diff --git a/common/.classpath b/common/.classpath
index ac1214e7bf805fa2d58fa060dadd812500601e69..df9d86de38585f0d17b5a5b65d9d8b2bdbc598c7 100644
--- a/common/.classpath
+++ b/common/.classpath
@@ -20,7 +20,7 @@
<classpathentry kind="lib" path="/libraries/cisd-base/cisd-base-test.jar" sourcepath="/libraries/cisd-base/cisd-base-src.zip"/>
<classpathentry kind="lib" path="/libraries/cisd-base/cisd-base.jar" sourcepath="/libraries/cisd-base/cisd-base-src.zip"/>
<classpathentry kind="lib" path="/libraries/fast-md5/fast-md5.jar" sourcepath="/libraries/fast-md5/src.zip"/>
- <classpathentry kind="lib" path="/libraries/jython/jython.jar" sourcepath="/libraries/jython/src.zip"/>
+ <classpathentry kind="lib" path="/libraries/jython/jython.jar" sourcepath="/libraries/jython/jython_src.zip"/>
<classpathentry kind="lib" path="/libraries/commons-httpclient/commons-httpclient.jar" sourcepath="/libraries/commons-httpclient/src.zip"/>
<classpathentry kind="lib" path="/libraries/commons-logging/commons-logging.jar" sourcepath="/libraries/commons-logging/src.zip"/>
<classpathentry kind="lib" path="/libraries/jaxb/jaxb-api.jar" sourcepath="/libraries/jaxb/jaxb-api-src.zip"/>
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 ed543e06047fde81f59b4870c28d429e8e2fa349..ea3ea599abbab6924dba61ea27ecccb4f35ed5a3 100644
--- a/common/source/java/ch/systemsx/cisd/common/evaluator/Evaluator.java
+++ b/common/source/java/ch/systemsx/cisd/common/evaluator/Evaluator.java
@@ -1,5 +1,3 @@
-package ch.systemsx.cisd.common.evaluator;
-
/*
* Copyright 2009 ETH Zuerich, CISD
*
@@ -16,17 +14,22 @@ package ch.systemsx.cisd.common.evaluator;
* limitations under the License.
*/
+package ch.systemsx.cisd.common.evaluator;
+
import java.math.BigInteger;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.lang.StringUtils;
+import org.python.core.CompileMode;
+import org.python.core.CompilerFlags;
+import org.python.core.Py;
+import org.python.core.PyBoolean;
import org.python.core.PyCode;
import org.python.core.PyException;
import org.python.core.PyFloat;
import org.python.core.PyFunction;
import org.python.core.PyInteger;
-import org.python.core.PyJavaInstance;
import org.python.core.PyList;
import org.python.core.PyLong;
import org.python.core.PyNone;
@@ -34,7 +37,6 @@ import org.python.core.PyObject;
import org.python.core.PyString;
import org.python.core.PyStringMap;
import org.python.core.PySystemState;
-import org.python.core.__builtin__;
import org.python.util.PythonInterpreter;
/**
@@ -45,7 +47,7 @@ import org.python.util.PythonInterpreter;
* <ol>
* <li>Construct an {@link Evaluator} with an appropriate expression.</li>
* <li>Set all variables needed for evaluation via {@link #set(String, Object)}</li>
- * <li>Call one of {@link #getType()}, {@link #evalAsString()}, {@link #evalToBoolean()},
+ * <li>Call one of {@link #getType()}, {@link #evalAsString}, {@link #evalToBoolean()},
* {@link #evalToInt()}, {@link #evalToBigInt()}, {@link #evalToDouble()}.</li>
* <li>Repeat from step 2</li>
* </ol>
@@ -73,7 +75,7 @@ public final class Evaluator
*/
public enum ReturnType
{
- INTEGER_OR_BOOLEAN, BIGINT, DOUBLE, STRING, OTHER
+ BOOLEAN, INTEGER, BIGINT, DOUBLE, STRING, OTHER
}
/**
@@ -173,7 +175,7 @@ public final class Evaluator
if (pyObject instanceof PyFunction == false)
{
throw new PyException(new PyString("Not a function"), "'" + functionName
- + "' is of type " + pyObject.getType().getFullName() + ".");
+ + "' is of type " + pyObject.getType().getName() + ".");
}
PyFunction func = (PyFunction) pyObject;
PyObject[] pyArgs = new PyObject[args.length];
@@ -204,7 +206,7 @@ public final class Evaluator
{
return new PyString((String) javaObject);
}
- return new PyJavaInstance(javaObject);
+ return Py.java2py(javaObject);
}
/**
@@ -215,8 +217,8 @@ public final class Evaluator
{
try
{
- return __builtin__.compile("__result__=(" + expression + ")", "expression: "
- + expression, "exec");
+ return Py.compile_flags("__result__=(" + expression + ")", "expression: " + expression,
+ CompileMode.exec, new CompilerFlags());
} catch (PyException ex)
{
throw toEvaluatorException(ex, expression);
@@ -255,9 +257,12 @@ public final class Evaluator
{
doEval();
final Object obj = getInterpreterResult();
- if (obj instanceof PyInteger)
+ if (obj instanceof PyBoolean)
{
- return ReturnType.INTEGER_OR_BOOLEAN;
+ return ReturnType.BOOLEAN;
+ } else if (obj instanceof PyInteger)
+ {
+ return ReturnType.INTEGER;
} else if (obj instanceof PyLong)
{
return ReturnType.BIGINT;
@@ -276,16 +281,19 @@ public final class Evaluator
/**
* Evaluates the expression of this evaluator and returns the result. Use this method if you do
* not know what will be the result type.
