diff --git a/common/source/java/ch/systemsx/cisd/common/jython/IJythonInterpreter.java b/common/source/java/ch/systemsx/cisd/common/jython/IJythonInterpreter.java
index 68ec87109e08fbeb6914a8157d94eb0dcb36699b..4e70806cd4ce82f10d4376161b4e5e97ea75e886 100644
--- a/common/source/java/ch/systemsx/cisd/common/jython/IJythonInterpreter.java
+++ b/common/source/java/ch/systemsx/cisd/common/jython/IJythonInterpreter.java
@@ -29,4 +29,6 @@ public interface IJythonInterpreter
void releaseResources();
IJythonFunction tryJythonFunction(String name);
+
+ boolean isNextCommand(String lines);
}
\ No newline at end of file
diff --git a/common/source/java/ch/systemsx/cisd/common/jython/JythonScriptCommand.java b/common/source/java/ch/systemsx/cisd/common/jython/JythonScriptCommand.java
deleted file mode 100644
index dc618c10537c65bd33e1276980621645d3bed7ac..0000000000000000000000000000000000000000
--- a/common/source/java/ch/systemsx/cisd/common/jython/JythonScriptCommand.java
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- * 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.jython;
-
-import org.python.core.CompileMode;
-import org.python.core.CompilerFlags;
-import org.python.core.Py;
-import org.python.core.PyException;
-import org.python.core.PyObject;
-
-/**
- * @author pkupczyk
- */
-public class JythonScriptCommand extends JythonScriptLines
-{
-
- public boolean isNextCommand(String line)
- {
- try
- {
- PyObject object =
- Py.compile_command_flags(getLines(), "<input>", CompileMode.single,
- new CompilerFlags(), true);
- return object != Py.None;
- } catch (PyException e)
- {
- return false;
- }
- }
-
-}
diff --git a/common/source/java/ch/systemsx/cisd/common/jython/JythonScriptSplitter.java b/common/source/java/ch/systemsx/cisd/common/jython/JythonScriptSplitter.java
index 3d5b5e8348d633d54b37a83945b9e9620a364401..4254f92143f44bc8f0bc5bd0dcea795416ac90fa 100644
--- a/common/source/java/ch/systemsx/cisd/common/jython/JythonScriptSplitter.java
+++ b/common/source/java/ch/systemsx/cisd/common/jython/JythonScriptSplitter.java
@@ -18,8 +18,6 @@ package ch.systemsx.cisd.common.jython;
import java.util.List;
-import org.python.core.PyException;
-
/**
* Splits jython code into smaller batches to overcome 64KB script size limitation.
*
@@ -32,16 +30,23 @@ public class JythonScriptSplitter
private int batchSize = DEFAULT_BATCH_SIZE;
- public List<String> split(String scriptToSplit) throws PyException
+ private IJythonInterpreter interpreter;
+
+ public JythonScriptSplitter(IJythonInterpreter interpreter)
+ {
+ this.interpreter = interpreter;
+ }
+
+ public List<String> split(String scriptToSplit)
{
JythonScript script = new JythonScript(scriptToSplit);
JythonScriptBatches batches = new JythonScriptBatches();
JythonScriptBatch batch = new JythonScriptBatch();
- JythonScriptCommand command = new JythonScriptCommand();
+ JythonScriptLines command = new JythonScriptLines();
for (String line : script.getLines())
{
- if (command.getSize() > 0 && command.isNextCommand(line))
+ if (command.getSize() > 0 && interpreter.isNextCommand(command.getLines()))
{
if (batch.getSize() > 0 && batch.getSize() + command.getSize() > getBatchSize())
{
@@ -49,7 +54,7 @@ public class JythonScriptSplitter
batch = new JythonScriptBatch();
}
batch.addLines(command);
- command = new JythonScriptCommand();
+ command = new JythonScriptLines();
command.addLine(line);
} else
{
diff --git a/common/source/java/ch/systemsx/cisd/common/jython/JythonUtils.java b/common/source/java/ch/systemsx/cisd/common/jython/JythonUtils.java
index 10b1be5b5a35ae2da32af08deaf955bc5675d998..7eadffe6d0813008a17dc02c38e833fa56258951 100644
--- a/common/source/java/ch/systemsx/cisd/common/jython/JythonUtils.java
+++ b/common/source/java/ch/systemsx/cisd/common/jython/JythonUtils.java
@@ -18,15 +18,7 @@ package ch.systemsx.cisd.common.jython;
import java.io.File;
import java.util.ArrayList;
-import java.util.HashMap;
import java.util.List;
-import java.util.Map;
-
-import org.python.core.Py;
-import org.python.core.PyDictionary;
-import org.python.core.PyFunction;
-import org.python.core.PyObject;
-import org.python.core.PySequenceList;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.jython.evaluator.EvaluatorException;
@@ -39,53 +31,6 @@ import ch.systemsx.cisd.common.shared.basic.string.StringUtils;
*/
public class JythonUtils
{
-
- /**
- * Converts a {@link PyDictionary} to a Java map.
