From cc6523be1f156b6c3fb9a5716264b0d0b13ddc20 Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Wed, 11 Apr 2012 11:22:59 +0000
Subject: [PATCH] Fix: SOB-38 by using Jython interpreters with isolated
PySystemState() objects.
SVN: 24864
---
.../cisd/common/evaluator/Evaluator.java | 4 +-
.../cisd/common/utilities/PythonUtils.java | 39 +++++++++++++++++++
.../JythonTopLevelDataSetHandler.java | 3 +-
.../v2/JythonTopLevelDataSetHandlerV2.java | 3 +-
.../v1/validation/ValidationScriptRunner.java | 3 +-
.../MasterDataRegistrationScriptRunner.java | 3 +-
.../etl/jython/JythonPlateDataSetHandler.java | 3 +-
7 files changed, 52 insertions(+), 6 deletions(-)
create mode 100644 common/source/java/ch/systemsx/cisd/common/utilities/PythonUtils.java
diff --git a/common/source/java/ch/systemsx/cisd/common/evaluator/Evaluator.java b/common/source/java/ch/systemsx/cisd/common/evaluator/Evaluator.java
index df230def7a4..499e168601b 100644
--- a/common/source/java/ch/systemsx/cisd/common/evaluator/Evaluator.java
+++ b/common/source/java/ch/systemsx/cisd/common/evaluator/Evaluator.java
@@ -39,6 +39,8 @@ import org.python.core.PyStringMap;
import org.python.core.PySystemState;
import org.python.util.PythonInterpreter;
+import ch.systemsx.cisd.common.utilities.PythonUtils;
+
/**
* A class for evaluating expressions, based on Jython.
* <p>
@@ -122,7 +124,7 @@ public final class Evaluator
{
throw new EvaluatorException("Expression '" + expression + "' contains line breaks");
}
- this.interpreter = new PythonInterpreter();
+ this.interpreter = PythonUtils.createIsolatedPythonInterpreter();
// Security: do not allow file access.
try
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/PythonUtils.java b/common/source/java/ch/systemsx/cisd/common/utilities/PythonUtils.java
new file mode 100644
index 00000000000..99a0d61dd35
--- /dev/null
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/PythonUtils.java
@@ -0,0 +1,39 @@
+/*
+ * Copyright 2012 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.common.utilities;
+
+import org.python.core.PySystemState;
+import org.python.util.PythonInterpreter;
+
+/**
+ * Utility functions for Jython.
+ *
+ * @author Bernd Rinn
+ */
+public class PythonUtils
+{
+
+ /**
+ * Creates a new Jython interpreter with a fully isolated system state (i.e. interpreters in
+ * different threads don't influence each other.
+ */
+ public static PythonInterpreter createIsolatedPythonInterpreter()
+ {
+ return new PythonInterpreter(null, new PySystemState());
+ }
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetHandler.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetHandler.java
index a5971fc0d90..99d9930c7c0 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetHandler.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetHandler.java
@@ -30,6 +30,7 @@ import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
+import ch.systemsx.cisd.common.utilities.PythonUtils;
import ch.systemsx.cisd.etlserver.ITopLevelDataSetRegistratorDelegate;
import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
import ch.systemsx.cisd.etlserver.registrator.api.v1.SecondaryTransactionFailure;
@@ -198,7 +199,7 @@ public class JythonTopLevelDataSetHandler<T extends DataSetInformation> extends
{
return createJythonDataSetRegistrationService(incomingDataSetFile,
callerDataSetInformationOrNull, cleanAfterwardsAction, delegate,
- new PythonInterpreter(), getGlobalState());
+ PythonUtils.createIsolatedPythonInterpreter(), getGlobalState());
}
/**
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/JythonTopLevelDataSetHandlerV2.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/JythonTopLevelDataSetHandlerV2.java
index 024d94d4a53..7278192638c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/JythonTopLevelDataSetHandlerV2.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/JythonTopLevelDataSetHandlerV2.java
@@ -21,6 +21,7 @@ import java.io.File;
import org.python.util.PythonInterpreter;
import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
+import ch.systemsx.cisd.common.utilities.PythonUtils;
import ch.systemsx.cisd.etlserver.ITopLevelDataSetRegistratorDelegate;
import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
import ch.systemsx.cisd.etlserver.registrator.DataSetFile;
@@ -60,7 +61,7 @@ public class JythonTopLevelDataSetHandlerV2<T extends DataSetInformation> extend
{
return createJythonDataSetRegistrationServiceV2(incomingDataSetFile,
callerDataSetInformationOrNull, cleanAfterwardsAction, delegate,
- new PythonInterpreter(), getGlobalState());
+ PythonUtils.createIsolatedPythonInterpreter(), getGlobalState());
}
/**
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/v1/validation/ValidationScriptRunner.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/v1/validation/ValidationScriptRunner.java
index 80503292525..92503c0467a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/v1/validation/ValidationScriptRunner.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/v1/validation/ValidationScriptRunner.java
@@ -32,6 +32,7 @@ import org.python.core.PyObject;
import org.python.util.PythonInterpreter;
import ch.systemsx.cisd.common.utilities.JythonUtils;
+import ch.systemsx.cisd.common.utilities.PythonUtils;
/**
* @author Chandrasekhar Ramakrishnan
@@ -76,7 +77,7 @@ public class ValidationScriptRunner
private ValidationScriptRunner(String scriptString)
{
- this.interpreter = new PythonInterpreter();
+ this.interpreter = PythonUtils.createIsolatedPythonInterpreter();
// Load the script
this.scriptString = scriptString;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/MasterDataRegistrationScriptRunner.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/MasterDataRegistrationScriptRunner.java
index 8c6f1b1fa9a..7fac147a409 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/MasterDataRegistrationScriptRunner.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/MasterDataRegistrationScriptRunner.java
@@ -21,6 +21,7 @@ import java.io.File;
import org.python.util.PythonInterpreter;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.utilities.PythonUtils;
/**
* A class for running python scripts that register master data.
@@ -51,7 +52,7 @@ public class MasterDataRegistrationScriptRunner implements IMasterDataScriptRegi
MasterDataRegistrationService service = new MasterDataRegistrationService(commonServer);
// Configure the evaluator
- PythonInterpreter interpreter = new PythonInterpreter();
+ PythonInterpreter interpreter = PythonUtils.createIsolatedPythonInterpreter();
interpreter.set(SERVICE_VARIABLE_NAME, service);
// Invoke the evaluator
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
index 51b0910ee50..c210e3d49e1 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
@@ -21,6 +21,7 @@ import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.io.FileBasedContentNode;
import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
+import ch.systemsx.cisd.common.utilities.PythonUtils;
import ch.systemsx.cisd.etlserver.ITopLevelDataSetRegistratorDelegate;
import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
import ch.systemsx.cisd.etlserver.registrator.AbstractDataSetRegistrationDetailsFactory;
@@ -346,7 +347,7 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
{
return new JythonDataSetRegistrationService<DataSetInformation>(this, incomingDataSetFile,
callerDataSetInformationOrNull, cleanAfterwardsAction, delegate,
- new PythonInterpreter(), getGlobalState())
+ PythonUtils.createIsolatedPythonInterpreter(), getGlobalState())
{
@SuppressWarnings("unchecked")
@Override
--
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