From e7bc45a0d64f152d50bdf001ebe032e6517ee1a7 Mon Sep 17 00:00:00 2001
From: Timm Fitschen <t.fitschen@indiscale.com>
Date: Mon, 14 Aug 2023 23:24:53 +0200
Subject: [PATCH 1/9] WIP: MAINT: refactor retrieve properties (move
backend-logic to backend)
---
.../caosdb/server/database/DatabaseUtils.java | 124 ++++++++++++++++--
.../MySQL/MySQLRetrieveProperties.java | 86 ++++++------
.../interfaces/RetrievePropertiesImpl.java | 4 +-
.../transaction/RetrieveProperties.java | 46 ++++---
.../server/database/proto/ProtoProperty.java | 19 ++-
.../server/entity/wrapper/Property.java | 48 ++++---
.../entity/xml/EntityToElementStrategy.java | 10 +-
.../entity/xml/PropertyToElementStrategy.java | 5 +
.../caosdb/server/database/InsertTest.java | 8 +-
9 files changed, 251 insertions(+), 99 deletions(-)
diff --git a/src/main/java/org/caosdb/server/database/DatabaseUtils.java b/src/main/java/org/caosdb/server/database/DatabaseUtils.java
index 5280de17..8f4a59bb 100644
--- a/src/main/java/org/caosdb/server/database/DatabaseUtils.java
+++ b/src/main/java/org/caosdb/server/database/DatabaseUtils.java
@@ -25,16 +25,21 @@ package org.caosdb.server.database;
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.HashMap;
+import java.util.Iterator;
+import java.util.LinkedList;
import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
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.datatype.IndexedSingleValue;
import org.caosdb.server.datatype.ReferenceValue;
import org.caosdb.server.datatype.SingleValue;
@@ -175,9 +180,9 @@ public class DatabaseUtils {
}
public static List<FlatProperty> parsePropertyResultset(final ResultSet rs) throws SQLException {
- final ArrayList<FlatProperty> ret = new ArrayList<FlatProperty>();
+ final List<FlatProperty> ret = new LinkedList<>();
while (rs.next()) {
- final FlatProperty fp = new FlatProperty();
+ FlatProperty fp = new FlatProperty();
fp.id = rs.getInt("PropertyID");
fp.value = bytes2UTF8(rs.getBytes("PropertyValue"));
fp.status = bytes2UTF8(rs.getBytes("PropertyStatus"));
@@ -354,27 +359,120 @@ public class DatabaseUtils {
}
}
- public static ArrayList<Property> parseFromProtoProperties(final List<ProtoProperty> protos) {
+ public static ArrayList<Property> parseFromProtoProperties(
+ EntityInterface entity, 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);
+ 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 {
+ final Property property = parseFlatProperty(pp);
+ // 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);
- }
+ final List<Property> properties, final List<ProtoProperty> props) {
+ if (props != null)
+ for (final ProtoProperty fp : props) {
+ final Property property = parseFlatProperty(fp);
+ parseFromFlatProperties(properties, fp.subProperties);
+ properties.add(property);
+ }
}
- private static Property parseFlatProperty(final FlatProperty fp) {
+ private static Property parseFlatProperty(final ProtoProperty fp) {
final Property property = new Property(new RetrieveEntity());
- property.parseFlatProperty(fp);
+ property.parseProtoProperty(fp);
return property;
}
+
+ @SuppressWarnings("unchecked")
+ public static LinkedList<ProtoProperty> transformToDeepPropertyTree(
+ List<ProtoProperty> properties) {
+ LinkedList<ProtoProperty> result = new LinkedList<>();
+ Map<String, ProtoProperty> replacements = new HashMap<>();
+ for (ProtoProperty pp : properties) {
+ if (pp.status.equals(StatementStatus.REPLACEMENT.toString())) {
+ 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(StatementStatus.REPLACEMENT.toString())) {
+ replace(pp, replacements.get(pp.value));
+ }
+ 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())
+ .toList();
+ }
+ result.add(pp);
+ }
+ return result;
+ }
+
+ private static void replace(ProtoProperty pp, ProtoProperty replacement) {
+ if (replacement == null) {
+ 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;
+ }
+ 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/MySQLRetrieveProperties.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java
index 6bcfeac0..b0c5d5b7 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
@@ -26,7 +26,7 @@ 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;
@@ -44,29 +44,23 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
private static final String stmtStr = "call retrieveEntityProperties(?,?,?)";
private static final String stmtStr2 = "call retrieveOverrides(?,?,?)";
+ private static final String isCollectionStmt = "call isCollection(?,?)";
@Override
- public ArrayList<ProtoProperty> execute(final EntityID entity, final String version)
+ public LinkedList<ProtoProperty> execute(final EntityID entity, final String version)
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);
} catch (final SQLException e) {
throw new TransactionException(e);
} catch (final ConnectionException e) {
@@ -74,68 +68,76 @@ 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 PreparedStatement stmt2 = prepareStatement(stmtStr2);
+ final PreparedStatement retrieveOverrides = prepareStatement(stmtStr2);
- retrieveOverrides(domain, entity, version, stmt2, props);
+ retrieveOverrides(domain, entity, version, retrieveOverrides, props);
- return props;
- } finally {
- if (rs != null && !rs.isClosed()) {
- rs.close();
- }
+ PreparedStatement isCollectionStatement = prepareStatement(isCollectionStmt);
+
+ return handleCollectionValues(props, isCollectionStatement);
}
}
+ public List<ProtoProperty> handleCollectionValues(
+ List<FlatProperty> props, PreparedStatement isCollectionStatement) throws SQLException {
+
+ List<ProtoProperty> result = new LinkedList<>();
+ for (FlatProperty fp : props) {
+ result.add(new ProtoProperty(fp));
+ }
+ return result;
+ }
+
private void retrieveOverrides(
final Integer domain,
final Integer entity,
final String version,
- final PreparedStatement stmt2,
+ final PreparedStatement retrieveOverrides,
final List<FlatProperty> 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/interfaces/RetrievePropertiesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePropertiesImpl.java
index dc1d5aa0..69fc9e70 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 +22,12 @@
*/
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) throws TransactionException;
}
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 726382f2..5cd7ace1 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
@@ -24,7 +24,8 @@
*/
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;
@@ -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 +62,45 @@ 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());
}
@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/proto/ProtoProperty.java b/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java
index 44acaa02..898565ac 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 +25,22 @@ 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 {
+
+ public ProtoProperty(FlatProperty fp) {
+ id = fp.id;
+ value = fp.value;
+ status = fp.status;
+ idx = fp.idx;
+ name = fp.name;
+ desc = fp.desc;
+ type = fp.type;
+ collection = fp.collection;
+ }
+
+ public ProtoProperty() {}
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/wrapper/Property.java b/src/main/java/org/caosdb/server/entity/wrapper/Property.java
