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Update NIHMS XML metadata to match latest version #66

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merged 4 commits into from
Nov 6, 2023
Merged

Update NIHMS XML metadata to match latest version #66

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f77cae0
Update NIHMS bulk submission dtd to latest version
markpatton Oct 20, 2023
49f3e63
Update NIHMS metadata serialization to latest version
markpatton Oct 20, 2023
3e42ddc
Handle embargo correctly in NIHMS XML. Also make some minor cleanups …
markpatton Nov 2, 2023
ce51c40
Update the file name for the NIHMS package to indicate the latest bul…
markpatton Nov 2, 2023
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17 changes: 3 additions & 14 deletions ...es/deposit-core/src/main/java/org/eclipse/pass/deposit/provider/nihms/NihmsAssembler.java
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Expand Up @@ -18,12 +18,10 @@

import static org.eclipse.pass.deposit.assembler.AssemblerSupport.buildMetadata;

import java.net.URI;
import java.time.ZonedDateTime;
import java.time.format.DateTimeFormatter;
import java.util.List;
import java.util.Map;
import java.util.UUID;

import org.eclipse.pass.deposit.assembler.AbstractAssembler;
import org.eclipse.pass.deposit.assembler.ArchivingPackageStream;
Expand All @@ -45,7 +43,7 @@ public class NihmsAssembler extends AbstractAssembler {
* Package specification URI identifying the NIHMS native packaging spec, as specified by their 07/2017
* bulk publishing pdf.
*/
public static final String SPEC_NIHMS_NATIVE_2017_07 = "nihms-native-2017-07";
public static final String SPEC_NIHMS_NATIVE_2022_05 = "nihms-native-2022-05";

/**
* Mime type of zip files.
Expand Down Expand Up @@ -81,20 +79,11 @@ protected PackageStream createPackageStream(DepositSubmission submission,
}

static void namePackage(DepositSubmission submission, MetadataBuilder mb) {
String submissionUuid = null;

try {
URI submissionUri = URI.create(submission.getId());
submissionUuid = submissionUri.getPath().substring(submissionUri.getPath().lastIndexOf("/") + 1);
} catch (Exception e) {
submissionUuid = UUID.randomUUID().toString();
}

String packageFileName = String.format(PACKAGE_FILE_NAME,
SPEC_NIHMS_NATIVE_2017_07,
SPEC_NIHMS_NATIVE_2022_05,
ZonedDateTime.now()
.format(DateTimeFormatter.ofPattern("uuuu-MM-dd_HH-MM-ss")),
submissionUuid);
submission.getId());

StringBuilder ext = new StringBuilder(packageFileName);
PackageStream.Metadata md = mb.build();
Expand Down
297 changes: 148 additions & 149 deletions ...t-core/src/main/java/org/eclipse/pass/deposit/provider/nihms/NihmsMetadataSerializer.java
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21 changes: 10 additions & 11 deletions .../deposit-core/src/test/java/org/eclipse/pass/deposit/provider/nihms/NihmsAssemblerIT.java
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Expand Up @@ -16,7 +16,7 @@
package org.eclipse.pass.deposit.provider.nihms;

import static org.eclipse.pass.deposit.provider.nihms.NihmsAssembler.APPLICATION_GZIP;
import static org.eclipse.pass.deposit.provider.nihms.NihmsAssembler.SPEC_NIHMS_NATIVE_2017_07;
import static org.eclipse.pass.deposit.provider.nihms.NihmsAssembler.SPEC_NIHMS_NATIVE_2022_05;
import static org.eclipse.pass.deposit.util.DepositTestUtil.asList;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
Expand Down Expand Up @@ -78,7 +78,7 @@ public void setUp() throws Exception {
protected Map<String, Object> getOptions() {
return new HashMap<>() {
{
put(Spec.KEY, SPEC_NIHMS_NATIVE_2017_07);
put(Spec.KEY, SPEC_NIHMS_NATIVE_2022_05);
put(Archive.KEY, Archive.OPTS.TAR);
put(Compression.KEY, Compression.OPTS.GZIP);
}
Expand All @@ -101,7 +101,7 @@ protected void verifyStreamMetadata(PackageStream.Metadata metadata) {
assertEquals(Compression.OPTS.GZIP, metadata.compression());
assertEquals(Archive.OPTS.TAR, metadata.archive());
assertTrue(metadata.archived());
assertEquals(SPEC_NIHMS_NATIVE_2017_07, metadata.spec());
assertEquals(SPEC_NIHMS_NATIVE_2022_05, metadata.spec());
assertEquals(APPLICATION_GZIP, metadata.mimeType());
}

