diff --git a/.gitlab/merge_request_templates/Default.md b/.gitlab/merge_request_templates/Default.md
index 35c6d01c5904289b77fc7f1de9419ef91a1510e9..3629e0ca3695000863d8c254516f64bf59a7bf60 100644
--- a/.gitlab/merge_request_templates/Default.md
+++ b/.gitlab/merge_request_templates/Default.md
@@ -28,6 +28,7 @@ guidelines](https://gitlab.com/caosdb/caosdb/-/blob/dev/REVIEW_GUIDELINES.md)
- [ ] Up-to-date CHANGELOG.md (or not necessary)
- [ ] Up-to-date JSON schema (or not necessary)
- [ ] Appropriate user and developer documentation (or not necessary)
+ - Update / write published documentation (`make doc`).
- How do I use the software? Assume "stupid" users.
- How do I develop or debug the software? Assume novice developers.
- [ ] Annotations in code (Gitlab comments)
@@ -41,7 +42,8 @@ guidelines](https://gitlab.com/caosdb/caosdb/-/blob/dev/REVIEW_GUIDELINES.md)
- [ ] I understand the intent of this MR
- [ ] All automated tests pass
- [ ] Up-to-date CHANGELOG.md (or not necessary)
-- [ ] Appropriate user and developer documentation (or not necessary)
+- [ ] Appropriate user and developer documentation (or not necessary), also in published
+ documentation.
- [ ] The test environment setup works and the intended behavior is reproducible in the test
environment
- [ ] In-code documentation and comments are up-to-date.
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2c1f5481af947c60e4f3192a7935183537ff3a05..be47de54cd33c917b8997eebaa55c31edfe71543 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,22 @@ 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).
+## [0.11.0] 2023-10-13 ##
+
+### Added ###
+
+* Configuration options `REST_RESPONSE_LOG_FORMAT` and
+ `GRPC_RESPONSE_LOG_FORMAT` which control the format and information included
+ in the log message of any response of the respective API. See
+ `conf/core/server.conf` for more information.
+* REST API: Permanent redirect from "FileSystem" to "FileSystem/".
+
+### Fixed ###
+
+* Wrong url returned by FileSystem resource behind proxy.
+* `NullPointerException` in GRPC API converters when executing SELECT query on
+ NULL values.
+
## [0.10.0] - 2023-06-02 ##
(Florian Spreckelsen)
diff --git a/CITATION.cff b/CITATION.cff
index a45e422c288822d0c34e1f5df2bcb83ceedd8e23..962c0cfce8443708de4094ea83658bd468ada26d 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -23,6 +23,6 @@ authors:
given-names: Stefan
orcid: https://orcid.org/0000-0001-7214-8125
title: "CaosDB - Server"
-version: 0.10.0
+version: 0.11.0
doi: 10.3390/data4020083
-date-released: 2023-06-02
+date-released: 2023-10-13
diff --git a/conf/core/log4j2-default.properties b/conf/core/log4j2-default.properties
index 5983f8e33d51729c70cd3d685fe299aa13e8f27c..39f5f0ead11bb5ccfa9e39d3007d40ee8fa3077c 100644
--- a/conf/core/log4j2-default.properties
+++ b/conf/core/log4j2-default.properties
@@ -8,6 +8,10 @@ verbose = true
property.LOG_DIR = log
property.REQUEST_TIME_LOGGER_LEVEL = OFF
+# the root logger has level "WARN" but we want to log the GRPC traffic in INFO level:
+logger.grpc_response_log.name = org.caosdb.server.grpc.LoggingInterceptor
+logger.grpc_response_log.level = INFO
+
## appenders
# stderr
appender.stderr.type = Console
diff --git a/conf/core/server.conf b/conf/core/server.conf
index c030d6eb63d61ad2d9adc6a174877b1006396537..5df6c40ca04a9c6f22d03f61c937ab5fbeab565f 100644
--- a/conf/core/server.conf
+++ b/conf/core/server.conf
@@ -100,6 +100,21 @@ GRPC_SERVER_PORT_HTTPS=8443
# HTTP port of the grpc end-point
GRPC_SERVER_PORT_HTTP=
+# --------------------------------------------------
+# Response Log formatting (this cannot be configured by the logging frame work
+# and thus has to be configured here).
+# --------------------------------------------------
+
+# Logging format of the GRPC API.
+# Known keys: user-agent, local-address, remote-address, method.
+# 'OFF' turns off the logging.
+GRPC_RESPONSE_LOG_FORMAT={method} {local-address} {remote-address} {user-agent}
+# Logging format of the REST API.
+# Known keys: see column "Variable name" at https://javadocs.restlet.talend.com/2.4/jse/api/index.html?org/restlet/util/Resolver.html
+# 'OFF' turns off the logging.
+# Leaving this empty means using restlet's default settings.
+REST_RESPONSE_LOG_FORMAT=
+
# --------------------------------------------------
# HTTPS options
# --------------------------------------------------
@@ -229,4 +244,4 @@ ENTITY_VERSIONING_ENABLED=true
# Enabling the state machine extension
-# EXT_STATE_ENTITY=ENABLE
\ No newline at end of file
+# EXT_STATE_ENTITY=ENABLE
diff --git a/pom.xml b/pom.xml
index 835de2d3eebef06cb10e9efd2e4aaf6890287357..05d1aa4b7d8e01b5cd3794b6fabbd01ea81a24ac 100644
--- a/pom.xml
+++ b/pom.xml
@@ -25,7 +25,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>org.caosdb</groupId>
<artifactId>caosdb-server</artifactId>
- <version>0.10.0</version>
+ <version>0.11.0</version>
<packaging>jar</packaging>
<name>CaosDB Server</name>
<scm>
diff --git a/src/doc/conf.py b/src/doc/conf.py
index 3c062b94cff76b69ac234ab7512a02c0b6d27247..434ed4623fbacd240d35142f855c1fd4301de915 100644
--- a/src/doc/conf.py
+++ b/src/doc/conf.py
@@ -26,9 +26,9 @@ copyright = '2023, IndiScale GmbH'
author = 'Daniel Hornung, Timm Fitschen'
# The short X.Y version
-version = '0.10.0'
+version = '0.11.0'
# The full version, including alpha/beta/rc tags
-release = '0.10.0'
+release = '0.11.0'
# -- General configuration ---------------------------------------------------
diff --git a/src/main/java/org/caosdb/server/CaosDBServer.java b/src/main/java/org/caosdb/server/CaosDBServer.java
index 9daabaed65aa39a9be868567581588625aba7a53..2a115c5cfa06ed0e3db85847c27fb4c8424eadaf 100644
--- a/src/main/java/org/caosdb/server/CaosDBServer.java
+++ b/src/main/java/org/caosdb/server/CaosDBServer.java
@@ -108,6 +108,7 @@ import org.restlet.data.Reference;
import org.restlet.data.ServerInfo;
import org.restlet.data.Status;
import org.restlet.engine.Engine;
+import org.restlet.routing.Redirector;
import org.restlet.routing.Route;
import org.restlet.routing.Router;
import org.restlet.routing.Template;
@@ -223,7 +224,6 @@ public class CaosDBServer extends Application {
public boolean notifyObserver(String e, Observable sender) {
if (e.equals(ServerProperties.KEY_TIMEZONE)) {
- String[] availableIDs = TimeZone.getAvailableIDs();
TimeZone newZoneId =
TimeZone.getTimeZone(getServerProperty(ServerProperties.KEY_TIMEZONE));
TimeZone.setDefault(newZoneId);
@@ -709,6 +709,9 @@ public class CaosDBServer extends Application {
protectedRouter.attach("/EntityPermissions/", EntityPermissionsResource.class);
protectedRouter.attach("/EntityPermissions/{specifier}", EntityPermissionsResource.class);
protectedRouter.attach("/Owner/{specifier}", EntityOwnerResource.class);
+ protectedRouter.attach(
+ "/FileSystem",
+ new Redirector(getContext(), "/FileSystem/", Redirector.MODE_CLIENT_PERMANENT));
protectedRouter.attach("/FileSystem/", FileSystemResource.class);
// FileSystem etc. needs to accept parameters which contain slashes and would otherwise be
// split at the first separator
@@ -894,6 +897,13 @@ class CaosDBComponent extends Component {
public CaosDBComponent() {
super();
+ String responseLogFormat =
+ CaosDBServer.getServerProperty(ServerProperties.KEY_REST_RESPONSE_LOG_FORMAT);
+ if ("OFF".equalsIgnoreCase(responseLogFormat)) {
+ getLogService().setEnabled(false);
+ } else if (responseLogFormat != null && !responseLogFormat.isEmpty()) {
+ getLogService().setResponseLogFormat(responseLogFormat);
+ }
setName(CaosDBServer.getServerProperty(ServerProperties.KEY_SERVER_NAME));
setOwner(CaosDBServer.getServerProperty(ServerProperties.KEY_SERVER_OWNER));
}
diff --git a/src/main/java/org/caosdb/server/ServerProperties.java b/src/main/java/org/caosdb/server/ServerProperties.java
index d58250242f691498288d765dd252986eda7fb09f..93a0c7473be1c31565e4b159ba55e01d557687e7 100644
--- a/src/main/java/org/caosdb/server/ServerProperties.java
+++ b/src/main/java/org/caosdb/server/ServerProperties.java
@@ -150,6 +150,8 @@ public class ServerProperties extends Properties implements Observable {
public static final String KEY_PASSWORD_STRENGTH_REGEX = "PASSWORD_VALID_REGEX";
public static final String KEY_PASSWORD_WEAK_MESSAGE = "PASSWORD_INVALID_MESSAGE";
+ public static final String KEY_REST_RESPONSE_LOG_FORMAT = "REST_RESPONSE_LOG_FORMAT";
+ public static final String KEY_GRPC_RESPONSE_LOG_FORMAT = "GRPC_RESPONSE_LOG_FORMAT";
/**
* Read the config files and initialize the server properties.
diff --git a/src/main/java/org/caosdb/server/accessControl/ACMPermissions.java b/src/main/java/org/caosdb/server/accessControl/ACMPermissions.java
index 854fc07f9ed93eda28e8aca99c1ea1983c73f4fe..075036921aba51acc05ff1b76df01763485c53c2 100644
--- a/src/main/java/org/caosdb/server/accessControl/ACMPermissions.java
+++ b/src/main/java/org/caosdb/server/accessControl/ACMPermissions.java
@@ -26,12 +26,9 @@ import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Set;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
public class ACMPermissions implements Comparable<ACMPermissions> {
- private static Logger LOGGER = LoggerFactory.getLogger(ACMPermissions.class);
public static final String USER_PARAMETER = "?USER?";
public static final String REALM_PARAMETER = "?REALM?";
public static final String ROLE_PARAMETER = "?ROLE?";
diff --git a/src/main/java/org/caosdb/server/database/BackendTransaction.java b/src/main/java/org/caosdb/server/database/BackendTransaction.java
index 5addf3f3f3e34a8e3e6a9152b9511046fe4b6a23..05ea26c255ae5b2bd1e75df7f3fdc4d94fca5e5a 100644
--- a/src/main/java/org/caosdb/server/database/BackendTransaction.java
+++ b/src/main/java/org/caosdb/server/database/BackendTransaction.java
@@ -47,7 +47,6 @@ import org.caosdb.server.database.backend.implementation.MySQL.MySQLIsSubType;
import org.caosdb.server.database.backend.implementation.MySQL.MySQLListRoles;
import org.caosdb.server.database.backend.implementation.MySQL.MySQLListUsers;
import org.caosdb.server.database.backend.implementation.MySQL.MySQLLogUserVisit;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRegisterSubDomain;
import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveAll;
import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveAllUncheckedFiles;
import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveDatatypes;
@@ -106,7 +105,6 @@ import org.caosdb.server.database.backend.interfaces.IsSubTypeImpl;
import org.caosdb.server.database.backend.interfaces.ListRolesImpl;
import org.caosdb.server.database.backend.interfaces.ListUsersImpl;
import org.caosdb.server.database.backend.interfaces.LogUserVisitImpl;
-import org.caosdb.server.database.backend.interfaces.RegisterSubDomainImpl;
import org.caosdb.server.database.backend.interfaces.RetrieveAllImpl;
import org.caosdb.server.database.backend.interfaces.RetrieveAllUncheckedFilesImpl;
import org.caosdb.server.database.backend.interfaces.RetrieveDatatypesImpl;
@@ -177,7 +175,6 @@ public abstract class BackendTransaction implements Undoable {
setImpl(IsSubTypeImpl.class, MySQLIsSubType.class);
setImpl(UpdateSparseEntityImpl.class, MySQLUpdateSparseEntity.class);
setImpl(RetrieveAllImpl.class, MySQLRetrieveAll.class);
- setImpl(RegisterSubDomainImpl.class, MySQLRegisterSubDomain.class);
setImpl(RetrieveDatatypesImpl.class, MySQLRetrieveDatatypes.class);
setImpl(RetrieveUserImpl.class, MySQLRetrieveUser.class);
setImpl(RetrieveParentsImpl.class, MySQLRetrieveParents.class);
diff --git a/src/main/java/org/caosdb/server/database/DatabaseUtils.java b/src/main/java/org/caosdb/server/database/DatabaseUtils.java
deleted file mode 100644
index 5280de17d91982db0481105af8c9ca760db1384f..0000000000000000000000000000000000000000
--- a/src/main/java/org/caosdb/server/database/DatabaseUtils.java
+++ /dev/null
@@ -1,380 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package org.caosdb.server.database;
-
-import com.google.common.base.Objects;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import org.caosdb.server.database.proto.FlatProperty;
-import org.caosdb.server.database.proto.ProtoProperty;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.IndexedSingleValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.datatype.SingleValue;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.wrapper.Domain;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.entity.wrapper.Property;
-
-public class DatabaseUtils {
-
- public static final String bytes2UTF8(final byte[] bytes) {
- if (bytes == null) {
- return null;
- } else {
- return new String(bytes);
- }
- }
-
- private static Domain makeReplacement(final EntityInterface p) {
- // add a new helper domain.
- final Domain d =
- new Domain(p.getProperties(), p.getDatatype(), p.getValue(), p.getStatementStatus());
- d.setDescOverride(p.isDescOverride());
- d.setNameOverride(p.isNameOverride());
- d.setDatatypeOverride(p.isDatatypeOverride());
- d.setName(p.getName());
- d.setDescription(p.getDescription());
- p.setReplacement(d);
- return d;
- }
-
- public static void deriveStage1Inserts(
- final List<EntityInterface> stage1Inserts, final EntityInterface e) {
- // entity value
- if (e.hasValue()) {
- final Property p = new Property(e);
- p.setStatementStatus(StatementStatus.FIX);
- p.setPIdx(0);
- p.setDatatype(e.getDatatype());
- p.setValue(e.getValue());
- processPropertiesStage1(stage1Inserts, p, e);
- }
-
- for (final EntityInterface p : e.getProperties()) {
- processPropertiesStage1(stage1Inserts, p, e);
- }
- }
-
- private static void processPropertiesStage1(
- final List<EntityInterface> stage1Inserts, final EntityInterface p, final EntityInterface e) {
- stage1Inserts.add(p);
- if (!p.isDescOverride()
- && !p.isNameOverride()
- && !p.isDatatypeOverride()
- && (!p.hasProperties() || hasUniquePropertyId(p, e))
- && !(p.getDatatype() instanceof AbstractCollectionDatatype)) {
- // this property can be represented without any replacement. We explicitly
- // setReplacement(null) because there is a corner case (related to the inheritance of
- // properties) where there is a replacement present which belongs to the parent entity, see
- // https://gitlab.com/caosdb/caosdb-server/-/issues/216.