- *
- * @return a map equivalent to the given Jython dictionary.
- */
- public static Map<String, String> convertPyDictToMap(PyDictionary result)
- {
- Map<String, String> javaMap = new HashMap<String, String>();
- for (Object item : result.items())
- {
- PySequenceList tuple = (PySequenceList) item;
- javaMap.put(tuple.get(0).toString(), tuple.get(1).toString());
- }
- return javaMap;
- }
-
- /**
- * Tries to get a function defined in jython script
- *
- * @return a Jython function object, or <code>null</code> if function doesn't exist.
- */
- public static PyFunction tryJythonFunction(PythonInterpreter interpreter, String functionName)
- {
- try
- {
- PyFunction function = interpreter.get(functionName, PyFunction.class);
- return function;
- } catch (Exception e)
- {
- return null;
- }
- }
-
- /**
- * Turn all arguments into a python objects, and calls the specified function.
- */
- public static PyObject invokeFunction(PyFunction function, Object... args)
- {
- PyObject[] pyArgs = new PyObject[args.length];
- for (int i = 0; i < args.length; i++)
- {
- pyArgs[i] = Py.java2py(args[i]);
- }
- return function.__call__(pyArgs);
- }
-
/**
* @return script string from file with given path
* @throws EvaluatorException if the file doesn't exist or is empty
diff --git a/common/source/java/ch/systemsx/cisd/common/jython/v25/Jython25InterpreterFactory.java b/common/source/java/ch/systemsx/cisd/common/jython/v25/Jython25InterpreterFactory.java
index f5fa157e0b3bc9feb659a8c386aae84f973cc98d..a8750976a494707ff6b63d9eb0cd7adec062a61b 100644
--- a/common/source/java/ch/systemsx/cisd/common/jython/v25/Jython25InterpreterFactory.java
+++ b/common/source/java/ch/systemsx/cisd/common/jython/v25/Jython25InterpreterFactory.java
@@ -16,7 +16,11 @@
package ch.systemsx.cisd.common.jython.v25;
+import org.python.core.CompileMode;
+import org.python.core.CompilerFlags;
+import org.python.core.Py;
import org.python.core.PyBaseCode;
+import org.python.core.PyException;
import org.python.core.PyFunction;
import org.python.core.PyInteger;
import org.python.core.PyObject;
@@ -25,7 +29,6 @@ import ch.systemsx.cisd.common.jython.IJythonFunction;
import ch.systemsx.cisd.common.jython.IJythonInterpreter;
import ch.systemsx.cisd.common.jython.IJythonInterpreterFactory;
import ch.systemsx.cisd.common.jython.IJythonObject;
-import ch.systemsx.cisd.common.jython.JythonUtils;
import ch.systemsx.cisd.common.jython.PythonInterpreter;
public class Jython25InterpreterFactory implements IJythonInterpreterFactory
@@ -48,7 +51,12 @@ public class Jython25InterpreterFactory implements IJythonInterpreterFactory
@Override
public IJythonObject invoke(Object... arguments)
{
- PyObject result = JythonUtils.invokeFunction(function, arguments);
+ PyObject[] pyArgs = new PyObject[arguments.length];
+ for (int i = 0; i < arguments.length; i++)
+ {
+ pyArgs[i] = Py.java2py(arguments[i]);
+ }
+ PyObject result = function.__call__(pyArgs);
if (result == null)
{
return null;
@@ -142,15 +150,30 @@ public class Jython25InterpreterFactory implements IJythonInterpreterFactory
@Override
public IJythonFunction tryJythonFunction(String name)
{
- PyFunction function = JythonUtils.tryJythonFunction(interpreter, name);
- if (function == null)
+ try
+ {
+ PyFunction function = interpreter.get(name, PyFunction.class);
+ return new Jython25Function(function);
+ } catch (Exception e)
{
return null;
}
- else
+ }
+
+ @Override
+ public boolean isNextCommand(String lines)
+ {
+ try
{
- return new Jython25Function(function);
+ PyObject object =
+ Py.compile_command_flags(lines, "<input>", CompileMode.single,
+ new CompilerFlags(), true);
+ return object != Py.None;
+ } catch (PyException e)
+ {
+ return false;
}
}
+
}
}
diff --git a/common/source/java/ch/systemsx/cisd/common/jython/v27/Jython27InterpreterFactory.java b/common/source/java/ch/systemsx/cisd/common/jython/v27/Jython27InterpreterFactory.java
index b7abfc09c1382bbaf065b9531dd6d9f6e54623ac..a9f3baa6f15ab81614a27b30e5f98b2b065b43a6 100644
--- a/common/source/java/ch/systemsx/cisd/common/jython/v27/Jython27InterpreterFactory.java
+++ b/common/source/java/ch/systemsx/cisd/common/jython/v27/Jython27InterpreterFactory.java
@@ -16,7 +16,11 @@
package ch.systemsx.cisd.common.jython.v27;
+import org.python27.core.CompileMode;
+import org.python27.core.CompilerFlags;
+import org.python27.core.Py;
import org.python27.core.PyBaseCode;
