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 107ecdf97707456dafe64522da753ab7ac859b41..807c9bac0b5544581fd59c554262dd11580dfaa1 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
@@ -39,6 +39,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteri
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.VocabularyTermWithStats;
import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetSearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
@@ -59,316 +60,377 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
*
* @author Franz-Josef Elmer
*/
-public interface ICommonClientService extends IClientService
-{
- /**
- * Returns a list of all groups which belong to the specified database instance.
- */
- public List<Group> listGroups(String databaseInstanceCode) throws UserFailureException;
-
- /**
- * Registers a new group with specified code and optional description and group leader ID.
- */
- public void registerGroup(String groupCode, String descriptionOrNull, String groupLeaderOrNull)
- throws UserFailureException;
-
- /**
- * Returns a list of all persons which belong to the current database instance.
- */
- public List<Person> listPersons() throws UserFailureException;
-
- /**
- * Registers a new person with specified code.
- */
- public void registerPerson(String code) throws UserFailureException;
-
- /**
- * Returns a list of all roles.
- */
- public List<RoleAssignment> listRoles() throws UserFailureException;
-
- /**
- * Registers a new role from given role set code, group code and person code
- */
- public void registerGroupRole(RoleSetCode roleSetCode, String group, String person)
- throws UserFailureException;
-
- /**
- * Deletes the role described by given role set code, group code and person code
- */
- public void deleteGroupRole(RoleSetCode roleSetCode, String group, String person)
- throws UserFailureException;
-
- /**
- * Registers a new role from given role set code and person code
- */
- public void registerInstanceRole(RoleSetCode roleSetCode, String person)
- throws UserFailureException;
-
- /**
- * Deletes the role described by given role set code and person code
- */
- public void deleteInstanceRole(RoleSetCode roleSetCode, String person)
- throws UserFailureException;
-
- /**
- * Returns a list of sample types.
- */
- public List<SampleType> listSampleTypes() throws UserFailureException;
-
- /**
- * Returns a list of samples for given sample type.
- */
- public ResultSet<Sample> listSamples(final ListSampleCriteria criteria)
- throws UserFailureException;
-
- /**
- * Returns a key which can be used be the export servlet (and eventually
- * {@link #getExportTable(String, String)}) to reference the export criteria in an easy way.
- */
- public String prepareExportSamples(final TableExportCriteria<Sample> criteria)
- throws UserFailureException;
-
- /**
- * Returns a list of experiments.
- */
- public ResultSet<Experiment> listExperiments(final ListExperimentsCriteria criteria)
- throws UserFailureException;
-
- /**
- * Returns a list of materials.
- */
- public ResultSet<Material> listMaterials(final ListMaterialCriteria criteria)
- throws UserFailureException;
-
- /**
- * Like {@link #prepareExportSamples(TableExportCriteria)}, but for experiments.
- */
-
- public String prepareExportExperiments(final TableExportCriteria<Experiment> criteria)
- throws UserFailureException;
-
- /**
- * Like {@link #prepareExportSamples(TableExportCriteria)}, but for data set search hits.
- */
- public String prepareExportDataSetSearchHits(TableExportCriteria<ExternalData> exportCriteria)
- throws UserFailureException;
-
- /**
- * Lists the entities matching the search.
- */
- public ResultSet<MatchingEntity> listMatchingEntities(
- final SearchableEntity searchableEntityOrNull, final String queryText,
- final IResultSetConfig<String, MatchingEntity> resultSetConfig)
- throws UserFailureException;
-
- /**
- * Like {@link #prepareExportSamples(TableExportCriteria)}, but for matching entites.
- */
- public String prepareExportMatchingEntities(final TableExportCriteria<MatchingEntity> criteria)
- throws UserFailureException;
-
- /**
- * Returns a chunk of the property types list.
- */
- public ResultSet<PropertyType> listPropertyTypes(
- DefaultResultSetConfig<String, PropertyType> criteria) throws UserFailureException;
-
- /**
- * Like {@link #prepareExportSamples(TableExportCriteria)}, but for property types.
- */
- public String prepareExportPropertyTypes(final TableExportCriteria<PropertyType> criteria)
- throws UserFailureException;
-
- /**
- * Returns a chunk of the property types assignment list.
- */
- public ResultSet<EntityTypePropertyType<?>> listPropertyTypeAssignments(
- DefaultResultSetConfig<String, EntityTypePropertyType<?>> criteria);
-
- /**
- * Like {@link #prepareExportSamples(TableExportCriteria)}, but for property types assignments.
- */
- public String prepareExportPropertyTypeAssignments(
- final TableExportCriteria<EntityTypePropertyType<?>> criteria)
- throws UserFailureException;
-
- /**
- * Returns a list of all projects.
- */
- public ResultSet<Project> listProjects(DefaultResultSetConfig<String, Project> criteria)
- throws UserFailureException;
-
- /**
- * Like {@link #prepareExportSamples(TableExportCriteria)}, but for projects.
- */
- public String prepareExportProjects(final TableExportCriteria<Project> criteria)
- throws UserFailureException;
-
- /**
- * Returns a list of all vocabularies.
- * <p>
- * Note that the vocabulary terms are included/loaded.
- * </p>
- */
- public ResultSet<Vocabulary> listVocabularies(boolean withTerms, boolean excludeInternal,
- DefaultResultSetConfig<String, Vocabulary> criteria) throws UserFailureException;
-
- /**
- * Like {@link #prepareExportSamples(TableExportCriteria)}, but for Vocabularies.
- */
- public String prepareExportVocabularies(final TableExportCriteria<Vocabulary> criteria)
- throws UserFailureException;
-
- /**
- * Returns a list of all vocabulary terms for a specified vocabulary.
- */
- public ResultSet<VocabularyTermWithStats> listVocabularyTerms(Vocabulary vocabulary,
- DefaultResultSetConfig<String, VocabularyTermWithStats> resultSetConfig);
-
- /**
- * Like {@link #prepareExportSamples(TableExportCriteria)}, but for Vocabulary Terms.
- */
- public String prepareExportVocabularyTerms(TableExportCriteria<VocabularyTermWithStats> criteria);
-
- public ResultSet<? extends EntityType> listMaterialTypes(
- DefaultResultSetConfig<String, MaterialType> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
-
- /**
- * Like {@link #prepareExportSamples(TableExportCriteria)}, but for MaterialType.
- */
- public String prepareExportMaterialTypes(final TableExportCriteria<MaterialType> criteria)
- throws UserFailureException;
-
- public ResultSet<? extends EntityType> listSampleTypes(
- DefaultResultSetConfig<String, SampleType> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
-
- /**
- * Like {@link #prepareExportSamples(TableExportCriteria)}, but for SampleType.
- */
- public String prepareExportSampleTypes(final TableExportCriteria<SampleType> criteria)
- throws UserFailureException;
-
- public ResultSet<? extends EntityType> listExperimentTypes(
- DefaultResultSetConfig<String, ExperimentType> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
-
- /**
- * Like {@link #prepareExportSamples(TableExportCriteria)}, but for ExperimentType.
- */
- public String prepareExportExperimentTypes(final TableExportCriteria<ExperimentType> criteria)
- throws UserFailureException;
-
- /**
- * Assumes that preparation of the export ({@link #prepareExportSamples(TableExportCriteria)}
- * or {@link #prepareExportExperiments(TableExportCriteria)} has been invoked before and
- * returned with an exportDataKey passed here as a parameter.
- */
- public String getExportTable(String exportDataKey, String lineSeparator)
- throws UserFailureException;
-
- /**
- * Removes the session result set associated with given key.
- */
- public void removeResultSet(final String resultSetKey) throws UserFailureException;
-
- /**
- * For given <var>sampleIdentifier</var> returns corresponding list of {@link ExternalData}.
- */
- public ResultSet<ExternalData> listSampleDataSets(final String sampleIdentifier,
- DefaultResultSetConfig<String, ExternalData> criteria) throws UserFailureException;
-
- public ResultSet<ExternalData> listExperimentDataSets(String experimentIdentifier,
- DefaultResultSetConfig<String, ExternalData> criteria) throws UserFailureException;
-
- /**
- * Lists the searchable entities.
- */
- public List<SearchableEntity> listSearchableEntities() throws UserFailureException;
-
- /**
- * Returns a list of all experiment types.
- */
- public List<ExperimentType> listExperimentTypes() throws UserFailureException;
-
- /**
- * Returns a list of all data types.
- */
- public List<DataType> listDataTypes() throws UserFailureException;
-
- /**
- * Assigns property type to entity type.
- */
- public String assignPropertyType(EntityKind entityKind, String propertyTypeCode,
- String entityTypeCode, boolean isMandatory, String defaultValue)
- throws UserFailureException;
-
- /**
- * Registers given {@link PropertyType}.
- */
- public void registerPropertyType(final PropertyType propertyType) throws UserFailureException;
-
- /**
- * Registers given {@link Vocabulary}.
- */
- public void registerVocabulary(final Vocabulary vocabulary) throws UserFailureException;
-
- /**
- * Registers given {@link Project}.
- */
- public void registerProject(final Project project) throws UserFailureException;
-
- /**
- * Returns {@link ExternalData} fulfilling given {@link DataSetSearchCriteria}.
- */
- public ResultSet<ExternalData> searchForDataSets(DataSetSearchCriteria criteria,
- final IResultSetConfig<String, ExternalData> resultSetConfig)
- throws UserFailureException;
-
- /**
- * Returns a list of all material types.
- */
- public List<MaterialType> listMaterialTypes() throws UserFailureException;
-
- /**
- * Like {@link #prepareExportSamples(TableExportCriteria)}, but for materials.
- */
- public String prepareExportMaterials(final TableExportCriteria<Material> criteria)
- throws UserFailureException;
-
- /** Registers a new material type */
- public void registerMaterialType(MaterialType entityType) throws UserFailureException;
-
- /** Registers a new sample type */
- public void registerSampleType(SampleType entityType) throws UserFailureException;
-
- /** Registers a new experiment type */
- public void registerExperimentType(ExperimentType entityType) throws UserFailureException;
-
- /**
- * Updates experiment.
- */
- public void updateExperiment(String attachmentSessionKey, final String experimentIdentifier,
- List<ExperimentProperty> properties, String newProjectIdentifier, Date version)
- throws UserFailureException;
-
- /**
- * Updates material.
- */
- public void updateMaterial(final String materialIdentifier, List<MaterialProperty> properties,
- Date version) throws UserFailureException;
-
- /**
- * Updates sample.
- */
- public void updateSample(final String sampleIdentifier, List<SampleProperty> properties,
- ExperimentIdentifier experimentIdentifierOrNull, Date version)
- throws UserFailureException;
-
- /** Deletes the specified data sets. */
- public void deleteDataSets(List<String> dataSetCodes, String reason)
- throws UserFailureException;
+public interface ICommonClientService extends IClientService {
+ /**
+ * Returns a list of all groups which belong to the specified database
+ * instance.
+ */
+ public List<Group> listGroups(String databaseInstanceCode)
+ throws UserFailureException;
+
+ /**
+ * Registers a new group with specified code and optional description and
+ * group leader ID.
+ */
+ public void registerGroup(String groupCode, String descriptionOrNull,
+ String groupLeaderOrNull) throws UserFailureException;
+
+ /**
+ * Returns a list of all persons which belong to the current database
+ * instance.
+ */
+ public List<Person> listPersons() throws UserFailureException;
+
+ /**
+ * Registers a new person with specified code.
+ */
+ public void registerPerson(String code) throws UserFailureException;
+
+ /**
+ * Returns a list of all roles.
+ */
+ public List<RoleAssignment> listRoles() throws UserFailureException;
+
+ /**
+ * Registers a new role from given role set code, group code and person code
+ */
+ public void registerGroupRole(RoleSetCode roleSetCode, String group,
+ String person) throws UserFailureException;
+
+ /**
+ * Deletes the role described by given role set code, group code and person
+ * code
+ */
+ public void deleteGroupRole(RoleSetCode roleSetCode, String group,
+ String person) throws UserFailureException;
+
+ /**
+ * Registers a new role from given role set code and person code
+ */
+ public void registerInstanceRole(RoleSetCode roleSetCode, String person)
+ throws UserFailureException;
+
+ /**
+ * Deletes the role described by given role set code and person code
+ */
+ public void deleteInstanceRole(RoleSetCode roleSetCode, String person)
+ throws UserFailureException;
+
+ /**
+ * Returns a list of sample types.
+ */
+ public List<SampleType> listSampleTypes() throws UserFailureException;
+
+ /**
+ * Returns a list of samples for given sample type.
+ */
+ public ResultSet<Sample> listSamples(final ListSampleCriteria criteria)
+ throws UserFailureException;
+
+ /**
+ * Returns a key which can be used be the export servlet (and eventually
+ * {@link #getExportTable(String, String)}) to reference the export criteria
+ * in an easy way.
+ */
+ public String prepareExportSamples(
+ final TableExportCriteria<Sample> criteria)
+ throws UserFailureException;
+
+ /**
+ * Returns a list of experiments.
+ */
+ public ResultSet<Experiment> listExperiments(
+ final ListExperimentsCriteria criteria) throws UserFailureException;
+
+ /**
+ * Returns a list of materials.
+ */
+ public ResultSet<Material> listMaterials(final ListMaterialCriteria criteria)
+ throws UserFailureException;
+
+ /**
+ * Like {@link #prepareExportSamples(TableExportCriteria)}, but for
+ * experiments.
+ */
+
+ public String prepareExportExperiments(
+ final TableExportCriteria<Experiment> criteria)
+ throws UserFailureException;
+
+ /**
+ * Like {@link #prepareExportSamples(TableExportCriteria)}, but for data set
+ * search hits.
+ */
+ public String prepareExportDataSetSearchHits(
+ TableExportCriteria<ExternalData> exportCriteria)
+ throws UserFailureException;
+
+ /**
+ * Lists the entities matching the search.
+ */
+ public ResultSet<MatchingEntity> listMatchingEntities(
+ final SearchableEntity searchableEntityOrNull,
+ final String queryText,
+ final IResultSetConfig<String, MatchingEntity> resultSetConfig)
+ throws UserFailureException;
+
+ /**
+ * Like {@link #prepareExportSamples(TableExportCriteria)}, but for matching
+ * entites.
+ */
+ public String prepareExportMatchingEntities(
+ final TableExportCriteria<MatchingEntity> criteria)
+ throws UserFailureException;
+
+ /**
+ * Returns a chunk of the property types list.
+ */
+ public ResultSet<PropertyType> listPropertyTypes(
+ DefaultResultSetConfig<String, PropertyType> criteria)
+ throws UserFailureException;
+
+ /**
+ * Like {@link #prepareExportSamples(TableExportCriteria)}, but for property
+ * types.
+ */
+ public String prepareExportPropertyTypes(
+ final TableExportCriteria<PropertyType> criteria)
+ throws UserFailureException;
+
+ /**
+ * Returns a chunk of the property types assignment list.
+ */
+ public ResultSet<EntityTypePropertyType<?>> listPropertyTypeAssignments(
+ DefaultResultSetConfig<String, EntityTypePropertyType<?>> criteria);
+
+ /**
+ * Like {@link #prepareExportSamples(TableExportCriteria)}, but for property
+ * types assignments.
+ */
+ public String prepareExportPropertyTypeAssignments(
+ final TableExportCriteria<EntityTypePropertyType<?>> criteria)
+ throws UserFailureException;
+
+ /**
+ * Returns a list of all projects.
+ */
+ public ResultSet<Project> listProjects(
+ DefaultResultSetConfig<String, Project> criteria)
+ throws UserFailureException;
+
+ /**
+ * Like {@link #prepareExportSamples(TableExportCriteria)}, but for
+ * projects.
+ */
+ public String prepareExportProjects(
+ final TableExportCriteria<Project> criteria)
+ throws UserFailureException;
+
+ /**
+ * Returns a list of all vocabularies.
+ * <p>
+ * Note that the vocabulary terms are included/loaded.
+ * </p>
+ */
+ public ResultSet<Vocabulary> listVocabularies(boolean withTerms,
+ boolean excludeInternal,
+ DefaultResultSetConfig<String, Vocabulary> criteria)
+ throws UserFailureException;
+
+ /**
+ * Like {@link #prepareExportSamples(TableExportCriteria)}, but for
+ * Vocabularies.
+ */
+ public String prepareExportVocabularies(
+ final TableExportCriteria<Vocabulary> criteria)
+ throws UserFailureException;
+
+ /**
+ * Returns a list of all vocabulary terms for a specified vocabulary.
+ */
+ public ResultSet<VocabularyTermWithStats> listVocabularyTerms(
+ Vocabulary vocabulary,
+ DefaultResultSetConfig<String, VocabularyTermWithStats> resultSetConfig);
+
+ /**
+ * Like {@link #prepareExportSamples(TableExportCriteria)}, but for
+ * Vocabulary Terms.
+ */
+ public String prepareExportVocabularyTerms(
+ TableExportCriteria<VocabularyTermWithStats> criteria);
+
+ public ResultSet<? extends EntityType> listMaterialTypes(
+ DefaultResultSetConfig<String, MaterialType> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
+
+ /**
+ * Like {@link #prepareExportSamples(TableExportCriteria)}, but for
+ * MaterialType.
+ */
+ public String prepareExportMaterialTypes(
+ final TableExportCriteria<MaterialType> criteria)
+ throws UserFailureException;
+
+ public ResultSet<? extends EntityType> listSampleTypes(
+ DefaultResultSetConfig<String, SampleType> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
+
+ /**
+ * Like {@link #prepareExportSamples(TableExportCriteria)}, but for
+ * SampleType.
+ */
+ public String prepareExportSampleTypes(
+ final TableExportCriteria<SampleType> criteria)
+ throws UserFailureException;
+
+ public ResultSet<? extends EntityType> listExperimentTypes(
+ DefaultResultSetConfig<String, ExperimentType> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
+
+ /**
+ * Like {@link #prepareExportSamples(TableExportCriteria)}, but for
+ * ExperimentType.
+ */
+ public String prepareExportExperimentTypes(
+ final TableExportCriteria<ExperimentType> criteria)
+ throws UserFailureException;
+
+ /**
+ * Assumes that preparation of the export (
+ * {@link #prepareExportSamples(TableExportCriteria)} or
+ * {@link #prepareExportExperiments(TableExportCriteria)} has been invoked
+ * before and returned with an exportDataKey passed here as a parameter.
+ */
+ public String getExportTable(String exportDataKey, String lineSeparator)
+ throws UserFailureException;
+
+ /**
+ * Removes the session result set associated with given key.
+ */
+ public void removeResultSet(final String resultSetKey)
+ throws UserFailureException;
+
+ /**
+ * For given <var>sampleIdentifier</var> returns corresponding list of
+ * {@link ExternalData}.
+ */
+ public ResultSet<ExternalData> listSampleDataSets(
+ final String sampleIdentifier,
+ DefaultResultSetConfig<String, ExternalData> criteria)
+ throws UserFailureException;
+
+ public ResultSet<ExternalData> listExperimentDataSets(
+ String experimentIdentifier,
+ DefaultResultSetConfig<String, ExternalData> criteria)
+ throws UserFailureException;
+
+ /**
+ * Lists the searchable entities.
+ */
+ public List<SearchableEntity> listSearchableEntities()
+ throws UserFailureException;
+
+ /**
+ * Returns a list of all experiment types.
+ */
+ public List<ExperimentType> listExperimentTypes()
+ throws UserFailureException;
+
+ /**
+ * Returns a list of all data types.
+ */
+ public List<DataType> listDataTypes() throws UserFailureException;
+
+ /**
+ * Assigns property type to entity type.
+ */
+ public String assignPropertyType(EntityKind entityKind,
+ String propertyTypeCode, String entityTypeCode,
+ boolean isMandatory, String defaultValue)
+ throws UserFailureException;
+
+ /**
+ * Registers given {@link PropertyType}.
+ */
+ public void registerPropertyType(final PropertyType propertyType)
+ throws UserFailureException;
+
+ /**
+ * Registers given {@link Vocabulary}.
+ */
+ public void registerVocabulary(final Vocabulary vocabulary)
+ throws UserFailureException;
+
+ /**
+ * Registers given {@link Project}.
+ */
+ public void registerProject(final Project project)
+ throws UserFailureException;
+
+ /**
+ * Returns {@link ExternalData} fulfilling given
+ * {@link DataSetSearchCriteria}.
+ */
+ public ResultSet<ExternalData> searchForDataSets(
+ DataSetSearchCriteria criteria,
+ final IResultSetConfig<String, ExternalData> resultSetConfig)
+ throws UserFailureException;
+
+ /**
+ * Returns a list of all material types.
+ */
+ public List<MaterialType> listMaterialTypes() throws UserFailureException;
+
+ /**
+ * Like {@link #prepareExportSamples(TableExportCriteria)}, but for
+ * materials.
+ */
+ public String prepareExportMaterials(
+ final TableExportCriteria<Material> criteria)
+ throws UserFailureException;
+
+ /** Registers a new material type */
+ public void registerMaterialType(MaterialType entityType)
+ throws UserFailureException;
+
+ /** Registers a new sample type */
+ public void registerSampleType(SampleType entityType)
+ throws UserFailureException;
+
+ /** Registers a new experiment type */
+ public void registerExperimentType(ExperimentType entityType)
+ throws UserFailureException;
+
+ /**
+ * Updates experiment.
+ */
+ public void updateExperiment(String attachmentSessionKey,
+ final String experimentIdentifier,
+ List<ExperimentProperty> properties, String newProjectIdentifier,
+ Date version) throws UserFailureException;
+
+ /**
+ * Updates material.
+ */
+ public void updateMaterial(final String materialIdentifier,
+ List<MaterialProperty> properties, Date version)
+ throws UserFailureException;
+
+ /**
+ * Updates sample.
+ */
+ public void updateSample(final String sampleIdentifier,
+ List<SampleProperty> properties,
+ ExperimentIdentifier experimentIdentifierOrNull, Date version)
+ throws UserFailureException;
+
+ /** Deletes the specified data sets. */
+ public void deleteDataSets(List<String> dataSetCodes, String reason)
+ throws UserFailureException;
+
+ /**
+ * Returns a list of all available data set types.
+ */
+ public List<DataSetType> listDataSetTypes() throws UserFailureException;
}
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 4abd04d10c62da42f9c13d85a1e36b595c0fc727..412354b5d668eb557c58c3d0698935539aea60cf 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
@@ -19,8 +19,6 @@ 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;
@@ -41,6 +39,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteri
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.VocabularyTermWithStats;
import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetSearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
@@ -56,273 +55,322 @@ 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}.
*
* @author Franz-Josef Elmer
*/
-public interface ICommonClientServiceAsync extends IClientServiceAsync
-{
- /** @see ICommonClientService#listGroups(String) */
- public void listGroups(String databaseInstanceCode, AsyncCallback<List<Group>> callback);
-
- /** @see ICommonClientService#registerGroup(String, String, String) */
- public void registerGroup(String groupCode, String descriptionOrNull, String groupLeaderOrNull,
- AsyncCallback<Void> callback);
-
- /** @see ICommonClientService#listPersons() */
- public void listPersons(AsyncCallback<List<Person>> asyncCallback);
-
- /** @see ICommonClientService#registerPerson(String) */
- public void registerPerson(String code, AsyncCallback<Void> asyncCallback);
-
- /** @see ICommonClientService#listRoles() */
- public void listRoles(AsyncCallback<List<RoleAssignment>> asyncCallback);
-
- /** @see ICommonClientService#registerGroupRole(RoleSetCode, String, String) */
- public void registerGroupRole(RoleSetCode roleSetCode, String group, String person,
- AsyncCallback<Void> asyncCallback);
-
- /** @see ICommonClientService#deleteGroupRole(RoleSetCode, String, String) */
- public void deleteGroupRole(RoleSetCode roleSetCode, String group, String person,
- AsyncCallback<Void> asyncCallback);
-
- /** @see ICommonClientService#registerInstanceRole(RoleSetCode, String) */
- public void registerInstanceRole(RoleSetCode roleSetCode, String person,
- AsyncCallback<Void> asyncCallback);
-
- /** @see ICommonClientService#deleteInstanceRole(RoleSetCode, String) */
- public void deleteInstanceRole(RoleSetCode roleSetCode, String person,
- AsyncCallback<Void> asyncCallback);
-
- /** @see ICommonClientService#listSampleTypes() */
- public void listSampleTypes(AsyncCallback<List<SampleType>> asyncCallback);
-
- /**
- * @see ICommonClientService#listSamples(ListSampleCriteria)
- */
- public void listSamples(final ListSampleCriteria criteria,
- AsyncCallback<ResultSet<Sample>> asyncCallback);
-
- /**
- * @see ICommonClientService#prepareExportSamples(TableExportCriteria)
- */
- public void prepareExportSamples(final TableExportCriteria<Sample> criteria,
- AsyncCallback<String> asyncCallback);
-
- /** @see ICommonClientService#listPropertyTypeAssignments(DefaultResultSetConfig) */
- public void listPropertyTypeAssignments(
- DefaultResultSetConfig<String, EntityTypePropertyType<?>> criteria,
- final AsyncCallback<ResultSet<EntityTypePropertyType<?>>> asyncCallback);
-
- /**
- * @see ICommonClientService#prepareExportPropertyTypeAssignments(TableExportCriteria)
- */
- public void prepareExportPropertyTypeAssignments(
- final TableExportCriteria<EntityTypePropertyType<?>> criteria,
- AsyncCallback<String> asyncCallback);
-
- /**
- * @see ICommonClientService#listExperiments(ListExperimentsCriteria)
- */
- public void listExperiments(
- final ListExperimentsCriteria criteria,
- AsyncCallback<ResultSet<ch.systemsx.cisd.openbis.generic.client.web.client.dto.Experiment>> asyncCallback);
-
- /**
- * @see ICommonClientService#prepareExportExperiments(TableExportCriteria)
- */
- public void prepareExportExperiments(TableExportCriteria<Experiment> exportCriteria,
- AsyncCallback<String> callback);
-
- /**
- * @see ICommonClientService#prepareExportDataSetSearchHits(TableExportCriteria)
- */
- public void prepareExportDataSetSearchHits(TableExportCriteria<ExternalData> exportCriteria,
- AsyncCallback<String> callback);
-
- /** @see ICommonClientService#listPropertyTypes(DefaultResultSetConfig) */
- public void listPropertyTypes(DefaultResultSetConfig<String, PropertyType> criteria,
- final AsyncCallback<ResultSet<PropertyType>> asyncCallback);
-
- /**
- * @see ICommonClientService#prepareExportPropertyTypes(TableExportCriteria)
- */
- public void prepareExportPropertyTypes(final TableExportCriteria<PropertyType> criteria,
- AsyncCallback<String> asyncCallback);
-
- /**
- * @see ICommonClientService#listMatchingEntities(SearchableEntity, String, IResultSetConfig)
- */
- public void listMatchingEntities(final SearchableEntity searchableEntity,
- final String queryText, final IResultSetConfig<String, MatchingEntity> resultSetConfig,
- final AsyncCallback<ResultSet<MatchingEntity>> asyncCallback);
-
- /** @see ICommonClientService#prepareExportMatchingEntities(TableExportCriteria) */
- public void prepareExportMatchingEntities(TableExportCriteria<MatchingEntity> exportCriteria,
- AsyncCallback<String> callback);
-
- /** @see ICommonClientService#listProjects(DefaultResultSetConfig) */
- public void listProjects(DefaultResultSetConfig<String, Project> criteria,
- final AsyncCallback<ResultSet<Project>> asyncCallback);
-
- /** @see ICommonClientService#prepareExportProjects(TableExportCriteria) */
- public void prepareExportProjects(TableExportCriteria<Project> exportCriteria,
- AsyncCallback<String> callback);
-
- /** @see ICommonClientService#listVocabularies(boolean, boolean, DefaultResultSetConfig) */
- public void listVocabularies(final boolean withTerms, boolean excludeInternal,
- DefaultResultSetConfig<String, Vocabulary> criteria,
- final AsyncCallback<ResultSet<Vocabulary>> asyncCallback);
-
- /** @see ICommonClientService#prepareExportVocabularies(TableExportCriteria) */
- public void prepareExportVocabularies(TableExportCriteria<Vocabulary> exportCriteria,
- AsyncCallback<String> callback);
-
- /** @see ICommonClientService#listVocabularyTerms(Vocabulary, DefaultResultSetConfig) */
- public void listVocabularyTerms(Vocabulary vocabulary,
- DefaultResultSetConfig<String, VocabularyTermWithStats> resultSetConfig,
- AsyncCallback<ResultSet<VocabularyTermWithStats>> callback);
-
- /** @see ICommonClientService#prepareExportVocabularyTerms(TableExportCriteria) */
- public void prepareExportVocabularyTerms(
- TableExportCriteria<VocabularyTermWithStats> exportCriteria,
- AsyncCallback<String> callback);
-
- /** @see ICommonClientService#listMaterialTypes(DefaultResultSetConfig) */
- public void listMaterialTypes(DefaultResultSetConfig<String, EntityType> criteria,
- final AsyncCallback<ResultSet<EntityType>> asyncCallback)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
-
- /** @see ICommonClientService#prepareExportMaterialTypes(TableExportCriteria) */
- public void prepareExportMaterialTypes(final TableExportCriteria<EntityType> criteria,
- AsyncCallback<String> callback);
-
- /** @see ICommonClientService#listSampleTypes(DefaultResultSetConfig) */
- public void listSampleTypes(DefaultResultSetConfig<String, EntityType> criteria,
- final AsyncCallback<ResultSet<EntityType>> asyncCallback)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
-
- /** @see ICommonClientService#prepareExportSampleTypes(TableExportCriteria) */
- public void prepareExportSampleTypes(final TableExportCriteria<EntityType> criteria,
- AsyncCallback<String> callback);
-
- /** @see ICommonClientService#listExperimentTypes(DefaultResultSetConfig) */
- public void listExperimentTypes(DefaultResultSetConfig<String, EntityType> criteria,
- final AsyncCallback<ResultSet<EntityType>> asyncCallback)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
-
- /** @see ICommonClientService#prepareExportExperimentTypes(TableExportCriteria) */
- public void prepareExportExperimentTypes(final TableExportCriteria<EntityType> criteria,
- AsyncCallback<String> callback);
-
- /**
- * @see ICommonClientService#getExportTable(String, String)
- */
- public void getExportTable(String exportDataKey, String lineSeparator,
- AsyncCallback<String> asyncCallback);
-
- /**
- * @see ICommonClientService#removeResultSet(String)
- */
- public void removeResultSet(final String resultSetKey, final AsyncCallback<Void> asyncCallback);
-
- /**
- * @see ICommonClientService#listSampleDataSets(String, DefaultResultSetConfig)
- */
- public void listSampleDataSets(String sampleIdentifier,
- DefaultResultSetConfig<String, ExternalData> criteria,
- AsyncCallback<ResultSet<ExternalData>> asyncCallback);
-
- /**
- * @see ICommonClientService#listExperimentDataSets(String, DefaultResultSetConfig)
- */
- public void listExperimentDataSets(String experimentIdentifier,
- DefaultResultSetConfig<String, ExternalData> criteria,
- AsyncCallback<ResultSet<ExternalData>> asyncCallback);
-
- /**
- * @see ICommonClientService#listSearchableEntities()
- */
- public void listSearchableEntities(final AsyncCallback<List<SearchableEntity>> asyncCallback);
-
- /** @see ICommonClientService#listExperimentTypes() */
- public void listExperimentTypes(
- final AsyncCallback<List<ExperimentType>> listExperimentTypesCallback);
-
- /** @see ICommonClientService#listDataTypes() */
- public void listDataTypes(final AsyncCallback<List<DataType>> asyncCallback);
-
- /** @see ICommonClientService#assignPropertyType(EntityKind, String, String, boolean, String) */
- public void assignPropertyType(EntityKind entityKind, String propertyTypeCode,
- String entityTypeCode, boolean isMandatory, String defaultValue,
- AsyncCallback<String> process);
-
- /** @see ICommonClientService#registerPropertyType(PropertyType) */
- public void registerPropertyType(final PropertyType propertyType,
- final AsyncCallback<Void> asyncCallback);
-
- /** @see ICommonClientService#registerVocabulary(Vocabulary) */
- public void registerVocabulary(final Vocabulary vocabulary,
- final AsyncCallback<Void> asyncCallback);
-
- /** @see ICommonClientService#registerProject(Project) */
- public void registerProject(Project project,
- final AsyncCallback<Void> projectRegistrationCallback);
-
- /**
- * @see ICommonClientService#searchForDataSets(DataSetSearchCriteria, IResultSetConfig)
- */
- public void searchForDataSets(DataSetSearchCriteria criteria,
- final IResultSetConfig<String, ExternalData> resultSetConfig,
- final AsyncCallback<ResultSet<ExternalData>> callback);
-
- /**
- * @see ICommonClientService#listMaterialTypes()
- */
- public void listMaterialTypes(AsyncCallback<List<MaterialType>> callback);
-
- /**
- * @see ICommonClientService#listMaterials(ListMaterialCriteria)
- */
- public void listMaterials(ListMaterialCriteria criteria,
- AsyncCallback<ResultSet<Material>> callback);
-
- /** @see ICommonClientService#prepareExportMaterials(TableExportCriteria) */
- public void prepareExportMaterials(TableExportCriteria<Material> exportCriteria,
- AsyncCallback<String> callback);
-
- /** @see ICommonClientService#registerMaterialType(MaterialType) */
- public void registerMaterialType(MaterialType entityType,
- final AsyncCallback<Void> asyncCallback);
-
- /** @see ICommonClientService#registerSampleType(SampleType) */
- public void registerSampleType(SampleType entityType, final AsyncCallback<Void> asyncCallback);
-
- /** @see ICommonClientService#registerExperimentType(ExperimentType) */
- public void registerExperimentType(ExperimentType entityType,
- final AsyncCallback<Void> asyncCallback);
-
- /**
- * @see ICommonClientService#updateExperiment(String, String, List, String, Date)
- */
- public void updateExperiment(String attachmentSessionKey, final String experimentIdentifier,
- List<ExperimentProperty> properties, String newProjectIdentifier, Date version,
- final AsyncCallback<Void> asyncCallback) throws UserFailureException;
-
- /**
- * @see ICommonClientService#updateMaterial(String, List, Date)
- */
- public void updateMaterial(final String materialIdentifier, List<MaterialProperty> properties,
- Date version, final AsyncCallback<Void> asyncCallback) throws UserFailureException;
-
- /**
- * @see ICommonClientService#updateSample(String, List, ExperimentIdentifier, Date)
- */
- public void updateSample(final String sampleIdentifier, List<SampleProperty> properties,
- ExperimentIdentifier experimentIdentifierOrNull, Date version, final AsyncCallback<Void> asyncCallback) throws UserFailureException;
-
- /** @see ICommonClientService#deleteDataSets(List, String) */
- public void deleteDataSets(List<String> dataSetCodes, String reason,
- AsyncCallback<Void> asyncCallback);
+public interface ICommonClientServiceAsync extends IClientServiceAsync {
+ /** @see ICommonClientService#listGroups(String) */
+ public void listGroups(String databaseInstanceCode,
+ AsyncCallback<List<Group>> callback);
+
+ /** @see ICommonClientService#registerGroup(String, String, String) */
+ public void registerGroup(String groupCode, String descriptionOrNull,
+ String groupLeaderOrNull, AsyncCallback<Void> callback);
+
+ /** @see ICommonClientService#listPersons() */
+ public void listPersons(AsyncCallback<List<Person>> asyncCallback);
+
+ /** @see ICommonClientService#registerPerson(String) */
+ public void registerPerson(String code, AsyncCallback<Void> asyncCallback);
+
+ /** @see ICommonClientService#listRoles() */
+ public void listRoles(AsyncCallback<List<RoleAssignment>> asyncCallback);
+
+ /** @see ICommonClientService#registerGroupRole(RoleSetCode, String, String) */
+ public void registerGroupRole(RoleSetCode roleSetCode, String group,
+ String person, AsyncCallback<Void> asyncCallback);
+
+ /** @see ICommonClientService#deleteGroupRole(RoleSetCode, String, String) */
+ public void deleteGroupRole(RoleSetCode roleSetCode, String group,
+ String person, AsyncCallback<Void> asyncCallback);
+
+ /** @see ICommonClientService#registerInstanceRole(RoleSetCode, String) */
+ public void registerInstanceRole(RoleSetCode roleSetCode, String person,
+ AsyncCallback<Void> asyncCallback);
+
+ /** @see ICommonClientService#deleteInstanceRole(RoleSetCode, String) */
+ public void deleteInstanceRole(RoleSetCode roleSetCode, String person,
+ AsyncCallback<Void> asyncCallback);
+
+ /** @see ICommonClientService#listSampleTypes() */
+ public void listSampleTypes(AsyncCallback<List<SampleType>> asyncCallback);
+
+ /**
+ * @see ICommonClientService#listSamples(ListSampleCriteria)
+ */
+ public void listSamples(final ListSampleCriteria criteria,
+ AsyncCallback<ResultSet<Sample>> asyncCallback);
+
+ /**
+ * @see ICommonClientService#prepareExportSamples(TableExportCriteria)
