import java.util.List;
+import org.apache.commons.lang3.StringUtils;
+
import eu.etaxonomy.cdm.common.CdmUtils;
import eu.etaxonomy.cdm.model.common.Language;
import eu.etaxonomy.cdm.model.description.CategoricalData;
protected String doFormat(CategoricalData catData, List<Language> preferredLanguages) {
List<StateData> stateDatas = catData.getStateData();
String stateDataText = getStateDatasText(stateDatas, preferredLanguages);
+ if (catData.getNoDataStatus() != null) {
+ String noDataStatus = catData.getNoDataStatus().getLabel();
+ stateDataText = StringUtils.isEmpty(stateDataText) ? noDataStatus : noDataStatus +" (" + stateDataText + ")";
+ }
return stateDataText;
}
import java.math.BigDecimal;
import java.util.List;
+import org.apache.commons.lang3.StringUtils;
+
import eu.etaxonomy.cdm.common.CdmUtils;
import eu.etaxonomy.cdm.common.UTF8;
import eu.etaxonomy.cdm.model.common.Language;
BigDecimal n = quantData.getSampleSize();
String size = (n == null) ? "" : "n="+String.valueOf(n);
String strBracket = isNotBlank(size) ? "[" + size + "]" : "";
+ result = CdmUtils.concat(" ", result, strBracket);
- //modif
+ //no data status
+ if (quantData.getNoDataStatus() != null) {
+ String noDataStatus = quantData.getNoDataStatus().getLabel();
+ result = StringUtils.isEmpty(result) ? noDataStatus : noDataStatus +" (" + result + ")";
+ }
- result = CdmUtils.concat(" ", result, strBracket);
return result;
}
}
\ No newline at end of file
import eu.etaxonomy.cdm.model.common.CdmClass;
import eu.etaxonomy.cdm.model.common.ExternallyManagedImport;
import eu.etaxonomy.cdm.model.description.DescriptionType;
+import eu.etaxonomy.cdm.model.description.NoDescriptiveDataStatus;
import eu.etaxonomy.cdm.model.media.ExternalLinkType;
import eu.etaxonomy.cdm.model.metadata.CdmMetaDataPropertyName;
import eu.etaxonomy.cdm.model.molecular.SequenceDirection;
//AuthorityType
}else if (clazz.equals(AuthorityType.class)){
return AuthorityType.getByKey(val);
+ //NoDescriptiveDataStatus
+ }else if (clazz.equals(NoDescriptiveDataStatus.class)){
+ return NoDescriptiveDataStatus.getByKey(val);
}else{
throw new IllegalArgumentException(String.format("EnumType %s not supported by %s.", clazz.getSimpleName(), EnumUserType.class.getSimpleName()));
}
import java.util.Arrays;
import java.util.List;
+import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.FetchType;
import javax.persistence.OneToMany;
import javax.validation.constraints.NotEmpty;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlElementWrapper;
import javax.xml.bind.annotation.XmlRootElement;
import org.apache.logging.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.Type;
import org.hibernate.envers.Audited;
import org.hibernate.search.annotations.Indexed;
import org.hibernate.search.annotations.IndexedEmbedded;
private List<StateData> stateData = new ArrayList<>();
@XmlElement(name = "UnknownData")
+ @Deprecated //will be replaced by #noDataStatus
private final Boolean unknownData = false;
+ @XmlAttribute(name ="NoDataStatus")
+ @Column(name="noDataStatus", length=10)
+ @Type(type = "eu.etaxonomy.cdm.hibernate.EnumUserType",
+ parameters = {@org.hibernate.annotations.Parameter(name = "enumClass", value = "eu.etaxonomy.cdm.model.description.NoDescriptiveDataStatus")}
+ )
+ //see also QuantitativeData.noDataStatus
+ private NoDescriptiveDataStatus noDataStatus;
+
//****************************** FACTORY METHOD *******************************/
/**
this.orderRelevant = orderRelevant;
}
+ //no data status, #2975
+ public NoDescriptiveDataStatus getNoDataStatus() {
+ return noDataStatus;
+ }
+ public void setNoDataStatus(NoDescriptiveDataStatus noDataStatus) {
+ this.noDataStatus = noDataStatus;
+ }
+
// ********************* CONVENIENCE ******************************************/
/**
return (getFeature()!=null ? getFeature().getLabel(): "") +
"[" + stateData +
(orderRelevant? ", orderRelevant=" + orderRelevant:"") +
- (unknownData? ", unknownData=" + unknownData:"")
+ (noDataStatus != null ? ", noDataStatus=" + noDataStatus.getLabel() :"")
+ "]";
}
--- /dev/null
+/**
+* Copyright (C) 2023 EDIT
+* European Distributed Institute of Taxonomy
+* http://www.e-taxonomy.eu
+*
+* The contents of this file are subject to the Mozilla Public License Version 1.1
+* See LICENSE.TXT at the top of this package for the full license terms.
