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..54c7166f9a6e848686ef369ba21916d8f46c03a8 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
*
@@ -16,25 +14,26 @@ 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;
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;
/**
@@ -73,7 +72,7 @@ public final class Evaluator
*/
public enum ReturnType
{
- INTEGER_OR_BOOLEAN, BIGINT, DOUBLE, STRING, OTHER
+ BOOLEAN, INTEGER, BIGINT, DOUBLE, STRING, OTHER
}
/**
@@ -173,7 +172,7 @@ 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 +203,7 @@ public final class Evaluator
{
return new PyString((String) javaObject);
}
- return new PyJavaInstance(javaObject);
+ return Py.java2py(javaObject);
}
/**
@@ -215,8 +214,8 @@ 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 +254,12 @@ public final class Evaluator
{
doEval();
final Object obj = getInterpreterResult();
- if (obj instanceof PyInteger)
+ if (obj instanceof PyBoolean)
+ {
+ return ReturnType.BOOLEAN;
+ } else if (obj instanceof PyInteger)
{
- return ReturnType.INTEGER_OR_BOOLEAN;
+ return ReturnType.INTEGER;
} else if (obj instanceof PyLong)
{
return ReturnType.BIGINT;
@@ -296,35 +298,7 @@ public final class Evaluator
private Object translateToJava(final PyObject obj)
{
- if (obj instanceof PyInteger)
- {
- return new Long(((PyInteger) obj).getValue());
- } else if (obj instanceof PyLong)
- {
- return new Long(((PyLong) obj).getValue().longValue());
- } else if (obj instanceof PyFloat)
- {
- return new Double(((PyFloat) obj).getValue());
- } else if (obj instanceof PyNone)
- {
- return null;
- } else if (obj instanceof PyList)
- {
- PyList pyList = (PyList) obj;
- PyObject[] array = pyList.getArray();
- List<Object> list = new ArrayList<Object>();
- for (int i = 0, n = pyList.size(); i < n; i++)
- {
- list.add(translateToJava(array[i]));
- }
- return list;
- } else if (obj instanceof PyJavaInstance)
- {
- return ((PyJavaInstance) obj).__tojava__(Object.class);
- } else
- {
- return obj == null ? null : obj.toString();
- }
+ return (obj == null) ? null : obj.__tojava__(Object.class);
}
private PyObject getInterpreterResult()
@@ -346,7 +320,7 @@ public final class Evaluator
{
final ReturnType type = getType();
throw new EvaluatorException("Expected a result of type "
- + ReturnType.INTEGER_OR_BOOLEAN + ", found " + type);
+ + ReturnType.INTEGER + ", found " + type);
}
}
@@ -364,7 +338,7 @@ public final class Evaluator
{
final ReturnType type = getType();
throw new EvaluatorException("Expected a result of type "
- + ReturnType.INTEGER_OR_BOOLEAN + ", found " + type);
+ + ReturnType.INTEGER + ", found " + type);
}
}
@@ -436,13 +410,10 @@ 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="${lib}/jython" />
<param name="jar" value="jython.jar" />
</antcall>
<antcall target="copy-and-sign-jar">
diff --git a/openbis/build/build.xml b/openbis/build/build.xml
index a4e192fcf6edadc523671a963fc4c8dd17165a55..b739cdb300f7bc355baf59c0d913c0c4e8d72b96 100644
--- a/openbis/build/build.xml
+++ b/openbis/build/build.xml
@@ -723,10 +723,6 @@
<lib dir="${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/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" />