diff --git a/common/source/java/ch/systemsx/cisd/common/servlet/HeaderFilter.java b/common/source/java/ch/systemsx/cisd/common/servlet/HeaderFilter.java
new file mode 100644
index 0000000000000000000000000000000000000000..acee6810f3d4b3a1700afe9bbc70b73fce7ed2e3
--- /dev/null
+++ b/common/source/java/ch/systemsx/cisd/common/servlet/HeaderFilter.java
@@ -0,0 +1,73 @@
+/*
+ * Copyright 2018 ETH Zuerich, SIS
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.common.servlet;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Enumeration;
+import java.util.List;
+
+import javax.servlet.Filter;
+import javax.servlet.FilterChain;
+import javax.servlet.FilterConfig;
+import javax.servlet.ServletException;
+import javax.servlet.ServletRequest;
+import javax.servlet.ServletResponse;
+import javax.servlet.http.HttpServletResponse;
+
+import org.springframework.util.StringUtils;
+
+/**
+ * @author Franz-Josef Elmer
+ *
+ */
+public class HeaderFilter implements Filter
+{
+ private List<String> headerNames;
+ private List<String> headerValues;
+
+ @Override
+ public void init(FilterConfig config) throws ServletException
+ {
+ Enumeration<String> initParameterNames = config.getInitParameterNames();
+ headerNames = Arrays.asList(StringUtils.toStringArray(initParameterNames));
+ headerValues = new ArrayList<>(headerNames.size());
+ for (String name : headerNames)
+ {
+ headerValues.add(config.getInitParameter(name));
+ }
+ }
+
+ @Override
+ public void doFilter(ServletRequest request, ServletResponse response, FilterChain filterChain) throws IOException, ServletException
+ {
+ HttpServletResponse httpResponse = (HttpServletResponse) response;
+
+ for (int i = 0; i < headerNames.size(); i++)
+ {
+ httpResponse.addHeader(headerNames.get(i), headerValues.get(i));
+ }
+ filterChain.doFilter(request, response);
+ }
+
+ @Override
+ public void destroy()
+ {
+ }
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServer.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServer.java
index a227191d4ae0d36aad2c7f5050d0e176a14e0326..f9ca5aa9dd93b8705ca01aa7bb4c731a9ef75b23 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServer.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServer.java
@@ -249,6 +249,7 @@ public class DataStoreServer
servletContextHandler.setAttribute(
WebApplicationContext.ROOT_WEB_APPLICATION_CONTEXT_ATTRIBUTE,
ServiceProvider.getApplicationContext());
+ servletContextHandler.getSessionHandler().getSessionCookieConfig().setHttpOnly(true);
// Disable URL rewriting (forces container to stop appending ";jsessionid=xxx" to urls)
// to avoid mistakes in URL parsing by download servlets
servletContextHandler.getSessionHandler()
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoProcessingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoProcessingPlugin.java
index 8a7ae2ec5744a651c2dc12b8a1ce26a60af54a2f..d43929f9d3f6e3150aed72b3091cb0f6a85be83b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoProcessingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoProcessingPlugin.java
@@ -57,12 +57,15 @@ public class DemoProcessingPlugin implements IProcessingPluginTask
DataSetProcessingContext context)
{
operationLog.info("Processing of the following datasets has been requested: " + datasets);
- Map<String, String> parameterBindings = context.getParameterBindings();
- if (parameterBindings.isEmpty() == false)
+ if (context != null)
{
- for (Entry<String, String> entry : parameterBindings.entrySet())
+ Map<String, String> parameterBindings = context.getParameterBindings();
+ if (parameterBindings != null && parameterBindings.isEmpty() == false)
{
- operationLog.info("Parameter: " + entry);
+ for (Entry<String, String> entry : parameterBindings.entrySet())
+ {
+ operationLog.info("Parameter: " + entry);
+ }
}
}
IHierarchicalContentProvider contentProvider =
diff --git a/datastore_server/sourceTest/java/ch/ethz/sis/openbis/generic/dss/systemtest/api/v3/AggregationServiceTest.java b/datastore_server/sourceTest/java/ch/ethz/sis/openbis/generic/dss/systemtest/api/v3/AggregationServiceTest.java
index c5faed5680534d6d0ab7628f63b426d4ffb33343..95f003d5c57bef0d4468c278dda5a38ed30e5176 100644
--- a/datastore_server/sourceTest/java/ch/ethz/sis/openbis/generic/dss/systemtest/api/v3/AggregationServiceTest.java
+++ b/datastore_server/sourceTest/java/ch/ethz/sis/openbis/generic/dss/systemtest/api/v3/AggregationServiceTest.java
@@ -226,6 +226,28 @@ public class AggregationServiceTest extends AbstractFileTest
"Cannot find the data store UNKNOWN");
as.logout(sessionToken);
}
+
+ @Test
+ public void testExecuteAggregationServiceOfUnspecifiedDataStore() throws Exception
+ {
+ // Given
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+ DssServicePermId id = new DssServicePermId("example-jython-aggregation-service-report");
+ AggregationServiceExecutionOptions options = new AggregationServiceExecutionOptions();
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ // When
+ as.executeAggregationService(sessionToken, id, options);
+ }
+ },
+ // Then
+ "Data store id cannot be null.");
+ as.logout(sessionToken);
+ }
@Test
public void testExecuteAggregationServiceWithMissingServiceId()
