diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientService.java
index 9ce4d92410bf1a3b88b2952d93f6b4a5b98d801f..a1045527de3f4710e9c0b4fe099d53c000a6565b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientService.java
@@ -360,6 +360,10 @@ public interface ICommonClientService extends IClientService {
*/
public void registerVocabulary(final Vocabulary vocabulary)
throws UserFailureException;
+
+ /** Adds specified terms to the specified vocabulary. */
+ public void addVocabularyTerms(String vocabularyCode, List<String> vocabularyTerms)
+ throws UserFailureException;
/**
* Registers given {@link Project}.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientServiceAsync.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientServiceAsync.java
index 219c0b3a621f692916e00432ef5fd5ebba50dbef..cf5123c7a0ba8cebdd7d633f82033b778f7d50e5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientServiceAsync.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientServiceAsync.java
@@ -19,6 +19,8 @@ package ch.systemsx.cisd.openbis.generic.client.web.client;
import java.util.Date;
import java.util.List;
+import com.google.gwt.user.client.rpc.AsyncCallback;
+
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ExperimentIdentifier;
@@ -55,8 +57,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
-import com.google.gwt.user.client.rpc.AsyncCallback;
-
/**
* Asynchronous version of {@link ICommonClientService}.
*
@@ -299,6 +299,10 @@ public interface ICommonClientServiceAsync extends IClientServiceAsync {
public void registerVocabulary(final Vocabulary vocabulary,
final AsyncCallback<Void> asyncCallback);
+ /** @see ICommonClientService#addVocabularyTerms(String, List) */
+ public void addVocabularyTerms(String vocabularyCode, List<String> vocabularyTerms,
+ AsyncCallback<Void> callback);
+
/** @see ICommonClientService#registerProject(Project) */
public void registerProject(Project project,
final AsyncCallback<Void> projectRegistrationCallback);
@@ -376,5 +380,6 @@ public interface ICommonClientServiceAsync extends IClientServiceAsync {
/** @see ICommonClientService#uploadDataSets(List, String, String) */
public void uploadDataSets(List<String> dataSetCodes, String cifexURL, String password,
- AsyncCallback<Void> abstractAsyncCallback);
+ AsyncCallback<Void> callback);
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/Dict.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/Dict.java
index 2b04cf16b6fce44ddead2a9d65404543d0dd37e5..8638774c6bb5108161c95d37fe7c72746ef4f04e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/Dict.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/Dict.java
@@ -419,6 +419,14 @@ public abstract class Dict {
public static final String TERM_FOR_MATERIALS_USAGE = "TERM_FOR_MATERIALS_USAGE";
public static final String TERM_TOTAL_USAGE = "TERM_TOTAL_USAGE";
+
+ public static final String ADD_VOCABULARY_TERMS_BUTTON = "add_vocabulary_terms_button";
+
+ public static final String ADD_VOCABULARY_TERMS_TITLE = "add_vocabulary_terms_title";
+
+ public static final String ADD_VOCABULARY_TERMS_OK_BUTTON = "add_vocabulary_terms_ok_button";
+
+ public static final String VOCABULARY_TERMS_VALIDATION_MESSAGE = "vocabulary_terms_validation_message";
//
// Project Browser
@@ -484,5 +492,7 @@ public abstract class Dict {
public static final String BUTTON_EDIT = "edit";
+
+
// ----- end generic ------------------
}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/vocabulary/VocabularyTermGrid.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/vocabulary/VocabularyTermGrid.java
index df7b6351757af2a83502d8b88266dae0577c73f6..46e0b7f1a9e7b9ee2d5efbb48d976ff21265fa18 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/vocabulary/VocabularyTermGrid.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/vocabulary/VocabularyTermGrid.java
@@ -18,14 +18,26 @@ package ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.vocabu
import java.util.List;
+import com.extjs.gxt.ui.client.event.ButtonEvent;
+import com.extjs.gxt.ui.client.event.ComponentEvent;
+import com.extjs.gxt.ui.client.event.KeyListener;
+import com.extjs.gxt.ui.client.event.SelectionListener;
+import com.extjs.gxt.ui.client.widget.HorizontalPanel;
+import com.extjs.gxt.ui.client.widget.button.Button;
+import com.extjs.gxt.ui.client.widget.form.TextArea;
+import com.extjs.gxt.ui.client.widget.toolbar.AdapterToolItem;
+
import ch.systemsx.cisd.openbis.generic.client.web.client.ICommonClientServiceAsync;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.IColumnDefinitionKind;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.specific.VocabularyTermColDefKind;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.AbstractSimpleBrowserGrid;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.DisposableComponent;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.SimpleDialog;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IDelegatedAction;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.IColumnDefinition;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
@@ -42,6 +54,20 @@ public class VocabularyTermGrid extends AbstractSimpleBrowserGrid<VocabularyTerm
{
// browser consists of the grid and the paging toolbar
private static final String BROWSER_ID = GenericConstants.ID_PREFIX + "vocabulary-term-browser";
+
+ final class VoidCallback extends AbstractAsyncCallback<Void>
+ {
+ private VoidCallback(IViewContext<?> viewContext)
+ {
+ super(viewContext);
+ }
+
+ @Override
+ protected void process(Void result)
+ {
+ refresh();
+ }
+ }
private final Vocabulary vocabulary;
@@ -56,6 +82,16 @@ public class VocabularyTermGrid extends AbstractSimpleBrowserGrid<VocabularyTerm
{
super(viewContext, createBrowserId(vocabulary), createGridId(vocabulary.getCode()));
this.vocabulary = vocabulary;
+ Button button = new Button(viewContext.getMessage(Dict.ADD_VOCABULARY_TERMS_BUTTON));
+ button.addSelectionListener(new SelectionListener<ButtonEvent>()
+ {
+ @Override
+ public void componentSelected(ButtonEvent ce)
+ {
+ askForNewTerms();
+ }
+ });
+ pagingToolbar.add(new AdapterToolItem(button));
}
public static String createGridId(String vocabularyCode)
@@ -100,4 +136,39 @@ public class VocabularyTermGrid extends AbstractSimpleBrowserGrid<VocabularyTerm
{
viewContext.getService().prepareExportVocabularyTerms(exportCriteria, callback);
}
+
+ private void askForNewTerms()
+ {
+ final TextArea textArea = new TextArea();
+ textArea.setWidth(250);
+ textArea.setHeight(200);
+ textArea.setEmptyText(viewContext.getMessage(Dict.VOCABULARY_TERMS_EMPTY));
+ textArea.setValidator(new VocabularyTermValidator(viewContext, vocabulary.getTerms()));
+ String heading = viewContext.getMessage(Dict.ADD_VOCABULARY_TERMS_TITLE);
+ String okButtonLabel = viewContext.getMessage(Dict.ADD_VOCABULARY_TERMS_OK_BUTTON);
+ HorizontalPanel panel = new HorizontalPanel();
+ panel.setWidth(300);
+ panel.add(textArea);
+ panel.setBorders(true);
+ final SimpleDialog dialog = new SimpleDialog(panel, heading, okButtonLabel, viewContext);
+ textArea.addKeyListener(new KeyListener()
+ {
+ @Override
+ public void handleEvent(ComponentEvent ce)
+ {
+ textArea.validate();
+ dialog.setEnableOfAcceptButton(textArea.isValid());
+ }
+ });
+ dialog.setAcceptAction(new IDelegatedAction()
+ {
+ public void execute()
+ {
+ viewContext.getCommonService().addVocabularyTerms(vocabulary.getCode(),
+ VocabularyTermValidator.getTerms(textArea.getValue()),
+ new VoidCallback(viewContext));
+ }
+ });
+ dialog.show();
+ }
}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/vocabulary/VocabularyTermValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/vocabulary/VocabularyTermValidator.java
index df599fd817a3216a288bfd1311992d8c6cd2565a..f83409e294593e46d28eed67fcc7919d2ba62980 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/vocabulary/VocabularyTermValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/vocabulary/VocabularyTermValidator.java
@@ -1,7 +1,10 @@
package ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.vocabulary;
import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashSet;
import java.util.List;
+import java.util.Set;
import com.extjs.gxt.ui.client.widget.form.TextArea;
import com.extjs.gxt.ui.client.widget.form.Validator;
@@ -10,6 +13,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.CodeField;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMessageProvider;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.StringUtils;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
/**
* A {@link Validator} implementation which validates vocabulary terms in a text area.
@@ -19,10 +23,22 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.Strin
final class VocabularyTermValidator implements Validator<String, TextArea>
{
private final IMessageProvider messageProvider;
+ private Set<String> existingTerms;
VocabularyTermValidator(final IMessageProvider messageProvider)
+ {
+ this(messageProvider, Collections.<VocabularyTerm>emptyList());
+ }
+
+ public VocabularyTermValidator(final IMessageProvider messageProvider,
+ List<VocabularyTerm> terms)
{
this.messageProvider = messageProvider;
+ existingTerms = new HashSet<String>();
+ for (VocabularyTerm vocabularyTerm : terms)
+ {
+ existingTerms.add(vocabularyTerm.getCode());
+ }
}
final static List<String> getTerms(final String value)
@@ -60,6 +76,10 @@ final class VocabularyTermValidator implements Validator<String, TextArea>
{
return messageProvider.getMessage(Dict.INVALID_CODE_MESSAGE, "Term '" + term + "'");
}
+ if (existingTerms.contains(term.toUpperCase()))
+ {
+ return messageProvider.getMessage(Dict.VOCABULARY_TERMS_VALIDATION_MESSAGE, term);
+ }
}
return null;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/widget/SimpleDialog.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/widget/SimpleDialog.java
index 86bb46bcb45a01117cc28fd5b8ba76d554a85501..88657cf1d7a26e670788224d4de650b6e79e461d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/widget/SimpleDialog.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/widget/SimpleDialog.java
@@ -42,10 +42,13 @@ public class SimpleDialog extends Dialog
private final IMessageProvider messageProvider;
+ private final Button acceptButton;
+
private IDelegatedAction acceptActionOrNull;
private IDelegatedAction cancelActionOrNull;
+
public SimpleDialog(final Widget widget, final String heading, String acceptButtonLabel,
IMessageProvider messageProvider)
{
@@ -58,7 +61,8 @@ public class SimpleDialog extends Dialog
setModal(true);
add(widget);
- addButton(createAcceptButton(acceptButtonLabel));
+ acceptButton = createAcceptButton(acceptButtonLabel);
+ addButton(acceptButton);
addButton(createCancelButton());
addWindowListener(new WindowListener()
@@ -70,7 +74,12 @@ public class SimpleDialog extends Dialog
}
});
}
-
+
+ public void setEnableOfAcceptButton(boolean enable)
+ {
+ acceptButton.setEnabled(enable);
+ }
+
private Button createCancelButton()
{
final Button button =
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java
index ec17b31014827f9288d7e0d143eea50fd749515c..f195acd9b5e637902ddd554dc249393dceafc8ed 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java
@@ -122,8 +122,9 @@ import ch.systemsx.cisd.openbis.plugin.AbstractClientService;
* @author Franz-Josef Elmer
*/
public final class CommonClientService extends AbstractClientService implements
- ICommonClientService {
- private final ICommonServer commonServer;
+ ICommonClientService
+{
+ private final ICommonServer commonServer;
private String dataStoreBaseURL;
@@ -139,12 +140,13 @@ public final class CommonClientService extends AbstractClientService implements
this.dataStoreBaseURL = dataStoreBaseURL + "/" + DATA_STORE_SERVER_WEB_APPLICATION_NAME;
}
- @Override
- protected final IServer getServer() {
- return commonServer;
- }
+ @Override
+ protected final IServer getServer()
+ {
+ return commonServer;
+ }
- // ----------- export and listing with cache generic functionality
+ // ----------- export and listing with cache generic functionality
@SuppressWarnings("unchecked")
private final <K> IResultSetManager<K> getResultSetManager()
@@ -159,802 +161,914 @@ public final class CommonClientService extends AbstractClientService implements
.getAttribute(SessionConstants.OPENBIS_RESULT_SET_MANAGER);
}
- @SuppressWarnings("unchecked")
- private final <T> CacheManager<String, T> getExportManager() {
- return (CacheManager<String, T>) getHttpSession().getAttribute(
- SessionConstants.OPENBIS_EXPORT_MANAGER);
- }
-
- /**
- * Returns and removes cached export criteria.
- */
- private final <T> TableExportCriteria<T> getAndRemoveExportCriteria(
- final String exportDataKey) {
- final CacheManager<String, TableExportCriteria<T>> exportManager = getExportManager();
- final TableExportCriteria<T> exportCriteria = exportManager
- .tryGetData(exportDataKey);
- assert exportCriteria != null : "No export criteria found at key "
- + exportDataKey;
- getExportManager().removeData(exportDataKey);
- return exportCriteria;
- }
-
- private final <T> List<T> fetchCachedEntities(
- final TableExportCriteria<T> exportCriteria) {
- final IResultSetManager<String> resultSetManager = getResultSetManager();
- IResultSetConfig<String, T> resultSetConfig = createExportListCriteria(exportCriteria);
- IOriginalDataProvider<T> dummyDataProvider = createDummyDataProvider();
- final IResultSet<String, T> result = resultSetManager.getResultSet(
- resultSetConfig, dummyDataProvider);
- final ResultSet<T> entities = ResultSetTranslator.translate(result);
- return entities.getList();
- }
-
- private static <T> IOriginalDataProvider<T> createDummyDataProvider() {
- return new IOriginalDataProvider<T>() {
- public List<T> getOriginalData() throws UserFailureException {
- throw new IllegalStateException("Data not found in the cache");
- }
- };
- }
-
- private static <T> IResultSetConfig<String, T> createExportListCriteria(
- final TableExportCriteria<T> exportCriteria) {
- final DefaultResultSetConfig<String, T> criteria = DefaultResultSetConfig
- .createFetchAll();
- criteria.setSortInfo(exportCriteria.getSortInfo());
- criteria.setFilterInfos(exportCriteria.getFilterInfos());
- criteria.setResultSetKey(exportCriteria.getResultSetKey());
- return criteria;
- }
-
- private <T> ResultSet<T> listEntities(
- final IResultSetConfig<String, T> criteria,
- IOriginalDataProvider<T> dataProvider)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final IResultSetManager<String> resultSetManager = getResultSetManager();
- final IResultSet<String, T> result = resultSetManager.getResultSet(
- criteria, dataProvider);
- return ResultSetTranslator.translate(result);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- /**
- * Assumes that preparation of the export (
- * {@link #prepareExportSamples(TableExportCriteria)} has been invoked
- * before and returned with an exportDataKey passed here as a parameter.
- */
- public final String getExportTable(final String exportDataKey,
- final String lineSeparator) {
- // NOTE: no generics in GWT
- return getGenericExportTable(exportDataKey, lineSeparator);
- }
-
- private final <T> String getGenericExportTable(final String exportDataKey,
- final String lineSeparator) {
- try {
- // Not directly needed but this refreshes the session.
- getSessionToken();
- final TableExportCriteria<T> exportCriteria = getAndRemoveExportCriteria(exportDataKey);
- final List<T> entities = fetchCachedEntities(exportCriteria);
- return TSVRenderer.createTable(entities, exportCriteria
- .getColumnDefs(), lineSeparator);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- private <T> String prepareExportEntities(TableExportCriteria<T> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- // Not directly needed but this refreshes the session.
- getSessionToken();
- final CacheManager<String, TableExportCriteria<T>> exportManager = getExportManager();
- return exportManager.saveData(criteria);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public final void removeResultSet(final String resultSetKey)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- // Not directly needed but this refreshes the session.
