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Upgrade jquery and format some expressions with c:out.
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meier-rene committed Dec 4, 2024
1 parent 2acbf05 commit e90225f
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Showing 15 changed files with 158 additions and 154 deletions.
12 changes: 6 additions & 6 deletions MassBank-Project/MassBank-lib/pom.xml
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Expand Up @@ -18,7 +18,7 @@
</dependency>
<dependency>
<groupId>jakarta.platform</groupId>
<artifactId>jakarta.jakartaee-api</artifactId>
<artifactId>jakarta.jakartaee-web-api</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
Expand Down Expand Up @@ -89,11 +89,11 @@
<groupId>io.github.dan2097</groupId>
<artifactId>jna-inchi-all</artifactId>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
<version>5.5.0</version>
</dependency>
<!-- <dependency>-->
<!-- <groupId>net.sourceforge.owlapi</groupId>-->
<!-- <artifactId>owlapi-distribution</artifactId>-->
<!-- <version>5.5.0</version>-->
<!-- </dependency>-->
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
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30 changes: 15 additions & 15 deletions MassBank-Project/MassBank-lib/src/main/java/massbank/CVUtil.java
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Expand Up @@ -10,21 +10,21 @@
import java.util.ArrayList;
import java.util.Set;

import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.reasoner.BufferingMode;
import org.semanticweb.owlapi.reasoner.InferenceType;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
import org.semanticweb.owlapi.reasoner.SimpleConfiguration;
import org.semanticweb.owlapi.reasoner.structural.StructuralReasoner;
import org.semanticweb.owlapi.reasoner.NodeSet;
import org.semanticweb.owlapi.model.OWLClass;
//import org.semanticweb.owlapi.apibinding.OWLManager;
//import org.semanticweb.owlapi.model.IRI;
//import org.semanticweb.owlapi.model.OWLAxiom;
//import org.semanticweb.owlapi.model.OWLDataFactory;
//import org.semanticweb.owlapi.model.OWLOntology;
//import org.semanticweb.owlapi.model.OWLOntologyCreationException;
//import org.semanticweb.owlapi.model.OWLOntologyManager;
//import org.semanticweb.owlapi.reasoner.BufferingMode;
//import org.semanticweb.owlapi.reasoner.InferenceType;
//import org.semanticweb.owlapi.reasoner.OWLReasoner;
//import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
//import org.semanticweb.owlapi.reasoner.SimpleConfiguration;
//import org.semanticweb.owlapi.reasoner.structural.StructuralReasoner;
//import org.semanticweb.owlapi.reasoner.NodeSet;
//import org.semanticweb.owlapi.model.OWLClass;


/**
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234 changes: 117 additions & 117 deletions MassBank-Project/MassBank-lib/src/test/java/massbank/CVUtilTest.java
Original file line number Diff line number Diff line change
Expand Up @@ -11,25 +11,25 @@

import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.formats.FunctionalSyntaxDocumentFormat;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;

import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
//import org.semanticweb.owlapi.apibinding.OWLManager;
//import org.semanticweb.owlapi.formats.FunctionalSyntaxDocumentFormat;
//import org.semanticweb.owlapi.model.IRI;
//import org.semanticweb.owlapi.model.OWLOntology;
//import org.semanticweb.owlapi.model.OWLOntologyCreationException;
//
//import org.semanticweb.owlapi.model.OWLOntologyManager;
//import org.semanticweb.owlapi.model.OWLOntologyStorageException;

import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.semanticweb.owlapi.model.parameters.Imports.INCLUDED;
import static org.semanticweb.owlapi.search.EntitySearcher.getAnnotationObjects;
import static org.semanticweb.owlapi.search.Searcher.sup;
import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.asList;
import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.asSet;
import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.asUnorderedSet;
import static org.semanticweb.owlapi.vocab.OWLFacet.MAX_EXCLUSIVE;
import static org.semanticweb.owlapi.vocab.OWLFacet.MIN_INCLUSIVE;
//import static org.semanticweb.owlapi.model.parameters.Imports.INCLUDED;
//import static org.semanticweb.owlapi.search.EntitySearcher.getAnnotationObjects;
//import static org.semanticweb.owlapi.search.Searcher.sup;
//import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.asList;
//import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.asSet;
//import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.asUnorderedSet;
//import static org.semanticweb.owlapi.vocab.OWLFacet.MAX_EXCLUSIVE;
//import static org.semanticweb.owlapi.vocab.OWLFacet.MIN_INCLUSIVE;

