diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataSetCommandExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataSetCommandExecutor.java
index 9acc523603c22fb16fc3f5183cc90da691768d67..e417992d562287b5165b2e8e99f1dfb100c8adaf 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataSetCommandExecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataSetCommandExecutor.java
@@ -146,11 +146,12 @@ class DataSetCommandExecutor implements IDataSetCommandExecutor
public void scheduleProcessDatasets(IProcessingPluginTask task,
List<DatasetDescription> datasets, Map<String, String> parameterBindings,
- String userEmailOrNull, DatastoreServiceDescription serviceDescription,
+ String userEmailOrNull, String sessionTokenOrNull,
+ DatastoreServiceDescription serviceDescription,
MailClientParameters mailClientParameters)
{
scheduleCommand(new ProcessDatasetsCommand(task, datasets, parameterBindings,
- userEmailOrNull, serviceDescription, mailClientParameters));
+ userEmailOrNull, sessionTokenOrNull, serviceDescription, mailClientParameters));
}
private void scheduleCommand(IDataSetCommand command)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java
index c80a5242f03da052b6c15d15e6fa55140e85280f..578e20ed9a78895f6db1d544b33ef9485791f28c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java
@@ -179,7 +179,8 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
{
operationLog.info("Command executor started.");
}
- getShareIdManager().isKnown(""); // initializes ShareIdManager: reading all share ids from the data base
+ getShareIdManager().isKnown(""); // initializes ShareIdManager: reading all share ids from
+ // the data base
if (operationLog.isInfoEnabled())
{
operationLog.info("Initialization finished.");
@@ -293,8 +294,8 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
return new CIFEXRPCServiceFactory(cifexURL);
}
- public TableModel createReportFromDatasets(String sessionToken, String serviceKey,
- List<DatasetDescription> datasets)
+ public TableModel createReportFromDatasets(String sessionToken, String userSessionToken,
+ String serviceKey, List<DatasetDescription> datasets)
{
sessionTokenManager.assertValidSessionToken(sessionToken);
@@ -310,7 +311,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
{
return task.createReport(datasets, new DataSetProcessingContext(
new DataSetDirectoryProvider(storeRoot, manager),
- new HashMap<String, String>(), null, null));
+ new HashMap<String, String>(), null, null, userSessionToken));
} finally
{
@@ -318,7 +319,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
}
}
- public void processDatasets(String sessionToken, String serviceKey,
+ public void processDatasets(String sessionToken, String userSessionToken, String serviceKey,
List<DatasetDescription> datasets, Map<String, String> parameterBindings,
String userEmailOrNull)
{
@@ -330,7 +331,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
IProcessingPluginTask task = plugins.getPluginInstance(serviceKey);
DatastoreServiceDescription pluginDescription = plugins.getPluginDescription(serviceKey);
commandExecutor.scheduleProcessDatasets(task, datasets, parameterBindings, userEmailOrNull,
- pluginDescription, mailClientParameters);
+ userSessionToken, pluginDescription, mailClientParameters);
}
public void unarchiveDatasets(String sessionToken, List<DatasetDescription> datasets,
@@ -372,7 +373,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
DatastoreServiceDescription.processing(description, description, null, null);
Map<String, String> parameterBindings = Collections.<String, String> emptyMap();
commandExecutor.scheduleProcessDatasets(processingTask, datasets, parameterBindings,
- userEmailOrNull, pluginDescription, mailClientParameters);
+ userEmailOrNull, sessionToken, pluginDescription, mailClientParameters);
}
private static class ArchiveProcessingPluginTask implements IProcessingPluginTask
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java
index 723c26c2a896c183757d8c4c3b4c43d44d8eb244..945fad6560ffb2ca72d1ee82237f8ed0e1fb88d7 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java
@@ -84,8 +84,8 @@ class DataStoreServiceLogger implements IDataStoreService, IInitializable
return 0;
}
- public List<String> getKnownDataSets(String sessionToken, List<DatasetDescription> dataSetLocations)
- throws InvalidAuthenticationException
+ public List<String> getKnownDataSets(String sessionToken,
+ List<DatasetDescription> dataSetLocations) throws InvalidAuthenticationException
{
log("getKnownDataSets", "DATA_SETS(%s)", dataSetLocations);
return null;
@@ -109,20 +109,21 @@ class DataStoreServiceLogger implements IDataStoreService, IInitializable
.toString().trim());
}
- public TableModel createReportFromDatasets(String sessionToken, String serviceKey,
- List<DatasetDescription> datasets)
+ public TableModel createReportFromDatasets(String sessionToken, String userSessionToken,
+ String serviceKey, List<DatasetDescription> datasets)
{
- log("createReportFromDatasets", "TASK_ID(%s) NO_OF_DATASETS(%s)", serviceKey,
- datasets.size());
+ log("createReportFromDatasets", "USER_SESSION(%s) TASK_ID(%s) NO_OF_DATASETS(%s)",
+ userSessionToken, serviceKey, datasets.size());
return null;
}
- public void processDatasets(String sessionToken, String serviceKey,
+ public void processDatasets(String sessionToken, String userSessionToken, String serviceKey,
List<DatasetDescription> datasets, Map<String, String> parameterBindings,
String userEmailOrNull)
{
- log("processDatasets", "TASK_ID(%s) NO_OF_DATASETS(%s) PARAMETERS(%s) USER_EMAIL(%s)",
- serviceKey, datasets.size(), parameterBindings, userEmailOrNull);
+ log("processDatasets",
+ "USER_SESSION(%s) TASK_ID(%s) NO_OF_DATASETS(%s) PARAMETERS(%s) USER_EMAIL(%s)",
