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[Treebase-guts] SF.net SVN: treebase:[974] trunk/treebase-core/src
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From: <rv...@us...> - 2011-10-27 16:58:23
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Revision: 974
http://treebase.svn.sourceforge.net/treebase/?rev=974&view=rev
Author: rvos
Date: 2011-10-27 16:58:16 +0000 (Thu, 27 Oct 2011)
Log Message:
-----------
So far, the NeXML converters were working on the assumption that a single study/nexusdataset would be converted to NeXML. It turns out there are use cases where a search result set needs to be converted. This means that we also want to be able to generate NeXML documents that don't have all the annotations that go with serializing a single study (e.g. its ID, authors, title, etc.), but rather a place holder document into which search results (e.g. entire studies, sets of taxa, matrices, trees) can be added and jointly serialized. This commit includes some refactorings in the Nexml*Writer classes and a JUnit test class that demonstrates this new behavior.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentWriter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUWriter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockWriter.java
Added Paths:
-----------
trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlSearchResultConverterTest.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentWriter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentWriter.java 2011-10-13 18:50:53 UTC (rev 973)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentWriter.java 2011-10-27 16:58:16 UTC (rev 974)
@@ -1,12 +1,28 @@
package org.cipres.treebase.domain.nexus.nexml;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
import org.cipres.treebase.Constants;
import org.cipres.treebase.domain.matrix.CharacterMatrix;
+import org.cipres.treebase.domain.matrix.Matrix;
import org.cipres.treebase.domain.nexus.NexusDataSet;
+import org.cipres.treebase.domain.search.MatrixSearchResults;
+import org.cipres.treebase.domain.search.SearchResults;
+import org.cipres.treebase.domain.search.SearchResultsType;
+import org.cipres.treebase.domain.search.StudySearchResults;
+import org.cipres.treebase.domain.search.TaxonSearchResults;
+import org.cipres.treebase.domain.search.TreeSearchResults;
import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.Taxon;
+import org.cipres.treebase.domain.taxon.TaxonLabel;
import org.cipres.treebase.domain.taxon.TaxonLabelHome;
import org.cipres.treebase.domain.taxon.TaxonLabelSet;
+import org.cipres.treebase.domain.tree.PhyloTree;
import org.nexml.model.Document;
+import org.nexml.model.OTUs;
+import org.nexml.model.TreeBlock;
public class NexmlDocumentWriter extends NexmlObjectConverter {
@@ -41,7 +57,7 @@
NexmlMatrixWriter nmc = new NexmlMatrixWriter(getStudy(),getTaxonLabelHome(),getDocument());
for (org.cipres.treebase.domain.matrix.Matrix matrix : pNexusDataSet.getMatrices() ) {
if ( matrix instanceof CharacterMatrix ) {
- nmc.fromTreeBaseToXml((CharacterMatrix)matrix);
+ nmc.fromTreeBaseToXml((CharacterMatrix)matrix,null);
}
}
@@ -71,7 +87,7 @@
NexmlMatrixWriter nmc = new NexmlMatrixWriter(getStudy(),getTaxonLabelHome(),getDocument());
for (org.cipres.treebase.domain.matrix.Matrix matrix : pStudy.getMatrices() ) {
if ( matrix instanceof CharacterMatrix ) {
- nmc.fromTreeBaseToXml((CharacterMatrix)matrix);
