[DSC-1125] Update Datacite schema on version 4

4Science · Aug 21, 2023 · 0f85176 · 0f85176
1 parent 6eb0a97
commit 0f85176
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diff --git a/dspace-api/src/main/java/org/dspace/identifier/doi/DataCiteConnector.java b/dspace-api/src/main/java/org/dspace/identifier/doi/DataCiteConnector.java
@@ -8,13 +8,14 @@
 package org.dspace.identifier.doi;
 
 import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.net.URISyntaxException;
 import java.sql.SQLException;
-import java.util.HashMap;
 import java.util.Iterator;
 import java.util.Map;
 
+import org.apache.commons.lang3.StringUtils;
 import org.apache.http.HttpEntity;
 import org.apache.http.HttpResponse;
 import org.apache.http.StatusLine;
@@ -35,13 +36,14 @@
 import org.apache.http.util.EntityUtils;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.DSpaceObject;
+import org.dspace.content.Item;
 import org.dspace.content.crosswalk.CrosswalkException;
-import org.dspace.content.crosswalk.DisseminationCrosswalk;
-import org.dspace.content.crosswalk.ParameterizedDisseminationCrosswalk;
+import org.dspace.content.crosswalk.StreamDisseminationCrosswalk;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.DSpaceObjectService;
+import org.dspace.content.service.ItemService;
+import org.dspace.core.Constants;
 import org.dspace.core.Context;
-import org.dspace.core.factory.CoreServiceFactory;
 import org.dspace.handle.service.HandleService;
 import org.dspace.identifier.DOI;
 import org.dspace.services.ConfigurationService;
@@ -99,18 +101,6 @@ public class DataCiteConnector
      * dependency injection.
      */
     protected String METADATA_PATH;
-    /**
-     * Name of crosswalk to convert metadata into DataCite Metadata Scheme. Set
-     * by spring dependency injection.
-     */
-    protected String CROSSWALK_NAME;
-    /**
-     * DisseminationCrosswalk to map local metadata into DataCite metadata.
-     * The name of the crosswalk is set by spring dependency injection using
-     * {@link #setDisseminationCrosswalkName(String) setDisseminationCrosswalkName} which
-     * instantiates the crosswalk.
-     */
-    protected ParameterizedDisseminationCrosswalk xwalk;
 
     protected ConfigurationService configurationService;
 
@@ -119,8 +109,12 @@ public class DataCiteConnector
     @Autowired
     protected HandleService handleService;
 
+    @Autowired
+    private ItemService itemService;
+
+    private Map<String, StreamDisseminationCrosswalk> disseminationCrosswalkByEntityType;
+
     public DataCiteConnector() {
-        this.xwalk = null;
         this.USERNAME = null;
         this.PASSWORD = null;
     }
@@ -189,34 +183,6 @@ public void setConfigurationService(ConfigurationService configurationService) {
         this.configurationService = configurationService;
     }
 
-    /**
-     * Set the name of the dissemination crosswalk used to convert the metadata
-     * into DataCite Metadata Schema. Used by spring dependency injection.
-     *
-     * @param CROSSWALK_NAME The name of the dissemination crosswalk to use. This
-     *                       crosswalk must be configured in dspace.cfg.
-     */
-    @Autowired(required = true)
-    public void setDisseminationCrosswalkName(String CROSSWALK_NAME) {
-        this.CROSSWALK_NAME = CROSSWALK_NAME;
-    }
-
-    protected void prepareXwalk() {
-        if (null != this.xwalk) {
-            return;
-        }
-
-        this.xwalk = (ParameterizedDisseminationCrosswalk) CoreServiceFactory.getInstance().getPluginService()
-                                                                             .getNamedPlugin(
-                                                                                 DisseminationCrosswalk.class,
-                                                                                 this.CROSSWALK_NAME);
-
-        if (this.xwalk == null) {
-            throw new RuntimeException("Can't find crosswalk '"
-                                           + CROSSWALK_NAME + "'!");
-        }
-    }
-
     protected String getUsername() {
         if (null == this.USERNAME) {
             this.USERNAME = this.configurationService.getProperty(CFG_USER);
@@ -350,64 +316,43 @@ public void deleteDOI(Context context, String doi)
     @Override
     public void reserveDOI(Context context, DSpaceObject dso, String doi)
         throws DOIIdentifierException {
-        this.prepareXwalk();
 