import java.io.ByteArrayOutputStream;
import java.io.File;
Expand All @@ -43,93 +43,93 @@

import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.formats.ManchesterSyntaxDocumentFormat;
import org.semanticweb.owlapi.formats.OWLXMLDocumentFormat;
import org.semanticweb.owlapi.formats.TurtleDocumentFormat;
import org.semanticweb.owlapi.io.StreamDocumentTarget;
import org.semanticweb.owlapi.io.StringDocumentSource;
import org.semanticweb.owlapi.io.StringDocumentTarget;
import org.semanticweb.owlapi.model.AddAxiom;
import org.semanticweb.owlapi.model.AddOntologyAnnotation;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotation;
import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLClassAssertionAxiom;
import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLClassExpressionVisitor;
import org.semanticweb.owlapi.model.OWLDataExactCardinality;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLDataProperty;
import org.semanticweb.owlapi.model.OWLDataPropertyAssertionAxiom;
import org.semanticweb.owlapi.model.OWLDataPropertyRangeAxiom;
import org.semanticweb.owlapi.model.OWLDataRange;
import org.semanticweb.owlapi.model.OWLDataSomeValuesFrom;
import org.semanticweb.owlapi.model.OWLDataUnionOf;
import org.semanticweb.owlapi.model.OWLDatatype;
import org.semanticweb.owlapi.model.OWLDatatypeDefinitionAxiom;
import org.semanticweb.owlapi.model.OWLDatatypeRestriction;
import org.semanticweb.owlapi.model.OWLDeclarationAxiom;
import org.semanticweb.owlapi.model.OWLDifferentIndividualsAxiom;
import org.semanticweb.owlapi.model.OWLDisjointClassesAxiom;
import org.semanticweb.owlapi.model.OWLDocumentFormat;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
import org.semanticweb.owlapi.model.OWLFacetRestriction;
import org.semanticweb.owlapi.model.OWLFunctionalDataPropertyAxiom;
import org.semanticweb.owlapi.model.OWLIndividual;
import org.semanticweb.owlapi.model.OWLLiteral;
import org.semanticweb.owlapi.model.OWLNamedIndividual;
import org.semanticweb.owlapi.model.OWLObjectAllValuesFrom;
import org.semanticweb.owlapi.model.OWLObjectExactCardinality;
import org.semanticweb.owlapi.model.OWLObjectHasValue;
import org.semanticweb.owlapi.model.OWLObjectIntersectionOf;
import org.semanticweb.owlapi.model.OWLObjectOneOf;
import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom;
import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyID;
import org.semanticweb.owlapi.model.OWLOntologyIRIMapper;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
import org.semanticweb.owlapi.model.OWLSubObjectPropertyOfAxiom;
import org.semanticweb.owlapi.model.PrefixManager;
import org.semanticweb.owlapi.model.SWRLAtom;
import org.semanticweb.owlapi.model.SWRLObjectPropertyAtom;
import org.semanticweb.owlapi.model.SWRLRule;
import org.semanticweb.owlapi.model.SWRLVariable;
import org.semanticweb.owlapi.model.SetOntologyID;
import org.semanticweb.owlapi.reasoner.BufferingMode;
import org.semanticweb.owlapi.reasoner.InferenceType;