+*/
+package eu.etaxonomy.cdm.model.description;
+
+import java.util.Set;
+import java.util.UUID;
+
+import javax.xml.bind.annotation.XmlEnumValue;
+
+import eu.etaxonomy.cdm.model.common.Language;
+import eu.etaxonomy.cdm.model.term.EnumeratedTermVoc;
+import eu.etaxonomy.cdm.model.term.IEnumTerm;
+
+/**
+ * Enumeration describing why descriptive data are not available.
+ * The enumeration values are taken from SDD.
+ *
+ * @see https://dev.e-taxonomy.eu/redmine/issues/2975
+ *
+ * @author a.mueller
+ * @date 27.06.2023
+ */
+public enum NoDescriptiveDataStatus implements IEnumTerm<NoDescriptiveDataStatus> {
+
+ @XmlEnumValue("NotApllicable")
+ NotApllicable(UUID.fromString("d8c7eedd-cd84-41e3-954f-910d73a367b0"), "not applicable","NA"),
+
+ @XmlEnumValue("DataUnavailable")
+ DataUnavailable(UUID.fromString("9826baa6-0bdb-4efa-957a-b5d4f0f4d7cc"), "data unavailable","DU"),
+
+ @XmlEnumValue("ToBeIgnored")
+ ToBeIgnored(UUID.fromString("47d3a9e6-22b5-4d12-bb53-c8a92afe5e83"), "to be ignored","TBI"),
+
+ @XmlEnumValue("ToBeChecked")
+ ToBeChecked(UUID.fromString("52952fe5-cb3d-4ab9-80a9-5cc93587cd0c"), "to be checked","TBC"),
+
+ @XmlEnumValue("NotInterpretable")
+ NotInterpretable(UUID.fromString("22305490-8ea5-487c-9068-b90d16045c8c"), "Not applicable","NI"),
+
+ @XmlEnumValue("DataWithheld")
+ DataWithheld(UUID.fromString("05b2abcf-0d41-463c-bd83-30a268fa32ae"), "data withheld","DW");
+
+ private NoDescriptiveDataStatus(UUID uuid, String defaultString, String key) {
+ this(uuid, defaultString, key, null);
+ }
+ private NoDescriptiveDataStatus(UUID uuid, String defaultString, String key, NoDescriptiveDataStatus parent) {
+ delegateVocTerm = EnumeratedTermVoc.addTerm(getClass(), this, uuid, defaultString, key, parent);
+ }
+
+ // *************************** DELEGATE **************************************/
+
+ private static EnumeratedTermVoc<NoDescriptiveDataStatus> delegateVoc;
+ private IEnumTerm<NoDescriptiveDataStatus> delegateVocTerm;
+
+ static {
+ delegateVoc = EnumeratedTermVoc.getVoc(NoDescriptiveDataStatus.class);
+ }
+
+ @Override
+ public String getKey(){return delegateVocTerm.getKey();}
+
+ @Override
+ public String getLabel(){return delegateVocTerm.getLabel();}
+
+ @Override
+ public String getLabel(Language language){return delegateVocTerm.getLabel(language);}
+
+
+ @Override
+ public UUID getUuid() {return delegateVocTerm.getUuid();}
+
+ @Override
+ public NoDescriptiveDataStatus getKindOf() {return delegateVocTerm.getKindOf();}
+
+ @Override
+ public Set<NoDescriptiveDataStatus> getGeneralizationOf() {return delegateVocTerm.getGeneralizationOf();}
+
+ @Override
+ public boolean isKindOf(NoDescriptiveDataStatus ancestor) {return delegateVocTerm.isKindOf(ancestor); }
+
+ @Override
+ public Set<NoDescriptiveDataStatus> getGeneralizationOf(boolean recursive) {return delegateVocTerm.getGeneralizationOf(recursive);}
+
+ public static NoDescriptiveDataStatus getByKey(String key){return delegateVoc.getByKey(key);}
+ public static NoDescriptiveDataStatus getByUuid(UUID uuid) {return delegateVoc.getByUuid(uuid);}
+}
\ No newline at end of file
import java.util.Iterator;
import java.util.Set;
+import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.FetchType;
import javax.persistence.ManyToOne;
import javax.validation.constraints.NotEmpty;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlElementWrapper;
import javax.xml.bind.annotation.XmlIDREF;
import org.apache.logging.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.Type;
import org.hibernate.envers.Audited;
import org.hibernate.search.annotations.Indexed;
// private Integer sampleSize;
@XmlElement(name = "UnknownData")
+ @Deprecated //will be replaced by #noDataStatus
private Boolean unknownData = false;
+ @XmlAttribute(name ="NoDataStatus")
+ @Column(name="noDataStatus", length=10)
+ @Type(type = "eu.etaxonomy.cdm.hibernate.EnumUserType",