+ */
+ public void prepareExportSamples(
+ final TableExportCriteria<Sample> criteria,
+ AsyncCallback<String> asyncCallback);
+
+ /** @see ICommonClientService#listPropertyTypeAssignments(DefaultResultSetConfig) */
+ public void listPropertyTypeAssignments(
+ DefaultResultSetConfig<String, EntityTypePropertyType<?>> criteria,
+ final AsyncCallback<ResultSet<EntityTypePropertyType<?>>> asyncCallback);
+
+ /**
+ * @see ICommonClientService#prepareExportPropertyTypeAssignments(TableExportCriteria)
+ */
+ public void prepareExportPropertyTypeAssignments(
+ final TableExportCriteria<EntityTypePropertyType<?>> criteria,
+ AsyncCallback<String> asyncCallback);
+
+ /**
+ * @see ICommonClientService#listExperiments(ListExperimentsCriteria)
+ */
+ public void listExperiments(
+ final ListExperimentsCriteria criteria,
+ AsyncCallback<ResultSet<ch.systemsx.cisd.openbis.generic.client.web.client.dto.Experiment>> asyncCallback);
+
+ /**
+ * @see ICommonClientService#prepareExportExperiments(TableExportCriteria)
+ */
+ public void prepareExportExperiments(
+ TableExportCriteria<Experiment> exportCriteria,
+ AsyncCallback<String> callback);
+
+ /**
+ * @see ICommonClientService#prepareExportDataSetSearchHits(TableExportCriteria)
+ */
+ public void prepareExportDataSetSearchHits(
+ TableExportCriteria<ExternalData> exportCriteria,
+ AsyncCallback<String> callback);
+
+ /** @see ICommonClientService#listPropertyTypes(DefaultResultSetConfig) */
+ public void listPropertyTypes(
+ DefaultResultSetConfig<String, PropertyType> criteria,
+ final AsyncCallback<ResultSet<PropertyType>> asyncCallback);
+
+ /**
+ * @see ICommonClientService#prepareExportPropertyTypes(TableExportCriteria)
+ */
+ public void prepareExportPropertyTypes(
+ final TableExportCriteria<PropertyType> criteria,
+ AsyncCallback<String> asyncCallback);
+
+ /**
+ * @see ICommonClientService#listMatchingEntities(SearchableEntity, String,
+ * IResultSetConfig)
+ */
+ public void listMatchingEntities(final SearchableEntity searchableEntity,
+ final String queryText,
+ final IResultSetConfig<String, MatchingEntity> resultSetConfig,
+ final AsyncCallback<ResultSet<MatchingEntity>> asyncCallback);
+
+ /** @see ICommonClientService#prepareExportMatchingEntities(TableExportCriteria) */
+ public void prepareExportMatchingEntities(
+ TableExportCriteria<MatchingEntity> exportCriteria,
+ AsyncCallback<String> callback);
+
+ /** @see ICommonClientService#listProjects(DefaultResultSetConfig) */
+ public void listProjects(DefaultResultSetConfig<String, Project> criteria,
+ final AsyncCallback<ResultSet<Project>> asyncCallback);
+
+ /** @see ICommonClientService#prepareExportProjects(TableExportCriteria) */
+ public void prepareExportProjects(
+ TableExportCriteria<Project> exportCriteria,
+ AsyncCallback<String> callback);
+
+ /**
+ * @see ICommonClientService#listVocabularies(boolean, boolean,
+ * DefaultResultSetConfig)
+ */
+ public void listVocabularies(final boolean withTerms,
+ boolean excludeInternal,
+ DefaultResultSetConfig<String, Vocabulary> criteria,
+ final AsyncCallback<ResultSet<Vocabulary>> asyncCallback);
+
+ /** @see ICommonClientService#prepareExportVocabularies(TableExportCriteria) */
+ public void prepareExportVocabularies(
+ TableExportCriteria<Vocabulary> exportCriteria,
+ AsyncCallback<String> callback);
+
+ /**
+ * @see ICommonClientService#listVocabularyTerms(Vocabulary,
+ * DefaultResultSetConfig)
+ */
+ public void listVocabularyTerms(
+ Vocabulary vocabulary,
+ DefaultResultSetConfig<String, VocabularyTermWithStats> resultSetConfig,
+ AsyncCallback<ResultSet<VocabularyTermWithStats>> callback);
+
+ /** @see ICommonClientService#prepareExportVocabularyTerms(TableExportCriteria) */
+ public void prepareExportVocabularyTerms(
+ TableExportCriteria<VocabularyTermWithStats> exportCriteria,
+ AsyncCallback<String> callback);
+
+ /** @see ICommonClientService#listMaterialTypes(DefaultResultSetConfig) */
+ public void listMaterialTypes(
+ DefaultResultSetConfig<String, EntityType> criteria,
+ final AsyncCallback<ResultSet<EntityType>> asyncCallback)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
+
+ /** @see ICommonClientService#prepareExportMaterialTypes(TableExportCriteria) */
+ public void prepareExportMaterialTypes(
+ final TableExportCriteria<EntityType> criteria,
+ AsyncCallback<String> callback);
+
+ /** @see ICommonClientService#listSampleTypes(DefaultResultSetConfig) */
+ public void listSampleTypes(
+ DefaultResultSetConfig<String, EntityType> criteria,
+ final AsyncCallback<ResultSet<EntityType>> asyncCallback)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
+
+ /** @see ICommonClientService#prepareExportSampleTypes(TableExportCriteria) */
+ public void prepareExportSampleTypes(
+ final TableExportCriteria<EntityType> criteria,
+ AsyncCallback<String> callback);
+
+ /** @see ICommonClientService#listExperimentTypes(DefaultResultSetConfig) */
+ public void listExperimentTypes(
+ DefaultResultSetConfig<String, EntityType> criteria,
+ final AsyncCallback<ResultSet<EntityType>> asyncCallback)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
+
+ /** @see ICommonClientService#prepareExportExperimentTypes(TableExportCriteria) */
+ public void prepareExportExperimentTypes(
+ final TableExportCriteria<EntityType> criteria,
+ AsyncCallback<String> callback);
+
+ /**
+ * @see ICommonClientService#getExportTable(String, String)
+ */
+ public void getExportTable(String exportDataKey, String lineSeparator,
+ AsyncCallback<String> asyncCallback);
+
+ /**
+ * @see ICommonClientService#removeResultSet(String)
+ */
+ public void removeResultSet(final String resultSetKey,
+ final AsyncCallback<Void> asyncCallback);
+
+ /**
+ * @see ICommonClientService#listSampleDataSets(String,
+ * DefaultResultSetConfig)
+ */
+ public void listSampleDataSets(String sampleIdentifier,
+ DefaultResultSetConfig<String, ExternalData> criteria,
+ AsyncCallback<ResultSet<ExternalData>> asyncCallback);
+
+ /**
+ * @see ICommonClientService#listExperimentDataSets(String,
+ * DefaultResultSetConfig)
+ */
+ public void listExperimentDataSets(String experimentIdentifier,
+ DefaultResultSetConfig<String, ExternalData> criteria,
+ AsyncCallback<ResultSet<ExternalData>> asyncCallback);
+
+ /**
+ * @see ICommonClientService#listSearchableEntities()
+ */
+ public void listSearchableEntities(
+ final AsyncCallback<List<SearchableEntity>> asyncCallback);
+
+ /** @see ICommonClientService#listExperimentTypes() */
+ public void listExperimentTypes(
+ final AsyncCallback<List<ExperimentType>> listExperimentTypesCallback);
+
+ /** @see ICommonClientService#listDataTypes() */
+ public void listDataTypes(final AsyncCallback<List<DataType>> asyncCallback);
+
+ /**
+ * @see ICommonClientService#assignPropertyType(EntityKind, String, String,
+ * boolean, String)
+ */
+ public void assignPropertyType(EntityKind entityKind,
+ String propertyTypeCode, String entityTypeCode,
+ boolean isMandatory, String defaultValue,
+ AsyncCallback<String> process);
+
+ /** @see ICommonClientService#registerPropertyType(PropertyType) */
+ public void registerPropertyType(final PropertyType propertyType,
+ final AsyncCallback<Void> asyncCallback);
+
+ /** @see ICommonClientService#registerVocabulary(Vocabulary) */
+ public void registerVocabulary(final Vocabulary vocabulary,
+ final AsyncCallback<Void> asyncCallback);
+
+ /** @see ICommonClientService#registerProject(Project) */
+ public void registerProject(Project project,
+ final AsyncCallback<Void> projectRegistrationCallback);
+
+ /**
+ * @see ICommonClientService#searchForDataSets(DataSetSearchCriteria,
+ * IResultSetConfig)
+ */
+ public void searchForDataSets(DataSetSearchCriteria criteria,
+ final IResultSetConfig<String, ExternalData> resultSetConfig,
+ final AsyncCallback<ResultSet<ExternalData>> callback);
+
+ /**
+ * @see ICommonClientService#listMaterialTypes()
+ */
+ public void listMaterialTypes(AsyncCallback<List<MaterialType>> callback);
+
+ /**
+ * @see ICommonClientService#listMaterials(ListMaterialCriteria)
+ */
+ public void listMaterials(ListMaterialCriteria criteria,
+ AsyncCallback<ResultSet<Material>> callback);
+
+ /** @see ICommonClientService#prepareExportMaterials(TableExportCriteria) */
+ public void prepareExportMaterials(
+ TableExportCriteria<Material> exportCriteria,
+ AsyncCallback<String> callback);
+
+ /** @see ICommonClientService#registerMaterialType(MaterialType) */
+ public void registerMaterialType(MaterialType entityType,
+ final AsyncCallback<Void> asyncCallback);
+
+ /** @see ICommonClientService#registerSampleType(SampleType) */
+ public void registerSampleType(SampleType entityType,
+ final AsyncCallback<Void> asyncCallback);
+
+ /** @see ICommonClientService#registerExperimentType(ExperimentType) */
+ public void registerExperimentType(ExperimentType entityType,
+ final AsyncCallback<Void> asyncCallback);
+
+ /**
+ * @see ICommonClientService#updateExperiment(String, String, List, String,
+ * Date)
+ */
+ public void updateExperiment(String attachmentSessionKey,
+ final String experimentIdentifier,
+ List<ExperimentProperty> properties, String newProjectIdentifier,
+ Date version, final AsyncCallback<Void> asyncCallback)
+ throws UserFailureException;
+
+ /**
+ * @see ICommonClientService#updateMaterial(String, List, Date)
+ */
+ public void updateMaterial(final String materialIdentifier,
+ List<MaterialProperty> properties, Date version,
+ final AsyncCallback<Void> asyncCallback)
+ throws UserFailureException;
+
+ /**
+ * @see ICommonClientService#updateSample(String, List,
+ * ExperimentIdentifier, Date)
+ */
+ public void updateSample(final String sampleIdentifier,
+ List<SampleProperty> properties,
+ ExperimentIdentifier experimentIdentifierOrNull, Date version,
+ final AsyncCallback<Void> asyncCallback)
+ throws UserFailureException;
+
+ /** @see ICommonClientService#deleteDataSets(List, String) */
+ public void deleteDataSets(List<String> dataSetCodes, String reason,
+ AsyncCallback<Void> asyncCallback);
+
+ /** @see ICommonClientService#listDataSetTypes() */
+ public void listDataSetTypes(AsyncCallback<List<DataSetType>> 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 76802ff98516a99a1ebbbbb527d67daa7239fc2f..126b776587c9a7f457f45a217372a637359c5905 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
@@ -19,463 +19,464 @@ package ch.systemsx.cisd.openbis.generic.client.web.client.application;
/**
* Contains keys of the localized messages.
* <p>
- * Use these constants instead of accessing messages with hard coded keys! Consider extending this
- * class for plugin specific keys. Currently this class contains message keys of the <i>common</i>
- * and <i>generic</i> technology.
+ * Use these constants instead of accessing messages with hard coded keys!
+ * Consider extending this class for plugin specific keys. Currently this class
+ * contains message keys of the <i>common</i> and <i>generic</i> technology.
* </p>
*
* @author Tomasz Pylak
*/
-public abstract class Dict
-{
+public abstract class Dict {
- protected Dict()
- {
- // Can not be instantiated.
- }
+ protected Dict() {
+ // Can not be instantiated.
+ }
- public static final String APPLICATION_NAME = "applicationName";
+ public static final String APPLICATION_NAME = "applicationName";
- public static final String WELCOME = "welcome";
+ public static final String WELCOME = "welcome";
- public static final String FOOTER = "footer";
+ public static final String FOOTER = "footer";
- //
- // Common Labels
- //
+ //
+ // Common Labels
+ //
- public static final String CODE = "code";
+ public static final String CODE = "code";
- public static final String REGISTRATOR = "registrator";
+ public static final String REGISTRATOR = "registrator";
- public static final String REGISTRATION_DATE = "registration_date";
+ public static final String REGISTRATION_DATE = "registration_date";
- public static final String NOT_IMPLEMENTED = "not_implemented";
+ public static final String NOT_IMPLEMENTED = "not_implemented";
- //
- // Field
- //
+ //
+ // Field
+ //
- public static final String COMBO_BOX_EMPTY = "combobox_empty";
+ public static final String COMBO_BOX_EMPTY = "combobox_empty";
- public static final String COMBO_BOX_CHOOSE = "combobox_choose";
+ public static final String COMBO_BOX_CHOOSE = "combobox_choose";
- public static final String INVALID_CODE_MESSAGE = "invalid_code_message";
+ public static final String INVALID_CODE_MESSAGE = "invalid_code_message";
- //
- // MessageBox
- //
+ //
+ // MessageBox
+ //
- public static final String MESSAGEBOX_ERROR = "messagebox_error";
+ public static final String MESSAGEBOX_ERROR = "messagebox_error";
- public static final String MESSAGEBOX_WARNING = "messagebox_warning";
+ public static final String MESSAGEBOX_WARNING = "messagebox_warning";
- public static final String MESSAGEBOX_INFO = "messagebox_info";
+ public static final String MESSAGEBOX_INFO = "messagebox_info";
- //
- // Buttons
- //
+ //
+ // Buttons
+ //
- public static final String TOOLTIP_REFRESH_ENABLED = "tooltip_refresh_enabled";
+ public static final String TOOLTIP_REFRESH_ENABLED = "tooltip_refresh_enabled";
- public static final String TOOLTIP_REFRESH_DISABLED = "tooltip_refresh_disabled";
+ public static final String TOOLTIP_REFRESH_DISABLED = "tooltip_refresh_disabled";
- public static final String TOOLTIP_EXPORT_ENABLED = "tooltip_export_enabled";
+ public static final String TOOLTIP_EXPORT_ENABLED = "tooltip_export_enabled";
- public static final String TOOLTIP_EXPORT_DISABLED = "tooltip_export_disabled";
+ public static final String TOOLTIP_EXPORT_DISABLED = "tooltip_export_disabled";
- public static final String BUTTON_SAVE = "button_save";
+ public static final String BUTTON_SAVE = "button_save";
- public static final String BUTTON_CHOOSE = "button_choose";
+ public static final String BUTTON_CHOOSE = "button_choose";
- public static final String BUTTON_CANCEL = "button_cancel";
+ public static final String BUTTON_CANCEL = "button_cancel";
- public static final String BUTTON_RESET = "button_reset";
+ public static final String BUTTON_RESET = "button_reset";
- public static final String BUTTON_SUBMIT = "button_submit";
+ public static final String BUTTON_SUBMIT = "button_submit";
- public static final String BUTTON_REFRESH = "button_refresh";
+ public static final String BUTTON_REFRESH = "button_refresh";
- public static final String BUTTON_SHOW = "button_show";
+ public static final String BUTTON_SHOW = "button_show";
- public static final String BUTTON_BROWSE = "button_browse";
+ public static final String BUTTON_BROWSE = "button_browse";
- public static final String BUTTON_SHOW_DETAILS = "button_show_details";
+ public static final String BUTTON_SHOW_DETAILS = "button_show_details";
- public static final String BUTTON_EXPORT_DATA = "button_exportData";
+ public static final String BUTTON_EXPORT_DATA = "button_exportData";
- public static final String BUTTON_ADD_GROUP = "button_add_group";
+ public static final String BUTTON_ADD_GROUP = "button_add_group";
- //
- // LoginWidget
- //
+ //
+ // LoginWidget
+ //
- public static final String LOGIN_INVITATION = "login_invitation";
+ public static final String LOGIN_INVITATION = "login_invitation";
- public static final String LOGIN_USER_LABEL = "login_userLabel";
+ public static final String LOGIN_USER_LABEL = "login_userLabel";
- public static final String LOGIN_PASSWORD_LABEL = "login_passwordLabel";
+ public static final String LOGIN_PASSWORD_LABEL = "login_passwordLabel";
- public static final String LOGIN_BUTTON_LABEL = "login_buttonLabel";
+ public static final String LOGIN_BUTTON_LABEL = "login_buttonLabel";
- public static final String LOGIN_FAILED = "login_failed";
+ public static final String LOGIN_FAILED = "login_failed";
- //
- // AbstractAsyncCallback
- //
+ //
+ // AbstractAsyncCallback
+ //
- public static final String EXCEPTION_INVOCATION_MESSAGE = "exception_invocationMessage";
+ public static final String EXCEPTION_INVOCATION_MESSAGE = "exception_invocationMessage";
- public static final String EXCEPTION_WITHOUT_MESSAGE = "exception_withoutMessage";
+ public static final String EXCEPTION_WITHOUT_MESSAGE = "exception_withoutMessage";
- //
- // Header
- //
+ //
+ // Header
+ //
- public static final String HEADER_USER_WITHOUT_HOMEGROUP = "header_userWithoutHomegroup";
+ public static final String HEADER_USER_WITHOUT_HOMEGROUP = "header_userWithoutHomegroup";
- public static final String HEADER_USER_WITH_HOMEGROUP = "header_userWithHomegroup";
+ public static final String HEADER_USER_WITH_HOMEGROUP = "header_userWithHomegroup";
- public static final String HEADER_LOGOUT_BUTTON_LABEL = "header_logoutButtonLabel";
+ public static final String HEADER_LOGOUT_BUTTON_LABEL = "header_logoutButtonLabel";
- //
- // Authorization Management Console
- //
+ //
+ // Authorization Management Console
+ //
- public static final String PERSONS_VIEW_HEADING = "personsView_heading";
+ public static final String PERSONS_VIEW_HEADING = "personsView_heading";
- public static final String GROUPS_VIEW_HEADING = "groupsView_heading";
+ public static final String GROUPS_VIEW_HEADING = "groupsView_heading";
- public static final String ROLES_VIEW_HEADING = "rolesView_heading";
+ public static final String ROLES_VIEW_HEADING = "rolesView_heading";
- //
- // Search
- //
+ //
+ // Search
+ //
- public static final String SEARCH_BUTTON = "search_button";
+ public static final String SEARCH_BUTTON = "search_button";
- public static final String GLOBAL_SEARCH = "global_search";
+ public static final String GLOBAL_SEARCH = "global_search";
- public static final String IDENTIFIER = "identifier";
+ public static final String IDENTIFIER = "identifier";
- public static final String NO_MATCH = "no_match";
+ public static final String NO_MATCH = "no_match";
- public static final String ENTITY_TYPE = "entity_type";
+ public static final String ENTITY_TYPE = "entity_type";
- public static final String ENTITY_KIND = "entity_kind";
+ public static final String ENTITY_KIND = "entity_kind";
- public static final String MATCHING_TEXT = "matching_text";
+ public static final String MATCHING_TEXT = "matching_text";
- public static final String MATCHING_FIELD = "matching_field";
+ public static final String MATCHING_FIELD = "matching_field";
- public static final String TOO_GENERIC = "too_generic";
+ public static final String TOO_GENERIC = "too_generic";
- //
- // Sample Browser
- //
+ //
+ // Sample Browser
+ //
- public static final String SAMPLE = "sample";
+ public static final String SAMPLE = "sample";
- public static final String SAMPLE_TYPE = "sample_type";
+ public static final String SAMPLE_TYPE = "sample_type";
- public static final String DATABASE_INSTANCE = "database_instance";
+ public static final String DATABASE_INSTANCE = "database_instance";
- public static final String SAMPLE_IDENTIFIER = "sample_identifier";
+ public static final String SAMPLE_IDENTIFIER = "sample_identifier";
- public static final String IS_INSTANCE_SAMPLE = "is_instance_sample";
+ public static final String IS_INSTANCE_SAMPLE = "is_instance_sample";
- public static final String IS_INVALID = "is_invalid";
+ public static final String IS_INVALID = "is_invalid";
- public static final String GROUP = "group";
+ public static final String GROUP = "group";
- public static final String PROJECT = "project";
+ public static final String PROJECT = "project";
- public static final String EXPERIMENT = "experiment";
+ public static final String EXPERIMENT = "experiment";
- public static final String EXPERIMENT_IDENTIFIER = "experiment_identifier";
+ public static final String EXPERIMENT_IDENTIFIER = "experiment_identifier";
- public static final String GENERATED_SAMPLES = "generated_samples";
+ public static final String GENERATED_SAMPLES = "generated_samples";
- public static final String GENERATED_FROM = "generated_from";
+ public static final String GENERATED_FROM = "generated_from";
- public static final String PART_OF = "part_of";
+ public static final String PART_OF = "part_of";
- //
- // Experiment Browser
- //
+ //
+ // Experiment Browser
+ //
- public static final String EXPERIMENT_TYPE = "experiment_type";
+ public static final String EXPERIMENT_TYPE = "experiment_type";
- //
- // Property Type Browser
- //
+ //
+ // Property Type Browser
+ //
- public static final String LABEL = "label";
+ public static final String LABEL = "label";
- public static final String DATA_TYPE = "data_type";
+ public static final String DATA_TYPE = "data_type";
- public static final String DATA_TYPE_CODE = "data_type_code";
+ public static final String DATA_TYPE_CODE = "data_type_code";
- public static final String DESCRIPTION = "description";
+ public static final String DESCRIPTION = "description";
- public static final String SAMPLE_TYPES = "sample_types";
+ public static final String SAMPLE_TYPES = "sample_types";
- public static final String MATERIAL_TYPES = "material_types";
+ public static final String MATERIAL_TYPES = "material_types";
- public static final String EXPERIMENT_TYPES = "experiment_types";
+ public static final String EXPERIMENT_TYPES = "experiment_types";
- public static final String IS_MANDATORY = "is_mandatory";
+ public static final String IS_MANDATORY = "is_mandatory";
- public static final String PROPERTY_TYPE = "property_type";
+ public static final String PROPERTY_TYPE = "property_type";
- public static final String PROPERTY_TYPE_CODE = "property_type_code";
+ public static final String PROPERTY_TYPE_CODE = "property_type_code";
- public static final String ASSIGNED_TO = "assigned_to";
+ public static final String ASSIGNED_TO = "assigned_to";
- public static final String TYPE_OF = "type_of";
+ public static final String TYPE_OF = "type_of";
- public static final String VOCABULARY = "vocabulary";
+ public static final String VOCABULARY = "vocabulary";
- public static final String VOCABULARY_TERMS = "vocabulary_terms";
+ public static final String VOCABULARY_TERMS = "vocabulary_terms";
- public static final String VOCABULARY_TERMS_EMPTY = "vocabulary_terms_empty";
+ public static final String VOCABULARY_TERMS_EMPTY = "vocabulary_terms_empty";
- public static final String MANDATORY = "mandatory";
+ public static final String MANDATORY = "mandatory";
- public static final String DEFAULT_VALUE = "default_value";
+ public static final String DEFAULT_VALUE = "default_value";
- public static final String DEFAULT_VALUE_TOOLTIP = "default_value_tooltip";
+ public static final String DEFAULT_VALUE_TOOLTIP = "default_value_tooltip";
- // -------- generic plugin dictionary -------------------
+ // -------- generic plugin dictionary -------------------
- //
- // Experiment Viewer
- //
+ //
+ // Experiment Viewer
+ //
- public static final String FILE_NAME = "file_name";
+ public static final String FILE_NAME = "file_name";
- public static final String VERSION_FILE_NAME = "version_file_name";
+ public static final String VERSION_FILE_NAME = "version_file_name";
- public static final String VERSION = "version";
+ public static final String VERSION = "version";
- public static final String VERSIONS = "versions";
+ public static final String VERSIONS = "versions";
- public static final String VERSIONS_TEMPLATE = "versions_template";
+ public static final String VERSIONS_TEMPLATE = "versions_template";
- public static final String NO_ATTACHMENTS_FOUND = "no_attachments_found";
+ public static final String NO_ATTACHMENTS_FOUND = "no_attachments_found";
- public static final String NO_SAMPLES_FOUND = "no_samples_found";
+ public static final String NO_SAMPLES_FOUND = "no_samples_found";
- public static final String PROCEDURE = "procedure";
+ public static final String PROCEDURE = "procedure";
- //
- // Sample Viewer
- //
+ //
+ // Sample Viewer
+ //
- public static final String SAMPLE_PROPERTIES_HEADING = "sample_properties_heading";
+ public static final String SAMPLE_PROPERTIES_HEADING = "sample_properties_heading";
- public static final String PART_OF_HEADING = "part_of_heading";
+ public static final String PART_OF_HEADING = "part_of_heading";
- public static final String EXTERNAL_DATA_HEADING = "external_data_heading";
+ public static final String EXTERNAL_DATA_HEADING = "external_data_heading";
- public static final String INVALIDATION = "invalidation";
+ public static final String INVALIDATION = "invalidation";
- public static final String INVALIDATION_TEMPLATE = "invalidation_template";
+ public static final String INVALIDATION_TEMPLATE = "invalidation_template";
- //
- // ExternalData Viewer
- //
+ //
+ // ExternalData Viewer
+ //
- public static final String PARENT_CODE = "parent_code";
+ public static final String PARENT_CODE = "parent_code";
- public static final String LOCATION = "location";
+ public static final String LOCATION = "location";
- public static final String FILE_FORMAT_TYPE = "file_format_type";
+ public static final String FILE_FORMAT_TYPE = "file_format_type";
- public static final String DATA_SET_TYPE = "data_set_type";
+ public static final String DATA_SET_TYPE = "data_set_type";
- public static final String PROCEDURE_TYPE = "procedure_type";
+ public static final String PROCEDURE_TYPE = "procedure_type";
- public static final String EXTERNAL_DATA_SAMPLE = "external_data_sample";
+ public static final String EXTERNAL_DATA_SAMPLE = "external_data_sample";
- public static final String IS_DERIVED = "is_derived";
+ public static final String IS_DERIVED = "is_derived";
- public static final String IS_COMPLETE = "is_complete";
+ public static final String IS_COMPLETE = "is_complete";
- public static final String PRODUCTION_DATE = "production_date";
+ public static final String PRODUCTION_DATE = "production_date";
- public static final String DATA_PRODUCER_CODE = "data_producer_code";
+ public static final String DATA_PRODUCER_CODE = "data_producer_code";
- public static final String BUTTON_DELETE_DATASETS = "button_delete_datasets";
+ public static final String BUTTON_DELETE_DATASETS = "button_delete_datasets";
- public static final String CONFIRM_DATASET_DELETION_TITLE = "confirm_dataset_deletion_title";
+ public static final String CONFIRM_DATASET_DELETION_TITLE = "confirm_dataset_deletion_title";
- public static final String CONFIRM_DATASET_DELETION_MSG = "confirm_dataset_deletion_msg";
+ public static final String CONFIRM_DATASET_DELETION_MSG = "confirm_dataset_deletion_msg";
- //
- // Sample Registration
- //
+ //
+ // Sample Registration
+ //
- public static final String INSTANCE_SAMPLE = "instance_sample";
+ public static final String INSTANCE_SAMPLE = "instance_sample";
- public static final String GENERATED_FROM_SAMPLE = "generated_from_sample";
+ public static final String GENERATED_FROM_SAMPLE = "generated_from_sample";
- public static final String PART_OF_SAMPLE = "part_of_sample";
+ public static final String PART_OF_SAMPLE = "part_of_sample";
- //
- // Menu Titles
- //
+ //
+ // Menu Titles
+ //
- public static final String MENU_ADMINISTRATION = "menu_administration";
+ public static final String MENU_ADMINISTRATION = "menu_administration";
- public static final String MENU_AUTHORIZATION = "menu_authorization";
+ public static final String MENU_AUTHORIZATION = "menu_authorization";
- public static final String MENU_PROJECT = "menu_project";
+ public static final String MENU_PROJECT = "menu_project";
- public static final String MENU_PROPERTY_TYPES = "menu_property_types";
+ public static final String MENU_PROPERTY_TYPES = "menu_property_types";
- public static final String MENU_VOCABULARY = "menu_vocabulary";
+ public static final String MENU_VOCABULARY = "menu_vocabulary";
- public static final String MENU_DATA_SET = "menu_data_set";
+ public static final String MENU_DATA_SET = "menu_data_set";
- public static final String MENU_EXPERIMENT = "menu_experiment";
+ public static final String MENU_EXPERIMENT = "menu_experiment";
- public static final String MENU_MATERIAL = "menu_material";
+ public static final String MENU_MATERIAL = "menu_material";
- public static final String MENU_SAMPLE = "menu_sample";
+ public static final String MENU_SAMPLE = "menu_sample";
- //
- // Tab Titles
- //
+ //
+ // Tab Titles
+ //
- public static final String ASSIGN_EXPERIMENT_PROPERTY_TYPE = "assign_experiment_property_type";
+ public static final String ASSIGN_EXPERIMENT_PROPERTY_TYPE = "assign_experiment_property_type";
- public static final String ASSIGN_SAMPLE_PROPERTY_TYPE = "assign_sample_property_type";
+ public static final String ASSIGN_MATERIAL_PROPERTY_TYPE = "assign_material_property_type";
- public static final String PROPERTY_TYPE_ASSIGNMENTS = "property_type_assignments";
+ public static final String ASSIGN_DATA_SET_PROPERTY_TYPE = "assign_data_set_property_type";
- public static final String PROPERTY_TYPE_REGISTRATION = "property_type_registration";
+ public static final String ASSIGN_SAMPLE_PROPERTY_TYPE = "assign_sample_property_type";
- public static final String PROPERTY_TYPES = "property_types";
+ public static final String PROPERTY_TYPE_ASSIGNMENTS = "property_type_assignments";
- public static final String EXPERIMENT_BROWSER = "experiment_browser";
+ public static final String PROPERTY_TYPE_REGISTRATION = "property_type_registration";
- public static final String VOCABULARY_REGISTRATION = "vocabulary_registration";
+ public static final String PROPERTY_TYPES = "property_types";
- public static final String SAMPLE_BATCH_REGISTRATION = "sample_batch_registration";
+ public static final String EXPERIMENT_BROWSER = "experiment_browser";
- public static final String SAMPLE_REGISTRATION = "sample_registration";
+ public static final String VOCABULARY_REGISTRATION = "vocabulary_registration";
- public static final String SAMPLE_BROWSER = "sample_broser";
+ public static final String SAMPLE_BATCH_REGISTRATION = "sample_batch_registration";
- public static final String LIST_GROUPS = "list_groups";
+ public static final String SAMPLE_REGISTRATION = "sample_registration";
- public static final String CONFIRM_TITLE = "confirm_title";
+ public static final String SAMPLE_BROWSER = "sample_broser";
- public static final String CONFIRM_CLOSE_MSG = "confirm_close_msg";
+ public static final String LIST_GROUPS = "list_groups";
- //
- // Role View
- //
- public static final String ROLE = "role";
+ public static final String CONFIRM_TITLE = "confirm_title";
- public static final String CONFIRM_ROLE_REMOVAL_MSG = "confirm_role_removal_msg";
+ public static final String CONFIRM_CLOSE_MSG = "confirm_close_msg";
- public static final String CONFIRM_ROLE_REMOVAL_TITLE = "confirm_role_removal_title";
+ //
+ // Role View
+ //
+ public static final String ROLE = "role";
- //
- // Experiment Registration
- //
+ public static final String CONFIRM_ROLE_REMOVAL_MSG = "confirm_role_removal_msg";
- public static final String EXPERIMENT_REGISTRATION = "experiment_registration";
+ public static final String CONFIRM_ROLE_REMOVAL_TITLE = "confirm_role_removal_title";
- public static final String SAMPLES = "samples";
+ //
+ // Experiment Registration
+ //
- public static final String SAMPLES_LIST = "samples_list";
+ public static final String EXPERIMENT_REGISTRATION = "experiment_registration";
- //
- // Vocabulary Browser
- //
- public static final String VOCABULARY_BROWSER = "vocabulary_browser";
+ public static final String SAMPLES = "samples";
- public static final String IS_MANAGED_INTERNALLY = "is_managed_internally";
+ public static final String SAMPLES_LIST = "samples_list";
- public static final String TERMS = "terms";
+ //
+ // Vocabulary Browser
+ //
+ public static final String VOCABULARY_BROWSER = "vocabulary_browser";
- public static final String VOCABULARY_TERMS_BROWSER = "VOCABULARY_TERMS_BROWSER";
+ public static final String IS_MANAGED_INTERNALLY = "is_managed_internally";
- public static final String TERM_FOR_SAMPLES_USAGE = "TERM_FOR_SAMPLES_USAGE";
+ public static final String TERMS = "terms";
- public static final String TERM_FOR_EXPERIMENTS_USAGE = "TERM_FOR_EXPERIMENTS_USAGE";
+ public static final String VOCABULARY_TERMS_BROWSER = "VOCABULARY_TERMS_BROWSER";
- public static final String TERM_FOR_MATERIALS_USAGE = "TERM_FOR_MATERIALS_USAGE";
+ public static final String TERM_FOR_SAMPLES_USAGE = "TERM_FOR_SAMPLES_USAGE";
- public static final String TERM_TOTAL_USAGE = "TERM_TOTAL_USAGE";
+ public static final String TERM_FOR_EXPERIMENTS_USAGE = "TERM_FOR_EXPERIMENTS_USAGE";
- //
- // Project Browser
- //
- public static final String PROJECT_BROWSER = "project_browser";
+ public static final String TERM_FOR_MATERIALS_USAGE = "TERM_FOR_MATERIALS_USAGE";
- //
- // Project Registration
- //
- public static final String PROJECT_REGISTRATION = "project_registration";
+ public static final String TERM_TOTAL_USAGE = "TERM_TOTAL_USAGE";
- //
- // Data Set Search
- //
- public static final String DATA_SET_SEARCH = "data_set_search";
+ //
+ // Project Browser
+ //
+ public static final String PROJECT_BROWSER = "project_browser";
- public static final String MATCH_ALL = "match_all";
+ //
+ // Project Registration
+ //
+ public static final String PROJECT_REGISTRATION = "project_registration";
- public static final String MATCH_ANY = "match_any";
+ //
+ // Data Set Search
+ //
+ public static final String DATA_SET_SEARCH = "data_set_search";
- public static final String BUTTON_CHANGE_QUERY = "button_change_query";
+ public static final String MATCH_ALL = "match_all";
- //
- // Material Browser
- //
- public static final String MATERIAL_TYPE = "material_type";
+ public static final String MATCH_ANY = "match_any";
- public static final String MATERIAL_BROWSER = "material_browser";
+ public static final String BUTTON_CHANGE_QUERY = "button_change_query";
- public static final String INHIBITOR_OF = "infibitor_of";
+ //
+ // Material Browser
+ //
+ public static final String MATERIAL_TYPE = "material_type";
- public static final String ALLOW_ANY_TYPE = "allow_any_type";
+ public static final String MATERIAL_BROWSER = "material_browser";
- //
- // Material Import
- //
- public static final String MATERIAL_IMPORT = "material_import";
+ public static final String INHIBITOR_OF = "infibitor_of";
- //
- // Material Chooser
- //
+ public static final String ALLOW_ANY_TYPE = "allow_any_type";
- public static final String TITLE_CHOOSE_MATERIAL = "title_choose_material";
+ //
+ // Material Import
+ //
+ public static final String MATERIAL_IMPORT = "material_import";
- public static final String CHOOSE_ANY_MATERIAL = "choose_any_material";
+ //
+ // Material Chooser
+ //
- public static final String INCORRECT_MATERIAL_SYNTAX = "incorrect_material_syntax";
+ public static final String TITLE_CHOOSE_MATERIAL = "title_choose_material";
- public static final String TITLE_CHOOSE_EXPERIMENT = "TITLE_CHOOSE_EXPERIMENT";
+ public static final String CHOOSE_ANY_MATERIAL = "choose_any_material";
- //
- // Unclassified
- //
- public static final String LEADER = "leader";
+ public static final String INCORRECT_MATERIAL_SYNTAX = "incorrect_material_syntax";
- public static final String FILTER = "filter";
+ public static final String TITLE_CHOOSE_EXPERIMENT = "TITLE_CHOOSE_EXPERIMENT";
- public static final String ENTITY_TYPE_ASSIGNMENTS = "entity_type_assignments";
+ //
+ // Unclassified
+ //
+ public static final String LEADER = "leader";
- public static final String COMBO_BOX_EXPECTED_VALUE_FROM_THE_LIST =
- "combo_box_expected_value_from_the_list";
+ public static final String FILTER = "filter";
- public static final String EDIT_TITLE = "edit_title";
+ public static final String ENTITY_TYPE_ASSIGNMENTS = "entity_type_assignments";
- public static final String BUTTON_EDIT = "edit";
+ public static final String COMBO_BOX_EXPECTED_VALUE_FROM_THE_LIST = "combo_box_expected_value_from_the_list";
- // ----- end generic ------------------
+ public static final String EDIT_TITLE = "edit_title";
+
+ 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/framework/ComponentProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/framework/ComponentProvider.java
index 80ddb0233351993b28f94ea162d8b8533e4373f7..9bbe1715446526e0a1a661ef5c9092c3f44c0d03 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/framework/ComponentProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/framework/ComponentProvider.java
@@ -16,8 +16,6 @@
package ch.systemsx.cisd.openbis.generic.client.web.client.application.framework;
-import com.extjs.gxt.ui.client.widget.Component;
-
import ch.systemsx.cisd.openbis.generic.client.web.client.application.CommonViewContext;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.GroupsView;
@@ -45,6 +43,8 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.vocabul
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.vocabulary.VocabularyRegistrationForm;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
+import com.extjs.gxt.ui.client.widget.Component;
+
/**
* Creates and provides GUI modules/components (such as sample browser).