+ * <p>
+ * <i>This is a legacy function to mimic the old Jython 2.2 Evaluator's behavior which will only
+ * return Long, Double or String and doesn't know boolean.</i>
*
* @return evaluation result which can be of Long, Double or String type. All other types are
* converted to String representation except {@link PyNone} that represents null value
* and will be converted to <code>null</code>.
*/
- public Object eval()
+ public Object evalLegacy2_2()
{
doEval();
final PyObject obj = getInterpreterResult();
- Object result = translateToJava(obj);
+ Object result = translateToJavaLegacy(obj);
if (result != null && result instanceof Long == false && result instanceof Double == false
&& result instanceof String == false)
{
@@ -294,7 +302,19 @@ public final class Evaluator
return result;
}
- private Object translateToJava(final PyObject obj)
+ /**
+ * Evaluates the expression of this evaluator and returns the result. Use this method if you do
+ * not know what will be the result type.
+ *
+ * @return evaluation result as translated by the Jython interpreter..
+ */
+ public Object eval()
+ {
+ doEval();
+ return translateToJava(getInterpreterResult());
+ }
+
+ private Object translateToJavaLegacy(final PyObject obj)
{
if (obj instanceof PyInteger)
{
@@ -315,18 +335,20 @@ public final class Evaluator
List<Object> list = new ArrayList<Object>();
for (int i = 0, n = pyList.size(); i < n; i++)
{
- list.add(translateToJava(array[i]));
+ list.add(translateToJavaLegacy(array[i]));
}
return list;
- } else if (obj instanceof PyJavaInstance)
- {
- return ((PyJavaInstance) obj).__tojava__(Object.class);
} else
{
- return obj == null ? null : obj.toString();
+ return translateToJava(obj);
}
}
+ private Object translateToJava(final PyObject obj)
+ {
+ return (obj == null) ? null : obj.__tojava__(Object.class);
+ }
+
private PyObject getInterpreterResult()
{
return interpreter.get("__result__");
@@ -341,12 +363,12 @@ public final class Evaluator
doEval();
try
{
- return ((PyInteger) getInterpreterResult()).getValue() > 0;
+ return ((PyBoolean) getInterpreterResult()).getValue() > 0;
} catch (ClassCastException ex)
{
final ReturnType type = getType();
- throw new EvaluatorException("Expected a result of type "
- + ReturnType.INTEGER_OR_BOOLEAN + ", found " + type);
+ throw new EvaluatorException("Expected a result of type " + ReturnType.INTEGER
+ + ", found " + type);
}
}
@@ -363,8 +385,8 @@ public final class Evaluator
} catch (ClassCastException ex)
{
final ReturnType type = getType();
- throw new EvaluatorException("Expected a result of type "
- + ReturnType.INTEGER_OR_BOOLEAN + ", found " + type);
+ throw new EvaluatorException("Expected a result of type " + ReturnType.INTEGER
+ + ", found " + type);
}
}
@@ -404,6 +426,21 @@ public final class Evaluator
}
}
+ /**
+ * Evaluates the expression of this evaluator and returns the result as a String. This method
+ * can always be called.
+ * <p>
+ * <i>This is a legacy function to mimic the old Jython 2.2 Evaluator's behavior which first
+ * translates to Long and Double and doesn't know boolean.</i>
+ * <p>
+ * NOTE: null will be returned if expression results in {@link PyNone}
+ */
+ public String evalAsStringLegacy2_2() throws EvaluatorException
+ {
+ Object result = evalLegacy2_2();
+ return result == null ? null : result.toString();
+ }
+
/**
* Evaluates the expression of this evaluator and returns the result as a String. This method
* can always be called.