diff --git a/datastore_server/sourceTest/java/ch/ethz/sis/openbis/generic/dss/systemtest/api/v3/ProcessingServiceTest.java b/datastore_server/sourceTest/java/ch/ethz/sis/openbis/generic/dss/systemtest/api/v3/ProcessingServiceTest.java
index 3871f0508c363357aae05c47774b3bcac99de182..bc16fd21b805903b1162fb4eb692cda8c91b46cb 100644
--- a/datastore_server/sourceTest/java/ch/ethz/sis/openbis/generic/dss/systemtest/api/v3/ProcessingServiceTest.java
+++ b/datastore_server/sourceTest/java/ch/ethz/sis/openbis/generic/dss/systemtest/api/v3/ProcessingServiceTest.java
@@ -139,7 +139,7 @@ public class ProcessingServiceTest extends AbstractFileTest
}
@Test
- public void testExecuteProcessingService() throws Exception
+ public void testExecuteProcessingServiceWithSpecifiedDataStore() throws Exception
{
// Given
String dataSetCode = registerDataSet();
@@ -200,6 +200,68 @@ public class ProcessingServiceTest extends AbstractFileTest
as.logout(sessionToken);
}
+ @Test
+ public void testExecuteProcessingService() throws Exception
+ {
+ // Given
+ String dataSetCode = registerDataSet();
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+ DssServicePermId id = new DssServicePermId("demo-processor");
+ ProcessingServiceExecutionOptions options = new ProcessingServiceExecutionOptions();
+ options.withDataSets(dataSetCode).withParameter("greetings", "hello world");
+
+ // When
+ as.executeProcessingService(sessionToken, id, options);
+
+ // Then
+ List<String> log = new ArrayList<>();
+ waitUntil(new ILogMonitoringStopCondition()
+ {
+ @Override
+ public boolean stopConditionFulfilled(ParsedLogEntry logEntry)
+ {
+ String logMessage = logEntry.getLogMessage();
+ if (logMessage.contains("DemoProcessingPlugin"))
+ {
+ log.add(logMessage.replace(dataSetCode, "<data set code>"));
+ }
+ return logMessage.contains("Processing done.");
+ }
+ }, 10);
+ Collections.sort(log);
+ assertEquals("OPERATION.DemoProcessingPlugin - Parameter: greetings=hello world\n"
+ + "OPERATION.DemoProcessingPlugin - Parameter: user=test\n"
+ + "OPERATION.DemoProcessingPlugin - Processing <data set code>/\n"
+ + "OPERATION.DemoProcessingPlugin - Processing <data set code>/original\n"
+ + "OPERATION.DemoProcessingPlugin - Processing <data set code>/original/<data set code>\n"
+ + "OPERATION.DemoProcessingPlugin - Processing <data set code>/original/<data set code>/file1.txt\n"
+ + "OPERATION.DemoProcessingPlugin - Processing <data set code>/original/<data set code>/file2.txt\n"
+ + "OPERATION.DemoProcessingPlugin - Processing <data set code>/original/<data set code>/subdir1\n"
+ + "OPERATION.DemoProcessingPlugin - Processing <data set code>/original/<data set code>/subdir1/file3.txt\n"
+ + "OPERATION.DemoProcessingPlugin - Processing <data set code>/original/<data set code>/subdir1/file4.txt\n"
+ + "OPERATION.DemoProcessingPlugin - Processing <data set code>/original/<data set code>/subdir1/subdir2\n"
+ + "OPERATION.DemoProcessingPlugin - Processing <data set code>/original/<data set code>/subdir1/subdir2/file5.txt\n"
+ + "OPERATION.DemoProcessingPlugin - Processing <data set code>/original/<data set code>/subdir3\n"
+ + "OPERATION.DemoProcessingPlugin - Processing <data set code>/original/<data set code>/subdir3/file6.txt\n"
+ + "OPERATION.DemoProcessingPlugin - Processing done.\n"
+ + "OPERATION.DemoProcessingPlugin - Processing of the following datasets has been requested: [Dataset '<data set code>']",
+ String.join("\n", log));
+ File[] emails = EMAIL_FOLDER.listFiles();
+ if (emails == null)
+ {
+ fail("Empty e-mails folder: " + EMAIL_FOLDER.getAbsolutePath());
+ }
+ File emailFile = Collections.max(new ArrayList<>(Arrays.asList(emails)));
+ String email = FileUtilities.loadToString(emailFile);
+ assertContains("'Demo Processing' [demo-processor] processing finished on 1 data set(s):", email);
+ assertContains(dataSetCode, email);
+ PersonPermId personPermId = new PersonPermId(TEST_USER);
+ PersonFetchOptions fetchOptions = new PersonFetchOptions();
+ String emailAddress = as.getPersons(sessionToken, Arrays.asList(personPermId), fetchOptions).get(personPermId).getEmail();
+ assertContains("To: " + emailAddress, email);
+ as.logout(sessionToken);
+ }
+
@Test
public void testExecuteProcessingServiceUsingReservedParameter() throws Exception
{
@@ -365,6 +427,7 @@ public class ProcessingServiceTest extends AbstractFileTest
// Given
String sessionToken = as.login(TEST_USER, PASSWORD);
ProcessingServiceExecutionOptions options = new ProcessingServiceExecutionOptions();
+ options.withDataSets("123");
assertUserFailureException(new IDelegatedAction()
{
@@ -387,6 +450,7 @@ public class ProcessingServiceTest extends AbstractFileTest
String sessionToken = as.login(TEST_USER, PASSWORD);
IDssServiceId id = new MyId();
ProcessingServiceExecutionOptions options = new ProcessingServiceExecutionOptions();
+ options.withDataSets("123");
assertUserFailureException(new IDelegatedAction()
{
@@ -410,6 +474,7 @@ public class ProcessingServiceTest extends AbstractFileTest
String sessionToken = as.login(TEST_USER, PASSWORD);
IDssServiceId id = new DssServicePermId("", new DataStorePermId("STANDARD"));
ProcessingServiceExecutionOptions options = new ProcessingServiceExecutionOptions();
+ options.withDataSets("123");
assertUserFailureException(new IDelegatedAction()
{
@@ -433,6 +498,7 @@ public class ProcessingServiceTest extends AbstractFileTest
String sessionToken = as.login(TEST_USER, PASSWORD);