* <p>
@@ -53,424 +53,373 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
*
* @author Izabela Adamczyk
*/
-public final class ComponentProvider
-{
- private final CommonViewContext viewContext;
-
- ComponentProvider(final CommonViewContext viewContext)
- {
- this.viewContext = viewContext;
- }
-
- private String getMessage(String key)
- {
- return viewContext.getMessage(key);
- }
-
- public final ITabItemFactory getSampleBrowser()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- DisposableComponent browser = SampleBrowserGrid.create(viewContext);
- return DefaultTabItem.create(getMessage(Dict.SAMPLE_BROWSER), browser);
- }
-
- public String getId()
- {
- return SampleBrowserGrid.BROWSER_ID;
- }
- };
- }
-
- public final ITabItemFactory getMaterialBrowser()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- DisposableComponent browser =
- MaterialBrowserGrid.createWithTypeChooser(viewContext);
- return DefaultTabItem.create(getMessage(Dict.MATERIAL_BROWSER), browser);
- }
-
- public String getId()
- {
- return MaterialBrowserGrid.BROWSER_ID;
- }
- };
- }
-
- public final ITabItemFactory getDummyComponent()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- return new DefaultTabItem(getMessage(Dict.NOT_IMPLEMENTED),
- new DummyComponent(), false);
- }
-
- public String getId()
- {
- return DummyComponent.ID;
- }
- };
- }
-
- public final ITabItemFactory getGroupsView()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- return new ContentPanelAdapter(new GroupsView(viewContext), false);
- }
-
- public String getId()
- {
- return GroupsView.ID;
- }
- };
- }
-
- public final ITabItemFactory getRolesView()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- return new ContentPanelAdapter(new RolesView(viewContext), false);
- }
-
- public String getId()
- {
- return RolesView.ID;
- }
- };
- }
-
- public final ITabItemFactory getPersonsView()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- return new ContentPanelAdapter(new PersonsView(viewContext), false);
- }
-
- public String getId()
- {
- return PersonsView.ID;
- }
- };
- }
-
- public final ITabItemFactory getSampleRegistration()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- Component component = new SampleRegistrationPanel(viewContext);
- return new DefaultTabItem(getMessage(Dict.SAMPLE_REGISTRATION), component, true);
- }
-
- public String getId()
- {
- return SampleRegistrationPanel.ID;
- }
- };
- }
-
- public final ITabItemFactory getExperimentRegistration()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- Component component = new ExperimentRegistrationPanel(viewContext);
- return new DefaultTabItem(getMessage(Dict.EXPERIMENT_REGISTRATION), component,
- true);
- }
-
- public String getId()
- {
- return ExperimentRegistrationPanel.ID;
- }
- };
- }
-
- public final ITabItemFactory getSampleBatchRegistration()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- Component component = new SampleBatchRegistrationPanel(viewContext);
- return new DefaultTabItem(getMessage(Dict.SAMPLE_BATCH_REGISTRATION),
- component, true);
- }
-
- public String getId()
- {
- return SampleBatchRegistrationPanel.ID;
- }
- };
- }
-
- public final ITabItemFactory getMaterialBatchRegistration()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- Component component = new MaterialBatchRegistrationPanel(viewContext);
- return new DefaultTabItem(getMessage(Dict.MATERIAL_IMPORT), component, true);
- }
-
- public String getId()
- {
- return MaterialBatchRegistrationPanel.ID;
- }
- };
- }
-
- public final ITabItemFactory getVocabularyRegistration()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- Component component = new VocabularyRegistrationForm(viewContext);
- return new DefaultTabItem(getMessage(Dict.VOCABULARY_REGISTRATION), component,
- true);
- }
-
- public String getId()
- {
- return VocabularyRegistrationForm.ID;
- }
- };
- }
-
- public final ITabItemFactory getProjectRegistration()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- Component component = new ProjectRegistrationForm(viewContext);
- return new DefaultTabItem(getMessage(Dict.PROJECT_REGISTRATION), component,
- true);
- }
-
- public String getId()
- {
- return ProjectRegistrationForm.ID;
- }
- };
- }
-
- public final ITabItemFactory getVocabularyBrowser()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- DisposableComponent component = VocabularyGrid.create(viewContext);
- return DefaultTabItem.create(getMessage(Dict.VOCABULARY_BROWSER), component);
- }
-
- public String getId()
- {
- return VocabularyGrid.GRID_ID;
- }
- };
- }
-
- public final ITabItemFactory getProjectBrowser()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- DisposableComponent component = ProjectGrid.create(viewContext);
- return DefaultTabItem.create(getMessage(Dict.PROJECT_BROWSER), component);
- }
-
- public String getId()
- {
- return ProjectGrid.BROWSER_ID;
- }
- };
- }
-
- public ITabItemFactory getExperimentBrowser()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- DisposableComponent browser = ExperimentBrowserGrid.create(viewContext);
- return DefaultTabItem.create(getMessage(Dict.EXPERIMENT_BROWSER), browser);
- }
-
- public String getId()
- {
- return ExperimentBrowserGrid.BROWSER_ID;
- }
- };
- }
-
- public ITabItemFactory getPropertyTypeBrowser()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- DisposableComponent component = PropertyTypeGrid.create(viewContext);
- return DefaultTabItem.create(getMessage(Dict.PROPERTY_TYPES), component);
- }
-
- public String getId()
- {
- return PropertyTypeGrid.BROWSER_ID;
- }
- };
- }
-
- public ITabItemFactory getPropertyTypeRegistration()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- Component component = new PropertyTypeRegistrationForm(viewContext);
- return new DefaultTabItem(getMessage(Dict.PROPERTY_TYPE_REGISTRATION),
- component, true);
- }
-
- public String getId()
- {
- return PropertyTypeRegistrationForm.ID;
- }
- };
- }
-
- public ITabItemFactory getPropertyTypeAssignmentBrowser()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- DisposableComponent component = PropertyTypeAssignmentGrid.create(viewContext);
- return DefaultTabItem.create(getMessage(Dict.PROPERTY_TYPE_ASSIGNMENTS),
- component);
- }
-
- public String getId()
- {
- return PropertyTypeAssignmentGrid.BROWSER_ID;
- }
- };
- }
-
- public ITabItemFactory getPropertyTypeExperimentTypeAssignmentForm()
- {
- return getPropertyTypeAssignmentForm(EntityKind.EXPERIMENT,
- Dict.ASSIGN_EXPERIMENT_PROPERTY_TYPE);
- }
-
- public ITabItemFactory getPropertyTypeSampleTypeAssignmentForm()
- {
- return getPropertyTypeAssignmentForm(EntityKind.SAMPLE, Dict.ASSIGN_SAMPLE_PROPERTY_TYPE);
- }
-
- private ITabItemFactory getPropertyTypeAssignmentForm(final EntityKind entityKind,
- final String messageKey)
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- Component component = new PropertyTypeAssignmentForm(viewContext, entityKind);
- return new DefaultTabItem(getMessage(messageKey), component, true);
- }
-
- public String getId()
- {
- return PropertyTypeAssignmentForm.createId(entityKind);
- }
- };
- }
-
- public ITabItemFactory getDataSetSearch()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- DisposableComponent browser = DataSetSearchHitGrid.create(viewContext);
- return DefaultTabItem.create(getMessage(Dict.DATA_SET_SEARCH), browser);
- }
-
- public String getId()
- {
- return DataSetSearchHitGrid.BROWSER_ID;
- }
- };
- }
-
- public ITabItemFactory getSampleTypeBrowser()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- DisposableComponent component = SampleTypeGrid.create(viewContext);
- return DefaultTabItem.create(getMessage(Dict.SAMPLE_TYPES), component);
- }
-
- public String getId()
- {
- return SampleTypeGrid.BROWSER_ID;
- }
- };
- }
-
- public ITabItemFactory getMaterialTypeBrowser()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- DisposableComponent component = MaterialTypeGrid.create(viewContext);
- return DefaultTabItem.create(getMessage(Dict.MATERIAL_TYPES), component);
- }
-
- public String getId()
- {
- return MaterialTypeGrid.BROWSER_ID;
- }
- };
- }
-
- public ITabItemFactory getExperimentTypeBrowser()
- {
- return new ITabItemFactory()
- {
- public ITabItem create()
- {
- DisposableComponent component = ExperimentTypeGrid.create(viewContext);
- return DefaultTabItem.create(getMessage(Dict.EXPERIMENT_TYPES), component);
- }
-
- public String getId()
- {
- return ExperimentTypeGrid.BROWSER_ID;
- }
- };
- }
+public final class ComponentProvider {
+ private final CommonViewContext viewContext;
+
+ ComponentProvider(final CommonViewContext viewContext) {
+ this.viewContext = viewContext;
+ }
+
+ private String getMessage(String key) {
+ return viewContext.getMessage(key);
+ }
+
+ public final ITabItemFactory getSampleBrowser() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ DisposableComponent browser = SampleBrowserGrid
+ .create(viewContext);
+ return DefaultTabItem.create(getMessage(Dict.SAMPLE_BROWSER),
+ browser);
+ }
+
+ public String getId() {
+ return SampleBrowserGrid.BROWSER_ID;
+ }
+ };
+ }
+
+ public final ITabItemFactory getMaterialBrowser() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ DisposableComponent browser = MaterialBrowserGrid
+ .createWithTypeChooser(viewContext);
+ return DefaultTabItem.create(getMessage(Dict.MATERIAL_BROWSER),
+ browser);
+ }
+
+ public String getId() {
+ return MaterialBrowserGrid.BROWSER_ID;
+ }
+ };
+ }
+
+ public final ITabItemFactory getDummyComponent() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ return new DefaultTabItem(getMessage(Dict.NOT_IMPLEMENTED),
+ new DummyComponent(), false);
+ }
+
+ public String getId() {
+ return DummyComponent.ID;
+ }
+ };
+ }
+
+ public final ITabItemFactory getGroupsView() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ return new ContentPanelAdapter(new GroupsView(viewContext),
+ false);
+ }
+
+ public String getId() {
+ return GroupsView.ID;
+ }
+ };
+ }
+
+ public final ITabItemFactory getRolesView() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ return new ContentPanelAdapter(new RolesView(viewContext),
+ false);
+ }
+
+ public String getId() {
+ return RolesView.ID;
+ }
+ };
+ }
+
+ public final ITabItemFactory getPersonsView() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ return new ContentPanelAdapter(new PersonsView(viewContext),
+ false);
+ }
+
+ public String getId() {
+ return PersonsView.ID;
+ }
+ };
+ }
+
+ public final ITabItemFactory getSampleRegistration() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ Component component = new SampleRegistrationPanel(viewContext);
+ return new DefaultTabItem(getMessage(Dict.SAMPLE_REGISTRATION),
+ component, true);
+ }
+
+ public String getId() {
+ return SampleRegistrationPanel.ID;
+ }
+ };
+ }
+
+ public final ITabItemFactory getExperimentRegistration() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ Component component = new ExperimentRegistrationPanel(
+ viewContext);
+ return new DefaultTabItem(
+ getMessage(Dict.EXPERIMENT_REGISTRATION), component,
+ true);
+ }
+
+ public String getId() {
+ return ExperimentRegistrationPanel.ID;
+ }
+ };
+ }
+
+ public final ITabItemFactory getSampleBatchRegistration() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ Component component = new SampleBatchRegistrationPanel(
+ viewContext);
+ return new DefaultTabItem(
+ getMessage(Dict.SAMPLE_BATCH_REGISTRATION), component,
+ true);
+ }
+
+ public String getId() {
+ return SampleBatchRegistrationPanel.ID;
+ }
+ };
+ }
+
+ public final ITabItemFactory getMaterialBatchRegistration() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ Component component = new MaterialBatchRegistrationPanel(
+ viewContext);
+ return new DefaultTabItem(getMessage(Dict.MATERIAL_IMPORT),
+ component, true);
+ }
+
+ public String getId() {
+ return MaterialBatchRegistrationPanel.ID;
+ }
+ };
+ }
+
+ public final ITabItemFactory getVocabularyRegistration() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ Component component = new VocabularyRegistrationForm(
+ viewContext);
+ return new DefaultTabItem(
+ getMessage(Dict.VOCABULARY_REGISTRATION), component,
+ true);
+ }
+
+ public String getId() {
+ return VocabularyRegistrationForm.ID;
+ }
+ };
+ }
+
+ public final ITabItemFactory getProjectRegistration() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ Component component = new ProjectRegistrationForm(viewContext);
+ return new DefaultTabItem(
+ getMessage(Dict.PROJECT_REGISTRATION), component, true);
+ }
+
+ public String getId() {
+ return ProjectRegistrationForm.ID;
+ }
+ };
+ }
+
+ public final ITabItemFactory getVocabularyBrowser() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ DisposableComponent component = VocabularyGrid
+ .create(viewContext);
+ return DefaultTabItem.create(
+ getMessage(Dict.VOCABULARY_BROWSER), component);
+ }
+
+ public String getId() {
+ return VocabularyGrid.GRID_ID;
+ }
+ };
+ }
+
+ public final ITabItemFactory getProjectBrowser() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ DisposableComponent component = ProjectGrid.create(viewContext);
+ return DefaultTabItem.create(getMessage(Dict.PROJECT_BROWSER),
+ component);
+ }
+
+ public String getId() {
+ return ProjectGrid.BROWSER_ID;
+ }
+ };
+ }
+
+ public ITabItemFactory getExperimentBrowser() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ DisposableComponent browser = ExperimentBrowserGrid
+ .create(viewContext);
+ return DefaultTabItem.create(
+ getMessage(Dict.EXPERIMENT_BROWSER), browser);
+ }
+
+ public String getId() {
+ return ExperimentBrowserGrid.BROWSER_ID;
+ }
+ };
+ }
+
+ public ITabItemFactory getPropertyTypeBrowser() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ DisposableComponent component = PropertyTypeGrid
+ .create(viewContext);
+ return DefaultTabItem.create(getMessage(Dict.PROPERTY_TYPES),
+ component);
+ }
+
+ public String getId() {
+ return PropertyTypeGrid.BROWSER_ID;
+ }
+ };
+ }
+
+ public ITabItemFactory getPropertyTypeRegistration() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ Component component = new PropertyTypeRegistrationForm(
+ viewContext);
+ return new DefaultTabItem(
+ getMessage(Dict.PROPERTY_TYPE_REGISTRATION), component,
+ true);
+ }
+
+ public String getId() {
+ return PropertyTypeRegistrationForm.ID;
+ }
+ };
+ }
+
+ public ITabItemFactory getPropertyTypeAssignmentBrowser() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ DisposableComponent component = PropertyTypeAssignmentGrid
+ .create(viewContext);
+ return DefaultTabItem.create(
+ getMessage(Dict.PROPERTY_TYPE_ASSIGNMENTS), component);
+ }
+
+ public String getId() {
+ return PropertyTypeAssignmentGrid.BROWSER_ID;
+ }
+ };
+ }
+
+ public ITabItemFactory getPropertyTypeExperimentTypeAssignmentForm() {
+ return getPropertyTypeAssignmentForm(EntityKind.EXPERIMENT,
+ Dict.ASSIGN_EXPERIMENT_PROPERTY_TYPE);
+ }
+
+ public ITabItemFactory getPropertyTypeMaterialTypeAssignmentForm() {
+ return getPropertyTypeAssignmentForm(EntityKind.MATERIAL,
+ Dict.ASSIGN_MATERIAL_PROPERTY_TYPE);
+ }
+
+ public ITabItemFactory getPropertyTypeDataSetTypeAssignmentForm() {
+ return getPropertyTypeAssignmentForm(EntityKind.DATA_SET,
+ Dict.ASSIGN_DATA_SET_PROPERTY_TYPE);
+ }
+
+ public ITabItemFactory getPropertyTypeSampleTypeAssignmentForm() {
+ return getPropertyTypeAssignmentForm(EntityKind.SAMPLE,
+ Dict.ASSIGN_SAMPLE_PROPERTY_TYPE);
+ }
+
+ private ITabItemFactory getPropertyTypeAssignmentForm(
+ final EntityKind entityKind, final String messageKey) {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ Component component = new PropertyTypeAssignmentForm(
+ viewContext, entityKind);
+ return new DefaultTabItem(getMessage(messageKey), component,
+ true);
+ }
+
+ public String getId() {
+ return PropertyTypeAssignmentForm.createId(entityKind);
+ }
+ };
+ }
+
+ public ITabItemFactory getDataSetSearch() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ DisposableComponent browser = DataSetSearchHitGrid
+ .create(viewContext);
+ return DefaultTabItem.create(getMessage(Dict.DATA_SET_SEARCH),
+ browser);
+ }
+
+ public String getId() {
+ return DataSetSearchHitGrid.BROWSER_ID;
+ }
+ };
+ }
+
+ public ITabItemFactory getSampleTypeBrowser() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ DisposableComponent component = SampleTypeGrid
+ .create(viewContext);
+ return DefaultTabItem.create(getMessage(Dict.SAMPLE_TYPES),
+ component);
+ }
+
+ public String getId() {
+ return SampleTypeGrid.BROWSER_ID;
+ }
+ };
+ }
+
+ public ITabItemFactory getMaterialTypeBrowser() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ DisposableComponent component = MaterialTypeGrid
+ .create(viewContext);
+ return DefaultTabItem.create(getMessage(Dict.MATERIAL_TYPES),
+ component);
+ }
+
+ public String getId() {
+ return MaterialTypeGrid.BROWSER_ID;
+ }
+ };
+ }
+
+ public ITabItemFactory getExperimentTypeBrowser() {
+ return new ITabItemFactory() {
+ public ITabItem create() {
+ DisposableComponent component = ExperimentTypeGrid
+ .create(viewContext);
+ return DefaultTabItem.create(getMessage(Dict.EXPERIMENT_TYPES),
+ component);
+ }
+
+ public String getId() {
+ return ExperimentTypeGrid.BROWSER_ID;
+ }
+ };
+ }
}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/menu/TopMenu.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/menu/TopMenu.java
index 2e77a6f83437e890eefafde58db4c38b35ff38ed..2ae4229efa8d5c58ee4dee7958a019f15a17b495 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/menu/TopMenu.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/menu/TopMenu.java
@@ -16,18 +16,6 @@
package ch.systemsx.cisd.openbis.generic.client.web.client.application.menu;
-import com.extjs.gxt.ui.client.event.ComponentEvent;
-import com.extjs.gxt.ui.client.event.SelectionListener;
-import com.extjs.gxt.ui.client.widget.Html;
-import com.extjs.gxt.ui.client.widget.LayoutContainer;
-import com.extjs.gxt.ui.client.widget.layout.FlowLayout;
-import com.extjs.gxt.ui.client.widget.toolbar.AdapterToolItem;
-import com.extjs.gxt.ui.client.widget.toolbar.FillToolItem;
-import com.extjs.gxt.ui.client.widget.toolbar.SeparatorToolItem;
-import com.extjs.gxt.ui.client.widget.toolbar.TextToolItem;
-import com.extjs.gxt.ui.client.widget.toolbar.ToolBar;
-import com.google.gwt.user.client.Element;
-
import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.CommonViewContext;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict;
@@ -43,6 +31,18 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMess
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.SessionContext;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.User;
+import com.extjs.gxt.ui.client.event.ComponentEvent;
+import com.extjs.gxt.ui.client.event.SelectionListener;
+import com.extjs.gxt.ui.client.widget.Html;
+import com.extjs.gxt.ui.client.widget.LayoutContainer;
+import com.extjs.gxt.ui.client.widget.layout.FlowLayout;
+import com.extjs.gxt.ui.client.widget.toolbar.AdapterToolItem;
+import com.extjs.gxt.ui.client.widget.toolbar.FillToolItem;
+import com.extjs.gxt.ui.client.widget.toolbar.SeparatorToolItem;
+import com.extjs.gxt.ui.client.widget.toolbar.TextToolItem;
+import com.extjs.gxt.ui.client.widget.toolbar.ToolBar;
+import com.google.gwt.user.client.Element;
+
/**
* Implements functionality of the top menu.
*
@@ -76,7 +76,9 @@ public class TopMenu extends LayoutContainer
PROJECT_MENU_BROWSE, PROJECT_MENU_NEW,
PROPERTY_TYPES_MENU_BROWSE_PROPERTY_TYPES, PROPERTY_TYPES_MENU_BROWSE_ASSIGNMENTS,
- PROPERTY_TYPES_MENU_NEW_PROPERTY_TYPES, PROPERTY_TYPES_MENU_ASSIGN_TO_EXPERIMENT_TYPE,
+ PROPERTY_TYPES_MENU_NEW_PROPERTY_TYPES, PROPERTY_TYPES_MENU_ASSIGN_TO_EXPERIMENT_TYPE,
+ PROPERTY_TYPES_MENU_ASSIGN_TO_MATERIAL_TYPE,
+ PROPERTY_TYPES_MENU_ASSIGN_TO_DATA_SET_TYPE,
PROPERTY_TYPES_MENU_ASSIGN_TO_SAMPLE_TYPE,
VOCABULARY_MENU_BROWSE, VOCABULARY_MENU_NEW;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/menu/administration/PropertyTypesMenu.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/menu/administration/PropertyTypesMenu.java
index e19c424edad1a9fa0c6020b19bfaca14a6437d25..ca22f406e3c392e5756d8a895da59b9c2d15dfe3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/menu/administration/PropertyTypesMenu.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/menu/administration/PropertyTypesMenu.java
@@ -48,6 +48,12 @@ public class PropertyTypesMenu extends MenuItem
menu.add(new ActionMenu(
TopMenu.ActionMenuKind.PROPERTY_TYPES_MENU_ASSIGN_TO_EXPERIMENT_TYPE,
messageProvider, componentProvider.getPropertyTypeExperimentTypeAssignmentForm()));
+ menu.add(new ActionMenu(
+ TopMenu.ActionMenuKind.PROPERTY_TYPES_MENU_ASSIGN_TO_MATERIAL_TYPE,
+ messageProvider, componentProvider.getPropertyTypeMaterialTypeAssignmentForm()));
+ menu.add(new ActionMenu(
+ TopMenu.ActionMenuKind.PROPERTY_TYPES_MENU_ASSIGN_TO_DATA_SET_TYPE,
+ messageProvider, componentProvider.getPropertyTypeDataSetTypeAssignmentForm()));
menu.add(new ActionMenu(TopMenu.ActionMenuKind.PROPERTY_TYPES_MENU_ASSIGN_TO_SAMPLE_TYPE,
messageProvider, componentProvider.getPropertyTypeSampleTypeAssignmentForm()));
setSubMenu(menu);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/model/DataSetTypeModel.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/model/DataSetTypeModel.java
new file mode 100644
index 0000000000000000000000000000000000000000..ee22e03243cb5ca0cb13533b6424f4f7db19de38
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/model/DataSetTypeModel.java
@@ -0,0 +1,53 @@
+/*
+ * Copyright 2008 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.client.web.client.application.model;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import com.extjs.gxt.ui.client.data.BaseModelData;
+import com.extjs.gxt.ui.client.data.ModelData;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
+
+/**
+ * {@link ModelData} for {@link DataSetType}.
+ *
+ * @author Izabela Adamczyk
+ */
+public class DataSetTypeModel extends BaseModelData
+{
+
+ private static final long serialVersionUID = 1L;
+
+ public DataSetTypeModel(final DataSetType dataSetType)
+ {
+ set(ModelDataPropertyNames.CODE, dataSetType.getCode());
+ set(ModelDataPropertyNames.OBJECT, dataSetType);
+ }
+
+ public final static List<DataSetTypeModel> convert(final List<DataSetType> dataSetTypes)
+ {
+ final List<DataSetTypeModel> result = new ArrayList<DataSetTypeModel>();
+ for (final DataSetType st : dataSetTypes)
+ {
+ result.add(new DataSetTypeModel(st));
+ }
+ return result;
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/DataSetTypeSelectionWidget.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/DataSetTypeSelectionWidget.java
new file mode 100644
index 0000000000000000000000000000000000000000..53cafc3c3b265a817996f6e1ec4347baef30b703
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/DataSetTypeSelectionWidget.java
@@ -0,0 +1,69 @@
+/*
+ * Copyright 2008 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.data;
+
+import java.util.List;
+
+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.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.DataSetTypeModel;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.ModelDataPropertyNames;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.sample.DropDownList;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
+
+import com.extjs.gxt.ui.client.widget.form.ComboBox;
+
+/**
+ * {@link ComboBox} containing list of data set types loaded from the server.
+ *
+ * @author Izabela Adamczyk
+ */
+public final class DataSetTypeSelectionWidget extends
+ DropDownList<DataSetTypeModel, DataSetType> {
+ public static final String SUFFIX = "data-set-type";
+
+ private final IViewContext<ICommonClientServiceAsync> viewContext;
+
+ public DataSetTypeSelectionWidget(
+ final IViewContext<ICommonClientServiceAsync> viewContext,
+ final String idSuffix) {
+ super(viewContext, SUFFIX + idSuffix, Dict.DATA_SET_TYPE,
+ ModelDataPropertyNames.CODE, "data set type", "data set types");
+ this.viewContext = viewContext;
+ }
+
+ /**
+ * Returns the {@link DataSetType} currently selected.
+ *
+ * @return <code>null</code> if nothing is selected yet.
+ */
+ public final DataSetType tryGetSelectedDataSetType() {
+ return super.tryGetSelected();
+ }
+
+ @Override
+ protected List<DataSetTypeModel> convertItems(List<DataSetType> result) {
+ return DataSetTypeModel.convert(result);
+ }
+
+ @Override
+ protected void loadData(AbstractAsyncCallback<List<DataSetType>> callback) {
+ viewContext.getService().listDataSetTypes(callback);
+ }
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/property_type/PropertyTypeAssignmentForm.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/property_type/PropertyTypeAssignmentForm.java
index b9b45284afecf396fdbfc05ca5cb309e6e8d5637..477b7f569bd0a4164a477ca4dc79cb90a3287336 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/property_type/PropertyTypeAssignmentForm.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/property_type/PropertyTypeAssignmentForm.java
@@ -16,6 +16,23 @@
package ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.property_type;
+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.InfoBoxCallbackListener;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AbstractRegistrationForm.InfoBoxResetListener;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.data.DataSetTypeSelectionWidget;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.experiment.ExperimentTypeSelectionWidget;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.PropertyFieldFactory;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.material.MaterialTypeSelectionWidget;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.sample.SampleTypeSelectionWidget;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.FieldUtil;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.InfoBox;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
+
import com.extjs.gxt.ui.client.Events;
import com.extjs.gxt.ui.client.Style.HorizontalAlignment;
import com.extjs.gxt.ui.client.Style.Scroll;
@@ -32,292 +49,289 @@ import com.extjs.gxt.ui.client.widget.form.FormPanel;
import com.extjs.gxt.ui.client.widget.layout.FlowLayout;
import com.google.gwt.user.client.Element;
-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.InfoBoxCallbackListener;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AbstractRegistrationForm.InfoBoxResetListener;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.experiment.ExperimentTypeSelectionWidget;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.PropertyFieldFactory;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.sample.SampleTypeSelectionWidget;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.FieldUtil;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.InfoBox;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
-
/**
* The property type assignment panel.
