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Compile the xpath at the instantiation of the patterns
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@lfoppiano
lfoppiano committed Aug 26, 2022
1 parent fc1445b commit d22a1ff
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Showing 2 changed files with 112 additions and 106 deletions.
64 changes: 32 additions & 32 deletions grobid-trainer/src/main/java/org/grobid/trainer/evaluation/EndToEndEvaluation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -28,14 +28,10 @@
import org.w3c.dom.*;

import javax.xml.namespace.QName;
import javax.xml.xpath.XPath;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
import javax.xml.xpath.*;
import javax.xml.parsers.*;
import org.xml.sax.*;

import javax.xml.xpath.XPathConstants;

import com.rockymadden.stringmetric.similarity.RatcliffObershelpMetric;
import scala.Option;

Expand Down Expand Up @@ -153,10 +149,14 @@ public EndToEndEvaluation(String path, String inType) {
headerLabels = new ArrayList<>();
fulltextLabels = new ArrayList<>();
citationsLabels = new ArrayList<>();

FieldSpecification.setUpFields(headerFields, fulltextFields, citationsFields,
headerLabels, fulltextLabels, citationsLabels);
}

try {
FieldSpecification.setUpFields(headerFields, fulltextFields, citationsFields,
headerLabels, fulltextLabels, citationsLabels);
} catch (XPathExpressionException e) {
throw new RuntimeException("Invalid XPaths for evaluation. ", e);
}
}

public String evaluationGrobid(boolean forceRun, StringBuilder reportMD) throws Exception {
if (xmlInputPath == null) {
Expand Down Expand Up @@ -530,27 +530,27 @@ public boolean accept(File dir, String name) {

XPathFactory xpf = XPathFactory.newInstance();
XPath xp = xpf.newXPath();
HashMap map = new HashMap();
// Map<String, String> map = new HashMap();
// explicit indication of the default namespace
map.put("tei", "http://www.tei-c.org/ns/1.0");
// map.put("tei", "http://www.tei-c.org/ns/1.0");

Map<String, String> mappings = new HashMap<String, String>();
Map<String, String> mappings = new HashMap<>();
mappings.put("tei", "http://www.tei-c.org/ns/1.0");
xp.setNamespaceContext(new NamespaceContextMap(mappings));

if (sectionType == this.CITATION) {
if (sectionType == CITATION) {
// we start by identifying each expected citation
// the first FieldSpecification object for the citation is the base path for
// each citation structure in the corresponding XML
FieldSpecification base = fields.get(0);

String path = null;
XPathExpression path = null;
if (inputType.equals("nlm"))
path = base.nlmPath.get(0).getLeft();
else
path = base.grobidPath.get(0).getLeft();

NodeList nodeList = (NodeList) xp.compile(path).
NodeList nodeList = (NodeList) path.
evaluate(gold.getDocumentElement(), XPathConstants.NODESET);
int nbCitationsGold = nodeList.getLength();
totalExpectedInstances += nbCitationsGold;
Expand Down Expand Up @@ -588,7 +588,7 @@ public boolean accept(File dir, String name) {
//p++;
continue;
}
List<Pair<String, QName>> subpaths = null;
List<Pair<XPathExpression, QName>> subpaths = null;
if (inputType.equals("nlm")) {
subpaths = field.nlmPath;
} else if (inputType.equals("tei")) {
Expand All @@ -598,8 +598,8 @@ public boolean accept(File dir, String name) {
if (subpaths == null)
continue;

for(Pair<String, QName> subpath : subpaths) {
NodeList nodeList2 = (NodeList) xp.compile(subpath.getLeft()).
for(Pair<XPathExpression, QName> subpath : subpaths) {
NodeList nodeList2 = (NodeList) subpath.getLeft().
evaluate(node, subpath.getRight());