@@ -436,13 +473,10 @@ public final class Evaluator
{
Exception exception = null;
PyObject value = ex.value;
- if (value instanceof PyJavaInstance)
+ Object object = value.__tojava__(Object.class);
+ if (object instanceof Exception)
{
- Object object = ((PyJavaInstance) value).__tojava__(Object.class);
- if (object instanceof Exception)
- {
- exception = (Exception) object;
- }
+ exception = (Exception) object;
}
String msg = extractExceptionMessage(ex);
if (expressionOrNull != null)
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/evaluator/EvaluatorTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/evaluator/EvaluatorTest.java
index f113c15bcfc6f3f94af709931305dc35004b0513..77d6e320df1ed707c8fa36cd5a2a88266b69a9d9 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/evaluator/EvaluatorTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/evaluator/EvaluatorTest.java
@@ -99,12 +99,12 @@ public class EvaluatorTest extends AssertJUnit
public static class Functions
{
- public static double Min(double a, double b)
+ public static double MinDbl(double a, double b)
{
return (a < b) ? a : b;
}
- public static double Min(double... vals)
+ public static double MinDbl(double[] vals)
{
double result = Double.MAX_VALUE;
for (double v : vals)
@@ -117,20 +117,21 @@ public class EvaluatorTest extends AssertJUnit
return result;
}
- public static int Min(int a, int b)
+ public static int MinInt(int a, int b)
{
return (a < b) ? a : b;
}
+
}
@Test
public void testFunctionEval()
{
- Evaluator eval = new Evaluator("Min(1,2)", Functions.class, null);
+ Evaluator eval = new Evaluator("MinInt(1,2)", Functions.class, null);
assertEquals(1, eval.evalToInt());
- eval = new Evaluator("Min([1,2,0.1])", Functions.class, null);
+ eval = new Evaluator("MinDbl([1,2,0.1])", Functions.class, null);
assertEquals(0.1, eval.evalToDouble(), 1e-15);
- eval = new Evaluator("Min(v)", Functions.class, null);
+ eval = new Evaluator("MinDbl(v)", Functions.class, null);
eval.set("v", new double[]
{ 1, 2, -99.9, 3 });
assertEquals(-99.9, eval.evalToDouble(), 1e-15);
@@ -149,7 +150,7 @@ public class EvaluatorTest extends AssertJUnit
{
final Evaluator eval = new Evaluator("a");
eval.set("a", 2);
- assertEquals(ReturnType.INTEGER_OR_BOOLEAN, eval.getType());
+ assertEquals(ReturnType.INTEGER, eval.getType());
eval.set("a", "2");
assertEquals(ReturnType.STRING, eval.getType());
}
@@ -178,15 +179,16 @@ public class EvaluatorTest extends AssertJUnit
{
final Evaluator eval = new Evaluator("a");
eval.set("a", true);
- assertEquals(ReturnType.INTEGER_OR_BOOLEAN, eval.getType());
- assertEquals("1", eval.evalAsString());
+ assertEquals(ReturnType.BOOLEAN, eval.getType());
+ assertEquals("true", eval.evalAsString());
try
{
eval.evalToDouble();
+ fail("Type mismatch not detected.");
} catch (EvaluatorException ex)
{
assertEquals(ex.getMessage(),
- "Expected a result of type DOUBLE, found INTEGER_OR_BOOLEAN", ex.getMessage());
+ "Expected a result of type DOUBLE, found BOOLEAN", ex.getMessage());
}
}
@@ -245,7 +247,7 @@ public class EvaluatorTest extends AssertJUnit
Evaluator evaluator = new Evaluator("", null, "def get():\n return ['a','b']");
Object result = evaluator.evalFunction("get");
assertEquals("Result " + result.getClass(), true, result instanceof List);
- assertEquals("[a, b]", result.toString());
+ assertEquals("['a', 'b']", result.toString());
}
@Test
@@ -258,7 +260,9 @@ public class EvaluatorTest extends AssertJUnit
fail("EvaluatorException expected");
} catch (EvaluatorException ex)
{
- assertEquals("Error evaluating 'hello(world)': NameError: unknown", ex.getMessage());
+ assertEquals(
+ "Error evaluating 'hello(world)': NameError: global name 'unknown' is not defined",
+ ex.getMessage());
}
}
@@ -316,7 +320,7 @@ public class EvaluatorTest extends AssertJUnit
} catch (EvaluatorException ex)
{
assertEquals("Error evaluating 'hello()': TypeError: "
- + "hello() takes at least 1 argument (0 given)", ex.getMessage());
+ + "hello() takes exactly 1 argument (0 given)", ex.getMessage());
}
}
@@ -331,7 +335,7 @@ public class EvaluatorTest extends AssertJUnit
} catch (EvaluatorException ex)
{
assertEquals("Error evaluating 'hello(world, universe)': TypeError: "
- + "hello() too many arguments; expected 1 got 2", ex.getMessage());
+ + "hello() takes exactly 1 argument (2 given)", ex.getMessage());
}
}
@@ -347,7 +351,7 @@ public class EvaluatorTest extends AssertJUnit
} catch (EvaluatorException ex)
{
assertEquals("Error evaluating 'get(world, universe)': AttributeError: "
- + "'string' object has no attribute 'get'", ex.getMessage());
+ + "'str' object has no attribute 'get'", ex.getMessage());
}
}
diff --git a/datastore_server/.classpath b/datastore_server/.classpath
index 6f8cb8ff0360c2606619b4b46636be9038132412..14e4742a6c6e51e3e90e16f02d75b91558a268f7 100644
--- a/datastore_server/.classpath
+++ b/datastore_server/.classpath
@@ -4,7 +4,6 @@
