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Minor: Code updates #61

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8ac6e09
add basic bibliographic data in response
lfoppiano Oct 30, 2025
3925911
make the code more readable
lfoppiano Oct 30, 2025
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248 changes: 248 additions & 0 deletions src/main/java/org/grobid/core/data/ArticleBiblio.java
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package org.grobid.core.data;

import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
import org.grobid.core.utilities.LayoutTokensUtil;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.NodeList;

import javax.xml.xpath.XPath;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathFactory;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;

/**
* Data class to hold article metadata (DOI, title, authors) extracted from documents.
* This class provides a clean separation from BiblioComponent which is designed
* for reference components within software mentions.
*/
public class ArticleBiblio {
private static final Logger LOGGER = LoggerFactory.getLogger(ArticleBiblio.class);

private String doi;
private String title;
private String authors;

public ArticleBiblio() {
}

public ArticleBiblio(String doi, String title, String authors) {
this.doi = doi;
this.title = title;
this.authors = authors;
}

// Getters and setters
public String getDoi() {
return doi;
}

public void setDoi(String doi) {
this.doi = doi;
}

public String getTitle() {
return title;
}

public void setTitle(String title) {
this.title = title;
}

public void setAuthors(String authors) {
this.authors = authors;
}

public String getAuthors() {
return this.authors;
}

/**
* Check if this metadata article has any meaningful content
*/
public boolean hasContent() {
return (StringUtils.isNotBlank(doi)) ||
(StringUtils.isNotBlank(title)) ||
(StringUtils.isNotBlank(authors));
}

/**
* Convert this MetadataArticle to JSON string for API response
*/
public String toJson() {
ObjectMapper mapper = new ObjectMapper();
StringBuilder json = new StringBuilder();

json.append("\"biblio\": {");
boolean firstField = true;

// Add DOI if available
if (doi != null && !doi.trim().isEmpty()) {
if (!firstField) json.append(", ");
try {
json.append("\"doi\": ").append(mapper.writeValueAsString(doi));
} catch (JsonProcessingException e) {
json.append("\"doi\": \"\"");
}
firstField = false;
}

// Add title if available
if (title != null && !title.trim().isEmpty()) {
if (!firstField) json.append(", ");
try {
json.append("\"title\": ").append(mapper.writeValueAsString(title));
} catch (JsonProcessingException e) {
json.append("\"title\": \"\"");
}
firstField = false;
}

// Add authors if available
if (StringUtils.isNotBlank(authors)) {
if (!firstField) json.append(", ");
json.append("\"authors\": \"" + authors + "\"");
}

json.append("}");
return json.toString();
}

/**
* Create MetadataArticle from BiblioItem
*/
public static Optional<ArticleBiblio> fromBiblioItem(BiblioItem biblioItem) {
if (biblioItem == null) {
LOGGER.debug("BiblioItem is null, cannot create MetadataArticle");
return Optional.empty();
}

LOGGER.debug("Creating MetadataArticle from BiblioItem");
ArticleBiblio metadata = new ArticleBiblio();

if (biblioItem.getDOI() != null && !biblioItem.getDOI().trim().isEmpty()) {
metadata.setDoi(biblioItem.getDOI());
LOGGER.debug("Extracted DOI: " + biblioItem.getDOI());
}

if (biblioItem.getTitle() != null && !biblioItem.getTitle().trim().isEmpty()) {
metadata.setTitle(biblioItem.getTitle());
LOGGER.debug("Extracted title: " + biblioItem.getTitle());
}

String authors = LayoutTokensUtil.normalizeText(biblioItem.getAuthors());
if (StringUtils.isNotBlank(authors)) {
metadata.setAuthors(authors);
}

return metadata.hasContent() ? Optional.of(metadata) : Optional.empty();
}

/**
* Extract article metadata from TEI XML Document using XPath
*/
public static Optional<ArticleBiblio> fromTeiDocument(org.w3c.dom.Document teiDocument) {
if (teiDocument == null) {
return Optional.empty();
}

try {
XPathFactory xPathFactory = XPathFactory.newInstance();
XPath xpath = xPathFactory.newXPath();

String title = extractTitle(teiDocument, xpath);
String doi = extractDOI(teiDocument, xpath);
List<String> authors = extractAuthors(teiDocument, xpath);

ArticleBiblio articleMetadata = new ArticleBiblio();
articleMetadata.setDoi(doi);
articleMetadata.setTitle(title);

if (CollectionUtils.isNotEmpty(authors)) {
articleMetadata.setAuthors(String.join(", ", authors));
}

return articleMetadata.hasContent() ? Optional.of(articleMetadata) : Optional.empty();
} catch (Exception e) {
return Optional.empty();
}
}

private static String extractTitle(org.w3c.dom.Document doc, XPath xpath) {
try {
NodeList titleNodes = (NodeList) xpath.evaluate("//teiHeader/fileDesc/titleStmt/title[@level='a'][@type='main']/text()", doc, XPathConstants.NODESET);
if (titleNodes != null && titleNodes.getLength() > 0) {
String title = titleNodes.item(0).getNodeValue().trim();
return title.isEmpty() ? "" : title;
}
} catch (Exception e) {
}
return "";
}

