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Merge branch 'main' into feature-relationship-versioning-contribution

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This commit is contained in:
Bruno Roemers
2022-05-04 11:46:28 +02:00
parent 9e654f7635 a235551fab
commit d119d842f8
326 changed files with 4742 additions and 5526 deletions
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176
dspace-api/pom.xml
View File

@@ -1,4 +1,6 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.dspace</groupId>
<artifactId>dspace-api</artifactId>
@@ -12,7 +14,7 @@
<parent>
<groupId>org.dspace</groupId>
<artifactId>dspace-parent</artifactId>
<version>7.2</version>
<version>7.3-SNAPSHOT</version>
<relativePath>..</relativePath>
</parent>
@@ -335,9 +337,13 @@
<dependencies>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-ehcache</artifactId>
<artifactId>hibernate-core</artifactId>
<exclusions>
<!-- Newer version pulled in via Jersey below -->
<exclusion>
@@ -346,6 +352,15 @@
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-jcache</artifactId>
</dependency>
<dependency>
<groupId>org.ehcache</groupId>
<artifactId>ehcache</artifactId>
<version>${ehcache.version}</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-jpamodelgen</artifactId>
@@ -358,7 +373,7 @@
<dependency>
<groupId>org.hibernate.javax.persistence</groupId>
<artifactId>hibernate-jpa-2.1-api</artifactId>
<version>1.0.0.Final</version>
<version>1.0.2.Final</version>
</dependency>
<dependency>
@@ -379,7 +394,7 @@
<groupId>org.ow2.asm</groupId>
<artifactId>asm-commons</artifactId>
</exclusion>
<!-- Newer version of Bouncycastle brought in via solr-cell -->
<!-- Newer version of Bouncycastle brought in via Tika -->
<exclusion>
<groupId>org.bouncycastle</groupId>
<artifactId>bcpkix-jdk15on</artifactId>
@@ -505,7 +520,7 @@
</dependency>
<dependency>
<groupId>org.jdom</groupId>
<artifactId>jdom</artifactId>
<artifactId>jdom2</artifactId>
</dependency>
<dependency>
<groupId>org.apache.pdfbox</groupId>
@@ -515,18 +530,6 @@
<groupId>org.apache.pdfbox</groupId>
<artifactId>fontbox</artifactId>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-scratchpad</artifactId>
</dependency>
<dependency>
<groupId>xalan</groupId>
<artifactId>xalan</artifactId>
</dependency>
<dependency>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
</dependency>
<dependency>
<groupId>com.ibm.icu</groupId>
<artifactId>icu4j</artifactId>
@@ -566,9 +569,12 @@
</dependency>
<!-- Used for RSS / ATOM syndication feeds -->
<dependency>
<groupId>org.rometools</groupId>
<groupId>com.rometools</groupId>
<artifactId>rome</artifactId>
</dependency>
<dependency>
<groupId>com.rometools</groupId>
<artifactId>rome-modules</artifactId>
<version>1.0</version>
</dependency>
<dependency>
<groupId>org.jbibtex</groupId>
@@ -579,28 +585,22 @@
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore</artifactId>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpmime</artifactId>
</dependency>
<!-- SolrJ is used to communicate with Solr throughout the dspace-api -->
<dependency>
<groupId>org.apache.solr</groupId>
<artifactId>solr-solrj</artifactId>
<version>${solr.client.version}</version>
<exclusions>
<!-- Newer Jetty version brought in via Parent POM -->
<exclusion>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-http</artifactId>
</exclusion>
<exclusion>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-io</artifactId>
</exclusion>
<exclusion>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-util</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- Solr Core is needed for Integration Tests (to run a MockSolrServer) -->
<!-- Solr Core is only needed for Integration Tests (to run a MockSolrServer) -->
<!-- The following Solr / Lucene dependencies also support integration tests -->
<dependency>
<groupId>org.apache.solr</groupId>
@@ -628,39 +628,10 @@
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.solr</groupId>
<artifactId>solr-cell</artifactId>
<exclusions>
<!-- Newer version brought in by opencsv -->
<exclusion>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
</exclusion>
<!-- Newer Jetty version brought in via Parent POM -->
<exclusion>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-http</artifactId>
</exclusion>
<exclusion>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-io</artifactId>
</exclusion>
<exclusion>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-util</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-core</artifactId>
</dependency>
<!-- Used for full-text indexing with Solr -->
<dependency>
<groupId>org.apache.tika</groupId>
<artifactId>tika-parsers</artifactId>
</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-analyzers-icu</artifactId>
@@ -676,9 +647,15 @@
<artifactId>lucene-analyzers-stempel</artifactId>
<scope>test</scope>
</dependency>
<!-- Tika is used to extract full text from documents in order to index in Solr -->
<dependency>
<groupId>org.apache.xmlbeans</groupId>
<artifactId>xmlbeans</artifactId>
<groupId>org.apache.tika</groupId>
<artifactId>tika-core</artifactId>
</dependency>
<dependency>
<groupId>org.apache.tika</groupId>
<artifactId>tika-parsers-standard-package</artifactId>
</dependency>
<dependency>
@@ -702,13 +679,6 @@
<version>1.1.1</version>
</dependency>
<!-- Gson: Java to Json conversion -->
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
@@ -736,7 +706,7 @@
<dependency>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-core</artifactId>
<version>6.5.7</version>
<version>8.4.4</version>
</dependency>
<!-- Google Analytics -->
@@ -792,44 +762,6 @@
<artifactId>jaxb-runtime</artifactId>
</dependency>
<!-- Apache Axiom -->
<dependency>
<groupId>org.apache.ws.commons.axiom</groupId>
<artifactId>axiom-impl</artifactId>
<version>${axiom.version}</version>
<exclusions>
<!-- Exclude Geronimo as it is NOT necessary when using javax.activation (which we use)
See: https://ws.apache.org/axiom/userguide/ch04.html#d0e732 -->
<exclusion>
<groupId>org.apache.geronimo.specs</groupId>
<artifactId>*</artifactId>
</exclusion>
<!-- Exclude Woodstox, as later version provided by Solr dependencies -->
<exclusion>
<groupId>org.codehaus.woodstox</groupId>
<artifactId>woodstox-core-asl</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.ws.commons.axiom</groupId>
<artifactId>axiom-api</artifactId>
<version>${axiom.version}</version>
<exclusions>
<!-- Exclude Geronimo as it is NOT necessary when using javax.activation (which we use)
See: https://ws.apache.org/axiom/userguide/ch04.html#d0e732 -->
<exclusion>
<groupId>org.apache.geronimo.specs</groupId>
<artifactId>*</artifactId>
</exclusion>
<!-- Exclude Woodstox, as later version provided by Solr dependencies -->
<exclusion>
<groupId>org.codehaus.woodstox</groupId>
<artifactId>woodstox-core-asl</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- Jersey / JAX-RS client (javax.ws.rs.*) dependencies needed to integrate with external sources/services -->
<dependency>
<groupId>org.glassfish.jersey.core</groupId>
@@ -885,6 +817,14 @@
<version>20180130</version>
</dependency>
<!-- Useful for testing command-line tools -->
<dependency>
<groupId>com.github.stefanbirkner</groupId>
<artifactId>system-rules</artifactId>
<version>1.19.0</version>
<scope>test</scope>
</dependency>
<!-- Used for Solr core export/import -->
<dependency>
<groupId>com.opencsv</groupId>
@@ -896,7 +836,6 @@
<dependency>
<groupId>org.apache.velocity</groupId>
<artifactId>velocity-engine-core</artifactId>
<type>jar</type>
</dependency>
<dependency>
@@ -918,13 +857,6 @@
<version>2.0.0</version>
</dependency>
<dependency>
<groupId>com.github.stefanbirkner</groupId>
<artifactId>system-rules</artifactId>
<version>1.19.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mock-server</groupId>
<artifactId>mockserver-junit-rule</artifactId>
@@ -971,7 +903,7 @@
<dependency>
<groupId>org.apache.velocity</groupId>
<artifactId>velocity-engine-core</artifactId>
<version>2.2</version>
<version>2.3</version>
</dependency>
<dependency>
<groupId>org.xmlunit</groupId>

26
dspace-api/src/main/java/org/dspace/administer/MetadataImporter.java
View File

@@ -11,13 +11,16 @@ import java.io.IOException;
import java.sql.SQLException;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.TransformerException;
import javax.xml.xpath.XPath;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.DefaultParser;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.xpath.XPathAPI;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.MetadataField;
import org.dspace.content.MetadataSchema;
@@ -90,7 +93,7 @@ public class MetadataImporter {
public static void main(String[] args)
throws ParseException, SQLException, IOException, TransformerException,
ParserConfigurationException, AuthorizeException, SAXException,
NonUniqueMetadataException, RegistryImportException {
NonUniqueMetadataException, RegistryImportException, XPathExpressionException {
// create an options object and populate it
CommandLineParser parser = new DefaultParser();
@@ -124,8 +127,8 @@ public class MetadataImporter {
* @throws RegistryImportException if import fails
*/
public static void loadRegistry(String file, boolean forceUpdate)
throws SQLException, IOException, TransformerException, ParserConfigurationException,
AuthorizeException, SAXException, NonUniqueMetadataException, RegistryImportException {
throws SQLException, IOException, TransformerException, ParserConfigurationException, AuthorizeException,
SAXException, NonUniqueMetadataException, RegistryImportException, XPathExpressionException {
Context context = null;
try {
@@ -137,7 +140,9 @@ public class MetadataImporter {
Document document = RegistryImporter.loadXML(file);
// Get the nodes corresponding to types
NodeList schemaNodes = XPathAPI.selectNodeList(document, "/dspace-dc-types/dc-schema");
XPath xPath = XPathFactory.newInstance().newXPath();
NodeList schemaNodes = (NodeList) xPath.compile("/dspace-dc-types/dc-schema")
.evaluate(document, XPathConstants.NODESET);
// Add each one as a new format to the registry
for (int i = 0; i < schemaNodes.getLength(); i++) {
@@ -146,7 +151,8 @@ public class MetadataImporter {
}
// Get the nodes corresponding to types
NodeList typeNodes = XPathAPI.selectNodeList(document, "/dspace-dc-types/dc-type");
NodeList typeNodes = (NodeList) xPath.compile("/dspace-dc-types/dc-type")
.evaluate(document, XPathConstants.NODESET);
// Add each one as a new format to the registry
for (int i = 0; i < typeNodes.getLength(); i++) {
@@ -178,8 +184,8 @@ public class MetadataImporter {
* @throws RegistryImportException if import fails
*/
private static void loadSchema(Context context, Node node, boolean updateExisting)
throws SQLException, IOException, TransformerException,
AuthorizeException, NonUniqueMetadataException, RegistryImportException {
throws SQLException, AuthorizeException, NonUniqueMetadataException, RegistryImportException,
XPathExpressionException {
// Get the values
String name = RegistryImporter.getElementData(node, "name");
String namespace = RegistryImporter.getElementData(node, "namespace");
@@ -236,8 +242,8 @@ public class MetadataImporter {
* @throws RegistryImportException if import fails
*/
private static void loadType(Context context, Node node)
throws SQLException, IOException, TransformerException,
AuthorizeException, NonUniqueMetadataException, RegistryImportException {
throws SQLException, IOException, AuthorizeException, NonUniqueMetadataException, RegistryImportException,
XPathExpressionException {
// Get the values
String schema = RegistryImporter.getElementData(node, "schema");
String element = RegistryImporter.getElementData(node, "element");

15
dspace-api/src/main/java/org/dspace/administer/RegistryImporter.java
View File

@@ -13,8 +13,11 @@ import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.TransformerException;
import javax.xml.xpath.XPath;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
import org.apache.xpath.XPathAPI;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
@@ -72,9 +75,10 @@ public class RegistryImporter {
* @throws TransformerException if error
*/
public static String getElementData(Node parentElement, String childName)
throws TransformerException {
throws XPathExpressionException {
// Grab the child node
Node childNode = XPathAPI.selectSingleNode(parentElement, childName);
XPath xPath = XPathFactory.newInstance().newXPath();
Node childNode = (Node) xPath.compile(childName).evaluate(parentElement, XPathConstants.NODE);
if (childNode == null) {
// No child node, so no values
@@ -115,9 +119,10 @@ public class RegistryImporter {
* @throws TransformerException if error
*/
public static String[] getRepeatedElementData(Node parentElement,
String childName) throws TransformerException {
String childName) throws XPathExpressionException {
// Grab the child node
NodeList childNodes = XPathAPI.selectNodeList(parentElement, childName);
XPath xPath = XPathFactory.newInstance().newXPath();
NodeList childNodes = (NodeList) xPath.compile(childName).evaluate(parentElement, XPathConstants.NODESET);
String[] data = new String[childNodes.getLength()];