+import org.python27.core.PyException;
import org.python27.core.PyFunction;
import org.python27.core.PyInteger;
import org.python27.core.PyObject;
@@ -153,6 +157,21 @@ public class Jython27InterpreterFactory implements IJythonInterpreterFactory
return new Jython27Function(function);
}
}
+
+ @Override
+ public boolean isNextCommand(String lines)
+ {
+ try
+ {
+ PyObject object =
+ Py.compile_command_flags(lines, "<input>", CompileMode.single,
+ new CompilerFlags(), true);
+ return object != Py.None;
+ } catch (PyException e)
+ {
+ return false;
+ }
+ }
}
}
\ No newline at end of file
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/jython/JythonScriptSplitterTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/jython/JythonScriptSplitterTest.java
index bfde3af37c23c21cf8174daeb0e88b0cfec29aa8..3c277c8c737870e4936cd5d13cec5afc7cac88b9 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/jython/JythonScriptSplitterTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/jython/JythonScriptSplitterTest.java
@@ -25,6 +25,7 @@ import org.testng.Assert;
import org.testng.annotations.Test;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.jython.v27.Jython27InterpreterFactory;
/**
* @author pkupczyk
@@ -38,7 +39,7 @@ public class JythonScriptSplitterTest
@Test
public void testSplittingNullScriptShouldReturnNoBatches()
{
- JythonScriptSplitter splitter = new JythonScriptSplitter();
+ JythonScriptSplitter splitter = new JythonScriptSplitter(new Jython27InterpreterFactory().createInterpreter());
List<String> batches = splitter.split(null);
Assert.assertNotNull(batches);
Assert.assertEquals(batches, Collections.emptyList());
@@ -47,7 +48,7 @@ public class JythonScriptSplitterTest
@Test
public void testSplittingEmptyScriptShouldReturnOneEmptyBatch()
{
- JythonScriptSplitter splitter = new JythonScriptSplitter();
+ JythonScriptSplitter splitter = new JythonScriptSplitter(new Jython27InterpreterFactory().createInterpreter());
List<String> batches = splitter.split("");
Assert.assertNotNull(batches);
Assert.assertEquals(batches.size(), 1);
@@ -89,7 +90,7 @@ public class JythonScriptSplitterTest
{
String originalScript = getTestScriptCode(scriptSize);
- JythonScriptSplitter splitter = new JythonScriptSplitter();
+ JythonScriptSplitter splitter = new JythonScriptSplitter(new Jython27InterpreterFactory().createInterpreter());
splitter.setBatchSize(batchSize);
List<String> batches = splitter.split(originalScript);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/DataSetRegistrationServiceV2.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/DataSetRegistrationServiceV2.java
index 6d815c8a3cefd4f0a286d966e126211d00f9e1d8..f122704e0549f468d751ced4c6c4054179bbdf8d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/DataSetRegistrationServiceV2.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/DataSetRegistrationServiceV2.java
@@ -73,6 +73,12 @@ public class DataSetRegistrationServiceV2<T extends DataSetInformation> extends
public void addToPath(String... pythonPaths)
{
}
+
+ @Override
+ public boolean isNextCommand(String line)
+ {
+ return false;
+ }
}, null);
}
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 c94df2b747c6e82b40e8b9fa8b8cea93eddd5e2e..d76e86bef6cb4211c7de4cf35c0538a400235a47 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
@@ -29,6 +29,7 @@ import org.python.core.Py;
import org.python.core.PyDictionary;
import org.python.core.PyFunction;
import org.python.core.PyObject;
+import org.python.core.PySequenceList;
import ch.systemsx.cisd.common.jython.JythonUtils;
import ch.systemsx.cisd.common.jython.PythonInterpreter;
@@ -161,7 +162,7 @@ public class ValidationScriptRunner
Map<String, String> javaResult = null;
if (result instanceof PyDictionary)
{
- javaResult = JythonUtils.convertPyDictToMap((PyDictionary) result);
+ javaResult = convertPyDictToMap((PyDictionary) result);
} else
{
javaResult = (Map<String, String>) result;
@@ -171,6 +172,17 @@ public class ValidationScriptRunner
return metadata;
}
+
+ private static Map<String, String> convertPyDictToMap(PyDictionary result)
+ {
+ Map<String, String> javaMap = new HashMap<String, String>();
+ for (Object item : result.items())
+ {
+ PySequenceList tuple = (PySequenceList) item;
+ javaMap.put(tuple.get(0).toString(), tuple.get(1).toString());
+ }
+ return javaMap;
+ }
public String getScriptString()
{