Revision a897c436
Added by Andreas Müller almost 6 years ago
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/bci/BciSchemaAdapter.java | ||
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/** |
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* Copyright (C) 2009 EDIT |
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* European Distributed Institute of Taxonomy
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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*
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* |
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* The contents of this file are subject to the Mozilla Public License Version 1.1 |
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* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 | 8 |
*/ |
| ... | ... | |
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* @since 25.08.2010 |
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*/ |
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public class BciSchemaAdapter extends SchemaAdapterBase<Reference>{
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static URI identifier = null; |
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static String nameSpace = "http://purl.org/dc/elements/1.1/"; |
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static {
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try {
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identifier = new URI("info:srw/schema/1/dc-v1.1");
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public String getShortName() {
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return "dc"; |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.ext.schema.SchemaAdapter#getCmdEntities(java.io.Reader) |
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*/ |
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logger.error(e); |
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} |
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DcSaxHandler handler = new DcSaxHandler(); |
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try {
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if(parser != null){
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parser.parse(inputStream, handler); |
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logger.error(e); |
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} |
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return handler.referenceList; |
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} |
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class DcSaxHandler extends DefaultHandler {
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private static final String DC_DC = "dc:dc"; |
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private static final String DC_TITLE = "dc:title"; |
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private static final String DC_CREATOR = "dc:creator"; |
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private static final String DC_PUBLISHER = "dc:publisher"; |
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private static final String DC_DATE = "dc:date"; |
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List<Reference> referenceList = new ArrayList<Reference>(); |
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Reference reference = null; |
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String dcFieldName = null; |
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@Override |
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public void startElement(String uri, String localName,
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public void startElement(String uri, String localName, |
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String qName, Attributes attributes) throws SAXException {
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if (uri.equals(nameSpace)) {
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logger.debug("Start Element :" + qName + "; " + uri);
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if (qName.equals(DC_DC)) {
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reference = ReferenceFactory.newGeneric(); |
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} else {
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if (uri.equals(nameSpace)) {
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if(reference != null) {
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logger.debug("End Element :" + qName + "; " + uri);
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if (qName.equals(DC_DC)) {
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referenceList.add(reference); |
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reference = null; |
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} else {
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dcFieldName = null; |
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} |
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}
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} |
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} |
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} |
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authorship.setTitleCache(text, true); |
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reference.setAuthorship(authorship); |
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} |
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} |
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} |
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} |
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} |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/dc/DublinCoreSchemaAdapter.java | ||
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| 1 | 1 |
/** |
| 2 | 2 |
* Copyright (C) 2009 EDIT |
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* European Distributed Institute of Taxonomy
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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*
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* |
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* The contents of this file are subject to the Mozilla Public License Version 1.1 |
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* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 | 8 |
*/ |
| ... | ... | |
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* @since 25.08.2010 |
| 38 | 38 |
*/ |
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public class DublinCoreSchemaAdapter extends SchemaAdapterBase<Reference>{
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static URI identifier = null; |