25
dspace-api/src/main/java/org/dspace/administer/RegistryLoader.java
View File

@@ -16,9 +16,12 @@ import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.TransformerException;
import javax.xml.xpath.XPath;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
import org.apache.logging.log4j.Logger;
import org.apache.xpath.XPathAPI;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.BitstreamFormat;
import org.dspace.content.factory.ContentServiceFactory;
@@ -122,12 +125,13 @@ public class RegistryLoader {
*/
public static void loadBitstreamFormats(Context context, String filename)
throws SQLException, IOException, ParserConfigurationException,
SAXException, TransformerException, AuthorizeException {
SAXException, TransformerException, AuthorizeException, XPathExpressionException {
Document document = loadXML(filename);
// Get the nodes corresponding to formats
NodeList typeNodes = XPathAPI.selectNodeList(document,
"dspace-bitstream-types/bitstream-type");
XPath xPath = XPathFactory.newInstance().newXPath();
NodeList typeNodes = (NodeList) xPath.compile("dspace-bitstream-types/bitstream-type")
.evaluate(document, XPathConstants.NODESET);
// Add each one as a new format to the registry
for (int i = 0; i < typeNodes.getLength(); i++) {
@@ -151,8 +155,7 @@ public class RegistryLoader {
* @throws AuthorizeException if authorization error
*/
private static void loadFormat(Context context, Node node)
throws SQLException, IOException, TransformerException,
AuthorizeException {
throws SQLException, AuthorizeException, XPathExpressionException {
// Get the values
String mimeType = getElementData(node, "mimetype");
String shortDesc = getElementData(node, "short_description");
@@ -231,9 +234,10 @@ public class RegistryLoader {
* @throws TransformerException if transformer error
*/
private static String getElementData(Node parentElement, String childName)
throws TransformerException {
throws XPathExpressionException {
// Grab the child node
Node childNode = XPathAPI.selectSingleNode(parentElement, childName);
XPath xPath = XPathFactory.newInstance().newXPath();
Node childNode = (Node) xPath.compile(childName).evaluate(parentElement, XPathConstants.NODE);
if (childNode == null) {
// No child node, so no values
@@ -274,9 +278,10 @@ public class RegistryLoader {
* @throws TransformerException if transformer error
*/
private static String[] getRepeatedElementData(Node parentElement,
String childName) throws TransformerException {
String childName) throws XPathExpressionException {
// Grab the child node
NodeList childNodes = XPathAPI.selectNodeList(parentElement, childName);
XPath xPath = XPathFactory.newInstance().newXPath();
NodeList childNodes = (NodeList) xPath.compile(childName).evaluate(parentElement, XPathConstants.NODESET);
String[] data = new String[childNodes.getLength()];

62
dspace-api/src/main/java/org/dspace/administer/StructBuilder.java
View File

@@ -30,6 +30,10 @@ import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.TransformerException;
import javax.xml.xpath.XPath;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
@@ -38,7 +42,6 @@ import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.xpath.XPathAPI;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Collection;
import org.dspace.content.Community;
@@ -52,9 +55,9 @@ import org.dspace.content.service.CommunityService;
import org.dspace.core.Context;
import org.dspace.eperson.factory.EPersonServiceFactory;
import org.dspace.eperson.service.EPersonService;
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;
@@ -138,7 +141,7 @@ public class StructBuilder {
*/
public static void main(String[] argv)
throws ParserConfigurationException, SQLException,
FileNotFoundException, IOException, TransformerException {
IOException, TransformerException, XPathExpressionException {
// Define command line options.
Options options = new Options();
@@ -240,7 +243,7 @@ public class StructBuilder {
* @throws SQLException
*/
static void importStructure(Context context, InputStream input, OutputStream output)
throws IOException, ParserConfigurationException, SQLException, TransformerException {
throws IOException, ParserConfigurationException, SQLException, TransformerException, XPathExpressionException {
// load the XML
Document document = null;
@@ -258,13 +261,15 @@ public class StructBuilder {
// is properly structured.
try {
validate(document);
} catch (TransformerException ex) {
} catch (XPathExpressionException ex) {
System.err.format("The input document is invalid: %s%n", ex.getMessage());
System.exit(1);
}
// Check for 'identifier' attributes -- possibly output by this class.
NodeList identifierNodes = XPathAPI.selectNodeList(document, "//*[@identifier]");
XPath xPath = XPathFactory.newInstance().newXPath();
NodeList identifierNodes = (NodeList) xPath.compile("//*[@identifier]")
.evaluate(document, XPathConstants.NODESET);
if (identifierNodes.getLength() > 0) {
System.err.println("The input document has 'identifier' attributes, which will be ignored.");
}
@@ -287,7 +292,8 @@ public class StructBuilder {
Element[] elements = new Element[]{};
try {
// get the top level community list
NodeList first = XPathAPI.selectNodeList(document, "/import_structure/community");
NodeList first = (NodeList) xPath.compile("/import_structure/community")
.evaluate(document, XPathConstants.NODESET);
// run the import starting with the top level communities
elements = handleCommunities(context, first, null);
@@ -307,7 +313,7 @@ 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) {
@@ -411,7 +417,7 @@ 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);
@@ -456,14 +462,16 @@ public class StructBuilder {
* @throws TransformerException if transformer error
*/
private static void validate(org.w3c.dom.Document document)
throws TransformerException {
throws XPathExpressionException {
StringBuilder err = new StringBuilder();
boolean trip = false;
err.append("The following errors were encountered parsing the source XML.\n");
err.append("No changes have been made to the DSpace instance.\n\n");
NodeList first = XPathAPI.selectNodeList(document, "/import_structure/community");
XPath xPath = XPathFactory.newInstance().newXPath();
NodeList first = (NodeList) xPath.compile("/import_structure/community")
.evaluate(document, XPathConstants.NODESET);
if (first.getLength() == 0) {
err.append("-There are no top level communities in the source document.");
System.out.println(err.toString());
@@ -493,14 +501,15 @@ public class StructBuilder {
* no errors.
*/
private static String validateCommunities(NodeList communities, int level)
throws TransformerException {
throws XPathExpressionException {
StringBuilder err = new StringBuilder();
boolean trip = false;
String errs = null;
XPath xPath = XPathFactory.newInstance().newXPath();
for (int i = 0; i < communities.getLength(); i++) {
Node n = communities.item(i);
NodeList name = XPathAPI.selectNodeList(n, "name");
NodeList name = (NodeList) xPath.compile("name").evaluate(n, XPathConstants.NODESET);
if (name.getLength() != 1) {
String pos = Integer.toString(i + 1);
err.append("-The level ").append(level)
@@ -510,7 +519,7 @@ public class StructBuilder {
}
// validate sub communities
NodeList subCommunities = XPathAPI.selectNodeList(n, "community");
NodeList subCommunities = (NodeList) xPath.compile("community").evaluate(n, XPathConstants.NODESET);
String comErrs = validateCommunities(subCommunities, level + 1);
if (comErrs != null) {
err.append(comErrs);
@@ -518,7 +527,7 @@ public class StructBuilder {
}
// validate collections
NodeList collections = XPathAPI.selectNodeList(n, "collection");
NodeList collections = (NodeList) xPath.compile("collection").evaluate(n, XPathConstants.NODESET);
String colErrs = validateCollections(collections, level + 1);
if (colErrs != null) {
err.append(colErrs);
@@ -542,14 +551,15 @@ public class StructBuilder {
* @return the errors to be generated by the calling method, or null if none
*/
private static String validateCollections(NodeList collections, int level)
throws TransformerException {
throws XPathExpressionException {
StringBuilder err = new StringBuilder();
boolean trip = false;
String errs = null;
XPath xPath = XPathFactory.newInstance().newXPath();
for (int i = 0; i < collections.getLength(); i++) {
Node n = collections.item(i);
NodeList name = XPathAPI.selectNodeList(n, "name");
NodeList name = (NodeList) xPath.compile("name").evaluate(n, XPathConstants.NODESET);
if (name.getLength() != 1) {
String pos = Integer.toString(i + 1);
err.append("-The level ").append(level)
@@ -613,8 +623,9 @@ public class StructBuilder {
* created communities (e.g. the handles they have been assigned)
*/
private static Element[] handleCommunities(Context context, NodeList communities, Community parent)
throws TransformerException, SQLException, AuthorizeException {
throws TransformerException, SQLException, AuthorizeException, XPathExpressionException {
Element[] elements = new Element[communities.getLength()];
XPath xPath = XPathFactory.newInstance().newXPath();
for (int i = 0; i < communities.getLength(); i++) {
Community community;
@@ -634,7 +645,7 @@ public class StructBuilder {
// now update the metadata
Node tn = communities.item(i);
for (Map.Entry<String, MetadataFieldName> entry : communityMap.entrySet()) {
NodeList nl = XPathAPI.selectNodeList(tn, entry.getKey());
NodeList nl = (NodeList) xPath.compile(entry.getKey()).evaluate(tn, XPathConstants.NODESET);
if (nl.getLength() == 1) {
communityService.setMetadataSingleValue(context, community,
entry.getValue(), null, getStringValue(nl.item(0)));
@@ -700,11 +711,11 @@ public class StructBuilder {
}
// handle sub communities
NodeList subCommunities = XPathAPI.selectNodeList(tn, "community");
NodeList subCommunities = (NodeList) xPath.compile("community").evaluate(tn, XPathConstants.NODESET);
Element[] subCommunityElements = handleCommunities(context, subCommunities, community);
// handle collections
NodeList collections = XPathAPI.selectNodeList(tn, "collection");
NodeList collections = (NodeList) xPath.compile("collection").evaluate(tn, XPathConstants.NODESET);
Element[] collectionElements = handleCollections(context, collections, community);
int j;
@@ -731,8 +742,9 @@ public class StructBuilder {
* created collections (e.g. the handle)
*/
private static Element[] handleCollections(Context context, NodeList collections, Community parent)
throws TransformerException, SQLException, AuthorizeException {
throws SQLException, AuthorizeException, XPathExpressionException {
Element[] elements = new Element[collections.getLength()];
XPath xPath = XPathFactory.newInstance().newXPath();
for (int i = 0; i < collections.getLength(); i++) {
Element element = new Element("collection");
@@ -745,7 +757,7 @@ public class StructBuilder {
// import the rest of the metadata
Node tn = collections.item(i);
for (Map.Entry<String, MetadataFieldName> entry : collectionMap.entrySet()) {
NodeList nl = XPathAPI.selectNodeList(tn, entry.getKey());
NodeList nl = (NodeList) xPath.compile(entry.getKey()).evaluate(tn, XPathConstants.NODESET);
if (nl.getLength() == 1) {
collectionService.setMetadataSingleValue(context, collection,
entry.getValue(), null, getStringValue(nl.item(0)));

2
dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataDeletionScriptConfiguration.java
View File

@@ -41,10 +41,8 @@ public class MetadataDeletionScriptConfiguration<T extends MetadataDeletion> ext
Options options = new Options();
options.addOption("m", "metadata", true, "metadata field name");
options.getOption("m").setType(String.class);
options.addOption("l", "list", false, "lists the metadata fields that can be deleted");
options.getOption("l").setType(boolean.class);
super.options = options;
}

3
dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataExportScriptConfiguration.java
View File

@@ -54,12 +54,9 @@ public class MetadataExportScriptConfiguration<T extends MetadataExport> extends
Options options = new Options();
options.addOption("i", "id", true, "ID or handle of thing to export (item, collection, or community)");
options.getOption("i").setType(String.class);
options.addOption("a", "all", false,
"include all metadata fields that are not normally changed (e.g. provenance)");
options.getOption("a").setType(boolean.class);
options.addOption("h", "help", false, "help");
options.getOption("h").setType(boolean.class);
super.options = options;

1
dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImportCliScriptConfiguration.java
View File

@@ -19,7 +19,6 @@ public class MetadataImportCliScriptConfiguration extends MetadataImportScriptCo
public Options getOptions() {
Options options = super.getOptions();
options.addOption("e", "email", true, "email address or user id of user (required if adding new items)");
options.getOption("e").setType(String.class);
options.getOption("e").setRequired(true);
super.options = options;
return options;

6
dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImportScriptConfiguration.java
View File

@@ -59,20 +59,14 @@ public class MetadataImportScriptConfiguration<T extends MetadataImport> extends
options.getOption("f").setRequired(true);
options.addOption("s", "silent", false,
"silent operation - doesn't request confirmation of changes USE WITH CAUTION");
options.getOption("s").setType(boolean.class);
options.addOption("w", "workflow", false, "workflow - when adding new items, use collection workflow");
options.getOption("w").setType(boolean.class);
options.addOption("n", "notify", false,
"notify - when adding new items using a workflow, send notification emails");
options.getOption("n").setType(boolean.class);
options.addOption("v", "validate-only", false,
"validate - just validate the csv, don't run the import");
options.getOption("v").setType(boolean.class);
options.addOption("t", "template", false,
"template - when adding new items, use the collection template (if it exists)");
options.getOption("t").setType(boolean.class);
options.addOption("h", "help", false, "help");
options.getOption("h").setType(boolean.class);
super.options = options;
}

9
dspace-api/src/main/java/org/dspace/app/harvest/HarvestScriptConfiguration.java
View File

