--- /dev/null
+/**
+* Copyright (C) 2020 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.io.fact.temporal.in;
+
+/**
+ * Analyzer for taxon based phenology import.
+ *
+ * TODO not yet implemented
+ *
+ * @author a.mueller
+ * @since 15.07.2020
+ */
+public class PhenologyExcelFormatAnalyzer
+ extends TemporalDataExcelFormatAnalyzer<PhenologyExcelImportConfigurator> {
+
+ protected PhenologyExcelFormatAnalyzer(PhenologyExcelImportConfigurator config) {
+ super(config, requiredWorksheets(), requiredColumns(), optionalColumns(), optionalMultiColumns());
+ }
+
+ private static String[] requiredWorksheets() {
+ return new String[]{"Data","Vocabulary"};
+ }
+
+ private static String[] requiredColumns() {
+ return new String[]{"taxonUuid", "xxx", "xxx"};
+ }
+
+ private static String[] optionalColumns() {
+ return new String[]{"nameCache", "nameFullCache"};
+ }
+ private static String[] optionalMultiColumns() {
+ return new String[]{};
+ }
+
+
+}
--- /dev/null
+/**
+* Copyright (C) 2017 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.io.fact.temporal.in;
+
+import java.util.Map;
+import java.util.UUID;
+
+import org.springframework.stereotype.Component;
+
+import eu.etaxonomy.cdm.model.description.Feature;
+import eu.etaxonomy.cdm.model.taxon.Taxon;
+
+/**
+ * Import for taxon based phenology data.
+ *
+ * @author a.mueller
+ * @since 15.07.2020
+ */
+@Component
+public class PhenologyExcelImport
+ extends TemporalDataExcelImport<PhenologyExcelImportState, PhenologyExcelImportConfigurator>{
+
+ private static final long serialVersionUID = 1050528888222978429L;
+
+ public static final String FLOWERING_START = "Flowering start";
+ public static final String FLOWERING_END = "Flowering end";
+ public static final String FRUITING_START = "Fruiting start";
+ public static final String FRUITING_END = "Fruiting end";
+
+ @Override
+ protected void doFirstPass(PhenologyExcelImportState state, Taxon taxon,
+ String line, String linePure){
+
+ super.doFirstPass(state, taxon, line, linePure);
+
+ if (taxon == null){
+// return;
+ taxon = Taxon.NewInstance(null, null);
+ }
+
+ Map<String, String> record = state.getOriginalRecord();
+
+ UUID uuidFeatureFruiting = state.getConfig().getFruitingFeatureUuid();
+ Feature featureFruiting = (Feature)getTermService().find(uuidFeatureFruiting);
+ String colFruitingStart = state.getConfig().getFruitingStartColumnLabel();
+ String colFruitingEnd = state.getConfig().getFruitingEndColumnLabel();
+
+ handleFeature(state, taxon, line, linePure, record, featureFruiting, colFruitingStart, colFruitingEnd);
+ }
+}
\ No newline at end of file
--- /dev/null
+/**
+* Copyright (C) 2017 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.io.fact.temporal.in;
+
+import java.net.URI;
+import java.util.UUID;
+
+import eu.etaxonomy.cdm.database.ICdmDataSource;
+import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
+import eu.etaxonomy.cdm.model.description.Feature;
+
+/**
+ * Configurator for taxon based phenology import.
