From 82f48d15a390562b835f33b176945743b1e61816 Mon Sep 17 00:00:00 2001
From: Timm Fitschen <t.fitschen@indiscale.com>
Date: Thu, 4 Jun 2020 00:55:57 +0200
Subject: [PATCH] WIP: versioning phase 8
---
.../backend/transaction/RetrieveParents.java | 13 ++++
.../transaction/RetrieveSparseEntity.java | 3 +-
.../server/datatype/ReferenceDatatype2.java | 2 +-
.../server/datatype/ReferenceValue.java | 64 ++++++++++++++++---
.../java/caosdb/server/entity/Entity.java | 6 +-
src/main/java/caosdb/server/jobs/Job.java | 32 +++++++++-
.../jobs/core/CheckDatatypePresent.java | 9 +--
.../server/jobs/core/CheckParValid.java | 2 +-
.../server/jobs/core/CheckPropValid.java | 2 +-
.../jobs/core/CheckRefidIsaParRefid.java | 3 +-
.../server/jobs/core/CheckRefidValid.java | 19 ++++--
src/main/java/caosdb/server/query/Query.java | 6 +-
.../server/transaction/ChecksumUpdater.java | 2 +-
13 files changed, 131 insertions(+), 32 deletions(-)
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveParents.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveParents.java
index 9fffcae8..eac5aa7f 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveParents.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveParents.java
@@ -34,6 +34,18 @@ import caosdb.server.entity.EntityInterface;
import java.util.ArrayList;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
+// TODO Problem with the caching.
+// When an old entity version has a parent which is deleted, the name is
+// still in the cached VerySparseEntity. This can be resolved by using a
+// similar strategy as in RetrieveProperties.java where the name etc. are
+// retrieved in a second step. Thus the deletion doesn't slips through
+// unnoticed.
+//
+// Changes are to be made in the backend-api, i.e. mysqlbackend and the
+// interfaces as well.
+//
+// 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>> {
@@ -67,6 +79,7 @@ public class RetrieveParents
@Override
protected void process(final ArrayList<VerySparseEntity> t) throws TransactionException {
this.entity.getParents().clear();
+
DatabaseUtils.parseParentsFromVerySparseEntity(this.entity, t);
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
index 6ad58df8..1eb0c4c5 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
@@ -58,8 +58,9 @@ public class RetrieveSparseEntity extends CacheableBackendTransaction<String, Sp
this.entity = entity;
}
- public RetrieveSparseEntity(final int id) {
+ public RetrieveSparseEntity(final int id, final String version) {
this(new Entity(id));
+ this.entity.getVersion().setId(version);
}
@Override
diff --git a/src/main/java/caosdb/server/datatype/ReferenceDatatype2.java b/src/main/java/caosdb/server/datatype/ReferenceDatatype2.java
index ce92aa02..87c17079 100644
--- a/src/main/java/caosdb/server/datatype/ReferenceDatatype2.java
+++ b/src/main/java/caosdb/server/datatype/ReferenceDatatype2.java
@@ -47,7 +47,7 @@ public class ReferenceDatatype2 extends ReferenceDatatype {
}
public void setEntity(final EntityInterface datatypeEntity) {
- this.refid.setEntity(datatypeEntity);
+ this.refid.setEntity(datatypeEntity, false);
}
@Override
diff --git a/src/main/java/caosdb/server/datatype/ReferenceValue.java b/src/main/java/caosdb/server/datatype/ReferenceValue.java
index 25fa0b38..3fa22c94 100644
--- a/src/main/java/caosdb/server/datatype/ReferenceValue.java
+++ b/src/main/java/caosdb/server/datatype/ReferenceValue.java
@@ -26,27 +26,28 @@ import caosdb.server.datatype.AbstractDatatype.Table;
import caosdb.server.entity.EntityInterface;
import caosdb.server.entity.Message;
import caosdb.server.utils.ServerMessages;
+import java.util.Objects;
import org.jdom2.Element;
public class ReferenceValue implements SingleValue {
private EntityInterface entity = null;
