-// $Id$
-/**
-* 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.io.specimen.abcd206.in;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.springframework.transaction.TransactionStatus;
-
-import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
-import eu.etaxonomy.cdm.io.common.CdmImportBase;
-import eu.etaxonomy.cdm.io.common.ImportStateBase;
-import eu.etaxonomy.cdm.model.common.OriginalSourceBase;
-import eu.etaxonomy.cdm.model.description.TaxonDescription;
-import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
-import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
-import eu.etaxonomy.cdm.model.reference.Reference;
-import eu.etaxonomy.cdm.model.taxon.Classification;
-
-/**
- * @author a.mueller
- * @created 11.05.2009
- * @version 1.0
- */
-public class Abcd206ImportState extends ImportStateBase<Abcd206ImportConfigurator, CdmImportBase<Abcd206ImportConfigurator,Abcd206ImportState>>{
- @SuppressWarnings("unused")
- private static final Logger logger = Logger.getLogger(Abcd206ImportState.class);
-
- private TransactionStatus tx;
-
- private ICdmApplicationConfiguration cdmRepository;
-
- private Classification classification = null;
- private Classification defaultClassification = null;
- private Reference<?> ref = null;
-
- private Abcd206DataHolder dataHolder;
- private DerivedUnit derivedUnitBase;
- private FieldUnit fieldUnit;
-
- private List<OriginalSourceBase<?>> associationRefs = new ArrayList<OriginalSourceBase<?>>();
- private boolean associationSourcesSet=false;
- private List<OriginalSourceBase<?>> descriptionRefs = new ArrayList<OriginalSourceBase<?>>();
- private boolean descriptionSourcesSet=false;
- private List<OriginalSourceBase<?>> derivedUnitSources = new ArrayList<OriginalSourceBase<?>>();
- private boolean derivedUnitSourcesSet=false;
- private boolean descriptionGroupSet = false;
- private TaxonDescription descriptionGroup = null;
-
-//****************** CONSTRUCTOR ***************************************************/
-
- public Abcd206ImportState(Abcd206ImportConfigurator config) {
- super(config);
- }
-
-//************************ GETTER / SETTER *****************************************/
-
- public TransactionStatus getTx() {
- return tx;
- }
-
- public void setTx(TransactionStatus tx) {
- this.tx = tx;
- }
-
- public ICdmApplicationConfiguration getCdmRepository() {
- return cdmRepository;
- }
-
- public void setCdmRepository(ICdmApplicationConfiguration cdmRepository) {
- this.cdmRepository = cdmRepository;
- }
-
- public Classification getClassification() {
- return classification;
- }
-
- public void setClassification(Classification classification) {
- this.classification = classification;
- }
-
- public Classification getDefaultClassification() {
- return defaultClassification;
- }
-
- public void setDefaultClassification(Classification defaultClassification) {
- this.defaultClassification = defaultClassification;
- }
-
- public Reference<?> getRef() {
- return ref;
- }
-
- public void setRef(Reference<?> ref) {
- this.ref = ref;
- }
-
- public Abcd206DataHolder getDataHolder() {
- return dataHolder;
- }
-
- public void setDataHolder(Abcd206DataHolder dataHolder) {
- this.dataHolder = dataHolder;
- }
-
- public DerivedUnit getDerivedUnitBase() {
- return derivedUnitBase;
- }
-
- public void setDerivedUnitBase(DerivedUnit derivedUnitBase) {
- this.derivedUnitBase = derivedUnitBase;
- }
-
- public FieldUnit getFieldUnit() {
- return fieldUnit;
- }
-
- public void setFieldUnit(FieldUnit fieldUnit) {
- this.fieldUnit = fieldUnit;
- }
-
- public List<OriginalSourceBase<?>> getAssociationRefs() {
- return associationRefs;
- }
-
- public void setAssociationRefs(List<OriginalSourceBase<?>> associationRefs) {
- this.associationRefs = associationRefs;
- }
-
- public boolean isAssociationSourcesSet() {
- return associationSourcesSet;
- }
-
- public void setAssociationSourcesSet(boolean associationSourcesSet) {
- this.associationSourcesSet = associationSourcesSet;
- }
-
- public List<OriginalSourceBase<?>> getDescriptionRefs() {
- return descriptionRefs;
- }
-
- public void setDescriptionRefs(List<OriginalSourceBase<?>> descriptionRefs) {
- this.descriptionRefs = descriptionRefs;
- }
-
- public boolean isDescriptionSourcesSet() {
- return descriptionSourcesSet;
- }
-
- public void setDescriptionSourcesSet(boolean descriptionSourcesSet) {
- this.descriptionSourcesSet = descriptionSourcesSet;
- }
-
- public List<OriginalSourceBase<?>> getDerivedUnitSources() {
- return derivedUnitSources;
- }
-
- public void setDerivedUnitSources(List<OriginalSourceBase<?>> derivedUnitSources) {
- this.derivedUnitSources = derivedUnitSources;
- }
-
- public boolean isDerivedUnitSourcesSet() {
- return derivedUnitSourcesSet;
- }
-
- public void setDerivedUnitSourcesSet(boolean derivedUnitSourcesSet) {
- this.derivedUnitSourcesSet = derivedUnitSourcesSet;
- }
-
- public boolean isDescriptionGroupSet() {
- return descriptionGroupSet;
- }
-
- public void setDescriptionGroupSet(boolean descriptionGroupSet) {
- this.descriptionGroupSet = descriptionGroupSet;
- }
-
- public TaxonDescription getDescriptionGroup() {
- return descriptionGroup;
- }
-
- public void setDescriptionGroup(TaxonDescription descriptionGroup) {
- this.descriptionGroup = descriptionGroup;
- }
-
-
-
-}
+// $Id$\r
+/**\r
+* Copyright (C) 2007 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+\r
+package eu.etaxonomy.cdm.io.specimen.abcd206.in;\r
+\r
+import java.util.ArrayList;\r
+import java.util.List;\r
+\r
+import org.apache.log4j.Logger;\r
+import org.springframework.transaction.TransactionStatus;\r
+\r
+import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;\r
+import eu.etaxonomy.cdm.io.common.CdmImportBase;\r
+import eu.etaxonomy.cdm.io.common.ImportStateBase;\r
+import eu.etaxonomy.cdm.model.common.OriginalSourceBase;\r
+import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
+import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;\r
+import eu.etaxonomy.cdm.model.occurrence.FieldUnit;\r
+import eu.etaxonomy.cdm.model.reference.Reference;\r
+import eu.etaxonomy.cdm.model.taxon.Classification;\r
+\r
+/**\r
+ * @author a.mueller\r
+ * @created 11.05.2009\r
+ * @version 1.0\r
+ */\r
+public class Abcd206ImportState extends ImportStateBase<Abcd206ImportConfigurator, CdmImportBase<Abcd206ImportConfigurator,Abcd206ImportState>>{\r
+ @SuppressWarnings("unused")\r
+ private static final Logger logger = Logger.getLogger(Abcd206ImportState.class);\r
+\r
+ private TransactionStatus tx;\r
+\r
+ private ICdmApplicationConfiguration cdmRepository;\r
+\r
+ private Classification classification = null;\r
+ private Classification defaultClassification = null;\r
+ private Reference<?> ref = null;\r
+\r
