diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ThreadParameters.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ThreadParameters.java
index 2a080ee0d7707b35ea1437085626f701b5650a50..eba8b7f1cbc2a0bbd0320c785c777511916bc782 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ThreadParameters.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ThreadParameters.java
@@ -59,7 +59,7 @@ public final class ThreadParameters
* A path to a script which should be invoked to validate the data set.
*/
@Private
- static final String VALIDATION_SCRIPT_KEY = "validation-script";
+ static final String VALIDATION_SCRIPT_KEY = "validation-script-path";
@Private
static final String GROUP_CODE_KEY = "group-code";
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/DataSetTypeToRegistratorMapper.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/DataSetTypeToRegistratorMapper.java
index f4dc90e03a07644f373713fbe3c6f855f1a5ec5e..672a82bb2441b1a7b49c0caa8ad0de66a4455c27 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/DataSetTypeToRegistratorMapper.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/DataSetTypeToRegistratorMapper.java
@@ -163,9 +163,9 @@ class DataSetTypeToRegistratorMapper
return ETLDaemon.createTopLevelDataSetRegistrator(params.getProperties(),
defaultThread, shareId, openBISService, mailClient, dataSetValidator, false,
- false, false, firstThread.tryGetPreRegistrationScript(),
- firstThread.tryGetPostRegistrationScript(), firstThread.tryValidationScript(),
- PutDataSetServerPluginHolder.class);
+ false, false, defaultThread.tryGetPreRegistrationScript(),
+ defaultThread.tryGetPostRegistrationScript(),
+ defaultThread.tryValidationScript(), PutDataSetServerPluginHolder.class);
}
public HashMap<String, ITopLevelDataSetRegistrator> getHandlerMap()
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetService.java
index 2915d47f77a2332a9103d2686139cfad9c61efd2..40e81371047dea32ea83274d67264211df794fa9 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetService.java
@@ -199,6 +199,11 @@ public class PutDataSetService
*/
public String getValidationScript(String dataSetTypeOrNull)
{
+ if (false == isInitialized)
+ {
+ doInitialization();
+ }
+
ITopLevelDataSetRegistrator registrator =
registratorMap.getRegistratorForType(dataSetTypeOrNull);
TopLevelDataSetRegistratorGlobalState globalState = registrator.getGlobalState();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandTestValid.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandTestValid.java
index 8a4216d4774914213451ce84e8bfb8d9637e7994..6e673d1ba557122413b8b343a1544618e4e40e1a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandTestValid.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandTestValid.java
@@ -243,7 +243,7 @@ class CommandTestValid extends AbstractDssCommand<CommandTestValid.CommandTestVa
@Override
protected String getRequiredArgumentsString()
{
- return "<owner type> <owner> <path> <script>";
+ return "<owner type> <owner> <path> [<script>]";
}
/**
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadClient.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadClient.java
index 1e1dfad27f1b0cd68fdf673d287a7a2906524e9d..e84b90853aa9daecb8e58038bd7542c660e15d23 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadClient.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadClient.java
@@ -27,6 +27,7 @@ import java.awt.GridBagLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.ArrayList;
+import java.util.Properties;
import javax.swing.Box;
import javax.swing.BoxLayout;
@@ -45,6 +46,8 @@ import javax.swing.event.ListSelectionListener;
import javax.swing.table.TableCellRenderer;
import javax.swing.table.TableColumn;
+import org.python.core.PySystemState;
+
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.utilities.ITimeProvider;
@@ -69,8 +72,31 @@ public class DataSetUploadClient extends AbstractSwingGUI
static
{
// Disable any logging output.