index efa1a685..9268d7f3 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 7f6e6dca..35d94aa7 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 23fd8a55..7109a0d8 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/test/java/org/caosdb/server/database/InsertTest.java b/src/test/java/org/caosdb/server/database/InsertTest.java
index 524e7add..59aa6f55 100644
--- a/src/test/java/org/caosdb/server/database/InsertTest.java
+++ b/src/test/java/org/caosdb/server/database/InsertTest.java
@@ -124,7 +124,7 @@ public class InsertTest {
final LinkedList<EntityInterface> stage1Inserts = new LinkedList<EntityInterface>();
final LinkedList<EntityInterface> stage2Inserts = new LinkedList<EntityInterface>();
- new LinkedList<EntityInterface>();
+
deriveStage1Inserts(stage1Inserts, r);
assertEquals(7, stage1Inserts.size());
@@ -166,34 +166,40 @@ public class InsertTest {
assertEquals(Role.Property, stage2Inserts.get(0).getRole());
assertEquals(new EntityID(3), stage2Inserts.get(0).getId());
assertEquals("V3", ((SingleValue) stage2Inserts.get(0).getValue()).toDatabaseString());
+ assertEquals(new EntityID(2), stage2Inserts.get(0).getDomain());
assertFalse(stage2Inserts.get(0).hasReplacement());
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(new EntityID(4), stage2Inserts.get(1).getDomain());
assertEquals(stage1Inserts.get(3), stage2Inserts.get(1).getReplacement());
assertEquals(Role.Property, stage2Inserts.get(2).getRole());
assertEquals(new EntityID(6), stage2Inserts.get(2).getId());
assertEquals("V6", ((SingleValue) stage2Inserts.get(2).getValue()).toDatabaseString());
+ assertEquals(new EntityID(5), stage2Inserts.get(2).getDomain());
assertFalse(stage2Inserts.get(2).hasReplacement());
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(new EntityID(7), stage2Inserts.get(3).getDomain());
assertEquals(stage1Inserts.get(5), stage2Inserts.get(3).getReplacement());
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(new EntityID(8), stage2Inserts.get(4).getDomain());
assertEquals(stage1Inserts.get(6), stage2Inserts.get(4).getReplacement());
assertEquals(Role.Property, stage2Inserts.get(5).getRole());
assertEquals(new EntityID(10), stage2Inserts.get(5).getId());
assertEquals("V10", ((SingleValue) stage2Inserts.get(5).getValue()).toDatabaseString());
+ assertEquals(new EntityID(9), stage2Inserts.get(5).getDomain());
assertFalse(stage2Inserts.get(5).hasReplacement());
}
--
GitLab
From 236a8d7bde090676b52a757be2e6cde4cc2f2026 Mon Sep 17 00:00:00 2001
From: Timm Fitschen <t.fitschen@indiscale.com>
Date: Tue, 15 Aug 2023 10:43:16 +0200
Subject: [PATCH 2/9] WIP: MAINT: refactor retrieve properties (move
backend-logic to backend)
---
.../caosdb/server/database/DatabaseUtils.java | 142 +++---------------
.../MySQL/MySQLRetrieveProperties.java | 15 +-
.../interfaces/RetrievePropertiesImpl.java | 3 +-
.../transaction/RetrieveProperties.java | 3 +-
4 files changed, 33 insertions(+), 130 deletions(-)
diff --git a/src/main/java/org/caosdb/server/database/DatabaseUtils.java b/src/main/java/org/caosdb/server/database/DatabaseUtils.java
index 8f4a59bb..5799d23f 100644
--- a/src/main/java/org/caosdb/server/database/DatabaseUtils.java
+++ b/src/main/java/org/caosdb/server/database/DatabaseUtils.java
@@ -40,9 +40,6 @@ 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.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;
@@ -55,6 +52,9 @@ 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;
@@ -265,100 +265,6 @@ public class DatabaseUtils {
}
}
- 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(
EntityInterface entity, List<ProtoProperty> protos) {
final ArrayList<Property> ret = new ArrayList<Property>();
@@ -380,24 +286,23 @@ public class DatabaseUtils {
}
} 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);
- // parseFromFlatProperties(property.getProperties(), pp.subProperties);
+ if (warning != null) {
+ property.addWarning(warning);
+ }
ret.add(property);
}
}
return ret;
}
- private static void parseFromFlatProperties(
- final List<Property> properties, final List<ProtoProperty> props) {
- if (props != null)
- for (final ProtoProperty fp : props) {
- final Property property = parseFlatProperty(fp);
- parseFromFlatProperties(properties, fp.subProperties);
- properties.add(property);
- }
- }
-
private static Property parseFlatProperty(final ProtoProperty fp) {
final Property property = new Property(new RetrieveEntity());
property.parseProtoProperty(fp);
@@ -406,7 +311,7 @@ public class DatabaseUtils {
@SuppressWarnings("unchecked")
public static LinkedList<ProtoProperty> transformToDeepPropertyTree(
- List<ProtoProperty> properties) {
+ List<ProtoProperty> properties, boolean isHead) {
LinkedList<ProtoProperty> result = new LinkedList<>();
Map<String, ProtoProperty> replacements = new HashMap<>();
for (ProtoProperty pp : properties) {
@@ -436,7 +341,7 @@ public class DatabaseUtils {
}
for (ProtoProperty pp : properties) {
if (pp.status.equals(StatementStatus.REPLACEMENT.toString())) {
- replace(pp, replacements.get(pp.value));
+ replace(pp, replacements.get(pp.value), isHead);
}
if (pp.collValues != null) {
// sort
@@ -455,16 +360,15 @@ public class DatabaseUtils {
return result;
}
- private static void replace(ProtoProperty pp, ProtoProperty replacement) {
+ private static void replace(ProtoProperty pp, ProtoProperty replacement, boolean isHead) {
if (replacement == null) {
- 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 (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;
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 b0c5d5b7..c8843f9c 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
@@ -44,11 +44,10 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
private static final String stmtStr = "call retrieveEntityProperties(?,?,?)";
private static final String stmtStr2 = "call retrieveOverrides(?,?,?)";
- private static final String isCollectionStmt = "call isCollection(?,?)";
@Override
- public LinkedList<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);
@@ -60,7 +59,7 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
p.subProperties =
retrieveFlatPropertiesStage1(entity.toInteger(), p.id, version, prepareStatement);
}
- return DatabaseUtils.transformToDeepPropertyTree(propsStage1);
+ return DatabaseUtils.transformToDeepPropertyTree(propsStage1, isHead);
} catch (final SQLException e) {
throw new TransactionException(e);
} catch (final ConnectionException e) {
@@ -99,14 +98,12 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
retrieveOverrides(domain, entity, version, retrieveOverrides, props);
- PreparedStatement isCollectionStatement = prepareStatement(isCollectionStmt);
-
- return handleCollectionValues(props, isCollectionStatement);
+ return handleCollectionValues(props);
}
}
- public List<ProtoProperty> handleCollectionValues(
- List<FlatProperty> props, PreparedStatement isCollectionStatement) throws SQLException {
+ @Deprecated
+ public List<ProtoProperty> handleCollectionValues(List<FlatProperty> props) throws SQLException {
List<ProtoProperty> result = new LinkedList<>();
for (FlatProperty fp : props) {
