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Merge branch 'main' into russ-856-email-intgr
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@rpoet-jh
rpoet-jh committed Jan 16, 2024
2 parents 3e53ca3 + 0c6a2e7 commit 3b65699
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Showing 15 changed files with 526 additions and 59 deletions.
7 changes: 7 additions & 0 deletions ...rvices/assembler-api/src/main/java/org/eclipse/pass/deposit/assembler/PackageOptions.java
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Expand Up @@ -98,4 +98,11 @@ enum OPTS {

}

/**
* Funder Mapping for Nihms Packages
*/
interface FunderMapping {
String KEY = "FUNDER-MAPPING";
}

}
12 changes: 12 additions & 0 deletions .../deposit-core/src/main/java/org/eclipse/pass/deposit/builder/DepositSubmissionMapper.java
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Expand Up @@ -100,6 +100,8 @@ public DepositSubmission createDepositSubmission(Submission submissionEntity, Li
metadata.setJournalMetadata(journal);
ArrayList<DepositMetadata.Person> persons = new ArrayList<>();
metadata.setPersons(persons);
ArrayList<DepositMetadata.Grant> grants = new ArrayList<>();
metadata.setGrantsMetadata(grants);

// Data from the Submission resource
submission.setId(submissionEntity.getId());
Expand Down Expand Up @@ -129,6 +131,7 @@ public DepositSubmission createDepositSubmission(Submission submissionEntity, Li
// Data from the User resources for the PI and CoPIs
User piEntity = grantEntity.getPi();
persons.add(createPerson(piEntity, DepositMetadata.PERSON_TYPE.pi));
grants.add(createGrant(piEntity, grantEntity));

for (User copiEntity : grantEntity.getCoPis()) {
persons.add(createPerson(copiEntity, DepositMetadata.PERSON_TYPE.copi));
Expand Down Expand Up @@ -188,6 +191,15 @@ private DepositMetadata.Person createAuthor(String fullName) {
return person;
}

private DepositMetadata.Grant createGrant(User userEntity, Grant grantEntity) {
DepositMetadata.Grant grant = new DepositMetadata.Grant();
grant.setGrantId(grantEntity.getAwardNumber());
grant.setGrantPi(createPerson(userEntity, DepositMetadata.PERSON_TYPE.pi));
grant.setFunder(grantEntity.getPrimaryFunder().getName());
grant.setFunderLocalKey(grantEntity.getPrimaryFunder().getLocalKey());
return grant;
}

/**
* Convenience method for retrieving a string property.
*
Expand Down
2 changes: 1 addition & 1 deletion ...ore/src/main/java/org/eclipse/pass/deposit/config/repository/RepositoryDepositConfig.java
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Expand Up @@ -72,6 +72,6 @@ public int hashCode() {
@Override
public String toString() {
return "RepositoryDepositConfig{" + "depositProcessing=" + depositProcessing +
", statusMapping=" + statusMapping + '}';
", statusMapping=" + statusMapping + "}";
}
}
117 changes: 99 additions & 18 deletions ...t-core/src/main/java/org/eclipse/pass/deposit/provider/nihms/NihmsMetadataSerializer.java
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Expand Up @@ -21,6 +21,8 @@
import java.time.Period;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.OutputKeys;
Expand All @@ -30,6 +32,8 @@
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;

import org.apache.commons.lang3.StringUtils;
import org.eclipse.pass.deposit.assembler.PackageOptions;
import org.eclipse.pass.deposit.assembler.SizedStream;
import org.eclipse.pass.deposit.model.DepositMetadata;
import org.eclipse.pass.deposit.model.JournalPublicationType;
Expand All @@ -48,9 +52,19 @@ public class NihmsMetadataSerializer implements StreamingSerializer {
private static final Logger LOG = LoggerFactory.getLogger(NihmsMetadataSerializer.class);

private DepositMetadata metadata;
private Map<String, String> funderMapping;

public NihmsMetadataSerializer(DepositMetadata metadata) {
public NihmsMetadataSerializer(DepositMetadata metadata, Map<String, Object> packageOptions) {
this.metadata = metadata;
Object funderMappingObj = packageOptions.get(PackageOptions.FunderMapping.KEY);
if (funderMappingObj instanceof Map<?, ?>) {
this.funderMapping = ((Map<?, ?>) funderMappingObj).entrySet().stream()
.collect(Collectors.toMap(
e -> (String) e.getKey(),
e -> (String) e.getValue()));
} else {
throw new ClassCastException("FunderMapping is not a Map<String, String>");
}
}

@Override
Expand Down Expand Up @@ -92,16 +106,27 @@ private void add_text_element(Document doc, Element parent, String name, String
}

private void write_metadata(Document doc) {
DepositMetadata.Manuscript manuscript = metadata.getManuscriptMetadata();
DepositMetadata.Article article = metadata.getArticleMetadata();
DepositMetadata.Journal journal = metadata.getJournalMetadata();