private static String extractDOI(org.w3c.dom.Document doc, XPath xpath) {
try {
NodeList doiNodes = (NodeList) xpath.evaluate("//teiHeader/fileDesc/sourceDesc/biblStruct/idno[2]/text()", doc, XPathConstants.NODESET);
if (doiNodes != null && doiNodes.getLength() > 0) {
String doi = doiNodes.item(0).getNodeValue().trim();
return doi.isEmpty() ? "" : doi;
}
} catch (Exception e) {
}
return "";
}

private static List<String> extractAuthors(org.w3c.dom.Document doc, XPath xpath) {
List<String> authors = new ArrayList<>();
try {
NodeList authorNodes = (NodeList) xpath.evaluate("//teiHeader/fileDesc/sourceDesc/biblStruct/analytic/author/persName", doc, XPathConstants.NODESET);
for (int i = 0; i < authorNodes.getLength(); i++) {
String author = formatAuthorFromNode(authorNodes.item(i));
if (!author.isEmpty() && !authors.contains(author)) {
authors.add(author);
}
}
} catch (Exception e) {
}
return authors;
}

/**
* Format author from XML node as "surname, name"
*/
private static String formatAuthorFromNode(org.w3c.dom.Node node) {
if (node == null) return "";

if (node.getNodeName().equals("persName")) {
String surname = "";
String forename = "";

NodeList childNodes = node.getChildNodes();
for (int i = 0; i < childNodes.getLength(); i++) {
org.w3c.dom.Node child = childNodes.item(i);
if (child.getNodeName().equals("surname")) {
surname = child.getTextContent().trim();
} else if (child.getNodeName().equals("forename")) {
forename = child.getTextContent().trim();
}
}

if (!surname.isEmpty()) {
return forename.isEmpty() ? surname : surname + ", " + forename;
}
}

return node.getTextContent().trim();
}

@Override
public String toString() {
return String.format("MetadataArticle{doi='%s', title='%s', authors=%s}",
doi, title, authors);
}
}
14 changes: 3 additions & 11 deletions src/main/java/org/grobid/core/data/BiblioComponent.java
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Original file line number Diff line number Diff line change
@@ -1,17 +1,9 @@
package org.grobid.core.data;

import org.grobid.core.engines.label.TaggingLabel;
import org.grobid.core.utilities.TextUtilities;
import org.grobid.core.utilities.OffsetPosition;
import org.grobid.core.lexicon.SoftwareLexicon;
import org.grobid.core.layout.BoundingBox;
import org.grobid.core.layout.LayoutToken;

import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;

import java.util.List;

import org.grobid.core.layout.BoundingBox;
import org.grobid.core.utilities.TextUtilities;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

Expand Down Expand Up @@ -82,7 +74,7 @@ public String toJson() {
}
}*/
buffer.append(", \"refKey\": " + refKey);

// knowledge information
if (wikidataId != null) {
buffer.append(", \"wikidataId\": \"" + wikidataId + "\"");
Expand Down
37 changes: 11 additions & 26 deletions src/main/java/org/grobid/core/engines/SoftwareContextClassifier.java
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Original file line number Diff line number Diff line change
@@ -1,36 +1,21 @@
package org.grobid.core.engines;

import java.util.*;

import org.apache.commons.io.FileUtils;
import org.grobid.core.GrobidModels;
import org.grobid.core.exceptions.GrobidException;
import org.grobid.core.factory.GrobidFactory;
import org.grobid.core.layout.LayoutToken;
import org.grobid.core.layout.LayoutTokenization;
import org.grobid.core.utilities.*;
import org.grobid.core.jni.PythonEnvironmentConfig;
import com.fasterxml.jackson.core.JsonParser;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
import org.grobid.core.data.SoftwareContextAttributes;
import org.grobid.core.data.SoftwareEntity;
import org.grobid.core.jni.DeLFTClassifierModel;
import org.grobid.core.utilities.GrobidConfig.ModelParameters;
import org.grobid.core.utilities.SoftwareConfiguration;
import org.grobid.core.utilities.TextUtilities;
import org.grobid.core.data.SoftwareEntity;
import org.grobid.core.data.SoftwareContextAttributes;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.ArrayUtils;
import org.apache.commons.lang3.SystemUtils;
import org.apache.commons.lang3.tuple.Pair;

import com.fasterxml.jackson.core.*;
import com.fasterxml.jackson.databind.*;
import com.fasterxml.jackson.databind.node.*;
import com.fasterxml.jackson.annotation.*;
import com.fasterxml.jackson.core.io.*;

import static org.apache.commons.lang3.ArrayUtils.isEmpty;
import java.util.*;

/**
* Use a Deep Learning multiclass and multilabel classifier to characterize the context of a recognized software mention.
Expand Down Expand Up @@ -132,7 +117,7 @@ public String classify(String text, MODEL_TYPE type) throws Exception {
* @return list of predicted labels/scores pairs for each text
*/
public String classify(List<String> texts, MODEL_TYPE type) throws Exception {
if (texts == null || texts.size() == 0)
if (CollectionUtils.isEmpty(texts))
return null;

LOGGER.info("classify: " + texts.size() + " sentence(s) for type " + type.toString());
Expand Down
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