Merge remote-tracking branch 'origin/clarin-dev' into clarin

.travis.yml

@@ -1,6 +1,6 @@
 language: java
 jdk:
-  - oraclejdk8
+  - openjdk8
 sudo: true
 addons:
   postgresql: '9.4'

README.md

@@ -9,7 +9,7 @@
 
 # clarin-dspace deployments
 
-* LINDAT/CLARIN: https://lindat.mff.cuni.cz/repository/xmlui/
+* LINDAT/CLARIAH-CZ: https://lindat.mff.cuni.cz/repository/xmlui/
 * CLARINO: https://repo.clarino.uib.no/xmlui/
 * CLARIN.SI: https://www.clarin.si/repository/xmlui/
 * CLARIN-PL: https://clarin-pl.eu/dspace/

dspace-api/src/main/java/cz/cuni/mff/ufal/FileTreeViewGenerator.java

@@ -1,6 +1,7 @@
 package cz.cuni.mff.ufal;
 
 import java.util.Hashtable;
+import java.util.concurrent.atomic.AtomicInteger;
 
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
@@ -44,25 +45,28 @@ public static String parse(NodeList nl) {
 
 		} while((n=n.getNextSibling())!=null);
 
-		int folderID = 0;
-		
+		AtomicInteger folderID = new AtomicInteger(0);
+
 		StringBuilder result = new StringBuilder();
 		result.append("<ul class='treeview'>");
 		for(FileInfo in : root.sub.values()) {
-			printFileInfo(in, result, ++folderID);
+			printFileInfo(in, result, folderID);
 		}
 		result.append("</ul>");
 
 		return result.toString();
 	}
 
-	static void printFileInfo(FileInfo f, StringBuilder result, int folderID) {
+	static void printFileInfo(FileInfo f, StringBuilder result, AtomicInteger folderID) {
+		String currentFolderId = "folder_" + folderID.incrementAndGet();
 		if(f.isDirectory) {
 			result.append("<li>");
-				result.append("<span class='foldername'><a role='button' data-toggle='collapse' href='#folder_" + folderID + "'>").append(f.name).append("</a></span>");
-				result.append("<ul id='folder_" + folderID + "' class='in' style='height: auto;'>");
+				result.append(String.format(
+						"<span class='foldername'><a role='button' data-toggle='collapse' href='#%s'>%s</a></span>",
+						currentFolderId, f.name));
+				result.append(String.format("<ul id='%s' class='in' style='height: auto;'>", currentFolderId));
 				for(FileInfo in : f.sub.values()) {
-					printFileInfo(in, result, ++folderID);
+					printFileInfo(in, result, folderID);
 				}
 				result.append("</ul>");
 			result.append("</li>");

dspace-api/src/main/java/cz/cuni/mff/ufal/curation/ProcessBitstreams.java

@@ -218,7 +218,8 @@ static int addBitstreamContent(Bitstream b) throws SQLException, AuthorizeExcept
 	                b.addMetadata( schema, element, qualifier, Item.ANY, content );
 	                //don't add more than 1000 files
 	                if(++i >= 1000){
-	                    b.addMetadata(schema, element, qualifier, Item.ANY, String.format("%s|%d", "...", 0));
+	                    b.addMetadata(schema, element, qualifier, Item.ANY, String.format("%s|%d", "... too many " +
+                                "files ...", 0));
 	                    break;
                     }
 	            }

dspace-api/src/main/java/cz/cuni/mff/ufal/tracker/PiwikTrackerFactory.java

@@ -32,7 +32,14 @@ public static Tracker createOAITrackerInstance(){
 
     public static Tracker createBitstreamTrackerInstance(Collection col){
         int defaultSiteId = configurationService.getPropertyAsType("lr.lr.tracker.bitstream.site_id", 0);
-        boolean disabled = configurationService.getPropertyAsType("lr.lr.tracker.collection."
+
+        if(col == null){
+            //There might be no collection for example if we try downloading as editors during review; the item has
+            // not been installed in any collection yet.
+            return new PiwikBitstreamTracker(defaultSiteId);
+        }
+
+        boolean disabled =  configurationService.getPropertyAsType("lr.lr.tracker.collection."
                 + col.getHandle() + ".disabled", false);
         if(disabled){
             return noopTracker;

dspace-api/src/main/java/org/dspace/app/util/MetadataExposure.java

@@ -229,27 +229,28 @@ else if (segment.length == 2)
                         hiddenElementSets.get(segment[0]).add(segment[1]);
                     }
 
