From 72b76510df0ea9646a8bde07cc462933123932eb Mon Sep 17 00:00:00 2001
From: Quazgar <quazgar@posteo.de>
Date: Tue, 25 Aug 2020 08:41:04 +0000
Subject: [PATCH] FIX: Forcing SRID initiation also for ChecksumUpdater
Necessary for bug #99.
---
CHANGELOG.md | 1 +
.../server/database/BackendTransaction.java | 2 ++
.../server/database/MySQLSetFileChecksum.java | 31 +++++++++++++++++++
.../interfaces/SetFileChecksumImpl.java | 6 ++++
.../backend/transaction/SetFileChecksum.java | 26 ++++++++++++++++
.../caosdb/server/entity/FileProperties.java | 6 ++--
.../server/transaction/ChecksumUpdater.java | 6 ++--
7 files changed, 73 insertions(+), 5 deletions(-)
create mode 100644 src/main/java/caosdb/server/database/MySQLSetFileChecksum.java
create mode 100644 src/main/java/caosdb/server/database/backend/interfaces/SetFileChecksumImpl.java
create mode 100644 src/main/java/caosdb/server/database/backend/transaction/SetFileChecksum.java
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 613ee315..71e19edb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -56,6 +56,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- #11 - pam_authentication leaks the password to unprivileged processes on the
same machine.
- #39 - quotes around datetimes in queries
+- #99 - Checksum updating resulted in infinite loop on server.
### Security (in case of vulnerabilities)
diff --git a/src/main/java/caosdb/server/database/BackendTransaction.java b/src/main/java/caosdb/server/database/BackendTransaction.java
index 55987005..c476fb5b 100644
--- a/src/main/java/caosdb/server/database/BackendTransaction.java
+++ b/src/main/java/caosdb/server/database/BackendTransaction.java
@@ -119,6 +119,7 @@ import caosdb.server.database.backend.interfaces.RetrieveUserImpl;
import caosdb.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
import caosdb.server.database.backend.interfaces.RuleLoaderImpl;
import caosdb.server.database.backend.interfaces.SetFileCheckedTimestampImpl;
+import caosdb.server.database.backend.interfaces.SetFileChecksumImpl;
import caosdb.server.database.backend.interfaces.SetPasswordImpl;
import caosdb.server.database.backend.interfaces.SetPermissionRulesImpl;
import caosdb.server.database.backend.interfaces.SetQueryTemplateDefinitionImpl;
@@ -209,6 +210,7 @@ public abstract class BackendTransaction implements Undoable {
RetrieveQueryTemplateDefinitionImpl.class, MySQLRetrieveQueryTemplateDefinition.class);
setImpl(InsertEntityDatatypeImpl.class, MySQLInsertEntityDatatype.class);
setImpl(RetrieveVersionHistoryImpl.class, MySQLRetrieveVersionHistory.class);
+ setImpl(SetFileChecksumImpl.class, MySQLSetFileChecksum.class);
}
}
diff --git a/src/main/java/caosdb/server/database/MySQLSetFileChecksum.java b/src/main/java/caosdb/server/database/MySQLSetFileChecksum.java
new file mode 100644
index 00000000..a74843b6
--- /dev/null
+++ b/src/main/java/caosdb/server/database/MySQLSetFileChecksum.java
@@ -0,0 +1,31 @@
+package caosdb.server.database;
+
+import caosdb.server.database.access.Access;
+import caosdb.server.database.backend.implementation.MySQL.ConnectionException;
+import caosdb.server.database.backend.implementation.MySQL.MySQLTransaction;
+import caosdb.server.database.backend.interfaces.SetFileChecksumImpl;
+import caosdb.server.database.exceptions.TransactionException;
+import java.sql.PreparedStatement;
+import java.sql.SQLException;
+
+public class MySQLSetFileChecksum extends MySQLTransaction implements SetFileChecksumImpl {
+
+ public MySQLSetFileChecksum(Access access) {
+ super(access);
+ }
+
+ public static final String STMT_SET_CHECKSUM =
+ "UPDATE files SET hash = unhex(?) WHERE file_id = ?";
+
+ @Override
+ public void execute(Integer id, String checksum) {
+ try {
+ PreparedStatement stmt = prepareStatement(STMT_SET_CHECKSUM);
+ stmt.setInt(2, id);
+ stmt.setString(1, checksum);
+ stmt.execute();
+ } catch (SQLException | ConnectionException e) {
+ throw new TransactionException(e);
+ }
+ }
+}
diff --git a/src/main/java/caosdb/server/database/backend/interfaces/SetFileChecksumImpl.java b/src/main/java/caosdb/server/database/backend/interfaces/SetFileChecksumImpl.java
