diff --git a/dspace-api/pom.xml b/dspace-api/pom.xml index 8dd36c9b19..6a54a96376 100644 --- a/dspace-api/pom.xml +++ b/dspace-api/pom.xml @@ -520,7 +520,7 @@ org.jdom - jdom + jdom2 org.apache.pdfbox @@ -581,9 +581,12 @@ - org.rometools + com.rometools + rome + + + com.rometools rome-modules - 1.0 org.jbibtex @@ -815,44 +818,6 @@ jaxb-runtime - - - org.apache.ws.commons.axiom - axiom-impl - ${axiom.version} - - - - org.apache.geronimo.specs - * - - - - org.codehaus.woodstox - woodstox-core-asl - - - - - org.apache.ws.commons.axiom - axiom-api - ${axiom.version} - - - - org.apache.geronimo.specs - * - - - - org.codehaus.woodstox - woodstox-core-asl - - - - org.glassfish.jersey.core diff --git a/dspace-api/src/main/java/org/dspace/administer/StructBuilder.java b/dspace-api/src/main/java/org/dspace/administer/StructBuilder.java index 6e69f93572..716e9330de 100644 --- a/dspace-api/src/main/java/org/dspace/administer/StructBuilder.java +++ b/dspace-api/src/main/java/org/dspace/administer/StructBuilder.java @@ -55,9 +55,9 @@ import org.dspace.eperson.factory.EPersonServiceFactory; import org.dspace.eperson.service.EPersonService; import org.dspace.handle.factory.HandleServiceFactory; import org.dspace.handle.service.HandleService; -import org.jdom.Element; -import org.jdom.output.Format; -import org.jdom.output.XMLOutputter; +import org.jdom2.Element; +import org.jdom2.output.Format; +import org.jdom2.output.XMLOutputter; import org.w3c.dom.Document; import org.w3c.dom.Node; import org.w3c.dom.NodeList; @@ -330,7 +330,7 @@ public class StructBuilder { } // finally write the string into the output file. - final org.jdom.Document xmlOutput = new org.jdom.Document(root); + final org.jdom2.Document xmlOutput = new org.jdom2.Document(root); try { new XMLOutputter().output(xmlOutput, output); } catch (IOException e) { @@ -434,7 +434,7 @@ public class StructBuilder { } // Now write the structure out. - org.jdom.Document xmlOutput = new org.jdom.Document(rootElement); + org.jdom2.Document xmlOutput = new org.jdom2.Document(rootElement); try { XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat()); outputter.output(xmlOutput, output); diff --git a/dspace-api/src/main/java/org/dspace/app/launcher/CommandRunner.java b/dspace-api/src/main/java/org/dspace/app/launcher/CommandRunner.java index ce33b6655b..06c2ddb483 100644 --- a/dspace-api/src/main/java/org/dspace/app/launcher/CommandRunner.java +++ b/dspace-api/src/main/java/org/dspace/app/launcher/CommandRunner.java @@ -16,7 +16,7 @@ import java.io.StreamTokenizer; import java.util.ArrayList; import java.util.List; -import org.jdom.Document; +import org.jdom2.Document; /** * @author mwood diff --git a/dspace-api/src/main/java/org/dspace/app/launcher/ScriptLauncher.java b/dspace-api/src/main/java/org/dspace/app/launcher/ScriptLauncher.java index d445f9bbf3..fcb2098bd0 100644 --- a/dspace-api/src/main/java/org/dspace/app/launcher/ScriptLauncher.java +++ b/dspace-api/src/main/java/org/dspace/app/launcher/ScriptLauncher.java @@ -29,9 +29,9 @@ import org.dspace.scripts.service.ScriptService; import org.dspace.servicemanager.DSpaceKernelImpl; import org.dspace.servicemanager.DSpaceKernelInit; import org.dspace.services.RequestService; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.input.SAXBuilder; +import org.jdom2.Document; +import org.jdom2.Element; +import org.jdom2.input.SAXBuilder; /** * A DSpace script launcher. diff --git a/dspace-api/src/main/java/org/dspace/app/util/GoogleMetadata.java b/dspace-api/src/main/java/org/dspace/app/util/GoogleMetadata.java index 0021f26700..72e2af409f 100644 --- a/dspace-api/src/main/java/org/dspace/app/util/GoogleMetadata.java +++ b/dspace-api/src/main/java/org/dspace/app/util/GoogleMetadata.java @@ -42,7 +42,7 @@ import org.dspace.core.Context; import org.dspace.handle.factory.HandleServiceFactory; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; -import org.jdom.Element; +import org.jdom2.Element; /** * Configuration and mapping for Google Scholar output metadata diff --git a/dspace-api/src/main/java/org/dspace/app/util/OpenSearchServiceImpl.java b/dspace-api/src/main/java/org/dspace/app/util/OpenSearchServiceImpl.java index 97f25cb2b2..89ca477442 100644 --- a/dspace-api/src/main/java/org/dspace/app/util/OpenSearchServiceImpl.java +++ b/dspace-api/src/main/java/org/dspace/app/util/OpenSearchServiceImpl.java @@ -16,10 +16,10 @@ import java.util.Arrays; import java.util.List; import java.util.Map; -import com.sun.syndication.feed.module.opensearch.OpenSearchModule; -import com.sun.syndication.feed.module.opensearch.entity.OSQuery; -import com.sun.syndication.feed.module.opensearch.impl.OpenSearchModuleImpl; -import com.sun.syndication.io.FeedException; +import com.rometools.modules.opensearch.OpenSearchModule; +import com.rometools.modules.opensearch.entity.OSQuery; +import com.rometools.modules.opensearch.impl.OpenSearchModuleImpl; +import com.rometools.rome.io.FeedException; import org.apache.logging.log4j.Logger; import org.dspace.app.util.service.OpenSearchService; import org.dspace.content.DSpaceObject; @@ -29,11 +29,11 @@ import org.dspace.discovery.IndexableObject; import org.dspace.handle.service.HandleService; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; -import org.jdom.Element; -import org.jdom.JDOMException; -import org.jdom.Namespace; -import org.jdom.output.DOMOutputter; -import org.jdom.output.XMLOutputter; +import org.jdom2.Element; +import org.jdom2.JDOMException; +import org.jdom2.Namespace; +import org.jdom2.output.DOMOutputter; +import org.jdom2.output.XMLOutputter; import org.springframework.beans.factory.annotation.Autowired; import org.w3c.dom.Document; @@ -192,7 +192,7 @@ public class OpenSearchServiceImpl implements OpenSearchService { * @param scope - null for the entire repository, or a collection/community handle * @return Service Document */ - protected org.jdom.Document getServiceDocument(String scope) { + protected org.jdom2.Document getServiceDocument(String scope) { ConfigurationService config = DSpaceServicesFactory.getInstance().getConfigurationService(); Namespace ns = Namespace.getNamespace(osNs); @@ -245,7 +245,7 @@ public class OpenSearchServiceImpl implements OpenSearchService { url.setAttribute("template", template.toString()); root.addContent(url); } - return new org.jdom.Document(root); + return new org.jdom2.Document(root); } /** @@ -255,7 +255,7 @@ public class OpenSearchServiceImpl implements OpenSearchService { * @return W3C Document object * @throws IOException if IO error */ - protected Document jDomToW3(org.jdom.Document jdomDoc) throws IOException { + protected Document jDomToW3(org.jdom2.Document jdomDoc) throws IOException { DOMOutputter domOut = new DOMOutputter(); try { return domOut.output(jdomDoc); diff --git a/dspace-api/src/main/java/org/dspace/app/util/SyndicationFeed.java b/dspace-api/src/main/java/org/dspace/app/util/SyndicationFeed.java index 2576df0193..8bbec234c9 100644 --- a/dspace-api/src/main/java/org/dspace/app/util/SyndicationFeed.java +++ b/dspace-api/src/main/java/org/dspace/app/util/SyndicationFeed.java @@ -15,26 +15,26 @@ import java.util.List; import java.util.Map; import javax.servlet.http.HttpServletRequest; -import com.sun.syndication.feed.module.DCModule; -import com.sun.syndication.feed.module.DCModuleImpl; -import com.sun.syndication.feed.module.Module; -import com.sun.syndication.feed.module.itunes.EntryInformation; -import com.sun.syndication.feed.module.itunes.EntryInformationImpl; -import com.sun.syndication.feed.module.itunes.types.Duration; -import com.sun.syndication.feed.synd.SyndContent; -import com.sun.syndication.feed.synd.SyndContentImpl; -import com.sun.syndication.feed.synd.SyndEnclosure; -import com.sun.syndication.feed.synd.SyndEnclosureImpl; -import com.sun.syndication.feed.synd.SyndEntry; -import com.sun.syndication.feed.synd.SyndEntryImpl; -import com.sun.syndication.feed.synd.SyndFeed; -import com.sun.syndication.feed.synd.SyndFeedImpl; -import com.sun.syndication.feed.synd.SyndImage; -import com.sun.syndication.feed.synd.SyndImageImpl; -import com.sun.syndication.feed.synd.SyndPerson; -import com.sun.syndication.feed.synd.SyndPersonImpl; -import com.sun.syndication.io.FeedException; -import com.sun.syndication.io.SyndFeedOutput; +import com.rometools.modules.itunes.EntryInformation; +import com.rometools.modules.itunes.EntryInformationImpl; +import com.rometools.modules.itunes.types.Duration; +import com.rometools.rome.feed.module.DCModule; +import com.rometools.rome.feed.module.DCModuleImpl; +import com.rometools.rome.feed.module.Module; +import com.rometools.rome.feed.synd.SyndContent; +import com.rometools.rome.feed.synd.SyndContentImpl; +import com.rometools.rome.feed.synd.SyndEnclosure; +import com.rometools.rome.feed.synd.SyndEnclosureImpl; +import com.rometools.rome.feed.synd.SyndEntry; +import com.rometools.rome.feed.synd.SyndEntryImpl; +import com.rometools.rome.feed.synd.SyndFeed; +import com.rometools.rome.feed.synd.SyndFeedImpl; +import com.rometools.rome.feed.synd.SyndImage; +import com.rometools.rome.feed.synd.SyndImageImpl; +import com.rometools.rome.feed.synd.SyndPerson; +import com.rometools.rome.feed.synd.SyndPersonImpl; +import com.rometools.rome.io.FeedException; +import com.rometools.rome.io.SyndFeedOutput; import org.apache.commons.lang3.ArrayUtils; import org.apache.commons.lang3.StringUtils; import org.apache.logging.log4j.Logger; diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/AIPDIMCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/AIPDIMCrosswalk.java index 2d919baa9d..4b77e4807a 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/AIPDIMCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/AIPDIMCrosswalk.java @@ -14,8 +14,8 @@ import java.util.List; import org.dspace.authorize.AuthorizeException; import org.dspace.content.DSpaceObject; import org.dspace.core.Context; -import org.jdom.Element; -import org.jdom.Namespace; +import