migration2clarin7/fix different separator in crosswalks and added met…

…asharev2 crosswalk. (#223) * Added missing metasharev2 crosswalk into xoai.xml - without it, this crosswalk would never be used. * Added a new metadata formats for the `metashare2.xsl` crosswalk * Working on separator and trying to fix metashare crosswalk * Created scripts for fast updating the crosswalks without rebuilding and installing the dspace project. * Added fast building script for oai-pmh package * Added fast building script for dspace-api package * str:split function replaced by the tokenize function. * Fixed creating NodeList * Refactoring * Added script for updating the configuration files * Refactoring and fixed checkstyle violations * `registry.metadata.load = metashare-schema.xml` property cannot be added in the `clarin-dspace.cfg` because then some Unit tests are failing.. --------- Co-authored-by: MilanMajchrák <milan.majchak@dataquest.sk>
dataquest-dev · Jun 19, 2024 · fa0c279 · fa0c279
1 parent 0bebdc4
commit fa0c279
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diff --git a/...dspace/storage/rdbms/sqlmigration/h2/V7.2_2022.07.28__Upgrade_to_Lindat_Clarin_schema.sql b/...dspace/storage/rdbms/sqlmigration/h2/V7.2_2022.07.28__Upgrade_to_Lindat_Clarin_schema.sql
@@ -11,6 +11,9 @@ ALTER TABLE handle ADD url varchar(2048);
 ALTER TABLE handle ADD dead BOOL;
 ALTER TABLE handle ADD dead_since TIMESTAMP;
 
+-- MetadataField table
+-- Because of metashareSchema
+ALTER TABLE metadatafieldregistry ALTER COLUMN element TYPE VARCHAR(128);
 
 -- LICENSES
 --

diff --git a/.../storage/rdbms/sqlmigration/postgres/V7.2_2022.07.28__Upgrade_to_Lindat_Clarin_schema.sql b/.../storage/rdbms/sqlmigration/postgres/V7.2_2022.07.28__Upgrade_to_Lindat_Clarin_schema.sql
@@ -11,6 +11,9 @@ ALTER TABLE handle ADD url varchar;
 ALTER TABLE handle ADD dead BOOL;
 ALTER TABLE handle ADD dead_since TIMESTAMP WITH TIME ZONE;
 
+-- MetadataField table
+-- Because of metashareSchema
+ALTER TABLE metadatafieldregistry ALTER COLUMN element TYPE VARCHAR(128);
 
 -- LICENSES
 --

diff --git a/dspace-oai/src/main/java/org/dspace/utils/LicenseUtil.java b/dspace-oai/src/main/java/org/dspace/utils/LicenseUtil.java
@@ -15,17 +15,19 @@
 import java.util.Map;
 import java.util.Objects;
 import java.util.Set;
-import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 
 /**
- *  Class is copied from the LINDAT/CLARIAH-CZ (This class is taken from UFAL-clarin. https://github.com/ufal/clarin-dspace/blob
+ *  Class is copied from the LINDAT/CLARIAH-CZ (This class is taken from UFAL-clarin.
+ *  https://github.com/ufal/clarin-dspace/blob
  *  * /si-master-origin/dspace-oai/src/main/java/cz/cuni/mff/ufal/utils/LicenseUtil.java) and modified by
+ *
  *  @author Marian Berger (marian.berger at dataquest.sk)
+ *  @author Milan Majchrak (milan.majchrak at dataquest.sk)
  */
 public class LicenseUtil {
 
@@ -198,15 +200,18 @@ public static String uriToAvailability(String uri) {
         return "available-restrictedUse";
     }
 
-    public static org.w3c.dom.NodeList uriToRestrictions(String uri) throws ParserConfigurationException {
+    public static org.w3c.dom.NodeList uriToRestrictions(String uri)
+            throws ParserConfigurationException {
+
         DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
-        DocumentBuilder builder = factory.newDocumentBuilder();
+        javax.xml.parsers.DocumentBuilder builder;
+        builder = factory.newDocumentBuilder();
 
         Document doc = builder.newDocument();
         Element root = doc.createElement("restrictions");
 
         String restrictions = _uri2restrictions.get(uri);
-        if (Objects.nonNull(restrictions)) {
+        if (Objects.isNull(restrictions)) {
             restrictions = "other";
         }
 