private String name = null;
private Integer id = null;
+ private String version = null;
+ private boolean versioned = false;
public static ReferenceValue parseReference(final Object reference) throws Message {
if (reference == null) {
return null;
}
if (reference instanceof EntityInterface) {
- return new ReferenceValue((EntityInterface) reference);
+ return new ReferenceValue(
+ (EntityInterface) reference, ((EntityInterface) reference).hasVersion());
} else if (reference instanceof ReferenceValue) {
return (ReferenceValue) reference;
} else if (reference instanceof GenericValue) {
- try {
- return new ReferenceValue(Integer.parseInt(((GenericValue) reference).toDatabaseString()));
- } catch (final NumberFormatException e) {
- return new ReferenceValue(((GenericValue) reference).toDatabaseString());
- }
+ String str = ((GenericValue) reference).toDatabaseString();
+ return parseFromString(str);
} else if (reference instanceof CollectionValue) {
throw ServerMessages.DATA_TYPE_DOES_NOT_ACCEPT_COLLECTION_VALUES;
} else {
@@ -58,17 +59,46 @@ public class ReferenceValue implements SingleValue {
}
}
+ public static ReferenceValue parseIdVersion(String str) {
+ String[] split = str.split("@", 2);
+ if (split.length == 2) {
+ return new ReferenceValue(Integer.parseInt(split[0]), split[1]);
+ } else {
+ return new ReferenceValue(Integer.parseInt(str));
+ }
+ }
+
+ public static ReferenceValue parseFromString(String str) {
+ try {
+ return parseIdVersion(str);
+ } catch (final NumberFormatException e) {
+ return new ReferenceValue(str);
+ }
+ }
+
@Override
public String toString() {
- if (this.entity != null) {
+ if (this.entity != null && versioned) {
+ return this.entity.getIdVersion().toString();
+ } else if (this.entity != null) {
return this.entity.getId().toString();
} else if (this.id == null && this.name != null) {
return this.name;
+ } else if (this.version != null) {
+ return getIdVersion();
}
return this.id.toString();
}
- public ReferenceValue(final EntityInterface entity) {
+ public String getIdVersion() {
+ if (this.version != null) {
+ return new StringBuilder().append(this.id).append("@").append(this.version).toString();
+ }
+ return this.id.toString();
+ }
+
+ public ReferenceValue(final EntityInterface entity, boolean versioned) {
+ this.versioned = versioned;
this.entity = entity;
}
@@ -76,6 +106,11 @@ public class ReferenceValue implements SingleValue {
this.id = id;
}
+ public ReferenceValue(final Integer id, final String version) {
+ this.id = id;
+ this.version = version;
+ }
+
public ReferenceValue(final String name) {
this.name = name;
}
@@ -84,7 +119,8 @@ public class ReferenceValue implements SingleValue {
return this.entity;
}
- public final void setEntity(final EntityInterface entity) {
+ public final void setEntity(final EntityInterface entity, boolean versioned) {
+ this.versioned = versioned;
this.entity = entity;
}
@@ -102,6 +138,13 @@ public class ReferenceValue implements SingleValue {
return this.id;
}
+ public final String getVersion() {
+ if (this.entity != null && versioned && this.entity.hasVersion()) {
+ return this.entity.getVersion().getId();
+ }
+ return this.version;
+ }
+
public final void setId(final Integer id) {
this.id = id;
}
@@ -126,7 +169,8 @@ public class ReferenceValue implements SingleValue {
if (obj instanceof ReferenceValue) {
final ReferenceValue that = (ReferenceValue) obj;
if (that.getId() != null && getId() != null) {
- return that.getId().equals(getId());
+ return that.getId().equals(getId())
+ && Objects.deepEquals(that.getVersion(), this.getVersion());
} else if (that.getName() != null && getName() != null) {
return that.getName().equals(getName());
}
diff --git a/src/main/java/caosdb/server/entity/Entity.java b/src/main/java/caosdb/server/entity/Entity.java