         DSpaceObjectService<DSpaceObject> dSpaceObjectService = ContentServiceFactory.getInstance()
                                                                                      .getDSpaceObjectService(dso);
 
-        if (!this.xwalk.canDisseminate(dso)) {
-            log.error("Crosswalk " + this.CROSSWALK_NAME
-                          + " cannot disseminate DSO with type " + dso.getType()
-                          + " and ID " + dso.getID() + ". Giving up reserving the DOI "
-                          + doi + ".");
-            throw new DOIIdentifierException("Cannot disseminate "
-                                                 + dSpaceObjectService.getTypeText(dso) + "/" + dso.getID()
-                                                 + " using crosswalk " + this.CROSSWALK_NAME + ".",
-                                             DOIIdentifierException.CONVERSION_ERROR);
-        }
+        StreamDisseminationCrosswalk xwalk = getStreamDisseminationCrosswalkByDso(dso);
 
-        // Set the transform's parameters.
-        // XXX Should the actual list be configurable?
-        Map<String, String> parameters = new HashMap<>();
-        if (configurationService.hasProperty(CFG_PREFIX)) {
-            parameters.put("prefix",
-                           configurationService.getProperty(CFG_PREFIX));
-        }
-        if (configurationService.hasProperty(CFG_PUBLISHER)) {
-            parameters.put("publisher",
-                           configurationService.getProperty(CFG_PUBLISHER));
-        }
-        if (configurationService.hasProperty(CFG_DATAMANAGER)) {
-            parameters.put("datamanager",
-                           configurationService.getProperty(CFG_DATAMANAGER));
-        }
-        if (configurationService.hasProperty(CFG_HOSTINGINSTITUTION)) {
-            parameters.put("hostinginstitution",
-                           configurationService.getProperty(CFG_HOSTINGINSTITUTION));
+        if (xwalk == null) {
+            log.error("No crosswalk found for DSO with type " + dso.getType()
+                + " and ID " + dso.getID() + ". Giving up reserving the DOI "
+                + doi + ".");
+            throw new DOIIdentifierException("Cannot disseminate "
+                + dSpaceObjectService.getTypeText(dso) + "/" + dso.getID() + ".",
+                DOIIdentifierException.CONVERSION_ERROR);
         }
 
         Element root = null;
         try {
-            root = xwalk.disseminateElement(context, dso, parameters);
+            ByteArrayOutputStream baos = new ByteArrayOutputStream();
+            xwalk.disseminate(context, dso, baos);
+            SAXBuilder builder = new SAXBuilder();
+            Document document = builder.build(new ByteArrayInputStream(baos.toByteArray()));
+            root = document.getRootElement();
         } catch (AuthorizeException ae) {
             log.error("Caught an AuthorizeException while disseminating DSO "
                           + "with type " + dso.getType() + " and ID " + dso.getID()
                           + ". Giving up to reserve DOI " + doi + ".", ae);
             throw new DOIIdentifierException("AuthorizeException occured while "
-                                                 + "converting " + dSpaceObjectService.getTypeText(dso) + "/" + dso
-                .getID()
-                                                 + " using crosswalk " + this.CROSSWALK_NAME + ".", ae,
+                + "converting " + dSpaceObjectService.getTypeText(dso) + "/" + dso + ".", ae,
                                              DOIIdentifierException.CONVERSION_ERROR);
         } catch (CrosswalkException ce) {
             log.error("Caught an CrosswalkException while reserving a DOI ("
                           + doi + ") for DSO with type " + dso.getType() + " and ID "
                           + dso.getID() + ". Won't reserve the doi.", ce);
             throw new DOIIdentifierException("CrosswalkException occured while "
-                                                 + "converting " + dSpaceObjectService.getTypeText(dso) + "/" + dso
-                .getID()
-                                                 + " using crosswalk " + this.CROSSWALK_NAME + ".", ce,
+                + "converting " + dSpaceObjectService.getTypeText(dso) + "/" + dso + ".", ce,
                                              DOIIdentifierException.CONVERSION_ERROR);
-        } catch (IOException | SQLException ex) {
+        } catch (IOException | SQLException | JDOMException ex) {
             throw new RuntimeException(ex);
         }
 