- p.setReplacement(null);
- } else {
- stage1Inserts.add(makeReplacement(p));
- }
- processSubPropertiesStage1(stage1Inserts, p);
- }
-
- public static int deriveStage2Inserts(
- final List<EntityInterface> stage2Inserts, final List<EntityInterface> stage1Inserts) {
- int domainCount = 0;
- for (final EntityInterface p : stage1Inserts) {
- if (p.hasRole() && p.getRole() == Role.Domain) {
- domainCount++;
- }
- if (!p.hasReplacement() && p.hasProperties()) {
- stage2Inserts.addAll(p.getProperties());
- }
- }
- return domainCount;
- }
-
- private static boolean hasUniquePropertyId(final EntityInterface p, final EntityInterface e) {
- final EntityID id = p.getId();
- for (final EntityInterface p2 : e.getProperties()) {
- if (Objects.equal(p2.getId(), id) && p2 != p) {
- return false;
- }
- }
- return true;
- }
-
- private static void processSubPropertiesStage1(
- final List<EntityInterface> stage1Inserts, final EntityInterface p) {
- for (final EntityInterface subP : p.getProperties()) {
- if (subP.hasProperties()) {
- stage1Inserts.add(makeReplacement(subP));
- processSubPropertiesStage1(stage1Inserts, subP);
- }
- }
- }
-
- public static void parseFromSparseEntities(final EntityInterface e, final SparseEntity spe) {
- if (spe != null) {
- e.parseSparseEntity(spe);
- }
- }
-
- public static void parseOverrides(final List<FlatProperty> properties, final ResultSet rs)
- throws SQLException {
- while (rs.next()) {
- final int property_id = rs.getInt("property_id");
- for (final FlatProperty p : properties) {
- if (p.id == property_id) {
- final String name = bytes2UTF8(rs.getBytes("name_override"));
- if (name != null) {
- p.name = name;
- }
- final String desc = bytes2UTF8(rs.getBytes("desc_override"));
- if (desc != null) {
- p.desc = desc;
- }
- final String type = bytes2UTF8(rs.getBytes("type_override"));
- if (type != null) {
- p.type = type;
- }
- final String coll = bytes2UTF8(rs.getBytes("collection_override"));
- if (coll != null) {
- p.collection = coll;
- }
- }
- }
- }
- }
-
- public static List<FlatProperty> parsePropertyResultset(final ResultSet rs) throws SQLException {
- final ArrayList<FlatProperty> ret = new ArrayList<FlatProperty>();
- while (rs.next()) {
- final FlatProperty fp = new FlatProperty();
- fp.id = rs.getInt("PropertyID");
- fp.value = bytes2UTF8(rs.getBytes("PropertyValue"));
- fp.status = bytes2UTF8(rs.getBytes("PropertyStatus"));
- fp.idx = rs.getInt("PropertyIndex");
- ret.add(fp);
- }
- return ret;
- }
-
- /**
- * Helper function for parsing MySQL results.
- *
- * <p>This function creates SparseEntities and parses only the name, the role and the acl of an
- * entity.
- *
- * <p>Never returns null.
- */
- public static SparseEntity parseNameRoleACL(final ResultSet rs) throws SQLException {
- final SparseEntity ret = new SparseEntity();
- ret.role = bytes2UTF8(rs.getBytes("EntityRole"));
- ret.name = bytes2UTF8(rs.getBytes("EntityName"));
- ret.acl = bytes2UTF8(rs.getBytes("ACL"));
- return ret;
- }
-
- /**
- * Helper function for parsing MySQL results.
- *
- * <p>This function creates SparseEntities and parses all fields which belong to a SparseEntity:
- * id, name, role, acl, description, datatype, and the file properties.
- *
- * <p>Never returns null.
- */
- public static SparseEntity parseEntityResultSet(final ResultSet rs) throws SQLException {
- final SparseEntity ret = parseNameRoleACL(rs);
- ret.id = rs.getInt("EntityID");
- ret.description = bytes2UTF8(rs.getBytes("EntityDesc"));
- ret.datatype = bytes2UTF8(rs.getBytes("Datatype"));
- ret.collection = bytes2UTF8(rs.getBytes("Collection"));
-
- ret.filePath = bytes2UTF8(rs.getBytes("FilePath"));
- ret.fileSize = rs.getLong("FileSize");
- ret.fileHash = bytes2UTF8(rs.getBytes("FileHash"));
-
- ret.versionId = bytes2UTF8(rs.getBytes("Version"));
- return ret;
- }
-
- public static ArrayList<VerySparseEntity> parseParentResultSet(final ResultSet rs)
- throws SQLException {
- final ArrayList<VerySparseEntity> ret = new ArrayList<VerySparseEntity>();
- while (rs.next()) {
- final VerySparseEntity vsp = new VerySparseEntity();
- vsp.id = rs.getInt("ParentID");
- vsp.name = bytes2UTF8(rs.getBytes("ParentName"));
- vsp.description = bytes2UTF8(rs.getBytes("ParentDescription"));
- vsp.role = bytes2UTF8(rs.getBytes("ParentRole"));
- vsp.acl = bytes2UTF8(rs.getBytes("ACL"));
- ret.add(vsp);
- }
- return ret;
- }
-
- public static <K extends EntityInterface> K parseEntityFromVerySparseEntity(
- final K entity, final VerySparseEntity vse) {
- entity.setId(new EntityID(vse.id));
- entity.setName(vse.name);
- entity.setRole(vse.role);
- entity.setDescription(vse.description);
- return entity;
- }
-
- public static void parseParentsFromVerySparseEntity(
- final EntityInterface entity, final List<VerySparseEntity> pars) {
- for (final VerySparseEntity vsp : pars) {
- final Parent p = new Parent(new RetrieveEntity(new EntityID(vsp.id)));
- p.setName(vsp.name);
- p.setDescription(vsp.description);
- entity.addParent(p);
- }
- }
-
- private static void replace(
- final Property p, final Map<EntityID, Property> domainMap, final boolean isHead) {
- // ... find the corresponding domain and replace it
- ReferenceValue ref;
- try {
- ref = ReferenceValue.parseReference(p.getValue());
- } catch (final Message e) {
- throw new RuntimeException("This should never happen.");
- }
- final EntityInterface replacement = domainMap.get(ref.getId());
- if (replacement == null) {
- if (isHead) {
- throw new NullPointerException("Replacement was null");
- }
- // entity has been deleted (we are processing properties of an old entity version)
- p.setValue(null);
- p.addWarning(
- new Message(
- "The referenced entity has been deleted in the mean time and is not longer available."));
- return;
- }
- if (replacement.isDescOverride()) {
- p.setDescOverride(true);
- p.setDescription(replacement.getDescription());
- }
- if (replacement.isNameOverride()) {
- p.setNameOverride(true);
- p.setName(replacement.getName());
- }
- if (replacement.isDatatypeOverride()) {
- p.setDatatypeOverride(true);
- p.setDatatype(replacement.getDatatype());
- }
- p.setProperties(replacement.getProperties());
- p.setStatementStatus(replacement.getStatementStatus());
- p.setValue(replacement.getValue());
- }
-
- public static void transformToDeepPropertyTree(
- final EntityInterface e, final List<Property> protoProperties) {
- // here we will store every domain we can find and we will index it by
- // its id.
- final Map<EntityID, Property> domainMap = new HashMap<>();
-
- // loop over all properties and collect the domains
- for (final Property p : protoProperties) {
- // if this is a domain it represents a deeper branch of the property
- // tree.
- if (p.getRole() == Role.Domain) {
- if (domainMap.containsKey(p.getId())) {
- // aggregate the multiple values.
- final Property domain = domainMap.get(p.getId());
- if (!(domain.getValue() instanceof CollectionValue)) {
- final SingleValue singleValue = (SingleValue) domain.getValue();
- final CollectionValue vals = new CollectionValue();
- final IndexedSingleValue iSingleValue =
- new IndexedSingleValue(domain.getPIdx(), singleValue);
- vals.add(iSingleValue);
- domain.setValue(vals);
- }
- ((CollectionValue) domain.getValue()).add(p.getPIdx(), p.getValue());
- } else {
- domainMap.put(p.getId(), p);
- }
- }
- }
-
- // loop over all properties
- final boolean isHead =
- e.getVersion().getSuccessors() == null || e.getVersion().getSuccessors().isEmpty();
- for (final Property p : protoProperties) {
-
- // if this is a replacement
- if (p.getStatementStatus() == StatementStatus.REPLACEMENT) {
- replace(p, domainMap, isHead);
- }
-
- for (final Property subP : p.getProperties()) {
- if (subP.getStatementStatus() == StatementStatus.REPLACEMENT) {
- replace(subP, domainMap, isHead);
- }
- }
-
- if (p.getId().equals(e.getId())) {
- // this is the value of an abstract property.
- e.setValue(p.getValue());
- } else if (p.getRole() != Role.Domain) {
- // if this is not a domain it is to be added to the properties
- // of e.
- e.addProperty(p);
- }
- }
- }
-
- public static ArrayList<Property> parseFromProtoProperties(final List<ProtoProperty> protos) {
- final ArrayList<Property> ret = new ArrayList<Property>();
- for (final ProtoProperty pp : protos) {
- final Property property = parseFlatProperty(pp.property);
- parseFromFlatProperties(property.getProperties(), pp.subProperties);
- ret.add(property);
- }
- return ret;
- }
-
- private static void parseFromFlatProperties(
- final List<Property> properties, final List<FlatProperty> props) {
- for (final FlatProperty fp : props) {
- final Property property = parseFlatProperty(fp);
- properties.add(property);
- }
- }
-
- private static Property parseFlatProperty(final FlatProperty fp) {
- final Property property = new Property(new RetrieveEntity());
- property.parseFlatProperty(fp);
- return property;
- }
-}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
new file mode 100644
index 0000000000000000000000000000000000000000..f7d364ae6376524ef892de3353d699547417717e
--- /dev/null
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
@@ -0,0 +1,365 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2018 Research Group Biomedical Physics,
+ * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ */
+package org.caosdb.server.database.backend.implementation.MySQL;
+
+import com.google.common.base.Objects;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.AbstractMap.SimpleEntry;
+import java.util.ArrayList;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.stream.Collectors;
+import org.caosdb.server.database.proto.FlatProperty;
+import org.caosdb.server.database.proto.ProtoProperty;
+import org.caosdb.server.database.proto.SparseEntity;
+import org.caosdb.server.database.proto.VerySparseEntity;
+import org.caosdb.server.datatype.AbstractCollectionDatatype;
+import org.caosdb.server.datatype.CollectionValue;
+import org.caosdb.server.datatype.GenericValue;
+import org.caosdb.server.entity.EntityID;
+import org.caosdb.server.entity.EntityInterface;
+import org.caosdb.server.entity.Message;
+import org.caosdb.server.entity.RetrieveEntity;
+import org.caosdb.server.entity.StatementStatus;
+import org.caosdb.server.entity.wrapper.Property;
+
+public class DatabaseUtils {
+
+ private static final String DELETED_REFERENCE_IN_PREVIOUS_VERSION =
+ "DELETED_REFERENCE_IN_PREVIOUS_VERSION";
+
+ public static final String bytes2UTF8(final byte[] bytes) {
+ if (bytes == null) {
+ return null;
+ } else {
+ return new String(bytes);
+ }
+ }
+
+ public static int deriveStage1Inserts(
+ final List<Property> stage1Inserts, final EntityInterface e) {
+ // entity value
+ if (e.hasValue()) {
+ final Property p = new Property(e);
+ p.setStatementStatus(StatementStatus.FIX);
+ p.setDatatype(e.getDatatype());
+ p.setValue(e.getValue());
+ p.setPIdx(0);
+ processPropertiesStage1(stage1Inserts, p, e);
+ }
+
+ for (final Property p : e.getProperties()) {
+ processPropertiesStage1(stage1Inserts, p, e);
+ }
+ int replacementCount = 0;
+ for (EntityInterface pp : stage1Inserts) {
+ if (pp instanceof Replacement) {
+ replacementCount++;
+ }
+ }
+ return replacementCount;
+ }
+
+ private static void processPropertiesStage1(
+ final List<Property> stage1Inserts, final Property p, final EntityInterface e) {
+
+ if (!p.isDescOverride()
+ && !p.isNameOverride()
+ && !p.isDatatypeOverride()
+ && (!p.hasProperties() || hasUniquePropertyId(p, e))
+ && !(p.getDatatype() instanceof AbstractCollectionDatatype)) {
+ stage1Inserts.add(p);
+ } else {
+ Replacement r = new Replacement(p);
+ stage1Inserts.add(r);
+ stage1Inserts.add(r.replacement);
+ }
+ processSubPropertiesStage1(stage1Inserts, p);
+ }
+
+ public static void deriveStage2Inserts(
+ final List<Property> stage2Inserts,
+ final List<Property> stage1Inserts,
+ Deque<EntityID> replacementIds,
+ EntityInterface entity) {
+ for (final Property p : stage1Inserts) {
+ if (p instanceof Replacement) {
+
+ EntityID replacementId = replacementIds.pop();
+ ((Replacement) p).setReplacementId(replacementId);
+
+ if (p.hasProperties()) {
+ for (Property subP : p.getProperties()) {
+ subP.setDomain(p);
+ stage2Inserts.add(subP);
+ }
+ }
+ } else {
+ if (p.hasProperties()) {
+ for (Property subP : p.getProperties()) {
+ stage2Inserts.add(subP);
+ }
+ }
+ }
+ }
+ }
+
+ private static boolean hasUniquePropertyId(final EntityInterface p, final EntityInterface e) {
+ final EntityID id = p.getId();
+ for (final EntityInterface p2 : e.getProperties()) {
+ if (Objects.equal(p2.getId(), id) && p2 != p) {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ private static void processSubPropertiesStage1(
+ final List<Property> stage1Inserts, final EntityInterface p) {
+ for (final Property subP : p.getProperties()) {
+ if (subP.hasProperties()) {
+ stage1Inserts.add(new Replacement(subP));
+ processSubPropertiesStage1(stage1Inserts, subP);
+ }
+ }
+ }
+
+ public static void parseOverrides(final List<ProtoProperty> properties, final ResultSet rs)
+ throws SQLException {
+ while (rs.next()) {
+ final int property_id = rs.getInt("property_id");
+ for (final FlatProperty p : properties) {
+ if (p.id == property_id) {
+ final String name = bytes2UTF8(rs.getBytes("name_override"));
+ if (name != null) {
+ p.name = name;
+ }
+ final String desc = bytes2UTF8(rs.getBytes("desc_override"));
+ if (desc != null) {
+ p.desc = desc;
+ }
+ final String type = bytes2UTF8(rs.getBytes("type_override"));
+ if (type != null) {
+ p.type = type;
+ }
+ final String coll = bytes2UTF8(rs.getBytes("collection_override"));
+ if (coll != null) {
+ p.collection = coll;
+ }
+ }
+ }
+ }
+ }
+
+ public static List<ProtoProperty> parsePropertyResultset(final ResultSet rs) throws SQLException {
+ final List<ProtoProperty> ret = new LinkedList<>();
+ while (rs.next()) {
+ ProtoProperty pp = new ProtoProperty();
+ pp.id = rs.getInt("PropertyID");
+ pp.value = bytes2UTF8(rs.getBytes("PropertyValue"));
+ pp.status = bytes2UTF8(rs.getBytes("PropertyStatus"));
+ pp.idx = rs.getInt("PropertyIndex");
+ ret.add(pp);
+ }
+ return ret;
+ }
+
+ /**
+ * Helper function for parsing MySQL results.
+ *
+ * <p>This function creates SparseEntities and parses only the name, the role and the acl of an
+ * entity.
+ *
+ * <p>Never returns null.
+ */
+ public static SparseEntity parseNameRoleACL(final ResultSet rs) throws SQLException {
+ final SparseEntity ret = new SparseEntity();
+ ret.role = bytes2UTF8(rs.getBytes("EntityRole"));
+ ret.name = bytes2UTF8(rs.getBytes("EntityName"));
+ ret.acl = bytes2UTF8(rs.getBytes("ACL"));
+ return ret;
+ }
+
+ /**
+ * Helper function for parsing MySQL results.
+ *
+ * <p>This function creates SparseEntities and parses all fields which belong to a SparseEntity:
+ * id, name, role, acl, description, datatype, and the file properties.
+ *
+ * <p>Never returns null.
