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Added the MedlineImporterTest and a testfile
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@mairdl
mairdl committed Dec 21, 2015
1 parent fc13a86 commit 7e61cc6
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89 changes: 89 additions & 0 deletions src/test/java/net/sf/jabref/importer/fileformat/MedlineImporterTest.java
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package net.sf.jabref.importer.fileformat;

import static org.junit.Assert.*;

import java.io.IOException;
import java.io.InputStream;
import java.util.Arrays;
import java.util.List;
import net.sf.jabref.Globals;
import net.sf.jabref.JabRefPreferences;
import net.sf.jabref.importer.OutputPrinterToNull;
import net.sf.jabref.model.entry.BibEntry;


import org.junit.Before;
import org.junit.Test;
import org.junit.Assert;

/**
* @author Daniel Mair/Bruehl
*
*/
public class MedlineImporterTest {

MedlineImporter medlineImporter;

@Before
public void setUp() throws Exception {
Globals.prefs = JabRefPreferences.getInstance();
this.medlineImporter = new MedlineImporter();
}

@Test
public void testIsRecognizedFormatAccept() throws Throwable {
List<String> list = Arrays.asList("MedlineImporterTest.xml");
for (String str : list) {
try (InputStream is = MedlineImporterTest.class.getResourceAsStream(str);) {
Assert.assertTrue(medlineImporter.isRecognizedFormat(is));
}
}
}

@Test
public void testIsRecognizedFormatReject() throws Throwable {
List<String> list = Arrays.asList("CopacImporterTest1.txt", "CopacImporterTest2.txt",
"IEEEImport1.txt", "IsiImporterTestWOS.isi");
for (String str : list) {
try (InputStream is = MedlineImporterTest.class.getResourceAsStream(str);) {
Assert.assertFalse(medlineImporter.isRecognizedFormat(is));
}
}
}

@Test
public void testImportEntries() throws IOException {
try (InputStream is = MedlineImporter.class.getResourceAsStream("MedlineImporterTest.xml")) {
List<BibEntry> entries = medlineImporter.importEntries(is, new OutputPrinterToNull());
Assert.assertEquals(1, entries.size());
}
}

@Test
public void testImportEntries2() throws IOException {
try (InputStream is = MedlineImporter.class.getResourceAsStream("CopacImporterTest1.txt")) {
// Trigger a catchblock
List<BibEntry> entries = medlineImporter.importEntries(is, new OutputPrinterToNull());
//Assert.fail("Error during XML parsing");
}
}

@Test
public void testGetFormatName() {
assertEquals("testGetFormatName failed", "Medline", medlineImporter.getFormatName());
}

@Test
public void testGetCLIId() {
assertEquals("testGetCLIID failed", "medline", medlineImporter.getCLIId());
}

@Test
public void testFetchMedline() {
List<BibEntry> validMedLine = medlineImporter.fetchMedline("1", new OutputPrinterToNull());
List<BibEntry> emptyMedLine = medlineImporter.fetchMedline("zzzzzz", new OutputPrinterToNull());
assertNotNull(validMedLine);
assertEquals(0, emptyMedLine.size());
}

}
167 changes: 167 additions & 0 deletions src/test/resources/net/sf/jabref/importer/fileformat/MedlineImporterTest.xml
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<PubmedArticleSet>
<PubmedArticle>
<MedlineCitation Owner="NLM" Status="MEDLINE">
<PMID Version="1">1</PMID>
<DateCreated>
<Year>1976</Year>
<Month>01</Month>
<Day>16</Day>
</DateCreated>
<DateCompleted>
<Year>1976</Year>
<Month>01</Month>
<Day>16</Day>
</DateCompleted>
<DateRevised>
<Year>2013</Year>
<Month>11</Month>
<Day>21</Day>
</DateRevised>
<Article PubModel="Print">
<Journal>
<ISSN IssnType="Print">0006-2944</ISSN>
<JournalIssue CitedMedium="Print">
<Volume>13</Volume>
<Issue>2</Issue>
<PubDate>
<Year>1975</Year>
<Month>Jun</Month>
</PubDate>
</JournalIssue>
<Title>Biochemical medicine</Title>
<ISOAbbreviation>Biochem Med</ISOAbbreviation>
</Journal>
<ArticleTitle>
Formate assay in body fluids: application in methanol poisoning.
</ArticleTitle>
<Pagination>
<MedlinePgn>117-26</MedlinePgn>
</Pagination>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Makar</LastName>
<ForeName>A B</ForeName>
<Initials>AB</Initials>
</Author>
<Author ValidYN="Y">
<LastName>McMartin</LastName>
<ForeName>K E</ForeName>
<Initials>KE</Initials>
</Author>
<Author ValidYN="Y">
<LastName>Palese</LastName>
<ForeName>M</ForeName>
<Initials>M</Initials>
</Author>
<Author ValidYN="Y">
<LastName>Tephly</LastName>
<ForeName>T R</ForeName>
<Initials>TR</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList>
<PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013487">Research Support, U.S. Gov't, P.H.S.</PublicationType>
</PublicationTypeList>
</Article>
<MedlineJournalInfo>
<Country>UNITED STATES</Country>
<MedlineTA>Biochem Med</MedlineTA>
<NlmUniqueID>0151424</NlmUniqueID>
<ISSNLinking>0006-2944</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D005561">Formates</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>142M471B3J</RegistryNumber>
<NameOfSubstance UI="D002245">Carbon Dioxide</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>EC 1.2.-</RegistryNumber>
<NameOfSubstance UI="D000445">Aldehyde Oxidoreductases</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>Y4S76JWI15</RegistryNumber>
<NameOfSubstance UI="D000432">Methanol</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList>
<MeshHeading>
<DescriptorName MajorTopicYN="N" UI="D000445">Aldehyde Oxidoreductases</DescriptorName>
<QualifierName MajorTopicYN="N" UI="Q000378">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N" UI="D000818">Animals</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N" UI="D001826">Body Fluids</DescriptorName>
<QualifierName MajorTopicYN="Y" UI="Q000032">analysis</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N" UI="D002245">Carbon Dioxide</DescriptorName>
<QualifierName MajorTopicYN="N" UI="Q000097">blood</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N" UI="D005561">Formates</DescriptorName>
<QualifierName MajorTopicYN="N" UI="Q000097">blood</QualifierName>
<QualifierName MajorTopicYN="Y" UI="Q000506">poisoning</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N" UI="D000882">Haplorhini</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N" UI="D006801">Humans</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N" UI="D006863">Hydrogen-Ion Concentration</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N" UI="D007700">Kinetics</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N" UI="D000432">Methanol</DescriptorName>
<QualifierName MajorTopicYN="N" UI="Q000097">blood</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N" UI="D008722">Methods</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N" UI="D011549">Pseudomonas</DescriptorName>
<QualifierName MajorTopicYN="N" UI="Q000201">enzymology</QualifierName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData>
<History>
<PubMedPubDate PubStatus="pubmed">
<Year>1975</Year>
<Month>6</Month>
<Day>1</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline">
<Year>1975</Year>
<Month>6</Month>
<Day>1</Day>
<Hour>0</Hour>
<Minute>1</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez">
<Year>1975</Year>
<Month>6</Month>
<Day>1</Day>
<Hour>0</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList>
<ArticleId IdType="pubmed">1</ArticleId>
</ArticleIdList>
</PubmedData>
</PubmedArticle>
</PubmedArticleSet>

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