Make sure, that if you want to be able to use the structure element path, to give unique names
+to the variables like:
+
+.. code-block:: yaml
+
+ description_text_block:
+ type: DictTextElement
+ match_value: (?P<description>.*)
+ match_name: description
+
+
+Scopes
+========
+
+Example:
+
+.. code-block:: yaml
+
+ DicomFile:
+ type: SimpleDicomFile
+ match: (?P<filename>.*)\.dicom
+ records:
+ DicomRecord:
+ name: $filename
+ subtree: # header of dicom file
+ PatientID:
+ type: DicomHeaderElement
+ match_name: PatientName
+ match_value: (?P<patient>.*)
+ records:
+ Patient:
+ name: $patient
+ dicom_name: $filename # $filename is in same scope!
+ ExperimentFile:
+ type: MarkdownFile
+ match: ^readme.md$
+ records:
+ Experiment:
+ dicom_name: $filename # does NOT work, because $filename is out of scope!
+
+
+# can variables be used within regexp?
+
+
+File Objects
+============
diff --git a/src/doc/conf.py b/src/doc/conf.py
index fb37cdd96c440300741aeb49e90caffe4370f5d7..30ce670eb8685e9701eeeb59bf22451a21fb16b9 100644
--- a/src/doc/conf.py
+++ b/src/doc/conf.py
@@ -53,6 +53,7 @@ extensions = [
'sphinx.ext.autosectionlabel',
'sphinx.ext.intersphinx',
'sphinx.ext.napoleon', # For Google style docstrings
+ "recommonmark", # For markdown files.
"sphinx_rtd_theme",
]
@@ -61,7 +62,7 @@ templates_path = ['_templates']
# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
-source_suffix = ['.rst']
+source_suffix = ['.rst', '.md']
# The master toctree document.
master_doc = 'index'
@@ -71,7 +72,7 @@ master_doc = 'index'
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
@@ -99,7 +100,7 @@ html_theme = "sphinx_rtd_theme"
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = [] # ['_static']
# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
diff --git a/src/doc/converters.rst b/src/doc/converters.rst
new file mode 100644
index 0000000000000000000000000000000000000000..640a1ddec04986960bcf41110c593bb73431ed75
--- /dev/null
+++ b/src/doc/converters.rst
@@ -0,0 +1,457 @@
+Converters
+))))))))))
+
+Converters treat StructureElements and thereby create the StructureElement that
+are the children of the treated StructureElement. Converters therefore create
+the tree of structure elements. The definition of a Converter also contains what
+Converters shall be used to treat the generated child-StructureElements. The
+definition is therefore a tree itself.
+
+Each StructureElement in the tree has a set of data values, i.e a dictionary of
+key value pairs.
+Some of those values are set due to the kind of StructureElement. For example,
+a file could have the file name as such a key value pair: 'filename': <sth>.
+Converters may define additional functions that create further values. For
+example, a regular expresion could be used to get a date from a file name.
+
+
+
+
+A converter is defined via a yml file or part of it. The definition states
+what kind of StructureElement it treats (typically one).
+Also, it defines how children of the current StructureElement are
+created and what Converters shall be used to treat those.
+
+The yaml definition looks like the following:
+
+TODO: outdated, see cfood-schema.yml
+
+.. code-block:: yaml
+
+ <NodeName>:
+ type: <ConverterName>
+ match: ".*"
+ records:
+ Experiment1:
+ parents:
+ - Experiment
+ - Blablabla
+ date: $DATUM
+ (...)
+ Experiment2:
+ parents:
+ - Experiment
+ subtree:
+ (...)
+
+The **<NodeName>** is a description of what it represents (e.g.
+'experiment-folder') and is used as identifier.
+
+**<type>** selects the converter that is going to be matched against the current structure
+element. If the structure element matches (this is a combination of a typecheck and a detailed
+match, see :py:class:`~caoscrawler.converters.Converter` for details) the converter is used
+to generate records (see :py:meth:`~caoscrawler.converters.Converter.create_records`) and to possibly process a subtree, as defined by the function :func:`caoscrawler.converters.create_children`.
+
+**records** is a dict of definitions that define the semantic structure
+(see details below).
+
+Subtree contains a list of Converter defnitions that look like the one
+described here.
+
+
+Standard Converters
++++++++++++++++++++
+
+Directory Converter
+===================
+
+Simple File Converter
+=====================
+
+Markdown File Converter
+=======================
+
+Dict Converter
+==============
+
+Typical Subtree converters
+--------------------------
+
+DictBooleanElementConverter
+DictFloatElementConverter
+DictTextElementConverter
+DictIntegerElementConverter
+DictListElementConverter
+DictDictElementConverter
+
+YAMLFileConverter
+=================
+
+A specialized Dict Converter for yaml files: Yaml files are opened and the contents are
+converted into dictionaries that can be further converted using the typical subtree converters
+of dict converter.
+
+**WARNING**: Currently unfinished implementation.
+
+JSONFileConverter
+=================
+
+
+
+TextElementConverter
+====================
+
+TableConverter
+==============
+
+A generic converter (abstract) for files containing tables.
+Currently, there are two specialized implementations for xlsx-files and csv-files.
+
+All table converters generate a subtree that can be converted with DictDictElementConverters:
+For each row in the table a DictDictElement (structure element) is generated. The key of the
+element is the row number. The value of the element is a dict containing the mapping of
+column names to values of the respective cell.
+
+Example:
+
+.. code-block:: yaml
+
+ subtree:
+ TABLE:
+ type: CSVTableConverter
+ match: ^test_table.csv$
+ records:
+ (...) # Records edited for the whole table file
+ subtree:
+ ROW:
+ type: DictDictElement
+ match_name: .*
+ match_value: .*
+ records:
+ (...) # Records edited for each row
+ subtree:
+ COLUMN:
+ type: DictFloatElement
+ match_name: measurement # Name of the column in the table file
+ match_value: (?P<column_value).*)
+ records:
+ (...) # Records edited for each cell
+
+
+XLSXTableConverter
+==================
+
+CSVTableConverter
+=================
+
+Custom Converters
++++++++++++++++++
+
+It was previously mentioned that it is possible to create custom converters.
+These custom converters can be used to integrate arbitrary data extraction and ETL capabilities
+into the caosdb-crawler and make these extensions available to any yaml specification.
+
+The basic syntax for adding a custom converter to a yaml cfood definition file is:
+
+.. code-block:: yaml
+
+ Converters:
+ <NameOfTheConverterInYamlFile>:
+ package: <python>.<module>.<name>
+ converter: <PythonClassName>
+
+The Converters-section can be either put into the first or second document of the cfood yaml file.
+It can be also part of a single-document yaml cfood file. Please refer to :doc:`the cfood documentation<cfood>` for more details.
+
+Details:
+
+- **<NameOfTheConverterInYamlFile>**: This is the name of the converter as it is going to be used in the present yaml file.
+- **<python>.<module>.<name>**: The name of the module where the converter class resides.
+- **<PythonClassName>**: Within this specified module there must be a class inheriting from base class :py:class:`caoscrawler.converters.Converter`.
+
+The following methods are abstract and need to be overwritten by your custom converter to make it work:
+
+- :py:meth:`~caoscrawler.converters.Converter.create_children`
+- :py:meth:`~caoscrawler.converters.Converter.match`
+- :py:meth:`~caoscrawler.converters.Converter.typecheck`
+
+
+Example
+=======
+
+In the following, we will explain the process of adding a custom converter to a yaml file using
+a SourceResolver that is able to attach a source element to another entity.
+
+**Note**: This example might become a standard crawler soon, as part of the scifolder specification. See https://doi.org/10.3390/data5020043 for details. In this documentation example we will, therefore, add it to a package called "scifolder".
+
+First we will create our package and module structure, which might be:
+
+.. code-block::
+
+ scifolder_package/
+ README.md
+ setup.cfg
+ setup.py
+ Makefile
+ tox.ini
+ src/
+ scifolder/
+ __init__.py
+ converters/
+ __init__.py
+ sources.py # <- the actual file containing
+ # the converter class
+ doc/
+ unittests/
+
+Now we need to create a class called "SourceResolver" in the file "sources.py". In this - more advanced - example, we will not inherit our converter directly from :py:class:`~caoscrawler.converters.Converter`, but use :py:class:`~caoscrawler.converters.TextElementConverter`. The latter already implements :py:meth:`~caoscrawler.converters.Converter.match` and :py:meth:`~caoscrawler.converters.Converter.typecheck`, so only an implementation for :py:meth:`~caoscrawler.converters.Converter.create_children` has to be provided by us.
