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[Treebase-guts] SF.net SVN: treebase:[971] trunk/treebase-core/src
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From: <rv...@us...> - 2011-10-13 16:26:56
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Revision: 971
http://treebase.svn.sourceforge.net/treebase/?rev=971&view=rev
Author: rvos
Date: 2011-10-13 16:26:47 +0000 (Thu, 13 Oct 2011)
Log Message:
-----------
This refactoring splits NeXML reading and writing into separate classes and hides some more of the visibility of methods that only deal with the conversion of deeply nested objects.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java
trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlAnalysisConverterTest.java
trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java
trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlSerializationTest.java
Added Paths:
-----------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentReader.java
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/NexmlMatrixReader.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/NexmlOTUReader.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/NexmlTreeBlockReader.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockWriter.java
Removed Paths:
-------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java 2011-10-05 17:43:48 UTC (rev 970)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java 2011-10-13 16:26:47 UTC (rev 971)
@@ -20,7 +20,8 @@
import org.cipres.treebase.domain.matrix.ContinuousMatrix;
import org.cipres.treebase.domain.matrix.ItemDefinition;
import org.cipres.treebase.domain.nexus.mesquite.MesquiteMatrixConverter;
-import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter;
+import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixWriter;
+import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixReader;
/**
* Helper class for direct Matrix related SQL operations. Bypass the hibernate framework for high
@@ -67,7 +68,7 @@
private org.nexml.model.ContinuousMatrix mNexmlCharacterData;
- private NexmlMatrixConverter mNexmlMatrixConverter;
+ private NexmlMatrixWriter mNexmlMatrixConverter;
// Note: currently we support only one set of item definitions for the entire matrix.
// It is modeled in continuousMatrix.itemDefinitions.
@@ -105,7 +106,7 @@
public ContinuousMatrixJDBC(ContinuousMatrix tbMatrix,
org.nexml.model.ContinuousMatrix xmlMatrix,
- NexmlMatrixConverter nexmlMatrixConverter) {
+ NexmlMatrixReader nexmlMatrixConverter) {
this();
setCharacterMatrix(tbMatrix);
setNexmlCharacterData(xmlMatrix);
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java 2011-10-05 17:43:48 UTC (rev 970)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java 2011-10-13 16:26:47 UTC (rev 971)
@@ -23,7 +23,8 @@
import org.cipres.treebase.domain.matrix.DiscreteChar;
import org.cipres.treebase.domain.matrix.DiscreteCharState;
import org.cipres.treebase.domain.nexus.mesquite.MesquiteMatrixConverter;
-import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter;
+import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixWriter;
+import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixReader;
/**
* Helper class for direct Matrix related SQL operations. Bypass the hibernate framework for high
@@ -107,7 +108,7 @@
public DiscreteMatrixJDBC(CharacterMatrix tbMatrix,
org.nexml.model.CategoricalMatrix xmlMatrix,
- NexmlMatrixConverter nexmlMatrixConverter) {
+ NexmlMatrixReader nexmlMatrixConverter) {
this();
setCharacterMatrix(tbMatrix);
setNexmlCharacterData(xmlMatrix);
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java 2011-10-05 17:43:48 UTC (rev 970)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java 2011-10-13 16:26:47 UTC (rev 971)
@@ -19,7 +19,8 @@
import org.cipres.treebase.domain.matrix.CharacterMatrix;
import org.cipres.treebase.domain.matrix.ContinuousMatrix;
import org.cipres.treebase.domain.nexus.mesquite.MesquiteMatrixConverter;
-import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter;
+import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixWriter;
+import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixReader;
/**
* Helper class for direct Matrix related SQL operations. Bypass the hibernate framework for high
@@ -69,7 +70,7 @@
private List<MatrixColumnJDBC> mMatrixColumnJDBCs;
private MesquiteMatrixConverter mMesqMatrixConverter;
- private NexmlMatrixConverter mNexmlMatrixConverter;
+ private NexmlMatrixReader mNexmlMatrixConverter;
private Matrix mNexmlCharacterData;
/**
@@ -295,7 +296,7 @@
}
protected void setNexmlMatrixConverter(
- NexmlMatrixConverter nexmlMatrixConverter) {
+ NexmlMatrixReader nexmlMatrixConverter) {
mNexmlMatrixConverter = nexmlMatrixConverter;
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlConverter.java 2011-10-05 17:43:48 UTC (rev 970)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlConverter.java 2011-10-13 16:26:47 UTC (rev 971)
@@ -42,13 +42,13 @@
}
// Taxa
- NexmlOTUConverter noc = new NexmlOTUConverter(pStudy,getTaxonLabelHome(),document);
+ NexmlOTUReader noc = new NexmlOTUReader(pStudy,getTaxonLabelHome(),document);
for ( OTUs xmlOTUs : document.getOTUsList() ) {
pDataSet.addTaxonLabelSet(xmlOTUs, noc.fromXmlToTreeBase(xmlOTUs));
}
// Matrices
- NexmlMatrixConverter nmc = new NexmlMatrixConverter(pStudy,getTaxonLabelHome(),document);
+ NexmlMatrixReader nmc = new NexmlMatrixReader(pStudy,getTaxonLabelHome(),document);
for ( org.nexml.model.Matrix<?> xmlMatrix : document.getMatrices() ) {
Matrix tbMatrix = nmc.fromXmlToTreeBase(xmlMatrix);
tbMatrix.setNexusFileName(pFile.getName());
@@ -56,7 +56,7 @@
}
// Trees
- NexmlTreeBlockConverter ntbc = new NexmlTreeBlockConverter(pStudy,getTaxonLabelHome(),document);
+ NexmlTreeBlockReader ntbc = new NexmlTreeBlockReader(pStudy,getTaxonLabelHome(),document);
for ( org.nexml.model.TreeBlock xmlTreeBlock : document.getTreeBlockList() ) {
TreeBlock tbTreeBlock = ntbc.fromXmlToTreeBase(xmlTreeBlock);
for ( PhyloTree phyloTree : tbTreeBlock.getTreeList() ) {
Deleted: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java 2011-10-05 17:43:48 UTC (rev 970)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java 2011-10-13 16:26:47 UTC (rev 971)
@@ -1,123 +0,0 @@
-package org.cipres.treebase.domain.nexus.nexml;
-
-//import org.cipres.treebase.Constants;
-//import org.cipres.treebase.domain.admin.Person;
-import org.cipres.treebase.Constants;
-import org.cipres.treebase.domain.matrix.CharacterMatrix;
-import org.cipres.treebase.domain.nexus.NexusDataSet;