*
* @author Izabela Adamczyk
*/
-public final class PropertyTypeAssignmentForm extends LayoutContainer
-{
- private static final String UNSUPPORTED_ENTITY_KIND = "Unsupported entity kind";
-
- private static final int LABEL_WIDTH = 130;
-
- private static final int FIELD_WIDTH = 400;
-
- private static final String PREFIX = "property-type-assignment_";
-
- public static final String ID_PREFIX = GenericConstants.ID_PREFIX + PREFIX;
-
- public static final String PROPERTY_TYPE_ID_SUFFIX = "property_type";
-
- public static final String SAMPLE_TYPE_ID_SUFFIX = ID_PREFIX + "sample_type";
-
- public static final String EXPERIMENT_TYPE_ID_SUFFIX = ID_PREFIX + "experiment_type";
-
- public static final String MANDATORY_CHECKBOX_ID_SUFFIX = "mandatory_checkbox";
-
- public static final String SAVE_BUTTON_ID_SUFFIX = "save-button";
-
- protected static final String DEFAULT_VALUE_ID_PART = "default_value";
-
- private final IViewContext<ICommonClientServiceAsync> viewContext;
-
- private SampleTypeSelectionWidget sampleTypeSelectionWidget;
-
- private ExperimentTypeSelectionWidget experimentTypeSelectionWidget;
-
- private PropertyTypeSelectionWidget propertyTypeSelectionWidget;
-
- private Field<?> defaultValueField;
-
- private CheckBox mandatoryCheckbox;
-
- private final InfoBox infoBox;
-
- private final FormPanel formPanel;
-
- private final EntityKind entityKind;
-
- public PropertyTypeAssignmentForm(final IViewContext<ICommonClientServiceAsync> viewContext,
- EntityKind entityKind)
- {
- this.entityKind = entityKind;
- setLayout(new FlowLayout(5));
- setId(createId(entityKind));
- this.viewContext = viewContext;
- setScrollMode(Scroll.AUTO);
- add(infoBox = createInfoBox());
- add(formPanel = createFormPanel());
- }
-
- public static final String createId(EntityKind entityKind)
- {
- return ID_PREFIX + entityKind.name();
- }
-
- private String createChildId(String childSuffix)
- {
- return getId() + childSuffix;
- }
-
- private final static InfoBox createInfoBox()
- {
- final InfoBox infoBox = new InfoBox();
- return infoBox;
- }
-
- private PropertyTypeSelectionWidget getPropertyTypeWidget()
- {
- if (propertyTypeSelectionWidget == null)
- {
- propertyTypeSelectionWidget =
- new PropertyTypeSelectionWidget(viewContext,
- createChildId(PROPERTY_TYPE_ID_SUFFIX));
- propertyTypeSelectionWidget
- .addListener(Events.Focus, new InfoBoxResetListener(infoBox));
- FieldUtil.markAsMandatory(propertyTypeSelectionWidget);
- propertyTypeSelectionWidget.addListener(Events.SelectionChange,
- new Listener<BaseEvent>()
- {
- public void handleEvent(BaseEvent be)
- {
- updateDefaultField();
- }
- });
- }
- return propertyTypeSelectionWidget;
- }
-
- private ComboBox<?> getTypeSelectionWidget()
- {
- switch (entityKind)
- {
- case EXPERIMENT:
- if (experimentTypeSelectionWidget == null)
- {
- experimentTypeSelectionWidget =
- new ExperimentTypeSelectionWidget(viewContext,
- EXPERIMENT_TYPE_ID_SUFFIX);
- experimentTypeSelectionWidget.addListener(Events.Focus,
- new InfoBoxResetListener(infoBox));
- FieldUtil.markAsMandatory(experimentTypeSelectionWidget);
- }
- return experimentTypeSelectionWidget;
- case SAMPLE:
- if (sampleTypeSelectionWidget == null)
- {
- sampleTypeSelectionWidget =
- new SampleTypeSelectionWidget(viewContext, SAMPLE_TYPE_ID_SUFFIX, false);
- sampleTypeSelectionWidget.addListener(Events.Focus, new InfoBoxResetListener(
- infoBox));
- FieldUtil.markAsMandatory(sampleTypeSelectionWidget);
- }
- return sampleTypeSelectionWidget;
- default:
- throw new IllegalArgumentException(UNSUPPORTED_ENTITY_KIND);
- }
- }
-
- private CheckBox getMandatoryCheckbox()
- {
- if (mandatoryCheckbox == null)
- {
- mandatoryCheckbox = new CheckBox();
- mandatoryCheckbox.setId(createChildId(MANDATORY_CHECKBOX_ID_SUFFIX));
- mandatoryCheckbox.setFieldLabel(viewContext.getMessage(Dict.MANDATORY));
- mandatoryCheckbox.setValue(false);
- mandatoryCheckbox.addListener(Events.Change, new InfoBoxResetListener(infoBox));
- }
- return mandatoryCheckbox;
- }
-
- private final FormPanel createFormPanel()
- {
- final FormPanel panel = new FormPanel();
- panel.setHeaderVisible(false);
- panel.setBodyBorder(false);
- panel.setWidth(LABEL_WIDTH + FIELD_WIDTH + 40);
- panel.setLabelWidth(LABEL_WIDTH);
- panel.setFieldWidth(FIELD_WIDTH);
- panel.setButtonAlign(HorizontalAlignment.RIGHT);
- final Button saveButton = new Button(viewContext.getMessage(Dict.BUTTON_SAVE));
- saveButton.setStyleAttribute("marginRight", "20px");
- saveButton.setId(createChildId(SAVE_BUTTON_ID_SUFFIX));
- saveButton.addSelectionListener(new SelectionListener<ButtonEvent>()
- {
- @Override
- public final void componentSelected(final ButtonEvent ce)
- {
- submitForm();
- }
- });
- final Button resetButton = new Button(viewContext.getMessage(Dict.BUTTON_RESET));
- resetButton.addSelectionListener(new SelectionListener<ButtonEvent>()
- {
- @Override
- public final void componentSelected(final ButtonEvent ce)
- {
- resetForm();
- }
- });
- panel.addButton(resetButton);
- panel.addButton(saveButton);
- return panel;
- }
-
- private String getDefaultValue()
- {
- if (defaultValueField != null)
- {
- return PropertyFieldFactory.valueToString(defaultValueField.getValue());
- }
- return null;
- }
-
- private String getSelectedEntityCode()
- {
- switch (entityKind)
- {
- case EXPERIMENT:
- return experimentTypeSelectionWidget.tryGetSelectedExperimentType().getCode();
- case SAMPLE:
- return sampleTypeSelectionWidget.tryGetSelectedSampleType().getCode();
- default:
- throw new IllegalArgumentException(UNSUPPORTED_ENTITY_KIND);
- }
- }
-
- private final void addFormFields()
- {
- formPanel.add(getPropertyTypeWidget());
- formPanel.add(getTypeSelectionWidget());
- formPanel.add(getMandatoryCheckbox());
- updateDefaultField();
- }
-
- @Override
- protected final void onRender(final Element target, final int index)
- {
- super.onRender(target, index);
- addFormFields();
- }
-
- public final class AssignPropertyTypeCallback extends AbstractAsyncCallback<String>
- {
- AssignPropertyTypeCallback(final IViewContext<?> viewContext)
- {
- super(viewContext, new InfoBoxCallbackListener<String>(infoBox));
- }
-
- @Override
- protected final void process(final String result)
- {
- infoBox.displayInfo(result);
- resetForm();
- }
- }
-
- private void updateDefaultField()
- {
- hideDefaultField();
- final PropertyType propertyType = propertyTypeSelectionWidget.tryGetSelectedPropertyType();
- if (propertyType != null)
- {
- String fieldId =
- createChildId(DEFAULT_VALUE_ID_PART + propertyType.isInternalNamespace()
- + propertyType.getSimpleCode());
- Field<?> field =
- PropertyFieldFactory.createField(propertyType, false, viewContext
- .getMessage(Dict.DEFAULT_VALUE), fieldId, null, viewContext);
- field.setToolTip(viewContext.getMessage(Dict.DEFAULT_VALUE_TOOLTIP));
- defaultValueField = field;
- defaultValueField.show();
- formPanel.add(defaultValueField);
- }
- layout();
- }
-
- private void hideDefaultField()
- {
- if (defaultValueField != null)
- {
- defaultValueField.hide();
- formPanel.remove(defaultValueField);
- defaultValueField = null;
- }
- }
-
- private final void submitForm()
- {
- if (formPanel.isValid())
- {
- viewContext.getService().assignPropertyType(entityKind,
- propertyTypeSelectionWidget.tryGetSelectedPropertyTypeCode(),
- getSelectedEntityCode(), getMandatoryCheckbox().getValue(), getDefaultValue(),
- new AssignPropertyTypeCallback(viewContext));
- }
- }
-
- private void resetForm()
- {
- formPanel.reset();
- updateDefaultField();
- }
+public final class PropertyTypeAssignmentForm extends LayoutContainer {
+ private static final String UNSUPPORTED_ENTITY_KIND = "Unsupported entity kind";
+
+ private static final int LABEL_WIDTH = 130;
+
+ private static final int FIELD_WIDTH = 400;
+
+ private static final String PREFIX = "property-type-assignment_";
+
+ public static final String ID_PREFIX = GenericConstants.ID_PREFIX + PREFIX;
+
+ public static final String PROPERTY_TYPE_ID_SUFFIX = "property_type";
+
+ public static final String SAMPLE_TYPE_ID_SUFFIX = ID_PREFIX
+ + "sample_type";
+
+ public static final String EXPERIMENT_TYPE_ID_SUFFIX = ID_PREFIX
+ + "experiment_type";
+
+ public static final String MATERIAL_TYPE_ID_SUFFIX = ID_PREFIX
+ + "material_type";
+
+ public static final String DATA_SET_TYPE_ID_SUFFIX = ID_PREFIX
+ + "data_set_type";
+
+ public static final String MANDATORY_CHECKBOX_ID_SUFFIX = "mandatory_checkbox";
+
+ public static final String SAVE_BUTTON_ID_SUFFIX = "save-button";
+
+ protected static final String DEFAULT_VALUE_ID_PART = "default_value";
+
+ private final IViewContext<ICommonClientServiceAsync> viewContext;
+
+ private SampleTypeSelectionWidget sampleTypeSelectionWidget;
+
+ private ExperimentTypeSelectionWidget experimentTypeSelectionWidget;
+
+ private MaterialTypeSelectionWidget materialTypeSelectionWidget;
+
+ private DataSetTypeSelectionWidget dataSetTypeSelectionWidget;
+
+ private PropertyTypeSelectionWidget propertyTypeSelectionWidget;
+
+ private Field<?> defaultValueField;
+
+ private CheckBox mandatoryCheckbox;
+
+ private final InfoBox infoBox;
+
+ private final FormPanel formPanel;
+
+ private final EntityKind entityKind;
+
+ public PropertyTypeAssignmentForm(
+ final IViewContext<ICommonClientServiceAsync> viewContext,
+ EntityKind entityKind) {
+ this.entityKind = entityKind;
+ setLayout(new FlowLayout(5));
+ setId(createId(entityKind));
+ this.viewContext = viewContext;
+ setScrollMode(Scroll.AUTO);
+ add(infoBox = createInfoBox());
+ add(formPanel = createFormPanel());
+ }
+
+ public static final String createId(EntityKind entityKind) {
+ return ID_PREFIX + entityKind.name();
+ }
+
+ private String createChildId(String childSuffix) {
+ return getId() + childSuffix;
+ }
+
+ private final static InfoBox createInfoBox() {
+ final InfoBox infoBox = new InfoBox();
+ return infoBox;
+ }
+
+ private PropertyTypeSelectionWidget getPropertyTypeWidget() {
+ if (propertyTypeSelectionWidget == null) {
+ propertyTypeSelectionWidget = new PropertyTypeSelectionWidget(
+ viewContext, createChildId(PROPERTY_TYPE_ID_SUFFIX));
+ propertyTypeSelectionWidget.addListener(Events.Focus,
+ new InfoBoxResetListener(infoBox));
+ FieldUtil.markAsMandatory(propertyTypeSelectionWidget);
+ propertyTypeSelectionWidget.addListener(Events.SelectionChange,
+ new Listener<BaseEvent>() {
+ public void handleEvent(BaseEvent be) {
+ updateDefaultField();
+ }
+ });
+ }
+ return propertyTypeSelectionWidget;
+ }
+
+ private ComboBox<?> getTypeSelectionWidget() {
+ switch (entityKind) {
+ case EXPERIMENT:
+ if (experimentTypeSelectionWidget == null) {
+ experimentTypeSelectionWidget = new ExperimentTypeSelectionWidget(
+ viewContext, EXPERIMENT_TYPE_ID_SUFFIX);
+ experimentTypeSelectionWidget.addListener(Events.Focus,
+ new InfoBoxResetListener(infoBox));
+ FieldUtil.markAsMandatory(experimentTypeSelectionWidget);
+ }
+ return experimentTypeSelectionWidget;
+ case SAMPLE:
+ if (sampleTypeSelectionWidget == null) {
+ sampleTypeSelectionWidget = new SampleTypeSelectionWidget(
+ viewContext, SAMPLE_TYPE_ID_SUFFIX, false);
+ sampleTypeSelectionWidget.addListener(Events.Focus,
+ new InfoBoxResetListener(infoBox));
+ FieldUtil.markAsMandatory(sampleTypeSelectionWidget);
+ }
+ return sampleTypeSelectionWidget;
+ case MATERIAL:
+ if (materialTypeSelectionWidget == null) {
+ materialTypeSelectionWidget = new MaterialTypeSelectionWidget(
+ viewContext, MATERIAL_TYPE_ID_SUFFIX);
+ materialTypeSelectionWidget.addListener(Events.Focus,
+ new InfoBoxResetListener(infoBox));
+ FieldUtil.markAsMandatory(materialTypeSelectionWidget);
+ }
+ return materialTypeSelectionWidget;
+ case DATA_SET:
+ if (dataSetTypeSelectionWidget == null) {
+ dataSetTypeSelectionWidget = new DataSetTypeSelectionWidget(
+ viewContext, DATA_SET_TYPE_ID_SUFFIX);
+ dataSetTypeSelectionWidget.addListener(Events.Focus,
+ new InfoBoxResetListener(infoBox));
+ FieldUtil.markAsMandatory(dataSetTypeSelectionWidget);
+ }
+ return dataSetTypeSelectionWidget;
+ }
+ throw new IllegalArgumentException(UNSUPPORTED_ENTITY_KIND);
+ }
+
+ private CheckBox getMandatoryCheckbox() {
+ if (mandatoryCheckbox == null) {
+ mandatoryCheckbox = new CheckBox();
+ mandatoryCheckbox
+ .setId(createChildId(MANDATORY_CHECKBOX_ID_SUFFIX));
+ mandatoryCheckbox.setFieldLabel(viewContext
+ .getMessage(Dict.MANDATORY));
+ mandatoryCheckbox.setValue(false);
+ mandatoryCheckbox.addListener(Events.Change,
+ new InfoBoxResetListener(infoBox));
+ }
+ return mandatoryCheckbox;
+ }
+
+ private final FormPanel createFormPanel() {
+ final FormPanel panel = new FormPanel();
+ panel.setHeaderVisible(false);
+ panel.setBodyBorder(false);
+ panel.setWidth(LABEL_WIDTH + FIELD_WIDTH + 40);
+ panel.setLabelWidth(LABEL_WIDTH);
+ panel.setFieldWidth(FIELD_WIDTH);
+ panel.setButtonAlign(HorizontalAlignment.RIGHT);
+ final Button saveButton = new Button(viewContext
+ .getMessage(Dict.BUTTON_SAVE));
+ saveButton.setStyleAttribute("marginRight", "20px");
+ saveButton.setId(createChildId(SAVE_BUTTON_ID_SUFFIX));
+ saveButton.addSelectionListener(new SelectionListener<ButtonEvent>() {
+ @Override
+ public final void componentSelected(final ButtonEvent ce) {
+ submitForm();
+ }
+ });
+ final Button resetButton = new Button(viewContext
+ .getMessage(Dict.BUTTON_RESET));
+ resetButton.addSelectionListener(new SelectionListener<ButtonEvent>() {
+ @Override
+ public final void componentSelected(final ButtonEvent ce) {
+ resetForm();
+ }
+ });
+ panel.addButton(resetButton);
+ panel.addButton(saveButton);
+ return panel;
+ }
+
+ private String getDefaultValue() {
+ if (defaultValueField != null) {
+ return PropertyFieldFactory.valueToString(defaultValueField
+ .getValue());
+ }
+ return null;
+ }
+
+ private String getSelectedEntityCode() {
+ switch (entityKind) {
+ case EXPERIMENT:
+ return experimentTypeSelectionWidget.tryGetSelectedExperimentType()
+ .getCode();
+ case SAMPLE:
+ return sampleTypeSelectionWidget.tryGetSelectedSampleType()
+ .getCode();
+ case MATERIAL:
+ return materialTypeSelectionWidget.tryGetSelectedMaterialType()
+ .getCode();
+ case DATA_SET:
+ return dataSetTypeSelectionWidget.tryGetSelectedDataSetType()
+ .getCode();
+ }
+ throw new IllegalArgumentException(UNSUPPORTED_ENTITY_KIND);
+ }
+
+ private final void addFormFields() {
+ formPanel.add(getPropertyTypeWidget());
+ formPanel.add(getTypeSelectionWidget());
+ formPanel.add(getMandatoryCheckbox());
+ updateDefaultField();
+ }
+
+ @Override
+ protected final void onRender(final Element target, final int index) {
+ super.onRender(target, index);
+ addFormFields();
+ }
+
+ public final class AssignPropertyTypeCallback extends
+ AbstractAsyncCallback<String> {
+ AssignPropertyTypeCallback(final IViewContext<?> viewContext) {
+ super(viewContext, new InfoBoxCallbackListener<String>(infoBox));
+ }
+
+ @Override
+ protected final void process(final String result) {
+ infoBox.displayInfo(result);
+ resetForm();
+ }
+ }
+
+ private void updateDefaultField() {
+ hideDefaultField();
+ final PropertyType propertyType = propertyTypeSelectionWidget
+ .tryGetSelectedPropertyType();
+ if (propertyType != null) {
+ String fieldId = createChildId(DEFAULT_VALUE_ID_PART
+ + propertyType.isInternalNamespace()
+ + propertyType.getSimpleCode());
+ Field<?> field = PropertyFieldFactory.createField(propertyType,
+ false, viewContext.getMessage(Dict.DEFAULT_VALUE), fieldId,
+ null, viewContext);
+ field
+ .setToolTip(viewContext
+ .getMessage(Dict.DEFAULT_VALUE_TOOLTIP));
+ defaultValueField = field;
+ defaultValueField.show();
+ formPanel.add(defaultValueField);
+ }
+ layout();
+ }
+
+ private void hideDefaultField() {
+ if (defaultValueField != null) {
+ defaultValueField.hide();
+ formPanel.remove(defaultValueField);
+ defaultValueField = null;
+ }
+ }
+
+ private final void submitForm() {
+ if (formPanel.isValid()) {
+ viewContext.getService().assignPropertyType(
+ entityKind,
+ propertyTypeSelectionWidget
+ .tryGetSelectedPropertyTypeCode(),
+ getSelectedEntityCode(), getMandatoryCheckbox().getValue(),
+ getDefaultValue(),
+ new AssignPropertyTypeCallback(viewContext));
+ }
+ }
+
+ private void resetForm() {
+ formPanel.reset();
+ updateDefaultField();
+ }
}
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 fd152a2624914fae8f0ba4641f085976bc20c544..35bd0fe7844f4eb455a007dd06ff0d34c8278172 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
@@ -52,6 +52,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.CacheManager
import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.IOriginalDataProvider;
import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.IResultSet;
import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.IResultSetManager;
+import ch.systemsx.cisd.openbis.generic.client.web.server.translator.DataSetTypeTranslator;
import ch.systemsx.cisd.openbis.generic.client.web.server.translator.DtoConverters;
import ch.systemsx.cisd.openbis.generic.client.web.server.translator.ExperimentTranslator;
import ch.systemsx.cisd.openbis.generic.client.web.server.translator.ExternalDataTranslator;
@@ -72,6 +73,7 @@ import ch.systemsx.cisd.openbis.generic.server.SessionConstants;
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetSearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
@@ -92,6 +94,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleTypePropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentContentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
@@ -119,957 +122,875 @@ import ch.systemsx.cisd.openbis.plugin.AbstractClientService;
* @author Franz-Josef Elmer
*/
public final class CommonClientService extends AbstractClientService implements
- ICommonClientService
-{
- private final ICommonServer commonServer;
-
- private final String dataStoreBaseURL;
-
- public CommonClientService(final ICommonServer commonServer,
- final IRequestContextProvider requestContextProvider, String dataStoreBaseURL)
- {
- super(requestContextProvider);
- this.commonServer = commonServer;
- this.dataStoreBaseURL = dataStoreBaseURL + "/" + DATA_STORE_SERVER_WEB_APPLICATION_NAME;
- }
-
- @Override
- protected final IServer getServer()
- {
- return commonServer;
- }
-
- // ----------- export and listing with cache generic functionality
-
- @SuppressWarnings("unchecked")
- private final <K> IResultSetManager<K> getResultSetManager()
- {
- return (IResultSetManager<K>) getHttpSession().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 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 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 updateMaterial(String materialIdentifier, List<MaterialProperty> properties,
- Date version)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
- {
- try
- {
- final String sessionToken = getSessionToken();
- final MaterialIdentifier identifier =
- MaterialIdentifier.tryParseIdentifier(materialIdentifier);
- commonServer.editMaterial(sessionToken, identifier, properties, version);
- } catch (final ch.systemsx.cisd.common.exceptions.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);
- }
-
- }
+ ICommonClientService {
+ private final ICommonServer commonServer;
+
+ private final String dataStoreBaseURL;
+
+ public CommonClientService(final ICommonServer commonServer,
+ final IRequestContextProvider requestContextProvider,
+ String dataStoreBaseURL) {
+ super(requestContextProvider);
+ this.commonServer = commonServer;
+ this.dataStoreBaseURL = dataStoreBaseURL + "/"
+ + DATA_STORE_SERVER_WEB_APPLICATION_NAME;
+ }
+
+ @Override
+ protected final IServer getServer() {
+ return commonServer;
+ }
+
+ // ----------- export and listing with cache generic functionality
+
+ @SuppressWarnings("unchecked")
+ private final <K> IResultSetManager<K> getResultSetManager() {
+ return (IResultSetManager<K>) getHttpSession().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);
+ }
+ }
+
+ }
+
+ 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 updateMaterial(String materialIdentifier,
+ List<MaterialProperty> properties, Date version)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
+ try {
+ final String sessionToken = getSessionToken();
+ final MaterialIdentifier identifier = MaterialIdentifier
+ .tryParseIdentifier(materialIdentifier);
+ commonServer.editMaterial(sessionToken, identifier, properties,
+ version);
+ } catch (final ch.systemsx.cisd.common.exceptions.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/client/web/server/ListDataSetsOriginalDataProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/ListDataSetsOriginalDataProvider.java
index e41bbcf8725ad6b3d2e465f8c364900252c9d5b0..c1c55ae85bc253cb49f7fa232ccec31874daf4b5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/ListDataSetsOriginalDataProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/ListDataSetsOriginalDataProvider.java
@@ -5,10 +5,11 @@ import java.util.List;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.IOriginalDataProvider;
-import ch.systemsx.cisd.openbis.generic.client.web.server.translator.DataSetSearchHitTranslator;
+import ch.systemsx.cisd.openbis.generic.client.web.server.translator.ExternalDataTranslator;
+import ch.systemsx.cisd.openbis.generic.client.web.server.translator.ExperimentTranslator.LoadableFields;
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetSearchCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetSearchHitDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
/**
* A {@link IOriginalDataProvider} implementation for search data sets.
@@ -35,12 +36,13 @@ final class ListDataSetsOriginalDataProvider extends AbstractOriginalDataProvide
public final List<ExternalData> getOriginalData()
{
- final List<DataSetSearchHitDTO> hits =
+ final List<ExternalDataPE> hits =
commonServer.searchForDataSets(sessionToken, criteria);
final List<ExternalData> list = new ArrayList<ExternalData>(hits.size());
- for (final DataSetSearchHitDTO hit : hits)
+ for (final ExternalDataPE hit : hits)
{
- list.add(DataSetSearchHitTranslator.translate(hit, dataStoreBaseURL));
+ list.add(ExternalDataTranslator.translate(hit, dataStoreBaseURL,true,
+ LoadableFields.PROPERTIES));
}
return list;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/translator/AbstractEntityTypePropertyTypeTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/translator/AbstractEntityTypePropertyTypeTranslator.java
index 900d5d36ad75fe41660aec3c517bbaa283abf233..d893aa314f8f16f2848fbd04af730506b0b45212 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/translator/AbstractEntityTypePropertyTypeTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/translator/AbstractEntityTypePropertyTypeTranslator.java
@@ -23,6 +23,7 @@ import java.util.Set;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityTypePropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePropertyTypePE;
@@ -65,7 +66,11 @@ abstract public class AbstractEntityTypePropertyTypeTranslator<ET extends Entity
result.setPropertyType(propertyType);
} else
{
- result.setPropertyType(PropertyTypeTranslator.translate(etptPE.getPropertyType()));
+ if(entityType != null && (entityType instanceof MaterialType)){
+ result.setPropertyType(PropertyTypeTranslator.translate(etptPE.getPropertyType(), (MaterialType)entityType));
+ }else{
+ result.setPropertyType(PropertyTypeTranslator.translate(etptPE.getPropertyType()));
+ }
}
if (entityType != null)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/translator/DataSetSearchHitTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/translator/DataSetSearchHitTranslator.java
deleted file mode 100644
index b53838bf963dd006e74bfce504fb4ed003c790b1..0000000000000000000000000000000000000000
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/translator/DataSetSearchHitTranslator.java
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.generic.client.web.server.translator;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ExternalData;
-import ch.systemsx.cisd.openbis.generic.client.web.server.translator.ExperimentTranslator.LoadableFields;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetSearchHitDTO;
-
-/**
- * Converts {@link DataSetSearchHitDTO}s to {@link ExternalData}s.
- *
- * @author Izabela Adamczyk
- */
-public class DataSetSearchHitTranslator
-{
- private DataSetSearchHitTranslator()
- {
- }
-
- public static List<ExternalData> translate(List<DataSetSearchHitDTO> list,
- String dataStoreBaseURL)
- {
- ArrayList<ExternalData> result = new ArrayList<ExternalData>(list.size());
- for (DataSetSearchHitDTO item : list)
- {
- result.add(translate(item, dataStoreBaseURL));
- }
- return result;
- }
-
- public static ExternalData translate(DataSetSearchHitDTO hit, String dataStoreBaseURL)
- {
- return ExternalDataTranslator.translate(hit.getDataSet(), dataStoreBaseURL, true,
- LoadableFields.PROPERTIES);
- }
-
-}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/translator/DataSetTypePropertyTypeTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/translator/DataSetTypePropertyTypeTranslator.java
new file mode 100644
index 0000000000000000000000000000000000000000..7211fcaee6b2235335b7e8d307d22798ebc9e54a
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/translator/DataSetTypePropertyTypeTranslator.java
@@ -0,0 +1,77 @@
+/*
+ * Copyright 2008 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.client.web.server.translator;
+
+import java.util.List;
+import java.util.Set;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypePropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePropertyTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
+
+/**
+ * Translates {@link DataSetTypePropertyTypePE} to
+ * {@link DataSetTypePropertyType}.
+ *
+ * @author Izabela Adamczyk
+ */
+public class DataSetTypePropertyTypeTranslator {
+
+ static private class DataSetTypePropertyTypeTranslatorHelper
+ extends
+ AbstractEntityTypePropertyTypeTranslator<DataSetType, DataSetTypePropertyType, DataSetTypePropertyTypePE> {
+ @Override
+ void setSpecificFields(DataSetTypePropertyType result,
+ DataSetTypePropertyTypePE etptPE) {
+ }
+
+ @Override
+ DataSetType translate(EntityTypePE entityTypePE) {
+ return DataSetTypeTranslator
+ .translate((DataSetTypePE) entityTypePE);
+ }
+
+ @Override
+ DataSetTypePropertyType create() {
+ return new DataSetTypePropertyType();
+ }
+ }
+
+ public static List<DataSetTypePropertyType> translate(
+ Set<DataSetTypePropertyTypePE> DataSetTypePropertyTypes,
+ PropertyType result) {
+ return new DataSetTypePropertyTypeTranslatorHelper().translate(
+ DataSetTypePropertyTypes, result);
+ }
+
+ public static DataSetTypePropertyType translate(
+ DataSetTypePropertyTypePE entityTypePropertyType) {
+ return new DataSetTypePropertyTypeTranslatorHelper()
+ .translate(entityTypePropertyType);
+ }
+
+ public static List<DataSetTypePropertyType> translate(
+ Set<DataSetTypePropertyTypePE> DataSetTypePropertyTypes,
+ DataSetType result) {
+ return new DataSetTypePropertyTypeTranslatorHelper().translate(
+ DataSetTypePropertyTypes, result);
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/translator/DataSetTypeTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/translator/DataSetTypeTranslator.java
new file mode 100644
index 0000000000000000000000000000000000000000..1b42a1b95dfa042bd081eaf70e5c5ee0c7992a51
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/translator/DataSetTypeTranslator.java
@@ -0,0 +1,58 @@
+/*
+ * Copyright 2008 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.client.web.server.translator;
+
+import org.apache.commons.lang.StringEscapeUtils;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
+
+/**
+ * Translates {@link DataSetTypePE} to {@link DataSetType}.
+ *
+ * @author Izabela Adamczyk
+ */
+public class DataSetTypeTranslator {
+
+ private DataSetTypeTranslator() {
+ }
+
+ public static DataSetType translate(DataSetTypePE entityTypeOrNull) {
+ if (entityTypeOrNull == null) {
+ return null;
+ }
+ final DataSetType result = new DataSetType();
+ result
+ .setCode(StringEscapeUtils.escapeHtml(entityTypeOrNull
+ .getCode()));
+ result.setDescription(StringEscapeUtils.escapeHtml(entityTypeOrNull
+ .getDescription()));
+ result.setDatabaseInstance(DatabaseInstanceTranslator
+ .translate(entityTypeOrNull.getDatabaseInstance()));
+ result.setDataSetTypePropertyTypes(DataSetTypePropertyTypeTranslator
+ .translate(entityTypeOrNull.getDataSetTypePropertyTypes(),
+ result));
+ return result;
+ }
+
+ public static DataSetTypePE translate(DataSetType type) {
+ final DataSetTypePE result = new DataSetTypePE();
+ result.setCode(type.getCode());
+ return result;
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/translator/PropertyTypeTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/translator/PropertyTypeTranslator.java
index cae7c1d7dd81b8e380d8c7f3b97a56a44bfee58b..3f5c1f15c89d85f18e2a0beb381368a6d6d6ef81 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/translator/PropertyTypeTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/translator/PropertyTypeTranslator.java
@@ -21,6 +21,7 @@ import java.util.List;
import org.apache.commons.lang.StringEscapeUtils;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
@@ -47,9 +48,8 @@ public final class PropertyTypeTranslator
return result;
}
- public final static PropertyType translate(final PropertyTypePE propertyType)
- {
- final PropertyType result = new PropertyType();
+ public final static PropertyType translate(final PropertyTypePE propertyType, MaterialType materialType){
+ final PropertyType result = new PropertyType();
result.setCode(StringEscapeUtils.escapeHtml(propertyType.getCode()));
result.setSimpleCode(StringEscapeUtils.escapeHtml(propertyType.getSimpleCode()));
result.setInternalNamespace(propertyType.isInternalNamespace());
@@ -57,7 +57,11 @@ public final class PropertyTypeTranslator
result.setLabel(StringEscapeUtils.escapeHtml(propertyType.getLabel()));
result.setDataType(DataTypeTranslator.translate(propertyType.getType()));
result.setVocabulary(VocabularyTranslator.translate(propertyType.getVocabulary()));
- result.setMaterialType(MaterialTypeTranslator.translate(propertyType.getMaterialType()));
+ if(materialType == null){
+ result.setMaterialType(MaterialTypeTranslator.translate(propertyType.getMaterialType()));
+ }else{
+ result.setMaterialType(materialType);
+ }
result.setDescription(StringEscapeUtils.escapeHtml(propertyType.getDescription()));
result.setSampleTypePropertyTypes(SampleTypePropertyTypeTranslator.translate(propertyType
.getSampleTypePropertyTypes(), result));
@@ -67,4 +71,9 @@ public final class PropertyTypeTranslator
propertyType.getExperimentTypePropertyTypes(), result));
return result;
}
-}
+
+ public final static PropertyType translate(final PropertyTypePE propertyType)
+ {
+ return translate(propertyType, null);
+ }
+}
\ No newline at end of file
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 0c38637d53ab84b5d6dc9e2ed88ffa48c6c1ee01..01fcb06ebe57e72252ef29e8a8e76a89539c3511 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
@@ -66,7 +66,7 @@ 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 ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetSearchHitDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerSession;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
@@ -104,640 +104,630 @@ import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
*
* @author Franz-Josef Elmer
*/
-public final class CommonServer extends AbstractServer<ICommonServer> implements ICommonServer
-{
- @Private static final String DELETION_DESCRIPTION = "single deletion";
-
- 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<DataSetSearchHitDTO> 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)
- {
- Session session = getSessionManager().getSession(sessionToken);
- IExternalDataDAO externalDataDAO = getDAOFactory().getExternalDataDAO();
- List<ExternalDataPE> dataSets = new ArrayList<ExternalDataPE>();
- List<String> locations = new ArrayList<String>();
- for (String dataSetCode : dataSetCodes)
- {
- ExternalDataPE dataSet = externalDataDAO.tryToFindFullDataSetByCode(dataSetCode);
- if (dataSet != null)
- {
- dataSets.add(dataSet);
- locations.add(dataSet.getLocation());
- }
- }
- assertDataSetsAreKnown(dataSets, locations);
-
- for (ExternalDataPE dataSet : dataSets)
- {
- externalDataDAO.markAsDeleted(dataSet, session.tryGetPerson(), DELETION_DESCRIPTION, reason);
- }
- Collection<DataStoreServerSession> sessions = dssSessionManager.getSessions();
- for (DataStoreServerSession dssSession : sessions)
- {
- dssSession.getService().deleteDataSets(dssSession.getSessionToken(), locations);
- }
- }
-
- private void assertDataSetsAreKnown(List<ExternalDataPE> dataSets, List<String> locations)
- {
- Set<String> knownLocations = new LinkedHashSet<String>();
- Collection<DataStoreServerSession> sessions = dssSessionManager.getSessions();
- for (DataStoreServerSession session : sessions)
- {
- IDataStoreService service = session.getService();
- String dssSessionToken = session.getSessionToken();
- knownLocations.addAll(service.getKnownDataSets(dssSessionToken, locations));
- }
- List<String> unknownDataSets = new ArrayList<String>();
- for (ExternalDataPE dataSet : dataSets)
- {
- if (knownLocations.contains(dataSet.getLocation()) == false)
- {
- unknownDataSets.add(dataSet.getCode());
- }
- }
- if (unknownDataSets.isEmpty() == false)
- {
- throw new UserFailureException(
- "The following data sets are unknown by any registered Data Store Server. "
- + "May be the responsible Data Store Server is not running.\n"
- + unknownDataSets);
- }
- }
-
- 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 final class CommonServer extends AbstractServer<ICommonServer> implements
+ ICommonServer {
+ @Private
+ static final String DELETION_DESCRIPTION = "single deletion";
+
+ 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);
+ }
+ }
+
+ public void deleteDataSets(String sessionToken, List<String> dataSetCodes,
+ String reason) {
+ Session session = getSessionManager().getSession(sessionToken);
+ IExternalDataDAO externalDataDAO = getDAOFactory().getExternalDataDAO();
+ List<ExternalDataPE> dataSets = new ArrayList<ExternalDataPE>();
+ List<String> locations = new ArrayList<String>();
+ for (String dataSetCode : dataSetCodes) {
+ ExternalDataPE dataSet = externalDataDAO
+ .tryToFindFullDataSetByCode(dataSetCode);
+ if (dataSet != null) {
+ dataSets.add(dataSet);
+ locations.add(dataSet.getLocation());
+ }
+ }
+ assertDataSetsAreKnown(dataSets, locations);
+
+ for (ExternalDataPE dataSet : dataSets) {
+ externalDataDAO.markAsDeleted(dataSet, session.tryGetPerson(),
+ DELETION_DESCRIPTION, reason);
+ }
+ Collection<DataStoreServerSession> sessions = dssSessionManager
+ .getSessions();
+ for (DataStoreServerSession dssSession : sessions) {
+ dssSession.getService().deleteDataSets(
+ dssSession.getSessionToken(), locations);
+ }
+ }
+
+ private void assertDataSetsAreKnown(List<ExternalDataPE> dataSets,
+ List<String> locations) {
+ Set<String> knownLocations = new LinkedHashSet<String>();
+ Collection<DataStoreServerSession> sessions = dssSessionManager
+ .getSessions();
+ for (DataStoreServerSession session : sessions) {
+ IDataStoreService service = session.getService();
+ String dssSessionToken = session.getSessionToken();
+ knownLocations.addAll(service.getKnownDataSets(dssSessionToken,
+ locations));
+ }
+ List<String> unknownDataSets = new ArrayList<String>();
+ for (ExternalDataPE dataSet : dataSets) {
+ if (knownLocations.contains(dataSet.getLocation()) == false) {
+ unknownDataSets.add(dataSet.getCode());
+ }
+ }
+ if (unknownDataSets.isEmpty() == false) {
+ throw new UserFailureException(
+ "The following data sets are unknown by any registered Data Store Server. "
+ + "May be the responsible Data Store Server is not running.\n"
+ + unknownDataSets);
+ }
+ }
+
+ 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 df7dca9dacd7a22b519a4d98b69924cbccbb8484..915965eb48eb9cf835bdc14dc58aaf3f23eda8d6 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
@@ -34,7 +34,7 @@ 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 ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetSearchHitDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
@@ -65,287 +65,291 @@ 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<DataSetSearchHitDTO> 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 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;
- }
+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);
+ }
+
+ 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;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IHibernateSearchDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IHibernateSearchDAO.java
index 941a9b32a605d4b4ebe7b1b2494ffd84e6e762a4..15cfe02484066b5b9569b9224ee59d35b384559e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IHibernateSearchDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IHibernateSearchDAO.java
@@ -21,7 +21,7 @@ import java.util.List;
import org.springframework.dao.DataAccessException;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetSearchCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetSearchHitDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.IMatchingEntity;
import ch.systemsx.cisd.openbis.generic.shared.dto.SearchHit;
@@ -42,5 +42,5 @@ public interface IHibernateSearchDAO
final Class<T> entityClass, final String searchTerm) throws DataAccessException;
/** search for datasets using the specified criteria */
- public List<DataSetSearchHitDTO> searchForDataSets(DataSetSearchCriteria criteria);
+ public List<ExternalDataPE> searchForDataSets(DataSetSearchCriteria criteria);
}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/HibernateSearchDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/HibernateSearchDAO.java
index 771d5ec64b4755baadff15dc478ff9da8ff8aa16..a8e65037adaa7e2ab426886820ec5f8786ddf7e8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/HibernateSearchDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/HibernateSearchDAO.java
@@ -62,7 +62,6 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IHibernateSearchDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.search.LuceneQueryBuilder;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.search.SearchAnalyzer;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetSearchCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetSearchHitDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.IMatchingEntity;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
@@ -328,9 +327,9 @@ final class HibernateSearchDAO extends HibernateDaoSupport implements IHibernate
}
}
- public List<DataSetSearchHitDTO> searchForDataSets(final DataSetSearchCriteria criteria)
+ public List<ExternalDataPE> searchForDataSets(final DataSetSearchCriteria criteria)
{
- final List<DataSetSearchHitDTO> list =
+ final List<ExternalDataPE> list =
AbstractDAO.cast((List<?>) getHibernateTemplate().execute(new HibernateCallback()
{
public final Object doInHibernate(final Session session)
@@ -348,7 +347,7 @@ final class HibernateSearchDAO extends HibernateDaoSupport implements IHibernate
return list;
}
- private List<DataSetSearchHitDTO> searchForDataSets(Session session,
+ private List<ExternalDataPE> searchForDataSets(Session session,
DataSetSearchCriteria datasetSearchCriteria)
{
BooleanQuery query = new BooleanQuery();
@@ -372,7 +371,7 @@ final class HibernateSearchDAO extends HibernateDaoSupport implements IHibernate
// NOTE: there is a limit on the number of JOINs, so we have to initialize sample properties
// manually
initSamplesWithProperties(datasets);
- return asDataSetHits(datasets);
+ return datasets;
}
private void initSamplesWithProperties(List<ExternalDataPE> datasets)
@@ -394,13 +393,5 @@ final class HibernateSearchDAO extends HibernateDaoSupport implements IHibernate
}
}
- private static List<DataSetSearchHitDTO> asDataSetHits(List<ExternalDataPE> datasets)
- {
- List<DataSetSearchHitDTO> result = new ArrayList<DataSetSearchHitDTO>();
- for (ExternalDataPE dataset : datasets)
- {
- result.add(new DataSetSearchHitDTO(dataset));
- }
- return result;
- }
+
}
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 ddc1db0ffef5f4ccf47d472b94f60000e99432b4..2f64236ae77a43fcc218ea71b93503d39b6aa47a 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
@@ -29,6 +29,7 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCo
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.GroupIdentifierPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.NullableGroupIdentifierPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.SampleOwnerIdentifierPredicate;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.ExternalDataValidator;
import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.GroupValidator;
import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.MatchingEntityValidator;
import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.ProjectValidator;
@@ -43,7 +44,7 @@ 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 ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetSearchHitDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
@@ -75,315 +76,346 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
*
* @author Franz-Josef Elmer
*/
-public interface ICommonServer extends IServer
-{
- /**
- * Returns all groups which belong to the specified database instance. *
- *
- * @return a sorted list of {@link GroupPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- @ReturnValueFilter(validatorClass = GroupValidator.class)
- public List<GroupPE> listGroups(String sessionToken, DatabaseInstanceIdentifier identifier);
-
- /**
- * Registers a new group with specified code and optional description and group leader ID.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerGroup(String sessionToken, String groupCode, String descriptionOrNull,
- String groupLeaderOrNull);
-
- /**
- * Returns all persons from current instance.