+Furthermore we will customize the method :py:meth:`~caoscrawler.converters.Converter.create_records` that allows us to specify a more complex record generation procedure than provided in the standard implementation. One specific limitation of the standard implementation is, that only a fixed
+number of records can be generated by the yaml definition. So for any applications - like here - that require an arbitrary number of records to be created, a customized implementation of :py:meth:`~caoscrawler.converters.Converter.create_records` is recommended.
+In this context it is recommended to make use of the function :func:`caoscrawler.converters.create_records` that implements creation of record objects from python dictionaries of the same structure
+that would be given using a yaml definition (see next section below).
+
+.. code-block:: python
+
+ import re
+ from caoscrawler.stores import GeneralStore, RecordStore
+ from caoscrawler.converters import TextElementConverter, create_records
+ from caoscrawler.structure_elements import StructureElement, TextElement
+
+
+ class SourceResolver(TextElementConverter):
+ """
+ This resolver uses a source list element (e.g. from the markdown readme file)
+ to link sources correctly.
+ """
+
+ def __init__(self, definition: dict, name: str,
+ converter_registry: dict):
+ """
+ Initialize a new directory converter.
+ """
+ super().__init__(definition, name, converter_registry)
+
+ def create_children(self, generalStore: GeneralStore,
+ element: StructureElement):
+
+ # The source resolver does not create children:
+
+ return []
+
+ def create_records(self, values: GeneralStore,
+ records: RecordStore,
+ element: StructureElement,
+ file_path_prefix):
+ if not isinstance(element, TextElement):
+ raise RuntimeError()
+
+ # This function must return a list containing tuples, each one for a modified
+ # property: (name_of_entity, name_of_property)
+ keys_modified = []
+
+ # This is the name of the entity where the source is going to be attached:
+ attach_to_scientific_activity = self.definition["scientific_activity"]
+ rec = records[attach_to_scientific_activity]
+
+ # The "source" is a path to a source project, so it should have the form:
+ # /<Category>/<project>/<scientific_activity>/
+ # obtain these information from the structure element:
+ val = element.value
+ regexp = (r'/(?P<category>(SimulationData)|(ExperimentalData)|(DataAnalysis))'
+ '/(?P<project_date>.*?)_(?P<project_identifier>.*)'
+ '/(?P<date>[0-9]{4,4}-[0-9]{2,2}-[0-9]{2,2})(_(?P<identifier>.*))?/')
+
+ res = re.match(regexp, val)
+ if res is None:
+ raise RuntimeError("Source cannot be parsed correctly.")
+
+ # Mapping of categories on the file system to corresponding record types in CaosDB:
+ cat_map = {
+ "SimulationData": "Simulation",
+ "ExperimentalData": "Experiment",
+ "DataAnalysis": "DataAnalysis"}
+ linkrt = cat_map[res.group("category")]
+
+ keys_modified.extend(create_records(values, records, {
+ "Project": {
+ "date": res.group("project_date"),
+ "identifier": res.group("project_identifier"),
+ },
+ linkrt: {
+ "date": res.group("date"),
+ "identifier": res.group("identifier"),
+ "project": "$Project"
+ },
+ attach_to_scientific_activity: {
+ "sources": "+$" + linkrt
+ }}, file_path_prefix))
+
+ # Process the records section of the yaml definition:
+ keys_modified.extend(
+ super().create_records(values, records, element, file_path_prefix))
+
+ # The create_records function must return the modified keys to make it compatible
+ # to the crawler functions:
+ return keys_modified
+
+
+If the recommended (python) package structure is used, the package containing the converter
+definition can just be installed using `pip install .` or `pip install -e .` from the
+`scifolder_package` directory.
+
+The following yaml block will register the converter in a yaml file:
+
+.. code-block:: yaml
+
+ Converters:
+ SourceResolver:
+ package: scifolder.converters.sources
+ converter: SourceResolver
+
+
+Using the `create_records` API function
+=======================================
+
+The function :func:`caoscrawler.converters.create_records` was already mentioned above and it is
+the recommended way to create new records from custom converters. Let's have a look at the
+function signature:
+
+.. code-block:: python
+
+ def create_records(values: GeneralStore, # <- pass the current variables store here
+ records: RecordStore, # <- pass the current store of CaosDB records here
+ def_records: dict): # <- This is the actual definition of new records!
+
+
+`def_records` is the actual definition of new records according to the yaml cfood specification
+(work in progress, in the docs). Essentially you can do everything here, that you could do
+in the yaml document as well, but using python source code.
+
+Let's have a look at a few examples:
+
+.. code-block:: yaml
+
+ DirConverter:
+ type: Directory
+ match: (?P<dir_name>.*)
+ records:
+ Experiment:
+ identifier: $dir_name
+
+This block will just create a new record with parent `Experiment` and one property
+`identifier` with a value derived from the matching regular expression.
+
+Let's formulate that using `create_records`:
+
+.. code-block:: python
+
+ dir_name = "directory name"
+
+ record_def = {
+ "Experiment": {
+ "identifier": dir_name
+ }
+ }
+
+ keys_modified = create_records(values, records,
+ record_def)
+
+The `dir_name` is set explicitely here, everything else is identical to the yaml statements.
+
+
+The role of `keys_modified`
+===========================
+
+You probably have noticed already, that :func:`caoscrawler.converters.create_records` returns
+`keys_modified` which is a list of tuples. Each element of `keys_modified` has two elements:
+
+- Element 0 is the name of the record that is modified (as used in the record store `records`).
+- Element 1 is the name of the property that is modified.
+
+It is important, that the correct list of modified keys is returned by
+:py:meth:`~caoscrawler.converters.Converter.create_records` to make the crawler process work.
+
+So, a sketch of a typical implementation within a custom converter could look like this:
+
+
+.. code-block:: python
+
+ def create_records(self, values: GeneralStore,
+ records: RecordStore,
+ element: StructureElement,
+ file_path_prefix: str):
+
+ # Modify some records:
+ record_def = {
+ # ...
+ }
+
+ keys_modified = create_records(values, records,
+ record_def)
+
+ # You can of course do it multiple times:
+ keys_modified.extend(create_records(values, records,
+ record_def))
+
+ # You can also process the records section of the yaml definition:
+ keys_modified.extend(
+ super().create_records(values, records, element, file_path_prefix))
+ # This essentially allows users of your converter to customize the creation of records
+ # by providing a custom "records" section additionally to the modifications provided
+ # in this implementation of the Converter.
+
+ # Important: Return the list of modified keys!
+ return keys_modified
+
+
+More complex example
+====================
+
+Let's have a look at a more complex examples, defining multiple records:
+
+.. code-block:: yaml
+
+ DirConverter:
+ type: Directory
+ match: (?P<dir_name>.*)
+ records:
+ Project:
+ identifier: project_name
+ Experiment:
+ identifier: $dir_name
+ Project: $Project
+ ProjectGroup:
+ projects: +$Project
+
+
+This block will create two new Records:
+
+- A project with a constant identifier
+- An experiment with an identifier, derived from a regular expression and a reference to the new project.
+
+Furthermore a Record `ProjectGroup` will be edited (its initial definition is not given in the
+yaml block): The project that was just created will be added as a list element to the property
+`projects`.
+
+Let's formulate that using `create_records` (again, `dir_name` is constant here):
+
+.. code-block:: python
+
+ dir_name = "directory name"
+
+ record_def = {
+ "Project": {
+ "identifier": "project_name",
+ }
+ "Experiment": {
+ "identifier": dir_name,
+ "Project": "$Project",
+ }
+ "ProjectGroup": {
+ "projects": "+$Project",
+ }
+
+ }
+
+ keys_modified = create_records(values, records,
+ record_def)
diff --git a/src/doc/index.rst b/src/doc/index.rst
index f11d73b58a3216b1d735d6565650148c150ebb68..724bcc543dd1cf0b9af451c487b1b3aab7fa95ca 100644
--- a/src/doc/index.rst
+++ b/src/doc/index.rst
@@ -1,8 +1,23 @@
Crawler 2.0 Documentation
=========================
-Introduction
-------------
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+ :hidden:
+
+ Getting started<README_SETUP>
+ Concepts<concepts>
+ Converters<converters>
+ CFoods (Crawler Definitions)<cfood>
+ Macros<macros>
+ Tutorials<tutorials/index>
+ API documentation<_apidoc/modules>
+
+
+
+This is the documentation for the crawler (previously known as crawler 2.0) for CaosDB, ``caosdb-crawler``.
The crawler is the main date integration tool for CaosDB.
Its task is to automatically synchronize data found on file systems or in other
@@ -15,172 +30,15 @@ The hierarchical sturcture can be for example a file tree. However it can be
also something different like the contents of a json file or a file tree with
json files.