+ private Abcd206DataHolder dataHolder;\r
+ private DerivedUnit derivedUnitBase;\r
+ private FieldUnit fieldUnit;\r
+\r
+ private List<OriginalSourceBase<?>> associationRefs = new ArrayList<OriginalSourceBase<?>>();\r
+ private boolean associationSourcesSet=false;\r
+ private List<OriginalSourceBase<?>> descriptionRefs = new ArrayList<OriginalSourceBase<?>>();\r
+ private boolean descriptionSourcesSet=false;\r
+ private List<OriginalSourceBase<?>> derivedUnitSources = new ArrayList<OriginalSourceBase<?>>();\r
+ private boolean derivedUnitSourcesSet=false;\r
+ private boolean descriptionGroupSet = false;\r
+ private TaxonDescription descriptionGroup = null;\r
+\r
+//****************** CONSTRUCTOR ***************************************************/\r
+\r
+ public Abcd206ImportState(Abcd206ImportConfigurator config) {\r
+ super(config);\r
+ }\r
+\r
+//************************ GETTER / SETTER *****************************************/\r
+\r
+ public TransactionStatus getTx() {\r
+ return tx;\r
+ }\r
+\r
+ public void setTx(TransactionStatus tx) {\r
+ this.tx = tx;\r
+ }\r
+\r
+ public ICdmApplicationConfiguration getCdmRepository() {\r
+ return cdmRepository;\r
+ }\r
+\r
+ public void setCdmRepository(ICdmApplicationConfiguration cdmRepository) {\r
+ this.cdmRepository = cdmRepository;\r
+ }\r
+\r
+ public Classification getClassification() {\r
+ return classification;\r
+ }\r
+\r
+ public void setClassification(Classification classification) {\r
+ this.classification = classification;\r
+ }\r
+\r
+ public Classification getDefaultClassification() {\r
+ return defaultClassification;\r
+ }\r
+\r
+ public void setDefaultClassification(Classification defaultClassification) {\r
+ this.defaultClassification = defaultClassification;\r
+ }\r
+\r
+ public Reference<?> getRef() {\r
+ return ref;\r
+ }\r
+\r
+ public void setRef(Reference<?> ref) {\r
+ this.ref = ref;\r
+ }\r
+\r
+ public Abcd206DataHolder getDataHolder() {\r
+ return dataHolder;\r
+ }\r
+\r
+ public void setDataHolder(Abcd206DataHolder dataHolder) {\r
+ this.dataHolder = dataHolder;\r
+ }\r
+\r
+ public DerivedUnit getDerivedUnitBase() {\r
+ return derivedUnitBase;\r
+ }\r
+\r
+ public void setDerivedUnitBase(DerivedUnit derivedUnitBase) {\r
+ this.derivedUnitBase = derivedUnitBase;\r
+ }\r
+\r
+ public FieldUnit getFieldUnit() {\r
+ return fieldUnit;\r
+ }\r
+\r
+ public void setFieldUnit(FieldUnit fieldUnit) {\r
+ this.fieldUnit = fieldUnit;\r
+ }\r
+\r
+ public List<OriginalSourceBase<?>> getAssociationRefs() {\r
+ return associationRefs;\r
+ }\r
+\r
+ public void setAssociationRefs(List<OriginalSourceBase<?>> associationRefs) {\r
+ this.associationRefs = associationRefs;\r
+ }\r
+\r
+ public boolean isAssociationSourcesSet() {\r
+ return associationSourcesSet;\r
+ }\r
+\r
+ public void setAssociationSourcesSet(boolean associationSourcesSet) {\r
+ this.associationSourcesSet = associationSourcesSet;\r
+ }\r
+\r
+ public List<OriginalSourceBase<?>> getDescriptionRefs() {\r
+ return descriptionRefs;\r
+ }\r
+\r
+ public void setDescriptionRefs(List<OriginalSourceBase<?>> descriptionRefs) {\r
+ this.descriptionRefs = descriptionRefs;\r
+ }\r
+\r
+ public boolean isDescriptionSourcesSet() {\r
+ return descriptionSourcesSet;\r
+ }\r
+\r
+ public void setDescriptionSourcesSet(boolean descriptionSourcesSet) {\r
+ this.descriptionSourcesSet = descriptionSourcesSet;\r
+ }\r
+\r
+ public List<OriginalSourceBase<?>> getDerivedUnitSources() {\r
+ return derivedUnitSources;\r
+ }\r
+\r
+ public void setDerivedUnitSources(List<OriginalSourceBase<?>> derivedUnitSources) {\r
+ this.derivedUnitSources = derivedUnitSources;\r
+ }\r
+\r
+ public boolean isDerivedUnitSourcesSet() {\r
+ return derivedUnitSourcesSet;\r
+ }\r
+\r
+ public void setDerivedUnitSourcesSet(boolean derivedUnitSourcesSet) {\r
+ this.derivedUnitSourcesSet = derivedUnitSourcesSet;\r
+ }\r
+\r
+ public boolean isDescriptionGroupSet() {\r
+ return descriptionGroupSet;\r
+ }\r
+\r
+ public void setDescriptionGroupSet(boolean descriptionGroupSet) {\r
+ this.descriptionGroupSet = descriptionGroupSet;\r
+ }\r
+\r
+ public TaxonDescription getDescriptionGroup() {\r
+ return descriptionGroup;\r
+ }\r
+\r
+ public void setDescriptionGroup(TaxonDescription descriptionGroup) {\r
+ this.descriptionGroup = descriptionGroup;\r
+ }\r
+\r
+\r
+\r
+}\r
-/**
-* 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.io.specimen.abcd206.in;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.io.FileNotFoundException;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.net.URL;
-import java.text.ParseException;
-import java.util.List;
-import java.util.Set;
-import java.util.UUID;
-
-import org.joda.time.DateTime;
-import org.junit.Assert;
-import org.junit.Test;
-import org.unitils.dbunit.annotation.DataSet;
-import org.unitils.spring.annotation.SpringBeanByName;
-import org.unitils.spring.annotation.SpringBeanByType;
-
-import eu.etaxonomy.cdm.api.service.IOccurrenceService;
-import eu.etaxonomy.cdm.api.service.IReferenceService;
-import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;
-import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport;
-import eu.etaxonomy.cdm.model.common.DefinedTerm;
-import eu.etaxonomy.cdm.model.media.MediaUtils;
-import eu.etaxonomy.cdm.model.molecular.Amplification;
-import eu.etaxonomy.cdm.model.molecular.AmplificationResult;
-import eu.etaxonomy.cdm.model.molecular.DnaQuality;
-import eu.etaxonomy.cdm.model.molecular.DnaSample;
-import eu.etaxonomy.cdm.model.molecular.Primer;
-import eu.etaxonomy.cdm.model.molecular.Sequence;
-import eu.etaxonomy.cdm.model.molecular.SequenceDirection;
-import eu.etaxonomy.cdm.model.molecular.SequenceString;
-import eu.etaxonomy.cdm.model.molecular.SingleRead;
-import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
-import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
-import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
-import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
-import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
-import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
-import eu.etaxonomy.cdm.model.reference.Reference;
-import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
-import eu.etaxonomy.cdm.test.unitils.CleanSweepInsertLoadStrategy;
-
-/**
- * @author a.mueller
- * @created 29.01.2009
- */
-public class AbcdGgbnImportTest extends CdmTransactionalIntegrationTest {
-
- @SpringBeanByName
- private CdmApplicationAwareDefaultImport<?> defaultImport;
-
- @SpringBeanByType
- private IOccurrenceService occurrenceService;
-
- @SpringBeanByType
- private IReferenceService referenceService;
-
- /**
- * Tests import import of DNA unit and all its parameters
- * and sub derivatives (sequence, amplification, etc.)