import org.semanticweb.owlapi.reasoner.Node;
import org.semanticweb.owlapi.reasoner.NodeSet;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
import org.semanticweb.owlapi.reasoner.SimpleConfiguration;
import org.semanticweb.owlapi.reasoner.structural.StructuralReasoner;
import org.semanticweb.owlapi.reasoner.structural.StructuralReasonerFactory;
import org.semanticweb.owlapi.search.Filters;
import org.semanticweb.owlapi.util.AutoIRIMapper;
import org.semanticweb.owlapi.util.DefaultPrefixManager;
import org.semanticweb.owlapi.util.InferredAxiomGenerator;
import org.semanticweb.owlapi.util.InferredOntologyGenerator;
import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;
import org.semanticweb.owlapi.util.OWLEntityRemover;
import org.semanticweb.owlapi.util.OWLOntologyMerger;
import org.semanticweb.owlapi.util.OWLOntologyWalker;
import org.semanticweb.owlapi.util.OWLOntologyWalkerVisitorEx;
import org.semanticweb.owlapi.util.SimpleIRIMapper;
import org.semanticweb.owlapi.vocab.OWL2Datatype;
import org.semanticweb.owlapi.vocab.OWLFacet;
//import org.semanticweb.owlapi.apibinding.OWLManager;
//import org.semanticweb.owlapi.formats.ManchesterSyntaxDocumentFormat;
//import org.semanticweb.owlapi.formats.OWLXMLDocumentFormat;
//import org.semanticweb.owlapi.formats.TurtleDocumentFormat;
//import org.semanticweb.owlapi.io.StreamDocumentTarget;
//import org.semanticweb.owlapi.io.StringDocumentSource;
//import org.semanticweb.owlapi.io.StringDocumentTarget;
//import org.semanticweb.owlapi.model.AddAxiom;
//import org.semanticweb.owlapi.model.AddOntologyAnnotation;
//import org.semanticweb.owlapi.model.IRI;
//import org.semanticweb.owlapi.model.OWLAnnotation;
//import org.semanticweb.owlapi.model.OWLAnnotationProperty;
//import org.semanticweb.owlapi.model.OWLAxiom;
//import org.semanticweb.owlapi.model.OWLClass;
//import org.semanticweb.owlapi.model.OWLClassAssertionAxiom;
//import org.semanticweb.owlapi.model.OWLClassExpression;
//import org.semanticweb.owlapi.model.OWLClassExpressionVisitor;
//import org.semanticweb.owlapi.model.OWLDataExactCardinality;
//import org.semanticweb.owlapi.model.OWLDataFactory;
//import org.semanticweb.owlapi.model.OWLDataProperty;
//import org.semanticweb.owlapi.model.OWLDataPropertyAssertionAxiom;
//import org.semanticweb.owlapi.model.OWLDataPropertyRangeAxiom;
//import org.semanticweb.owlapi.model.OWLDataRange;
//import org.semanticweb.owlapi.model.OWLDataSomeValuesFrom;
//import org.semanticweb.owlapi.model.OWLDataUnionOf;
//import org.semanticweb.owlapi.model.OWLDatatype;
//import org.semanticweb.owlapi.model.OWLDatatypeDefinitionAxiom;
//import org.semanticweb.owlapi.model.OWLDatatypeRestriction;
//import org.semanticweb.owlapi.model.OWLDeclarationAxiom;
//import org.semanticweb.owlapi.model.OWLDifferentIndividualsAxiom;
//import org.semanticweb.owlapi.model.OWLDisjointClassesAxiom;
//import org.semanticweb.owlapi.model.OWLDocumentFormat;
//import org.semanticweb.owlapi.model.OWLEntity;