-Concepts
---------
-
-Structure Elements
-++++++++++++++++++
-
-This hierarchical structure is assumed to be consituted of a tree of
-StructureElements. The tree is created on the fly by so called Converters which
-are defined in a yaml file. The tree of StructureElements is a model
-of the existing data (For example could a tree of Python file objects
-(StructureElements) represent a file tree that exists on some file server).
-
-Relevant sources in:
-src/structure_elements.py
-
-Converters
-++++++++++
-
-Converters treat StructureElements and thereby create the StructureElement that
-are the children of the treated StructureElement. Converters therefore create
-the above named tree. The definition of a Converter also contains what
-Converters shall be used to treat the generated child-StructureElements. The
-definition is there a tree itself. (Question: Should there be global Converters
-that are always checked when treating a StructureElement? Should Converters be
-associated with generated child-StructureElements? Currently, all children are
-created and checked against all Converters. It could be that one would like to
-check file-StructureElements against one set of Converters and
-directory-StructureElements against another)
-
-Each StructureElement in the tree has a set of data values, i.e a dictionary of
-key value pairs.
-Some of those values are set due to the kind of StructureElement. For example,
-a file could have the file name as such a key value pair: 'filename': <sth>.
-Converters may define additional functions that create further values. For
-example, a regular expresion could be used to get a date from a file name.
-
-
-
-
-A converter is defined via a yml file or part of it. The definition states
-what kind of StructureElement it treats (typically one).
-Also, it defines how children of the current StructureElement are
-created and what Converters shall be used to treat those.
-
-The yaml definition looks like the following:
-
-TODO: outdated, see cfood-schema.yml
-
-converter-name:
- type: <StructureElement Type>
- match: ".*"
- records:
- Experiment1:
- parents:
- - Experiment
- - Blablabla
- date: $DATUM
- <...>
- Experiment2:
- parents:
- - Experiment
- valuegenerators:
- datepattern:
- <...>
- childrengenerators:
- create_children_from_directory:
- sort-by-date: true
- subtree:
-
-
-records:
- Measurement: <- wird automatisch ein value im valueStore
- run_number: 25
- Experiment1:
- Measurement: +Measurement <- Element in List (list is cleared before run)
- *Measurement <- Multi Property (properties are removed before run)
- Measurement <- Overwrite
-
-UPDATE-Stage prüft ob es z.B. Gleichheit zwischen Listen gibt (die dadurch definiert sein
-kann, dass alle Elemente vorhanden, aber nicht zwingend in der richtigen Reihenfolge sind)
-evtl. brauchen wir das nicht, weil crawler eh schon deterministisch ist.
-
-The converter-name is a description of what it represents (e.g.
-'experiment-folder') and is used as identifier.
-
-The type restricts what kind of StructureElements are treated.
-The match is by default a regular expression, that is matche against the
-name of StructureElements. Discussion: StructureElements might not have a
-name (e.g. a dict) or should a name be created artificially if necessary
-(e.g. "root-dict")? It might make sense to allow keywords like "always" and
-other kinds of checks. For example a dictionary could be checked against a
-json-schema definition.
-
-recordtypes is a list of definitions that define the semantic structure
-(see details below).
-
-valuegenerators allow to provide additional functionality that creates
-data values in addition to the ones given by default via the
-StructureElement. This can be for example a match group of a regular
-expression applied to the filename.
-It should be possible to access the values of parent nodes. For example,
-the name of a parent node could be accessed with $converter-name.name.
-Discussion: This can introduce conflicts, if the key <converver-name>
-already exists. An alternative would be to identify those lookups. E.g.
-$$converter-name.name (2x$).
-
-childrengenerators denotes how StructureElements shall be created that are
-children of the current one.
-
-subtree contains a list of Converter defnitions that look like the one
-described here.
-
-those keywords should be allowed but not required. I.e. if no
-valuegenerators shall be defined, the keyword may be omitted.
-
-
-Relevant sources in:
-src/converters.py
-
-Identifiables
-+++++++++++++
-
-Relevant sources in:
-src/identifiable_adapters.py
-
-The Crawler
-+++++++++++
-
-The crawler can be considered the main program doing the synchronization in basically two steps:
-1. Based on a yaml-specification scan the file system (or other sources) and create a set
- of CaosDB Entities that are supposed to be inserted or updated in a CaosDB instance.
-2. Compare the current state of the CaosDB instance with the set of CaosDB Entities created in
- step 1, taking into account the :ref:`registered identifiables<Identifiables>`. Insert or
- update entites accordingly.
-
-Relevant sources in:
-src/crawl.py
-
-
-
-Special Cases
-=============
-
-Variable Precedence
-++++++++++++
-
-Let's assume the following situation
-
-.. code-block:: yaml
- description:
- type: DictTextElement
- match_value: (?P<description>.*)
- match_name: description
+This documentation helps you to :doc:`get started<README_SETUP>`, explains the most important
+:doc:`concepts<concepts>` and offers a range of :doc:`tutorials<tutorials/index>`.
-Making use of the $description variable could refer to two different variables created here:
-1. The structure element path.
-2. The value of the matched expression.
+Indices and tables
+==================
-The matched expression does take precedence over the structure element path and shadows it.
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
-Make sure, that if you want to be able to use the structure element path, to give unique names
-to the variables like:
-.. code-block:: yaml
- description_text_block:
- type: DictTextElement
- match_value: (?P<description>.*)
- match_name: description
diff --git a/src/doc/macros.rst b/src/doc/macros.rst
new file mode 100644
index 0000000000000000000000000000000000000000..d3a3e9b9634a4e1d72228dd46692a824e1d5acfd
--- /dev/null
+++ b/src/doc/macros.rst
@@ -0,0 +1,233 @@
+Macros
+------
+
+Macros highly facilitate the writing of complex :doc:`CFoods<cfood>`. Consider the following prevalent example:
+
+.. _example_files:
+.. code-block:: yaml
+
+ ExperimentalData:
+ type: Directory
+ match: ExperimentalData
+ subtree:
+ README:
+ type: SimpleFile
+ match: ^README.md$
+ records:
+ ReadmeFile:
+ parents:
+ - MarkdownFile
+ role: File
+ path: $README
+ file: $README
+
+This example just inserts a file called ``README.md`` contained in Folder ``ExpreimentalData/`` into CaosDB, assigns the parent (RecordType) ``MarkdownFile`` and allows for later referencing this entity within the cfood. As file objects are created in the cfood specification using the ``records`` section with the special role ``File``, defining and using many files can become very cumbersome and make the cfood file difficult to read.
+
+The same version using cfood macros could be defined as follows:
+
+.. _example_files_2:
+.. code-block:: yaml
+
+ ---
+ metadata:
+ macros:
+ - !defmacro
+ name: MarkdownFile
+ params:
+ name: null
+ filename: null
+ definition:
+ ${name}_filename:
+ type: SimpleFile
+ match: $filename
+ records:
+ $name:
+ parents:
+ - MarkdownFile
+ role: File
+ path: ${name}_filename
+ file: ${name}_filename
+ ---
+ ExperimentalData:
+ type: Directory
+ match: ExperimentalData
+ subtree: !macro
+ MarkdownFile:
+ - name: README
+ filename: ^README.md$
+
+The "MarkdownFile" key and its value will be replaced by everything that is
+given below "definition" in the Macro.
+
+The expanded version of `ExperimentalData` will look like:
+
+.. _example_files_2_expanded:
+.. code-block:: yaml
+
+ ExperimentalData:
+ match: ExperimentalData
+ subtree:
+ README_filename:
+ match: ^README.md$
+ records:
+ README:
+ file: README_filename
+ parents:
+ - MarkdownFile
+ path: README_filename
+ role: File
+ type: SimpleFile
+ type: Directory
+
+This :ref:`example<_example_files_2>` can also be found in the macro unit tests (see :func:`unittests.test_macros.test_documentation_example_2`).
+
+
+Complex Example
+===============
+
+The following, more complex example, demonstrates the use
+of macro variable substitutions that generate crawler variable substitutions:
+
+- `$$$nodename` will lead to a macro variable substitution of variable `$nodename` during macro expansion.
+- `$$` will be turned into `$`
+- So in the crawler cfood, the string will appear as `$value` if variable `nodename` would be set to `value` when using the macro.
+
+
+.. _example_1:
+.. code-block:: yaml
+
+ macros:
+ - !defmacro
+ name: SimulationDatasetFile
+ params:
+ match: null
+ recordtype: null
+ nodename: null
+ definition:
+ $nodename:
+ match: $match
+ type: SimpleFile
+ records:
+ File:
+ parents:
+ - $recordtype
+ role: File
+ path: $$$nodename
+ file: $$$nodename
+ Simulation:
+ $recordtype: +$File
+
+The expanded version of :ref:`example<_example_1>` can be seen in :ref:`example<_example_1_expanded>`.