org.jdom2.Element; +import org.jdom2.Namespace; /** * Crosswalk descriptive metadata to and from DIM (DSpace Intermediate diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/AIPTechMDCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/AIPTechMDCrosswalk.java index 8ffddf715f..978cabfb4b 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/AIPTechMDCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/AIPTechMDCrosswalk.java @@ -40,8 +40,8 @@ import org.dspace.handle.factory.HandleServiceFactory; import org.dspace.handle.service.HandleService; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; -import org.jdom.Element; -import org.jdom.Namespace; +import org.jdom2.Element; +import org.jdom2.Namespace; /** * Crosswalk of technical metadata for DSpace AIP. This is diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/DIMDisseminationCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/DIMDisseminationCrosswalk.java index 3f4d6bd44e..4365d9a485 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/DIMDisseminationCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/DIMDisseminationCrosswalk.java @@ -23,8 +23,8 @@ import org.dspace.content.factory.ContentServiceFactory; import org.dspace.content.service.ItemService; import org.dspace.core.Constants; import org.dspace.core.Context; -import org.jdom.Element; -import org.jdom.Namespace; +import org.jdom2.Element; +import org.jdom2.Namespace; /** * DIM dissemination crosswalk diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/DIMIngestionCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/DIMIngestionCrosswalk.java index ad922a65f2..4217308e65 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/DIMIngestionCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/DIMIngestionCrosswalk.java @@ -19,8 +19,8 @@ import org.dspace.content.factory.ContentServiceFactory; import org.dspace.content.service.ItemService; import org.dspace.core.Constants; import org.dspace.core.Context; -import org.jdom.Element; -import org.jdom.Namespace; +import org.jdom2.Element; +import org.jdom2.Namespace; /** * DIM ingestion crosswalk diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/DisseminationCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/DisseminationCrosswalk.java index 23e1965d7b..3e4fe21f8f 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/DisseminationCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/DisseminationCrosswalk.java @@ -14,8 +14,8 @@ import java.util.List; import org.dspace.authorize.AuthorizeException; import org.dspace.content.DSpaceObject; import org.dspace.core.Context; -import org.jdom.Element; -import org.jdom.Namespace; +import org.jdom2.Element; +import org.jdom2.Namespace; /** * Dissemination Crosswalk plugin -- translate DSpace native diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/IngestionCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/IngestionCrosswalk.java index 7edfb6f79f..bb73c83c45 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/IngestionCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/IngestionCrosswalk.java @@ -14,7 +14,7 @@ import java.util.List; import org.dspace.authorize.AuthorizeException; import org.dspace.content.DSpaceObject; import org.dspace.core.Context; -import org.jdom.Element; +import org.jdom2.Element; /** * Ingestion Crosswalk plugin -- translate an external metadata format diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/METSDisseminationCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/METSDisseminationCrosswalk.java index e44774a672..b8a4a8aef3 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/METSDisseminationCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/METSDisseminationCrosswalk.java @@ -24,11 +24,11 @@ import org.dspace.core.Context; import org.dspace.core.factory.CoreServiceFactory; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.JDOMException; -import org.jdom.Namespace; -import org.jdom.input.SAXBuilder; +import org.jdom2.Document; +import org.jdom2.Element; +import org.jdom2.JDOMException; +import org.jdom2.Namespace; +import org.jdom2.input.SAXBuilder; /** * METS dissemination crosswalk diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/METSRightsCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/METSRightsCrosswalk.java index 559d463be2..7f6622841b 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/METSRightsCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/METSRightsCrosswalk.java @@ -35,8 +35,8 @@ import org.dspace.eperson.Group; import org.dspace.eperson.factory.EPersonServiceFactory; import org.dspace.eperson.service.EPersonService; import org.dspace.eperson.service.GroupService; -import org.jdom.Element; -import org.jdom.Namespace; +import org.jdom2.Element; +import org.jdom2.Namespace; /** * METSRights Ingestion and Dissemination Crosswalk diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/MODSDisseminationCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/MODSDisseminationCrosswalk.java index 182fcebe2f..57202f656e 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/MODSDisseminationCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/MODSDisseminationCrosswalk.java @@ -15,7 +15,6 @@ import java.sql.SQLException; import java.util.ArrayList; import java.util.Enumeration; import java.util.HashMap; -import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Properties; @@ -42,16 +41,18 @@ import org.dspace.handle.factory.HandleServiceFactory; import org.dspace.handle.service.HandleService; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; -import org.jdom.Attribute; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.JDOMException; -import org.jdom.Namespace; -import org.jdom.Text; -import org.jdom.Verifier; -import org.jdom.input.SAXBuilder; -import org.jdom.output.XMLOutputter; -import org.jdom.xpath.XPath; +import org.jdom2.Attribute; +import org.jdom2.Document; +import org.jdom2.Element; +import org.jdom2.JDOMException; +import org.jdom2.Namespace; +import org.jdom2.Text; +import org.jdom2.Verifier; +import org.jdom2.filter.Filters; +import org.jdom2.input.SAXBuilder; +import org.jdom2.output.XMLOutputter; +import org.jdom2.xpath.XPathExpression; +import org.jdom2.xpath.XPathFactory; /** * Configurable MODS Crosswalk @@ -156,7 +157,7 @@ public class MODSDisseminationCrosswalk extends SelfNamedPlugin static class modsTriple { public String qdc = null; public Element xml = null; - public XPath xpath = null; + public XPathExpression xpath = null; /** * Initialize from text versions of QDC, XML and XPath. @@ -171,9 +172,9 @@ public class MODSDisseminationCrosswalk extends SelfNamedPlugin final String postlog = ""; try { result.qdc = qdc; - result.xpath = XPath.newInstance(xpath); - result.xpath.addNamespace(MODS_NS.getPrefix(), MODS_NS.getURI()); - result.xpath.addNamespace(XLINK_NS); + result.xpath = + XPathFactory.instance() + .compile(xpath, Filters.fpassthrough(), null, MODS_NS, XLINK_NS); Document d = builder.build(new StringReader(prolog + xml + postlog)); result.xml = (Element) d.getRootElement().getContent(0); } catch (JDOMException | IOException je) { @@ -295,6 +296,7 @@ public class MODSDisseminationCrosswalk extends SelfNamedPlugin * @throws IOException if IO error * @throws SQLException if database error * @throws AuthorizeException if authorization error + * @return List of Elements */ @Override public List disseminateList(Context context, DSpaceObject dso) @@ -352,37 +354,29 @@ public class MODSDisseminationCrosswalk extends SelfNamedPlugin if (trip == null) { log.warn("WARNING: " + getPluginInstanceName() + ": No MODS mapping for \"" + qdc + "\""); } else { - try { - Element me = (Element) trip.xml.clone(); - if (addSchema) { - me.setAttribute("schemaLocation", schemaLocation, XSI_NS); - } - Iterator ni = trip.xpath.selectNodes(me).iterator(); - if (!ni.hasNext()) { - log.warn("XPath \"" + trip.xpath.getXPath() + - "\" found no elements in \"" + - outputUgly.outputString(me) + - "\", qdc=" + qdc); - } - while (ni.hasNext()) { - Object what = ni.next(); - if (what instanceof Element) { - ((Element) what).setText(checkedString(value)); - } else if (what instanceof Attribute) { - ((Attribute) what).setValue(checkedString(value)); - } else if (what instanceof Text) { - ((Text) what).setText(checkedString(value)); - } else { - log.warn("Got unknown object from XPath, class=" + what.getClass().getName()); - } - } - result.add(me); - } catch (JDOMException je) { - log.error("Error following XPath in modsTriple: context=" + - outputUgly.outputString(trip.xml) + - ", xpath=" + trip.xpath.getXPath() + ", exception=" + - je.toString()); + Element me = (Element) trip.xml.clone(); + if (addSchema) { + me.setAttribute("schemaLocation", schemaLocation, XSI_NS); } + List matches = trip.xpath.evaluate(me); + if (matches.isEmpty()) { + log.warn("XPath \"" + trip.xpath.getExpression() + + "\" found no elements in \"" + + outputUgly.outputString(me) + + "\", qdc=" + qdc); + } + for (Object match: matches) { + if (match instanceof Element) { + ((Element) match).setText(checkedString(value)); + } else if (match instanceof Attribute) { + ((Attribute) match).setValue(checkedString(value)); + } else if (match instanceof Text) { + ((Text) match).setText(checkedString(value)); + } else { + log.warn("Got unknown object from XPath, class=" + match.getClass().getName()); + } + } + result.add(me); } } return result; diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/NullIngestionCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/NullIngestionCrosswalk.java index 994e15601d..562dadaca0 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/NullIngestionCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/NullIngestionCrosswalk.java @@ -15,9 +15,9 @@ import org.apache.logging.log4j.Logger; import org.dspace.authorize.AuthorizeException; import org.dspace.content.DSpaceObject; import org.dspace.core.Context; -import org.jdom.Element; -import