- getSessionToken();
- getResultSetManager().removeResultSet(resultSetKey);
- } catch (final ch.systemsx.cisd.common.exceptions.UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- // --------------- end export & listing
-
- //
- // IGenericClientService
- //
-
- public final List<Group> listGroups(final String databaseInstanceCode) {
- try {
- final String sessionToken = getSessionToken();
- final DatabaseInstanceIdentifier identifier = new DatabaseInstanceIdentifier(
- databaseInstanceCode);
- final List<Group> result = new ArrayList<Group>();
- final List<GroupPE> groups = commonServer.listGroups(sessionToken,
- identifier);
- for (final GroupPE group : groups) {
- result.add(GroupTranslator.translate(group));
- }
- return result;
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public final void registerGroup(final String groupCode,
- final String descriptionOrNull, final String groupLeaderOrNull) {
- try {
- final String sessionToken = getSessionToken();
- commonServer.registerGroup(sessionToken, groupCode,
- descriptionOrNull, groupLeaderOrNull);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public final List<Person> listPersons()
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
-
- try {
- final String sessionToken = getSessionToken();
- final List<Person> result = new ArrayList<Person>();
- final List<PersonPE> persons = commonServer
- .listPersons(sessionToken);
- for (final PersonPE person : persons) {
- result.add(PersonTranslator.translate(person));
- }
- return result;
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public final void registerPerson(final String code) {
- try {
- final String sessionToken = getSessionToken();
- commonServer.registerPerson(sessionToken, code);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public final List<RoleAssignment> listRoles()
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- final List<RoleAssignment> result = new ArrayList<RoleAssignment>();
- final List<RoleAssignmentPE> roles = commonServer
- .listRoles(sessionToken);
- for (final RoleAssignmentPE role : roles) {
- result.add(RoleAssignmentTranslator.translate(role));
- }
- return result;
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public final void registerGroupRole(final RoleSetCode roleSetCode,
- final String group, final String person)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- final GroupIdentifier groupIdentifier = new GroupIdentifier(
- DatabaseInstanceIdentifier.HOME, group);
- commonServer.registerGroupRole(sessionToken, RoleCodeTranslator
- .translate(roleSetCode), groupIdentifier, person);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public final void registerInstanceRole(final RoleSetCode roleSetCode,
- final String person)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- commonServer.registerInstanceRole(sessionToken, RoleCodeTranslator
- .translate(roleSetCode), person);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public final void deleteGroupRole(final RoleSetCode roleSetCode,
- final String group, final String person)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- final GroupIdentifier groupIdentifier = new GroupIdentifier(
- DatabaseInstanceIdentifier.HOME, group);
- commonServer.deleteGroupRole(sessionToken, RoleCodeTranslator
- .translate(roleSetCode), groupIdentifier, person);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
-
- }
-
- public final void deleteInstanceRole(final RoleSetCode roleSetCode,
- final String person)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- commonServer.deleteInstanceRole(sessionToken, RoleCodeTranslator
- .translate(roleSetCode), person);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
-
- }
-
- public final List<SampleType> listSampleTypes()
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- final List<SampleTypePE> sampleTypes = commonServer
- .listSampleTypes(sessionToken);
- final List<SampleType> result = new ArrayList<SampleType>();
- for (final SampleTypePE sampleTypePE : sampleTypes) {
- result.add(SampleTypeTranslator.translate(sampleTypePE));
- }
- return result;
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- // --------- methods preparing exported content. Note: GWT does not support
- // generic methods :(
-
- public final String prepareExportSamples(
- final TableExportCriteria<Sample> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- return prepareExportEntities(criteria);
- }
-
- public final String prepareExportExperiments(
- final TableExportCriteria<Experiment> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- return prepareExportEntities(criteria);
- }
-
- public final String prepareExportMatchingEntities(
- final TableExportCriteria<MatchingEntity> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- return prepareExportEntities(criteria);
- }
-
- public String prepareExportPropertyTypes(
- TableExportCriteria<PropertyType> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- return prepareExportEntities(criteria);
- }
-
- public String prepareExportPropertyTypeAssignments(
- TableExportCriteria<EntityTypePropertyType<?>> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- return prepareExportEntities(criteria);
- }
-
- public String prepareExportProjects(TableExportCriteria<Project> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- return prepareExportEntities(criteria);
- }
-
- public String prepareExportVocabularies(
- final TableExportCriteria<Vocabulary> criteria)
- throws UserFailureException {
- return prepareExportEntities(criteria);
- }
-
- public String prepareExportVocabularyTerms(
- TableExportCriteria<VocabularyTermWithStats> criteria) {
- return prepareExportEntities(criteria);
- }
-
- public String prepareExportMaterialTypes(
- final TableExportCriteria<MaterialType> criteria)
- throws UserFailureException {
- return prepareExportEntities(criteria);
- }
-
- public String prepareExportExperimentTypes(
- final TableExportCriteria<ExperimentType> criteria)
- throws UserFailureException {
- return prepareExportEntities(criteria);
- }
-
- public String prepareExportSampleTypes(
- final TableExportCriteria<SampleType> criteria)
- throws UserFailureException {
- return prepareExportEntities(criteria);
- }
-
- // ---------------- methods which list entities using cache
-
- public final ResultSet<Sample> listSamples(
- final ListSampleCriteria listCriteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- final String sessionToken = getSessionToken();
- return listEntities(listCriteria, new ListSamplesOriginalDataProvider(
- commonServer, sessionToken, listCriteria));
- }
-
- public ResultSet<ExternalData> searchForDataSets(
- DataSetSearchCriteria criteria,
- final IResultSetConfig<String, ExternalData> resultSetConfig)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- final String sessionToken = getSessionToken();
- return listEntities(resultSetConfig,
- new ListDataSetsOriginalDataProvider(commonServer,
- sessionToken, criteria, dataStoreBaseURL));
- }
-
- public final ResultSet<Experiment> listExperiments(
- final ListExperimentsCriteria listCriteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- final String sessionToken = getSessionToken();
- return listEntities(listCriteria,
- new ListExperimentsOriginalDataProvider(commonServer,
- listCriteria, sessionToken));
- }
-
- public ResultSet<PropertyType> listPropertyTypes(
- DefaultResultSetConfig<String, PropertyType> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- return listEntities(criteria,
- new IOriginalDataProvider<PropertyType>() {
- public List<PropertyType> getOriginalData()
- throws UserFailureException {
- return listPropertyTypes();
- }
- });
- }
-
- public final ResultSet<MatchingEntity> listMatchingEntities(
- final SearchableEntity searchableEntityOrNull,
- final String queryText,
- final IResultSetConfig<String, MatchingEntity> resultSetConfig)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- final String sessionToken = getSessionToken();
- final ch.systemsx.cisd.openbis.generic.shared.dto.SearchableEntity[] matchingEntities = SearchableEntityTranslator
- .translate(searchableEntityOrNull);
- return listEntities(resultSetConfig,
- new ListMatchingEntitiesOriginalDataProvider(commonServer,
- sessionToken, matchingEntities, queryText));
- }
-
- public ResultSet<EntityTypePropertyType<?>> listPropertyTypeAssignments(
- DefaultResultSetConfig<String, EntityTypePropertyType<?>> criteria) {
- return listEntities(criteria,
- new IOriginalDataProvider<EntityTypePropertyType<?>>() {
- public List<EntityTypePropertyType<?>> getOriginalData()
- throws UserFailureException {
- return extractAssignments(listPropertyTypes());
- }
- });
- }
-
- private static List<EntityTypePropertyType<?>> extractAssignments(
- List<PropertyType> listPropertyTypes) {
- List<EntityTypePropertyType<?>> result = new ArrayList<EntityTypePropertyType<?>>();
- for (PropertyType propertyType : listPropertyTypes) {
- extractAssignments(result, propertyType);
- }
- return result;
- }
-
- private static void extractAssignments(
- List<EntityTypePropertyType<?>> result,
- final PropertyType propertyType) {
- for (ExperimentTypePropertyType etpt : propertyType
- .getExperimentTypePropertyTypes()) {
- result.add(etpt);
- }
- for (SampleTypePropertyType etpt : propertyType
- .getSampleTypePropertyTypes()) {
- result.add(etpt);
- }
- for (MaterialTypePropertyType etpt : propertyType
- .getMaterialTypePropertyTypes()) {
- result.add(etpt);
- }
- }
-
- public ResultSet<Project> listProjects(
- DefaultResultSetConfig<String, Project> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- return listEntities(criteria, new IOriginalDataProvider<Project>() {
- public List<Project> getOriginalData() throws UserFailureException {
- return listProjects();
- }
- });
- }
-
- private List<Project> listProjects()
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- final List<ProjectPE> projects = commonServer
- .listProjects(sessionToken);
- return ProjectTranslator.translate(projects);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public ResultSet<Vocabulary> listVocabularies(final boolean withTerms,
- final boolean excludeInternal,
- DefaultResultSetConfig<String, Vocabulary> criteria)
- throws UserFailureException {
- return listEntities(criteria, new IOriginalDataProvider<Vocabulary>() {
- public List<Vocabulary> getOriginalData()
- throws UserFailureException {
- return listVocabularies(withTerms, excludeInternal);
- }
- });
- }
-
- private List<Vocabulary> listVocabularies(final boolean withTerms,
- boolean excludeInternal)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- final List<VocabularyPE> vocabularies = commonServer
- .listVocabularies(sessionToken, withTerms, excludeInternal);
- return BeanUtils.createBeanList(Vocabulary.class, vocabularies,
- DtoConverters.getVocabularyConverter());
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public ResultSet<VocabularyTermWithStats> listVocabularyTerms(
- final Vocabulary vocabulary,
- DefaultResultSetConfig<String, VocabularyTermWithStats> criteria) {
- return listEntities(criteria,
- new IOriginalDataProvider<VocabularyTermWithStats>() {
- public List<VocabularyTermWithStats> getOriginalData()
- throws UserFailureException {
- List<ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyTermWithStats> terms = commonServer
- .listVocabularyTerms(getSessionToken(),
- vocabulary);
- return VocabularyTermTranslator.translate(terms);
- }
- });
- }
-
- public ResultSet<? extends EntityType> listMaterialTypes(
- DefaultResultSetConfig<String, MaterialType> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- return listEntities(criteria,
- new IOriginalDataProvider<MaterialType>() {
- public List<MaterialType> getOriginalData()
- throws UserFailureException {
- return listMaterialTypes();
- }
- });
- }
-
- public ResultSet<? extends EntityType> listSampleTypes(
- DefaultResultSetConfig<String, SampleType> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- return listEntities(criteria, new IOriginalDataProvider<SampleType>() {
- public List<SampleType> getOriginalData()
- throws UserFailureException {
- return listSampleTypes();
- }
- });
- }
-
- public ResultSet<? extends EntityType> listExperimentTypes(
- DefaultResultSetConfig<String, ExperimentType> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- return listEntities(criteria,
- new IOriginalDataProvider<ExperimentType>() {
- public List<ExperimentType> getOriginalData()
- throws UserFailureException {
- return listExperimentTypes();
- }
- });
- }
-
- public ResultSet<ExternalData> listSampleDataSets(
- final String sampleIdentifier,
- DefaultResultSetConfig<String, ExternalData> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- return listEntities(criteria,
- new IOriginalDataProvider<ExternalData>() {
- public List<ExternalData> getOriginalData()
- throws UserFailureException {
- final String sessionToken = getSessionToken();
- final SampleIdentifier identifier = SampleIdentifierFactory
- .parse(sampleIdentifier);
- final List<ExternalDataPE> externalData = commonServer
- .listExternalData(sessionToken, identifier);
- return ExternalDataTranslator.translate(externalData,
- dataStoreBaseURL);
- }
- });
- }
-
- public ResultSet<ExternalData> listExperimentDataSets(
- final String experimentIdentifier,
- DefaultResultSetConfig<String, ExternalData> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- return listEntities(criteria,
- new IOriginalDataProvider<ExternalData>() {
-
- public List<ExternalData> getOriginalData()
- throws UserFailureException {
- final String sessionToken = getSessionToken();
- final ExperimentIdentifier identifier = new ExperimentIdentifierFactory(
- experimentIdentifier).createIdentifier();
- final List<ExternalDataPE> externalData = commonServer
- .listExternalData(sessionToken, identifier);
- return ExternalDataTranslator.translate(externalData,
- dataStoreBaseURL);
- }
-
- });
- }
-
- // ---------------- end list using cache ----------
-
- public final List<SearchableEntity> listSearchableEntities()
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- // Not directly needed but this refreshes the session.
- getSessionToken();
- final List<SearchableEntity> searchableEntities = BeanUtils
- .createBeanList(
- SearchableEntity.class,
- Arrays
- .asList(ch.systemsx.cisd.openbis.generic.shared.dto.SearchableEntity
- .values()));
- Collections.sort(searchableEntities);
- return searchableEntities;
- } catch (final ch.systemsx.cisd.common.exceptions.UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public List<ExperimentType> listExperimentTypes()
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- final List<ExperimentType> result = new ArrayList<ExperimentType>();
- final List<ExperimentTypePE> experiments = commonServer
- .listExperimentTypes(sessionToken);
- for (final ExperimentTypePE expType : experiments) {
- result.add(ExperimentTranslator.translate(expType));
- }
- return result;
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- private List<PropertyType> listPropertyTypes()
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- final List<PropertyTypePE> propertyTypes = commonServer
- .listPropertyTypes(sessionToken);
- return PropertyTypeTranslator.translate(propertyTypes);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public final List<DataType> listDataTypes()
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- final List<DataTypePE> dataTypes = commonServer
- .listDataTypes(sessionToken);
- return BeanUtils.createBeanList(DataType.class, dataTypes,
- DtoConverters.getDataTypeConverter());
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public String assignPropertyType(final EntityKind entityKind,
- final String propertyTypeCode, final String entityTypeCode,
- final boolean isMandatory, final String defaultValue)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- return commonServer.assignPropertyType(sessionToken, DtoConverters
- .convertEntityKind(entityKind), propertyTypeCode,
- entityTypeCode, isMandatory, defaultValue);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public final void registerPropertyType(final PropertyType propertyType)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- assert propertyType != null : "Unspecified property type.";
- try {
- final String sessionToken = getSessionToken();
- commonServer.registerPropertyType(sessionToken, propertyType);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public final void registerVocabulary(final Vocabulary vocabulary)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- assert vocabulary != null : "Unspecified vocabulary.";
- try {
- final String sessionToken = getSessionToken();
- commonServer.registerVocabulary(sessionToken, vocabulary);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public void registerProject(Project project)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- assert project != null : "Unspecified project.";
- try {
- final String sessionToken = getSessionToken();
- final ProjectIdentifier projectIdentifier = new ProjectIdentifierFactory(
- project.getIdentifier()).createIdentifier();
- Person leader = project.getProjectLeader();
- final String leaderId = leader == null ? null : project
- .getProjectLeader().getUserId();
- commonServer.registerProject(sessionToken, projectIdentifier,
- project.getDescription(), leaderId);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public String prepareExportDataSetSearchHits(
- TableExportCriteria<ExternalData> exportCriteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- return prepareExportEntities(exportCriteria);
- }
-
- public List<MaterialType> listMaterialTypes()
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- final List<MaterialType> result = new ArrayList<MaterialType>();
- final List<MaterialTypePE> projects = commonServer
- .listMaterialTypes(sessionToken);
- for (final MaterialTypePE expType : projects) {
- result.add(MaterialTypeTranslator.translate(expType));
- }
- return result;
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public List<DataSetType> listDataSetTypes()
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- final List<DataSetType> result = new ArrayList<DataSetType>();
- final List<DataSetTypePE> types = commonServer
- .listDataSetTypes(sessionToken);
- for (final DataSetTypePE type : types) {
- result.add(DataSetTypeTranslator.translate(type));
- }
- return result;
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public ResultSet<Material> listMaterials(ListMaterialCriteria criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- final String sessionToken = getSessionToken();
- return listEntities(criteria, new ListMaterialOriginalDataProvider(
- commonServer, sessionToken, criteria));
- }
-
- public String prepareExportMaterials(TableExportCriteria<Material> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- return prepareExportEntities(criteria);
- }
-
- public void registerMaterialType(MaterialType entityType)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- commonServer.registerMaterialType(sessionToken, entityType);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public void registerExperimentType(ExperimentType entityType)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- commonServer.registerExperimentType(sessionToken, entityType);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public void registerSampleType(SampleType entityType)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- commonServer.registerSampleType(sessionToken, entityType);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- private final static AttachmentPE createAttachment(String fileName,
- final byte[] content) {
- final AttachmentPE attachment = new AttachmentPE();
- attachment.setFileName(fileName);
- final AttachmentContentPE attachmentContent = new AttachmentContentPE();
- attachmentContent.setValue(content);
- attachment.setAttachmentContent(attachmentContent);
- return attachment;
- }
-
- public void updateExperiment(String sessionKey,
- String experimentIdentifier, List<ExperimentProperty> properties,
- String newProjectIdentifier, Date version)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
-
- UploadedFilesBean uploadedFiles = null;
- HttpSession session = null;
- try {
- final String sessionToken = getSessionToken();
- session = getHttpSession();
- uploadedFiles = (UploadedFilesBean) session
- .getAttribute(sessionKey);
- List<AttachmentPE> attachments = new ArrayList<AttachmentPE>();
- if (uploadedFiles != null) {
- for (final IUncheckedMultipartFile multipartFile : uploadedFiles
- .iterable()) {
- String fileName = multipartFile.getOriginalFilename();
- byte[] content = multipartFile.getBytes();
- attachments.add(createAttachment(fileName, content));
- }
- }
- final ExperimentIdentifier identifier = new ExperimentIdentifierFactory(
- experimentIdentifier).createIdentifier();
- final ProjectIdentifier project = new ProjectIdentifierFactory(
- newProjectIdentifier).createIdentifier();
- commonServer.editExperiment(sessionToken, identifier, properties,
- attachments, project, version);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- } finally {
- if (uploadedFiles != null) {
- uploadedFiles.deleteTransferredFiles();
- }
- if (session != null) {
- session.removeAttribute(sessionKey);
- }
- }
-
- }
+ @SuppressWarnings("unchecked")
+ private final <T> CacheManager<String, T> getExportManager()
+ {
+ return (CacheManager<String, T>) getHttpSession().getAttribute(
+ SessionConstants.OPENBIS_EXPORT_MANAGER);
+ }
+
+ /**
+ * Returns and removes cached export criteria.