IDssServiceId id = new DssServicePermId("key", new MyId());
ProcessingServiceExecutionOptions options = new ProcessingServiceExecutionOptions();
+ options.withDataSets("123");
assertUserFailureException(new IDelegatedAction()
{
@@ -456,6 +522,7 @@ public class ProcessingServiceTest extends AbstractFileTest
String sessionToken = as.login(TEST_USER, PASSWORD);
IDssServiceId id = new DssServicePermId("key", new DataStorePermId(""));
ProcessingServiceExecutionOptions options = new ProcessingServiceExecutionOptions();
+ options.withDataSets("123");
assertUserFailureException(new IDelegatedAction()
{
diff --git a/datastore_server/sourceTest/java/ch/ethz/sis/openbis/generic/dss/systemtest/api/v3/ReportingServiceTest.java b/datastore_server/sourceTest/java/ch/ethz/sis/openbis/generic/dss/systemtest/api/v3/ReportingServiceTest.java
index 624c038e39e42b1251379846c234af8180a1ee4a..3e1930a9f471044a9a65551aaae362d2e95c7eda 100644
--- a/datastore_server/sourceTest/java/ch/ethz/sis/openbis/generic/dss/systemtest/api/v3/ReportingServiceTest.java
+++ b/datastore_server/sourceTest/java/ch/ethz/sis/openbis/generic/dss/systemtest/api/v3/ReportingServiceTest.java
@@ -110,6 +110,7 @@ public class ReportingServiceTest extends AbstractFileTest
List<String> allDataSetTypeCodes = as.searchDataSetTypes(sessionToken, new DataSetTypeSearchCriteria(),
new DataSetTypeFetchOptions()).getObjects().stream().map(t -> t.getCode()).collect(Collectors.toList());
Collections.sort(allDataSetTypeCodes);
+ System.err.println(allDataSetTypeCodes);
// When
List<ReportingService> services = as.searchReportingServices(sessionToken, searchCriteria, fetchOptions).getObjects();
@@ -131,7 +132,7 @@ public class ReportingServiceTest extends AbstractFileTest
}
@Test
- public void testExecuteReportingService() throws Exception
+ public void testExecuteReportingServiceWithSpecifiedDataStore() throws Exception
{
// Given
String dataSetCode = registerDataSet();
@@ -152,6 +153,28 @@ public class ReportingServiceTest extends AbstractFileTest
as.logout(sessionToken);
}
+ @Test
+ public void testExecuteReportingService() throws Exception
+ {
+ // Given
+ String dataSetCode = registerDataSet();
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+ DssServicePermId id = new DssServicePermId("example-jython-report");
+ ReportingServiceExecutionOptions options = new ReportingServiceExecutionOptions();
+ options.withDataSets(dataSetCode);
+
+ // When
+ TableModel tableModel = as.executeReportingService(sessionToken, id, options);
+
+ // Then
+ assertEquals("[Data Set, Data Set Type]", tableModel.getColumns().toString());
+ assertEquals("[[" + dataSetCode + ", UNKNOWN]]", tableModel.getRows().toString());
+ assertEquals(tableModel.getRows().get(0).get(0).getClass(), TableStringCell.class);
+ assertEquals(tableModel.getRows().get(0).get(1).getClass(), TableStringCell.class);
+
+ as.logout(sessionToken);
+ }
+
@Test
public void testExecuteUnknownReportingService() throws Exception
{
diff --git a/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/common.js b/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/common.js
index 8b2033c55333b4dc27695bb507a9048405f32b33..8802daed52ec5f6558b181c44cf8f9fdf90f8568 100644
--- a/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/common.js
+++ b/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/common.js
@@ -81,7 +81,6 @@ define(
this.MaterialDeletionOptions = dtos.MaterialDeletionOptions;
this.PluginDeletionOptions = dtos.PluginDeletionOptions;
this.VocabularyTermDeletionOptions = dtos.VocabularyTermDeletionOptions;
- this.EntityTypeDeletionOptions = dtos.EntityTypeDeletionOptions;
this.ExternalDmsDeletionOptions = dtos.ExternalDmsDeletionOptions;
this.TagDeletionOptions = dtos.TagDeletionOptions;
this.AuthorizationGroupDeletionOptions = dtos.AuthorizationGroupDeletionOptions;
@@ -315,7 +314,6 @@ define(
this.DeleteSampleTypesOperation = dtos.DeleteSampleTypesOperation;
this.DeleteDataSetTypesOperation = dtos.DeleteDataSetTypesOperation;
this.DeleteMaterialTypesOperation = dtos.DeleteMaterialTypesOperation;
- this.DeleteEntityTypesOperation = dtos.DeleteEntityTypesOperation;
this.DeleteTagsOperation = dtos.DeleteTagsOperation;
this.DeleteAuthorizationGroupsOperation = dtos.DeleteAuthorizationGroupsOperation;
this.DeleteRoleAssignmentsOperation = dtos.DeleteRoleAssignmentsOperation;
@@ -1055,13 +1053,6 @@ define(
return facade.deleteMaterialTypes([ id ], options);
}.bind(this);
- this.deleteEntityType = function(facade, id) {
- var c = this;
- var options = new dtos.EntityTypeDeletionOptions();
- options.setReason("test reason");
- return facade.deleteEntityTypes([ id ], options);
- }.bind(this);
-
this.deletePlugin = function(facade, id) {
var c = this;
var options = new dtos.PluginDeletionOptions();
diff --git a/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-dss-services.js b/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-dss-services.js
index f6c6377930a8593ecf9c9cdb39c027d651cda935..f5ce0bdafdff2657eda1dcc7059a71c1ab9d8241 100644
--- a/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-dss-services.js
+++ b/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-dss-services.js
@@ -212,7 +212,7 @@ define([ 'jquery', 'underscore', 'openbis', 'test/openbis-execute-operations', '