//import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
//import org.semanticweb.owlapi.model.OWLFacetRestriction;
//import org.semanticweb.owlapi.model.OWLFunctionalDataPropertyAxiom;
//import org.semanticweb.owlapi.model.OWLIndividual;
//import org.semanticweb.owlapi.model.OWLLiteral;
//import org.semanticweb.owlapi.model.OWLNamedIndividual;
//import org.semanticweb.owlapi.model.OWLObjectAllValuesFrom;
//import org.semanticweb.owlapi.model.OWLObjectExactCardinality;
//import org.semanticweb.owlapi.model.OWLObjectHasValue;
//import org.semanticweb.owlapi.model.OWLObjectIntersectionOf;
//import org.semanticweb.owlapi.model.OWLObjectOneOf;
//import org.semanticweb.owlapi.model.OWLObjectProperty;
//import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom;
//import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
//import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom;
//import org.semanticweb.owlapi.model.OWLOntology;
//import org.semanticweb.owlapi.model.OWLOntologyCreationException;
//import org.semanticweb.owlapi.model.OWLOntologyID;
//import org.semanticweb.owlapi.model.OWLOntologyIRIMapper;
//import org.semanticweb.owlapi.model.OWLOntologyManager;
//import org.semanticweb.owlapi.model.OWLOntologyStorageException;
//import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
//import org.semanticweb.owlapi.model.OWLSubObjectPropertyOfAxiom;
//import org.semanticweb.owlapi.model.PrefixManager;
//import org.semanticweb.owlapi.model.SWRLAtom;
//import org.semanticweb.owlapi.model.SWRLObjectPropertyAtom;
//import org.semanticweb.owlapi.model.SWRLRule;
//import org.semanticweb.owlapi.model.SWRLVariable;
//import org.semanticweb.owlapi.model.SetOntologyID;
//import org.semanticweb.owlapi.reasoner.BufferingMode;
//import org.semanticweb.owlapi.reasoner.InferenceType;
//import org.semanticweb.owlapi.reasoner.Node;
//import org.semanticweb.owlapi.reasoner.NodeSet;
//import org.semanticweb.owlapi.reasoner.OWLReasoner;
//import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
//import org.semanticweb.owlapi.reasoner.SimpleConfiguration;
//import org.semanticweb.owlapi.reasoner.structural.StructuralReasoner;
//import org.semanticweb.owlapi.reasoner.structural.StructuralReasonerFactory;
//import org.semanticweb.owlapi.search.Filters;
//import org.semanticweb.owlapi.util.AutoIRIMapper;
//import org.semanticweb.owlapi.util.DefaultPrefixManager;
//import org.semanticweb.owlapi.util.InferredAxiomGenerator;
//import org.semanticweb.owlapi.util.InferredOntologyGenerator;
//import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;
//import org.semanticweb.owlapi.util.OWLEntityRemover;
//import org.semanticweb.owlapi.util.OWLOntologyMerger;
//import org.semanticweb.owlapi.util.OWLOntologyWalker;
//import org.semanticweb.owlapi.util.OWLOntologyWalkerVisitorEx;
//import org.semanticweb.owlapi.util.SimpleIRIMapper;
//import org.semanticweb.owlapi.vocab.OWL2Datatype;
//import org.semanticweb.owlapi.vocab.OWLFacet;