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 69fc9e70..6bf2051a 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
@@ -29,5 +29,6 @@ import org.caosdb.server.entity.EntityID;
public interface RetrievePropertiesImpl extends BackendTransactionImpl {
- public LinkedList<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/RetrieveProperties.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveProperties.java
index 5cd7ace1..caa4b6cf 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
@@ -64,7 +64,8 @@ public class RetrieveProperties
@Override
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
--
GitLab
From 0326111fc575abeddfad65c546cf6f075464c8bf Mon Sep 17 00:00:00 2001
From: Timm Fitschen <t.fitschen@indiscale.com>
Date: Wed, 16 Aug 2023 00:00:44 +0200
Subject: [PATCH 3/9] WIP: MAINT: refactor retrieve properties (move
backend-logic to backend)
---
.../server/database/BackendTransaction.java | 3 -
.../caosdb/server/database/DatabaseUtils.java | 80 +++++----
.../caosdb/server/database/Replacement.java | 41 +++++
.../MySQL/MySQLInsertEntityProperties.java | 147 ++++++++++++++++-
.../MySQL/MySQLRegisterSubDomain.java | 64 -------
.../InsertEntityPropertiesImpl.java | 9 +-
.../interfaces/RegisterSubDomainImpl.java | 32 ----
.../transaction/InsertEntityProperties.java | 137 +--------------
.../transaction/InsertEntityTransaction.java | 4 +-
.../transaction/RegisterSubDomain.java | 49 ------
.../server/database/proto/FlatProperty.java | 13 ++
.../server/database/proto/ProtoProperty.java | 11 +-
.../caosdb/server/database/InsertTest.java | 156 ++++++++----------
.../caosdb/server/database/InsertTest2.java | 148 +++++++++++++++++
14 files changed, 466 insertions(+), 428 deletions(-)
create mode 100644 src/main/java/org/caosdb/server/database/Replacement.java
delete mode 100644 src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRegisterSubDomain.java
delete mode 100644 src/main/java/org/caosdb/server/database/backend/interfaces/RegisterSubDomainImpl.java
delete mode 100644 src/main/java/org/caosdb/server/database/backend/transaction/RegisterSubDomain.java
create mode 100644 src/test/java/org/caosdb/server/database/InsertTest2.java
diff --git a/src/main/java/org/caosdb/server/database/BackendTransaction.java b/src/main/java/org/caosdb/server/database/BackendTransaction.java
index 5addf3f3..05ea26c2 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
index 5799d23f..6d72d965 100644
--- a/src/main/java/org/caosdb/server/database/DatabaseUtils.java
+++ b/src/main/java/org/caosdb/server/database/DatabaseUtils.java
@@ -27,6 +27,7 @@ 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;
@@ -44,9 +45,7 @@ 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;
@@ -63,39 +62,33 @@ public class DatabaseUtils {
}
}
- 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) {
+ 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.setPIdx(0);
p.setDatatype(e.getDatatype());
p.setValue(e.getValue());
+ p.setPIdx(0);
processPropertiesStage1(stage1Inserts, p, e);
}
- for (final EntityInterface p : e.getProperties()) {
+ 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<EntityInterface> stage1Inserts, final EntityInterface p, final EntityInterface e) {
- stage1Inserts.add(p);
+ final List<Property> stage1Inserts, final Property p, final EntityInterface e) {
+
if (!p.isDescOverride()
&& !p.isNameOverride()
&& !p.isDatatypeOverride()
@@ -105,25 +98,40 @@ public class DatabaseUtils {
// 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);
+ stage1Inserts.add(p);
} else {
- stage1Inserts.add(makeReplacement(p));
+ Replacement r = new Replacement(p);
+ stage1Inserts.add(r);
+ stage1Inserts.add(r.replacement);
}
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());
+ 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);
+ }
+ }
}
}
- return domainCount;
}
private static boolean hasUniquePropertyId(final EntityInterface p, final EntityInterface e) {
@@ -137,10 +145,10 @@ public class DatabaseUtils {
}
private static void processSubPropertiesStage1(
- final List<EntityInterface> stage1Inserts, final EntityInterface p) {
- for (final EntityInterface subP : p.getProperties()) {
+ final List<Property> stage1Inserts, final EntityInterface p) {
+ for (final Property subP : p.getProperties()) {
if (subP.hasProperties()) {
- stage1Inserts.add(makeReplacement(subP));
+ stage1Inserts.add(new Replacement(subP));
processSubPropertiesStage1(stage1Inserts, subP);
}
}
diff --git a/src/main/java/org/caosdb/server/database/Replacement.java b/src/main/java/org/caosdb/server/database/Replacement.java
new file mode 100644
index 00000000..8606d51b
--- /dev/null
+++ b/src/main/java/org/caosdb/server/database/Replacement.java
@@ -0,0 +1,41 @@
+package org.caosdb.server.database;
+
+import org.caosdb.server.datatype.ReferenceValue;
+import org.caosdb.server.entity.EntityID;
+import org.caosdb.server.entity.RetrieveEntity;
+import org.caosdb.server.entity.StatementStatus;
+import org.caosdb.server.entity.wrapper.Property;
+
+public class Replacement extends Property {
+
+ public Property replacement;
+ public EntityID replacementId;
+
+ @Override
+ public EntityID getId() {
+ return replacementId;
+ }
+
+ public void setReplacementId(EntityID id) {
+ replacementId.link(id);
+ }
+
+ public Replacement(Property p) {
+ super(p);
+ replacementId = new EntityID();
+ replacement = new Property(new RetrieveEntity());
+
+ replacement.setDomain(p.getDomainEntity());
+ // replacement.setDatatypeOverride(p.isDatatypeOverride());
+ // replacement.setDatatype(p.getDatatype());
+ // replacement.setNameOverride(p.isNameOverride());
+ // replacement.setName(p.getName());
+ // replacement.setDescOverride(p.isDescOverride());
+ // replacement.setDescription(p.getDescription());
+
+ replacement.setId(replacementId);
+ replacement.setStatementStatus(StatementStatus.REPLACEMENT);
+ replacement.setValue(new ReferenceValue(p.getId()));
+ replacement.setPIdx(0);
+ }
+}
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 7c3c5a33..5c9ca6f9 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 +25,30 @@ 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.DatabaseUtils;
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.StatementStatus;
+import org.caosdb.server.entity.wrapper.Property;
public class MySQLInsertEntityProperties extends MySQLTransaction
implements InsertEntityPropertiesImpl {
@@ -46,7 +61,27 @@ 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 +111,114 @@ 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> stage1Inserts, final EntityID domain, final EntityID entity)
+ throws TransactionException {
+
+ for (final Property property : stage1Inserts) {
+
+ // 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() == StatementStatus.REPLACEMENT) {
+ table = Table.reference_data;
+ fp.value = fp.id.toString();
+ fp.id = ((ReferenceValue) property.getValue()).getId().toInteger();
+ } 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/MySQLRegisterSubDomain.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRegisterSubDomain.java
deleted file mode 100644
index 1e14600e..00000000
--- 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/interfaces/InsertEntityPropertiesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityPropertiesImpl.java
