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Switch publication date in deposit metadata to be an actual date and …
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…not a string
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@markpatton
markpatton committed Nov 26, 2024
1 parent d4a366b commit ee7134d
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Showing 7 changed files with 42 additions and 39 deletions.
32 changes: 21 additions & 11 deletions .../deposit-core/src/main/java/org/eclipse/pass/deposit/builder/DepositSubmissionMapper.java
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Expand Up @@ -20,10 +20,10 @@

import java.net.URI;
import java.time.LocalDate;
import java.time.LocalDateTime;
import java.time.ZoneId;
import java.time.ZonedDateTime;
import java.time.format.DateTimeFormatter;
import java.time.format.DateTimeParseException;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
Expand Down Expand Up @@ -73,8 +73,8 @@ public class DepositSubmissionMapper {
private static final String AUTHORS_KEY = "authors";
private static final String AUTHOR_KEY = "author";
private static final String PUB_TYPE_KEY = "pubType";
private static final String EMBARGO_END_DATE_PATTERN = "yyyy-MM-dd";
private static final String NLMTA_KEY = "journal-NLMTA-ID";
private static final String DEFAULT_DATE_TIME_ZONE = "America/New_York";

/**
* Creates a DepositSubmission by walking the tree of PassEntity objects, starting with the Submission entity,
Expand Down Expand Up @@ -267,7 +267,7 @@ private void processCommonMetadata(DepositMetadata metadata, JsonObject submissi
.ifPresent(pName -> metadata.getJournalMetadata().setPublisherName(pName));

getStringProperty(submissionData, PUBLICATION_DATE_KEY)
.ifPresent(pName -> metadata.getJournalMetadata().setPublicationDate(pName));
.ifPresent(date -> metadata.getJournalMetadata().setPublicationDate(parseDate(date)));

getArrayProperty(submissionData, ISSNS).ifPresent(issns -> {
issns.forEach(issnObjAsStr -> {
Expand All @@ -290,19 +290,29 @@ private void processCommonMetadata(DepositMetadata metadata, JsonObject submissi

getStringProperty(submissionData, EMBARGO_END_DATE_KEY).ifPresent(endDate -> {
try {
// TODO - Resolve inconsistent date/date-time formats in metadata and deposit data model
// TODO - Fix assumption of local timezone
DateTimeFormatter formatter = DateTimeFormatter.ofPattern(EMBARGO_END_DATE_PATTERN);
LocalDateTime localEndDate = LocalDate.parse(endDate, formatter).atStartOfDay();
ZonedDateTime zonedEndDate = localEndDate.atZone(ZoneId.of("America/New_York"));
metadata.getArticleMetadata().setEmbargoLiftDate(zonedEndDate);
} catch (Exception e) {
metadata.getArticleMetadata().setEmbargoLiftDate(parseDate(endDate));
} catch (DateTimeParseException e) {
throw new DepositServiceRuntimeException(
String.format("Data file contained an invalid Date: '%s'.", endDate), e);
String.format("Data file contained an invalid Date: '%s'.", endDate), e);
}
});
}

// Parse an ISO 8601 date with or without a time zone
public ZonedDateTime parseDate(String date) {
try {
return ZonedDateTime.parse(date, DateTimeFormatter.ISO_DATE);
} catch (DateTimeParseException e) {
try {
return LocalDate.parse(date, DateTimeFormatter.ISO_LOCAL_DATE).atStartOfDay()
.atZone(ZoneId.of(DEFAULT_DATE_TIME_ZONE));
} catch (DateTimeParseException e2) {
throw new DepositServiceRuntimeException(
String.format("Metadata contained an invalid Date: '%s'.", date), e2);
}
}
}

private void processCrossrefMetadata(DepositMetadata metadata, JsonObject submissionData) {
getStringProperty(submissionData, DOI_KEY).ifPresent(doi -> {
try {
Expand Down
12 changes: 6 additions & 6 deletions ...sit-core/src/main/java/org/eclipse/pass/deposit/provider/dspace/DSpaceMetadataMapper.java
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Expand Up @@ -79,10 +79,9 @@ public String patchWorkspaceItem(DepositSubmission submission) {
metadata.add(add_array("traditionalpageone", "dc.identifier.citation", citation));
}

// TODO: Must format YYYY-MM-DD
// Required by DSpace
String publicationDate = journalMd.getPublicationDate();
metadata.add(add_array("traditionalpageone", "dc.date.issued", publicationDate));
// Required by DSpace as ISO 8601 local date
metadata.add(add_array("traditionalpageone", "dc.date.issued", journalMd.getPublicationDate().
format(DateTimeFormatter.ISO_LOCAL_DATE)));

// Add non-submitters as authors
// TODO This is different from before
Expand Down Expand Up @@ -171,8 +170,9 @@ private String createCitation(DepositSubmission submission) {