import uk.ac.manchester.cs.owlapi.modularity.ModuleType;
import uk.ac.manchester.cs.owlapi.modularity.SyntacticLocalityModuleExtractor;
//import uk.ac.manchester.cs.owlapi.modularity.ModuleType;
//import uk.ac.manchester.cs.owlapi.modularity.SyntacticLocalityModuleExtractor;

public class CVUtilTest {

Expand All @@ -149,22 +149,22 @@ public class CVUtilTest {
// Assertions.assertFalse(cvUtil.ontology.containsTerm("MS:2000000"));
// }

@Test
public void testTermIsA() throws IOException, OWLOntologyStorageException, OWLOntologyCreationException {
CVUtil cvUtil = CVUtil.get();
Assertions.assertTrue(cvUtil.termIsA("MS:1003294","MS:1000250"));
// IOHelper ioHelper = new IOHelper();
// OWLOntology full = ioHelper.loadOntology("/home/rene/GIT/MassBank-web/MassBank-Project/MassBank-lib/src/main/resources/cv/psi-ms.owl");
//
//
// OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
// OWLOntology ontology = manager.loadOntology(IRI.create("https://protege.stanford.edu/ontologies/pizza/pizza.owl"));
// ontology.saveOntology(new FunctionalSyntaxDocumentFormat(), System.out);
// @Test
// public void testTermIsA() throws IOException, OWLOntologyStorageException, OWLOntologyCreationException {
// CVUtil cvUtil = CVUtil.get();
// Assertions.assertTrue(cvUtil.termIsA("MS:1003294","MS:1000250"));
//// IOHelper ioHelper = new IOHelper();
//// OWLOntology full = ioHelper.loadOntology("/home/rene/GIT/MassBank-web/MassBank-Project/MassBank-lib/src/main/resources/cv/psi-ms.owl");
////
////
//// OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
//// OWLOntology ontology = manager.loadOntology(IRI.create("https://protege.stanford.edu/ontologies/pizza/pizza.owl"));
//// ontology.saveOntology(new FunctionalSyntaxDocumentFormat(), System.out);
////
//// OWLOntologyManager man = OWLManager.createOWLOntologyManager();
//// System.out.println(man.getOntologies().size());
//
// OWLOntologyManager man = OWLManager.createOWLOntologyManager();
// System.out.println(man.getOntologies().size());

}
// }



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8 changes: 7 additions & 1 deletion MassBank-Project/MassBank-web/pom.xml
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,13 @@
</dependency>
<dependency>
<groupId>jakarta.platform</groupId>
<artifactId>jakarta.jakartaee-api</artifactId>
<artifactId>jakarta.jakartaee-web-api</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.glassfish.web</groupId>
<artifactId>jakarta.servlet.jsp.jstl</artifactId>
<version>2.0.0</version>
<scope>provided</scope>
</dependency>
<dependency>
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2 changes: 1 addition & 1 deletion MassBank-Project/MassBank-web/src/main/webapp/About.jsp
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Expand Up @@ -35,7 +35,7 @@
<link rel="stylesheet" type="text/css" href="css/massbank.css">
<link rel="preconnect" href="https://fonts.gstatic.com">
<link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Mulish:ital,wght@0,400;0,600;1,400;1,600">
<script src="js/jquery-3.5.1.min.js"></script>
<script src="js/jquery-3.7.1.min.js"></script>
<script src="js/iframeResizer.min.js"></script>
<script src="js/svg4everybody-2.1.9.min.js"></script>
<script>svg4everybody();</script>
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2 changes: 1 addition & 1 deletion MassBank-Project/MassBank-web/src/main/webapp/Contents.jsp
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Expand Up @@ -35,7 +35,7 @@
<link rel="stylesheet" type="text/css" href="css/massbank.css">
<link rel="preconnect" href="https://fonts.gstatic.com">
<link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Mulish:ital,wght@0,400;0,600;1,400;1,600">
<script src="js/jquery-3.5.1.min.js"></script>
<script src="js/jquery-3.7.1.min.js"></script>
<script src="js/svg4everybody-2.1.9.min.js"></script>
<script>svg4everybody();</script>
</head>
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2 changes: 1 addition & 1 deletion MassBank-Project/MassBank-web/src/main/webapp/Index.jsp
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Expand Up @@ -35,7 +35,7 @@
<link rel="stylesheet" type="text/css" href="css/massbank.css">
<link rel="preconnect" href="https://fonts.gstatic.com">
<link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Mulish:ital,wght@0,400;0,600;1,400;1,600">
<script src="js/jquery-3.5.1.min.js"></script>
<script src="js/jquery-3.7.1.min.js"></script>
<script src="js/svg4everybody-2.1.9.min.js"></script>
<script src="js/iframeResizer.min.js"></script>
<script>svg4everybody();</script>
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@
<link rel="stylesheet" type="text/css" href="css/massbank.css">
<link rel="preconnect" href="https://fonts.gstatic.com">
<link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Mulish:ital,wght@0,400;0,600;1,400;1,600">
<script src="js/jquery-3.5.1.min.js"></script>
<script src="js/jquery-3.7.1.min.js"></script>
<script src="js/iframeResizer.min.js"></script>
<script src="js/svg4everybody-2.1.9.min.js"></script>
<script>svg4everybody();</script>
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