-//import org.cipres.treebase.domain.study.ArticleCitation;
-//import org.cipres.treebase.domain.study.Citation;
-import org.cipres.treebase.domain.study.Study;
-import org.cipres.treebase.domain.taxon.TaxonLabelHome;
-import org.cipres.treebase.domain.taxon.TaxonLabelSet;
-import org.nexml.model.Document;
-import org.nexml.model.Matrix;
-import org.nexml.model.OTUs;
-import org.nexml.model.TreeBlock;
-
-public class NexmlDocumentConverter extends NexmlObjectConverter {
-
- /**
- *
- * @param study
- * @param taxonLabelHome
- * @param document
- */
- public NexmlDocumentConverter(Study study, TaxonLabelHome taxonLabelHome,
- Document document) {
- super(study, taxonLabelHome, document);
- }
-
- public NexmlDocumentConverter(Study study, TaxonLabelHome taxonLabelHome,
- Document document,String baseURI) {
- super(study, taxonLabelHome, document,baseURI);
- }
-
- /**
- *
- * @param pDocument
- * @return
- */
- public NexusDataSet fromXmlToTreeBase(Document pDocument) {
- NexusDataSet nexusDataSet = new NexusDataSet();
- nexusDataSet.setNexmlProject(pDocument);
-
- NexmlOTUConverter noc = new NexmlOTUConverter(getStudy(),getTaxonLabelHome(),pDocument);
- for ( OTUs xmlOTUs : pDocument.getOTUsList() ) {
- TaxonLabelSet taxonLabelSet = noc.fromXmlToTreeBase(xmlOTUs);
- nexusDataSet.addTaxonLabelSet(xmlOTUs, taxonLabelSet);
- }
-
- NexmlMatrixConverter nmc = new NexmlMatrixConverter(getStudy(),getTaxonLabelHome(),pDocument);
- for ( Matrix<?> xmlMatrix : pDocument.getMatrices() ) {
- org.cipres.treebase.domain.matrix.Matrix matrix = nmc.fromXmlToTreeBase(xmlMatrix);
- nexusDataSet.getMatrices().add(matrix);
- }
-
- NexmlTreeBlockConverter ntc = new NexmlTreeBlockConverter(getStudy(),getTaxonLabelHome(),pDocument);
- for ( TreeBlock xmlTreeBlock : pDocument.getTreeBlockList() ) {
- org.cipres.treebase.domain.tree.TreeBlock treeBlock = ntc.fromXmlToTreeBase(xmlTreeBlock);
- nexusDataSet.getTreeBlocks().add(treeBlock);
- }
-
- return nexusDataSet;
- }
-
- /**
- *
- * @param pNexusDataSet
- * @return
- */
- public Document fromTreeBaseToXml(NexusDataSet pNexusDataSet) {
-
- NexmlOTUConverter noc = new NexmlOTUConverter(getStudy(),getTaxonLabelHome(),getDocument());
- for ( TaxonLabelSet taxonLabelSet : pNexusDataSet.getTaxonLabelSets() ) {
- noc.fromTreeBaseToXml(taxonLabelSet);
- }
-
- NexmlMatrixConverter nmc = new NexmlMatrixConverter(getStudy(),getTaxonLabelHome(),getDocument());
- for (org.cipres.treebase.domain.matrix.Matrix matrix : pNexusDataSet.getMatrices() ) {
- if ( matrix instanceof CharacterMatrix ) {
- nmc.fromTreeBaseToXml((CharacterMatrix)matrix);
- }
- }
-
- NexmlTreeBlockConverter ntc = new NexmlTreeBlockConverter(getStudy(),getTaxonLabelHome(),getDocument());
- for ( org.cipres.treebase.domain.tree.TreeBlock treeBlock : pNexusDataSet.getTreeBlocks() ) {
- ntc.fromTreeBaseToXML(treeBlock);
- }
-
- return getDocument();
-
- }
-
- /**
- *
- * @param pStudy
- * @return
- */
- public Document fromTreeBaseToXml(Study pStudy) {
- attachTreeBaseID(getDocument(), pStudy,Study.class);
- getDocument().addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlDocumentConverter $Rev$");
-
- NexmlOTUConverter noc = new NexmlOTUConverter(getStudy(),getTaxonLabelHome(),getDocument());
- for ( TaxonLabelSet taxonLabelSet : pStudy.getTaxonLabelSets() ) {
- noc.fromTreeBaseToXml(taxonLabelSet);
- }
-
- NexmlMatrixConverter nmc = new NexmlMatrixConverter(getStudy(),getTaxonLabelHome(),getDocument());
- for (org.cipres.treebase.domain.matrix.Matrix matrix : pStudy.getMatrices() ) {
- if ( matrix instanceof CharacterMatrix ) {
- nmc.fromTreeBaseToXml((CharacterMatrix)matrix);
- }
- }
-
- NexmlTreeBlockConverter ntc = new NexmlTreeBlockConverter(getStudy(),getTaxonLabelHome(),getDocument());
- for ( org.cipres.treebase.domain.tree.TreeBlock treeBlock : pStudy.getTreeBlocks() ) {
- ntc.fromTreeBaseToXML(treeBlock);
- }
-
- return getDocument();
- }
-
-}
Added: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentReader.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentReader.java (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentReader.java 2011-10-13 16:26:47 UTC (rev 971)
@@ -0,0 +1,49 @@
+package org.cipres.treebase.domain.nexus.nexml;
+
+import org.cipres.treebase.domain.nexus.NexusDataSet;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.cipres.treebase.domain.taxon.TaxonLabelSet;
+import org.nexml.model.Document;
+import org.nexml.model.Matrix;
+import org.nexml.model.OTUs;
+import org.nexml.model.TreeBlock;
+
+public class NexmlDocumentReader extends NexmlObjectConverter {
+
+ public NexmlDocumentReader(Study study, TaxonLabelHome taxonLabelHome,
+ Document document) {
+ super(study, taxonLabelHome, document);
+ }
+
+ /**
+ *
+ * @param pDocument
+ * @return
+ */
+ public NexusDataSet fromXmlToTreeBase(Document pDocument) {
+ NexusDataSet nexusDataSet = new NexusDataSet();
+ nexusDataSet.setNexmlProject(pDocument);
+
+ NexmlOTUReader noc = new NexmlOTUReader(getStudy(),getTaxonLabelHome(),pDocument);
+ for ( OTUs xmlOTUs : pDocument.getOTUsList() ) {
+ TaxonLabelSet taxonLabelSet = noc.fromXmlToTreeBase(xmlOTUs);
+ nexusDataSet.addTaxonLabelSet(xmlOTUs, taxonLabelSet);
+ }
+
+ NexmlMatrixReader nmc = new NexmlMatrixReader(getStudy(),getTaxonLabelHome(),pDocument);
+ for ( Matrix<?> xmlMatrix : pDocument.getMatrices() ) {
+ org.cipres.treebase.domain.matrix.Matrix matrix = nmc.fromXmlToTreeBase(xmlMatrix);
+ nexusDataSet.getMatrices().add(matrix);
+ }
+
+ NexmlTreeBlockReader ntc = new NexmlTreeBlockReader(getStudy(),getTaxonLabelHome(),pDocument);
+ for ( TreeBlock xmlTreeBlock : pDocument.getTreeBlockList() ) {
+ org.cipres.treebase.domain.tree.TreeBlock treeBlock = ntc.fromXmlToTreeBase(xmlTreeBlock);
+ nexusDataSet.getTreeBlocks().add(treeBlock);
+ }
+
+ return nexusDataSet;
+ }
+
+}
Copied: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentWriter.java (from rev 970, trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java)
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentWriter.java (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentWriter.java 2011-10-13 16:26:47 UTC (rev 971)
@@ -0,0 +1,86 @@
+package org.cipres.treebase.domain.nexus.nexml;
+
+import org.cipres.treebase.Constants;
+import org.cipres.treebase.domain.matrix.CharacterMatrix;
+import org.cipres.treebase.domain.nexus.NexusDataSet;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.cipres.treebase.domain.taxon.TaxonLabelSet;
+import org.nexml.model.Document;
+
+public class NexmlDocumentWriter extends NexmlObjectConverter {
+