+ // System.setProperty("org.apache.commons.logging.Log",
+ // "org.apache.commons.logging.impl.NoOpLog");
+
+ // Provide some logging
System.setProperty("org.apache.commons.logging.Log",
- "org.apache.commons.logging.impl.NoOpLog");
+ "org.apache.commons.logging.impl.SimpleLog");
+ System.setProperty("org.apache.commons.logging.simplelog.showdatetime", "true");
+
+ // Properties baseProperties = System.getProperties();
+ // String path =
+ // PySystemState.class.getProtectionDomain().getCodeSource().getLocation().getPath();
+ // System.out.println(path);
+ // baseProperties.setProperty("python.home", path);
+ //
+ // PySystemState.initialize(baseProperties, null, new String[]
+ // { "" });
+
+ Properties baseProperties = System.getProperties();
+ String path = PySystemState.class.getResource("PySystemState.class").getPath();
+ path = path.substring(5, path.indexOf("!"));
+ System.out.println(path);
+ baseProperties.setProperty("python.home", path);
+
+ PySystemState.initialize(baseProperties, null, new String[]
+ { "" });
}
private static final String TITLE = "Data Set Uploader";
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponent.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponent.java
index a572760ad4e461d2125a5e5da4224b38d7704696..f7cb501d317c0122026f5a4cf08d334485c3db60 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponent.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponent.java
@@ -24,6 +24,8 @@ import java.util.Collections;
import java.util.HashMap;
import java.util.List;
+import org.python.core.Py;
+import org.python.core.PyException;
import org.springframework.remoting.RemoteAccessException;
import org.springframework.remoting.RemoteConnectFailureException;
@@ -319,7 +321,8 @@ class AuthenticatedState extends AbstractDssComponentState
private final IRpcServiceFactory dssServiceFactory;
- private final HashMap<String, String> validationScriptCache = new HashMap<String, String>();
+ private final HashMap<String, ValidationScriptRunner> validationScriptRunnerCache =
+ new HashMap<String, ValidationScriptRunner>();
AuthenticatedState(IGeneralInformationService generalOpenBisService,
IRpcServiceFactory dssServiceFactory, String sessionToken)
@@ -573,22 +576,50 @@ class AuthenticatedState extends AbstractDssComponentState
}
String dataSetTypeOrNull = newDataset.tryDataSetType();
- String validationScript;
+ ValidationScriptRunner runner;
+
// Check if the script is in the cache
- if (validationScriptCache.containsKey(dataSetTypeOrNull))
+ if (validationScriptRunnerCache.containsKey(dataSetTypeOrNull))
{
- validationScript = validationScriptCache.get(dataSetTypeOrNull);
+ runner = validationScriptRunnerCache.get(dataSetTypeOrNull);
} else
{
- validationScript = dssService.getValidationScript(sessionToken, dataSetTypeOrNull);
- validationScriptCache.put(dataSetTypeOrNull, validationScript);
+
+ String validationScript =
+ dssService.getValidationScript(sessionToken, dataSetTypeOrNull);
+ try
+ {
+ runner = ValidationScriptRunner.createValidatorFromScriptString(validationScript);
+ validationScriptRunnerCache.put(dataSetTypeOrNull, runner);
+ } catch (PyException ex)
+ {
+ System.err.println("Could not create validation script ");
+ System.err.println(validationScript);
+ System.err.println(ex);
+ ex.printStackTrace(System.err);
+ System.err.println(Py.getSystemState().modules);
+
+ return new ArrayList<ValidationError>();
+ } catch (Throwable ex)
+ {
+ System.err.println("Could not create validation script ");
+ System.err.println(validationScript);
+ System.err.println(ex);
+ ex.printStackTrace(System.err);
+
+ return new ArrayList<ValidationError>();
+ }
}
- if (null == validationScript)
+
+ try
+ {
+ return runner.validate(dataSetFile);
+ } catch (Throwable ex)
{
+ System.err.println("Could not run validation script: ");
+ System.err.println(runner.getScriptString());
+ ex.printStackTrace(System.err);
return new ArrayList<ValidationError>();
}
- ValidationScriptRunner runner =
- ValidationScriptRunner.createValidatorFromScriptString(validationScript);
- return runner.validate(dataSetFile);
}
}
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 73d065f0106f5a30c7289231ea74f770a4875ea1..ff64c5dc1e89ab67d7b655d241afbcf0cb6c45f7 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
@@ -61,6 +61,10 @@ public class ValidationScriptRunner
*/
public static ValidationScriptRunner createValidatorFromScriptString(String scriptString)
{
+ if (scriptString == null)
+ {
+ return new NullValidationScriptRunner();
+ }
String theScriptString = getValidationScriptString(scriptString);
return new ValidationScriptRunner(theScriptString);
}
@@ -111,6 +115,11 @@ public class ValidationScriptRunner
return errors;
}
+ public String getScriptString()
+ {
+ return scriptString;
+ }
+
private PyFunction tryJythonFunction(String functionName)
{
try