dataSetCode = permId;
var serviceId = new c.DssServicePermId("test-reporting-service", new c.DataStorePermId("DSS1"));
var options = new c.ReportingServiceExecutionOptions();
- options.withDataSets([dataSetCode]);
+ options.withDataSets(dataSetCode);
return facade.executeReportingService(serviceId, options);
});
}
diff --git a/openbis/resource/server/bis-common.xml b/openbis/resource/server/bis-common.xml
index 85934415b690e825409e2efe08f75abd3755930c..b7f83dd0102db34f719b92a5a1b917f17a90ffaa 100644
--- a/openbis/resource/server/bis-common.xml
+++ b/openbis/resource/server/bis-common.xml
@@ -14,6 +14,19 @@
</listener-class>
</listener>
+ <filter>
+ <filter-name>HeaderFilter</filter-name>
+ <filter-class>ch.systemsx.cisd.common.servlet.HeaderFilter</filter-class>
+ <init-param>
+ <param-name>X-Frame-Options</param-name>
+ <param-value>SAMEORIGIN</param-value>
+ </init-param>
+ </filter>
+ <filter-mapping>
+ <filter-name>HeaderFilter</filter-name>
+ <url-pattern>/*</url-pattern>
+ </filter-mapping>
+
<filter>
<filter-name>CacheFilter</filter-name>
<filter-class>ch.systemsx.cisd.openbis.generic.server.CacheFilter</filter-class>
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/dataset/CreateDataSetTypesExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/dataset/CreateDataSetTypesExecutor.java
index c938d62c3e6a6d1ca8293c1c734e75989b13e51f..1454df00f7266d6084003723668bef9f952b299d 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/dataset/CreateDataSetTypesExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/dataset/CreateDataSetTypesExecutor.java
@@ -16,12 +16,15 @@
package ch.ethz.sis.openbis.generic.server.asapi.v3.executor.dataset;
+import org.springframework.beans.factory.InitializingBean;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.DataSetTypeCreation;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.IOperationContext;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.entity.AbstractCreateEntityTypeExecutor;
+import ch.systemsx.cisd.openbis.generic.server.DataStoreServiceRegistrator;
+import ch.systemsx.cisd.openbis.generic.server.IDataStoreServiceRegistrator;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IEntityTypeBO;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
@@ -32,12 +35,19 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
*/
@Component
public class CreateDataSetTypesExecutor extends AbstractCreateEntityTypeExecutor<DataSetTypeCreation, DataSetType, DataSetTypePE>
- implements ICreateDataSetTypeExecutor
+ implements ICreateDataSetTypeExecutor, InitializingBean
{
-
@Autowired
private IDataSetTypeAuthorizationExecutor authorizationExecutor;
+ private IDataStoreServiceRegistrator dataStoreServiceRegistrator;
+
+ @Override
+ public void afterPropertiesSet() throws Exception
+ {
+ dataStoreServiceRegistrator = new DataStoreServiceRegistrator(daoFactory);
+ }
+
@Override
protected ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind getPEEntityKind()
{
@@ -75,6 +85,7 @@ public class CreateDataSetTypesExecutor extends AbstractCreateEntityTypeExecutor
IEntityTypeBO typeBO = businessObjectFactory.createEntityTypeBO(context.getSession());
typeBO.define(type);
typeBO.save();
+ dataStoreServiceRegistrator.register(type);
}
@Override
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/entity/AbstractCreateEntityTypeExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/entity/AbstractCreateEntityTypeExecutor.java
index 4961683ca576799e172fb0e8f45009bcac6f39fc..0acad5bb582748b45b161472336ec90bee3732cc 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/entity/AbstractCreateEntityTypeExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/entity/AbstractCreateEntityTypeExecutor.java
@@ -58,7 +58,7 @@ public abstract class AbstractCreateEntityTypeExecutor<CREATION extends IEntityT
{
@Autowired
- private IDAOFactory daoFactory;
+ protected IDAOFactory daoFactory;
@Resource(name = ComponentNames.COMMON_BUSINESS_OBJECT_FACTORY)
protected ICommonBusinessObjectFactory businessObjectFactory;
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/AbstractDssServiceExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/AbstractDssServiceExecutor.java
index 541211a1050e44f41a510de044394269c05db088..b82a69140a7d0158669412446cccf39a1159314a 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/AbstractDssServiceExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/AbstractDssServiceExecutor.java
@@ -43,7 +43,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
/**
* @author Franz-Josef Elmer
- *
*/
abstract class AbstractDssServiceExecutor
{
@@ -63,54 +62,61 @@ abstract class AbstractDssServiceExecutor
throw new UserFailureException("Service key cannot be empty.");
}
IDataStoreId dataStoreId = permId.getDataStoreId();
- if (dataStoreId == null)
- {
- throw new UserFailureException("Data store id cannot be null.");
- }
- if (dataStoreId instanceof DataStorePermId == false)
- {
- throw new UserFailureException("Unknown data store id type: " + dataStoreId.getClass().getName());
- }
- if (StringUtils.isBlank(((DataStorePermId) dataStoreId).getPermId()))
+ if (dataStoreId != null)
{
- throw new UserFailureException("Data store code cannot be empty.");
+ if (dataStoreId instanceof DataStorePermId == false)
+ {