@@ -43,22 +43,14 @@ public class HarvestScriptConfiguration<T extends Harvest> extends ScriptConfigu
public Options getOptions() {
Options options = new Options();
options.addOption("p", "purge", false, "delete all items in the collection");
options.getOption("p").setType(boolean.class);
options.addOption("r", "run", false, "run the standard harvest procedure");
options.getOption("r").setType(boolean.class);
options.addOption("g", "ping", false, "test the OAI server and set");
options.getOption("g").setType(boolean.class);
options.addOption("s", "setup", false, "Set the collection up for harvesting");
options.getOption("s").setType(boolean.class);
options.addOption("S", "start", false, "start the harvest loop");
options.getOption("S").setType(boolean.class);
options.addOption("R", "reset", false, "reset harvest status on all collections");
options.getOption("R").setType(boolean.class);
options.addOption("P", "purgeCollections", false, "purge all harvestable collections");
options.getOption("P").setType(boolean.class);
options.addOption("o", "reimport", false, "reimport all items in the collection, " +
"this is equivalent to -p -r, purging all items in a collection and reimporting them");
options.getOption("o").setType(boolean.class);
options.addOption("c", "collection", true,
"harvesting collection (handle or id)");
options.addOption("t", "type", true,
@@ -72,7 +64,6 @@ public class HarvestScriptConfiguration<T extends Harvest> extends ScriptConfigu
"crosswalk in dspace.cfg");
options.addOption("h", "help", false, "help");
options.getOption("h").setType(boolean.class);
return options;
}

15
dspace-api/src/main/java/org/dspace/app/itemimport/ItemImportServiceImpl.java
View File

@@ -51,6 +51,10 @@ import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.TransformerException;
import javax.xml.xpath.XPath;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
import org.apache.commons.collections4.ComparatorUtils;
import org.apache.commons.io.FileDeleteStrategy;
@@ -59,7 +63,6 @@ import org.apache.commons.lang3.RandomStringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.exception.ExceptionUtils;
import org.apache.logging.log4j.Logger;
import org.apache.xpath.XPathAPI;
import org.dspace.app.itemimport.service.ItemImportService;
import org.dspace.app.util.LocalSchemaFilenameFilter;
import org.dspace.app.util.RelationshipUtils;
@@ -861,7 +864,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
// Load all metadata schemas into the item.
protected void loadMetadata(Context c, Item myitem, String path)
throws SQLException, IOException, ParserConfigurationException,
SAXException, TransformerException, AuthorizeException {
SAXException, TransformerException, AuthorizeException, XPathExpressionException {
// Load the dublin core metadata
loadDublinCore(c, myitem, path + "dublin_core.xml");
@@ -875,14 +878,15 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
protected void loadDublinCore(Context c, Item myitem, String filename)
throws SQLException, IOException, ParserConfigurationException,
SAXException, TransformerException, AuthorizeException {
SAXException, TransformerException, AuthorizeException, XPathExpressionException {
Document document = loadXML(filename);
// Get the schema, for backward compatibility we will default to the
// dublin core schema if the schema name is not available in the import
// file
String schema;
NodeList metadata = XPathAPI.selectNodeList(document, "/dublin_core");
XPath xPath = XPathFactory.newInstance().newXPath();
NodeList metadata = (NodeList) xPath.compile("/dublin_core").evaluate(document, XPathConstants.NODESET);
Node schemaAttr = metadata.item(0).getAttributes().getNamedItem(
"schema");
if (schemaAttr == null) {
@@ -892,8 +896,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
}
// Get the nodes corresponding to formats
NodeList dcNodes = XPathAPI.selectNodeList(document,
"/dublin_core/dcvalue");
NodeList dcNodes = (NodeList) xPath.compile("/dublin_core/dcvalue").evaluate(document, XPathConstants.NODESET);
if (!isQuiet) {
System.out.println("\tLoading dublin core from " + filename);

19
dspace-api/src/main/java/org/dspace/app/itemupdate/MetadataUtilities.java
View File

@@ -27,10 +27,12 @@ import javax.xml.transform.TransformerConfigurationException;
import javax.xml.transform.TransformerException;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import javax.xml.xpath.XPath;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
import org.apache.commons.lang3.StringUtils;
import org.apache.xpath.XPathAPI;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Item;
import org.dspace.content.MetadataField;
import org.dspace.content.MetadataSchema;
@@ -170,24 +172,21 @@ public class MetadataUtilities {
* @param docBuilder DocumentBuilder
* @param is - InputStream of dublin_core.xml
* @return list of DtoMetadata representing the metadata fields relating to an Item
* @throws SQLException if database error
* @throws IOException if IO error
* @throws ParserConfigurationException if parser config error
* @throws SAXException if XML error
* @throws TransformerException if transformer error
* @throws AuthorizeException if authorization error
*/
public static List<DtoMetadata> loadDublinCore(DocumentBuilder docBuilder, InputStream is)
throws SQLException, IOException, ParserConfigurationException,
SAXException, TransformerException, AuthorizeException {
throws IOException, XPathExpressionException, SAXException {
Document document = docBuilder.parse(is);
List<DtoMetadata> dtomList = new ArrayList<DtoMetadata>();
// Get the schema, for backward compatibility we will default to the
// dublin core schema if the schema name is not available in the import file
String schema = null;
NodeList metadata = XPathAPI.selectNodeList(document, "/dublin_core");
String schema;
XPath xPath = XPathFactory.newInstance().newXPath();
NodeList metadata = (NodeList) xPath.compile("/dublin_core").evaluate(document, XPathConstants.NODESET);
Node schemaAttr = metadata.item(0).getAttributes().getNamedItem("schema");
if (schemaAttr == null) {
schema = MetadataSchemaEnum.DC.getName();
@@ -196,7 +195,7 @@ public class MetadataUtilities {
}
// Get the nodes corresponding to formats
NodeList dcNodes = XPathAPI.selectNodeList(document, "/dublin_core/dcvalue");
NodeList dcNodes = (NodeList) xPath.compile("/dublin_core/dcvalue").evaluate(document, XPathConstants.NODESET);
for (int i = 0; i < dcNodes.getLength(); i++) {
Node n = dcNodes.item(i);

2
dspace-api/src/main/java/org/dspace/app/launcher/CommandRunner.java
View File

@@ -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

6
dspace-api/src/main/java/org/dspace/app/launcher/ScriptLauncher.java
View File

@@ -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.

99
dspace-api/src/main/java/org/dspace/app/mediafilter/ExcelFilter.java
View File

@@ -1,99 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.app.mediafilter;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import org.apache.commons.io.IOUtils;
import org.apache.logging.log4j.Logger;
import org.apache.poi.POITextExtractor;
import org.apache.poi.extractor.ExtractorFactory;
import org.apache.poi.hssf.extractor.ExcelExtractor;
import org.apache.poi.xssf.extractor.XSSFExcelExtractor;
import org.dspace.content.Item;
/*
* ExcelFilter
*
* Entries you must add to dspace.cfg:
*
* filter.plugins = blah, \
* Excel Text Extractor
*
* plugin.named.org.dspace.app.mediafilter.FormatFilter = \
* blah = blah, \
* org.dspace.app.mediafilter.ExcelFilter = Excel Text Extractor
*
* #Configure each filter's input Formats
* filter.org.dspace.app.mediafilter.ExcelFilter.inputFormats = Microsoft Excel, Microsoft Excel XML
*
*/
public class ExcelFilter extends MediaFilter {
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(ExcelFilter.class);
public String getFilteredName(String oldFilename) {
return oldFilename + ".txt";
}
/**
* @return String bundle name
*/
public String getBundleName() {
return "TEXT";
}
/**
* @return String bitstream format
*/
public String getFormatString() {
return "Text";
}
/**
* @return String description
*/
public String getDescription() {
return "Extracted text";
}
/**
* @param item item
* @param source source input stream
* @param verbose verbose mode
* @return InputStream the resulting input stream
* @throws Exception if error
*/
@Override
public InputStream getDestinationStream(Item item, InputStream source, boolean verbose)
throws Exception {
String extractedText = null;
try {
POITextExtractor theExtractor = ExtractorFactory.createExtractor(source);
if (theExtractor instanceof ExcelExtractor) {
// for xls file
extractedText = (theExtractor).getText();
} else if (theExtractor instanceof XSSFExcelExtractor) {
// for xlsx file
extractedText = (theExtractor).getText();
}
} catch (Exception e) {
log.error("Error filtering bitstream: " + e.getMessage(), e);
throw e;
}
if (extractedText != null) {
// generate an input stream with the extracted text
return IOUtils.toInputStream(extractedText, StandardCharsets.UTF_8);
}
return null;
}
}

82
dspace-api/src/main/java/org/dspace/app/mediafilter/HTMLFilter.java
View File

@@ -1,82 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.app.mediafilter;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import javax.swing.text.Document;
import javax.swing.text.html.HTMLEditorKit;
import org.dspace.content.Item;
/*
*
* to do: helpful error messages - can't find mediafilter.cfg - can't
* instantiate filter - bitstream format doesn't exist
*
*/
public class HTMLFilter extends MediaFilter {
@Override
public String getFilteredName(String oldFilename) {
return oldFilename + ".txt";
}
/**
* @return String bundle name
*/
@Override
public String getBundleName() {
return "TEXT";
}
/**
* @return String bitstream format
*/
@Override
public String getFormatString() {
return "Text";
}
/**
* @return String description
*/
@Override
public String getDescription() {
return "Extracted text";
}
/**
* @param currentItem item
* @param source source input stream
* @param verbose verbose mode
* @return InputStream the resulting input stream
* @throws Exception if error
*/
@Override
public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
throws Exception {
// try and read the document - set to ignore character set directive,
// assuming that the input stream is already set properly (I hope)
HTMLEditorKit kit = new HTMLEditorKit();
Document doc = kit.createDefaultDocument();
doc.putProperty("IgnoreCharsetDirective", Boolean.TRUE);
kit.read(source, doc, 0);
String extractedText = doc.getText(0, doc.getLength());
// generate an input stream with the extracted text
byte[] textBytes = extractedText.getBytes(StandardCharsets.UTF_8);
ByteArrayInputStream bais = new ByteArrayInputStream(textBytes);
return bais;
}
}

4
dspace-api/src/main/java/org/dspace/app/mediafilter/MediaFilterScriptConfiguration.java
View File

@@ -50,15 +50,11 @@ public class MediaFilterScriptConfiguration<T extends MediaFilterScript> extends
public Options getOptions() {
Options options = new Options();
options.addOption("v", "verbose", false, "print all extracted text and other details to STDOUT");
options.getOption("v").setType(boolean.class);
options.addOption("q", "quiet", false, "do not print anything except in the event of errors.");
options.getOption("q").setType(boolean.class);
options.addOption("f", "force", false, "force all bitstreams to be processed");
options.getOption("f").setType(boolean.class);
options.addOption("i", "identifier", true, "ONLY process bitstreams belonging to identifier");
options.addOption("m", "maximum", true, "process no more than maximum items");
options.addOption("h", "help", false, "help");
options.getOption("h").setType(boolean.class);
Option pluginOption = Option.builder("p")
.longOpt("plugins")

137
dspace-api/src/main/java/org/dspace/app/mediafilter/PDFFilter.java
View File

@@ -1,137 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.app.mediafilter;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.InputStream;
import java.io.OutputStreamWriter;
import java.io.Writer;
import org.apache.logging.log4j.Logger;
import org.apache.pdfbox.pdmodel.PDDocument;
import org.apache.pdfbox.pdmodel.encryption.InvalidPasswordException;
import org.apache.pdfbox.text.PDFTextStripper;
import org.dspace.content.Item;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
/*
*
* to do: helpful error messages - can't find mediafilter.cfg - can't
* instantiate filter - bitstream format doesn't exist
*
*/
public class PDFFilter extends MediaFilter {
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(PDFFilter.class);
@Override
public String getFilteredName(String oldFilename) {
return oldFilename + ".txt";
}
/**
* @return String bundle name
*/
@Override
public String getBundleName() {
return "TEXT";
}
/**
* @return String bitstreamformat
*/
@Override
public String getFormatString() {
return "Text";
}
/**
* @return String description
*/
@Override
public String getDescription() {
return "Extracted text";
}
/**
* @param currentItem item
* @param source source input stream
* @param verbose verbose mode
* @return InputStream the resulting input stream
* @throws Exception if error
*/
@Override
public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
throws Exception {
ConfigurationService configurationService
= DSpaceServicesFactory.getInstance().getConfigurationService();
try {
boolean useTemporaryFile = configurationService.getBooleanProperty("pdffilter.largepdfs", false);
// get input stream from bitstream
// pass to filter, get string back
PDFTextStripper pts = new PDFTextStripper();
pts.setSortByPosition(true);
PDDocument pdfDoc = null;
Writer writer = null;
File tempTextFile = null;
ByteArrayOutputStream byteStream = null;
if (useTemporaryFile) {
tempTextFile = File.createTempFile("dspacepdfextract" + source.hashCode(), ".txt");
tempTextFile.deleteOnExit();
writer = new OutputStreamWriter(new FileOutputStream(tempTextFile));
} else {
byteStream = new ByteArrayOutputStream();
writer = new OutputStreamWriter(byteStream);
}
try {
pdfDoc = PDDocument.load(source);
pts.writeText(pdfDoc, writer);
} catch (InvalidPasswordException ex) {
log.error("PDF is encrypted. Cannot extract text (item: {})",
() -> currentItem.getHandle());
return null;
} finally {
try {
if (pdfDoc != null) {
pdfDoc.close();
}
} catch (Exception e) {
log.error("Error closing PDF file: " + e.getMessage(), e);
}
try {
writer.close();
} catch (Exception e) {
log.error("Error closing temporary extract file: " + e.getMessage(), e);
}
}
if (useTemporaryFile) {
return new FileInputStream(tempTextFile);
} else {
byte[] bytes = byteStream.toByteArray();
return new ByteArrayInputStream(bytes);
}
} catch (OutOfMemoryError oome) {
log.error("Error parsing PDF document " + oome.getMessage(), oome);
if (!configurationService.getBooleanProperty("pdffilter.skiponmemoryexception", false)) {
throw oome;
}
}
return null;
}
}