List<String> goldResults = new ArrayList<String>();
Expand Down Expand Up @@ -704,7 +704,7 @@ public boolean accept(File dir, String name) {
* - third rule: matching of "soft" inTitle (title of Journal or Conference), volume and first page
* - forth rule: matching of first author last name and title, or inTitle if title is empty
*/
String signature1 = null;
String signature1 = null;
if ( (goldTitleSoft.length()>0) && (goldDate.length()>0) ) {
signature1 = goldTitleSoft + goldDate;
//signature1 = signature1.replaceAll("[^\\x00-\\x7F]", "");
Expand Down Expand Up @@ -742,7 +742,7 @@ public boolean accept(File dir, String name) {
// get the Grobid citations
path = base.grobidPath.get(0).getLeft();
QName nodeType = base.grobidPath.get(0).getRight();
nodeList = (NodeList) xp.compile(path).
nodeList = (NodeList) path.
evaluate(tei.getDocumentElement(), nodeType);
int nbCitationsGrobid = nodeList.getLength();
totalObservedInstances += nbCitationsGrobid;
Expand All @@ -758,8 +758,8 @@ public boolean accept(File dir, String name) {
//p++;
continue;
}
for(Pair<String, QName> subpath : field.grobidPath) {
NodeList nodeList2 = (NodeList) xp.compile(subpath.getLeft()).
for(Pair<XPathExpression, QName> subpath : field.grobidPath) {
NodeList nodeList2 = (NodeList) subpath.getLeft().
evaluate(node, subpath.getRight());
List<String> grobidResults = new ArrayList<String>();
for (int j = 0; j < nodeList2.getLength(); j++) {
Expand Down Expand Up @@ -1239,8 +1239,8 @@ else if (goldResultSoft.length() > 0) {

List<String> grobidResults = new ArrayList<>();
int nbGrobidResults = 0;
for(Pair<String, QName> path : field.grobidPath) {
NodeList nodeList = (NodeList) xp.compile(path.getLeft()).
for(Pair<XPathExpression, QName> path : field.grobidPath) {
NodeList nodeList = (NodeList) path.getLeft().
evaluate(tei.getDocumentElement(), path.getRight());
nbGrobidResults = nodeList.getLength();
for (int i = 0; i < nodeList.getLength(); i++) {
Expand All @@ -1262,7 +1262,7 @@ else if (goldResultSoft.length() > 0) {

List<String> goldResults = new ArrayList<String>();
int nbGoldResults = 0;
List<Pair<String, QName>> subpaths = null;
List<Pair<XPathExpression, QName>> subpaths = null;
if (inputType.equals("nlm")) {
subpaths = field.nlmPath;
} else if (inputType.equals("tei")) {
Expand All @@ -1272,8 +1272,8 @@ else if (goldResultSoft.length() > 0) {
if (subpaths == null)
continue;

for(Pair<String, QName> path : subpaths) {
NodeList nodeList = (NodeList) xp.compile(path.getLeft()).
for(Pair<XPathExpression, QName> path : subpaths) {
NodeList nodeList = (NodeList) path.getLeft().
evaluate(gold.getDocumentElement(), path.getRight());
//System.out.println(path + ": " + nodeList.getLength() + " nodes");
nbGoldResults = nodeList.getLength();
Expand Down Expand Up @@ -1462,7 +1462,7 @@ else if (sectionType == this.FULLTEXT) {

// List<String> goldResults = new ArrayList<>();
// int nbgoldResults = 0;
List<Pair<String, QName>> subpaths = null;
List<Pair<XPathExpression, QName>> subpaths = null;
if (inputType.equals("nlm")) {
subpaths = field.nlmPath;
} else if (inputType.equals("tei")) {
Expand Down Expand Up @@ -1841,16 +1841,16 @@ else if (sectionType == this.HEADER) {
return report.toString();
}

private static List<String> extractFromXPath(Document xmlDocument, List<Pair<String, QName>> extractionPaths, XPath xPath, FieldSpecification field) throws XPathExpressionException {
private static List<String> extractFromXPath(Document xmlDocument, List<Pair<XPathExpression, QName>> extractionPaths, XPath xPath, FieldSpecification field) throws XPathExpressionException {
List<String> results = new ArrayList<>();
for(Pair<String, QName> path : extractionPaths) {
for(Pair<XPathExpression, QName> path : extractionPaths) {
if (path.getRight() == XPathConstants.NODESET) {
NodeList nodeList = (NodeList) xPath.compile(path.getLeft()).evaluate(xmlDocument.getDocumentElement(), path.getRight());
NodeList nodeList = (NodeList) path.getLeft().evaluate(xmlDocument.getDocumentElement(), path.getRight());
for (int i = 0; i < nodeList.getLength(); i++) {
results.add(basicNormalizationFullText(nodeList.item(i).getNodeValue(), field.fieldName));
}
} else if (path.getRight() == XPathConstants.STRING) {
String string = (String) xPath.compile(path.getLeft()).evaluate(xmlDocument, path.getRight());
String string = (String) path.getLeft().evaluate(xmlDocument, path.getRight());
results.add(basicNormalizationFullText(string, field.fieldName));
} else {
throw new UnsupportedOperationException("Extraction from XPath works only with STRING or NODESET. Used: " + path.getRight().toString());
Expand Down
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