+ parameters = {@org.hibernate.annotations.Parameter(name = "enumClass", value = "eu.etaxonomy.cdm.model.description.NoDescriptiveDataStatus")}
+ )
+ //see also CategoricalData.noDataStatus
+ private NoDescriptiveDataStatus noDataStatus;
+
// ******************************** FACTORY METHODS *******************************/
/**
// return result;
// }
+ @Deprecated //will be replaced by #noDataStatus
public Boolean getUnknownData() {
return unknownData;
}
-
+ @Deprecated //will be replaced by #noDataStatus
public void setUnknownData(Boolean unknownData) {
this.unknownData = unknownData;
}
+ //no data status, #2975
+ public NoDescriptiveDataStatus getNoDataStatus() {
+ return noDataStatus;
+ }
+ public void setNoDataStatus(NoDescriptiveDataStatus noDataStatus) {
+ this.noDataStatus = noDataStatus;
+ }
+
//
// public BigDecimal getMinimum() {
// return minimum;
return (getFeature()!=null ? getFeature().getLabel(): "") +
"[" + statisticalValues +
(unit!=null ? ", unit=" + unit : "") +
- (unknownData? ", unknownData=" + unknownData:"")
+ (noDataStatus != null ? ", noDataStatus=" + noDataStatus.getLabel() :"")
+ "]";
}
-
-}
+}
\ No newline at end of file
* be handled by SCHEMA_VALIDATION.UPDATE
* The last number represents the date of change.
*/
- private static final String dbSchemaVersion = CdmVersion.V_05_38_00.versionString;
+ private static final String dbSchemaVersion = CdmVersion.V_05_40_00.versionString;
public enum CdmVersion {
V_05_12_00("5.12.0.0.20191202"),
V_05_35_01("5.35.1.0.20221218"),
V_05_36_00("5.36.0.0.20230106"),
V_05_36_01("5.36.1.0.20230323"),
- V_05_38_00("5.38.0.0.20230510")
+ V_05_38_00("5.38.0.0.20230510"),
+ V_05_40_00("5.40.0.0.20230627")
;
private String versionString;
import eu.etaxonomy.cdm.model.common.Language;
import eu.etaxonomy.cdm.model.description.CategoricalData;
import eu.etaxonomy.cdm.model.description.Feature;
+import eu.etaxonomy.cdm.model.description.NoDescriptiveDataStatus;
import eu.etaxonomy.cdm.model.description.State;
import eu.etaxonomy.cdm.model.description.StateData;
import eu.etaxonomy.cdm.model.term.DefinedTerm;
Assert.assertEquals("female state1s, textmodi state2, male unknown state3", text);
//TODO test with additional basedata like timeperiod etc.
+
+
}
-}
+ @Test
+ public void testFormatNoData() {
+ //no data status
+ CategoricalData catData = CategoricalData.NewInstance(Feature.HABITAT());
+ FormatKey[] formatKey = null;
+ CategoricalDataFormatter formatter = new CategoricalDataFormatter(catData, formatKey);
+
+ //fully empty
+ String text = formatter.format(catData, formatKey);
+ Assert.assertEquals("", text); //behavior may change in future
+
+ //data unavailable
+ catData.setNoDataStatus(NoDescriptiveDataStatus.DataUnavailable);
+ text = formatter.format(catData, formatKey);
+ Assert.assertEquals("data unavailable", text);
+
+ //data unavailable, but still data exists
+ catData.addStateData(stateData2);
+ text = formatter.format(catData, formatKey);
+ Assert.assertEquals("data unavailable (state2)", text);
+ }
+}
\ No newline at end of file
import eu.etaxonomy.cdm.model.common.Language;
import eu.etaxonomy.cdm.model.description.Feature;
import eu.etaxonomy.cdm.model.description.MeasurementUnit;
+import eu.etaxonomy.cdm.model.description.NoDescriptiveDataStatus;
import eu.etaxonomy.cdm.model.description.QuantitativeData;
import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;
public void testFormatWithModifier() {
QuantitativeData quantData = QuantitativeData.NewInstance(Feature.CHROMOSOME_NUMBER());
FormatKey[] formatKey = null;
+ QuantitativeDataFormatter formatter = new QuantitativeDataFormatter(quantData, formatKey);
quantData.addStatisticalValue(min1);
quantData.addStatisticalValue(max1);
MeasurementUnit unit = MeasurementUnit.METER();
quantData.setUnit(unit);
- QuantitativeDataFormatter formatter = new QuantitativeDataFormatter(quantData, formatKey);
String text = formatter.format(quantData, formatKey);
Assert.assertEquals("0.1"+lowerUpperSep+"1.3 m [n=2]", text);
