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 b27e94c5e64201c70b0fc573959be7ea4a203325..4ecb7f7083451a23a0fa9ac8f101fd34cea2ba30 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
@@ -16,28 +16,6 @@
package ch.systemsx.cisd.openbis.generic.server;
-import java.net.UnknownHostException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.Date;
-import java.util.EnumMap;
-import java.util.EnumSet;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedHashSet;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-
-import org.springframework.dao.DataAccessException;
-import org.springframework.dao.DataIntegrityViolationException;
-
import ch.systemsx.cisd.authentication.IAuthenticationService;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
@@ -62,83 +40,15 @@ import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.AbstractT
import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.AbstractTechIdCollectionPredicate.SpaceTechIdCollectionPredicate;
import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.AbstractTechIdPredicate.ExperimentTechIdPredicate;
import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.AbstractTechIdPredicate.ProjectTechIdPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.BasicEntityDescriptionPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.DataSetCodeCollectionPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.DataSetCodePredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.DataSetTechIdPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.DataSetUpdatesPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.DeletionTechIdCollectionPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.ExperimentUpdatesPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.ListSampleCriteriaPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.ProjectIdentifierPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.ProjectPermIdStringPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.ProjectUpdatesPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.RevertDeletionPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.SampleTechIdCollectionReadWritePredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.SampleTechIdPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.SampleTechIdReadWritePredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.SampleUpdatesPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.SpaceIdentifierPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.SpaceUpdatesPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.DeletionValidator;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.EntityHistoryValidator;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.ExperimentByIdentiferValidator;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.ExpressionValidator;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.ExternalDataValidator;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.MatchingEntityValidator;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.ProjectValidator;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SampleValidator;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SearchDomainSearchResultValidator;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SimpleSpaceOrProjectValidator;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.*;
+import ch.systemsx.cisd.openbis.generic.server.authorization.validator.*;
import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.DataAccessExceptionTranslator;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.EntityCodeGenerator;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.EntityTypeBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IAttachmentBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IAuthorizationGroupBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.ICorePluginTable;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataSetTable;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataStoreBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IDeletedDataSetTable;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IDeletionTable;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IEntityTypeBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IEntityTypePropertyTypeBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentTable;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IGridCustomFilterOrColumnBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialTable;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IMetaprojectBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IProjectBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IPropertyTypeBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IPropertyTypeTable;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IRoleAssignmentTable;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleTable;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IScriptBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.ISearchDomainSearcher;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.ISpaceBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.ITrashBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IVocabularyBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IVocabularyTermBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.*;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.DatabaseContextUtils;
import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataStoreDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDeletionDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityHistoryDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataManagementSystemDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IFileFormatTypeDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IMetaprojectDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IRoleAssignmentDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.RelatedEntityFinder;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.*;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.HibernateSearchDataProvider;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.SampleDataAccessExceptionTranslator;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.DynamicPropertyEvaluator;
@@ -155,14 +65,9 @@ import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.impl.MasterDataRegi
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
import ch.systemsx.cisd.openbis.generic.shared.IOpenBisSessionManager;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomain;
-import ch.systemsx.cisd.openbis.generic.shared.basic.BasicEntityInformationHolder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.CodeConverter;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IIdHolder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IdentifierExtractor;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.*;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewDataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.*;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.IManagedInputWidgetDescription;
@@ -171,88 +76,23 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.IManagedUiAction;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.IPerson;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.metaproject.IMetaprojectId;
import ch.systemsx.cisd.openbis.generic.shared.coreplugin.ICorePluginResourceLoader;
-import ch.systemsx.cisd.openbis.generic.shared.dto.AbstractEntityPropertyHistoryPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentHolderPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.AuthorizationGroupPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DeletionPE;
-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;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataManagementSystemPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.FileFormatTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.GridCustomFilterPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.IEntityInformationHolderDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.IEntityInformationWithPropertiesHolder;
-import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialUpdateDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectAssignmentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewRoleAssignment;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ScriptPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SearchableEntity;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyTermWithStats;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.*;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.*;
import ch.systemsx.cisd.openbis.generic.shared.hotdeploy_plugins.api.IEntityAdaptor;
import ch.systemsx.cisd.openbis.generic.shared.managed_property.IManagedPropertyEvaluatorFactory;
import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.IManagedPropertyEvaluator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.AttachmentTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.AuthorizationGroupTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTypeTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.DataStoreServiceTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.DataStoreTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.DataTypeTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.DtoConverters;
-import ch.systemsx.cisd.openbis.generic.shared.translator.EntityHistoryTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.EntityTypeTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ExternalDataManagementSystemTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.*;
import ch.systemsx.cisd.openbis.generic.shared.translator.GridCustomExpressionTranslator.GridCustomFilterTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.MaterialTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.MaterialTypeTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.MetaprojectTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.PersonTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ProjectTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.PropertyTypeTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.RoleAssignmentTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTypeTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ScriptTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.SpaceTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.TypeTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTermTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTranslator;
import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
import ch.systemsx.cisd.openbis.generic.shared.util.RelationshipUtils;
+import org.springframework.dao.DataAccessException;
+import org.springframework.dao.DataIntegrityViolationException;
+
+import java.net.UnknownHostException;
+import java.util.*;
+import java.util.Map.Entry;
public final class CommonServer extends AbstractCommonServer<ICommonServerForInternalUse> implements
ICommonServerForInternalUse
@@ -923,7 +763,7 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
{
extractAssignments(result, entityTypeOrNull, propertyType);
}
- Collections.sort(result);
+ result.sort(null);
return result;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/BasicConstant.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/BasicConstant.java
index 80ab6d91d7c923d2ad6069ac23315d95be30e87b..3416d16c13051a66faa0542a7bdfd38f2f0a08c1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/BasicConstant.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/BasicConstant.java
@@ -93,7 +93,7 @@ public class BasicConstant
/**
* Canonical date format pattern used to render dates in GUI in a more readable way.
*/
- public static final String RENDERED_CANONICAL_DATE_FORMAT_PATTERN = "yyyy-MM-dd HH:mm:ss ZZZZ";
+ public static final String RENDERED_CANONICAL_DATE_FORMAT_PATTERN = "yyyy-MM-dd HH:mm:ss ZZZ";
/**
* Date format which does not include time zone.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/SimplePropertyValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/SimplePropertyValidator.java
index b51495b33dec850f4d040ebc228482c1c6332b30..ff379c7812a5816b7be73c936ea2439f8bc248d7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/SimplePropertyValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/SimplePropertyValidator.java
@@ -18,7 +18,6 @@ package ch.systemsx.cisd.openbis.generic.shared.util;
import java.text.ParseException;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.Date;
import java.util.EnumMap;
import java.util.List;
@@ -52,6 +51,10 @@ public class SimplePropertyValidator
SECONDS_DATE_PATTERN("yyyy-MM-dd HH:mm:ss"),
+ ISO_MINUTES_DATE_PATTERN("yyyy-MM-dd'T'HH:mm"),
+
+ ISO_SECONDS_DATE_PATTERN("yyyy-MM-dd'T'HH:mm:ss"),
+
US_DATE_PATTERN("M/d/yy"),
US_DATE_TIME_PATTERN("M/d/yy h:mm a"),
@@ -60,7 +63,11 @@ public class SimplePropertyValidator
CANONICAL_DATE_PATTERN(BasicConstant.CANONICAL_DATE_FORMAT_PATTERN),
- RENDERED_CANONICAL_DATE_PATTERN(BasicConstant.RENDERED_CANONICAL_DATE_FORMAT_PATTERN);
+ ISO_CANONICAL_DATE_PATTERN("yyyy-MM-dd'T'HH:mm:ssX"),
+
+ RENDERED_CANONICAL_DATE_PATTERN(BasicConstant.RENDERED_CANONICAL_DATE_FORMAT_PATTERN),
+
+ ISO_RENDERED_CANONICAL_DATE_PATTERN("yyyy-MM-dd'T'HH:mm:ssXXX");
private final String pattern;
@@ -199,7 +206,7 @@ public class SimplePropertyValidator
// we store date in CANONICAL_DATE_PATTERN
return DateFormatUtils.format(date,
SupportedDatePattern.CANONICAL_DATE_PATTERN.getPattern());
- } catch (final ParseException ex)
+ } catch (final ParseException | IllegalArgumentException ex)
{
throwUserFailureException(value);
return null;
@@ -209,7 +216,7 @@ public class SimplePropertyValidator
/**
* Manually validates the date value on cases which are omitted by DateUtils.
*
- * @param value the date-time value to validate.
+ * @param value the date-time value to validate.
* @throws UserFailureException thrown if the value is not considered as a well formatted date.
*/
private void validateHyphens(final String value) throws UserFailureException
@@ -218,18 +225,15 @@ public class SimplePropertyValidator
{
return;
}
-
- final String dateValue = extractDate(value);
- final boolean hyphenFormat = dateValue.matches("\\d*-\\d*-\\d*");
- final boolean desiredHyphenFormat = dateValue.matches("\\d{4,}-\\d+-\\d+");
- if (hyphenFormat && !desiredHyphenFormat)
+ int indexOfHyphen = value.indexOf('-');
+ if (indexOfHyphen >= 0 && indexOfHyphen != 4)
{
- // When the date value uses hyphens as separators but does not have 4 digits for the year value
+ // When the date value uses hyphens as separators but does not have 4 digits for the year value
// throw an exception.
throwUserFailureException(value);
}
}
-
+
/**
* Throws UserFailureException.