- *
- * @return a sorted list of {@link PersonPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<PersonPE> listPersons(String sessionToken);
-
- /**
- * Returns all projects.
- *
- * @return a sorted list of {@link ProjectPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- @ReturnValueFilter(validatorClass = ProjectValidator.class)
- public List<ProjectPE> listProjects(String sessionToken);
-
- /**
- * Registers a new person.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerPerson(String sessionToken, String userID);
-
- /**
- * Returns a list of all roles.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.GROUP_ADMIN)
- public List<RoleAssignmentPE> listRoles(String sessionToken);
-
- /**
- * Registers a new group role.
- */
- @Transactional
- @RolesAllowed(RoleSet.GROUP_ADMIN)
- public void registerGroupRole(String sessionToken, RoleCode roleCode,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class)
- GroupIdentifier identifier, String person);
-
- /**
- * Registers a new instance role.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerInstanceRole(String sessionToken, RoleCode roleCode, String person);
-
- /**
- * Deletes role described by given role code, group identifier and user id.
- */
- @Transactional
- @RolesAllowed(RoleSet.GROUP_ADMIN)
- public void deleteGroupRole(String sessionToken, RoleCode roleCode,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class)
- GroupIdentifier groupIdentifier, String person);
-
- /**
- * Deletes role described by given role code and user id.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void deleteInstanceRole(String sessionToken, RoleCode roleCode, String person);
-
- /**
- * Lists sample types which are appropriate for listing.
- *
- * @return a sorted list of {@link SampleTypePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<SampleTypePE> listSampleTypes(String sessionToken);
-
- /**
- * Lists samples using given configuration.
- *
- * @return a sorted list of {@link SamplePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<SamplePE> listSamples(final String sessionToken,
- final ListSampleCriteriaDTO criteria);
-
- /**
- * Lists experiments.
- *
- * @return a sorted list of {@link ExperimentPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<ExperimentPE> listExperiments(final String sessionToken,
- ExperimentTypePE experimentType,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class)
- ProjectIdentifier project);
-
- /**
- * For given {@link SampleIdentifier} returns the corresponding list of {@link ExternalDataPE}.
- *
- * @return a sorted list of {@link ExternalDataPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<ExternalDataPE> listExternalData(final String sessionToken,
- @AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class)
- final SampleIdentifier identifier);
-
- /**
- * For given {@link ExperimentIdentifier} returns the corresponding list of
- * {@link ExternalDataPE}.
- *
- * @return a sorted list of {@link ExternalDataPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<ExternalDataPE> listExternalData(final String sessionToken,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class)
- final ExperimentIdentifier identifier);
-
- /**
- * Performs an <i>Hibernate Search</i> based on given parameters.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- @ReturnValueFilter(validatorClass = MatchingEntityValidator.class)
- public List<SearchHit> listMatchingEntities(final String sessionToken,
- final SearchableEntity[] searchableEntities, final String queryText);
-
- /**
- * List experiment types.
- *
- * @return a sorted list of {@link ExperimentTypePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<ExperimentTypePE> listExperimentTypes(String sessionToken);
-
- /**
- * List property types.
- *
- * @return a sorted list of {@link PropertyTypePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<PropertyTypePE> listPropertyTypes(final String sessionToken);
-
- /**
- * Lists data types.
- *
- * @return a sorted list of {@link DataTypePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<DataTypePE> listDataTypes(final String sessionToken);
-
- /**
- * Lists vocabularies.
- *
- * @return a sorted list of {@link VocabularyPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<VocabularyPE> listVocabularies(final String sessionToken, final boolean withTerms,
- boolean excludeInternal);
-
- /**
- * Registers given {@link PropertyType}.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerPropertyType(final String sessionToken, final PropertyType propertyType);
-
- /**
- * Assigns property type to entity type.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public String assignPropertyType(final String sessionToken, final EntityKind entityKind,
- final String propertyTypeCode, final String entityTypeCode, final boolean isMandatory,
- final String defaultValue);
-
- /**
- * Registers given {@link Vocabulary}.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerVocabulary(final String sessionToken, final Vocabulary vocabulary);
-
- /**
- * Registers new project.
- */
- @Transactional
- @RolesAllowed(RoleSet.GROUP_ADMIN)
- public void registerProject(String sessionToken,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class)
- ProjectIdentifier projectIdentifier, String description, String leaderId);
-
- /**
- * Performs an <i>Hibernate Search</i> based on given parameters.
- */
- // TODO 2009-03-16 FJE, @ReturnValueFilter missing
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<DataSetSearchHitDTO> searchForDataSets(String sessionToken,
- DataSetSearchCriteria criteria);
-
- /**
- * List material types.
- *
- * @return a sorted list of {@link MaterialTypePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<MaterialTypePE> listMaterialTypes(String sessionToken);
-
- /**
- * Lists materials.
- *
- * @return a sorted list of {@link MaterialPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<MaterialPE> listMaterials(String sessionToken, MaterialTypePE materialType);
-
- /**
- * Creates a new material type.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerMaterialType(String sessionToken, MaterialType entityType);
-
- /**
- * Creates a new sample type.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerSampleType(String sessionToken, SampleType entityType);
-
- /**
- * Creates a new experiment type.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerExperimentType(String sessionToken, ExperimentType entityType);
-
- /**
- * Deletes specified data sets.
- */
- @Transactional
- @RolesAllowed(RoleSet.GROUP_ADMIN)
- public void deleteDataSets(String sessionToken,
- @AuthorizationGuard(guardClass = DataSetCodePredicate.class)
- List<String> dataSetCodes, String reason);
-
- /**
- * Saves changed experiment.
- */
- @Transactional
- @RolesAllowed(RoleSet.USER)
- public void editExperiment(String sessionToken,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class)
- ExperimentIdentifier experimentIdentifier, List<ExperimentProperty> properties,
- List<AttachmentPE> attachments,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class)
- ProjectIdentifier newProjectIdentifier, Date version);
-
- /**
- * Saves changed material.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void editMaterial(String sessionToken, MaterialIdentifier identifier,
- List<MaterialProperty> properties, Date version);
-
- /**
- * Saves changed sample.
- */
- @Transactional
- @RolesAllowed(RoleSet.USER)
- public void editSample(String sessionToken,
- @AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class)
- SampleIdentifier identifier, List<SampleProperty> properties,
- @AuthorizationGuard(guardClass = NullableGroupIdentifierPredicate.class)
- ExperimentIdentifier experimentIdentifierOrNull, Date version);
-
- /** Lists vocabulary terms of a given vocabulary. Includes terms usage statistics. */
- @Transactional
- @RolesAllowed(RoleSet.USER)
- public List<VocabularyTermWithStats> listVocabularyTerms(String sessionToken,
- Vocabulary vocabulary);
+public interface ICommonServer extends IServer {
+ /**
+ * Returns all groups which belong to the specified database instance. *
+ *
+ * @return a sorted list of {@link GroupPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ @ReturnValueFilter(validatorClass = GroupValidator.class)
+ public List<GroupPE> listGroups(String sessionToken,
+ DatabaseInstanceIdentifier identifier);
+
+ /**
+ * Registers a new group with specified code and optional description and
+ * group leader ID.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerGroup(String sessionToken, String groupCode,
+ String descriptionOrNull, String groupLeaderOrNull);
+
+ /**
+ * Returns all persons from current instance.
+ *
+ * @return a sorted list of {@link PersonPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<PersonPE> listPersons(String sessionToken);
+
+ /**
+ * Returns all projects.
+ *
+ * @return a sorted list of {@link ProjectPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ @ReturnValueFilter(validatorClass = ProjectValidator.class)
+ public List<ProjectPE> listProjects(String sessionToken);
+
+ /**
+ * Registers a new person.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerPerson(String sessionToken, String userID);
+
+ /**
+ * Returns a list of all roles.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.GROUP_ADMIN)
+ public List<RoleAssignmentPE> listRoles(String sessionToken);
+
+ /**
+ * Registers a new group role.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.GROUP_ADMIN)
+ public void registerGroupRole(
+ String sessionToken,
+ RoleCode roleCode,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) GroupIdentifier identifier,
+ String person);
+
+ /**
+ * Registers a new instance role.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerInstanceRole(String sessionToken, RoleCode roleCode,
+ String person);
+
+ /**
+ * Deletes role described by given role code, group identifier and user id.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.GROUP_ADMIN)
+ public void deleteGroupRole(
+ String sessionToken,
+ RoleCode roleCode,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) GroupIdentifier groupIdentifier,
+ String person);
+
+ /**
+ * Deletes role described by given role code and user id.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void deleteInstanceRole(String sessionToken, RoleCode roleCode,
+ String person);
+
+ /**
+ * Lists sample types which are appropriate for listing.
+ *
+ * @return a sorted list of {@link SampleTypePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<SampleTypePE> listSampleTypes(String sessionToken);
+
+ /**
+ * Lists samples using given configuration.
+ *
+ * @return a sorted list of {@link SamplePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<SamplePE> listSamples(final String sessionToken,
+ final ListSampleCriteriaDTO criteria);
+
+ /**
+ * Lists experiments.
+ *
+ * @return a sorted list of {@link ExperimentPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<ExperimentPE> listExperiments(
+ final String sessionToken,
+ ExperimentTypePE experimentType,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) ProjectIdentifier project);
+
+ /**
+ * For given {@link SampleIdentifier} returns the corresponding list of
+ * {@link ExternalDataPE}.
+ *
+ * @return a sorted list of {@link ExternalDataPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<ExternalDataPE> listExternalData(
+ final String sessionToken,
+ @AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class) final SampleIdentifier identifier);
+
+ /**
+ * For given {@link ExperimentIdentifier} returns the corresponding list of
+ * {@link ExternalDataPE}.
+ *
+ * @return a sorted list of {@link ExternalDataPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<ExternalDataPE> listExternalData(
+ final String sessionToken,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) final ExperimentIdentifier identifier);
+
+ /**
+ * Performs an <i>Hibernate Search</i> based on given parameters.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ @ReturnValueFilter(validatorClass = MatchingEntityValidator.class)
+ public List<SearchHit> listMatchingEntities(final String sessionToken,
+ final SearchableEntity[] searchableEntities, final String queryText);
+
+ /**
+ * List experiment types.
+ *
+ * @return a sorted list of {@link ExperimentTypePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<ExperimentTypePE> listExperimentTypes(String sessionToken);
+
+ /**
+ * List property types.
+ *
+ * @return a sorted list of {@link PropertyTypePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<PropertyTypePE> listPropertyTypes(final String sessionToken);
+
+ /**
+ * Lists data types.
+ *
+ * @return a sorted list of {@link DataTypePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<DataTypePE> listDataTypes(final String sessionToken);
+
+ /**
+ * Lists vocabularies.
+ *
+ * @return a sorted list of {@link VocabularyPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<VocabularyPE> listVocabularies(final String sessionToken,
+ final boolean withTerms, boolean excludeInternal);
+
+ /**
+ * Registers given {@link PropertyType}.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerPropertyType(final String sessionToken,
+ final PropertyType propertyType);
+
+ /**
+ * Assigns property type to entity type.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public String assignPropertyType(final String sessionToken,
+ final EntityKind entityKind, final String propertyTypeCode,
+ final String entityTypeCode, final boolean isMandatory,
+ final String defaultValue);
+
+ /**
+ * Registers given {@link Vocabulary}.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerVocabulary(final String sessionToken,
+ final Vocabulary vocabulary);
+
+ /**
+ * Registers new project.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.GROUP_ADMIN)
+ public void registerProject(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) ProjectIdentifier projectIdentifier,
+ String description, String leaderId);
+
+ /**
+ * Performs an <i>Hibernate Search</i> based on given parameters.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ @ReturnValueFilter(validatorClass = ExternalDataValidator.class)
+ public List<ExternalDataPE> searchForDataSets(String sessionToken,
+ DataSetSearchCriteria criteria);
+
+ /**
+ * List material types.
+ *
+ * @return a sorted list of {@link MaterialTypePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<MaterialTypePE> listMaterialTypes(String sessionToken);
+
+ /**
+ * Lists materials.
+ *
+ * @return a sorted list of {@link MaterialPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<MaterialPE> listMaterials(String sessionToken,
+ MaterialTypePE materialType);
+
+ /**
+ * Creates a new material type.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerMaterialType(String sessionToken,
+ MaterialType entityType);
+
+ /**
+ * Creates a new sample type.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerSampleType(String sessionToken, SampleType entityType);
+
+ /**
+ * Creates a new experiment type.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerExperimentType(String sessionToken,
+ ExperimentType entityType);
+
+ /**
+ * Deletes specified data sets.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.GROUP_ADMIN)
+ public void deleteDataSets(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodePredicate.class) List<String> dataSetCodes,
+ String reason);
+
+ /**
+ * Saves changed experiment.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.USER)
+ public void editExperiment(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) ExperimentIdentifier experimentIdentifier,
+ List<ExperimentProperty> properties,
+ List<AttachmentPE> attachments,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) ProjectIdentifier newProjectIdentifier,
+ Date version);
+
+ /**
+ * Saves changed material.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void editMaterial(String sessionToken,
+ MaterialIdentifier identifier, List<MaterialProperty> properties,
+ Date version);
+
+ /**
+ * Saves changed sample.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.USER)
+ public void editSample(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class) SampleIdentifier identifier,
+ List<SampleProperty> properties,
+ @AuthorizationGuard(guardClass = NullableGroupIdentifierPredicate.class) ExperimentIdentifier experimentIdentifierOrNull,
+ Date version);
+
+ /**
+ * Lists vocabulary terms of a given vocabulary. Includes terms usage
+ * statistics.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.USER)
+ public List<VocabularyTermWithStats> listVocabularyTerms(
+ String sessionToken, Vocabulary vocabulary);
+
+ /**
+ * List data set types.
+ *
+ * @return a sorted list of {@link DataSetTypePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<DataSetTypePE> listDataSetTypes(String sessionToken);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DataSetType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DataSetType.java
new file mode 100644
index 0000000000000000000000000000000000000000..57ffddc0904d88bd030f22ecee07cccd22e7f0b7
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DataSetType.java
@@ -0,0 +1,42 @@
+/*
+ * Copyright 2008 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
+
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
+
+/**
+ * The <i>GWT</i> equivalent to {@link DataSetTypePE}.
+ *
+ * @author Izabela Adamczyk
+ */
+public class DataSetType extends EntityType
+{
+ private List<DataSetTypePropertyType> dataSetTypePropertyTypes;
+
+ public List<DataSetTypePropertyType> getDataSetTypePropertyTypes()
+ {
+ return dataSetTypePropertyTypes;
+ }
+
+ public void setDataSetTypePropertyTypes(
+ List<DataSetTypePropertyType> dataSetTypePropertyTypes)
+ {
+ this.dataSetTypePropertyTypes = dataSetTypePropertyTypes;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetSearchHitDTO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DataSetTypePropertyType.java
similarity index 63%
rename from openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetSearchHitDTO.java
rename to openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DataSetTypePropertyType.java
index fa5e37fc470ae5b7a343b257bbcc538edc7530bb..3b8e5d8c7502ace7f20535079e3a0d3d89a3b105 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetSearchHitDTO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DataSetTypePropertyType.java
@@ -14,25 +14,21 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.generic.shared.dto;
+package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
+
+import com.google.gwt.user.client.rpc.IsSerializable;
+
/**
- * Single result of data set search.
+ * The {@link EntityTypePropertyType} extension for <i>Data Set Type</i>.
*
* @author Izabela Adamczyk
*/
-public class DataSetSearchHitDTO
+public class DataSetTypePropertyType extends EntityTypePropertyType<DataSetType> implements
+ IsSerializable
{
- private final ExternalDataPE dataSet;
-
- public DataSetSearchHitDTO(ExternalDataPE dataSet)
+ public DataSetTypePropertyType()
{
- this.dataSet = dataSet;
+ super(EntityKind.DATA_SET);
}
-
- public ExternalDataPE getDataSet()
- {
- return dataSet;
- }
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityKind.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityKind.java
index 82cf07fcb0a495fca5a375cdb2445807d5630e09..27ae7bd42c34ea002fb257af7f719b2eb5d4d097 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityKind.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityKind.java
@@ -26,7 +26,7 @@ import com.google.gwt.user.client.rpc.IsSerializable;
*/
public enum EntityKind implements IsSerializable
{
- MATERIAL("Material"), EXPERIMENT("Experiment"), SAMPLE("Sample");
+ MATERIAL("Material"), EXPERIMENT("Experiment"), SAMPLE("Sample"), DATA_SET("Data Set");
private final String description;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ColumnNames.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ColumnNames.java
index a7c1389b290203747a2a8fc64d0bf6574953605e..61df9c9a4fa15cb37b9bd645aeb6bebcea58d82c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ColumnNames.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ColumnNames.java
@@ -21,164 +21,167 @@ package ch.systemsx.cisd.openbis.generic.shared.dto;
*
* @author Christian Ribeaud
*/
-public final class ColumnNames
-{
+public final class ColumnNames {
- public static final String AMOUNT_COLUMN = "amount";
+ public static final String AMOUNT_COLUMN = "amount";
- public static final String CODE_COLUMN = "code";
+ public static final String CODE_COLUMN = "code";
- public static final String CONTROL_LAYOUT_SAMPLE_COLUMN = "samp_id_control_layout";
+ public static final String CONTROL_LAYOUT_SAMPLE_COLUMN = "samp_id_control_layout";
- public static final String CONTROLLED_VOCABULARY_COLUMN = "covo_id";
+ public static final String CONTROLLED_VOCABULARY_COLUMN = "covo_id";
- public static final String DATA_CHILD_COLUMN = "data_id_child";
+ public static final String DATA_CHILD_COLUMN = "data_id_child";
- public static final String DATA_ID_COLUMN = "data_id";
+ public static final String DATA_ID_COLUMN = "data_id";
- public static final String DATA_PARENT_COLUMN = "data_id_parent";
+ public static final String DATA_PARENT_COLUMN = "data_id_parent";
- public static final String DATA_PRODUCER_CODE_COLUMN = "data_producer_code";
+ public static final String DATA_PRODUCER_CODE_COLUMN = "data_producer_code";
- public static final String DATA_SET_TYPE_COLUMN = "dsty_id";
+ public static final String DATA_SET_TYPE_COLUMN = "dsty_id";
- public static final String DATA_STORE_COLUMN = "dast_id";
+ public static final String DATA_STORE_COLUMN = "dast_id";
- public static final String DATA_TYPE_COLUMN = "daty_id";
+ public static final String DATA_TYPE_COLUMN = "daty_id";
- public final static String DATABASE_INSTANCE_COLUMN = "dbin_id";
+ public final static String DATABASE_INSTANCE_COLUMN = "dbin_id";
- public static final String DESCRIPTION_COLUMN = "description";
+ public static final String DESCRIPTION_COLUMN = "description";
- public static final String DOWNLOAD_URL_COLUMN = "download_url";
+ public static final String DOWNLOAD_URL_COLUMN = "download_url";
- public static final String EXPERIMENT_ATTACHMENT_CONTENT_COLUMN = "exac_id";
+ public static final String EXPERIMENT_ATTACHMENT_CONTENT_COLUMN = "exac_id";
- public static final String EXPERIMENT_COLUMN = "expe_id";
+ public static final String EXPERIMENT_COLUMN = "expe_id";
- public static final String EXPERIMENT_TYPE_COLUMN = "exty_id";
+ public static final String DATA_SET_COLUMN = "ds_id";
- public static final String EXPERIMENT_TYPE_PROPERTY_TYPE_COLUMN = "etpt_id";
+ public static final String EXPERIMENT_TYPE_COLUMN = "exty_id";
- public static final String FILE_FORMAT_TYPE = "ffty_id";
+ public static final String EXPERIMENT_TYPE_PROPERTY_TYPE_COLUMN = "etpt_id";
- public static final String FILE_NAME_COLUMN = "file_name";
+ public static final String DATA_SET_TYPE_PROPERTY_TYPE_COLUMN = "dstpt_id";
- public final static String FIRST_NAME_COLUMN = "first_name";
+ public static final String FILE_FORMAT_TYPE = "ffty_id";
- public static final String GENERATED_FROM_DEPTH = "generated_from_depth";
+ public static final String FILE_NAME_COLUMN = "file_name";
- public static final String GENERATED_FROM_SAMPLE_COLUMN = "samp_id_generated_from";
+ public final static String FIRST_NAME_COLUMN = "first_name";
- public static final String GROUP_COLUMN = "grou_id";
+ public static final String GENERATED_FROM_DEPTH = "generated_from_depth";
- public static final String GROUP_PARENT_COLUMN = "grou_id_parent";
+ public static final String GENERATED_FROM_SAMPLE_COLUMN = "samp_id_generated_from";
- public static final String ID_COLUMN = "id";
+ public static final String GROUP_COLUMN = "grou_id";
- public static final String INHIBITOR_OF_COLUMN = "mate_id_inhibitor_of";
+ public static final String GROUP_PARENT_COLUMN = "grou_id_parent";
- public static final String INVALIDATION_COLUMN = "inva_id";
+ public static final String ID_COLUMN = "id";
- public static final String IS_COMPLETE_COLUMN = "is_complete";
+ public static final String INHIBITOR_OF_COLUMN = "mate_id_inhibitor_of";
- public static final String IS_DATA_ACQUSITION = "is_data_acquisition";
+ public static final String INVALIDATION_COLUMN = "inva_id";
- public static final String IS_DISPLAYED = "is_displayed";
+ public static final String IS_COMPLETE_COLUMN = "is_complete";
- public static final String IS_INTERNAL_NAMESPACE = "is_internal_namespace";
+ public static final String IS_DATA_ACQUSITION = "is_data_acquisition";
- public static final String IS_LISTABLE = "IS_LISTABLE";
+ public static final String IS_DISPLAYED = "is_displayed";
- public static final String IS_MANAGED_INTERNALLY = "is_managed_internally";
+ public static final String IS_INTERNAL_NAMESPACE = "is_internal_namespace";
- public static final String IS_MANDATORY = "is_mandatory";
+ public static final String IS_LISTABLE = "IS_LISTABLE";
- public static final String IS_ORIGINAL_SOURCE_COLUMN = "is_original_source";
+ public static final String IS_MANAGED_INTERNALLY = "is_managed_internally";
- public static final String IS_PLACEHOLDER_COLUMN = "is_placeholder";
-
- public static final String IS_DELETED_COLUMN = "is_deleted";
+ public static final String IS_MANDATORY = "is_mandatory";
- public static final String LABEL_COLUMN = "label";
+ public static final String IS_ORIGINAL_SOURCE_COLUMN = "is_original_source";
- public final static String LAST_NAME_COLUMN = "last_name";
+ public static final String IS_PLACEHOLDER_COLUMN = "is_placeholder";
- public static final String LOCATION_COLUMN = "location";
+ public static final String IS_DELETED_COLUMN = "is_deleted";
- public static final String LOCATOR_TYPE_COLUMN = "loty_id";
+ public static final String LABEL_COLUMN = "label";
- public static final String MATERIAL_BATCH_COLUMN = "maba_id";
+ public final static String LAST_NAME_COLUMN = "last_name";
- public static final String MATERIAL_COLUMN = "mate_id";
+ public static final String LOCATION_COLUMN = "location";
- public static final String MATERIAL_TYPE_COLUMN = "maty_id";
+ public static final String LOCATOR_TYPE_COLUMN = "loty_id";
- public static final String MATERIAL_TYPE_PROPERTY_TYPE_COLUMN = "mtpt_id";
+ public static final String MATERIAL_BATCH_COLUMN = "maba_id";
- public static final String PARENT_DATA_SET_CODE_COLUMN = "data_producer_code";
+ public static final String MATERIAL_COLUMN = "mate_id";
- public static final String PART_OF_DEPTH = "part_of_depth";
+ public static final String MATERIAL_TYPE_COLUMN = "maty_id";
- public static final String PART_OF_SAMPLE_COLUMN = "samp_id_part_of";
+ public static final String MATERIAL_TYPE_PROPERTY_TYPE_COLUMN = "mtpt_id";
- public static final String PERSON_GRANTEE_COLUMN = "pers_id_grantee";
+ public static final String PARENT_DATA_SET_CODE_COLUMN = "data_producer_code";
- public static final String PERSON_LEADER_COLUMN = "pers_id_leader";
+ public static final String PART_OF_DEPTH = "part_of_depth";
- public static final String PERSON_REGISTERER_COLUMN = "pers_id_registerer";
+ public static final String PART_OF_SAMPLE_COLUMN = "samp_id_part_of";
- public static final String PROCEDURE_COLUMN = "proc_id";
+ public static final String PERSON_GRANTEE_COLUMN = "pers_id_grantee";
- public static final String PROCEDURE_PRODUCED_BY_COLUMN = "proc_id_produced_by";
+ public static final String PERSON_LEADER_COLUMN = "pers_id_leader";
- public static final String PROCEDURE_TYPE_COLUMN = "pcty_id";
+ public static final String PERSON_REGISTERER_COLUMN = "pers_id_registerer";
- public static final String PRODUCTION_TIMESTAMP_COLUMN = "production_timestamp";
+ public static final String PROCEDURE_COLUMN = "proc_id";
- public static final String PROJECT_COLUMN = "proj_id";
+ public static final String PROCEDURE_PRODUCED_BY_COLUMN = "proc_id_produced_by";
- public static final String PROPERTY_TYPE_COLUMN = "prty_id";
+ public static final String PROCEDURE_TYPE_COLUMN = "pcty_id";
- public static final String REGISTRATION_TIMESTAMP_COLUMN = "registration_timestamp";
+ public static final String PRODUCTION_TIMESTAMP_COLUMN = "production_timestamp";
- public final static String ROLE_COLUMN = "role_code";
+ public static final String PROJECT_COLUMN = "proj_id";
- public static final String SAMPLE_ACQUIRED_FROM = "samp_id_acquired_from";
+ public static final String PROPERTY_TYPE_COLUMN = "prty_id";
- public static final String SAMPLE_COLUMN = "samp_id";
+ public static final String REGISTRATION_TIMESTAMP_COLUMN = "registration_timestamp";
- public static final String SAMPLE_DERIVED_FROM = "samp_id_derived_from";
+ public final static String ROLE_COLUMN = "role_code";
- public static final String SAMPLE_TYPE_COLUMN = "saty_id";
+ public static final String SAMPLE_ACQUIRED_FROM = "samp_id_acquired_from";
- public static final String SAMPLE_TYPE_PROPERTY_TYPE_COLUMN = "stpt_id";
+ public static final String SAMPLE_COLUMN = "samp_id";
- public static final String STORAGE_FORMAT_COLUMN = "cvte_id_stor_fmt";
+ public static final String SAMPLE_DERIVED_FROM = "samp_id_derived_from";
- public static final String STUDY_OBJECT_COLUMN = "mate_id_study_object";
+ public static final String SAMPLE_TYPE_COLUMN = "saty_id";
- public static final String TOP_SAMPLE_COLUMN = "samp_id_top";
+ public static final String SAMPLE_TYPE_PROPERTY_TYPE_COLUMN = "stpt_id";
- public final static String USER_COLUMN = "user_id";
+ public static final String STORAGE_FORMAT_COLUMN = "cvte_id_stor_fmt";
- public static final String UUID_COLUMN = "uuid";
+ public static final String STUDY_OBJECT_COLUMN = "mate_id_study_object";
- public static final String VALUE_COLUMN = "value";
+ public static final String TOP_SAMPLE_COLUMN = "samp_id_top";
- public static final String VERSION_COLUMN = "version";
+ public final static String USER_COLUMN = "user_id";
- public static final String VOCABULARY_TERM_COLUMN = "cvte_id";
+ public static final String UUID_COLUMN = "uuid";
- public static final String MODIFICATION_TIMESTAMP_COLUMN = "modification_timestamp";
-
- public static final String EVENT_TYPE = "event_type";
-
- public static final String MATERIAL_PROP_COLUMN = "mate_prop_id";
-
- public static final String PROPERTY_MATERIAL_TYPE_COLUMN = "maty_prop_id";
- private ColumnNames()
- {
- // Can not be instantiated.
- }
+ public static final String VALUE_COLUMN = "value";
+
+ public static final String VERSION_COLUMN = "version";
+
+ public static final String VOCABULARY_TERM_COLUMN = "cvte_id";
+
+ public static final String MODIFICATION_TIMESTAMP_COLUMN = "modification_timestamp";
+
+ public static final String EVENT_TYPE = "event_type";
+
+ public static final String MATERIAL_PROP_COLUMN = "mate_prop_id";
+
+ public static final String PROPERTY_MATERIAL_TYPE_COLUMN = "maty_prop_id";
+
+ private ColumnNames() {
+ // Can not be instantiated.
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java
index b438501ce33a47724d56f032e9bc68959b3ecf50..944994f99e07ac1cec2e04620437d790c3eb5e19 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java
@@ -39,6 +39,9 @@ import javax.persistence.Table;
import javax.persistence.Transient;
import javax.persistence.UniqueConstraint;
+import org.hibernate.annotations.Cache;
+import org.hibernate.annotations.CacheConcurrencyStrategy;
+import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.Check;
import org.hibernate.annotations.Generated;
import org.hibernate.annotations.GenerationTime;
@@ -57,296 +60,310 @@ import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
import ch.systemsx.cisd.openbis.generic.shared.dto.hibernate.SearchFieldConstants;
/**
- * Kind of <i>Java Bean</i> or <i>Value Object</i> which contains any information we would like to
- * know about one DATA.
+ * Kind of <i>Java Bean</i> or <i>Value Object</i> which contains any
+ * information we would like to know about one DATA.
* <p>
- * This class is the <i>Java Object</i> representation of the corresponding data in the database.
+ * This class is the <i>Java Object</i> representation of the corresponding data
+ * in the database.