<classpathentry kind="src" path="resource"/>
<classpathentry kind="src" path="sourceTest/java"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
- <classpathentry kind="lib" path="/libraries/jython/standalone/jython.jar" sourcepath="/Users/gpawel/Downloads/jython_installer-2.2.1.jar"/>
<classpathentry combineaccessrules="false" exported="true" kind="src" path="/common"/>
<classpathentry kind="lib" path="/libraries/log4j/log4j.jar" sourcepath="/libraries/log4j/src.zip"/>
<classpathentry kind="lib" path="/libraries/commons-lang/commons-lang.jar" sourcepath="/libraries/commons-lang/src.zip"/>
@@ -71,5 +70,6 @@
<classpathentry kind="lib" path="/libraries/poi/ooxml-lib/xmlbeans-2.3.0.jar"/>
<classpathentry kind="lib" path="/libraries/ftpserver/ftpserver-core.jar"/>
<classpathentry kind="lib" path="/libraries/mina/mina-core.jar"/>
+ <classpathentry kind="lib" path="/libraries/jython/jython.jar" sourcepath="/libraries/jython/jython_src.zip"/>
<classpathentry kind="output" path="targets/classes"/>
</classpath>
diff --git a/datastore_server/build/build.xml b/datastore_server/build/build.xml
index 784f88a139653c6bb00763bdbadaeb8775f4656d..99b94a69f8047c5a472d8230780021947f03d329 100644
--- a/datastore_server/build/build.xml
+++ b/datastore_server/build/build.xml
@@ -150,9 +150,6 @@
<copy file="${lib}/jython/jython.jar" todir="${dist.datastore_server.lib}" />
<copy file="${lib}/mina/mina-core.jar" todir="${dist.datastore_server.lib}" />
<copy file="${lib}/ftpserver/ftpserver-core.jar" todir="${dist.datastore_server.lib}" />
- <copy todir="${dist.datastore_server.lib}/jython-lib" >
- <fileset dir="${lib}/jython/jython-lib" />
- </copy>
<copy file="${lib}/truezip/truezip.jar" todir="${dist.datastore_server.lib}" />
<copy todir="${dist.datastore_server.lib}/${dss_upload_gui}" >
<fileset dir="${dist.dss_upload_gui.lib}" />
@@ -283,7 +280,7 @@
<copy file="${lib}/commons-httpclient/commons-httpclient.jar" todir="${dist.dss_client.lib}" />
<copy file="${lib}/spring/spring.jar" todir="${dist.dss_client.lib}" />
<copy file="${lib}/jline/jline.jar" todir="${dist.dss_client.lib}" />
- <copy file="${lib}/jython/standalone/jython.jar" todir="${dist.dss_client.lib}" />
+ <copy file="${lib}/jython/jython.jar" todir="${dist.dss_client.lib}" />
<copy file="${lib}/poi/poi-3.7-20101029.jar" todir="${dist.dss_client.lib}" />
<copy file="${lib}/poi/poi-ooxml-3.7-20101029.jar" todir="${dist.dss_client.lib}" />
<copy file="${lib}/poi/poi-ooxml-schemas-3.7-20101029.jar" todir="${dist.dss_client.lib}" />
@@ -400,7 +397,7 @@
<param name="jar" value="stream-supporting-httpinvoker.jar" />
</antcall>
<antcall target="copy-and-sign-jar">
- <param name="dir" value="${lib}/jython/standalone" />
+ <param name="dir" value="${lib}/jython" />
<param name="jar" value="jython.jar" />
</antcall>
<antcall target="copy-and-sign-jar">
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java
index ed13b1384a4e3f1dee116dab12f57b5766517632..a937efa69b1169d1b40da26a432981f10b7a315e 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java
@@ -298,7 +298,7 @@ public class DataSetRegistrationService<T extends DataSetInformation> implements
return encounteredErrors;
}
- protected IDataSetRegistrationDetailsFactory<T> getDataSetRegistrationDetailsFactory()
+ public IDataSetRegistrationDetailsFactory<T> getDataSetRegistrationDetailsFactory()
{
return dataSetRegistrationDetailsFactory;
}
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 e0fa3ee68af987ee35f235f25c32f8fc8254ff38..9ef358fcf7e55ed2a26257b03f0e5a4f6116097b 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
@@ -101,7 +101,7 @@ public class JythonTopLevelDataSetHandler<T extends DataSetInformation> extends
}
@Override
- protected void handleDataSet(File dataSetFile, DataSetRegistrationService<T> genericService)
+ public void handleDataSet(File dataSetFile, DataSetRegistrationService<T> genericService)
throws Throwable
{
// Load the script
@@ -221,7 +221,7 @@ public class JythonTopLevelDataSetHandler<T extends DataSetInformation> extends
{
try
{
- PyFunction function = (PyFunction) interpreter.get(functionName, PyFunction.class);
+ PyFunction function = interpreter.get(functionName, PyFunction.class);
return function;
} catch (Exception e)
{
@@ -317,7 +317,7 @@ public class JythonTopLevelDataSetHandler<T extends DataSetInformation> extends
}
}
- protected static class JythonDataSetRegistrationService<T extends DataSetInformation> extends
+ public static class JythonDataSetRegistrationService<T extends DataSetInformation> extends
DataSetRegistrationService<T>
{
private final PythonInterpreter interpreter;
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 9e450cd5fd77b6644b074620a73b840c206507bb..80503292525d76fcd2480fe45f249a6925df3fd2 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
@@ -146,7 +146,7 @@ public class ValidationScriptRunner
{
try
{