+ /**
+ *
+ * @param study
+ * @param taxonLabelHome
+ * @param document
+ */
+ public NexmlDocumentWriter(Study study, TaxonLabelHome taxonLabelHome,
+ Document document) {
+ super(study, taxonLabelHome, document);
+ }
+
+ public NexmlDocumentWriter(Study study, TaxonLabelHome taxonLabelHome,
+ Document document,String baseURI) {
+ super(study, taxonLabelHome, document,baseURI);
+ }
+
+ /**
+ *
+ * @param pNexusDataSet
+ * @return
+ */
+ public Document fromTreeBaseToXml(NexusDataSet pNexusDataSet) {
+
+ NexmlOTUWriter noc = new NexmlOTUWriter(getStudy(),getTaxonLabelHome(),getDocument());
+ for ( TaxonLabelSet taxonLabelSet : pNexusDataSet.getTaxonLabelSets() ) {
+ noc.fromTreeBaseToXml(taxonLabelSet);
+ }
+
+ 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);
+ }
+ }
+
+ NexmlTreeBlockWriter ntc = new NexmlTreeBlockWriter(getStudy(),getTaxonLabelHome(),getDocument());
+ for ( org.cipres.treebase.domain.tree.TreeBlock treeBlock : pNexusDataSet.getTreeBlocks() ) {
+ ntc.fromTreeBaseToXML(treeBlock);
+ }
+
+ return getDocument();
+
+ }
+
+ /**
+ *
+ * @param pStudy
+ * @return
+ */
+ public Document fromTreeBaseToXml(Study pStudy) {
+ attachTreeBaseID(getDocument(), pStudy,Study.class);
+ getDocument().addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlDocumentConverter $Rev$");
+
+ NexmlOTUWriter noc = new NexmlOTUWriter(getStudy(),getTaxonLabelHome(),getDocument());
+ for ( TaxonLabelSet taxonLabelSet : pStudy.getTaxonLabelSets() ) {
+ noc.fromTreeBaseToXml(taxonLabelSet);
+ }
+
+ 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);
+ }
+ }
+
+ NexmlTreeBlockWriter ntc = new NexmlTreeBlockWriter(getStudy(),getTaxonLabelHome(),getDocument());
+ for ( org.cipres.treebase.domain.tree.TreeBlock treeBlock : pStudy.getTreeBlocks() ) {
+ ntc.fromTreeBaseToXML(treeBlock);
+ }
+
+ return getDocument();
+ }
+
+}
Deleted: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2011-10-05 17:43:48 UTC (rev 970)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2011-10-13 16:26:47 UTC (rev 971)
@@ -1,739 +0,0 @@
-package org.cipres.treebase.domain.nexus.nexml;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.cipres.treebase.Constants;
-import org.cipres.treebase.dao.jdbc.ContinuousMatrixElementJDBC;
-import org.cipres.treebase.dao.jdbc.ContinuousMatrixJDBC;
-import org.cipres.treebase.dao.jdbc.DiscreteMatrixElementJDBC;
-import org.cipres.treebase.dao.jdbc.DiscreteMatrixJDBC;
-import org.cipres.treebase.dao.jdbc.MatrixColumnJDBC;
-import org.cipres.treebase.domain.matrix.CharSet;
-import org.cipres.treebase.domain.matrix.CharacterMatrix;
-import org.cipres.treebase.domain.matrix.ColumnRange;
-import org.cipres.treebase.domain.matrix.ContinuousChar;
-import org.cipres.treebase.domain.matrix.ContinuousMatrix;
-import org.cipres.treebase.domain.matrix.ContinuousMatrixElement;
-import org.cipres.treebase.domain.matrix.DiscreteChar;
-import org.cipres.treebase.domain.matrix.DiscreteCharState;
-import org.cipres.treebase.domain.matrix.DiscreteMatrix;
-import org.cipres.treebase.domain.matrix.DiscreteMatrixElement;
-import org.cipres.treebase.domain.matrix.Matrix;
-import org.cipres.treebase.domain.matrix.MatrixColumn;
-import org.cipres.treebase.domain.matrix.MatrixDataType;
-import org.cipres.treebase.domain.matrix.MatrixElement;
-import org.cipres.treebase.domain.matrix.MatrixRow;
-import org.cipres.treebase.domain.matrix.PhyloChar;
-import org.cipres.treebase.domain.matrix.RowSegment;
-import org.cipres.treebase.domain.matrix.StandardMatrix;
-import org.cipres.treebase.domain.matrix.StateSet;
-import org.cipres.treebase.domain.study.Study;
-import org.cipres.treebase.domain.taxon.TaxonLabelHome;
-import org.cipres.treebase.domain.taxon.TaxonLabelSet;
-import org.nexml.model.Annotatable;
-import org.nexml.model.CategoricalMatrix;
-import org.nexml.model.CharacterState;
-import org.nexml.model.CharacterStateSet;
-import org.nexml.model.Document;
-import org.nexml.model.MatrixCell;
-import org.nexml.model.MolecularMatrix;
-import org.nexml.model.OTUs;
-import org.nexml.model.OTU;
-import org.nexml.model.Subset;
-
-public class NexmlMatrixConverter extends NexmlObjectConverter {
-
- private static final int MAX_GRANULAR_NCHAR = 1000;
- private static final int MAX_GRANULAR_NTAX = 30;
-
- /**
- *
- * @param study
- * @param taxonLabelHome
- */
- public NexmlMatrixConverter(Study study,TaxonLabelHome taxonLabelHome,Document document) {
- super(study,taxonLabelHome,document);
- }
-
- /**
- *
- * @param xmlMatrix
- * @return
- */
- public Matrix fromXmlToTreeBase(CategoricalMatrix xmlMatrix) {
- DiscreteMatrix tbMatrix = new DiscreteMatrix();
- DiscreteMatrixJDBC matrixJDBC = new DiscreteMatrixJDBC(tbMatrix, xmlMatrix, this);
- List<MatrixColumnJDBC> columnJDBCs = new ArrayList<MatrixColumnJDBC>();
- long[] colIds = matrixJDBC.getColIDs();
- long[] rowIds = matrixJDBC.getRowIDs();
- List<DiscreteMatrixElementJDBC> elements = new ArrayList<DiscreteMatrixElementJDBC>();
- int colIndex = 0;
- for ( org.nexml.model.Character xmlCharacter : xmlMatrix.getCharacters() ) {
- String charName = xmlCharacter.getLabel();
- DiscreteChar tbChar = new DiscreteChar();
- tbChar.setDescription(charName);
- MatrixColumnJDBC aColumnJDBC = new MatrixColumnJDBC();
- aColumnJDBC.setPhyloChar(tbChar);
- columnJDBCs.add(aColumnJDBC);
- int rowIndex = 0;
- for ( OTU xmlOTU : xmlMatrix.getOTUs().getAllOTUs() ) {
- @SuppressWarnings("unused")
- MatrixCell<CharacterState> xmlCell = xmlMatrix.getCell(xmlOTU, xmlCharacter);
- DiscreteMatrixElementJDBC element = new DiscreteMatrixElementJDBC();
- //element.setValue(xmlCell.getValue()); // XXX nested stateset lookup song & dance here
- element.setElementOrder(colIndex);
- element.setMatrixRowID(rowIds[rowIndex]);
- element.setMatrixColID(colIds[colIndex]);
- elements.add(element);
- rowIndex++;
- }
- colIndex++;
- }
- DiscreteMatrixElementJDBC.batchDiscreteElements(elements, getTaxonLabelHome().getConnection());
- return tbMatrix;
- }
-
- /**
- *
- * @param xmlMatrix
- * @return
- */
- public Matrix fromXmlToTreeBase(org.nexml.model.ContinuousMatrix xmlMatrix) {
- ContinuousMatrix tbMatrix = new ContinuousMatrix();
- ContinuousMatrixJDBC matrixJDBC = new ContinuousMatrixJDBC(tbMatrix, xmlMatrix, this);
- List<MatrixColumnJDBC> columnJDBCs = new ArrayList<MatrixColumnJDBC>();
- long[] colIds = matrixJDBC.getColIDs();
- long[] rowIds = matrixJDBC.getRowIDs();
- List<ContinuousMatrixElementJDBC> elements = new ArrayList<ContinuousMatrixElementJDBC>();
-
- int colIndex = 0;