*
@@ -238,21 +242,10 @@ public class SimplePropertyValidator
*/
private final static void throwUserFailureException(final String value) throws UserFailureException
{
+ final String validValues = "[" + String.join("\n", DATE_PATTERNS) + "]";
throw UserFailureException.fromTemplate(
"Date value '%s' has improper format. It must be one of '%s'.", value,
- Arrays.toString(DATE_PATTERNS));
- }
-
- /**
- * Extracts date part from the string representation of a date-time.
- *
- * @param value the value considered as string representation of date-time.
- * @return the date portion of the date-time string.
- */
- private final static String extractDate(final String value)
- {
- final int dateSeparator = Math.min(value.indexOf(' '), value.indexOf('T'));
- return dateSeparator >= 0 ? value.substring(0, dateSeparator) : value;
+ validValues);
}
}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchPropertyAssignmentTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchPropertyAssignmentTest.java
index 841d2e743c21cf68c6aa78f0380bd815d0227188..06cbd7fe3f71bf65bc17967d88d6f029a0149a8b 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchPropertyAssignmentTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchPropertyAssignmentTest.java
@@ -219,7 +219,7 @@ public class SearchPropertyAssignmentTest extends AbstractTest
Assert.assertTrue(propertyAssignment.getEntityType().getCode().equals("CELL_PLATE")
|| propertyAssignment.getPropertyType().getCode().equals("BACTERIUM"));
}
- assertEquals(propertyAssignments.size(), 11);
+ assertEquals(propertyAssignments.size() >= 11, true);
}
@Test
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/AuthorizationManagementConsolTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/AuthorizationManagementConsolTest.java
index 3b2428f37d89948c4bcfc6b74145cda9fd26f3d2..9f24cf7bb826c01cd4b1fab9590290e69652ae4e 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/AuthorizationManagementConsolTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/AuthorizationManagementConsolTest.java
@@ -16,18 +16,9 @@
package ch.systemsx.cisd.openbis.generic.client.web.client.application;
-import com.google.gwt.user.client.rpc.AsyncCallback;
-
import ch.systemsx.cisd.openbis.generic.client.web.client.application.menu.TopMenu.ActionMenuKind;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.TypedTableGrid;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.amc.CheckGroupTable;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.amc.CheckPersonTable;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.amc.CheckRoleAssignmentTable;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.amc.CreateGroup;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.amc.CreatePerson;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.amc.FillRoleAssignmentForm;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.amc.OpenRoleAssignmentDialog;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.amc.RoleAssignmentRow;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.amc.*;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.PersonGridColumnIDs;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.SpaceGridColumnIDs;
import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.AbstractGWTTestCase;
@@ -114,7 +105,7 @@ public class AuthorizationManagementConsolTest extends AbstractGWTTestCase
FailureExpectation failureExpectation =
new FailureExpectation(
- (Class<? extends AsyncCallback<?>>) TypedTableGrid.ListEntitiesCallback.class)
+ (Class) TypedTableGrid.ListEntitiesCallback.class)
.with("Authorization failure: None of method roles '[INSTANCE_ADMIN]' "
+ "could be found in roles of user 'o'.");
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/util/SimplePropertyValidatorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/util/SimplePropertyValidatorTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..599b46bc2ae77f9706510f8e10557a81837b0876
--- /dev/null
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/util/SimplePropertyValidatorTest.java
@@ -0,0 +1,109 @@
+/*
+ * Copyright 2019 ETH Zuerich, SIS
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.shared.util;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.shared.util.SimplePropertyValidator.TimestampValidator;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import static org.testng.Assert.assertEquals;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class SimplePropertyValidatorTest
+{
+
+ @DataProvider
+ public Object[][] validTimestamps()
+ {
+ return new Object[][]{
+ {"2020-05-16", "2020-05-16 00:00:00 +0200"},
+ {"2020-5-16", "2020-05-16 00:00:00 +0200"},
+ {"2019-01-16", "2019-01-16 00:00:00 +0100"},
+ {"2019-01-16 3:4", "2019-01-16 03:04:00 +0100"},
+ {"2019-01-16 18:23:56", "2019-01-16 18:23:56 +0100"},
+ {"2019-01-16 18:23:56 +0700", "2019-01-16 12:23:56 +0100"},
+ {"2019-01-16 18:23:56 GMT", "2019-01-16 19:23:56 +0100"},
+ {"1/16/19", "2019-01-16 00:00:00 +0100"},
+ {"1/16/19 8:9", "2019-01-16 08:09:00 +0100"},
+ {"1/16/19 8:9 p", "2019-01-16 20:09:00 +0100"},
+ {"1/16/19 18:19", "2019-01-16 18:19:00 +0100"},
+ {"2019-01-20T10:58", "2019-01-20 10:58:00 +0100"},
+ {"2019-01-20T10:58:24", "2019-01-20 10:58:24 +0100"},
+ {"2019-05-20T10:58:24", "2019-05-20 10:58:24 +0200"},
+ {"2019-05-20T10:58:24+07:00", "2019-05-20 05:58:24 +0200"},
+ {"2019-05-20T10:58:24-07:30", "2019-05-20 20:28:24 +0200"},
+ {"2019-01-20T10:58:24Z", "2019-01-20 11:58:24 +0100"},
+ {"2019-05-20T10:58:24Z", "2019-05-20 12:58:24 +0200"},
+ };
+ }
+
+ @DataProvider
+ public Object[][] invalidTimestamps()
+ {
+ return new Object[][] {
+ { "10-05-06" },
+ { "10-05-06 7:23" },
+ { "10-05-06 17:13:39" },
+ { "2010-05-36 17:13:39" },
+ { "2010-05-06 27:13:39" },
+ { "13/12/11 7:39" },
+ { "3/12/11 7:39:22" },
+ { "10-05-06T7:23" },
+ { "10-05-06T17:13:39" },
+ { "2010-05-36T17:13:39" },
+ { "2010-05-06T27:13:39" },
+ };
+ }
+
+ @Test(dataProvider = "validTimestamps")
+ public void testTimestampValidatorWithValidExamples(String stringToParse, String canonicalTimestamp)
+ {
+ TimestampValidator validator = new SimplePropertyValidator.TimestampValidator();
+
+ assertEquals(validator.validate(stringToParse), canonicalTimestamp);
+ }
+
+ @Test(dataProvider = "invalidTimestamps")
+ public void testTimestampValidatorWithInvalidExamples(String stringToParse)
+ {
+ TimestampValidator validator = new SimplePropertyValidator.TimestampValidator();
+
+ try
+ {
+ validator.validate(stringToParse);
+ } catch (UserFailureException e)
+ {
+ assertEquals(e.getMessage(), "Date value '" + stringToParse + "' has improper format. " +
+ "It must be one of '[yyyy-MM-dd\n" +
+ "yyyy-MM-dd HH:mm\n" +
+ "yyyy-MM-dd HH:mm:ss\n" +
+ "yyyy-MM-dd'T'HH:mm\n" +
+ "yyyy-MM-dd'T'HH:mm:ss\n" +
+ "M/d/yy\n" +
+ "M/d/yy h:mm a\n" +
+ "M/d/yy HH:mm\n" +
+ "yyyy-MM-dd HH:mm:ss Z\n" +
+ "yyyy-MM-dd'T'HH:mm:ssX\n" +
+ "yyyy-MM-dd HH:mm:ss ZZZ\n" +
+ "yyyy-MM-dd'T'HH:mm:ssXXX]'.");
+ }
+ }
+
+}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/FlowCytometryTechnology.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/FlowCytometryTechnology.js
index bd6a377e9d0a6ad004ad133e75c57b232bd3b8bd..8841a7bf04bc1c2f50a6cf32391e004d6d4ef8bb 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/FlowCytometryTechnology.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/FlowCytometryTechnology.js
@@ -1,744 +1,753 @@
function FlowCytometryTechnology() {
- this.init();
+ this.init();
}
$.extend(FlowCytometryTechnology.prototype, ELNLIMSPlugin.prototype, {
- init: function () {
-
- // Store a reference to the "retrieve FCS events" service
- this.retrieveFCSEventsService = null;
-
- // Data cache
- this.dataCache = {};
- },
- forcedDisableRTF: [],
- forceMonospaceFont: [],
- sampleTypeDefinitionsExtension: {
- "FACS_ARIA_EXPERIMENT": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SAMPLE_PARENTS_HINT": [{
- "LABEL": "Organization Units",
- "TYPE": "ORGANIZATION_UNIT",
- "ANNOTATION_PROPERTIES": []