index 9bd0b6dd..23fb170d 100644
--- a/src/main/java/caosdb/server/entity/Entity.java
+++ b/src/main/java/caosdb/server/entity/Entity.java
@@ -1142,7 +1142,11 @@ public class Entity extends AbstractObservable implements EntityInterface {
if (!this.hasId()) {
return null;
} else if (this.hasVersion()) {
- return new StringBuilder().append(getId()).append(getVersion().getId()).toString();
+ return new StringBuilder()
+ .append(getId())
+ .append("@")
+ .append(getVersion().getId())
+ .toString();
}
return getId().toString();
}
diff --git a/src/main/java/caosdb/server/jobs/Job.java b/src/main/java/caosdb/server/jobs/Job.java
index 110809e7..8d98cbc3 100644
--- a/src/main/java/caosdb/server/jobs/Job.java
+++ b/src/main/java/caosdb/server/jobs/Job.java
@@ -171,11 +171,37 @@ public abstract class Job extends AbstractObservable implements Observer {
protected final EntityInterface retrieveValidSparseEntityByName(final String name)
throws Message {
- return retrieveValidSparseEntityById(retrieveValidIDByName(name));
+ return retrieveValidSparseEntityById(retrieveValidIDByName(name), null);
}
- protected final EntityInterface retrieveValidSparseEntityById(final Integer id) throws Message {
- final EntityInterface ret = execute(new RetrieveSparseEntity(id)).getEntity();
+ protected final EntityInterface retrieveValidSparseEntityById(
+ final Integer id, final String version) throws Message {
+
+ String resulting_version = version;
+ if (version == null || version.equals("HEAD")) {
+ // the targeted entity version is the entity after the transaction or the
+ // entity without a specific version. Thus we have to fetch the entity
+ // from the container if possible.
+ EntityInterface ret = getEntityById(id);
+ if (ret != null) {
+ return ret;
+ }
+ } else if (version.startsWith("HEAD~")) {
+ // if version is HEAD~{OFFSET} with {OFFSET} > 0 and the targeted entity is
+ // part of this request (i.e. is to be updated), the actual offset has to be
+ // reduced by 1. HEAD always denotes the entity@HEAD *after* the successful
+ // transaction.
+ int offset = Integer.parseInt(version.substring(5)) - 1;
+ if (offset == 0) {
+ // special case HEAD~1
+ resulting_version = "HEAD";
+ } else {
+ resulting_version = new StringBuilder().append("HEAD~").append(offset).toString();
+ }
+ }
+
+ final EntityInterface ret =
+ execute(new RetrieveSparseEntity(id, resulting_version)).getEntity();
if (ret.getEntityStatus() == EntityStatus.NONEXISTENT) {
throw ServerMessages.ENTITY_DOES_NOT_EXIST;
}
diff --git a/src/main/java/caosdb/server/jobs/core/CheckDatatypePresent.java b/src/main/java/caosdb/server/jobs/core/CheckDatatypePresent.java
index 69d36f42..faf481db 100644
--- a/src/main/java/caosdb/server/jobs/core/CheckDatatypePresent.java
+++ b/src/main/java/caosdb/server/jobs/core/CheckDatatypePresent.java
@@ -138,7 +138,8 @@ public final class CheckDatatypePresent extends EntityJob {
}
} else {
- final EntityInterface validDatatypeEntity = retrieveValidSparseEntityById(datatype.getId());
+ final EntityInterface validDatatypeEntity =
+ retrieveValidSparseEntityById(datatype.getId(), null);
assertAllowedToUse(validDatatypeEntity);
datatype.setEntity(validDatatypeEntity);
}
@@ -151,7 +152,7 @@ public final class CheckDatatypePresent extends EntityJob {
private void checkIfOverride() throws Message {
if (getEntity().hasId() && getEntity().getId() > 0) {
// get data type from database
- final EntityInterface foreign = retrieveValidSparseEntityById(getEntity().getId());
+ final EntityInterface foreign = retrieveValidSparseEntityById(getEntity().getId(), null);
if (foreign.hasDatatype() && !foreign.getDatatype().equals(getEntity().getDatatype())) {
// is override!