Element root = doc.createElement("manuscript-submit");
doc.appendChild(root);

if (manuscript.getNihmsId() != null) {
addManuscriptMetadata(root);
addArticleMetadata(root);
addJournalMetadata(doc, root);
addManuscriptTitle(doc, root);
addContacts(doc, root);
addGrants(doc, root);
}

private void addManuscriptMetadata(Element root) {
DepositMetadata.Manuscript manuscript = metadata.getManuscriptMetadata();

if (StringUtils.isNotBlank(manuscript.getNihmsId())) {
root.setAttribute("manuscript-id", manuscript.getNihmsId());
}
}

private void addArticleMetadata(Element root) {
DepositMetadata.Article article = metadata.getArticleMetadata();

if (article != null && metadata.getArticleMetadata().getEmbargoLiftDate() != null) {
LocalDate lift = article.getEmbargoLiftDate().toLocalDate();
Expand All @@ -128,6 +153,10 @@ private void write_metadata(Document doc) {

root.setAttribute("doi", path);
}
}

private void addJournalMetadata(Document doc, Element root) {
DepositMetadata.Journal journal = metadata.getJournalMetadata();

// There is an optional agency attribute.
// Should only be used for non-NIH funders when grant information is also given
Expand All @@ -143,7 +172,7 @@ private void write_metadata(Document doc) {
// See https://github.com/OA-PASS/metadata-schemas/pull/28 and
// https://github.com/OA-PASS/jhu-package-providers/issues/16
journal.getIssnPubTypes().values().forEach(issnPubType -> {
if (issnPubType.pubType == null || issnPubType.issn == null || issnPubType.issn.trim().isEmpty()) {
if (issnPubType.pubType == null || StringUtils.isBlank(issnPubType.issn)) {
LOG.debug("Discarding incomplete ISSN: {}", issnPubType);
return;
}
Expand All @@ -159,15 +188,21 @@ private void write_metadata(Document doc) {
add_text_element(doc, journal_meta, "journal-title", journal.getJournalTitle());
}

if (manuscript != null && manuscript.title != null) {
}

private void addManuscriptTitle(Document doc, Element root) {
DepositMetadata.Manuscript manuscript = metadata.getManuscriptMetadata();

if (manuscript != null && StringUtils.isNotBlank(manuscript.title)) {
add_text_element(doc, root, "manuscript-title", manuscript.title);
}

// Could add a citation element if we had all the information
}

private void addContacts(Document doc, Element root) {
List<DepositMetadata.Person> persons = metadata.getPersons();

if (persons != null && persons.size() > 0) {
if (persons != null && !persons.isEmpty()) {
Element contacts = doc.createElement("contacts");
root.appendChild(contacts);

Expand All @@ -177,20 +212,20 @@ private void write_metadata(Document doc) {
Element p = doc.createElement("person");
contacts.appendChild(p);

if (person.getFirstName() != null) {
if (StringUtils.isNotBlank(person.getFirstName())) {
p.setAttribute("fname", person.getFirstName());
} else {
if (person.getFullName() != null) {
if (StringUtils.isNotBlank(person.getFullName())) {
p.setAttribute("fname", person.getFullName().split("\\s")[0]);
}
}
if (person.getMiddleName() != null) {
if (StringUtils.isNotBlank(person.getMiddleName())) {
p.setAttribute("mname", person.getMiddleName());
}
if (person.getLastName() != null) {
if (StringUtils.isNotBlank(person.getLastName())) {
p.setAttribute("lname", person.getLastName());
} else {
if (person.getFullName() != null) {
if (StringUtils.isNotBlank(person.getFullName())) {
String[] split = person.getFullName().split("\\s");
if (split.length > 2) {
// middle name is present
Expand All @@ -201,16 +236,62 @@ private void write_metadata(Document doc) {
}
}
}
if (person.getEmail() != null) {
if (StringUtils.isNotBlank(person.getEmail())) {
p.setAttribute("email", person.getEmail());
}

p.setAttribute("person-type", "author");
}
}
}
}

private void addGrants(Document doc, Element root) {
List<DepositMetadata.Grant> grantsList = metadata.getGrantsMetadata();

if (grantsList != null && !grantsList.isEmpty()) {
List<String> funderKeys = grantsList.stream()
.map(DepositMetadata.Grant::getFunderLocalKey)
.toList();

//Only create the top level grant element if at least one of the keys is associated with nihms
if (funderKeys.stream().anyMatch(funderMapping::containsKey)) {

Element grantsElement = doc.createElement("grants");
root.appendChild(grantsElement);

for (DepositMetadata.Grant grant : grantsList) {
if (funderMapping.containsKey(grant.getFunderLocalKey())) {
if (StringUtils.isNotBlank(grant.getFunder())) {
Element grantElement = doc.createElement("grant");
grantsElement.appendChild(grantElement);