org.jdom.output.Format; -import org.jdom.output.XMLOutputter; +import org.jdom2.Element; +import org.jdom2.output.Format; +import org.jdom2.output.XMLOutputter; /** * "Null" ingestion crosswalk diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/OAIDCIngestionCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/OAIDCIngestionCrosswalk.java index 10bd5ce6fa..6b0ecae780 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/OAIDCIngestionCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/OAIDCIngestionCrosswalk.java @@ -20,8 +20,8 @@ import org.dspace.content.factory.ContentServiceFactory; import org.dspace.content.service.ItemService; import org.dspace.core.Constants; import org.dspace.core.Context; -import org.jdom.Element; -import org.jdom.Namespace; +import org.jdom2.Element; +import org.jdom2.Namespace; /** * DIM ingestion crosswalk diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/OREDisseminationCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/OREDisseminationCrosswalk.java index 3dde093784..ac1c434322 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/OREDisseminationCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/OREDisseminationCrosswalk.java @@ -31,8 +31,8 @@ import org.dspace.core.Context; import org.dspace.core.Utils; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; -import org.jdom.Element; -import org.jdom.Namespace; +import org.jdom2.Element; +import org.jdom2.Namespace; /** * ORE dissemination crosswalk diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/OREIngestionCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/OREIngestionCrosswalk.java index 80c424e782..f756aae225 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/OREIngestionCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/OREIngestionCrosswalk.java @@ -34,12 +34,13 @@ import org.dspace.content.service.BundleService; import org.dspace.content.service.ItemService; import org.dspace.core.Constants; import org.dspace.core.Context; -import org.jdom.Attribute; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.JDOMException; -import org.jdom.Namespace; -import org.jdom.xpath.XPath; +import org.jdom2.Attribute; +import org.jdom2.Document; +import org.jdom2.Element; +import org.jdom2.Namespace; +import org.jdom2.filter.Filters; +import org.jdom2.xpath.XPathExpression; +import org.jdom2.xpath.XPathFactory; /** * ORE ingestion crosswalk @@ -113,23 +114,21 @@ public class OREIngestionCrosswalk Document doc = new Document(); doc.addContent(root.detach()); - XPath xpathLinks; List aggregatedResources; String entryId; - try { - xpathLinks = XPath.newInstance("/atom:entry/atom:link[@rel=\"" + ORE_NS.getURI() + "aggregates" + "\"]"); - xpathLinks.addNamespace(ATOM_NS); - aggregatedResources = xpathLinks.selectNodes(doc); + XPathExpression xpathLinks = + XPathFactory.instance() + .compile("/atom:entry/atom:link[@rel=\"" + ORE_NS.getURI() + "aggregates" + "\"]", + Filters.element(), null, ATOM_NS); + aggregatedResources = xpathLinks.evaluate(doc); - xpathLinks = XPath.newInstance("/atom:entry/atom:link[@rel='alternate']/@href"); - xpathLinks.addNamespace(ATOM_NS); - entryId = ((Attribute) xpathLinks.selectSingleNode(doc)).getValue(); - } catch (JDOMException e) { - throw new CrosswalkException("JDOM exception occurred while ingesting the ORE", e); - } + XPathExpression xpathAltHref = + XPathFactory.instance() + .compile("/atom:entry/atom:link[@rel='alternate']/@href", + Filters.attribute(), null, ATOM_NS); + entryId = xpathAltHref.evaluateFirst(doc).getValue(); // Next for each resource, create a bitstream - XPath xpathDesc; NumberFormat nf = NumberFormat.getInstance(); nf.setGroupingUsed(false); nf.setMinimumIntegerDigits(4); @@ -140,16 +139,12 @@ public class OREIngestionCrosswalk String bundleName; Element desc = null; - try { - xpathDesc = XPath.newInstance( - "/atom:entry/oreatom:triples/rdf:Description[@rdf:about=\"" + this.encodeForURL(href) + "\"][1]"); - xpathDesc.addNamespace(ATOM_NS); - xpathDesc.addNamespace(ORE_ATOM); - xpathDesc.addNamespace(RDF_NS); - desc = (Element) xpathDesc.selectSingleNode(doc); - } catch (JDOMException e) { - log.warn("Could not find description for {}", href, e); - } + XPathExpression xpathDesc = + XPathFactory.instance() + .compile("/atom:entry/oreatom:triples/rdf:Description[@rdf:about=\"" + + this.encodeForURL(href) + "\"][1]", + Filters.element(), null, ATOM_NS, ORE_ATOM, RDF_NS); + desc = xpathDesc.evaluateFirst(doc); if (desc != null && desc.getChild("type", RDF_NS).getAttributeValue("resource", RDF_NS) .equals(DS_NS.getURI() + "DSpaceBitstream")) { diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/PREMISCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/PREMISCrosswalk.java index e4e387a3ec..39b6c8f29c 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/PREMISCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/PREMISCrosswalk.java @@ -30,8 +30,8 @@ import org.dspace.core.Constants; import org.dspace.core.Context; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; -import org.jdom.Element; -import org.jdom.Namespace; +import org.jdom2.Element; +import org.jdom2.Namespace; /** * PREMIS Crosswalk diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/ParameterizedDisseminationCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/ParameterizedDisseminationCrosswalk.java index 312aed3543..5d9322339d 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/ParameterizedDisseminationCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/ParameterizedDisseminationCrosswalk.java @@ -14,7 +14,7 @@ import java.util.Map; import org.dspace.authorize.AuthorizeException; import org.dspace.content.DSpaceObject; import org.dspace.core.Context; -import org.jdom.Element; +import org.jdom2.Element; /** * Translate DSpace native metadata into an external XML format, with parameters. diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/QDCCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/QDCCrosswalk.java index f3c51a5d46..2fdbaaad00 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/QDCCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/QDCCrosswalk.java @@ -36,10 +36,10 @@ import org.dspace.core.Context; import org.dspace.core.SelfNamedPlugin; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.Namespace; -import org.jdom.input.SAXBuilder; +import org.jdom2.Document; +import org.jdom2.Element; +import org.jdom2.Namespace; +import org.jdom2.input.SAXBuilder; /** * Configurable QDC Crosswalk @@ -290,7 +290,7 @@ public class QDCCrosswalk extends SelfNamedPlugin qdc2element.put(qdc, element); element2qdc.put(makeQualifiedTagName(element), qdc); log.debug("Building Maps: qdc=\"" + qdc + "\", element=\"" + element.toString() + "\""); - } catch (org.jdom.JDOMException je) { + } catch (org.jdom2.JDOMException je) { throw new CrosswalkInternalException( "Failed parsing XML fragment in properties file: \"" + prolog + val + postlog + "\": " + je .toString(), je); @@ -326,6 +326,7 @@ public class QDCCrosswalk extends SelfNamedPlugin * @throws IOException if IO error * @throws SQLException if database error * @throws AuthorizeException if authorization error + * @return List of Elements */ @Override public List disseminateList(Context context, DSpaceObject dso) diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/RoleCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/RoleCrosswalk.java index d36ff3edf5..2c763036ce 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/RoleCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/RoleCrosswalk.java @@ -26,12 +26,12 @@ import org.dspace.core.factory.CoreServiceFactory; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; import org.dspace.workflow.WorkflowException; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.JDOMException; -import org.jdom.Namespace; -import org.jdom.input.SAXBuilder; -import org.jdom.output.XMLOutputter; +import org.jdom2.Document; +import org.jdom2.Element; +import org.jdom2.JDOMException; +import org.jdom2.Namespace; +import org.jdom2.input.SAXBuilder; +import org.jdom2.output.XMLOutputter; /** * Role Crosswalk diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/SimpleDCDisseminationCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/SimpleDCDisseminationCrosswalk.java index 22ec68070a..2f91c3aa07 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/SimpleDCDisseminationCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/SimpleDCDisseminationCrosswalk.java @@ -24,8 +24,8 @@ import org.dspace.content.service.ItemService; import org.dspace.core.Constants; import org.dspace.core.Context; import org.dspace.core.SelfNamedPlugin; -import org.jdom.Element; -import org.jdom.Namespace; +import org.jdom2.Element; +import org.jdom2.Namespace; /** * Disseminator for Simple Dublin Core metadata in XML format. @@ -84,6 +84,7 @@ public class SimpleDCDisseminationCrosswalk extends SelfNamedPlugin * @throws IOException if IO error * @throws SQLException if database error * @throws AuthorizeException if authorization error + * @return List of Elements */ @Override public List disseminateList(Context context, DSpaceObject dso) diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/XHTMLHeadDisseminationCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/XHTMLHeadDisseminationCrosswalk.java index d03d2dd887..2fbbdd9756 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/XHTMLHeadDisseminationCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/XHTMLHeadDisseminationCrosswalk.java @@ -34,9 +34,9 @@ import org.dspace.core.Context; import org.dspace.core.SelfNamedPlugin; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; -import org.jdom.Element; -import org.jdom.Namespace; -import org.jdom.Verifier; +import org.jdom2.Element; +import org.jdom2.Namespace; +import org.jdom2.Verifier; /** * Crosswalk for creating appropriate <meta> elements to appear in the @@ -178,6 +178,7 @@ public class XHTMLHeadDisseminationCrosswalk * @throws IOException if IO