+ */
+ public static SparseEntity parseEntityResultSet(final ResultSet rs) throws SQLException {
+ final SparseEntity ret = parseNameRoleACL(rs);
+ ret.id = rs.getInt("EntityID");
+ ret.description = bytes2UTF8(rs.getBytes("EntityDesc"));
+ ret.datatype = bytes2UTF8(rs.getBytes("Datatype"));
+ ret.collection = bytes2UTF8(rs.getBytes("Collection"));
+
+ ret.filePath = bytes2UTF8(rs.getBytes("FilePath"));
+ ret.fileSize = rs.getLong("FileSize");
+ ret.fileHash = bytes2UTF8(rs.getBytes("FileHash"));
+
+ ret.versionId = bytes2UTF8(rs.getBytes("Version"));
+ return ret;
+ }
+
+ public static LinkedList<VerySparseEntity> parseParentResultSet(final ResultSet rs)
+ throws SQLException {
+ final LinkedList<VerySparseEntity> ret = new LinkedList<>();
+ while (rs.next()) {
+ final VerySparseEntity vsp = new VerySparseEntity();
+ vsp.id = rs.getInt("ParentID");
+ vsp.name = bytes2UTF8(rs.getBytes("ParentName"));
+ vsp.description = bytes2UTF8(rs.getBytes("ParentDescription"));
+ vsp.role = bytes2UTF8(rs.getBytes("ParentRole"));
+ vsp.acl = bytes2UTF8(rs.getBytes("ACL"));
+ ret.add(vsp);
+ }
+ return ret;
+ }
+
+ public static ArrayList<Property> parseFromProtoProperties(
+ EntityInterface entity, List<ProtoProperty> protos) {
+ final ArrayList<Property> ret = new ArrayList<Property>();
+ for (final ProtoProperty pp : protos) {
+ if (pp.id.equals(entity.getId().toInteger())) {
+ if (pp.value != null) {
+ entity.setValue(new GenericValue(pp.value));
+ }
+ if (pp.collValues != null) {
+ CollectionValue value = new CollectionValue();
+ for (Object next : pp.collValues) {
+ if (next == null) {
+ value.add(null);
+ } else {
+ value.add(new GenericValue(next.toString()));
+ }
+ }
+ entity.setValue(value);
+ }
+
+ } else {
+ Message warning = null;
+ if (pp.status == DELETED_REFERENCE_IN_PREVIOUS_VERSION) {
+ pp.status = StatementStatus.FIX.name();
+ warning =
+ new Message(
+ "The referenced entity has been deleted in the mean time and is not longer available.");
+ }
+ final Property property = parseFlatProperty(pp);
+ if (warning != null) {
+ property.addWarning(warning);
+ }
+ ret.add(property);
+ }
+ }
+ return ret;
+ }
+
+ private static Property parseFlatProperty(final ProtoProperty fp) {
+ final Property property = new Property(new RetrieveEntity());
+ property.parseProtoProperty(fp);
+ return property;
+ }
+
+ @SuppressWarnings("unchecked")
+ public static LinkedList<ProtoProperty> transformToDeepPropertyTree(
+ List<ProtoProperty> properties, boolean isHead) {
+ LinkedList<ProtoProperty> result = new LinkedList<>();
+ Map<String, ProtoProperty> replacements = new HashMap<>();
+ for (ProtoProperty pp : properties) {
+ if (pp.status.equals(ReplacementStatus.REPLACEMENT.name())) {
+ replacements.put(pp.value, null);
+ }
+ }
+ Iterator<ProtoProperty> iterator = properties.iterator();
+ while (iterator.hasNext()) {
+ ProtoProperty pp = iterator.next();
+ if (replacements.containsKey(pp.id.toString())) {
+ ProtoProperty other = replacements.get(pp.id.toString());
+ // handle collection values
+ if (other != null) {
+ if (other.collValues == null) {
+ other.collValues = new LinkedList<>();
+ Entry<Integer, String> obj = new SimpleEntry<>(other.idx, other.value);
+ other.collValues.add(obj);
+ other.value = null;
+ }
+ other.collValues.add(new SimpleEntry<>(pp.idx, pp.value));
+ } else {
+ replacements.put(pp.id.toString(), pp);
+ }
+ iterator.remove();
+ }
+ }
+ for (ProtoProperty pp : properties) {
+ if (pp.status.equals(ReplacementStatus.REPLACEMENT.name())) {
+ replace(pp, replacements.get(pp.value), isHead);
+ }
+ if (pp.collValues != null) {
+ // sort
+ pp.collValues.sort(
+ (x, y) -> {
+ return ((Entry<Integer, String>) x).getKey() - ((Entry<Integer, String>) y).getKey();
+ });
+ pp.collValues =
+ pp.collValues
+ .stream()
+ .map((x) -> (Object) ((Entry<Integer, String>) x).getValue())
+ .collect(Collectors.toList());
+ }
+ result.add(pp);
+ }
+ return result;
+ }
+
+ /*
+ * This replace function is used during the retrieval of properties. It is
+ * basically the opposite of the Replacement class. It copies the information
+ * from the replacement object back into the Property.
+ */
+ private static void replace(ProtoProperty pp, ProtoProperty replacement, boolean isHead) {
+ if (replacement == null) {
+ if (isHead) {
+ throw new NullPointerException("Replacement was null");
+ }
+ // entity has been deleted (we are processing properties of an old entity version)
+ pp.value = null;
+ pp.status = DELETED_REFERENCE_IN_PREVIOUS_VERSION;
+ return;
+ }
+ pp.desc = replacement.desc;
+ pp.name = replacement.name;
+ pp.type = replacement.type;
+ pp.collection = replacement.collection;
+ pp.value = replacement.value;
+ pp.collValues = replacement.collValues;
+ pp.status = replacement.status;
+ pp.subProperties = replacement.subProperties;
+ }
+}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java
index 09cae6886c2daa94d93ab76539a3e1343f5aecbe..474048f1a72331c3a2e35b38c5cb4c9b3e4d6543 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java
@@ -5,7 +5,6 @@ import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.List;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.GetAllNamesImpl;
import org.caosdb.server.database.exceptions.TransactionException;
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityProperties.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityProperties.java
index 7c3c5a33e160f3da6a8c2b89fe0487e0317c99da..becb56a2397fffa323f005507463a586bdecc0cf 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityProperties.java
@@ -25,15 +25,28 @@ package org.caosdb.server.database.backend.implementation.MySQL;
import static java.sql.Types.BIGINT;
import java.sql.PreparedStatement;
+import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.SQLIntegrityConstraintViolationException;
+import java.util.ArrayDeque;
+import java.util.Deque;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.InsertEntityPropertiesImpl;
import org.caosdb.server.database.exceptions.IntegrityException;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.proto.FlatProperty;
+import org.caosdb.server.datatype.AbstractCollectionDatatype;
import org.caosdb.server.datatype.AbstractDatatype.Table;
+import org.caosdb.server.datatype.CollectionValue;
+import org.caosdb.server.datatype.IndexedSingleValue;
+import org.caosdb.server.datatype.ReferenceValue;
+import org.caosdb.server.datatype.SingleValue;
import org.caosdb.server.entity.EntityID;
+import org.caosdb.server.entity.EntityInterface;
+import org.caosdb.server.entity.wrapper.Property;
public class MySQLInsertEntityProperties extends MySQLTransaction
implements InsertEntityPropertiesImpl {
@@ -46,7 +59,27 @@ public class MySQLInsertEntityProperties extends MySQLTransaction
}
@Override
- public void execute(
+ public void execute(EntityInterface entity) {
+ final List<Property> stage1Inserts = new LinkedList<>();
+ final List<Property> stage2Inserts = new LinkedList<>();
+
+ final int domainCount = DatabaseUtils.deriveStage1Inserts(stage1Inserts, entity);
+
+ try {
+ final Deque<EntityID> replacementIds = registerReplacementId(domainCount);
+
+ DatabaseUtils.deriveStage2Inserts(stage2Inserts, stage1Inserts, replacementIds, entity);
+
+ insertStages(stage1Inserts, entity.getDomain(), entity.getId());
+ insertStages(stage2Inserts, entity.getId(), null);
+ } catch (final SQLIntegrityConstraintViolationException exc) {
+ throw new IntegrityException(exc);
+ } catch (SQLException | ConnectionException e) {
+ throw new TransactionException(e);
+ }
+ }
+
+ private void insertFlatProperty(
final EntityID domain,
final EntityID entity,
final FlatProperty fp,
@@ -76,10 +109,124 @@ public class MySQLInsertEntityProperties extends MySQLTransaction
stmt.execute();
} catch (final SQLIntegrityConstraintViolationException exc) {
throw new IntegrityException(exc);
- } catch (final SQLException exc) {
- throw new TransactionException(exc);
- } catch (final ConnectionException exc) {
+ } catch (final SQLException | ConnectionException exc) {
throw new TransactionException(exc);
}
}
+
+ private void insertStages(
+ final List<Property> inserts, final EntityID domain, final EntityID entity)
+ throws TransactionException {
+
+ for (final Property property : inserts) {
+
+ // prepare flat property
+ final FlatProperty fp = new FlatProperty();
+ Table table = Table.null_data;
+ Long unit_sig = null;
+ fp.id = property.getId().toInteger();
+ fp.idx = property.getPIdx();
+ fp.status = property.getStatementStatus().name();
+
+ if (property.getStatementStatus() == ReplacementStatus.REPLACEMENT) {
+ // special treatment: swap value and id. This is part of the back-end specification for the
+ // representation of replacement. The reason why this happens here (and
+ // not in the replacement class for instance) is that the original
+ // Property must not be changed for this. Otherwise we would have to
+ // change it back after the insertion or internally used replacement ids
+ // would be leaked.
+
+ // value is to be the id of the property which is being replaced
+ fp.value = fp.id.toString();
+
+ // id is to be the replacement id (an internally used/private id)
+ fp.id = ((ReferenceValue) property.getValue()).getId().toInteger();
+ table = Table.reference_data;
+ } else {
+
+ if (property.hasUnit()) {
+ unit_sig = property.getUnit().getSignature();
+ }
+ if (property.hasValue()) {
+ if (property.getValue() instanceof CollectionValue) {
+ // insert collection of values
+ final CollectionValue v = (CollectionValue) property.getValue();
+ final Iterator<IndexedSingleValue> iterator = v.iterator();
+ final SingleValue firstValue = iterator.next();
+
+ // insert 2nd to nth item
+ for (int i = 1; i < v.size(); i++) {
+ final SingleValue vi = iterator.next();
+ fp.idx = i;
+ if (vi == null) {
+ fp.value = null;
+ table = Table.null_data;
+ } else {
+ fp.value = vi.toDatabaseString();
+ table = vi.getTable();
+ }
+ insertFlatProperty(
+ domain, entity != null ? entity : property.getDomain(), fp, table, unit_sig);
+ }
+
+ // insert first item
+ fp.idx = 0;
+ if (firstValue == null) {
+ fp.value = null;
+ table = Table.null_data;
+ } else {
+ fp.value = firstValue.toDatabaseString();
+ table = firstValue.getTable();
+ }
+
+ } else {
+ // insert single value
+ fp.value = ((SingleValue) property.getValue()).toDatabaseString();
+ if (property instanceof Property && ((Property) property).isName()) {
+ table = Table.name_data;
+ } else {
+ table = ((SingleValue) property.getValue()).getTable();
+ }
+ }
+ }
+ if (property.isNameOverride()) {
+ fp.name = property.getName();
+ }
+ if (property.isDescOverride()) {
+ fp.desc = property.getDescription();
+ }
+ if (property.isDatatypeOverride()) {
+ if (property.getDatatype() instanceof AbstractCollectionDatatype) {
+ fp.type =
+ ((AbstractCollectionDatatype) property.getDatatype())
+ .getDatatype()
+ .getId()
+ .toString();
+ fp.collection =
+ ((AbstractCollectionDatatype) property.getDatatype()).getCollectionName();
+ } else {
+ fp.type = property.getDatatype().getId().toString();
+ }
+ }
+ }
+
+ insertFlatProperty(
+ domain, entity != null ? entity : property.getDomain(), fp, table, unit_sig);
+ }
+ }
+
+ public static final String STMT_REGISTER_SUBDOMAIN = "call registerSubdomain(?)";
+
+ public Deque<EntityID> registerReplacementId(final int domainCount)
+ throws SQLException, ConnectionException {
+ final PreparedStatement stmt = prepareStatement(STMT_REGISTER_SUBDOMAIN);
+ stmt.setInt(1, domainCount);
+ try (final ResultSet rs = stmt.executeQuery()) {
+ final Deque<EntityID> ret = new ArrayDeque<>();
+ while (rs.next()) {
+ ret.add(new EntityID(rs.getInt(1)));
+ }
+ return ret;
+ }
+ }
}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
index 1b945acf566db938f12847f758636dbfddeac3d1..27227926156fc9b35ab75473e1efa2cce55f152e 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
@@ -26,7 +26,6 @@ import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLIntegrityConstraintViolationException;
import java.sql.Types;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.InsertSparseEntityImpl;
import org.caosdb.server.database.exceptions.IntegrityException;
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRegisterSubDomain.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRegisterSubDomain.java
deleted file mode 100644
index 1e14600e71023dff544a09910fabe0dc8b17ca42..0000000000000000000000000000000000000000
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRegisterSubDomain.java
+++ /dev/null
@@ -1,64 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package org.caosdb.server.database.backend.implementation.MySQL;
-
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.util.ArrayDeque;
-import java.util.Deque;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RegisterSubDomainImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-
-public class MySQLRegisterSubDomain extends MySQLTransaction implements RegisterSubDomainImpl {
-
- public MySQLRegisterSubDomain(final Access access) {
- super(access);
- }
-
- public static final String STMT_REGISTER_SUBDOMAIN = "call registerSubdomain(?)";
-
- @Override
- public Deque<EntityID> execute(final int domainCount) throws TransactionException {
- try {
- final PreparedStatement stmt = prepareStatement(STMT_REGISTER_SUBDOMAIN);
- stmt.setInt(1, domainCount);
- final ResultSet rs = stmt.executeQuery();
- try {
- final Deque<EntityID> ret = new ArrayDeque<>();
- while (rs.next()) {
- ret.add(new EntityID(rs.getInt(1)));
- }
- return ret;
- } finally {
- rs.close();
- }
- } catch (final SQLException e) {
- throw new TransactionException(e);
- } catch (final ConnectionException e) {
- throw new TransactionException(e);
- }
- }
-}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java
index f847bf63e9f72b4632cecf55ee4a132f141a2cd1..9a2ea81629853e3baf9de7757e1abe6c8f01fe28 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java
@@ -27,7 +27,6 @@ import java.sql.SQLException;
import java.util.LinkedList;
import java.util.List;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.RetrieveAllImpl;
import org.caosdb.server.database.exceptions.TransactionException;
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java
index e085f0510a5c0a95f1e0a3bc2f702b4e345d706e..685249417ca9c1664cc1a30af3fc3a597788c29f 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java
@@ -25,8 +25,7 @@ package org.caosdb.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import java.util.ArrayList;
-import org.caosdb.server.database.DatabaseUtils;
+import java.util.List;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.RetrieveDatatypesImpl;
import org.caosdb.server.database.exceptions.TransactionException;
@@ -53,7 +52,7 @@ public class MySQLRetrieveDatatypes extends MySQLTransaction implements Retrieve
+ "FROM entities AS e WHERE e.role='DATATYPE'";
@Override
- public ArrayList<VerySparseEntity> execute() throws TransactionException {
+ public List<VerySparseEntity> execute() throws TransactionException {
try {
final PreparedStatement stmt = prepareStatement(STMT_GET_DATATYPE);
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java
index 64ce7e9023bd18506a4b13610033923fa7320ca8..1e2a6621d2fb85a5a5260b1a607670e970f54701 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java
@@ -26,8 +26,7 @@ import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Types;
-import java.util.ArrayList;
-import org.caosdb.server.database.DatabaseUtils;
+import java.util.LinkedList;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.RetrieveParentsImpl;
import org.caosdb.server.database.exceptions.TransactionException;
@@ -43,7 +42,7 @@ public class MySQLRetrieveParents extends MySQLTransaction implements RetrievePa
private static final String stmtStr = "call retrieveEntityParents(?, ?)";
@Override
- public ArrayList<VerySparseEntity> execute(final EntityID id, final String version)
+ public LinkedList<VerySparseEntity> execute(final EntityID id, final String version)
throws TransactionException {
try {
ResultSet rs = null;
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePasswordValidator.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePasswordValidator.java
index 1ff7dd7afd0b468a90d9e3b82faca1adc5cae84f..9fd7e0a8e441b3ede2a3447ec364c24e16898fb5 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePasswordValidator.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePasswordValidator.java
@@ -22,7 +22,7 @@
*/
package org.caosdb.server.database.backend.implementation.MySQL;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.security.NoSuchAlgorithmException;
import java.sql.PreparedStatement;
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java
index 6bcfeac05cd3631f05615d26741c47f4c5c1bf63..100df4ce72ebae75d3022866b345bacc9752ad91 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java
@@ -26,13 +26,11 @@ import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Types;
-import java.util.ArrayList;
+import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.RetrievePropertiesImpl;
import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.FlatProperty;
import org.caosdb.server.database.proto.ProtoProperty;
import org.caosdb.server.entity.EntityID;
@@ -46,27 +44,20 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
private static final String stmtStr2 = "call retrieveOverrides(?,?,?)";
@Override
- public ArrayList<ProtoProperty> execute(final EntityID entity, final String version)
- throws TransactionException {
+ public LinkedList<ProtoProperty> execute(
+ final EntityID entity, final String version, boolean isHead) throws TransactionException {
try {
final PreparedStatement prepareStatement = prepareStatement(stmtStr);
- final List<FlatProperty> props =
+ final List<ProtoProperty> propsStage1 =
retrieveFlatPropertiesStage1(0, entity.toInteger(), version, prepareStatement);
- final ArrayList<ProtoProperty> protos = new ArrayList<ProtoProperty>();
- for (final FlatProperty p : props) {
- final ProtoProperty proto = new ProtoProperty();
- proto.property = p;
+ for (final ProtoProperty p : propsStage1) {
- final List<FlatProperty> subProps =
+ p.subProperties =
retrieveFlatPropertiesStage1(entity.toInteger(), p.id, version, prepareStatement);
-
- proto.subProperties = subProps;
-
- protos.add(proto);
}
- return protos;
+ return DatabaseUtils.transformToDeepPropertyTree(propsStage1, isHead);