72
dspace-api/src/main/java/org/dspace/app/mediafilter/PoiWordFilter.java
View File

@@ -1,72 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.app.mediafilter;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import org.apache.poi.POITextExtractor;
import org.apache.poi.extractor.ExtractorFactory;
import org.apache.poi.openxml4j.exceptions.OpenXML4JException;
import org.apache.xmlbeans.XmlException;
import org.dspace.content.Item;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Extract flat text from Microsoft Word documents (.doc, .docx).
*/
public class PoiWordFilter
extends MediaFilter {
private static final Logger LOG = LoggerFactory.getLogger(PoiWordFilter.class);
@Override
public String getFilteredName(String oldFilename) {
return oldFilename + ".txt";
}
@Override
public String getBundleName() {
return "TEXT";
}
@Override
public String getFormatString() {
return "Text";
}
@Override
public String getDescription() {
return "Extracted text";
}
@Override
public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
throws Exception {
String text;
try {
// get input stream from bitstream, pass to filter, get string back
POITextExtractor extractor = ExtractorFactory.createExtractor(source);
text = extractor.getText();
} catch (IOException | OpenXML4JException | XmlException e) {
System.err.format("Invalid File Format: %s%n", e.getMessage());
LOG.error("Unable to parse the bitstream: ", e);
throw e;
}
// if verbose flag is set, print out extracted text to STDOUT
if (verbose) {
System.out.println(text);
}
// return the extracted text as a stream.
return new ByteArrayInputStream(text.getBytes(StandardCharsets.UTF_8));
}
}

113
dspace-api/src/main/java/org/dspace/app/mediafilter/PowerPointFilter.java
View File

@@ -1,113 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.app.mediafilter;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import org.apache.logging.log4j.Logger;
import org.apache.poi.POITextExtractor;
import org.apache.poi.extractor.ExtractorFactory;
import org.apache.poi.hslf.extractor.PowerPointExtractor;
import org.apache.poi.xslf.extractor.XSLFPowerPointExtractor;
import org.dspace.content.Item;
/*
* TODO: Allow user to configure extraction of only text or only notes
*
*/
public class PowerPointFilter extends MediaFilter {
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(PowerPointFilter.class);
@Override
public String getFilteredName(String oldFilename) {
return oldFilename + ".txt";
}
/**
* @return String bundle name
*/
@Override
public String getBundleName() {
return "TEXT";
}
/**
* @return String bitstream format
*
* TODO: Check that this is correct
*/
@Override
public String getFormatString() {
return "Text";
}
/**
* @return String description
*/
@Override
public String getDescription() {
return "Extracted text";
}
/**
* @param currentItem item
* @param source source input stream
* @param verbose verbose mode
* @return InputStream the resulting input stream
* @throws Exception if error
*/
@Override
public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
throws Exception {
try {
String extractedText = null;
new ExtractorFactory();
POITextExtractor pptExtractor = ExtractorFactory
.createExtractor(source);
// PowerPoint XML files and legacy format PowerPoint files
// require different classes and APIs for text extraction
// If this is a PowerPoint XML file, extract accordingly
if (pptExtractor instanceof XSLFPowerPointExtractor) {
// The true method arguments indicate that text from
// the slides and the notes is desired
extractedText = ((XSLFPowerPointExtractor) pptExtractor)
.getText(true, true);
} else if (pptExtractor instanceof PowerPointExtractor) { // Legacy PowerPoint files
extractedText = ((PowerPointExtractor) pptExtractor).getText()
+ " " + ((PowerPointExtractor) pptExtractor).getNotes();
}
if (extractedText != null) {
// if verbose flag is set, print out extracted text
// to STDOUT
if (verbose) {
System.out.println(extractedText);
}
// generate an input stream with the extracted text
byte[] textBytes = extractedText.getBytes();
ByteArrayInputStream bais = new ByteArrayInputStream(textBytes);
return bais;
}
} catch (Exception e) {
log.error("Error filtering bitstream: " + e.getMessage(), e);
throw e;
}
return null;
}
}

183
dspace-api/src/main/java/org/dspace/app/mediafilter/TikaTextExtractionFilter.java Normal file
View File

@@ -0,0 +1,183 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.app.mediafilter;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import org.apache.commons.lang.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.apache.tika.Tika;
import org.apache.tika.exception.TikaException;
import org.apache.tika.metadata.Metadata;
import org.apache.tika.parser.AutoDetectParser;
import org.apache.tika.sax.BodyContentHandler;
import org.apache.tika.sax.ContentHandlerDecorator;
import org.dspace.content.Item;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.xml.sax.SAXException;
/**
* Text Extraction media filter which uses Apache Tika to extract text from a large number of file formats (including
* all Microsoft formats, PDF, HTML, Text, etc). For a more complete list of file formats supported by Tika see the
* Tika documentation: https://tika.apache.org/2.3.0/formats.html
*/
public class TikaTextExtractionFilter
extends MediaFilter {
private final static Logger log = LogManager.getLogger();
@Override
public String getFilteredName(String oldFilename) {
return oldFilename + ".txt";
}
@Override
public String getBundleName() {
return "TEXT";
}
@Override
public String getFormatString() {
return "Text";
}
@Override
public String getDescription() {
return "Extracted text";
}
@Override
public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
throws Exception {
ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
boolean useTemporaryFile = configurationService.getBooleanProperty("textextractor.use-temp-file", false);
if (useTemporaryFile) {
// Extract text out of source file using a temp file, returning results as InputStream
return extractUsingTempFile(source, verbose);
}
// Not using temporary file. We'll use Tika's default in-memory parsing.
// Get maximum characters to extract. Default is 100,000 chars, which is also Tika's default setting.
String extractedText;
int maxChars = configurationService.getIntProperty("textextractor.max-chars", 100000);
try {
// Use Tika to extract text from input. Tika will automatically detect the file type.
Tika tika = new Tika();
tika.setMaxStringLength(maxChars); // Tell Tika the maximum number of characters to extract
extractedText = tika.parseToString(source);
} catch (IOException e) {
System.err.format("Unable to extract text from bitstream in Item %s%n", currentItem.getID().toString());
e.printStackTrace();
log.error("Unable to extract text from bitstream in Item {}", currentItem.getID().toString(), e);
throw e;
} catch (OutOfMemoryError oe) {
System.err.format("OutOfMemoryError occurred when extracting text from bitstream in Item %s. " +
"You may wish to enable 'textextractor.use-temp-file'.%n", currentItem.getID().toString());
oe.printStackTrace();
log.error("OutOfMemoryError occurred when extracting text from bitstream in Item {}. " +
"You may wish to enable 'textextractor.use-temp-file'.", currentItem.getID().toString(), oe);
throw oe;
}
if (StringUtils.isNotEmpty(extractedText)) {
// if verbose flag is set, print out extracted text to STDOUT
if (verbose) {
System.out.println("(Verbose mode) Extracted text:");
System.out.println(extractedText);
}
// return the extracted text as a UTF-8 stream.
return new ByteArrayInputStream(extractedText.getBytes(StandardCharsets.UTF_8));
}
return null;
}
/**
* Extracts the text out of a given source InputStream, using a temporary file. This decreases the amount of memory
* necessary for text extraction, but can be slower as it requires writing extracted text to a temporary file.
* @param source source InputStream
* @param verbose verbose mode enabled/disabled
* @return InputStream for temporary file containing extracted text
* @throws IOException
* @throws SAXException
* @throws TikaException
*/
private InputStream extractUsingTempFile(InputStream source, boolean verbose)
throws IOException, TikaException, SAXException {
File tempExtractedTextFile = File.createTempFile("dspacetextextract" + source.hashCode(), ".txt");
if (verbose) {
System.out.println("(Verbose mode) Extracted text was written to temporary file at " +
tempExtractedTextFile.getAbsolutePath());
} else {
tempExtractedTextFile.deleteOnExit();
}
// Open temp file for writing
try (FileWriter writer = new FileWriter(tempExtractedTextFile, StandardCharsets.UTF_8)) {
// Initialize a custom ContentHandlerDecorator which is a BodyContentHandler.
// This mimics the behavior of Tika().parseToString(), which only extracts text from the body of the file.
// This custom Handler writes any extracted text to the temp file.
ContentHandlerDecorator handler = new BodyContentHandler(new ContentHandlerDecorator() {
/**
* Write all extracted characters directly to the temp file.
*/
@Override
public void characters(char[] ch, int start, int length) throws SAXException {
try {
writer.append(new String(ch), start, length);
} catch (IOException e) {
String errorMsg = String.format("Could not append to temporary file at %s " +
"when performing text extraction",
tempExtractedTextFile.getAbsolutePath());
log.error(errorMsg, e);
throw new SAXException(errorMsg, e);
}
}
/**
* Write all ignorable whitespace directly to the temp file.
* This mimics the behaviour of Tika().parseToString() which extracts ignorableWhitespace characters
* (like blank lines, indentations, etc.), so that we get the same extracted text either way.
*/
@Override
public void ignorableWhitespace(char[] ch, int start, int length) throws SAXException {
try {
writer.append(new String(ch), start, length);
} catch (IOException e) {
String errorMsg = String.format("Could not append to temporary file at %s " +
"when performing text extraction",
tempExtractedTextFile.getAbsolutePath());
log.error(errorMsg, e);
throw new SAXException(errorMsg, e);
}
}
});
AutoDetectParser parser = new AutoDetectParser();
Metadata metadata = new Metadata();
// parse our source InputStream using the above custom handler
parser.parse(source, handler, metadata);
}
// At this point, all extracted text is written to our temp file. So, return a FileInputStream for that file
return new FileInputStream(tempExtractedTextFile);
}
}

58
dspace-api/src/main/java/org/dspace/app/util/CacheSnooper.java
View File

@@ -1,58 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.app.util;
import net.sf.ehcache.Cache;
import net.sf.ehcache.CacheManager;
import org.dspace.core.Context;
import org.dspace.servicemanager.DSpaceKernelImpl;
import org.dspace.servicemanager.DSpaceKernelInit;
import org.dspace.services.CachingService;
/**
* List all EhCache CacheManager and Cache instances.
*
* <p>This is a debugging tool, not used in the daily operation of DSpace.
* Just run it from the installed instance using
* {@code bin/dspace dsrun org.dspace.app.util.CacheSnooper}
* to check that the cache configuration is what you expect it to be,
* given your configuration.
*
* <p>This was created to prove a specific cache configuration patch,
* but I leave it here in the hope that it may be useful to others.
*
* @author Mark H. Wood <mwood@iupui.edu>
*/
public class CacheSnooper {
private CacheSnooper() { }
public static void main(String[] argv) {
// Ensure that the DSpace kernel is started.
DSpaceKernelImpl kernel = DSpaceKernelInit.getKernel(null);
// Ensure that the services cache manager is started.
CachingService serviceCaches = kernel.getServiceManager()
.getServiceByName(null, CachingService.class);
// Ensure that the database layer is started.
Context ctx = new Context();
// List those caches!
for (CacheManager manager : CacheManager.ALL_CACHE_MANAGERS) {
System.out.format("CacheManager: %s%n", manager);
for (String cacheName : manager.getCacheNames()) {
Cache cache = manager.getCache(cacheName);
System.out.format(" Cache: '%s'; maxHeap: %d; maxDisk: %d%n",
cacheName,
cache.getCacheConfiguration().getMaxEntriesLocalHeap(),
cache.getCacheConfiguration().getMaxEntriesLocalDisk());
}
}
}
}

30
dspace-api/src/main/java/org/dspace/app/util/Configuration.java
View File

@@ -37,6 +37,7 @@ public class Configuration {
* <li>{@code --property name} prints the value of the DSpace configuration
* property {@code name} to the standard output.</li>
* <li>{@code --raw} suppresses parameter substitution in the output.</li>
* <li>{@code --first} print only the first of multiple values.</li>
* <li>{@code --help} describes these options.</li>
* </ul>
* If the property does not exist, nothing is written.
@@ -51,6 +52,8 @@ public class Configuration {
"optional name of the module in which 'property' exists");
options.addOption("r", "raw", false,
"do not do property substitution on the value");
options.addOption("f", "first", false,
"display only the first value of an array property");
options.addOption("?", "Get help");
options.addOption("h", "help", false, "Get help");
@@ -90,19 +93,36 @@ public class Configuration {
propNameBuilder.append(cmd.getOptionValue('p'));
String propName = propNameBuilder.toString();
// Print the property's value, if it exists
// Print the property's value(s), if it exists
ConfigurationService cfg = DSpaceServicesFactory.getInstance().getConfigurationService();
if (!cfg.hasProperty(propName)) {
System.out.println();
} else {
String val;
if (cmd.hasOption('r')) {
val = cfg.getPropertyValue(propName).toString();
// Print "raw" values (without property substitutions)
Object rawValue = cfg.getPropertyValue(propName);
if (rawValue.getClass().isArray()) {
for (Object value : (Object[]) rawValue) {
System.out.println(value.toString());
if (cmd.hasOption('f')) {
break; // If --first print only one value
}
}
} else { // Not an array
System.out.println(rawValue.toString());
}
} else {
val = cfg.getProperty(propName);
// Print values with property substitutions
String[] values = cfg.getArrayProperty(propName);
for (String value : values) {
System.out.println(value);
if (cmd.hasOption('f')) {
break; // If --first print only one value
}
System.out.println(val);
}
}
}
System.exit(0);
}
}