error * @throws SQLException if database error * @throws AuthorizeException if authorization error + * @return List of Elements */ @Override public List disseminateList(Context context, DSpaceObject dso) throws CrosswalkException, diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTCrosswalk.java index 1c85fd82c5..ba3d5717d6 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTCrosswalk.java @@ -21,7 +21,7 @@ import javax.xml.transform.stream.StreamSource; import org.dspace.core.SelfNamedPlugin; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; -import org.jdom.Namespace; +import org.jdom2.Namespace; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTDisseminationCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTDisseminationCrosswalk.java index 6c30c1b1a4..26371b46aa 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTDisseminationCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTDisseminationCrosswalk.java @@ -18,6 +18,7 @@ import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; +import java.util.stream.Collectors; import javax.xml.transform.Transformer; import javax.xml.transform.TransformerException; @@ -41,14 +42,15 @@ import org.dspace.core.factory.CoreServiceFactory; import org.dspace.handle.factory.HandleServiceFactory; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.Namespace; -import org.jdom.Verifier; -import org.jdom.output.Format; -import org.jdom.output.XMLOutputter; -import org.jdom.transform.JDOMResult; -import org.jdom.transform.JDOMSource; +import org.jdom2.Content; +import org.jdom2.Document; +import org.jdom2.Element; +import org.jdom2.Namespace; +import org.jdom2.Verifier; +import org.jdom2.output.Format; +import org.jdom2.output.XMLOutputter; +import org.jdom2.transform.JDOMResult; +import org.jdom2.transform.JDOMSource; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -244,6 +246,7 @@ public class XSLTDisseminationCrosswalk * @throws SQLException if database error * @throws AuthorizeException if authorization error * @see DisseminationCrosswalk + * @return List of Elements */ @Override public List disseminateList(Context context, DSpaceObject dso) @@ -268,7 +271,12 @@ public class XSLTDisseminationCrosswalk try { JDOMResult result = new JDOMResult(); xform.transform(new JDOMSource(createDIM(dso).getChildren()), result); - return result.getResult(); + List contentList = result.getResult(); + // Transform List into List + List elementList = contentList.stream() + .filter(obj -> obj instanceof Element) + .map(Element.class::cast).collect(Collectors.toList()); + return elementList; } catch (TransformerException e) { LOG.error("Got error: " + e.toString()); throw new CrosswalkInternalException("XSL translation failed: " + e.toString(), e); diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTIngestionCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTIngestionCrosswalk.java index 37a822374d..63ef5f7336 100644 --- a/dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTIngestionCrosswalk.java +++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTIngestionCrosswalk.java @@ -12,6 +12,7 @@ import java.io.IOException; import java.sql.SQLException; import java.util.Iterator; import java.util.List; +import java.util.stream.Collectors; import javax.xml.transform.Transformer; import javax.xml.transform.TransformerException; @@ -34,13 +35,14 @@ import org.dspace.content.service.ItemService; import org.dspace.core.Constants; import org.dspace.core.Context; import org.dspace.core.factory.CoreServiceFactory; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.input.SAXBuilder; -import org.jdom.output.Format; -import org.jdom.output.XMLOutputter; -import org.jdom.transform.JDOMResult; -import org.jdom.transform.JDOMSource; +import org.jdom2.Content; +import org.jdom2.Document; +import org.jdom2.Element; +import org.jdom2.input.SAXBuilder; +import org.jdom2.output.Format; +import org.jdom2.output.XMLOutputter; +import org.jdom2.transform.JDOMResult; +import org.jdom2.transform.JDOMSource; /** * Configurable XSLT-driven ingestion Crosswalk @@ -141,7 +143,12 @@ public class XSLTIngestionCrosswalk try { JDOMResult result = new JDOMResult(); xform.transform(new JDOMSource(metadata), result); - ingestDIM(context, dso, result.getResult(), createMissingMetadataFields); + List contentList = result.getResult(); + // Transform List into List + List elementList = contentList.stream() + .filter(obj -> obj instanceof Element) + .map(Element.class::cast).collect(Collectors.toList()); + ingestDIM(context, dso, elementList, createMissingMetadataFields); } catch (TransformerException e) { log.error("Got error: " + e.toString()); throw new CrosswalkInternalException("XSL Transformation failed: " + e.toString(), e); diff --git a/dspace-api/src/main/java/org/dspace/content/packager/AbstractMETSDisseminator.java b/dspace-api/src/main/java/org/dspace/content/packager/AbstractMETSDisseminator.java index 471b9ba27c..03afb5e852 100644 --- a/dspace-api/src/main/java/org/dspace/content/packager/AbstractMETSDisseminator.java +++ b/dspace-api/src/main/java/org/dspace/content/packager/AbstractMETSDisseminator.java @@ -83,10 +83,10 @@ import org.dspace.license.factory.LicenseServiceFactory; import org.dspace.license.service.CreativeCommonsService; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; -import org.jdom.Element; -import org.jdom.Namespace; -import org.jdom.output.Format; -import org.jdom.output.XMLOutputter; +import org.jdom2.Element; +import org.jdom2.Namespace; +import org.jdom2.output.Format; +import org.jdom2.output.XMLOutputter; /** * Base class for disseminator of diff --git a/dspace-api/src/main/java/org/dspace/content/packager/AbstractMETSIngester.java b/dspace-api/src/main/java/org/dspace/content/packager/AbstractMETSIngester.java index 9a7fffdec5..98277c4f9c 100644 --- a/dspace-api/src/main/java/org/dspace/content/packager/AbstractMETSIngester.java +++ b/dspace-api/src/main/java/org/dspace/content/packager/AbstractMETSIngester.java @@ -51,7 +51,7 @@ import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; import org.dspace.workflow.WorkflowException; import org.dspace.workflow.factory.WorkflowServiceFactory; -import org.jdom.Element; +import org.jdom2.Element; /** * Base class for package ingester of METS (Metadata Encoding and Transmission diff --git a/dspace-api/src/main/java/org/dspace/content/packager/DSpaceAIPIngester.java b/dspace-api/src/main/java/org/dspace/content/packager/DSpaceAIPIngester.java index 954a68bfc1..e7be7ab511 100644 --- a/dspace-api/src/main/java/org/dspace/content/packager/DSpaceAIPIngester.java +++ b/dspace-api/src/main/java/org/dspace/content/packager/DSpaceAIPIngester.java @@ -20,7 +20,7 @@ import org.dspace.content.crosswalk.CrosswalkException; import org.dspace.content.crosswalk.MetadataValidationException; import org.dspace.core.Constants; import org.dspace.core.Context; -import org.jdom.Element; +import org.jdom2.Element; /** * Subclass of the METS packager framework to ingest a DSpace diff --git a/dspace-api/src/main/java/org/dspace/content/packager/DSpaceMETSIngester.java b/dspace-api/src/main/java/org/dspace/content/packager/DSpaceMETSIngester.java index da3965534f..380764268c 100644 --- a/dspace-api/src/main/java/org/dspace/content/packager/DSpaceMETSIngester.java +++ b/dspace-api/src/main/java/org/dspace/content/packager/DSpaceMETSIngester.java @@ -23,7 +23,7 @@ import org.dspace.core.Constants; import org.dspace.core.Context; import org.dspace.core.factory.CoreServiceFactory; import org.dspace.core.service.PluginService; -import org.jdom.Element; +import org.jdom2.Element; /** * Packager plugin to ingest a diff --git a/dspace-api/src/main/java/org/dspace/content/packager/METSManifest.java b/dspace-api/src/main/java/org/dspace/content/packager/METSManifest.java index 8fb8172aeb..3399bdf0f0 100644 --- a/dspace-api/src/main/java/org/dspace/content/packager/METSManifest.java +++ b/dspace-api/src/main/java/org/dspace/content/packager/METSManifest.java @@ -35,15 +35,17 @@ import org.dspace.core.Context; import org.dspace.core.factory.CoreServiceFactory; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; -import org.jdom.Content; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.JDOMException; -import org.jdom.Namespace; -import org.jdom.input.SAXBuilder; -import org.jdom.output.Format; -import org.jdom.output.XMLOutputter; -import org.jdom.xpath.XPath; +import org.jdom2.Content; +import org.jdom2.Document; +import org.jdom2.Element; +import org.jdom2.JDOMException; +import org.jdom2.Namespace; +import org.jdom2.filter.Filters; +import org.jdom2.input.SAXBuilder; +import org.jdom2.output.Format; +import org.jdom2.output.XMLOutputter; +import org.jdom2.xpath.XPathExpression; +import org.jdom2.xpath.XPathFactory; /** *