+
+
+.. _example_1_expanded:
+.. code-block:: yaml
+
+ SimulationData:
+ match: SimulationData
+ subtree:
+ Dataset:
+ match: .*
+ records:
+ File:
+ file: $Dataset
+ parents:
+ - DatasetFile
+ path: $Dataset
+ role: File
+ Simulation:
+ DatasetFile: +$File
+ type: SimpleFile
+ type: Directory
+
+This :ref:`example<_example_1>` can also be found in the macro unit tests (see :func:`unittests.test_macros.test_documentation_example_1`).
+
+
+
+Using Macros Multiple Times
+===========================
+
+To use the same macro multiple times in the same yaml node, lists can be used:
+
+.. _example_multiple:
+.. code-block:: yaml
+
+ ---
+ metadata:
+ macros:
+ - !defmacro
+ name: test_twice
+ params:
+ macro_name: default_name
+ a: 4
+ definition:
+ $macro_name:
+ something:
+ a: $a
+ ---
+ extroot: !macro
+ test_twice:
+ - macro_name: once # <- This is the first replacement of the macro
+ - macro_name: twice # <- This is the second one, with different arguments
+ a: 5
+ - {} # <- This is the third one, just using default arguments
+
+
+This :ref:`example<_example_multiple>` is taken from the macro unit tests (see :func:`unittests.test_macros.test_use_macro_twice`).
+
+The example will be expanded to:
+
+.. _example_multiple_expanded:
+.. code-block:: yaml
+
+ extroot:
+ default_name:
+ something:
+ a: '4'
+ once:
+ something:
+ a: '4'
+ twice:
+ something:
+ a: '5'
+
+
+
+
+Limitation
+----------
+
+Currently it is not possible to use the same macro twice in the same yaml node, but in different
+positions. Consider:
+
+.. _example_multiple_limitation:
+.. code-block:: yaml
+
+ ---
+ metadata:
+ macros:
+ - !defmacro
+ name: test_twice
+ params:
+ macro_name: default_name
+ a: 4
+ definition:
+ $macro_name:
+ something:
+ a: $a
+ ---
+ extroot: !macro
+ test_twice:
+ - macro_name: once # <- This is the first replacement of the macro
+
+ Other_node:
+ type: test
+
+ test_twice: # This is NOT possible as each
+ # dictionary element can only appear once in a yaml node.
+ - macro_name: twice # <- This is the second one, with different arguments
+ a: 5
+ - {} # <- This is the third one, just using default arguments
+
+However, this should not be a real limitation, as the crawler is designed in a way,
+that the order of the nodes in the same level should not matter.
diff --git a/src/doc/tutorials/index.rst b/src/doc/tutorials/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..1652515968c3b0025a2916604632d57c042f119b
--- /dev/null
+++ b/src/doc/tutorials/index.rst
@@ -0,0 +1,2 @@
+Tutorials
++++++++++
diff --git a/synchronize.md b/synchronize.md
index 7d240095a770a33d55370d9e48a1ab89b60c02dd..30cf342cd4c4342ab43ed05799faf8b89abce71a 100644
--- a/synchronize.md
+++ b/synchronize.md
@@ -28,7 +28,7 @@ b) identifiable does not exist: check the to_be_inserted dict(key is a hash comp
Maybe keep another dict that tracks what Record objects are in the to_be_updated dict (id(rec) as key?)
-After treating leave Records, Records that could not be checked before can be checked: Either referenced Records now have an ID or they are in the to_be_inserted dict such that it is clear that the identifiable at hand does not exist in the server.
+After treating leaf Records, Records that could not be checked before can be checked: Either referenced Records now have an ID or they are in the to_be_inserted dict such that it is clear that the identifiable at hand does not exist in the server.
This way, the whole structure can be resolved except if there are circular dependencies: Those can be added fully to the to_be_inserted dict. (???)
diff --git a/unittests/cfoods_scalar.yml b/unittests/cfoods_scalar.yml
new file mode 100644
index 0000000000000000000000000000000000000000..d0a728c35c27e331114cc5c18ebcfd1aa0905e31
--- /dev/null
+++ b/unittests/cfoods_scalar.yml
@@ -0,0 +1,14 @@
+# This is a test cfood for:
+# https://gitlab.com/caosdb/caosdb-crawler/-/issues/9
+
+Data: # name of the converter
+ type: Directory
+ match: (.*)
+ subtree:
+ DataAnalysis: # name of the converter
+ type: Directory
+ match: DataAnalysis
+ records:
+ RecordThatGetsParentsLater:
+ someId: 23 # <- this scalar causes problems
+
diff --git a/unittests/simulated_server_data.py b/unittests/simulated_server_data.py
index 6a523dbb06397b380510f72502a76cc6bda5f06c..dd0c6b4e8693d64c9d96cafc5db2f447613daa1b 100644
--- a/unittests/simulated_server_data.py
+++ b/unittests/simulated_server_data.py
@@ -1,20 +1,20 @@
import caosdb as db
-data_model = {"person": (db.RecordType(id=10001, name="Person")
+data_model = {"person": (db.RecordType(id=259, name="Person")
.add_property(name="first_name")
.add_property(name="last_name")),
- "measurement": (db.RecordType(id=10002, name="Measurement")
+ "measurement": (db.RecordType(id=278, name="Measurement")
.add_property(name="identifier")
.add_property(name="date")
.add_property(name="project")),
- "project": (db.RecordType(id=10003, name="Project")
+ "project": (db.RecordType(id=250, name="Project")
.add_property(name="date")
.add_property(name="identifier")),
- "first_name": db.Property(name="first_name", datatype=db.TEXT, id=10004),
- "responsible": db.Property(name="responsible", datatype="Person", id=10005),
- "last_name": db.Property(name="last_name", datatype=db.TEXT, id=10006),
- "identifier": db.Property(name="identifier", datatype=db.TEXT, id=10007),
- "date": db.Property(name="date", datatype=db.DATETIME, id=10008),
+ "first_name": db.Property(name="first_name", datatype=db.TEXT, id=261),
+ "responsible": db.Property(name="responsible", datatype="Person", id=249),
+ "last_name": db.Property(name="last_name", datatype=db.TEXT, id=262),
+ "identifier": db.Property(name="identifier", datatype=db.TEXT, id=248),
+ "date": db.Property(name="date", datatype=db.DATETIME, id=247),
}
existing_data = {
}
diff --git a/unittests/test_converters.py b/unittests/test_converters.py
index 7a6987b8b3fae9d747f2440de202df5d10a34cc0..802483c1d1eaf7f63096591ac7df7362f25f599a 100644
--- a/unittests/test_converters.py
+++ b/unittests/test_converters.py
@@ -23,26 +23,26 @@
"""
test the converters module
"""
-
-from caoscrawler.converters import Converter
+import importlib
+import os
+import pytest
+import yaml
+
+from caoscrawler.converters import (Converter, ConverterValidationError,
+ DictConverter, DirectoryConverter,
+ handle_value, MarkdownFileConverter,
+ JSONFileConverter)
+from caoscrawler.converters import _AbstractDictElementConverter
+from caoscrawler.crawl import Crawler
from caoscrawler.stores import GeneralStore
-from caoscrawler.converters import (ConverterValidationError,
- MarkdownFileConverter, JSONFileConverter,
- DictConverter)
-from caoscrawler.structure_elements import Directory
from caoscrawler.structure_elements import (File, DictTextElement,
DictListElement, DictElement,
DictBooleanElement, DictDictElement,
- DictIntegerElement, DictFloatElement)
-
-from caoscrawler.converters import handle_value
+ DictIntegerElement,
+ DictFloatElement, Directory)
from test_tool import rfp
-import pytest
-import os
-import importlib
-
@pytest.fixture
def converter_registry():
@@ -272,3 +272,135 @@ def test_variable_replacement():
assert handle_value(["a", "b"], values) == (["a", "b"], "single")
assert handle_value(["$a", "$b"], values) == (["4", "68"], "single")
+
+
+def test_filter_children_of_directory(converter_registry):
+ """Verify that children (i.e., files) in a directory are filtered or sorted
+ correctly.
+
+ """
+ test_dir = Directory("examples_filter_children", rfp(
+ "test_directories", "examples_filter_children"))
+
+ dc = DirectoryConverter(
+ definition={
+ "match": "(.*)",
+ "filter": {
+ "expr": "test_(?P<date>[0-9]{4,4}-[0-9]{2,2}-[0-9]{2,2}).json",
+ "group": "date",
+ "rule": "only_max"
+ }
+ },
+ name="TestOnlyMaxDirectoryConverter",
+ converter_registry=converter_registry
+ )
+
+ m = dc.match(test_dir)
+ assert m is not None
+
+ # This should only contain the youngest json and the csv that doesn't match
+ # the above filter expression.