+ */
+ private final <T> TableExportCriteria<T> getAndRemoveExportCriteria(final String exportDataKey)
+ {
+ final CacheManager<String, TableExportCriteria<T>> exportManager = getExportManager();
+ final TableExportCriteria<T> exportCriteria = exportManager.tryGetData(exportDataKey);
+ assert exportCriteria != null : "No export criteria found at key " + exportDataKey;
+ getExportManager().removeData(exportDataKey);
+ return exportCriteria;
+ }
+
+ private final <T> List<T> fetchCachedEntities(final TableExportCriteria<T> exportCriteria)
+ {
+ final IResultSetManager<String> resultSetManager = getResultSetManager();
+ IResultSetConfig<String, T> resultSetConfig = createExportListCriteria(exportCriteria);
+ IOriginalDataProvider<T> dummyDataProvider = createDummyDataProvider();
+ final IResultSet<String, T> result =
+ resultSetManager.getResultSet(resultSetConfig, dummyDataProvider);
+ final ResultSet<T> entities = ResultSetTranslator.translate(result);
+ return entities.getList();
+ }
+
+ private static <T> IOriginalDataProvider<T> createDummyDataProvider()
+ {
+ return new IOriginalDataProvider<T>()
+ {
+ public List<T> getOriginalData() throws UserFailureException
+ {
+ throw new IllegalStateException("Data not found in the cache");
+ }
+ };
+ }
+
+ private static <T> IResultSetConfig<String, T> createExportListCriteria(
+ final TableExportCriteria<T> exportCriteria)
+ {
+ final DefaultResultSetConfig<String, T> criteria = DefaultResultSetConfig.createFetchAll();
+ criteria.setSortInfo(exportCriteria.getSortInfo());
+ criteria.setFilterInfos(exportCriteria.getFilterInfos());
+ criteria.setResultSetKey(exportCriteria.getResultSetKey());
+ return criteria;
+ }
+
+ private <T> ResultSet<T> listEntities(final IResultSetConfig<String, T> criteria,
+ IOriginalDataProvider<T> dataProvider)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final IResultSetManager<String> resultSetManager = getResultSetManager();
+ final IResultSet<String, T> result =
+ resultSetManager.getResultSet(criteria, dataProvider);
+ return ResultSetTranslator.translate(result);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ /**
+ * Assumes that preparation of the export ( {@link #prepareExportSamples(TableExportCriteria)}
+ * has been invoked before and returned with an exportDataKey passed here as a parameter.
+ */
+ public final String getExportTable(final String exportDataKey, final String lineSeparator)
+ {
+ // NOTE: no generics in GWT
+ return getGenericExportTable(exportDataKey, lineSeparator);
+ }
+
+ private final <T> String getGenericExportTable(final String exportDataKey,
+ final String lineSeparator)
+ {
+ try
+ {
+ // Not directly needed but this refreshes the session.
+ getSessionToken();
+ final TableExportCriteria<T> exportCriteria = getAndRemoveExportCriteria(exportDataKey);
+ final List<T> entities = fetchCachedEntities(exportCriteria);
+ return TSVRenderer.createTable(entities, exportCriteria.getColumnDefs(), lineSeparator);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ private <T> String prepareExportEntities(TableExportCriteria<T> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ // Not directly needed but this refreshes the session.
+ getSessionToken();
+ final CacheManager<String, TableExportCriteria<T>> exportManager = getExportManager();
+ return exportManager.saveData(criteria);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public final void removeResultSet(final String resultSetKey)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ // Not directly needed but this refreshes the session.
+ getSessionToken();
+ getResultSetManager().removeResultSet(resultSetKey);
+ } catch (final ch.systemsx.cisd.common.exceptions.UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ // --------------- end export & listing
+
+ //
+ // IGenericClientService
+ //
+
+ public final List<Group> listGroups(final String databaseInstanceCode)
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ final DatabaseInstanceIdentifier identifier =
+ new DatabaseInstanceIdentifier(databaseInstanceCode);
+ final List<Group> result = new ArrayList<Group>();
+ final List<GroupPE> groups = commonServer.listGroups(sessionToken, identifier);
+ for (final GroupPE group : groups)
+ {
+ result.add(GroupTranslator.translate(group));
+ }
+ return result;
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public final void registerGroup(final String groupCode, final String descriptionOrNull,
+ final String groupLeaderOrNull)
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ commonServer.registerGroup(sessionToken, groupCode, descriptionOrNull,
+ groupLeaderOrNull);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public final List<Person> listPersons()
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+
+ try
+ {
+ final String sessionToken = getSessionToken();
+ final List<Person> result = new ArrayList<Person>();
+ final List<PersonPE> persons = commonServer.listPersons(sessionToken);
+ for (final PersonPE person : persons)
+ {
+ result.add(PersonTranslator.translate(person));
+ }
+ return result;
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public final void registerPerson(final String code)
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ commonServer.registerPerson(sessionToken, code);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public final List<RoleAssignment> listRoles()
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ final List<RoleAssignment> result = new ArrayList<RoleAssignment>();
+ final List<RoleAssignmentPE> roles = commonServer.listRoles(sessionToken);
+ for (final RoleAssignmentPE role : roles)
+ {
+ result.add(RoleAssignmentTranslator.translate(role));
+ }
+ return result;
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public final void registerGroupRole(final RoleSetCode roleSetCode, final String group,
+ final String person)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ final GroupIdentifier groupIdentifier =
+ new GroupIdentifier(DatabaseInstanceIdentifier.HOME, group);
+ commonServer.registerGroupRole(sessionToken, RoleCodeTranslator.translate(roleSetCode),
+ groupIdentifier, person);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public final void registerInstanceRole(final RoleSetCode roleSetCode, final String person)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ commonServer.registerInstanceRole(sessionToken, RoleCodeTranslator
+ .translate(roleSetCode), person);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public final void deleteGroupRole(final RoleSetCode roleSetCode, final String group,
+ final String person)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ final GroupIdentifier groupIdentifier =
+ new GroupIdentifier(DatabaseInstanceIdentifier.HOME, group);
+ commonServer.deleteGroupRole(sessionToken, RoleCodeTranslator.translate(roleSetCode),
+ groupIdentifier, person);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+
+ }
+
+ public final void deleteInstanceRole(final RoleSetCode roleSetCode, final String person)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ commonServer.deleteInstanceRole(sessionToken,
+ RoleCodeTranslator.translate(roleSetCode), person);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+
+ }
+
+ public final List<SampleType> listSampleTypes()
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ final List<SampleTypePE> sampleTypes = commonServer.listSampleTypes(sessionToken);
+ final List<SampleType> result = new ArrayList<SampleType>();
+ for (final SampleTypePE sampleTypePE : sampleTypes)
+ {
+ result.add(SampleTypeTranslator.translate(sampleTypePE));
+ }
+ return result;
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ // --------- methods preparing exported content. Note: GWT does not support
+ // generic methods :(
+
+ public final String prepareExportSamples(final TableExportCriteria<Sample> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return prepareExportEntities(criteria);
+ }
+
+ public final String prepareExportExperiments(final TableExportCriteria<Experiment> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return prepareExportEntities(criteria);
+ }
+
+ public final String prepareExportMatchingEntities(
+ final TableExportCriteria<MatchingEntity> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return prepareExportEntities(criteria);
+ }
+
+ public String prepareExportPropertyTypes(TableExportCriteria<PropertyType> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return prepareExportEntities(criteria);
+ }
+
+ public String prepareExportPropertyTypeAssignments(
+ TableExportCriteria<EntityTypePropertyType<?>> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return prepareExportEntities(criteria);
+ }
+
+ public String prepareExportProjects(TableExportCriteria<Project> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return prepareExportEntities(criteria);
+ }
+
+ public String prepareExportVocabularies(final TableExportCriteria<Vocabulary> criteria)
+ throws UserFailureException
+ {
+ return prepareExportEntities(criteria);
+ }
+
+ public String prepareExportVocabularyTerms(TableExportCriteria<VocabularyTermWithStats> criteria)
+ {
+ return prepareExportEntities(criteria);
+ }
+
+ public String prepareExportMaterialTypes(final TableExportCriteria<MaterialType> criteria)
+ throws UserFailureException
+ {
+ return prepareExportEntities(criteria);
+ }
+
+ public String prepareExportExperimentTypes(final TableExportCriteria<ExperimentType> criteria)
+ throws UserFailureException
+ {
+ return prepareExportEntities(criteria);
+ }
+
+ public String prepareExportSampleTypes(final TableExportCriteria<SampleType> criteria)
+ throws UserFailureException
+ {
+ return prepareExportEntities(criteria);
+ }
+
+ // ---------------- methods which list entities using cache
+
+ public final ResultSet<Sample> listSamples(final ListSampleCriteria listCriteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ final String sessionToken = getSessionToken();
+ return listEntities(listCriteria, new ListSamplesOriginalDataProvider(commonServer,
+ sessionToken, listCriteria));
+ }
+
+ public ResultSet<ExternalData> searchForDataSets(DataSetSearchCriteria criteria,
+ final IResultSetConfig<String, ExternalData> resultSetConfig)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ final String sessionToken = getSessionToken();
+ return listEntities(resultSetConfig, new ListDataSetsOriginalDataProvider(commonServer,
+ sessionToken, criteria, dataStoreBaseURL));
+ }
+
+ public final ResultSet<Experiment> listExperiments(final ListExperimentsCriteria listCriteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ final String sessionToken = getSessionToken();
+ return listEntities(listCriteria, new ListExperimentsOriginalDataProvider(commonServer,
+ listCriteria, sessionToken));
+ }
+
+ public ResultSet<PropertyType> listPropertyTypes(
+ DefaultResultSetConfig<String, PropertyType> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return listEntities(criteria, new IOriginalDataProvider<PropertyType>()
+ {
+ public List<PropertyType> getOriginalData() throws UserFailureException
+ {
+ return listPropertyTypes();
+ }
+ });
+ }
+
+ public final ResultSet<MatchingEntity> listMatchingEntities(
+ final SearchableEntity searchableEntityOrNull, final String queryText,
+ final IResultSetConfig<String, MatchingEntity> resultSetConfig)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ final String sessionToken = getSessionToken();
+ final ch.systemsx.cisd.openbis.generic.shared.dto.SearchableEntity[] matchingEntities =
+ SearchableEntityTranslator.translate(searchableEntityOrNull);
+ return listEntities(resultSetConfig, new ListMatchingEntitiesOriginalDataProvider(
+ commonServer, sessionToken, matchingEntities, queryText));
+ }
+
+ public ResultSet<EntityTypePropertyType<?>> listPropertyTypeAssignments(
+ DefaultResultSetConfig<String, EntityTypePropertyType<?>> criteria)
+ {
+ return listEntities(criteria, new IOriginalDataProvider<EntityTypePropertyType<?>>()
+ {
+ public List<EntityTypePropertyType<?>> getOriginalData()
+ throws UserFailureException
+ {
+ return extractAssignments(listPropertyTypes());
+ }
+ });
+ }
+
+ private static List<EntityTypePropertyType<?>> extractAssignments(
+ List<PropertyType> listPropertyTypes)
+ {
+ List<EntityTypePropertyType<?>> result = new ArrayList<EntityTypePropertyType<?>>();
+ for (PropertyType propertyType : listPropertyTypes)
+ {
+ extractAssignments(result, propertyType);
+ }
+ return result;
+ }
+
+ private static void extractAssignments(List<EntityTypePropertyType<?>> result,
+ final PropertyType propertyType)
+ {
+ for (ExperimentTypePropertyType etpt : propertyType.getExperimentTypePropertyTypes())
+ {
+ result.add(etpt);
+ }
+ for (SampleTypePropertyType etpt : propertyType.getSampleTypePropertyTypes())
+ {
+ result.add(etpt);
+ }
+ for (MaterialTypePropertyType etpt : propertyType.getMaterialTypePropertyTypes())
+ {
+ result.add(etpt);
+ }
+ }
+
+ public ResultSet<Project> listProjects(DefaultResultSetConfig<String, Project> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return listEntities(criteria, new IOriginalDataProvider<Project>()
+ {
+ public List<Project> getOriginalData() throws UserFailureException
+ {
+ return listProjects();
+ }
+ });
+ }
+
+ private List<Project> listProjects()
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ final List<ProjectPE> projects = commonServer.listProjects(sessionToken);
+ return ProjectTranslator.translate(projects);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public ResultSet<Vocabulary> listVocabularies(final boolean withTerms,
+ final boolean excludeInternal, DefaultResultSetConfig<String, Vocabulary> criteria)
+ throws UserFailureException
+ {
+ return listEntities(criteria, new IOriginalDataProvider<Vocabulary>()
+ {
+ public List<Vocabulary> getOriginalData() throws UserFailureException
+ {
+ return listVocabularies(withTerms, excludeInternal);
+ }
+ });
+ }
+
+ private List<Vocabulary> listVocabularies(final boolean withTerms, boolean excludeInternal)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ final List<VocabularyPE> vocabularies =
+ commonServer.listVocabularies(sessionToken, withTerms, excludeInternal);
+ return BeanUtils.createBeanList(Vocabulary.class, vocabularies, DtoConverters
+ .getVocabularyConverter());
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public ResultSet<VocabularyTermWithStats> listVocabularyTerms(final Vocabulary vocabulary,
+ DefaultResultSetConfig<String, VocabularyTermWithStats> criteria)
+ {
+ return listEntities(criteria, new IOriginalDataProvider<VocabularyTermWithStats>()
+ {
+ public List<VocabularyTermWithStats> getOriginalData() throws UserFailureException
+ {
+ List<ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyTermWithStats> terms =
+ commonServer.listVocabularyTerms(getSessionToken(), vocabulary);
+ return VocabularyTermTranslator.translate(terms);
+ }
+ });
+ }
+
+ public ResultSet<? extends EntityType> listMaterialTypes(
+ DefaultResultSetConfig<String, MaterialType> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return listEntities(criteria, new IOriginalDataProvider<MaterialType>()
+ {
+ public List<MaterialType> getOriginalData() throws UserFailureException
+ {
+ return listMaterialTypes();
+ }
+ });
+ }
+
+ public ResultSet<? extends EntityType> listSampleTypes(
+ DefaultResultSetConfig<String, SampleType> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return listEntities(criteria, new IOriginalDataProvider<SampleType>()
+ {
+ public List<SampleType> getOriginalData() throws UserFailureException
+ {
+ return listSampleTypes();
+ }
+ });
+ }
+
+ public ResultSet<? extends EntityType> listExperimentTypes(
+ DefaultResultSetConfig<String, ExperimentType> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return listEntities(criteria, new IOriginalDataProvider<ExperimentType>()
+ {
+ public List<ExperimentType> getOriginalData() throws UserFailureException
+ {
+ return listExperimentTypes();
+ }
+ });
+ }
+
+ public ResultSet<ExternalData> listSampleDataSets(final String sampleIdentifier,
+ DefaultResultSetConfig<String, ExternalData> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return listEntities(criteria, new IOriginalDataProvider<ExternalData>()
+ {
+ public List<ExternalData> getOriginalData() throws UserFailureException
+ {
+ final String sessionToken = getSessionToken();
+ final SampleIdentifier identifier =
+ SampleIdentifierFactory.parse(sampleIdentifier);
+ final List<ExternalDataPE> externalData =
+ commonServer.listExternalData(sessionToken, identifier);
+ return ExternalDataTranslator.translate(externalData, dataStoreBaseURL);
+ }
+ });
+ }
+
+ public ResultSet<ExternalData> listExperimentDataSets(final String experimentIdentifier,
+ DefaultResultSetConfig<String, ExternalData> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return listEntities(criteria, new IOriginalDataProvider<ExternalData>()
+ {
+
+ public List<ExternalData> getOriginalData() throws UserFailureException
+ {
+ final String sessionToken = getSessionToken();
+ final ExperimentIdentifier identifier =
+ new ExperimentIdentifierFactory(experimentIdentifier)
+ .createIdentifier();
+ final List<ExternalDataPE> externalData =
+ commonServer.listExternalData(sessionToken, identifier);
+ return ExternalDataTranslator.translate(externalData, dataStoreBaseURL);
+ }
+
+ });
+ }
+
+ // ---------------- end list using cache ----------
+
+ public final List<SearchableEntity> listSearchableEntities()
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ // Not directly needed but this refreshes the session.