@@ -382,15 +384,12 @@ public class METSManifest { public List getMdFiles() throws MetadataValidationException { if (mdFiles == null) { - try { - // Use a special namespace with known prefix - // so we get the right prefix. - XPath xpath = XPath.newInstance("descendant::mets:mdRef"); - xpath.addNamespace(metsNS); - mdFiles = xpath.selectNodes(mets); - } catch (JDOMException je) { - throw new MetadataValidationException("Failed while searching for mdRef elements in manifest: ", je); - } + // Use a special namespace with known prefix + // so we get the right prefix. + XPathExpression xpath = + XPathFactory.instance() + .compile("descendant::mets:mdRef", Filters.element(), null, metsNS); + mdFiles = xpath.evaluate(mets); } return mdFiles; } @@ -414,25 +413,22 @@ public class METSManifest { return null; } - try { - XPath xpath = XPath.newInstance( - "mets:fileSec/mets:fileGrp[@USE=\"CONTENT\"]/mets:file[@GROUPID=\"" + groupID + "\"]"); - xpath.addNamespace(metsNS); - List oFiles = xpath.selectNodes(mets); - if (oFiles.size() > 0) { - if (log.isDebugEnabled()) { - log.debug("Got ORIGINAL file for derived=" + file.toString()); - } - Element flocat = ((Element) oFiles.get(0)).getChild("FLocat", metsNS); - if (flocat != null) { - return flocat.getAttributeValue("href", xlinkNS); - } + XPathExpression xpath = + XPathFactory.instance() + .compile( + "mets:fileSec/mets:fileGrp[@USE=\"CONTENT\"]/mets:file[@GROUPID=\"" + groupID + "\"]", + Filters.element(), null, metsNS); + List oFiles = xpath.evaluate(mets); + if (oFiles.size() > 0) { + if (log.isDebugEnabled()) { + log.debug("Got ORIGINAL file for derived=" + file.toString()); + } + Element flocat = oFiles.get(0).getChild("FLocat", metsNS); + if (flocat != null) { + return flocat.getAttributeValue("href", xlinkNS); } - return null; - } catch (JDOMException je) { - log.warn("Got exception on XPATH looking for Original file, " + je.toString()); - return null; } + return null; } // translate bundle name from METS to DSpace; METS may be "CONTENT" @@ -888,20 +884,16 @@ public class METSManifest { // use only when path varies each time you call it. protected Element getElementByXPath(String path, boolean nullOk) throws MetadataValidationException { - try { - XPath xpath = XPath.newInstance(path); - xpath.addNamespace(metsNS); - xpath.addNamespace(xlinkNS); - Object result = xpath.selectSingleNode(mets); - if (result == null && nullOk) { - return null; - } else if (result instanceof Element) { - return (Element) result; - } else { - throw new MetadataValidationException("METSManifest: Failed to resolve XPath, path=\"" + path + "\""); - } - } catch (JDOMException je) { - throw new MetadataValidationException("METSManifest: Failed to resolve XPath, path=\"" + path + "\"", je); + XPathExpression xpath = + XPathFactory.instance() + .compile(path, Filters.element(), null, metsNS, xlinkNS); + Element result = xpath.evaluateFirst(mets); + if (result == null && nullOk) { + return null; + } else if (result == null && !nullOk) { + throw new MetadataValidationException("METSManifest: Failed to resolve XPath, path=\"" + path + "\""); + } else { + return result; } } diff --git a/dspace-api/src/main/java/org/dspace/content/packager/RoleDisseminator.java b/dspace-api/src/main/java/org/dspace/content/packager/RoleDisseminator.java index 8643f60f6c..f627779af8 100644 --- a/dspace-api/src/main/java/org/dspace/content/packager/RoleDisseminator.java +++ b/dspace-api/src/main/java/org/dspace/content/packager/RoleDisseminator.java @@ -35,7 +35,7 @@ import org.dspace.eperson.PasswordHash; import org.dspace.eperson.factory.EPersonServiceFactory; import org.dspace.eperson.service.EPersonService; import org.dspace.eperson.service.GroupService; -import org.jdom.Namespace; +import org.jdom2.Namespace; /** * Plugin to export all Group and EPerson objects in XML, perhaps for reloading. diff --git a/dspace-api/src/main/java/org/dspace/harvest/HarvestedCollectionServiceImpl.java b/dspace-api/src/main/java/org/dspace/harvest/HarvestedCollectionServiceImpl.java index 88cec74a58..d4bb37cf94 100644 --- a/dspace-api/src/main/java/org/dspace/harvest/HarvestedCollectionServiceImpl.java +++ b/dspace-api/src/main/java/org/dspace/harvest/HarvestedCollectionServiceImpl.java @@ -29,10 +29,10 @@ import org.dspace.harvest.dao.HarvestedCollectionDAO; import org.dspace.harvest.service.HarvestedCollectionService; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.Namespace; -import org.jdom.input.DOMBuilder; +import org.jdom2.Document; +import org.jdom2.Element; +import org.jdom2.Namespace; +import org.jdom2.input.DOMBuilder; import org.springframework.beans.factory.annotation.Autowired; import org.w3c.dom.DOMException; import org.xml.sax.SAXException; diff --git a/dspace-api/src/main/java/org/dspace/harvest/OAIHarvester.java b/dspace-api/src/main/java/org/dspace/harvest/OAIHarvester.java index 71e00d73d7..a15ed53a93 100644 --- a/dspace-api/src/main/java/org/dspace/harvest/OAIHarvester.java +++ b/dspace-api/src/main/java/org/dspace/harvest/OAIHarvester.java @@ -70,11 +70,11 @@ import org.dspace.harvest.service.HarvestedCollectionService; import org.dspace.harvest.service.HarvestedItemService; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.Namespace; -import org.jdom.input.DOMBuilder; -import org.jdom.output.XMLOutputter; +import org.jdom2.Document; +import org.jdom2.Element; +import org.jdom2.Namespace; +import org.jdom2.input.DOMBuilder; +import org.jdom2.output.XMLOutputter; import org.xml.sax.SAXException; diff --git a/dspace-api/src/main/java/org/dspace/identifier/DataCiteXMLCreator.java b/dspace-api/src/main/java/org/dspace/identifier/DataCiteXMLCreator.java index 0ea25ff3a4..ae2cd248d4 100644 --- a/dspace-api/src/main/java/org/dspace/identifier/DataCiteXMLCreator.java +++ b/dspace-api/src/main/java/org/dspace/identifier/DataCiteXMLCreator.java @@ -23,8 +23,8 @@ import org.dspace.core.factory.CoreServiceFactory; import org.dspace.handle.factory.HandleServiceFactory; import org.dspace.services.ConfigurationService; import org.dspace.utils.DSpace; -import org.jdom.Element; -import org.jdom.output.XMLOutputter; +import org.jdom2.Element; +import org.jdom2.output.XMLOutputter; import org.slf4j.Logger; import org.slf4j.LoggerFactory; 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 index bc8ea90957..57136d6143 100644 --- a/dspace-api/src/main/java/org/dspace/identifier/doi/DataCiteConnector.java +++ b/dspace-api/src/main/java/org/dspace/identifier/doi/DataCiteConnector.java @@ -45,13 +45,13 @@ import org.dspace.core.factory.CoreServiceFactory; import org.dspace.handle.service.HandleService; import org.dspace.identifier.DOI; import org.dspace.services.ConfigurationService; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.JDOMException; -import org.jdom.filter.ElementFilter; -import org.jdom.input.SAXBuilder; -import org.jdom.output.Format; -import org.jdom.output.XMLOutputter; +import org.jdom2.Document; +import org.jdom2.Element; +import org.jdom2.JDOMException; +import org.jdom2.filter.ElementFilter; +import org.jdom2.input.SAXBuilder; +import org.jdom2.output.Format; +import org.jdom2.output.XMLOutputter; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.annotation.Autowired; diff --git a/dspace-api/src/main/java/org/dspace/importer/external/arxiv/metadatamapping/contributor/ArXivIdMetadataContributor.java b/dspace-api/src/main/java/org/dspace/importer/external/arxiv/metadatamapping/contributor/ArXivIdMetadataContributor.java index ed5ac5960b..7bd42cf07a 100644 --- a/dspace-api/src/main/java/org/dspace/importer/external/arxiv/metadatamapping/contributor/ArXivIdMetadataContributor.java +++ b/dspace-api/src/main/java/org/dspace/importer/external/arxiv/metadatamapping/contributor/ArXivIdMetadataContributor.java @@ -9,10 +9,10 @@ package org.dspace.importer.external.arxiv.metadatamapping.contributor; import java.util.Collection; -import org.apache.axiom.om.OMElement; import org.dspace.importer.external.metadatamapping.MetadatumDTO; import org.dspace.importer.external.metadatamapping.contributor.MetadataContributor; import org.dspace.importer.external.metadatamapping.contributor.SimpleXpathMetadatumContributor; +import org.jdom2.Element; /** * Arxiv specific implementation of {@link MetadataContributor} @@ -32,7 +32,7 @@ public class ArXivIdMetadataContributor extends SimpleXpathMetadatumContributor * @return a collection of import records. Only the identifier of the found records may be put in the record. */ @Override - public Collection contributeMetadata(OMElement t) { + public Collection contributeMetadata(Element t) { Collection values = super.contributeMetadata(t); parseValue(values); return values; diff --git a/dspace-api/src/main/java/org/dspace/importer/external/arxiv/service/ArXivImportMetadataSourceServiceImpl.java b/dspace-api/src/main/java/org/dspace/importer/external/arxiv/service/ArXivImportMetadataSourceServiceImpl.java index 6b418423fa..96689e62ba 100644 --- a/dspace-api/src/main/java/org/dspace/importer/external/arxiv/service/ArXivImportMetadataSourceServiceImpl.java +++ b/dspace-api/src/main/java/org/dspace/importer/external/arxiv/service/ArXivImportMetadataSourceServiceImpl.java @@ -7,8 +7,10 @@ */ package org.dspace.importer.external.arxiv.service; +import java.io.IOException; import java.io.StringReader; import java.util.ArrayList; +import java.util.Arrays; import java.util.Collection; import java.util.List; import java.util.concurrent.Callable; @@ -20,10 +22,6 @@ import javax.ws.rs.client.WebTarget; import javax.ws.rs.core.MediaType; import javax.ws.rs.core.Response; -import org.apache.axiom.om.OMElement; -import org.apache.axiom.om.OMXMLBuilderFactory; -import org.apache.axiom.om.OMXMLParserWrapper; -import org.apache.axiom.om.xpath.AXIOMXPath; import org.apache.commons.lang3.StringUtils; import org.dspace.content.Item; import org.dspace.importer.external.datamodel.ImportRecord; @@ -31,7 +29,14 @@ import org.dspace.importer.external.datamodel.Query; import org.dspace.importer.external.exception.MetadataSourceException; import org.dspace.importer.external.service.AbstractImportMetadataSourceService; import org.dspace.importer.external.service.components.QuerySource; -import org.jaxen.JaxenException; +import org.jdom2.Document; +import org.jdom2.Element; +import org.jdom2.JDOMException; +import org.jdom2.Namespace; +import org.jdom2.filter.Filters; +import org.jdom2.input.SAXBuilder; +import org.jdom2.xpath.XPathExpression; +import org.jdom2.xpath.XPathFactory; /** * Implements a data source for querying ArXiv @@ -39,7 +44,7 @@ import org.jaxen.JaxenException; * @author Pasquale Cavallo (pasquale.cavallo at 4Science dot it) * */ -public class ArXivImportMetadataSourceServiceImpl extends AbstractImportMetadataSourceService +public class ArXivImportMetadataSourceServiceImpl extends AbstractImportMetadataSourceService implements QuerySource { private WebTarget webTarget; @@ -213,15 +218,20 @@ public class ArXivImportMetadataSourceServiceImpl extends AbstractImportMetadata Response response = invocationBuilder.get(); if (response.getStatus() == 200) { String responseString = response.readEntity(String.class); - OMXMLParserWrapper