Update NIHMS metadata, Adding Grant and Funder to bulk_meta.xml

pass-deposit-services/assembler-api/src/main/java/org/eclipse/pass/deposit/assembler/PackageOptions.java

@@ -98,4 +98,11 @@ enum OPTS {
 
     }
 
+    /**
+     * Funder Mapping for Nihms Packages
+     */
+    interface FunderMapping {
+        String KEY = "FUNDER-MAPPING";
+    }
+
 }

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/builder/DepositSubmissionMapper.java

@@ -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());
@@ -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));
@@ -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.
      *

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/config/repository/RepositoryDepositConfig.java

@@ -72,6 +72,6 @@ public int hashCode() {
     @Override
     public String toString() {
         return "RepositoryDepositConfig{" + "depositProcessing=" + depositProcessing +
-               ", statusMapping=" + statusMapping + '}';
+               ", statusMapping=" + statusMapping + "}";
     }
 }

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/provider/nihms/NihmsMetadataSerializer.java

@@ -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;
@@ -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;
@@ -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
@@ -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();
@@ -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
@@ -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;
                 }
@@ -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);
 
@@ -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
@@ -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());
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        }
     }
 }

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/provider/nihms/NihmsPackageProvider.java

@@ -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);
     }
 
     /**

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/service/DepositTask.java

@@ -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();

pass-deposit-services/deposit-core/src/test/java/org/eclipse/pass/deposit/builder/DepositSubmissionModelBuilderIT.java

@@ -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<>() {
             {
@@ -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"));
     }
-
 }

pass-deposit-services/deposit-core/src/test/java/org/eclipse/pass/deposit/provider/j10p/MetadataIT.java

@@ -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.