@@ -217,7 +222,6 @@ public static org.w3c.dom.NodeList uriToRestrictions(String uri) throws ParserCo
         }
 
         return root.getElementsByTagName("restriction");
-
     }
 
     public static void main(String[] args) throws Exception {

diff --git a/dspace-oai/src/main/java/org/dspace/xoai/services/impl/resources/functions/LogMissingFn.java b/dspace-oai/src/main/java/org/dspace/xoai/services/impl/resources/functions/LogMissingFn.java
@@ -54,7 +54,7 @@ public XdmValue call(XdmValue[] xdmValues) throws SaxonApiException {
             return new XdmAtomicValue("");
         }
         return new XdmAtomicValue(checks(XslLogUtil.logMissing(xdmValues[0].itemAt(0).getStringValue(),
-                xdmValues[0].itemAt(1).getStringValue())));
+                xdmValues[1].itemAt(0).getStringValue())));
     }
 
     private String checks(String got) {

diff --git a/.../src/main/java/org/dspace/xoai/services/impl/resources/functions/NodeListXslFunction.java b/.../src/main/java/org/dspace/xoai/services/impl/resources/functions/NodeListXslFunction.java
@@ -8,11 +8,10 @@
 
 package org.dspace.xoai.services.impl.resources.functions;
 
+import static org.apache.logging.log4j.LogManager.getLogger;
 import static org.dspace.xoai.services.impl.resources.functions.StringXSLFunction.BASE;
 
 import java.util.Objects;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.dom.DOMSource;
 
 import net.sf.saxon.s9api.DocumentBuilder;
@@ -25,21 +24,26 @@
 import net.sf.saxon.s9api.SequenceType;
 import net.sf.saxon.s9api.XdmAtomicValue;
 import net.sf.saxon.s9api.XdmValue;
+import org.apache.logging.log4j.Logger;
 import org.bouncycastle.util.Arrays;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 
 
 /**
  * Serves as proxy for call from XSL engine.
+ *
  * @author Marian Berger (marian.berger at dataquest.sk)
+ * @author Milan Majchrak (milan.majchrak at dataquest.sk)
  */
 public abstract class NodeListXslFunction implements ExtensionFunction {
 
     protected abstract String getFnName();
 
     protected abstract NodeList getNodeList(String param);
 
+    private static final Logger log = getLogger(NodeListXslFunction.class);
+
     @Override
     final public QName getName() {
         return new QName(BASE, getFnName());
@@ -62,26 +66,13 @@ final public XdmValue call(XdmValue[] xdmValues) throws SaxonApiException {
         if (Objects.isNull(xdmValues) || Arrays.isNullOrContainsNull(xdmValues)) {
             return new XdmAtomicValue("");
         }
+
         NodeList nodeList = getNodeList(xdmValues[0].itemAt(0).getStringValue());
+        Node oneNode = nodeList.item(0);
+
         DocumentBuilder db = new Processor(false).newDocumentBuilder();
-        if (Objects.isNull(nodeList)) {
-            try {
-                nodeList = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument().getChildNodes();
-            } catch (ParserConfigurationException e) {
-                e.printStackTrace();
-                return null;
-            }
-        }
-        Node parent = null;
-        try {
-            parent = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
-            for (int i = 0; i < nodeList.getLength(); i++) {
-                parent.appendChild(nodeList.item(i));
-            }
-            return db.build(new DOMSource(parent));
-        } catch (ParserConfigurationException e) {
-            e.printStackTrace();
-            return null;
-        }
+        DOMSource sourceObj = new DOMSource(oneNode);
+        var res = db.wrap(sourceObj);
+        return res;
     }
 }
diff --git a/dspace/config/crosswalks/oai/metadataFormats/metasharev2.xsl b/dspace/config/crosswalks/oai/metadataFormats/metasharev2.xsl
@@ -1,13 +1,10 @@
 <?xml version="1.0" encoding="UTF-8" ?>
-<!-- 
--->
 <xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
     xmlns:doc="http://www.lyncode.com/xoai"
-    xmlns:str="http://exslt.org/strings"
     xmlns:ms="http://www.ilsp.gr/META-XMLSchema"
     xmlns:fn="http://custom.crosswalk.functions"
-    exclude-result-prefixes="doc fn str"
-    version="1.0">
+    exclude-result-prefixes="doc fn"
+    version="2.0">
 