* </p>
*
* @author Bernd Rinn
*/
@Entity
@Table(name = TableNames.DATA_TABLE, uniqueConstraints = @UniqueConstraint(columnNames = ColumnNames.CODE_COLUMN))
-@Check(constraints = "(" + ColumnNames.SAMPLE_ACQUIRED_FROM + " IS NOT NULL AND "
- + ColumnNames.SAMPLE_DERIVED_FROM + " IS NULL) OR (" + ColumnNames.SAMPLE_ACQUIRED_FROM
- + " IS NULL AND " + ColumnNames.SAMPLE_DERIVED_FROM + " IS NOT NULL)")
+@Check(constraints = "(" + ColumnNames.SAMPLE_ACQUIRED_FROM
+ + " IS NOT NULL AND " + ColumnNames.SAMPLE_DERIVED_FROM
+ + " IS NULL) OR (" + ColumnNames.SAMPLE_ACQUIRED_FROM + " IS NULL AND "
+ + ColumnNames.SAMPLE_DERIVED_FROM + " IS NOT NULL)")
@Inheritance(strategy = InheritanceType.JOINED)
@Friend(toClasses = EventPE.class)
-public class DataPE extends AbstractIdAndCodeHolder<DataPE>
+public class DataPE extends AbstractIdAndCodeHolder<DataPE> implements
+ IEntityPropertiesHolder<DataSetPropertyPE>
{
- private static final long serialVersionUID = GenericSharedConstants.VERSION;
-
- public static final DataPE[] EMPTY_ARRAY = new DataPE[0];
-
- private transient Long id;
-
- private String code;
-
- private boolean placeholder;
-
- private boolean deleted;
-
- /** Registration date of the database instance. */
- private Date registrationDate;
-
- private DataSetTypePE dataSetType;
-
- private ProcedurePE procedure;
-
- private Date productionDate;
-
- private String dataProducerCode;
-
- private SamplePE sampleAcquiredFrom;
-
- private SamplePE sampleDerivedFrom;
-
- private Set<DataPE> parents = new HashSet<DataPE>();
-
- private Set<EventPE> events = new HashSet<EventPE>();
-
- @Column(name = ColumnNames.REGISTRATION_TIMESTAMP_COLUMN, nullable = false, insertable = false)
- @Generated(GenerationTime.ALWAYS)
- public Date getRegistrationDate()
- {
- return HibernateAbstractRegistrationHolder.getDate(registrationDate);
- }
-
- public void setRegistrationDate(final Date registrationDate)
- {
- this.registrationDate = registrationDate;
- }
-
- @ManyToOne(fetch = FetchType.EAGER)
- @NotNull(message = ValidationMessages.DATA_SET_TYPE_NOT_NULL_MESSAGE)
- @JoinColumn(name = ColumnNames.DATA_SET_TYPE_COLUMN)
- @IndexedEmbedded(prefix = SearchFieldConstants.PREFIX_DATASET_TYPE)
- /** Returns <code>dataSetType</code>. */
- public DataSetTypePE getDataSetType()
- {
- return dataSetType;
- }
-
- /** Sets <code>dataSetType</code>. */
- public void setDataSetType(final DataSetTypePE dataSetType)
- {
- this.dataSetType = dataSetType;
- }
-
- /**
- * Returns <code>true</code> if this data set is a placeholder for a data set yet to arrive.
- */
- @Column(name = ColumnNames.IS_PLACEHOLDER_COLUMN)
- public boolean isPlaceholder()
- {
- return placeholder;
- }
-
- /**
- * Set to <code>true</code> if this data set is a placeholder for a data set yet to arrive.
- */
- public void setPlaceholder(final boolean placeholder)
- {
- this.placeholder = placeholder;
- }
-
- @Column(name = ColumnNames.IS_DELETED_COLUMN)
- @Field(index = Index.UN_TOKENIZED, store = Store.YES, name = SearchFieldConstants.DELETED)
- public boolean isDeleted()
- {
- return deleted;
- }
-
- public void setDeleted(boolean deleted)
- {
- this.deleted = deleted;
- }
-
- @ManyToOne(fetch = FetchType.EAGER)
- @JoinColumn(name = ColumnNames.SAMPLE_ACQUIRED_FROM)
- @IndexedEmbedded(prefix = SearchFieldConstants.PREFIX_SAMPLE)
- public SamplePE getSampleAcquiredFrom()
- {
- return sampleAcquiredFrom;
- }
-
- @ManyToOne(fetch = FetchType.EAGER)
- @JoinColumn(name = ColumnNames.SAMPLE_DERIVED_FROM)
- @IndexedEmbedded(prefix = SearchFieldConstants.PREFIX_SAMPLE)
- public SamplePE getSampleDerivedFrom()
- {
- return sampleDerivedFrom;
- }
-
- public void setSampleAcquiredFrom(final SamplePE sampleAcquiredFrom)
- {
- this.sampleAcquiredFrom = sampleAcquiredFrom;
- }
-
- public void setSampleDerivedFrom(final SamplePE sampleDerivedFrom)
- {
- this.sampleDerivedFrom = sampleDerivedFrom;
- }
-
- @Transient
- public String getAssociatedSampleCode()
- {
- final SamplePE sample = sampleAcquiredFrom != null ? sampleAcquiredFrom : sampleDerivedFrom;
- return sample != null ? sample.getCode() : null;
- }
-
- /**
- * Returns the date when the measurement / calculation that produced this external data set has
- * been performed.
- * <p>
- * This may not be known in which case this method will return <code>null</code>.
- */
- @Column(name = ColumnNames.PRODUCTION_TIMESTAMP_COLUMN)
- public Date getProductionDate()
- {
- return HibernateAbstractRegistrationHolder.getDate(productionDate);
- }
-
- /**
- * Sets the date when the measurement / calculation that produced this external data set has
- * been performed.
- */
- public void setProductionDate(final Date productionDate)
- {
- this.productionDate = productionDate;
- }
-
- /**
- * Returns the code identifying the data source (i.e. measurement device or software pipeline)
- * that produced this external data set.
- * <p>
- * This may not be known in which case this method will return <code>null</code>.
- * </p>
- */
- @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
- @Column(name = ColumnNames.DATA_PRODUCER_CODE_COLUMN)
- public String getDataProducerCode()
- {
- return dataProducerCode;
- }
-
- /**
- * Sets the code identifying the data source (i.e. measurement device or software pipeline) that
- * produced this external data set.
- */
- public void setDataProducerCode(final String dataProducerCode)
- {
- this.dataProducerCode = dataProducerCode;
- }
-
- public void setId(final Long id)
- {
- this.id = id;
- }
-
- /**
- * Sets the code (i.e. the externally used unique identifier) of this external data.
- */
- public void setCode(final String code)
- {
- this.code = code;
- }
-
- @ManyToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL)
- @JoinTable(name = TableNames.DATA_SET_RELATIONSHIPS_TABLE, joinColumns = @JoinColumn(name = ColumnNames.DATA_CHILD_COLUMN), inverseJoinColumns = @JoinColumn(name = ColumnNames.DATA_PARENT_COLUMN))
- public Set<DataPE> getParents()
- {
- return parents;
- }
-
- public void setParents(final Set<DataPE> parents)
- {
- this.parents = parents;
- }
-
- //
- // AbstractIdAndCodeHolder
- //
-
- @Id
- @SequenceGenerator(name = SequenceNames.DATA_SEQUENCE, sequenceName = SequenceNames.DATA_SEQUENCE, allocationSize = 1)
- @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.DATA_SEQUENCE)
- @DocumentId
- public Long getId()
- {
- return id;
- }
-
- @Column(unique = true)
- @NotNull(message = ValidationMessages.CODE_NOT_NULL_MESSAGE)
- @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
- @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
- @Field(index = Index.TOKENIZED, store = Store.YES, name = SearchFieldConstants.CODE)
- public String getCode()
- {
- return code;
- }
-
- /** Returns <code>procedure</code>. */
- @ManyToOne(fetch = FetchType.LAZY)
- @NotNull(message = ValidationMessages.PROCEDURE_NOT_NULL_MESSAGE)
- @JoinColumn(name = ColumnNames.PROCEDURE_PRODUCED_BY_COLUMN)
- @IndexedEmbedded(prefix = SearchFieldConstants.PREFIX_PROCEDURE)
- public ProcedurePE getProcedure()
- {
- return procedure;
- }
-
- /** Sets <code>procedure</code>. */
- public void setProcedure(final ProcedurePE procedure)
- {
- this.procedure = procedure;
- }
-
- @OneToMany(fetch = FetchType.LAZY, mappedBy = "dataInternal", cascade = CascadeType.ALL)
- private final Set<EventPE> getEventsInternal()
- {
- return events;
- }
-
- // Required by Hibernate.
- @SuppressWarnings("unused")
- private final void setEventsInternal(final Set<EventPE> events)
- {
- this.events = events;
- }
-
- public final void setEvents(final Set<EventPE> events)
- {
- getEventsInternal().clear();
- for (final EventPE child : events)
- {
- addEvent(child);
- }
- }
-
- @Transient
- public final Set<EventPE> getEvents()
- {
- return new UnmodifiableSetDecorator<EventPE>(getEventsInternal());
- }
-
- public void addEvent(final EventPE event)
- {
- final DataPE data = event.getData();
- if (data != null)
- {
- data.removeEvent(event);
- }
- event.setDataInternal(this);
- getEventsInternal().add(event);
- }
-
- public void removeEvent(final EventPE event)
- {
- assert event != null : "Unspecified event.";
- getEventsInternal().remove(event);
- event.setDataInternal(null);
- }
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final DataPE[] EMPTY_ARRAY = new DataPE[0];
+
+ private transient Long id;
+
+ private String code;
+
+ private boolean placeholder;
+
+ private boolean deleted;
+
+ /** Registration date of the database instance. */
+ private Date registrationDate;
+
+ private DataSetTypePE dataSetType;
+
+ private ProcedurePE procedure;
+
+ private Date productionDate;
+
+ private String dataProducerCode;
+
+ private SamplePE sampleAcquiredFrom;
+
+ private SamplePE sampleDerivedFrom;
+
+ private Set<DataPE> parents = new HashSet<DataPE>();
+
+ private Set<EventPE> events = new HashSet<EventPE>();
+
+ @Column(name = ColumnNames.REGISTRATION_TIMESTAMP_COLUMN, nullable = false, insertable = false)
+ @Generated(GenerationTime.ALWAYS)
+ public Date getRegistrationDate() {
+ return HibernateAbstractRegistrationHolder.getDate(registrationDate);
+ }
+
+ public void setRegistrationDate(final Date registrationDate) {
+ this.registrationDate = registrationDate;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.DATA_SET_TYPE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.DATA_SET_TYPE_COLUMN)
+ @IndexedEmbedded(prefix = SearchFieldConstants.PREFIX_DATASET_TYPE)
+ /* * Returns <code>dataSetType</code>. */
+ public DataSetTypePE getDataSetType() {
+ return dataSetType;
+ }
+
+ /** Sets <code>dataSetType</code>. */
+ public void setDataSetType(final DataSetTypePE dataSetType) {
+ this.dataSetType = dataSetType;
+ }
+
+ /**
+ * Returns <code>true</code> if this data set is a placeholder for a data
+ * set yet to arrive.
+ */
+ @Column(name = ColumnNames.IS_PLACEHOLDER_COLUMN)
+ public boolean isPlaceholder() {
+ return placeholder;
+ }
+
+ /**
+ * Set to <code>true</code> if this data set is a placeholder for a data set
+ * yet to arrive.
+ */
+ public void setPlaceholder(final boolean placeholder) {
+ this.placeholder = placeholder;
+ }
+
+ @Column(name = ColumnNames.IS_DELETED_COLUMN)
+ @Field(index = Index.UN_TOKENIZED, store = Store.YES, name = SearchFieldConstants.DELETED)
+ public boolean isDeleted() {
+ return deleted;
+ }
+
+ public void setDeleted(boolean deleted) {
+ this.deleted = deleted;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.SAMPLE_ACQUIRED_FROM)
+ @IndexedEmbedded(prefix = SearchFieldConstants.PREFIX_SAMPLE)
+ public SamplePE getSampleAcquiredFrom() {
+ return sampleAcquiredFrom;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.SAMPLE_DERIVED_FROM)
+ @IndexedEmbedded(prefix = SearchFieldConstants.PREFIX_SAMPLE)
+ public SamplePE getSampleDerivedFrom() {
+ return sampleDerivedFrom;
+ }
+
+ public void setSampleAcquiredFrom(final SamplePE sampleAcquiredFrom) {
+ this.sampleAcquiredFrom = sampleAcquiredFrom;
+ }
+
+ public void setSampleDerivedFrom(final SamplePE sampleDerivedFrom) {
+ this.sampleDerivedFrom = sampleDerivedFrom;
+ }
+
+ @Transient
+ public String getAssociatedSampleCode() {
+ final SamplePE sample = sampleAcquiredFrom != null ? sampleAcquiredFrom
+ : sampleDerivedFrom;
+ return sample != null ? sample.getCode() : null;
+ }
+
+ /**
+ * Returns the date when the measurement / calculation that produced this
+ * external data set has been performed.
+ * <p>
+ * This may not be known in which case this method will return
+ * <code>null</code>.
+ */
+ @Column(name = ColumnNames.PRODUCTION_TIMESTAMP_COLUMN)
+ public Date getProductionDate() {
+ return HibernateAbstractRegistrationHolder.getDate(productionDate);
+ }
+
+ /**
+ * Sets the date when the measurement / calculation that produced this
+ * external data set has been performed.
+ */
+ public void setProductionDate(final Date productionDate) {
+ this.productionDate = productionDate;
+ }
+
+ /**
+ * Returns the code identifying the data source (i.e. measurement device or
+ * software pipeline) that produced this external data set.
+ * <p>
+ * This may not be known in which case this method will return
+ * <code>null</code>.
+ * </p>
+ */
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @Column(name = ColumnNames.DATA_PRODUCER_CODE_COLUMN)
+ public String getDataProducerCode() {
+ return dataProducerCode;
+ }
+
+ /**
+ * Sets the code identifying the data source (i.e. measurement device or
+ * software pipeline) that produced this external data set.
+ */
+ public void setDataProducerCode(final String dataProducerCode) {
+ this.dataProducerCode = dataProducerCode;
+ }
+
+ public void setId(final Long id) {
+ this.id = id;
+ }
+
+ /**
+ * Sets the code (i.e. the externally used unique identifier) of this
+ * external data.
+ */
+ public void setCode(final String code) {
+ this.code = code;
+ }
+
+ @ManyToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL)
+ @JoinTable(name = TableNames.DATA_SET_RELATIONSHIPS_TABLE, joinColumns = @JoinColumn(name = ColumnNames.DATA_CHILD_COLUMN), inverseJoinColumns = @JoinColumn(name = ColumnNames.DATA_PARENT_COLUMN))
+ public Set<DataPE> getParents() {
+ return parents;
+ }
+
+ public void setParents(final Set<DataPE> parents) {
+ this.parents = parents;
+ }
+
+ //
+ // AbstractIdAndCodeHolder
+ //
+
+ @Id
+ @SequenceGenerator(name = SequenceNames.DATA_SEQUENCE, sequenceName = SequenceNames.DATA_SEQUENCE, allocationSize = 1)
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.DATA_SEQUENCE)
+ @DocumentId
+ public Long getId() {
+ return id;
+ }
+
+ @Column(unique = true)
+ @NotNull(message = ValidationMessages.CODE_NOT_NULL_MESSAGE)
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
+ @Field(index = Index.TOKENIZED, store = Store.YES, name = SearchFieldConstants.CODE)
+ public String getCode() {
+ return code;
+ }
+
+ /** Returns <code>procedure</code>. */
+ @ManyToOne(fetch = FetchType.LAZY)
+ @NotNull(message = ValidationMessages.PROCEDURE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.PROCEDURE_PRODUCED_BY_COLUMN)
+ @IndexedEmbedded(prefix = SearchFieldConstants.PREFIX_PROCEDURE)
+ public ProcedurePE getProcedure() {
+ return procedure;
+ }
+
+ /** Sets <code>procedure</code>. */
+ public void setProcedure(final ProcedurePE procedure) {
+ this.procedure = procedure;
+ }
+
+ @OneToMany(fetch = FetchType.LAZY, mappedBy = "dataInternal", cascade = CascadeType.ALL)
+ private final Set<EventPE> getEventsInternal() {
+ return events;
+ }
+
+ // Required by Hibernate.
+ @SuppressWarnings("unused")
+ private final void setEventsInternal(final Set<EventPE> events) {
+ this.events = events;
+ }
+
+ public final void setEvents(final Set<EventPE> events) {
+ getEventsInternal().clear();
+ for (final EventPE child : events) {
+ addEvent(child);
+ }
+ }
+
+ @Transient
+ public final Set<EventPE> getEvents() {
+ return new UnmodifiableSetDecorator<EventPE>(getEventsInternal());
+ }
+
+ public void addEvent(final EventPE event) {
+ final DataPE data = event.getData();
+ if (data != null) {
+ data.removeEvent(event);
+ }
+ event.setDataInternal(this);
+ getEventsInternal().add(event);
+ }
+
+ public void removeEvent(final EventPE event) {
+ assert event != null : "Unspecified event.";
+ getEventsInternal().remove(event);
+ event.setDataInternal(null);
+ }
+
+ private Set<DataSetPropertyPE> properties = new HashSet<DataSetPropertyPE>();
+
+ @Cascade(value = org.hibernate.annotations.CascadeType.DELETE_ORPHAN)
+ @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL, mappedBy = "entity")
+ @Cache(usage = CacheConcurrencyStrategy.READ_WRITE)
+ @IndexedEmbedded(prefix = SearchFieldConstants.PREFIX_PROPERTIES)
+ private Set<DataSetPropertyPE> getDataSetProperties() {
+ return properties;
+ }
+
+ // Required by Hibernate.
+ @SuppressWarnings("unused")
+ private void setDataSetProperties(final Set<DataSetPropertyPE> properties) {
+ this.properties = properties;
+ }
+
+ public void addProperty(final DataSetPropertyPE property) {
+ property.setEntity(this);
+ getDataSetProperties().add(property);
+ }
+
+ public void setProperties(final Set<DataSetPropertyPE> properties) {
+ getDataSetProperties().clear();
+ for (final DataSetPropertyPE property : properties) {
+ final DataPE parent = property.getDataSet();
+ if (parent != null) {
+ parent.getDataSetProperties().remove(property);
+ }
+ addProperty(property);
+ }
+ }
+
+ @Transient
+ public Set<DataSetPropertyPE> getProperties() {
+ return new UnmodifiableSetDecorator<DataSetPropertyPE>(
+ getDataSetProperties());
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetPropertyPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetPropertyPE.java
new file mode 100644
index 0000000000000000000000000000000000000000..e4f333ad1701e2b2f4b21e2ec68b7a827cce1238
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetPropertyPE.java
@@ -0,0 +1,98 @@
+/*
+ * Copyright 2008 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.shared.dto;
+
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+import javax.persistence.UniqueConstraint;
+
+import org.hibernate.annotations.Cache;
+import org.hibernate.annotations.CacheConcurrencyStrategy;
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistence entity representing data set property.
+ *
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.DATA_SET_PROPERTIES_TABLE, uniqueConstraints = @UniqueConstraint(columnNames = {
+ ColumnNames.DATA_SET_COLUMN,
+ ColumnNames.DATA_SET_TYPE_PROPERTY_TYPE_COLUMN }))
+@Cache(usage = CacheConcurrencyStrategy.READ_WRITE)
+public class DataSetPropertyPE extends EntityPropertyPE {
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public final static DataSetPropertyPE[] EMPTY_ARRAY = new DataSetPropertyPE[0];
+
+ private DataPE dataSet;
+
+ @Transient
+ public final DataPE getDataSet() {
+ return dataSet;
+ }
+
+ //
+ // EntityPropertyPE
+ //
+
+ @NotNull(message = ValidationMessages.DATA_SET_TYPE_NOT_NULL_MESSAGE)
+ @ManyToOne(fetch = FetchType.EAGER, targetEntity = DataSetTypePropertyTypePE.class)
+ @JoinColumn(name = ColumnNames.DATA_SET_TYPE_PROPERTY_TYPE_COLUMN, updatable = false)
+ public EntityTypePropertyTypePE getEntityTypePropertyType() {
+ return entityTypePropertyType;
+ }
+
+ @SequenceGenerator(name = SequenceNames.DATA_SET_PROPERTY_SEQUENCE, sequenceName = SequenceNames.DATA_SET_PROPERTY_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.DATA_SET_PROPERTY_SEQUENCE)
+ public Long getId() {
+ return id;
+ }
+
+ @ManyToOne(fetch = FetchType.LAZY, targetEntity = DataPE.class)
+ @JoinColumn(name = ColumnNames.DATA_SET_COLUMN, updatable = false)
+ public IIdAndCodeHolder getEntity() {
+ return getDataSet();
+ }
+
+ /**
+ * Sets the <var>data set</var> of this property.
+ * <p>
+ * <i>Do not use directly, instead, call
+ * {@link DataPE#addProperty(DataSetPropertyPE)} with <code>this</code>
+ * object!</i>
+ */
+ void setEntity(final IIdAndCodeHolder entity) {
+ this.dataSet = (DataPE) entity;
+ }
+
+ @Override
+ public void setHolder(final IIdAndCodeHolder entity) {
+ ((DataPE) entity).addProperty(this);
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetTypePE.java
index f0821591c8ce38c1a7ff0c5d2507c98c6d44793e..a6a8d81443be0773b7a620910ab284922f68b398 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetTypePE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetTypePE.java
@@ -16,55 +16,75 @@
package ch.systemsx.cisd.openbis.generic.shared.dto;
+import java.util.HashSet;
+import java.util.Set;
+
import javax.persistence.Entity;
import javax.persistence.FetchType;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
+import javax.persistence.Transient;
import javax.persistence.UniqueConstraint;
-import org.hibernate.validator.NotNull;
-
import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
/**
* Persistence Entity representing data set type.
*
- * @author Christian Ribeaud
* @author Izabela Adamczyk
*/
@Entity
-@Table(name = TableNames.DATA_SET_TYPES_TABLE, uniqueConstraints =
- { @UniqueConstraint(columnNames =
- { ColumnNames.CODE_COLUMN, ColumnNames.DATABASE_INSTANCE_COLUMN }) })
-public class DataSetTypePE extends AbstractTypePE
-{
- private static final long serialVersionUID = GenericSharedConstants.VERSION;
+@Table(name = TableNames.DATA_SET_TYPES_TABLE, uniqueConstraints = { @UniqueConstraint(columnNames = {
+ ColumnNames.CODE_COLUMN, ColumnNames.DATABASE_INSTANCE_COLUMN }) })
+public class DataSetTypePE extends EntityTypePE {
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private Set<DataSetTypePropertyTypePE> dataSetTypePropertyTypes = new HashSet<DataSetTypePropertyTypePE>();
+
+ @SequenceGenerator(name = SequenceNames.DATA_SET_TYPE_SEQUENCE, sequenceName = SequenceNames.DATA_SET_TYPE_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.DATA_SET_TYPE_SEQUENCE)
+ public final Long getId() {
+ return id;
+ }
+
+ public void addDataSetTypePropertyType(final DataSetTypePropertyTypePE child) {
+ final DataSetTypePE parent = (DataSetTypePE) child.getEntityType();
+ if (parent != null) {
+ parent.getDataSetTypePropertyTypesInternal().remove(child);
+ }
+ child.setEntityTypeInternal(this);
+ getDataSetTypePropertyTypesInternal().add(child);
+ }
- private DatabaseInstancePE databaseInstance;
+ @OneToMany(fetch = FetchType.LAZY, mappedBy = "entityTypeInternal")
+ @JoinColumn(name = ColumnNames.DATA_SET_TYPE_COLUMN, updatable = false)
+ private Set<DataSetTypePropertyTypePE> getDataSetTypePropertyTypesInternal() {
+ return dataSetTypePropertyTypes;
+ }
- @SequenceGenerator(name = SequenceNames.DATA_SET_TYPE_SEQUENCE, sequenceName = SequenceNames.DATA_SET_TYPE_SEQUENCE, allocationSize = 1)
- @Id
- @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.DATA_SET_TYPE_SEQUENCE)
- public final Long getId()
- {
- return id;
- }
+ // Required by Hibernate.
+ @SuppressWarnings("unused")
+ private void setDataSetTypePropertyTypesInternal(
+ final Set<DataSetTypePropertyTypePE> dataSetTypePropertyTypes) {
+ this.dataSetTypePropertyTypes = dataSetTypePropertyTypes;
+ }
- @ManyToOne(fetch = FetchType.EAGER)
- @NotNull(message = ValidationMessages.DATABASE_INSTANCE_NOT_NULL_MESSAGE)
- @JoinColumn(name = ColumnNames.DATABASE_INSTANCE_COLUMN, updatable = false)
- public DatabaseInstancePE getDatabaseInstance()
- {
- return databaseInstance;
- }
+ @Transient
+ public Set<DataSetTypePropertyTypePE> getDataSetTypePropertyTypes() {
+ return getDataSetTypePropertyTypesInternal();
+ }
- public void setDatabaseInstance(final DatabaseInstancePE databaseInstance)
- {
- this.databaseInstance = databaseInstance;
- }
+ public final void setDataSetTypePropertyTypes(
+ final Set<DataSetTypePropertyTypePE> dataSetTypePropertyTypes) {
+ getDataSetTypePropertyTypesInternal().clear();
+ for (final DataSetTypePropertyTypePE child : dataSetTypePropertyTypes) {
+ addDataSetTypePropertyType(child);
+ }
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetTypePropertyTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetTypePropertyTypePE.java
new file mode 100644
index 0000000000000000000000000000000000000000..3de079bae414b5761a313159f899458000e67c3e
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetTypePropertyTypePE.java
@@ -0,0 +1,94 @@
+/*
+ * Copyright 2008 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.shared.dto;
+
+import java.util.Set;
+
+import javax.persistence.CascadeType;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+import javax.persistence.UniqueConstraint;
+
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistence entity representing experiment type - property type relation.
+ *
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.DATA_SET_TYPE_PROPERTY_TYPE_TABLE, uniqueConstraints = { @UniqueConstraint(columnNames = {
+ ColumnNames.DATA_SET_TYPE_COLUMN, ColumnNames.PROPERTY_TYPE_COLUMN }) })
+public class DataSetTypePropertyTypePE extends EntityTypePropertyTypePE {
+
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final DataSetTypePropertyTypePE[] EMPTY_ARRAY = new DataSetTypePropertyTypePE[0];
+
+ @NotNull(message = ValidationMessages.DATA_SET_TYPE_NOT_NULL_MESSAGE)
+ @ManyToOne(fetch = FetchType.EAGER, targetEntity = ExperimentTypePE.class)
+ @JoinColumn(name = ColumnNames.DATA_SET_TYPE_COLUMN)
+ private EntityTypePE getEntityTypeInternal() {
+ return entityType;
+ }
+
+ //
+ // EntityTypePropertyTypePE
+ //
+
+ @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL, mappedBy = "entityTypePropertyType", targetEntity = DataSetPropertyPE.class)
+ public Set<EntityPropertyPE> getPropertyValues() {
+ return propertyValues;
+ }
+
+ @Transient
+ public EntityTypePE getEntityType() {
+ return getEntityTypeInternal();
+ }
+
+ @Override
+ // This setter sets the bidirectional connection. That's why we must have an
+ // another internal
+ // plain setter for Hibernate.
+ public void setEntityType(EntityTypePE entityType) {
+ ((DataSetTypePE) entityType).addDataSetTypePropertyType(this);
+ }
+
+ @SequenceGenerator(name = SequenceNames.DATA_SET_TYPE_PROPERTY_TYPE_SEQUENCE, sequenceName = SequenceNames.DATA_SET_TYPE_PROPERTY_TYPE_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.DATA_SET_TYPE_PROPERTY_TYPE_SEQUENCE)
+ public Long getId() {
+ return id;
+ }
+
+ @Override
+ public void setPropertyType(PropertyTypePE propertyType) {
+ propertyType.addDataSetTypePropertyType(this);
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalDataPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalDataPE.java
index d284288895a5ae6735cf8f15d68a4b56e7d226b5..8842d026ab3a88b895759cdd9764b0334478e493 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalDataPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalDataPE.java
@@ -57,7 +57,6 @@ public final class ExternalDataPE extends DataPE
private static final long serialVersionUID = GenericSharedConstants.VERSION;
/** An empty array of <code>ExternalData</code>. */
- @SuppressWarnings("hiding")
public final static ExternalDataPE[] EMPTY_ARRAY = new ExternalDataPE[0];
private String location;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewSampleComponent.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewSampleComponent.java
index b8f48dfaac8fda20ec6ac647aef1ca32084c5735..98a9a3052c1574dbba7433e570bba6fd7ddd5598 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewSampleComponent.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewSampleComponent.java
@@ -31,7 +31,6 @@ public final class NewSampleComponent extends NewSampleComponentWithFixedMateria
{
private static final long serialVersionUID = GenericSharedConstants.VERSION;
- @SuppressWarnings("hiding")
public final static NewSampleComponent[] EMPTY_ARRAY = new NewSampleComponent[0];
private String materialTypeCode;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PropertyTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PropertyTypePE.java
index 323085c2b8e2bb133099a484b86760be897a2713..5a145b3f7d3a743c4f9e8cd5e4d4330896853ef8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PropertyTypePE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PropertyTypePE.java
@@ -54,371 +54,352 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.hibernate.InternalNamespace;
* @author Izabela Adamczyk
*/
@Entity
-@Table(name = TableNames.PROPERTY_TYPES_TABLE, uniqueConstraints =
- { @UniqueConstraint(columnNames =
- { ColumnNames.CODE_COLUMN, ColumnNames.IS_INTERNAL_NAMESPACE,
- ColumnNames.DATABASE_INSTANCE_COLUMN }) })
-public final class PropertyTypePE extends HibernateAbstractRegistrationHolder implements
- Comparable<PropertyTypePE>, IIdAndCodeHolder
-{
- public static final PropertyTypePE[] EMPTY_ARRAY = new PropertyTypePE[0];
-
- private static final long serialVersionUID = GenericSharedConstants.VERSION;
-
- private String simpleCode;
-
- private DataTypePE type;
-
- private String description;
-
- private String label;
-
- /** can be null. Is always null when {@link #materialType} is not null. */
- private VocabularyPE vocabulary;
-
- /**
- * If this field is set, then it specifies the type of the materials, which are values of this
- * property type.<br>
- * Note that this field can be null and the data type can be still MATERIAL, it means that, that
- * material of any type can be a valid property value.
- */
- private MaterialTypePE materialType;
-
- private boolean internalNamespace;
-
- private boolean managedInternally;
-
- private transient Long id;
-
- private DatabaseInstancePE databaseInstance;
-
- private Set<MaterialTypePropertyTypePE> materialTypePropertyTypes =
- new HashSet<MaterialTypePropertyTypePE>();
-
- private Set<ExperimentTypePropertyTypePE> experimentTypePropertyTypes =
- new HashSet<ExperimentTypePropertyTypePE>();
-
- private Set<SampleTypePropertyTypePE> sampleTypePropertyTypes =
- new HashSet<SampleTypePropertyTypePE>();
-
- @ManyToOne(fetch = FetchType.EAGER)
- @JoinColumn(name = ColumnNames.CONTROLLED_VOCABULARY_COLUMN, updatable = false)
- public VocabularyPE getVocabulary()
- {
- return vocabulary;
- }
-
- public void setVocabulary(final VocabularyPE vocabulary)
- {
- assert materialType == null || vocabulary == null : "Property cannot be of controled vocabulary and material type at the same moment";
- this.vocabulary = vocabulary;
- }
-
- @ManyToOne(fetch = FetchType.EAGER)
- @JoinColumn(name = ColumnNames.PROPERTY_MATERIAL_TYPE_COLUMN, updatable = false)
- public MaterialTypePE getMaterialType()
- {
- return materialType;
- }
-
- public void setMaterialType(MaterialTypePE materialType)
- {
- assert materialType == null || vocabulary == null : "Property cannot be of controled vocabulary and material type at the same moment";
- this.materialType = materialType;
- }
-
- /**
- * Sets code in 'database format' - without 'user prefix'. To set full code (with user prefix
- * use {@link #setCode(String)}).
- */
- public void setSimpleCode(final String simpleCode)
- {
- this.simpleCode = simpleCode.toUpperCase();
- }
-
- @NotNull(message = ValidationMessages.DATABASE_INSTANCE_NOT_NULL_MESSAGE)
- @ManyToOne(fetch = FetchType.EAGER)
- @JoinColumn(name = ColumnNames.DATABASE_INSTANCE_COLUMN, updatable = false)
- public DatabaseInstancePE getDatabaseInstance()
- {
- return databaseInstance;
- }
-
- public void setDatabaseInstance(final DatabaseInstancePE databaseInstance)
- {
- this.databaseInstance = databaseInstance;
- }
-
- @Column(name = ColumnNames.CODE_COLUMN)
- @NotNull(message = ValidationMessages.CODE_NOT_NULL_MESSAGE)
- @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
- @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
- public String getSimpleCode()
- {
- return simpleCode;
- }
-
- public void setCode(final String fullCode)
- {
- setInternalNamespace(CodeConverter.isInternalNamespace(fullCode));
- setSimpleCode(CodeConverter.tryToDatabase(fullCode));
- }
-
- @Transient
- public String getCode()
- {
- return CodeConverter.tryToBusinessLayer(getSimpleCode(), isInternalNamespace() == false);
- }
-
- @NotNull(message = ValidationMessages.DATA_TYPE_NOT_NULL_MESSAGE)
- @ManyToOne(fetch = FetchType.EAGER)
- @JoinColumn(name = ColumnNames.DATA_TYPE_COLUMN, updatable = false)
- public final DataTypePE getType()
- {
- return type;
- }
-
- public final void setType(final DataTypePE type)
- {
- this.type = type;
- }
-
- @NotNull(message = ValidationMessages.DESCRIPTION_NOT_NULL_MESSAGE)
- @Column(name = ColumnNames.DESCRIPTION_COLUMN)
- @Length(max = 80, message = ValidationMessages.DESCRIPTION_LENGTH_MESSAGE)
- public final String getDescription()
- {
- return description;
- }
-
- public final void setDescription(final String description)
- {
- this.description = description;
- }
-
- @NotNull(message = ValidationMessages.LABEL_NOT_NULL_MESSAGE)
- @Column(name = ColumnNames.LABEL_COLUMN)
- @Length(max = 40, message = ValidationMessages.LABEL_LENGTH_MESSAGE)
- public final String getLabel()
- {
- return label;
- }
-
- public final void setLabel(final String label)
- {
- this.label = label;
- }
-
- @NotNull
- @Column(name = ColumnNames.IS_MANAGED_INTERNALLY)
- public boolean isManagedInternally()
- {
- return managedInternally;
- }
-
- public void setManagedInternally(final boolean managedInternally)
- {
- this.managedInternally = managedInternally;
- }
-
- @NotNull
- @Column(name = ColumnNames.IS_INTERNAL_NAMESPACE)
- @InternalNamespace(message = ValidationMessages.CODE_NOT_USER_NAMESPACE)
- public boolean isInternalNamespace()
- {
- return internalNamespace;
- }
-
- public void setInternalNamespace(final boolean internalNamespace)
- {
- this.internalNamespace = internalNamespace;
- }
-
- @SequenceGenerator(name = SequenceNames.PROPERTY_TYPES_SEQUENCE, sequenceName = SequenceNames.PROPERTY_TYPES_SEQUENCE, allocationSize = 1)
- @Id
- @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.PROPERTY_TYPES_SEQUENCE)
- public Long getId()
- {
- return id;
- }
-
- public void setId(final Long id)
- {
- this.id = id;
- }
-
- //
- // Comparable
- //
-
- /**
- * If <code>null</code> values are present for <code>code</code>, then they come first.