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static String nameSpace = "http://purl.org/dc/elements/1.1/"; |
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static {
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try {
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identifier = new URI("info:srw/schema/1/dc-v1.1");
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public String getShortName() {
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return "dc"; |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.ext.schema.SchemaAdapter#getCmdEntities(java.io.Reader) |
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*/ |
| ... | ... | |
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logger.error(e); |
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} |
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DcSaxHandler handler = new DcSaxHandler(); |
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try {
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if(parser != null){
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parser.parse(inputStream, handler); |
| ... | ... | |
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logger.error(e); |
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} |
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return handler.referenceList; |
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} |
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class DcSaxHandler extends DefaultHandler {
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private static final String DC_DC = "dc:dc"; |
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private static final String DC_TITLE = "dc:title"; |
| 112 | 112 |
private static final String DC_CREATOR = "dc:creator"; |
| 113 | 113 |
private static final String DC_PUBLISHER = "dc:publisher"; |
| 114 | 114 |
private static final String DC_DATE = "dc:date"; |
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private static final String DC_IDENTIFIER = "dc:identifier"; //TODO map this |
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List<Reference> referenceList = new ArrayList<Reference>(); |
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Reference reference = null; |
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String dcFieldName = null; |
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@Override |
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public void startElement(String uri, String localName,
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public void startElement(String uri, String localName, |
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String qName, Attributes attributes) throws SAXException {
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if (uri.equals(nameSpace)) {
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logger.debug("Start Element :" + qName + "; " + uri);
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if (qName.equals(DC_DC)) {
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reference = ReferenceFactory.newGeneric(); |
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} else {
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if (uri.equals(nameSpace)) {
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if(reference != null) {
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logger.debug("End Element :" + qName + "; " + uri);
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if (qName.equals(DC_DC)) {
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referenceList.add(reference); |
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reference = null; |
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} else {
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dcFieldName = null; |
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} |
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}
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} |
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} |
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} |
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authorship.setTitleCache(text, true); |
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reference.setAuthorship(authorship); |
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} |
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} |
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} |
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} |
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} |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/openurl/MobotOpenUrlResponseSchemaAdapter.java | ||
|---|---|---|
| 1 | 1 |
/** |
| 2 | 2 |
* Copyright (C) 2009 EDIT |
| 3 |
* European Distributed Institute of Taxonomy
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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*
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* |
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* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 7 | 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 | 8 |
*/ |
| ... | ... | |
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public URI getIdentifier() {
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return identifier; |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.ext.schema.SchemaAdapter#getShortName() |
| 55 | 55 |
*/ |
| ... | ... | |
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public String getShortName() {
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return "MOBOT.OpenUrl.Utilities.OpenUrlResponse"; |
| 59 | 59 |
} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.ext.schema.SchemaAdapter#getCmdEntities(java.io.Reader) |
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*/ |
| ... | ... | |
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logger.error(e); |
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} |
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OpenUrlResponseHandler handler = new OpenUrlResponseHandler(); |
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try {
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if(parser != null){
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Reader reader = new InputStreamReader(inputStream, "UTF-8"); |
| ... | ... | |
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} |
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} catch (SAXException e) {
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logger.error(e); |
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} |
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} |
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return handler.referenceList; |