- for ( org.nexml.model.Character xmlCharacter : xmlMatrix.getCharacters() ) {
- String charName = xmlCharacter.getLabel();
- ContinuousChar tbChar = new ContinuousChar();
- tbChar.setDescription(charName);
- MatrixColumnJDBC aColumnJDBC = new MatrixColumnJDBC();
- aColumnJDBC.setPhyloChar(tbChar);
- columnJDBCs.add(aColumnJDBC);
- int rowIndex = 0;
- for ( OTU xmlOTU : xmlMatrix.getOTUs().getAllOTUs() ) {
- MatrixCell<Double> xmlCell = xmlMatrix.getCell(xmlOTU, xmlCharacter);
- ContinuousMatrixElementJDBC element = new ContinuousMatrixElementJDBC();
- element.setValue(xmlCell.getValue());
- element.setElementOrder(colIndex);
- element.setMatrixRowID(rowIds[rowIndex]);
- element.setMatrixColID(colIds[colIndex]);
- elements.add(element);
- rowIndex++;
- }
- colIndex++;
- }
- ContinuousMatrixElementJDBC.batchContinuousElements(elements, getTaxonLabelHome().getConnection());
- return tbMatrix;
- }
-
- /**
- *
- * @param xmlMatrix
- * @return
- */
- public Matrix fromXmlToTreeBase(org.nexml.model.Matrix<?> xmlMatrix) {
- OTUs xmlOTUs = xmlMatrix.getOTUs();
- Matrix tbMatrix = null;
- TaxonLabelSet tbTaxa = null;
- Long tbTaxonLabelSetID = readTreeBaseID((Annotatable) xmlOTUs);
- if ( null != tbTaxonLabelSetID ) {
- tbTaxa = getTaxonLabelHome()
- .findPersistedObjectByID(TaxonLabelSet.class, tbTaxonLabelSetID);
- }
- if ( xmlMatrix instanceof CategoricalMatrix ) {
- tbMatrix = fromXmlToTreeBase((CategoricalMatrix) xmlMatrix);
- }
- else if ( xmlMatrix instanceof org.nexml.model.ContinuousMatrix ) {
- tbMatrix = fromXmlToTreeBase((org.nexml.model.ContinuousMatrix) xmlMatrix);
- }
- if ( null != tbMatrix ) {
- attachTreeBaseID((Annotatable) xmlMatrix, tbMatrix,Matrix.class);
- if ( null != tbTaxa ) {
- tbMatrix.setTaxa(tbTaxa);
- }
- tbMatrix.setStudy(getStudy());
- tbMatrix.setTitle(xmlMatrix.getLabel());
- tbMatrix.setPublished(false);
- }
- return tbMatrix;
- }
-
- /**
- * Creates and populates characters (i.e. columns) with their annotations,
- * and state sets, with their annotations
- *
- * @param tbMatrix
- * @return an xml matrix with empty rows
- */
- public CategoricalMatrix fromTreeBaseToXml(StandardMatrix tbMatrix) {
- OTUs xmlOTUs = getOTUsById(tbMatrix.getTaxa().getId());
- CategoricalMatrix xmlMatrix = getDocument().createCategoricalMatrix(xmlOTUs);
-
- // attach base uri and history note
- xmlMatrix.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlMatrixConverter $Rev$");
- xmlMatrix.setBaseURI(mMatrixBaseURI);
-
- List<List<DiscreteCharState>> tbStateLabels = tbMatrix.getStateLabels();
- List<MatrixColumn> tbColumns = tbMatrix.getColumnsReadOnly();
- for ( int i = 0; i < tbColumns.size(); i++ ) {
- CharacterStateSet xmlStateSet = xmlMatrix.createCharacterStateSet();
- for ( DiscreteCharState tbState : tbStateLabels.get(i) ) {
- CharacterState xmlState = xmlStateSet.createCharacterState(tbState.getSymbol().toString());
- if ( null != tbState.getDescription() ) {
- xmlState.setLabel(tbState.getDescription());
- }
- attachTreeBaseID((Annotatable)xmlState,tbState,DiscreteCharState.class);
- }
- org.nexml.model.Character xmlCharacter = xmlMatrix.createCharacter(xmlStateSet);
- PhyloChar tbCharacter = tbColumns.get(i).getCharacter();
- if ( null != tbCharacter.getDescription() ) {
- xmlCharacter.setLabel(tbCharacter.getDescription());
- }
- attachTreeBaseID((Annotatable)xmlCharacter,tbColumns.get(i),MatrixColumn.class);
- }
- return xmlMatrix;
- }
-
- /**
- * Creates and populates characters (i.e. columns) with their annotations,
- * and state sets, with their annotations
- *
- * @param tbMatrix
- * @return an xml matrix with empty rows
- */
- public MolecularMatrix fromTreeBaseToXml(DiscreteMatrix tbMatrix) {
- OTUs xmlOTUs = getOTUsById(tbMatrix.getTaxa().getId());
- String tbDataType = tbMatrix.getDataType().getDescription();
- MolecularMatrix xmlMatrix = null;
- CharacterStateSet xmlStateSet = null;
-
- // create the matrix and constant state set
- if ( tbDataType.equals(MatrixDataType.MATRIX_DATATYPE_DNA) ) {
- xmlMatrix = getDocument().createMolecularMatrix(xmlOTUs, MolecularMatrix.DNA);
- xmlStateSet = ((MolecularMatrix)xmlMatrix).getDNACharacterStateSet();
- }
- else if ( tbDataType.equals(MatrixDataType.MATRIX_DATATYPE_RNA) ) {
- xmlMatrix = getDocument().createMolecularMatrix(xmlOTUs, MolecularMatrix.RNA);
- xmlStateSet = ((MolecularMatrix)xmlMatrix).getRNACharacterStateSet();
- }
- else if ( tbDataType.equals(MatrixDataType.MATRIX_DATATYPE_PROTEIN) ) {
- xmlMatrix = getDocument().createMolecularMatrix(xmlOTUs, MolecularMatrix.Protein);
- xmlStateSet = ((MolecularMatrix)xmlMatrix).getProteinCharacterStateSet();
- }
-
- // attach base uri and history note
- xmlMatrix.setBaseURI(mMatrixBaseURI);
- xmlMatrix.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlMatrixConverter $Rev$");
-
- // lookup the equivalent state in tb and attach identifiers
- for(StateSet tbStateSet : tbMatrix.getStateSets() ) {
- for (DiscreteCharState tbState : tbStateSet.getStates() ) {
- String tbSymbol = tbState.getSymbol().toString().toUpperCase();
- CharacterState xmlState = xmlStateSet.lookupCharacterStateBySymbol(tbSymbol);
- if ( null == xmlState ) {
- xmlState = xmlStateSet.createCharacterState(tbSymbol);
- }
- attachTreeBaseID((Annotatable)xmlState,tbState,DiscreteCharState.class);
- }
- }
-
- // create columns and attach identifiers
- for ( MatrixColumn tbColumn : tbMatrix.getColumnsReadOnly() ) {
- org.nexml.model.Character xmlCharacter = xmlMatrix.createCharacter(xmlStateSet);
- attachTreeBaseID((Annotatable)xmlCharacter,tbColumn,MatrixColumn.class);
- }
- return xmlMatrix;
- }
-
- /**
- * Creates and populates characters (i.e. columns) with their annotations,
- * and state sets, with their annotations
- *
- * @param tbMatrix
- * @return an xml matrix with empty rows
- */
- public org.nexml.model.ContinuousMatrix fromTreeBaseToXml(ContinuousMatrix tbMatrix) {
- OTUs xmlOTUs = getOTUsById(tbMatrix.getTaxa().getId());
- org.nexml.model.ContinuousMatrix xmlMatrix = getDocument().createContinuousMatrix(xmlOTUs);
-
- // attach base uri and history note
- xmlMatrix.setBaseURI(mMatrixBaseURI);
- xmlMatrix.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlMatrixConverter $Rev$");
-
- for ( MatrixColumn tbColumn : tbMatrix.getColumnsReadOnly() ) {
- org.nexml.model.Character xmlCharacter = xmlMatrix.createCharacter();
- PhyloChar tbCharacter = tbColumn.getCharacter();
- if ( null != tbCharacter.getDescription() ) {
- xmlCharacter.setLabel(tbCharacter.getDescription());
- ((Annotatable)xmlCharacter).addAnnotationValue("dcterms:description", Constants.DCTermsURI, tbCharacter.getDescription());