+ userSessionToken, serviceKey, datasets.size(), parameterBindings, userEmailOrNull);
}
public void unarchiveDatasets(String sessionToken, List<DatasetDescription> datasets,
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetImageOverviewServlet.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetImageOverviewServlet.java
index 2482e11e0e9a81adec0f836aefa43b0322efd13d..0126ccb34f3391ac3ab270b4a93d17a4f5d47930 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetImageOverviewServlet.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetImageOverviewServlet.java
@@ -131,6 +131,7 @@ public class DatasetImageOverviewServlet extends AbstractDatasetDownloadServlet
private ResponseContentStream createImageResponse(HttpSession session, String datasetCode,
String datasetTypeCode, ImageResolutionKind resolution)
{
+ @SuppressWarnings("deprecation")
File datasetRoot = createDataSetRootDirectory(datasetCode, session);
IDatasetImageOverviewPlugin plugin =
configuration.getDatasetImageOverviewPlugin(datasetTypeCode);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/IDataSetCommandExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/IDataSetCommandExecutor.java
index bbe4781700bdca7a3352eae6d9daeaa2deb8e6b7..60bf90eba6fee6c6fe546c1fb39731251110d92f 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/IDataSetCommandExecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/IDataSetCommandExecutor.java
@@ -63,16 +63,18 @@ public interface IDataSetCommandExecutor extends IDataSetDeleter
String cifexAdminPasswordOrNull);
/**
- * Schedules the specified processing task with specified parameter bindings for provided datasets.
+ * Schedules the specified processing task with specified parameter bindings for provided
+ * datasets.
*
- * @param parameterBindings Contains at least the parameter {@link Constants#USER_PARAMETER} with
- * the ID of the user who initiated processing.
+ * @param parameterBindings Contains at least the parameter {@link Constants#USER_PARAMETER}
+ * with the ID of the user who initiated processing.
* @param userEmailOrNull Email of user who initiated processing and will get a message after
* the processing is finished. It may be null if the user doesn't have email and no
* message will be send in such case.
+ * @param sessionTokenOrNull The session token of the user that requested the processing.
*/
void scheduleProcessDatasets(IProcessingPluginTask task, List<DatasetDescription> datasets,
Map<String, String> parameterBindings, String userEmailOrNull,
- DatastoreServiceDescription serviceDescription,
+ String sessionTokenOrNull, DatastoreServiceDescription serviceDescription,
MailClientParameters mailClientParameters);
}
\ No newline at end of file
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ProcessDatasetsCommand.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ProcessDatasetsCommand.java
index 430ee2f90f1ea24f5cf9126b43b934bc9df82360..0962aaa9a1818c266684e623c6ad6e5b1e751bdf 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ProcessDatasetsCommand.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ProcessDatasetsCommand.java
@@ -59,6 +59,8 @@ public class ProcessDatasetsCommand extends AbstractDataSetDescriptionBasedComma
private final String userEmailOrNull;
+ private final String sessionTokenOrNull;
+
private final DatastoreServiceDescription serviceDescription;
private MailClientParameters mailClientParameters;
@@ -67,22 +69,24 @@ public class ProcessDatasetsCommand extends AbstractDataSetDescriptionBasedComma
public ProcessDatasetsCommand(IProcessingPluginTask task, List<DatasetDescription> datasets,
Map<String, String> parameterBindings, String userEmailOrNull,
- DatastoreServiceDescription serviceDescription,
+ String sessionTokenOrNull, DatastoreServiceDescription serviceDescription,
MailClientParameters mailClientParameters)
{
- this(task, datasets, parameterBindings, userEmailOrNull, serviceDescription,
- new MailClient(mailClientParameters));
+ this(task, datasets, parameterBindings, userEmailOrNull, sessionTokenOrNull,
+ serviceDescription, new MailClient(mailClientParameters));
this.mailClientParameters = mailClientParameters;
}
ProcessDatasetsCommand(IProcessingPluginTask task, List<DatasetDescription> datasets,
Map<String, String> parameterBindings, String userEmailOrNull,
- DatastoreServiceDescription serviceDescription, IMailClient mailClient)
+ String sessionTokenOrNull, DatastoreServiceDescription serviceDescription,
+ IMailClient mailClient)
{
super(datasets);
this.task = task;
this.parameterBindings = parameterBindings;
this.userEmailOrNull = userEmailOrNull;
+ this.sessionTokenOrNull = sessionTokenOrNull;
this.serviceDescription = serviceDescription;
this.mailClient = mailClient;
}
@@ -153,7 +157,7 @@ public class ProcessDatasetsCommand extends AbstractDataSetDescriptionBasedComma
{
DataSetProcessingContext context =
new DataSetProcessingContext(dataSetDirectoryProvider, parameterBindings,
- proxyMailClient, userEmailOrNull);
+ proxyMailClient, userEmailOrNull, sessionTokenOrNull);
processingStatusOrNull = task.process(dataSets, context);
} catch (RuntimeException e)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/openbisauth/OpenBISSessionHolder.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/openbisauth/OpenBISSessionHolder.java
index 3263ba849293af3f163a4a8949eb9cb3802a28d8..3ce260e2de4aa9ccae0c08eb460c4dc9796478ac 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/openbisauth/OpenBISSessionHolder.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/openbisauth/OpenBISSessionHolder.java
@@ -17,6 +17,9 @@
package ch.systemsx.cisd.openbis.dss.generic.server.openbisauth;
/**
+ * A class that holds information about the openBIS session. It has the information necessary to
+ * connect to any of the openBIS APIs.