4
dspace-api/src/main/java/org/dspace/app/util/GoogleBitstreamComparator.java
View File

@@ -86,8 +86,10 @@ public class GoogleBitstreamComparator implements Comparator<Bitstream> {
if (priority1 > priority2) {
return 1;
} else if (priority1 == priority2) {
if (b1.getSizeBytes() <= b2.getSizeBytes()) {
if (b1.getSizeBytes() < b2.getSizeBytes()) {
return 1;
} else if (b1.getSizeBytes() == b2.getSizeBytes()) {
return 0;
} else {
return -1;
}

2
dspace-api/src/main/java/org/dspace/app/util/GoogleMetadata.java
View File

@@ -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

24
dspace-api/src/main/java/org/dspace/app/util/OpenSearchServiceImpl.java
View File

@@ -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);

40
dspace-api/src/main/java/org/dspace/app/util/SyndicationFeed.java
View File

@@ -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;

24
dspace-api/src/main/java/org/dspace/authenticate/ShibAuthentication.java
View File

@@ -20,7 +20,6 @@ import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.UUID;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
@@ -290,20 +289,13 @@ public class ShibAuthentication implements AuthenticationMethod {
try {
// User has not successfuly authenticated via shibboleth.
if (request == null ||
context.getCurrentUser() == null ||
request.getSession().getAttribute("shib.authenticated") == null) {
context.getCurrentUser() == null) {
return Collections.EMPTY_LIST;
}
// If we have already calculated the special groups then return them.
if (request.getSession().getAttribute("shib.specialgroup") != null) {
if (context.getSpecialGroups().size() > 0 ) {
log.debug("Returning cached special groups.");
List<UUID> sessionGroupIds = (List<UUID>) request.getSession().getAttribute("shib.specialgroup");
List<Group> result = new ArrayList<>();
for (UUID uuid : sessionGroupIds) {
result.add(groupService.find(context, uuid));
}
return result;
return context.getSpecialGroups();
}
log.debug("Starting to determine special groups");
@@ -396,16 +388,8 @@ public class ShibAuthentication implements AuthenticationMethod {
log.info("Added current EPerson to special groups: " + groups);
List<UUID> groupIds = new ArrayList<>();
for (Group group : groups) {
groupIds.add(group.getID());
}
// Cache the special groups, so we don't have to recalculate them again
// for this session.
request.setAttribute("shib.specialgroup", groupIds);
return new ArrayList<>(groups);
} catch (Throwable t) {
log.error("Unable to validate any sepcial groups this user may belong too because of an exception.", t);
return Collections.EMPTY_LIST;

5
dspace-api/src/main/java/org/dspace/authority/orcid/Orcidv3SolrAuthorityImpl.java
View File

@@ -21,7 +21,8 @@ import org.apache.http.HttpResponse;
import org.apache.http.client.HttpClient;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.authority.AuthorityValue;
import org.dspace.authority.SolrAuthorityInterface;
import org.dspace.external.OrcidRestConnector;
@@ -40,7 +41,7 @@ import org.orcid.jaxb.model.v3.release.search.Result;
*/
public class Orcidv3SolrAuthorityImpl implements SolrAuthorityInterface {
private static Logger log = Logger.getLogger(Orcidv3SolrAuthorityImpl.class);
private final static Logger log = LogManager.getLogger();
private OrcidRestConnector orcidRestConnector;
private String OAUTHUrl;

31
dspace-api/src/main/java/org/dspace/authority/util/XMLUtils.java
View File

@@ -14,11 +14,12 @@ import java.util.Iterator;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.TransformerException;
import javax.xml.xpath.XPath;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
import org.apache.logging.log4j.Logger;
import org.apache.xpath.XPathAPI;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
@@ -62,36 +63,26 @@ public class XMLUtils {
/**
* @param xml The starting context (a Node or a Document, for example).
* @param NodeListXPath xpath
* @param nodeListXPath xpath
* @return A Node matches the NodeListXPath
* null if nothing matches the NodeListXPath
* @throws XPathExpressionException if xpath error
*/
public static Node getNode(Node xml, String NodeListXPath) throws XPathExpressionException {
Node result = null;
try {
result = XPathAPI.selectSingleNode(xml, NodeListXPath);
} catch (TransformerException e) {
log.error("Error", e);
}
return result;
public static Node getNode(Node xml, String nodeListXPath) throws XPathExpressionException {
XPath xPath = XPathFactory.newInstance().newXPath();
return (Node) xPath.compile(nodeListXPath).evaluate(xml, XPathConstants.NODE);
}
/**
* @param xml The starting context (a Node or a Document, for example).
* @param NodeListXPath xpath
* @param nodeListXPath xpath
* @return A NodeList containing the nodes that match the NodeListXPath
* null if nothing matches the NodeListXPath
* @throws XPathExpressionException if xpath error
*/
public static NodeList getNodeList(Node xml, String NodeListXPath) throws XPathExpressionException {
NodeList nodeList = null;
try {
nodeList = XPathAPI.selectNodeList(xml, NodeListXPath);
} catch (TransformerException e) {
log.error("Error", e);
}
return nodeList;
public static NodeList getNodeList(Node xml, String nodeListXPath) throws XPathExpressionException {
XPath xPath = XPathFactory.newInstance().newXPath();
return (NodeList) xPath.compile(nodeListXPath).evaluate(xml, XPathConstants.NODESET);
}
public static Iterator<Node> getNodeListIterator(Node xml, String NodeListXPath) throws XPathExpressionException {

2
dspace-api/src/main/java/org/dspace/authorize/ResourcePolicy.java
View File

@@ -93,7 +93,7 @@ public class ResourcePolicy implements ReloadableEntity<Integer> {
private String rptype;
@Lob
@Type(type = "org.hibernate.type.MaterializedClobType")
@Type(type = "org.dspace.storage.rdbms.hibernate.DatabaseAwareLobType")
@Column(name = "rpdescription")
private String rpdescription;

15
dspace-api/src/main/java/org/dspace/browse/BrowseEngine.java
View File

@@ -11,6 +11,7 @@ import java.sql.SQLException;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Collection;
import org.dspace.content.Community;
@@ -202,6 +203,8 @@ public class BrowseEngine {
// get the table name that we are going to be getting our data from
dao.setTable(browseIndex.getTableName());
dao.setStartsWith(StringUtils.lowerCase(scope.getStartsWith()));
// tell the browse query whether we are ascending or descending on the value
dao.setAscending(scope.isAscending());
@@ -248,9 +251,6 @@ public class BrowseEngine {
}
}
// this is the total number of results in answer to the query
int total = getTotalResults();
// assemble the ORDER BY clause
String orderBy = browseIndex.getSortField(scope.isSecondLevel());
if (scope.getSortBy() > 0) {
@@ -258,6 +258,9 @@ public class BrowseEngine {
}
dao.setOrderField(orderBy);
// this is the total number of results in answer to the query
int total = getTotalResults();
int offset = scope.getOffset();
String rawFocusValue = null;
if (offset < 1 && (scope.hasJumpToItem() || scope.hasJumpToValue() || scope.hasStartsWith())) {
@@ -269,9 +272,6 @@ public class BrowseEngine {
String focusValue = normalizeJumpToValue(rawFocusValue);
log.debug("browsing using focus: " + focusValue);
// Convert the focus value into an offset
offset = getOffsetForValue(focusValue);
}
dao.setOffset(offset);
@@ -684,13 +684,11 @@ public class BrowseEngine {
// our count, storing them locally to reinstate later
String focusField = dao.getJumpToField();
String focusValue = dao.getJumpToValue();
String orderField = dao.getOrderField();
int limit = dao.getLimit();
int offset = dao.getOffset();
dao.setJumpToField(null);
dao.setJumpToValue(null);
dao.setOrderField(null);
dao.setLimit(-1);
dao.setOffset(-1);
@@ -700,7 +698,6 @@ public class BrowseEngine {
// now put back the values we removed for this method
dao.setJumpToField(focusField);
dao.setJumpToValue(focusValue);
dao.setOrderField(orderField);
dao.setLimit(limit);
dao.setOffset(offset);
dao.setCountValues(null);

3
dspace-api/src/main/java/org/dspace/browse/SolrBrowseDAO.java
View File

@@ -205,6 +205,9 @@ public class SolrBrowseDAO implements BrowseDAO {
} else if (valuePartial) {
query.addFilterQueries("{!field f=" + facetField + "_partial}" + value);
}
if (StringUtils.isNotBlank(startsWith) && orderField != null) {
query.addFilterQueries("bi_" + orderField + "_sort:" + startsWith + "*");
}
// filter on item to be sure to don't include any other object
// indexed in the Discovery Search core
query.addFilterQueries("search.resourcetype:" + IndexableItem.TYPE);

9
dspace-api/src/main/java/org/dspace/content/DSpaceObjectServiceImpl.java
View File

@@ -243,11 +243,11 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
boolean authorityControlled = metadataAuthorityService.isAuthorityControlled(metadataField);
boolean authorityRequired = metadataAuthorityService.isAuthorityRequired(metadataField);
List<MetadataValue> newMetadata = new ArrayList<>(values.size());
List<MetadataValue> newMetadata = new ArrayList<>();
// We will not verify that they are valid entries in the registry
// until update() is called.
for (int i = 0; i < values.size(); i++) {
if (values.get(i) != null) {
if (authorities != null && authorities.size() >= i) {
if (StringUtils.startsWith(authorities.get(i), Constants.VIRTUAL_AUTHORITY_PREFIX)) {
continue;
@@ -285,7 +285,6 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
.get(i) + "\"");
}
}
if (values.get(i) != null) {
// remove control unicode char
String temp = values.get(i).trim();
char[] dcvalue = temp.toCharArray();
@@ -298,13 +297,11 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
}
}
metadataValue.setValue(String.valueOf(dcvalue));
} else {
metadataValue.setValue(null);
}
//An update here isn't needed, this is persited upon the merge of the owning object
// metadataValueService.update(context, metadataValue);
dso.addDetails(metadataField.toString());
}
}
setMetadataModified(dso);
return newMetadata;
}

6
dspace-api/src/main/java/org/dspace/content/ItemServiceImpl.java
View File

@@ -911,6 +911,12 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
@Override
public void move(Context context, Item item, Collection from, Collection to)
throws SQLException, AuthorizeException, IOException {
// If the two collections are the same, do nothing.
if (from.equals(to)) {
return;
}
// Use the normal move method, and default to not inherit permissions
this.move(context, item, from, to, false);
}

2
dspace-api/src/main/java/org/dspace/content/MetadataValue.java
View File

@@ -59,7 +59,7 @@ public class MetadataValue implements ReloadableEntity<Integer> {
* The value of the field
*/
@Lob
@Type(type = "org.hibernate.type.MaterializedClobType")
@Type(type = "org.dspace.storage.rdbms.hibernate.DatabaseAwareLobType")
@Column(name = "text_value")
private String value;

4
dspace-api/src/main/java/org/dspace/content/crosswalk/AIPDIMCrosswalk.java
View File

@@ -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

4
dspace-api/src/main/java/org/dspace/content/crosswalk/AIPTechMDCrosswalk.java
View File

@@ -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

4
dspace-api/src/main/java/org/dspace/content/crosswalk/DIMDisseminationCrosswalk.java
View File

@@ -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

4
dspace-api/src/main/java/org/dspace/content/crosswalk/DIMIngestionCrosswalk.java
View File

@@ -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

4
dspace-api/src/main/java/org/dspace/content/crosswalk/DisseminationCrosswalk.java
View File

@@ -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

2
dspace-api/src/main/java/org/dspace/content/crosswalk/IngestionCrosswalk.java
View File

@@ -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

10
dspace-api/src/main/java/org/dspace/content/crosswalk/METSDisseminationCrosswalk.java
View File

@@ -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

4
dspace-api/src/main/java/org/dspace/content/crosswalk/METSRightsCrosswalk.java
View File

@@ -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

62
dspace-api/src/main/java/org/dspace/content/crosswalk/MODSDisseminationCrosswalk.java
View File

@@ -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 = "</mods>";
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<Element> 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() +
List<Object> matches = trip.xpath.evaluate(me);
if (matches.isEmpty()) {
log.warn("XPath \"" + trip.xpath.getExpression() +
"\" 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));
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=" + what.getClass().getName());
log.warn("Got unknown object from XPath, class=" + match.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());
}
}
}
return result;

6
dspace-api/src/main/java/org/dspace/content/crosswalk/NullIngestionCrosswalk.java
View File

@@ -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

4
dspace-api/src/main/java/org/dspace/content/crosswalk/OAIDCIngestionCrosswalk.java
View File

@@ -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

4
dspace-api/src/main/java/org/dspace/content/crosswalk/OREDisseminationCrosswalk.java
View File

@@ -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

51
dspace-api/src/main/java/org/dspace/content/crosswalk/OREIngestionCrosswalk.java
View File

@@ -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<Element> 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<Element> 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<Attribute> 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<Element> 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")) {

4
dspace-api/src/main/java/org/dspace/content/crosswalk/PREMISCrosswalk.java
View File

@@ -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

2
dspace-api/src/main/java/org/dspace/content/crosswalk/ParameterizedDisseminationCrosswalk.java
View File

@@ -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.