@@ -179,7 +180,7 @@ public final class CheckDatatypePresent extends EntityJob {
// the data type of the corresponding abstract property.
if (getEntity().hasId() && getEntity().getId() > 0) {
// get from data base
- final EntityInterface foreign = retrieveValidSparseEntityById(getEntity().getId());
+ final EntityInterface foreign = retrieveValidSparseEntityById(getEntity().getId(), null);
inheritDatatypeFromForeignEntity(foreign);
} else if (getEntity().hasId() && getEntity().getId() < 0) {
// get from container
@@ -218,7 +219,7 @@ public final class CheckDatatypePresent extends EntityJob {
for (final EntityInterface parent : getEntity().getParents()) {
EntityInterface parentEntity = null;
if (parent.getId() > 0) {
- parentEntity = retrieveValidSparseEntityById(parent.getId());
+ parentEntity = retrieveValidSparseEntityById(parent.getId(), null);
} else {
parentEntity = getEntityById(parent.getId());
runJobFromSchedule(parentEntity, CheckDatatypePresent.class);
diff --git a/src/main/java/caosdb/server/jobs/core/CheckParValid.java b/src/main/java/caosdb/server/jobs/core/CheckParValid.java
index 005053a4..560558dc 100644
--- a/src/main/java/caosdb/server/jobs/core/CheckParValid.java
+++ b/src/main/java/caosdb/server/jobs/core/CheckParValid.java
@@ -65,7 +65,7 @@ public class CheckParValid extends EntityJob {
if (parent.getId() >= 0) {
// id >= 0 (parent is yet in the database)
// retrieve parent by id
- final EntityInterface foreign = retrieveValidSparseEntityById(parent.getId());
+ final EntityInterface foreign = retrieveValidSparseEntityById(parent.getId(), null);
// check permissions for this
// parentforeign.acceptObserver(o)
assertAllowedToUse(foreign);
diff --git a/src/main/java/caosdb/server/jobs/core/CheckPropValid.java b/src/main/java/caosdb/server/jobs/core/CheckPropValid.java
index 6a7cbb51..5e199e84 100644
--- a/src/main/java/caosdb/server/jobs/core/CheckPropValid.java
+++ b/src/main/java/caosdb/server/jobs/core/CheckPropValid.java
@@ -55,7 +55,7 @@ public class CheckPropValid extends EntityJob {
if (property.getId() >= 0) {
final EntityInterface abstractProperty =
- retrieveValidSparseEntityById(property.getId());
+ retrieveValidSparseEntityById(property.getId(), null);
assertAllowedToUse(abstractProperty);
diff --git a/src/main/java/caosdb/server/jobs/core/CheckRefidIsaParRefid.java b/src/main/java/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
index fa2b21cc..04a1ac8c 100644
--- a/src/main/java/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
+++ b/src/main/java/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
@@ -94,7 +94,8 @@ public class CheckRefidIsaParRefid extends EntityJob {
&& getEntityByName(rv.getName()).getRole() == Role.File) {
} else if (rv.getId() != null
&& rv.getId() > 0
- && retrieveValidSparseEntityById(rv.getId()).getRole() == Role.File) {
+ && retrieveValidSparseEntityById(rv.getId(), rv.getVersion()).getRole()
+ == Role.File) {
} else if (rv.getName() != null
&& retrieveValidSparseEntityByName(rv.getName()).getRole() == Role.File) {
} else {
diff --git a/src/main/java/caosdb/server/jobs/core/CheckRefidValid.java b/src/main/java/caosdb/server/jobs/core/CheckRefidValid.java
index 14d98962..0139b98f 100644
--- a/src/main/java/caosdb/server/jobs/core/CheckRefidValid.java
+++ b/src/main/java/caosdb/server/jobs/core/CheckRefidValid.java
@@ -85,9 +85,12 @@ public class CheckRefidValid extends EntityJob {
private void checkRefValue(final ReferenceValue ref) throws Message {
if (ref.getId() != null) {
if (ref.getId() >= 0) {
- final EntityInterface referencedValidEntity = retrieveValidSparseEntityById(ref.getId());
+ final EntityInterface referencedValidEntity =
