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package eu.dnetlib.iis.ingest.pmc.metadata;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Stack;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.jdom.Element;
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import org.xml.sax.Attributes;
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import org.xml.sax.SAXException;
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import org.xml.sax.helpers.DefaultHandler;
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import pl.edu.icm.cermine.metadata.affiliation.CRFAffiliationParser;
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import eu.dnetlib.iis.common.affiliation.AffiliationBuilder;
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import eu.dnetlib.iis.ingest.pmc.metadata.schemas.ExtractedDocumentMetadata;
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import eu.dnetlib.iis.ingest.pmc.metadata.schemas.Range;
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import eu.dnetlib.iis.ingest.pmc.metadata.schemas.ReferenceBasicMetadata;
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import eu.dnetlib.iis.ingest.pmc.metadata.schemas.ReferenceMetadata;
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import eu.dnetlib.iis.metadataextraction.schemas.Affiliation;
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/**
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* PMC XML SAX handler.
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*
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* @author mhorst
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*
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*/
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public class PmcXmlHandler extends DefaultHandler {
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// front journal
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private static final String ELEM_JOURNAL_TITLE = "journal-title";
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private static final String ELEM_JOURNAL_TITLE_GROUP = "journal-title-group";
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// front article
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private static final String ELEM_ARTICLE_META = "article-meta";
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private static final String ELEM_ARTICLE_ID = "article-id";
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private static final String ELEM_AFFILIATION = "aff";
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private static final String ELEM_LABEL = "label";
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// back citations
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private static final String ELEM_REF_LIST = "ref-list";
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private static final String ELEM_REF = "ref";
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private static final String ELEM_PUB_ID = "pub-id";
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// back citations meta
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private static final String ELEM_ARTICLE_TITLE = "article-title";
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private static final String ELEM_SOURCE = "source";
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private static final String ELEM_YEAR = "year";
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private static final String ELEM_VOLUME = "volume";
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private static final String ELEM_ISSUE = "issue";
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private static final String ELEM_FPAGE = "fpage";
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private static final String ELEM_LPAGE = "lpage";
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// back citations author
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private static final String ELEM_NAME = "name";
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private static final String ELEM_SURNAME = "surname";
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private static final String ELEM_GIVEN_NAMES = "given-names";
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// back citations contains text child
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private static final String ELEM_CITATION = "citation";
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private static final String ELEM_ELEMENT_CITATION = "element-citation";
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private static final String ELEM_MIXED_CITATION = "mixed-citation";
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// attributes
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private static final String PUB_ID_TYPE = "pub-id-type";
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private static final String ATTR_ARTICLE_TYPE = "article-type";
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private static final String PUB_ID_TYPE_PMID = "pmid";
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private final Logger log = Logger.getLogger(this.getClass());
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private Stack<String> parents;
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private StringBuilder currentValue = new StringBuilder();
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private ReferenceMetadata.Builder currentRefMetaBuilder;
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private String currentSurname = null;
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private String currentGivenNames = null;
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private List<CharSequence> currentRefAuthorList;
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private StringBuffer currentReferenceText;
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private boolean currentReferenceTextExplicitlySet = false;
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private String currentReferenceIdType = null;
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private String currentArticleIdType = null;
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boolean containsTextChild = false;
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boolean rootElement = true;
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private final ExtractedDocumentMetadata.Builder builder;
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/**
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* Default constructor.