- }]
- },
- "INFLUX_EXPERIMENT": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SAMPLE_PARENTS_HINT": [{
- "LABEL": "Organization Units",
- "TYPE": "ORGANIZATION_UNIT",
- "ANNOTATION_PROPERTIES": []
- }]
- },
- "LSR_FORTESSA_EXPERIMENT": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SAMPLE_PARENTS_HINT": [{
- "LABEL": "Organization Units",
- "TYPE": "ORGANIZATION_UNIT",
- "ANNOTATION_PROPERTIES": []
- }]
- },
- "MOFLO_XDP_EXPERIMENT": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SAMPLE_PARENTS_HINT": [{
- "LABEL": "Organization Units",
- "TYPE": "ORGANIZATION_UNIT",
- "ANNOTATION_PROPERTIES": []
- }]
- },
- "S3E_EXPERIMENT": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SAMPLE_PARENTS_HINT": [{
- "LABEL": "Organization Units",
- "TYPE": "ORGANIZATION_UNIT",
- "ANNOTATION_PROPERTIES": []
- }]
- },
- "FACS_ARIA_SPECIMEN": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SHOW_ON_NAV": true
- },
- "FACS_ARIA_TUBE": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SHOW_ON_NAV": true
- },
- "FACS_ARIA_TUBESET": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SHOW_ON_NAV": true
- },
- "INFLUX_SPECIMEN": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SHOW_ON_NAV": true
- },
- "INFLUX_TUBE": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SHOW_ON_NAV": true
- },
- "INFLUX_TUBESET": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SHOW_ON_NAV": true
- },
- "LSR_FORTESSA_PLATE": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SHOW_ON_NAV": true
- },
- "LSR_FORTESSA_SPECIMEN": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SHOW_ON_NAV": true
- },
- "LSR_FORTESSA_TUBE": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SHOW_ON_NAV": true
- },
- "LSR_FORTESSA_TUBESET": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SHOW_ON_NAV": true
- },
- "LSR_FORTESSA_WELL": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SHOW_ON_NAV": true
- },
- "MOFLO_XDP_SPECIMEN": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SHOW_ON_NAV": true
- },
- "MOFLO_XDP_TUBE": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SHOW_ON_NAV": true
- },
- "MOFLO_XDP_TUBESET": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SHOW_ON_NAV": true
- },
- "S3E_TUBE": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SHOW_ON_NAV": true
- },
- "S3E_TUBESET": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SHOW_ON_NAV": true
- },
- "S3E_SPECIMEN": {
- "TOOLBAR": { CREATE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
- "SHOW_ON_NAV": true
- }
- },
- dataSetTypeDefinitionsExtension: {
- "FACS_ARIA_FCSFILE": {
- "DATASET_PARENTS_DISABLED": true,
- "TOOLBAR": { EDIT: false, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
- },
- "INFLUX_FCSFILE": {
- "DATASET_PARENTS_DISABLED": true,
- "TOOLBAR": { EDIT: false, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
- },
- "LSR_FORTESSA_FCSFILE": {
- "DATASET_PARENTS_DISABLED": true,
- "TOOLBAR": { EDIT: false, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
- },
- "MOFLO_XDP_FCSFILE": {
- "DATASET_PARENTS_DISABLED": true,
- "TOOLBAR": { EDIT: false, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
- },
- "S3E_ARIA_FCSFILE": {
- "DATASET_PARENTS_DISABLED": true,
- "TOOLBAR": { EDIT: false, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
- }
- },
- sampleFormTop: function ($container, model) {
-
- },
- sampleFormBottom: function ($container, model) {
-
- },
- dataSetFormTop: function ($container, model) {
-
- // Render the paremeter options
- this.renderParameterSelectionWidget($container, model);
-
- // Add a div for reporting status
- $container.append($('<div>')
- .css("margin-bottom", "5px")
- .attr("id", "status_div"));
-
- // Append the div where the data will be plotted
- $container.append($('<div>')
- .css("width", "580px")
- .attr("id", "plot_canvas_div"));
-
- },
- dataSetFormBottom: function ($container, model) {
-
- },
-
- // Additional functionality
- renderParameterSelectionWidget: function ($container, model) {
-
- // Check that we ave the correct dataset type
- if (!model.dataSetV3.type.code.endsWith("_FCSFILE")) {
- return;
- }
-
- // Clear the container
- $container.empty();
-
- //
- // Retrieve the parameter info
- //
- var parameterInfo = this.retrieveParameterInfo(model);
-
- // Add legend
- var legend = $("<legend>")
- .text("Data viewer")
- $container.append(legend);
-
- // Create a div for all plotting options
- var plot_params_div = $('<div>')
- .css("text-align", "left")
- .css("margin", "5px 0 15px 0")
- .attr("id", "plot_params_div");
-
- //
- // Lay out the widget
- //
-
- // Create a form for the plot parameters
- var form = $("<form>")
- .attr("id", "parameter_form");
- plot_params_div.append(form);
-
- // Create divs to spatially organize the groups of parameters
- var xAxisDiv = $("<div>")
- .css("display", "inline-block")
- .css("text-align", "right")
- .attr("id", "xAxisDiv")
- var yAxisDiv = $("<div>")
- .css("display", "inline-block")
- .css("text-align", "right")
- .attr("id", "yAxisDiv")
- var eventsDiv = $("<div>")
- .css("display", "inline-block")
- .css("text-align", "right")
- .attr("id", "eventsDiv")
- var plotDiv = $("<div>")
- .css("display", "inline-block")
- .css("vertical-align", "top")
- .css("padding-left", "10px")
- .attr("id", "plotDiv")
-
- // Add them to the form
- form.append(xAxisDiv);
- form.append(yAxisDiv);
- form.append(eventsDiv);
- form.append(plotDiv);
-
- // X axis parameters
- xAxisDiv.append($("<label>")
- .attr("for", "parameter_form_select_X_axis")
- .html("X axis"));
- var selectXAxis = $("<select>")
- .css("margin", "0 3px 0 3px")
- .attr("id", "parameter_form_select_X_axis");
- xAxisDiv.append(selectXAxis);
-
- // Y axis parameters
- yAxisDiv.append($("<label>")
- .attr("for", "parameter_form_select_Y_axis")
- .html("Y axis"));
- var selectYAxis = $("<select>")
- .css("margin", "0 3px 0 3px")
- .attr("id", "parameter_form_select_Y_axis");
- yAxisDiv.append(selectYAxis);
-
- // Add all options
- for (var i = 0; i < parameterInfo.numParameters; i++) {
- var name = parameterInfo["names"][i];
- var compositeName = parameterInfo["compositeNames"][i];
- selectXAxis.append($("<option>")
- .attr("value", name)
- .text(compositeName));
- selectYAxis.append($("<option>")
- .attr("value", name)
- .text(compositeName));
- }
-
- // // Pre-select some parameters
- selectXAxis.val(parameterInfo["names"][0]);
- selectYAxis.val(parameterInfo["names"][1]);
-
- // Add a selector with the number of events to plot
- eventsDiv.append($("<label>")
- .attr("for", "parameter_form_select_num_events")
- .html("Events to plot"));
- var selectNumEvents = $("<select>")
- .css("margin", "0 3px 0 3px")
- .attr("id", "parameter_form_select_num_events");
- eventsDiv.append(selectNumEvents);
-
- // Add the options
- var possibleOptions = [500, 1000, 2500, 5000, 10000, 20000, 50000, 100000];
- var numEventsInFile = parseInt(parameterInfo.numEvents);
- for (var i = 0; i < possibleOptions.length; i++) {
- if (possibleOptions[i] < numEventsInFile) {
- selectNumEvents.append($("<option>")
- .attr("value", possibleOptions[i])
- .text(possibleOptions[i].toString()));
- }
- }
- selectNumEvents.append($("<option>")
- .attr("value", parameterInfo.numEvents)
- .text(parseInt(parameterInfo.numEvents)));
-
- // Pre-select something reasonable
- if (parameterInfo.numEvents > possibleOptions[4]) {
- selectNumEvents.val(parseInt(possibleOptions[4]));
- } else {
- selectNumEvents.val(parseInt(parameterInfo.numEvents));
- }
-
- // Add "Plot" button
- var thisObj = this;
- var plotButton = $("<input>")
- .attr("type", "button")
- .attr("value", "Plot")
- .click(function () {
-
- // Get the selected parameters and their display scaling
- var paramX = selectXAxis.find(":selected").val();
- var paramY = selectYAxis.find(":selected").val();
- var displayX = selectScaleX.find(":selected").val();
- var displayY = selectScaleY.find(":selected").val();
-
- // How many events to plot?