+ throw new UserFailureException("Unknown data store id type: " + dataStoreId.getClass().getName());
+ }
+ if (StringUtils.isBlank(((DataStorePermId) dataStoreId).getPermId()))
+ {
+ throw new UserFailureException("Data store code cannot be empty.");
+ }
}
}
protected TableModel translate(ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel tableModel)
{
- List<TableModelColumnHeader> headers = tableModel.getHeader();
- List<TableColumn> columns = new ArrayList<>(headers.size());
- for (TableModelColumnHeader header : headers)
- {
- columns.add(new TableColumn(header.getTitle()));
- }
- SimpleDateFormat format = new SimpleDateFormat(BasicConstant.CANONICAL_DATE_FORMAT_PATTERN);
- List<TableModelRow> rows = tableModel.getRows();
- List<List<ITableCell>> translatedRows = new ArrayList<>(rows.size());
- for (TableModelRow row : rows)
+ ArrayList<TableColumn> columns = new ArrayList<>();
+ ArrayList<List<ITableCell>> translatedRows = new ArrayList<>();
+ if (tableModel != null && tableModel.getHeader() != null && tableModel.getRows() != null)
{
- List<ISerializableComparable> values = row.getValues();
- List<ITableCell> cells = new ArrayList<>(values.size());
- for (ISerializableComparable value : values)
+ List<TableModelColumnHeader> headers = tableModel.getHeader();
+ columns.ensureCapacity(headers.size());
+ for (TableModelColumnHeader header : headers)
{
- ITableCell cell = null;
- if (value instanceof IntegerTableCell)
- {
- cell = new TableLongCell(((IntegerTableCell) value).getNumber());
- } else if (value instanceof DoubleTableCell)
- {
- cell = new TableDoubleCell(((DoubleTableCell) value).getNumber());
- } else if (value instanceof DateTableCell)
- {
- cell = new TableStringCell(format.format(((DateTableCell) value).getDateTime()));
- } else if (value != null)
+ columns.add(new TableColumn(header.getTitle()));
+ }
+ SimpleDateFormat format = new SimpleDateFormat(BasicConstant.CANONICAL_DATE_FORMAT_PATTERN);
+ List<TableModelRow> rows = tableModel.getRows();
+ translatedRows.ensureCapacity(rows.size());
+ for (TableModelRow row : rows)
+ {
+ List<ISerializableComparable> values = row.getValues();
+ if (values != null)
{
- cell = new TableStringCell(value.toString());
+ List<ITableCell> cells = new ArrayList<>(values.size());
+ for (ISerializableComparable value : values)
+ {
+ ITableCell cell = null;
+ if (value instanceof IntegerTableCell)
+ {
+ cell = new TableLongCell(((IntegerTableCell) value).getNumber());
+ } else if (value instanceof DoubleTableCell)
+ {
+ cell = new TableDoubleCell(((DoubleTableCell) value).getNumber());
+ } else if (value instanceof DateTableCell)
+ {
+ cell = new TableStringCell(format.format(((DateTableCell) value).getDateTime()));
+ } else if (value != null)
+ {
+ cell = new TableStringCell(value.toString());
+ }
+ cells.add(cell);
+ }
+ translatedRows.add(cells);
}
- cells.add(cell);
}
- translatedRows.add(cells);
}
return new TableModel(columns, translatedRows);
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/ExecuteAggregationServiceExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/ExecuteAggregationServiceExecutor.java
index 7a4f3ca1cf9e135f08ed786e3658dc8ebd1b67db..3b8e0e3d3aae16f17bc2ac816e79d0dd09e98209 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/ExecuteAggregationServiceExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/ExecuteAggregationServiceExecutor.java
@@ -22,11 +22,13 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.datastore.id.DataStorePermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.datastore.id.IDataStoreId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.service.execute.AggregationServiceExecutionOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.service.execute.TableModel;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.service.id.DssServicePermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.service.id.IDssServiceId;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.IOperationContext;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.ComponentNames;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataSetTable;
@@ -56,4 +58,15 @@ public class ExecuteAggregationServiceExecutor extends AbstractDssServiceExecuto
return translate(dataSetTable.createReportFromAggregationService(key, datastoreCode, options.getParameters()));
}
+ @Override
+ protected void checkData(IDssServiceId serviceId)
+ {
+ super.checkData(serviceId);
+ IDataStoreId dataStoreId = ((DssServicePermId) serviceId).getDataStoreId();
+ if (dataStoreId == null)
+ {
+ throw new UserFailureException("Data store id cannot be null.");
+ }
+ }
+
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/ExecuteProcessingServiceExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/ExecuteProcessingServiceExecutor.java
index 28e545f80c42bbbfa45e2df74792f361b323c959..240ae48f6a2f1570875e619e0bff1a61a0701231 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/ExecuteProcessingServiceExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/ExecuteProcessingServiceExecutor.java
@@ -16,12 +16,16 @@
package ch.ethz.sis.openbis.generic.server.asapi.v3.executor.service;
+import java.util.List;
+import java.util.Map;
+