- }
- attachTreeBaseID((Annotatable)xmlCharacter,tbColumn,MatrixColumn.class);
-
- //coerce the tbMatrix into a character matrix to get its character sets
- CharacterMatrix tbCharacterMatrix = (CharacterMatrix)tbMatrix;
- Set<CharSet> tbCharSets = tbCharacterMatrix.getCharSets();
- for ( CharSet tbCharSet : tbCharSets ) {
- Collection<ColumnRange> tbColumnRanges = tbCharSet.getColumns(tbCharacterMatrix);
-
- for ( ColumnRange tbColumnRange : tbColumnRanges ) {
-
- // these are the beginning and end of the range
- int tbStart = tbColumnRange.getStartColIndex();
- int tbStop = tbColumnRange.getEndColIndex();
-
- // increment from beginning to end. This number is probably either null, for a
- // contiguous range, or perhaps 3 for codon positions
- int tbInc = 1;
- // create the equivalent nexml character set
- Subset nexSubset = xmlMatrix.createSubset(tbCharSet.getLabel());
-
- // assign character objects to the subset. Here we get the full list
- List<org.nexml.model.Character> nexCharacters = xmlMatrix.getCharacters();
-
- // now we iterate over the coordinates and assign the nexml characters to the set
- for ( int i = tbStart; i <= tbStop; i += tbInc ) {
- nexSubset.addThing(nexCharacters.get(i));
- }
- }
- }
-
- }
-
- return xmlMatrix;
- }
-
-
-// XXX doesn't handle the following data types:
-// public static final String MATRIX_DATATYPE_NUCLEOTIDE = "Nucleotide";
-// 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) {
- org.nexml.model.Matrix<?> xmlMatrix = null;
- if ( tbMatrix instanceof DiscreteMatrix ) {
- if ( tbMatrix.getDataType().getDescription().equals(MatrixDataType.MATRIX_DATATYPE_STANDARD) ) {
- xmlMatrix = fromTreeBaseToXml((StandardMatrix) tbMatrix);
- }
- else {
- xmlMatrix = fromTreeBaseToXml((DiscreteMatrix) tbMatrix);
- }
- populateXmlMatrix((org.nexml.model.Matrix<CharacterState>)xmlMatrix,(DiscreteMatrix)tbMatrix);
- }
- else if ( tbMatrix instanceof ContinuousMatrix ) {
- xmlMatrix = fromTreeBaseToXml((ContinuousMatrix) tbMatrix);
- populateXmlMatrix((org.nexml.model.ContinuousMatrix)xmlMatrix,(ContinuousMatrix)tbMatrix);
- }
- xmlMatrix.setLabel(tbMatrix.getTitle());
- attachTreeBaseID((Annotatable)xmlMatrix, tbMatrix,Matrix.class);
- String tb1MatrixID = tbMatrix.getTB1MatrixID();
- if ( null != tb1MatrixID ) {
- ((Annotatable)xmlMatrix).addAnnotationValue("tb:identifier.matrix.tb1", Constants.TBTermsURI, tb1MatrixID);
- }
- Set<CharSet> tbCharSets = tbMatrix.getCharSets();
- for ( CharSet tbCharSet : tbCharSets ) {
- Collection<ColumnRange> tbColumnRanges = tbCharSet.getColumns(tbMatrix);
-
- for ( ColumnRange tbColumnRange : tbColumnRanges ) {
-
- // these are the beginning and end of the range
- int tbStart = tbColumnRange.getStartColIndex();
- int tbStop = tbColumnRange.getEndColIndex();
-
- // increment from beginning to end. This number is probably either null, for a
- // contiguous range, or perhaps 3 for codon positions
- int tbInc = 1;
- // create the equivalent nexml character set
- Subset nexSubset = xmlMatrix.createSubset(tbCharSet.getLabel());
-
- // assign character objects to the subset. Here we get the full list
- List<org.nexml.model.Character> nexCharacters = xmlMatrix.getCharacters();
-
- // now we iterate over the coordinates and assign the nexml characters to the set
- for ( int i = tbStart; i <= tbStop; i += tbInc ) {
- nexSubset.addThing(nexCharacters.get(i));
- }
- }
- }
-
- return xmlMatrix;
- }
-
- /**
- *
- * @param xmlMatrix
- * @param tbMatrix
- * @param xmlOTUs
- * @param stateSet
- */
- private void populateXmlMatrix(
- org.nexml.model.Matrix<CharacterState> xmlMatrix,
- DiscreteMatrix tbMatrix) {
- OTUs xmlOTUs = xmlMatrix.getOTUs();
- List<org.nexml.model.Character> characterList = xmlMatrix.getCharacters();
- for ( MatrixRow tbRow : tbMatrix.getRowsReadOnly() ) {
- Set<RowSegment> tbSegments = tbRow.getSegmentsReadOnly();
- OTU xmlOTU = getOTUById(xmlOTUs, tbRow.getTaxonLabel().getId());
- int charIndex = 0;
- if ( characterList.size() <= MAX_GRANULAR_NCHAR && xmlOTUs.getAllOTUs().size() <= MAX_GRANULAR_NTAX ) {
- for ( MatrixColumn tbColumn : ((CharacterMatrix)tbMatrix).getColumns() ) {
- String seq = tbRow.buildElementAsString();
- xmlMatrix.setSeq(seq, xmlOTU);
- org.nexml.model.Character xmlCharacter = characterList.get(charIndex);
- MatrixCell<CharacterState> xmlCell = xmlMatrix.getCell(xmlOTU, xmlCharacter);
-
- attachTreeBaseID ((Annotatable) xmlCell, tbColumn , DiscreteMatrixElement.class);
-
- //The following is commented out as tbRow.getElements() does not work directly and crashes the loop.
- //The above for loop fixes this issue.
- /*
- for ( MatrixElement tbCell : tbRow.getElements() ) {
- org.nexml.model.Character xmlCharacter = characterList.get(charIndex);
- MatrixCell<CharacterState> xmlCell = xmlMatrix.getCell(xmlOTU, xmlCharacter);
- DiscreteCharState tbState = ((DiscreteMatrixElement)tbCell).getCharState();
- String tbSymbolString = ( null == tbState ) ? "?" : tbState.getSymbol().toString();
- CharacterState xmlState = xmlCharacter.getCharacterStateSet().lookupCharacterStateBySymbol(tbSymbolString);
- xmlCell.setValue(xmlState);
- attachTreeBaseID((Annotatable)xmlCell,tbCell,DiscreteMatrixElement.class);
- */
-
- for ( RowSegment tbSegment : tbSegments ) {
- if ( tbSegment.getStartIndex() <= charIndex && charIndex <= tbSegment.getEndIndex() ) {
- //declare variables for row-segment annotations
- String title = tbSegment.getTitle();
- String institutionCode = tbSegment.getSpecimenLabel().getInstAcronym();
- String collectionCode = tbSegment.getSpecimenLabel().getCollectionCode();
- String catalogNumber = tbSegment.getSpecimenLabel().getCatalogNumber();
- String accessionNumber = tbSegment.getSpecimenLabel().getGenBankAccession();
- String otherAccessionNumber = tbSegment.getSpecimenLabel().getOtherAccession();
- String dateSampled = tbSegment.getSpecimenLabel().getSampleDateString();
- String scientificName = tbSegment.getSpecimenTaxonLabelAsString();
- String collector = tbSegment.getSpecimenLabel().getCollector();
- Double latitude = tbSegment.getSpecimenLabel().getLatitude();
- Double longitude = tbSegment.getSpecimenLabel().getLongitude();
- Double elevation = tbSegment.getSpecimenLabel().getElevation();
- String country = tbSegment.getSpecimenLabel().getCountry();
- String state = tbSegment.getSpecimenLabel().getState();
- String locality = tbSegment.getSpecimenLabel().getLocality();
- String notes = tbSegment.getSpecimenLabel().getNotes();
-
- //if the value is not null, output the xmlOTU annotation.