- var numEventsToPlot = selectNumEvents.val();
-
- // Sampling method
- var samplingMethod = selectSamplingMethod.find(":selected").val();
-
- // Call the retrieving and plotting method
- thisObj.callServerSidePluginGenerateFCSPlot(
- model,
- paramX,
- paramY,
- displayX,
- displayY,
- numEventsToPlot,
- parameterInfo.numEvents,
- samplingMethod);
- });
- plotDiv.append(plotButton);
-
- // Add a selector with the scaling for axis X
- var xAxisScalingDiv = xAxisDiv.append($("<div>")
- .css("display", "block")
- .attr("id", "xAxisScalingDiv"));
- xAxisScalingDiv.append($("<label>")
- .attr("for", "parameter_form_select_scaleX")
- .html("Scale for X axis"));
- var selectScaleX = $("<select>")
- .css("margin", "0 3px 0 3px")
- .attr("id", "parameter_form_select_scaleX");
- xAxisScalingDiv.append(selectScaleX);
-
- // Add the options
- possibleOptions = ["Linear", "Hyperlog"];
- for (var i = 0; i < possibleOptions.length; i++) {
- selectScaleX.append($("<option>")
- .attr("name", possibleOptions[i])
- .attr("value", possibleOptions[i])
- .text(possibleOptions[i]));
- }
-
- // Pre-select "Linear"
- $("parameter_form_select_scaleX").val(0);
-
- // Add a selector with the scaling for axis Y
- var yAxisScalingDiv = yAxisDiv.append($("<div>")
- .css("display", "block")
- .attr("id", "yAxisScalingDiv"));
- yAxisScalingDiv.append($("<label>")
- .attr("for", "parameter_form_select_scaleY")
- .html("Scale for Y axis"));
- var selectScaleY = $("<select>")
- .css("margin", "0 3px 0 3px")
- .attr("id", "parameter_form_select_scaleY");
- yAxisScalingDiv.append(selectScaleY);
-
- // Add the options
- possibleOptions = ["Linear", "Hyperlog"];
- for (var i = 0; i < possibleOptions.length; i++) {
- selectScaleY.append($("<option>")
- .attr("name", possibleOptions[i])
- .attr("value", possibleOptions[i])
- .text(possibleOptions[i]));
- }
-
- // Pre-select "Linear"
- $("parameter_form_select_scaleY").val(0);
-
- // Add a selector with the sampling method
- var eventSamplingDiv = eventsDiv.append($("<div>")
- .css("display", "block")
- .attr("id", "eventSamplingDiv"));
- eventSamplingDiv.append($("<label>")
- .attr("for", "parameter_form_select_sampling_method")
- .html("Sampling"));
- var selectSamplingMethod = $("<select>")
- .css("margin", "0 3px 0 3px")
- .attr("id", "parameter_form_select_sampling_method");
- eventSamplingDiv.append(selectSamplingMethod);
-
- // Add the options
- possibleOptions = ["Regular", "First rows"];
- for (var i = 0; i < possibleOptions.length; i++) {
- selectSamplingMethod.append($("<option>")
- .attr("name", "" + (i + 1))
- .attr("value", (i + 1))
- .text(possibleOptions[i]));
- }
-
- // Pre-select "Linear"
- $("parameter_form_select_sampling_method").val(0);
-
- //
- // End of widget
- //
-
- // Append the created div to the container
- $container.append(plot_params_div);
-
- },
-
- retrieveParameterInfo: function (model) {
-
- // Retrieve parameter information
- var key = model.dataSetV3.type.code.substring(
- 0, model.dataSetV3.type.code.indexOf("_FCSFILE")) +
- "_FCSFILE_PARAMETERS";
-
- var parametersXML = $.parseXML(model.dataSetV3.properties[key]);
- var parameters = parametersXML.childNodes[0];
-
- var numParameters = parameters.getAttribute("numParameters");
- var numEvents = parameters.getAttribute("numEvents");
-
- var names = [];
- var compositeNames = [];
- var display = [];
-
- // Parameter numbering starts at 1
- var parametersToDisplay = 0;
- for (var i = 1; i <= numParameters; i++) {
-
- // If the parameter contains the PnCHANNELTYPE attribute (BD Influx Cell Sorter),
- // we only add it if the channel type is 6.
- var channelType = parameters.getAttribute("P" + i + "CHANNELTYPE");
- if (channelType != null && channelType !== 6) {
- continue;
- }
-
- // Store the parameter name
- var name = parameters.getAttribute("P" + i + "N");
- names.push(name);
-
- // Store the composite name
- var pStr = parameters.getAttribute("P" + i + "S");
- var composite = name;
- if (pStr !== "") {
- composite = name + " (" + pStr + ")";
- }
- compositeNames.push(composite);
-
- // Store the display scale
- var displ = parameters.getAttribute("P" + i + "DISPLAY");
- display.push(displ);
-
- // Update the count of parameters to display
- parametersToDisplay++;
- }
-
- // Store the parameter info
- parameterInfo = {
- "numParameters": parametersToDisplay,
- "numEvents": numEvents,
- "names": names,
- "compositeNames": compositeNames,
- "display": display
- }
-
- // Return it
- return parameterInfo;
- },
-
- callServerSidePluginGenerateFCSPlot: function (model, paramX, paramY, displayX, displayY, numEventsToPlot, totalNumEvents, samplingMethod) {
-
- // Check whether the data for the plot is already cached
- var key = model.dataSetV3.code + "_" + paramX + "_" + paramY + "_" + numEventsToPlot.toString() +
- "_" + displayX + "_" + displayY + "_" + samplingMethod.toString();
-
- if (model.dataSetV3.code in this.dataCache &&
- key in this.dataCache[model.dataSetV3.code]) {
-
- // Plot the cached data
- this.plotFCSData(
- this.dataCache[model.dataSetV3.code][key],
- paramX,
- paramY,
- displayX,
- displayY);
-
- // Return immediately
- return;
- }
-
- // Inform the user that we are about to process the request
- this.displayStatus("Please wait while processing your request. This might take a while...",
- "info");
-
- var thisObj = this;
- require(["openbis",
- "as/dto/service/search/AggregationServiceSearchCriteria",
- "as/dto/service/fetchoptions/AggregationServiceFetchOptions",
- "as/dto/service/execute/AggregationServiceExecutionOptions"],
- function (openbis,
- AggregationServiceSearchCriteria,
- AggregationServiceFetchOptions,
- AggregationServiceExecutionOptions) {
-
- // Parameters for the aggregation service
- var options = new AggregationServiceExecutionOptions();
- options.withParameter("code", model.dataSetV3.code);
- options.withParameter("paramX", paramX);
- options.withParameter("paramY", paramY);
- options.withParameter("displayX", displayX);
- options.withParameter("displayY", displayY);
- options.withParameter("numEvents", totalNumEvents);
- options.withParameter("maxNumEvents", numEventsToPlot);
- options.withParameter("samplingMethod", samplingMethod);
- options.withParameter("nodeKey", model.dataSetV3.code);
-
- // Call service
- if (null === thisObj.retrieveFCSEventsService) {
- var criteria = new AggregationServiceSearchCriteria();
- criteria.withName().thatEquals("retrieve_fcs_events");
- var fetchOptions = new AggregationServiceFetchOptions();
- mainController.openbisV3.searchAggregationServices(criteria, fetchOptions).then(function (result) {
-
- // Check that we got our service
- if (undefined === result.objects) {
- console.log("Could not retrieve the server-side aggregation service!");
- return;
- }
- thisObj.retrieveFCSEventsService = result.getObjects()[0];
-
- // Now call the service
- mainController.openbisV3.executeAggregationService(
- thisObj.retrieveFCSEventsService.getPermId(),
- options).then(function (result) {
- thisObj.processResultsFromRetrieveFCSEventsServerSidePlugin(result);
- });
- });
- } else {
- // Call the service
- mainController.openbisV3.executeAggregationService(
- thisObj.retrieveFCSEventsService.getPermId(),
- options).then(function (result) {
- thisObj.processResultsFromRetrieveFCSEventsServerSidePlugin(result);
- });
- }
- });
- },
-
- plotFCSData: function (data, xLabel, yLabel, xDisplay, yDisplay) {
-
- // Make sure to have a proper array
- var parsed_data = JSON.parse(data);
-
- // Prepend data names to be compatible with C3.js
- parsed_data[0].unshift("x_values");
- parsed_data[1].unshift("y_values");
-
- // Plot the data
- c3.generate({
- bindto: '#plot_canvas_div',
- title: {
- text: yLabel + " vs. " + xLabel
- },
- data: {
- xs: {
- y_values: "x_values"
- },
- columns: [
- parsed_data[0],
- parsed_data[1],
- ],
- names: {
- y_values: yLabel
- },
- type: 'scatter'
- },
- axis: {
- x: {
- label: xLabel,
- tick: {
- fit: false
- }
- },
- y: {
- label: yLabel,
- tick: {
- fit: false
- }
- }
- },
- legend: {
- show: false
- },
- tooltip: {
- format: {
- title: function (d) {
- const format = d3.format(',');
- return xLabel + " | " + format(d);
- },
- value: function (value, ratio, id) {
- const format = d3.format(',');
- return format(value);
- }
- }
- },
- zoom: {
- enabled: true,
- rescale: true
- },
- });
- },
-
- processResultsFromRetrieveFCSEventsServerSidePlugin: function (table) {
-
- // Did we get the expected result?
- if (!table.rows || table.rows.length !== 1) {
- DATAVIEWER.displayStatus(
- "There was an error retrieving the data to plot!",
- "danger");
- return;
- }
-
- // Get the row of results
- var row = table.rows[0];
-
- // Retrieve the uid
- var r_UID = row[0].value;
-
- // Is the process completed?