+ *
* @author Kaloyan Enimanev
*/
public class OpenBISSessionHolder
@@ -25,6 +28,17 @@ public class OpenBISSessionHolder
private String dataStoreCode;
+ private String serverUrl;
+
+ public String getServerUrl()
+ {
+ return serverUrl;
+ }
+
+ public void setServerUrl(String serverUrl)
+ {
+ this.serverUrl = serverUrl;
+ }
public String getDataStoreCode()
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/IPluginScriptRunnerFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/IPluginScriptRunnerFactory.java
index c0781268c48caec0c3e088fbc2ad1364f93c47e6..7a89415f5b970a6a159bd5141b6c9c32d5b64d4d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/IPluginScriptRunnerFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/IPluginScriptRunnerFactory.java
@@ -24,6 +24,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
*/
public interface IPluginScriptRunnerFactory extends ISerializable
{
+ String getScriptPath();
+
IReportingPluginScriptRunner createReportingPluginRunner(DataSetProcessingContext context);
IProcessingPluginScriptRunner createProcessingPluginRunner(DataSetProcessingContext context);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedProcessingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedProcessingPlugin.java
index 8b390f5ee3f6d6d96ebca5eacb4e59268e7074a0..19f22fe7cab10d101f9a52157d91dfd4e58be529 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedProcessingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedProcessingPlugin.java
@@ -52,14 +52,18 @@ public class JythonBasedProcessingPlugin implements IProcessingPluginTask
transient IHierarchicalContentProvider hierarchicalContentProvider;
+ protected static String getScriptPathProperty(Properties properties)
+ {
+ return PropertyUtils.getMandatoryProperty(properties, SCRIPT_PATH);
+ }
+
public JythonBasedProcessingPlugin(Properties properties, File storeRoot)
{
- this(new PluginScriptRunnerFactory(PropertyUtils.getMandatoryProperty(properties,
- SCRIPT_PATH)), null);
+ this(new PluginScriptRunnerFactory(getScriptPathProperty(properties)), null);
}
// for tests
- JythonBasedProcessingPlugin(IPluginScriptRunnerFactory scriptRunnerFactory,
+ protected JythonBasedProcessingPlugin(IPluginScriptRunnerFactory scriptRunnerFactory,
IHierarchicalContentProvider contentProvider)
{
this.scriptRunnerFactory = scriptRunnerFactory;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedReportingPlugin.java
index 33c3a2ab4587d247205651bbe4a6d5ebfb1499cb..2ec8fc096210bdee29177a8ee8b14743841f9f6b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedReportingPlugin.java
@@ -22,10 +22,10 @@ import java.util.Properties;
import org.apache.log4j.Logger;
+import ch.systemsx.cisd.common.evaluator.EvaluatorException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.api.IDataSet;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDatastorePlugin;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractTableModelReportingPlugin;
@@ -45,23 +45,26 @@ public class JythonBasedReportingPlugin extends AbstractTableModelReportingPlugi
{
private static final long serialVersionUID = 1L;
- private static final String SCRIPT_PATH = "script-path";
-
private static final Logger notifyLog = LogFactory.getLogger(LogCategory.NOTIFY,
AbstractDatastorePlugin.class);
+ protected static String getScriptPathProperty(Properties properties)
+ {
+ return JythonBasedProcessingPlugin.getScriptPathProperty(properties);
+ }
+
private final IPluginScriptRunnerFactory scriptRunnerFactory;
transient IHierarchicalContentProvider hierarchicalContentProvider;
public JythonBasedReportingPlugin(Properties properties, File storeRoot)
{
- this(properties, storeRoot, new PluginScriptRunnerFactory(
- PropertyUtils.getMandatoryProperty(properties, SCRIPT_PATH)), null);
+ this(properties, storeRoot,
+ new PluginScriptRunnerFactory(getScriptPathProperty(properties)), null);
}
// for tests
- JythonBasedReportingPlugin(Properties properties, File storeRoot,
+ protected JythonBasedReportingPlugin(Properties properties, File storeRoot,
IPluginScriptRunnerFactory scriptRunnerFactory,
IHierarchicalContentProvider contentProvider)
{
@@ -108,9 +111,25 @@ public class JythonBasedReportingPlugin extends AbstractTableModelReportingPlugi
operationLog.info("Reporting done");
JythonBasedPluginUtils.closeContent(iDataSets);
}
+ } catch (EvaluatorException ex)
+ {
+ StringBuilder errorString = new StringBuilder();
+ errorString
+ .append("Could not run report script " + scriptRunnerFactory.getScriptPath());
+ if (null != ex.getCause())
+ {
+ notifyLog.error(errorString.toString(), ex.getCause());
+ } else
+ {
+ notifyLog.error(errorString.toString(), ex);
+ }
+ throw new UserFailureException("Chosen plugin failed to create a report.");
} catch (RuntimeException ex)
{