import javax.annotation.Resource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.datastore.id.DataStorePermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.datastore.id.IDataStoreId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.service.execute.ProcessingServiceExecutionOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.service.id.DssServicePermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.service.id.IDssServiceId;
@@ -48,12 +52,20 @@ public class ExecuteProcessingServiceExecutor
public void execute(IOperationContext context, IDssServiceId serviceId, ProcessingServiceExecutionOptions options)
{
checkData(serviceId, options);
- authorizationExecutor.canExecute(context, options.getDataSetCodes());
+ List<String> dataSetCodes = options.getDataSetCodes();
+ authorizationExecutor.canExecute(context, dataSetCodes);
IDataSetTable dataSetTable = businessObjectFactory.createDataSetTable(context.getSession());
DssServicePermId permId = (DssServicePermId) serviceId;
String key = permId.getPermId();
- String datastoreCode = ((DataStorePermId) permId.getDataStoreId()).getPermId();
- dataSetTable.processDatasets(key, datastoreCode, options.getDataSetCodes(), options.getParameters());
+ IDataStoreId dataStoreId = permId.getDataStoreId();
+ Map<String, String> parameters = options.getParameters();
+ if (dataStoreId instanceof DataStorePermId)
+ {
+ dataSetTable.processDatasets(key, ((DataStorePermId) dataStoreId).getPermId(), dataSetCodes, parameters);
+ } else
+ {
+ dataSetTable.processDatasets(key, dataSetCodes, parameters);
+ }
}
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/ExecuteReportingServiceExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/ExecuteReportingServiceExecutor.java
index b1ab79cb2f6dd691a3523270ff1490f923369816..cb22400b3e16254c5de39af2f1fdd9b7c5ef7e2f 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/ExecuteReportingServiceExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/ExecuteReportingServiceExecutor.java
@@ -22,6 +22,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.datastore.id.DataStorePermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.datastore.id.IDataStoreId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.service.execute.ReportingServiceExecutionOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.service.execute.TableModel;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.service.id.DssServicePermId;
@@ -54,8 +55,16 @@ public class ExecuteReportingServiceExecutor
IDataSetTable dataSetTable = businessObjectFactory.createDataSetTable(context.getSession());
DssServicePermId permId = (DssServicePermId) serviceId;
String key = permId.getPermId();
- String datastoreCode = ((DataStorePermId) permId.getDataStoreId()).getPermId();
- return translate(dataSetTable.createReportFromDatasets(key, datastoreCode, options.getDataSetCodes()));
+ IDataStoreId dataStoreId = permId.getDataStoreId();
+ if (dataStoreId instanceof DataStorePermId)
+ {
+ DataStorePermId n = (DataStorePermId) dataStoreId;
+ String dataStoreCode = n.getPermId();
+ return translate(dataSetTable.createReportFromDatasets(key, dataStoreCode, options.getDataSetCodes()));
+ } else
+ {
+ return translate(dataSetTable.createReportFromDatasets(key, options.getDataSetCodes()));
+ }
}
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/ProcessingServiceAuthorizationExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/ProcessingServiceAuthorizationExecutor.java
index a96acccffa8e8f9f2acba09d0af941147ca0cfda..ace11b5b96bc3b7b85f77d1a2479b8aaea3b9362 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/ProcessingServiceAuthorizationExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/service/ProcessingServiceAuthorizationExecutor.java
@@ -43,7 +43,7 @@ public class ProcessingServiceAuthorizationExecutor implements IProcessingServic
}
@Override
- @RolesAllowed({ RoleWithHierarchy.PROJECT_OBSERVER })
+ @RolesAllowed({ RoleWithHierarchy.PROJECT_USER })
@Capability("EXECUTE_PROCESSING_SERVICES")
public void canExecute(IOperationContext context,
@AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class) List<String> dataSetCodes)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/service/execute/ProcessingServiceExecutionOptions.js b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/service/execute/ProcessingServiceExecutionOptions.js
index cbe328d016c0ee27a5c5889a287cf0d57ff00d4f..dfb463fec417622a52661d7a2fa6862905c0febd 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/service/execute/ProcessingServiceExecutionOptions.js
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/service/execute/ProcessingServiceExecutionOptions.js
@@ -3,12 +3,16 @@ define([ "stjs", "as/dto/service/execute/AbstractExecutionOptionsWithParameters"
AbstractExecutionOptionsWithParameters.call(this);
this.dataSetCodes = [];
};
- stjs.extend(ProcessingServiceExecutionOptions, null, [ ], function(constructor, prototype) {
+ stjs.extend(ProcessingServiceExecutionOptions, AbstractExecutionOptionsWithParameters, [AbstractExecutionOptionsWithParameters], function(constructor, prototype) {
prototype['@type'] = 'as.dto.service.execute.ProcessingServiceExecutionOptions';
constructor.serialVersionUID = 1;
prototype.dataSetCodes = null;
prototype.withDataSets = function(dataSetCodes) {
- this.dataSetCodes = dataSetCodes;
+ if (Object.prototype.toString.call( dataSetCodes ) === '[object Array]' ) {