- * @throws ParseException
- */
- @Test
- @DataSet( value="../../../BlankDataSet.xml", loadStrategy=CleanSweepInsertLoadStrategy.class)
- public void testImportGgbn() throws ParseException {
- String inputFile = "/eu/etaxonomy/cdm/io/specimen/abcd206/in/db6.xml";
- URL url = this.getClass().getResource(inputFile);
- assertNotNull("URL for the test file '" + inputFile + "' does not exist", url);
-
- Abcd206ImportConfigurator importConfigurator = null;
- try {
- importConfigurator = Abcd206ImportConfigurator.NewInstance(url.toURI(), null,false);
- } catch (URISyntaxException e) {
- e.printStackTrace();
- Assert.fail();
- }
- assertNotNull("Configurator could not be created", importConfigurator);
-
- boolean result = defaultImport.invoke(importConfigurator);
- assertTrue("Return value for import.invoke should be true", result);
- assertEquals("Number of derived units is incorrect", 1, occurrenceService.count(DerivedUnit.class));
- assertEquals("Number of dna samples is incorrect", 1, occurrenceService.count(DnaSample.class));
- assertEquals("Number of field units is incorrect", 1, occurrenceService.count(FieldUnit.class));
-
- //associated specimen
- FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();
- config.setSignificantIdentifier("B 10 0066577");
- List<SpecimenOrObservationBase> records = occurrenceService.findByTitle(config).getRecords();
- assertEquals(1, records.size());
- SpecimenOrObservationBase derivedUnitSpecimen = records.iterator().next();
- assertEquals(DerivedUnit.class, derivedUnitSpecimen.getClass());
- DerivedUnit specimen = (DerivedUnit) derivedUnitSpecimen;
- assertEquals("Herbarium Berolinense", specimen.getCollection().getName());
- assertTrue(SpecimenOrObservationType.DnaSample!=specimen.getRecordBasis());
-
- //dna sample
- FindOccurrencesConfigurator dnaConfig = new FindOccurrencesConfigurator();
- dnaConfig.setSignificantIdentifier("DB 6");
- List<SpecimenOrObservationBase> dnaRecords = occurrenceService.findByTitle(dnaConfig).getRecords();
- assertEquals(1, dnaRecords.size());
- SpecimenOrObservationBase dnaSpecimen = dnaRecords.iterator().next();
- assertEquals(DnaSample.class, dnaSpecimen.getClass());
- DnaSample dnaSample = (DnaSample) dnaSpecimen;
- DerivationEvent derivedFrom = dnaSample.getDerivedFrom();
- assertNotNull(derivedFrom);
- assertEquals("Wrong derivation type!", DerivationEventType.DNA_EXTRACTION(), derivedFrom.getType());
- assertEquals("Wrong number of originals", 1, derivedFrom.getOriginals().size());
- assertEquals("DNA Bank", dnaSample.getCollection().getCode());
- assertEquals(SpecimenOrObservationType.DnaSample, dnaSample.getRecordBasis());
- //preservation/preparation
- assertNotNull(derivedFrom.getActor());
- assertEquals("Bansemer, Jana", derivedFrom.getActor().getTitleCache());
- assertNotNull(derivedFrom.getTimeperiod());
- assertEquals((Integer)2002,derivedFrom.getTimeperiod().getStartYear());
- assertEquals((Integer)8,derivedFrom.getTimeperiod().getStartMonth());
- assertEquals((Integer)13,derivedFrom.getTimeperiod().getStartDay());
- assertNotNull(dnaSample.getPreservation());
-
-
- //dna quality
- DnaQuality dnaQuality = dnaSample.getDnaQuality();
- assertNotNull("Dna quality is null", dnaQuality!=null);
- assertEquals(new Double("0.77"),dnaQuality.getRatioOfAbsorbance260_230());
- assertEquals(new Double("1.38"),dnaQuality.getRatioOfAbsorbance260_280());
- assertEquals(new DateTime(2008, 4, 15, 0, 0),dnaQuality.getQualityCheckDate());
-// assertEquals(MeasurementUnit.NewInstance(, label, labelAbbrev)DateTime(2008, 4, 15, 0, 0),dnaQuality.getQualityCheckDate());
-
- //amplifications
- Set<AmplificationResult> amplificationResults = dnaSample.getAmplificationResults();
- assertNotNull(amplificationResults);
- assertEquals(1, amplificationResults.size());
- AmplificationResult amplificationResult = amplificationResults.iterator().next();
- Amplification amplification = amplificationResult.getAmplification();
- assertNotNull("Amplification is null", amplification);
- DefinedTerm dnaMarker = amplification.getDnaMarker();
- assertNotNull(dnaMarker);
- assertEquals("ITS (ITS1, 5.8S rRNA, ITS2)", dnaMarker.getLabel());
-
- //amplification primers
- Primer forwardPrimer = amplification.getForwardPrimer();
- assertNotNull(forwardPrimer);
- assertEquals("PIpetB1411F", forwardPrimer.getLabel());
- assertEquals("5´-GCCGTMTTTATGTTAATGC-3´", forwardPrimer.getSequence().getString());
- assertNotNull(forwardPrimer.getPublishedIn());
- assertEquals("Löhne & Borsch 2005", forwardPrimer.getPublishedIn().getTitle());
-
- Primer reversePrimer = amplification.getReversePrimer();
- assertNotNull(reversePrimer);
- assertEquals("PIpetD738R", reversePrimer.getLabel());
- assertEquals("5´-AATTTAGCYCTTAATACAGG-3´", reversePrimer.getSequence().getString());
-
- //sequencing
- Set<Sequence> sequences = dnaSample.getSequences();
- assertNotNull(sequences);
- assertEquals(1, sequences.size());
- Sequence sequence = sequences.iterator().next();
- SequenceString consensusSequence = sequence.getConsensusSequence();
- assertNotNull(consensusSequence);
- assertEquals(
- "TTTCGGGTCC TTTATAGTGA AGATATAGCA TAGATAGTTG TAATCCATTA" +
- " TGTATCATTG GGGAAGGAAG GAGAATATTT TTTTGATAGA ATACAAGTAT" +
- " GGATTATTGA AACTAATACG CCATGTATTT GGATATTTCC CTTGAACTGC" +