+ getSessionToken();
+ final List<SearchableEntity> searchableEntities =
+ BeanUtils.createBeanList(SearchableEntity.class, Arrays
+ .asList(ch.systemsx.cisd.openbis.generic.shared.dto.SearchableEntity
+ .values()));
+ Collections.sort(searchableEntities);
+ return searchableEntities;
+ } catch (final ch.systemsx.cisd.common.exceptions.UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public List<ExperimentType> listExperimentTypes()
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ final List<ExperimentType> result = new ArrayList<ExperimentType>();
+ final List<ExperimentTypePE> experiments =
+ commonServer.listExperimentTypes(sessionToken);
+ for (final ExperimentTypePE expType : experiments)
+ {
+ result.add(ExperimentTranslator.translate(expType));
+ }
+ return result;
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ private List<PropertyType> listPropertyTypes()
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ final List<PropertyTypePE> propertyTypes = commonServer.listPropertyTypes(sessionToken);
+ return PropertyTypeTranslator.translate(propertyTypes);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public final List<DataType> listDataTypes()
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ final List<DataTypePE> dataTypes = commonServer.listDataTypes(sessionToken);
+ return BeanUtils.createBeanList(DataType.class, dataTypes, DtoConverters
+ .getDataTypeConverter());
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public String assignPropertyType(final EntityKind entityKind, final String propertyTypeCode,
+ final String entityTypeCode, final boolean isMandatory, final String defaultValue)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ return commonServer.assignPropertyType(sessionToken, DtoConverters
+ .convertEntityKind(entityKind), propertyTypeCode, entityTypeCode, isMandatory,
+ defaultValue);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public final void registerPropertyType(final PropertyType propertyType)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ assert propertyType != null : "Unspecified property type.";
+ try
+ {
+ final String sessionToken = getSessionToken();
+ commonServer.registerPropertyType(sessionToken, propertyType);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public final void registerVocabulary(final Vocabulary vocabulary)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ assert vocabulary != null : "Unspecified vocabulary.";
+ try
+ {
+ final String sessionToken = getSessionToken();
+ commonServer.registerVocabulary(sessionToken, vocabulary);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public void addVocabularyTerms(String vocabularyCode, List<String> vocabularyTerms)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ assert vocabularyCode != null : "Unspecified vocabulary code.";
+
+ if (vocabularyTerms != null && vocabularyTerms.isEmpty() == false)
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ commonServer.addVocabularyTerms(sessionToken, vocabularyCode, vocabularyTerms);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+ }
+
+ public void registerProject(Project project)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ assert project != null : "Unspecified project.";
+ try
+ {
+ final String sessionToken = getSessionToken();
+ final ProjectIdentifier projectIdentifier =
+ new ProjectIdentifierFactory(project.getIdentifier()).createIdentifier();
+ Person leader = project.getProjectLeader();
+ final String leaderId = leader == null ? null : project.getProjectLeader().getUserId();
+ commonServer.registerProject(sessionToken, projectIdentifier, project.getDescription(),
+ leaderId);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public String prepareExportDataSetSearchHits(TableExportCriteria<ExternalData> exportCriteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return prepareExportEntities(exportCriteria);
+ }
+
+ public List<MaterialType> listMaterialTypes()
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ final List<MaterialType> result = new ArrayList<MaterialType>();
+ final List<MaterialTypePE> projects = commonServer.listMaterialTypes(sessionToken);
+ for (final MaterialTypePE expType : projects)
+ {
+ result.add(MaterialTypeTranslator.translate(expType));
+ }
+ return result;
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public List<DataSetType> listDataSetTypes()
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ final List<DataSetType> result = new ArrayList<DataSetType>();
+ final List<DataSetTypePE> types = commonServer.listDataSetTypes(sessionToken);
+ for (final DataSetTypePE type : types)
+ {
+ result.add(DataSetTypeTranslator.translate(type));
+ }
+ return result;
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public ResultSet<Material> listMaterials(ListMaterialCriteria criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ final String sessionToken = getSessionToken();
+ return listEntities(criteria, new ListMaterialOriginalDataProvider(commonServer,
+ sessionToken, criteria));
+ }
+
+ public String prepareExportMaterials(TableExportCriteria<Material> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return prepareExportEntities(criteria);
+ }
+
+ public void registerMaterialType(MaterialType entityType)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ commonServer.registerMaterialType(sessionToken, entityType);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public void registerExperimentType(ExperimentType entityType)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ commonServer.registerExperimentType(sessionToken, entityType);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public void registerSampleType(SampleType entityType)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ commonServer.registerSampleType(sessionToken, entityType);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ private final static AttachmentPE createAttachment(String fileName, final byte[] content)
+ {
+ final AttachmentPE attachment = new AttachmentPE();
+ attachment.setFileName(fileName);
+ final AttachmentContentPE attachmentContent = new AttachmentContentPE();
+ attachmentContent.setValue(content);
+ attachment.setAttachmentContent(attachmentContent);
+ return attachment;
+ }
+
+ public void updateExperiment(String sessionKey, String experimentIdentifier,
+ List<ExperimentProperty> properties, String newProjectIdentifier, Date version)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+
+ UploadedFilesBean uploadedFiles = null;
+ HttpSession session = null;
+ try
+ {
+ final String sessionToken = getSessionToken();
+ session = getHttpSession();
+ uploadedFiles = (UploadedFilesBean) session.getAttribute(sessionKey);
+ List<AttachmentPE> attachments = new ArrayList<AttachmentPE>();
+ if (uploadedFiles != null)
+ {
+ for (final IUncheckedMultipartFile multipartFile : uploadedFiles.iterable())
+ {
+ String fileName = multipartFile.getOriginalFilename();
+ byte[] content = multipartFile.getBytes();
+ attachments.add(createAttachment(fileName, content));
+ }
+ }
+ final ExperimentIdentifier identifier =
+ new ExperimentIdentifierFactory(experimentIdentifier).createIdentifier();
+ final ProjectIdentifier project =
+ new ProjectIdentifierFactory(newProjectIdentifier).createIdentifier();
+ commonServer.editExperiment(sessionToken, identifier, properties, attachments, project,
+ version);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ } finally
+ {
+ if (uploadedFiles != null)
+ {
+ uploadedFiles.deleteTransferredFiles();
+ }
+ if (session != null)
+ {
+ session.removeAttribute(sessionKey);
+ }
+ }
+
+ }
public void uploadDataSets(List<String> dataSetCodes, String cifexURL, String password)
throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
@@ -984,37 +1098,45 @@ public final class CommonClientService extends AbstractClientService implements
throw UserFailureExceptionTranslator.translate(e);
}
}
-
- public void deleteDataSets(List<String> dataSetCodes, String reason)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- commonServer.deleteDataSets(sessionToken, dataSetCodes, reason);
- } catch (final UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
- }
-
- public void updateSample(
- String sampleIdentifier,
- List<SampleProperty> properties,
- ch.systemsx.cisd.openbis.generic.client.web.client.dto.ExperimentIdentifier experimentIdentifierOrNull,
- Date version)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- final SampleIdentifier identifier = new SampleIdentifierFactory(
- sampleIdentifier).createIdentifier();
- ExperimentIdentifier convExperimentIdentifierOrNull = null;
- if (experimentIdentifierOrNull != null) {
- convExperimentIdentifierOrNull = BeanUtils.createBean(
- ExperimentIdentifier.class, experimentIdentifierOrNull);
- }
- commonServer.editSample(sessionToken, identifier, properties,
- convExperimentIdentifierOrNull, version);
- } catch (final ch.systemsx.cisd.common.exceptions.UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
-
- }
+
+ public void deleteDataSets(List<String> dataSetCodes, String reason)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ commonServer.deleteDataSets(sessionToken, dataSetCodes, reason);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public void updateSample(
+ String sampleIdentifier,
+ List<SampleProperty> properties,
+ ch.systemsx.cisd.openbis.generic.client.web.client.dto.ExperimentIdentifier experimentIdentifierOrNull,
+ Date version)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ final SampleIdentifier identifier =
+ new SampleIdentifierFactory(sampleIdentifier).createIdentifier();
+ ExperimentIdentifier convExperimentIdentifierOrNull = null;
+ if (experimentIdentifierOrNull != null)
+ {
+ convExperimentIdentifierOrNull =
+ BeanUtils
+ .createBean(ExperimentIdentifier.class, experimentIdentifierOrNull);
+ }
+ commonServer.editSample(sessionToken, identifier, properties,
+ convExperimentIdentifierOrNull, version);
+ } catch (final ch.systemsx.cisd.common.exceptions.UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
index ed64bb70eba0da0b141a12d442b26bf9535b93a1..5cba4c15b2ae3dc47fe99977305b06f4647bab65 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
@@ -100,473 +100,495 @@ import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
*/
public final class CommonServer extends AbstractServer<ICommonServer> implements ICommonServer
{
- private final IAuthenticationService authenticationService;
-
- private final ICommonBusinessObjectFactory businessObjectFactory;
-
- private final DataStoreServerSessionManager dssSessionManager;
-
- public CommonServer(final IAuthenticationService authenticationService,
- final ISessionManager<Session> sessionManager,
- DataStoreServerSessionManager dssSessionManager,
- final IDAOFactory daoFactory,
- final ICommonBusinessObjectFactory businessObjectFactory) {
- super(sessionManager, daoFactory);
- this.authenticationService = authenticationService;
- this.dssSessionManager = dssSessionManager;
- this.businessObjectFactory = businessObjectFactory;
- }
-
- ICommonBusinessObjectFactory getBusinessObjectFactory() {
- return businessObjectFactory;
- }
-
- // Call this when session object is not needed but you want just to
- // refresh/check the session.
- private void checkSession(final String sessionToken) {
- getSessionManager().getSession(sessionToken);
- }
-
- private static UserFailureException createUserFailureException(
- final DataAccessException ex) {
- return new UserFailureException(ex.getMostSpecificCause().getMessage(),
- ex);
- }
-
- //
- // AbstractServerWithLogger
- //
-
- @Override
- protected final Class<ICommonServer> getProxyInterface() {
- return ICommonServer.class;
- }
-
- //
- // IInvocationLoggerFactory
- //
-
- /**
- * Creates a logger used to log invocations of objects of this class.