+ nmc.fromTreeBaseToXml((CharacterMatrix)matrix,null);
}
}
@@ -82,5 +98,91 @@
return getDocument();
}
+
+ public Document fromTreeBaseToXml(SearchResults<?> searchResults) {
+ getDocument().addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using "+this.toString()+" $Rev$");
+ SearchResultsType srt = searchResults.resultType();
+ switch(srt) {
+ case STUDY : return fromTreeBaseToXml((StudySearchResults) searchResults);
+ case MATRIX : return fromTreeBaseToXml((MatrixSearchResults) searchResults);
+ case TREE : return fromTreeBaseToXml((TreeSearchResults) searchResults);
+ case TAXON : return fromTreeBaseToXml((TaxonSearchResults) searchResults);
+ case NONE : ; break;
+ }
+ return null;
+ }
+
+ public Document fromTreeBaseToXml(StudySearchResults searchResults) {
+ NexmlOTUWriter noc = new NexmlOTUWriter(null,getTaxonLabelHome(),getDocument());
+ NexmlMatrixWriter nmc = new NexmlMatrixWriter(null,getTaxonLabelHome(),getDocument());
+ NexmlTreeBlockWriter ntc = new NexmlTreeBlockWriter(null,getTaxonLabelHome(),getDocument());
+ for ( Study pStudy : searchResults.getResults() ) {
+ for ( TaxonLabelSet taxonLabelSet : pStudy.getTaxonLabelSets() ) {
+ noc.fromTreeBaseToXml(taxonLabelSet);
+ }
+ for (org.cipres.treebase.domain.matrix.Matrix matrix : pStudy.getMatrices() ) {
+ if ( matrix instanceof CharacterMatrix ) {
+ nmc.fromTreeBaseToXml((CharacterMatrix)matrix,null);
+ }
+ }
+ for ( org.cipres.treebase.domain.tree.TreeBlock treeBlock : pStudy.getTreeBlocks() ) {
+ ntc.fromTreeBaseToXML(treeBlock);
+ }
+ }
+ return getDocument();
+ }
+
+ public Document fromTreeBaseToXml(MatrixSearchResults searchResults) {
+
+ // create a merged set of all taxon labels in all matrices
+ Set<TaxonLabel> mergedLabels = new HashSet<TaxonLabel>();
+ for (Matrix m : searchResults.getResults()) {
+ List<TaxonLabel> labelsInTree = m.getAllTaxonLabels();
+ mergedLabels.addAll(labelsInTree);
+ }
+
+ // convert merged set of taxon labels to XML OTUs
+ NexmlOTUWriter noc = new NexmlOTUWriter(null,getTaxonLabelHome(),getDocument());
+ OTUs xmlOTUs = noc.fromTreeBaseToXml(mergedLabels);
+
+ // convert matrices to XML trees
+ NexmlMatrixWriter nmc = new NexmlMatrixWriter(null,getTaxonLabelHome(),getDocument());
+ for (Matrix m : searchResults.getResults()) {
+ nmc.fromTreeBaseToXml((CharacterMatrix)m,xmlOTUs);
+ }
+
+ return getDocument();
+ }
+ public Document fromTreeBaseToXml(TreeSearchResults searchResults) {
+
+ // create a merged set of all taxon labels in all trees
+ Set<TaxonLabel> mergedLabels = new HashSet<TaxonLabel>();
+ for (PhyloTree t : searchResults.getResults()) {
+ Set<TaxonLabel> labelsInTree = t.getAllTaxonLabels();
+ mergedLabels.addAll(labelsInTree);
+ }
+
+ // convert merged set of taxon labels to XML OTUs
+ NexmlOTUWriter noc = new NexmlOTUWriter(null,getTaxonLabelHome(),getDocument());
+ OTUs xmlOTUs = noc.fromTreeBaseToXml(mergedLabels);
+
+ // convert phylotrees to XML trees
+ NexmlTreeBlockWriter ntc = new NexmlTreeBlockWriter(null,getTaxonLabelHome(),getDocument());
+ TreeBlock xmlTreeBlock = getDocument().createTreeBlock(xmlOTUs);
+ for (PhyloTree t : searchResults.getResults()) {
+ ntc.fromTreeBaseToXml(t, xmlTreeBlock);
+ }
+ return getDocument();
+ }
+
+ public Document fromTreeBaseToXml(TaxonSearchResults searchResults) {
+ NexmlOTUWriter noc = new NexmlOTUWriter(null,getTaxonLabelHome(),getDocument());
+ OTUs xmlOTUs = getDocument().createOTUs();
+ for (Taxon t : searchResults.getResults()) {