// Could add grant information here if it was useful.
// Can only be used for a set list of funders
if (StringUtils.isNotBlank(grant.getGrantId())) {
grantElement.setAttribute("id", grant.getGrantId());
}

//use the nihms abbreviations for funders, the accepted list is in the nihms DTD
grantElement.setAttribute("funder", funderMapping.get(grant.getFunderLocalKey()));

DepositMetadata.Person pi = grant.getGrantPi();
if (pi != null) {
Element piElement = doc.createElement("PI");
grantElement.appendChild(piElement);

if (StringUtils.isNotBlank(pi.getFirstName())) {
piElement.setAttribute("fname", pi.getFirstName());
}
if (StringUtils.isNotBlank(pi.getLastName())) {
piElement.setAttribute("lname", pi.getLastName());
}
if (StringUtils.isNotBlank(pi.getEmail())) {
piElement.setAttribute("email", pi.getEmail());
}
}
}
}
}
}
}
}
}
2 changes: 1 addition & 1 deletion ...osit-core/src/main/java/org/eclipse/pass/deposit/provider/nihms/NihmsPackageProvider.java
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Expand Up @@ -74,7 +74,7 @@ public static String getNonCollidingFilename(String fileName, DepositFileType fi
public void start(DepositSubmission submission, List<DepositFileResource> custodialResources,
Map<String, Object> packageOptions) {
manifestSerializer = new NihmsManifestSerializer(submission.getManifest());
metadataSerializer = new NihmsMetadataSerializer(submission.getMetadata());
metadataSerializer = new NihmsMetadataSerializer(submission.getMetadata(), packageOptions);
}

/**
Expand Down
1 change: 1 addition & 0 deletions ...sit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/service/DepositTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -424,6 +424,7 @@ static Function<Deposit, TransportResponse> performDeposit(DepositWorkerContext

try {
packager = dc.packager();

packageStream = packager.getAssembler().assemble(
dc.depositSubmission(), packager.getAssemblerOptions());
packagerConfig = packager.getConfiguration();
Expand Down
13 changes: 10 additions & 3 deletions ...-core/src/test/java/org/eclipse/pass/deposit/builder/DepositSubmissionModelBuilderIT.java
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Original file line number Diff line number Diff line change
Expand Up @@ -49,10 +49,12 @@ public class DepositSubmissionModelBuilderIT extends AbstractDepositSubmissionIT
private static final String EXPECTED_DOI = "10.1039/c7fo01251a";
private static final String EXPECTED_EMBARGO_END_DATE = "2018-06-30";
private static final int EXPECTED_SUBMITER_COUNT = 1;
private static final int EXPECTED_PI_COUNT = 1;
private static final int EXPECTED_CO_PI_COUNT = 2;
private static final int EXPECTED_PI_COUNT = 2;
private static final int EXPECTED_CO_PI_COUNT = 4;
private static final int EXPECTED_AUTHOR_COUNT = 6;
private static final String EXPECTED_NLMTA = "Food Funct";
private static final String EXPECTED_GRANT1 = "R01EY026617";
private static final String EXPECTED_GRANT2 = "R01EY026618";
private static final Map<String, DepositMetadata.IssnPubType> EXPECTED_ISSNS =
new HashMap<>() {
{
Expand Down Expand Up @@ -159,10 +161,15 @@ public void testBuildDepositSubmission() throws IOException {
.anyMatch(author ->
author.getName().equals("Raymond J. Playford")));

//test the grants associated with the submission
List<DepositMetadata.Grant> grants = submission.getMetadata().getGrantsMetadata();

assertNotNull(grants.stream().filter(matchGrant -> matchGrant.getGrantId() == EXPECTED_GRANT1));
assertNotNull(grants.stream().filter(matchGrant -> matchGrant.getGrantId() == EXPECTED_GRANT2));

// Read something out of the submission metadata
assertTrue(submission.getSubmissionMeta().has("agreements"));
JsonObject agreement = submission.getSubmissionMeta().getAsJsonObject("agreements");
assertTrue(agreement.has("JScholarship"));
}

}
2 changes: 1 addition & 1 deletion ...ervices/deposit-core/src/test/java/org/eclipse/pass/deposit/provider/j10p/MetadataIT.java
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ public void commonContributorsAndFewAuthors() throws Exception {
assertEquals("Elsevier", qdc.getElementsByTagNameNS(DC_NS, DC_PUBLISHER).item(0).getTextContent());

// Contributor list does not include submitting user, only PIs (from Grant) and authors (from metadata)
assertEquals(5, qdc.getElementsByTagNameNS(DC_NS, DC_CONTRIBUTOR).getLength());
assertEquals(8, qdc.getElementsByTagNameNS(DC_NS, DC_CONTRIBUTOR).getLength());
for (int i = 0; i < 5; i++) {
// Contributors must have names, whether they come from
// first/middle/last or only display name (in Submission), or from metadata.
Expand Down
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