Merge remote-tracking branch 'upstream/develop' into capabilitiesLink…

…Service-PR

.gitignore

@@ -14,6 +14,7 @@ geonetwork*.db
 changes-*
 web/coverage.ec
 */target/
+*/.externalToolBuilders
 web/src/main/webapp/data/
 web/src/main/webapp/WEB-INF/lucene/
 web/src/main/webapp/WEB-INF/metadata_subversion/
@@ -40,3 +41,6 @@ web/src/main/webapp/WEB-INF/data/index
 web-itest/jcs_caching
 datadir/
 web/src/main/webapp/WEB-INF/data/removed/
+web-ui/src/main/resources/catalog/lib/gn*.min.js
+web-ui/src/main/resources/catalog/style/gn*.css
+web-ui/src/main/resources/catalog/style/gn.css

core/src/main/java/org/fao/geonet/constants/Geonet.java

@@ -138,6 +138,7 @@ public static final class Path {
 		public static final String CSW                = Jeeves.Path.XML + "csw/";
 		public static final String VALIDATION         = Jeeves.Path.XML + "validation/";
 		public static final String STYLESHEETS        = "/xsl";
+        public static final String XSLT_FOLDER        = java.io.File.separator + "xslt";
 		public static final String CONV_STYLESHEETS   = STYLESHEETS + "/conversion";
 		public static final String IMPORT_STYLESHEETS = CONV_STYLESHEETS + "/import";
 		public static final String WFS_STYLESHEETS    = "/convert/WFSToFragments";

core/src/main/java/org/fao/geonet/kernel/DataManager.java

@@ -27,6 +27,27 @@
 
 package org.fao.geonet.kernel;
 
+import java.io.File;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.UUID;
+import java.util.Vector;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+
+import javax.annotation.CheckForNull;
+import javax.annotation.Nonnull;
+
 import jeeves.config.springutil.JeevesApplicationContext;
 import jeeves.constants.Jeeves;
 import jeeves.exceptions.JeevesException;
@@ -42,6 +63,7 @@
 import jeeves.utils.Xml;
 import jeeves.utils.Xml.ErrorHandler;
 import jeeves.xlink.Processor;
+
 import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.lang.StringUtils;
 import org.fao.geonet.GeonetContext;
@@ -67,25 +89,6 @@
 import org.jdom.Namespace;
 import org.jdom.filter.ElementFilter;
 
-import javax.annotation.CheckForNull;
-import javax.annotation.Nonnull;
-import java.io.File;
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.UUID;
-import java.util.Vector;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-
 /**
  * Handles all operations on metadata (select,insert,update,delete etc...).
  *
@@ -101,6 +104,7 @@ public class DataManager {
     //---
     //--------------------------------------------------------------------------
 
+    private static final String MD_ON_HARV = "(SELECT id FROM Metadata WHERE harvestUuid=?)";
     /**
      *
      * @return
@@ -1592,6 +1596,24 @@ public Element getMetadata(Dbms dbms, String id) throws Exception {
      */
     public Element getMetadata(ServiceContext srvContext, String id, boolean forEditing, boolean withEditorValidationErrors, boolean keepXlinkAttributes) throws Exception {
         Dbms dbms = (Dbms) srvContext.getResourceManager().open(Geonet.Res.MAIN_DB);
+
+        return getMetadata(srvContext, dbms, id, forEditing, withEditorValidationErrors, keepXlinkAttributes);
+    }
+
+    /**
+     * Retrieves a metadata (in xml) given its id; adds editing information if requested and validation errors if
+     * requested.
+     *
+     * @param srvContext
+     * @param dbms
+     * @param id
+     * @param forEditing        Add extra element to build metadocument {@link EditLib#expandElements(String, Element)}
+     * @param withEditorValidationErrors
+     * @param keepXlinkAttributes When XLinks are resolved in non edit mode, do not remove XLink attributes.
+     * @return
+     * @throws Exception
+     */
+    public Element getMetadata(ServiceContext srvContext, Dbms dbms, String id, boolean forEditing, boolean withEditorValidationErrors, boolean keepXlinkAttributes) throws Exception {
         boolean doXLinks = xmlSerializer.resolveXLinks();
         Element md = xmlSerializer.selectNoXLinkResolver(dbms, "Metadata", id, false);
         if (md == null) return null;
@@ -1732,7 +1754,8 @@ public synchronized boolean updateMetadata(ServiceContext context, Dbms dbms, St
         }
 
         String uuid = null;
-        if (schemaMan.getSchema(schema).isReadwriteUUID()) {
+        if (schemaMan.getSchema(schema).isReadwriteUUID()
+                && !getMetadataTemplate(dbms, id).equals("s")) {
             uuid = extractUUID(schema, md);
         }
 
@@ -2048,6 +2071,69 @@ public synchronized void deleteMetadata(ServiceContext context, Dbms dbms, Strin
         searchMan.delete("_id", id+"");
     }
 