+ noc.fromTreeBaseToXml(t, xmlOTUs);
+ }
+ return getDocument();
+ }
+
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java 2011-10-13 18:50:53 UTC (rev 973)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java 2011-10-27 16:58:16 UTC (rev 974)
@@ -57,8 +57,10 @@
* @param tbMatrix
* @return an xml matrix with empty rows
*/
- private CategoricalMatrix fromTreeBaseToXml(StandardMatrix tbMatrix) {
- OTUs xmlOTUs = getOTUsById(tbMatrix.getTaxa().getId());
+ private CategoricalMatrix fromTreeBaseToXml(StandardMatrix tbMatrix,OTUs xmlOTUs) {
+ if ( null == xmlOTUs ) {
+ xmlOTUs = getOTUsById(tbMatrix.getTaxa().getId());
+ }
CategoricalMatrix xmlMatrix = getDocument().createCategoricalMatrix(xmlOTUs);
setMatrixAttributes(xmlMatrix,tbMatrix);
@@ -108,8 +110,10 @@
* @param tbMatrix
* @return an xml matrix with empty rows
*/
- private MolecularMatrix fromTreeBaseToXml(DiscreteMatrix tbMatrix) {
- OTUs xmlOTUs = getOTUsById(tbMatrix.getTaxa().getId());
+ private MolecularMatrix fromTreeBaseToXml(DiscreteMatrix tbMatrix,OTUs xmlOTUs) {
+ if ( null == xmlOTUs ) {
+ xmlOTUs = getOTUsById(tbMatrix.getTaxa().getId());
+ }
String tbDataType = tbMatrix.getDataType().getDescription();
MolecularMatrix xmlMatrix = null;
CharacterStateSet xmlStateSet = null;
@@ -156,8 +160,10 @@
* @param tbMatrix
* @return an xml matrix with empty rows
*/
- private org.nexml.model.ContinuousMatrix fromTreeBaseToXml(ContinuousMatrix tbMatrix) {
- OTUs xmlOTUs = getOTUsById(tbMatrix.getTaxa().getId());
+ private org.nexml.model.ContinuousMatrix fromTreeBaseToXml(ContinuousMatrix tbMatrix,OTUs xmlOTUs) {
+ if ( null == xmlOTUs ) {
+ xmlOTUs = getOTUsById(tbMatrix.getTaxa().getId());
+ }
org.nexml.model.ContinuousMatrix xmlMatrix = getDocument().createContinuousMatrix(xmlOTUs);
setMatrixAttributes(xmlMatrix,tbMatrix);
@@ -204,19 +210,19 @@
// public static final String MATRIX_DATATYPE_DISTANCE = "Distance";
// public static final String MATRIX_DATATYPE_MIXED = "Mixed";
@SuppressWarnings("unchecked")
- public org.nexml.model.Matrix<?> fromTreeBaseToXml(CharacterMatrix tbMatrix) {
+ public org.nexml.model.Matrix<?> fromTreeBaseToXml(CharacterMatrix tbMatrix,OTUs xmlOTUs) {
org.nexml.model.Matrix<?> xmlMatrix = null;
if ( tbMatrix instanceof DiscreteMatrix ) {
if ( tbMatrix.getDataType().getDescription().equals(MatrixDataType.MATRIX_DATATYPE_STANDARD) ) {
- xmlMatrix = fromTreeBaseToXml((StandardMatrix) tbMatrix);
+ xmlMatrix = fromTreeBaseToXml((StandardMatrix) tbMatrix,xmlOTUs);
}
else {
- xmlMatrix = fromTreeBaseToXml((DiscreteMatrix) tbMatrix);
+ xmlMatrix = fromTreeBaseToXml((DiscreteMatrix) tbMatrix,xmlOTUs);
}
populateXmlMatrix((org.nexml.model.Matrix<CharacterState>)xmlMatrix,(DiscreteMatrix)tbMatrix);
}
else if ( tbMatrix instanceof ContinuousMatrix ) {
- xmlMatrix = fromTreeBaseToXml((ContinuousMatrix) tbMatrix);
+ xmlMatrix = fromTreeBaseToXml((ContinuousMatrix) tbMatrix,xmlOTUs);
populateXmlMatrix((org.nexml.model.ContinuousMatrix)xmlMatrix,(ContinuousMatrix)tbMatrix);
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUWriter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUWriter.java 2011-10-13 18:50:53 UTC (rev 973)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUWriter.java 2011-10-27 16:58:16 UTC (rev 974)
@@ -1,7 +1,10 @@
package org.cipres.treebase.domain.nexus.nexml;
+import java.util.Set;
+
import org.cipres.treebase.Constants;
import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.Taxon;