     <xsl:output omit-xml-declaration="yes" method="xml" indent="yes"/>
 
@@ -142,7 +139,7 @@
 				</xsl:when>
                 <xsl:when
                     test="doc:metadata/doc:element[@name='local']/doc:element[@name='contact']/doc:element[@name='person']/doc:element/doc:field[@name='value']">
-                    <xsl:value-of select="str:split(doc:metadata/doc:element[@name='local']/doc:element[@name='contact']/doc:element[@name='person']/doc:element/doc:field[@name='value'], '@@')[2]"/>
+                    <xsl:value-of select="tokenize(doc:metadata/doc:element[@name='local']/doc:element[@name='contact']/doc:element[@name='person']/doc:element/doc:field[@name='value'], ';')[2]"/>
                 </xsl:when>
 				<xsl:otherwise>
 					<xsl:value-of select="fn:logMissing('surname',$handle)" />
@@ -158,7 +155,7 @@
                 </xsl:when>
                 <xsl:when
                     test="doc:metadata/doc:element[@name='local']/doc:element[@name='contact']/doc:element[@name='person']/doc:element/doc:field[@name='value']">
-                    <xsl:value-of select="str:split(doc:metadata/doc:element[@name='local']/doc:element[@name='contact']/doc:element[@name='person']/doc:element/doc:field[@name='value'], '@@')[1]"/>
+                    <xsl:value-of select="tokenize(doc:metadata/doc:element[@name='local']/doc:element[@name='contact']/doc:element[@name='person']/doc:element/doc:field[@name='value'], ';')[1]"/>
                 </xsl:when>
                 <xsl:otherwise>
                     <xsl:value-of select="fn:logMissing('givenName',$handle)" />
@@ -177,11 +174,11 @@
 					<xsl:call-template name="CommunicationInfo" />
 				</ms:affiliation>
 			</xsl:when>
-			<xsl:when 
+			<xsl:when
                 test="doc:metadata/doc:element[@name='local']/doc:element[@name='contact']/doc:element[@name='person']/doc:element/doc:field[@name='value']">
 				<ms:affiliation>
 				    <ms:organizationName>
-					   <xsl:value-of select="str:split(doc:metadata/doc:element[@name='local']/doc:element[@name='contact']/doc:element[@name='person']/doc:element/doc:field[@name='value'], '@@')[4]" />
+					   <xsl:value-of select="tokenize(doc:metadata/doc:element[@name='local']/doc:element[@name='contact']/doc:element[@name='person']/doc:element/doc:field[@name='value'], ';')[4]" />
 					</ms:organizationName>
 					<!--another communicationInfo needed -->
 					<xsl:call-template name="CommunicationInfo" />
@@ -202,7 +199,7 @@
                         </xsl:when>
                         <xsl:when
                             test="doc:metadata/doc:element[@name='local']/doc:element[@name='contact']/doc:element[@name='person']/doc:element/doc:field[@name='value']">
-                            <xsl:value-of select="str:split(doc:metadata/doc:element[@name='local']/doc:element[@name='contact']/doc:element[@name='person']/doc:element/doc:field[@name='value'], '@@')[3]"/>
+                            <xsl:value-of select="tokenize(doc:metadata/doc:element[@name='local']/doc:element[@name='contact']/doc:element[@name='person']/doc:element/doc:field[@name='value'], ';')[3]"/>
                         </xsl:when>
                         <xsl:otherwise>
                             <xsl:value-of select="fn:logMissing('email',$handle)" />
@@ -288,10 +285,10 @@
                                 <xsl:for-each select="doc:metadata/doc:element[@name='local']/doc:element[@name='sponsor']/doc:element/doc:field[@name='value']">
                                                 <ms:fundingProject>
                                                     <ms:projectName>
-                                                            <xsl:value-of select="str:split(., '@@')[3]"/>
+                                                            <xsl:value-of select="tokenize(., ';')[3]"/>
                                                     </ms:projectName>
                                                     <ms:fundingType>
-                                                            <xsl:value-of select="str:split(., '@@')[4]"/>
+                                                            <xsl:value-of select="tokenize(., ';')[4]"/>
                                                     </ms:fundingType>
                                                 </ms:fundingProject>
                                 </xsl:for-each>
@@ -459,7 +456,7 @@
 					</xsl:when>
                     <xsl:when
                         test="doc:metadata/doc:element[@name='local']/doc:element[@name='size']/doc:element[@name='info']/doc:element/doc:field[@name='value']">
-                        <xsl:value-of select="str:split(doc:metadata/doc:element[@name='local']/doc:element[@name='size']/doc:element[@name='info']/doc:element/doc:field[@name='value'], '@@')[1]"/>
+                        <xsl:value-of select="tokenize(doc:metadata/doc:element[@name='local']/doc:element[@name='size']/doc:element[@name='info']/doc:element/doc:field[@name='value'], ';')[1]"/>
                     </xsl:when>
 					<xsl:otherwise>
                         			<xsl:variable name="iJustWantToLog" select="fn:logMissing('size',$handle)" />
@@ -476,7 +473,7 @@
 					</xsl:when>
                     <xsl:when
                         test="doc:metadata/doc:element[@name='local']/doc:element[@name='size']/doc:element[@name='info']/doc:element/doc:field[@name='value']">
-                        <xsl:value-of select="str:split(doc:metadata/doc:element[@name='local']/doc:element[@name='size']/doc:element[@name='info']/doc:element/doc:field[@name='value'], '@@')[2]"/>
+                        <xsl:value-of select="tokenize(doc:metadata/doc:element[@name='local']/doc:element[@name='size']/doc:element[@name='info']/doc:element/doc:field[@name='value'], ';')[2]"/>
                     </xsl:when>
 					<xsl:otherwise>
                         			<xsl:variable name="iJustWantToLog" select="fn:logMissing('size',$handle)" />