11
dspace-api/src/main/java/org/dspace/content/crosswalk/QDCCrosswalk.java
View File

@@ -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<Element> disseminateList(Context context, DSpaceObject dso)

12
dspace-api/src/main/java/org/dspace/content/crosswalk/RoleCrosswalk.java
View File

@@ -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

5
dspace-api/src/main/java/org/dspace/content/crosswalk/SimpleDCDisseminationCrosswalk.java
View File

@@ -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<Element> disseminateList(Context context, DSpaceObject dso)

7
dspace-api/src/main/java/org/dspace/content/crosswalk/XHTMLHeadDisseminationCrosswalk.java
View File

@@ -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 &lt;meta&gt; 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<Element> disseminateList(Context context, DSpaceObject dso) throws CrosswalkException,

11
dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTCrosswalk.java
View File

@@ -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;
@@ -130,12 +130,6 @@ public abstract class XSLTCrosswalk extends SelfNamedPlugin {
return aliasList.toArray(new String[aliasList.size()]);
}
/**
* We need to force this, because some dependency elsewhere interferes.
*/
private static final String TRANSFORMER_FACTORY_CLASS
= "com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl";
private Transformer transformer = null;
private File transformFile = null;
private long transformLastModified = 0;
@@ -181,8 +175,7 @@ public abstract class XSLTCrosswalk extends SelfNamedPlugin {
Source transformSource
= new StreamSource(new FileInputStream(transformFile));
TransformerFactory transformerFactory
= TransformerFactory.newInstance(
TRANSFORMER_FACTORY_CLASS, null);
= TransformerFactory.newInstance();
transformer = transformerFactory.newTransformer(transformSource);
transformLastModified = transformFile.lastModified();
} catch (TransformerConfigurationException | FileNotFoundException e) {

26
dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTDisseminationCrosswalk.java
View File

@@ -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<Element> 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<Content> contentList = result.getResult();
// Transform List<Content> into List<Element>
List<Element> 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);

23
dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTIngestionCrosswalk.java
View File

@@ -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<Content> contentList = result.getResult();
// Transform List<Content> into List<Element>
List<Element> 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);

5
dspace-api/src/main/java/org/dspace/content/logic/DefaultFilter.java
View File

@@ -7,7 +7,8 @@
*/
package org.dspace.content.logic;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Item;
import org.dspace.core.Context;
@@ -21,7 +22,7 @@ import org.dspace.core.Context;
*/
public class DefaultFilter implements Filter {
private LogicalStatement statement;
private static Logger log = Logger.getLogger(Filter.class);
private final static Logger log = LogManager.getLogger();
/**
* Set statement from Spring configuration in item-filters.xml

5
dspace-api/src/main/java/org/dspace/content/logic/condition/InCommunityCondition.java
View File

@@ -10,7 +10,8 @@ package org.dspace.content.logic.condition;
import java.sql.SQLException;
import java.util.List;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Collection;
import org.dspace.content.Community;
import org.dspace.content.DSpaceObject;
@@ -26,7 +27,7 @@ import org.dspace.core.Context;
* @version $Revision$
*/
public class InCommunityCondition extends AbstractCondition {
private static Logger log = Logger.getLogger(InCommunityCondition.class);
private final static Logger log = LogManager.getLogger();
/**
* Return true if item is in one of the specified collections

5
dspace-api/src/main/java/org/dspace/content/logic/condition/IsWithdrawnCondition.java
View File

@@ -7,7 +7,8 @@
*/
package org.dspace.content.logic.condition;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Item;
import org.dspace.content.logic.LogicalStatementException;
import org.dspace.core.Context;
@@ -19,7 +20,7 @@ import org.dspace.core.Context;
* @version $Revision$
*/
public class IsWithdrawnCondition extends AbstractCondition {
private static Logger log = Logger.getLogger(IsWithdrawnCondition.class);
private final static Logger log = LogManager.getLogger();
/**
* Return true if item is withdrawn

5
dspace-api/src/main/java/org/dspace/content/logic/condition/MetadataValueMatchCondition.java
View File

@@ -11,7 +11,8 @@ import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Item;
import org.dspace.content.MetadataValue;
import org.dspace.content.logic.LogicalStatementException;
@@ -26,7 +27,7 @@ import org.dspace.core.Context;
*/
public class MetadataValueMatchCondition extends AbstractCondition {
private static Logger log = Logger.getLogger(MetadataValueMatchCondition.class);
private final static Logger log = LogManager.getLogger();
/**
* Return true if any value for a specified field in the item matches a specified regex pattern

5
dspace-api/src/main/java/org/dspace/content/logic/condition/MetadataValuesMatchCondition.java
View File

@@ -11,7 +11,8 @@ import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Item;
import org.dspace.content.MetadataValue;
import org.dspace.content.logic.LogicalStatementException;
@@ -26,7 +27,7 @@ import org.dspace.core.Context;
*/
public class MetadataValuesMatchCondition extends AbstractCondition {
private static Logger log = Logger.getLogger(MetadataValuesMatchCondition.class);
private final static Logger log = LogManager.getLogger();
/**
* Return true if any value for a specified field in the item matches any of the specified regex patterns

5
dspace-api/src/main/java/org/dspace/content/logic/condition/ReadableByGroupCondition.java
View File

@@ -10,7 +10,8 @@ package org.dspace.content.logic.condition;
import java.sql.SQLException;
import java.util.List;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.ResourcePolicy;
import org.dspace.authorize.factory.AuthorizeServiceFactory;
import org.dspace.authorize.service.AuthorizeService;
@@ -27,7 +28,7 @@ import org.dspace.core.Context;
* @version $Revision$
*/
public class ReadableByGroupCondition extends AbstractCondition {
private static Logger log = Logger.getLogger(ReadableByGroupCondition.class);
private final static Logger log = LogManager.getLogger();
// Authorize service
AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();

8
dspace-api/src/main/java/org/dspace/content/packager/AbstractMETSDisseminator.java
View File

@@ -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

2
dspace-api/src/main/java/org/dspace/content/packager/AbstractMETSIngester.java
View File

@@ -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

2
dspace-api/src/main/java/org/dspace/content/packager/DSpaceAIPIngester.java
View File

@@ -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

2
dspace-api/src/main/java/org/dspace/content/packager/DSpaceMETSIngester.java
View File

@@ -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

66
dspace-api/src/main/java/org/dspace/content/packager/METSManifest.java
View File

@@ -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;
/**
* <P>
@@ -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);
}
XPathExpression<Element> 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);
XPathExpression<Element> xpath =
XPathFactory.instance()
.compile(
"mets:fileSec/mets:fileGrp[@USE=\"CONTENT\"]/mets:file[@GROUPID=\"" + groupID + "\"]",
Filters.element(), null, metsNS);
List<Element> oFiles = xpath.evaluate(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);
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;
}
}
// 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);
XPathExpression<Element> xpath =
XPathFactory.instance()
.compile(path, Filters.element(), null, metsNS, xlinkNS);
Element result = xpath.evaluateFirst(mets);
if (result == null && nullOk) {
return null;
} else if (result instanceof Element) {
return (Element) result;
} else {
} else if (result == null && !nullOk) {
throw new MetadataValidationException("METSManifest: Failed to resolve XPath, path=\"" + path + "\"");
}
} catch (JDOMException je) {
throw new MetadataValidationException("METSManifest: Failed to resolve XPath, path=\"" + path + "\"", je);
} else {
return result;
}
}

2
dspace-api/src/main/java/org/dspace/content/packager/RoleDisseminator.java
View File

@@ -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.

10
dspace-api/src/main/java/org/dspace/core/Email.java
View File

@@ -152,14 +152,14 @@ public class Email {
private static final String RESOURCE_REPOSITORY_NAME = "Email";
private static final Properties VELOCITY_PROPERTIES = new Properties();
static {
VELOCITY_PROPERTIES.put(Velocity.RESOURCE_LOADER, "string");
VELOCITY_PROPERTIES.put("string.resource.loader.description",
VELOCITY_PROPERTIES.put(Velocity.RESOURCE_LOADERS, "string");
VELOCITY_PROPERTIES.put("resource.loader.string.description",
"Velocity StringResource loader");
VELOCITY_PROPERTIES.put("string.resource.loader.class",
VELOCITY_PROPERTIES.put("resource.loader.string.class",
StringResourceLoader.class.getName());
VELOCITY_PROPERTIES.put("string.resource.loader.repository.name",
VELOCITY_PROPERTIES.put("resource.loader.string.repository.name",
RESOURCE_REPOSITORY_NAME);
VELOCITY_PROPERTIES.put("string.resource.loader.repository.static",
VELOCITY_PROPERTIES.put("resource.loader.string.repository.static",
"false");
}

4
dspace-api/src/main/java/org/dspace/curate/CitationPage.java
View File

@@ -7,6 +7,7 @@
*/
package org.dspace.curate;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.sql.SQLException;
@@ -154,7 +155,8 @@ public class CitationPage extends AbstractCurationTask {
try {
//Create the cited document
InputStream citedInputStream =
citationDocument.makeCitedDocument(Curator.curationContext(), bitstream).getLeft();
new ByteArrayInputStream(
citationDocument.makeCitedDocument(Curator.curationContext(), bitstream).getLeft());
//Add the cited document to the approiate bundle
this.addCitedPageToItem(citedInputStream, bundle, pBundle,
dBundle, displayMap, item, bitstream);

1
dspace-api/src/main/java/org/dspace/curate/CurationCliScriptConfiguration.java
View File

@@ -19,7 +19,6 @@ public class CurationCliScriptConfiguration extends CurationScriptConfiguration<
public Options getOptions() {
options = super.getOptions();
options.addOption("e", "eperson", true, "email address of curating eperson");
options.getOption("e").setType(String.class);
options.getOption("e").setRequired(true);
return options;
}

8
dspace-api/src/main/java/org/dspace/discovery/IndexClientOptions.java
View File

@@ -74,25 +74,17 @@ public enum IndexClientOptions {
options
.addOption("r", "remove", true, "remove an Item, Collection or Community from index based on its handle");
options.getOption("r").setType(String.class);
options.addOption("i", "index", true,
"add or update an Item, Collection or Community based on its handle or uuid");
options.getOption("i").setType(boolean.class);
options.addOption("c", "clean", false,
"clean existing index removing any documents that no longer exist in the db");
options.getOption("c").setType(boolean.class);
options.addOption("d", "delete", false,
"delete all records from existing index");
options.getOption("d").setType(boolean.class);
options.addOption("b", "build", false, "(re)build index, wiping out current one if it exists");
options.getOption("b").setType(boolean.class);
options.addOption("s", "spellchecker", false, "Rebuild the spellchecker, can be combined with -b and -f.");
options.getOption("s").setType(boolean.class);
options.addOption("f", "force", false,
"if updating existing index, force each handle to be reindexed even if uptodate");
options.getOption("f").setType(boolean.class);
options.addOption("h", "help", false, "print this help message");
options.getOption("h").setType(boolean.class);
return options;
}
}

1
dspace-api/src/main/java/org/dspace/discovery/indexobject/IndexFactoryImpl.java
View File

@@ -95,7 +95,6 @@ public abstract class IndexFactoryImpl<T extends IndexableObject, S> implements
100000);
// Use Tika's Text parser as the streams are always from the TEXT bundle (i.e. already extracted text)
// TODO: We may wish to consider using Tika to extract the text in the future.
TextAndCSVParser tikaParser = new TextAndCSVParser();
BodyContentHandler tikaHandler = new BodyContentHandler(charLimit);
Metadata tikaMetadata = new Metadata();

5
dspace-api/src/main/java/org/dspace/disseminate/CitationDocumentServiceImpl.java
View File

@@ -8,7 +8,6 @@
package org.dspace.disseminate;
import java.awt.Color;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.IOException;
@@ -297,7 +296,7 @@ public class CitationDocumentServiceImpl implements CitationDocumentService, Ini
}
@Override
public Pair<InputStream, Long> makeCitedDocument(Context context, Bitstream bitstream)
public Pair<byte[], Long> makeCitedDocument(Context context, Bitstream bitstream)
throws IOException, SQLException, AuthorizeException {
PDDocument document = new PDDocument();
PDDocument sourceDocument = new PDDocument();
@@ -318,7 +317,7 @@ public class CitationDocumentServiceImpl implements CitationDocumentService, Ini
document.save(out);
byte[] data = out.toByteArray();
return Pair.of(new ByteArrayInputStream(data), Long.valueOf(data.length));
return Pair.of(data, Long.valueOf(data.length));
}
} finally {

3
dspace-api/src/main/java/org/dspace/disseminate/service/CitationDocumentService.java
View File