- */
- public final int compareTo(final PropertyTypePE o)
- {
- return AbstractIdAndCodeHolder.compare(this, o);
- }
-
- //
- // Object
- //
-
- @Override
- public final boolean equals(final Object obj)
- {
- if (obj == this)
- {
- return true;
- }
- if (obj instanceof PropertyTypePE == false)
- {
- return false;
- }
- final PropertyTypePE that = (PropertyTypePE) obj;
- final EqualsBuilder builder = new EqualsBuilder();
- builder.append(getSimpleCode(), that.getSimpleCode());
- builder.append(getDatabaseInstance(), that.getDatabaseInstance());
- builder.append(isInternalNamespace(), that.isInternalNamespace());
- return builder.isEquals();
- }
-
- @Override
- public final int hashCode()
- {
- final HashCodeBuilder builder = new HashCodeBuilder();
- builder.append(getSimpleCode());
- builder.append(getDatabaseInstance());
- builder.append(isInternalNamespace());
- return builder.toHashCode();
- }
-
- @Override
- public final String toString()
- {
- return getCode();
- }
-
- @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL, mappedBy = "propertyTypeInternal")
- private Set<SampleTypePropertyTypePE> getSampleTypePropertyTypesInternal()
- {
- return sampleTypePropertyTypes;
- }
-
- // Required by Hibernate.
- @SuppressWarnings("unused")
- private void setSampleTypePropertyTypesInternal(
- Set<SampleTypePropertyTypePE> sampleTypePropertyTypes)
- {
- this.sampleTypePropertyTypes = sampleTypePropertyTypes;
- }
-
- @Transient
- public Set<SampleTypePropertyTypePE> getSampleTypePropertyTypes()
- {
- return new UnmodifiableSetDecorator<SampleTypePropertyTypePE>(
- getSampleTypePropertyTypesInternal());
- }
-
- public final void setSampleTypePropertyTypes(final Iterable<SampleTypePropertyTypePE> childs)
- {
- getSampleTypePropertyTypesInternal().clear();
- for (final SampleTypePropertyTypePE child : childs)
- {
- addSampleTypePropertyType(child);
- }
- }
-
- public void addSampleTypePropertyType(final SampleTypePropertyTypePE child)
- {
- final PropertyTypePE parent = child.getPropertyType();
- if (parent != null)
- {
- parent.getSampleTypePropertyTypesInternal().remove(child);
- }
- child.setPropertyTypeInternal(this);
- getSampleTypePropertyTypesInternal().add(child);
- }
-
- @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL, mappedBy = "propertyTypeInternal")
- private Set<ExperimentTypePropertyTypePE> getExperimentTypePropertyTypesInternal()
- {
- return experimentTypePropertyTypes;
- }
-
- // Required by Hibernate.
- @SuppressWarnings("unused")
- private void setExperimentTypePropertyTypesInternal(
- Set<ExperimentTypePropertyTypePE> experimentTypePropertyTypes)
- {
- this.experimentTypePropertyTypes = experimentTypePropertyTypes;
- }
-
- @Transient
- public Set<ExperimentTypePropertyTypePE> getExperimentTypePropertyTypes()
- {
- return new UnmodifiableSetDecorator<ExperimentTypePropertyTypePE>(
- getExperimentTypePropertyTypesInternal());
- }
-
- public final void setExperimentTypePropertyTypes(
- final Iterable<ExperimentTypePropertyTypePE> childs)
- {
- getExperimentTypePropertyTypesInternal().clear();
- for (final ExperimentTypePropertyTypePE child : childs)
- {
- addExperimentTypePropertyType(child);
- }
- }
-
- public void addExperimentTypePropertyType(final ExperimentTypePropertyTypePE child)
- {
- final PropertyTypePE parent = child.getPropertyType();
- if (parent != null)
- {
- parent.getExperimentTypePropertyTypesInternal().remove(child);
- }
- child.setPropertyTypeInternal(this);
- getExperimentTypePropertyTypesInternal().add(child);
- }
-
- @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL, mappedBy = "propertyTypeInternal")
- private Set<MaterialTypePropertyTypePE> getMaterialTypePropertyTypesInternal()
- {
- return materialTypePropertyTypes;
- }
-
- // Required by Hibernate.
- @SuppressWarnings("unused")
- private void setMaterialTypePropertyTypesInternal(
- Set<MaterialTypePropertyTypePE> materialTypePropertyTypes)
- {
- this.materialTypePropertyTypes = materialTypePropertyTypes;
- }
-
- @Transient
- public Set<MaterialTypePropertyTypePE> getMaterialTypePropertyTypes()
- {
- return new UnmodifiableSetDecorator<MaterialTypePropertyTypePE>(
- getMaterialTypePropertyTypesInternal());
- }
-
- public final void setMaterialTypePropertyTypes(final Iterable<MaterialTypePropertyTypePE> childs)
- {
- getMaterialTypePropertyTypesInternal().clear();
- for (final MaterialTypePropertyTypePE child : childs)
- {
- addMaterialTypePropertyType(child);
- }
- }
-
- public void addMaterialTypePropertyType(final MaterialTypePropertyTypePE child)
- {
- final PropertyTypePE parent = child.getPropertyType();
- if (parent != null)
- {
- parent.getMaterialTypePropertyTypesInternal().remove(child);
- }
- child.setPropertyTypeInternal(this);
- getMaterialTypePropertyTypesInternal().add(child);
- }
+@Table(name = TableNames.PROPERTY_TYPES_TABLE, uniqueConstraints = { @UniqueConstraint(columnNames = {
+ ColumnNames.CODE_COLUMN, ColumnNames.IS_INTERNAL_NAMESPACE,
+ ColumnNames.DATABASE_INSTANCE_COLUMN }) })
+public final class PropertyTypePE extends HibernateAbstractRegistrationHolder
+ implements Comparable<PropertyTypePE>, IIdAndCodeHolder {
+ public static final PropertyTypePE[] EMPTY_ARRAY = new PropertyTypePE[0];
+
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private String simpleCode;
+
+ private DataTypePE type;
+
+ private String description;
+
+ private String label;
+
+ /** can be null. Is always null when {@link #materialType} is not null. */
+ private VocabularyPE vocabulary;
+
+ /**
+ * If this field is set, then it specifies the type of the materials, which
+ * are values of this property type.<br>
+ * Note that this field can be null and the data type can be still MATERIAL,
+ * it means that, that material of any type can be a valid property value.
+ */
+ private MaterialTypePE materialType;
+
+ private boolean internalNamespace;
+
+ private boolean managedInternally;
+
+ private transient Long id;
+
+ private DatabaseInstancePE databaseInstance;
+
+ private Set<MaterialTypePropertyTypePE> materialTypePropertyTypes = new HashSet<MaterialTypePropertyTypePE>();
+
+ private Set<ExperimentTypePropertyTypePE> experimentTypePropertyTypes = new HashSet<ExperimentTypePropertyTypePE>();
+
+ private Set<SampleTypePropertyTypePE> sampleTypePropertyTypes = new HashSet<SampleTypePropertyTypePE>();
+
+ private Set<DataSetTypePropertyTypePE> dataSetTypePropertyTypes = new HashSet<DataSetTypePropertyTypePE>();
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.CONTROLLED_VOCABULARY_COLUMN, updatable = false)
+ public VocabularyPE getVocabulary() {
+ return vocabulary;
+ }
+
+ public void setVocabulary(final VocabularyPE vocabulary) {
+ assert materialType == null || vocabulary == null : "Property cannot be of controled vocabulary and material type at the same moment";
+ this.vocabulary = vocabulary;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.PROPERTY_MATERIAL_TYPE_COLUMN, updatable = false)
+ public MaterialTypePE getMaterialType() {
+ return materialType;
+ }
+
+ public void setMaterialType(MaterialTypePE materialType) {
+ assert materialType == null || vocabulary == null : "Property cannot be of controled vocabulary and material type at the same moment";
+ this.materialType = materialType;
+ }
+
+ /**
+ * Sets code in 'database format' - without 'user prefix'. To set full code
+ * (with user prefix use {@link #setCode(String)}).
+ */
+ public void setSimpleCode(final String simpleCode) {
+ this.simpleCode = simpleCode.toUpperCase();
+ }
+
+ @NotNull(message = ValidationMessages.DATABASE_INSTANCE_NOT_NULL_MESSAGE)
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.DATABASE_INSTANCE_COLUMN, updatable = false)
+ public DatabaseInstancePE getDatabaseInstance() {
+ return databaseInstance;
+ }
+
+ public void setDatabaseInstance(final DatabaseInstancePE databaseInstance) {
+ this.databaseInstance = databaseInstance;
+ }
+
+ @Column(name = ColumnNames.CODE_COLUMN)
+ @NotNull(message = ValidationMessages.CODE_NOT_NULL_MESSAGE)
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
+ public String getSimpleCode() {
+ return simpleCode;
+ }
+
+ public void setCode(final String fullCode) {
+ setInternalNamespace(CodeConverter.isInternalNamespace(fullCode));
+ setSimpleCode(CodeConverter.tryToDatabase(fullCode));
+ }
+
+ @Transient
+ public String getCode() {
+ return CodeConverter.tryToBusinessLayer(getSimpleCode(),
+ isInternalNamespace() == false);
+ }
+
+ @NotNull(message = ValidationMessages.DATA_TYPE_NOT_NULL_MESSAGE)
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.DATA_TYPE_COLUMN, updatable = false)
+ public final DataTypePE getType() {
+ return type;
+ }
+
+ public final void setType(final DataTypePE type) {
+ this.type = type;
+ }
+
+ @NotNull(message = ValidationMessages.DESCRIPTION_NOT_NULL_MESSAGE)
+ @Column(name = ColumnNames.DESCRIPTION_COLUMN)
+ @Length(max = 80, message = ValidationMessages.DESCRIPTION_LENGTH_MESSAGE)
+ public final String getDescription() {
+ return description;
+ }
+
+ public final void setDescription(final String description) {
+ this.description = description;
+ }
+
+ @NotNull(message = ValidationMessages.LABEL_NOT_NULL_MESSAGE)
+ @Column(name = ColumnNames.LABEL_COLUMN)
+ @Length(max = 40, message = ValidationMessages.LABEL_LENGTH_MESSAGE)
+ public final String getLabel() {
+ return label;
+ }
+
+ public final void setLabel(final String label) {
+ this.label = label;
+ }
+
+ @NotNull
+ @Column(name = ColumnNames.IS_MANAGED_INTERNALLY)
+ public boolean isManagedInternally() {
+ return managedInternally;
+ }
+
+ public void setManagedInternally(final boolean managedInternally) {
+ this.managedInternally = managedInternally;
+ }
+
+ @NotNull
+ @Column(name = ColumnNames.IS_INTERNAL_NAMESPACE)
+ @InternalNamespace(message = ValidationMessages.CODE_NOT_USER_NAMESPACE)
+ public boolean isInternalNamespace() {
+ return internalNamespace;
+ }
+
+ public void setInternalNamespace(final boolean internalNamespace) {
+ this.internalNamespace = internalNamespace;
+ }
+
+ @SequenceGenerator(name = SequenceNames.PROPERTY_TYPES_SEQUENCE, sequenceName = SequenceNames.PROPERTY_TYPES_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.PROPERTY_TYPES_SEQUENCE)
+ public Long getId() {
+ return id;
+ }
+
+ public void setId(final Long id) {
+ this.id = id;
+ }
+
+ //
+ // Comparable
+ //
+
+ /**
+ * If <code>null</code> values are present for <code>code</code>, then they
+ * come first.
+ */
+ public final int compareTo(final PropertyTypePE o) {
+ return AbstractIdAndCodeHolder.compare(this, o);
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj) {
+ if (obj == this) {
+ return true;
+ }
+ if (obj instanceof PropertyTypePE == false) {
+ return false;
+ }
+ final PropertyTypePE that = (PropertyTypePE) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(getSimpleCode(), that.getSimpleCode());
+ builder.append(getDatabaseInstance(), that.getDatabaseInstance());
+ builder.append(isInternalNamespace(), that.isInternalNamespace());
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode() {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getSimpleCode());
+ builder.append(getDatabaseInstance());
+ builder.append(isInternalNamespace());
+ return builder.toHashCode();
+ }
+
+ @Override
+ public final String toString() {
+ return getCode();
+ }
+
+ @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL, mappedBy = "propertyTypeInternal")
+ private Set<SampleTypePropertyTypePE> getSampleTypePropertyTypesInternal() {
+ return sampleTypePropertyTypes;
+ }
+
+ // Required by Hibernate.
+ @SuppressWarnings("unused")
+ private void setSampleTypePropertyTypesInternal(
+ Set<SampleTypePropertyTypePE> sampleTypePropertyTypes) {
+ this.sampleTypePropertyTypes = sampleTypePropertyTypes;
+ }
+
+ @Transient
+ public Set<SampleTypePropertyTypePE> getSampleTypePropertyTypes() {
+ return new UnmodifiableSetDecorator<SampleTypePropertyTypePE>(
+ getSampleTypePropertyTypesInternal());
+ }
+
+ public final void setSampleTypePropertyTypes(
+ final Iterable<SampleTypePropertyTypePE> childs) {
+ getSampleTypePropertyTypesInternal().clear();
+ for (final SampleTypePropertyTypePE child : childs) {
+ addSampleTypePropertyType(child);
+ }
+ }
+
+ public void addSampleTypePropertyType(final SampleTypePropertyTypePE child) {
+ final PropertyTypePE parent = child.getPropertyType();
+ if (parent != null) {
+ parent.getSampleTypePropertyTypesInternal().remove(child);
+ }
+ child.setPropertyTypeInternal(this);
+ getSampleTypePropertyTypesInternal().add(child);
+ }
+
+ @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL, mappedBy = "propertyTypeInternal")
+ private Set<ExperimentTypePropertyTypePE> getExperimentTypePropertyTypesInternal() {
+ return experimentTypePropertyTypes;
+ }
+
+ // Required by Hibernate.
+ @SuppressWarnings("unused")
+ private void setExperimentTypePropertyTypesInternal(
+ Set<ExperimentTypePropertyTypePE> experimentTypePropertyTypes) {
+ this.experimentTypePropertyTypes = experimentTypePropertyTypes;
+ }
+
+ @Transient
+ public Set<ExperimentTypePropertyTypePE> getExperimentTypePropertyTypes() {
+ return new UnmodifiableSetDecorator<ExperimentTypePropertyTypePE>(
+ getExperimentTypePropertyTypesInternal());
+ }
+
+ public final void setExperimentTypePropertyTypes(
+ final Iterable<ExperimentTypePropertyTypePE> childs) {
+ getExperimentTypePropertyTypesInternal().clear();
+ for (final ExperimentTypePropertyTypePE child : childs) {
+ addExperimentTypePropertyType(child);
+ }
+ }
+
+ public void addExperimentTypePropertyType(
+ final ExperimentTypePropertyTypePE child) {
+ final PropertyTypePE parent = child.getPropertyType();
+ if (parent != null) {
+ parent.getExperimentTypePropertyTypesInternal().remove(child);
+ }
+ child.setPropertyTypeInternal(this);
+ getExperimentTypePropertyTypesInternal().add(child);
+ }
+
+ @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL, mappedBy = "propertyTypeInternal")
+ private Set<MaterialTypePropertyTypePE> getMaterialTypePropertyTypesInternal() {
+ return materialTypePropertyTypes;
+ }
+
+ // Required by Hibernate.
+ @SuppressWarnings("unused")
+ private void setMaterialTypePropertyTypesInternal(
+ Set<MaterialTypePropertyTypePE> materialTypePropertyTypes) {
+ this.materialTypePropertyTypes = materialTypePropertyTypes;
+ }
+
+ @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL, mappedBy = "propertyTypeInternal")
+ private Set<DataSetTypePropertyTypePE> getDataSetTypePropertyTypesInternal() {
+ return dataSetTypePropertyTypes;
+ }
+
+ // Required by Hibernate.
+ @SuppressWarnings("unused")
+ private void setDataSetTypePropertyTypesInternal(
+ Set<DataSetTypePropertyTypePE> dataSetTypePropertyTypes) {
+ this.dataSetTypePropertyTypes = dataSetTypePropertyTypes;
+ }
+
+ @Transient
+ public Set<MaterialTypePropertyTypePE> getMaterialTypePropertyTypes() {
+ return new UnmodifiableSetDecorator<MaterialTypePropertyTypePE>(
+ getMaterialTypePropertyTypesInternal());
+ }
+
+ public final void setMaterialTypePropertyTypes(
+ final Iterable<MaterialTypePropertyTypePE> childs) {
+ getMaterialTypePropertyTypesInternal().clear();
+ for (final MaterialTypePropertyTypePE child : childs) {
+ addMaterialTypePropertyType(child);
+ }
+ }
+
+ public void addMaterialTypePropertyType(
+ final MaterialTypePropertyTypePE child) {
+ final PropertyTypePE parent = child.getPropertyType();
+ if (parent != null) {
+ parent.getMaterialTypePropertyTypesInternal().remove(child);
+ }
+ child.setPropertyTypeInternal(this);
+ getMaterialTypePropertyTypesInternal().add(child);
+ }
+
+ public void addDataSetTypePropertyType(DataSetTypePropertyTypePE child) {
+ final PropertyTypePE parent = child.getPropertyType();
+ if (parent != null) {
+ parent.getDataSetTypePropertyTypesInternal().remove(child);
+ }
+ child.setPropertyTypeInternal(this);
+ getDataSetTypePropertyTypesInternal().add(child);
+ }
+
+ @Transient
+ public Set<DataSetTypePropertyTypePE> getDataSetTypePropertyTypes() {
+ return new UnmodifiableSetDecorator<DataSetTypePropertyTypePE>(
+ getDataSetTypePropertyTypesInternal());
+ }
}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePropertyPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePropertyPE.java
index 5daa0847a98ac7ee3a4ec18de39b90e40fd937d9..d955f93de9e5daec1084dbfa42caf3f4877c5ca9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePropertyPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePropertyPE.java
@@ -88,12 +88,13 @@ public class SamplePropertyPE extends EntityPropertyPE
return getSample();
}
- /**
- * Sets the <var>sample</var> of this property.
- * <p>
- * <i>Do not use directly, instead, call {@link MaterialPE#addProperty(MaterialPropertyPE)} with
- * <code>this</code> object!</i>
- */
+ /**
+ * Sets the <var>sample</var> of this property.
+ * <p>
+ * <i>Do not use directly, instead, call
+ * {@link SamplePE#addProperty(SamplePropertyPE)} with <code>this</code>
+ * object!</i>
+ */
void setEntity(final IIdAndCodeHolder entity)
{
this.sample = (SamplePE) entity;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleTypePropertyTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleTypePropertyTypePE.java
index 543fa348f11b40851fabc0b62161dfce00676918..c3098da38dbe314f2bdd3d49f57e1efb0f4b5054 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleTypePropertyTypePE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleTypePropertyTypePE.java
@@ -43,73 +43,64 @@ import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
* @author Izabela Adamczyk
*/
@Entity
-@Table(name = TableNames.SAMPLE_TYPE_PROPERTY_TYPE_TABLE, uniqueConstraints =
- { @UniqueConstraint(columnNames =
- { ColumnNames.SAMPLE_TYPE_COLUMN, ColumnNames.PROPERTY_TYPE_COLUMN }) })
-public class SampleTypePropertyTypePE extends EntityTypePropertyTypePE
-{
- private static final long serialVersionUID = GenericSharedConstants.VERSION;
-
- public static final SampleTypePropertyTypePE[] EMPTY_ARRAY = new SampleTypePropertyTypePE[0];
-
- private boolean displayed;
-
- @Column(name = ColumnNames.IS_DISPLAYED)
- public boolean isDisplayed()
- {
- return displayed;
- }
-
- public void setDisplayed(final boolean displayed)
- {
- this.displayed = displayed;
- }
-
- @NotNull(message = ValidationMessages.SAMPLE_TYPE_NOT_NULL_MESSAGE)
- @ManyToOne(fetch = FetchType.EAGER, targetEntity = SampleTypePE.class)
- @JoinColumn(name = ColumnNames.SAMPLE_TYPE_COLUMN)
- private EntityTypePE getEntityTypeInternal()
- {
- return entityType;
- }
-
- //
- // EntityTypePropertyTypePE
- //
-
- @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL, mappedBy = "entityTypePropertyType", targetEntity = SamplePropertyPE.class)
- public Set<EntityPropertyPE> getPropertyValues()
- {
- return propertyValues;
- }
-
- @Transient
- public EntityTypePE getEntityType()
- {
- return getEntityTypeInternal();
- }
-
- @Override
- // This setter sets the bidirectional connection. That's why we must have an another internal
- // plain setter for Hibernate.
- public void setEntityType(EntityTypePE entityType)
- {
- ((SampleTypePE) entityType).addSampleTypePropertyType(this);
- }
-
- @SequenceGenerator(name = SequenceNames.SAMPLE_TYPE_PROPERTY_TYPE_SEQUENCE, sequenceName = SequenceNames.SAMPLE_TYPE_PROPERTY_TYPE_SEQUENCE, allocationSize = 1)
- @Id
- @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.SAMPLE_TYPE_PROPERTY_TYPE_SEQUENCE)
- @Column(insertable = false, updatable = false)
- public Long getId()
- {
- return id;
- }
-
- @Override
- public void setPropertyType(PropertyTypePE propertyType)
- {
- propertyType.addSampleTypePropertyType(this);
- }
+@Table(name = TableNames.SAMPLE_TYPE_PROPERTY_TYPE_TABLE, uniqueConstraints = { @UniqueConstraint(columnNames = {
+ ColumnNames.SAMPLE_TYPE_COLUMN, ColumnNames.PROPERTY_TYPE_COLUMN }) })
+public class SampleTypePropertyTypePE extends EntityTypePropertyTypePE {
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final SampleTypePropertyTypePE[] EMPTY_ARRAY = new SampleTypePropertyTypePE[0];
+
+ private boolean displayed;
+
+ @Column(name = ColumnNames.IS_DISPLAYED)
+ public boolean isDisplayed() {
+ return displayed;
+ }
+
+ public void setDisplayed(final boolean displayed) {
+ this.displayed = displayed;
+ }
+
+ @NotNull(message = ValidationMessages.SAMPLE_TYPE_NOT_NULL_MESSAGE)
+ @ManyToOne(fetch = FetchType.EAGER, targetEntity = SampleTypePE.class)
+ @JoinColumn(name = ColumnNames.SAMPLE_TYPE_COLUMN)
+ private EntityTypePE getEntityTypeInternal() {
+ return entityType;
+ }
+
+ //
+ // EntityTypePropertyTypePE
+ //
+
+ @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL, mappedBy = "entityTypePropertyType", targetEntity = SamplePropertyPE.class)
+ public Set<EntityPropertyPE> getPropertyValues() {
+ return propertyValues;
+ }
+
+ @Transient
+ public EntityTypePE getEntityType() {
+ return getEntityTypeInternal();
+ }
+
+ @Override
+ // This setter sets the bidirectional connection. That's why we must have an
+ // another internal
+ // plain setter for Hibernate.
+ public void setEntityType(EntityTypePE entityType) {
+ ((SampleTypePE) entityType).addSampleTypePropertyType(this);
+ }
+
+ @SequenceGenerator(name = SequenceNames.SAMPLE_TYPE_PROPERTY_TYPE_SEQUENCE, sequenceName = SequenceNames.SAMPLE_TYPE_PROPERTY_TYPE_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.SAMPLE_TYPE_PROPERTY_TYPE_SEQUENCE)
+ @Column(insertable = false, updatable = false)
+ public Long getId() {
+ return id;
+ }
+
+ @Override
+ public void setPropertyType(PropertyTypePE propertyType) {
+ propertyType.addSampleTypePropertyType(this);
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SequenceNames.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SequenceNames.java
index 7dac00f42914a7b7645cadb7ca1e14230d52f89a..b8a339d972ad07e31d88797ce76e9183d7f58393 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SequenceNames.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SequenceNames.java
@@ -21,84 +21,85 @@ package ch.systemsx.cisd.openbis.generic.shared.dto;
*
* @author Christian Ribeaud
*/
-public final class SequenceNames
-{
+public final class SequenceNames {
- public static final String CONTROLLED_VOCABULARY_SEQUENCE = "CONTROLLED_VOCABULARY_ID_SEQ";
+ public static final String CONTROLLED_VOCABULARY_SEQUENCE = "CONTROLLED_VOCABULARY_ID_SEQ";
- public static final String CONTROLLED_VOCABULARY_TERM_SEQUENCE = "CVTE_ID_SEQ";
+ public static final String CONTROLLED_VOCABULARY_TERM_SEQUENCE = "CVTE_ID_SEQ";
- public static final String DATA_SEQUENCE = "DATA_ID_SEQ";
+ public static final String DATA_SEQUENCE = "DATA_ID_SEQ";
- public static final String DATA_SET_RELATIONSHIP_SEQUENCE = "DATA_SET_RELATIONSHIP_ID_SEQ";
+ public static final String DATA_SET_RELATIONSHIP_SEQUENCE = "DATA_SET_RELATIONSHIP_ID_SEQ";
- public static final String DATA_SET_TYPE_SEQUENCE = "DATA_SET_TYPE_ID_SEQ";
+ public static final String DATA_SET_TYPE_SEQUENCE = "DATA_SET_TYPE_ID_SEQ";
- public static final String DATA_STORE_SEQUENCE = "DATA_STORE_ID_SEQ";
+ public static final String DATA_STORE_SEQUENCE = "DATA_STORE_ID_SEQ";
- public static final String DATA_TYPE_SEQUENCE = "DATA_TYPE_ID_SEQ";
+ public static final String DATA_TYPE_SEQUENCE = "DATA_TYPE_ID_SEQ";
- public static final String DATABASE_INSTANCE_SEQUENCE = "DATABASE_INSTANCE_ID_SEQ";
+ public static final String DATABASE_INSTANCE_SEQUENCE = "DATABASE_INSTANCE_ID_SEQ";
- public static final String EXPERIMENT_ATTACHMENT_CONTENT_SEQUENCE =
- "EXPERIMENT_ATTACHMENT_CONTENT_ID_SEQ";
+ public static final String EXPERIMENT_ATTACHMENT_CONTENT_SEQUENCE = "EXPERIMENT_ATTACHMENT_CONTENT_ID_SEQ";
- public static final String EXPERIMENT_ATTACHMENT_SEQUENCE = "EXPERIMENT_ATTACHMENT_ID_SEQ";
+ public static final String EXPERIMENT_ATTACHMENT_SEQUENCE = "EXPERIMENT_ATTACHMENT_ID_SEQ";
- public static final String EXPERIMENT_PROPERTY_SEQUENCE = "EXPERIMENT_PROPERTY_ID_SEQ";
+ public static final String EXPERIMENT_PROPERTY_SEQUENCE = "EXPERIMENT_PROPERTY_ID_SEQ";
- public static final String EXPERIMENT_SEQUENCE = "EXPERIMENT_ID_SEQ";
+ public static final String DATA_SET_PROPERTY_SEQUENCE = "DATA_SET_PROPERTY_ID_SEQ";
- public static final String EXPERIMENT_TYPE_PROPERTY_TYPE_SEQUENCE = "ETPT_ID_SEQ";
+ public static final String EXPERIMENT_SEQUENCE = "EXPERIMENT_ID_SEQ";
- public static final String EXPERIMENT_TYPE_SEQUENCE = "EXPERIMENT_TYPE_ID_SEQ";
+ public static final String EXPERIMENT_TYPE_PROPERTY_TYPE_SEQUENCE = "ETPT_ID_SEQ";
- public static final String FILE_FORMAT_TYPE_SEQUENCE = "FILE_FORMAT_TYPE_ID_SEQ";
+ public static final String DATA_SET_TYPE_PROPERTY_TYPE_SEQUENCE = "DSTPT_ID_SEQ";
- public static final String GROUP_SEQUENCE = "GROUP_ID_SEQ";
+ public static final String EXPERIMENT_TYPE_SEQUENCE = "EXPERIMENT_TYPE_ID_SEQ";
- public static final String INVALIDATION_SEQUENCE = "INVALIDATION_ID_SEQ";
+ public static final String FILE_FORMAT_TYPE_SEQUENCE = "FILE_FORMAT_TYPE_ID_SEQ";
- public static final String LOCATOR_TYPE_SEQUENCE = "LOCATOR_TYPE_ID_SEQ";
+ public static final String GROUP_SEQUENCE = "GROUP_ID_SEQ";
- public static final String MATERIAL_BATCH_SEQUENCE = "MATERIAL_BATCH_ID_SEQ";
+ public static final String INVALIDATION_SEQUENCE = "INVALIDATION_ID_SEQ";
- public static final String MATERIAL_PROPERTY_SEQUENCE = "MATERIAL_PROPERTY_ID_SEQ";
+ public static final String LOCATOR_TYPE_SEQUENCE = "LOCATOR_TYPE_ID_SEQ";
- public static final String MATERIAL_SEQUENCE = "MATERIAL_ID_SEQ";
+ public static final String MATERIAL_BATCH_SEQUENCE = "MATERIAL_BATCH_ID_SEQ";
- public static final String MATERIAL_TYPE_PROPERTY_TYPE_SEQUENCE = "MTPT_ID_SEQ";
+ public static final String MATERIAL_PROPERTY_SEQUENCE = "MATERIAL_PROPERTY_ID_SEQ";
- public static final String MATERIAL_TYPE_SEQUENCE = "MATERIAL_TYPE_ID_SEQ";
+ public static final String MATERIAL_SEQUENCE = "MATERIAL_ID_SEQ";
- public final static String PERSON_SEQUENCE = "PERSON_ID_SEQ";
+ public static final String MATERIAL_TYPE_PROPERTY_TYPE_SEQUENCE = "MTPT_ID_SEQ";
- public static final String PROCEDURE_SEQUENCE = "PROCEDURE_ID_SEQ";
+ public static final String MATERIAL_TYPE_SEQUENCE = "MATERIAL_TYPE_ID_SEQ";
- public static final String PROCEDURE_TYPE_SEQUENCE = "PROCEDURE_TYPE_ID_SEQ";
+ public final static String PERSON_SEQUENCE = "PERSON_ID_SEQ";
- public static final String PROJECT_SEQUENCE = "PROJECT_ID_SEQ";
+ public static final String PROCEDURE_SEQUENCE = "PROCEDURE_ID_SEQ";
- public static final String PROPERTY_TYPES_SEQUENCE = "PROPERTY_TYPE_ID_SEQ";
+ public static final String PROCEDURE_TYPE_SEQUENCE = "PROCEDURE_TYPE_ID_SEQ";
- public static final String ROLE_ASSIGNMENT_SEQUENCE = "ROLE_ASSIGNMENT_ID_SEQ";
+ public static final String PROJECT_SEQUENCE = "PROJECT_ID_SEQ";
- public static final String SAMPLE_INPUT_SEQUENCE = "SAMPLE_INPUT_ID_SEQ";
+ public static final String PROPERTY_TYPES_SEQUENCE = "PROPERTY_TYPE_ID_SEQ";
- public static final String SAMPLE_MATERIAL_BATCH_SEQUENCE = "SAMPLE_MATERIAL_BATCH_ID_SEQ";
+ public static final String ROLE_ASSIGNMENT_SEQUENCE = "ROLE_ASSIGNMENT_ID_SEQ";
- public static final String SAMPLE_PROPERTY_SEQUENCE = "SAMPLE_PROPERTY_ID_SEQ";
+ public static final String SAMPLE_INPUT_SEQUENCE = "SAMPLE_INPUT_ID_SEQ";
- public static final String SAMPLE_SEQUENCE = "SAMPLE_ID_SEQ";
+ public static final String SAMPLE_MATERIAL_BATCH_SEQUENCE = "SAMPLE_MATERIAL_BATCH_ID_SEQ";
- public static final String SAMPLE_TYPE_PROPERTY_TYPE_SEQUENCE = "STPT_ID_SEQ";
+ public static final String SAMPLE_PROPERTY_SEQUENCE = "SAMPLE_PROPERTY_ID_SEQ";
- public static final String SAMPLE_TYPE_SEQUENCE = "SAMPLE_TYPE_ID_SEQ";
-
- public static final String EVENT_SEQUENCE = "EVENT_ID_SEQ";
+ public static final String SAMPLE_SEQUENCE = "SAMPLE_ID_SEQ";
- private SequenceNames()
- {
- // Can not be instantiated.
- }
+ public static final String SAMPLE_TYPE_PROPERTY_TYPE_SEQUENCE = "STPT_ID_SEQ";
+
+ public static final String SAMPLE_TYPE_SEQUENCE = "SAMPLE_TYPE_ID_SEQ";
+
+ public static final String EVENT_SEQUENCE = "EVENT_ID_SEQ";
+
+ private SequenceNames() {
+ // Can not be instantiated.