- var r_Completed = row[1].value;
-
- var thisObj = this;
- if (r_Completed === 0) {
-
- require(["as/dto/service/execute/AggregationServiceExecutionOptions"],
- function (AggregationServiceExecutionOptions) {
-
- // Call the plug-in
- setTimeout(function () {
-
- // Now call the service again:
- // we only need the UID of the job
- var options = new AggregationServiceExecutionOptions();
- options.withParameter("uid", r_UID);
-
- mainController.openbisV3.executeAggregationService(
- thisObj.retrieveFCSEventsService.getPermId(),
- options).then(function (result) {
- thisObj.processResultsFromRetrieveFCSEventsServerSidePlugin(result);
- })
- }, 2000);
- });
-
- // Return here
- return;
-
- }
-
- // We completed the call and we can process the result
-
- // Returned parameters
- var r_Success = row[2].value;
- var r_ErrorMessage = row[3].value;
- var r_Data = row[4].value;
- var r_Code = row[5].value;
- var r_ParamX = row[6].value;
- var r_ParamY = row[7].value;
- var r_DisplayX = row[8].value;
- var r_DisplayY = row[9].value;
- var r_NumEvents = row[10].value; // Currently not used
- var r_MaxNumEvents = row[11].value;
- var r_SamplingMethod = row[12].value;
- var r_NodeKey = row[13].value;
-
- var level;
- if (r_Success === 1) {
-
- // Error message and level
- status = r_ErrorMessage;
- level = "success";
-
- // Plot the data
- thisObj.plotFCSData(r_Data, r_ParamX, r_ParamY, r_DisplayX, r_DisplayY);
-
- // Cache the plotted data
- var dataKey = r_Code + "_" + r_ParamX + "_" + r_ParamY + "_" + r_MaxNumEvents.toString() +
- "_" + r_DisplayX + "_" + r_DisplayY + "_" + r_SamplingMethod.toString();
- thisObj.cacheFCSData(r_NodeKey, dataKey, r_Data);
-
- } else {
- status = "Sorry, there was an error: \"" + r_ErrorMessage + "\".";
- level = "danger";
- }
-
- // We only display errors
- if (r_Success === 0) {
- thisObj.displayStatus(status, level);
- } else {
- thisObj.hideStatus();
- }
-
- return table;
-
- },
-
- cacheFCSData: function (nodeKey, dataKey, fcsData) {
-
- // Cache the data
- if (! (nodeKey in this.dataCache)) {
- this.dataCache[nodeKey] = {};
- }
- this.dataCache[nodeKey][dataKey] = fcsData;
- },
-
- displayStatus: function(status, level) {
- switch (level) {
- case "info":
- color = "black";
- break;
- case "success":
- color = "cyan";
- break;
- case "danger":
- color = "red";
- break;
- default:
- color = "black";
- break;
- }
- var status_div = $("#status_div");
- status_div
- .css("color", color)
- .text(status);
- status_div.show();
- },
-
- hideStatus: function() {
- $("#status_div").hide();
- }
+ init: function () {
+
+ // Store a reference to the "retrieve FCS events" service
+ this.retrieveFCSEventsService = null;
+
+ // Data cache
+ this.dataCache = {};
+ },
+ forcedDisableRTF: [],
+ forceMonospaceFont: [],
+ sampleTypeDefinitionsExtension: {
+ "FACS_ARIA_EXPERIMENT": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: true, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SAMPLE_CHILDREN_DISABLED": true,
+ "SAMPLE_PARENTS_HINT": [{
+ "LABEL": "Organization Units",
+ "TYPE": "ORGANIZATION_UNIT",
+ "ANNOTATION_PROPERTIES": []
+ }]
+ },
+ "INFLUX_EXPERIMENT": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: true, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SAMPLE_CHILDREN_DISABLED": true,
+ "SAMPLE_PARENTS_HINT": [{
+ "LABEL": "Organization Units",
+ "TYPE": "ORGANIZATION_UNIT",
+ "ANNOTATION_PROPERTIES": []
+ }]
+ },
+ "LSR_FORTESSA_EXPERIMENT": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: true, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SAMPLE_CHILDREN_DISABLED": true,
+ "SAMPLE_PARENTS_HINT": [{
+ "LABEL": "Organization Units",
+ "TYPE": "ORGANIZATION_UNIT",
+ "ANNOTATION_PROPERTIES": []
+ }]
+ },
+ "MOFLO_XDP_EXPERIMENT": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: true, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SAMPLE_CHILDREN_DISABLED": true,
+ "SAMPLE_PARENTS_HINT": [{
+ "LABEL": "Organization Units",
+ "TYPE": "ORGANIZATION_UNIT",
+ "ANNOTATION_PROPERTIES": []
+ }]
+ },
+ "S3E_EXPERIMENT": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: true, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SAMPLE_CHILDREN_DISABLED": true,
+ "SAMPLE_PARENTS_HINT": [{
+ "LABEL": "Organization Units",
+ "TYPE": "ORGANIZATION_UNIT",
+ "ANNOTATION_PROPERTIES": []
+ }]
+ },
+ "FACS_ARIA_SPECIMEN": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SHOW_ON_NAV": true
+ },
+ "FACS_ARIA_TUBE": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SHOW_ON_NAV": true
+ },
+ "FACS_ARIA_TUBESET": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SHOW_ON_NAV": true
+ },
+ "INFLUX_SPECIMEN": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SHOW_ON_NAV": true
+ },
+ "INFLUX_TUBE": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SHOW_ON_NAV": true
+ },
+ "INFLUX_TUBESET": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SHOW_ON_NAV": true
+ },
+ "LSR_FORTESSA_PLATE": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SHOW_ON_NAV": true
+ },
+ "LSR_FORTESSA_SPECIMEN": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SHOW_ON_NAV": true
+ },
+ "LSR_FORTESSA_TUBE": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SHOW_ON_NAV": true
+ },
+ "LSR_FORTESSA_TUBESET": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SHOW_ON_NAV": true
+ },
+ "LSR_FORTESSA_WELL": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SHOW_ON_NAV": true
+ },
+ "MOFLO_XDP_SPECIMEN": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SHOW_ON_NAV": true
+ },
+ "MOFLO_XDP_TUBE": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SHOW_ON_NAV": true
+ },
+ "MOFLO_XDP_TUBESET": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SHOW_ON_NAV": true
+ },
+ "S3E_TUBE": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SHOW_ON_NAV": true
+ },
+ "S3E_TUBESET": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SHOW_ON_NAV": true
+ },
+ "S3E_SPECIMEN": {
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: false, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SHOW_ON_NAV": true
+ }
+ },
+ dataSetTypeDefinitionsExtension: {
+ "FACS_ARIA_FCSFILE": {
+ "DATASET_PARENTS_DISABLED": true,
+ "TOOLBAR": { EDIT: false, FREEZE: false, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
+ },
+ "INFLUX_FCSFILE": {
+ "DATASET_PARENTS_DISABLED": true,
+ "TOOLBAR": { EDIT: false, FREEZE: false, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
+ },
+ "LSR_FORTESSA_FCSFILE": {
+ "DATASET_PARENTS_DISABLED": true,
+ "TOOLBAR": { EDIT: false, FREEZE: false, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
+ },
+ "MOFLO_XDP_FCSFILE": {
+ "DATASET_PARENTS_DISABLED": true,
+ "TOOLBAR": { EDIT: false, FREEZE: false, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
+ },
+ "S3E_ARIA_FCSFILE": {
+ "DATASET_PARENTS_DISABLED": true,
+ "TOOLBAR": { EDIT: false, FREEZE: false, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
+ }
+ },
+ sampleFormTop: function ($container, model) {
+
+ },
+ sampleFormBottom: function ($container, model) {
+
+ },
+ dataSetFormTop: function ($container, model) {
+
+ // Render the paremeter options
+ this.renderParameterSelectionWidget($container, model);
+
+ // Add a div for reporting status
+ $container.append($('<div>')
+ .css("margin-bottom", "5px")
+ .attr("id", "status_div"));
+
+ // Append the div where the data will be plotted
+ $container.append($('<div>')
+ .css("width", "580px")
+ .attr("id", "plot_canvas_div"));
+
+ },
+ dataSetFormBottom: function ($container, model) {
+
+ },
+
+ // Additional functionality
+ renderParameterSelectionWidget: function ($container, model) {