text = formatter.format(quantData, formatKey);
Assert.assertEquals("about new mod (min"+modifierSep+"0.1"+minSep+")0.2"+lowerUpperSep+"max"+modifierSep+"1.3 m [n=2]", text);
}
+
+ @Test
+ public void testFormatNoData() {
+ //no data status
+ QuantitativeData quantData = QuantitativeData.NewInstance(Feature.CHROMOSOME_NUMBER());
+ FormatKey[] formatKey = null;
+ QuantitativeDataFormatter formatter = new QuantitativeDataFormatter(quantData, formatKey);
+
+ //fully empty
+ String text = formatter.format(quantData, formatKey);
+ Assert.assertEquals("", text); //behavior may change in future
+
+ //data unavailable
+ quantData.setNoDataStatus(NoDescriptiveDataStatus.DataUnavailable);
+ text = formatter.format(quantData, formatKey);
+ Assert.assertEquals("data unavailable", text);
+
+ //data unavailable, but still data exists
+ quantData.addStatisticalValue(min1);
+ quantData.addStatisticalValue(max1);
+ quantData.addStatisticalValue(n1);
+ MeasurementUnit unit = MeasurementUnit.METER();
+ quantData.setUnit(unit);
+ text = formatter.format(quantData, formatKey);
+ Assert.assertEquals("data unavailable (0.1"+lowerUpperSep+"1.3 m [n=2])", text);
+ }
}
\ No newline at end of file
import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
import eu.etaxonomy.cdm.database.CdmDataSource;
import eu.etaxonomy.cdm.database.ICdmDataSource;
-import eu.etaxonomy.cdm.database.update.v536_538.SchemaUpdater_5361_5380;
+import eu.etaxonomy.cdm.database.update.v538_540.SchemaUpdater_5380_5400;
import eu.etaxonomy.cdm.model.metadata.CdmMetaData;
/**
private static final Logger logger = LogManager.getLogger();
private static final ISchemaUpdater getCurrentSchemaUpdater() {
- return SchemaUpdater_5361_5380.NewInstance();
+ return SchemaUpdater_5380_5400.NewInstance();
}
public static CdmUpdater NewInstance(){
--- /dev/null
+/**
+ * Copyright (C) 2007 EDIT
+ * European Distributed Institute of Taxonomy
+ * http://www.e-taxonomy.eu
+ *
+ * The contents of this file are subject to the Mozilla Public License Version 1.1
+ * See LICENSE.TXT at the top of this package for the full license terms.
+ */
+package eu.etaxonomy.cdm.database.update.v538_540;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import eu.etaxonomy.cdm.database.update.ColumnAdder;
+import eu.etaxonomy.cdm.database.update.ISchemaUpdater;
+import eu.etaxonomy.cdm.database.update.ISchemaUpdaterStep;
+import eu.etaxonomy.cdm.database.update.SchemaUpdaterBase;
+import eu.etaxonomy.cdm.database.update.v536_538.SchemaUpdater_5361_5380;
+import eu.etaxonomy.cdm.model.metadata.CdmMetaData.CdmVersion;
+
+/**
+ * @author a.mueller
+ * @date 27.06.2023
+ */
+public class SchemaUpdater_5380_5400 extends SchemaUpdaterBase {
+
+ @SuppressWarnings("unused")
+ private static final Logger logger = LogManager.getLogger();
+
+ private static final CdmVersion startSchemaVersion = CdmVersion.V_05_38_00;
+ private static final CdmVersion endSchemaVersion = CdmVersion.V_05_40_00;
+
+// ********************** FACTORY METHOD *************************************
+
+ @Override
+ public ISchemaUpdater getPreviousUpdater() {
+ return SchemaUpdater_5361_5380.NewInstance();
+ }
+
+ public static SchemaUpdater_5380_5400 NewInstance() {
+ return new SchemaUpdater_5380_5400();
+ }
+
+ protected SchemaUpdater_5380_5400() {
+ super(startSchemaVersion.versionString(), endSchemaVersion.versionString());
+ }
+
+
+ @Override
+ protected List<ISchemaUpdaterStep> getUpdaterList() {
+
+ String stepName;
+ String tableName;
+ String columnName;
+
+ List<ISchemaUpdaterStep> stepList = new ArrayList<>();
+
+ //#2975 add noDataStatus column for descriptive data
+ stepName = "Add noDataStatus column for descriptive data";
+ tableName = "DescriptionElementBase";
+ columnName = "noDataStatus";
+ ColumnAdder.NewStringInstance(stepList, stepName, tableName, columnName, 10, INCLUDE_AUDIT);
+
+ return stepList;
+ }
+}
\ No newline at end of file
BGBM BDI Projects / cdmlib.git / commitdiff