- PyFunction function = (PyFunction) interpreter.get(functionName, PyFunction.class);
+ PyFunction function = interpreter.get(functionName, PyFunction.class);
return function;
} catch (Exception e)
{
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
index a91d9ae12786a9777452ea748d336a3038baec69..13a64e918e23a09acdb0e2fda87e12d4c275f972 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
@@ -1150,7 +1150,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
((JythonDataSetRegistrationService<DataSetInformation>) service)
.getInterpreter();
didRollbackServiceFunctionRun =
- (Boolean) interpreter.get("didRollbackServiceFunctionRun", Boolean.class);
+ interpreter.get("didRollbackServiceFunctionRun", Boolean.class);
}
@Override
@@ -1165,7 +1165,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
((JythonDataSetRegistrationService<DataSetInformation>) service)
.getInterpreter();
didRollbackDataSetRegistrationFunctionRun =
- (Boolean) interpreter.get("didRollbackServiceFunctionRun", Boolean.class);
+ interpreter.get("didRollbackServiceFunctionRun", Boolean.class);
}
@Override
@@ -1182,7 +1182,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
((JythonDataSetRegistrationService<DataSetInformation>) service)
.getInterpreter();
didRollbackTransactionFunctionRunHappen =
- (Boolean) interpreter.get("didTransactionRollbackHappen", Boolean.class);
+ interpreter.get("didTransactionRollbackHappen", Boolean.class);
}
@Override
@@ -1196,7 +1196,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
((JythonDataSetRegistrationService<DataSetInformation>) service)
.getInterpreter();
didCommitTransactionFunctionRunHappen =
- (Boolean) interpreter.get("didTransactionCommitHappen", Boolean.class);
+ interpreter.get("didTransactionCommitHappen", Boolean.class);
}
@Override
diff --git a/openbis/build/build.xml b/openbis/build/build.xml
index a4e192fcf6edadc523671a963fc4c8dd17165a55..b739cdb300f7bc355baf59c0d913c0c4e8d72b96 100644
--- a/openbis/build/build.xml
+++ b/openbis/build/build.xml
@@ -723,10 +723,6 @@
<lib dir="${lib}/jython">
<include name="jython.jar" />
</lib>
- <!-- modules for jython scripting -->
- <webinf dir="${lib}/jython/">
- <include name="jython-lib/**/*.*" />
- </webinf>
</war>
<!-- Does some cleaning. -->
<delete file="${jar.file}" failonerror="true" />
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/ColumnDefinition.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/ColumnDefinition.java
index 370119023c8f531c171158a73bbf9bf72a810b78..67d79c522f8819a21f7a6063fd5eb39ffbae5629 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/ColumnDefinition.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/ColumnDefinition.java
@@ -25,7 +25,7 @@ package ch.systemsx.cisd.openbis.generic.client.web.server.calculator;
*
* @author Franz-Josef Elmer
*/
-class ColumnDefinition
+public class ColumnDefinition
{
private final String columnID;
private final ITableDataProvider provider;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/ColumnGroup.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/ColumnGroup.java
index 01f6832676e8c2d70674f16dfa0a5b513a9ddc05..ace1228476225c2b767c59c3de6606c6a07eee10 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/ColumnGroup.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/ColumnGroup.java
@@ -26,7 +26,7 @@ import java.util.List;
*
* @author Franz-Josef Elmer
*/
-class ColumnGroup
+public class ColumnGroup
{
private final String propertyValue;
private final List<Object> values;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/Row.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/Row.java
index 3e8dff34ce15a6e2497f4d2cddcda72346039c28..c79c2c637b783c992e763832409eea3fd8c47db5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/Row.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/Row.java
@@ -35,7 +35,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable
*
* @author Franz-Josef Elmer
*/
-final class Row
+public final class Row
{
private final Map<String, List<ColumnDefinition>> definitionsByProperties =
new HashMap<String, List<ColumnDefinition>>();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/RowCalculator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/RowCalculator.java
index f3d7af2e31457c8e9430ba5bdecff4af8ce2c38f..175a5f753d44a29a1336a56eaf5cf48cfd13748f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/RowCalculator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/RowCalculator.java
@@ -28,7 +28,7 @@ import ch.systemsx.cisd.openbis.generic.shared.calculator.AbstractCalculator;
/**
* @author Franz-Josef Elmer
*/
-class RowCalculator extends AbstractCalculator
+public class RowCalculator extends AbstractCalculator
{
private final Row row;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/calculator/DynamicPropertyAdaptor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/calculator/DynamicPropertyAdaptor.java