import org.cipres.treebase.domain.taxon.TaxonLabel;
import org.cipres.treebase.domain.taxon.TaxonLabelHome;
import org.cipres.treebase.domain.taxon.TaxonLabelSet;
@@ -42,11 +45,30 @@
/**
*
+ * @param taxonLabelSet
+ * @return
+ */
+ protected OTUs fromTreeBaseToXml(Set<TaxonLabel> taxonLabelSet) {
+ OTUs xmlOTUs = getDocument().createOTUs();
+
+ // attach base uri and skos:historyNote
+ xmlOTUs.setBaseURI(mTaxonBaseURI);
+ xmlOTUs.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using "+this.toString()+" $Rev$");
+
+ for ( TaxonLabel taxonLabel : taxonLabelSet ) {
+ fromTreeBaseToXml(taxonLabel,xmlOTUs);
+ }
+ return xmlOTUs;
+
+ }
+
+ /**
+ *
* @param taxonLabel
* @param xmlOTUs
* @return
*/
- private OTU fromTreeBaseToXml(TaxonLabel taxonLabel,OTUs xmlOTUs) {
+ protected OTU fromTreeBaseToXml(TaxonLabel taxonLabel,OTUs xmlOTUs) {
OTU xmlOTU = xmlOTUs.createOTU();
if ( null != taxonLabel.getTaxonLabel() ) {
xmlOTU.setLabel(taxonLabel.getTaxonLabel());
@@ -54,5 +76,20 @@
attachTreeBaseID(xmlOTU,taxonLabel,TaxonLabel.class);
return xmlOTU;
}
+
+ /**
+ *
+ * @param taxon
+ * @param xmlOTUs
+ * @return
+ */
+ protected OTU fromTreeBaseToXml(Taxon taxon,OTUs xmlOTUs) {
+ OTU xmlOTU = xmlOTUs.createOTU();
+ if ( null != taxon.getLabel() ) {
+ xmlOTU.setLabel(taxon.getLabel());
+ }
+ attachTreeBaseID(xmlOTU,taxon,Taxon.class);
+ return xmlOTU;
+ }
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java 2011-10-13 18:50:53 UTC (rev 973)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java 2011-10-27 16:58:16 UTC (rev 974)
@@ -36,7 +36,9 @@
if ( null != baseURI ) {
document.setBaseURI(URI.create(baseURI));
}
- document.setId(study.getTreebaseIDString().toString());
+ if ( null != study ) {
+ document.setId(study.getTreebaseIDString().toString());
+ }
setTaxonLabelHome(taxonLabelHome);
setStudy(study);
setDocument(document);
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockWriter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockWriter.java 2011-10-13 18:50:53 UTC (rev 973)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockWriter.java 2011-10-27 16:58:16 UTC (rev 974)
@@ -33,7 +33,7 @@
* @param phyloTree
* @return
*/
- private Tree<?> fromTreeBaseToXml(PhyloTree phyloTree,org.nexml.model.TreeBlock xmlTreeBlock) {
+ protected Tree<?> fromTreeBaseToXml(PhyloTree phyloTree,org.nexml.model.TreeBlock xmlTreeBlock) {
Tree<FloatEdge> xmlTree = xmlTreeBlock.createFloatTree();
if ( null != phyloTree.getLabel() ) {
xmlTree.setLabel(phyloTree.getLabel());
Added: trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlSearchResultConverterTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlSearchResultConverterTest.java (rev 0)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlSearchResultConverterTest.java 2011-10-27 16:58:16 UTC (rev 974)
@@ -0,0 +1,133 @@
+package org.cipres.treebase.domain.nexus;
+
+import java.util.Collection;
+import java.util.HashSet;
+
+import org.cipres.treebase.dao.AbstractDAOTest;
+import org.cipres.treebase.domain.matrix.Matrix;
+import org.cipres.treebase.domain.search.MatrixSearchResults;
+import org.cipres.treebase.domain.search.StudySearchResults;
+import org.cipres.treebase.domain.search.TaxonSearchResults;
+import org.cipres.treebase.domain.search.TreeSearchResults;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.study.StudyHome;
+import org.cipres.treebase.domain.taxon.TaxonLabel;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.cipres.treebase.domain.tree.PhyloTree;
