Revision 30986
Added by Marek Horst over 9 years ago
| ResolvedCitation.java | ||
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package eu.dnetlib.iis.ingest.pmc.citations; |
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import eu.dnetlib.data.proto.TypeProtos.Type; |
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import eu.dnetlib.data.transform.xml.AbstractDNetOafXsltFunctions; |
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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.Map; |
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import org.apache.commons.io.IOUtils; |
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import org.apache.commons.lang.StringUtils; |
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import pl.edu.icm.ceon.scala_commons.xml.XPathEvaluator; |
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import scala.collection.JavaConversions; |
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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.Map; |
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/** |
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* A model of resolved citation from PMC. |
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* |
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* @author Mateusz Fedoryszak (m.fedoryszak@icm.edu.pl) |
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*/ |
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public class ResolvedCitation {
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private final String sourcePmid;
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private final String sourceOaid;
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private final int position; |
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private final String rawText; |
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private final Map<String, String> targetIds; |
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private static final String PUBMED_NS_PREFIX = "od_______908"; |
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private static final String PUBMED_ID_PREFIX = "oai:europepmc.org:"; |
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private static final String PMID_KEY = "pmid"; |
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private static final String DOI_KEY = "doi"; |
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public ResolvedCitation(final String sourcePmid, final int position, final String rawText, final Map<String, String> targetIds) {
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this.sourcePmid = sourcePmid;
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public ResolvedCitation(final String sourceOaid, final int position, final String rawText, final Map<String, String> targetIds) {
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this.sourceOaid = sourceOaid;
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this.position = position; |
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this.rawText = rawText; |
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this.targetIds = targetIds; |
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} |
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/** |
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* @return Source (citing) document PubMedID |
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*/ |
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public String getSourcePmid() {
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return sourcePmid; |
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} |
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/** |
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* @return Source (citing) document OpenAIRE ID (before dedup) |
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*/ |
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public String getSourceOaid() {
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return pmidToOaid(sourcePmid);
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return sourceOaid;
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} |
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public int getPosition() {
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return targetIds.get(PMID_KEY); |
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} |
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/** |
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* @return Target (cited) document OpenAIRE ID (before dedup)
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* @return Target (cited) document DOI
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*/ |
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public String getTargetOaid() {
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final String pmid = getTargetPmid(); |
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if (pmid != null) {
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return pmidToOaid(pmid); |
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} else {
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return null; |
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} |
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public String getTargetDoi() {
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return targetIds.get(DOI_KEY); |
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} |
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public String getTargetIdsJson() {
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return new JSONObject(targetIds).toString(); |
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} |
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/** |
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* Transforms PubMed ID into OpenAIRE ID (before dedup) |
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*/ |
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public static String pmidToOaid(final String pmid) {
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return AbstractDNetOafXsltFunctions.oafId( |
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Type.result.name(), PUBMED_NS_PREFIX, PUBMED_ID_PREFIX + pmid); |
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} |
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/** |
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* Parses NLM file and extracts resolved citations. |
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*/ |
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public static List<ResolvedCitation> extractFromNlm(final String text) {
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XPathEvaluator evaluator = XPathEvaluator.fromString(text); |
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String id = evaluator.apply("/article/front/article-meta/article-id[@pub-id-type='pmid']");
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public static List<ResolvedCitation> extractFromNlm(final String oaSourceId, final String text) {
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XPathEvaluator evaluator = XPathEvaluator.fromInputStream(IOUtils.toInputStream(text)); |
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List<ResolvedCitation> result = new ArrayList<ResolvedCitation>(); |
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int position = 1; |
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final String idValue = citId.getTextContent(); |
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targetIds.put(idType, idValue); |
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} |
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result.add(new ResolvedCitation(id, position, rawTextGenerator(ref), targetIds));
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result.add(new ResolvedCitation(oaSourceId, position, rawTextGenerator(ref), targetIds));
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++position; |
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} |
Also available in: Unified diff
#757 fixing pmid and doi matching, fixing sourceDocumentId and destinationDocumentId generation