index 4a4d0749ab28918865e47aeafd60b22beb369a6f..314a0e77f96750d8af015de8cf8c5768d6d370bc 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/calculator/DynamicPropertyAdaptor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/calculator/DynamicPropertyAdaptor.java
@@ -29,7 +29,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePropertyTypePE;
*
* @author Piotr Buczek
*/
-class DynamicPropertyAdaptor implements IEntityPropertyAdaptor
+public class DynamicPropertyAdaptor implements IEntityPropertyAdaptor
{
/** state of lazy evaluation of the property value (analogy to graph search) */
private enum State
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/calculator/DynamicPropertyFunctions.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/calculator/DynamicPropertyFunctions.java
index 8eb7e7eee3393abdb96ebf92a005f776ace89374..dd3f2cf97db3be255347ad717ebab862a20f1ad6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/calculator/DynamicPropertyFunctions.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/calculator/DynamicPropertyFunctions.java
@@ -25,7 +25,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
*
* @author Piotr Buczek
*/
-final class DynamicPropertyFunctions
+public final class DynamicPropertyFunctions
{
/**
* @return String representation of material identifier for given material code and material
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/calculator/XmlPropertyAdaptor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/calculator/XmlPropertyAdaptor.java
index 88e7ef2d7f34cf085a3c3ef2bbff421ccea8b604..5aebf854808eb3449afb9801cd39a2be32ef8ae2 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/calculator/XmlPropertyAdaptor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/calculator/XmlPropertyAdaptor.java
@@ -26,7 +26,7 @@ import ch.systemsx.cisd.openbis.generic.shared.util.XmlUtils;
*
* @author Piotr Buczek
*/
-class XmlPropertyAdaptor extends BasicPropertyAdaptor
+public class XmlPropertyAdaptor extends BasicPropertyAdaptor
{
private final String xsltTransformation;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/calculator/AbstractCalculator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/calculator/AbstractCalculator.java
index 8fb658111e4517d706efbfb3d1e19d51c44039c5..61687562acb6def5495284b59b5ca1f13d5e44f8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/calculator/AbstractCalculator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/calculator/AbstractCalculator.java
@@ -49,7 +49,7 @@ public class AbstractCalculator
public PrimitiveValue getTypedResult()
{
- Object value = evaluator.eval();
+ Object value = evaluator.evalLegacy2_2();
if (value == null)
{
return PrimitiveValue.NULL;
@@ -88,12 +88,12 @@ public class AbstractCalculator
public String evalAsString() throws EvaluatorException
{
- return evaluator.evalAsString();
+ return evaluator.evalAsStringLegacy2_2();
}
public Object eval() throws EvaluatorException
{
- return evaluator.eval();
+ return evaluator.evalLegacy2_2();
}
}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/calculator/StandardFunctions.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/calculator/StandardFunctions.java
index c4610eae9e4924bf5ab48ad081672b118d2655f7..72976e74a34ea690ce48a5b64abd520b8ad374a8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/calculator/StandardFunctions.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/calculator/StandardFunctions.java
@@ -41,7 +41,7 @@ import ch.systemsx.cisd.common.utilities.ExceptionUtils;
*
* @author Franz-Josef Elmer
*/
-final class StandardFunctions
+public final class StandardFunctions
{
static final Double DOUBLE_DEFAULT_VALUE = new Double(-Double.MAX_VALUE);
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/CachedResultSetManagerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/CachedResultSetManagerTest.java
index c68706ffaf6c01f5c98508fb8879c3b8893d033a..74bbb35a033f08e2ae50397c4291f8e89fc2c9e7 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/CachedResultSetManagerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/CachedResultSetManagerTest.java
@@ -115,7 +115,6 @@ public final class CachedResultSetManagerTest extends AssertJUnit
{
resultSetConfig.setAvailableColumns(new LinkedHashSet<IColumnDefinition<DataHolder>>(
cols.values()));
- System.out.println(resultSetConfig.getAvailableColumns().size());
if (columnFilters.isEmpty() == false)
{
resultSetConfig.setFilters(GridFilters.createColumnFilter(columnFilters));
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/CustomColumnUtilsTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/CustomColumnUtilsTest.java
index 73bbc123f90938d8b4435a1b138bba686080dad4..a4ed41e054f3d1fa6eaf7b27819bda675f745c40 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/CustomColumnUtilsTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/CustomColumnUtilsTest.java
@@ -39,6 +39,7 @@ public class CustomColumnUtilsTest extends AssertJUnit