- notifyLog.error(ex.getMessage());
+ StringBuilder errorString = new StringBuilder();
+ errorString
+ .append("Could not run report script " + scriptRunnerFactory.getScriptPath());
+ notifyLog.error(errorString.toString(), ex);
throw new UserFailureException("Chosen plugin failed to create a report.");
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/PluginScriptRunnerFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/PluginScriptRunnerFactory.java
index d9fbdd21f07fa5c314a6ba27393cbdf7ad89d710..36abacd746ed50d71b31e60a89c41398a182be42 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/PluginScriptRunnerFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/PluginScriptRunnerFactory.java
@@ -39,7 +39,7 @@ import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.ISimpleTable
/**
* @author Piotr Buczek
*/
-class PluginScriptRunnerFactory implements IPluginScriptRunnerFactory
+public class PluginScriptRunnerFactory implements IPluginScriptRunnerFactory
{
private static final long serialVersionUID = 1L;
@@ -57,6 +57,7 @@ class PluginScriptRunnerFactory implements IPluginScriptRunnerFactory
public PluginScriptRunnerFactory(String scriptPath)
{
this.scriptPath = scriptPath;
+ Evaluator.initialize();
}
/**
@@ -124,8 +125,8 @@ class PluginScriptRunnerFactory implements IPluginScriptRunnerFactory
/**
* Factory method for creating an IReportingPluginScriptRunner given the script as a string.
*/
- static IReportingPluginScriptRunner createReportingPluginRunnerFromScriptString(
- String scriptString, DataSetProcessingContext context)
+ IReportingPluginScriptRunner createReportingPluginRunnerFromScriptString(String scriptString,
+ DataSetProcessingContext context)
{
return new ReportingPluginScriptRunner(createEvaluator(scriptString, context));
}
@@ -133,13 +134,13 @@ class PluginScriptRunnerFactory implements IPluginScriptRunnerFactory
/**
* Factory method for creating an IProcessingPluginScriptRunner given the script as a string.
*/
- static IProcessingPluginScriptRunner createProcessingPluginRunnerFromScriptString(
- String scriptString, DataSetProcessingContext context)
+ IProcessingPluginScriptRunner createProcessingPluginRunnerFromScriptString(String scriptString,
+ DataSetProcessingContext context)
{
return new ProcessingPluginScriptRunner(createEvaluator(scriptString, context));
}
- private static Evaluator createEvaluator(String scriptString, DataSetProcessingContext context)
+ protected Evaluator createEvaluator(String scriptString, DataSetProcessingContext context)
{
final Evaluator evaluator = new Evaluator("", null, scriptString, false);
evaluator.set(SEARCH_SERVICE_VARIABLE_NAME, createSearchService());
@@ -218,4 +219,9 @@ class PluginScriptRunnerFactory implements IPluginScriptRunnerFactory
}
+ public String getScriptPath()
+ {
+ return scriptPath;
+ }
+
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/ReportingBasedProcessingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/ReportingBasedProcessingPlugin.java
index 0de1afdc1bb7d31c2cbb6e2122efe4624afa667f..8d2febc5808acffe36a25ff60d6b89c6fa34378d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/ReportingBasedProcessingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/ReportingBasedProcessingPlugin.java
@@ -34,6 +34,7 @@ import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractTabl
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IProcessingPluginTask;
import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
import ch.systemsx.cisd.openbis.dss.generic.shared.ProcessingStatus;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
@@ -53,8 +54,6 @@ public class ReportingBasedProcessingPlugin implements IProcessingPluginTask
// keys of properties
- private static final String SCRIPT_PATH = "script-path"; // the only mandatory property
-
private static final String EMAIL_SUBJECT = "email-subject";
private static final String EMAIL_BODY = "email-body";
@@ -71,6 +70,11 @@ public class ReportingBasedProcessingPlugin implements IProcessingPluginTask
private static final boolean DEFAULT_SINGLE_REPORT_FOR_ALL = false;
+ protected static String getScriptPathProperty(Properties properties)
+ {
+ return JythonBasedProcessingPlugin.getScriptPathProperty(properties);
+ }
+
private final String emailSubject;
private final String emailBody;
@@ -83,9 +87,17 @@ public class ReportingBasedProcessingPlugin implements IProcessingPluginTask
public ReportingBasedProcessingPlugin(Properties properties, File storeRoot)
{
- this.scriptRunnerFactory =
- new PluginScriptRunnerFactory(PropertyUtils.getMandatoryProperty(properties,
- SCRIPT_PATH));
+ this(new PluginScriptRunnerFactory(getScriptPathProperty(properties)), properties,
+ storeRoot);
+ }
+
+ /**
+ * Internal constructor for use by subclasses.