- //DwC refers to the Darwin Core term vocabulary for the associated annotation
- if (null != title){
- //output name identifying the data set from which the record was derived
- ((Annotatable)xmlCell).addAnnotationValue("DwC:datasetName", Constants.DwCURI, title);
- }
- if ( null != institutionCode ) {
- //output name or acronym of institution that has custody of information referred to in record
- ((Annotatable)xmlCell).addAnnotationValue("DwC:institutionCode", Constants.DwCURI, institutionCode);
- }
- if ( null != collectionCode ) {
- //output name or code that identifies collection or data set from which record was derived
- ((Annotatable)xmlCell).addAnnotationValue ("DwC:collectionCode", Constants.DwCURI, collectionCode);
- }
- if ( null != catalogNumber ){
- //output unique (usually) identifier for the record within data set or collection
- ((Annotatable)xmlCell).addAnnotationValue("DwC:catalogNumber", Constants.DwCURI, catalogNumber);
- }
- if ( null != accessionNumber) {
- //output a list of genetic sequence information associated with occurrence
- ((Annotatable)xmlCell).addAnnotationValue("DwC:associatedSequences", Constants.DwCURI, accessionNumber);
- }
- if ( null != otherAccessionNumber ) {
- //list of previous or alternate fully catalog numbers (i.e. Genbank) or human-used identifiers
- ((Annotatable)xmlCell).addAnnotationValue("DwC:otherCatalogNumbers", Constants.DwCURI, otherAccessionNumber);
- }
- if ( null != dateSampled ) {
- //output date sampled in ISO 8601 format
- ((Annotatable)xmlCell).addAnnotationValue("DwC:eventDate", Constants.DwCURI, dateSampled);
- }
- if ( null != scientificName ) {
- //output full scientific name
- ((Annotatable)xmlCell).addAnnotationValue("DwC:scientificName", Constants.DwCURI, scientificName);
- }
- if ( null != collector ) {
- //output names of people associated with recording of original occurrence
- ((Annotatable)xmlCell).addAnnotationValue("DwC:recordedBy", Constants.DwCURI, collector);
- }
- if ( null != latitude ) {
- //output geographic latitude in decimal degrees using geodeticDatum spatial reference system
- ((Annotatable)xmlCell).addAnnotationValue("DwC:decimalLatitude", Constants.DwCURI, latitude);
- }
- if ( null != longitude ) {
- //output geographic longitude in decimal degrees using geodeticDatum spatial reference system
- ((Annotatable)xmlCell).addAnnotationValue("DwC:decimalLongitude", Constants.DwCURI, longitude);
- }
- if ( null != elevation ) {
- //there are two different Darwin Core terms for elevation depending on elevation value
- //outputs geographic elevation of sample
- if ( elevation >= 0) {
- //above local surface in meters
- ((Annotatable)xmlCell).addAnnotationValue("DwC:verbatimElevation", Constants.DwCURI, elevation);
- }
- else {
- //below local surface in meters
- ((Annotatable)xmlCell).addAnnotationValue("DwC:verbatimDepth", Constants.DwCURI, elevation);
- }
- }
- if ( null != country ) {
- //output country in which location occurs
- ((Annotatable)xmlCell).addAnnotationValue("DwC:country", Constants.DwCURI, country);
- }
- if ( null != state ) {
- //output name of next smaller administrative region than country (i.e. state, province, region)
- ((Annotatable)xmlCell).addAnnotationValue ("DwC:stateProvince", Constants.DwCURI, state);
- }
- if ( null != locality) {
- //output brief description of sample location
- ((Annotatable)xmlCell).addAnnotationValue("DwC:locality", Constants.DwCURI, locality);
- }
- if ( null != notes ) {
- //output any additional information about specimen
- ((Annotatable)xmlCell).addAnnotationValue("DwC:occurenceRemarks", Constants.DwCURI, notes);
- }
- }
- }
- charIndex++;
- }
- }
- else {
- String seq = tbRow.buildElementAsString();
- if ( tbMatrix.getDataType().getDescription().equals(MatrixDataType.MATRIX_DATATYPE_STANDARD) ) {
- StringBuilder sb = new StringBuilder();
- for ( int i = 0; i < seq.length(); i++ ) {
- sb.append(seq.charAt(i));
- if ( i < seq.length() - 1 ) {
- sb.append(' ');
- }
- }
- }
- xmlMatrix.setSeq(seq,xmlOTU);
- }
- for ( RowSegment tbSegment : tbSegments ) {
- //declare variables for row-segment annotations
- String title = tbSegment.getTitle();
- String institutionCode = tbSegment.getSpecimenLabel().getInstAcronym();
- String collectionCode = tbSegment.getSpecimenLabel().getCollectionCode();
- String catalogNumber = tbSegment.getSpecimenLabel().getCatalogNumber();
- String accessionNumber = tbSegment.getSpecimenLabel().getGenBankAccession();
- String otherAccessionNumber = tbSegment.getSpecimenLabel().getOtherAccession();
- String dateSampled = tbSegment.getSpecimenLabel().getSampleDateString();
- String scientificName = tbSegment.getSpecimenTaxonLabelAsString();
- String collector = tbSegment.getSpecimenLabel().getCollector();
- Double latitude = tbSegment.getSpecimenLabel().getLatitude();
- Double longitude = tbSegment.getSpecimenLabel().getLongitude();
- Double elevation = tbSegment.getSpecimenLabel().getElevation();
- String country = tbSegment.getSpecimenLabel().getCountry();
- String state = tbSegment.getSpecimenLabel().getState();
- String locality = tbSegment.getSpecimenLabel().getLocality();
- String notes = tbSegment.getSpecimenLabel().getNotes();
-
- //if the value is not null, output the xmlOTU annotation.