@@ -462,6 +407,21 @@ public void reserveDOI(Context context, DSpaceObject dso, String doi)
         }
     }
 
+    private StreamDisseminationCrosswalk getStreamDisseminationCrosswalkByDso(DSpaceObject dso) {
+
+        if (dso.getType() != Constants.ITEM) {
+            return null;
+        }
+
+        String entityType = itemService.getEntityType((Item) dso);
+        if (StringUtils.isBlank(entityType)) {
+            entityType = "Publication";
+        }
+
+        return disseminationCrosswalkByEntityType.get(entityType);
+
+    }
+
     @Override
     public void registerDOI(Context context, DSpaceObject dso, String doi)
         throws DOIIdentifierException {
@@ -631,7 +591,7 @@ protected DataCiteResponse sendMetadataPostRequest(String doi, Element metadataR
         Format format = Format.getCompactFormat();
         format.setEncoding("UTF-8");
         XMLOutputter xout = new XMLOutputter(format);
-        return sendMetadataPostRequest(doi, xout.outputString(new Document(metadataRoot)));
+        return sendMetadataPostRequest(doi, xout.outputString(metadataRoot.getDocument()));
     }
 
     protected DataCiteResponse sendMetadataPostRequest(String doi, String metadata)
@@ -848,6 +808,15 @@ protected Element addDOI(String doi, Element root) {
         return root.addContent(0, identifier);
     }
 
+    public Map<String, StreamDisseminationCrosswalk> getDisseminationCrosswalkByEntityType() {
+        return disseminationCrosswalkByEntityType;
+    }
+
+    public void setDisseminationCrosswalkByEntityType(
+        Map<String, StreamDisseminationCrosswalk> disseminationCrosswalkByEntityType) {
+        this.disseminationCrosswalkByEntityType = disseminationCrosswalkByEntityType;
+    }
+
     protected class DataCiteResponse {
         private final int statusCode;
         private final String content;