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* @param receiver
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*/
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public PmcXmlHandler(ExtractedDocumentMetadata.Builder builder) {
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super();
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this.builder = builder;
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}
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@Override
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public void startDocument() throws SAXException {
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this.parents = new Stack<String>();
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clearAllFields();
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}
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@Override
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public void startElement(String uri, String localName, String qName,
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Attributes attributes) throws SAXException {
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if (rootElement) {
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rootElement = false;
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builder.setEntityType(attributes.getValue(ATTR_ARTICLE_TYPE));
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} else if (isWithinElement(qName, ELEM_JOURNAL_TITLE, ELEM_JOURNAL_TITLE_GROUP)) {
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this.currentValue = new StringBuilder();
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} else if (isWithinElement(qName, ELEM_ARTICLE_ID, ELEM_ARTICLE_META)) {
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this.currentArticleIdType = attributes.getValue(PUB_ID_TYPE);
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this.currentValue = new StringBuilder();
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} else if (isWithinElement(qName, ELEM_FPAGE, ELEM_ARTICLE_META) ||
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isWithinElement(qName, ELEM_LPAGE, ELEM_ARTICLE_META)) {
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this.currentValue = new StringBuilder();
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} else if (hasAmongParents(qName, ELEM_AFFILIATION, this.parents, ELEM_ARTICLE_META)) {
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this.currentValue = new StringBuilder();
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} else if (hasAmongParents(qName, ELEM_ARTICLE_TITLE, this.parents, ELEM_REF, ELEM_REF_LIST) ||
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hasAmongParents(qName, ELEM_SOURCE, this.parents, ELEM_REF, ELEM_REF_LIST) ||
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hasAmongParents(qName, ELEM_YEAR, this.parents, ELEM_REF, ELEM_REF_LIST) ||
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hasAmongParents(qName, ELEM_VOLUME, this.parents, ELEM_REF, ELEM_REF_LIST) ||
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hasAmongParents(qName, ELEM_ISSUE, this.parents, ELEM_REF, ELEM_REF_LIST) ||
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hasAmongParents(qName, ELEM_FPAGE, this.parents, ELEM_REF, ELEM_REF_LIST) ||
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hasAmongParents(qName, ELEM_LPAGE, this.parents, ELEM_REF, ELEM_REF_LIST)) {
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this.currentValue = new StringBuilder();
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} else if (isWithinElement(qName, ELEM_SURNAME, ELEM_NAME) ||
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isWithinElement(qName, ELEM_GIVEN_NAMES, ELEM_NAME)) {
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this.currentValue = new StringBuilder();
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} else if (isWithinElement(qName, ELEM_PUB_ID, ELEM_CITATION) ||
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isWithinElement(qName, ELEM_PUB_ID, ELEM_ELEMENT_CITATION) ||
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isWithinElement(qName, ELEM_PUB_ID, ELEM_MIXED_CITATION)) {
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this.currentReferenceIdType = attributes.getValue(PUB_ID_TYPE);
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this.currentValue = new StringBuilder();
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} else if (isWithinElement(qName, ELEM_REF, ELEM_REF_LIST)) {
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this.currentRefMetaBuilder = ReferenceMetadata.newBuilder();
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this.currentRefAuthorList = new ArrayList<CharSequence>();
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this.currentReferenceText = new StringBuffer();
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ReferenceBasicMetadata.Builder basicMetaBuilder = ReferenceBasicMetadata.newBuilder();
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basicMetaBuilder.setExternalIds(new HashMap<CharSequence, CharSequence>());
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this.currentRefMetaBuilder.setBasicMetadata(basicMetaBuilder.build());
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}
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this.parents.push(qName);
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}
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@Override
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public void endElement(String uri, String localName, String qName)
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throws SAXException {
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try {
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this.parents.pop();
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if (isWithinElement(qName, ELEM_JOURNAL_TITLE, ELEM_JOURNAL_TITLE_GROUP)) {
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builder.setJournal(this.currentValue.toString().trim());
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} else if (isWithinElement(qName, ELEM_ARTICLE_ID, ELEM_ARTICLE_META) &&
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PUB_ID_TYPE_PMID.equals(this.currentArticleIdType)) {
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builder.setPmid(this.currentValue.toString().trim());
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} else if (isWithinElement(qName, ELEM_FPAGE, ELEM_ARTICLE_META)) {
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if (builder.getPages()==null) {
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builder.setPages(Range.newBuilder().build());
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}
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builder.getPages().setStart(this.currentValue.toString().trim());
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} else if (isWithinElement(qName, ELEM_LPAGE, ELEM_ARTICLE_META)) {
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if (builder.getPages()==null) {
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builder.setPages(Range.newBuilder().build());
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}
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builder.getPages().setEnd(this.currentValue.toString().trim());
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} else if (hasAmongParents(qName, ELEM_AFFILIATION, this.parents, ELEM_ARTICLE_META)) {
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CRFAffiliationParser affiliationParser = new CRFAffiliationParser();