} catch (final SQLException e) {
throw new TransactionException(e);
} catch (final ConnectionException e) {
@@ -74,43 +65,38 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
}
}
- private List<FlatProperty> retrieveFlatPropertiesStage1(
+ private List<ProtoProperty> retrieveFlatPropertiesStage1(
final Integer domain,
final Integer entity,
final String version,
final PreparedStatement stmt)
throws SQLException, ConnectionException {
- ResultSet rs = null;
- try {
- if (domain != null && domain >= 0) {
- stmt.setInt(1, domain);
- } else {
- stmt.setInt(1, 0);
- }
+ if (domain != null && domain >= 0) {
+ stmt.setInt(1, domain);
+ } else {
+ stmt.setInt(1, 0);
+ }
- stmt.setInt(2, entity);
- if (version == null) {
- stmt.setNull(3, Types.VARBINARY);
- } else {
- stmt.setString(3, version);
- }
+ stmt.setInt(2, entity);
+ if (version == null) {
+ stmt.setNull(3, Types.VARBINARY);
+ } else {
+ stmt.setString(3, version);
+ }
- final long t1 = System.currentTimeMillis();
- rs = stmt.executeQuery();
+ final long t1 = System.currentTimeMillis();
+
+ try (ResultSet rs = stmt.executeQuery()) {
final long t2 = System.currentTimeMillis();
addMeasurement(this.getClass().getSimpleName() + ".retrieveFlatPropertiesStage1", t2 - t1);
- final List<FlatProperty> props = DatabaseUtils.parsePropertyResultset(rs);
+ final List<ProtoProperty> properties = DatabaseUtils.parsePropertyResultset(rs);
- final PreparedStatement stmt2 = prepareStatement(stmtStr2);
+ final PreparedStatement retrieveOverrides = prepareStatement(stmtStr2);
- retrieveOverrides(domain, entity, version, stmt2, props);
+ retrieveOverrides(domain, entity, version, retrieveOverrides, properties);
- return props;
- } finally {
- if (rs != null && !rs.isClosed()) {
- rs.close();
- }
+ return properties;
}
}
@@ -118,24 +104,25 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
final Integer domain,
final Integer entity,
final String version,
- final PreparedStatement stmt2,
- final List<FlatProperty> props)
+ final PreparedStatement retrieveOverrides,
+ final List<ProtoProperty> props)
throws SQLException {
ResultSet rs = null;
try {
- stmt2.setInt(1, domain);
- stmt2.setInt(2, entity);
+ retrieveOverrides.setInt(1, domain);
+ retrieveOverrides.setInt(2, entity);
if (version == null) {
- stmt2.setNull(3, Types.VARBINARY);
+ retrieveOverrides.setNull(3, Types.VARBINARY);
} else {
- stmt2.setString(3, version);
+ retrieveOverrides.setString(3, version);
}
final long t1 = System.currentTimeMillis();
- rs = stmt2.executeQuery();
+ rs = retrieveOverrides.executeQuery();
final long t2 = System.currentTimeMillis();
addMeasurement(this.getClass().getSimpleName() + ".retrieveOverrides", t2 - t1);
DatabaseUtils.parseOverrides(props, rs);
+
} finally {
if (rs != null && !rs.isClosed()) {
rs.close();
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java
index ca3bd078daba4c72e7f516ce64b1da1515a1a6eb..48cd84b3869262ba7f1d8129fdde2335bed6cd8e 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java
@@ -26,7 +26,6 @@ import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Types;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.RetrieveSparseEntityImpl;
import org.caosdb.server.database.exceptions.TransactionException;
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveUser.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveUser.java
index bde1878db5d49b2da201b7d589c1ee8b8d73f656..40f036f1d63753c0be9e6153f741db7d4f9d04ad 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveUser.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveUser.java
@@ -22,7 +22,7 @@
*/
package org.caosdb.server.database.backend.implementation.MySQL;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java
index 585be49afe93dc94c6ba2bc4f058c5d46fcf40f6..6c4c2629a5effee25128f478bef20f5558a027ba 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java
@@ -27,7 +27,6 @@ import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.HashMap;
import java.util.LinkedList;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
import org.caosdb.server.database.exceptions.TransactionException;
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
index 1c8039253b4c5e74a8054dfa937fec23c55440e8..b2d0fb9e3b7615e7e95243a2a7bde2fa99e98ca2 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
@@ -27,7 +27,6 @@ import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.SQLIntegrityConstraintViolationException;
import java.sql.Types;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.UpdateSparseEntityImpl;
import org.caosdb.server.database.exceptions.IntegrityException;
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java
new file mode 100644
index 0000000000000000000000000000000000000000..61e431bab60b9973f6aa1f0b824ffc3e3b60744e
--- /dev/null
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java
@@ -0,0 +1,63 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ */
+package org.caosdb.server.database.backend.implementation.MySQL;
+
+import org.caosdb.server.datatype.ReferenceValue;
+import org.caosdb.server.entity.EntityID;
+import org.caosdb.server.entity.RetrieveEntity;
+import org.caosdb.server.entity.StatementStatusInterface;
+import org.caosdb.server.entity.wrapper.Property;
+
+enum ReplacementStatus implements StatementStatusInterface {
+ REPLACEMENT
+}
+/**
+ * A wrapper of {@link Property} objects used by the back-end implementation for the MySQL/MariaDB
+ * back-end.
+ *
+ * <p>This class helps to transform deeply nested properties, properties with overridden data types,
+ * and much more to the flat (row-like) representation used internally by the back-end (which is an
+ * implementation detail of the back-end or part of the non-public API of the back-end from that
+ * point of view).
+ */
+public class Replacement extends Property {
+
+ public Property replacement;
+
+ @Override
+ public EntityID getId() {
+ return replacement.getId();
+ }
+
+ public void setReplacementId(EntityID id) {
+ replacement.getId().link(id);
+ }
+
+ public Replacement(Property p) {
+ super(p);
+ replacement = new Property(new RetrieveEntity());
+
+ replacement.setDomain(p.getDomainEntity());
+ replacement.setId(new EntityID());
+ replacement.setStatementStatus(ReplacementStatus.REPLACEMENT);
+ replacement.setValue(new ReferenceValue(p.getId()));
+ replacement.setPIdx(0);
+ }
+}
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityPropertiesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityPropertiesImpl.java
index 2406d4895487bdec5f271b41bf46207a48c7375d..f17643fd6ff0e980aef122a318fd9fc2668e2b79 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityPropertiesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityPropertiesImpl.java
@@ -22,15 +22,10 @@
*/
package org.caosdb.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.FlatProperty;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
-import org.caosdb.server.entity.EntityID;
+import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.utils.Undoable;
public interface InsertEntityPropertiesImpl extends BackendTransactionImpl, Undoable {
- public abstract void execute(
- EntityID domain, EntityID entity, FlatProperty fp, Table table, Long unit_sig)
- throws TransactionException;
+ public abstract void execute(EntityInterface entity);
}
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveDatatypesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveDatatypesImpl.java
index 91c68dc56a31fe520d6b29c4b6780afe433f9039..0886ff4374e846acfd14e37b8d2414be912d6e3d 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveDatatypesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveDatatypesImpl.java
@@ -22,11 +22,11 @@
*/
package org.caosdb.server.database.backend.interfaces;
-import java.util.ArrayList;
+import java.util.List;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.proto.VerySparseEntity;
public interface RetrieveDatatypesImpl extends BackendTransactionImpl {
- public abstract ArrayList<VerySparseEntity> execute() throws TransactionException;
+ public abstract List<VerySparseEntity> execute() throws TransactionException;
}
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java
index 9bfddba10a8b548d1259adb22aac392a127a8b5e..9f7eba821e8038befa47f35b31e017aa042bb28f 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java
@@ -22,13 +22,13 @@
*/
package org.caosdb.server.database.backend.interfaces;
-import java.util.ArrayList;
+import java.util.LinkedList;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.proto.VerySparseEntity;
import org.caosdb.server.entity.EntityID;
public interface RetrieveParentsImpl extends BackendTransactionImpl {
- public ArrayList<VerySparseEntity> execute(EntityID id, String version)
+ public LinkedList<VerySparseEntity> execute(EntityID id, String version)
throws TransactionException;
}
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePropertiesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePropertiesImpl.java
index dc1d5aa09653c9a4905dcc456a7037f4009bb838..6bf2051ab1ada80bd09ca074b4b50b6af3abf574 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePropertiesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePropertiesImpl.java
@@ -22,12 +22,13 @@
*/
package org.caosdb.server.database.backend.interfaces;
-import java.util.ArrayList;
+import java.util.LinkedList;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.proto.ProtoProperty;
import org.caosdb.server.entity.EntityID;
public interface RetrievePropertiesImpl extends BackendTransactionImpl {
- public ArrayList<ProtoProperty> execute(EntityID id, String version) throws TransactionException;
+ public LinkedList<ProtoProperty> execute(EntityID id, String version, boolean isHead)
+ throws TransactionException;
}
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityProperties.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityProperties.java
index f9af6a482efaccf896a1a85fc65d0e1217bd6a53..8de8afc084ae16dea370a519a4fde3524fa8c7c9 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityProperties.java
@@ -22,25 +22,10 @@
*/
package org.caosdb.server.database.backend.transaction;
-import java.util.ArrayList;
-import java.util.Deque;
-import java.util.Iterator;
-import java.util.List;
import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.backend.interfaces.InsertEntityPropertiesImpl;
import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.FlatProperty;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.IndexedSingleValue;
-import org.caosdb.server.datatype.SingleValue;
-import org.caosdb.server.entity.EntityID;
import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.wrapper.Property;
public class InsertEntityProperties extends BackendTransaction {
@@ -54,126 +39,6 @@ public class InsertEntityProperties extends BackendTransaction {
public void execute() throws TransactionException {
final InsertEntityPropertiesImpl t = getImplementation(InsertEntityPropertiesImpl.class);
-
- final ArrayList<EntityInterface> stage1Inserts = new ArrayList<EntityInterface>();
- final ArrayList<EntityInterface> stage2Inserts = new ArrayList<EntityInterface>();
-
- DatabaseUtils.deriveStage1Inserts(stage1Inserts, this.entity);
-
- final int domainCount = DatabaseUtils.deriveStage2Inserts(stage2Inserts, stage1Inserts);
-
- final Deque<EntityID> domainIds = execute(new RegisterSubDomain(domainCount)).getDomains();
-
- insertStages(t, domainIds, stage1Inserts, this.entity.getDomain(), this.entity.getId());
- insertStages(t, domainIds, stage2Inserts, this.entity.getId(), null);
- }
-
- private void insertStages(
- final InsertEntityPropertiesImpl t,
- final Deque<EntityID> domainIds,
- final List<EntityInterface> stage1Inserts,
- final EntityID domain,
- final EntityID entity)
- throws TransactionException {
-
- for (final EntityInterface property : stage1Inserts) {
- if (property.hasRole() && property.getRole() == Role.Domain && !property.hasId()) {
- property.setId(domainIds.removeFirst());
- }
- int pIdx;
- if (property instanceof Property) {
- // this is a normal property
- pIdx = ((Property) property).getPIdx();
- } else {
- // this is a replacement
- pIdx = 0;
- }
-
- // prepare flat property
- final FlatProperty fp = new FlatProperty();
- Table table = Table.null_data;
- Long unit_sig = null;
- fp.id = property.getId().toInteger();
- fp.idx = pIdx;
-
- if (property.hasReplacement()) {
- if (!property.getReplacement().hasId()) {
- property.getReplacement().setId(domainIds.removeFirst());
- }
-
- fp.value = property.getReplacement().getId().toString();
- fp.status = StatementStatus.REPLACEMENT.toString();
-
- table = Table.reference_data;
- } else {
- if (property.hasUnit()) {
- unit_sig = property.getUnit().getSignature();
- }
- fp.status = property.getStatementStatus().toString();
- if (property.hasValue()) {
- if (property.getValue() instanceof CollectionValue) {
- // insert collection of values
- final CollectionValue v = (CollectionValue) property.getValue();
- final Iterator<IndexedSingleValue> iterator = v.iterator();
- final SingleValue firstValue = iterator.next();
-
- // insert 2nd to nth item
- for (int i = 1; i < v.size(); i++) {
- final SingleValue vi = iterator.next();
- fp.idx = i;
- if (vi == null) {
- fp.value = null;
- table = Table.null_data;
- } else {
- fp.value = vi.toDatabaseString();
- table = vi.getTable();
- }
- t.execute(
- domain, entity != null ? entity : property.getDomain(), fp, table, unit_sig);
- }
-
- // insert first item
- fp.idx = 0;
- if (firstValue == null) {
- fp.value = null;
- table = Table.null_data;
- } else {
- fp.value = firstValue.toDatabaseString();
- table = firstValue.getTable();
- }
-
- } else {
- // insert single value
- fp.value = ((SingleValue) property.getValue()).toDatabaseString();
- if (property instanceof Property && ((Property) property).isName()) {
- table = Table.name_data;
- } else {
- table = ((SingleValue) property.getValue()).getTable();
- }
- }
- }
- if (property.isNameOverride()) {
- fp.name = property.getName();
- }
- if (property.isDescOverride()) {
- fp.desc = property.getDescription();
- }
- if (property.isDatatypeOverride()) {
- if (property.getDatatype() instanceof AbstractCollectionDatatype) {
- fp.type =
- ((AbstractCollectionDatatype) property.getDatatype())
- .getDatatype()
- .getId()
- .toString();
- fp.collection =
- ((AbstractCollectionDatatype) property.getDatatype()).getCollectionName();
- } else {
- fp.type = property.getDatatype().getId().toString();
- }
- }
- }
-
- t.execute(domain, entity != null ? entity : property.getDomain(), fp, table, unit_sig);
- }
+ t.execute(this.entity);
}
}
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityTransaction.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityTransaction.java
index 5871c97e8ff172fe58b37627cc93824e96c7b32e..2846fa64d56ea696d4ecb0412a88de449d0483a1 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityTransaction.java
@@ -54,7 +54,9 @@ public class InsertEntityTransaction extends BackendTransaction {
if (newEntity.hasFileProperties()) {
execute(new InsertFile(newEntity));
}
- execute(new InsertEntityProperties(newEntity));
+ if (newEntity.hasProperties() || newEntity.hasValue()) {
+ execute(new InsertEntityProperties(newEntity));
+ }
execute(new InsertParents(newEntity));
if (newEntity.getEntityStatus() == EntityStatus.QUALIFIED) {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RegisterSubDomain.java b/src/main/java/org/caosdb/server/database/backend/transaction/RegisterSubDomain.java
deleted file mode 100644
index 0321a621a82a9ae2841d31b55b05a46743f963bd..0000000000000000000000000000000000000000
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RegisterSubDomain.java
+++ /dev/null
@@ -1,49 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package org.caosdb.server.database.backend.transaction;
-
-import java.util.Deque;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RegisterSubDomainImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-
-public class RegisterSubDomain extends BackendTransaction {
-
- private final int domainCount;
- private Deque<EntityID> list;
-
- public RegisterSubDomain(final int domainCount) {
- this.domainCount = domainCount;
- }
-
- @Override
- public void execute() throws TransactionException {
- final RegisterSubDomainImpl t = getImplementation(RegisterSubDomainImpl.class);
- this.list = t.execute(this.domainCount);
- }
-
- public Deque<EntityID> getDomains() {
- return this.list;
- }
-}
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveDatatypes.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveDatatypes.java
index b4a726da8d7b352f69df23a54371feef2d2201c5..1ca9f60e964f1e18ca49b749dde21f8e8785aaa6 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveDatatypes.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveDatatypes.java
@@ -22,7 +22,7 @@
*/
package org.caosdb.server.database.backend.transaction;
-import java.util.ArrayList;
+import java.util.List;
import org.caosdb.server.database.BackendTransaction;
import org.caosdb.server.database.backend.interfaces.RetrieveDatatypesImpl;
import org.caosdb.server.database.exceptions.TransactionException;
@@ -35,7 +35,7 @@ import org.caosdb.server.entity.container.Container;
public class RetrieveDatatypes extends BackendTransaction {
- private ArrayList<VerySparseEntity> list;
+ private List<VerySparseEntity> list;
@Override
public void execute() throws TransactionException {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveParents.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveParents.java
index b551430a26ed6a254789258aca688521f5a57ae4..262ee271acf5b6d3652a0177b0818cbf1e9f74ee 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveParents.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveParents.java
@@ -24,15 +24,18 @@
*/
package org.caosdb.server.database.backend.transaction;
-import java.util.ArrayList;
+import java.util.LinkedList;
+import java.util.List;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
import org.caosdb.server.caching.Cache;
import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.backend.interfaces.RetrieveParentsImpl;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.proto.VerySparseEntity;
+import org.caosdb.server.entity.EntityID;
import org.caosdb.server.entity.EntityInterface;
+import org.caosdb.server.entity.RetrieveEntity;
+import org.caosdb.server.entity.wrapper.Parent;
// TODO Problem with the caching.