+ this.dataSetCodes = this.dataSetCodes.concat(dataSetCodes);
+ } else {
+ this.dataSetCodes.push(dataSetCodes);
+ }
};
prototype.getDataSetCodes = function() {
return this.dataSetCodes;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/service/execute/ReportingServiceExecutionOptions.js b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/service/execute/ReportingServiceExecutionOptions.js
index 33a4f7067b2907476315586953fc36d307062043..375c988347351c91fcfe8a3445d0de8d5580d959 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/service/execute/ReportingServiceExecutionOptions.js
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/service/execute/ReportingServiceExecutionOptions.js
@@ -7,7 +7,11 @@ define([ "stjs"], function(stjs) {
constructor.serialVersionUID = 1;
prototype.dataSetCodes = null;
prototype.withDataSets = function(dataSetCodes) {
- this.dataSetCodes = dataSetCodes;
+ if (Object.prototype.toString.call( dataSetCodes ) === '[object Array]' ) {
+ this.dataSetCodes = this.dataSetCodes.concat(dataSetCodes);
+ } else {
+ this.dataSetCodes.push(dataSetCodes);
+ }
};
prototype.getDataSetCodes = function() {
return this.dataSetCodes;
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/CommonServerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/CommonServerTest.java
index 7b5e16a3bf7a6c2ee36417a3130cebe08c90b73c..2c81d317054df145084aa61c5ff653722e2d8aa0 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/CommonServerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/CommonServerTest.java
@@ -2107,7 +2107,7 @@ public class CommonServerTest extends SystemTestCase
commonServer.createReportFromDatasets(session.getSessionToken(), serviceKey, Arrays.asList(dataSetCode));
} catch (Exception e)
{
- assertEquals(e.getMessage(), "Data store 'STANDARD' does not have '" + serviceKey + "' report configured.");
+ assertEquals(e.getMessage(), "Data store 'STANDARD' does not have '" + serviceKey + "' reporting plugin configured.");
}
} else
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/CommonAuthorizationSystemTestService.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/CommonAuthorizationSystemTestService.java
index 925891f6641aa0301fbc57f3a750e0640bb15c14..57c6a533170bfe109056cba8bdb3707b2f834b28 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/CommonAuthorizationSystemTestService.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/CommonAuthorizationSystemTestService.java
@@ -26,10 +26,13 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import org.springframework.transaction.annotation.Transactional;
+import ch.systemsx.cisd.openbis.generic.server.DataStoreServiceRegistrator;
+import ch.systemsx.cisd.openbis.generic.server.IDataStoreServiceRegistrator;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
import ch.systemsx.cisd.openbis.generic.shared.basic.IIdHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Deletion;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletionType;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
@@ -66,6 +69,17 @@ public class CommonAuthorizationSystemTestService
private ICommonServer commonServer;
private List<IIdHolder> createdObjects;
+
+ private IDataStoreServiceRegistrator dataStoreServiceRegistrator;
+
+ private IDataStoreServiceRegistrator getDataStoreServiceRegistrator()
+ {
+ if (dataStoreServiceRegistrator == null)
+ {
+ dataStoreServiceRegistrator = new DataStoreServiceRegistrator(daoFactory);
+ }
+ return dataStoreServiceRegistrator;
+ }
@Transactional
public void createPerson(PersonPE person)
@@ -115,6 +129,12 @@ public class CommonAuthorizationSystemTestService
public void createType(EntityTypePE entityType, EntityKind entityKind)
{
daoFactory.getEntityTypeDAO(entityKind).createOrUpdateEntityType(entityType);
+ if (EntityKind.DATA_SET.equals(entityKind))
+ {
+ DataSetType dataSetType = new DataSetType();
+ dataSetType.setCode(entityType.getCode());
+ getDataStoreServiceRegistrator().register(dataSetType);
+ }
createdObjects.add(entityType);
}
diff --git a/openbis_all/source/bash/build/branch.sh b/openbis_all/source/bash/build/branch.sh
index c433d8f0eeba80940fdf08696913fb1be45b83cf..576581e2a327a4dff4e20b2da804148c84dee0e4 100755
--- a/openbis_all/source/bash/build/branch.sh
+++ b/openbis_all/source/bash/build/branch.sh
@@ -10,7 +10,7 @@ then
fi
# exit if branch already exists
-branch_heads=`git ls-remote --heads git@sissource.ethz.ch:sis/openbis.git $1`
+branch_heads=`git ls-remote --heads git@sissource.ethz.ch:sispub/openbis.git $1`
if [ -n "$branch_heads" ]; then
echo "Branch already exists!"
exit 1
diff --git a/openbis_all/source/bash/build/build.sh b/openbis_all/source/bash/build/build.sh
index 9744734ce2614d2cbd51c4712fa72e6dde7de258..769c63088399140ccb669cdf8d40c23777cd2f10 100755
--- a/openbis_all/source/bash/build/build.sh
+++ b/openbis_all/source/bash/build/build.sh
@@ -37,12 +37,12 @@ if [ $? -ne 0 ]; then echo "Tag does not exist!"; exit 1; fi
# build
cd openbis_standard_technologies
-./gradlew :clientsAndApis -x test
-./gradlew :generateJavadoc
+./gradlew :clean :clientsAndApis -x test
+./gradlew :clean :generateJavadoc
cd ../installation
-./gradlew :build -x test
+./gradlew :clean :build -x test
cd ../plasmid
-./gradlew :build -x test
+./gradlew :clean :build -x test
cd ../..