- */
- public final ICommonServer createLogger(final boolean invocationSuccessful) {
- return new CommonServerLogger(getSessionManager(), invocationSuccessful);
- }
-
- //
- // IGenericServer
- //
-
- public final List<GroupPE> listGroups(final String sessionToken,
- final DatabaseInstanceIdentifier identifier) {
- final Session session = getSessionManager().getSession(sessionToken);
- final DatabaseInstancePE databaseInstance = GroupIdentifierHelper
- .getDatabaseInstance(identifier, getDAOFactory());
- final List<GroupPE> groups = getDAOFactory().getGroupDAO().listGroups(
- databaseInstance);
- final Long homeGroupID = session.tryGetHomeGroupId();
- for (final GroupPE group : groups) {
- group.setHome(homeGroupID != null
- && homeGroupID.equals(group.getId()));
- }
- Collections.sort(groups);
- return groups;
- }
-
- public final void registerGroup(final String sessionToken,
- final String groupCode, final String descriptionOrNull,
- final String groupLeaderOrNull) {
- final Session session = getSessionManager().getSession(sessionToken);
- final IGroupBO groupBO = businessObjectFactory.createGroupBO(session);
- groupBO.define(groupCode, descriptionOrNull, groupLeaderOrNull);
- groupBO.save();
- }
-
- public final void registerPerson(final String sessionToken,
- final String userID) {
- final Session session = getSessionManager().getSession(sessionToken);
- final PersonPE person = getDAOFactory().getPersonDAO()
- .tryFindPersonByUserId(userID);
- if (person != null) {
- throw UserFailureException.fromTemplate(
- "Person '%s' already exists.", userID);
- }
- final String applicationToken = authenticationService
- .authenticateApplication();
- if (applicationToken == null) {
- throw new EnvironmentFailureException(
- "Authentication service cannot be accessed.");
- }
- try {
- final Principal principal = authenticationService.getPrincipal(
- applicationToken, userID);
- createPerson(principal, session.tryGetPerson());
- } catch (final IllegalArgumentException e) {
- throw new UserFailureException("Person '" + userID
- + "' unknown by the authentication service.");
- }
- }
-
- public final List<RoleAssignmentPE> listRoles(final String sessionToken) {
- checkSession(sessionToken);
- return getDAOFactory().getRoleAssignmentDAO().listRoleAssignments();
- }
-
- public final void registerGroupRole(final String sessionToken,
- final RoleCode roleCode, final GroupIdentifier groupIdentifier,
- final String person) {
- final Session session = getSessionManager().getSession(sessionToken);
-
- final NewRoleAssignment newRoleAssignment = new NewRoleAssignment();
- newRoleAssignment.setUserId(person);
- newRoleAssignment.setGroupIdentifier(groupIdentifier);
- newRoleAssignment.setRole(roleCode);
-
- final IRoleAssignmentTable table = businessObjectFactory
- .createRoleAssignmentTable(session);
- table.add(newRoleAssignment);
- table.save();
-
- }
-
- public final void registerInstanceRole(final String sessionToken,
- final RoleCode roleCode, final String person) {
- final Session session = getSessionManager().getSession(sessionToken);
-
- final NewRoleAssignment newRoleAssignment = new NewRoleAssignment();
- newRoleAssignment.setUserId(person);
- newRoleAssignment
- .setDatabaseInstanceIdentifier(new DatabaseInstanceIdentifier(
- DatabaseInstanceIdentifier.HOME));
- newRoleAssignment.setRole(roleCode);
-
- final IRoleAssignmentTable table = businessObjectFactory
- .createRoleAssignmentTable(session);
- table.add(newRoleAssignment);
- table.save();
-
- }
-
- public final void deleteGroupRole(final String sessionToken,
- final RoleCode roleCode, final GroupIdentifier groupIdentifier,
- final String person) {
- final Session session = getSessionManager().getSession(sessionToken);
-
- final RoleAssignmentPE roleAssignment = getDAOFactory()
- .getRoleAssignmentDAO().tryFindGroupRoleAssignment(roleCode,
- groupIdentifier.getGroupCode(), person);
- if (roleAssignment == null) {
- throw new UserFailureException("Given group role does not exist.");
- }
- final PersonPE personPE = session.tryGetPerson();
- if (roleAssignment.getPerson().equals(personPE)
- && roleAssignment.getRole().equals(RoleCode.ADMIN)) {
- boolean isInstanceAdmin = false;
- for (final RoleAssignmentPE roleAssigment : personPE
- .getRoleAssignments()) {
- if (roleAssigment.getDatabaseInstance() != null
- && roleAssigment.getRole().equals(RoleCode.ADMIN)) {
- isInstanceAdmin = true;
- }
- }
- if (isInstanceAdmin == false) {
- throw new UserFailureException(
- "For safety reason you cannot give away your own group admin power. "
- + "Ask instance admin to do that for you.");
- }
- }
- getDAOFactory().getRoleAssignmentDAO().deleteRoleAssignment(
- roleAssignment);
- }
-
- public final void deleteInstanceRole(final String sessionToken,
- final RoleCode roleCode, final String person) {
- final Session session = getSessionManager().getSession(sessionToken);
- final IRoleAssignmentDAO roleAssignmentDAO = getDAOFactory()
- .getRoleAssignmentDAO();
- final RoleAssignmentPE roleAssignment = roleAssignmentDAO
- .tryFindInstanceRoleAssignment(roleCode, person);
- if (roleAssignment == null) {
- throw new UserFailureException(
- "Given database instance role does not exist.");
- }
- if (roleAssignment.getPerson().equals(session.tryGetPerson())
- && roleAssignment.getRole().equals(RoleCode.ADMIN)
- && roleAssignment.getDatabaseInstance() != null) {
- throw new UserFailureException(
- "For safety reason you cannot give away your own omnipotence. "
- + "Ask another instance admin to do that for you.");
- }
- roleAssignmentDAO.deleteRoleAssignment(roleAssignment);
- }
-
- public final List<PersonPE> listPersons(final String sessionToken) {
- checkSession(sessionToken);
- final List<PersonPE> persons = getDAOFactory().getPersonDAO()
- .listPersons();
- Collections.sort(persons);
- return persons;
- }
-
- public final List<ProjectPE> listProjects(final String sessionToken) {
- checkSession(sessionToken);
- final List<ProjectPE> projects = getDAOFactory().getProjectDAO()
- .listProjects();
- Collections.sort(projects);
- return projects;
- }
-
- public final List<SampleTypePE> listSampleTypes(final String sessionToken) {
- checkSession(sessionToken);
- final List<SampleTypePE> sampleTypes = getDAOFactory()
- .getSampleTypeDAO().listSampleTypes();
- Collections.sort(sampleTypes);
- return sampleTypes;
- }
-
- public final List<SamplePE> listSamples(final String sessionToken,
- final ListSampleCriteriaDTO criteria) {
- final Session session = getSessionManager().getSession(sessionToken);
- final ISampleTable sampleTable = businessObjectFactory
- .createSampleTable(session);
- sampleTable.loadSamplesByCriteria(criteria);
- sampleTable.enrichWithValidProcedure();
- sampleTable.enrichWithProperties();
- final List<SamplePE> samples = sampleTable.getSamples();
- Collections.sort(samples);
- return samples;
- }
-
- public final List<ExternalDataPE> listExternalData(
- final String sessionToken, final SampleIdentifier identifier) {
- final Session session = getSessionManager().getSession(sessionToken);
- final IExternalDataTable externalDataTable = businessObjectFactory
- .createExternalDataTable(session);
- externalDataTable.loadBySampleIdentifier(identifier);
- return getSortedExternalDataFrom(externalDataTable);
- }
-
- public List<ExternalDataPE> listExternalData(String sessionToken,
- ExperimentIdentifier identifier) {
- final Session session = getSessionManager().getSession(sessionToken);
- final IExternalDataTable externalDataTable = businessObjectFactory
- .createExternalDataTable(session);
- externalDataTable.loadByExperimentIdentifier(identifier);
- return getSortedExternalDataFrom(externalDataTable);
- }
-
- private List<ExternalDataPE> getSortedExternalDataFrom(
- final IExternalDataTable externalDataTable) {
- final List<ExternalDataPE> externalData = externalDataTable
- .getExternalData();
- Collections.sort(externalData);
- return externalData;
- }
-
- public final List<PropertyTypePE> listPropertyTypes(
- final String sessionToken) {
- final Session session = getSessionManager().getSession(sessionToken);
- final IPropertyTypeTable propertyTypeTable = businessObjectFactory
- .createPropertyTypeTable(session);
- propertyTypeTable.load();
- propertyTypeTable.enrichWithRelations();
- final List<PropertyTypePE> propertyTypes = propertyTypeTable
- .getPropertyTypes();
- Collections.sort(propertyTypes);
- return propertyTypes;
- }
-
- public final List<SearchHit> listMatchingEntities(
- final String sessionToken,
- final SearchableEntity[] searchableEntities, final String queryText) {
- checkSession(sessionToken);
- final List<SearchHit> list = new ArrayList<SearchHit>();
- try {
- for (final SearchableEntity searchableEntity : searchableEntities) {
- final List<SearchHit> entities = getDAOFactory()
- .getHibernateSearchDAO().searchEntitiesByTerm(
- searchableEntity.getMatchingEntityClass(),
- queryText);
- list.addAll(entities);
- }
- } catch (final DataAccessException ex) {
- throw createUserFailureException(ex);
- }
- return list;
- }
-
- public final List<ExperimentPE> listExperiments(final String sessionToken,
- final ExperimentTypePE experimentType,
- final ProjectIdentifier projectIdentifier) {
- final Session session = getSessionManager().getSession(sessionToken);
- final IExperimentTable experimentTable = businessObjectFactory
- .createExperimentTable(session);
- experimentTable.load(experimentType.getCode(), projectIdentifier);
- experimentTable.enrichWithProperties();
- final List<ExperimentPE> experiments = experimentTable.getExperiments();
- Collections.sort(experiments);
- return experiments;
- }
-
- public final List<ExperimentTypePE> listExperimentTypes(
- final String sessionToken) {
- return listEntityTypes(sessionToken, EntityKind.EXPERIMENT);
- }
-
- public List<MaterialTypePE> listMaterialTypes(String sessionToken) {
- return listEntityTypes(sessionToken, EntityKind.MATERIAL);
- }
-
- private <T extends EntityTypePE> List<T> listEntityTypes(
- String sessionToken, EntityKind entityKind) {
- checkSession(sessionToken);
- final List<T> types = getDAOFactory().getEntityTypeDAO(entityKind)
- .listEntityTypes();
- Collections.sort(types);
- return types;
- }
-
- public final List<DataTypePE> listDataTypes(final String sessionToken) {
- assert sessionToken != null : "Unspecified session token";
- checkSession(sessionToken);
- final List<DataTypePE> dataTypes = getDAOFactory().getPropertyTypeDAO()
- .listDataTypes();
- Collections.sort(dataTypes);
- return dataTypes;
- }
-
- public final List<VocabularyPE> listVocabularies(final String sessionToken,
- final boolean withTerms, boolean excludeInternal) {
- assert sessionToken != null : "Unspecified session token";
- checkSession(sessionToken);
- final List<VocabularyPE> vocabularies = getDAOFactory()
- .getVocabularyDAO().listVocabularies(excludeInternal);
- if (withTerms) {
- for (final VocabularyPE vocabularyPE : vocabularies) {
- enrichWithTerms(vocabularyPE);
- }
- }
- Collections.sort(vocabularies);
- return vocabularies;
- }
-
- private void enrichWithTerms(final VocabularyPE vocabularyPE) {
- HibernateUtils.initialize(vocabularyPE.getTerms());
- }
-
- public String assignPropertyType(final String sessionToken,
- final EntityKind entityKind, final String propertyTypeCode,
- final String entityTypeCode, final boolean isMandatory,
- final String defaultValue) {
- assert sessionToken != null : "Unspecified session token";
- Session session = getSessionManager().getSession(sessionToken);
-
- IEntityTypePropertyTypeBO etptBO = businessObjectFactory
- .createEntityTypePropertyTypeBO(session, entityKind);
- etptBO.createAssignment(propertyTypeCode, entityTypeCode, isMandatory,
- defaultValue);
- return String.format(
- "%s property type '%s' successfully assigned to %s type '%s'",
- isMandatory ? "Mandatory" : "Optional", propertyTypeCode,
- entityKind.getLabel(), entityTypeCode);
-
- }
-
- public final void registerPropertyType(final String sessionToken,
- final PropertyType propertyType) {
- assert sessionToken != null : "Unspecified session token";
- assert propertyType != null : "Unspecified property type";
-
- final Session session = getSessionManager().getSession(sessionToken);
- final IPropertyTypeBO propertyTypeBO = businessObjectFactory
- .createPropertyTypeBO(session);
- propertyTypeBO.define(propertyType);
- propertyTypeBO.save();
- }
-
- public final void registerVocabulary(final String sessionToken,
- final Vocabulary vocabulary) {
- assert sessionToken != null : "Unspecified session token";
- assert vocabulary != null : "Unspecified vocabulary";
-
- final Session session = getSessionManager().getSession(sessionToken);
- final IVocabularyBO vocabularyBO = businessObjectFactory
- .createVocabularyBO(session);
- vocabularyBO.define(vocabulary);
- vocabularyBO.save();
- }
-
- public void registerProject(String sessionToken,
- ProjectIdentifier projectIdentifier, String description,
- String leaderId) {
- final Session session = getSessionManager().getSession(sessionToken);
- final IProjectBO projectBO = businessObjectFactory
- .createProjectBO(session);
- projectBO.define(projectIdentifier, description, leaderId);
- projectBO.save();
-
- }
-
- public List<ExternalDataPE> searchForDataSets(String sessionToken,
- DataSetSearchCriteria criteria) {
- checkSession(sessionToken);
- try {
- IHibernateSearchDAO searchDAO = getDAOFactory()
- .getHibernateSearchDAO();
- return searchDAO.searchForDataSets(criteria);
- } catch (final DataAccessException ex) {
- throw createUserFailureException(ex);
- }
- }
-
- public List<MaterialPE> listMaterials(String sessionToken,
- MaterialTypePE materialType) {
- final Session session = getSessionManager().getSession(sessionToken);
- final IMaterialTable materialTable = businessObjectFactory
- .createMaterialTable(session);
- materialTable.load(materialType.getCode());
- final List<MaterialPE> materials = materialTable.getMaterials();
- Collections.sort(materials);
- return materials;
- }
-
- public void registerSampleType(String sessionToken, SampleType entityType) {
- final Session session = getSessionManager().getSession(sessionToken);
- try {
- IEntityTypeBO entityTypeBO = businessObjectFactory
- .createEntityTypeBO(session);
- entityTypeBO.define(entityType);
- entityTypeBO.save();
- } catch (final DataAccessException ex) {
- throw createUserFailureException(ex);
- }
- }
-
- public void registerMaterialType(String sessionToken,
- MaterialType entityType) {
- final Session session = getSessionManager().getSession(sessionToken);
- try {
- IEntityTypeBO entityTypeBO = businessObjectFactory
- .createEntityTypeBO(session);
- entityTypeBO.define(entityType);
- entityTypeBO.save();
- } catch (final DataAccessException ex) {
- throw createUserFailureException(ex);
- }
- }
-
- public void registerExperimentType(String sessionToken,
- ExperimentType entityType) {
- final Session session = getSessionManager().getSession(sessionToken);
- try {
- IEntityTypeBO entityTypeBO = businessObjectFactory
- .createEntityTypeBO(session);
- entityTypeBO.define(entityType);
- entityTypeBO.save();
- } catch (final DataAccessException ex) {
- throw createUserFailureException(ex);
- }
- }
+ private final IAuthenticationService authenticationService;
+
+ private final ICommonBusinessObjectFactory businessObjectFactory;
+
+ private final DataStoreServerSessionManager dssSessionManager;
+
+ public CommonServer(final IAuthenticationService authenticationService,
+ final ISessionManager<Session> sessionManager,
+ DataStoreServerSessionManager dssSessionManager, final IDAOFactory daoFactory,
+ final ICommonBusinessObjectFactory businessObjectFactory)
+ {
+ super(sessionManager, daoFactory);
+ this.authenticationService = authenticationService;
+ this.dssSessionManager = dssSessionManager;
+ this.businessObjectFactory = businessObjectFactory;
+ }
+
+ ICommonBusinessObjectFactory getBusinessObjectFactory()
+ {
+ return businessObjectFactory;
+ }
+
+ // Call this when session object is not needed but you want just to
+ // refresh/check the session.
+ private void checkSession(final String sessionToken)
+ {
+ getSessionManager().getSession(sessionToken);
+ }
+
+ private static UserFailureException createUserFailureException(final DataAccessException ex)
+ {
+ return new UserFailureException(ex.getMostSpecificCause().getMessage(), ex);
+ }
+
+ //
+ // AbstractServerWithLogger
+ //
+
+ @Override
+ protected final Class<ICommonServer> getProxyInterface()
+ {
+ return ICommonServer.class;
+ }
+
+ //
+ // IInvocationLoggerFactory
+ //
+
+ /**
+ * Creates a logger used to log invocations of objects of this class.