+
+    /**
+     * Removes all metadata associated to one harvester. Faster than doing one by one.
+     * 
+     * @param context
+     * @param dbms
+     * @param id
+     * @throws Exception
+     */
+    public synchronized void deleteBatchMetadata(ServiceContext context,
+            Dbms dbms, String harvesterId) throws Exception {
+
+        // --- remove operations
+        deleteBatchMetadataOper(dbms, harvesterId, false);
+
+        // --- remove categories
+        deleteBatchAllMetadataCateg(dbms, harvesterId);
+
+        dbms.execute(
+                "DELETE FROM MetadataRating WHERE metadataId in " + DataManager.MD_ON_HARV,
+                harvesterId);
+        dbms.execute(
+                "DELETE FROM Validation WHERE metadataId in " + DataManager.MD_ON_HARV,
+                harvesterId);
+
+        dbms.execute(
+                "DELETE FROM MetadataStatus WHERE metadataId in " + DataManager.MD_ON_HARV,
+                harvesterId);
+
+
+        //Notify templates in Batch
+        String getQuery = "SELECT id, uuid FROM Metadata WHERE harvestUuid=? AND isTemplate like 'n'";
+        for (Object o : dbms.select(getQuery, harvesterId).getChildren())
+        {
+            Element el = (Element) o;
+            String  id = el.getChildText("id");
+            String uuid = el.getChildText("uuid");
+            notifyMetadataDelete(dbms, id, uuid);
+        }
+
+        //TODO improve this, try to do it batch too
+        getQuery = "SELECT id FROM Metadata WHERE harvestUuid=?";
+        List<String> ids = new LinkedList<String>();
+        for (Object o : dbms.select(getQuery, harvesterId).getChildren())
+        {
+            Element el = (Element) o;
+            String  id = el.getChildText("id");
+
+            // --- remove metadata
+            xmlSerializer.delete(dbms, "Metadata", id, context);
+
+            ids.add(id);
+        }
+
+        // --- update search criteria
+        searchMan.delete("_id", ids);
+
+        dbms.execute(
+                "DELETE FROM Metadata WHERE harvestUuid = ?",
+                harvesterId);
+        dbms.commit();
+    }
+
     /**
      *
      * @param context
@@ -2076,7 +2162,21 @@ public void deleteMetadataOper(Dbms dbms, String id, boolean skipAllIntranet) th
 
         dbms.execute(query, Integer.valueOf(id));
     }
+    /**
+     * Removes all operations stored for all metadata on a harvester.
+     * @param dbms
+     * @param harvesterId
+     * @param skipAllIntranet
+     * @throws Exception
+     */
+    public void deleteBatchMetadataOper(Dbms dbms, String harvesterId, boolean skipAllIntranet) throws Exception {
+        String query = "DELETE FROM OperationAllowed WHERE metadataId in " + DataManager.MD_ON_HARV;
 
+        if (skipAllIntranet)
+            query += " AND groupId>1";
+
+        dbms.execute(query, harvesterId);
+    }
     /**
      * Removes all categories stored for a metadata.
      *
@@ -2090,6 +2190,19 @@ public void deleteAllMetadataCateg(Dbms dbms, String id) throws Exception {
         dbms.execute(query, Integer.valueOf(id));
     }
 
+    /**
+     * Removes all categories stored for all metadata in a harvester
+     *
+     * @param dbms
+     * @param harvesterId
+     * @throws Exception
+     */
+    public void deleteBatchAllMetadataCateg(Dbms dbms, String harvesterId) throws Exception {
+        String query = "DELETE FROM MetadataCateg WHERE metadataId in " + DataManager.MD_ON_HARV;
+
+        dbms.execute(query, harvesterId);
+    }
+
     //--------------------------------------------------------------------------
     //---
     //--- Metadata thumbnail API
@@ -2175,7 +2288,7 @@ public void unsetThumbnail(ServiceContext context, Dbms dbms, String id, boolean
     private void manageThumbnail(ServiceContext context, Dbms dbms, String id, boolean small, Element env,
                                  String styleSheet, boolean indexAfterChange) throws Exception {
         boolean forEditing = false, withValidationErrors = false, keepXlinkAttributes = true;
-        Element md = getMetadata(context, id, forEditing, withValidationErrors, keepXlinkAttributes);
+        Element md = getMetadata(context, dbms, id, forEditing, withValidationErrors, keepXlinkAttributes);
 
         if (md == null)
             return;
@@ -3364,4 +3477,4 @@ public void run() {
     public enum UpdateDatestamp {
         yes, no
     }
-}
+}

core/src/main/java/org/fao/geonet/kernel/search/SearchManager.java

@@ -924,6 +924,22 @@ public void delete(String fld, String txt) throws Exception {
 		_indexWriter.deleteDocuments(new Term(fld, txt));
 		_spatial.writer().delete(txt);
 	}
+
+    /**
+     *  deletes a list of documents.
+     *
+     * @param fld
+     * @param txt
+     * @throws Exception
+     */
+    public void delete(String fld, List<String> txts) throws Exception {
+        // possibly remove old document
+        for(String txt : txts) {
+            _indexWriter.deleteDocuments(new Term(fld, txt));
+        }
+        _spatial.writer().delete(txts);
+    }
+
 