records = OMXMLBuilderFactory.createOMBuilder(new StringReader(responseString)); - OMElement element = records.getDocumentElement(); - AXIOMXPath xpath = null; + + SAXBuilder saxBuilder = new SAXBuilder(); + Document document = saxBuilder.build(new StringReader(responseString)); + Element root = document.getRootElement(); + + List namespaces = Arrays.asList(Namespace.getNamespace("opensearch", + "http://a9.com/-/spec/opensearch/1.1/")); + XPathExpression xpath = + XPathFactory.instance().compile("opensearch:totalResults", Filters.element(), null, namespaces); + + Element count = xpath.evaluateFirst(root); try { - xpath = new AXIOMXPath("opensearch:totalResults"); - xpath.addNamespace("opensearch", "http://a9.com/-/spec/opensearch/1.1/"); - OMElement count = (OMElement) xpath.selectSingleNode(element); return Integer.parseInt(count.getText()); - } catch (JaxenException e) { + } catch (NumberFormatException e) { return null; } } else { @@ -274,8 +284,8 @@ public class ArXivImportMetadataSourceServiceImpl extends AbstractImportMetadata Response response = invocationBuilder.get(); if (response.getStatus() == 200) { String responseString = response.readEntity(String.class); - List omElements = splitToRecords(responseString); - for (OMElement record : omElements) { + List elements = splitToRecords(responseString); + for (Element record : elements) { results.add(transformSourceRecords(record)); } return results; @@ -321,8 +331,8 @@ public class ArXivImportMetadataSourceServiceImpl extends AbstractImportMetadata Response response = invocationBuilder.get(); if (response.getStatus() == 200) { String responseString = response.readEntity(String.class); - List omElements = splitToRecords(responseString); - for (OMElement record : omElements) { + List elements = splitToRecords(responseString); + for (Element record : elements) { results.add(transformSourceRecords(record)); } return results; @@ -359,8 +369,8 @@ public class ArXivImportMetadataSourceServiceImpl extends AbstractImportMetadata Response response = invocationBuilder.get(); if (response.getStatus() == 200) { String responseString = response.readEntity(String.class); - List omElements = splitToRecords(responseString); - for (OMElement record : omElements) { + List elements = splitToRecords(responseString); + for (Element record : elements) { results.add(transformSourceRecords(record)); } return results; @@ -387,16 +397,21 @@ public class ArXivImportMetadataSourceServiceImpl extends AbstractImportMetadata } } - private List splitToRecords(String recordsSrc) { - OMXMLParserWrapper records = OMXMLBuilderFactory.createOMBuilder(new StringReader(recordsSrc)); - OMElement element = records.getDocumentElement(); - AXIOMXPath xpath = null; + private List splitToRecords(String recordsSrc) { + try { - xpath = new AXIOMXPath("ns:entry"); - xpath.addNamespace("ns", "http://www.w3.org/2005/Atom"); - List recordsList = xpath.selectNodes(element); + SAXBuilder saxBuilder = new SAXBuilder(); + Document document = saxBuilder.build(new StringReader(recordsSrc)); + Element root = document.getRootElement(); + + List namespaces = Arrays.asList(Namespace.getNamespace("ns", + "http://www.w3.org/2005/Atom")); + XPathExpression xpath = + XPathFactory.instance().compile("ns:entry", Filters.element(), null, namespaces); + + List recordsList = xpath.evaluate(root); return recordsList; - } catch (JaxenException e) { + } catch (JDOMException | IOException e) { return null; } } diff --git a/dspace-api/src/main/java/org/dspace/importer/external/metadatamapping/contributor/SimpleXpathMetadatumContributor.java b/dspace-api/src/main/java/org/dspace/importer/external/metadatamapping/contributor/SimpleXpathMetadatumContributor.java index 87cdbfa6ed..65d6d66947 100644 --- a/dspace-api/src/main/java/org/dspace/importer/external/metadatamapping/contributor/SimpleXpathMetadatumContributor.java +++ b/dspace-api/src/main/java/org/dspace/importer/external/metadatamapping/contributor/SimpleXpathMetadatumContributor.java @@ -7,33 +7,36 @@ */ package org.dspace.importer.external.metadatamapping.contributor; +import java.util.ArrayList; import java.util.Collection; import java.util.LinkedList; import java.util.List; import java.util.Map; import javax.annotation.Resource; -import org.apache.axiom.om.OMAttribute; -import org.apache.axiom.om.OMElement; -import org.apache.axiom.om.OMText; -import org.apache.axiom.om.xpath.AXIOMXPath; +import org.apache.logging.log4j.Logger; import org.dspace.importer.external.metadatamapping.MetadataFieldConfig; import org.dspace.importer.external.metadatamapping.MetadataFieldMapping; import org.dspace.importer.external.metadatamapping.MetadatumDTO; -import org.jaxen.JaxenException; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; +import org.jdom2.Attribute; +import org.jdom2.Element; +import org.jdom2.Namespace; +import org.jdom2.Text; +import org.jdom2.filter.Filters; +import org.jdom2.xpath.XPathExpression; +import org.jdom2.xpath.XPathFactory; import org.springframework.beans.factory.annotation.Autowired; /** - * Metadata contributor that takes an axiom OMElement and turns it into a metadatum + * Metadata contributor that takes a JDOM Element and turns it into a metadatum * * @author Roeland Dillen (roeland at atmire dot com) */ -public class SimpleXpathMetadatumContributor implements MetadataContributor { +public class SimpleXpathMetadatumContributor implements MetadataContributor { private MetadataFieldConfig field; - private static final Logger log = LoggerFactory.getLogger(SimpleXpathMetadatumContributor.class); + private static final Logger log + = org.apache.logging.log4j.LogManager.getLogger(); /** * Return prefixToNamespaceMapping @@ -44,14 +47,14 @@ public class SimpleXpathMetadatumContributor implements MetadataContributor> metadataFieldMapping; + private MetadataFieldMapping> metadataFieldMapping; /** * Return metadataFieldMapping * * @return MetadataFieldMapping */ - public MetadataFieldMapping> getMetadataFieldMapping() { + public MetadataFieldMapping> getMetadataFieldMapping() { return metadataFieldMapping; } @@ -62,7 +65,7 @@ public class SimpleXpathMetadatumContributor implements MetadataContributor> metadataFieldMapping) { + MetadataFieldMapping> metadataFieldMapping) { this.metadataFieldMapping = metadataFieldMapping; } @@ -140,36 +143,35 @@ public class SimpleXpathMetadatumContributor implements MetadataContributor contributeMetadata(OMElement t) { + public Collection contributeMetadata(Element t) { List values = new LinkedList<>(); - try { - AXIOMXPath xpath = new AXIOMXPath(query); - for (String ns : prefixToNamespaceMapping.keySet()) { - xpath.addNamespace(prefixToNamespaceMapping.get(ns), ns); - } - List nodes = xpath.selectNodes(t); - for (Object el : nodes) { - if (el instanceof OMElement) { - values.add(metadataFieldMapping.toDCValue(field, ((OMElement) el).getText())); - } else if (el instanceof OMAttribute) { - values.add(metadataFieldMapping.toDCValue(field, ((OMAttribute) el).getAttributeValue())); - } else if (el instanceof String) { - values.add(metadataFieldMapping.toDCValue(field, (String) el)); - } else if (el instanceof OMText) { - values.add(metadataFieldMapping.toDCValue(field, ((OMText) el).getText())); - } else { - log.error("node of type: " + el.getClass()); - } - } - return values; - } catch (JaxenException e) { - log.error(query, e); - throw new RuntimeException(e); + + List namespaces = new ArrayList<>(); + for (String ns : prefixToNamespaceMapping.keySet()) { + namespaces.add(Namespace.getNamespace(prefixToNamespaceMapping.get(ns), ns)); } + XPathExpression xpath = + XPathFactory.instance().compile(query, Filters.fpassthrough(), null, namespaces); + + List nodes = xpath.evaluate(t); + for (Object el : nodes) { + if (el instanceof Element) { + values.add(metadataFieldMapping.toDCValue(field, ((Element) el).getText())); + } else if (el instanceof Attribute) { + values.add(metadataFieldMapping.toDCValue(field, ((Attribute) el).getValue())); + } else if (el instanceof String) { + values.add(metadataFieldMapping.toDCValue(field, (String) el)); + } else if (el instanceof Text) { + values.add(metadataFieldMapping.toDCValue(field, ((Text) el).getText())); + } else { + log.error("Encountered unsupported XML node of type: {}. Skipped that node.", el.getClass()); + } + } + return values; } } diff --git a/dspace-api/src/main/java/org/dspace/importer/external/pubmed/service/PubmedImportMetadataSourceServiceImpl.java b/dspace-api/src/main/java/org/dspace/importer/external/pubmed/service/PubmedImportMetadataSourceServiceImpl.java index 4802dcfa17..73768330d8 100644 --- a/dspace-api/src/main/java/org/dspace/importer/external/pubmed/service/PubmedImportMetadataSourceServiceImpl.java +++ b/dspace-api/src/main/java/org/dspace/importer/external/pubmed/service/PubmedImportMetadataSourceServiceImpl.java @@ -25,10 +25,6 @@ import javax.ws.rs.core.MediaType; import javax.ws.rs.core.Response; import com.google.common.io.CharStreams; -import org.apache.axiom.om.OMElement; -import org.apache.axiom.om.OMXMLBuilderFactory; -import org.apache.axiom.om.OMXMLParserWrapper; -import org.apache.axiom.om.xpath.AXIOMXPath; import org.dspace.content.Item; import org.dspace.importer.external.datamodel.ImportRecord; import org.dspace.importer.external.datamodel.Query; @@ -38,7 +34,13 @@ import org.dspace.importer.external.exception.MetadataSourceException; import org.dspace.importer.external.service.AbstractImportMetadataSourceService; import org.dspace.importer.external.service.components.FileSource; import org.dspace.importer.external.service.components.QuerySource; -import org.jaxen.JaxenException; +import org.jdom2.Document; +import org.jdom2.Element; +import org.jdom2.JDOMException; +import org.jdom2.filter.Filters; +import org.jdom2.input.SAXBuilder; +import org.jdom2.xpath.XPathExpression; +import org.jdom2.xpath.XPathFactory; /** * Implements a data source for querying PubMed Central @@ -46,7 +48,7 @@ import org.jaxen.JaxenException; * @author Roeland Dillen (roeland at atmire dot com) * @author Pasquale Cavallo (pasquale.cavallo at 4science dot it) */ -public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadataSourceService +public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadataSourceService implements QuerySource, FileSource { private String baseAddress; @@ -59,7 +61,7 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat /** * Set the file extensions supported by this metadata service * - * @param supportedExtensionsthe file extensions (xml,txt,...) supported by this service + * @param supportedExtensions the file extensions (xml,txt,...) supported by this service */ public void setSupportedExtensions(List supportedExtensions) { this.supportedExtensions = supportedExtensions; @@ -243,17 +245,21 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat private String getSingleElementValue(String src, String elementName) { - OMXMLParserWrapper records = OMXMLBuilderFactory.createOMBuilder(new StringReader(src)); - OMElement element = records.getDocumentElement(); - AXIOMXPath xpath = null; String value = null; + try { - xpath = new AXIOMXPath("//" + elementName); - List recordsList = xpath.selectNodes(element); - if (!recordsList.isEmpty()) { - value = recordsList.get(0).getText(); + SAXBuilder saxBuilder = new SAXBuilder(); + Document document = saxBuilder.build(new StringReader(src)); + Element root = document.getRootElement(); + + XPathExpression xpath = + XPathFactory.instance().compile("//" + elementName, Filters.element()); + + Element record = xpath.evaluateFirst(root); + if (record != null) { + value = record.getText(); } - } catch (JaxenException e) { + } catch (JDOMException | IOException e) { value = null; } return value; @@ -314,9 +320,9 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat invocationBuilder = getRecordsTarget.request(MediaType.TEXT_PLAIN_TYPE); response = invocationBuilder.get(); - List omElements = splitToRecords(response.readEntity(String.class)); + List elements = splitToRecords(response.readEntity(String.class)); - for (OMElement record : omElements) { + for (Element record : elements) { records.add(transformSourceRecords(record)); } @@ -324,15 +330,18 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat } } - private List splitToRecords(String recordsSrc) { - OMXMLParserWrapper records = OMXMLBuilderFactory.createOMBuilder(new StringReader(recordsSrc)); - OMElement element = records.getDocumentElement(); - AXIOMXPath xpath = null; + private List splitToRecords(String recordsSrc) { try { - xpath = new AXIOMXPath("//PubmedArticle"); - List recordsList = xpath.selectNodes(element); + SAXBuilder saxBuilder = new SAXBuilder(); + Document document = saxBuilder.build(new StringReader(recordsSrc)); + Element root = document.getRootElement(); + + XPathExpression xpath = + XPathFactory.instance().compile("//PubmedArticle", Filters.element()); + + List recordsList = xpath.evaluate(root); return recordsList; - } catch (JaxenException e) { + } catch (JDOMException | IOException e) { return null; } } @@ -362,13 +371,13 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat Response response = invocationBuilder.get(); - List omElements = splitToRecords(response.readEntity(String.class)); + List elements = splitToRecords(response.readEntity(String.class)); - if (omElements.size() == 0) { + if (elements.isEmpty()) { return null; } - return transformSourceRecords(omElements.get(0)); + return transformSourceRecords(elements.get(0)); } } @@ -441,8 +450,8 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat private List parseXMLString(String xml) { List records = new LinkedList(); - List omElements = splitToRecords(xml); - for (OMElement record : omElements) { + List elements = splitToRecords(xml); + for (Element record : elements) { records.add(transformSourceRecords(record)); } return records; diff --git a/dspace-api/src/main/java/org/dspace/license/CCLicenseConnectorService.java b/dspace-api/src/main/java/org/dspace/license/CCLicenseConnectorService.java index 0c061d2d64..64450b796c 100644 --- a/dspace-api/src/main/java/org/dspace/license/CCLicenseConnectorService.java +++ b/dspace-api/src/main/java/org/dspace/license/CCLicenseConnectorService.java @@ -10,7 +10,7 @@ package org.dspace.license; import java.io.IOException; import java.util.Map; -import org.jdom.Document; +import org.jdom2.Document; /** * Service interface class for the Creative commons license connector service. diff --git a/dspace-api/src/main/java/org/dspace/license/CCLicenseConnectorServiceImpl.java b/dspace-api/src/main/java/org/dspace/license/CCLicenseConnectorServiceImpl.java index 792c25d629..619227432d 100644 --- a/dspace-api/src/main/java/org/dspace/license/CCLicenseConnectorServiceImpl.java +++ b/dspace-api/src/main/java/org/dspace/license/CCLicenseConnectorServiceImpl.java @@ -32,13 +32,14 @@ import org.apache.http.impl.client.HttpClientBuilder; import org.apache.http.util.EntityUtils; import org.apache.logging.log4j.Logger; import org.dspace.services.ConfigurationService; -import org.jaxen.JaxenException; -import org.jaxen.jdom.JDOMXPath; -import org.jdom.Attribute; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.JDOMException; -import org.jdom.input.SAXBuilder; +import org.jdom2.Attribute; +import org.jdom2.Document; +import org.jdom2.Element; +import org.jdom2.JDOMException; +import org.jdom2.filter.Filters; +import org.jdom2.input.SAXBuilder; +import org.jdom2.xpath.XPathExpression; +import org.jdom2.xpath.XPathFactory; import org.springframework.beans.factory.InitializingBean; import org.springframework.beans.factory.annotation.Autowired; import org.xml.sax.InputSource; @@ -96,7 +97,7 @@ public class CCLicenseConnectorServiceImpl implements CCLicenseConnectorService, List licenses; try (CloseableHttpResponse response = client.execute(httpGet)) { licenses = retrieveLicenses(response); - } catch (JDOMException | JaxenException | IOException e) { + } catch (JDOMException | IOException e) { log.error("Error while retrieving the license details using url: " + uri, e); licenses = Collections.emptyList(); } @@ -110,7 +111,7 @@ public class CCLicenseConnectorServiceImpl implements CCLicenseConnectorService, try (CloseableHttpResponse response = client.execute(licenseHttpGet)) { CCLicense ccLicense = retrieveLicenseObject(license, response); ccLicenses.put(ccLicense.getLicenseId(), ccLicense); - } catch (JaxenException | JDOMException | IOException e) { + } catch (JDOMException | IOException e) { log.error("Error while retrieving the license details using url: " + licenseUri, e); } } @@ -125,25 +126,23 @@ public class CCLicenseConnectorServiceImpl implements CCLicenseConnectorService, * @param response The response from the API * @return a list of license identifiers for which details need to be retrieved * @throws IOException - * @throws JaxenException * @throws JDOMException */ private List retrieveLicenses(CloseableHttpResponse response) - throws IOException, JaxenException, JDOMException { + throws IOException, JDOMException { List domains = new LinkedList<>(); String[] excludedLicenses = configurationService.getArrayProperty("cc.license.classfilter"); - String responseString = EntityUtils.toString(response.getEntity()); - JDOMXPath licenseClassXpath = new JDOMXPath("//licenses/license"); - + XPathExpression licenseClassXpath = + XPathFactory.instance().compile("//licenses/license", Filters.element()); try (StringReader stringReader = new StringReader(responseString)) { InputSource is = new InputSource(stringReader); - org.jdom.Document classDoc = this.parser.build(is); + org.jdom2.Document classDoc = this.parser.build(is); - List elements = licenseClassXpath.selectNodes(classDoc); + List elements = licenseClassXpath.evaluate(classDoc); for (Element element : elements) { String licenseId = getSingleNodeValue(element, "@id"); if (StringUtils.isNotBlank(licenseId) && !ArrayUtils.contains(excludedLicenses, licenseId)) { @@ -163,30 +162,29 @@ public class CCLicenseConnectorServiceImpl implements CCLicenseConnectorService, * @param response for a specific CC License response * @return the corresponding CC License Object * @throws IOException - * @throws JaxenException * @throws JDOMException */ private CCLicense retrieveLicenseObject(final String licenseId, CloseableHttpResponse response) - throws IOException, JaxenException, JDOMException { + throws IOException, JDOMException { String responseString = EntityUtils.toString(response.getEntity()); - - JDOMXPath licenseClassXpath = new JDOMXPath("//licenseclass"); - JDOMXPath licenseFieldXpath = new JDOMXPath("field"); - + XPathExpression licenseClassXpath = + XPathFactory.instance().compile("//licenseclass", Filters.fpassthrough()); + XPathExpression licenseFieldXpath = + XPathFactory.instance().compile("field", Filters.element()); try (StringReader stringReader = new StringReader(responseString)) { InputSource is = new InputSource(stringReader); - org.jdom.Document classDoc = this.parser.build(is); + org.jdom2.Document classDoc = this.parser.build(is); - Object element = licenseClassXpath.selectSingleNode(classDoc); + Object element = licenseClassXpath.evaluateFirst(classDoc); String licenseLabel = getSingleNodeValue(element, "label"); List ccLicenseFields = new LinkedList<>(); - List licenseFields = licenseFieldXpath.selectNodes(element); + List licenseFields = licenseFieldXpath.evaluate(element); for (Element licenseField : licenseFields) { CCLicenseField ccLicenseField = parseLicenseField(licenseField); ccLicenseFields.add(ccLicenseField); @@ -196,13 +194,14 @@ public class CCLicenseConnectorServiceImpl implements CCLicenseConnectorService, } } - private CCLicenseField parseLicenseField(final Element licenseField) throws JaxenException { + private CCLicenseField parseLicenseField(final Element licenseField) { String id = getSingleNodeValue(licenseField, "@id"); String label = getSingleNodeValue(licenseField, "label"); String description = getSingleNodeValue(licenseField, "description"); - JDOMXPath enumXpath = new JDOMXPath("enum"); - List enums = enumXpath.selectNodes(licenseField); + XPathExpression enumXpath = + XPathFactory.instance().compile("enum", Filters.element()); + List enums = enumXpath.evaluate(licenseField); List ccLicenseFieldEnumList = new LinkedList<>(); @@ -215,7 +214,7 @@ public class CCLicenseConnectorServiceImpl implements CCLicenseConnectorService, } - private CCLicenseFieldEnum parseEnum(final Element enumElement) throws JaxenException { + private CCLicenseFieldEnum parseEnum(final Element enumElement) { String id = getSingleNodeValue(enumElement, "@id"); String label = getSingleNodeValue(enumElement, "label"); String description = getSingleNodeValue(enumElement, "description"); @@ -236,9 +235,10 @@ public class CCLicenseConnectorServiceImpl implements CCLicenseConnectorService, } } - private String getSingleNodeValue(final Object t, String query) throws JaxenException { - JDOMXPath xpath = new JDOMXPath(query); - Object singleNode = xpath.selectSingleNode(t); + private String getSingleNodeValue(final Object t, String query) { + XPathExpression xpath = + XPathFactory.instance().compile(query, Filters.fpassthrough()); + Object singleNode = xpath.evaluateFirst(t); return getNodeValue(singleNode); } @@ -273,7 +273,7 @@ public class CCLicenseConnectorServiceImpl implements CCLicenseConnectorService, try (CloseableHttpResponse response = client.execute(httpPost)) { return retrieveLicenseUri(response); - } catch (JDOMException | JaxenException | IOException e) { + } catch (JDOMException | IOException e) { log.error("Error while retrieving the license uri for license : " + licenseId + " with answers " + answerMap.toString(), e); } @@ -286,21 +286,20 @@ public class CCLicenseConnectorServiceImpl implements CCLicenseConnectorService, * @param response for a specific CC License URI response * @return the corresponding CC License URI as a string * @throws IOException - * @throws JaxenException * @throws JDOMException */ private String retrieveLicenseUri(final CloseableHttpResponse response) - throws IOException, JaxenException, JDOMException { + throws IOException, JDOMException { String responseString = EntityUtils.toString(response.getEntity()); - JDOMXPath licenseClassXpath = new JDOMXPath("//result/license-uri"); - + XPathExpression licenseClassXpath = + XPathFactory.instance().compile("//result/license-uri", Filters.fpassthrough()); try (StringReader stringReader = new StringReader(responseString)) { InputSource is = new InputSource(stringReader); - org.jdom.Document classDoc = this.parser.build(is); + org.jdom2.Document classDoc = this.parser.build(is); - Object node = licenseClassXpath.selectSingleNode(classDoc); + Object node = licenseClassXpath.evaluateFirst(classDoc); String nodeValue = getNodeValue(node); if (StringUtils.isNotBlank(nodeValue)) { @@ -364,12 +363,7 @@ public class CCLicenseConnectorServiceImpl implements CCLicenseConnectorService, * @return the license name */ public String retrieveLicenseName(final Document doc) { - try { - return getSingleNodeValue(doc, "//result/license-name"); - } catch (JaxenException e) { - log.error("Error while retrieving the license name from the license document", e); - } - return null; + return getSingleNodeValue(doc, "//result/license-name"); } } diff --git a/dspace-api/src/main/java/org/dspace/license/CreativeCommonsServiceImpl.java b/dspace-api/src/main/java/org/dspace/license/CreativeCommonsServiceImpl.java index ccc660b63b..96f110c101 100644 --- a/dspace-api/src/main/java/org/dspace/license/CreativeCommonsServiceImpl.java +++ b/dspace-api/src/main/java/org/dspace/license/CreativeCommonsServiceImpl.java @@ -40,8 +40,8 @@ import org.dspace.core.Utils; import org.dspace.license.service.CreativeCommonsService; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; -import org.jdom.Document; -import org.jdom.transform.JDOMSource; +import org.jdom2.Document; +import org.jdom2.transform.JDOMSource; import org.springframework.beans.factory.InitializingBean; import org.springframework.beans.factory.annotation.Autowired; diff --git a/dspace-api/src/main/java/org/dspace/license/service/CreativeCommonsService.java b/dspace-api/src/main/java/org/dspace/license/service/CreativeCommonsService.java index 1f5f1ddd02..0f4911aa3e 100644 --- a/dspace-api/src/main/java/org/dspace/license/service/CreativeCommonsService.java +++ b/dspace-api/src/main/java/org/dspace/license/service/CreativeCommonsService.java @@ -18,7 +18,7 @@ import org.dspace.content.Bitstream; import org.dspace.content.Item; import org.dspace.core.Context; import org.dspace.license.CCLicense; -import org.jdom.Document; +import org.jdom2.Document; /** * Service interface class for the Creative commons licensing. diff --git a/dspace-api/src/main/java/org/dspace/testing/PubMedToImport.java b/dspace-api/src/main/java/org/dspace/testing/PubMedToImport.java index b7ded5ecbf..ec51528429 100644 --- a/dspace-api/src/main/java/org/dspace/testing/PubMedToImport.java +++ b/dspace-api/src/main/java/org/dspace/testing/PubMedToImport.java @@ -24,10 +24,10 @@ import org.apache.commons.cli.Options; import org.apache.commons.lang3.StringUtils; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.output.Format; -import org.jdom.output.XMLOutputter; +import org.jdom2.Document; +import org.jdom2.Element; +import org.jdom2.output.Format; +import org.jdom2.output.XMLOutputter; import org.xml.sax.Attributes; import org.xml.sax.SAXException; import org.xml.sax.helpers.DefaultHandler; diff --git a/dspace-api/src/test/java/org/dspace/AbstractIntegrationTestWithDatabase.java b/dspace-api/src/test/java/org/dspace/AbstractIntegrationTestWithDatabase.java index 402947b966..cada4944e3 100644 --- a/dspace-api/src/test/java/org/dspace/AbstractIntegrationTestWithDatabase.java +++ b/dspace-api/src/test/java/org/dspace/AbstractIntegrationTestWithDatabase.java @@ -32,7 +32,7 @@ import org.dspace.services.factory.DSpaceServicesFactory; import org.dspace.statistics.MockSolrLoggerServiceImpl; import org.dspace.statistics.MockSolrStatisticsCore; import org.dspace.storage.rdbms.DatabaseUtils; -import org.jdom.Document; +import org.jdom2.Document; import org.junit.After; import org.junit.Before; import org.junit.BeforeClass; diff --git a/dspace-api/src/test/java/org/dspace/app/packager/PackagerIT.java b/dspace-api/src/test/java/org/dspace/app/packager/PackagerIT.java index c814d2d9f6..7d808ab871 100644 --- a/dspace-api/src/test/java/org/dspace/app/packager/PackagerIT.java +++ b/dspace-api/src/test/java/org/dspace/app/packager/PackagerIT.java @@ -38,7 +38,7 @@ import org.dspace.content.service.ItemService; import org.dspace.content.service.WorkspaceItemService; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; -import org.jdom.Element; +import org.jdom2.Element; import org.junit.After; import org.junit.Before; import org.junit.Test; diff --git a/dspace-api/src/test/java/org/dspace/content/crosswalk/QDCCrosswalkTest.java b/dspace-api/src/test/java/org/dspace/content/crosswalk/QDCCrosswalkTest.java index efed8ad8dc..2eafc03986 100644 --- a/dspace-api/src/test/java/org/dspace/content/crosswalk/QDCCrosswalkTest.java +++ b/dspace-api/src/test/java/org/dspace/content/crosswalk/QDCCrosswalkTest.java @@ -14,7 +14,7 @@ import org.dspace.AbstractDSpaceTest; import org.dspace.core.service.PluginService; import org.dspace.services.ConfigurationService; import org.dspace.services.factory.DSpaceServicesFactory; -import org.jdom.Namespace; +import org.jdom2.Namespace; import org.junit.After; import org.junit.AfterClass; import org.junit.Before; diff --git a/dspace-api/src/test/java/org/dspace/license/MockCCLicenseConnectorServiceImpl.java b/dspace-api/src/test/java/org/dspace/license/MockCCLicenseConnectorServiceImpl.java index 8545c4187d..30a5a3a9b5 100644 --- a/dspace-api/src/test/java/org/dspace/license/MockCCLicenseConnectorServiceImpl.java +++ b/dspace-api/src/test/java/org/dspace/license/MockCCLicenseConnectorServiceImpl.java @@ -15,8 +15,8 @@ import java.util.List; import java.util.Map; import org.apache.commons.lang3.StringUtils; -import org.jdom.Document; -import org.jdom.JDOMException; +import org.jdom2.Document; +import org.jdom2.JDOMException; /** * Mock implementation for the Creative commons license connector service. diff --git a/dspace-server-webapp/src/test/java/org/dspace/license/MockCCLicenseConnectorServiceImpl.java b/dspace-server-webapp/src/test/java/org/dspace/license/MockCCLicenseConnectorServiceImpl.java index bb443ab4a4..d70499d096 100644 --- a/dspace-server-webapp/src/test/java/org/dspace/license/MockCCLicenseConnectorServiceImpl.java +++ b/dspace-server-webapp/src/test/java/org/dspace/license/MockCCLicenseConnectorServiceImpl.java @@ -15,8 +15,8 @@ import java.util.List; import java.util.Map; import org.apache.commons.lang3.StringUtils; -import org.jdom.Document; -import org.jdom.JDOMException; +import org.jdom2.Document; +import org.jdom2.JDOMException; /** * Mock implementation for the Creative commons license connector service. diff --git a/dspace-swordv2/pom.xml b/dspace-swordv2/pom.xml index 3fbc6cf469..6bf09475ef 100644 --- a/dspace-swordv2/pom.xml +++ b/dspace-swordv2/pom.xml @@ -135,7 +135,8 @@ org.apache.ws.commons.axiom fom-impl - ${axiom.version} + + 1.2.22 diff --git a/pom.xml b/pom.xml index 27f6597caa..e03dcb3b07 100644 --- a/pom.xml +++ b/pom.xml @@ -27,7 +27,6 @@ 42.3.3 8.8.1 - 1.2.22 3.4.0 2.10.0 @@ -41,6 +40,7 @@ 2.17.1 2.0.24 3.17 + 1.18.0 1.7.25 @@ -1116,7 +1116,7 @@ 3.4.14 - + org.apache.james apache-mime4j-core @@ -1161,6 +1161,23 @@ ${hibernate-validator.version} + + + com.rometools + rome + ${rome.version} + + + com.rometools + rome-modules + ${rome.version} + + + com.rometools + rome-utils + ${rome.version} + + org.springframework spring-orm @@ -1468,6 +1485,7 @@ 3.1.0 + jaxen jaxen @@ -1481,8 +1499,8 @@ org.jdom - jdom - 1.1.3 + jdom2 + 2.0.6.1