Expand Down Expand Up @@ -205,10 +205,10 @@ public void testPackageMetadata() throws Exception {

// root element is <nihms-submit>
Element root = metaDom.getDocumentElement();
assertEquals("nihms-submit", root.getTagName());
assertEquals("manuscript-submit", root.getTagName());

// required <title> element is present with the manuscript title as the value
Element title = asList(root.getElementsByTagName("title")).get(0);
// required <manuscript-title> element is present with the manuscript title as the value
Element title = asList(root.getElementsByTagName("manuscript-title")).get(0);
assertEquals(submission.getMetadata().getManuscriptMetadata().getTitle(), title.getTextContent());

// Insure that only one <person> element is present in the submission metadata
Expand Down Expand Up @@ -242,8 +242,7 @@ public void testPackageMetadata() throws Exception {
});

// Assert that the DOI is present in the metadata
Element ms = asList(root.getElementsByTagName("manuscript")).get(0);
assertEquals(submission.getMetadata().getArticleMetadata().getDoi().toString(), ms.getAttribute("doi"));
assertEquals(submission.getMetadata().getArticleMetadata().getDoi().toString(), root.getAttribute("doi"));

// Assert that the ISSNs are present in the metadata as the <issn> element
List<Element> issns = asList(root.getElementsByTagName("issn"));
Expand All @@ -255,10 +254,10 @@ public void testPackageMetadata() throws Exception {
issns.forEach(issn -> assertTrue(issnPubTypes.containsKey(issn.getTextContent())));
issns.forEach(issn -> {
DepositMetadata.IssnPubType pubType = issnPubTypes.get(issn.getTextContent());
if (pubType.pubType == JournalPublicationType.OPUB) {
assertEquals(issn.getAttribute("pub-type"), JournalPublicationType.EPUB.name().toLowerCase());
if (pubType.pubType == JournalPublicationType.OPUB || pubType.pubType == JournalPublicationType.EPUB) {
assertEquals(issn.getAttribute("issn-type"), "electronic");
} else {
assertEquals(issn.getAttribute("pub-type"), pubType.pubType.name().toLowerCase());
assertEquals(issn.getAttribute("issn-type"), "print");
}
});

Expand Down
2 changes: 1 addition & 1 deletion ...eposit-core/src/test/java/org/eclipse/pass/deposit/provider/nihms/NihmsAssemblerTest.java
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Expand Up @@ -55,7 +55,7 @@ public void setUp() throws Exception {
mdBuilder = mock(MetadataBuilder.class);

String expectedSubmissionUuid = UUID.randomUUID().toString();
when(submission.getId()).thenReturn("http://example.org/" + expectedSubmissionUuid);
when(submission.getId()).thenReturn(expectedSubmissionUuid);

when(mdBuilder.build()).thenReturn(metadata);

Expand Down
28 changes: 19 additions & 9 deletions ...re/src/test/java/org/eclipse/pass/deposit/provider/nihms/NihmsMetadataSerializerTest.java
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Expand Up @@ -31,6 +31,7 @@
import java.net.URI;
import java.net.URL;
import java.nio.file.Path;
import java.time.ZonedDateTime;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
Expand All @@ -42,6 +43,7 @@
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.stream.StreamSource;

import com.github.jknack.handlebars.internal.Files;
import org.apache.commons.io.IOUtils;
import org.eclipse.pass.deposit.assembler.SizedStream;
import org.eclipse.pass.deposit.model.DepositMetadata;
Expand Down Expand Up @@ -101,6 +103,7 @@ public void setup() throws Exception {

// populate article metadata
article.setDoi(URI.create("10.1234/smh0000001"));
article.setEmbargoLiftDate(ZonedDateTime.now().plusYears(100));

//populate persons
DepositMetadata.Person person1 = new DepositMetadata.Person();
Expand All @@ -113,8 +116,8 @@ public void setup() throws Exception {

// Enter the first person twice, as both an author and a PI
DepositMetadata.Person person1a = new DepositMetadata.Person(person1);
person1.setType(DepositMetadata.PERSON_TYPE.pi);
personList.add(person1);
person1a.setType(DepositMetadata.PERSON_TYPE.pi);
personList.add(person1a);