+ children = dc.create_children(None, test_dir)
+ assert len(children) == 2
+ assert children[0].__class__ == File
+ assert children[0].name == "test_2022-02-02.json"
+ assert children[1].__class__ == File
+ assert children[1].name == "some_other_file.csv"
+
+ dc = DirectoryConverter(
+ definition={
+ "match": "(.*)",
+ "filter": {
+ "expr": "test_(?P<date>[0-9]{4,4}-[0-9]{2,2}-[0-9]{2,2}).json",
+ "group": "date",
+ "rule": "only_min"
+ }
+ },
+ name="TestOnlyMinDirectoryConverter",
+ converter_registry=converter_registry
+ )
+
+ m = dc.match(test_dir)
+ assert m is not None
+
+ # This should only contain the youngest json and the csv that doesn't match
+ # the above filter expression.
+ children = dc.create_children(None, test_dir)
+ assert len(children) == 2
+ assert children[0].__class__ == File
+ assert children[0].name == "test_2022-01-01.json"
+ assert children[1].__class__ == File
+ assert children[1].name == "some_other_file.csv"
+
+ dc = DirectoryConverter(
+ definition={
+ "match": "(.*)",
+ "filter": {
+ "expr": "test_(?P<date>[0-9]{4,4}-[0-9]{2,2}-[0-9]{2,2}).json",
+ "group": "date",
+ "rule": "does_not_exist"
+ }
+ },
+ name="TestBrokenDirectoryConverter",
+ converter_registry=converter_registry
+ )
+
+ m = dc.match(test_dir)
+ assert m is not None
+
+ with pytest.raises(RuntimeError):
+ children = dc.create_children(None, test_dir)
+
+
+def test_validate_custom_converters():
+ one_doc_yaml = """
+Converters:
+ MyNewType:
+ converter: MyNewTypeConverter
+ package: some_package.my_converters
+MyElement:
+ type: MyNewType
+ match: something
+ """
+ crawler1 = Crawler()
+ one_doc_definitions = crawler1._load_definition_from_yaml_dict(
+ [yaml.load(one_doc_yaml, Loader=yaml.SafeLoader)])
+ assert "MyElement" in one_doc_definitions
+ assert one_doc_definitions["MyElement"]["type"] == "MyNewType"
+
+ # this has to be equivalent
+ two_doc_yaml = """
+---
+metadata:
+ Converters:
+ MyNewType:
+ converter: MyNewTypeConverter
+ package: some_package.my_converters
+---
+MyElement:
+ type: MyNewType
+ match: something
+ """
+ crawler2 = Crawler()
+ two_doc_definitions = crawler2._load_definition_from_yaml_dict(
+ list(yaml.safe_load_all(two_doc_yaml)))
+ assert "MyElement" in two_doc_definitions
+ assert two_doc_definitions["MyElement"]["type"] == one_doc_definitions["MyElement"]["type"]
+
+
+def test_abstract_dict_element_converter():
+ definition = yaml.safe_load("""
+match_name: text
+match_value: .*begin(?P<text>.*)end
+ """)
+ converter = _AbstractDictElementConverter(
+ definition, "test_converter",
+ None # This is possible when "subtree" is not used
+ )
+ element = DictTextElement("text", """
+begin
+bla
+end""")
+ val = converter.match(element)
+ assert val is not None
+ assert val["text"] == "\nbla\n"
diff --git a/unittests/test_directories/examples_article/SimulationData/2020_climate-model-predict/2020-02-01/README.md b/unittests/test_directories/examples_article/SimulationData/2020_climate-model-predict/2020-02-01/README.md
index 0e7726d941d86ca357149f28ef98311b33808f11..0c91d6b5f7601334b84a77328b888d227e779a93 100644
--- a/unittests/test_directories/examples_article/SimulationData/2020_climate-model-predict/2020-02-01/README.md
+++ b/unittests/test_directories/examples_article/SimulationData/2020_climate-model-predict/2020-02-01/README.md
@@ -1,6 +1,6 @@
---
responsible: AuthorE
-description: >
+description: >-
Code for fitting the predictive model to the
training data and for predicting the average
annual temperature for all measurement stations
diff --git a/unittests/test_directories/examples_filter_children/some_other_file.csv b/unittests/test_directories/examples_filter_children/some_other_file.csv
new file mode 100644
index 0000000000000000000000000000000000000000..bc715fe81656397eae98aa4b04f9af2e3fdd9e43
--- /dev/null
+++ b/unittests/test_directories/examples_filter_children/some_other_file.csv
@@ -0,0 +1,2 @@
+some,other,data
+1,2,3
diff --git a/unittests/test_directories/examples_filter_children/test_2022-01-01.json b/unittests/test_directories/examples_filter_children/test_2022-01-01.json
new file mode 100644
index 0000000000000000000000000000000000000000..8de42f29d2eed374a0aba356c7fce2daa3e08e49
--- /dev/null
+++ b/unittests/test_directories/examples_filter_children/test_2022-01-01.json
@@ -0,0 +1,3 @@
+{
+ "key": "value",
+}
diff --git a/unittests/test_directories/examples_filter_children/test_2022-01-02.json b/unittests/test_directories/examples_filter_children/test_2022-01-02.json
new file mode 100644
index 0000000000000000000000000000000000000000..8de42f29d2eed374a0aba356c7fce2daa3e08e49
--- /dev/null
+++ b/unittests/test_directories/examples_filter_children/test_2022-01-02.json
@@ -0,0 +1,3 @@
+{
+ "key": "value",
+}
diff --git a/unittests/test_directories/examples_filter_children/test_2022-02-02.json b/unittests/test_directories/examples_filter_children/test_2022-02-02.json
new file mode 100644
index 0000000000000000000000000000000000000000..8de42f29d2eed374a0aba356c7fce2daa3e08e49
--- /dev/null
+++ b/unittests/test_directories/examples_filter_children/test_2022-02-02.json
@@ -0,0 +1,3 @@
+{
+ "key": "value",
+}
diff --git a/unittests/test_directories/examples_json/testjson.json b/unittests/test_directories/examples_json/testjson.json
index b893b608a6a2119c5c3252cd9cff4c4100f404da..d37ea2defc21d767e4e13ad3b39d6682b3c452ef 100644
--- a/unittests/test_directories/examples_json/testjson.json
+++ b/unittests/test_directories/examples_json/testjson.json
@@ -6,6 +6,7 @@
{
"firstname": "Miri",
"lastname": "Mueller",
+ "other": null,
"email": "miri.mueller@science.de"
},
{
diff --git a/unittests/test_identified_cache.py b/unittests/test_identified_cache.py
index 33add97d4309d87705144ec5331366d0bcd05541..aeb5f0afcd9fc9912579bf5320bbb36b52899f07 100644
--- a/unittests/test_identified_cache.py
+++ b/unittests/test_identified_cache.py
@@ -53,6 +53,10 @@ def test_create_hash():
db.Record("A")
.add_parent("B")
.add_property('a', [db.Record(id=12), 11])) == "P<B>N<A>a:[12, 11]")
+ assert (_create_hashable_string(
+ db.Record().add_parent("B").add_property('a', [db.Record()]))
+ != _create_hashable_string(
+ db.Record().add_parent("B").add_property('a', [db.Record()])))
def test_IdentifiedCache():
diff --git a/unittests/test_issues.py b/unittests/test_issues.py
new file mode 100644
index 0000000000000000000000000000000000000000..6e77b0c7f26f4b2970203cfc4b8cc786fe24121b
--- /dev/null
+++ b/unittests/test_issues.py
@@ -0,0 +1,70 @@
+#!/usr/bin/env python3
+# encoding: utf-8
+#
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2022 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2022 Florian Spreckelsen <f.spreckelsen@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/>.
+#
+
+from pytest import mark
+
+from caoscrawler.crawl import Crawler
+from caoscrawler.structure_elements import Dict
+from test_tool import rfp
+
+
+@mark.xfail(
+ reason="Wait until value conversion in dicts is fixed, see "
+ "https://gitlab.com/caosdb/caosdb-crawler/-/issues/10."