- " ATAATATTCT TTATTTTCCA TGAATAGTGT AAGGGAATTT TTCGAAGAGA" +
- " AAATGGATTA TGGGAGTGTG TGACTTGAGC TATTGATTGG TCTGTGCAGA" +
- " TACGGGCTTT TATCTATCTG CCACATTGTA ATTCACAAAC CAATGTGTCT" +
- " TTGTTCCAAC CATCGCGTAA GCCCCATACA GAAGATAGGC TGGTTCGCTT" +
- " GAAGAGAATC TTTTCTATGA TCAGATCCGA ATTATGTCGT ACATGAGCAG" +
- " GCTCCGTAAG ATCTAGTTGA CTTAAGTCAA ACTTCAATAG TATAAAAATG" +
- " CACTCATTTC CTCTGCATTG ACACGAGCTA TGAGACTATC GGAGTGAAAG" +
- " AAAGGGTCTA AAGAAGAAGA AAGCTTGGGC TAGATTAGTA ACAAGTAAAT" +
- " CCTTTGTGTG TGTGTTTGTA ATTAGTAAAT GGGCTCTCAA TATTTTGGGG" +
- " CTAATTACTG ATCCTAAGGT TTGAGACGAC CCAGAAAGCA CTTGATCATA" +
- " TCACGATTGA CTTTGTAAGC CTACTTGGGT ATTGAGTATT TACTTGTAAG" +
- " AACCGAATTC TTTGGGGGAT AGTTGCAAAA AGAATCCAGT CAATTGTTCT" +
- " TACGTAAAAC CATTCATATC TCGTATATGG ATATGTCTAG ATAGGCTATC" +
- " GATTTTCGAT GGATTCGTTT GGTTCTTTTG ATTATTGCTC GAGCTGGATG" +
- " ATGAAAAATT ATCATGTCCG GTTCCTTCG",consensusSequence.getString());
-// assertEquals((Integer)912, consensusSequence.getLength());
- assertNotNull(sequence.getContigFile());
- assertEquals(URI.create("http://ww2.biocase.org/websvn/filedetails.php?repname=campanula&path=%2FCAM385_Campa_drabifolia.pde"), MediaUtils.getFirstMediaRepresentationPart(sequence.getContigFile()).getUri());
- assertEquals(1, sequence.getCitations().size());
- Reference<?> reference = sequence.getCitations().iterator().next();
- assertEquals("Gemeinholzer,B., Bachmann,K. (2005): Examining morphological "
- + "and molecular diagnostic character states in "
- + "Cichorium intybus L. (Asteraceae) and Cichorium spinosum L."
- + " Plant Systematics and Evolution 253 (1-3): 105-123.", reference.getTitle());
-
- //single reads
- Set<SingleRead> singleReads = sequence.getSingleReads();
- assertNotNull(singleReads);
- assertEquals(2, singleReads.size());
- for (SingleRead singleRead : singleReads) {
- if(singleRead.getDirection().equals(SequenceDirection.Forward)){
- assertNotNull(singleRead.getPherogram());
- assertEquals(URI.create("http://ww2.biocase.org/websvn/filedetails.php?repname=campanula&path=%2FCAM385_GM312-petD_F.ab1"), MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram()).getUri());
- }
- else{
- assertNotNull(singleRead.getPherogram());
- assertEquals(URI.create("http://ww2.biocase.org/websvn/filedetails.php?repname=campanula&path=%2FCAM385_GM312-petD_R.ab1"), MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram()).getUri());
- }
- }
- assertNotNull(amplificationResult.getSingleReads());
- assertEquals(amplificationResult.getSingleReads(), singleReads);
-
-
- }
-
- /**
- * Tests import of DNA unit and attaching it to an existing specimen to which
- * it has a UnitAssociation.
- */
- @Test
- @DataSet( value="AbcdGgbnImportTest.testAttachDnaSampleToDerivedUnit.xml", loadStrategy=CleanSweepInsertLoadStrategy.class)
- public void testAttachDnaSampleToDerivedUnit(){
- UUID derivedUnit1Uuid = UUID.fromString("eb40cb0f-efb2-4985-819e-a9168f6d61fe");
-
-// DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
-// derivedUnit.setAccessionNumber("B 10 0066577");
-// derivedUnit.setTitleCache("testUnit1", true);
-//
-// derivedUnit.setUuid(derivedUnit1Uuid );
-//
-// occurrenceService.save(derivedUnit);
-//
-// commitAndStartNewTransaction(null);
-//
-// setComplete();
-// endTransaction();
-//
-//
-// try {
-// writeDbUnitDataSetFile(new String[] {
-// "SpecimenOrObservationBase",
-// }, "testAttachDnaSampleToDerivedUnit");
-// } catch (FileNotFoundException e) {
-// e.printStackTrace();
-// }
-
-
- String inputFile = "/eu/etaxonomy/cdm/io/specimen/abcd206/in/db6.xml";
- URL url = this.getClass().getResource(inputFile);
- assertNotNull("URL for the test file '" + inputFile + "' does not exist", url);
-
- Abcd206ImportConfigurator importConfigurator = null;
- try {
- importConfigurator = Abcd206ImportConfigurator.NewInstance(url.toURI(), null,false);
- } catch (URISyntaxException e) {
- e.printStackTrace();
- Assert.fail();
- }
- assertNotNull("Configurator could not be created", importConfigurator);
-
- boolean result = defaultImport.invoke(importConfigurator);
- assertTrue("Return value for import.invoke should be true", result);
- assertEquals("Number of derived units is incorrect", 2, occurrenceService.count(DerivedUnit.class));
- List<DerivedUnit> derivedUnits = occurrenceService.list(DerivedUnit.class, null, null, null, null);
- assertEquals("Number of derived units is incorrect", 2, derivedUnits.size());
- assertEquals("Number of field units is incorrect", 1, occurrenceService.count(FieldUnit.class));
- assertEquals("Number of dna samples is incorrect", 1, occurrenceService.count(DnaSample.class));
-
- DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(derivedUnit1Uuid);
- assertTrue(derivedUnits.contains(derivedUnit));
-
- assertEquals("Number of dna samples is incorrect", 1, occurrenceService.count(DnaSample.class));
- DnaSample dnaSample = occurrenceService.list(DnaSample.class, null, null, null, null).get(0);
- assertEquals("Wrong derivation type!", DerivationEventType.DNA_EXTRACTION(), dnaSample.getDerivedFrom().getType());
-
- assertEquals("Wrong number of originals", 1, dnaSample.getDerivedFrom().getOriginals().size());
-
- }
-
- /**
- * Tests importing of DNA unit without attaching it to an existing specimen.
