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Add CI runner for ELAN vocabulary generation #307

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f75bac1
Add CI runner for ECV generation
ayden175 Sep 25, 2023
16456df
Remove some comments and unused import
ayden175 Sep 25, 2023
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5 changes: 4 additions & 1 deletion scripts/java/src/main/java/main/CIRunner.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,9 @@ public class CIRunner implements CommandLineRunner {
@Autowired
private SubclassNothingRewriter gciRewriter;

@Autowired
private ElanCVGenerator elanCVGenerator;

@Autowired
private IRINamespaceChecker iriNamespaceChecker;

Expand All @@ -32,7 +35,7 @@ public class CIRunner implements CommandLineRunner {

@Override
public void run(final String... args) throws Exception {
final CIRunnable[] toRun = {iriNamespaceChecker, gciRewriter, isDefinedInAdder, versionInfoAdder, collapser, ontologySaver};
final CIRunnable[] toRun = {iriNamespaceChecker, elanCVGenerator, gciRewriter, isDefinedInAdder, versionInfoAdder, collapser, ontologySaver};
for (final var next : toRun) {
next.run();
}
Expand Down
244 changes: 244 additions & 0 deletions scripts/java/src/main/java/main/ci_runners/ElanCVGenerator.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,244 @@
package main.ci_runners;

import main.OntologyManager;
import org.semanticweb.owlapi.model.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.annotation.Lazy;
import org.springframework.stereotype.Component;
import org.w3c.dom.Document;
import org.w3c.dom.Element;

import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.OutputKeys;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.*;

import static org.semanticweb.owlapi.search.EntitySearcher.*;

@Component
@Lazy
public class ElanCVGenerator implements CIRunnable {
private static final Logger LOGGER = LoggerFactory.getLogger(ElanCVGenerator.class);

private final OntologyManager ontologyManager;
private final String outputPath = "../SOMA.ecv";
private final String version;
private final List<OWLOntology> ontologies;
private final String langRef = "und";
private final String langLabel = "und";
private final HashMap<String, List<String>> vocabs;
private final OWLAnnotationProperty elanNameAnnot;
private final OWLAnnotationProperty elanUsageAnnot;

@Autowired
public ElanCVGenerator(final OntologyManager ontologyManager, @Value("${versionInfo}") final String versionInfo) {
this.ontologyManager = ontologyManager;
this.version = versionInfo;

String[] ontologyStrings = {"SOMA", "SOMA-NEEM", "SOMA-OBJ", "SOMA-PROC", "SOMA-STATE", "SOMA-ACT", "SOMA-ELAN"};
ontologies = new ArrayList<>();
for (OWLOntology ontology : ontologyManager.getOntologyManager().getOntologies()) {
for (String ontologyString : ontologyStrings) {
if (ontology.getOntologyID().getOntologyIRI().get().toString().contains(ontologyString + ".owl")) {
ontologies.add(ontology);
}
}
}

String ease = "http://www.ease-crc.org/ont/SOMA.owl#";
vocabs = new HashMap<>();
vocabs.put("lvl1-ease_tsd-motion", List.of(ease + "Locomotion",
ease + "BodyMovement",
ease + "Manipulating",
ease + "Actuating"));
vocabs.put("lvl_2-ease_tsd-task_step", List.of(ease + "PhysicalTask"));
vocabs.put("think-aloud_coding", List.of(ease + "ThinkAloudTopic"));

elanNameAnnot = getAnnotationByIRI(ease + "ELANName");
elanUsageAnnot = getAnnotationByIRI(ease + "ELANUsageGuideline");
}

@Override
public void run() {
if (elanNameAnnot == null) {
LOGGER.error("Could not find ELANName annotation property. ELAN CV will not be generated.");
return;
}

HashMap<String, List<OWLClass>> vocabWords = new HashMap<>();

for (String cv_id : vocabs.keySet()) {
Set<OWLClass> actionWords = new HashSet<>();
Set<OWLClass> actionParents = new HashSet<>();
for (String classIRIString : vocabs.get(cv_id)) {
OWLClass owlClass = getClassByIRI(classIRIString);
if (owlClass != null) {
actionParents.add(owlClass);
if (!Objects.equals(getAnnotationValue(owlClass, elanNameAnnot), "")) {
actionWords.add(owlClass);
}
} else {
LOGGER.error("Could not find class with IRI {}", classIRIString);
}
}

while (!actionParents.isEmpty()) {
Set<OWLClass> newActionParents = new HashSet<>();
for (OWLClass actionParent : actionParents) {
getSubClasses(actionParent, ontologies.stream()).forEach((classExpression) -> {
if (classExpression.isNamed()) {
OWLClass owlClass = classExpression.asOWLClass();
actionWords.add(owlClass);
newActionParents.add(owlClass);
}
});
}
actionParents = newActionParents;
}
vocabWords.put(cv_id, actionWords.stream().sorted(Comparator.comparing(this::getElanName)).toList());
}