+)
+def test_issue_10():
+ """Test integer-to-float conversion in dictionaries"""
+ crawler_definition = {
+ "DictTest": {
+ "type": "Dict",
+ "match": "(.*)",
+ "records": {
+ "TestRec": {}
+ },
+ "subtree": {
+ "float_element": {
+ "type": "DictFloatElement",
+ "match_name": "float_value",
+ "match_value": "(?P<float_value>.*)",
+ "records": {
+ "TestRec": {
+ "float_prop": "$float_value"
+ }
+ }
+ }
+ }
+ }
+ }
+
+ crawler = Crawler(debug=True)
+ converter_registry = crawler.load_converters(crawler_definition)
+
+ test_dict = {
+ "float_value": 4
+ }
+
+ records = crawler.start_crawling(
+ Dict("TestDict", test_dict), crawler_definition, converter_registry)
+ assert len(records) == 1
+ assert records[0].parents[0].name == "TestRec"
+ assert records[0].get_property("float_prop") is not None
+ assert float(records[0].get_property("float_prop").value) == 4.0
diff --git a/unittests/test_macros.py b/unittests/test_macros.py
new file mode 100644
index 0000000000000000000000000000000000000000..2934d7902a2f7be6925491f73412b0350265145d
--- /dev/null
+++ b/unittests/test_macros.py
@@ -0,0 +1,411 @@
+#!/usr/bin/env python3
+# encoding: utf-8
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2022 Alexander Schlemmer
+#
+# 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
+#
+
+from caoscrawler.macros import defmacro_constructor, macro_constructor
+from caoscrawler.macros.macro_yaml_object import macro_store
+from caoscrawler.crawl import Crawler
+
+from tempfile import NamedTemporaryFile
+
+import yaml
+import pytest
+
+
+@pytest.fixture
+def register_macros():
+ yaml.SafeLoader.add_constructor("!defmacro", defmacro_constructor)
+ yaml.SafeLoader.add_constructor("!macro", macro_constructor)
+
+
+@pytest.fixture
+def macro_store_reset():
+ macro_store.clear()
+
+
+def _temp_file_load(txt: str):
+ """
+ Create a temporary file with txt and load the crawler
+ definition using load_definition from Crawler.
+ """
+ definition = None
+ with NamedTemporaryFile() as f:
+ f.write(txt.encode())
+ f.flush()
+ c = Crawler()
+ definition = c.load_definition(f.name)
+ return definition
+
+
+def test_macros(register_macros, macro_store_reset):
+ dat = yaml.load("""
+defs:
+- !defmacro
+ name: test
+ params:
+ a: 2
+ b: bla
+ c: $variable
+ definition:
+ expanded_$b:
+ blubb: ok$a
+ $b: $c
+
+testnode:
+ obl: !macro
+ test:
+ a: 4
+ b: yea
+""", Loader=yaml.SafeLoader)
+ assert dat["testnode"]["obl"]["expanded_yea"]["blubb"] == "ok4"
+ assert dat["testnode"]["obl"]["expanded_yea"]["yea"] == "$variable"
+ assert "expanded_bla" not in dat["testnode"]["obl"]
+ assert "bla" not in dat["testnode"]["obl"]["expanded_yea"]
+
+
+def test_macro_list_replacment(register_macros, macro_store_reset):
+ dat = yaml.load("""
+defs:
+- !defmacro
+ name: test
+ params:
+ a: 2
+ b: bla
+ c: $variable
+ definition:
+ expanded_$b:
+ blubb:
+ - ok$a
+ - $b: $c
+
+testnode:
+ obl: !macro
+ test:
+ a: 4
+ b: yea
+""", Loader=yaml.SafeLoader)
+ assert isinstance(dat["testnode"]["obl"]["expanded_yea"]["blubb"], list)
+ assert len(dat["testnode"]["obl"]["expanded_yea"]["blubb"]) == 2
+ assert dat["testnode"]["obl"]["expanded_yea"]["blubb"][0] == "ok4"
+ assert dat["testnode"]["obl"]["expanded_yea"]["blubb"][1]["yea"] == "$variable"
+
+
+def test_multi_macros(register_macros, macro_store_reset):
+ dat = yaml.load("""
+defs:
+- !defmacro
+ name: test_one
+ params: {}
+ definition:
+ replaced1: ok
+- !defmacro
+ name: test_two
+ params: {}
+ definition:
+ replaced2: ok
+ replaced3: ok
+
+testnode:
+ obl: !macro
+ test_one:
+ test_two:
+""", Loader=yaml.SafeLoader)
+ assert dat["testnode"]["obl"]["replaced1"] == "ok"
+ assert dat["testnode"]["obl"]["replaced2"] == "ok"
+ assert dat["testnode"]["obl"]["replaced3"] == "ok"
+
+
+def test_multi_macros_toplevel(register_macros, macro_store_reset):
+ """
+ See: https://gitlab.indiscale.com/caosdb/src/caosdb-crawler/-/issues/23
+ """
+ dat_loader = list(yaml.safe_load_all("""
+---
+metadata:
+ macros:
+ - !defmacro
+ name: test_one
+ params: {}
+ definition:
+ replaced1: ok
+ - !defmacro
+ name: test_two
+ params: {}
+ definition:
+ replaced2: ok
+ replaced3: ok
+---
+testnode: !macro
+ test_one:
+ test_two:
+"""))
+ assert len(dat_loader) == 2
+ dat = dat_loader[1]
+ assert dat["testnode"]["replaced1"] == "ok"
+ assert dat["testnode"]["replaced2"] == "ok"
+ assert dat["testnode"]["replaced3"] == "ok"
+
+
+def test_load_definition(register_macros, macro_store_reset):
+ txt = """
+extroot:
+ type: Directory
+ match: extroot
+ subtree:
+ SimulationData:
+ type: Directory
+ match: SimulationData
+ """
+ # Check whether simple cfoods can be loaded:
+ cfood = _temp_file_load(txt)
+ assert cfood["extroot"]["subtree"]["SimulationData"]["match"] == "SimulationData"
+
+ cfood = _temp_file_load("""
+---
+metadata:
+ macros:
+ - !defmacro
+ name: test_one
+ params: {}
+ definition:
+ replaced1: ok
+ - !defmacro
+ name: test_two
+ params:
+ match_name: null
+ definition:
+ type: Directory
+ match: $match_name
+---
+extroot:
+ type: Directory
+ match: extroot
+ subtree:
+ SimulationData:
+ type: Directory
+ match: SimulationData
+extroot2: !macro # test top level macro
+ test_one:
+extroot3:
+ subtree:
+ SimulationData: !macro
+ test_two:
+ match_name: SimulationData
+ """)
+ assert cfood["extroot"]["subtree"]["SimulationData"]["match"] == "SimulationData"
+ assert cfood["extroot2"]["replaced1"] == "ok"
+ assert cfood["extroot3"]["subtree"]["SimulationData"]["match"] == "SimulationData"
+
+
+@pytest.mark.xfail
+def test_replace_arbitrary_objects(register_macros, macro_store_reset):
+ """
+ See: https://gitlab.indiscale.com/caosdb/src/caosdb-crawler/-/issues/24
+ """
+ dat = yaml.load("""
+defs:
+- !defmacro
+ name: test
+ params:
+ b: 25
+ testvar_list:
+ - a
+ - $b
+ testvar_dict:
+ t1: a
+ t2: $b
+ definition:
+ replaced1:
+ $b: ok
+ c: $testvar_dict
+ d: $testvar_list
+
+testnode:
+ obl: !macro
+ test:
+""", Loader=yaml.SafeLoader)
+ print(yaml.dump(dat))
+ assert dat["testnode"]["obl"]["replaced1"]["c"]["t1"] == "a"
+ assert dat["testnode"]["obl"]["replaced1"]["c"]["t2"] == "25"
+ assert dat["testnode"]["obl"]["replaced1"]["d"][0] == "a"
+ assert dat["testnode"]["obl"]["replaced1"]["d"][1] == "25"
+
+
+def test_circular_macro_definition(register_macros, macro_store_reset):
+ """Test the (ab-)use of macros to create an infinite loop."""
+ cfood = _temp_file_load("""
+---
+metadata:
+ macros:
+ - !defmacro
+ name: test_one
+ params: {}
+ definition: !macro
+ test_two:
+ - !defmacro
+ name: test_two
+ params: {}
+ definition: !macro
+ test_one:
+ - !defmacro
+ name: test_three
+ params: {}
+ definition: !macro
+ test_two:
+ - !defmacro
+ name: test_four
+ params: {}
+ definition: !macro
+ test_four:
+---
+extroot: !macro
+ test_one:
+extroot2: !macro
+ test_three:
+extroot3: !macro
+ test_four:
+ """)
+ # macros in macros can be used, but there are no circles; they stop at the first one.
+ assert "test_one" not in cfood["extroot"]
+ assert cfood["extroot"]["test_two"] is None
+ assert "test_three" not in cfood["extroot2"]
+ assert "test_one" not in cfood["extroot2"]
+ assert cfood["extroot2"]["test_two"] is None
+ # No recursion
+ assert cfood["extroot3"]["test_four"] is None
+
+
+def test_use_macro_twice():
+ """Test that the same macro can be used twice with different parameters in
+ the same CFood element if the name depends on the parameters.