- //DwC refers to the Darwin Core term vocabulary for the associated annotation
- if (null != title){
- //output name identifying the data set from which the record was derived
- xmlOTU.addAnnotationValue("DwC:datasetName", Constants.DwCURI, title);
- }
- if ( null != institutionCode ) {
- //output name or acronym of institution that has custody of information referred to in record
- xmlOTU.addAnnotationValue("DwC:institutionCode", Constants.DwCURI, institutionCode);
- }
- if ( null != collectionCode ) {
- //output name or code that identifies collection or data set from which record was derived
- xmlOTU.addAnnotationValue ("DwC:collectionCode", Constants.DwCURI, collectionCode);
- }
- if ( null != catalogNumber ){
- //output unique (usually) identifier for the record within data set or collection
- xmlOTU.addAnnotationValue("DwC:catalogNumber", Constants.DwCURI, catalogNumber);
- }
- if ( null != accessionNumber) {
- //output a list of genetic sequence information associated with occurrence
- xmlOTU.addAnnotationValue("DwC:associatedSequences", Constants.DwCURI, accessionNumber);
- }
- if ( null != otherAccessionNumber ) {
- //list of previous or alternate fully catalog numbers (i.e. Genbank) or human-used identifiers
- xmlOTU.addAnnotationValue("DwC:otherCatalogNumbers", Constants.DwCURI, otherAccessionNumber);
- }
- if ( null != dateSampled ) {
- //output date sampled in ISO 8601 format
- xmlOTU.addAnnotationValue("DwC:eventDate", Constants.DwCURI, dateSampled);
- }
- if ( null != scientificName ) {
- //output full scientific name
- xmlOTU.addAnnotationValue("DwC:scientificName", Constants.DwCURI, scientificName);
- }
- if ( null != collector ) {
- //output names of people associated with recording of original occurrence
- xmlOTU.addAnnotationValue("DwC:recordedBy", Constants.DwCURI, collector);
- }
- if ( null != latitude ) {
- //output geographic latitude in decimal degrees using geodeticDatum spatial reference system
- xmlOTU.addAnnotationValue("DwC:decimalLatitude", Constants.DwCURI, latitude);
- }
- if ( null != longitude ) {
- //output geographic longitude in decimal degrees using geodeticDatum spatial reference system
- xmlOTU.addAnnotationValue("DwC:decimalLongitude", Constants.DwCURI, longitude);
- }
- if ( null != elevation ) {
- //there are two different Darwin Core terms for elevation depending on elevation value
- //outputs geographic elevation of sample
- if ( elevation >= 0) {
- //above local surface in meters
- xmlOTU.addAnnotationValue("DwC:verbatimElevation", Constants.DwCURI, elevation);
- }
- else {
- //below local surface in meters
- xmlOTU.addAnnotationValue("DwC:verbatimDepth", Constants.DwCURI, elevation);
- }
- }
- if ( null != country ) {
- //output country in which location occurs
- xmlOTU.addAnnotationValue("DwC:country", Constants.DwCURI, country);
- }
- if ( null != state ) {
- //output name of next smaller administrative region than country (i.e. state, province, region)
- xmlOTU.addAnnotationValue ("DwC:stateProvince", Constants.DwCURI, state);
- }
- if ( null != locality) {
- //output brief description of sample location
- xmlOTU.addAnnotationValue("DwC:locality", Constants.DwCURI, locality);
- }
- if ( null != notes ) {
- //output any additional information about specimen
- xmlOTU.addAnnotationValue("DwC:occurenceRemarks", Constants.DwCURI, notes);
- }
- }
- }
- }
-
- /**
- *
- * @param xmlMatrix
- * @param tbMatrix
- */
- private void populateXmlMatrix(org.nexml.model.ContinuousMatrix xmlMatrix,
- ContinuousMatrix tbMatrix) {
- List<org.nexml.model.Character> characterList = xmlMatrix.getCharacters();
- OTUs xmlOTUs = xmlMatrix.getOTUs();
- for ( MatrixRow tbRow : tbMatrix.getRowsReadOnly() ) {
- List<MatrixElement> elements = tbRow.getElements();
- OTU xmlOTU = getOTUById(xmlOTUs, tbRow.getTaxonLabel().getId());
- if ( characterList.size() <= MAX_GRANULAR_NCHAR && xmlOTUs.getAllOTUs().size() <= MAX_GRANULAR_NTAX ) {
- for ( int elementIndex = 0; elementIndex < tbMatrix.getnChar(); elementIndex++ ) {
- ContinuousMatrixElement tbCell = (ContinuousMatrixElement)elements.get(elementIndex);
- MatrixCell<Double> xmlCell = xmlMatrix.getCell(xmlOTU, characterList.get(elementIndex));
- xmlCell.setValue(tbCell.getValue());
- attachTreeBaseID((Annotatable)xmlCell,tbCell,DiscreteMatrixElement.class);
- }
- }
- else {
- String seq = tbRow.buildElementAsString();
- xmlMatrix.setSeq(seq,xmlOTU);
- }
- Set<RowSegment> tbSegments = tbRow.getSegmentsReadOnly();
- for ( RowSegment tbSegment : tbSegments ) {
- //declare variables for row-segment annotations
- String title = tbSegment.getTitle();
- String institutionCode = tbSegment.getSpecimenLabel().getInstAcronym();
- String collectionCode = tbSegment.getSpecimenLabel().getCollectionCode();
- String catalogNumber = tbSegment.getSpecimenLabel().getCatalogNumber();
- String accessionNumber = tbSegment.getSpecimenLabel().getGenBankAccession();
- String otherAccessionNumber = tbSegment.getSpecimenLabel().getOtherAccession();
- String dateSampled = tbSegment.getSpecimenLabel().getSampleDateString();
- String scientificName = tbSegment.getSpecimenTaxonLabelAsString();
- String collector = tbSegment.getSpecimenLabel().getCollector();
- Double latitude = tbSegment.getSpecimenLabel().getLatitude();
- Double longitude = tbSegment.getSpecimenLabel().getLongitude();
- Double elevation = tbSegment.getSpecimenLabel().getElevation();
- String country = tbSegment.getSpecimenLabel().getCountry();
- String state = tbSegment.getSpecimenLabel().getState();
- String locality = tbSegment.getSpecimenLabel().getLocality();
- String notes = tbSegment.getSpecimenLabel().getNotes();
-
- //if the value is not null, output the xmlOTU annotation.
- //DwC refers to the Darwin Core term vocabulary for the associated annotation
- if (null != title){
- //output name identifying the data set from which the record was derived
- xmlOTU.addAnnotationValue("DwC:datasetName", Constants.DwCURI, title);
- }
- if ( null != institutionCode ) {
- //output name or acronym of institution that has custody of information referred to in record
- xmlOTU.addAnnotationValue("DwC:institutionCode", Constants.DwCURI, institutionCode);
- }
- if ( null != collectionCode ) {
- //output name or code that identifies collection or data set from which record was derived
- xmlOTU.addAnnotationValue ("DwC:collectionCode", Constants.DwCURI, collectionCode);
- }
- if ( null != catalogNumber ){
- //output unique (usually) identifier for the record within data set or collection
- xmlOTU.addAnnotationValue("DwC:catalogNumber", Constants.DwCURI, catalogNumber);
- }
- if ( null != accessionNumber) {
- //output a list of genetic sequence information associated with occurrence
- xmlOTU.addAnnotationValue("DwC:associatedSequences", Constants.DwCURI, accessionNumber);
- }
- if ( null != otherAccessionNumber ) {
- //list of previous or alternate fully catalog numbers (i.e. Genbank) or human-used identifiers
- xmlOTU.addAnnotationValue("DwC:otherCatalogNumbers", Constants.DwCURI, otherAccessionNumber);
- }
- if ( null != dateSampled ) {
- //output date sampled in ISO 8601 format
- xmlOTU.addAnnotationValue("DwC:eventDate", Constants.DwCURI, dateSampled);
- }
- if ( null != scientificName ) {
- //output full scientific name
- xmlOTU.addAnnotationValue("DwC:scientificName", Constants.DwCURI, scientificName);
- }
- if ( null != collector ) {
- //output names of people associated with recording of original occurrence
- xmlOTU.addAnnotationValue("DwC:recordedBy", Constants.DwCURI, collector);
- }
- if ( null != latitude ) {