- * Creates a FieldUnit with an attached DnaSample.
- */
- @Test
- @DataSet( value="AbcdGgbnImportTest.testNoAttachDnaSampleToDerivedUnit.xml", loadStrategy=CleanSweepInsertLoadStrategy.class)
- public void testNoAttachDnaSampleToDerivedUnit(){
- UUID derivedUnit1Uuid = UUID.fromString("eb40cb0f-efb2-4985-819e-a9168f6d61fe");
-
-// DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
-// derivedUnit.setAccessionNumber("B 10 0066577");
-// derivedUnit.setTitleCache("testUnit1", true);
-//
-// derivedUnit.setUuid(derivedUnit1Uuid );
-//
-// occurrenceService.save(derivedUnit);
-//
-// commitAndStartNewTransaction(null);
-//
-// setComplete();
-// endTransaction();
-//
-//
-// try {
-// writeDbUnitDataSetFile(new String[] {
-// "SpecimenOrObservationBase",
-// }, "testAttachDnaSampleToDerivedUnit");
-// } catch (FileNotFoundException e) {
-// e.printStackTrace();
-// }
-
-
- String inputFile = "/eu/etaxonomy/cdm/io/specimen/abcd206/in/db6.xml";
- URL url = this.getClass().getResource(inputFile);
- assertNotNull("URL for the test file '" + inputFile + "' does not exist", url);
-
- Abcd206ImportConfigurator importConfigurator = null;
- try {
- importConfigurator = Abcd206ImportConfigurator.NewInstance(url.toURI(), null,false);
- } catch (URISyntaxException e) {
- e.printStackTrace();
- Assert.fail();
- }
- assertNotNull("Configurator could not be created", importConfigurator);
-
- assertEquals("Number of derived units is incorrect", 1, occurrenceService.count(DerivedUnit.class));
- boolean result = defaultImport.invoke(importConfigurator);
- assertTrue("Return value for import.invoke should be true", result);
- assertEquals("Number of derived units is incorrect", 3, occurrenceService.count(DerivedUnit.class));
- List<DerivedUnit> derivedUnits = occurrenceService.list(DerivedUnit.class, null, null, null, null);
- assertEquals("Number of derived units is incorrect", 3, derivedUnits.size());
- assertEquals("Number of field units is incorrect", 1, occurrenceService.count(FieldUnit.class));
- assertEquals("Number of dna samples is incorrect", 1, occurrenceService.count(DnaSample.class));
-
- DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(derivedUnit1Uuid);
- assertTrue(derivedUnits.contains(derivedUnit));
-
- assertEquals("Number of dna samples is incorrect", 1, occurrenceService.count(DnaSample.class));
- DnaSample dnaSample = occurrenceService.list(DnaSample.class, null, null, null, null).get(0);
- assertEquals("Wrong derivation type!", DerivationEventType.DNA_EXTRACTION(), dnaSample.getDerivedFrom().getType());
-
- assertEquals("Wrong number of originals", 1, dnaSample.getDerivedFrom().getOriginals().size());
-
- }
-
- @Override
- public void createTestDataSet() throws FileNotFoundException {
- UUID derivedUnit1Uuid = UUID.fromString("eb40cb0f-efb2-4985-819e-a9168f6d61fe");
-
- DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
- derivedUnit.setAccessionNumber("B 10 0066577");
- derivedUnit.setTitleCache("testUnit1", true);
-
- derivedUnit.setUuid(derivedUnit1Uuid );
-
- occurrenceService.save(derivedUnit);
-
- commitAndStartNewTransaction(null);
-
- setComplete();
- endTransaction();
-
-
- try {
- writeDbUnitDataSetFile(new String[] {
- "SpecimenOrObservationBase",
- }, "testAttachDnaSampleToDerivedUnit");
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- }
- }
-
-}
+/**\r
+* Copyright (C) 2007 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+\r
+package eu.etaxonomy.cdm.io.specimen.abcd206.in;\r
+\r
+import static org.junit.Assert.assertEquals;\r
+import static org.junit.Assert.assertNotNull;\r
+import static org.junit.Assert.assertTrue;\r
+\r
+import java.io.FileNotFoundException;\r
+import java.net.URI;\r
+import java.net.URISyntaxException;\r
+import java.net.URL;\r
+import java.text.ParseException;\r
+import java.util.List;\r
+import java.util.Set;\r
+import java.util.UUID;\r
+\r
+import org.joda.time.DateTime;\r
+import org.junit.Assert;\r
+import org.junit.Test;\r
+import org.unitils.dbunit.annotation.DataSet;\r
+import org.unitils.spring.annotation.SpringBeanByName;\r
+import org.unitils.spring.annotation.SpringBeanByType;\r
+\r
+import eu.etaxonomy.cdm.api.service.IOccurrenceService;\r
+import eu.etaxonomy.cdm.api.service.IReferenceService;\r
+import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;\r
+import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport;\r
+import eu.etaxonomy.cdm.model.common.DefinedTerm;\r
+import eu.etaxonomy.cdm.model.media.MediaUtils;\r
+import eu.etaxonomy.cdm.model.molecular.Amplification;\r
+import eu.etaxonomy.cdm.model.molecular.AmplificationResult;\r
+import eu.etaxonomy.cdm.model.molecular.DnaQuality;\r
+import eu.etaxonomy.cdm.model.molecular.DnaSample;\r
+import eu.etaxonomy.cdm.model.molecular.Primer;\r
+import eu.etaxonomy.cdm.model.molecular.Sequence;\r
+import eu.etaxonomy.cdm.model.molecular.SequenceDirection;\r
+import eu.etaxonomy.cdm.model.molecular.SequenceString;\r
+import eu.etaxonomy.cdm.model.molecular.SingleRead;\r
+import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;\r
+import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;\r