DepositMetadata.Person person2 = new DepositMetadata.Person();
person2.setType(DepositMetadata.PERSON_TYPE.submitter);
Expand Down Expand Up @@ -160,7 +163,7 @@ public void testSerializedMetadataValidity() throws Exception {
OutputStream os = new FileOutputStream(targetFile);

os.write("<?xml version=\"1.0\" encoding=\"utf-8\"?>\n".getBytes());
os.write("<!DOCTYPE nihms-submit SYSTEM \"bulksubmission.dtd\">\n".getBytes());
os.write("<!DOCTYPE manuscript-submit SYSTEM \"bulksubmission.dtd\">\n".getBytes());
os.write(buffer);
os.close();

Expand All @@ -170,6 +173,15 @@ public void testSerializedMetadataValidity() throws Exception {
v.setSchemaSource(dtd);
StreamSource s = new StreamSource(targetFile);
ValidationResult r = v.validateInstance(s);

if (!r.isValid()) {
System.err.println(Files.read(targetFile, UTF_8));

r.getProblems().forEach(p -> {
System.err.println(p);
});
}

assertTrue(r.isValid());
}

Expand All @@ -186,15 +198,15 @@ public void testSerializedMetadataDoi() throws Exception {
metadata.getArticleMetadata().setDoi(URI.create(path));
sizedStream = underTest.serialize();
is = sizedStream.getInputStream();
node = builder.parse(is).getDocumentElement().getFirstChild().getNextSibling();
node = builder.parse(is).getDocumentElement();
doi = node.getAttributes().getNamedItem("doi").getTextContent();
is.close();
assertTrue(doi.contentEquals(path));

metadata.getArticleMetadata().setDoi(URI.create("http://dx.doi.org/" + path));
sizedStream = underTest.serialize();
is = sizedStream.getInputStream();
node = builder.parse(is).getDocumentElement().getFirstChild().getNextSibling();
node = builder.parse(is).getDocumentElement();
doi = node.getAttributes().getNamedItem("doi").getTextContent();
is.close();
assertTrue(doi.contentEquals(path));
Expand All @@ -208,9 +220,7 @@ public void completeIssnPubtype() throws IOException, ParserConfigurationExcepti
DepositMetadata metadata = new DepositMetadata();
DepositMetadata.Journal journalMd = new DepositMetadata.Journal();
String expectedIssn = "foo";
String expectedPubType = JournalPublicationType.EPUB.name()
.toLowerCase(); // remember OPUB is mapped to EPUB when
// serializing
String expectedPubType = "electronic";

DepositMetadata.IssnPubType issn = new DepositMetadata.IssnPubType(expectedIssn, JournalPublicationType.OPUB);
journalMd.setIssnPubTypes(new HashMap<>() {
Expand All @@ -236,7 +246,7 @@ public void completeIssnPubtype() throws IOException, ParserConfigurationExcepti
new RuntimeException(
"Missing expected <issn> element for " + expectedIssn + " and " + expectedPubType));

assertEquals(expectedPubType, actualIssn.getAttributes().getNamedItem("pub-type").getNodeValue());
assertEquals(expectedPubType, actualIssn.getAttributes().getNamedItem("issn-type").getNodeValue());
}

/**
Expand Down
4 changes: 2 additions & 2 deletions ...t-core/src/test/java/org/eclipse/pass/deposit/provider/nihms/NihmsThreadedAssemblyIT.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
package org.eclipse.pass.deposit.provider.nihms;

import static java.util.Collections.singletonList;
import static org.eclipse.pass.deposit.provider.nihms.NihmsAssembler.SPEC_NIHMS_NATIVE_2017_07;
import static org.eclipse.pass.deposit.provider.nihms.NihmsAssembler.SPEC_NIHMS_NATIVE_2022_05;

import java.util.HashMap;
import java.util.Map;
Expand All @@ -41,7 +41,7 @@ protected AbstractAssembler assemblerUnderTest() {
protected Map<String, Object> packageOptions() {
return new HashMap<>() {
{
put(PackageOptions.Spec.KEY, SPEC_NIHMS_NATIVE_2017_07);
put(PackageOptions.Spec.KEY, SPEC_NIHMS_NATIVE_2022_05);
put(PackageOptions.Archive.KEY, PackageOptions.Archive.OPTS.TAR);
put(PackageOptions.Compression.KEY, PackageOptions.Compression.OPTS.GZIP);
put(PackageOptions.Checksum.KEY, singletonList(PackageOptions.Checksum.OPTS.SHA256));
Expand Down
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