+ *
+ * @author a.mueller
+ * @since 15.07.2020
+ */
+public class PhenologyExcelImportConfigurator
+ extends TemporalDataExcelImportConfigurator<PhenologyExcelFormatAnalyzer>{
+
+ private static final long serialVersionUID = 2413575026028295925L;
+
+ private String floweringStartColumnLabel = PhenologyExcelImport.FLOWERING_START;
+ private String floweringEndColumnLabel = PhenologyExcelImport.FLOWERING_END;
+ private String fruitingStartColumnLabel = PhenologyExcelImport.FRUITING_START;
+ private String fruitingEndColumnLabel = PhenologyExcelImport.FRUITING_END;
+
+ public static PhenologyExcelImportConfigurator NewInstance(URI uri, ICdmDataSource destination){
+ return new PhenologyExcelImportConfigurator(uri, destination, null);
+ }
+
+ private PhenologyExcelImportConfigurator(URI uri, ICdmDataSource destination, IInputTransformer transformer) {
+ super(uri, destination, transformer);
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public PhenologyExcelImportState getNewState() {
+ return new PhenologyExcelImportState(this);
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ protected void makeIoClassList() {
+ ioClassList = new Class[]{
+ PhenologyExcelImport.class,
+ };
+ }
+
+ @Override
+ public PhenologyExcelFormatAnalyzer getAnalyzer() {
+ return new PhenologyExcelFormatAnalyzer(this);
+ }
+
+ @Override
+ //Used for flowering uuid
+ public UUID getFeatureUuid() {
+ return Feature.uuidFloweringPeriod;
+ }
+
+ public UUID getFruitingFeatureUuid() {
+ return Feature.uuidFruitingPeriod;
+ }
+
+ @Override
+ @Deprecated
+ public String getColumnLabelStart() {
+ return getFloweringStartColumnLabel();
+ }
+ @Override
+ @Deprecated
+ public void setColumnLabelStart(String columnLabelStart) {
+ setFloweringStartColumnLabel(columnLabelStart);
+ }
+
+ @Override
+ @Deprecated
+ public String getColumnLabelEnd() {
+ return getFloweringEndColumnLabel();
+ }
+ @Override
+ @Deprecated
+ public void setColumnLabelEnd(String columnLabelEnd) {
+ setFloweringEndColumnLabel(columnLabelEnd);
+ }
+
+ public String getFloweringStartColumnLabel() {
+ return floweringStartColumnLabel;
+ }
+ public void setFloweringStartColumnLabel(String floweringStartColumnLabel) {
+ this.floweringStartColumnLabel = floweringStartColumnLabel;
+ }
+
+ public String getFloweringEndColumnLabel() {
+ return floweringEndColumnLabel;
+ }
+ public void setFloweringEndColumnLabel(String floweringEndColumnLabel) {
+ this.floweringEndColumnLabel = floweringEndColumnLabel;
+ }
+
+ public String getFruitingStartColumnLabel() {
+ return fruitingStartColumnLabel;
+ }
+ public void setFruitingStartColumnLabel(String fruitingStartColumnLabel) {
+ this.fruitingStartColumnLabel = fruitingStartColumnLabel;
+ }
+
+ public String getFruitingEndColumnLabel() {
+ return fruitingEndColumnLabel;
+ }
+ public void setFruitingEndColumnLabel(String fruitingEndColumnLabel) {
+ this.fruitingEndColumnLabel = fruitingEndColumnLabel;
+ }
+}
--- /dev/null
+/**
+* Copyright (C) 2017 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.io.fact.temporal.in;
+
+/**
+ * State for taxon based phenology import.
+ *
+ * @author a.mueller
+ * @since 15.07.2020
+ */
+public class PhenologyExcelImportState
+ extends TemporalDataExcelImportState<PhenologyExcelImportConfigurator>{
+
+ public PhenologyExcelImportState(PhenologyExcelImportConfigurator config) {
+ super(config);
+ }
+}
--- /dev/null
+/**
+* Copyright (C) 2020 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.io.fact.temporal.in;
+
+import eu.etaxonomy.cdm.io.fact.altitude.in.analyze.ExcelFormatAnalyzer;
+
+/**
+ * Analyzer for taxon based temporal data import.