+ */
+ protected ReportingBasedProcessingPlugin(IPluginScriptRunnerFactory scriptRunnerFactory,
+ Properties properties, File storeRoot)
+ {
+ this.scriptRunnerFactory = scriptRunnerFactory;
this.singleReport =
PropertyUtils.getBoolean(properties, SINGLE_REPORT, DEFAULT_SINGLE_REPORT_FOR_ALL);
this.emailSubject =
@@ -144,8 +156,8 @@ public class ReportingBasedProcessingPlugin implements IProcessingPluginTask
public TableModel createTableModel(List<DatasetDescription> dataSets,
DataSetProcessingContext context)
{
- return JythonBasedReportingPlugin
- .createReport(dataSets, context, scriptRunnerFactory, null);
+ return JythonBasedReportingPlugin.createReport(dataSets, context, scriptRunnerFactory,
+ ServiceProvider.getHierarchicalContentProvider());
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/DataSetProcessingContext.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/DataSetProcessingContext.java
index aacfdac3678540a1b7d2c14c673e3f5d729cb57c..380e9e3d94af19e1724be2dd64dc5cb0df9f77be 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/DataSetProcessingContext.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/DataSetProcessingContext.java
@@ -23,7 +23,7 @@ import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IProcessingPlug
/**
* Context for processing data sets by a {@link IProcessingPluginTask}.
- *
+ *
* @author Franz-Josef Elmer
*/
public class DataSetProcessingContext
@@ -36,17 +36,31 @@ public class DataSetProcessingContext
private final IDataSetDirectoryProvider directoryProvider;
+ private final String sessionTokenOrNull;
+
/**
* Creates an instance for specified directory provider, parameter bindings, e-mail client, and
- * optional user e-mail address.
+ * optional user e-mail address and sessionToken.
*/
public DataSetProcessingContext(IDataSetDirectoryProvider directoryProvider,
Map<String, String> parameterBindings, IMailClient mailClient, String userEmailOrNull)
+ {
+ this(directoryProvider, parameterBindings, mailClient, userEmailOrNull, null);
+ }
+
+ /**
+ * Creates an instance for specified directory provider, parameter bindings, e-mail client, and
+ * optional user e-mail address and sessionToken.
+ */
+ public DataSetProcessingContext(IDataSetDirectoryProvider directoryProvider,
+ Map<String, String> parameterBindings, IMailClient mailClient, String userEmailOrNull,
+ String sessionTokenOrNull)
{
this.directoryProvider = directoryProvider;
this.parameterBindings = parameterBindings;
this.mailClient = mailClient;
this.userEmailOrNull = userEmailOrNull;
+ this.sessionTokenOrNull = sessionTokenOrNull;
}
public IDataSetDirectoryProvider getDirectoryProvider()
@@ -68,4 +82,9 @@ public class DataSetProcessingContext
{
return userEmailOrNull;
}
+
+ public String trySessionToken()
+ {
+ return sessionTokenOrNull;
+ }
}
diff --git a/datastore_server/source/java/dssApplicationContext.xml b/datastore_server/source/java/dssApplicationContext.xml
index 2c07fc869d6f02f62a95219379b09566227a3fde..71e4cc80850fc5da0644a02d4d799e1bef2e38f6 100644
--- a/datastore_server/source/java/dssApplicationContext.xml
+++ b/datastore_server/source/java/dssApplicationContext.xml
@@ -35,6 +35,7 @@
<bean id="sessionHolder" class="ch.systemsx.cisd.openbis.dss.generic.server.openbisauth.OpenBISSessionHolder">
<property name="dataStoreCode" value="${data-store-server-code}"/>
+ <property name="serverUrl" value="${server-url}"/>
</bean>
<bean id="reauthenticateInterceptor" class="ch.systemsx.cisd.openbis.dss.generic.server.openbisauth.OpenBISAuthenticationInterceptor">
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ProcessDatasetsCommandTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ProcessDatasetsCommandTest.java
index aeaf67ca8d07b1d7d605e852d5d83a373d1efd1d..8e84a77ac76721ffa223cf1421dd9ccb25bfa8c3 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ProcessDatasetsCommandTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ProcessDatasetsCommandTest.java
@@ -87,7 +87,7 @@ public class ProcessDatasetsCommandTest extends AssertJUnit
parameterBindings = new HashMap<String, String>();
dataSets = Arrays.<DatasetDescription> asList(ds1, ds2);
command =
- new ProcessDatasetsCommand(task, dataSets, parameterBindings, E_MAIL,
+ new ProcessDatasetsCommand(task, dataSets, parameterBindings, E_MAIL, null,
DatastoreServiceDescription.processing("MY_TASK", EXAMPLE_TASK_LABEL,
new String[0], "DSS1"), mailClient);
subjectRecorder = new RecordingMatcher<String>();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
index caa7470515686168799e849e18dc40a3d5fa3505..170707cc51d3ea5f7c6a69e91f8c260dbcfa784c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
@@ -551,9 +551,10 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
}
List<DatasetDescription> locations = loadAvailableDatasetDescriptions(datasetCodes);
String sessionToken = dataStore.getSessionToken();
+ String userSessionToken = session.getSessionToken();
parameterBindings.put(Constants.USER_PARAMETER, session.tryGetPerson().getUserId());
- service.processDatasets(sessionToken, datastoreServiceKey, locations, parameterBindings,
- tryGetLoggedUserEmail());
+ service.processDatasets(sessionToken, userSessionToken, datastoreServiceKey, locations,
+ parameterBindings, tryGetLoggedUserEmail());
}
private String tryGetLoggedUserEmail()
@@ -579,7 +580,9 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
}
List<DatasetDescription> locations = loadAvailableDatasetDescriptions(datasetCodes);
String sessionToken = dataStore.getSessionToken();
- return service.createReportFromDatasets(sessionToken, datastoreServiceKey, locations);
+ String userSessionToken = session.getSessionToken();
+ return service.createReportFromDatasets(sessionToken, userSessionToken,
+ datastoreServiceKey, locations);
}
private List<DatasetDescription> loadAvailableDatasetDescriptions(List<String> dataSetCodes)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java
index 8fcce253dfca48b9914b9db178406157cfc6500a..16274c3c277941bec98b0b21c23b189fa11f2091 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java
@@ -78,20 +78,21 @@ public interface IDataStoreService
DataSetUploadContext context) throws InvalidAuthenticationException;
/** Runs the reporting task with the specified id for provided datasets */
- public TableModel createReportFromDatasets(String sessionToken, String serviceKey,
- List<DatasetDescription> datasets);
+ public TableModel createReportFromDatasets(String sessionToken, String userSessionToken,
+ String serviceKey, List<DatasetDescription> datasets);
/**
* Schedules the processing task with the specified id for provided datasets and specified
* parameter bindings.