// When an old entity version has a parent which is deleted, the name is
@@ -47,9 +50,9 @@ import org.caosdb.server.entity.EntityInterface;
// See also a failing test in caosdb-pyinttest:
// tests/test_version.py::test_bug_cached_parent_name_in_old_version
public class RetrieveParents
- extends CacheableBackendTransaction<String, ArrayList<VerySparseEntity>> {
+ extends CacheableBackendTransaction<String, LinkedList<VerySparseEntity>> {
- private static final ICacheAccess<String, ArrayList<VerySparseEntity>> cache =
+ private static final ICacheAccess<String, LinkedList<VerySparseEntity>> cache =
Cache.getCache("BACKEND_EntityParents");
/**
@@ -71,16 +74,26 @@ public class RetrieveParents
}
@Override
- public ArrayList<VerySparseEntity> executeNoCache() throws TransactionException {
+ public LinkedList<VerySparseEntity> executeNoCache() throws TransactionException {
final RetrieveParentsImpl t = getImplementation(RetrieveParentsImpl.class);
return t.execute(this.entity.getId(), this.entity.getVersion().getId());
}
@Override
- protected void process(final ArrayList<VerySparseEntity> t) throws TransactionException {
+ protected void process(final LinkedList<VerySparseEntity> t) throws TransactionException {
this.entity.getParents().clear();
- DatabaseUtils.parseParentsFromVerySparseEntity(this.entity, t);
+ parseParentsFromVerySparseEntity(this.entity, t);
+ }
+
+ private void parseParentsFromVerySparseEntity(
+ final EntityInterface entity, final List<VerySparseEntity> pars) {
+ for (final VerySparseEntity vsp : pars) {
+ final Parent p = new Parent(new RetrieveEntity(new EntityID(vsp.id)));
+ p.setName(vsp.name);
+ p.setDescription(vsp.description);
+ entity.addParent(p);
+ }
}
@Override
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveProperties.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveProperties.java
index 726382f28c59a45a647098c3d227288fa1fabff6..f9c11303b31ac81696873876b532f9db95f3dbac 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveProperties.java
@@ -24,11 +24,12 @@
*/
package org.caosdb.server.database.backend.transaction;
-import java.util.ArrayList;
+import java.util.LinkedList;
+import java.util.List;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
import org.caosdb.server.caching.Cache;
import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.DatabaseUtils;
+import org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils;
import org.caosdb.server.database.backend.interfaces.RetrievePropertiesImpl;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.proto.ProtoProperty;
@@ -37,11 +38,11 @@ import org.caosdb.server.entity.Role;
import org.caosdb.server.entity.wrapper.Property;
public class RetrieveProperties
- extends CacheableBackendTransaction<String, ArrayList<ProtoProperty>> {
+ extends CacheableBackendTransaction<String, LinkedList<ProtoProperty>> {
private final EntityInterface entity;
public static final String CACHE_REGION = "BACKEND_EntityProperties";
- private static final ICacheAccess<String, ArrayList<ProtoProperty>> cache =
+ private static final ICacheAccess<String, LinkedList<ProtoProperty>> cache =
Cache.getCache(CACHE_REGION);
/**
@@ -61,40 +62,46 @@ public class RetrieveProperties
}
@Override
- public ArrayList<ProtoProperty> executeNoCache() throws TransactionException {
+ public LinkedList<ProtoProperty> executeNoCache() throws TransactionException {
final RetrievePropertiesImpl t = getImplementation(RetrievePropertiesImpl.class);
- return t.execute(this.entity.getId(), this.entity.getVersion().getId());
+ return t.execute(
+ this.entity.getId(), this.entity.getVersion().getId(), this.entity.getVersion().isHead());
}
@Override
- protected void process(final ArrayList<ProtoProperty> t) throws TransactionException {
+ protected void process(final LinkedList<ProtoProperty> t) throws TransactionException {
this.entity.getProperties().clear();
- final ArrayList<Property> props = DatabaseUtils.parseFromProtoProperties(t);
+ final List<Property> props = DatabaseUtils.parseFromProtoProperties(this.entity, t);
+ this.entity.getProperties().addAll(props);
- for (final Property p : props) {
+ retrieveSparseSubproperties(props);
+ }
+
+ private void retrieveSparseSubproperties(List<Property> properties) {
+ for (final Property p : properties) {
// retrieve sparse properties stage 1
+
+ // handle corner case where a record type is used as a property with an overridden name.
+ boolean isNameOverride = p.isNameOverride();
+ String overrideName = p.getName();
+ p.setNameOverride(false);
+
final RetrieveSparseEntity t1 = new RetrieveSparseEntity(p);
execute(t1);
+ String originalName = p.getName();
+ if (isNameOverride) {
+ p.setNameOverride(isNameOverride);
+ p.setName(overrideName);
+ }
- // add default data type for record types
if (!p.hasDatatype() && p.getRole() == Role.RecordType) {
- p.setDatatype(p.getName());
+ p.setDatatype(originalName);
}
// retrieve sparse properties stage 2
- for (final EntityInterface subP : p.getProperties()) {
- final RetrieveSparseEntity t2 = new RetrieveSparseEntity(subP);
- execute(t2);
-
- // add default data type for record types
- if (!subP.hasDatatype() && subP.getRole() == Role.RecordType) {
- subP.setDatatype(subP.getName());
- }
- }
+ retrieveSparseSubproperties(p.getProperties());
}
-
- DatabaseUtils.transformToDeepPropertyTree(this.entity, props);
}
@Override
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
index aabd490b0fb8a6b5e801f6132113726a9361d258..f1ba8354f98fb0f6716fcfe0a742a597b69dd0a3 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
@@ -27,7 +27,6 @@ package org.caosdb.server.database.backend.transaction;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
import org.caosdb.server.caching.Cache;
import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.backend.interfaces.RetrieveSparseEntityImpl;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.proto.SparseEntity;
@@ -81,8 +80,10 @@ public class RetrieveSparseEntity extends CacheableBackendTransaction<String, Sp
@Override
protected void process(final SparseEntity t) throws TransactionException {
- DatabaseUtils.parseFromSparseEntities(this.entity, t);
- this.entity.setEntityStatus(EntityStatus.VALID);
+ if (t != null) {
+ this.entity.parseSparseEntity(t);
+ this.entity.setEntityStatus(EntityStatus.VALID);
+ }
}
@Override
diff --git a/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java b/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java
index 44acaa024513d3f4b8d89c3f59bda9baf9de3044..7a11cd4daf6369649a0205a5637d3e86fbafbffe 100644
--- a/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java
+++ b/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java
@@ -25,9 +25,9 @@ package org.caosdb.server.database.proto;
import java.io.Serializable;
import java.util.List;
-public class ProtoProperty implements Serializable {
-
+public class ProtoProperty extends FlatProperty implements Serializable {
private static final long serialVersionUID = 7731301985162924975L;
- public List<FlatProperty> subProperties = null;
- public FlatProperty property = null;
+
+ public List<ProtoProperty> subProperties = null;
+ public List<Object> collValues = null;
}
diff --git a/src/main/java/org/caosdb/server/entity/Entity.java b/src/main/java/org/caosdb/server/entity/Entity.java
index 48367508112c2c3267abd771fa84eb21ea16a534..614397c50526606176fc50b06e2f07e76cbfb9ff 100644
--- a/src/main/java/org/caosdb/server/entity/Entity.java
+++ b/src/main/java/org/caosdb/server/entity/Entity.java
@@ -47,7 +47,6 @@ import org.caosdb.server.datatype.Value;
import org.caosdb.server.entity.Message.MessageType;
import org.caosdb.server.entity.container.ParentContainer;
import org.caosdb.server.entity.container.PropertyContainer;
-import org.caosdb.server.entity.wrapper.Domain;
import org.caosdb.server.entity.wrapper.Parent;
import org.caosdb.server.entity.wrapper.Property;
import org.caosdb.server.entity.xml.EntityToElementStrategy;
@@ -422,7 +421,7 @@ public abstract class Entity extends AbstractObservable implements EntityInterfa
}
}
- private StatementStatus statementStatus = null;
+ private StatementStatusInterface statementStatus = null;
/**
* statementStatus getter.
@@ -430,7 +429,7 @@ public abstract class Entity extends AbstractObservable implements EntityInterfa
* @return
*/
@Override
- public StatementStatus getStatementStatus() {
+ public StatementStatusInterface getStatementStatus() {
return this.statementStatus;
}
@@ -440,7 +439,7 @@ public abstract class Entity extends AbstractObservable implements EntityInterfa
* @return
*/
@Override
- public void setStatementStatus(final StatementStatus statementStatus) {
+ public void setStatementStatus(final StatementStatusInterface statementStatus) {
this.statementStatus = statementStatus;
}
@@ -609,10 +608,11 @@ public abstract class Entity extends AbstractObservable implements EntityInterfa
@Override
public void parseValue() throws Message {
- if (!this.isParsed) {
- this.isParsed = true;
- setValue(getDatatype().parseValue(getValue()));
+ if (this.isParsed) {
+ return;
}
+ this.isParsed = true;
+ if (getValue() != null) setValue(getDatatype().parseValue(getValue()));
}
@Override
@@ -848,23 +848,6 @@ public abstract class Entity extends AbstractObservable implements EntityInterfa
}
}
- @Override
- public void setReplacement(final Domain d) {
- this.replacement = d;
- }
-
- @Override
- public boolean hasReplacement() {
- return this.replacement != null;
- }
-
- @Override
- public Domain getReplacement() {
- return this.replacement;
- }
-
- private Domain replacement = null;
-
private final HashMap<String, String> flags = new HashMap<String, String>();
@Override
diff --git a/src/main/java/org/caosdb/server/entity/EntityInterface.java b/src/main/java/org/caosdb/server/entity/EntityInterface.java
index f967b307a1ea13a16d7e9225cb038a15f6883727..ba77b5c4ac8b5c833d2046dec506655531ff62cb 100644
--- a/src/main/java/org/caosdb/server/entity/EntityInterface.java
+++ b/src/main/java/org/caosdb/server/entity/EntityInterface.java
@@ -31,7 +31,6 @@ import org.caosdb.server.datatype.AbstractDatatype;
import org.caosdb.server.datatype.Value;
import org.caosdb.server.entity.container.ParentContainer;
import org.caosdb.server.entity.container.PropertyContainer;
-import org.caosdb.server.entity.wrapper.Domain;
import org.caosdb.server.entity.wrapper.Parent;
import org.caosdb.server.entity.wrapper.Property;
import org.caosdb.server.entity.xml.SerializeFieldStrategy;
@@ -58,9 +57,9 @@ public interface EntityInterface
public abstract boolean hasId();
- public abstract StatementStatus getStatementStatus();
+ public abstract StatementStatusInterface getStatementStatus();
- public abstract void setStatementStatus(StatementStatus statementStatus);
+ public abstract void setStatementStatus(StatementStatusInterface statementStatus);
public abstract void setStatementStatus(String statementStatus);
@@ -127,12 +126,6 @@ public interface EntityInterface
public abstract void setProperties(PropertyContainer properties);
- public abstract void setReplacement(Domain d);
-
- public abstract boolean hasReplacement();
-
- public abstract Domain getReplacement();
-
public abstract EntityInterface setDescOverride(boolean b);
public abstract boolean isDescOverride();
diff --git a/src/main/java/org/caosdb/server/entity/StatementStatus.java b/src/main/java/org/caosdb/server/entity/StatementStatus.java
index 0a7971751bffcdfc0323835433fc006bf5269ec9..83d0c57e4ece787e53efa2e149ff0910e1850ed5 100644
--- a/src/main/java/org/caosdb/server/entity/StatementStatus.java
+++ b/src/main/java/org/caosdb/server/entity/StatementStatus.java
@@ -33,17 +33,11 @@ package org.caosdb.server.entity;
* href="../../../../../specification/RecordType.html">the documentation of RecordTypes</a> for more
* information.
*
- * <p>2. Marking an entity as a ``REPLACEMENT`` which is needed for flat representation of deeply
- * nested properties. This constant is only used for internal processes and has no meaning in the
- * API. That is also the reason why this enum is not called "Importance". Apart from that, in most
- * cases its meaning is identical to the importance of an entity.
- *
* @author Timm Fitschen (t.fitschen@indiscale.com)
*/
-public enum StatementStatus {
+public enum StatementStatus implements StatementStatusInterface {
OBLIGATORY,
RECOMMENDED,
SUGGESTED,
FIX,
- REPLACEMENT
}
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RegisterSubDomainImpl.java b/src/main/java/org/caosdb/server/entity/StatementStatusInterface.java
similarity index 58%
rename from src/main/java/org/caosdb/server/database/backend/interfaces/RegisterSubDomainImpl.java
rename to src/main/java/org/caosdb/server/entity/StatementStatusInterface.java
index 87ea0c85db6a698f49c103506b520342deff2fb0..d1596afda95a4836dcd84fc79b67cf2e0b4f12a4 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RegisterSubDomainImpl.java
+++ b/src/main/java/org/caosdb/server/entity/StatementStatusInterface.java
@@ -1,9 +1,8 @@
/*
- * ** header v3.0
* This file is a part of the CaosDB Project.
*
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -17,16 +16,14 @@
*
* 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
*/
-package org.caosdb.server.database.backend.interfaces;
-
-import java.util.Deque;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+package org.caosdb.server.entity;
-public interface RegisterSubDomainImpl extends BackendTransactionImpl {
-
- public abstract Deque<EntityID> execute(int domainCount) throws TransactionException;
+/**
+ * Interface for the StatementStatus. This may be used by back-end implementations to use back-end
+ * specific implementations (e.g.
+ * org.caosdb.server.database.backend.implementation.MySQL.ReplacementStatus).