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} |
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class OpenUrlResponseHandler extends DefaultHandler {
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/* |
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* Fields of OpenUrlResponse |
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* see http://code.google.com/p/bhl-bits/source/browse/trunk/portal/OpenUrlUtilities/OpenUrlResponse.cs |
| ... | ... | |
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private static final String MESSAGE = "Message"; |
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private static final String CITATIONS = "citations"; |
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private static final String OPENURL_RESPONSE_CITATION = "OpenUrlResponseCitation"; |
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/* |
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* Fields of OpenUrlResponseCitation |
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* see http://code.google.com/p/bhl-bits/source/browse/trunk/portal/OpenUrlUtilities/OpenUrlResponseCitation.cs |
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*/ |
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/** |
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* references the specific page in the title |
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*/ |
| ... | ... | |
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private static final String SPAGE = "SPage"; |
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private static final String EPAGE = "EPage"; |
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private static final String PAGES = "Pages"; |
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List<Reference> referenceList = new ArrayList<Reference>(); |
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OpenUrlReference reference = null; |
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ResponseStatus status = null; |
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Team authorship = null; |
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String message = null; |
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String elementName = null; |
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private String elementNameToStore; |
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private StringBuilder textBuffer = new StringBuilder(); |
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@Override |
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public void startElement(String uri, String localName,
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public void startElement(String uri, String localName, |
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String qName, Attributes attributes) throws SAXException {
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| 170 | 170 |
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if (qName.equals(OPENURL_RESPONSE)) {
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| ... | ... | |
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} else if (reference != null && qName.equals(AUTHORS)) {
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authorship = Team.NewInstance(); |
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} else if (reference != null && qName.equals(SUBJECTS)) {
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//TODO implement, but no equivalent in the cdm model
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//TODO implement, but no equivalent in the cdm model |
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} else {
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elementName = qName; |
| 182 | 182 |
} |
| ... | ... | |
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public void endElement(String uri, String localName, String qName) throws SAXException {
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if (qName.equals(OPENURL_RESPONSE)) {
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} else if (qName.equals(OPENURL_RESPONSE_CITATION)) {
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referenceList.add(reference); |
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reference = null; |
| ... | ... | |
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reference.setAuthorship(authorship); |
| 195 | 195 |
authorship = null; |
| 196 | 196 |
} else if (reference != null && qName.equals(SUBJECTS)) {
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//TODO implement, but no equivalent in the cdm model
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//TODO implement, but no equivalent in the cdm model |
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| 198 | 198 |
}else {
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elementNameToStore = elementName; |
| 200 | 200 |
elementName = null; |
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| 205 | 205 |
@Override |
| 206 | 206 |
public void characters(char ch[], int start, int length) |
| 207 | 207 |
throws SAXException {
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| 209 | 209 |
if(elementNameToStore == null){
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textBuffer.append(new String(ch, start, length)); |
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} else {
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logger.debug("Characters [" + elementNameToStore + "]: " + textBuffer);
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String trimmedText = textBuffer.toString().trim(); |
| 217 | 217 |
// empty the text buffer |
| 218 | 218 |
textBuffer.delete(0, textBuffer.length()); |
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// --- Reference --- //
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// --- Reference --- // |
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| 221 | 221 |
if(reference != null){
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| 223 | 223 |
if(elementNameToStore.equals(URL)){
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try {
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reference.setUri(new URI(trimmedText)); |
| ... | ... | |
| 308 | 308 |
reference.setIssn(trimmedText); |
| 309 | 309 |
} |
| 310 | 310 |
} |
| 311 |
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| 312 | 312 |
// --- Reference.authorship --- // |
| 313 | 313 |
if(authorship != null && reference != null){
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| 314 | 314 |
if(elementNameToStore.equals("String")){
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authorship.addTeamMember(Person.NewTitledInstance(trimmedText)); |