@@ -8,7 +8,6 @@
package org.dspace.disseminate.service;
import java.io.IOException;
import java.io.InputStream;
import java.sql.SQLException;
import org.apache.commons.lang3.tuple.Pair;
@@ -84,7 +83,7 @@ public interface CitationDocumentService {
* @throws SQLException if database error
* @throws AuthorizeException if authorization error
*/
public Pair<InputStream, Long> makeCitedDocument(Context context, Bitstream bitstream)
public Pair<byte[], Long> makeCitedDocument(Context context, Bitstream bitstream)
throws IOException, SQLException, AuthorizeException;
/**

29
dspace-api/src/main/java/org/dspace/eperson/EPersonConsumer.java
View File

@@ -7,10 +7,12 @@
*/
package org.dspace.eperson;
import java.io.IOException;
import java.util.Date;
import java.util.UUID;
import javax.mail.MessagingException;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.core.Constants;
import org.dspace.core.Context;
@@ -30,16 +32,17 @@ import org.dspace.services.factory.DSpaceServicesFactory;
* Recommended filter: EPerson+Create
*
* @author Stuart Lewis
* @version $Revision$
*/
public class EPersonConsumer implements Consumer {
/**
* log4j logger
*/
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(EPersonConsumer.class);
private static final Logger log
= org.apache.logging.log4j.LogManager.getLogger(EPersonConsumer.class);
protected EPersonService ePersonService
= EPersonServiceFactory.getInstance().getEPersonService();
protected ConfigurationService configurationService
= DSpaceServicesFactory.getInstance().getConfigurationService();
@@ -74,6 +77,7 @@ public class EPersonConsumer implements Consumer {
if (et == Event.CREATE) {
// Notify of new user registration
String notifyRecipient = configurationService.getProperty("registration.notify");
EPerson eperson = ePersonService.find(context, id);
if (notifyRecipient == null) {
notifyRecipient = "";
}
@@ -81,7 +85,6 @@ public class EPersonConsumer implements Consumer {
if (!notifyRecipient.equals("")) {
try {
EPerson eperson = ePersonService.find(context, id);
Email adminEmail = Email
.getEmail(I18nUtil.getEmailFilename(context.getCurrentLocale(), "registration_notify"));
adminEmail.addRecipient(notifyRecipient);
@@ -103,6 +106,26 @@ public class EPersonConsumer implements Consumer {
"error_emailing_administrator", ""), me);
}
}
// If enabled, send a "welcome" message to the new EPerson.
if (configurationService.getBooleanProperty("mail.welcome.enabled", false)) {
String addressee = eperson.getEmail();
if (StringUtils.isNotBlank(addressee)) {
log.debug("Sending welcome email to {}", addressee);
try {
Email message = Email.getEmail(
I18nUtil.getEmailFilename(context.getCurrentLocale(), "welcome"));
message.addRecipient(addressee);
message.send();
} catch (IOException | MessagingException ex) {
log.warn("Welcome message not sent to {}: {}",
addressee, ex.getMessage());
}
} else {
log.warn("Welcome message not sent to EPerson {} because it has no email address.",
eperson.getID().toString());
}
}
} else if (et == Event.DELETE) {
// TODO: Implement this if required
}

2
dspace-api/src/main/java/org/dspace/eperson/Group.java
View File

@@ -201,7 +201,7 @@ public class Group extends DSpaceObject implements DSpaceObjectLegacySupport {
void setName(String name) throws SQLException {
if (!StringUtils.equals(this.name, name) && !isPermanent()) {
this.name = name;
groupsChanged = true;
setMetadataModified();
}
}

5
dspace-api/src/main/java/org/dspace/google/GoogleAsyncEventListener.java
View File

@@ -31,7 +31,8 @@ import org.apache.http.client.methods.HttpPost;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.core.Constants;
import org.dspace.core.Context;
@@ -55,7 +56,7 @@ public class GoogleAsyncEventListener extends AbstractUsageEventListener {
// 20 is the event max set by the GA API
private static final int GA_MAX_EVENTS = 20;
private static final String ANALYTICS_BATCH_ENDPOINT = "https://www.google-analytics.com/batch";
private static Logger log = Logger.getLogger(GoogleAsyncEventListener.class);
private final static Logger log = LogManager.getLogger();
private static String analyticsKey;
private static CloseableHttpClient httpclient;
private static Buffer buffer;

8
dspace-api/src/main/java/org/dspace/harvest/HarvestedCollectionServiceImpl.java
View File

@@ -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;

10
dspace-api/src/main/java/org/dspace/harvest/OAIHarvester.java
View File

@@ -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;

2
dspace-api/src/main/java/org/dspace/identifier/DOI.java
View File

@@ -34,8 +34,6 @@ public class DOI
implements Identifier, ReloadableEntity<Integer> {
public static final String SCHEME = "doi:";
public static final String RESOLVER = "http://dx.doi.org";
@Id
@Column(name = "doi_id")
@GeneratedValue(strategy = GenerationType.SEQUENCE, generator = "doi_seq")

2
dspace-api/src/main/java/org/dspace/identifier/DOIIdentifierProvider.java
View File

@@ -1028,7 +1028,7 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
Item item = (Item) dso;
List<MetadataValue> metadata = itemService.getMetadata(item, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null);
String leftPart = DOI.RESOLVER + SLASH + getPrefix() + SLASH + getNamespaceSeparator();
String leftPart = doiService.getResolver() + SLASH + getPrefix() + SLASH + getNamespaceSeparator();
for (MetadataValue id : metadata) {
if (id.getValue().startsWith(leftPart)) {
return doiService.DOIFromExternalFormat(id.getValue());

82
dspace-api/src/main/java/org/dspace/identifier/DOIServiceImpl.java
View File

@@ -17,11 +17,13 @@ import org.dspace.core.Context;
import org.dspace.identifier.dao.DOIDAO;
import org.dspace.identifier.doi.DOIIdentifierException;
import org.dspace.identifier.service.DOIService;
import org.dspace.services.ConfigurationService;
import org.springframework.beans.factory.annotation.Autowired;
/**
* Service implementation for the DOI object.
* This class is responsible for all business logic calls for the DOI object and is autowired by spring.
* Service implementation for the {@link DOI} object.
* This class is responsible for all business logic calls for the DOI object
* and is autowired by Spring.
* This class should never be accessed directly.
*
* @author kevinvandevelde at atmire.com
@@ -31,6 +33,16 @@ public class DOIServiceImpl implements DOIService {
@Autowired(required = true)
protected DOIDAO doiDAO;
@Autowired(required = true)
protected ConfigurationService configurationService;
private static final Pattern DOI_URL_PATTERN
= Pattern.compile("http(s)?://([a-z0-9-.]+)?doi.org(?<path>/.*)",
Pattern.CASE_INSENSITIVE);
private static final String DOI_URL_PATTERN_PATH_GROUP = "path";
private static final String RESOLVER_DEFAULT = "https://doi.org";
protected DOIServiceImpl() {
}
@@ -66,25 +78,46 @@ public class DOIServiceImpl implements DOIService {
if (null == identifier) {
throw new IllegalArgumentException("Identifier is null.", new NullPointerException());
}
if (identifier.isEmpty()) {
throw new IllegalArgumentException("Cannot format an empty identifier.");
}
if (identifier.startsWith(DOI.SCHEME)) {
return DOI.RESOLVER + "/" + identifier.substring(DOI.SCHEME.length());
String resolver = getResolver();
if (identifier.startsWith(DOI.SCHEME)) { // doi:something
StringBuilder result = new StringBuilder(resolver);
if (!resolver.endsWith("/")) {
result.append('/');
}
if (identifier.startsWith("10.") && identifier.contains("/")) {
return DOI.RESOLVER + "/" + identifier;
result.append(identifier.substring(DOI.SCHEME.length()));
return result.toString();
}
if (identifier.startsWith(DOI.RESOLVER + "/10.")) {
if (identifier.startsWith("10.") && identifier.contains("/")) { // 10.something
StringBuilder result = new StringBuilder(resolver);
if (!resolver.endsWith("/")) {
result.append('/');
}
result.append(identifier);
return result.toString();
}
if (identifier.startsWith(resolver + "/10.")) { // https://doi.org/10.something
return identifier;
}
Matcher matcher = DOI_URL_PATTERN.matcher(identifier);
if (matcher.matches()) { // various old URL forms
return resolver + matcher.group(DOI_URL_PATTERN_PATH_GROUP);
}
throw new IdentifierException(identifier + "does not seem to be a DOI.");
}
@Override
public String DOIFromExternalFormat(String identifier) throws DOIIdentifierException {
Pattern pattern = Pattern.compile("^" + DOI.RESOLVER + "/+(10\\..*)$");
Pattern pattern = Pattern.compile("^" + getResolver() + "/+(10\\..*)$");
Matcher matcher = pattern.matcher(identifier);
if (matcher.find()) {
return DOI.SCHEME + matcher.group(1);
@@ -99,18 +132,29 @@ public class DOIServiceImpl implements DOIService {
if (null == identifier) {
throw new IllegalArgumentException("Identifier is null.", new NullPointerException());
}
if (identifier.startsWith(DOI.SCHEME)) {
return identifier;
}
if (identifier.isEmpty()) {
throw new IllegalArgumentException("Cannot format an empty identifier.");
}
if (identifier.startsWith("10.") && identifier.contains("/")) {
if (identifier.startsWith(DOI.SCHEME)) { // doi:something
return identifier;
}
if (identifier.startsWith("10.") && identifier.contains("/")) { // 10.something
return DOI.SCHEME + identifier;
}
if (identifier.startsWith(DOI.RESOLVER + "/10.")) {
return DOI.SCHEME + identifier.substring(18);
String resolver = getResolver();
if (identifier.startsWith(resolver + "/10.")) { //https://doi.org/10.something
return DOI.SCHEME + identifier.substring(resolver.length());
}
Matcher matcher = DOI_URL_PATTERN.matcher(identifier);
if (matcher.matches()) { // various old URL forms
return DOI.SCHEME + matcher.group(DOI_URL_PATTERN_PATH_GROUP).substring(1);
}
throw new DOIIdentifierException(identifier + "does not seem to be a DOI.",
DOIIdentifierException.UNRECOGNIZED);
}
@@ -126,4 +170,14 @@ public class DOIServiceImpl implements DOIService {
throws SQLException {
return doiDAO.findSimilarNotInState(context, doiPattern, statuses, dsoIsNotNull);
}
@Override
public String getResolver() {
String resolver = configurationService.getProperty("identifier.doi.resolver",
RESOLVER_DEFAULT);
if (resolver.endsWith("/")) {
resolver = resolver.substring(0, resolver.length() - 1);
}
return resolver;
}
}

4
dspace-api/src/main/java/org/dspace/identifier/DataCiteXMLCreator.java
View File

@@ -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;

14
dspace-api/src/main/java/org/dspace/identifier/doi/DataCiteConnector.java
View File

@@ -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;

74
dspace-api/src/main/java/org/dspace/identifier/service/DOIService.java
View File

@@ -17,26 +17,65 @@ import org.dspace.identifier.IdentifierException;
import org.dspace.identifier.doi.DOIIdentifierException;
/**
* Service interface class for the DOI object.
* The implementation of this class is responsible for all business logic calls for the DOI object and is autowired
* by spring
* Service interface class for the {@link DOI} object.
* The implementation of this class is responsible for all business logic calls
* for the {@link DOI} object and is autowired by Spring.
*
* @author kevinvandevelde at atmire.com
*/
public interface DOIService {
/**
* Update a DOI in storage.
*
* @param context current DSpace session.
* @param doi the DOI to persist.
* @throws SQLException passed through.
*/
public void update(Context context, DOI doi) throws SQLException;
/**
* Create a new DOI in storage.
*
* @param context current DSpace session.
* @return the new DOI.
* @throws SQLException passed through.
*/
public DOI create(Context context) throws SQLException;
/**
* Find a specific DOI in storage.
*
* @param context current DSpace session.
* @param doi string representation of the DOI.
* @return the DOI object found.
* @throws SQLException passed through, can mean none found.
*/
public DOI findByDoi(Context context, String doi) throws SQLException;
/**
* Find the DOI assigned to a given DSpace Object.
*
* @param context current DSpace session.
* @param dso The DSpace Object.
* @return the DSO's DOI.
* @throws SQLException passed through.
*/
public DOI findDOIByDSpaceObject(Context context, DSpaceObject dso) throws SQLException;
/**
* Find the DOI assigned to a given DSpace Object, unless it has one of a
* given set of statuses.
*
* @param context current DSpace context.
* @param dso the DSpace Object.
* @param statusToExclude uninteresting statuses.
* @return the DSO's DOI.
* @throws SQLException passed through.
*/
public DOI findDOIByDSpaceObject(Context context, DSpaceObject dso, List<Integer> statusToExclude)
throws SQLException;
/**
* This method helps to convert a DOI into a URL. It takes DOIs in one of
* the following formats and returns it as URL (f.e.
@@ -50,11 +89,17 @@ public interface DOIService {
* @param identifier A DOI that should be returned in external form.
* @return A String containing a URL to the official DOI resolver.
* @throws IllegalArgumentException If identifier is null or an empty String.
* @throws org.dspace.identifier.IdentifierException If identifier could not be recognized as valid DOI.
* @throws IdentifierException If identifier could not be recognized as valid DOI.
*/
public String DOIToExternalForm(String identifier)
throws IdentifierException;
/**
* Convert an HTTP DOI URL (https://doi.org/10.something) to a "doi:" URI.
* @param identifier HTTP URL
* @return DOI URI
* @throws DOIIdentifierException if {@link identifier} is not recognizable.
*/
public String DOIFromExternalFormat(String identifier)
throws DOIIdentifierException;
@@ -65,15 +110,23 @@ public interface DOIService {
* f.e. 10.123/456, doi:10.123/456, http://dx.doi.org/10.123/456.
* @return Given Identifier with DOI-Scheme, f.e. doi:10.123/456.
* @throws IllegalArgumentException If identifier is empty or null.
* @throws org.dspace.identifier.doi.DOIIdentifierException If DOI could not be recognized.
* @throws DOIIdentifierException If DOI could not be recognized.
*/
public String formatIdentifier(String identifier)
throws DOIIdentifierException;
/**
* Find all DOIs that have one of a given set of statuses.
* @param context current DSpace session.
* @param statuses desired statuses.
* @return all DOIs having any of the given statuses.
* @throws SQLException passed through.
*/
public List<DOI> getDOIsByStatus(Context context, List<Integer> statuses) throws SQLException;
/**
* Find all DOIs that are similar to the specified pattern ant not in the specified states.
* Find all DOIs that are similar to the specified pattern and not in the
* specified states.
*
* @param context DSpace context
* @param doiPattern The pattern, e.g. "10.5072/123.%"
@@ -85,4 +138,11 @@ public interface DOIService {
public List<DOI> getSimilarDOIsNotInState(Context context, String doiPattern, List<Integer> statuses,
boolean dsoIsNotNull)
throws SQLException;
/**
* Get the URL stem of the DOI resolver, e.g. "https://doi.org/".
*
* @return URL to the DOI resolver.
*/
public String getResolver();
}