+ *
+ * TODO not yet implemented
+ *
+ * @author a.mueller
+ * @since 15.07.2020
+ */
+public class TemporalDataExcelFormatAnalyzer<CONFIG extends TemporalDataExcelImportConfigurator<?>>
+ extends ExcelFormatAnalyzer<CONFIG> {
+
+ public TemporalDataExcelFormatAnalyzer(CONFIG config,
+ String[] requiredWorksheets,
+ String[] requiredColumns,
+ String[] optionalColumns,
+ String[] optionalMultiColumns) {
+ super(config, requiredWorksheets, requiredColumns, optionalColumns, optionalMultiColumns);
+ }
+
+ protected TemporalDataExcelFormatAnalyzer(CONFIG config) {
+ super(config, requiredWorksheets(), requiredColumns(), optionalColumns(), optionalMultiColumns());
+ }
+
+ private static String[] requiredWorksheets() {
+ return new String[]{"Data","Vocabulary"};
+ }
+
+ private static String[] requiredColumns() {
+ return new String[]{"taxonUuid", "xxx", "xxx"};
+ }
+
+ private static String[] optionalColumns() {
+ return new String[]{"nameCache", "nameFullCache"};
+ }
+ private static String[] optionalMultiColumns() {
+ return new String[]{};
+ }
+
+
+}
--- /dev/null
+/**
+* Copyright (C) 2017 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.io.fact.temporal.in;
+
+import java.util.Map;
+import java.util.UUID;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.commons.lang3.StringUtils;
+import org.springframework.stereotype.Component;
+
+import eu.etaxonomy.cdm.io.excel.common.ExcelRowBase;
+import eu.etaxonomy.cdm.io.fact.in.FactExcelImportBase;
+import eu.etaxonomy.cdm.model.common.ExtendedTimePeriod;
+import eu.etaxonomy.cdm.model.description.Feature;
+import eu.etaxonomy.cdm.model.description.TaxonDescription;
+import eu.etaxonomy.cdm.model.description.TemporalData;
+import eu.etaxonomy.cdm.model.reference.Reference;
+import eu.etaxonomy.cdm.model.taxon.Taxon;
+
+/**
+ * Import for taxon based temporal data.
+ *
+ * @author a.mueller
+ * @since 15.07.2020
+ */
+@Component
+public class TemporalDataExcelImport<STATE extends TemporalDataExcelImportState<CONFIG>, CONFIG extends TemporalDataExcelImportConfigurator<?>>
+ extends FactExcelImportBase<STATE, CONFIG, ExcelRowBase>{
+
+ private static final long serialVersionUID = -2885338554616141176L;
+
+ @Override
+ protected String getWorksheetName(CONFIG config) {
+ return "Data";
+ }
+
+ @Override
+ protected void doFirstPass(STATE state, Taxon taxon,
+ String line, String linePure){
+
+ if (taxon == null){
+// return;
+ taxon = Taxon.NewInstance(null, null);
+ }
+
+ Map<String, String> record = state.getOriginalRecord();
+
+ Feature feature = null;
+ UUID uuidFeature = state.getConfig().getFeatureUuid();
+ if (uuidFeature != null){
+ feature = (Feature)getTermService().find(uuidFeature);
+ }
+ if (feature == null){
+ String message = "Feature could not be defined. Import not possible.";
+ state.addError(message);
+ return;
+ }
+
+ String colLabelStart = state.getConfig().getColumnLabelStart();
+ String colLabelEnd = state.getConfig().getColumnLabelEnd();
+
+ handleFeature(state, taxon, line, linePure, record, feature, colLabelStart, colLabelEnd);
+
+ }
+
+ protected void handleFeature(STATE state, Taxon taxon, String line, String linePure,
+ Map<String, String> record, Feature feature, String startColLabel, String endColLabel) {
+
+ TemporalData temporalData = TemporalData.NewInstance(feature);
+ String startMonthStr = getValue(record, startColLabel);
+ String endMonthStr = getValue(record, endColLabel);
+ Integer startMonth = monthToInteger(state, startMonthStr, startColLabel, false);
+ Integer startMonthExtreme = monthToInteger(state, startMonthStr, startColLabel, true);