+ */
+public interface StatementStatusInterface {
+ public String name();
}
diff --git a/src/main/java/org/caosdb/server/entity/wrapper/Domain.java b/src/main/java/org/caosdb/server/entity/wrapper/Domain.java
deleted file mode 100644
index 146706efd2caa74ff1399568bf499f37683bfdbe..0000000000000000000000000000000000000000
--- a/src/main/java/org/caosdb/server/entity/wrapper/Domain.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package org.caosdb.server.entity.wrapper;
-
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.datatype.Value;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.container.PropertyContainer;
-
-public class Domain extends Entity {
-
- private boolean descO;
-
- public Domain(
- final PropertyContainer properties,
- final AbstractDatatype datatype,
- final Value value,
- final org.caosdb.server.entity.StatementStatus statementStatus) {
-
- setRole(Role.Domain);
- setProperties(properties);
- setDatatype(datatype);
- setValue(value);
- setStatementStatus(statementStatus);
- }
-
- @Override
- public EntityInterface setDescOverride(final boolean b) {
- this.descO = b;
- return this;
- }
-
- @Override
- public boolean isDescOverride() {
- return this.descO;
- }
-}
diff --git a/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java b/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java
index 7da945738ac966114a020098171c049a6fa387a3..b294a17e5ea68ee02e529735ec39a748bc4f2c83 100644
--- a/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java
+++ b/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java
@@ -38,7 +38,7 @@ import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.entity.FileProperties;
import org.caosdb.server.entity.Message;
import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.StatementStatus;
+import org.caosdb.server.entity.StatementStatusInterface;
import org.caosdb.server.entity.Version;
import org.caosdb.server.entity.container.ParentContainer;
import org.caosdb.server.entity.container.PropertyContainer;
@@ -112,13 +112,13 @@ public abstract class EntityWrapper implements EntityInterface {
}
@Override
- public StatementStatus getStatementStatus() {
+ public StatementStatusInterface getStatementStatus() {
return this.entity.getStatementStatus();
}
@Override
- public void setStatementStatus(final StatementStatus statementStatus) {
- this.entity.setStatementStatus(statementStatus);
+ public void setStatementStatus(final StatementStatusInterface replacement) {
+ this.entity.setStatementStatus(replacement);
}
@Override
@@ -376,21 +376,6 @@ public abstract class EntityWrapper implements EntityInterface {
this.entity.setProperties(properties);
}
- @Override
- public void setReplacement(final Domain d) {
- this.entity.setReplacement(d);
- }
-
- @Override
- public boolean hasReplacement() {
- return this.entity.hasReplacement();
- }
-
- @Override
- public Domain getReplacement() {
- return this.entity.getReplacement();
- }
-
@Override
public Map<String, String> getFlags() {
return this.entity.getFlags();
diff --git a/src/main/java/org/caosdb/server/entity/wrapper/Property.java b/src/main/java/org/caosdb/server/entity/wrapper/Property.java
index efa1a6857a8dec0b3d7dcc45ec689d5b3bc0f745..9268d7f3cb327a70a4cca872657d72e2779fc344 100644
--- a/src/main/java/org/caosdb/server/entity/wrapper/Property.java
+++ b/src/main/java/org/caosdb/server/entity/wrapper/Property.java
@@ -25,11 +25,13 @@ package org.caosdb.server.entity.wrapper;
import org.apache.shiro.authz.AuthorizationException;
import org.apache.shiro.authz.Permission;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.proto.FlatProperty;
+import org.caosdb.server.database.proto.ProtoProperty;
import org.caosdb.server.datatype.AbstractCollectionDatatype;
+import org.caosdb.server.datatype.CollectionValue;
import org.caosdb.server.datatype.GenericValue;
import org.caosdb.server.entity.EntityID;
import org.caosdb.server.entity.EntityInterface;
+import org.caosdb.server.entity.RetrieveEntity;
import org.caosdb.server.entity.xml.PropertyToElementStrategy;
public class Property extends EntityWrapper {
@@ -72,29 +74,45 @@ public class Property extends EntityWrapper {
return this;
}
- public Property parseFlatProperty(final FlatProperty fp) {
- setId(new EntityID(fp.id));
- setStatementStatus(fp.status);
- setPIdx(fp.idx);
- if (fp.name != null) {
- setName(fp.name);
+ public Property parseProtoProperty(final ProtoProperty pp) {
+ setId(new EntityID(pp.id));
+ setStatementStatus(pp.status);
+ setPIdx(pp.idx);
+ if (pp.name != null) {
+ setName(pp.name);
setNameOverride(true);
}
- if (fp.desc != null) {
- setDescription(fp.desc);
+ if (pp.desc != null) {
+ setDescription(pp.desc);
setDescOverride(true);
}
- if (fp.type != null) {
- if (fp.collection != null) {
+ if (pp.type != null) {
+ if (pp.collection != null) {
this.setDatatype(
- AbstractCollectionDatatype.collectionDatatypeFactory(fp.collection, fp.type));
+ AbstractCollectionDatatype.collectionDatatypeFactory(pp.collection, pp.type));
} else {
- this.setDatatype(fp.type);
+ this.setDatatype(pp.type);
}
setDatatypeOverride(true);
}
- if (fp.value != null) {
- setValue(new GenericValue(fp.value));
+ if (pp.value != null) {
+ setValue(new GenericValue(pp.value));
+ }
+ if (pp.collValues != null) {
+ CollectionValue value = new CollectionValue();
+ for (Object next : pp.collValues) {
+ if (next == null) {
+ value.add(null);
+ } else {
+ value.add(new GenericValue(next.toString()));
+ }
+ }
+ setValue(value);
+ }
+ if (pp.subProperties != null) {
+ for (ProtoProperty subP : pp.subProperties) {
+ this.addProperty(new Property(new RetrieveEntity()).parseProtoProperty(subP));
+ }
}
return this;
}
diff --git a/src/main/java/org/caosdb/server/entity/xml/EntityToElementStrategy.java b/src/main/java/org/caosdb/server/entity/xml/EntityToElementStrategy.java
index 7f6e6dcae9152091b854007149b0793cbff45542..35d94aa79fd62a04f8b0dae1a17829a1106c2d97 100644
--- a/src/main/java/org/caosdb/server/entity/xml/EntityToElementStrategy.java
+++ b/src/main/java/org/caosdb/server/entity/xml/EntityToElementStrategy.java
@@ -85,9 +85,7 @@ public class EntityToElementStrategy implements ToElementStrategy {
// @review Florian Spreckelsen 2022-03-22
- if (entity.getEntityACL() != null) {
- element.addContent(entity.getEntityACL().getPermissionsFor(SecurityUtils.getSubject()));
- }
+ addPermissions(entity, element);
if (serializeFieldStrategy.isToBeSet("id") && entity.hasId()) {
element.setAttribute("id", entity.getId().toString());
}
@@ -135,6 +133,12 @@ public class EntityToElementStrategy implements ToElementStrategy {
}
}
+ protected void addPermissions(EntityInterface entity, Element element) {
+ if (entity.getEntityACL() != null) {
+ element.addContent(entity.getEntityACL().getPermissionsFor(SecurityUtils.getSubject()));
+ }
+ }
+
/**
* Set the value of the entity.
*
diff --git a/src/main/java/org/caosdb/server/entity/xml/PropertyToElementStrategy.java b/src/main/java/org/caosdb/server/entity/xml/PropertyToElementStrategy.java
index 23fd8a553e66df23349c20e8539e3154f3e2ac0a..7109a0d8d5312dcb7cbdecc587dc28fe0a4146ba 100644
--- a/src/main/java/org/caosdb/server/entity/xml/PropertyToElementStrategy.java
+++ b/src/main/java/org/caosdb/server/entity/xml/PropertyToElementStrategy.java
@@ -35,6 +35,11 @@ public class PropertyToElementStrategy extends EntityToElementStrategy {
super("Property");
}
+ @Override
+ protected void addPermissions(EntityInterface entity, Element element) {
+ // don't
+ }
+
@Override
public Element addToElement(
final EntityInterface entity,
diff --git a/src/main/java/org/caosdb/server/grpc/CaosDBToGrpcConverters.java b/src/main/java/org/caosdb/server/grpc/CaosDBToGrpcConverters.java
index 6fef590746bbf2c3ff802baec73385e4b061ec95..8ab8b0579bd6d0a32976ac6e2e28e776f00d4850 100644
--- a/src/main/java/org/caosdb/server/grpc/CaosDBToGrpcConverters.java
+++ b/src/main/java/org/caosdb/server/grpc/CaosDBToGrpcConverters.java
@@ -75,6 +75,7 @@ import org.caosdb.server.entity.MagicTypes;
import org.caosdb.server.entity.Message;
import org.caosdb.server.entity.Role;
import org.caosdb.server.entity.StatementStatus;
+import org.caosdb.server.entity.StatementStatusInterface;
import org.caosdb.server.entity.container.ParentContainer;
import org.caosdb.server.entity.container.RetrieveContainer;
import org.caosdb.server.entity.wrapper.Property;
@@ -298,6 +299,8 @@ public class CaosDBToGrpcConverters {
} else if (value instanceof GenericValue) {
return convertGenericValue((GenericValue) value);
+ } else if (value == null) {
+ return ScalarValue.newBuilder().setSpecialValue(SpecialValue.SPECIAL_VALUE_UNSPECIFIED);
}
return null;
}
@@ -357,8 +360,8 @@ public class CaosDBToGrpcConverters {
return convertScalarValue(v.getWrapped()).build();
}
- private Importance convert(final StatementStatus statementStatus) {
- switch (statementStatus) {
+ private Importance convert(final StatementStatusInterface statementStatus) {
+ switch ((StatementStatus) statementStatus) {
case FIX:
return Importance.IMPORTANCE_FIX;
case OBLIGATORY:
@@ -704,7 +707,7 @@ public class CaosDBToGrpcConverters {
return null;
}
- private org.caosdb.api.entity.v1.Value.Builder getSelectedValue(Selection s, EntityInterface e) {
+ org.caosdb.api.entity.v1.Value.Builder getSelectedValue(Selection s, EntityInterface e) {
org.caosdb.api.entity.v1.Value.Builder result = null;
String selector = s.getSelector();
result = handleSpecialSelectors(selector, e);
@@ -735,8 +738,9 @@ public class CaosDBToGrpcConverters {
result = getSelectedValue(s.getSubselection(), referenced_entity);
} else if (v instanceof CollectionValue) {
for (Value i : (CollectionValue) v) {
- if (i instanceof ReferenceValue) {
- EntityInterface referenced_entity = ((ReferenceValue) i).getEntity();
+ Value wrapped = ((IndexedSingleValue) i).getWrapped();
+ if (wrapped instanceof ReferenceValue) {
+ EntityInterface referenced_entity = ((ReferenceValue) wrapped).getEntity();
result = getSelectedValue(s.getSubselection(), referenced_entity);
results.add(result);
} else {
diff --git a/src/main/java/org/caosdb/server/grpc/LoggingInterceptor.java b/src/main/java/org/caosdb/server/grpc/LoggingInterceptor.java
index 9edd35090659e908ecf7f3fb502d34c36ac7e829..4e52485d4af4357b90a560baee6095c3b14683ae 100644
--- a/src/main/java/org/caosdb/server/grpc/LoggingInterceptor.java
+++ b/src/main/java/org/caosdb/server/grpc/LoggingInterceptor.java
@@ -1,5 +1,6 @@
package org.caosdb.server.grpc;
+import io.grpc.Attributes.Key;
import io.grpc.Context;
import io.grpc.Contexts;
import io.grpc.Metadata;
@@ -7,18 +8,70 @@ import io.grpc.ServerCall;
import io.grpc.ServerCall.Listener;
import io.grpc.ServerCallHandler;
import io.grpc.ServerInterceptor;
+import java.net.SocketAddress;
+import org.caosdb.server.CaosDBServer;
+import org.caosdb.server.ServerProperties;
+import org.restlet.routing.Template;
+import org.restlet.util.Resolver;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+class CallResolver<ReqT, RespT> extends Resolver<String> {
+
+ private ServerCall<ReqT, RespT> call;
+ private Metadata headers;
+
+ public static final Metadata.Key<String> KEY_USER_AGENT =
+ Metadata.Key.of("user-agent", Metadata.ASCII_STRING_MARSHALLER);
+ public static final Key<SocketAddress> KEY_LOCAL_ADDRESS = io.grpc.Grpc.TRANSPORT_ATTR_LOCAL_ADDR;
+ public static final Key<SocketAddress> KEY_REMOTE_ADDRESS =
+ io.grpc.Grpc.TRANSPORT_ATTR_REMOTE_ADDR;
+
+ public CallResolver(
+ ServerCall<ReqT, RespT> call, Metadata headers, ServerCallHandler<ReqT, RespT> next) {
+ this.call = call;
+ this.headers = headers;
+ }
+
+ @Override
+ public String resolve(String name) {
+ switch (name) {
+ case "user-agent":
+ return headers.get(KEY_USER_AGENT);
+ case "remote-address":
+ return call.getAttributes().get(KEY_REMOTE_ADDRESS).toString();
+ case "local-address":
+ return call.getAttributes().get(KEY_LOCAL_ADDRESS).toString();
+ case "method":
+ return call.getMethodDescriptor().getFullMethodName();
+ default:
+ break;
+ }
+ return null;
+ }
+}
+
public class LoggingInterceptor implements ServerInterceptor {
+ private Template template;
+
+ public LoggingInterceptor() {
+ String format = CaosDBServer.getServerProperty(ServerProperties.KEY_GRPC_RESPONSE_LOG_FORMAT);
+ if ("OFF".equalsIgnoreCase(format)) {
+ this.template = null;
+ } else if (format != null) {
+ this.template = new Template(format);
+ }
+ }
+
private static final Logger logger = LoggerFactory.getLogger(LoggingInterceptor.class.getName());
@Override
public <ReqT, RespT> Listener<ReqT> interceptCall(
ServerCall<ReqT, RespT> call, Metadata headers, ServerCallHandler<ReqT, RespT> next) {
-
- logger.info(call.getMethodDescriptor().getFullMethodName() + " - " + call.getAttributes());
+ if (template != null) {
+ logger.info(template.format(new CallResolver<ReqT, RespT>(call, headers, next)));
+ }
return Contexts.interceptCall(Context.current(), call, headers, next);
}
}
diff --git a/src/main/java/org/caosdb/server/logging/log4j/CustomConfigurationFactory.java b/src/main/java/org/caosdb/server/logging/log4j/CustomConfigurationFactory.java
index 62722317f882dffae4168808514a6d972ae8bfe6..4416227f9672a9b3be3ffb34306e78de04a20a2f 100644
--- a/src/main/java/org/caosdb/server/logging/log4j/CustomConfigurationFactory.java
+++ b/src/main/java/org/caosdb/server/logging/log4j/CustomConfigurationFactory.java
@@ -54,7 +54,7 @@ public class CustomConfigurationFactory extends PropertiesConfigurationFactory {
LOGGER.debug("Reconfiguration is done by {}", getClass().toString());
List<String> sources = getConfigFiles();
- if (sources.size() > 1) {
+ if (sources.size() > 0) {
final List<AbstractConfiguration> configs = new ArrayList<>();
for (final String sourceLocation : sources) {
LOGGER.debug("Reconfigure with {}", sourceLocation);
diff --git a/src/main/java/org/caosdb/server/query/Backreference.java b/src/main/java/org/caosdb/server/query/Backreference.java
index 7d551fd45e761a54d2c2508dcbb1b98ffc72891c..b801ffaf396a3ba9f98531ca06fc274b05c70b96 100644
--- a/src/main/java/org/caosdb/server/query/Backreference.java
+++ b/src/main/java/org/caosdb/server/query/Backreference.java
@@ -23,7 +23,7 @@
package org.caosdb.server.query;
import static java.sql.Types.VARCHAR;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
diff --git a/src/main/java/org/caosdb/server/query/Conjunction.java b/src/main/java/org/caosdb/server/query/Conjunction.java
index 03b331242e239a26f108973ca7a37624ab80ea64..59dfd57b20ed8bce443e670e767dc42bb91ac6ac 100644