// Attach a <dc:identifier:citation> if not empty
// publication date - after a single space, in parens, followed by "."
if (journalMd != null && journalMd.getPublicationDate() != null && !journalMd.getPublicationDate().isEmpty()) {
citationBldr.append(" (" + journalMd.getPublicationDate() + ").");
if (journalMd != null && journalMd.getPublicationDate() != null) {
citationBldr.append(" (" + journalMd.getPublicationDate().
format(DateTimeFormatter.ISO_LOCAL_DATE) + ").");
}
// article title - after single space, in double quotes with "." inside
if (articleMd != null && articleMd.getTitle() != null && !articleMd.getTitle().isEmpty()) {
Expand Down
6 changes: 4 additions & 2 deletions .../src/main/java/org/eclipse/pass/deposit/provider/inveniordm/InvenioRdmMetadataMapper.java
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Expand Up @@ -15,6 +15,7 @@
*/
package org.eclipse.pass.deposit.provider.inveniordm;

import java.time.format.DateTimeFormatter;
import java.util.Objects;

import net.minidev.json.JSONArray;
Expand Down Expand Up @@ -49,8 +50,9 @@ public JSONObject toInvenioMetadata(DepositSubmission depositSubmission) {
invenioMetadata.put("creators", creators);
String title = depositSubmission.getSubmissionMeta().get("title").getAsString();
invenioMetadata.put("title", title);
String publicationDate = depositMetadata.getJournalMetadata().getPublicationDate();
invenioMetadata.put("publication_date", publicationDate);

invenioMetadata.put("publication_date", depositMetadata.getJournalMetadata().
getPublicationDate().format(DateTimeFormatter.ISO_LOCAL_DATE));
JSONObject resourceType = new JSONObject();
resourceType.put("id", "publication-article");
invenioMetadata.put("resource_type", resourceType);
Expand Down
4 changes: 2 additions & 2 deletions ...it-core/src/main/java/org/eclipse/pass/deposit/provider/j10p/DspaceMetadataDomWriter.java
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Expand Up @@ -469,8 +469,8 @@ Element createDublinCoreMetadataDCMES(DepositSubmission submission) {

// Attach a <dc:identifier:citation> if not empty
// publication date - after a single space, in parens, followed by "."
if (journalMd != null && journalMd.getPublicationDate() != null && !journalMd.getPublicationDate().isEmpty()) {
citationBldr.append(" (" + journalMd.getPublicationDate() + ").");
if (journalMd != null && journalMd.getPublicationDate() != null) {
citationBldr.append(" (" + journalMd.getPublicationDate().format(DateTimeFormatter.ISO_LOCAL_DATE) + ").");
}
// article title - after single space, in double quotes with "." inside
if (articleMd != null && articleMd.getTitle() != null && !articleMd.getTitle().isEmpty()) {
Expand Down
13 changes: 2 additions & 11 deletions ...ore/src/test/java/org/eclipse/pass/deposit/provider/j10p/DspaceMetadataDomWriterTest.java
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Expand Up @@ -104,8 +104,6 @@
import org.junit.jupiter.api.io.TempDir;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.core.io.ClassPathResource;
import org.springframework.core.io.Resource;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NodeList;
Expand All @@ -120,10 +118,6 @@ public class DspaceMetadataDomWriterTest {
@TempDir
private Path tempDir;

private List<Resource> custodialContent = Arrays.asList(
new ClassPathResource(this.getClass().getPackage().getName().replace(".", "/") + "/manuscript.txt"),
new ClassPathResource(this.getClass().getPackage().getName().replace(".", "/") + "/figure.jpg"));

private final DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();

private DspaceMetadataDomWriter underTest;
Expand Down Expand Up @@ -229,7 +223,7 @@ public void writeSampleMets() throws Exception {
when(journal.getJournalTitle()).thenReturn("American Journal of XYZ Research");
when(journal.getJournalId()).thenReturn("Am J of XYZ Res");
when(journal.getPublisherName()).thenReturn("Super Publisher");
when(journal.getPublicationDate()).thenReturn("2018-09-12");
when(journal.getPublicationDate()).thenReturn(ZonedDateTime.now());

underTest.addResource(r);
underTest.addSubmission(submission);
Expand Down Expand Up @@ -296,8 +290,6 @@ public void testAddResource() throws Exception {
String type = "text/plain";
String checksumMd5Val = "abcdef12345";
String checksumMd5 = Checksum.OPTS.MD5.name();
String checksumShaVal = "123456abcdef";
String checksumSha = Checksum.OPTS.SHA256.name();

PackageStream.Checksum checksum = mock(PackageStream.Checksum.class);
when(checksum.algorithm()).thenReturn(Checksum.OPTS.MD5);
Expand Down Expand Up @@ -448,8 +440,7 @@ public void testCreateDublinCoreMetadata() throws Exception {
DepositMetadata.Journal jMd = mock(DepositMetadata.Journal.class);
String publisherName = "Big Publisher";
when(jMd.getPublisherName()).thenReturn(publisherName);
String publicationDate = "1/9/1919";
when(jMd.getPublicationDate()).thenReturn(publicationDate);
when(jMd.getPublicationDate()).thenReturn(ZonedDateTime.now());