private static final class MockDataProvider implements ITableDataProvider
{
private final String expectedColumnID;
+
private final List<List<? extends Comparable<?>>> rows;
MockDataProvider(String expectedColumnID, List<? extends Comparable<?>>... rows)
@@ -74,7 +75,7 @@ public class CustomColumnUtilsTest extends AssertJUnit
return null;
}
}
-
+
GridCustomColumn customColumn;
List<GridCustomColumn> customColumns;
@@ -105,9 +106,10 @@ public class CustomColumnUtilsTest extends AssertJUnit
public void testCorrectExpression()
{
customColumn.setExpression("row.col('VALUE') + 10");
-
- List<PrimitiveValue> values = GridExpressionUtils.evalCustomColumn(dataProvider, customColumn, false);
-
+
+ List<PrimitiveValue> values =
+ GridExpressionUtils.evalCustomColumn(dataProvider, customColumn, false);
+
assertEquals("[52]", values.toString());
}
@@ -120,9 +122,12 @@ public class CustomColumnUtilsTest extends AssertJUnit
// incorrect expression
customColumn.setExpression("junk + 10");
- List<PrimitiveValue> values = GridExpressionUtils.evalCustomColumn(dataProvider, customColumn, false);
-
- assertEquals("[Error. Please contact 'Jane Doe <jane.doe@nowhere.com>', who defined this column.]", values.toString());
+ List<PrimitiveValue> values =
+ GridExpressionUtils.evalCustomColumn(dataProvider, customColumn, false);
+
+ assertEquals(
+ "[Error. Please contact 'Jane Doe <jane.doe@nowhere.com>', who defined this column.]",
+ values.toString());
}
@Test
@@ -131,10 +136,12 @@ public class CustomColumnUtilsTest extends AssertJUnit
// incorrect expression
customColumn.setExpression("junk + 10");
- List<PrimitiveValue> values = GridExpressionUtils.evalCustomColumn(dataProvider, customColumn, true);
+ List<PrimitiveValue> values =
+ GridExpressionUtils.evalCustomColumn(dataProvider, customColumn, true);
- assertEquals("[Error: (Error evaluating 'junk + 10': NameError: junk).]", values.toString());
+ assertEquals(
+ "[Error: (Error evaluating 'junk + 10': NameError: name 'junk' is not defined).]",
+ values.toString());
}
-
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ScriptBOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ScriptBOTest.java
index 0956a1503a18e59f7660cd6e24900181004b2f9b..60933aeb880d5af85bbe61499913b179e759b920 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ScriptBOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ScriptBOTest.java
@@ -53,10 +53,13 @@ public final class ScriptBOTest extends AbstractBOTest
{
{
ScriptType.DYNAMIC_PROPERTY,
- "Error evaluating '1+': SyntaxError: ('invalid syntax', "
- + "('expression: 1+', 1, 15, '__result__=(1+)'))" },
- { ScriptType.MANAGED_PROPERTY,
- "SyntaxError: ('invalid syntax', ('<string>', 1, 3, '1+'))" }
+ "Error evaluating '1+': SyntaxError: "
+ + "(\"no viable alternative at input ')'\", "
+ + "('expression: 1+', 1, 14, '__result__=(1+)\\n'))" },
+ {
+ ScriptType.MANAGED_PROPERTY,
+ "SyntaxError: (\"no viable alternative at input '\\\\n\\\\n'\", "
+ + "('<string>', 1, 2, '1+\\n'))" }
};
}
@@ -126,7 +129,8 @@ public final class ScriptBOTest extends AbstractBOTest
}
@Test(dataProvider = "scriptTypes")
- public final void testDefineAndSaveScriptCompilationFail(ScriptType scriptType, String expectedErrorMessage)
+ public final void testDefineAndSaveScriptCompilationFail(ScriptType scriptType,
+ String expectedErrorMessage)
{
final ScriptBO scriptBO = createScriptBO();
final DatabaseInstancePE instance = createDatabaseInstance();
@@ -239,7 +243,8 @@ public final class ScriptBOTest extends AbstractBOTest
}
@Test(dataProvider = "scriptTypes")
- public void testUpdateScriptNotChanged(ScriptType scriptType, String expectedErrorMessage) throws Exception
+ public void testUpdateScriptNotChanged(ScriptType scriptType, String expectedErrorMessage)
+ throws Exception
{
final ScriptBO scriptBO = createScriptBO();
@@ -282,7 +287,8 @@ public final class ScriptBOTest extends AbstractBOTest
@SuppressWarnings("deprecation")
@Test(dataProvider = "scriptTypes")
- public void testUpdateScriptChanged(final ScriptType scriptType, String expectedErrorMessage) throws Exception
+ public void testUpdateScriptChanged(final ScriptType scriptType, String expectedErrorMessage)
+ throws Exception
{
final ScriptBO scriptBO = createScriptBO();
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/DynamicPropertyEvaluatorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/DynamicPropertyEvaluatorTest.java
index c29152784b2db599b1391cfb0e2a7cb275516b0e..036b58e6e7fad80df8950360298839c24a1a4ece 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/DynamicPropertyEvaluatorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/DynamicPropertyEvaluatorTest.java
@@ -150,7 +150,9 @@ public class DynamicPropertyEvaluatorTest extends AbstractBOTest
assertEquals(expectedDp1ErrorValue, dp1Error.getValue());
assertEquals(properties.size() + "", dp2.getValue());