*
+ * @param userSessionToken The session token of the user that initiated the processing.
* @param parameterBindings Contains at least the parameter {@link Constants#USER_PARAMETER}
* with the ID of the user who initiated processing.
* @param userEmailOrNull Email of user who initiated processing and will get a message after
* the processing is finished. It may be null if the user doesn't have email and no
* message will be send in such case.
*/
- public void processDatasets(String sessionToken, String serviceKey,
+ public void processDatasets(String sessionToken, String userSessionToken, String serviceKey,
List<DatasetDescription> datasets, Map<String, String> parameterBindings,
String userEmailOrNull);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonBasedProcessingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonBasedProcessingPlugin.java
new file mode 100644
index 0000000000000000000000000000000000000000..528ba994f26e7f2bfb9d05b11edbe42b63ddf9d2
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonBasedProcessingPlugin.java
@@ -0,0 +1,59 @@
+/*
+ * Copyright 2011 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.openbis.dss.screening.server.plugins.jython;
+
+import java.io.File;
+import java.util.Properties;
+
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.IPluginScriptRunnerFactory;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonBasedProcessingPlugin;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
+
+/**
+ * A version of the {@link JythonBasedProcessingPlugin} with extra support for screening.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class ScreeningJythonBasedProcessingPlugin extends JythonBasedProcessingPlugin
+{
+
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Public constructor.
+ *
+ * @param properties
+ * @param storeRoot
+ */
+ public ScreeningJythonBasedProcessingPlugin(Properties properties, File storeRoot)
+ {
+ this(new ScreeningPluginScriptRunnerFactory(getScriptPathProperty(properties)), null);
+ }
+
+ /**
+ * Constructor for tests.
+ *
+ * @param scriptRunnerFactory
+ * @param contentProvider
+ */
+ ScreeningJythonBasedProcessingPlugin(IPluginScriptRunnerFactory scriptRunnerFactory,
+ IHierarchicalContentProvider contentProvider)
+ {
+ super(scriptRunnerFactory, contentProvider);
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonBasedReportingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonBasedReportingPlugin.java
new file mode 100644
index 0000000000000000000000000000000000000000..57fd993f2bb53dc5163dda811060b1c661ab5e20
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonBasedReportingPlugin.java
@@ -0,0 +1,63 @@
+/*
+ * Copyright 2011 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.openbis.dss.screening.server.plugins.jython;
+
+import java.io.File;
+import java.util.Properties;
+
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.IPluginScriptRunnerFactory;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonBasedReportingPlugin;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
+
+/**
+ * A version of the {@link JythonBasedReportingPlugin} with extra support for screening.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class ScreeningJythonBasedReportingPlugin extends JythonBasedReportingPlugin
+{
+
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Public constructor.
+ *
+ * @param properties
+ * @param storeRoot
+ */
+ public ScreeningJythonBasedReportingPlugin(Properties properties, File storeRoot)
+ {
+ this(properties, storeRoot, new ScreeningPluginScriptRunnerFactory(
+ getScriptPathProperty(properties)), null);
+ }
+
+ /**
+ * Constructor for tests.