new file mode 100644
index 00000000..be73b33e
--- /dev/null
+++ b/src/main/java/caosdb/server/database/backend/interfaces/SetFileChecksumImpl.java
@@ -0,0 +1,6 @@
+package caosdb.server.database.backend.interfaces;
+
+public interface SetFileChecksumImpl extends BackendTransactionImpl {
+
+ void execute(Integer id, String checksum);
+}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/SetFileChecksum.java b/src/main/java/caosdb/server/database/backend/transaction/SetFileChecksum.java
new file mode 100644
index 00000000..b19bceab
--- /dev/null
+++ b/src/main/java/caosdb/server/database/backend/transaction/SetFileChecksum.java
@@ -0,0 +1,26 @@
+package caosdb.server.database.backend.transaction;
+
+import caosdb.server.database.BackendTransaction;
+import caosdb.server.database.backend.interfaces.SetFileChecksumImpl;
+import caosdb.server.entity.EntityInterface;
+
+public class SetFileChecksum extends BackendTransaction {
+
+ private EntityInterface entity;
+
+ public SetFileChecksum(EntityInterface entity) {
+ this.entity = entity;
+ }
+
+ @Override
+ protected void execute() {
+ RetrieveSparseEntity.removeCached(this.entity);
+ if (entity.hasFileProperties()) {
+ GetFileRecordByPath.removeCached(this.entity.getFileProperties().getPath());
+
+ final SetFileChecksumImpl t = getImplementation(SetFileChecksumImpl.class);
+
+ t.execute(this.entity.getId(), this.entity.getFileProperties().getChecksum());
+ }
+ }
+}
diff --git a/src/main/java/caosdb/server/entity/FileProperties.java b/src/main/java/caosdb/server/entity/FileProperties.java
index fbf8031f..c0fcaa46 100644
--- a/src/main/java/caosdb/server/entity/FileProperties.java
+++ b/src/main/java/caosdb/server/entity/FileProperties.java
@@ -220,10 +220,10 @@ public class FileProperties {
if (file.getAbsolutePath().startsWith(FileSystem.getBasepath())) {
final Undoable d;
final File parent = file.getParentFile();
- if (file.getCanonicalPath().startsWith(FileSystem.getBasepath())) {
- d = FileUtils.delete(file, file.isDirectory());
- } else if (FileUtils.isSymlink(file)) {
+ if (FileUtils.isSymlink(file)) {
d = FileUtils.unlink(file);
+ } else if (file.getCanonicalPath().startsWith(FileSystem.getBasepath())) {
+ d = FileUtils.delete(file, file.isDirectory());
} else {
throw new CaosDBException(
"File is in Filesystem, but it is neither a normal file nor a symlink.");
diff --git a/src/main/java/caosdb/server/transaction/ChecksumUpdater.java b/src/main/java/caosdb/server/transaction/ChecksumUpdater.java
index 29603fc5..ec923bec 100644
--- a/src/main/java/caosdb/server/transaction/ChecksumUpdater.java
+++ b/src/main/java/caosdb/server/transaction/ChecksumUpdater.java
@@ -27,7 +27,7 @@ import caosdb.server.database.DatabaseMonitor;
import caosdb.server.database.access.Access;
import caosdb.server.database.backend.transaction.GetUpdateableChecksums;
import caosdb.server.database.backend.transaction.RetrieveSparseEntity;
-import caosdb.server.database.backend.transaction.UpdateSparseEntity;
+import caosdb.server.database.backend.transaction.SetFileChecksum;
import caosdb.server.database.exceptions.TransactionException;
import caosdb.server.entity.EntityInterface;
import caosdb.server.entity.FileProperties;
@@ -46,6 +46,7 @@ import java.security.NoSuchAlgorithmException;
public class ChecksumUpdater extends WriteTransaction<TransactionContainer> implements Runnable {
private Boolean running = false;
+
private static final ChecksumUpdater instance = new ChecksumUpdater();
private ChecksumUpdater() {
@@ -85,7 +86,7 @@ public class ChecksumUpdater extends WriteTransaction<TransactionContainer> impl
DatabaseMonitor.getInstance().acquireStrongAccess(this);
// update
- execute(new UpdateSparseEntity(fileEntity), strongAccess);
+ execute(new SetFileChecksum(fileEntity), strongAccess);
strongAccess.commit();
} catch (final InterruptedException e) {
@@ -145,6 +146,7 @@ public class ChecksumUpdater extends WriteTransaction<TransactionContainer> impl
}
} catch (final Exception e) {
e.printStackTrace();
+ instance.running = false;
return null;
} finally {
weakAccess.release();
--
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