+ */
+ public final ICommonServer createLogger(final boolean invocationSuccessful)
+ {
+ return new CommonServerLogger(getSessionManager(), invocationSuccessful);
+ }
+
+ //
+ // IGenericServer
+ //
+
+ public final List<GroupPE> listGroups(final String sessionToken,
+ final DatabaseInstanceIdentifier identifier)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ final DatabaseInstancePE databaseInstance =
+ GroupIdentifierHelper.getDatabaseInstance(identifier, getDAOFactory());
+ final List<GroupPE> groups = getDAOFactory().getGroupDAO().listGroups(databaseInstance);
+ final Long homeGroupID = session.tryGetHomeGroupId();
+ for (final GroupPE group : groups)
+ {
+ group.setHome(homeGroupID != null && homeGroupID.equals(group.getId()));
+ }
+ Collections.sort(groups);
+ return groups;
+ }
+
+ public final void registerGroup(final String sessionToken, final String groupCode,
+ final String descriptionOrNull, final String groupLeaderOrNull)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ final IGroupBO groupBO = businessObjectFactory.createGroupBO(session);
+ groupBO.define(groupCode, descriptionOrNull, groupLeaderOrNull);
+ groupBO.save();
+ }
+
+ public final void registerPerson(final String sessionToken, final String userID)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ final PersonPE person = getDAOFactory().getPersonDAO().tryFindPersonByUserId(userID);
+ if (person != null)
+ {
+ throw UserFailureException.fromTemplate("Person '%s' already exists.", userID);
+ }
+ final String applicationToken = authenticationService.authenticateApplication();
+ if (applicationToken == null)
+ {
+ throw new EnvironmentFailureException("Authentication service cannot be accessed.");
+ }
+ try
+ {
+ final Principal principal =
+ authenticationService.getPrincipal(applicationToken, userID);
+ createPerson(principal, session.tryGetPerson());
+ } catch (final IllegalArgumentException e)
+ {
+ throw new UserFailureException("Person '" + userID
+ + "' unknown by the authentication service.");
+ }
+ }
+
+ public final List<RoleAssignmentPE> listRoles(final String sessionToken)
+ {
+ checkSession(sessionToken);
+ return getDAOFactory().getRoleAssignmentDAO().listRoleAssignments();
+ }
+
+ public final void registerGroupRole(final String sessionToken, final RoleCode roleCode,
+ final GroupIdentifier groupIdentifier, final String person)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+
+ final NewRoleAssignment newRoleAssignment = new NewRoleAssignment();
+ newRoleAssignment.setUserId(person);
+ newRoleAssignment.setGroupIdentifier(groupIdentifier);
+ newRoleAssignment.setRole(roleCode);
+
+ final IRoleAssignmentTable table = businessObjectFactory.createRoleAssignmentTable(session);
+ table.add(newRoleAssignment);
+ table.save();
+
+ }
+
+ public final void registerInstanceRole(final String sessionToken, final RoleCode roleCode,
+ final String person)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+
+ final NewRoleAssignment newRoleAssignment = new NewRoleAssignment();
+ newRoleAssignment.setUserId(person);
+ newRoleAssignment.setDatabaseInstanceIdentifier(new DatabaseInstanceIdentifier(
+ DatabaseInstanceIdentifier.HOME));
+ newRoleAssignment.setRole(roleCode);
+
+ final IRoleAssignmentTable table = businessObjectFactory.createRoleAssignmentTable(session);
+ table.add(newRoleAssignment);
+ table.save();
+
+ }
+
+ public final void deleteGroupRole(final String sessionToken, final RoleCode roleCode,
+ final GroupIdentifier groupIdentifier, final String person)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+
+ final RoleAssignmentPE roleAssignment =
+ getDAOFactory().getRoleAssignmentDAO().tryFindGroupRoleAssignment(roleCode,
+ groupIdentifier.getGroupCode(), person);
+ if (roleAssignment == null)
+ {
+ throw new UserFailureException("Given group role does not exist.");
+ }
+ final PersonPE personPE = session.tryGetPerson();
+ if (roleAssignment.getPerson().equals(personPE)
+ && roleAssignment.getRole().equals(RoleCode.ADMIN))
+ {
+ boolean isInstanceAdmin = false;
+ for (final RoleAssignmentPE roleAssigment : personPE.getRoleAssignments())
+ {
+ if (roleAssigment.getDatabaseInstance() != null
+ && roleAssigment.getRole().equals(RoleCode.ADMIN))
+ {
+ isInstanceAdmin = true;
+ }
+ }
+ if (isInstanceAdmin == false)
+ {
+ throw new UserFailureException(
+ "For safety reason you cannot give away your own group admin power. "
+ + "Ask instance admin to do that for you.");
+ }
+ }
+ getDAOFactory().getRoleAssignmentDAO().deleteRoleAssignment(roleAssignment);
+ }
+
+ public final void deleteInstanceRole(final String sessionToken, final RoleCode roleCode,
+ final String person)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ final IRoleAssignmentDAO roleAssignmentDAO = getDAOFactory().getRoleAssignmentDAO();
+ final RoleAssignmentPE roleAssignment =
+ roleAssignmentDAO.tryFindInstanceRoleAssignment(roleCode, person);
+ if (roleAssignment == null)
+ {
+ throw new UserFailureException("Given database instance role does not exist.");
+ }
+ if (roleAssignment.getPerson().equals(session.tryGetPerson())
+ && roleAssignment.getRole().equals(RoleCode.ADMIN)
+ && roleAssignment.getDatabaseInstance() != null)
+ {
+ throw new UserFailureException(
+ "For safety reason you cannot give away your own omnipotence. "
+ + "Ask another instance admin to do that for you.");
+ }
+ roleAssignmentDAO.deleteRoleAssignment(roleAssignment);
+ }
+
+ public final List<PersonPE> listPersons(final String sessionToken)
+ {
+ checkSession(sessionToken);
+ final List<PersonPE> persons = getDAOFactory().getPersonDAO().listPersons();
+ Collections.sort(persons);
+ return persons;
+ }
+
+ public final List<ProjectPE> listProjects(final String sessionToken)
+ {
+ checkSession(sessionToken);
+ final List<ProjectPE> projects = getDAOFactory().getProjectDAO().listProjects();
+ Collections.sort(projects);
+ return projects;
+ }
+
+ public final List<SampleTypePE> listSampleTypes(final String sessionToken)
+ {
+ checkSession(sessionToken);
+ final List<SampleTypePE> sampleTypes = getDAOFactory().getSampleTypeDAO().listSampleTypes();
+ Collections.sort(sampleTypes);
+ return sampleTypes;
+ }
+
+ public final List<SamplePE> listSamples(final String sessionToken,
+ final ListSampleCriteriaDTO criteria)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ final ISampleTable sampleTable = businessObjectFactory.createSampleTable(session);
+ sampleTable.loadSamplesByCriteria(criteria);
+ sampleTable.enrichWithValidProcedure();
+ sampleTable.enrichWithProperties();
+ final List<SamplePE> samples = sampleTable.getSamples();
+ Collections.sort(samples);
+ return samples;
+ }
+
+ public final List<ExternalDataPE> listExternalData(final String sessionToken,
+ final SampleIdentifier identifier)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ final IExternalDataTable externalDataTable =
+ businessObjectFactory.createExternalDataTable(session);
+ externalDataTable.loadBySampleIdentifier(identifier);
+ return getSortedExternalDataFrom(externalDataTable);
+ }
+
+ public List<ExternalDataPE> listExternalData(String sessionToken,
+ ExperimentIdentifier identifier)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ final IExternalDataTable externalDataTable =
+ businessObjectFactory.createExternalDataTable(session);
+ externalDataTable.loadByExperimentIdentifier(identifier);
+ return getSortedExternalDataFrom(externalDataTable);
+ }
+
+ private List<ExternalDataPE> getSortedExternalDataFrom(
+ final IExternalDataTable externalDataTable)
+ {
+ final List<ExternalDataPE> externalData = externalDataTable.getExternalData();
+ Collections.sort(externalData);
+ return externalData;
+ }
+
+ public final List<PropertyTypePE> listPropertyTypes(final String sessionToken)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ final IPropertyTypeTable propertyTypeTable =
+ businessObjectFactory.createPropertyTypeTable(session);
+ propertyTypeTable.load();
+ propertyTypeTable.enrichWithRelations();
+ final List<PropertyTypePE> propertyTypes = propertyTypeTable.getPropertyTypes();
+ Collections.sort(propertyTypes);
+ return propertyTypes;
+ }
+
+ public final List<SearchHit> listMatchingEntities(final String sessionToken,
+ final SearchableEntity[] searchableEntities, final String queryText)
+ {
+ checkSession(sessionToken);
+ final List<SearchHit> list = new ArrayList<SearchHit>();
+ try
+ {
+ for (final SearchableEntity searchableEntity : searchableEntities)
+ {
+ final List<SearchHit> entities =
+ getDAOFactory().getHibernateSearchDAO().searchEntitiesByTerm(
+ searchableEntity.getMatchingEntityClass(), queryText);
+ list.addAll(entities);
+ }
+ } catch (final DataAccessException ex)
+ {
+ throw createUserFailureException(ex);
+ }
+ return list;
+ }
+
+ public final List<ExperimentPE> listExperiments(final String sessionToken,
+ final ExperimentTypePE experimentType, final ProjectIdentifier projectIdentifier)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ final IExperimentTable experimentTable =
+ businessObjectFactory.createExperimentTable(session);
+ experimentTable.load(experimentType.getCode(), projectIdentifier);
+ experimentTable.enrichWithProperties();
+ final List<ExperimentPE> experiments = experimentTable.getExperiments();
+ Collections.sort(experiments);
+ return experiments;
+ }
+
+ public final List<ExperimentTypePE> listExperimentTypes(final String sessionToken)
+ {
+ return listEntityTypes(sessionToken, EntityKind.EXPERIMENT);
+ }
+
+ public List<MaterialTypePE> listMaterialTypes(String sessionToken)
+ {
+ return listEntityTypes(sessionToken, EntityKind.MATERIAL);
+ }
+
+ private <T extends EntityTypePE> List<T> listEntityTypes(String sessionToken,
+ EntityKind entityKind)
+ {
+ checkSession(sessionToken);
+ final List<T> types = getDAOFactory().getEntityTypeDAO(entityKind).listEntityTypes();
+ Collections.sort(types);
+ return types;
+ }
+
+ public final List<DataTypePE> listDataTypes(final String sessionToken)
+ {
+ assert sessionToken != null : "Unspecified session token";
+ checkSession(sessionToken);
+ final List<DataTypePE> dataTypes = getDAOFactory().getPropertyTypeDAO().listDataTypes();
+ Collections.sort(dataTypes);
+ return dataTypes;
+ }
+
+ public final List<VocabularyPE> listVocabularies(final String sessionToken,
+ final boolean withTerms, boolean excludeInternal)
+ {
+ assert sessionToken != null : "Unspecified session token";
+ checkSession(sessionToken);
+ final List<VocabularyPE> vocabularies =
+ getDAOFactory().getVocabularyDAO().listVocabularies(excludeInternal);
+ if (withTerms)
+ {
+ for (final VocabularyPE vocabularyPE : vocabularies)
+ {
+ enrichWithTerms(vocabularyPE);
+ }
+ }
+ Collections.sort(vocabularies);
+ return vocabularies;
+ }
+
+ private void enrichWithTerms(final VocabularyPE vocabularyPE)
+ {
+ HibernateUtils.initialize(vocabularyPE.getTerms());
+ }
+
+ public String assignPropertyType(final String sessionToken, final EntityKind entityKind,
+ final String propertyTypeCode, final String entityTypeCode, final boolean isMandatory,
+ final String defaultValue)
+ {
+ assert sessionToken != null : "Unspecified session token";
+ Session session = getSessionManager().getSession(sessionToken);
+
+ IEntityTypePropertyTypeBO etptBO =
+ businessObjectFactory.createEntityTypePropertyTypeBO(session, entityKind);
+ etptBO.createAssignment(propertyTypeCode, entityTypeCode, isMandatory, defaultValue);
+ return String.format("%s property type '%s' successfully assigned to %s type '%s'",
+ isMandatory ? "Mandatory" : "Optional", propertyTypeCode, entityKind.getLabel(),
+ entityTypeCode);
+
+ }
+
+ public final void registerPropertyType(final String sessionToken,
+ final PropertyType propertyType)
+ {
+ assert sessionToken != null : "Unspecified session token";
+ assert propertyType != null : "Unspecified property type";
+
+ final Session session = getSessionManager().getSession(sessionToken);
+ final IPropertyTypeBO propertyTypeBO = businessObjectFactory.createPropertyTypeBO(session);
+ propertyTypeBO.define(propertyType);
+ propertyTypeBO.save();
+ }
+
+ public final void registerVocabulary(final String sessionToken, final Vocabulary vocabulary)
+ {
+ assert sessionToken != null : "Unspecified session token";
+ assert vocabulary != null : "Unspecified vocabulary";
+
+ final Session session = getSessionManager().getSession(sessionToken);
+ final IVocabularyBO vocabularyBO = businessObjectFactory.createVocabularyBO(session);
+ vocabularyBO.define(vocabulary);
+ vocabularyBO.save();
+ }
+
+ public void addVocabularyTerms(String sessionToken, String vocabularyCode,
+ List<String> vocabularyTerms)
+ {
+ System.out.println(vocabularyCode+":"+vocabularyTerms);
+
+ }
+
+ public void registerProject(String sessionToken, ProjectIdentifier projectIdentifier,
+ String description, String leaderId)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ final IProjectBO projectBO = businessObjectFactory.createProjectBO(session);
+ projectBO.define(projectIdentifier, description, leaderId);
+ projectBO.save();
+
+ }
+
+ public List<ExternalDataPE> searchForDataSets(String sessionToken,
+ DataSetSearchCriteria criteria)
+ {
+ checkSession(sessionToken);
+ try
+ {
+ IHibernateSearchDAO searchDAO = getDAOFactory().getHibernateSearchDAO();
+ return searchDAO.searchForDataSets(criteria);
+ } catch (final DataAccessException ex)
+ {
+ throw createUserFailureException(ex);
+ }
+ }
+
+ public List<MaterialPE> listMaterials(String sessionToken, MaterialTypePE materialType)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ final IMaterialTable materialTable = businessObjectFactory.createMaterialTable(session);
+ materialTable.load(materialType.getCode());
+ final List<MaterialPE> materials = materialTable.getMaterials();
+ Collections.sort(materials);
+ return materials;
+ }
+
+ public void registerSampleType(String sessionToken, SampleType entityType)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ try
+ {
+ IEntityTypeBO entityTypeBO = businessObjectFactory.createEntityTypeBO(session);
+ entityTypeBO.define(entityType);
+ entityTypeBO.save();
+ } catch (final DataAccessException ex)
+ {
+ throw createUserFailureException(ex);
+ }
+ }
+
+ public void registerMaterialType(String sessionToken, MaterialType entityType)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ try
+ {
+ IEntityTypeBO entityTypeBO = businessObjectFactory.createEntityTypeBO(session);
+ entityTypeBO.define(entityType);
+ entityTypeBO.save();
+ } catch (final DataAccessException ex)
+ {
+ throw createUserFailureException(ex);
+ }
+ }
+
+ public void registerExperimentType(String sessionToken, ExperimentType entityType)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ try
+ {
+ IEntityTypeBO entityTypeBO = businessObjectFactory.createEntityTypeBO(session);
+ entityTypeBO.define(entityType);
+ entityTypeBO.save();
+ } catch (final DataAccessException ex)
+ {
+ throw createUserFailureException(ex);
+ }
+ }
public void deleteDataSets(String sessionToken, List<String> dataSetCodes, String reason)
{
@@ -598,105 +620,105 @@ public final class CommonServer extends AbstractServer<ICommonServer> implements
throw createUserFailureException(ex);
}
}
-
- public void editExperiment(String sessionToken,
- ExperimentIdentifier identifier,
- List<ExperimentProperty> properties,
- List<AttachmentPE> attachments,
- ProjectIdentifier newProjectIdentifier, Date version) {
- final Session session = getSessionManager().getSession(sessionToken);
- if (newProjectIdentifier.equals(identifier) == false) {
- checkExternalData(identifier, session);
- checkSampleConsistency(identifier, newProjectIdentifier, session);
- }
-
- final IExperimentBO experimentBO = businessObjectFactory
- .createExperimentBO(session);
- experimentBO.edit(identifier, properties, attachments,
- newProjectIdentifier, version);
- experimentBO.save();
- }
-
- private void checkExternalData(ExperimentIdentifier identifier,