- //output geographic latitude in decimal degrees using geodeticDatum spatial reference system
- xmlOTU.addAnnotationValue("DwC:decimalLatitude", Constants.DwCURI, latitude);
- }
- if ( null != longitude ) {
- //output geographic longitude in decimal degrees using geodeticDatum spatial reference system
- xmlOTU.addAnnotationValue("DwC:decimalLongitude", Constants.DwCURI, longitude);
- }
- if ( null != elevation ) {
- //there are two different Darwin Core terms for elevation depending on elevation value
- //outputs geographic elevation of sample
- if ( elevation >= 0) {
- //above local surface in meters
- xmlOTU.addAnnotationValue("DwC:verbatimElevation", Constants.DwCURI, elevation);
- }
- else {
- //below local surface in meters
- xmlOTU.addAnnotationValue("DwC:verbatimDepth", Constants.DwCURI, elevation);
- }
- }
- if ( null != country ) {
- //output country in which location occurs
- xmlOTU.addAnnotationValue("DwC:country", Constants.DwCURI, country);
- }
- if ( null != state ) {
- //output name of next smaller administrative region than country (i.e. state, province, region)
- xmlOTU.addAnnotationValue ("DwC:stateProvince", Constants.DwCURI, state);
- }
- if ( null != locality) {
- //output brief description of sample location
- xmlOTU.addAnnotationValue("DwC:locality", Constants.DwCURI, locality);
- }
- if ( null != notes ) {
- //output any additional information about specimen
- xmlOTU.addAnnotationValue("DwC:occurenceRemarks", Constants.DwCURI, notes);
- }
- }
- }
- }
-
-}
Added: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixReader.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixReader.java (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixReader.java 2011-10-13 16:26:47 UTC (rev 971)
@@ -0,0 +1,142 @@
+package org.cipres.treebase.domain.nexus.nexml;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.cipres.treebase.dao.jdbc.ContinuousMatrixElementJDBC;
+import org.cipres.treebase.dao.jdbc.ContinuousMatrixJDBC;
+import org.cipres.treebase.dao.jdbc.DiscreteMatrixElementJDBC;
+import org.cipres.treebase.dao.jdbc.DiscreteMatrixJDBC;
+import org.cipres.treebase.dao.jdbc.MatrixColumnJDBC;
+import org.cipres.treebase.domain.matrix.ContinuousChar;
+import org.cipres.treebase.domain.matrix.ContinuousMatrix;
+import org.cipres.treebase.domain.matrix.DiscreteChar;
+import org.cipres.treebase.domain.matrix.DiscreteMatrix;
+import org.cipres.treebase.domain.matrix.Matrix;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.cipres.treebase.domain.taxon.TaxonLabelSet;
+import org.nexml.model.Annotatable;
+import org.nexml.model.CategoricalMatrix;
+import org.nexml.model.CharacterState;
+import org.nexml.model.Document;
+import org.nexml.model.MatrixCell;
+import org.nexml.model.OTU;
+import org.nexml.model.OTUs;
+
+public class NexmlMatrixReader extends NexmlObjectConverter {
+
+ public NexmlMatrixReader(Study study, TaxonLabelHome taxonLabelHome,
+ Document document) {
+ super(study, taxonLabelHome, document);
+ }
+
+ /**
+ *
+ * @param xmlMatrix
+ * @return
+ */
+ private Matrix fromXmlToTreeBase(CategoricalMatrix xmlMatrix) {
+ DiscreteMatrix tbMatrix = new DiscreteMatrix();
+ DiscreteMatrixJDBC matrixJDBC = new DiscreteMatrixJDBC(tbMatrix, xmlMatrix, this);
+ List<MatrixColumnJDBC> columnJDBCs = new ArrayList<MatrixColumnJDBC>();
+ long[] colIds = matrixJDBC.getColIDs();
+ long[] rowIds = matrixJDBC.getRowIDs();
+ List<DiscreteMatrixElementJDBC> elements = new ArrayList<DiscreteMatrixElementJDBC>();
+ int colIndex = 0;
+ for ( org.nexml.model.Character xmlCharacter : xmlMatrix.getCharacters() ) {
+ String charName = xmlCharacter.getLabel();
+ DiscreteChar tbChar = new DiscreteChar();
+ tbChar.setDescription(charName);
+ MatrixColumnJDBC aColumnJDBC = new MatrixColumnJDBC();
+ aColumnJDBC.setPhyloChar(tbChar);
+ columnJDBCs.add(aColumnJDBC);
+ int rowIndex = 0;
+ for ( OTU xmlOTU : xmlMatrix.getOTUs().getAllOTUs() ) {
+ @SuppressWarnings("unused")
+ MatrixCell<CharacterState> xmlCell = xmlMatrix.getCell(xmlOTU, xmlCharacter);
+ DiscreteMatrixElementJDBC element = new DiscreteMatrixElementJDBC();
+ //element.setValue(xmlCell.getValue()); // XXX nested stateset lookup song & dance here
+ element.setElementOrder(colIndex);
+ element.setMatrixRowID(rowIds[rowIndex]);
+ element.setMatrixColID(colIds[colIndex]);
+ elements.add(element);
+ rowIndex++;
+ }
+ colIndex++;
+ }
+ DiscreteMatrixElementJDBC.batchDiscreteElements(elements, getTaxonLabelHome().getConnection());
+ return tbMatrix;
+ }
+
+ /**
+ *
+ * @param xmlMatrix
+ * @return
+ */
+ private Matrix fromXmlToTreeBase(org.nexml.model.ContinuousMatrix xmlMatrix) {
+ ContinuousMatrix tbMatrix = new ContinuousMatrix();
+ ContinuousMatrixJDBC matrixJDBC = new ContinuousMatrixJDBC(tbMatrix, xmlMatrix, this);
+ List<MatrixColumnJDBC> columnJDBCs = new ArrayList<MatrixColumnJDBC>();
+ long[] colIds = matrixJDBC.getColIDs();
+ long[] rowIds = matrixJDBC.getRowIDs();
+ List<ContinuousMatrixElementJDBC> elements = new ArrayList<ContinuousMatrixElementJDBC>();
+
+ int colIndex = 0;
+ for ( org.nexml.model.Character xmlCharacter : xmlMatrix.getCharacters() ) {
+ String charName = xmlCharacter.getLabel();
+ ContinuousChar tbChar = new ContinuousChar();
+ tbChar.setDescription(charName);
+ MatrixColumnJDBC aColumnJDBC = new MatrixColumnJDBC();
+ aColumnJDBC.setPhyloChar(tbChar);
+ columnJDBCs.add(aColumnJDBC);
+ int rowIndex = 0;
+ for ( OTU xmlOTU : xmlMatrix.getOTUs().getAllOTUs() ) {
+ MatrixCell<Double> xmlCell = xmlMatrix.getCell(xmlOTU, xmlCharacter);
+ ContinuousMatrixElementJDBC element = new ContinuousMatrixElementJDBC();
+ element.setValue(xmlCell.getValue());
+ element.setElementOrder(colIndex);
+ element.setMatrixRowID(rowIds[rowIndex]);
+ element.setMatrixColID(colIds[colIndex]);
+ elements.add(element);
+ rowIndex++;
+ }
+ colIndex++;
+ }
+ ContinuousMatrixElementJDBC.batchContinuousElements(elements, getTaxonLabelHome().getConnection());
+ return tbMatrix;
+ }
+
+ /**
+ *
+ * @param xmlMatrix
+ * @return
+ */
+ public Matrix fromXmlToTreeBase(org.nexml.model.Matrix<?> xmlMatrix) {
+ OTUs xmlOTUs = xmlMatrix.getOTUs();
+ Matrix tbMatrix = null;
+ TaxonLabelSet tbTaxa = null;
+ Long tbTaxonLabelSetID = readTreeBaseID((Annotatable) xmlOTUs);
+ if ( null != tbTaxonLabelSetID ) {
+ tbTaxa = getTaxonLabelHome()
+ .findPersistedObjectByID(TaxonLabelSet.class, tbTaxonLabelSetID);
+ }
+ if ( xmlMatrix instanceof CategoricalMatrix ) {
+ tbMatrix = fromXmlToTreeBase((CategoricalMatrix) xmlMatrix);
+ }
+ else if ( xmlMatrix instanceof org.nexml.model.ContinuousMatrix ) {
+ tbMatrix = fromXmlToTreeBase((org.nexml.model.ContinuousMatrix) xmlMatrix);
+ }
+ if ( null != tbMatrix ) {
+ attachTreeBaseID((Annotatable) xmlMatrix, tbMatrix,Matrix.class);
+ if ( null != tbTaxa ) {
+ tbMatrix.setTaxa(tbTaxa);
+ }
+ tbMatrix.setStudy(getStudy());
+ tbMatrix.setTitle(xmlMatrix.getLabel());
+ tbMatrix.setPublished(false);
+ }
+ return tbMatrix;
+ }
+
+}
Copied: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java (from rev 970, trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java)
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java 2011-10-13 16:26:47 UTC (rev 971)
@@ -0,0 +1,622 @@
+package org.cipres.treebase.domain.nexus.nexml;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Set;
+
+import org.cipres.treebase.Constants;
+import org.cipres.treebase.domain.matrix.CharSet;
+import org.cipres.treebase.domain.matrix.CharacterMatrix;
+import org.cipres.treebase.domain.matrix.ColumnRange;
+impo...
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