index 2406d489..f17643fd 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/RegisterSubDomainImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RegisterSubDomainImpl.java
deleted file mode 100644
index 87ea0c85..00000000
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RegisterSubDomainImpl.java
+++ /dev/null
@@ -1,32 +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.interfaces;
-
-import java.util.Deque;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-
-public interface RegisterSubDomainImpl extends BackendTransactionImpl {
-
- public abstract Deque<EntityID> execute(int domainCount) 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 f9af6a48..8de8afc0 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 5871c97e..2846fa64 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 0321a621..00000000
--- 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/proto/FlatProperty.java b/src/main/java/org/caosdb/server/database/proto/FlatProperty.java
index b92d3def..b4f0f62a 100644
--- a/src/main/java/org/caosdb/server/database/proto/FlatProperty.java
+++ b/src/main/java/org/caosdb/server/database/proto/FlatProperty.java
@@ -26,6 +26,19 @@ import java.io.Serializable;
public class FlatProperty implements Serializable {
+ public FlatProperty() {}
+
+ public FlatProperty(FlatProperty fp) {
+ id = fp.id;
+ value = fp.value;
+ status = fp.status;
+ idx = fp.idx;
+ name = fp.name;
+ desc = fp.desc;
+ type = fp.type;
+ collection = fp.collection;
+ }
+
private static final long serialVersionUID = 6039288034435124195L;
public Integer id = null;
public String value = null;
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 898565ac..c6cdbd54 100644
--- a/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java
+++ b/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java
@@ -26,21 +26,14 @@ import java.io.Serializable;
import java.util.List;
public class ProtoProperty extends FlatProperty implements Serializable {
+ private static final long serialVersionUID = 7731301985162924975L;
public ProtoProperty(FlatProperty fp) {
- id = fp.id;
- value = fp.value;
- status = fp.status;
- idx = fp.idx;
- name = fp.name;
- desc = fp.desc;
- type = fp.type;
- collection = fp.collection;
+ super(fp);
}
public ProtoProperty() {}
- private static final long serialVersionUID = 7731301985162924975L;
public List<ProtoProperty> subProperties = null;
public List<Object> collValues = null;
}
diff --git a/src/test/java/org/caosdb/server/database/InsertTest.java b/src/test/java/org/caosdb/server/database/InsertTest.java
index 59aa6f55..e385d6cb 100644
--- a/src/test/java/org/caosdb/server/database/InsertTest.java
+++ b/src/test/java/org/caosdb/server/database/InsertTest.java
@@ -28,13 +28,15 @@ 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 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 +46,14 @@ 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.
*
@@ -122,85 +132,67 @@ public class InsertTest {
p10.setStatementStatus(StatementStatus.OBLIGATORY);
p9.addProperty(p10);
- final LinkedList<EntityInterface> stage1Inserts = new LinkedList<EntityInterface>();
- final LinkedList<EntityInterface> stage2Inserts = new LinkedList<EntityInterface>();
+ final LinkedList<Property> stage1Inserts = new LinkedList<>();
+ final LinkedList<Property> stage2Inserts = new LinkedList<>();
- deriveStage1Inserts(stage1Inserts, r);
+ 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(5, 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(8, 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(9, 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());
assertEquals(new EntityID(2), stage2Inserts.get(0).getDomain());
- assertFalse(stage2Inserts.get(0).hasReplacement());
- 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(new EntityID(4), stage2Inserts.get(1).getDomain());
- assertEquals(stage1Inserts.get(3), stage2Inserts.get(1).getReplacement());
- assertEquals(Role.Property, stage2Inserts.get(2).getRole());
assertEquals(new EntityID(6), stage2Inserts.get(2).getId());
assertEquals("V6", ((SingleValue) stage2Inserts.get(2).getValue()).toDatabaseString());
- assertEquals(new EntityID(5), stage2Inserts.get(2).getDomain());
- 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(new EntityID(7), stage2Inserts.get(3).getDomain());
- assertEquals(stage1Inserts.get(5), stage2Inserts.get(3).getReplacement());
- 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(new EntityID(8), stage2Inserts.get(4).getDomain());
- 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());
- assertEquals(new EntityID(9), stage2Inserts.get(5).getDomain());
- assertFalse(stage2Inserts.get(5).hasReplacement());
+ assertEquals(new EntityID(-3), stage2Inserts.get(5).getDomain());
}
/**
@@ -233,34 +225,31 @@ 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(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());
}
/**
@@ -297,39 +286,33 @@ 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());
+ assertTrue(stage1Inserts.get(0) instanceof Replacement);
assertEquals(new EntityID(1), stage1Inserts.get(0).getId());
- assertTrue(stage1Inserts.get(0).hasReplacement());
- assertEquals(stage1Inserts.get(1), stage1Inserts.get(0).getReplacement());
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());
}
/**
@@ -366,32 +349,31 @@ 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());
+ assertTrue(stage1Inserts.get(1) instanceof Replacement);
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).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());
}
}
diff --git a/src/test/java/org/caosdb/server/database/InsertTest2.java b/src/test/java/org/caosdb/server/database/InsertTest2.java
new file mode 100644
index 00000000..58cc5850
--- /dev/null
+++ b/src/test/java/org/caosdb/server/database/InsertTest2.java
@@ -0,0 +1,148 @@
+package org.caosdb.server.database;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.util.ArrayDeque;
+import java.util.Deque;
+import java.util.LinkedList;
+import java.util.List;
+import org.caosdb.server.entity.Entity;
+import org.caosdb.server.entity.EntityID;
+import org.caosdb.server.entity.InsertEntity;
+import org.caosdb.server.entity.RetrieveEntity;
+import org.caosdb.server.entity.Role;
+import org.caosdb.server.entity.StatementStatus;
+import org.caosdb.server.entity.wrapper.Property;
+import org.junit.jupiter.api.Test;
+
+public class InsertTest2 {
+
+ 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;
+ }
+
+ @Test
+ public void transformation5() {
+ 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.RECOMMENDED);
+ 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.RECOMMENDED);
+ 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.RECOMMENDED);
+ 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.RECOMMENDED);
+ 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.RECOMMENDED);
+ 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.RECOMMENDED);
+ 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.RECOMMENDED);
+ 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.RECOMMENDED);