--- a/src/main/java/org/caosdb/server/query/Conjunction.java
+++ b/src/main/java/org/caosdb/server/query/Conjunction.java
@@ -22,7 +22,7 @@
*/
package org.caosdb.server.query;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
diff --git a/src/main/java/org/caosdb/server/query/Disjunction.java b/src/main/java/org/caosdb/server/query/Disjunction.java
index edd2e6daf243cd25ea112fdbfb946f2b80ee80b1..925ef85952e2d31783a6f7447074d0384e508a98 100644
--- a/src/main/java/org/caosdb/server/query/Disjunction.java
+++ b/src/main/java/org/caosdb/server/query/Disjunction.java
@@ -22,7 +22,7 @@
*/
package org.caosdb.server.query;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
diff --git a/src/main/java/org/caosdb/server/query/Negation.java b/src/main/java/org/caosdb/server/query/Negation.java
index cfdfd05e286030f525b8d4f3c291e2bdfb27b100..431124df7b995faf6aa493363a51095e7028b9b8 100644
--- a/src/main/java/org/caosdb/server/query/Negation.java
+++ b/src/main/java/org/caosdb/server/query/Negation.java
@@ -22,7 +22,7 @@
*/
package org.caosdb.server.query;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
diff --git a/src/main/java/org/caosdb/server/query/POV.java b/src/main/java/org/caosdb/server/query/POV.java
index 0de160cdb6249ffaea10f4eeeafdf4884323a186..ebc35a16b1495accf8cd4a114dd688c2b2529c1b 100644
--- a/src/main/java/org/caosdb/server/query/POV.java
+++ b/src/main/java/org/caosdb/server/query/POV.java
@@ -25,7 +25,7 @@ package org.caosdb.server.query;
import static java.sql.Types.DOUBLE;
import static java.sql.Types.INTEGER;
import static java.sql.Types.VARCHAR;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import de.timmfitschen.easyunits.parser.ParserException;
import java.sql.CallableStatement;
diff --git a/src/main/java/org/caosdb/server/query/Query.java b/src/main/java/org/caosdb/server/query/Query.java
index c4a458630456d057ccddf26c48def0e72ccf3789..abaca4365e54c21ee2ba8cf8bf7727fe746c7277 100644
--- a/src/main/java/org/caosdb/server/query/Query.java
+++ b/src/main/java/org/caosdb/server/query/Query.java
@@ -21,7 +21,7 @@
*/
package org.caosdb.server.query;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.io.Serializable;
import java.sql.CallableStatement;
diff --git a/src/main/java/org/caosdb/server/query/SubProperty.java b/src/main/java/org/caosdb/server/query/SubProperty.java
index 8ff167eac1e045875576a75f3d922f5c6461c68e..d5ce923449b45cb45dab77e4c30b5d8b343e01e3 100644
--- a/src/main/java/org/caosdb/server/query/SubProperty.java
+++ b/src/main/java/org/caosdb/server/query/SubProperty.java
@@ -23,7 +23,7 @@
package org.caosdb.server.query;
import static java.sql.Types.VARCHAR;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
diff --git a/src/main/java/org/caosdb/server/resource/FileSystemResource.java b/src/main/java/org/caosdb/server/resource/FileSystemResource.java
index 1e601cb2116c92ae3aa31aaca4be01b429f9e826..9c0d615833148f706b190d7dfbc1aafdca61a75f 100644
--- a/src/main/java/org/caosdb/server/resource/FileSystemResource.java
+++ b/src/main/java/org/caosdb/server/resource/FileSystemResource.java
@@ -86,14 +86,16 @@ public class FileSystemResource extends AbstractCaosDBServerResource {
}
if (file.isDirectory()) {
- String referenceString = getReference().toString();
- if (!referenceString.endsWith("/")) {
- referenceString = referenceString + "/";
- }
+ String path = (specifier.endsWith("/") ? specifier : specifier + "/");
+ String url =
+ getUtils().getServerRootURI()
+ + "/FileSystem"
+ + (path.startsWith("/") ? path : ("/" + path));
+
final Element folder = new Element("dir");
- folder.setAttribute("path", (specifier.endsWith("/") ? specifier : specifier + "/"));
+ folder.setAttribute("path", path);
folder.setAttribute("name", file.getName());
- folder.setAttribute("url", referenceString);
+ folder.setAttribute("url", url);
final boolean thumbnailsExist =
new File(file.getAbsolutePath() + File.separator + ".thumbnails").exists();
@@ -110,7 +112,7 @@ public class FileSystemResource extends AbstractCaosDBServerResource {
}
if (thumbnailsExist) {
- final Attribute thumbnailAttribute = getThumbnailAttribute(file, child, referenceString);
+ final Attribute thumbnailAttribute = getThumbnailAttribute(file, child, url);
if (thumbnailAttribute != null) {
celem.setAttribute(thumbnailAttribute);
}
diff --git a/src/main/java/org/caosdb/server/utils/ResultSetIterator.java b/src/main/java/org/caosdb/server/utils/ResultSetIterator.java
index 0912d278c7158c9b7b75a585c2827d851951f29b..71429f1a704299555ab1d86be0695e3104be828d 100644
--- a/src/main/java/org/caosdb/server/utils/ResultSetIterator.java
+++ b/src/main/java/org/caosdb/server/utils/ResultSetIterator.java
@@ -1,6 +1,6 @@
package org.caosdb.server.utils;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.ResultSet;
import java.sql.SQLException;
diff --git a/src/main/java/org/caosdb/server/utils/WebinterfaceUtils.java b/src/main/java/org/caosdb/server/utils/WebinterfaceUtils.java
index 375d6b5e7bbced84cec5bdcdee26a9e436f0215a..6c583fccce77471ae4a4272f35d94ec2c886afd3 100644
--- a/src/main/java/org/caosdb/server/utils/WebinterfaceUtils.java
+++ b/src/main/java/org/caosdb/server/utils/WebinterfaceUtils.java
@@ -61,6 +61,23 @@ public class WebinterfaceUtils {
private long buildNumberDate;
private static final Map<String, WebinterfaceUtils> instances = new HashMap<>();
+ public static String getForwardedProto(Request request) {
+ String scheme = null;
+ String forwarded = request.getHeaders().getFirstValue("Forwarded", true);
+ if (forwarded != null) {
+ for (String directive : forwarded.split(";")) {
+ String[] s = directive.split("=", 2);
+ if (s.length == 2 && "proto".equalsIgnoreCase(s[0])) {
+ scheme = s[1];
+ }
+ }
+ }
+ if (scheme == null) {
+ scheme = request.getHeaders().getFirstValue("X-Forwarded-Proto", true);
+ }
+ return scheme;
+ }
+
/**
* Retrieve an instance of {@link WebinterfaceUtils} for the request. The instance can be shared
* with other callers.
@@ -70,7 +87,7 @@ public class WebinterfaceUtils {
*/
public static WebinterfaceUtils getInstance(Request request) {
String hostStr = request.getHostRef().getHostIdentifier();
- String scheme = request.getHeaders().getFirstValue("X-Forwarded-Proto", true);
+ String scheme = getForwardedProto(request);
if (scheme != null) {
hostStr = hostStr.replaceFirst("^" + request.getHostRef().getScheme(), scheme);
}
diff --git a/src/test/java/org/caosdb/server/database/InsertTest.java b/src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java
similarity index 55%
rename from src/test/java/org/caosdb/server/database/InsertTest.java
rename to src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java
index 524e7addd20581db349082f91206605a97bdee8e..03bd185c8884822f89f8ff323a1c32125b66f88b 100644
--- a/src/test/java/org/caosdb/server/database/InsertTest.java
+++ b/src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java
@@ -20,21 +20,24 @@
*
* ** end header
*/
-package org.caosdb.server.database;
+package org.caosdb.server.database.backend.implementation.MySQL;
-import static org.caosdb.server.database.DatabaseUtils.deriveStage1Inserts;
-import static org.caosdb.server.database.DatabaseUtils.deriveStage2Inserts;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.deriveStage1Inserts;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.deriveStage2Inserts;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
+import java.util.ArrayDeque;
+import java.util.Deque;
import java.util.LinkedList;
+import java.util.List;
import org.caosdb.server.datatype.CollectionValue;
import org.caosdb.server.datatype.GenericValue;
+import org.caosdb.server.datatype.ReferenceValue;
import org.caosdb.server.datatype.SingleValue;
import org.caosdb.server.entity.Entity;
import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.entity.InsertEntity;
import org.caosdb.server.entity.RetrieveEntity;
import org.caosdb.server.entity.Role;
@@ -44,6 +47,14 @@ import org.junit.jupiter.api.Test;
public class InsertTest {
+ private Deque<EntityID> registerReplacementIds(int count) {
+ Deque<EntityID> replacementIds = new ArrayDeque<>();
+ for (int i = 1; i < count + 1; i++) {
+ replacementIds.add(new EntityID(-i));
+ }
+ return replacementIds;
+ }
+
/**
* Record with very deep property tree.
*
@@ -122,79 +133,67 @@ public class InsertTest {
p10.setStatementStatus(StatementStatus.OBLIGATORY);
p9.addProperty(p10);
- final LinkedList<EntityInterface> stage1Inserts = new LinkedList<EntityInterface>();
- final LinkedList<EntityInterface> stage2Inserts = new LinkedList<EntityInterface>();
- new LinkedList<EntityInterface>();
- deriveStage1Inserts(stage1Inserts, r);
+ final LinkedList<Property> stage1Inserts = new LinkedList<>();
+ final LinkedList<Property> stage2Inserts = new LinkedList<>();
+
+ int replacementCount = deriveStage1Inserts(stage1Inserts, r);
+ assertEquals(3, replacementCount);
+
+ deriveStage2Inserts(stage2Inserts, stage1Inserts, registerReplacementIds(replacementCount), r);
assertEquals(7, stage1Inserts.size());
- assertEquals(Role.Property, stage1Inserts.get(0).getRole());
- assertEquals(new EntityID(1), stage1Inserts.get(0).getId());
+ assertFalse(stage1Inserts.get(0) instanceof Replacement);
+ assertEquals(1, stage1Inserts.get(0).getId().toInteger());
assertEquals("V1", ((SingleValue) stage1Inserts.get(0).getValue()).toDatabaseString());
- assertFalse(stage1Inserts.get(0).hasReplacement());
- assertEquals(Role.Property, stage1Inserts.get(1).getRole());
- assertEquals(new EntityID(2), stage1Inserts.get(1).getId());
+ assertFalse(stage1Inserts.get(1) instanceof Replacement);
+ assertEquals(2, stage1Inserts.get(1).getId().toInteger());
assertEquals("V2", ((SingleValue) stage1Inserts.get(1).getValue()).toDatabaseString());
- assertFalse(stage1Inserts.get(1).hasReplacement());
- assertEquals(Role.Property, stage1Inserts.get(2).getRole());
- assertEquals(new EntityID(4), stage1Inserts.get(2).getId());
+ assertFalse(stage1Inserts.get(2) instanceof Replacement);
+ assertEquals(4, stage1Inserts.get(2).getId().toInteger());
assertEquals("V4", ((SingleValue) stage1Inserts.get(2).getValue()).toDatabaseString());
- assertFalse(stage1Inserts.get(2).hasReplacement());
- assertEquals(Role.Domain, stage1Inserts.get(3).getRole());
+ assertTrue(stage1Inserts.get(3) instanceof Replacement);
+ assertEquals(-1, stage1Inserts.get(3).getId().toInteger());
assertEquals("V5", ((SingleValue) stage1Inserts.get(3).getValue()).toDatabaseString());
- assertFalse(stage1Inserts.get(3).hasReplacement());
- assertEquals(Role.Property, stage1Inserts.get(4).getRole());
- assertEquals(new EntityID(7), stage1Inserts.get(4).getId());
+ assertFalse(stage1Inserts.get(4) instanceof Replacement);
+ assertEquals(7, stage1Inserts.get(4).getId().toInteger());
assertEquals("V7", ((SingleValue) stage1Inserts.get(4).getValue()).toDatabaseString());
- assertFalse(stage1Inserts.get(4).hasReplacement());
- assertEquals(Role.Domain, stage1Inserts.get(5).getRole());
+ assertTrue(stage1Inserts.get(5) instanceof Replacement);
+ assertEquals(-2, stage1Inserts.get(5).getId().toInteger());
assertEquals("V8", ((SingleValue) stage1Inserts.get(5).getValue()).toDatabaseString());
- assertFalse(stage1Inserts.get(5).hasReplacement());
- assertEquals(Role.Domain, stage1Inserts.get(6).getRole());
+ assertTrue(stage1Inserts.get(6) instanceof Replacement);
+ assertEquals(-3, stage1Inserts.get(6).getId().toInteger());
assertEquals("V9", ((SingleValue) stage1Inserts.get(6).getValue()).toDatabaseString());
- assertFalse(stage1Inserts.get(6).hasReplacement());
-
- deriveStage2Inserts(stage2Inserts, stage1Inserts);
assertEquals(6, stage2Inserts.size());
- assertEquals(Role.Property, stage2Inserts.get(0).getRole());
assertEquals(new EntityID(3), stage2Inserts.get(0).getId());
assertEquals("V3", ((SingleValue) stage2Inserts.get(0).getValue()).toDatabaseString());
- assertFalse(stage2Inserts.get(0).hasReplacement());
+ assertEquals(new EntityID(2), stage2Inserts.get(0).getDomain());
- assertEquals(Role.Property, stage2Inserts.get(1).getRole());
assertEquals(new EntityID(5), stage2Inserts.get(1).getId());
assertEquals("V5", ((SingleValue) stage2Inserts.get(1).getValue()).toDatabaseString());
- assertTrue(stage2Inserts.get(1).hasReplacement());
- assertEquals(stage1Inserts.get(3), stage2Inserts.get(1).getReplacement());
+ assertEquals(new EntityID(4), stage2Inserts.get(1).getDomain());
- assertEquals(Role.Property, stage2Inserts.get(2).getRole());
assertEquals(new EntityID(6), stage2Inserts.get(2).getId());
assertEquals("V6", ((SingleValue) stage2Inserts.get(2).getValue()).toDatabaseString());
- assertFalse(stage2Inserts.get(2).hasReplacement());
+ assertEquals(new EntityID(-1), stage2Inserts.get(2).getDomain());
- assertEquals(Role.Property, stage2Inserts.get(3).getRole());
assertEquals(new EntityID(8), stage2Inserts.get(3).getId());
assertEquals("V8", ((SingleValue) stage2Inserts.get(3).getValue()).toDatabaseString());
- assertTrue(stage2Inserts.get(3).hasReplacement());
- assertEquals(stage1Inserts.get(5), stage2Inserts.get(3).getReplacement());
+ assertEquals(new EntityID(7), stage2Inserts.get(3).getDomain());
- assertEquals(Role.Property, stage2Inserts.get(4).getRole());
assertEquals(new EntityID(9), stage2Inserts.get(4).getId());
assertEquals("V9", ((SingleValue) stage2Inserts.get(4).getValue()).toDatabaseString());
- assertTrue(stage2Inserts.get(4).hasReplacement());
- assertEquals(stage1Inserts.get(6), stage2Inserts.get(4).getReplacement());
+ assertEquals(new EntityID(-2), stage2Inserts.get(4).getDomain());
- assertEquals(Role.Property, stage2Inserts.get(5).getRole());
assertEquals(new EntityID(10), stage2Inserts.get(5).getId());
assertEquals("V10", ((SingleValue) stage2Inserts.get(5).getValue()).toDatabaseString());
- assertFalse(stage2Inserts.get(5).hasReplacement());
+ assertEquals(new EntityID(-3), stage2Inserts.get(5).getDomain());
}
/**
@@ -227,34 +226,31 @@ public class InsertTest {
subp.setStatementStatus(StatementStatus.FIX);
p2.addProperty(subp);
- final LinkedList<EntityInterface> stage1Inserts = new LinkedList<EntityInterface>();
- final LinkedList<EntityInterface> stage2Inserts = new LinkedList<EntityInterface>();
+ final LinkedList<Property> stage1Inserts = new LinkedList<>();
+ final LinkedList<Property> stage2Inserts = new LinkedList<>();
- deriveStage1Inserts(stage1Inserts, r);
+ int replacementCount = deriveStage1Inserts(stage1Inserts, r);
+ deriveStage2Inserts(stage2Inserts, stage1Inserts, registerReplacementIds(replacementCount), r);
assertEquals(3, stage1Inserts.size());