diff --git a/dspace/config/crosswalks/oai/xoai.xml b/dspace/config/crosswalks/oai/xoai.xml
@@ -10,6 +10,7 @@
             <Format ref="oaidc"/>
             <Format ref="mets"/>
             <Format ref="cmdi" />
+            <Format ref="oai_metasharev2" />
             <Format ref="olac" />
             <Format ref="xoai"/>
             <Format ref="didl"/>
@@ -122,6 +123,12 @@
             <SchemaLocation>http://catalog.clarin.eu/ds/ComponentRegistry/rest/registry/profiles/clarin.eu:cr1:p_1349361150622/xsd</SchemaLocation>
 <!--            <Filter ref="ExcludeItemsInComOrCol"/>-->
         </Format>
+        <Format id="oai_metasharev2">
+            <Prefix>oai_metasharev2</Prefix>
+            <XSLT>metadataFormats/metasharev2.xsl</XSLT>
+            <Namespace>http://www.ilsp.gr/META-XMLSchema</Namespace>
+            <SchemaLocation>http://metashare.ilsp.gr/META-XMLSchema/v2.0/META-SHARE-Resource.xsd</SchemaLocation>
+        </Format>
         <Format id="mets">
             <Prefix>mets</Prefix>
             <XSLT>metadataFormats/mets.xsl</XSLT>

diff --git a/dspace/config/dspace.cfg b/dspace/config/dspace.cfg
@@ -928,7 +928,9 @@ registry.metadata.load = schema-publicationVolume-types.xml
 registry.metadata.load = openaire4-types.xml
 registry.metadata.load = dspace-types.xml
 registry.metadata.load = iiif-types.xml
-
+### CLARIN ###
+# This property cannot be added in the `clarin-dspace.cfg` because then some Unit tests are failing..
+registry.metadata.load = metashare-schema.xml
 
 #---------------------------------------------------------------#
 #-----------------UI-Related CONFIGURATIONS---------------------#

diff --git a/dspace/config/registries/local-types.xml b/dspace/config/registries/local-types.xml
@@ -90,4 +90,52 @@
     <scope_note>Links to data in TEITOK</scope_note>
   </dc-type>
 
+  <dc-type>
+    <schema>local</schema>
+    <element>demo</element>
+    <qualifier>uri</qualifier>
+    <scope_note>URL of the demo</scope_note>
+  </dc-type>
+
+  <dc-type>
+    <schema>local</schema>
+    <element>size</element>
+    <qualifier>info</qualifier>
+  </dc-type>
+
+  <dc-type>
+    <schema>local</schema>
+    <element>submission</element>
+    <qualifier>note</qualifier>
+    <scope_note>A submitter's note for editor/reviewer</scope_note>
+  </dc-type>
+
+  <dc-type>
+    <schema>local</schema>
+    <element>has</element>
+    <qualifier>files</qualifier>
+    <scope_note>True if the item contains any bitstreams</scope_note>
+  </dc-type>
+
+  <dc-type>
+    <schema>local</schema>
+    <element>branding</element>
+    <scope_note>LRT/LINDAT (Name of Community)</scope_note>
+  </dc-type>
+
+  <dc-type>
+    <schema>local</schema>
+    <element>bitstream</element>
+    <qualifier>file</qualifier>
+    <scope_note>Files inside a bitstream if an archive</scope_note>
+  </dc-type>
+
+  <dc-type>
+    <schema>local</schema>
+    <element>refbox</element>
+    <qualifier>format</qualifier>
+    <scope_note>If the default refbox citation is not enough, use this field to provide a format string
+      . Check/extend html.xsl for available variables.</scope_note>
+  </dc-type>
+
 </dspace-dc-types>