+import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;\r
+import eu.etaxonomy.cdm.model.occurrence.FieldUnit;\r
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;\r
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;\r
+import eu.etaxonomy.cdm.model.reference.Reference;\r
+import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;\r
+import eu.etaxonomy.cdm.test.unitils.CleanSweepInsertLoadStrategy;\r
+\r
+/**\r
+ * @author a.mueller\r
+ * @created 29.01.2009\r
+ */\r
+public class AbcdGgbnImportTest extends CdmTransactionalIntegrationTest {\r
+\r
+ @SpringBeanByName\r
+ private CdmApplicationAwareDefaultImport<?> defaultImport;\r
+\r
+ @SpringBeanByType\r
+ private IOccurrenceService occurrenceService;\r
+\r
+ @SpringBeanByType\r
+ private IReferenceService referenceService;\r
+\r
+ /**\r
+ * Tests import import of DNA unit and all its parameters\r
+ * and sub derivatives (sequence, amplification, etc.)\r
+ * @throws ParseException\r
+ */\r
+ @Test\r
+ @DataSet( value="../../../BlankDataSet.xml", loadStrategy=CleanSweepInsertLoadStrategy.class)\r
+ public void testImportGgbn() throws ParseException {\r
+ String inputFile = "/eu/etaxonomy/cdm/io/specimen/abcd206/in/db6.xml";\r
+ URL url = this.getClass().getResource(inputFile);\r
+ assertNotNull("URL for the test file '" + inputFile + "' does not exist", url);\r
+\r
+ Abcd206ImportConfigurator importConfigurator = null;\r
+ try {\r
+ importConfigurator = Abcd206ImportConfigurator.NewInstance(url.toURI(), null,false);\r
+ } catch (URISyntaxException e) {\r
+ e.printStackTrace();\r
+ Assert.fail();\r
+ }\r
+ assertNotNull("Configurator could not be created", importConfigurator);\r
+\r
+ boolean result = defaultImport.invoke(importConfigurator);\r
+ assertTrue("Return value for import.invoke should be true", result);\r
+ assertEquals("Number of derived units is incorrect", 1, occurrenceService.count(DerivedUnit.class));\r
+ assertEquals("Number of dna samples is incorrect", 1, occurrenceService.count(DnaSample.class));\r
+ assertEquals("Number of field units is incorrect", 1, occurrenceService.count(FieldUnit.class));\r
+\r
+ //associated specimen\r
+ FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();\r
+ config.setSignificantIdentifier("B 10 0066577");\r
+ List<SpecimenOrObservationBase> records = occurrenceService.findByTitle(config).getRecords();\r
+ assertEquals(1, records.size());\r
+ SpecimenOrObservationBase derivedUnitSpecimen = records.iterator().next();\r
+ assertEquals(DerivedUnit.class, derivedUnitSpecimen.getClass());\r
+ DerivedUnit specimen = (DerivedUnit) derivedUnitSpecimen;\r
+ assertEquals("Herbarium Berolinense", specimen.getCollection().getName());\r
+ assertTrue(SpecimenOrObservationType.DnaSample!=specimen.getRecordBasis());\r
+\r
+ //dna sample\r
+ FindOccurrencesConfigurator dnaConfig = new FindOccurrencesConfigurator();\r
+ dnaConfig.setSignificantIdentifier("DB 6");\r
+ List<SpecimenOrObservationBase> dnaRecords = occurrenceService.findByTitle(dnaConfig).getRecords();\r
+ assertEquals(1, dnaRecords.size());\r
+ SpecimenOrObservationBase dnaSpecimen = dnaRecords.iterator().next();\r
+ assertEquals(DnaSample.class, dnaSpecimen.getClass());\r
+ DnaSample dnaSample = (DnaSample) dnaSpecimen;\r
+ DerivationEvent derivedFrom = dnaSample.getDerivedFrom();\r
+ assertNotNull(derivedFrom);\r
+ assertEquals("Wrong derivation type!", DerivationEventType.DNA_EXTRACTION(), derivedFrom.getType());\r
+ assertEquals("Wrong number of originals", 1, derivedFrom.getOriginals().size());\r
+ assertEquals("DNA Bank", dnaSample.getCollection().getCode());\r
+ assertEquals(SpecimenOrObservationType.DnaSample, dnaSample.getRecordBasis());\r
+ //preservation/preparation\r
+ assertNotNull(derivedFrom.getActor());\r
+ assertEquals("Bansemer, Jana", derivedFrom.getActor().getTitleCache());\r
+ assertNotNull(derivedFrom.getTimeperiod());\r
+ assertEquals((Integer)2002,derivedFrom.getTimeperiod().getStartYear());\r
+ assertEquals((Integer)8,derivedFrom.getTimeperiod().getStartMonth());\r
+ assertEquals((Integer)13,derivedFrom.getTimeperiod().getStartDay());\r
+ assertNotNull(dnaSample.getPreservation());\r
+\r
+\r
+ //dna quality\r
+ DnaQuality dnaQuality = dnaSample.getDnaQuality();\r
+ assertNotNull("Dna quality is null", dnaQuality!=null);\r
+ assertEquals(new Double("0.77"),dnaQuality.getRatioOfAbsorbance260_230());\r
+ assertEquals(new Double("1.38"),dnaQuality.getRatioOfAbsorbance260_280());\r
+ assertEquals(new DateTime(2008, 4, 15, 0, 0),dnaQuality.getQualityCheckDate());\r
+// assertEquals(MeasurementUnit.NewInstance(, label, labelAbbrev)DateTime(2008, 4, 15, 0, 0),dnaQuality.getQualityCheckDate());\r
+\r
+ //amplifications\r
+ Set<AmplificationResult> amplificationResults = dnaSample.getAmplificationResults();\r
+ assertNotNull(amplificationResults);\r
+ assertEquals(1, amplificationResults.size());\r
+ AmplificationResult amplificationResult = amplificationResults.iterator().next();\r
+ Amplification amplification = amplificationResult.getAmplification();\r
+ assertNotNull("Amplification is null", amplification);\r
+ DefinedTerm dnaMarker = amplification.getDnaMarker();\r
+ assertNotNull(dnaMarker);\r