+ retrieveValidSparseEntityById(ref.getId(), ref.getVersion());
assertAllowedToUse(referencedValidEntity);
- ref.setEntity(referencedValidEntity);
+
+ // link the entity as versioned entity iff the reference specified a version
+ ref.setEntity(referencedValidEntity, ref.getVersion() != null);
} else {
@@ -100,7 +103,9 @@ public class CheckRefidValid extends EntityJob {
final EntityInterface referencedEntity = getEntityById(ref.getId());
if (referencedEntity != null) {
assertAllowedToUse(referencedEntity);
- ref.setEntity(referencedEntity);
+
+ // link the entity as versioned entity iff the reference specified a version
+ ref.setEntity(referencedEntity, ref.getVersion() != null);
} else {
throw ServerMessages.REFERENCED_ENTITY_DOES_NOT_EXIST;
}
@@ -117,7 +122,9 @@ public class CheckRefidValid extends EntityJob {
if (referencedEntity != null) {
assertAllowedToUse(referencedEntity);
- ref.setEntity(referencedEntity);
+
+ // link the entity as versioned entity iff the reference specified a version
+ ref.setEntity(referencedEntity, ref.getVersion() != null);
if (checkRefEntity(ref)) {
ref.getEntity().acceptObserver(this);
}
@@ -125,7 +132,9 @@ public class CheckRefidValid extends EntityJob {
final EntityInterface referencedValidEntity =
retrieveValidSparseEntityByName(ref.getName());
assertAllowedToUse(referencedValidEntity);
- ref.setEntity(referencedValidEntity);
+
+ // link the entity as versioned entity iff the reference specified a version
+ ref.setEntity(referencedValidEntity, ref.getVersion() != null);
}
}
}
diff --git a/src/main/java/caosdb/server/query/Query.java b/src/main/java/caosdb/server/query/Query.java
index 1f858269..c235a34e 100644
--- a/src/main/java/caosdb/server/query/Query.java
+++ b/src/main/java/caosdb/server/query/Query.java
@@ -299,7 +299,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
// ... check for RETRIEVE:ENTITY permission...
final EntityInterface e =
- execute(new RetrieveSparseEntity(q.getKey()), query.getAccess()).getEntity();
+ execute(new RetrieveSparseEntity(q.getKey(), null), query.getAccess()).getEntity();
final EntityACL entityACL = e.getEntityACL();
if (!entityACL.isPermitted(query.getUser(), EntityPermission.RETRIEVE_ENTITY)) {
// ... and ignore if not.
@@ -553,7 +553,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
while (rs.next()) {
final long t1 = System.currentTimeMillis();
final Integer id = rs.getInt("id");
- if (!execute(new RetrieveSparseEntity(id), query.getAccess())
+ if (!execute(new RetrieveSparseEntity(id, null), query.getAccess())
.getEntity()
.getEntityACL()
.isPermitted(query.getUser(), EntityPermission.RETRIEVE_ENTITY)) {
@@ -586,7 +586,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
while (iterator.hasNext()) {
final long t1 = System.currentTimeMillis();
final Integer id = iterator.next();
- if (!execute(new RetrieveSparseEntity(id), getAccess())
+ if (!execute(new RetrieveSparseEntity(id, null), getAccess())
.getEntity()
.getEntityACL()
.isPermitted(getUser(), EntityPermission.RETRIEVE_ENTITY)) {
diff --git a/src/main/java/caosdb/server/transaction/ChecksumUpdater.java b/src/main/java/caosdb/server/transaction/ChecksumUpdater.java
index 30313478..29603fc5 100644
--- a/src/main/java/caosdb/server/transaction/ChecksumUpdater.java
+++ b/src/main/java/caosdb/server/transaction/ChecksumUpdater.java
@@ -141,7 +141,7 @@ public class ChecksumUpdater extends WriteTransaction<TransactionContainer> impl
instance.running = false;
return null;
}
- return execute(new RetrieveSparseEntity(id), weakAccess).getEntity();
+ return execute(new RetrieveSparseEntity(id, null), weakAccess).getEntity();
}
} catch (final Exception e) {
e.printStackTrace();
--
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