- assertEquals(Role.Property, stage1Inserts.get(0).getRole());
+
+ assertFalse(stage1Inserts.get(0) instanceof Replacement);
assertEquals(new EntityID(1), stage1Inserts.get(0).getId());
assertEquals("V1-1", ((SingleValue) stage1Inserts.get(0).getValue()).toDatabaseString());
- assertFalse(stage1Inserts.get(0).hasReplacement());
- assertEquals(Role.Property, stage1Inserts.get(1).getRole());
+ assertTrue(stage1Inserts.get(1) instanceof Replacement);
assertEquals("V1-2", ((SingleValue) stage1Inserts.get(1).getValue()).toDatabaseString());
- assertEquals(new EntityID(1), stage1Inserts.get(1).getId());
- assertTrue(stage1Inserts.get(1).hasReplacement());
- assertEquals(stage1Inserts.get(2), stage1Inserts.get(1).getReplacement());
+ assertEquals(new EntityID(-1), stage1Inserts.get(1).getId());
- assertEquals(Role.Domain, stage1Inserts.get(2).getRole());
- assertEquals("V1-2", ((SingleValue) stage1Inserts.get(2).getValue()).toDatabaseString());
- assertFalse(stage1Inserts.get(2).hasReplacement());
-
- deriveStage2Inserts(stage2Inserts, stage1Inserts);
+ assertFalse(stage1Inserts.get(2) instanceof Replacement);
+ assertEquals(new EntityID(-1), stage1Inserts.get(2).getId());
+ assertEquals("1", ((SingleValue) stage1Inserts.get(2).getValue()).toDatabaseString());
assertEquals(1, stage2Inserts.size());
- assertEquals(Role.Property, stage2Inserts.get(0).getRole());
+
+ assertFalse(stage2Inserts.get(0) instanceof Replacement);
assertEquals(new EntityID(2), stage2Inserts.get(0).getId());
assertEquals("V2", ((SingleValue) stage2Inserts.get(0).getValue()).toDatabaseString());
- assertFalse(stage2Inserts.get(0).hasReplacement());
}
/**
@@ -291,39 +287,33 @@ public class InsertTest {
sub1.setStatementStatus(StatementStatus.FIX);
p1.addProperty(sub1);
- final LinkedList<EntityInterface> stage1Inserts = new LinkedList<EntityInterface>();
- final LinkedList<EntityInterface> stage2Inserts = new LinkedList<EntityInterface>();
+ final LinkedList<Property> stage1Inserts = new LinkedList<>();
+ final LinkedList<Property> stage2Inserts = new LinkedList<>();
- deriveStage1Inserts(stage1Inserts, r);
+ int count = deriveStage1Inserts(stage1Inserts, r);
+ deriveStage2Inserts(stage2Inserts, stage1Inserts, registerReplacementIds(count), r);
assertEquals(4, stage1Inserts.size());
- assertEquals(Role.Property, stage1Inserts.get(0).getRole());
- assertEquals(new EntityID(1), stage1Inserts.get(0).getId());
- assertTrue(stage1Inserts.get(0).hasReplacement());
- assertEquals(stage1Inserts.get(1), stage1Inserts.get(0).getReplacement());
+ assertTrue(stage1Inserts.get(0) instanceof Replacement);
+ assertEquals(new EntityID(-1), stage1Inserts.get(0).getId());
assertEquals(null, stage1Inserts.get(0).getValue());
- assertEquals(Role.Domain, stage1Inserts.get(1).getRole());
- assertFalse(stage1Inserts.get(1).hasReplacement());
- assertEquals(null, stage1Inserts.get(1).getValue());
+ assertFalse(stage1Inserts.get(1) instanceof Replacement);
+ assertEquals(new EntityID(-1), stage1Inserts.get(1).getId());
+ assertEquals(1, ((ReferenceValue) stage1Inserts.get(1).getValue()).getId().toInteger());
- assertEquals(Role.Property, stage1Inserts.get(2).getRole());
+ assertFalse(stage1Inserts.get(2) instanceof Replacement);
assertEquals(new EntityID(1), stage1Inserts.get(2).getId());
- assertFalse(stage1Inserts.get(2).hasReplacement());
assertEquals(null, stage1Inserts.get(2).getValue());
- assertEquals(Role.Property, stage1Inserts.get(3).getRole());
+ assertFalse(stage1Inserts.get(3) instanceof Replacement);
assertEquals(new EntityID(1), stage1Inserts.get(3).getId());
- assertFalse(stage1Inserts.get(3).hasReplacement());
assertEquals(null, stage1Inserts.get(3).getValue());
- deriveStage2Inserts(stage2Inserts, stage1Inserts);
-
assertEquals(1, stage2Inserts.size());
- assertEquals(Role.Property, stage2Inserts.get(0).getRole());
assertEquals(new EntityID(2), stage2Inserts.get(0).getId());
assertEquals("V1", ((SingleValue) stage2Inserts.get(0).getValue()).toDatabaseString());
- assertFalse(stage2Inserts.get(0).hasReplacement());
+ assertEquals(new EntityID(-1), stage2Inserts.get(0).getDomain());
}
/**
@@ -360,32 +350,154 @@ public class InsertTest {
p3.setStatementStatus(StatementStatus.FIX);
r.addProperty(p3);
- final LinkedList<EntityInterface> stage1Inserts = new LinkedList<EntityInterface>();
- final LinkedList<EntityInterface> stage2Inserts = new LinkedList<EntityInterface>();
+ final LinkedList<Property> stage1Inserts = new LinkedList<>();
+ final LinkedList<Property> stage2Inserts = new LinkedList<>();
- deriveStage1Inserts(stage1Inserts, r);
+ int count = deriveStage1Inserts(stage1Inserts, r);
+ deriveStage2Inserts(stage2Inserts, stage1Inserts, registerReplacementIds(count), r);
assertEquals(4, stage1Inserts.size());
- assertEquals(Role.Property, stage1Inserts.get(0).getRole());
+
+ assertFalse(stage1Inserts.get(0) instanceof Replacement);
assertEquals(new EntityID(1), stage1Inserts.get(0).getId());
- assertFalse(stage1Inserts.get(0).hasReplacement());
assertEquals("V1", ((SingleValue) stage1Inserts.get(0).getValue()).toDatabaseString());
- assertEquals(Role.Property, stage1Inserts.get(1).getRole());
- assertEquals(new EntityID(2), stage1Inserts.get(1).getId());
- assertTrue(stage1Inserts.get(1).hasReplacement());
- assertEquals(stage1Inserts.get(2), stage1Inserts.get(1).getReplacement());
+ assertTrue(stage1Inserts.get(1) instanceof Replacement);
+ assertEquals(new EntityID(-1), stage1Inserts.get(1).getId());
assertTrue(stage1Inserts.get(1).getValue() instanceof CollectionValue);
- assertEquals(Role.Domain, stage1Inserts.get(2).getRole());
- assertFalse(stage1Inserts.get(2).hasReplacement());
- assertTrue(stage1Inserts.get(2).getValue() instanceof CollectionValue);
+ assertFalse(stage1Inserts.get(2) instanceof Replacement);
+ assertEquals(new EntityID(-1), stage1Inserts.get(2).getId());
+ assertEquals(2, ((ReferenceValue) stage1Inserts.get(2).getValue()).getId().toInteger());
- assertEquals(Role.Property, stage1Inserts.get(3).getRole());
+ assertFalse(stage1Inserts.get(3) instanceof Replacement);
assertEquals(new EntityID(3), stage1Inserts.get(3).getId());
- assertFalse(stage1Inserts.get(3).hasReplacement());
assertEquals("V3", ((SingleValue) stage1Inserts.get(3).getValue()).toDatabaseString());
- deriveStage2Inserts(stage2Inserts, stage1Inserts);
+ assertEquals(0, stage2Inserts.size());
+ }
+
+ /** Deeply nested properties without any values, with overridden name and description */
+ @Test
+ public void testTransformation5() {
+ final Entity r = new InsertEntity("Test", Role.RecordType);
+ final Property p1 = new Property(new RetrieveEntity(new EntityID(1)));
+ p1.setRole("Property");
+ p1.setDatatype("TEXT");
+ p1.setDescription("desc1");
+ p1.setDescOverride(true);
+ p1.setName("P1");
+ p1.setNameOverride(true);
+ p1.setStatementStatus(StatementStatus.RECOMMENDED);
+ r.addProperty(p1);
+
+ final Property p2 = new Property(new RetrieveEntity(new EntityID(2)));
+ p2.setRole("Property");
+ p2.setDatatype("TEXT");
+ p2.setDescription("desc2");
+ p2.setDescOverride(true);
+ p2.setName("P2");
+ p2.setNameOverride(true);
+ p2.setStatementStatus(StatementStatus.RECOMMENDED);
+ r.addProperty(p2);
+
+ final Property p21 = new Property(new RetrieveEntity(new EntityID(1)));
+ p21.setRole("Property");
+ p21.setDatatype("TEXT");
+ p21.setDescription("desc21");
+ p21.setDescOverride(true);
+ p21.setName("P21");
+ p21.setNameOverride(true);
+ p21.setStatementStatus(StatementStatus.FIX);
+ p2.addProperty(p21);
+
+ final Property p22 = new Property(new RetrieveEntity(new EntityID(2)));
+ p22.setRole("Property");
+ p22.setDatatype("TEXT");
+ p22.setDescription("desc22");
+ p22.setDescOverride(true);
+ p22.setName("P22");
+ p22.setNameOverride(true);
+ p22.setStatementStatus(StatementStatus.FIX);
+ p2.addProperty(p22);
+
+ final Property p3 = new Property(new RetrieveEntity(new EntityID(3)));
+ p3.setRole("Property");
+ p3.setDatatype("TEXT");
+ p3.setDescription("desc3");
+ p3.setDescOverride(true);
+ p3.setName("P3");
+ p3.setNameOverride(true);
+ p3.setStatementStatus(StatementStatus.RECOMMENDED);
+ r.addProperty(p3);
+
+ final Property p31 = new Property(new RetrieveEntity(new EntityID(1)));
+ p31.setRole("Property");
+ p31.setDatatype("TEXT");
+ p31.setDescription("desc31");
+ p31.setDescOverride(true);
+ p31.setName("P31");
+ p31.setNameOverride(true);
+ p31.setStatementStatus(StatementStatus.FIX);
+ p3.addProperty(p31);
+
+ final Property p32 = new Property(new RetrieveEntity(new EntityID(2)));
+ p32.setRole("Property");
+ p32.setDatatype("TEXT");
+ p32.setDescription("desc32");
+ p32.setDescOverride(true);
+ p32.setName("P32");
+ p32.setNameOverride(true);
+ p32.setStatementStatus(StatementStatus.FIX);
+ p3.addProperty(p32);
+
+ final Property p321 = new Property(new RetrieveEntity(new EntityID(1)));
+ p321.setRole("Property");
+ p321.setDatatype("TEXT");
+ p321.setDescription("desc321");
+ p321.setDescOverride(true);
+ p321.setName("P321");
+ p321.setNameOverride(true);
+ p321.setStatementStatus(StatementStatus.FIX);
+ p32.addProperty(p321);
+
+ final Property p322 = new Property(new RetrieveEntity(new EntityID(2)));
+ p322.setRole("Property");
+ p322.setDatatype("TEXT");
+ p322.setDescription("desc322");
+ p322.setDescOverride(true);
+ p322.setName("P322");
+ p322.setNameOverride(true);
+ p322.setStatementStatus(StatementStatus.FIX);
+ p32.addProperty(p322);
+
+ final Property p323 = new Property(new RetrieveEntity(new EntityID(3)));
+ p323.setRole("Property");
+ p323.setDatatype("TEXT");
+ p323.setDescription("desc323");
+ p323.setDescOverride(true);
+ p323.setName("P323");
+ p323.setNameOverride(true);
+ p323.setStatementStatus(StatementStatus.FIX);
+ p32.addProperty(p323);
+
+ final Property p33 = new Property(new RetrieveEntity(new EntityID(3)));
+ p33.setRole("Property");
+ p33.setDatatype("TEXT");
+ p33.setDescription("desc33");
+ p33.setDescOverride(true);
+ p33.setName("P33");
+ p33.setNameOverride(true);
+ p33.setStatementStatus(StatementStatus.FIX);
+ p3.addProperty(p33);
+
+ List<Property> stage1Inserts = new LinkedList<>();
+ List<Property> stage2Inserts = new LinkedList<>();
+ int c = DatabaseUtils.deriveStage1Inserts(stage1Inserts, r);
+ DatabaseUtils.deriveStage2Inserts(stage2Inserts, stage1Inserts, registerReplacementIds(c), r);
+
+ assertEquals(4, c);
+ assertEquals(7, stage1Inserts.size());
+ assertEquals(8, stage2Inserts.size());
}
}
diff --git a/src/test/java/org/caosdb/server/grpc/CaosDBToGrpcConvertersTest.java b/src/test/java/org/caosdb/server/grpc/CaosDBToGrpcConvertersTest.java
index d39a803f9cfe3ce0a4cf23265683d121b3bc688d..d46c187324b76e179ef8d562cd5a150ab7968a45 100644
--- a/src/test/java/org/caosdb/server/grpc/CaosDBToGrpcConvertersTest.java
+++ b/src/test/java/org/caosdb/server/grpc/CaosDBToGrpcConvertersTest.java
@@ -1,12 +1,14 @@
package org.caosdb.server.grpc;
import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.util.TimeZone;
+import org.caosdb.api.entity.v1.Value.Builder;
import org.caosdb.datetime.DateTimeFactory2;
+import org.caosdb.server.datatype.CollectionValue;
import org.caosdb.server.datatype.GenericValue;
+import org.caosdb.server.datatype.ReferenceValue;
import org.caosdb.server.datatype.Value;
import org.caosdb.server.entity.EntityID;
import org.caosdb.server.entity.FileProperties;
@@ -17,6 +19,7 @@ import org.caosdb.server.entity.StatementStatus;
import org.caosdb.server.entity.wrapper.Parent;
import org.caosdb.server.entity.wrapper.Property;
import org.caosdb.server.entity.xml.IdAndServerMessagesOnlyStrategy;
+import org.caosdb.server.query.Query.Selection;
import org.junit.jupiter.api.Test;
public class CaosDBToGrpcConvertersTest {
@@ -27,7 +30,9 @@ public class CaosDBToGrpcConvertersTest {
DateTimeFactory2 factory = new DateTimeFactory2(timeZone);
CaosDBToGrpcConverters converters = new CaosDBToGrpcConverters(timeZone);
Value value = null;
- assertNull(converters.convertScalarValue(value));
+ assertEquals(
+ converters.convertScalarValue(value).toString(),
+ "special_value: SPECIAL_VALUE_UNSPECIFIED\n");
value = factory.parse("2022");
assertEquals(converters.convertScalarValue(value).toString(), "string_value: \"2022\"\n");
value = factory.parse("2022-12");
@@ -101,4 +106,68 @@ public class CaosDBToGrpcConvertersTest {
converters.convert(entity).toString(),
"entity {\n id: \"1234\"\n}\nerrors {\n code: 1\n description: \"error\"\n}\nwarnings {\n code: 1\n description: \"warning\"\n}\ninfos {\n code: 1\n description: \"info\"\n}\n");
}
+
+ @Test
+ public void testGetSelectedValueWithNullValue() {
+ Property p = new Property(new RetrieveEntity());
+ p.setName("p0");
+ p.setDatatype("DOUBLE");
+ RetrieveEntity entity = new RetrieveEntity();
+ entity.addProperty(p);
+
+ CaosDBToGrpcConverters converters = new CaosDBToGrpcConverters(null);
+ Builder value = converters.getSelectedValue(new Selection("p0"), entity);
+ assertEquals(
+ "scalar_value {\n" + " special_value: SPECIAL_VALUE_UNSPECIFIED\n" + "}\n",
+ value.toString());
+ }
+
+ @Test
+ public void testGetSelectedValueWithListOfReferenceValue() {
+ CollectionValue col = new CollectionValue();
+ Property p = new Property(new RetrieveEntity());
+ p.setName("Person");
+ p.setDatatype("List<Person>");
+
+ Property fullName1 = new Property(new RetrieveEntity());
+ fullName1.setName("full name");
+ fullName1.setDatatype("TEXT");
+ fullName1.setValue(new GenericValue("Harry Belafonte"));
+
+ RetrieveEntity person1 = new RetrieveEntity();
+ person1.addProperty(fullName1);
+ ReferenceValue val1 = new ReferenceValue(new EntityID(1234));
+ val1.setEntity(person1, false);
+ col.add(val1);
+
+ Property fullName2 = new Property(new RetrieveEntity());
+ fullName2.setName("full name");
+ fullName2.setDatatype("TEXT");
+ fullName2.setValue(new GenericValue("Louis Prima"));
+
+ RetrieveEntity person2 = new RetrieveEntity();
+ person2.addProperty(fullName2);
+ ReferenceValue val2 = new ReferenceValue(new EntityID(1234));
+ val2.setEntity(person2, false);
+ col.add(val2);
+ p.setValue(col);
+
+ RetrieveEntity entity = new RetrieveEntity();
+ entity.addProperty(p);
+
+ CaosDBToGrpcConverters converters = new CaosDBToGrpcConverters(null);
+ Builder value =
+ converters.getSelectedValue(
+ new Selection("Person").setSubSelection(new Selection("full name")), entity);
+ assertEquals(
+ "list_values {\n"
+ + " values {\n"
+ + " string_value: \"Harry Belafonte\"\n"
+ + " }\n"
+ + " values {\n"
+ + " string_value: \"Louis Prima\"\n"
+ + " }\n"
+ + "}\n",
+ value.toString());
+ }
}