+ 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(7, stage1Inserts.size());
+ assertEquals(8, stage2Inserts.size());
+ }
+}
--
GitLab
From d186c1b94b24f52cd2919660401431e9fcfab18c Mon Sep 17 00:00:00 2001
From: Timm Fitschen <t.fitschen@indiscale.com>
Date: Wed, 16 Aug 2023 00:10:26 +0200
Subject: [PATCH 4/9] WIP: MAINT: refactor retrieve properties (move
backend-logic to backend)
---
.../java/org/caosdb/server/entity/Entity.java | 18 ---
.../caosdb/server/entity/EntityInterface.java | 7 -
.../caosdb/server/entity/wrapper/Domain.java | 59 -------
.../server/entity/wrapper/EntityWrapper.java | 15 --
.../caosdb/server/database/InsertTest.java | 138 +++++++++++++++-
.../caosdb/server/database/InsertTest2.java | 148 ------------------
6 files changed, 131 insertions(+), 254 deletions(-)
delete mode 100644 src/main/java/org/caosdb/server/entity/wrapper/Domain.java
delete mode 100644 src/test/java/org/caosdb/server/database/InsertTest2.java
diff --git a/src/main/java/org/caosdb/server/entity/Entity.java b/src/main/java/org/caosdb/server/entity/Entity.java
index e1acfbdc..843449ce 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;
@@ -849,23 +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 f967b307..d97970de 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;
@@ -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/wrapper/Domain.java b/src/main/java/org/caosdb/server/entity/wrapper/Domain.java
deleted file mode 100644
index 146706ef..00000000
--- 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 7da94573..f23408df 100644
--- a/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java
+++ b/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java
@@ -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/test/java/org/caosdb/server/database/InsertTest.java b/src/test/java/org/caosdb/server/database/InsertTest.java
index e385d6cb..0484e623 100644
--- a/src/test/java/org/caosdb/server/database/InsertTest.java
+++ b/src/test/java/org/caosdb/server/database/InsertTest.java
@@ -31,6 +31,7 @@ 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;
@@ -154,7 +155,7 @@ public class InsertTest {
assertEquals("V4", ((SingleValue) stage1Inserts.get(2).getValue()).toDatabaseString());
assertTrue(stage1Inserts.get(3) instanceof Replacement);
- assertEquals(5, stage1Inserts.get(3).getId().toInteger());
+ assertEquals(-1, stage1Inserts.get(3).getId().toInteger());
assertEquals("V5", ((SingleValue) stage1Inserts.get(3).getValue()).toDatabaseString());
assertFalse(stage1Inserts.get(4) instanceof Replacement);
@@ -162,11 +163,11 @@ public class InsertTest {
assertEquals("V7", ((SingleValue) stage1Inserts.get(4).getValue()).toDatabaseString());
assertTrue(stage1Inserts.get(5) instanceof Replacement);
- assertEquals(8, stage1Inserts.get(5).getId().toInteger());
+ assertEquals(-2, stage1Inserts.get(5).getId().toInteger());
assertEquals("V8", ((SingleValue) stage1Inserts.get(5).getValue()).toDatabaseString());
assertTrue(stage1Inserts.get(6) instanceof Replacement);
- assertEquals(9, stage1Inserts.get(6).getId().toInteger());
+ assertEquals(-3, stage1Inserts.get(6).getId().toInteger());
assertEquals("V9", ((SingleValue) stage1Inserts.get(6).getValue()).toDatabaseString());
assertEquals(6, stage2Inserts.size());
@@ -239,7 +240,7 @@ public class InsertTest {
assertTrue(stage1Inserts.get(1) instanceof Replacement);
assertEquals("V1-2", ((SingleValue) stage1Inserts.get(1).getValue()).toDatabaseString());
- assertEquals(new EntityID(1), stage1Inserts.get(1).getId());
+ assertEquals(new EntityID(-1), stage1Inserts.get(1).getId());
assertFalse(stage1Inserts.get(2) instanceof Replacement);
assertEquals(new EntityID(-1), stage1Inserts.get(2).getId());
@@ -294,7 +295,7 @@ public class InsertTest {
assertEquals(4, stage1Inserts.size());
assertTrue(stage1Inserts.get(0) instanceof Replacement);
- assertEquals(new EntityID(1), stage1Inserts.get(0).getId());
+ assertEquals(new EntityID(-1), stage1Inserts.get(0).getId());
assertEquals(null, stage1Inserts.get(0).getValue());
assertFalse(stage1Inserts.get(1) instanceof Replacement);
@@ -359,11 +360,10 @@ public class InsertTest {
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());
assertTrue(stage1Inserts.get(1) instanceof Replacement);
- assertEquals(new EntityID(2), stage1Inserts.get(1).getId());
+ assertEquals(new EntityID(-1), stage1Inserts.get(1).getId());
assertTrue(stage1Inserts.get(1).getValue() instanceof CollectionValue);
assertFalse(stage1Inserts.get(2) instanceof Replacement);
@@ -376,4 +376,128 @@ public class InsertTest {
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/database/InsertTest2.java b/src/test/java/org/caosdb/server/database/InsertTest2.java
deleted file mode 100644
index 58cc5850..00000000
--- a/src/test/java/org/caosdb/server/database/InsertTest2.java
+++ /dev/null
@@ -1,148 +0,0 @@
-package org.caosdb.server.database;
-
-import static org.junit.jupiter.api.Assertions.assertEquals;
-
-import java.util.ArrayDeque;
-import java.util.Deque;
-import java.util.LinkedList;
-import java.util.List;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.wrapper.Property;
-import org.junit.jupiter.api.Test;
-
-public class InsertTest2 {
-
- 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;
- }
-
- @Test
- public void transformation5() {
- 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.RECOMMENDED);
- 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.RECOMMENDED);
- 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.RECOMMENDED);
- 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.RECOMMENDED);
- 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.RECOMMENDED);
- 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.RECOMMENDED);
- 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.RECOMMENDED);
- 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.RECOMMENDED);
- 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(7, stage1Inserts.size());
- assertEquals(8, stage2Inserts.size());
- }
-}
--
GitLab
From ce345f40b927ac1bcd1d159ec4383d768a678bbe Mon Sep 17 00:00:00 2001
From: Timm Fitschen <t.fitschen@indiscale.com>
Date: Wed, 16 Aug 2023 00:59:18 +0200
Subject: [PATCH 5/9] WIP: MAINT: refactor retrieve properties (move
backend-logic to backend)
---
.../java/org/caosdb/server/CaosDBServer.java | 1 -
.../server/accessControl/ACMPermissions.java | 3 -
.../caosdb/server/database/Replacement.java | 41 --------------
.../implementation/MySQL}/DatabaseUtils.java | 55 +++++--------------
.../MySQL/MySQLGetAllNames.java | 1 -
.../MySQL/MySQLInsertEntityProperties.java | 1 -
.../MySQL/MySQLInsertSparseEntity.java | 1 -
.../MySQL/MySQLRetrieveAll.java | 1 -
.../MySQL/MySQLRetrieveDatatypes.java | 5 +-
.../MySQL/MySQLRetrieveParents.java | 5 +-
.../MySQL/MySQLRetrievePasswordValidator.java | 2 +-
.../MySQL/MySQLRetrieveProperties.java | 20 ++-----
.../MySQL/MySQLRetrieveSparseEntity.java | 1 -
.../MySQL/MySQLRetrieveUser.java | 2 +-
.../MySQL/MySQLRetrieveVersionHistory.java | 1 -
.../MySQL/MySQLUpdateSparseEntity.java | 1 -
.../implementation/MySQL/Replacement.java | 53 ++++++++++++++++++
.../interfaces/RetrieveDatatypesImpl.java | 4 +-
.../interfaces/RetrieveParentsImpl.java | 4 +-