+
+ """
+
+ cfood = _temp_file_load("""
+---
+metadata:
+ macros:
+ - !defmacro
+ name: test_twice
+ params:
+ macro_name: default_name
+ a: 4
+ definition:
+ $macro_name:
+ something:
+ a: $a
+---
+extroot: !macro
+ test_twice:
+ - macro_name: once
+ - macro_name: twice
+ a: 5
+ - {}
+ """)
+ for name in ["once", "twice", "default_name"]:
+ assert name in cfood["extroot"]
+ assert cfood["extroot"]["once"]["something"]["a"] == "4"
+ assert cfood["extroot"]["twice"]["something"]["a"] == "5"
+ assert cfood["extroot"]["default_name"]["something"]["a"] == "4"
+
+ # Code sample to generate the expanded macro:
+ # with open("expanded_test_macro.yaml", "w") as f:
+ # f.write(yaml.dump(cfood))
+
+
+def test_documentation_example_2():
+
+ cfood = _temp_file_load("""
+---
+metadata:
+ macros:
+ - !defmacro
+ name: MarkdownFile
+ params:
+ name: null
+ filename: null
+ definition:
+ ${name}_filename:
+ type: SimpleFile
+ match: $filename
+ records:
+ $name:
+ parents:
+ - MarkdownFile
+ role: File
+ path: ${name}_filename
+ file: ${name}_filename
+---
+ExperimentalData:
+ type: Directory
+ match: ExperimentalData
+ subtree: !macro
+ MarkdownFile:
+ - name: README
+ filename: ^README.md$
+ """)
+
+ # Code sample to generate the expanded macro:
+ # with open("expanded_test_macro.yaml", "w") as f:
+ # f.write(yaml.dump(cfood))
+
+
+def test_documentation_example_1():
+
+ cfood = _temp_file_load("""
+---
+metadata:
+ macros:
+ - !defmacro
+ name: SimulationDatasetFile
+ params:
+ match: null
+ recordtype: null
+ nodename: null
+ definition:
+ $nodename:
+ match: $match
+ type: SimpleFile
+ records:
+ File:
+ parents:
+ - $recordtype
+ role: File
+ path: $$$nodename
+ file: $$$nodename
+ Simulation:
+ $recordtype: +$File
+---
+SimulationData:
+ type: Directory
+ match: SimulationData
+ subtree: !macro
+ SimulationDatasetFile:
+ - match: .*
+ recordtype: DatasetFile
+ nodename: Dataset
+ """)
+
+ # Code sample to generate the expanded macro:
+ # with open("expanded_test_macro.yaml", "w") as f:
+ # f.write(yaml.dump(cfood))
diff --git a/unittests/test_scalars_cfood.py b/unittests/test_scalars_cfood.py
new file mode 100644
index 0000000000000000000000000000000000000000..1bf8f0b7d67f00f2018b5b68424d6b9cc17602eb
--- /dev/null
+++ b/unittests/test_scalars_cfood.py
@@ -0,0 +1,57 @@
+#!/bin/python
+# Tests for:
+# https://gitlab.com/caosdb/caosdb-crawler/-/issues/9
+# A. Schlemmer, 06/2021
+
+import pytest
+
+# The main function that is affected by this issue:
+from caoscrawler.converters import handle_value
+from caoscrawler.crawl import Crawler
+# We need the store for the above function
+from caoscrawler.stores import GeneralStore
+
+from test_tool import dircheckstr, rfp
+
+
+@pytest.fixture
+def crawler():
+ crawler = Crawler(debug=True)
+ crawler.crawl_directory(rfp("test_directories", "examples_article"),
+ rfp("cfoods_scalar.yml"))
+ return crawler
+
+
+def test_handle_value():
+ # Note that we will need this store only, if we also want to test variables substitution:
+ store = GeneralStore()
+
+ # This one should work:
+ assert handle_value("bla", store) == ("bla", "single")
+
+ # These failed:
+ assert handle_value(4, store) == (4, "single")
+ assert handle_value(4.2, store) == (4.2, "single")
+ assert handle_value(True, store) == (True, "single")
+
+ # List test:
+ assert handle_value([4, 3, 2], store) == ([4, 3, 2], "single")
+
+
+def test_record_structure_generation(crawler):
+ subd = crawler.debug_tree[dircheckstr("DataAnalysis")]
+ assert len(subd) == 2
+ # variables store on Data Analysis node of debug tree
+ assert len(subd[0]) == 3
+ assert "Data" in subd[0]
+ assert "DataAnalysis" in subd[0]
+ assert "RecordThatGetsParentsLater" in subd[0]
+
+ prop = subd[0]["RecordThatGetsParentsLater"].get_property("someId")
+ assert type(prop.value) == int
+ assert prop.value == 23
+
+ # record store on Data Analysis node of debug tree
+ assert len(subd[1]) == 1
+ prop2 = subd[1]["RecordThatGetsParentsLater"].get_property("someId")
+ assert prop == prop2
diff --git a/unittests/test_tool.py b/unittests/test_tool.py
index 59573756fe61ef697976e480dd1550cb0ead0998..0eef86b3a9f5ef6f64d9ccb9ce0102cd87208fa4 100755
--- a/unittests/test_tool.py
+++ b/unittests/test_tool.py
@@ -29,11 +29,19 @@ def rfp(*pathcomponents):
return join(dirname(__file__), *pathcomponents)
+ident = LocalStorageIdentifiableAdapter()
+ident.restore_state(rfp("records.xml"))
+full_data.update({el.name: el for el in ident._records if el.name is not None})
+full_data.update({el.id: el for el in ident._records if el.name is None})
+
+
def dircheckstr(*pathcomponents):
"""
Return the debug tree identifier for a given path.
"""
- return "caoscrawler.structure_elements.Directory: " + basename(join(*pathcomponents)) + ", " + rfp("test_directories", "examples_article", *pathcomponents)
+ return ("caoscrawler.structure_elements.Directory: " + basename(
+ join(*pathcomponents)) + ", " + rfp(
+ "test_directories", "examples_article", *pathcomponents))
@pytest.fixture
@@ -87,7 +95,7 @@ def test_record_structure_generation(crawler):
# The data analysis node creates one variable for the node itself:
assert subd[0]["DataAnalysis"] == "examples_article/DataAnalysis"
- assert subc[0]["DataAnalysis"] == False
+ assert subc[0]["DataAnalysis"] is False
subd = crawler.debug_tree[dircheckstr(
"DataAnalysis", "2020_climate-model-predict")]
@@ -107,9 +115,9 @@ def test_record_structure_generation(crawler):
assert subd[0]["Project"].__class__ == db.Record
assert subd[0]["DataAnalysis"] == "examples_article/DataAnalysis"
- assert subc[0]["DataAnalysis"] == True
+ assert subc[0]["DataAnalysis"] is True
assert subd[0]["project_dir"] == "examples_article/DataAnalysis/2020_climate-model-predict"
- assert subc[0]["project_dir"] == False
+ assert subc[0]["project_dir"] is False
# Check the copy flags for the first level in the hierarchy:
assert len(subc[0]) == 6
@@ -176,7 +184,7 @@ def test_record_structure_generation(crawler):
def test_ambigious_records(crawler, ident):
ident.get_records().clear()
- ident.get_records().extend(crawler.target_data)
+ ident.get_records().extend(crawler.crawled_data)
r = ident.get_records()
id_r0 = ident.get_identifiable(r[0])
with raises(RuntimeError, match=".*unambigiously.*"):
@@ -198,10 +206,11 @@ def test_crawler_update_list(crawler, ident):
) == 2
# The crawler contains lots of duplicates, because identifiables have not been resolved yet:
- assert len(ident.get_records()) != len(crawler.target_data)
+ assert len(ident.get_records()) != len(crawler.crawled_data)
# Check consistency:
- # Check whether identifiables retrieved from current identifiable store return the same results.
+ # Check whether identifiables retrieved from current identifiable store return
+ # the same results.