diff --git a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/execute/AbstractExecutionOptionsWithParameters.java b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/execute/AbstractExecutionOptionsWithParameters.java
index 91a170c94478989bbd97bf86885906d1dce732d5..3e71de2ce6a9e3547ac4eff45f28e6325e63000f 100644
--- a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/execute/AbstractExecutionOptionsWithParameters.java
+++ b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/execute/AbstractExecutionOptionsWithParameters.java
@@ -45,4 +45,10 @@ public abstract class AbstractExecutionOptionsWithParameters<EO extends Abstract
return parameters;
}
+ @Override
+ public String toString()
+ {
+ return getClass().getSimpleName() + ": parameters=" + parameters;
+ }
+
}
diff --git a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/execute/ProcessingServiceExecutionOptions.java b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/execute/ProcessingServiceExecutionOptions.java
index 2c4506c7107a3a6ed6b0996008fee2308d93c398..962578beb4a1dc0938d27bf3bdbdaf2905ea330f 100644
--- a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/execute/ProcessingServiceExecutionOptions.java
+++ b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/execute/ProcessingServiceExecutionOptions.java
@@ -52,4 +52,10 @@ public class ProcessingServiceExecutionOptions
return dataSetCodes;
}
+ @Override
+ public String toString()
+ {
+ return super.toString() + ", data sets=" + dataSetCodes;
+ }
+
}
diff --git a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/execute/ReportingServiceExecutionOptions.java b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/execute/ReportingServiceExecutionOptions.java
index fd6caa7b40c1ca314ef0f35a306f10ee834d04ca..29f465fca3160c7a5fbfacf0c4bf219b43121a4b 100644
--- a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/execute/ReportingServiceExecutionOptions.java
+++ b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/execute/ReportingServiceExecutionOptions.java
@@ -51,4 +51,10 @@ public class ReportingServiceExecutionOptions implements Serializable, IDataSetC
return dataSetCodes;
}
+ @Override
+ public String toString()
+ {
+ return getClass().getSimpleName() + ": data sets=" + dataSetCodes;
+ }
+
}
diff --git a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/execute/SearchDomainServiceExecutionOptions.java b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/execute/SearchDomainServiceExecutionOptions.java
index 6d12a23f09b9febc36c4d0fd1a3eb2c78cf5eb12..87da62444aa538965f0748ff9d0c822affd6ed3f 100644
--- a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/execute/SearchDomainServiceExecutionOptions.java
+++ b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/execute/SearchDomainServiceExecutionOptions.java
@@ -53,4 +53,19 @@ public class SearchDomainServiceExecutionOptions extends AbstractExecutionOption
return searchString;
}
+ @Override
+ public String toString()
+ {
+ StringBuilder builder = new StringBuilder(super.toString());
+ if (searchString != null)
+ {
+ builder.append(", search string='").append(searchString).append("'");
+ }
+ if (preferredSearchDomain != null)
+ {
+ builder.append(", preferred serach domain=").append(preferredSearchDomain);
+ }
+ return builder.toString();
+ }
+
}
diff --git a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/id/DssServicePermId.java b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/id/DssServicePermId.java
index 959be45f2bb4b2357c09fb92f377088f5512b4f0..5f83f235e5f7e03fd234fbb8973307799a272981 100644
--- a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/id/DssServicePermId.java
+++ b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/service/id/DssServicePermId.java
@@ -33,21 +33,22 @@ public class DssServicePermId extends ObjectPermId implements IDssServiceId
@JsonProperty
private IDataStoreId dataStoreId;
+
+ public DssServicePermId(String permId)
+ {
+ this(permId, null);
+ }
public DssServicePermId(String permId, IDataStoreId dataStoreId)
{
super(permId);
- if (dataStoreId == null)
- {
- throw new IllegalArgumentException("Data store id cannot be null.");
- }
this.dataStoreId = dataStoreId;
}
@Override
public String toString()
{
- return dataStoreId + ":" + super.toString();
+ return dataStoreId == null ? super.toString() : dataStoreId + ":" + super.toString();
}
@Override
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exports-api.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exports-api.py
index ba912cf8d232b5daee7614c97f53b39b781b282c..28e199de7ec1a2058de164a844a54d93aac3ea2d 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exports-api.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exports-api.py
@@ -595,7 +595,7 @@ def getFilePath(spaceCode, projCode, expCode, sampCode, dataCode):
def addToZipFile(path, file, zos):
fis = FileInputStream(file);
- zipEntry = ZipEntry(path);
+ zipEntry = ZipEntry(path[1:]); # Making paths relative to make them compatible with Windows zip implementation
zos.putNextEntry(zipEntry);
bytes = jarray.zeros(1024, "b");
diff --git a/openbis_standard_technologies/resource/server/jetty-web.xml b/openbis_standard_technologies/resource/server/jetty-web.xml
index 0ddbc770e44fa5ba1c66e97fcfca0ee7f0777d70..c5d95dbcbaf382e28530bb2113e58d0d5c7fdc34 100644
--- a/openbis_standard_technologies/resource/server/jetty-web.xml
+++ b/openbis_standard_technologies/resource/server/jetty-web.xml
@@ -5,4 +5,9 @@
<Call name="addAliasCheck">
<Arg><New class="org.eclipse.jetty.server.handler.AllowSymLinkAliasChecker"/></Arg>
</Call>
+ <Get name="sessionHandler">
+ <Get name="sessionCookieConfig">
+ <Set name="httpOnly" type="boolean">true</Set>
+ </Get>
+ </Get>
</Configure>
\ No newline at end of file