+ *
+ * @param properties
+ * @param storeRoot
+ * @param scriptRunnerFactory
+ * @param contentProvider
+ */
+ public ScreeningJythonBasedReportingPlugin(Properties properties, File storeRoot,
+ IPluginScriptRunnerFactory scriptRunnerFactory,
+ IHierarchicalContentProvider contentProvider)
+ {
+ super(properties, storeRoot, scriptRunnerFactory, contentProvider);
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningPluginScriptRunnerFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningPluginScriptRunnerFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..eb7e4f3016dbb4888b4bd5d66c2a042568ca5e71
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningPluginScriptRunnerFactory.java
@@ -0,0 +1,66 @@
+/*
+ * Copyright 2011 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.openbis.dss.screening.server.plugins.jython;
+
+import org.springframework.beans.factory.BeanFactory;
+
+import ch.systemsx.cisd.common.evaluator.Evaluator;
+import ch.systemsx.cisd.openbis.dss.generic.server.openbisauth.OpenBISSessionHolder;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.PluginScriptRunnerFactory;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade;
+import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacadeFactory;
+
+/**
+ * A version of the {@link PluginScriptRunnerFactory} with extra support for screening.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class ScreeningPluginScriptRunnerFactory extends PluginScriptRunnerFactory
+{
+ private static final long serialVersionUID = 1L;
+
+ private final static String SCREENING_FACADE_VARIABLE_NAME = "screeningFacade";
+
+ /**
+ * Public constructor
+ *
+ * @param scriptPath
+ */
+ public ScreeningPluginScriptRunnerFactory(String scriptPath)
+ {
+ super(scriptPath);
+ }
+
+ @Override
+ protected Evaluator createEvaluator(String scriptString, DataSetProcessingContext context)
+ {
+ Evaluator evaluator = super.createEvaluator(scriptString, context);
+ evaluator.set(SCREENING_FACADE_VARIABLE_NAME, createScreeningFacade(context));
+ return evaluator;
+ }
+
+ private IScreeningOpenbisServiceFacade createScreeningFacade(DataSetProcessingContext context)
+ {
+ BeanFactory applicationContext = ServiceProvider.getApplicationContext();
+ OpenBISSessionHolder sessionContextHolder =
+ (OpenBISSessionHolder) applicationContext.getBean("sessionHolder");
+ return ScreeningOpenbisServiceFacadeFactory.tryCreate(context.trySessionToken(),
+ sessionContextHolder.getServerUrl());
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningReportingBasedProcessingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningReportingBasedProcessingPlugin.java
new file mode 100644
index 0000000000000000000000000000000000000000..664210935c3369d8651ddc01d6866cdea7db197b
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningReportingBasedProcessingPlugin.java
@@ -0,0 +1,44 @@
+/*
+ * Copyright 2011 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.openbis.dss.screening.server.plugins.jython;
+
+import java.io.File;
+import java.util.Properties;
+
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.ReportingBasedProcessingPlugin;
+
+/**
+ * A version of the {@link ReportingBasedProcessingPlugin} with extra support for screening.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class ScreeningReportingBasedProcessingPlugin extends ReportingBasedProcessingPlugin
+{
+
+ /**
+ * @param properties
+ * @param storeRoot
+ */
+ public ScreeningReportingBasedProcessingPlugin(Properties properties, File storeRoot)
+ {
+ super(new ScreeningPluginScriptRunnerFactory(getScriptPathProperty(properties)),
+ properties, storeRoot);
+ }
+
+ private static final long serialVersionUID = 1L;
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeFactory.java
index 97f4e987cc6ae5661d69335fde806e291de40fb4..abe4f80ed8d585ad4b7707a33602c6999f738e57 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeFactory.java
@@ -20,7 +20,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.client.api.v1;
* Default implementation of {@link IScreeningOpenbisServiceFacadeFactory}.
*
* @author Chandrasekhar Ramakrishnan
- * @author Franze-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public class ScreeningOpenbisServiceFacadeFactory implements IScreeningOpenbisServiceFacadeFactory
{
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonBasedReportingPluginTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonBasedReportingPluginTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..063e017173cc20b7049c4a64d989f4561473d669
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonBasedReportingPluginTest.java
@@ -0,0 +1,187 @@
+/*
+ * Copyright 2009 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.openbis.dss.screening.server.plugins.jython;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Properties;
+
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent;
+import ch.systemsx.cisd.common.logging.LogInitializer;
+import ch.systemsx.cisd.common.test.RecordingMatcher;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.IPluginScriptRunnerFactory;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.IReportingPluginScriptRunner;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.api.IDataSet;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
+import ch.systemsx.cisd.openbis.dss.screening.server.plugins.jython.ScreeningJythonBasedReportingPlugin;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.ISimpleTableModelBuilderAdaptor;