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String affStr = this.currentValue.toString();
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if (affStr.trim().length()>0) {
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try {
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Element parsedAffiliation = affiliationParser.parse(affStr);
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if (parsedAffiliation!=null) {
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if (builder.getAffiliations()==null) {
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builder.setAffiliations(new ArrayList<Affiliation>());
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}
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Affiliation aff = AffiliationBuilder.build(parsedAffiliation);
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if (aff.getRawText().length()>0) {
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builder.getAffiliations().add(aff);
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} else {
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aff.setRawText(affStr);
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}
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}
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} catch (IndexOutOfBoundsException e) {
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// FIXME remove this catch block when upgrading cermine version
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log.error("exception occurred when parsing affiliation: " + affStr, e);
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}
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}
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} else if (hasAmongParents(qName, ELEM_ARTICLE_TITLE, this.parents, ELEM_REF, ELEM_REF_LIST)) {
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currentRefMetaBuilder.getBasicMetadata().setTitle(this.currentValue.toString());
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} else if (hasAmongParents(qName, ELEM_SOURCE, this.parents, ELEM_REF, ELEM_REF_LIST)) {
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currentRefMetaBuilder.getBasicMetadata().setSource(this.currentValue.toString());
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} else if (hasAmongParents(qName, ELEM_YEAR, this.parents, ELEM_REF, ELEM_REF_LIST)) {
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currentRefMetaBuilder.getBasicMetadata().setYear(this.currentValue.toString());
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} else if (hasAmongParents(qName, ELEM_VOLUME, this.parents, ELEM_REF, ELEM_REF_LIST)) {
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currentRefMetaBuilder.getBasicMetadata().setVolume(this.currentValue.toString());
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} else if (hasAmongParents(qName, ELEM_ISSUE, this.parents, ELEM_REF, ELEM_REF_LIST)) {
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201
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currentRefMetaBuilder.getBasicMetadata().setIssue(this.currentValue.toString());
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202
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} else if (hasAmongParents(qName, ELEM_FPAGE, this.parents, ELEM_REF, ELEM_REF_LIST)) {
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203
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if (currentRefMetaBuilder.getBasicMetadata().getPages()==null) {
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204
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currentRefMetaBuilder.getBasicMetadata().setPages(Range.newBuilder().build());
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205
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}
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206
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currentRefMetaBuilder.getBasicMetadata().getPages().setStart(this.currentValue.toString());
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207
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} else if (hasAmongParents(qName, ELEM_LPAGE, this.parents, ELEM_REF, ELEM_REF_LIST)) {
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208
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if (currentRefMetaBuilder.getBasicMetadata().getPages()==null) {
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209
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currentRefMetaBuilder.getBasicMetadata().setPages(Range.newBuilder().build());
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210
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}
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211
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currentRefMetaBuilder.getBasicMetadata().getPages().setEnd(this.currentValue.toString());
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212
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} else if (hasAmongParents(qName, ELEM_PUB_ID, this.parents, ELEM_REF, ELEM_REF_LIST)) {
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213
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if (this.currentReferenceIdType!=null) {
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214
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currentRefMetaBuilder.getBasicMetadata().getExternalIds().put(
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215
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this.currentReferenceIdType, this.currentValue.toString());
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216
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}
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217
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} else if (isWithinElement(qName, ELEM_SURNAME, ELEM_NAME)) {
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218
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this.currentSurname = this.currentValue.toString();
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219
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} else if (isWithinElement(qName, ELEM_GIVEN_NAMES, ELEM_NAME)) {
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220
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this.currentGivenNames = this.currentValue.toString();
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221
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} else if (hasAmongParents(qName, ELEM_NAME, this.parents, ELEM_REF)) {
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222
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// in element-citation names are nested in person-group
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223
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this.currentRefAuthorList.add(
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224
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this.currentSurname + ", " + this.currentGivenNames);
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225
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this.currentSurname = null;
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226
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this.currentGivenNames = null;
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227
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} else if (isWithinElement(qName, ELEM_CITATION, ELEM_REF) ||
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228
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isWithinElement(qName, ELEM_ELEMENT_CITATION, ELEM_REF) ||