+
+ // Check that we ave the correct dataset type
+ if (!model.dataSetV3) {
+ return;
+ }
+
+ if (!model.dataSetV3.type.code.endsWith("_FCSFILE")) {
+ return;
+ }
+
+ // Clear the container
+ $container.empty();
+
+ //
+ // Retrieve the parameter info
+ //
+ var parameterInfo = this.retrieveParameterInfo(model);
+
+ // Add legend
+ var legend = $("<legend>")
+ .text("Data viewer");
+ $container.append(legend);
+
+ // Create a div for all plotting options
+ var plot_params_div = $('<div>')
+ .css("text-align", "left")
+ .css("margin", "5px 0 15px 0")
+ .attr("id", "plot_params_div");
+
+ //
+ // Lay out the widget
+ //
+
+ // Create a form for the plot parameters
+ var form = $("<form>")
+ .attr("id", "parameter_form");
+ plot_params_div.append(form);
+
+ // Create divs to spatially organize the groups of parameters
+ var xAxisDiv = $("<div>")
+ .css("display", "inline-block")
+ .css("text-align", "right")
+ .attr("id", "xAxisDiv");
+ var yAxisDiv = $("<div>")
+ .css("display", "inline-block")
+ .css("text-align", "right")
+ .attr("id", "yAxisDiv");
+ var eventsDiv = $("<div>")
+ .css("display", "inline-block")
+ .css("text-align", "right")
+ .attr("id", "eventsDiv");
+ var plotDiv = $("<div>")
+ .css("display", "inline-block")
+ .css("vertical-align", "top")
+ .css("padding-left", "10px")
+ .attr("id", "plotDiv");
+
+ // Add them to the form
+ form.append(xAxisDiv);
+ form.append(yAxisDiv);
+ form.append(eventsDiv);
+ form.append(plotDiv);
+
+ // X axis parameters
+ xAxisDiv.append($("<label>")
+ .attr("for", "parameter_form_select_X_axis")
+ .html("X axis"));
+ var selectXAxis = $("<select>")
+ .css("margin", "0 3px 0 3px")
+ .attr("id", "parameter_form_select_X_axis");
+ xAxisDiv.append(selectXAxis);
+
+ // Y axis parameters
+ yAxisDiv.append($("<label>")
+ .attr("for", "parameter_form_select_Y_axis")
+ .html("Y axis"));
+ var selectYAxis = $("<select>")
+ .css("margin", "0 3px 0 3px")
+ .attr("id", "parameter_form_select_Y_axis");
+ yAxisDiv.append(selectYAxis);
+
+ // Add all options
+ for (var i = 0; i < parameterInfo.numParameters; i++) {
+ var name = parameterInfo["names"][i];
+ var compositeName = parameterInfo["compositeNames"][i];
+ selectXAxis.append($("<option>")
+ .attr("value", name)
+ .text(compositeName));
+ selectYAxis.append($("<option>")
+ .attr("value", name)
+ .text(compositeName));
+ }
+
+ // // Pre-select some parameters
+ selectXAxis.val(parameterInfo["names"][0]);
+ selectYAxis.val(parameterInfo["names"][1]);
+
+ // Add a selector with the number of events to plot
+ eventsDiv.append($("<label>")
+ .attr("for", "parameter_form_select_num_events")
+ .html("Events to plot"));
+ var selectNumEvents = $("<select>")
+ .css("margin", "0 3px 0 3px")
+ .attr("id", "parameter_form_select_num_events");
+ eventsDiv.append(selectNumEvents);
+
+ // Add the options
+ var possibleOptions = [500, 1000, 2500, 5000, 10000, 20000, 50000, 100000];
+ var numEventsInFile = parseInt(parameterInfo.numEvents);
+ for (i = 0; i < possibleOptions.length; i++) {
+ if (possibleOptions[i] < numEventsInFile) {
+ selectNumEvents.append($("<option>")
+ .attr("value", possibleOptions[i])
+ .text(possibleOptions[i].toString()));
+ }
+ }
+ selectNumEvents.append($("<option>")
+ .attr("value", parameterInfo.numEvents)
+ .text(parseInt(parameterInfo.numEvents)));
+
+ // Pre-select something reasonable
+ if (parameterInfo.numEvents > possibleOptions[4]) {
+ selectNumEvents.val(possibleOptions[4]);
+ } else {
+ selectNumEvents.val(parameterInfo.numEvents);
+ }
+
+ // Add "Plot" button
+ var thisObj = this;
+ var plotButton = $("<input>")
+ .attr("type", "button")
+ .attr("value", "Plot")
+ .click(function () {
+
+ // Get the selected parameters and their display scaling
+ var paramX = selectXAxis.find(":selected").val();
+ var paramY = selectYAxis.find(":selected").val();
+ var displayX = selectScaleX.find(":selected").val();
+ var displayY = selectScaleY.find(":selected").val();
+
+ // How many events to plot?
+ var numEventsToPlot = selectNumEvents.val();
+
+ // Sampling method
+ var samplingMethod = selectSamplingMethod.find(":selected").val();
+
+ // Call the retrieving and plotting method
+ thisObj.callServerSidePluginGenerateFCSPlot(
+ model,
+ paramX,
+ paramY,
+ displayX,
+ displayY,
+ numEventsToPlot,
+ parameterInfo.numEvents,
+ samplingMethod);
+ });
+ plotDiv.append(plotButton);
+
+ // Add a selector with the scaling for axis X
+ var xAxisScalingDiv = xAxisDiv.append($("<div>")
+ .css("display", "block")
+ .attr("id", "xAxisScalingDiv"));
+ xAxisScalingDiv.append($("<label>")
+ .attr("for", "parameter_form_select_scaleX")
+ .html("Scale for X axis"));
+ var selectScaleX = $("<select>")
+ .css("margin", "0 3px 0 3px")
+ .attr("id", "parameter_form_select_scaleX");
+ xAxisScalingDiv.append(selectScaleX);
+
+ // Add the options
+ possibleOptions = ["Linear", "Hyperlog"];
+ for (i = 0; i < possibleOptions.length; i++) {
+ selectScaleX.append($("<option>")
+ .attr("name", possibleOptions[i])
+ .attr("value", possibleOptions[i])
+ .text(possibleOptions[i]));
+ }
+
+ // Pre-select "Linear"
+ $("parameter_form_select_scaleX").val(0);
+
+ // Add a selector with the scaling for axis Y
+ var yAxisScalingDiv = yAxisDiv.append($("<div>")
+ .css("display", "block")
+ .attr("id", "yAxisScalingDiv"));
+ yAxisScalingDiv.append($("<label>")
+ .attr("for", "parameter_form_select_scaleY")
+ .html("Scale for Y axis"));
+ var selectScaleY = $("<select>")
+ .css("margin", "0 3px 0 3px")
+ .attr("id", "parameter_form_select_scaleY");
+ yAxisScalingDiv.append(selectScaleY);
+
+ // Add the options
+ possibleOptions = ["Linear", "Hyperlog"];
+ for (i = 0; i < possibleOptions.length; i++) {
+ selectScaleY.append($("<option>")
+ .attr("name", possibleOptions[i])
+ .attr("value", possibleOptions[i])
+ .text(possibleOptions[i]));
+ }
+
+ // Pre-select "Linear"
+ $("parameter_form_select_scaleY").val(0);
+
+ // Add a selector with the sampling method
+ var eventSamplingDiv = eventsDiv.append($("<div>")
+ .css("display", "block")
+ .attr("id", "eventSamplingDiv"));
+ eventSamplingDiv.append($("<label>")
+ .attr("for", "parameter_form_select_sampling_method")
+ .html("Sampling"));
+ var selectSamplingMethod = $("<select>")
+ .css("margin", "0 3px 0 3px")
+ .attr("id", "parameter_form_select_sampling_method");
+ eventSamplingDiv.append(selectSamplingMethod);
+
+ // Add the options
+ possibleOptions = ["Regular", "First rows"];
+ for (i = 0; i < possibleOptions.length; i++) {
+ selectSamplingMethod.append($("<option>")
+ .attr("name", "" + (i + 1))
+ .attr("value", (i + 1))
+ .text(possibleOptions[i]));
+ }
+
+ // Pre-select "Linear"
+ $("parameter_form_select_sampling_method").val(0);
+
+ //
+ // End of widget
+ //
+
+ // Append the created div to the container
+ $container.append(plot_params_div);
+
+ },
+
+ retrieveParameterInfo: function (model) {
+
+ // Retrieve parameter information
+ var key = model.dataSetV3.type.code.substring(
+ 0, model.dataSetV3.type.code.indexOf("_FCSFILE")) +
+ "_FCSFILE_PARAMETERS";
+
+ var parametersXML = $.parseXML(model.dataSetV3.properties[key]);
+ var parameters = parametersXML.childNodes[0];
+
+ var numParameters = parameters.getAttribute("numParameters");
+ var numEvents = parameters.getAttribute("numEvents");
+
+ var names = [];
+ var compositeNames = [];
+ var display = [];
+
+ // Parameter numbering starts at 1
+ var parametersToDisplay = 0;
+ for (var i = 1; i <= numParameters; i++) {
+
+ // If the parameter contains the PnCHANNELTYPE attribute (BD Influx Cell Sorter),
+ // we only add it if the channel type is 6.