+ Integer endMonth = monthToInteger(state, endMonthStr, endColLabel, false);
+ Integer endMonthExtreme = monthToInteger(state, endMonthStr, endColLabel, true);
+ ExtendedTimePeriod period = ExtendedTimePeriod.NewExtendedMonthInstance(startMonth, endMonth, startMonthExtreme, endMonthExtreme);
+ temporalData.setPeriod(period);
+
+ //source
+ String id = null;
+ String idNamespace = getWorksheetName(state.getConfig());
+ Reference reference = getSourceReference(state);
+
+ //description
+ if (!temporalData.getPeriod().isEmpty()){
+ TaxonDescription taxonDescription = this.getTaxonDescription(taxon, reference, !IMAGE_GALLERY, true);
+ taxonDescription.addElement(temporalData);
+ temporalData.addImportSource(id, idNamespace, reference, linePure);
+ }
+ }
+
+ private Integer monthToInteger(STATE state, String monthStr, String colLabel, boolean isExtreme) {
+ if(StringUtils.isBlank(monthStr)){
+ return null;
+ }else {
+ Matcher matcher = getPattern().matcher(monthStr);
+ if (matcher.matches()){
+ if(isExtreme){
+ if (matcher.group(2) != null){
+ String extreme = matcher.group(2);
+ return Integer.valueOf(extreme);
+ }else{
+ return null; //extreme value does not exist
+ }
+ }else{
+ String normal = matcher.group(1);
+ return Integer.valueOf(normal);
+ }
+ }else{
+ if (!isExtreme){ //we have to record this only once
+ String message = "Value " + monthStr + " for " + colLabel + " could not be transformed to a valid month number. Value not imported." ;
+ state.addError(message);
+ }
+ }
+ }
+ return null;
+ }
+
+ private Pattern monthPattern;
+ private Pattern getPattern() {
+ if (monthPattern == null){
+ String nr = "(0?[1-9]|1[0-2])";
+ monthPattern = Pattern.compile(nr + "\\s*(?:\\(" + nr + "\\))?");
+ }
+ return monthPattern;
+ }
+
+ @Override
+ protected boolean requiresNomenclaturalCode() {
+ return false;
+ }
+
+ @Override
+ protected boolean isIgnore(STATE state) {
+ return false;
+ }
+}
\ No newline at end of file
--- /dev/null
+/**
+* Copyright (C) 2017 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.io.fact.temporal.in;
+
+import java.net.URI;
+
+import eu.etaxonomy.cdm.database.ICdmDataSource;
+import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
+import eu.etaxonomy.cdm.io.fact.in.FactExcelImportConfiguratorBase;
+import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
+
+/**
+ * Configurator for taxon based temporal data import.
+ *
+ * @author a.mueller
+ * @since 15.07.2020
+ */
+public class TemporalDataExcelImportConfigurator<ANALYZE extends TemporalDataExcelFormatAnalyzer<?>>
+ extends FactExcelImportConfiguratorBase<ANALYZE>{
+
+ private static final long serialVersionUID = 2413575026028295925L;
+
+ private String columnLabelStart = "Start";
+ private String columnLabelEnd = "End";
+
+ public static final TemporalDataExcelImportConfigurator<TemporalDataExcelFormatAnalyzer<?>> NewTemporalInstance(URI uri, ICdmDataSource destination){
+ return new TemporalDataExcelImportConfigurator<TemporalDataExcelFormatAnalyzer<?>>(uri, destination, null);
+ }
+
+ protected TemporalDataExcelImportConfigurator(URI uri, ICdmDataSource destination, IInputTransformer transformer) {
+ super(uri, destination, transformer);
+ }
+
+ @SuppressWarnings({ "unchecked" })
+ @Override
+ public TemporalDataExcelImportState<?> getNewState() {
+ return new TemporalDataExcelImportState<>(this);
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ protected void makeIoClassList() {
+ ioClassList = new Class[]{
+ TemporalDataExcelImport.class,
+ };
+ }
+
+ /**
+ * Note: This method needs to be overriden by potential subclasses.