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229
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isWithinElement(qName, ELEM_MIXED_CITATION, ELEM_REF)) {
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230
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if (!this.currentRefMetaBuilder.hasText() &&
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231
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this.currentReferenceTextExplicitlySet &&
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232
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this.currentReferenceText!=null && this.currentReferenceText.length()>0) {
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233
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String trimmedRefText = this.currentReferenceText.toString().trim().replaceAll(" +", " ");
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234
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if (!trimmedRefText.isEmpty()) {
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235
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this.currentRefMetaBuilder.setText(trimmedRefText);
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236
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}
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237
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}
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238
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} else if (isWithinElement(qName, ELEM_REF, ELEM_REF_LIST)) {
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239
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if (this.builder.getReferences()==null) {
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240
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this.builder.setReferences(new ArrayList<ReferenceMetadata>());
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241
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}
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242
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this.currentRefMetaBuilder.setPosition(this.builder.getReferences().size()+1);
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243
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244
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if (this.currentRefAuthorList!=null && this.currentRefAuthorList.size()>0) {
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245
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this.currentRefMetaBuilder.getBasicMetadata().setAuthors(this.currentRefAuthorList);
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246
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}
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247
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248
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if (!this.currentRefMetaBuilder.hasText()) {
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249
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this.currentRefMetaBuilder.setText(generateReferenceRawText(
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250
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this.currentRefMetaBuilder.getBasicMetadata()));
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251
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}
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252
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this.builder.getReferences().add(this.currentRefMetaBuilder.build());
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253
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// reference fields cleanup
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254
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this.currentRefMetaBuilder = null;
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255
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this.currentRefAuthorList = null;
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256
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this.currentReferenceText = null;
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257
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this.currentReferenceTextExplicitlySet = false;
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258
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this.currentReferenceIdType = null;
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259
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}
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260
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} catch (Exception e) {
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261
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// FIXME remote this catch
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262
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throw new RuntimeException("unexpected exception while processing doc: " +
|
|
263
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builder.getId(), e);
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|
264
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}
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|
265
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}
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|
266
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267
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@Override
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268
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public void endDocument() throws SAXException {
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|
269
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parents.clear();
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270
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parents = null;
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|
271
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}
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|
272
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|
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273
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@Override
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|
274
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public void characters(char[] ch, int start, int length)
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|
275
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throws SAXException {
|
|
276
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String currentElement = this.parents.pop();
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|
277
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try {
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278
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// skipping affiliation position element
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279
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if (isWithinElement(currentElement, ELEM_LABEL, ELEM_AFFILIATION)) {
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|
280
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return;
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|
281
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}
|
|
282
|
|
|
283
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this.currentValue.append(ch, start, length);
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284
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// handing reference text