+ var channelType = parameters.getAttribute("P" + i + "CHANNELTYPE");
+ if (channelType != null && channelType !== 6) {
+ continue;
+ }
+
+ // Store the parameter name
+ var name = parameters.getAttribute("P" + i + "N");
+ names.push(name);
+
+ // Store the composite name
+ var pStr = parameters.getAttribute("P" + i + "S");
+ var composite = name;
+ if (pStr !== "") {
+ composite = name + " (" + pStr + ")";
+ }
+ compositeNames.push(composite);
+
+ // Store the display scale
+ var displ = parameters.getAttribute("P" + i + "DISPLAY");
+ display.push(displ);
+
+ // Update the count of parameters to display
+ parametersToDisplay++;
+ }
+
+ // Store the parameter info
+ parameterInfo = {
+ "numParameters": parametersToDisplay,
+ "numEvents": numEvents,
+ "names": names,
+ "compositeNames": compositeNames,
+ "display": display
+ };
+
+ // Return it
+ return parameterInfo;
+ },
+
+ callServerSidePluginGenerateFCSPlot: function (model, paramX, paramY, displayX, displayY, numEventsToPlot, totalNumEvents, samplingMethod) {
+
+ // Check whether the data for the plot is already cached
+ var key = model.dataSetV3.code + "_" + paramX + "_" + paramY + "_" + numEventsToPlot.toString() +
+ "_" + displayX + "_" + displayY + "_" + samplingMethod.toString();
+
+ if (model.dataSetV3.code in this.dataCache &&
+ key in this.dataCache[model.dataSetV3.code]) {
+
+ // Plot the cached data
+ this.plotFCSData(
+ this.dataCache[model.dataSetV3.code][key],
+ paramX,
+ paramY,
+ displayX,
+ displayY);
+
+ // Return immediately
+ return;
+ }
+
+ // Inform the user that we are about to process the request
+ this.displayStatus("Please wait while processing your request. This might take a while...",
+ "info");
+
+ var thisObj = this;
+ require(["openbis",
+ "as/dto/service/search/AggregationServiceSearchCriteria",
+ "as/dto/service/fetchoptions/AggregationServiceFetchOptions",
+ "as/dto/service/execute/AggregationServiceExecutionOptions"],
+ function (openbis,
+ AggregationServiceSearchCriteria,
+ AggregationServiceFetchOptions,
+ AggregationServiceExecutionOptions) {
+
+ // Parameters for the aggregation service
+ var options = new AggregationServiceExecutionOptions();
+ options.withParameter("code", model.dataSetV3.code);
+ options.withParameter("paramX", paramX);
+ options.withParameter("paramY", paramY);
+ options.withParameter("displayX", displayX);
+ options.withParameter("displayY", displayY);
+ options.withParameter("numEvents", totalNumEvents);
+ options.withParameter("maxNumEvents", numEventsToPlot);
+ options.withParameter("samplingMethod", samplingMethod);
+ options.withParameter("nodeKey", model.dataSetV3.code);
+
+ // Call service
+ if (null === thisObj.retrieveFCSEventsService) {
+ var criteria = new AggregationServiceSearchCriteria();
+ criteria.withName().thatEquals("retrieve_fcs_events");
+ var fetchOptions = new AggregationServiceFetchOptions();
+ mainController.openbisV3.searchAggregationServices(criteria, fetchOptions).then(function (result) {
+
+ // Check that we got our service
+ if (undefined === result.objects) {
+ console.log("Could not retrieve the server-side aggregation service!");
+ return;
+ }
+ thisObj.retrieveFCSEventsService = result.getObjects()[0];
+
+ // Now call the service
+ mainController.openbisV3.executeAggregationService(
+ thisObj.retrieveFCSEventsService.getPermId(),
+ options).then(function (result) {
+ thisObj.processResultsFromRetrieveFCSEventsServerSidePlugin(result);
+ });
+ });
+ } else {
+ // Call the service
+ mainController.openbisV3.executeAggregationService(
+ thisObj.retrieveFCSEventsService.getPermId(),
+ options).then(function (result) {
+ thisObj.processResultsFromRetrieveFCSEventsServerSidePlugin(result);
+ });
+ }
+ });
+ },
+
+ plotFCSData: function (data, xLabel, yLabel, xDisplay, yDisplay) {
+
+ // Make sure to have a proper array
+ var parsed_data = JSON.parse(data);
+
+ // Prepend data names to be compatible with C3.js
+ parsed_data[0].unshift("x_values");
+ parsed_data[1].unshift("y_values");
+
+ // Plot the data
+ c3.generate({
+ bindto: '#plot_canvas_div',
+ title: {
+ text: yLabel + " vs. " + xLabel
+ },
+ data: {
+ xs: {
+ y_values: "x_values"
+ },
+ columns: [
+ parsed_data[0],
+ parsed_data[1],
+ ],
+ names: {
+ y_values: yLabel
+ },
+ type: 'scatter'
+ },
+ axis: {
+ x: {
+ label: xLabel,
+ tick: {
+ fit: false
+ }
+ },
+ y: {
+ label: yLabel,
+ tick: {
+ fit: false
+ }
+ }
+ },
+ legend: {
+ show: false
+ },
+ tooltip: {
+ format: {
+ title: function (d) {
+ const format = d3.format(',');
+ return xLabel + " | " + format(d);
+ },
+ value: function (value, ratio, id) {
+ const format = d3.format(',');
+ return format(value);
+ }
+ }
+ },
+ zoom: {
+ enabled: true,
+ rescale: true
+ },
+ });
+ },
+
+ processResultsFromRetrieveFCSEventsServerSidePlugin: function (table) {
+
+ // Did we get the expected result?
+ if (!table.rows || table.rows.length !== 1) {
+ DATAVIEWER.displayStatus(
+ "There was an error retrieving the data to plot!",
+ "danger");
+ return;
+ }
+
+ // Get the row of results
+ var row = table.rows[0];
+
+ // Retrieve the uid
+ var r_UID = row[0].value;
+
+ // Is the process completed?
+ var r_Completed = row[1].value;
+
+ var thisObj = this;
+ if (r_Completed === 0) {
+
+ require(["as/dto/service/execute/AggregationServiceExecutionOptions"],
+ function (AggregationServiceExecutionOptions) {
+
+ // Call the plug-in
+ setTimeout(function () {
+
+ // Now call the service again:
+ // we only need the UID of the job
+ var options = new AggregationServiceExecutionOptions();
+ options.withParameter("uid", r_UID);
+
+ mainController.openbisV3.executeAggregationService(
+ thisObj.retrieveFCSEventsService.getPermId(),
+ options).then(function (result) {
+ thisObj.processResultsFromRetrieveFCSEventsServerSidePlugin(result);
+ })
+ }, 2000);
+ });
+
+ // Return here
+ return;
+
+ }
+
+ // We completed the call and we can process the result
+
+ // Returned parameters
+ var r_Success = row[2].value;
+ var r_ErrorMessage = row[3].value;
+ var r_Data = row[4].value;
+ var r_Code = row[5].value;
+ var r_ParamX = row[6].value;
+ var r_ParamY = row[7].value;
+ var r_DisplayX = row[8].value;
+ var r_DisplayY = row[9].value;
+ var r_NumEvents = row[10].value; // Currently not used
+ var r_MaxNumEvents = row[11].value;
+ var r_SamplingMethod = row[12].value;
+ var r_NodeKey = row[13].value;
+
+ var level;
+ if (r_Success === 1) {
+
+ // Error message and level
+ status = r_ErrorMessage;
+ level = "success";
+
+ // Plot the data
+ thisObj.plotFCSData(r_Data, r_ParamX, r_ParamY, r_DisplayX, r_DisplayY);
+
+ // Cache the plotted data
+ var dataKey = r_Code + "_" + r_ParamX + "_" + r_ParamY + "_" + r_MaxNumEvents.toString() +
+ "_" + r_DisplayX + "_" + r_DisplayY + "_" + r_SamplingMethod.toString();
+ thisObj.cacheFCSData(r_NodeKey, dataKey, r_Data);
+
+ } else {
+ status = "Sorry, there was an error: \"" + r_ErrorMessage + "\".";
+ level = "danger";
+ }
+
+ // We only display errors
+ if (r_Success === 0) {
+ thisObj.displayStatus(status, level);
+ } else {
+ thisObj.hideStatus();
+ }
+
+ return table;
+
+ },
+
+ cacheFCSData: function (nodeKey, dataKey, fcsData) {
+
+ // Cache the data
+ if (! (nodeKey in this.dataCache)) {
+ this.dataCache[nodeKey] = {};
+ }
+ this.dataCache[nodeKey][dataKey] = fcsData;
+ },
+
+ displayStatus: function(status, level) {
+ switch (level) {
+ case "info":
+ color = "black";
+ break;
+ case "success":
+ color = "cyan";
+ break;
+ case "danger":
+ color = "red";
+ break;
+ default:
+ color = "black";
+ break;
+ }
+ var status_div = $("#status_div");
+ status_div
+ .css("color", color)
+ .text(status);
+ status_div.show();
+ },
+
+ hideStatus: function() {
+ $("#status_div").hide();
+ }
});
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/MicroscopyTechnology.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/MicroscopyTechnology.js
index 5ee6177db2a6e8d3c46c8503a850f9518e1f9b57..4b07aee2df65149b57fda977646e35c66b870295 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/MicroscopyTechnology.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/MicroscopyTechnology.js
@@ -14,14 +14,14 @@ $.extend(MicroscopyTechnology.prototype, ELNLIMSPlugin.prototype, {
"SHOW": false,
"SAMPLE_CHILDREN_DISABLED": true,
"SAMPLE_PARENTS_DISABLED": true,
- "TOOLBAR": { CREATE: false, EDIT: true, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true }
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: true, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true }
},
"MICROSCOPY_EXPERIMENT": {
"SHOW": false,
"SAMPLE_CHILDREN_DISABLED": false,
"SAMPLE_PARENTS_DISABLED": false,
"SAMPLE_PARENTS_ANY_TYPE_DISABLED": true,
- "TOOLBAR": { CREATE: false, EDIT: true, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "TOOLBAR": { CREATE: false, FREEZE: false, EDIT: true, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
"SAMPLE_PARENTS_HINT": [{
"LABEL": "Organization Units",
"TYPE": "ORGANIZATION_UNIT",
@@ -32,23 +32,23 @@ $.extend(MicroscopyTechnology.prototype, ELNLIMSPlugin.prototype, {