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/TableNames.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/TableNames.java
index d054fe704cbf7874fea8c47a0c4f1a076fd915ed..56a25bf60a5cf17c027c118ad6241dec9955decc 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/TableNames.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/TableNames.java
@@ -37,6 +37,11 @@ public final class TableNames
public static final String DATA_STORES_TABLE = "data_stores";
public static final String DATA_TABLE = "data";
+
+ public static final String DATA_SET_PROPERTIES_TABLE = "data_set_properties";
+
+ public static final String DATA_SET_TYPE_PROPERTY_TYPE_TABLE =
+ "data_set_type_property_types";
public static final String DATA_TYPES_TABLE = "data_types";
@@ -48,7 +53,7 @@ public final class TableNames
public static final String EXPERIMENT_ATTACHMENTS_TABLE = "experiment_attachments";
public static final String EXPERIMENT_PROPERTIES_TABLE = "experiment_properties";
-
+
public static final String EXPERIMENT_TYPE_PROPERTY_TYPE_TABLE =
"experiment_type_property_types";
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ValidationMessages.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ValidationMessages.java
index 5119f194e1d9c4e562251afe21749ef4dcdc1900..8e564fe22c91c66af67ba79cbc527fb7c8c73e1e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ValidationMessages.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ValidationMessages.java
@@ -25,136 +25,159 @@ package ch.systemsx.cisd.openbis.generic.shared.dto;
*
* @author Christian Ribeaud
*/
-public final class ValidationMessages
-{
+public final class ValidationMessages {
- private static final String CAN_NOT_BE_NULL = " can not be null.";
+ private static final String CAN_NOT_BE_NULL = " can not be null.";
- private static final String LENGTH_PREFIX = "Given ";
+ private static final String LENGTH_PREFIX = "Given ";
- private static final String LENGTH_SUFFIX =
- " '%s' is too long (maximal length: {max} characters).";
+ private static final String LENGTH_SUFFIX = " '%s' is too long (maximal length: {max} characters).";
- public static final String ATTACHMENT_CONTENT_NOT_NULL_MESSAGE =
- "The content of the attachment" + CAN_NOT_BE_NULL;
+ public static final String ATTACHMENT_CONTENT_NOT_NULL_MESSAGE = "The content of the attachment"
+ + CAN_NOT_BE_NULL;
- public static final String CODE_LENGTH_MESSAGE =
- "Given code '%s' is either too short (minimal length: {min} character) "
- + "or too long (maximal length: {max} characters).";
+ public static final String CODE_LENGTH_MESSAGE = "Given code '%s' is either too short (minimal length: {min} character) "
+ + "or too long (maximal length: {max} characters).";
- public static final String CODE_NOT_NULL_MESSAGE = "Code" + CAN_NOT_BE_NULL;
+ public static final String CODE_NOT_NULL_MESSAGE = "Code" + CAN_NOT_BE_NULL;
- public static final String CODE_PATTERN_MESSAGE =
- "Given code '%s' contains illegal characters (allowed: A-Z, a-z, 0-9, _ and -)";
+ public static final String CODE_PATTERN_MESSAGE = "Given code '%s' contains illegal characters (allowed: A-Z, a-z, 0-9, _ and -)";
- public static final String DATA_SET_TYPE_NOT_NULL_MESSAGE = "Data set type" + CAN_NOT_BE_NULL;
+ public static final String DATA_SET_TYPE_NOT_NULL_MESSAGE = "Data set type"
+ + CAN_NOT_BE_NULL;
- public static final String DATA_TYPE_NOT_NULL_MESSAGE = "Data type" + CAN_NOT_BE_NULL;
+ public static final String DATA_TYPE_NOT_NULL_MESSAGE = "Data type"
+ + CAN_NOT_BE_NULL;
- public static final String DATABASE_INSTANCE_NOT_NULL_MESSAGE =
- "Database instance" + CAN_NOT_BE_NULL;
+ public static final String DATABASE_INSTANCE_NOT_NULL_MESSAGE = "Database instance"
+ + CAN_NOT_BE_NULL;
- public final static String DESCRIPTION_LENGTH_MESSAGE =
- LENGTH_PREFIX + "description" + LENGTH_SUFFIX;
+ public final static String DESCRIPTION_LENGTH_MESSAGE = LENGTH_PREFIX
+ + "description" + LENGTH_SUFFIX;
- public static final String DESCRIPTION_NOT_NULL_MESSAGE = "Description" + CAN_NOT_BE_NULL;
+ public static final String DESCRIPTION_NOT_NULL_MESSAGE = "Description"
+ + CAN_NOT_BE_NULL;
- public static final String DOWNLOAD_URL_NOT_NULL_MESSAGE = "Download URL" + CAN_NOT_BE_NULL;
+ public static final String DOWNLOAD_URL_NOT_NULL_MESSAGE = "Download URL"
+ + CAN_NOT_BE_NULL;
- public static final String EMAIL_EMAIL_MESSAGE = "Given email address '%s' is not a valid one.";
+ public static final String EMAIL_EMAIL_MESSAGE = "Given email address '%s' is not a valid one.";
- public static final String EMAIL_LENGTH_MESSAGE =
- LENGTH_PREFIX + "email address" + LENGTH_SUFFIX;
+ public static final String EMAIL_LENGTH_MESSAGE = LENGTH_PREFIX
+ + "email address" + LENGTH_SUFFIX;
- public static final String EXPERIMENT_NOT_NULL_MESSAGE = "Experiment " + CAN_NOT_BE_NULL;
+ public static final String EXPERIMENT_NOT_NULL_MESSAGE = "Experiment "
+ + CAN_NOT_BE_NULL;
- public static final String EXPERIMENT_TYPE_NOT_NULL_MESSAGE =
- "Experiment type" + CAN_NOT_BE_NULL;
+ public static final String EXPERIMENT_TYPE_NOT_NULL_MESSAGE = "Experiment type"
+ + CAN_NOT_BE_NULL;
- public static final String EXPERIMENT_TYPE_PROPERTY_TYPE_NOT_NULL_MESSAGE =
- "Experiment type - property type" + CAN_NOT_BE_NULL;
+ public static final String EXPERIMENT_TYPE_PROPERTY_TYPE_NOT_NULL_MESSAGE = "Experiment type - property type"
+ + CAN_NOT_BE_NULL;
- public static final String FILE_FORMAT_TYPE_NOT_NULL_MESSAGE =
- "File format type" + CAN_NOT_BE_NULL;
+ public static final String FILE_FORMAT_TYPE_NOT_NULL_MESSAGE = "File format type"
+ + CAN_NOT_BE_NULL;
- public static final String FILE_NAME_LENGTH_MESSAGE =
- LENGTH_PREFIX + "file name" + LENGTH_SUFFIX;
+ public static final String FILE_NAME_LENGTH_MESSAGE = LENGTH_PREFIX
+ + "file name" + LENGTH_SUFFIX;
- public static final String FILE_NAME_NOT_NULL_MESSAGE = "File name" + CAN_NOT_BE_NULL;
+ public static final String FILE_NAME_NOT_NULL_MESSAGE = "File name"
+ + CAN_NOT_BE_NULL;
- public static final String FIRST_NAME_LENGTH_MESSAGE =
- LENGTH_PREFIX + "first name" + LENGTH_SUFFIX;
+ public static final String FIRST_NAME_LENGTH_MESSAGE = LENGTH_PREFIX
+ + "first name" + LENGTH_SUFFIX;
- public static final String GROUP_NOT_NULL_MESSAGE = "Group" + CAN_NOT_BE_NULL;
+ public static final String GROUP_NOT_NULL_MESSAGE = "Group"
+ + CAN_NOT_BE_NULL;
- public static final String IS_COMPLETE_NOT_NULL_MESSAGE = "Complete flag" + CAN_NOT_BE_NULL;
+ public static final String IS_COMPLETE_NOT_NULL_MESSAGE = "Complete flag"
+ + CAN_NOT_BE_NULL;
- public static final String LABEL_LENGTH_MESSAGE = LENGTH_PREFIX + "label" + LENGTH_SUFFIX;
+ public static final String LABEL_LENGTH_MESSAGE = LENGTH_PREFIX + "label"
+ + LENGTH_SUFFIX;
- public static final String LABEL_NOT_NULL_MESSAGE = "Label" + CAN_NOT_BE_NULL;
+ public static final String LABEL_NOT_NULL_MESSAGE = "Label"
+ + CAN_NOT_BE_NULL;
- public static final String LAST_NAME_LENGTH_MESSAGE =
- LENGTH_PREFIX + "last name" + LENGTH_SUFFIX;
+ public static final String LAST_NAME_LENGTH_MESSAGE = LENGTH_PREFIX
+ + "last name" + LENGTH_SUFFIX;
- public static final String LOCATION_LENGTH_MESSAGE = LENGTH_PREFIX + "location" + LENGTH_SUFFIX;
+ public static final String LOCATION_LENGTH_MESSAGE = LENGTH_PREFIX
+ + "location" + LENGTH_SUFFIX;
- public static final String LOCATION_NOT_NULL_MESSAGE = "Location" + CAN_NOT_BE_NULL;
+ public static final String LOCATION_NOT_NULL_MESSAGE = "Location"
+ + CAN_NOT_BE_NULL;
- public static final String LOCATION_NOT_RELATIVE = "Location is not relative";
+ public static final String LOCATION_NOT_RELATIVE = "Location is not relative";
- public static final String CODE_NOT_USER_NAMESPACE =
- "Code does not contain '" + CodeConverter.USER_PROPERTY_PREFIX + "' prefix.";
+ public static final String CODE_NOT_USER_NAMESPACE = "Code does not contain '"
+ + CodeConverter.USER_PROPERTY_PREFIX + "' prefix.";
- public static final String LOCATOR_TYPE_NOT_NULL_MESSAGE = "Locator type" + CAN_NOT_BE_NULL;
+ public static final String LOCATOR_TYPE_NOT_NULL_MESSAGE = "Locator type"
+ + CAN_NOT_BE_NULL;
- public static final String MATERIAL_NOT_NULL_MESSAGE = "Material" + CAN_NOT_BE_NULL;
+ public static final String MATERIAL_NOT_NULL_MESSAGE = "Material"
+ + CAN_NOT_BE_NULL;
- public static final String MATERIAL_TYPE_NOT_NULL_MESSAGE = "Material type" + CAN_NOT_BE_NULL;
+ public static final String MATERIAL_TYPE_NOT_NULL_MESSAGE = "Material type"
+ + CAN_NOT_BE_NULL;
- public static final String MATERIAL_TYPE_PROPERTY_TYPE_NOT_NULL_MESSAGE =
- "Material type - property type" + CAN_NOT_BE_NULL;
+ public static final String MATERIAL_TYPE_PROPERTY_TYPE_NOT_NULL_MESSAGE = "Material type - property type"
+ + CAN_NOT_BE_NULL;
- public static final String PERSON_NOT_NULL_MESSAGE = "Person" + CAN_NOT_BE_NULL;
+ public static final String PERSON_NOT_NULL_MESSAGE = "Person"
+ + CAN_NOT_BE_NULL;
- public static final String PROCEDURE_NOT_NULL_MESSAGE = "Procedure" + CAN_NOT_BE_NULL;
+ public static final String PROCEDURE_NOT_NULL_MESSAGE = "Procedure"
+ + CAN_NOT_BE_NULL;
- public static final String PROJECT_NOT_NULL_MESSAGE = "Project" + CAN_NOT_BE_NULL;
+ public static final String PROJECT_NOT_NULL_MESSAGE = "Project"
+ + CAN_NOT_BE_NULL;
- public static final String PROPERTY_TYPE_NOT_NULL_MESSAGE = "Property type" + CAN_NOT_BE_NULL;
+ public static final String PROPERTY_TYPE_NOT_NULL_MESSAGE = "Property type"
+ + CAN_NOT_BE_NULL;
- public static final String ROLE_NOT_NULL_MESSAGE = "Role" + CAN_NOT_BE_NULL;
+ public static final String ROLE_NOT_NULL_MESSAGE = "Role" + CAN_NOT_BE_NULL;
- public static final String SAMPLE_TYPE_NOT_NULL_MESSAGE = "Sample type" + CAN_NOT_BE_NULL;
+ public static final String SAMPLE_TYPE_NOT_NULL_MESSAGE = "Sample type"
+ + CAN_NOT_BE_NULL;
- public static final String SAMPLE_TYPE_PROPERTY_TYPE_NOT_NULL_MESSAGE =
- "Sample type - property type" + CAN_NOT_BE_NULL;
+ public static final String SAMPLE_TYPE_PROPERTY_TYPE_NOT_NULL_MESSAGE = "Sample type - property type"
+ + CAN_NOT_BE_NULL;
- public static final String STORAGE_FORMAT_NOT_NULL_MESSAGE = "Storage format" + CAN_NOT_BE_NULL;
+ public static final String STORAGE_FORMAT_NOT_NULL_MESSAGE = "Storage format"
+ + CAN_NOT_BE_NULL;
- public static final String USER_ID_LENGTH_MESSAGE = LENGTH_PREFIX + "user id" + LENGTH_SUFFIX;
+ public static final String USER_ID_LENGTH_MESSAGE = LENGTH_PREFIX
+ + "user id" + LENGTH_SUFFIX;
- public static final String USER_ID_NOT_NULL_MESSAGE = "User id" + CAN_NOT_BE_NULL;
+ public static final String USER_ID_NOT_NULL_MESSAGE = "User id"
+ + CAN_NOT_BE_NULL;
- public static final String UUID_NOT_NULL_MESSAGE = "UUID" + CAN_NOT_BE_NULL;
+ public static final String UUID_NOT_NULL_MESSAGE = "UUID" + CAN_NOT_BE_NULL;
- public static final String VALUE_LENGTH_MESSAGE = LENGTH_PREFIX + "value" + LENGTH_SUFFIX;
+ public static final String VALUE_LENGTH_MESSAGE = LENGTH_PREFIX + "value"
+ + LENGTH_SUFFIX;
- public static final String VALUE_NOT_NULL_MESSAGE = "Value" + CAN_NOT_BE_NULL;
+ public static final String VALUE_NOT_NULL_MESSAGE = "Value"
+ + CAN_NOT_BE_NULL;
- public static final String VERSION_NOT_NULL_MESSAGE = "Version" + CAN_NOT_BE_NULL;
+ public static final String VERSION_NOT_NULL_MESSAGE = "Version"
+ + CAN_NOT_BE_NULL;
- public static final String VOCABULARY_NOT_NULL_MESSAGE = "Vocabulary" + CAN_NOT_BE_NULL;
+ public static final String VOCABULARY_NOT_NULL_MESSAGE = "Vocabulary"
+ + CAN_NOT_BE_NULL;
- public static final String VALID_USER_CODE_DESCRIPTION =
- "User code must not be empty and must contain only allowed characters: "
- + "letters, digits, '_', '.', '-', '@'. Note that whitespaces are not allowed.";
+ public static final String VALID_USER_CODE_DESCRIPTION = "User code must not be empty and must contain only allowed characters: "
+ + "letters, digits, '_', '.', '-', '@'. Note that whitespaces are not allowed.";
- public static final String EVENT_TYPE_NOT_NULL_MESSAGE = "Event Type" + CAN_NOT_BE_NULL;
+ public static final String EVENT_TYPE_NOT_NULL_MESSAGE = "Event Type"
+ + CAN_NOT_BE_NULL;
- public static final String DATA_NOT_NULL_MESSAGE = "Data " + CAN_NOT_BE_NULL;
+ public static final String DATA_NOT_NULL_MESSAGE = "Data "
+ + CAN_NOT_BE_NULL;
- private ValidationMessages()
- {
- // Can not be instantiated.
- }
+ private ValidationMessages() {
+ // Can not be instantiated.
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityKind.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityKind.java
index 5380544775b5c62cdfe78f7f1b9bc7e08c91c62c..1a2777950a2a1f17c2effb99f56e01f099248016 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityKind.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityKind.java
@@ -16,6 +16,10 @@
package ch.systemsx.cisd.openbis.generic.shared.dto.properties;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetPropertyPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityPropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePropertyTypePE;
@@ -37,70 +41,65 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePropertyTypePE;
*
* @author Franz-Josef Elmer
*/
-public enum EntityKind
-{
- MATERIAL("material", MaterialPE.class, MaterialTypePE.class, MaterialTypePropertyTypePE.class,
- MaterialPropertyPE.class),
-
- EXPERIMENT("experiment", ExperimentPE.class, ExperimentTypePE.class,
- ExperimentTypePropertyTypePE.class, ExperimentPropertyPE.class),
-
- SAMPLE("sample", SamplePE.class, SampleTypePE.class, SampleTypePropertyTypePE.class,
- SamplePropertyPE.class);
-
- private final String entityLabel;
-
- private transient final Class<?> entityClass;
-
- private transient final Class<?> typeClass;
-
- private transient final Class<?> assignmentClass;
-
- private transient final Class<?> propertyClass;
-
- private EntityKind(final String entityLabel, final Class<?> entityClass,
- final Class<?> typeClass, final Class<?> assignmentClass, Class<?> propertyClass)
- {
- this.entityLabel = entityLabel;
- this.entityClass = entityClass;
- this.typeClass = typeClass;
- this.assignmentClass = assignmentClass;
- this.propertyClass = propertyClass;
- }
-
- @SuppressWarnings("unchecked")
- private final static <T> Class<T> cast(final Class<?> clazz)
- {
- return (Class<T>) clazz;
- }
-
- public final String getLabel()
- {
- return entityLabel;
- }
-
- public final <T extends EntityTypePE> Class<T> getTypeClass()
- {
- return cast(typeClass);
- }
-
- public final <T extends EntityTypePropertyTypePE> Class<T> getEntityTypePropertyTypeAssignmentClass()
- {
- return cast(assignmentClass);
- }
-
- public final <T extends EntityPropertyPE> Class<T> getEntityPropertyClass()
- {
- return cast(propertyClass);
- }
-
- public final <T> Class<T> getEntityClass()
- {
- return cast(entityClass);
- }
-
- public final String getEntityTypeFieldName()
- {
- return entityLabel + "Type";
- }
+public enum EntityKind {
+ MATERIAL("material", MaterialPE.class, MaterialTypePE.class,
+ MaterialTypePropertyTypePE.class, MaterialPropertyPE.class),
+
+ EXPERIMENT("experiment", ExperimentPE.class, ExperimentTypePE.class,
+ ExperimentTypePropertyTypePE.class, ExperimentPropertyPE.class),
+
+ SAMPLE("sample", SamplePE.class, SampleTypePE.class,
+ SampleTypePropertyTypePE.class, SamplePropertyPE.class),
+
+ DATA_SET("dataSet", DataPE.class, DataSetTypePE.class,
+ DataSetTypePropertyTypePE.class, DataSetPropertyPE.class);
+
+ private final String entityLabel;
+
+ private transient final Class<?> entityClass;
+
+ private transient final Class<?> typeClass;
+
+ private transient final Class<?> assignmentClass;
+
+ private transient final Class<?> propertyClass;
+
+ private EntityKind(final String entityLabel, final Class<?> entityClass,
+ final Class<?> typeClass, final Class<?> assignmentClass,
+ Class<?> propertyClass) {
+ this.entityLabel = entityLabel;
+ this.entityClass = entityClass;
+ this.typeClass = typeClass;
+ this.assignmentClass = assignmentClass;
+ this.propertyClass = propertyClass;
+ }
+
+ @SuppressWarnings("unchecked")
+ private final static <T> Class<T> cast(final Class<?> clazz) {
+ return (Class<T>) clazz;
+ }
+
+ public final String getLabel() {
+ return entityLabel;
+ }
+
+ public final <T extends EntityTypePE> Class<T> getTypeClass() {
+ return cast(typeClass);
+ }
+
+ public final <T extends EntityTypePropertyTypePE> Class<T> getEntityTypePropertyTypeAssignmentClass() {
+ return cast(assignmentClass);
+ }
+
+ public final <T extends EntityPropertyPE> Class<T> getEntityPropertyClass() {
+ return cast(propertyClass);
+ }
+
+ public final <T> Class<T> getEntityClass() {
+ return cast(entityClass);
+ }
+
+ public final String getEntityTypeFieldName() {
+ return entityLabel + "Type";
+ }
}
diff --git a/openbis/source/java/hibernateContext.xml b/openbis/source/java/hibernateContext.xml
index 501bb209bb45c4272d7f9e3e0168c2290a2fe341..2ecfa4b9e28b18b9c848c75db6b6d721b0b43522 100644
--- a/openbis/source/java/hibernateContext.xml
+++ b/openbis/source/java/hibernateContext.xml
@@ -70,6 +70,9 @@
<value>ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE</value>
<value>ch.systemsx.cisd.openbis.generic.shared.dto.MaterialBatchPE</value>
+
+ <value>ch.systemsx.cisd.openbis.generic.shared.dto.DataSetPropertyPE</value>
+ <value>ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePropertyTypePE</value>
</list>
</property>
<!--
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/HibernateSearchDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/HibernateSearchDAOTest.java
index 8e72b2d138095e930687651bf2d397a080306071..dd5f78ab08502a70999669a4146e0ca1e9b41e07 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/HibernateSearchDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/HibernateSearchDAOTest.java
@@ -46,13 +46,13 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetSearchCriterion;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetSearchField;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetSearchFieldKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchCriteriaConnection;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetSearchHitDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityPropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.HierarchyType;
import ch.systemsx.cisd.openbis.generic.shared.dto.IEntityPropertiesHolder;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
@@ -239,7 +239,7 @@ public final class HibernateSearchDAOTest extends AbstractDAOTest
return codes;
}
- private List<DataSetSearchHitDTO> searchForDatasets(DataSetSearchCriteria criteria)
+ private List<ExternalDataPE> searchForDatasets(DataSetSearchCriteria criteria)
{
final IHibernateSearchDAO hibernateSearchDAO = daoFactory.getHibernateSearchDAO();
return hibernateSearchDAO.searchForDataSets(criteria);
@@ -250,11 +250,11 @@ public final class HibernateSearchDAOTest extends AbstractDAOTest
private void assertCorrectDatasetsFound(DataSetSearchCriteria criteria,
DSLoc... expectedLocations)
{
- List<DataSetSearchHitDTO> dataSets = searchForDatasets(criteria);
+ List<ExternalDataPE> dataSets = searchForDatasets(criteria);
AssertJUnit.assertEquals(expectedLocations.length, dataSets.size());
- for (DataSetSearchHitDTO dataSet : dataSets)
+ for (ExternalDataPE dataSet : dataSets)
{
- assertContains(expectedLocations, dataSet.getDataSet().getLocation());
+ assertContains(expectedLocations, dataSet.getLocation());
}
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java.expected b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java.expected
index f06f868779a27c6e3f85659ff37057194c6974ef..b81a82be2b514c863f1f54cd9391b5e990715afd 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java.expected
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java.expected
@@ -29,6 +29,7 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCo
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.GroupIdentifierPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.NullableGroupIdentifierPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.SampleOwnerIdentifierPredicate;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.ExternalDataValidator;
import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.GroupValidator;
import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.MatchingEntityValidator;
import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.ProjectValidator;
@@ -43,7 +44,7 @@ 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 ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetSearchHitDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
@@ -75,315 +76,346 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
*
* @author Franz-Josef Elmer
*/
-public interface ICommonServer extends IServer
-{
- /**
- * Returns all groups which belong to the specified database instance. *
- *
- * @return a sorted list of {@link GroupPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- @ReturnValueFilter(validatorClass = GroupValidator.class)
- public List<GroupPE> listGroups(String sessionToken, DatabaseInstanceIdentifier identifier);
-
- /**
- * Registers a new group with specified code and optional description and group leader ID.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerGroup(String sessionToken, String groupCode, String descriptionOrNull,
- String groupLeaderOrNull);
-
- /**
- * Returns all persons from current instance.
- *
- * @return a sorted list of {@link PersonPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<PersonPE> listPersons(String sessionToken);
-
- /**
- * Returns all projects.
- *
- * @return a sorted list of {@link ProjectPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- @ReturnValueFilter(validatorClass = ProjectValidator.class)
- public List<ProjectPE> listProjects(String sessionToken);
-
- /**
- * Registers a new person.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerPerson(String sessionToken, String userID);
-
- /**
- * Returns a list of all roles.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.GROUP_ADMIN)
- public List<RoleAssignmentPE> listRoles(String sessionToken);
-
- /**
- * Registers a new group role.
- */
- @Transactional
- @RolesAllowed(RoleSet.GROUP_ADMIN)
- public void registerGroupRole(String sessionToken, RoleCode roleCode,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class)
- GroupIdentifier identifier, String person);
-
- /**
- * Registers a new instance role.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerInstanceRole(String sessionToken, RoleCode roleCode, String person);
-
- /**
- * Deletes role described by given role code, group identifier and user id.
- */
- @Transactional
- @RolesAllowed(RoleSet.GROUP_ADMIN)
- public void deleteGroupRole(String sessionToken, RoleCode roleCode,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class)
- GroupIdentifier groupIdentifier, String person);
-
- /**
- * Deletes role described by given role code and user id.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void deleteInstanceRole(String sessionToken, RoleCode roleCode, String person);
-
- /**
- * Lists sample types which are appropriate for listing.
- *
- * @return a sorted list of {@link SampleTypePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<SampleTypePE> listSampleTypes(String sessionToken);
-
- /**
- * Lists samples using given configuration.
- *
- * @return a sorted list of {@link SamplePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<SamplePE> listSamples(final String sessionToken,
- final ListSampleCriteriaDTO criteria);
-
- /**
- * Lists experiments.
- *
- * @return a sorted list of {@link ExperimentPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<ExperimentPE> listExperiments(final String sessionToken,
- ExperimentTypePE experimentType,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class)
- ProjectIdentifier project);
-
- /**
- * For given {@link SampleIdentifier} returns the corresponding list of {@link ExternalDataPE}.
- *
- * @return a sorted list of {@link ExternalDataPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<ExternalDataPE> listExternalData(final String sessionToken,
- @AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class)
- final SampleIdentifier identifier);
-
- /**
- * For given {@link ExperimentIdentifier} returns the corresponding list of
- * {@link ExternalDataPE}.
- *
- * @return a sorted list of {@link ExternalDataPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<ExternalDataPE> listExternalData(final String sessionToken,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class)
- final ExperimentIdentifier identifier);
-
- /**
- * Performs an <i>Hibernate Search</i> based on given parameters.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- @ReturnValueFilter(validatorClass = MatchingEntityValidator.class)
- public List<SearchHit> listMatchingEntities(final String sessionToken,
- final SearchableEntity[] searchableEntities, final String queryText);
-
- /**
- * List experiment types.
- *
- * @return a sorted list of {@link ExperimentTypePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<ExperimentTypePE> listExperimentTypes(String sessionToken);
-
- /**
- * List property types.
- *
- * @return a sorted list of {@link PropertyTypePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<PropertyTypePE> listPropertyTypes(final String sessionToken);
-
- /**
- * Lists data types.
- *
- * @return a sorted list of {@link DataTypePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<DataTypePE> listDataTypes(final String sessionToken);
-
- /**
- * Lists vocabularies.
- *
- * @return a sorted list of {@link VocabularyPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<VocabularyPE> listVocabularies(final String sessionToken, final boolean withTerms,
- boolean excludeInternal);
-
- /**
- * Registers given {@link PropertyType}.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerPropertyType(final String sessionToken, final PropertyType propertyType);
-
- /**
- * Assigns property type to entity type.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public String assignPropertyType(final String sessionToken, final EntityKind entityKind,
- final String propertyTypeCode, final String entityTypeCode, final boolean isMandatory,
- final String defaultValue);
-
- /**
- * Registers given {@link Vocabulary}.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerVocabulary(final String sessionToken, final Vocabulary vocabulary);
-
- /**
- * Registers new project.
- */
- @Transactional
- @RolesAllowed(RoleSet.GROUP_ADMIN)
- public void registerProject(String sessionToken,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class)
- ProjectIdentifier projectIdentifier, String description, String leaderId);
-
- /**
- * Performs an <i>Hibernate Search</i> based on given parameters.
- */
- // TODO 2009-03-16 FJE, @ReturnValueFilter missing
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<DataSetSearchHitDTO> searchForDataSets(String sessionToken,
- DataSetSearchCriteria criteria);
-
- /**
- * List material types.
- *
- * @return a sorted list of {@link MaterialTypePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<MaterialTypePE> listMaterialTypes(String sessionToken);
-
- /**
- * Lists materials.
- *
- * @return a sorted list of {@link MaterialPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<MaterialPE> listMaterials(String sessionToken, MaterialTypePE materialType);
-
- /**
- * Creates a new material type.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerMaterialType(String sessionToken, MaterialType entityType);
-
- /**
- * Creates a new sample type.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerSampleType(String sessionToken, SampleType entityType);
-
- /**
- * Creates a new experiment type.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerExperimentType(String sessionToken, ExperimentType entityType);
-
- /**
- * Deletes specified data sets.
- */
- @Transactional
- @RolesAllowed(RoleSet.GROUP_ADMIN)
- public void deleteDataSets(String sessionToken,
- @AuthorizationGuard(guardClass = DataSetCodePredicate.class)
- List<String> dataSetCodes, String reason);
-
- /**
- * Saves changed experiment.
- */
- @Transactional
- @RolesAllowed(RoleSet.USER)
- public void editExperiment(String sessionToken,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class)
- ExperimentIdentifier experimentIdentifier, List<ExperimentProperty> properties,
- List<AttachmentPE> attachments,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class)
- ProjectIdentifier newProjectIdentifier, Date version);
-
- /**
- * Saves changed material.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void editMaterial(String sessionToken, MaterialIdentifier identifier,
- List<MaterialProperty> properties, Date version);
-
- /**
- * Saves changed sample.
- */
- @Transactional
- @RolesAllowed(RoleSet.USER)
- public void editSample(String sessionToken,
- @AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class)
- SampleIdentifier identifier, List<SampleProperty> properties,
- @AuthorizationGuard(guardClass = NullableGroupIdentifierPredicate.class)
- ExperimentIdentifier experimentIdentifierOrNull, Date version);
-
- /** Lists vocabulary terms of a given vocabulary. Includes terms usage statistics. */
- @Transactional
- @RolesAllowed(RoleSet.USER)
- public List<VocabularyTermWithStats> listVocabularyTerms(String sessionToken,
- Vocabulary vocabulary);
+public interface ICommonServer extends IServer {
+ /**
+ * Returns all groups which belong to the specified database instance. *
+ *
+ * @return a sorted list of {@link GroupPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ @ReturnValueFilter(validatorClass = GroupValidator.class)
+ public List<GroupPE> listGroups(String sessionToken,
+ DatabaseInstanceIdentifier identifier);
+
+ /**
+ * Registers a new group with specified code and optional description and
+ * group leader ID.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerGroup(String sessionToken, String groupCode,
+ String descriptionOrNull, String groupLeaderOrNull);
+
+ /**
+ * Returns all persons from current instance.
+ *
+ * @return a sorted list of {@link PersonPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<PersonPE> listPersons(String sessionToken);
+
+ /**
+ * Returns all projects.
+ *
+ * @return a sorted list of {@link ProjectPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ @ReturnValueFilter(validatorClass = ProjectValidator.class)
+ public List<ProjectPE> listProjects(String sessionToken);
+
+ /**
+ * Registers a new person.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerPerson(String sessionToken, String userID);
+
+ /**
+ * Returns a list of all roles.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.GROUP_ADMIN)
+ public List<RoleAssignmentPE> listRoles(String sessionToken);
+
+ /**
+ * Registers a new group role.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.GROUP_ADMIN)
+ public void registerGroupRole(
+ String sessionToken,
+ RoleCode roleCode,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) GroupIdentifier identifier,
+ String person);
+
+ /**
+ * Registers a new instance role.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerInstanceRole(String sessionToken, RoleCode roleCode,
+ String person);
+
+ /**
+ * Deletes role described by given role code, group identifier and user id.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.GROUP_ADMIN)
+ public void deleteGroupRole(
+ String sessionToken,
+ RoleCode roleCode,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) GroupIdentifier groupIdentifier,
+ String person);
+
+ /**
+ * Deletes role described by given role code and user id.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void deleteInstanceRole(String sessionToken, RoleCode roleCode,
+ String person);
+
+ /**
+ * Lists sample types which are appropriate for listing.
+ *
+ * @return a sorted list of {@link SampleTypePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<SampleTypePE> listSampleTypes(String sessionToken);
+
+ /**
+ * Lists samples using given configuration.
+ *
+ * @return a sorted list of {@link SamplePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<SamplePE> listSamples(final String sessionToken,
+ final ListSampleCriteriaDTO criteria);
+
+ /**
+ * Lists experiments.
+ *
+ * @return a sorted list of {@link ExperimentPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<ExperimentPE> listExperiments(
+ final String sessionToken,
+ ExperimentTypePE experimentType,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) ProjectIdentifier project);
+
+ /**
+ * For given {@link SampleIdentifier} returns the corresponding list of
+ * {@link ExternalDataPE}.
+ *
+ * @return a sorted list of {@link ExternalDataPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<ExternalDataPE> listExternalData(
+ final String sessionToken,
+ @AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class) final SampleIdentifier identifier);
+
+ /**
+ * For given {@link ExperimentIdentifier} returns the corresponding list of
+ * {@link ExternalDataPE}.
+ *
+ * @return a sorted list of {@link ExternalDataPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<ExternalDataPE> listExternalData(
+ final String sessionToken,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) final ExperimentIdentifier identifier);
+
+ /**
+ * Performs an <i>Hibernate Search</i> based on given parameters.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ @ReturnValueFilter(validatorClass = MatchingEntityValidator.class)
+ public List<SearchHit> listMatchingEntities(final String sessionToken,
+ final SearchableEntity[] searchableEntities, final String queryText);
+
+ /**
+ * List experiment types.
+ *
+ * @return a sorted list of {@link ExperimentTypePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<ExperimentTypePE> listExperimentTypes(String sessionToken);
+
+ /**
+ * List property types.
+ *
+ * @return a sorted list of {@link PropertyTypePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<PropertyTypePE> listPropertyTypes(final String sessionToken);
+
+ /**
+ * Lists data types.
+ *
+ * @return a sorted list of {@link DataTypePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<DataTypePE> listDataTypes(final String sessionToken);
+
+ /**
+ * Lists vocabularies.
+ *
+ * @return a sorted list of {@link VocabularyPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<VocabularyPE> listVocabularies(final String sessionToken,
+ final boolean withTerms, boolean excludeInternal);
+
+ /**
+ * Registers given {@link PropertyType}.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerPropertyType(final String sessionToken,
+ final PropertyType propertyType);
+
+ /**
+ * Assigns property type to entity type.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public String assignPropertyType(final String sessionToken,
+ final EntityKind entityKind, final String propertyTypeCode,
+ final String entityTypeCode, final boolean isMandatory,
+ final String defaultValue);
+
+ /**
+ * Registers given {@link Vocabulary}.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerVocabulary(final String sessionToken,
+ final Vocabulary vocabulary);
+
+ /**
+ * Registers new project.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.GROUP_ADMIN)
+ public void registerProject(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) ProjectIdentifier projectIdentifier,
+ String description, String leaderId);
+
+ /**
+ * Performs an <i>Hibernate Search</i> based on given parameters.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ @ReturnValueFilter(validatorClass = ExternalDataValidator.class)
+ public List<ExternalDataPE> searchForDataSets(String sessionToken,
+ DataSetSearchCriteria criteria);
+
+ /**
+ * List material types.
+ *
+ * @return a sorted list of {@link MaterialTypePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<MaterialTypePE> listMaterialTypes(String sessionToken);
+
+ /**
+ * Lists materials.
+ *
+ * @return a sorted list of {@link MaterialPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<MaterialPE> listMaterials(String sessionToken,
+ MaterialTypePE materialType);
+
+ /**
+ * Creates a new material type.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerMaterialType(String sessionToken,
+ MaterialType entityType);
+
+ /**
+ * Creates a new sample type.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerSampleType(String sessionToken, SampleType entityType);
+
+ /**
+ * Creates a new experiment type.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerExperimentType(String sessionToken,
+ ExperimentType entityType);
+
+ /**
+ * Deletes specified data sets.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.GROUP_ADMIN)
+ public void deleteDataSets(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodePredicate.class) List<String> dataSetCodes,
+ String reason);
+
+ /**
+ * Saves changed experiment.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.USER)
+ public void editExperiment(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) ExperimentIdentifier experimentIdentifier,
+ List<ExperimentProperty> properties,
+ List<AttachmentPE> attachments,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) ProjectIdentifier newProjectIdentifier,
+ Date version);
+
+ /**
+ * Saves changed material.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void editMaterial(String sessionToken,
+ MaterialIdentifier identifier, List<MaterialProperty> properties,
+ Date version);
+
+ /**
+ * Saves changed sample.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.USER)
+ public void editSample(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class) SampleIdentifier identifier,
+ List<SampleProperty> properties,
+ @AuthorizationGuard(guardClass = NullableGroupIdentifierPredicate.class) ExperimentIdentifier experimentIdentifierOrNull,
+ Date version);
+
+ /**
+ * Lists vocabulary terms of a given vocabulary. Includes terms usage
+ * statistics.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.USER)
+ public List<VocabularyTermWithStats> listVocabularyTerms(
+ String sessionToken, Vocabulary vocabulary);
+
+ /**
+ * List data set types.
+ *
+ * @return a sorted list of {@link DataSetTypePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<DataSetTypePE> listDataSetTypes(String sessionToken);
}