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285
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if (hasAmongParents(this.parents, ELEM_REF)) {
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286
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if (isWithinElement(currentElement, ELEM_CITATION, ELEM_REF) ||
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287
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isWithinElement(currentElement, ELEM_ELEMENT_CITATION, ELEM_REF) ||
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288
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isWithinElement(currentElement, ELEM_MIXED_CITATION, ELEM_REF)) {
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289
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// citation element contents
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290
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char[] chunk = new char[length];
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291
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System.arraycopy(ch, start, chunk, 0, length);
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|
292
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if (containsNonWhiteCharacter(chunk)) {
|
|
293
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this.currentReferenceTextExplicitlySet = true;
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|
294
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}
|
|
295
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}
|
|
296
|
if (this.currentReferenceText.length()>0 &&
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297
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isAlphanumeric(ch[start]) &&
|
|
298
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isAlphanumeric(this.currentReferenceText.charAt(
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|
299
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this.currentReferenceText.length()-1))) {
|
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300
|
// adding missing space separator between two alphanumeric characters
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|
301
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this.currentReferenceText.append(' ');
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|
302
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}
|
|
303
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this.currentReferenceText.append(ch, start, length);
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304
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}
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|
305
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} finally {
|
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306
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this.parents.push(currentElement);
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|
307
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}
|
|
308
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}
|
|
309
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|
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310
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private void clearAllFields() {
|
|
311
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this.currentArticleIdType = null;
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|
312
|
this.rootElement = true;
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313
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}
|
|
314
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|
|
315
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static boolean isAlphanumeric(char c) {
|
|
316
|
return !(c < 0x30 || (c >= 0x3a && c <= 0x40) || (c > 0x5a && c <= 0x60) || c > 0x7a);
|
|
317
|
}
|
|
318
|
|
|
319
|
boolean isWithinElement(String qName,
|
|
320
|
String expectedElement, String expectedParent) {
|
|
321
|
return qName.equals(expectedElement) &&
|
|
322
|
(expectedParent==null || !this.parents.isEmpty() && expectedParent.equals(this.parents.peek()));
|
|
323
|
}
|
|
324
|
|
|
325
|
public static boolean hasAmongParents(String qName,
|
|
326
|
String expectedElement, Stack<String> parentStack, String... expectedParents) {
|
|
327
|
if (qName.equals(expectedElement)) {
|
|
328
|
return hasAmongParents(parentStack, expectedParents);
|
|
329
|
} else {
|
|
330
|
return false;
|
|
331
|
}
|
|
332
|
}
|
|
333
|
|
|
334
|
public static boolean hasAmongParents(Stack<String> parentStack, String... expectedParents) {
|
|
335
|
if (expectedParents.length <= parentStack.size()) {
|
|
336
|
int startIterationIdx = 0;
|
|
337
|
for (String currentParent : expectedParents) {
|
|
338
|
boolean found = false;
|
|
339
|
for (int i=startIterationIdx; i<parentStack.size(); i++) {
|
|
340
|
// iteration starts from the bottom while we want to check from top
|
|
341
|
if (currentParent.equals(parentStack.get(parentStack.size()-(i+1)))) {
|
|
342
|
startIterationIdx = i+1;
|
|
343
|
found = true;
|
|
344
|
break;
|
|
345
|
}
|
|
346
|
}
|
|
347
|
if (!found) {
|
|
348
|
return false;
|
|
349
|
}
|
|
350
|
}
|
|
351
|
return true;
|
|
352
|
}
|
|
353
|
return false;
|
|
354
|
}
|
|
355
|
|
|
356
|
static boolean containsNonWhiteCharacter(char[] ch) {
|
|
357
|
if (ch!=null && ch.length>0) {
|
|
358
|
for (char currentCh : ch) {
|
|
359
|
if (!Character.isWhitespace(currentCh)) {
|
|
360
|
return true;
|
|
361
|
}
|
|
362
|
}
|
|
363
|
}
|
|
364
|
return false;
|
|
365
|
}
|
|
366
|
|
|
367
|
public static String generateReferenceRawText(ReferenceBasicMetadata refMeta) {
|
|
368
|
String authors = refMeta.getAuthors()!=null?
|
|
369
|
StringUtils.join(refMeta.getAuthors(), ", "):"";
|
|
370
|
String title = refMeta.getTitle()!=null?refMeta.getTitle().toString():null;
|
|
371
|
String source = refMeta.getSource()!=null?refMeta.getSource().toString():null;
|
|
372
|
String year = refMeta.getYear()!=null?refMeta.getYear().toString():null;
|
|
373
|
String volume = refMeta.getVolume()!=null?refMeta.getVolume().toString():null;
|
|
374
|
String issue = refMeta.getIssue()!=null?refMeta.getIssue().toString():null;
|
|
375
|
String fpage = refMeta.getPages()!=null && refMeta.getPages().getStart()!=null
|
|
376
|
?refMeta.getPages().getStart().toString():null;
|
|
377
|
String lpage = refMeta.getPages()!=null && refMeta.getPages().getEnd()!=null
|
|
378
|
?refMeta.getPages().getEnd().toString():null;
|
|
379
|
|
|
380
|
StringBuilder builder = new StringBuilder();
|
|
381
|
|
|
382
|
if (StringUtils.isNotBlank(authors)) {
|
|
383
|
builder.append(authors);
|
|
384
|
builder.append(". ");
|
|
385
|
}
|
|
386
|
if (StringUtils.isNotBlank(title)) {
|
|
387
|
builder.append(title);
|
|
388
|
builder.append(". ");
|
|
389
|
}
|
|
390
|
if (StringUtils.isNotBlank(source)) {
|
|
391
|
builder.append(source);
|
|
392
|
builder.append(". ");
|
|
393
|
}
|
|
394
|
if (StringUtils.isNotBlank(year)) {
|
|
395
|
builder.append(year);
|
|
396
|
}
|
|
397
|
if (StringUtils.isNotBlank(volume)) {
|
|
398
|
builder.append("; ");
|
|
399
|
builder.append(volume);
|
|
400
|
}
|
|
401
|
if (StringUtils.isNotBlank(issue)) {
|
|
402
|
builder.append(" (");
|
|
403
|
builder.append(issue);
|
|
404
|
builder.append(")");
|
|
405
|
}
|
|
406
|
if (StringUtils.isNotBlank(fpage)) {
|
|
407
|
builder.append(": ");
|
|
408
|
builder.append(fpage);
|
|
409
|
}
|
|
410
|
if (StringUtils.isNotBlank(lpage)) {
|
|
411
|
builder.append("-");
|
|
412
|
builder.append(lpage);
|
|
413
|
}
|
|
414
|
return builder.toString();
|
|
415
|
}
|
|
416
|
}
|