+
+/**
+ * Tests for {@link ScreeningJythonBasedReportingPlugin} class.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class ScreeningJythonBasedReportingPluginTest extends AbstractFileSystemTestCase
+{
+ private Mockery context;
+
+ private IHierarchicalContentProvider hierarchicalContentProvider;
+
+ private IPluginScriptRunnerFactory scriptRunnerFactory;
+
+ private IReportingPluginScriptRunner reportingPluginScriptRunner;
+
+ private DataSetProcessingContext processingContext;
+
+ private File store;
+
+ private DatasetDescription datasetDescription1;
+
+ private DatasetDescription datasetDescription2;
+
+ private IHierarchicalContent content1;
+
+ private IHierarchicalContent content2;
+
+ @BeforeMethod
+ public void beforeMethod()
+ {
+ LogInitializer.init();
+ store = new File(workingDirectory, "store");
+ store.mkdirs();
+
+ datasetDescription1 = createDatasetDescription(1);
+ datasetDescription2 = createDatasetDescription(2);
+ context = new Mockery();
+ scriptRunnerFactory = context.mock(IPluginScriptRunnerFactory.class);
+ reportingPluginScriptRunner = context.mock(IReportingPluginScriptRunner.class);
+ hierarchicalContentProvider = context.mock(IHierarchicalContentProvider.class);
+ content1 = context.mock(IHierarchicalContent.class, "content1");
+ content2 = context.mock(IHierarchicalContent.class, "content2");
+ }
+
+ @AfterMethod
+ public void afterTest()
+ {
+ context.assertIsSatisfied();
+ }
+
+ private ScreeningJythonBasedReportingPlugin createPlugin()
+ {
+ return new ScreeningJythonBasedReportingPlugin(new Properties(), store,
+ scriptRunnerFactory, hierarchicalContentProvider);
+ }
+
+ @Test
+ public void testCreateReportHappyCase()
+ {
+ final ScreeningJythonBasedReportingPlugin plugin = createPlugin();
+ final RecordingMatcher<List<IDataSet>> iDataSetsMatcher =
+ new RecordingMatcher<List<IDataSet>>();
+ commonPrepare();
+ context.checking(new Expectations()
+ {
+ {
+ one(reportingPluginScriptRunner).describe(with(iDataSetsMatcher),
+ with(any(ISimpleTableModelBuilderAdaptor.class)));
+ }
+ });
+ plugin.createReport(Arrays.asList(datasetDescription1, datasetDescription2),
+ processingContext);
+ // verify data sets
+ assertEquals(2, iDataSetsMatcher.recordedObject().size());
+ verifyDataset(content1, 1, iDataSetsMatcher.recordedObject().get(0));
+ verifyDataset(content2, 2, iDataSetsMatcher.recordedObject().get(1));
+
+ context.assertIsSatisfied();
+ }
+
+ private void commonPrepare()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(scriptRunnerFactory).createReportingPluginRunner(processingContext);
+ will(returnValue(reportingPluginScriptRunner));
+
+ one(hierarchicalContentProvider).asContent("code1");
+ will(returnValue(content1));
+ one(hierarchicalContentProvider).asContent("code2");
+ will(returnValue(content2));
+
+ // in the end all contents should be closed automatically
+ // (both for success and failure)
+ one(content1).close();
+ one(content2).close();
+ }
+ });
+ }
+
+ private static DatasetDescription createDatasetDescription(int nr)
+ {
+ DatasetDescription result = new DatasetDescription();
+ result.setDatabaseInstanceCode("databaseInstanceCode" + nr);
+ result.setDataSetCode("code" + nr);
+ result.setDataSetLocation("dataSetLocation" + nr);
+ result.setDataSetSize(new Long(nr));
+ result.setDatasetTypeCode("datasetTypeCode" + nr);
+ result.setExperimentCode("experimentCode" + nr);
+ result.setExperimentIdentifier("experimentIdentifier" + nr);
+ result.setExperimentTypeCode("experimentTypeCode" + nr);
+ result.setMainDataSetPath("mainDataSetPath" + nr);
+ result.setMainDataSetPattern("mainDataSetPattern" + nr);
+ result.setProjectCode("projectCode" + nr);
+ result.setSampleCode("sampleCode" + nr);
+ result.setSampleIdentifier("sampleIdentifier" + nr);
+ result.setSampleTypeCode("sampleTypeCode" + nr);
+ result.setSpaceCode("spaceCode" + nr);
+ result.setSpeedHint(nr);
+ return result;
+ }
+
+ private static void verifyDataset(IHierarchicalContent expectedContent, int expectedNr,
+ IDataSet dataSet)
+ {
+ assertSame(expectedContent, dataSet.getContent());
+ assertEquals("databaseInstanceCode" + expectedNr, dataSet.getDatabaseInstanceCode());
+ assertEquals("code" + expectedNr, dataSet.getDataSetCode());
+ assertEquals("dataSetLocation" + expectedNr, dataSet.getDataSetLocation());
+ assertEquals(new Long(expectedNr), dataSet.getDataSetSize());
+ assertEquals("datasetTypeCode" + expectedNr, dataSet.getDataSetTypeCode());
+ assertEquals("experimentCode" + expectedNr, dataSet.getExperimentCode());
+ assertEquals("experimentIdentifier" + expectedNr, dataSet.getExperimentIdentifier());
+ assertEquals("experimentTypeCode" + expectedNr, dataSet.getExperimentTypeCode());
+ assertEquals("mainDataSetPath" + expectedNr, dataSet.getMainDataSetPath());
+ assertEquals("mainDataSetPattern" + expectedNr, dataSet.getMainDataSetPattern());
+ assertEquals("projectCode" + expectedNr, dataSet.getProjectCode());
+ assertEquals("sampleCode" + expectedNr, dataSet.getSampleCode());
+ assertEquals("sampleIdentifier" + expectedNr, dataSet.getSampleIdentifier());
+ assertEquals("sampleTypeCode" + expectedNr, dataSet.getSampleTypeCode());
+ assertEquals("spaceCode" + expectedNr, dataSet.getSpaceCode());
+ assertEquals(expectedNr, dataSet.getSpeedHint());
+ }
+}