diff --git a/dspace/config/crosswalks/mapConverter-datacitePublicationLicense.properties b/dspace/config/crosswalks/mapConverter-datacitePublicationLicense.properties
@@ -0,0 +1,8 @@
+CC\ BY = https://creativecommons.org/licenses/by/4.0/legalcode
+CC\ BY\-SA = https://creativecommons.org/licenses/by-sa/4.0/legalcode
+CC\ BY\-ND = https://creativecommons.org/licenses/by-nd/4.0/legalcode
+CC\ BY\-NC = https://creativecommons.org/licenses/by-nc/4.0/legalcode
+CC\ BY\-NC\-SA = https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
+CC\ BY\-NC\-ND = https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
+CC0 = https://creativecommons.org/share-your-work/public-domain/cc0/
+PDM = https://creativecommons.org/publicdomain/mark/1.0/
diff --git a/dspace/config/crosswalks/mapConverter-datacitePublicationRights.properties b/dspace/config/crosswalks/mapConverter-datacitePublicationRights.properties
@@ -0,0 +1,4 @@
+openaccess = http://purl.org/coar/access_right/c_abf2
+embargoed = http://purl.org/coar/access_right/c_f1cf
+restricted = http://purl.org/coar/access_right/c_16ec
+metadata\ only = http://purl.org/coar/access_right/c_14cb
diff --git a/dspace/config/crosswalks/mapConverter-datacitePublicationTypes.properties b/dspace/config/crosswalks/mapConverter-datacitePublicationTypes.properties
@@ -0,0 +1,50 @@
+Resource\ Types\:\:text = Text
+Resource\ Types\:\:text\:\:annotation = Text
+Resource\ Types\:\:text\:\:bibliography = Text
+Resource\ Types\:\:text\:\:blog\ post = Text
+Resource\ Types\:\:text\:\:book = Book
+Resource\ Types\:\:text\:\:book\:\:book\ part = BookChapter
+Resource\ Types\:\:text\:\:conference\ output = ConferencePaper
+Resource\ Types\:\:text\:\:conference\ output\:\:conference paper not in proceedings = ConferencePaper
+Resource\ Types\:\:text\:\:conference\ output\:\:conference poster not in proceedings = ConferencePaper
+Resource\ Types\:\:text\:\:conference\ output\:\:conference presentation = ConferenceProceeding
+Resource\ Types\:\:text\:\:conference\ output\:\:conference proceedings = ConferenceProceeding
+Resource\ Types\:\:text\:\:journal = Journal
+Resource\ Types\:\:text\:\:journal\:\:editorial = Journal
+Resource\ Types\:\:text\:\:journal\:\:journal\ article = JournalArticle
+Resource\ Types\:\:text\:\:journal\:\:journal\ article\:\:corrigendum = JournalArticle
+Resource\ Types\:\:text\:\:journal\:\:journal\ article\:\:data\ paper = JournalArticle
+Resource\ Types\:\:text\:\:journal\:\:journal\ article\:\:research\ article = JournalArticle
+Resource\ Types\:\:text\:\:journal\:\:journal\ article\:\:review\ article = JournalArticle
+Resource\ Types\:\:text\:\:journal\:\:journal\ article\:\:software\ paper = JournalArticle
+Resource\ Types\:\:text\:\:journal\:\:letter\ to\ the\ editor = Journal
+Resource\ Types\:\:text\:\:lecture = Text
+Resource\ Types\:\:text\:\:letter = Text
+Resource\ Types\:\:text\:\:magazine = Text
+Resource\ Types\:\:text\:\:manuscript = Text
+Resource\ Types\:\:text\:\:musical\ notation = Sound
+Resource\ Types\:\:text\:\:newspaper = Text
+Resource\ Types\:\:text\:\:newspaper\:\:newspaper\ article = Text
+Resource\ Types\:\:text\:\:other\ periodical = Text
+Resource\ Types\:\:text\:\:preprint = Preprint
+Resource\ Types\:\:text\:\:report = Report
+Resource\ Types\:\:text\:\:report\:\:clinical\ study = Report
+Resource\ Types\:\:text\:\:report\:\:data\ management\ plan = OutputManagementPlan
+Resource\ Types\:\:text\:\:report\:\:memorandum = Report
+Resource\ Types\:\:text\:\:report\:\:policy\ report = Report
+Resource\ Types\:\:text\:\:report\:\:project\ deliverable = Report
+Resource\ Types\:\:text\:\:report\:\:research\ protocol = Report
+Resource\ Types\:\:text\:\:report\:\:research\ report = Report
+Resource\ Types\:\:text\:\:report\:\:technical\ report = Report
+Resource\ Types\:\:text\:\:research\ proposal = Text
+Resource\ Types\:\:text\:\:review = PeerReview
+Resource\ Types\:\:text\:\:review\:\:book\ review = PeerReview
+Resource\ Types\:\:text\:\:review\:\:commentary = PeerReview
+Resource\ Types\:\:text\:\:review\:\:peer\ review = PeerReview
+Resource\ Types\:\:text\:\:technical\ documentation = Text
+Resource\ Types\:\:text\:\:thesis = Dissertation
+Resource\ Types\:\:text\:\:thesis\:\:bachelor\ thesis = Dissertation