.../transaction/RetrieveDatatypes.java | 4 +-
.../backend/transaction/RetrieveParents.java | 27 ++++++---
.../transaction/RetrieveProperties.java | 2 +-
.../transaction/RetrieveSparseEntity.java | 7 ++-
.../server/database/proto/FlatProperty.java | 13 -----
.../server/database/proto/ProtoProperty.java | 6 --
.../caosdb/server/query/Backreference.java | 2 +-
.../org/caosdb/server/query/Conjunction.java | 2 +-
.../org/caosdb/server/query/Disjunction.java | 2 +-
.../org/caosdb/server/query/Negation.java | 2 +-
.../java/org/caosdb/server/query/POV.java | 2 +-
.../java/org/caosdb/server/query/Query.java | 2 +-
.../org/caosdb/server/query/SubProperty.java | 2 +-
.../server/utils/ResultSetIterator.java | 2 +-
.../implementation/MySQL}/InsertTest.java | 6 +-
34 files changed, 119 insertions(+), 164 deletions(-)
delete mode 100644 src/main/java/org/caosdb/server/database/Replacement.java
rename src/main/java/org/caosdb/server/database/{ => backend/implementation/MySQL}/DatabaseUtils.java (87%)
create mode 100644 src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java
rename src/test/java/org/caosdb/server/database/{ => backend/implementation/MySQL}/InsertTest.java (98%)
diff --git a/src/main/java/org/caosdb/server/CaosDBServer.java b/src/main/java/org/caosdb/server/CaosDBServer.java
index 05fb9485..deca9aae 100644
--- a/src/main/java/org/caosdb/server/CaosDBServer.java
+++ b/src/main/java/org/caosdb/server/CaosDBServer.java
@@ -223,7 +223,6 @@ 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);
diff --git a/src/main/java/org/caosdb/server/accessControl/ACMPermissions.java b/src/main/java/org/caosdb/server/accessControl/ACMPermissions.java
index 854fc07f..07503692 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/Replacement.java b/src/main/java/org/caosdb/server/database/Replacement.java
deleted file mode 100644
index 8606d51b..00000000
--- a/src/main/java/org/caosdb/server/database/Replacement.java
+++ /dev/null
@@ -1,41 +0,0 @@
-package org.caosdb.server.database;
-
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.wrapper.Property;
-
-public class Replacement extends Property {
-
- public Property replacement;
- public EntityID replacementId;
-
- @Override
- public EntityID getId() {
- return replacementId;
- }
-
- public void setReplacementId(EntityID id) {
- replacementId.link(id);
- }
-
- public Replacement(Property p) {
- super(p);
- replacementId = new EntityID();
- replacement = new Property(new RetrieveEntity());
-
- replacement.setDomain(p.getDomainEntity());
- // replacement.setDatatypeOverride(p.isDatatypeOverride());
- // replacement.setDatatype(p.getDatatype());
- // replacement.setNameOverride(p.isNameOverride());
- // replacement.setName(p.getName());
- // replacement.setDescOverride(p.isDescOverride());
- // replacement.setDescription(p.getDescription());
-
- replacement.setId(replacementId);
- replacement.setStatementStatus(StatementStatus.REPLACEMENT);
- replacement.setValue(new ReferenceValue(p.getId()));
- replacement.setPIdx(0);
- }
-}
diff --git a/src/main/java/org/caosdb/server/database/DatabaseUtils.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
similarity index 87%
rename from src/main/java/org/caosdb/server/database/DatabaseUtils.java
rename to src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
index 6d72d965..0347028b 100644
--- a/src/main/java/org/caosdb/server/database/DatabaseUtils.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
@@ -1,9 +1,10 @@
/*
- * ** 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
@@ -17,10 +18,8 @@
*
* 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;
+package org.caosdb.server.database.backend.implementation.MySQL;
import com.google.common.base.Objects;
import java.sql.ResultSet;
@@ -46,7 +45,6 @@ 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.Parent;
import org.caosdb.server.entity.wrapper.Property;
public class DatabaseUtils {
@@ -154,13 +152,7 @@ public class DatabaseUtils {
}
}
- 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)
+ public static void parseOverrides(final List<ProtoProperty> properties, final ResultSet rs)
throws SQLException {
while (rs.next()) {
final int property_id = rs.getInt("property_id");
@@ -187,15 +179,15 @@ public class DatabaseUtils {
}
}
- public static List<FlatProperty> parsePropertyResultset(final ResultSet rs) throws SQLException {
- final List<FlatProperty> ret = new LinkedList<>();
+ public static List<ProtoProperty> parsePropertyResultset(final ResultSet rs) throws SQLException {
+ final List<ProtoProperty> ret = new LinkedList<>();
while (rs.next()) {
- 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);
+ 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;
}
@@ -239,9 +231,9 @@ public class DatabaseUtils {
return ret;
}
- public static ArrayList<VerySparseEntity> parseParentResultSet(final ResultSet rs)
+ public static LinkedList<VerySparseEntity> parseParentResultSet(final ResultSet rs)
throws SQLException {
- final ArrayList<VerySparseEntity> ret = new ArrayList<VerySparseEntity>();
+ final LinkedList<VerySparseEntity> ret = new LinkedList<>();
while (rs.next()) {
final VerySparseEntity vsp = new VerySparseEntity();
vsp.id = rs.getInt("ParentID");
@@ -254,25 +246,6 @@ public class DatabaseUtils {
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);
- }
- }
-
public static ArrayList<Property> parseFromProtoProperties(
EntityInterface entity, List<ProtoProperty> protos) {
final ArrayList<Property> ret = new ArrayList<Property>();
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 09cae688..474048f1 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 5c9ca6f9..f3977068 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
@@ -33,7 +33,6 @@ import java.util.Deque;
import java.util.Iterator;
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.InsertEntityPropertiesImpl;
import org.caosdb.server.database.exceptions.IntegrityException;
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 1b945acf..27227926 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/MySQLRetrieveAll.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java
index f847bf63..9a2ea816 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 e085f051..68524941 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 64ce7e90..1e2a6621 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 1ff7dd7a..9fd7e0a8 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 c8843f9c..100df4ce 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
@@ -28,11 +28,9 @@ import java.sql.SQLException;
import java.sql.Types;
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;
@@ -92,32 +90,22 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
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 retrieveOverrides = prepareStatement(stmtStr2);
- retrieveOverrides(domain, entity, version, retrieveOverrides, props);
+ retrieveOverrides(domain, entity, version, retrieveOverrides, properties);
- return handleCollectionValues(props);
+ return properties;
}
}
- @Deprecated
- public List<ProtoProperty> handleCollectionValues(List<FlatProperty> props) throws SQLException {
-
- List<ProtoProperty> result = new LinkedList<>();