- final Session session) {
- final IExternalDataTable externalDataTable = businessObjectFactory
- .createExternalDataTable(session);
- externalDataTable.loadByExperimentIdentifier(identifier);
- if (externalDataTable.getExternalData().size() > 0) {
- throw new UserFailureException(
- "Changing the project of experiment containing data sets is not allowed.");
- }
- }
-
- private void checkSampleConsistency(ExperimentIdentifier identifier,
- ProjectIdentifier newProjectIdentifier, final Session session) {
- ListSampleCriteriaDTO criteria = ListSampleCriteriaDTO
- .createExperimentIdentifier(identifier);
- final ISampleTable sampleTable = businessObjectFactory
- .createSampleTable(session);
- sampleTable.loadSamplesByCriteria(criteria);
- final List<SamplePE> samples = sampleTable.getSamples();
- if (samples.size() > 0) {
- checkExperimentGroupMatches(samples.get(0).getSampleIdentifier(),
- newProjectIdentifier);
- }
- }
-
- private void checkExperimentGroupMatches(SampleIdentifier sampleIdentifier,
- ProjectIdentifier newProjectIdentifier) {
- assert sampleIdentifier != null : "Sample identifier not specified";
- assert newProjectIdentifier != null : "Project identifier not specified";
- final GroupIdentifier sampleGroup = sampleIdentifier.getGroupLevel();
- if (sampleGroup == null) {
- throw new UserFailureException(
- "Inconsistency detected: shared sample found in experiment.");
- }
- if (sampleGroup.getDatabaseInstanceCode().equals(
- newProjectIdentifier.getDatabaseInstanceCode()) == false
- || sampleGroup.getGroupCode().equals(
- newProjectIdentifier.getGroupCode()) == false) {
- throw new UserFailureException(
- String
- .format(
- "Project cannot be changed to '%s' because experiment containes samples from group '%s'.",
- newProjectIdentifier, sampleGroup));
- }
- }
-
- public void editMaterial(String sessionToken,
- MaterialIdentifier identifier, List<MaterialProperty> properties,
- Date version) {
- final Session session = getSessionManager().getSession(sessionToken);
- final IMaterialBO materialBO = businessObjectFactory
- .createMaterialBO(session);
- materialBO.edit(identifier, properties, version);
- materialBO.save();
-
- }
-
- public void editSample(String sessionToken, SampleIdentifier identifier,
- List<SampleProperty> properties,
- ExperimentIdentifier experimentIdentifierOrNull, Date version) {
- final Session session = getSessionManager().getSession(sessionToken);
- final ISampleBO sampleBO = businessObjectFactory
- .createSampleBO(session);
- sampleBO.edit(identifier, properties, experimentIdentifierOrNull,
- version);
- sampleBO.save();
-
- }
-
- public List<VocabularyTermWithStats> listVocabularyTerms(
- String sessionToken, Vocabulary vocabulary) {
- final Session session = getSessionManager().getSession(sessionToken);
- final IVocabularyBO vocabularyBO = businessObjectFactory
- .createVocabularyBO(session);
- vocabularyBO.load(vocabulary);
- return vocabularyBO.countTermsUsageStatistics();
- }
-
- public List<DataSetTypePE> listDataSetTypes(String sessionToken) {
- return listEntityTypes(sessionToken, EntityKind.DATA_SET);
- }
+
+ public void editExperiment(String sessionToken, ExperimentIdentifier identifier,
+ List<ExperimentProperty> properties, List<AttachmentPE> attachments,
+ ProjectIdentifier newProjectIdentifier, Date version)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ if (newProjectIdentifier.equals(identifier) == false)
+ {
+ checkExternalData(identifier, session);
+ checkSampleConsistency(identifier, newProjectIdentifier, session);
+ }
+
+ final IExperimentBO experimentBO = businessObjectFactory.createExperimentBO(session);
+ experimentBO.edit(identifier, properties, attachments, newProjectIdentifier, version);
+ experimentBO.save();
+ }
+
+ private void checkExternalData(ExperimentIdentifier identifier, final Session session)
+ {
+ final IExternalDataTable externalDataTable =
+ businessObjectFactory.createExternalDataTable(session);
+ externalDataTable.loadByExperimentIdentifier(identifier);
+ if (externalDataTable.getExternalData().size() > 0)
+ {
+ throw new UserFailureException(
+ "Changing the project of experiment containing data sets is not allowed.");
+ }
+ }
+
+ private void checkSampleConsistency(ExperimentIdentifier identifier,
+ ProjectIdentifier newProjectIdentifier, final Session session)
+ {
+ ListSampleCriteriaDTO criteria =
+ ListSampleCriteriaDTO.createExperimentIdentifier(identifier);
+ final ISampleTable sampleTable = businessObjectFactory.createSampleTable(session);
+ sampleTable.loadSamplesByCriteria(criteria);
+ final List<SamplePE> samples = sampleTable.getSamples();
+ if (samples.size() > 0)
+ {
+ checkExperimentGroupMatches(samples.get(0).getSampleIdentifier(), newProjectIdentifier);
+ }
+ }
+
+ private void checkExperimentGroupMatches(SampleIdentifier sampleIdentifier,
+ ProjectIdentifier newProjectIdentifier)
+ {
+ assert sampleIdentifier != null : "Sample identifier not specified";
+ assert newProjectIdentifier != null : "Project identifier not specified";
+ final GroupIdentifier sampleGroup = sampleIdentifier.getGroupLevel();
+ if (sampleGroup == null)
+ {
+ throw new UserFailureException(
+ "Inconsistency detected: shared sample found in experiment.");
+ }
+ if (sampleGroup.getDatabaseInstanceCode().equals(
+ newProjectIdentifier.getDatabaseInstanceCode()) == false
+ || sampleGroup.getGroupCode().equals(newProjectIdentifier.getGroupCode()) == false)
+ {
+ throw new UserFailureException(
+ String
+ .format(
+ "Project cannot be changed to '%s' because experiment containes samples from group '%s'.",
+ newProjectIdentifier, sampleGroup));
+ }
+ }
+
+ public void editMaterial(String sessionToken, MaterialIdentifier identifier,
+ List<MaterialProperty> properties, Date version)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ final IMaterialBO materialBO = businessObjectFactory.createMaterialBO(session);
+ materialBO.edit(identifier, properties, version);
+ materialBO.save();
+
+ }
+
+ public void editSample(String sessionToken, SampleIdentifier identifier,
+ List<SampleProperty> properties, ExperimentIdentifier experimentIdentifierOrNull,
+ Date version)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ final ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
+ sampleBO.edit(identifier, properties, experimentIdentifierOrNull, version);
+ sampleBO.save();
+
+ }
+
+ public List<VocabularyTermWithStats> listVocabularyTerms(String sessionToken,
+ Vocabulary vocabulary)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ final IVocabularyBO vocabularyBO = businessObjectFactory.createVocabularyBO(session);
+ vocabularyBO.load(vocabulary);
+ return vocabularyBO.countTermsUsageStatistics();
+ }
+
+ public List<DataSetTypePE> listDataSetTypes(String sessionToken)
+ {
+ return listEntityTypes(sessionToken, EntityKind.DATA_SET);
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java
index ef782cd1d0c2e608a91739f7c878f92b5f9dd3b0..adc6c5dfa0ffdbbf16e931fce5d95a5bf77682bd 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java
@@ -65,296 +65,306 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
/**
- * Logger class for {@link CommonServer} which creates readable logs of method
- * invocations.
+ * Logger class for {@link CommonServer} which creates readable logs of method invocations.
*
* @author Franz-Josef Elmer
*/
-final class CommonServerLogger extends AbstractServerLogger implements
- ICommonServer {
- /**
- * Creates an instance for the specified session manager and invocation
- * status. The session manager is used to retrieve user information which
- * will be a part of the log message.
- */
- CommonServerLogger(final ISessionManager<Session> sessionManager,
- final boolean invocationSuccessful) {
- super(sessionManager, invocationSuccessful);
- }
-
- //
- // IGenericServer
- //
-
- public List<GroupPE> listGroups(final String sessionToken,
- final DatabaseInstanceIdentifier identifier) {
- final String command = "list_groups";
- if (identifier == null || identifier.getDatabaseInstanceCode() == null) {
- logAccess(sessionToken, command);
- } else {
- logAccess(sessionToken, command, "DATABASE-INSTANCE(%s)",
- identifier);
- }
- return null;
- }
-
- public void registerGroup(final String sessionToken,
- final String groupCode, final String descriptionOrNull,
- final String groupLeaderOrNull) {
- logTracking(sessionToken, "register_group", "CODE(%s)", groupCode);
- }
-
- public List<PersonPE> listPersons(final String sessionToken) {
- logAccess(sessionToken, "list_persons");
- return null;
- }
-
- public void registerPerson(final String sessionToken, final String userID) {
- logTracking(sessionToken, "register_person", "CODE(%s)", userID);
-
- }
-
- public List<RoleAssignmentPE> listRoles(final String sessionToken) {
- logAccess(sessionToken, "list_roles");
- return null;
- }
-
- public void registerGroupRole(final String sessionToken,
- final RoleCode roleCode, final GroupIdentifier groupIdentifier,
- final String person) {
- logTracking(sessionToken, "register_role",
- "ROLE(%s) GROUP(%s) PERSON(%s)", roleCode, groupIdentifier,
- person);
-
- }
-
- public void registerInstanceRole(final String sessionToken,
- final RoleCode roleCode, final String person) {
- logTracking(sessionToken, "register_role", "ROLE(%s) PERSON(%s)",
- roleCode, person);
-
- }
-
- public void deleteGroupRole(final String sessionToken,
- final RoleCode roleCode, final GroupIdentifier groupIdentifier,
- final String person) {
- logTracking(sessionToken, "delete_role",
- "ROLE(%s) GROUP(%s) PERSON(%s)", roleCode, groupIdentifier,
- person);
-
- }
-
- public void deleteInstanceRole(final String sessionToken,
- final RoleCode roleCode, final String person) {
- logTracking(sessionToken, "delete_role", "ROLE(%s) PERSON(%s)",
- roleCode, person);
-
- }
-
- public final List<SampleTypePE> listSampleTypes(final String sessionToken) {
- logAccess(sessionToken, "list_sample_types");
- return null;
- }
-
- public final List<SamplePE> listSamples(final String sessionToken,
- final ListSampleCriteriaDTO criteria) {
- logAccess(sessionToken, "list_samples",
- "TYPE(%s) OWNERS(%s) CONTAINER(%s) EXPERIMENT(%s)", criteria
- .getSampleType(), criteria.getOwnerIdentifiers(),
- criteria.getContainerIdentifier(), criteria
- .getExperimentIdentifier());
- return null;
- }
-
- public final List<SamplePropertyPE> listSamplesProperties(
- final String sessionToken, final ListSampleCriteriaDTO criteria,
- final List<PropertyTypePE> propertyCodes) {
- logAccess(sessionToken, "list_samples_properties",
- "CRITERIA(%s) PROPERTIES(%s)", criteria, propertyCodes.size());
- return null;
- }
-
- public final SampleGenerationDTO getSampleInfo(final String sessionToken,
- final SampleIdentifier identifier) {
- logAccess(sessionToken, "get_sample_info", "IDENTIFIER(%s)", identifier);
- return null;
- }
-
- public final List<ExternalDataPE> listExternalData(
- final String sessionToken, final SampleIdentifier identifier) {
- logAccess(sessionToken, "list_external_data", "IDENTIFIER(%s)",
- identifier);
- return null;
- }
-
- public List<ExternalDataPE> listExternalData(String sessionToken,
- ExperimentIdentifier identifier) {
- logAccess(sessionToken, "list_external_data", "IDENTIFIER(%s)",
- identifier);
- return null;
- }
-
- public final List<SearchHit> listMatchingEntities(
- final String sessionToken,
- final SearchableEntity[] searchableEntities, final String queryText) {
- logAccess(sessionToken, "list_matching_entities",
- "SEARCHABLE-ENTITIES(%s) QUERY-TEXT(%s)", Arrays
- .toString(searchableEntities), queryText);
- return null;
- }
-
- public void registerSample(final String sessionToken,
- final NewSample newSample) {
- logTracking(sessionToken, "register_sample",
- "SAMPLE_TYPE(%s) SAMPLE(%S)", newSample.getSampleType(),
- newSample.getIdentifier());
- }
-
- public List<ExperimentPE> listExperiments(final String sessionToken,
- final ExperimentTypePE experimentType,
- final ProjectIdentifier project) {
- logAccess(sessionToken, "list_experiments", "TYPE(%s) PROJECT(%s)",
- experimentType, project);
- return null;
- }
-
- public List<ProjectPE> listProjects(final String sessionToken) {
- logAccess(sessionToken, "list_projects");
- return null;
- }
-
- public List<ExperimentTypePE> listExperimentTypes(final String sessionToken) {
- logAccess(sessionToken, "list_experiment_types");
- return null;
- }
-
- public List<PropertyTypePE> listPropertyTypes(final String sessionToken) {
- logAccess(sessionToken, "list_property_types");
- return null;
- }
-
- public final List<DataTypePE> listDataTypes(final String sessionToken) {
- logAccess(sessionToken, "list_data_types");
- return null;
- }
-
- public final List<VocabularyPE> listVocabularies(final String sessionToken,
- boolean withTerms, boolean excludeInternal) {
- logAccess(sessionToken, "list_vocabularies");
- return null;
- }
-
- public String assignPropertyType(final String sessionToken,
- final EntityKind entityKind, final String propertyTypeCode,
- final String entityTypeCode, final boolean isMandatory,
- final String defaultValue) {
- final String entityTypeFormat = entityKind.name() + "_TYPE(%S)";
- logTracking(sessionToken, "assign_property_type", " PROPERTY_TYPE(%S) "
- + entityTypeFormat + " MANDATORY(%S) DEFAULT(%S)",
- propertyTypeCode, entityTypeCode, isMandatory, defaultValue);
- return null;
- }
-
- public final void registerPropertyType(final String sessionToken,
- final PropertyType propertyType) {
- logTracking(sessionToken, "register_property_type",
- "PROPERTY_TYPE(%s)", propertyType.getCode());
- }
-
- public final void registerVocabulary(final String sessionToken,
- final Vocabulary vocabulary) {
- logTracking(sessionToken, "register_vocabulary", "VOCABULARY(%s)",
- vocabulary.getCode());
- }
-
- public void registerProject(String sessionToken,
- ProjectIdentifier projectIdentifier, String description,
- String leaderId) {
- logTracking(sessionToken, "register_project", "PROJECT(%s)",
- projectIdentifier);
- }
-
- public List<ExternalDataPE> searchForDataSets(String sessionToken,
- DataSetSearchCriteria criteria) {
- logAccess(sessionToken, "search_for_datasets");
- return null;
- }
-
- public List<MaterialTypePE> listMaterialTypes(String sessionToken) {
- logAccess(sessionToken, "list_material_types");
- return null;
- }
-
- public List<MaterialPE> listMaterials(String sessionToken,
- MaterialTypePE materialType) {
- logAccess(sessionToken, "list_materials", "TYPE(%s)", materialType);
- return null;
- }
-
- public void registerMaterialType(String sessionToken,
- MaterialType entityType) {
- logTracking(sessionToken, "register_material_type", "CODE(%s)",
- entityType.getCode());
- }
-
- public void registerSampleType(String sessionToken, SampleType entityType) {
- logTracking(sessionToken, "register_sample_type", "CODE(%s)",
- entityType.getCode());
- }
-
- public void registerExperimentType(String sessionToken,
- ExperimentType entityType) {
- logTracking(sessionToken, "register_experiment_type", "CODE(%s)",
- entityType.getCode());
- }
-
- public void editExperiment(String sessionToken,
- ExperimentIdentifier experimentIdentifier,
- List<ExperimentProperty> properties,
- List<AttachmentPE> attachments,
- ProjectIdentifier newProjectIdentifierOrNull, Date version) {
- logTracking(sessionToken, "edit_experiment",
- "EXPERIMENT(%s) ATTACHMENTS_ADDED(%s) NEW_PROJECT(%s)",
- experimentIdentifier, attachments.size(),
- newProjectIdentifierOrNull);
- }
-
- public void deleteDataSets(String sessionToken, List<String> dataSetCodes,
- String reason) {
- logTracking(sessionToken, "delete_data_sets", "CODES(%s) REASON(%s)",
- dataSetCodes, reason);
- }
+final class CommonServerLogger extends AbstractServerLogger implements ICommonServer
+{
+ /**
+ * Creates an instance for the specified session manager and invocation status. The session
+ * manager is used to retrieve user information which will be a part of the log message.