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} |
| 317 | 317 |
} |
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// openUrlResponse //
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// openUrlResponse // |
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if(reference == null){
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| 321 | 321 |
if(elementNameToStore.equals(STATUS)){
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status = ResponseStatus.valueOf(trimmedText); |
| ... | ... | |
| 326 | 326 |
elementNameToStore = null; |
| 327 | 327 |
} |
| 328 | 328 |
} |
| 329 |
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| 330 | 330 |
} |
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| 332 | 332 |
/** |
| 333 | 333 |
* @see http://code.google.com/p/bhl-bits/source/browse/trunk/portal/OpenUrlUtilities/IOpenUrlResponse.cs |
| 334 | 334 |
*/ |
| ... | ... | |
| 337 | 337 |
Success, Error |
| 338 | 338 |
} |
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| 340 |
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| 340 |
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| 341 | 341 |
} |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/in/GbifReferenceCsv2CdmConverter.java | ||
|---|---|---|
| 103 | 103 |
Reference inRef = handleInRef(strSource); |
| 104 | 104 |
if (inRef != null){
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| 105 | 105 |
reference.setInReference(inRef); |
| 106 |
resultList.add(new MappedCdmBase<CdmBase>(inRef));
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| 106 |
resultList.add(new MappedCdmBase<>(inRef)); |
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| 107 | 107 |
} |
| 108 | 108 |
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| 109 | 109 |
//URI |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsxml/DefaultTcsXmlPlaceholders.java | ||
|---|---|---|
| 1 | 1 |
/** |
| 2 | 2 |
* Copyright (C) 2007 EDIT |
| 3 |
* European Distributed Institute of Taxonomy
|
|
| 3 |
* European Distributed Institute of Taxonomy |
|
| 4 | 4 |
* http://www.e-taxonomy.eu |
| 5 |
*
|
|
| 5 |
* |
|
| 6 | 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 7 | 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 | 8 |
*/ |
| ... | ... | |
| 26 | 26 |
*/ |
| 27 | 27 |
public class DefaultTcsXmlPlaceholders implements ITcsXmlPlaceholderClass {
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| 28 | 28 |
private static final Logger logger = Logger.getLogger(DefaultTcsXmlPlaceholders.class); |
| 29 |
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| 29 |
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| 30 | 30 |
/* (non-Javadoc) |
| 31 | 31 |
* @see tcsxml.ITcsXmlPlaceholderClass#makeMetaDataDetailed(tcsxml.TcsXmlImportConfigurator, org.jdom.Element) |
| 32 | 32 |
*/ |
| 33 |
public boolean makeMetaDataDetailed(TcsXmlImportConfigurator tcsConfig, Element elMetaDataDetailed){
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| 33 |
@Override |
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| 34 |
public boolean makeMetaDataDetailed(TcsXmlImportConfigurator tcsConfig, Element elMetaDataDetailed){
|
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| 34 | 35 |
if (tcsConfig == null){
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| 35 | 36 |
return false; |
| 36 | 37 |
} |
| 37 | 38 |
if (elMetaDataDetailed == null){
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| 38 | 39 |
return true; |
| 39 | 40 |
} |
| 40 |
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| 41 |
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| 41 | 42 |
//Do nothing |
| 42 | 43 |
//TODO implement EDIT TcsMetaData extension |
| 43 | 44 |
logger.info("MetaDataElement found: " + elMetaDataDetailed.getName());
|
| ... | ... | |
| 47 | 48 |
/* (non-Javadoc) |
| 48 | 49 |
* @see tcsxml.ITcsXmlPlaceholderClass#makePublicationDetailed(tcsxml.TcsXmlImportConfigurator, org.jdom.Element, eu.etaxonomy.cdm.model.reference.Reference) |
| 49 | 50 |
*/ |
| 50 |
public boolean makePublicationDetailed(TcsXmlImportConfigurator config, Element elPublicationDetailed, Reference publication){
|
|
| 51 |
@Override |
|
| 52 |
public boolean makePublicationDetailed(TcsXmlImportConfigurator config, Element elPublicationDetailed, Reference publication){
|
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| 51 | 53 |
ResultWrapper<Boolean> success = ResultWrapper.NewInstance(true); |
| 52 | 54 |
if (config == null){
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| 53 | 55 |
return false; |
| ... | ... | |
| 57 | 59 |
}else{
|
| 58 | 60 |
publication.setProtectedTitleCache(false); |
| 59 | 61 |
} |
| 60 |
|
|
| 62 |
|
|
| 61 | 63 |
String childName; |
| 62 | 64 |
Namespace tcsNs = config.getTcsXmlNamespace(); |
| 63 | 65 |
for (Object o : elPublicationDetailed.getChildren()){
|
| 64 | 66 |
Element element = (Element)o; |
| 65 | 67 |
String value = element.getTextNormalize(); |
| 66 |
|
|
| 68 |
|
|
| 67 | 69 |
childName = "Title"; |
| 68 | 70 |
if (element.getName().equalsIgnoreCase(childName) && element.getNamespace().equals(tcsNs)){
|
| 69 | 71 |
publication.setTitle(value); |
| ... | ... | |
| 76 | 78 |
publication.setDatePublished(datePublished); |
| 77 | 79 |
continue; |
| 78 | 80 |
} |
| 79 |
|
|
| 81 |
|
|
| 80 | 82 |
logger.warn("Unhandled Publication Detailed child element: " + element.getName());
|
| 81 |
|
|
| 83 |
|
|
| 82 | 84 |
} |
| 83 | 85 |
// String childName = "Title"; |
| 84 | 86 |
// boolean obligatory = false; |
| ... | ... | |
| 97 | 99 |
// TimePeriod datePublished = TimePeriodParser.parseString(strDatePublished); |
| 98 | 100 |
// publication.setDatePublished(datePublished); |
| 99 | 101 |
// } |
| 100 |
|
|
| 102 |
|
|
| 101 | 103 |
//Do nothing |
| 102 | 104 |
//TODO implement EDIT TcsMetaData extension |
| 103 | 105 |
if (logger.isDebugEnabled()){logger.debug("PublicationDetailed element found: " + elPublicationDetailed.getName());}
|
| 104 | 106 |
return success.getValue(); |
| 105 | 107 |
} |
| 106 |
|
|
| 107 |
|
|
| 108 |
|
|
| 109 |
|
|
| 108 |
|
|
| 109 |
|
|
| 110 |
|
|
| 111 |
|
|
| 110 | 112 |
|
| 111 | 113 |
} |
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/Taxon.java | ||
|---|---|---|
| 810 | 810 |
} |
| 811 | 811 |
|
| 812 | 812 |
/** |
| 813 |
* Counts the number of misapplied name relationships (including pro parte misapplied
|
|
| 814 |
* names) where this taxon represents the |
|
| 813 |
* Counts the number of misapplied name relationships (including pro parte and partial
|
|
| 814 |
* misapplied names) where this taxon represents the
|
|
| 815 | 815 |
* misapplied name for another taxon. |
| 816 | 816 |
* @return |
| 817 | 817 |
*/ |
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