- for (FlatProperty fp : props) {
- result.add(new ProtoProperty(fp));
- }
- return result;
- }
-
private void retrieveOverrides(
final Integer domain,
final Integer entity,
final String version,
final PreparedStatement retrieveOverrides,
- final List<FlatProperty> props)
+ final List<ProtoProperty> props)
throws SQLException {
ResultSet rs = null;
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 ca3bd078..48cd84b3 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 bde1878d..40f036f1 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 585be49a..6c4c2629 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 1c803925..b2d0fb9e 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 00000000..66bf99c4
--- /dev/null
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java
@@ -0,0 +1,53 @@
+/*
+ * 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.StatementStatus;
+import org.caosdb.server.entity.wrapper.Property;
+
+public class Replacement extends Property {
+
+ public Property replacement;
+ public EntityID replacementId;
+
+ @Override
+ public EntityID getId() {
+ return replacementId;
+ }
+
+ public void setReplacementId(EntityID id) {
+ replacementId.link(id);
+ }
+
+ public Replacement(Property p) {
+ super(p);
+ replacementId = new EntityID();
+ replacement = new Property(new RetrieveEntity());
+
+ replacement.setDomain(p.getDomainEntity());
+ replacement.setId(replacementId);
+ replacement.setStatementStatus(StatementStatus.REPLACEMENT);
+ replacement.setValue(new ReferenceValue(p.getId()));
+ replacement.setPIdx(0);
+ }
+}
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 91c68dc5..0886ff43 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 9bfddba1..9f7eba82 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/transaction/RetrieveDatatypes.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveDatatypes.java
index b4a726da..1ca9f60e 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 b551430a..262ee271 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 caa4b6cf..f9c11303 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
@@ -29,7 +29,7 @@ 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;
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 aabd490b..f1ba8354 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/FlatProperty.java b/src/main/java/org/caosdb/server/database/proto/FlatProperty.java
index b4f0f62a..b92d3def 100644
--- a/src/main/java/org/caosdb/server/database/proto/FlatProperty.java
+++ b/src/main/java/org/caosdb/server/database/proto/FlatProperty.java
@@ -26,19 +26,6 @@ import java.io.Serializable;
public class FlatProperty implements Serializable {
- public FlatProperty() {}
-
- public FlatProperty(FlatProperty fp) {
- id = fp.id;
- value = fp.value;
- status = fp.status;
- idx = fp.idx;
- name = fp.name;
- desc = fp.desc;
- type = fp.type;
- collection = fp.collection;
- }
-
private static final long serialVersionUID = 6039288034435124195L;
public Integer id = null;
public String value = null;
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 c6cdbd54..7a11cd4d 100644
--- a/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java
+++ b/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java
@@ -28,12 +28,6 @@ import java.util.List;
public class ProtoProperty extends FlatProperty implements Serializable {
private static final long serialVersionUID = 7731301985162924975L;
- public ProtoProperty(FlatProperty fp) {
- super(fp);
- }
-
- public ProtoProperty() {}
-
public List<ProtoProperty> subProperties = null;
public List<Object> collValues = null;
}
diff --git a/src/main/java/org/caosdb/server/query/Backreference.java b/src/main/java/org/caosdb/server/query/Backreference.java
index 7d551fd4..b801ffaf 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 03b33124..59dfd57b 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 edd2e6da..925ef859 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 cfdfd05e..431124df 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 0de160cd..ebc35a16 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 c4a45863..abaca436 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 8ff167ea..d5ce9234 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/utils/ResultSetIterator.java b/src/main/java/org/caosdb/server/utils/ResultSetIterator.java
index 0912d278..71429f1a 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/test/java/org/caosdb/server/database/InsertTest.java b/src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java
similarity index 98%
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 0484e623..03bd185c 100644
--- a/src/test/java/org/caosdb/server/database/InsertTest.java
+++ b/src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java
@@ -20,10 +20,10 @@
*
* ** 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;
--
GitLab
From ac56b7746d683050512ef58288e526f92c056397 Mon Sep 17 00:00:00 2001
From: Timm Fitschen <t.fitschen@indiscale.com>
Date: Wed, 16 Aug 2023 01:10:28 +0200
Subject: [PATCH 6/9] WIP: MAINT: refactor retrieve properties (move
backend-logic to backend)
---
.../backend/implementation/MySQL/DatabaseUtils.java | 3 ++-
.../backend/implementation/MySQL/Replacement.java | 8 +++-----
2 files changed, 5 insertions(+), 6 deletions(-)
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
index 0347028b..20d43389 100644
--- 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
@@ -33,6 +33,7 @@ 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;
@@ -334,7 +335,7 @@ public class DatabaseUtils {
pp.collValues
.stream()
.map((x) -> (Object) ((Entry<Integer, String>) x).getValue())
- .toList();
+ .collect(Collectors.toList());
}
result.add(pp);
}
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
index 66bf99c4..fa2fb7cb 100644
--- 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
@@ -28,24 +28,22 @@ import org.caosdb.server.entity.wrapper.Property;
public class Replacement extends Property {
public Property replacement;
- public EntityID replacementId;
@Override
public EntityID getId() {
- return replacementId;
+ return replacement.getId();
}
public void setReplacementId(EntityID id) {
- replacementId.link(id);
+ replacement.getId().link(id);
}
public Replacement(Property p) {
super(p);
- replacementId = new EntityID();
replacement = new Property(new RetrieveEntity());
replacement.setDomain(p.getDomainEntity());
- replacement.setId(replacementId);
+ replacement.setId(new EntityID());
replacement.setStatementStatus(StatementStatus.REPLACEMENT);
replacement.setValue(new ReferenceValue(p.getId()));
replacement.setPIdx(0);
--
GitLab
From cc12cb76926f2e01eb1c64aa51aa22aedd701d7e Mon Sep 17 00:00:00 2001
From: Timm Fitschen <t.fitschen@indiscale.com>
Date: Wed, 16 Aug 2023 11:11:32 +0200
Subject: [PATCH 7/9] WIP: MAINT: refactor retrieve properties (move
backend-logic to backend)
---
.../implementation/MySQL/DatabaseUtils.java | 9 ++++--
.../MySQL/MySQLInsertEntityProperties.java | 14 +++++----
.../implementation/MySQL/Replacement.java | 16 ++++++++--
.../java/org/caosdb/server/entity/Entity.java | 6 ++--
.../caosdb/server/entity/EntityInterface.java | 4 +--
.../caosdb/server/entity/StatementStatus.java | 8 +----