+ */
+ @SuppressWarnings("unchecked")
+ @Override
+ public ANALYZE getAnalyzer() {
+ return (ANALYZE)new TemporalDataExcelFormatAnalyzer(this);
+ }
+
+ @Override
+ public NomenclaturalCode getNomenclaturalCode() {
+ NomenclaturalCode result = super.getNomenclaturalCode();
+ if (result == null){
+ result = NomenclaturalCode.ICNAFP;
+ }
+ return result;
+ }
+
+ public void setRowToNeglect(int row){
+
+ }
+
+ public String getColumnLabelStart() {
+ return columnLabelStart;
+ }
+ public void setColumnLabelStart(String columnLabelStart) {
+ this.columnLabelStart = columnLabelStart;
+ }
+
+ public String getColumnLabelEnd() {
+ return columnLabelEnd;
+ }
+ public void setColumnLabelEnd(String columnLabelEnd) {
+ this.columnLabelEnd = columnLabelEnd;
+ }
+
+}
--- /dev/null
+/**
+* Copyright (C) 2017 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.io.fact.temporal.in;
+
+import eu.etaxonomy.cdm.io.fact.in.FactExcelImportStateBase;
+
+/**
+ * State for taxon based temporal data import.
+ *
+ * @author a.mueller
+ * @since 15.07.2020
+ */
+public class TemporalDataExcelImportState<CONFIG extends TemporalDataExcelImportConfigurator>
+ extends FactExcelImportStateBase<CONFIG>{
+
+ public TemporalDataExcelImportState(CONFIG config) {
+ super(config);
+ }
+}
private static final UUID uuidUseRecord = UUID.fromString("8125a59d-b4d5-4485-89ea-67306297b599");
private static final UUID uuidNotes = UUID.fromString("b5780b45-6439-4f3c-9818-d89d26d36eb2");
public static final UUID uuidLifeform = UUID.fromString("db9228d3-8bbf-4460-abfe-0b1326c82f8e");
- private static final UUID uuidFloweringPeriod = UUID.fromString("03710cb5-606e-444a-a3e6-594268e3cc47");
- private static final UUID uuidFruitingPeriod = UUID.fromString("04aa8993-24b4-43e3-888c-5afaa733376e");
+ public static final UUID uuidFloweringPeriod = UUID.fromString("03710cb5-606e-444a-a3e6-594268e3cc47");
+ public static final UUID uuidFruitingPeriod = UUID.fromString("04aa8993-24b4-43e3-888c-5afaa733376e");
public static final UUID uuidAltitude = UUID.fromString("1a28ed59-e15f-4001-b5c2-ea89f0012671");
/* ***************** CONSTRUCTOR AND FACTORY METHODS **********************************/
@XmlElement(name = "Period")
private ExtendedTimePeriod period = ExtendedTimePeriod.NewExtendedInstance();
-
/**
- * Creates a period fact with the given period.
+ * Creates a temporal fact with the given period.
*/
public static TemporalData NewInstance(ExtendedTimePeriod period){
TemporalData result = new TemporalData();
return result;
}
+ public static TemporalData NewInstance(Feature feature){
+ TemporalData result = new TemporalData();
+ result.setFeature(feature);
+ return result;
+ }
+
+ public static TemporalData NewInstance(Feature feature, ExtendedTimePeriod period){
+ TemporalData result = new TemporalData();
+ result.setFeature(feature);
+ result.setPeriod(period);
+ return result;
+ }
+
// *************************** CONSTRUCTOR *************************************/
/**
BGBM BDI Projects / cdmlib.git / commitdiff