+ assertEquals("ITS (ITS1, 5.8S rRNA, ITS2)", dnaMarker.getLabel());\r
+\r
+ //amplification primers\r
+ Primer forwardPrimer = amplification.getForwardPrimer();\r
+ assertNotNull(forwardPrimer);\r
+ assertEquals("PIpetB1411F", forwardPrimer.getLabel());\r
+ assertEquals("5´-GCCGTMTTTATGTTAATGC-3´", forwardPrimer.getSequence().getString());\r
+ assertNotNull(forwardPrimer.getPublishedIn());\r
+ assertEquals("Löhne & Borsch 2005", forwardPrimer.getPublishedIn().getTitle());\r
+\r
+ Primer reversePrimer = amplification.getReversePrimer();\r
+ assertNotNull(reversePrimer);\r
+ assertEquals("PIpetD738R", reversePrimer.getLabel());\r
+ assertEquals("5´-AATTTAGCYCTTAATACAGG-3´", reversePrimer.getSequence().getString());\r
+\r
+ //sequencing\r
+ Set<Sequence> sequences = dnaSample.getSequences();\r
+ assertNotNull(sequences);\r
+ assertEquals(1, sequences.size());\r
+ Sequence sequence = sequences.iterator().next();\r
+ SequenceString consensusSequence = sequence.getConsensusSequence();\r
+ assertNotNull(consensusSequence);\r
+ assertEquals(\r
+ "TTTCGGGTCC TTTATAGTGA AGATATAGCA TAGATAGTTG TAATCCATTA" +\r
+ " TGTATCATTG GGGAAGGAAG GAGAATATTT TTTTGATAGA ATACAAGTAT" +\r
+ " GGATTATTGA AACTAATACG CCATGTATTT GGATATTTCC CTTGAACTGC" +\r
+ " ATAATATTCT TTATTTTCCA TGAATAGTGT AAGGGAATTT TTCGAAGAGA" +\r
+ " AAATGGATTA TGGGAGTGTG TGACTTGAGC TATTGATTGG TCTGTGCAGA" +\r
+ " TACGGGCTTT TATCTATCTG CCACATTGTA ATTCACAAAC CAATGTGTCT" +\r
+ " TTGTTCCAAC CATCGCGTAA GCCCCATACA GAAGATAGGC TGGTTCGCTT" +\r
+ " GAAGAGAATC TTTTCTATGA TCAGATCCGA ATTATGTCGT ACATGAGCAG" +\r
+ " GCTCCGTAAG ATCTAGTTGA CTTAAGTCAA ACTTCAATAG TATAAAAATG" +\r
+ " CACTCATTTC CTCTGCATTG ACACGAGCTA TGAGACTATC GGAGTGAAAG" +\r
+ " AAAGGGTCTA AAGAAGAAGA AAGCTTGGGC TAGATTAGTA ACAAGTAAAT" +\r
+ " CCTTTGTGTG TGTGTTTGTA ATTAGTAAAT GGGCTCTCAA TATTTTGGGG" +\r
+ " CTAATTACTG ATCCTAAGGT TTGAGACGAC CCAGAAAGCA CTTGATCATA" +\r
+ " TCACGATTGA CTTTGTAAGC CTACTTGGGT ATTGAGTATT TACTTGTAAG" +\r
+ " AACCGAATTC TTTGGGGGAT AGTTGCAAAA AGAATCCAGT CAATTGTTCT" +\r
+ " TACGTAAAAC CATTCATATC TCGTATATGG ATATGTCTAG ATAGGCTATC" +\r
+ " GATTTTCGAT GGATTCGTTT GGTTCTTTTG ATTATTGCTC GAGCTGGATG" +\r
+ " ATGAAAAATT ATCATGTCCG GTTCCTTCG",consensusSequence.getString());\r
+// assertEquals((Integer)912, consensusSequence.getLength());\r
+ assertNotNull(sequence.getContigFile());\r
+ assertEquals(URI.create("http://ww2.biocase.org/websvn/filedetails.php?repname=campanula&path=%2FCAM385_Campa_drabifolia.pde"), MediaUtils.getFirstMediaRepresentationPart(sequence.getContigFile()).getUri());\r
+ assertEquals(1, sequence.getCitations().size());\r
+ Reference<?> reference = sequence.getCitations().iterator().next();\r
+ assertEquals("Gemeinholzer,B., Bachmann,K. (2005): Examining morphological "\r
+ + "and molecular diagnostic character states in "\r
+ + "Cichorium intybus L. (Asteraceae) and Cichorium spinosum L."\r
+ + " Plant Systematics and Evolution 253 (1-3): 105-123.", reference.getTitle());\r
+\r
+ //single reads\r
+ Set<SingleRead> singleReads = sequence.getSingleReads();\r
+ assertNotNull(singleReads);\r
+ assertEquals(2, singleReads.size());\r
+ for (SingleRead singleRead : singleReads) {\r
+ if(singleRead.getDirection().equals(SequenceDirection.Forward)){\r
+ assertNotNull(singleRead.getPherogram());\r
+ assertEquals(URI.create("http://ww2.biocase.org/websvn/filedetails.php?repname=campanula&path=%2FCAM385_GM312-petD_F.ab1"), MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram()).getUri());\r
+ }\r
+ else{\r
+ assertNotNull(singleRead.getPherogram());\r
+ assertEquals(URI.create("http://ww2.biocase.org/websvn/filedetails.php?repname=campanula&path=%2FCAM385_GM312-petD_R.ab1"), MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram()).getUri());\r
+ }\r
+ }\r
+ assertNotNull(amplificationResult.getSingleReads());\r
+ assertEquals(amplificationResult.getSingleReads(), singleReads);\r
+\r
+\r
+ }\r
+\r
+ /**\r
+ * Tests import of DNA unit and attaching it to an existing specimen to which\r
+ * it has a UnitAssociation.\r
+ */\r
+ @Test\r
+ @DataSet( value="AbcdGgbnImportTest.testAttachDnaSampleToDerivedUnit.xml", loadStrategy=CleanSweepInsertLoadStrategy.class)\r
+ public void testAttachDnaSampleToDerivedUnit(){\r
+ UUID derivedUnit1Uuid = UUID.fromString("eb40cb0f-efb2-4985-819e-a9168f6d61fe");\r
+\r
+// DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);\r
+// derivedUnit.setAccessionNumber("B 10 0066577");\r
+// derivedUnit.setTitleCache("testUnit1", true);\r
+//\r
+// derivedUnit.setUuid(derivedUnit1Uuid );\r
+//\r
+// occurrenceService.save(derivedUnit);\r
+//\r
+// commitAndStartNewTransaction(null);\r
+//\r
+// setComplete();\r
+// endTransaction();\r
+//\r
+//\r
+// try {\r
+// writeDbUnitDataSetFile(new String[] {\r
+// "SpecimenOrObservationBase",\r
+// }, "testAttachDnaSampleToDerivedUnit");\r
+// } catch (FileNotFoundException e) {\r
+// e.printStackTrace();\r
+// }\r
+\r
+\r
+ String inputFile = "/eu/etaxonomy/cdm/io/specimen/abcd206/in/db6.xml";\r
+ URL url = this.getClass().getResource(inputFile);\r
+ assertNotNull("URL for the test file '" + inputFile + "' does not exist", url);\r
+\r