# take the first person in the list of records:
for r in ident.get_records():
@@ -287,8 +296,8 @@ def test_remove_unnecessary_updates():
# test trvial case
upl = [db.Record().add_parent("A")]
irs = [db.Record().add_parent("A")]
- Crawler.remove_unnecessary_updates(upl, irs)
- assert len(upl) == 0
+ updates = Crawler.remove_unnecessary_updates(upl, irs)
+ assert len(updates) == 0
# test property difference case
# TODO this should work right?
@@ -300,24 +309,24 @@ def test_remove_unnecessary_updates():
# test value difference case
upl = [db.Record().add_parent("A").add_property("a", 5)]
irs = [db.Record().add_parent("A").add_property("a")]
- Crawler.remove_unnecessary_updates(upl, irs)
- assert len(upl) == 1
+ updates = Crawler.remove_unnecessary_updates(upl, irs)
+ assert len(updates) == 1
upl = [db.Record().add_parent("A").add_property("a", 5)]
irs = [db.Record().add_parent("A").add_property("a", 5)]
- Crawler.remove_unnecessary_updates(upl, irs)
- assert len(upl) == 0
+ updates = Crawler.remove_unnecessary_updates(upl, irs)
+ assert len(updates) == 0
# test unit difference case
upl = [db.Record().add_parent("A").add_property("a", unit='cm')]
irs = [db.Record().add_parent("A").add_property("a")]
- Crawler.remove_unnecessary_updates(upl, irs)
- assert len(upl) == 1
+ updates = Crawler.remove_unnecessary_updates(upl, irs)
+ assert len(updates) == 1
# test None difference case
upl = [db.Record().add_parent("A").add_property("a")]
irs = [db.Record().add_parent("A").add_property("a", 5)]
- Crawler.remove_unnecessary_updates(upl, irs)
- assert len(upl) == 1
+ updates = Crawler.remove_unnecessary_updates(upl, irs)
+ assert len(updates) == 1
# Current status:
@@ -330,7 +339,7 @@ def test_identifiable_adapter_no_identifiable(crawler, ident):
insl, updl = crawler.synchronize()
assert len(updl) == 0
- pers = [r for r in crawler.target_data if r.parents[0].name == "Person"]
+ pers = [r for r in crawler.crawled_data if r.parents[0].name == "Person"]
# All persons are inserted, because they are not identifiable:
assert len(insl) == len(pers)
@@ -381,10 +390,10 @@ def test_split_into_inserts_and_updates_single(crawler_mocked_identifiable_retri
entlist = [db.Record(name="A").add_parent(
"C"), db.Record(name="B").add_parent("C")]
- assert crawler.get_identified_record_from_local_cache(entlist[0]) is None
- assert crawler.get_identified_record_from_local_cache(entlist[1]) is None
- assert crawler.can_be_checked_externally(entlist[0])
- assert crawler.can_be_checked_externally(entlist[1])
+ assert crawler.get_from_any_cache(entlist[0]) is None
+ assert crawler.get_from_any_cache(entlist[1]) is None
+ assert not crawler.has_reference_value_without_id(entlist[0])
+ assert not crawler.has_reference_value_without_id(entlist[1])
assert crawler.identifiableAdapter.retrieve_identified_record_for_record(
entlist[0]).id == 1111
assert crawler.identifiableAdapter.retrieve_identified_record_for_record(
@@ -489,45 +498,67 @@ def test_split_into_inserts_and_updates_with_copy_attr(crawler_mocked_identifiab
crawler.identifiableAdapter.retrieve_identified_record_for_record.assert_called()
-def test_all_references_are_existing_already(crawler):
+def test_has_missing_object_in_references(crawler):
# Simulate remote server content by using the names to identify records
# There are only two known Records with name A and B
crawler.identifiableAdapter.get_registered_identifiable = Mock(side_effect=partial(
- basic_retrieve_by_name_mock_up, known={"A": db.Record(name="A").add_parent("C"),
- "B": db.Record(name="B").add_parent("C")}))
-
- assert crawler.all_references_are_existing_already(
- db.Record().add_property('a', 123))
- assert crawler.all_references_are_existing_already(db.Record()
- .add_property('a', db.Record(id=123)))
- assert crawler.all_references_are_existing_already(db.Record()
- .add_property('a', 123)
- .add_property('b', db.Record(id=123)))
- assert not crawler.all_references_are_existing_already(db.Record()
- .add_property('a', 123)
- .add_property('b', db.Record(name="A")
- .add_parent("C")))
- a = db.Record(name="A").add_parent("C")
- crawler.add_identified_record_to_local_cache(a)
- assert crawler.all_references_are_existing_already(db.Record()
- .add_property('a', 123)
- .add_property('b', a))
+ basic_retrieve_by_name_mock_up, known={"C": db.Record(name="C").add_parent("RTC")
+ .add_property("d"),
+ "D": db.Record(name="D").add_parent("RTD")
+ .add_property("d").add_property("e"),
+ }))
+
+ # one reference with id -> check
+ assert not crawler.has_missing_object_in_references(db.Record(name="C")
+ .add_parent("RTC").add_property('d', 123))
+ # one ref with Entity with id -> check
+ assert not crawler.has_missing_object_in_references(db.Record(name="C")
+ .add_parent("RTC")
+ .add_property('d', db.Record(id=123)
+ .add_parent("C")))
+ # one ref with id one with Entity with id (mixed) -> check
+ assert not crawler.has_missing_object_in_references(db.Record(name="C").add_parent("RTD")
+ .add_property('d', 123)
+ .add_property('b', db.Record(id=123)
+ .add_parent("RTC")))
+ # entity to be referenced in the following
+ a = db.Record(name="C").add_parent("C").add_property("d", 12311)
+ # one ref with id one with Entity without id (but not identifying) -> fail
+ assert not crawler.has_missing_object_in_references(db.Record(name="C").add_parent("RTC")
+ .add_property('d', 123)
+ .add_property('e', a))
+
+ # one ref with id one with Entity without id (mixed) -> fail
+ assert not crawler.has_missing_object_in_references(db.Record(name="D").add_parent("RTD")
+ .add_property('d', 123)
+ .add_property('e', a))
+ crawler.add_to_remote_missing_cache(a)
+ # one ref with id one with Entity without id but in cache -> check
+ assert crawler.has_missing_object_in_references(db.Record(name="D").add_parent("RTD")
+ .add_property('d', 123)
+ .add_property('e', a))
# if this ever fails, the mock up may be removed
crawler.identifiableAdapter.get_registered_identifiable.assert_called()
-def test_can_be_checked_externally(crawler):
- assert crawler.can_be_checked_externally(
- db.Record().add_property('a', 123))
- assert crawler.can_be_checked_externally(db.Record()
- .add_property('a', db.Record(id=123)))
- assert crawler.can_be_checked_externally(db.Record()
- .add_property('a', 123)
- .add_property('b', db.Record(id=123)))
+def test_references_entities_without_ids(crawler, ident):
+ assert not crawler.has_reference_value_without_id(db.Record().add_parent("Person")
+ .add_property('last_name', 123)
+ .add_property('first_name', 123))
+ # id and rec with id
+ assert not crawler.has_reference_value_without_id(db.Record().add_parent("Person")
+ .add_property('first_name', 123)
+ .add_property('last_name', db.Record(id=123)))
+ # id and rec with id and one unneeded prop
+ assert crawler.has_reference_value_without_id(db.Record().add_parent("Person")
+ .add_property('first_name', 123)
+ .add_property('stuff', db.Record())
+ .add_property('last_name', db.Record(id=123)))
- assert not crawler.can_be_checked_externally(db.Record()
- .add_property('a', 123)
- .add_property('b', db.Record()))
+ # one identifying prop is missing
+ assert crawler.has_reference_value_without_id(db.Record().add_parent("Person")
+ .add_property('first_name', 123)
+ .add_property('last_name', db.Record()))
def test_replace_entities_with_ids(crawler):
@@ -541,12 +572,21 @@ def test_replace_entities_with_ids(crawler):
assert a.get_property("C").value == [12345, 233324]
+def mock_get_entity_by_id(id):
+ candidates = [el for el in list(full_data.values()) if el.id == id]
+ if len(candidates) > 0:
+ return candidates[0]
+ else:
+ raise ValueError()
+
+
def mock_get_entity_by_name(name):
- candidates = [el for el in full_data.values() if el.name.lower() == name.lower()]
+ candidates = [el for el in full_data.values()
+ if (el.name is not None and el.name.lower() == name.lower())]
if len(candidates) > 0:
return candidates[0]
else:
- return None
+ raise ValueError()
def prepare_crawler_with_sec_mode(mode, ident):
@@ -584,6 +624,8 @@ def change_non_identifiable_prop(ident):
del resps.value[-1]
+@patch("caoscrawler.crawl.Crawler._get_entity_by_id",
+ new=Mock(side_effect=mock_get_entity_by_id))
@patch("caoscrawler.crawl.Crawler._get_entity_by_name",
new=Mock(side_effect=mock_get_entity_by_name))
@patch("caoscrawler.crawl.db.Container.insert")
@@ -671,3 +713,9 @@ def test_security_mode(updateCacheMock, upmock, insmock, ident):
reset_mocks([updateCacheMock, insmock, upmock])
# restore original ident
ident._records = deepcopy(records_backup)
+
+
+def test_create_flat_list():
+ a = db.Record()
+ a.add_property(name="a", value=a)
+ Crawler.create_flat_list([a], [])