final String expectedDp3ErrorValue =
- expectedErrorMessage("Error evaluating '" + s3 + "': AttributeError: getCode");
+ expectedErrorMessage("Error evaluating '" + s3
+ + "': AttributeError: 'ch.systemsx.cisd.openbis.generic.server.business.b'"
+ + " object has no attribute 'getCode'");
assertEquals(expectedDp3ErrorValue, dp3Error.getValue());
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/calculator/DynamicPropertyCalculatorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/calculator/DynamicPropertyCalculatorTest.java
index cc90c988b647999ab11cb283f4e8c2703181b9c0..70d3a8d18c22bdb9ff13d044c71f036195ad82c0 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/calculator/DynamicPropertyCalculatorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/dynamic_property/calculator/DynamicPropertyCalculatorTest.java
@@ -127,7 +127,7 @@ public class DynamicPropertyCalculatorTest extends AssertJUnit
fail("expected EvaluatorException");
} catch (EvaluatorException e)
{
- final String expectedMsg = "Error evaluating 'calculate()': NameError: calculate";
+ final String expectedMsg = "Error evaluating 'calculate()': NameError: name 'calculate' is not defined";
assertEquals("expected exception message: " + expectedMsg, expectedMsg, e.getMessage());
}
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/ManagedPropertyEvaluatorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/ManagedPropertyEvaluatorTest.java
index 900619eccab116730b8b77cbc8fc8a7a2842a593..cbdde2e1240d7c9fa0791f212897812870de98b9 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/ManagedPropertyEvaluatorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/ManagedPropertyEvaluatorTest.java
@@ -71,8 +71,8 @@ public class ManagedPropertyEvaluatorTest extends AssertJUnit
fail("EvaluatorException expected");
} catch (EvaluatorException ex)
{
- assertEquals("SyntaxError: ('invalid syntax', ('<string>', 1, 4, 'a ='))",
- ex.getMessage());
+ assertEquals("SyntaxError: (\"no viable alternative at input '='\", "
+ + "('<string>', 1, 2, 'a =\\n'))", ex.getMessage());
}
}
@@ -306,7 +306,7 @@ public class ManagedPropertyEvaluatorTest extends AssertJUnit
} catch (EvaluatorException ex)
{
assertEquals("Function 'batchColumnNames' doesn't return a List "
- + "but an object of type 'java.lang.Long': 42", ex.getMessage());
+ + "but an object of type 'java.lang.Integer': 42", ex.getMessage());
}
}
diff --git a/sanofi/.classpath b/sanofi/.classpath
index dc1aac1a05c9f18d34503f26441c2ecaa11697f0..b33c8c47a8d577a2558a2e91e97b70f7a5ec7e70 100644
--- a/sanofi/.classpath
+++ b/sanofi/.classpath
@@ -21,9 +21,9 @@
<classpathentry kind="lib" path="/libraries/spring/spring.jar" sourcepath="/libraries/spring/src.jar"/>
<classpathentry kind="lib" path="/libraries/cisd-args4j/cisd-args4j.jar" sourcepath="/libraries/cisd-args4j/cisd-args4j-src.zip"/>
<classpathentry kind="lib" path="/libraries/poi/poi-3.7-20101029.jar"/>
- <classpathentry kind="lib" path="/libraries/jython/standalone/jython.jar" sourcepath="/Users/gpawel/Downloads/jython_installer-2.2.1.jar"/>
<classpathentry combineaccessrules="false" kind="src" path="/datastore_server"/>
<classpathentry combineaccessrules="false" kind="src" path="/openbis"/>
<classpathentry kind="lib" path="/libraries/eodsql/eodsql.jar" sourcepath="/libraries/eodsql/eodsql_src.zip"/>
+ <classpathentry kind="lib" path="/libraries/jython/jython.jar" sourcepath="/libraries/jython/jython_src.zip"/>
<classpathentry kind="output" path="targets/classes"/>
</classpath>
diff --git a/screening/build/build.xml b/screening/build/build.xml
index 7826973eb4cee48a336e84fd0db38dcb170196ae..5a04c171121a9427b2431ced2bdb441410e53a11 100644
--- a/screening/build/build.xml
+++ b/screening/build/build.xml
@@ -353,7 +353,7 @@
<param name="jar" value="ij.jar" />
</antcall>
<antcall target="copy-and-sign-jar">
- <param name="dir" value="${lib}/jython/standalone" />
+ <param name="dir" value="${lib}/jython" />
<param name="jar" value="jython.jar" />
</antcall>
<zip destfile="${jars.to.be.signed.zip}"
@@ -501,7 +501,7 @@
<zipfileset src="${lib}/jline/jline.jar" />
<zipfileset src="${lib}/cisd-args4j/cisd-args4j.jar" />
<zipfileset src="${lib}/cisd-base/cisd-base.jar" />
- <zipfileset src="${lib}/jython/standalone/jython.jar" />
+ <zipfileset src="${lib}/jython/jython.jar" />
</recursive-jar>
<recursive-jar destfile="${dist.screening-api-batteries-included.jar}">
<zipfileset src="${dist.screening-api.lib}/spring-ext.jar" />
@@ -570,7 +570,7 @@
<zipfileset src="${lib}/jline/jline.jar" />
<zipfileset src="${lib}/cisd-args4j/cisd-args4j.jar" />
<zipfileset src="${lib}/cisd-base/cisd-base.jar" />
- <zipfileset src="${lib}/jython/standalone/jython.jar" />
+ <zipfileset src="${lib}/jython/jython.jar" />
</recursive-jar>
<recursive-jar destfile="${dist.screening-api-batteries-included.jar}">
<zipfileset src="${dist.screening-api.lib}/spring-ext.jar" />