+ Abcd206ImportConfigurator importConfigurator = null;\r
+ try {\r
+ importConfigurator = Abcd206ImportConfigurator.NewInstance(url.toURI(), null,false);\r
+ } catch (URISyntaxException e) {\r
+ e.printStackTrace();\r
+ Assert.fail();\r
+ }\r
+ assertNotNull("Configurator could not be created", importConfigurator);\r
+\r
+ boolean result = defaultImport.invoke(importConfigurator);\r
+ assertTrue("Return value for import.invoke should be true", result);\r
+ assertEquals("Number of derived units is incorrect", 2, occurrenceService.count(DerivedUnit.class));\r
+ List<DerivedUnit> derivedUnits = occurrenceService.list(DerivedUnit.class, null, null, null, null);\r
+ assertEquals("Number of derived units is incorrect", 2, derivedUnits.size());\r
+ assertEquals("Number of field units is incorrect", 1, occurrenceService.count(FieldUnit.class));\r
+ assertEquals("Number of dna samples is incorrect", 1, occurrenceService.count(DnaSample.class));\r
+\r
+ DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(derivedUnit1Uuid);\r
+ assertTrue(derivedUnits.contains(derivedUnit));\r
+\r
+ assertEquals("Number of dna samples is incorrect", 1, occurrenceService.count(DnaSample.class));\r
+ DnaSample dnaSample = occurrenceService.list(DnaSample.class, null, null, null, null).get(0);\r
+ assertEquals("Wrong derivation type!", DerivationEventType.DNA_EXTRACTION(), dnaSample.getDerivedFrom().getType());\r
+\r
+ assertEquals("Wrong number of originals", 1, dnaSample.getDerivedFrom().getOriginals().size());\r
+\r
+ }\r
+\r
+ /**\r
+ * Tests importing of DNA unit without attaching it to an existing specimen.\r
+ * Creates a FieldUnit with an attached DnaSample.\r
+ */\r
+ @Test\r
+ @DataSet( value="AbcdGgbnImportTest.testNoAttachDnaSampleToDerivedUnit.xml", loadStrategy=CleanSweepInsertLoadStrategy.class)\r
+ public void testNoAttachDnaSampleToDerivedUnit(){\r
+ UUID derivedUnit1Uuid = UUID.fromString("eb40cb0f-efb2-4985-819e-a9168f6d61fe");\r
+\r
+// DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);\r
+// derivedUnit.setAccessionNumber("B 10 0066577");\r
+// derivedUnit.setTitleCache("testUnit1", true);\r
+//\r
+// derivedUnit.setUuid(derivedUnit1Uuid );\r
+//\r
+// occurrenceService.save(derivedUnit);\r
+//\r
+// commitAndStartNewTransaction(null);\r
+//\r
+// setComplete();\r
+// endTransaction();\r
+//\r
+//\r
+// try {\r
+// writeDbUnitDataSetFile(new String[] {\r
+// "SpecimenOrObservationBase",\r
+// }, "testAttachDnaSampleToDerivedUnit");\r
+// } catch (FileNotFoundException e) {\r
+// e.printStackTrace();\r
+// }\r
+\r
+\r
+ String inputFile = "/eu/etaxonomy/cdm/io/specimen/abcd206/in/db6.xml";\r
+ URL url = this.getClass().getResource(inputFile);\r
+ assertNotNull("URL for the test file '" + inputFile + "' does not exist", url);\r
+\r
+ Abcd206ImportConfigurator importConfigurator = null;\r
+ try {\r
+ importConfigurator = Abcd206ImportConfigurator.NewInstance(url.toURI(), null,false);\r
+ } catch (URISyntaxException e) {\r
+ e.printStackTrace();\r
+ Assert.fail();\r
+ }\r
+ assertNotNull("Configurator could not be created", importConfigurator);\r
+\r
+ assertEquals("Number of derived units is incorrect", 1, occurrenceService.count(DerivedUnit.class));\r
+ boolean result = defaultImport.invoke(importConfigurator);\r
+ assertTrue("Return value for import.invoke should be true", result);\r
+ assertEquals("Number of derived units is incorrect", 3, occurrenceService.count(DerivedUnit.class));\r
+ List<DerivedUnit> derivedUnits = occurrenceService.list(DerivedUnit.class, null, null, null, null);\r
+ assertEquals("Number of derived units is incorrect", 3, derivedUnits.size());\r
+ assertEquals("Number of field units is incorrect", 1, occurrenceService.count(FieldUnit.class));\r
+ assertEquals("Number of dna samples is incorrect", 1, occurrenceService.count(DnaSample.class));\r
+\r
+ DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(derivedUnit1Uuid);\r
+ assertTrue(derivedUnits.contains(derivedUnit));\r
+\r
+ assertEquals("Number of dna samples is incorrect", 1, occurrenceService.count(DnaSample.class));\r
+ DnaSample dnaSample = occurrenceService.list(DnaSample.class, null, null, null, null).get(0);\r
+ assertEquals("Wrong derivation type!", DerivationEventType.DNA_EXTRACTION(), dnaSample.getDerivedFrom().getType());\r
+\r
+ assertEquals("Wrong number of originals", 1, dnaSample.getDerivedFrom().getOriginals().size());\r
+\r
+ }\r
+\r
+ @Override\r
+ public void createTestDataSet() throws FileNotFoundException {\r
+ UUID derivedUnit1Uuid = UUID.fromString("eb40cb0f-efb2-4985-819e-a9168f6d61fe");\r
+\r
+ DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);\r
+ derivedUnit.setAccessionNumber("B 10 0066577");\r
+ derivedUnit.setTitleCache("testUnit1", true);\r
+\r
+ derivedUnit.setUuid(derivedUnit1Uuid );\r
+\r
+ occurrenceService.save(derivedUnit);\r
+\r
+ commitAndStartNewTransaction(null);\r
+\r
+ setComplete();\r
+ endTransaction();\r
+\r
+\r
+ try {\r
+ writeDbUnitDataSetFile(new String[] {\r
+ "SpecimenOrObservationBase",\r
+ }, "testAttachDnaSampleToDerivedUnit");\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+\r
+}\r
BGBM BDI Projects / cdmlib.git / commitdiff