2
dspace-api/src/main/java/org/dspace/iiif/consumer/CanvasCacheEvictService.java
View File

@@ -23,7 +23,7 @@ public class CanvasCacheEvictService {
CacheManager cacheManager;
public void evictSingleCacheValue(String cacheKey) {
Objects.requireNonNull(cacheManager.getCache(CACHE_NAME)).evict(cacheKey);
Objects.requireNonNull(cacheManager.getCache(CACHE_NAME)).evictIfPresent(cacheKey);
}
}

4
dspace-api/src/main/java/org/dspace/iiif/consumer/ManifestsCacheEvictService.java
View File

@@ -26,11 +26,11 @@ public class ManifestsCacheEvictService {
CacheManager cacheManager;
public void evictSingleCacheValue(String cacheKey) {
Objects.requireNonNull(cacheManager.getCache(CACHE_NAME)).evict(cacheKey);
Objects.requireNonNull(cacheManager.getCache(CACHE_NAME)).evictIfPresent(cacheKey);
}
public void evictAllCacheValues() {
Objects.requireNonNull(cacheManager.getCache(CACHE_NAME)).clear();
Objects.requireNonNull(cacheManager.getCache(CACHE_NAME)).invalidate();
}
}

4
dspace-api/src/main/java/org/dspace/importer/external/arxiv/metadatamapping/contributor/ArXivIdMetadataContributor.java vendored
View File

@@ -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<MetadatumDTO> contributeMetadata(OMElement t) {
public Collection<MetadatumDTO> contributeMetadata(Element t) {
Collection<MetadatumDTO> values = super.contributeMetadata(t);
parseValue(values);
return values;

69
dspace-api/src/main/java/org/dspace/importer/external/arxiv/service/ArXivImportMetadataSourceServiceImpl.java vendored
View File

@@ -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<OMElement>
public class ArXivImportMetadataSourceServiceImpl extends AbstractImportMetadataSourceService<Element>
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<Element> 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<OMElement> omElements = splitToRecords(responseString);
for (OMElement record : omElements) {
List<Element> 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<OMElement> omElements = splitToRecords(responseString);
for (OMElement record : omElements) {
List<Element> 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<OMElement> omElements = splitToRecords(responseString);
for (OMElement record : omElements) {
List<Element> elements = splitToRecords(responseString);
for (Element record : elements) {
results.add(transformSourceRecords(record));
}
return results;
@@ -387,16 +397,21 @@ public class ArXivImportMetadataSourceServiceImpl extends AbstractImportMetadata
}
}
private List<OMElement> splitToRecords(String recordsSrc) {
OMXMLParserWrapper records = OMXMLBuilderFactory.createOMBuilder(new StringReader(recordsSrc));
OMElement element = records.getDocumentElement();
AXIOMXPath xpath = null;
private List<Element> splitToRecords(String recordsSrc) {
try {
xpath = new AXIOMXPath("ns:entry");
xpath.addNamespace("ns", "http://www.w3.org/2005/Atom");
List<OMElement> 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<Element> xpath =
XPathFactory.instance().compile("ns:entry", Filters.element(), null, namespaces);
List<Element> recordsList = xpath.evaluate(root);
return recordsList;
} catch (JaxenException e) {
} catch (JDOMException | IOException e) {
return null;
}
}

64
dspace-api/src/main/java/org/dspace/importer/external/metadatamapping/contributor/SimpleXpathMetadatumContributor.java vendored
View File

@@ -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<OMElement> {
public class SimpleXpathMetadatumContributor implements MetadataContributor<Element> {
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<OMEl
return prefixToNamespaceMapping;
}
private MetadataFieldMapping<OMElement, MetadataContributor<OMElement>> metadataFieldMapping;
private MetadataFieldMapping<Element, MetadataContributor<Element>> metadataFieldMapping;
/**
* Return metadataFieldMapping
*
* @return MetadataFieldMapping
*/
public MetadataFieldMapping<OMElement, MetadataContributor<OMElement>> getMetadataFieldMapping() {
public MetadataFieldMapping<Element, MetadataContributor<Element>> getMetadataFieldMapping() {
return metadataFieldMapping;
}
@@ -62,7 +65,7 @@ public class SimpleXpathMetadatumContributor implements MetadataContributor<OMEl
*/
@Override
public void setMetadataFieldMapping(
MetadataFieldMapping<OMElement, MetadataContributor<OMElement>> metadataFieldMapping) {
MetadataFieldMapping<Element, MetadataContributor<Element>> metadataFieldMapping) {
this.metadataFieldMapping = metadataFieldMapping;
}
@@ -140,36 +143,35 @@ public class SimpleXpathMetadatumContributor implements MetadataContributor<OMEl
* Depending on the retrieved node (using the query), different types of values will be added to the MetadatumDTO
* list
*
* @param t A class to retrieve metadata from.
* @param t An element to retrieve metadata from.
* @return a collection of import records. Only the identifier of the found records may be put in the record.
*/
@Override
public Collection<MetadatumDTO> contributeMetadata(OMElement t) {
public Collection<MetadatumDTO> contributeMetadata(Element t) {
List<MetadatumDTO> values = new LinkedList<>();
try {
AXIOMXPath xpath = new AXIOMXPath(query);
List<Namespace> namespaces = new ArrayList<>();
for (String ns : prefixToNamespaceMapping.keySet()) {
xpath.addNamespace(prefixToNamespaceMapping.get(ns), ns);
namespaces.add(Namespace.getNamespace(prefixToNamespaceMapping.get(ns), ns));
}
List<Object> nodes = xpath.selectNodes(t);
XPathExpression<Object> xpath =
XPathFactory.instance().compile(query, Filters.fpassthrough(), null, namespaces);
List<Object> nodes = xpath.evaluate(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()));
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 OMText) {
values.add(metadataFieldMapping.toDCValue(field, ((OMText) el).getText()));
} else if (el instanceof Text) {
values.add(metadataFieldMapping.toDCValue(field, ((Text) el).getText()));
} else {
log.error("node of type: " + el.getClass());
log.error("Encountered unsupported XML node of type: {}. Skipped that node.", el.getClass());
}
}
return values;
} catch (JaxenException e) {
log.error(query, e);
throw new RuntimeException(e);
}
}
}

65
dspace-api/src/main/java/org/dspace/importer/external/pubmed/service/PubmedImportMetadataSourceServiceImpl.java vendored
View File

@@ -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<OMElement>
public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadataSourceService<Element>
implements QuerySource, FileSource {
private String baseAddress;
@@ -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<OMElement> 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<Element> 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<OMElement> omElements = splitToRecords(response.readEntity(String.class));
List<Element> 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<OMElement> splitToRecords(String recordsSrc) {
OMXMLParserWrapper records = OMXMLBuilderFactory.createOMBuilder(new StringReader(recordsSrc));
OMElement element = records.getDocumentElement();
AXIOMXPath xpath = null;
private List<Element> splitToRecords(String recordsSrc) {
try {
xpath = new AXIOMXPath("//PubmedArticle");
List<OMElement> recordsList = xpath.selectNodes(element);
SAXBuilder saxBuilder = new SAXBuilder();
Document document = saxBuilder.build(new StringReader(recordsSrc));
Element root = document.getRootElement();
XPathExpression<Element> xpath =
XPathFactory.instance().compile("//PubmedArticle", Filters.element());
List<Element> 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<OMElement> omElements = splitToRecords(response.readEntity(String.class));
List<Element> 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<ImportRecord> parseXMLString(String xml) {
List<ImportRecord> records = new LinkedList<ImportRecord>();
List<OMElement> omElements = splitToRecords(xml);
for (OMElement record : omElements) {
List<Element> elements = splitToRecords(xml);
for (Element record : elements) {
records.add(transformSourceRecords(record));
}
return records;

2
dspace-api/src/main/java/org/dspace/license/CCLicenseConnectorService.java
View File

@@ -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.

82
dspace-api/src/main/java/org/dspace/license/CCLicenseConnectorServiceImpl.java
View File

@@ -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<String> 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<String> retrieveLicenses(CloseableHttpResponse response)
throws IOException, JaxenException, JDOMException {
throws IOException, JDOMException {
List<String> domains = new LinkedList<>();
String[] excludedLicenses = configurationService.getArrayProperty("cc.license.classfilter");
String responseString = EntityUtils.toString(response.getEntity());
JDOMXPath licenseClassXpath = new JDOMXPath("//licenses/license");
XPathExpression<Element> 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<Element> elements = licenseClassXpath.selectNodes(classDoc);
List<Element> 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<Object> licenseClassXpath =
XPathFactory.instance().compile("//licenseclass", Filters.fpassthrough());
XPathExpression<Element> 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<CCLicenseField> ccLicenseFields = new LinkedList<>();
List<Element> licenseFields = licenseFieldXpath.selectNodes(element);
List<Element> 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<Element> enums = enumXpath.selectNodes(licenseField);
XPathExpression<Element> enumXpath =
XPathFactory.instance().compile("enum", Filters.element());
List<Element> enums = enumXpath.evaluate(licenseField);
List<CCLicenseFieldEnum> 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<Object> 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;
}
}

4
dspace-api/src/main/java/org/dspace/license/CreativeCommonsServiceImpl.java
View File

@@ -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;

2
dspace-api/src/main/java/org/dspace/license/service/CreativeCommonsService.java
View File

@@ -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.

13
dspace-api/src/main/java/org/dspace/rdf/RDFConsumer.java
View File

@@ -286,10 +286,10 @@ public class RDFConsumer implements Consumer {
@Override
public void end(Context ctx) throws Exception {
log.debug("Started processing of queued events.");
// create a new context, to be sure to work as anonymous user
// we don't want to store private data in a triplestore with public
// SPARQL endpoint.
ctx = new Context(Context.Mode.READ_ONLY);
// store the context mode, set context read only for performance reasons, and restore the old mode
Context.Mode oldMode = ctx.getCurrentMode();
try {
ctx.setMode(Context.Mode.READ_ONLY);
if (toDelete == null) {
log.debug("Deletion queue does not exists, creating empty queue.");
this.toDelete = new LinkedList<>();
@@ -330,7 +330,10 @@ public class RDFConsumer implements Consumer {
+ id.id.toString() + ".");
delete(ctx, id);
}
ctx.abort();
} finally {
// restore context mode
ctx.setMode(oldMode);
}
log.debug("Deletion finished.");
}

70
dspace-api/src/main/java/org/dspace/statistics/DataTermsFacet.java
View File

@@ -1,70 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.statistics;
import java.util.ArrayList;
import java.util.List;
import com.google.gson.Gson;
/**
* A neutral data object to hold data for statistics.
*/
public class DataTermsFacet {
private List<TermsFacet> terms;
public DataTermsFacet() {
terms = new ArrayList<TermsFacet>();
}
public void addTermFacet(TermsFacet termsFacet) {
terms.add(termsFacet);
}
/**
* Render this data object into JSON format.
*
* An example of the output could be of the format:
* [{"term":"247166","count":10},{"term":"247168","count":6}]
*
* @return JSON-formatted data.
*/
public String toJson() {
Gson gson = new Gson();
return gson.toJson(terms);
}
public static class TermsFacet {
private String term;
private Integer count;
public TermsFacet(String term, Integer count) {
setTerm(term);
setCount(count);
}
public String getTerm() {
return term;
}
public void setTerm(String term) {
this.term = term;
}
public Integer getCount() {
return count;
}
public void setCount(Integer count) {
this.count = count;
}
}
}

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