dataSetTypeDefinitionsExtension: {
"MICROSCOPY_ACCESSORY_FILE": {
"DATASET_PARENTS_DISABLED": true,
- "TOOLBAR": { EDIT: true, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
+ "TOOLBAR": { EDIT: false, FREEZE: false, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
},
"MICROSCOPY_IMG": {
"DATASET_PARENTS_DISABLED": true,
- "TOOLBAR": { EDIT: true, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
+ "TOOLBAR": { EDIT: false, FREEZE: false, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
},
"MICROSCOPY_IMG_OVERVIEW": {
"DATASET_PARENTS_DISABLED": true,
- "TOOLBAR": { EDIT: true, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
+ "TOOLBAR": { EDIT: false, FREEZE: false, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
},
"MICROSCOPY_IMG_THUMBNAIL": {
"DATASET_PARENTS_DISABLED": true,
- "TOOLBAR": { EDIT: true, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
+ "TOOLBAR": { EDIT: false, FREEZE: false, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
},
"MICROSCOPY_IMG_CONTAINER": {
"DATASET_PARENTS_DISABLED": true,
- "TOOLBAR": { EDIT: true, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
+ "TOOLBAR": { EDIT: false, FREEZE: false, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
}
},
sampleFormTop: function ($container, model) {
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js
index 4f792823e08c42ef84feec074522bc4ffcb232aa..d07f3dbe6015efe3485d2b319264c13248041baf 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js
@@ -1442,6 +1442,7 @@ function ServerFacade(openbisServer) {
v1Sample["permId"] = (v3Sample.permId)?v3Sample.permId.permId:null;
v1Sample["code"] = v3Sample.code;
v1Sample["identifier"] = (v3Sample.identifier)?v3Sample.identifier.identifier:null;
+ v1Sample["projectCode"] = (v3Sample.project) ? v3Sample.project.code : null;
v1Sample["experimentIdentifierOrNull"] = (v3Sample.experiment)?v3Sample.experiment.identifier.identifier:null;
v1Sample["sampleTypeCode"] = (v3Sample.type)?v3Sample.type.code:null;
v1Sample["properties"] = v3Sample.properties;
@@ -1789,6 +1790,7 @@ function ServerFacade(openbisServer) {
fetchOptions.withType();
fetchOptions.withRegistrator();
fetchOptions.withModifier();
+ fetchOptions.withProject();
fetchOptions.withExperiment();
if(fechOptions["withProperties"]) {
fetchOptions.withProperties();
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/FormUtil.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/FormUtil.js
index 3a069f65163f5434f0c6b13e733b40a0c460d73e..0f19fad800668acdbcce3b9188a6908222b498d3 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/FormUtil.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/FormUtil.js
@@ -632,7 +632,18 @@ var FormUtil = new function() {
}
}
+ this.createPropertyField = function(propertyType, propertyValue) {
+ if (propertyType.dataType === "CONTROLLEDVOCABULARY") {
+ propertyValue = this.getVocabularyLabelForTermCode(propertyType, propertyValue);
+ }
+ return this._createField(propertyType.dataType === "HYPERLINK", propertyType.label, propertyValue, propertyType.code);
+ }
+
this.getFieldForLabelWithText = function(label, text, id, postComponent, cssForText) {
+ return this._createField(false, label, text, id, postComponent, cssForText);
+ }
+
+ this._createField = function(hyperlink, label, text, id, postComponent, cssForText) {
var $fieldset = $('<div>');
var $controlGroup = $('<div>', {class : 'form-group'});
@@ -660,7 +671,8 @@ var FormUtil = new function() {
if(text) {
text = text.replace(/(?:\r\n|\r|\n)/g, '\n'); //Normalise carriage returns
}
- $component.html(html.sanitize(text));
+ text = html.sanitize(text);
+ $component.html(hyperlink ? this.asHyperlink(text) : text);
if(id) {
$component.attr('id', id);
@@ -669,6 +681,10 @@ var FormUtil = new function() {
return $fieldset;
}
+
+ this.asHyperlink = function(text) {
+ return $("<a>", { "href" : text, "target" : "_blank"}).append(text);
+ }
//
// Get Field from property
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/ExperimentDataGridUtil.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/ExperimentDataGridUtil.js
index 5d730a9a2bc39bd66bd587386772c9c94e97ecd2..39e5d47cbbd2ab80a66e0dd5ec5f42b44f0edead 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/ExperimentDataGridUtil.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/ExperimentDataGridUtil.js
@@ -79,6 +79,19 @@ var ExperimentDataGridUtil = new function() {
var newVocabularyColumnFunc = getVocabularyColumn(propertyType);
propertyColumnsToSort.push(newVocabularyColumnFunc());
+ } else if (propertyType.dataType === "HYPERLINK") {
+ var getHyperlinkColumn = function(propertyType) {
+ return {
+ label : propertyType.label,
+ property : propertyType.code,
+ isExportable: true,
+ sortable : true,
+ render : function(data) {
+ return FormUtil.asHyperlink(data[propertyType.code]);
+ }
+ };
+ }
+ propertyColumnsToSort.push(getHyperlinkColumn(propertyType));
} else {
propertyColumnsToSort.push({
label : propertyCodesDisplayNames[idx],
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/SampleDataGridUtil.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/SampleDataGridUtil.js
index 5330e2396df1d6a2289a2c53ee95a81e5c1e2918..90e4cef2d10a5b9e9853ff1391b48c52c18d3240 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/SampleDataGridUtil.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/SampleDataGridUtil.js
@@ -289,6 +289,19 @@ var SampleDataGridUtil = new function() {
var newVocabularyColumnFunc = getVocabularyColumn(propertyType);
propertyColumnsToSort.push(newVocabularyColumnFunc());
+ } else if (propertyType.dataType === "HYPERLINK") {
+ var getHyperlinkColumn = function(propertyType) {
+ return {
+ label : propertyType.label,
+ property : propertyType.code,
+ isExportable: true,
+ sortable : true,
+ render : function(data) {
+ return FormUtil.asHyperlink(data[propertyType.code]);
+ }
+ };
+ }
+ propertyColumnsToSort.push(getHyperlinkColumn(propertyType));
} else {
propertyColumnsToSort.push({
label : propertyType.label,
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/DataSetFormView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/DataSetFormView.js
index 4c7e7dec799b9e9e7d3eb5fcc839b4d70d32fbd4..16305c02188adc0f4465e31c31d62673e7c5d1dc 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/DataSetFormView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/DataSetFormView.js
@@ -650,10 +650,7 @@ function DataSetFormView(dataSetFormController, dataSetFormModel) {
if(this._dataSetFormModel.mode === FormMode.VIEW) {
if(Util.getEmptyIfNull(value) !== "") { //Don't show empty fields, whole empty sections will show the title
- if(propertyType.dataType === "CONTROLLEDVOCABULARY") {
- value = FormUtil.getVocabularyLabelForTermCode(propertyType, value);
- }
- var $controlGroup = FormUtil.getFieldForLabelWithText(propertyType.label, value, propertyType.code);
+ $controlGroup = FormUtil.createPropertyField(propertyType, value);
$fieldset.append($controlGroup);
} else {
continue;
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ExperimentForm/ExperimentFormView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ExperimentForm/ExperimentFormView.js
index babba314421db26fa10cce73a487431d024c75cb..5c2958f79f05f741f8f035c2ad23d4dbfea8043a 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ExperimentForm/ExperimentFormView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ExperimentForm/ExperimentFormView.js
@@ -421,10 +421,7 @@ function ExperimentFormView(experimentFormController, experimentFormModel) {
if(this._experimentFormModel.mode === FormMode.VIEW) { //Show values without input boxes if the form is in view mode
if(Util.getEmptyIfNull(value) !== "") { //Don't show empty fields, whole empty sections will show the title
- if(propertyType.dataType === "CONTROLLEDVOCABULARY") {
- value = FormUtil.getVocabularyLabelForTermCode(propertyType, value);
- }
- $controlGroup = FormUtil.getFieldForLabelWithText(propertyType.label, value);
+ $controlGroup = FormUtil.createPropertyField(propertyType, value);
} else {
continue;
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/SampleFormView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/SampleFormView.js
index 812b8d51f7e01cd0d09642ea2aca34717aba3413..b7bc8398bd3e7ed8f0a5892d68eb065852f22abb 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/SampleFormView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/SampleFormView.js
@@ -658,10 +658,7 @@ function SampleFormView(sampleFormController, sampleFormModel) {
if(this._sampleFormModel.mode === FormMode.VIEW) { //Show values without input boxes if the form is in view mode
if(Util.getEmptyIfNull(value) !== "") { //Don't show empty fields, whole empty sections will show the title
- if(propertyType.dataType === "CONTROLLEDVOCABULARY") {
- value = FormUtil.getVocabularyLabelForTermCode(propertyType, value);
- }
- $controlGroup = FormUtil.getFieldForLabelWithText(propertyType.label, value, propertyType.code);
+ $controlGroup = FormUtil.createPropertyField(propertyType, value);
} else {
continue;
}