-                    if(value != null && !value.equals("") && !"true".equals(value)){
-                    	//select schema
-                    	Map<String, Map<String,String>> elements = hiddenConditions.get(segment[0]);
-                    	if(elements == null){
-                    		elements = new HashMap<String, Map<String,String>>();
-                    		hiddenConditions.put(segment[0], elements);
-                    	}
-                    	//select element
-                    	Map<String,String> qualifiers = elements.get(segment[1]);
-                    	if(qualifiers == null){
-                    		qualifiers = new HashMap<String,String>();
-                    		elements.put(segment[1], qualifiers);
-                    	}
-                    	qualifiers.put(qualifier, value);
-                    }
-
                     // oops..
                     else
                     {
                         log.warn("Bad format in hidden metadata directive, field=\""+mdField+"\", config property="+key);
                     }
+
+                    if(value != null && !value.equals("") && !"true".equals(value)){
+                        //select schema
+                        Map<String, Map<String,String>> elements = hiddenConditions.get(segment[0]);
+                        if(elements == null){
+                            elements = new HashMap<String, Map<String,String>>();
+                            hiddenConditions.put(segment[0], elements);
+                        }
+                        //select element
+                        Map<String,String> qualifiers = elements.get(segment[1]);
+                        if(qualifiers == null){
+                            qualifiers = new HashMap<String,String>();
+                            elements.put(segment[1], qualifiers);
+                        }
+                        qualifiers.put(qualifier, value);
+                    }
+
                 }
             }
         }

dspace-api/src/main/java/org/dspace/eperson/EPerson.java

@@ -315,7 +315,10 @@ public static EPerson[] search(Context context, String query, int offset, int li
                 " LEFT JOIN metadatavalue fn on (resource_id=e.eperson_id AND fn.resource_type_id=? and fn.metadata_field_id=?) " +
                 " LEFT JOIN metadatavalue ln on (ln.resource_id=e.eperson_id AND ln.resource_type_id=? and ln.metadata_field_id=?) " +
                 " WHERE e.eperson_id = ? OR " +
-                "LOWER(fn.text_value) LIKE LOWER(?) OR LOWER(ln.text_value) LIKE LOWER(?) OR LOWER(email) LIKE LOWER(?) ORDER BY  ");
+                "COALESCE(LOWER(fn.text_value),'') LIKE LOWER(?) OR " +
+                "COALESCE(LOWER(ln.text_value),'') LIKE LOWER(?) OR " +
+                "COALESCE(LOWER(email),'') LIKE LOWER(?) " +
+                "ORDER BY  ");
 
         queryBuf.append(order_by);
 
@@ -455,26 +458,22 @@ public static int searchResultCount(Context context, String query)
 		}
 
 		// Get all the epeople that match the query
-		TableRow row = DatabaseManager.querySingle(context,
-		        "SELECT count(*) as epcount FROM eperson " +
-                "WHERE eperson_id = ? OR " +
-		        "LOWER((select text_value from metadatavalue where resource_id=? and resource_type_id=? and metadata_field_id=?)) LIKE LOWER(?) " +
-                "OR LOWER((select text_value from metadatavalue where resource_id=? and resource_type_id=? and metadata_field_id=?)) LIKE LOWER(?) " +
-                "OR LOWER(eperson.email) LIKE LOWER(?)",
+		TableRow row = DatabaseManager.querySingle(context,"select count(e.*) as epcount from eperson e " +
+                        " LEFT JOIN metadatavalue fn on (resource_id=e.eperson_id AND fn.resource_type_id=? and fn.metadata_field_id=?) " +
+                        " LEFT JOIN metadatavalue ln on (ln.resource_id=e.eperson_id AND ln.resource_type_id=? and ln.metadata_field_id=?) " +
+                        " WHERE e.eperson_id = ? OR " +
+                        "COALESCE(LOWER(fn.text_value),'') LIKE LOWER(?) OR " +
+                        "COALESCE(LOWER(ln.text_value),'') LIKE LOWER(?) OR " +
+                        "COALESCE(LOWER(email),'') LIKE LOWER(?)",
 		        new Object[] {
-                        int_param,
-
-                        int_param,
                         Constants.EPERSON,
                         MetadataField.findByElement(context, MetadataSchema.find(context, "eperson").getSchemaID(), "firstname", null).getFieldID(),
-                        dbquery,
 
