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[Treebase-guts] SF.net SVN: treebase:[927] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlMatrixConverter.java
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From: <lol...@us...> - 2011-07-11 19:11:23
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Revision: 927
http://treebase.svn.sourceforge.net/treebase/?rev=927&view=rev
Author: loloyohe
Date: 2011-07-11 19:11:16 +0000 (Mon, 11 Jul 2011)
Log Message:
-----------
Extended fromTreeBaseToXml() methods to include more row-segment metadata annotations.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
Modified: 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 2011-06-29 15:09:55 UTC (rev 926)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2011-07-11 19:11:16 UTC (rev 927)
@@ -377,14 +377,98 @@
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 ) {
- ((Annotatable)xmlCell).addAnnotationValue("DwC:DecimalLatitude", Constants.DwCURI, latitude);
+ //output geographic latitude in decimal degrees using geodeticDatum spatial reference system
+ ((Annotatable)xmlCell).addAnnotationValue("DwC:decimalLatitude", Constants.DwCURI, latitude);
}
if ( null != longitude ) {
- ((Annotatable)xmlCell).addAnnotationValue("DwC:DecimalLongitude", Constants.DwCURI, 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++;
@@ -404,30 +488,98 @@
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 collector = tbSegment.getSpecimenLabel().getCollector();
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) {
- xmlOTU.addAnnotationValue("DwC:StringGenbankAcessionNumber", Constants.DwCURI, 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 ) {
- xmlOTU.addAnnotationValue("DwC:DecimalLatitude", Constants.DwCURI, latitude);
+ //output geographic latitude in decimal degrees using geodeticDatum spatial reference system
+ xmlOTU.addAnnotationValue("DwC:decimalLatitude", Constants.DwCURI, latitude);
}
if ( null != longitude ) {
- xmlOTU.addAnnotationValue("DwC:DecimalLongitude", Constants.DwCURI, longitude);
+ //output geographic longitude in decimal degrees using geodeticDatum spatial reference system
+ xmlOTU.addAnnotationValue("DwC:decimalLongitude", Constants.DwCURI, longitude);
}
if ( null != elevation ) {
- xmlOTU.addAnnotationValue("DwC:DecimalElevation", Constants.DwCURI, 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 != collector ) {
- xmlOTU.addAnnotationValue("DwC:StringCollector", Constants.DwCURI, collector);
- }
if ( null != country ) {
- xmlOTU.addAnnotationValue("DwC:StringCountry", Constants.DwCURI, 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);
+ }
}
}
}
@@ -458,30 +610,98 @@
}
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 collector = tbSegment.getSpecimenLabel().getCollector();
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) {
- xmlOTU.addAnnotationValue("DwC:StringGenbankAcessionNumber", Constants.DwCURI, 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 ) {
- xmlOTU.addAnnotationValue("DwC:DecimalLatitude", Constants.DwCURI, latitude);
+ //output geographic latitude in decimal degrees using geodeticDatum spatial reference system
+ xmlOTU.addAnnotationValue("DwC:decimalLatitude", Constants.DwCURI, latitude);
}
if ( null != longitude ) {
- xmlOTU.addAnnotationValue("DwC:DecimalLongitude", Constants.DwCURI, longitude);
+ //output geographic longitude in decimal degrees using geodeticDatum spatial reference system
+ xmlOTU.addAnnotationValue("DwC:decimalLongitude", Constants.DwCURI, longitude);
}
if ( null != elevation ) {
- xmlOTU.addAnnotationValue("DwC:DecimalElevation", Constants.DwCURI, 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 != collector ) {
- xmlOTU.addAnnotationValue("DwC:StringCollector", Constants.DwCURI, collector);
- }
if ( null != country ) {
- xmlOTU.addAnnotationValue("DwC:StringCountry", Constants.DwCURI, 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);
+ }
}
}
}
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