.../entity/StatementStatusInterface.java | 29 +++++++++++++++++++
.../server/entity/wrapper/EntityWrapper.java | 8 ++---
.../server/grpc/CaosDBToGrpcConverters.java | 5 ++--
9 files changed, 72 insertions(+), 27 deletions(-)
create mode 100644 src/main/java/org/caosdb/server/entity/StatementStatusInterface.java
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
index 20d43389..c123b467 100644
--- 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
@@ -297,7 +297,7 @@ public class DatabaseUtils {
LinkedList<ProtoProperty> result = new LinkedList<>();
Map<String, ProtoProperty> replacements = new HashMap<>();
for (ProtoProperty pp : properties) {
- if (pp.status.equals(StatementStatus.REPLACEMENT.toString())) {
+ if (pp.status.equals(ReplacementStatus.REPLACEMENT.name())) {
replacements.put(pp.value, null);
}
}
@@ -322,7 +322,7 @@ public class DatabaseUtils {
}
}
for (ProtoProperty pp : properties) {
- if (pp.status.equals(StatementStatus.REPLACEMENT.toString())) {
+ if (pp.status.equals(ReplacementStatus.REPLACEMENT.name())) {
replace(pp, replacements.get(pp.value), isHead);
}
if (pp.collValues != null) {
@@ -342,6 +342,11 @@ public class DatabaseUtils {
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) {
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 f3977068..b57719f5 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
@@ -46,7 +46,6 @@ 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.StatementStatus;
import org.caosdb.server.entity.wrapper.Property;
public class MySQLInsertEntityProperties extends MySQLTransaction
@@ -116,10 +115,10 @@ public class MySQLInsertEntityProperties extends MySQLTransaction
}
private void insertStages(
- final List<Property> stage1Inserts, final EntityID domain, final EntityID entity)
+ final List<Property> inserts, final EntityID domain, final EntityID entity)
throws TransactionException {
- for (final Property property : stage1Inserts) {
+ for (final Property property : inserts) {
// prepare flat property
final FlatProperty fp = new FlatProperty();
@@ -129,10 +128,15 @@ public class MySQLInsertEntityProperties extends MySQLTransaction
fp.idx = property.getPIdx();
fp.status = property.getStatementStatus().name();
- if (property.getStatementStatus() == StatementStatus.REPLACEMENT) {
- table = Table.reference_data;
+ if (property.getStatementStatus() == ReplacementStatus.REPLACEMENT) {
+ // special treatment: swap value and id. This is part of the back-end specification for the
+ // representation of replacement.
+
+ // value should be the
fp.value = fp.id.toString();
+
fp.id = ((ReferenceValue) property.getValue()).getId().toInteger();
+ table = Table.reference_data;
} else {
if (property.hasUnit()) {
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
index fa2fb7cb..61e431ba 100644
--- 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
@@ -22,9 +22,21 @@ 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.StatementStatus;
+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;
@@ -44,7 +56,7 @@ public class Replacement extends Property {
replacement.setDomain(p.getDomainEntity());
replacement.setId(new EntityID());
- replacement.setStatementStatus(StatementStatus.REPLACEMENT);
+ replacement.setStatementStatus(ReplacementStatus.REPLACEMENT);
replacement.setValue(new ReferenceValue(p.getId()));
replacement.setPIdx(0);
}
diff --git a/src/main/java/org/caosdb/server/entity/Entity.java b/src/main/java/org/caosdb/server/entity/Entity.java
index 843449ce..614397c5 100644
--- a/src/main/java/org/caosdb/server/entity/Entity.java
+++ b/src/main/java/org/caosdb/server/entity/Entity.java
@@ -421,7 +421,7 @@ public abstract class Entity extends AbstractObservable implements EntityInterfa
}
}
- private StatementStatus statementStatus = null;
+ private StatementStatusInterface statementStatus = null;
/**
* statementStatus getter.
@@ -429,7 +429,7 @@ public abstract class Entity extends AbstractObservable implements EntityInterfa
* @return
*/
@Override
- public StatementStatus getStatementStatus() {
+ public StatementStatusInterface getStatementStatus() {
return this.statementStatus;
}
@@ -439,7 +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;
}
diff --git a/src/main/java/org/caosdb/server/entity/EntityInterface.java b/src/main/java/org/caosdb/server/entity/EntityInterface.java
index d97970de..ba77b5c4 100644
--- a/src/main/java/org/caosdb/server/entity/EntityInterface.java
+++ b/src/main/java/org/caosdb/server/entity/EntityInterface.java
@@ -57,9 +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);
diff --git a/src/main/java/org/caosdb/server/entity/StatementStatus.java b/src/main/java/org/caosdb/server/entity/StatementStatus.java
index 0a797175..83d0c57e 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/entity/StatementStatusInterface.java b/src/main/java/org/caosdb/server/entity/StatementStatusInterface.java
new file mode 100644
index 00000000..d1596afd
--- /dev/null
+++ b/src/main/java/org/caosdb/server/entity/StatementStatusInterface.java
@@ -0,0 +1,29 @@
+/*
+ * 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.entity;
+
+/**
+ * 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/EntityWrapper.java b/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java
index f23408df..b294a17e 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
diff --git a/src/main/java/org/caosdb/server/grpc/CaosDBToGrpcConverters.java b/src/main/java/org/caosdb/server/grpc/CaosDBToGrpcConverters.java
index 1b70a729..8ab8b057 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;
@@ -359,8 +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:
--
GitLab
From 5d5ea96303228064c854194d1ce60b7c4ab298d7 Mon Sep 17 00:00:00 2001
From: Timm Fitschen <t.fitschen@indiscale.com>
Date: Wed, 16 Aug 2023 11:24:17 +0200
Subject: [PATCH 8/9] WIP: MAINT: refactor retrieve properties (move
backend-logic to backend)
---
.../MySQL/MySQLInsertEntityProperties.java | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
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 b57719f5..becb56a2 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
@@ -130,11 +130,16 @@ public class MySQLInsertEntityProperties extends MySQLTransaction
if (property.getStatementStatus() == ReplacementStatus.REPLACEMENT) {
// special treatment: swap value and id. This is part of the back-end specification for the
- // representation of replacement.
+ // 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 should be the
+ // 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 {
--
GitLab
From f9f540e17d9eaee27d542f90e5eb10b94a7ce6be Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Thu, 17 Aug 2023 17:48:21 +0000
Subject: [PATCH 9/9] REVIEW: apply suggested changes
---
.../database/backend/implementation/MySQL/DatabaseUtils.java | 4 ----
1 file changed, 4 deletions(-)
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
index c123b467..f7d364ae 100644
--- 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
@@ -93,10 +93,6 @@ public class DatabaseUtils {
&& !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.
stage1Inserts.add(p);
} else {
Replacement r = new Replacement(p);
--
GitLab