-                        int_param,
                         Constants.EPERSON,
                         MetadataField.findByElement(context, MetadataSchema.find(context, "eperson").getSchemaID(), "lastname", null).getFieldID(),
-                        dbquery,
 
-                        dbquery
+                        int_param,
+                        dbquery, dbquery, dbquery
                 });
 
 		// use getIntColumn for Oracle count data

dspace-oai/src/main/java/org/dspace/xoai/controller/DSpaceOAIDataProvider.java

@@ -189,7 +189,7 @@ public String contextAction (Model model, HttpServletRequest request, HttpServle
 
         if(configurationService.getBooleanProperty("lr", "lr.tracker.enabled", false)) {
             // Track the OAI request for analytics platform
-            TrackerFactory.createOAITrackerInstance().trackPage(request, "LINDAT/CLARIN OAI-PMH Data Provider " +
+            TrackerFactory.createOAITrackerInstance().trackPage(request, "Repository OAI-PMH Data Provider " +
                     "Endpoint");
         }
 

dspace-oai/src/main/webapp/static/style.xsl

@@ -21,7 +21,7 @@
 	<xsl:template match="/">
 		<html>
 			<head>
-                <title>LINDAT/CLARIN OAI-PMH Data Provider Endpoint</title>
+                <title>LINDAT/CLARIAH-CZ OAI-PMH Data Provider Endpoint</title>
                 <meta name="viewport" content="width=device-width, initial-scale=1.0" />
                 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
                 <script src="static/js/jquery.js" type="text/javascript"></script>
@@ -35,7 +35,7 @@
                 <div class="container">
                     <div class="navbar navbar-default" role="navigation">
                         <div class="navbar-header">
-                            <a class="navbar-brand" href="#">LINDAT/CLARIN OAI-PMH Data Provider Endpoint</a>
+                            <a class="navbar-brand" href="#">LINDAT/CLARIAH-CZ OAI-PMH Data Provider Endpoint</a>
                         </div>
                         <div class="navbar-collapse collapse">
                             <ul class="nav navbar-nav navbar-right">

dspace-xmlui/src/main/webapp/exception2html.xslt

@@ -18,7 +18,6 @@
     xmlns:dim="http://www.dspace.org/xmlns/dspace/dim"
     xmlns:xhtml="http://www.w3.org/1999/xhtml"
     xmlns:mods="http://www.loc.gov/mods/v3"
-    xmlns:file="java.io.File"
     xmlns:dc="http://purl.org/dc/elements/1.1/"
 	xmlns:confman="org.dspace.core.ConfigurationManager"
     xmlns="http://www.w3.org/1999/xhtml"
@@ -259,21 +258,8 @@
 	        <script type="text/javascript" src="{$contextPath}/themes/UFAL/lib/js/jquery-ui.js">&#160;</script>
                 <script type="text/javascript" src="{$contextPath}/themes/UFAL/lib/js/jquery.i18n.js">&#160;</script>
 		<script type="text/javascript">
-		    <xsl:variable name="currentLocale">
-                        <xsl:value-of select="/dri:document/dri:meta/dri:pageMeta/dri:metadata[@element='page'][@qualifier='currentLocale']"/>
-                    </xsl:variable>
                     <xsl:attribute name="src">
-                        <xsl:variable name="localizedContextPath" select="concat($theme-path,'/lib/js/messages/messages_',$currentLocale,'.js')" />
-                        <xsl:variable name="localizedDiskPath" select="concat($theme-path-on-disk,'/lib/js/messages/messages_',$currentLocale,'.js')" />
-                        <xsl:variable name="path" select="file:new($localizedDiskPath)"/>
-                        <xsl:choose>
-                            <xsl:when test="file:isFile($path)">
-                                <xsl:value-of select="$localizedContextPath" />
-                            </xsl:when>
-                            <xsl:otherwise>
-                                <xsl:value-of select="concat($theme-path,'/lib/js/messages/messages.js')" />
-                            </xsl:otherwise>
-                        </xsl:choose>
+                        <xsl:value-of select="concat($contextPath,$theme-path,'/lib/js/messages/messages.js')" />
                     </xsl:attribute>&#160;</script>
 