+Resource\ Types\:\:text\:\:thesis\:\:doctoral\ thesis = Dissertation
+Resource\ Types\:\:text\:\:thesis\:\:master\ thesis = Dissertation
+Resource\ Types\:\:text\:\:transcription = Text
+Resource\ Types\:\:text\:\:working\ paper = Preprint
diff --git a/dspace/config/crosswalks/template/patent-datacite-xml.template b/dspace/config/crosswalks/template/patent-datacite-xml.template
@@ -0,0 +1,43 @@
+<?xml version='1.0' encoding='utf-8'?>
+<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.4/metadata.xsd">
+  <identifier identifierType="DOI">@dc.identifier.doi@</identifier>
+  <creators>
+      @group.dc-contributor-author.start@
+      <creator>
+            <creatorName>@dc.contributor.author@</creatorName>
+            @relation.dc-contributor-author.start@
+            <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">@person.identifier.orcid@</nameIdentifier>       
+            @relation.dc-contributor-author.end@
+            <affiliation>@oairecerif.author.affiliation@</affiliation>
+      </creator>
+      @group.dc-contributor-author.end@
+    </creators>
+  <titles>
+    <title>@dc.title@</title>
+  </titles>
+  <publisher>@dc.publisher@</publisher>
+  <publicationYear>@virtual.date.dc-date-issued.YYYY@</publicationYear>
+  <subjects>
+    <subject>@dc.subject@</subject>
+  </subjects>
+  <dates>
+    <date dateType="Issued">@dc.date.issued@</date>
+    <date dateType="Available">@datacite.available@</date>
+  </dates>
+  <language>@dc.language.iso@</language>
+  <resourceType resourceTypeGeneral="@virtual.mapConverter.type2datacite.dc-type@" />
+  <alternateIdentifiers>
+    <alternateIdentifier alternateIdentifierType="url">@dc.identifier.uri@</alternateIdentifier>
+  </alternateIdentifiers>
+  <version>@dc.description.version@</version>
+  <rightsList>
+    <rights rightsURI="@virtual.mapConverter.right2licenseUrl.oaire-licenseCondition@">
+        @oaire.licenseCondition@</rights>
+    <rights rightsURI="@virtual.mapConverter.right2conceptUrl.datacite-rights@">
+        @datacite.rights@</rights>
+  </rightsList>
+  <descriptions>
+    <description descriptionType="Abstract">@dc.description.abstract@</description>
+    <description descriptionType="Other">@dc.description@</description>
+  </descriptions>
+</resource>
diff --git a/dspace/config/crosswalks/template/product-datacite-xml.template b/dspace/config/crosswalks/template/product-datacite-xml.template
@@ -0,0 +1,42 @@
+<?xml version='1.0' encoding='utf-8'?>
+<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.4/metadata.xsd">
+  <identifier identifierType="DOI">@dc.identifier.doi@</identifier>
+  <creators>
+      @group.dc-contributor-author.start@
+      <creator>
+            <creatorName>@dc.contributor.author@</creatorName>
+            @relation.dc-contributor-author.start@
+            <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">@person.identifier.orcid@</nameIdentifier>       
+            @relation.dc-contributor-author.end@
+            <affiliation>@oairecerif.author.affiliation@</affiliation>
+      </creator>
+      @group.dc-contributor-author.end@
+    </creators>
+  <titles>
+    <title>@dc.title@</title>
+  </titles>
+  <publisher>@dc.publisher@</publisher>
+  <publicationYear>@virtual.date.dc-date-issued.YYYY@</publicationYear>
+  <subjects>
+    <subject>@dc.subject@</subject>
+  </subjects>
+  <dates>
+    <date dateType="Issued">@dc.date.issued@</date>
+  </dates>
+  <language>@dc.language.iso@</language>
+  <resourceType resourceTypeGeneral="Dataset" />
+  <alternateIdentifiers>
+    <alternateIdentifier alternateIdentifierType="url">@dc.identifier.uri@</alternateIdentifier>
+  </alternateIdentifiers>
+  <version>@dc.description.version@</version>
+  <rightsList>
+    <rights rightsURI="@virtual.mapConverter.right2licenseUrl.oaire-licenseCondition@">
+        @oaire.licenseCondition@</rights>
+    <rights rightsURI="@virtual.mapConverter.right2conceptUrl.datacite-rights@">
+        @datacite.rights@</rights>
+  </rightsList>
+  <descriptions>
+    <description descriptionType="Abstract">@dc.description.abstract@</description>
+    <description descriptionType="Other">@dc.description@</description>
+  </descriptions>
+</resource>