DepositMetadata md = mock(DepositMetadata.class);
when(md.getArticleMetadata()).thenReturn(artMd);
Expand Down
8 changes: 4 additions & 4 deletions ...ervices/deposit-core/src/test/java/org/eclipse/pass/deposit/provider/j10p/MetadataIT.java
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Expand Up @@ -51,7 +51,7 @@ public class MetadataIT extends AbstractDepositSubmissionIT {
" },\n {\n \"author\": \"Mary Beth Lacey\"\n }\n ],\n \"agreements\": {\n " +
"\"JScholarship\": \"Text removed.\"\n },\n \"title\": \"My Test Article\",\n \"journal-title\": " +
"\"Nature Communications\",\n \"issns\": [\n {\n \"issn\": \"2041-1723\",\n \"pubType\": " +
"\"Print\"\n }\n ],\n \"publisher\": \"Elsevier\",\n \"publicationDate\": \"Fall 2016\",\n " +
"\"Print\"\n }\n ],\n \"publisher\": \"Elsevier\",\n \"publicationDate\": \"2001-03-05\",\n " +
"\"abstract\": \"Abstract text\",\n \"journal-NLMTA-ID\": \"Nat Commun\",\n \"agent_information\": " +
"{\n \"name\": \"Chrome\",\n \"version\": \"69\"\n }\n}";

Expand All @@ -61,7 +61,7 @@ public class MetadataIT extends AbstractDepositSubmissionIT {
"\"JScholarship\": \"Text removed.\"\n },\n \"title\": \"My Test Article\",\n \"journal-title\": " +
"\"Nature Communications\",\n \"issns\": [\n {\n \"issn\": \"2041-1723\",\n " +
"\"pubType\": \"Print\"\n }\n ],\n \"publisher\": \"Elsevier\",\n \"publicationDate\": " +
"\"Fall 2016\",\n \"abstract\": \"Abstract text\",\n \"journal-NLMTA-ID\": \"Nat Commun\",\n " +
"\"2020-05-06\",\n \"abstract\": \"Abstract text\",\n \"journal-NLMTA-ID\": \"Nat Commun\",\n " +
"\"agent_information\": {\n \"name\": \"Chrome\",\n \"version\": \"69\"\n }\n}";

@Autowired private SubmissionTestUtil submissionTestUtil;
Expand Down Expand Up @@ -96,7 +96,7 @@ public void commonContributorsAndFewAuthors() throws Exception {

// In citation, list up to three authors. Take publication date from "common" if not in "crossref".
assertNotNull(qdc.getElementsByTagNameNS(DCTERMS_NS, DCT_BIBLIOCITATION).item(0).getTextContent());
assertEquals("Christine Cagney, Mary Beth Lacey. (Fall 2016). \"My Test Article.\" Nature Communications.",
assertEquals("Christine Cagney, Mary Beth Lacey. (2001-03-05). \"My Test Article.\" Nature Communications.",
qdc.getElementsByTagNameNS(DCTERMS_NS, DCT_BIBLIOCITATION).item(0).getTextContent());
}

Expand All @@ -116,7 +116,7 @@ public void crossrefAndManyAuthors() throws Exception {
// Publication date in "crossref" has precedence over one in "common".
assertNotNull(qdc.getElementsByTagNameNS(DCTERMS_NS, DCT_BIBLIOCITATION).item(0).getTextContent());
assertEquals(
"Christine Cagney, Mary Beth Lacey, David Michael Starsky, et al. (Fall 2016). \"My Test Article.\" " +
"Christine Cagney, Mary Beth Lacey, David Michael Starsky, et al. (2020-05-06). \"My Test Article.\" " +
"Nature Communications.",
qdc.getElementsByTagNameNS(DCTERMS_NS, DCT_BIBLIOCITATION).item(0).getTextContent());
}
Expand Down
6 changes: 3 additions & 3 deletions ...-services/deposit-model/src/main/java/org/eclipse/pass/deposit/model/DepositMetadata.java
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Original file line number Diff line number Diff line change
Expand Up @@ -237,7 +237,7 @@ public static class Journal {
/**
* Date of publication
*/
public String publicationDate;
public ZonedDateTime publicationDate;

/**
* ISSN mapped to journal publication type
Expand Down Expand Up @@ -302,14 +302,14 @@ public void setPublisherName(String publisherName) {
/**
* @return {@link #publicationDate}
*/
public String getPublicationDate() {
public ZonedDateTime getPublicationDate() {
return publicationDate;
}

/**
* @param publicationDate {@link #publicationDate}
*/
public void setPublicationDate(String publicationDate) {
public void setPublicationDate(ZonedDateTime publicationDate) {
this.publicationDate = publicationDate;
}

Expand Down

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