+import org.cipres.treebase.domain.nexus.nexml.NexmlDocumentWriter;
+import org.nexml.model.Document;
+import org.nexml.model.DocumentFactory;
+
+public class NexmlSearchResultConverterTest extends AbstractDAOTest {
+
+ private TaxonLabelHome mTaxonLabelHome;
+ private StudyHome mStudyHome;
+
+ private StudySearchResults ssr = null;
+
+ private Collection<Study> studies = null;
+ private Collection<Matrix> matrices = null;
+ private Collection<PhyloTree> trees = null;
+ private Collection<TaxonLabel> taxa = null;
+
+ @Override
+ protected void onSetUp() throws Exception {
+ super.onSetUp();
+
+ studies = getTestData();
+ ssr = new StudySearchResults(studies);
+
+ // populate set of matrices from test data
+ matrices = new HashSet<Matrix> ();
+ for (Study s : studies) {
+ matrices.addAll(s.getMatrices());
+ }
+
+ // populate set of trees from test data
+ trees = new HashSet<PhyloTree> ();
+ for (Study s : studies) {
+ trees.addAll(s.getTrees());
+ }
+
+ // populate set of taxa from test data
+ taxa = new HashSet<TaxonLabel>();
+ for ( Study s : studies) {
+ taxa.addAll(s.getTaxonLabels());
+ }
+ }
+
+ public NexmlSearchResultConverterTest() {
+ super();
+ }
+
+ public void testTrivial() {
+ assertNotNull(getTaxonLabelHome());
+ assertNotNull(getStudyHome());
+ }
+
+ public void testQuickCheck() {
+ assertFalse(studies.size() == 0);
+ assertFalse(matrices.size() == 0);
+ assertFalse(trees.size() == 0);
+ assertFalse(taxa.size() == 0);
+ }
+
+ private Collection<Study> getTestData(String accessionNumber) {
+ Collection<Study> studies = new HashSet<Study>();
+ studies.add(getStudyHome().findByAccessionNumber(accessionNumber));
+ assertFalse(studies.size() == 0);
+ return studies;
+ }
+
+ private Collection<Study> getTestData() {
+ return getTestData("S1787");
+ }
+
+ public void testStudySearchSerialization() {
+ Document doc = DocumentFactory.safeCreateDocument();
+ NexmlDocumentWriter ndw = new NexmlDocumentWriter(null, mTaxonLabelHome, doc);
+ ndw.fromTreeBaseToXml(ssr);
+ assertNotNull(doc.getXmlString());
+ }
+
+ public void testTaxonSearchSerialization() {
+ Document doc = DocumentFactory.safeCreateDocument();
+ NexmlDocumentWriter ndw = new NexmlDocumentWriter(null, mTaxonLabelHome, doc);
+ TaxonSearchResults tasr = ssr.convertToTaxa();
+ ndw.fromTreeBaseToXml(tasr);
+ assertNotNull(doc.getXmlString());
+ }
+
+ public void testMatrixSearchSerialization() {
+ Document doc = DocumentFactory.safeCreateDocument();
+ NexmlDocumentWriter ndw = new NexmlDocumentWriter(null, mTaxonLabelHome, doc);
+ MatrixSearchResults msr = ssr.convertToMatrices();
+ ndw.fromTreeBaseToXml(msr);
+ assertNotNull(doc.getXmlString());
+ }
+
+ public void testTreeSearchSerialization() {
+ Document doc = DocumentFactory.safeCreateDocument();
+ NexmlDocumentWriter ndw = new NexmlDocumentWriter(null, mTaxonLabelHome, doc);
+ TreeSearchResults tsr = ssr.convertToTrees();
+ ndw.fromTreeBaseToXml(tsr);
+ assertNotNull(doc.getXmlString());
+ }
+
+ public TaxonLabelHome getTaxonLabelHome() {
+ return mTaxonLabelHome;
+ }
+
+ public void setTaxonLabelHome(TaxonLabelHome pNewTaxonLabelHome) {
+ mTaxonLabelHome = pNewTaxonLabelHome;
+ }
+
+ public StudyHome getStudyHome() {
+ return mStudyHome;
+ }
+
+ public void setStudyHome(StudyHome studyHome) {
+ mStudyHome = studyHome;
+ }
+
+}
\ No newline at end of file
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