try {
exportCV(vocabWords);
} catch (ParserConfigurationException | TransformerException | IOException e) {
LOGGER.error("Could not export CV", e);
}
}

private OWLClass getClassByIRI(String classIRIString) {
OWLOntologyManager owlOntologyManager = ontologyManager.getOntologyManager();
OWLDataFactory dataFactory = owlOntologyManager.getOWLDataFactory();
IRI classIRI = IRI.create(classIRIString);
for (OWLOntology ontology : ontologies) {
if (ontology.containsEntityInSignature(classIRI)) {
return dataFactory.getOWLClass(classIRI);
}
}

return null; // Class not found
}

private String getElanName(OWLClass owlClass) {
String elanName = getAnnotationValue(owlClass, elanNameAnnot);
if (Objects.equals(elanName, "")) {
elanName = owlClass.getIRI().getShortForm();
}
return elanName;
}

private String getAnnotationValue(OWLClass owlClass, OWLAnnotationProperty annotationProperty) {
try {
return getAnnotations(owlClass, ontologies.stream(), annotationProperty).findAny().get().getValue().asLiteral().get().getLiteral();
} catch (java.util.NoSuchElementException e) {
return "";
}
}

private OWLAnnotationProperty getAnnotationByIRI(String annotationIRIString) {
OWLDataFactory dataFactory = ontologyManager.getOntologyManager().getOWLDataFactory();
IRI annotationPropertyIRI = IRI.create(annotationIRIString);
return dataFactory.getOWLAnnotationProperty(annotationPropertyIRI);
}

private String getCVEID(String cvId, String elanName) {
String input = langRef + cvId + elanName;

try {
MessageDigest md = MessageDigest.getInstance("MD5");
md.update(input.getBytes());
byte[] digest = md.digest();

StringBuilder hexString = new StringBuilder();
hexString.append("cveid_");
for (byte b : digest) {
hexString.append(String.format("%02x", b));
}

return hexString.toString();
} catch (NoSuchAlgorithmException e) {
LOGGER.error("Could not generate CVE ID for {}", input);
return "";
}
}

private void exportCV(HashMap<String, List<OWLClass>> vocabWords) throws ParserConfigurationException, TransformerException, IOException {
DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder docBuilder = docFactory.newDocumentBuilder();
DateFormat df = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");

Document doc = docBuilder.newDocument();
doc.setXmlStandalone(true);
Element rootElement = doc.createElement("CV_RESOURCE");
rootElement.setAttribute("AUTHOR", "");
rootElement.setAttribute("DATE", df.format(Calendar.getInstance().getTime()));
rootElement.setAttribute("VERSION", version);
rootElement.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance");
rootElement.setAttribute("xsi:noNamespaceSchemaLocation", "http://www.mpi.nl/tools/elan/EAFv2.8.xsd");
doc.appendChild(rootElement);

Element lang = doc.createElement("LANGUAGE");
lang.setAttribute("LANG_DEF", "http://cdb.iso.org/lg/CDB-00130975-001");
lang.setAttribute("LANG_ID", langRef);
lang.setAttribute("LANG_LABEL", langLabel);
rootElement.appendChild(lang);

ArrayList<String> cvIdsSorted = new ArrayList<>(vocabWords.keySet());
cvIdsSorted.sort(String::compareTo);
for (String cv_id : cvIdsSorted) {
Element cv = doc.createElement("CONTROLLED_VOCABULARY");
cv.setAttribute("CV_ID", cv_id);
rootElement.appendChild(cv);
Element cvDesc = doc.createElement("DESCRIPTION");
cvDesc.setAttribute("LANG_REF", langRef);
cv.appendChild(cvDesc);

for (OWLClass actionWord : vocabWords.get(cv_id)) {
String elanName = getElanName(actionWord);
String elanUsage = getAnnotationValue(actionWord, elanUsageAnnot);
String cveId = getCVEID(cv_id, elanName);

Element cvEntry = doc.createElement("CVE_ENTRY_ML");
cvEntry.setAttribute("CVE_ID", cveId);
cv.appendChild(cvEntry);
Element cvEntryVal = doc.createElement("CVE_VALUE");
cvEntryVal.setTextContent(elanName);
cvEntryVal.setAttribute("DESCRIPTION", elanUsage);
cvEntryVal.setAttribute("LANG_REF", langRef);
cvEntry.appendChild(cvEntryVal);
}
}

try (FileOutputStream output = new FileOutputStream(outputPath)) {
writeXml(doc, output);
}
}

private static void writeXml(Document doc, OutputStream output) throws TransformerException {
TransformerFactory transformerFactory = TransformerFactory.newInstance();
Transformer transformer = transformerFactory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty(OutputKeys.DOCTYPE_PUBLIC, "");

DOMSource source = new DOMSource(doc);
StreamResult result = new StreamResult(output);

transformer.transform(source, result);
LOGGER.info("ECV exported");
}
}