+ */
+ CommonServerLogger(final ISessionManager<Session> sessionManager,
+ final boolean invocationSuccessful)
+ {
+ super(sessionManager, invocationSuccessful);
+ }
+
+ //
+ // IGenericServer
+ //
+
+ public List<GroupPE> listGroups(final String sessionToken,
+ final DatabaseInstanceIdentifier identifier)
+ {
+ final String command = "list_groups";
+ if (identifier == null || identifier.getDatabaseInstanceCode() == null)
+ {
+ logAccess(sessionToken, command);
+ } else
+ {
+ logAccess(sessionToken, command, "DATABASE-INSTANCE(%s)", identifier);
+ }
+ return null;
+ }
+
+ public void registerGroup(final String sessionToken, final String groupCode,
+ final String descriptionOrNull, final String groupLeaderOrNull)
+ {
+ logTracking(sessionToken, "register_group", "CODE(%s)", groupCode);
+ }
+
+ public List<PersonPE> listPersons(final String sessionToken)
+ {
+ logAccess(sessionToken, "list_persons");
+ return null;
+ }
+
+ public void registerPerson(final String sessionToken, final String userID)
+ {
+ logTracking(sessionToken, "register_person", "CODE(%s)", userID);
+
+ }
+
+ public List<RoleAssignmentPE> listRoles(final String sessionToken)
+ {
+ logAccess(sessionToken, "list_roles");
+ return null;
+ }
+
+ public void registerGroupRole(final String sessionToken, final RoleCode roleCode,
+ final GroupIdentifier groupIdentifier, final String person)
+ {
+ logTracking(sessionToken, "register_role", "ROLE(%s) GROUP(%s) PERSON(%s)", roleCode,
+ groupIdentifier, person);
+
+ }
+
+ public void registerInstanceRole(final String sessionToken, final RoleCode roleCode,
+ final String person)
+ {
+ logTracking(sessionToken, "register_role", "ROLE(%s) PERSON(%s)", roleCode, person);
+
+ }
+
+ public void deleteGroupRole(final String sessionToken, final RoleCode roleCode,
+ final GroupIdentifier groupIdentifier, final String person)
+ {
+ logTracking(sessionToken, "delete_role", "ROLE(%s) GROUP(%s) PERSON(%s)", roleCode,
+ groupIdentifier, person);
+
+ }
+
+ public void deleteInstanceRole(final String sessionToken, final RoleCode roleCode,
+ final String person)
+ {
+ logTracking(sessionToken, "delete_role", "ROLE(%s) PERSON(%s)", roleCode, person);
+
+ }
+
+ public final List<SampleTypePE> listSampleTypes(final String sessionToken)
+ {
+ logAccess(sessionToken, "list_sample_types");
+ return null;
+ }
+
+ public final List<SamplePE> listSamples(final String sessionToken,
+ final ListSampleCriteriaDTO criteria)
+ {
+ logAccess(sessionToken, "list_samples", "TYPE(%s) OWNERS(%s) CONTAINER(%s) EXPERIMENT(%s)",
+ criteria.getSampleType(), criteria.getOwnerIdentifiers(), criteria
+ .getContainerIdentifier(), criteria.getExperimentIdentifier());
+ return null;
+ }
+
+ public final List<SamplePropertyPE> listSamplesProperties(final String sessionToken,
+ final ListSampleCriteriaDTO criteria, final List<PropertyTypePE> propertyCodes)
+ {
+ logAccess(sessionToken, "list_samples_properties", "CRITERIA(%s) PROPERTIES(%s)", criteria,
+ propertyCodes.size());
+ return null;
+ }
+
+ public final SampleGenerationDTO getSampleInfo(final String sessionToken,
+ final SampleIdentifier identifier)
+ {
+ logAccess(sessionToken, "get_sample_info", "IDENTIFIER(%s)", identifier);
+ return null;
+ }
+
+ public final List<ExternalDataPE> listExternalData(final String sessionToken,
+ final SampleIdentifier identifier)
+ {
+ logAccess(sessionToken, "list_external_data", "IDENTIFIER(%s)", identifier);
+ return null;
+ }
+
+ public List<ExternalDataPE> listExternalData(String sessionToken,
+ ExperimentIdentifier identifier)
+ {
+ logAccess(sessionToken, "list_external_data", "IDENTIFIER(%s)", identifier);
+ return null;
+ }
+
+ public final List<SearchHit> listMatchingEntities(final String sessionToken,
+ final SearchableEntity[] searchableEntities, final String queryText)
+ {
+ logAccess(sessionToken, "list_matching_entities", "SEARCHABLE-ENTITIES(%s) QUERY-TEXT(%s)",
+ Arrays.toString(searchableEntities), queryText);
+ return null;
+ }
+
+ public void registerSample(final String sessionToken, final NewSample newSample)
+ {
+ logTracking(sessionToken, "register_sample", "SAMPLE_TYPE(%s) SAMPLE(%S)", newSample
+ .getSampleType(), newSample.getIdentifier());
+ }
+
+ public List<ExperimentPE> listExperiments(final String sessionToken,
+ final ExperimentTypePE experimentType, final ProjectIdentifier project)
+ {
+ logAccess(sessionToken, "list_experiments", "TYPE(%s) PROJECT(%s)", experimentType, project);
+ return null;
+ }
+
+ public List<ProjectPE> listProjects(final String sessionToken)
+ {
+ logAccess(sessionToken, "list_projects");
+ return null;
+ }
+
+ public List<ExperimentTypePE> listExperimentTypes(final String sessionToken)
+ {
+ logAccess(sessionToken, "list_experiment_types");
+ return null;
+ }
+
+ public List<PropertyTypePE> listPropertyTypes(final String sessionToken)
+ {
+ logAccess(sessionToken, "list_property_types");
+ return null;
+ }
+
+ public final List<DataTypePE> listDataTypes(final String sessionToken)
+ {
+ logAccess(sessionToken, "list_data_types");
+ return null;
+ }
+
+ public final List<VocabularyPE> listVocabularies(final String sessionToken, boolean withTerms,
+ boolean excludeInternal)
+ {
+ logAccess(sessionToken, "list_vocabularies");
+ return null;
+ }
+
+ public String assignPropertyType(final String sessionToken, final EntityKind entityKind,
+ final String propertyTypeCode, final String entityTypeCode, final boolean isMandatory,
+ final String defaultValue)
+ {
+ final String entityTypeFormat = entityKind.name() + "_TYPE(%S)";
+ logTracking(sessionToken, "assign_property_type", " PROPERTY_TYPE(%S) " + entityTypeFormat
+ + " MANDATORY(%S) DEFAULT(%S)", propertyTypeCode, entityTypeCode, isMandatory,
+ defaultValue);
+ return null;
+ }
+
+ public final void registerPropertyType(final String sessionToken,
+ final PropertyType propertyType)
+ {
+ logTracking(sessionToken, "register_property_type", "PROPERTY_TYPE(%s)", propertyType
+ .getCode());
+ }
+
+ public final void registerVocabulary(final String sessionToken, final Vocabulary vocabulary)
+ {
+ logTracking(sessionToken, "register_vocabulary", "VOCABULARY(%s)", vocabulary.getCode());
+ }
+
+ public void addVocabularyTerms(String sessionToken, String vocabularyCode,
+ List<String> vocabularyTerms)
+ {
+ logTracking(sessionToken, "add_vocabulary_terms", "VOCABULARY(%s) NUMBER_OF_TERMS(%s)",
+ vocabularyCode, Integer.toString(vocabularyTerms.size()));
+ }
+
+ public void registerProject(String sessionToken, ProjectIdentifier projectIdentifier,
+ String description, String leaderId)
+ {
+ logTracking(sessionToken, "register_project", "PROJECT(%s)", projectIdentifier);
+ }
+
+ public List<ExternalDataPE> searchForDataSets(String sessionToken,
+ DataSetSearchCriteria criteria)
+ {
+ logAccess(sessionToken, "search_for_datasets");
+ return null;
+ }
+
+ public List<MaterialTypePE> listMaterialTypes(String sessionToken)
+ {
+ logAccess(sessionToken, "list_material_types");
+ return null;
+ }
+
+ public List<MaterialPE> listMaterials(String sessionToken, MaterialTypePE materialType)
+ {
+ logAccess(sessionToken, "list_materials", "TYPE(%s)", materialType);
+ return null;
+ }
+
+ public void registerMaterialType(String sessionToken, MaterialType entityType)
+ {
+ logTracking(sessionToken, "register_material_type", "CODE(%s)", entityType.getCode());
+ }
+
+ public void registerSampleType(String sessionToken, SampleType entityType)
+ {
+ logTracking(sessionToken, "register_sample_type", "CODE(%s)", entityType.getCode());
+ }
+
+ public void registerExperimentType(String sessionToken, ExperimentType entityType)
+ {
+ logTracking(sessionToken, "register_experiment_type", "CODE(%s)", entityType.getCode());
+ }
+
+ public void editExperiment(String sessionToken, ExperimentIdentifier experimentIdentifier,
+ List<ExperimentProperty> properties, List<AttachmentPE> attachments,
+ ProjectIdentifier newProjectIdentifierOrNull, Date version)
+ {
+ logTracking(sessionToken, "edit_experiment",
+ "EXPERIMENT(%s) ATTACHMENTS_ADDED(%s) NEW_PROJECT(%s)", experimentIdentifier,
+ attachments.size(), newProjectIdentifierOrNull);
+ }
+
+ public void deleteDataSets(String sessionToken, List<String> dataSetCodes, String reason)
+ {
+ logTracking(sessionToken, "delete_data_sets", "CODES(%s) REASON(%s)", dataSetCodes, reason);
+ }
public void uploadDataSets(String sessionToken, List<String> dataSetCodes, String cifexURL,
String password)
{
- logTracking(sessionToken, "upload_data_sets", "CODES(%s) CIFEX-URL(%s)", dataSetCodes, cifexURL);
+ logTracking(sessionToken, "upload_data_sets", "CODES(%s) CIFEX-URL(%s)", dataSetCodes,
+ cifexURL);
}
public void editMaterial(String sessionToken, MaterialIdentifier identifier,
List<MaterialProperty> properties, Date version)
{
logTracking(sessionToken, "edit_material", "MATERIAL(%s)", identifier);
- }
-
- public void editSample(String sessionToken, SampleIdentifier identifier,
- List<SampleProperty> properties,
- ExperimentIdentifier experimentIdentifierOrNull, Date version) {
- logTracking(sessionToken, "edit_sample",
- "SAMPLE(%s), CHANGE_TO_EXPERIMENT(%S)", identifier,
- experimentIdentifierOrNull);
-
- }
-
- public List<VocabularyTermWithStats> listVocabularyTerms(
- String sessionToken, Vocabulary vocabulary) {
- logAccess(sessionToken, "list_vocabulary_terms", "VOCABULARY(%s)",
- vocabulary.getCode());
- return null;
- }
-
- public List<DataSetTypePE> listDataSetTypes(String sessionToken) {
- logAccess(sessionToken, "list_data_set_types");
- return null;
- }
+ }
+
+ public void editSample(String sessionToken, SampleIdentifier identifier,
+ List<SampleProperty> properties, ExperimentIdentifier experimentIdentifierOrNull,
+ Date version)
+ {
+ logTracking(sessionToken, "edit_sample", "SAMPLE(%s), CHANGE_TO_EXPERIMENT(%S)",
+ identifier, experimentIdentifierOrNull);
+
+ }
+
+ public List<VocabularyTermWithStats> listVocabularyTerms(String sessionToken,
+ Vocabulary vocabulary)
+ {
+ logAccess(sessionToken, "list_vocabulary_terms", "VOCABULARY(%s)", vocabulary.getCode());
+ return null;
+ }
+
+ public List<DataSetTypePE> listDataSetTypes(String sessionToken)
+ {
+ logAccess(sessionToken, "list_data_set_types");
+ return null;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
index 7d069ee3a1532fa32e4c5e2a534c259762189886..e67f1eb952164c490cc8f5b265f51f164d2018f0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
@@ -284,6 +284,14 @@ public interface ICommonServer extends IServer
@RolesAllowed(RoleSet.INSTANCE_ADMIN)
public void registerVocabulary(final String sessionToken, final Vocabulary vocabulary);
+ /**
+ * Adds new terms to a vocabulary.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void addVocabularyTerms(String sessionToken, String vocabularyCode,
+ List<String> vocabularyTerms);
+
/**
* Registers new project.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/public/common-dictionary.js b/openbis/source/java/ch/systemsx/cisd/openbis/public/common-dictionary.js
index e57053c22a95f040b95556ceaa8b9fdeda4fc485..9d15068eedf5a349cc0c70e7e4e4b0885e55efcc 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/public/common-dictionary.js
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/public/common-dictionary.js
@@ -145,7 +145,7 @@ var common = {
type_of: "Entity",
vocabulary: "Vocabulary",
vocabulary_terms: "Terms",
- vocabulary_terms_empty: "White space or comma separated list",
+ vocabulary_terms_empty: "Space or comma separated list",
mandatory: "Mandatory",
default_value: "Initial Value",
default_value_tooltip: "The value of the assigned property for all currently existing entities.",
@@ -248,6 +248,10 @@ var common = {
TERM_FOR_EXPERIMENTS_USAGE: "Usages for Experiments",
TERM_FOR_MATERIALS_USAGE: "Usages for Materials",
TERM_TOTAL_USAGE: "Total Usages Number",
+ add_vocabulary_terms_button: "Add New Terms",
+ add_vocabulary_terms_title: "Add New Terms",
+ add_vocabulary_terms_ok_button: "OK",
+ vocabulary_terms_validation_message: "Term '{0}' already exists.",
//
// Project Browser