             <script type="text/javascript" src="{concat($aaiURL, '/discojuice/discojuice-2.1.en.min.js')}">&#160;</script>

dspace-xmlui/src/main/webapp/i18n/messages.xml

@@ -24,7 +24,7 @@
 		-->
 
 	<!-- General keys -->
-    <message key="xmlui.general.dspace_home">LINDAT/CLARIN Repository Home</message>
+    <message key="xmlui.general.dspace_home">LINDAT/CLARIAH-CZ Repository Home</message>
 	<message key="xmlui.general.search">Search</message>
 	<message key="xmlui.general.go">Go</message>
     <message key="xmlui.general.go_home">Back to repository homepage</message>
@@ -74,7 +74,7 @@
 	<!--
 		This section is for feed syndication (RSS, atom, etc)
 	-->
-    <message key="xmlui.feed.general_description">The LINDAT/CLARIN digital repository system captures, stores, indexes, preserves, and distributes digital research material.</message>
+    <message key="xmlui.feed.general_description">The LINDAT/CLARIAH-CZ digital repository system captures, stores, indexes, preserves, and distributes digital research material.</message>
     <message key="xmlui.feed.header">RSS Feeds</message>
 	<message key="xmlui.feed.logo_title">The Channel Image</message>
 	<message key="xmlui.feed.untitled">Untitled</message>
@@ -611,7 +611,7 @@
     <!-- org.dspace.app.xmlui.eperson.WelcomeLogin.java -->
     <message key="xmlui.EPerson.WelcomeLogin.title">Welcome message</message>
     <message key="xmlui.EPerson.WelcomeLogin.trail">Welcome message</message>
-    <message key="xmlui.EPerson.WelcomeLogin.head1">Welcome to LINDAT/CLARIN Repository</message>
+    <message key="xmlui.EPerson.WelcomeLogin.head1">Welcome to LINDAT/CLARIAH-CZ Repository</message>
     <message key="xmlui.EPerson.WelcomeLogin.head2">Privacy Statement</message>
     <message key="xmlui.EPerson.WelcomeLogin.para1">The information released by your IdP (home organisation) is shown below.</message>
     <message key="xmlui.EPerson.WelcomeLogin.warn1"><div class="bold text-error">We use only the required attributes as stated in <a href="http://lindat.mff.cuni.cz/privacypolicy.html" target="_blank" class="bold">http://lindat.mff.cuni.cz/privacypolicy.html</a>.<BR />However, we may log the attributes and keep them for a time period.</div></message>
@@ -2939,7 +2939,7 @@
 
     <!-- ufal theme -->
   <message key="UFAL.firstpage.title">Repository</message>
-  <message key="UFAL.firstpage.title.text">Welcome to LINDAT/CLARIN - Centre for Language Research Infrastructure in the Czech Republic</message>
+  <message key="UFAL.firstpage.title.text">Welcome to LINDAT/CLARIAH-CZ - Centre for Language Research Infrastructure in the Czech Republic</message>
 
   <!-- UFAL/lib/xsl/aspect/artifactbrowser/item-list.xsl -->
   <message key="xmlui.UFAL.artifactbrowser.item-contains-one-file">This item contains {0} file ({1}).</message>