     /**
      * TODO javadoc.

core/src/main/java/org/fao/geonet/kernel/search/spatial/SpatialIndexWriter.java

@@ -29,6 +29,7 @@
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
+import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 import java.util.concurrent.locks.Lock;
@@ -228,6 +229,34 @@ public void delete(String id) throws IOException
         }
     }
 
+
+    public void delete(List<String> ids) throws IOException
+    {
+        _lock.lock();
+        try {
+            FilterFactory2 factory = CommonFactoryFinder
+                    .getFilterFactory2(GeoTools.getDefaultHints());
+
+            List<Filter> filters = new LinkedList<Filter>();
+
+            for(String id : ids) {
+                filters.add(factory.equals(
+                    factory.property(_idColumn), factory.literal(id)));
+            }
+
+            _index = null;
+
+            _featureStore.removeFeatures(factory.or(filters));
+            try {
+                SpatialFilter.getJCSCache().clear();
+            } catch (Throwable e) {
+                e.printStackTrace();
+            }
+            _writes++;
+        } finally {
+            _lock.unlock();
+        }
+    }
     public void commit() throws IOException
     {
         _lock.lock();

core/src/main/java/org/fao/geonet/kernel/setting/SettingManager.java

@@ -311,6 +311,7 @@ public boolean setValues(Dbms dbms, Map<String, String> values) throws Exception
                 }
                 setting.setValue(value);
             } catch (Exception e) {
+            	e.printStackTrace();
                 Log.warning(Geonet.SETTINGS, "Failed to save setting with name: " + key + ", value: " + value + ". Error: " + e.getMessage());
                 throw e;
             }

core/src/main/java/org/fao/geonet/services/main/Info.java

@@ -139,6 +139,12 @@ else if (type.equals("harvester"))
                         new String[]{
                                 "system/harvester/enableEditing"
                                 }));
+
+			else if (type.equals("userGroupOnly"))
+                result.addContent(gc.getBean(SettingManager.class).getValues(
+                        new String[]{
+                                "system/metadataprivs/usergrouponly"
+                                }));
 
 			else if (type.equals("categories"))
 				result.addContent(Lib.local.retrieve(dbms, "Categories"));

core/src/main/java/org/fao/geonet/util/ISODate.java

@@ -129,28 +129,41 @@ public void setDate(String isoDate)
 
 		try
 		{
-			year  = Integer.parseInt(isoDate.substring(0,  4));
-			month = Integer.parseInt(isoDate.substring(5,  7));
-			day   = Integer.parseInt(isoDate.substring(8, 10));
+            if (isoDate.contains("T")) {
+                // Check if iso date contains time info and if using non UTC time zone to parse the date with
+                // JODAISODate. This class converts to UTC format to avoid timezones issues.
+                boolean timeZoneInfo = ((isoDate.split("T")[1].contains("+")) || (isoDate.split("T")[1].contains("-")));
 
-			isShort = true;
+                if (timeZoneInfo) {
+                    isoDate = JODAISODate.parseISODateTime(isoDate);
+                }
+            }
 
-			hour = 0;
-			min  = 0;
-			sec  = 0;
+            year  = Integer.parseInt(isoDate.substring(0,  4));
+            month = Integer.parseInt(isoDate.substring(5,  7));
+            day   = Integer.parseInt(isoDate.substring(8, 10));
 
-			//--- is the date in 'yyyy-mm-dd' or 'yyyy-mm-ddZ' format?
+            isShort = true;
 
-			if (isoDate.length() < 12)
-				return;
+            hour = 0;
+            min  = 0;
+            sec  = 0;
 
-			isoDate = isoDate.substring(11);
+            //--- is the date in 'yyyy-mm-dd' or 'yyyy-mm-ddZ' format?
 
-			hour  = Integer.parseInt(isoDate.substring(0,2));
-			min   = Integer.parseInt(isoDate.substring(3,5));
-			sec   = Integer.parseInt(isoDate.substring(6,8));
+            if (isoDate.length() < 12)
+                return;
+
+            isoDate = isoDate.substring(11);
+
+            hour  = Integer.parseInt(isoDate.substring(0,2));
+            min   = Integer.parseInt(isoDate.substring(3,5));
+            sec   = Integer.parseInt(isoDate.substring(6,8));
+
+
+
+            isShort = false;
 
-			isShort = false;
 		}
 		catch(Exception e)
 		{