Merge branch 'release-2017.02' into clarin

ufal · Mar 29, 2017 · 5a5d2bb · 5a5d2bb
2 parents 8bb548b + 57b4be7
commit 5a5d2bb
Show file tree

Hide file tree

Showing 28 changed files with 279 additions and 159 deletions.
diff --git a/dspace-api/src/main/java/cz/cuni/mff/ufal/curation/ItemMetadataQAChecker.java b/dspace-api/src/main/java/cz/cuni/mff/ufal/curation/ItemMetadataQAChecker.java
@@ -234,7 +234,7 @@ private void validate_dc_type(Item item, Metadatum[] dcs, StringBuilder results)
         Metadatum[] dcs_type = item.getMetadataByMetadataString("dc.type");
         // no metadata?
         if ( dcs_type == null || dcs_type.length == 0) {
-            throw new CurateException("Does not dc.type metadata",
+            throw new CurateException("Does not have dc.type metadata",
                 Curator.CURATE_FAIL );
         }
 

diff --git a/dspace-api/src/main/java/cz/cuni/mff/ufal/health/AdditionalInfoCheck.java b/dspace-api/src/main/java/cz/cuni/mff/ufal/health/AdditionalInfoCheck.java
@@ -16,10 +16,14 @@
 import org.dspace.health.ReportInfo;
 
 import java.io.File;
+import java.nio.file.Files;
+import java.nio.file.Paths;
 import java.text.SimpleDateFormat;
 
 public class AdditionalInfoCheck extends Check {
 
+    public static final String beancountersPath = "/proc/user_beancounters";
+
     @Override
     public String run( ReportInfo ri ) {
         String ret = "";
@@ -54,9 +58,11 @@ public String run( ReportInfo ri ) {
         ret +=
             "Clarin centers:   https://centres.clarin.eu/\n";
 
-        ret += IOUtils.run(
-            new File(ConfigurationManager.getProperty("dspace.dir")),
-            new String[]{"sudo", "cat", "/proc/user_beancounters"});
+        if(Files.exists(Paths.get(beancountersPath))) {
+            ret += IOUtils.run(
+                    new File(ConfigurationManager.getProperty("dspace.dir")),
+                    new String[]{"sudo", "cat", beancountersPath});
+        }
 
         return ret;
     }

diff --git a/dspace-api/src/main/java/cz/cuni/mff/ufal/health/ShibbolethCheck.java b/dspace-api/src/main/java/cz/cuni/mff/ufal/health/ShibbolethCheck.java
@@ -105,10 +105,8 @@ public boolean accept(File dir, String name) {
             org.apache.commons.io.IOUtils.copy(
                 new URL(ConfigurationManager.getProperty("dspace.url")
                     + "/discojuice/feeds").openStream(), writer);
-            String jsonp = writer.toString();
+            String json = writer.toString();
             // end download
-            String json = jsonp.substring(jsonp.indexOf("(") + 1,
-                jsonp.lastIndexOf(")")); // strip the dj_md_1()
             Set<String> entities = new HashSet<String>();
             JSONParser parser = new JSONParser();
             JSONArray entityArray = (JSONArray) parser.parse(json);

diff --git a/dspace-api/src/main/java/org/dspace/health/Core.java b/dspace-api/src/main/java/org/dspace/health/Core.java
@@ -107,16 +107,17 @@ public static String getTypeXcollectionCounts() throws SQLException {
         StringBuilder ret = new StringBuilder();
         Map<String, Map<String, Integer>> table = new HashMap<>();
         Set<String> colnames = new HashSet<>();
-        int lenColname = 0;
+        int lenColname = 1;
         Context context = new Context();
         TableRowIterator rows = DatabaseManager.query(context,
-                "SELECT text_value AS type, colname, count(text_value) AS count FROM item JOIN metadatavalue ON item_id=resource_id " +
-                "NATURAL JOIN metadatafieldregistry NATURAL JOIN metadataschemaregistry JOIN " +
-                "(SELECT resource_id, text_value AS colname FROM metadatavalue NATURAL JOIN metadatafieldregistry NATURAL JOIN metadataschemaregistry "+
+                "SELECT text_value AS type, colname, count(*) AS count FROM metadatavalue " +
+                "NATURAL JOIN metadatafieldregistry NATURAL JOIN metadataschemaregistry " +
+                "RIGHT JOIN item ON item_id=resource_id AND resource_type_id=? AND short_id='dc' AND element='type' AND withdrawn=false AND in_archive=true " +
+                "JOIN (SELECT resource_id, text_value AS colname FROM metadatavalue NATURAL JOIN metadatafieldregistry NATURAL JOIN metadataschemaregistry "+
                     "WHERE short_id='dc' AND element='title' AND qualifier IS NULL AND resource_type_id=?) " +
                         "AS colnames ON colnames.resource_id=owning_collection " +
-                "WHERE resource_type_id=? AND short_id='dc' AND element='type' AND withdrawn=false AND in_archive=true GROUP BY text_value, colname;",
-                Constants.COLLECTION, Constants.ITEM);
+                "GROUP BY text_value, colname;",
+                Constants.ITEM, Constants.COLLECTION);
         for(TableRow row : rows.toList()){
             String type = row.getStringColumn("type");
             String colname = row.getStringColumn("colname");

diff --git a/dspace-rest/pom.xml b/dspace-rest/pom.xml
@@ -18,7 +18,7 @@
     <properties>
         <!-- This is the path to the root [dspace-src] directory. -->
         <root.basedir>${basedir}/..</root.basedir>
-        <jersey.version>2.21</jersey.version>
+        <jersey.version>2.25.1</jersey.version>
     </properties>
     <build>
         <plugins>
@@ -101,6 +101,10 @@
                     <groupId>org.springframework</groupId>
                     <artifactId>spring-aop</artifactId>
                 </exclusion>
+                <exclusion>
+                    <groupId>org.jboss.logging</groupId>
+                    <artifactId>jboss-logging</artifactId>
+                </exclusion>
             </exclusions>
         </dependency>
 

diff --git a/dspace-rest/src/main/java/org/dspace/rest/BitstreamResource.java b/dspace-rest/src/main/java/org/dspace/rest/BitstreamResource.java
@@ -36,7 +36,6 @@
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.authorize.AuthorizeManager;
 import org.dspace.content.BitstreamFormat;
-import org.dspace.content.Bundle;
 import org.dspace.eperson.Group;
 import org.dspace.rest.common.Bitstream;
 import org.dspace.rest.common.ResourcePolicy;
@@ -97,7 +96,7 @@ public Bitstream getBitstream(@PathParam("bitstream_id") Integer bitstreamId, @Q
 
         try
         {
-            context = createContext(getUser(headers));
+            context = createContext(headers);
             org.dspace.content.Bitstream dspaceBitstream = findBitstream(context, bitstreamId, org.dspace.core.Constants.READ);
 
             writeStats(dspaceBitstream, UsageEvent.Action.VIEW, user_ip, user_agent, xforwardedfor, headers,
@@ -150,7 +149,7 @@ public ResourcePolicy[] getBitstreamPolicies(@PathParam("bitstream_id") Integer
 
         try
         {
-            context = createContext(getUser(headers));
+            context = createContext(headers);
             org.dspace.content.Bitstream dspaceBitstream = findBitstream(context, bitstreamId, org.dspace.core.Constants.READ);
             AuthorizeManager.getPolicies(context, dspaceBitstream);
 
@@ -212,7 +211,7 @@ public Bitstream[] getBitstreams(@QueryParam("expand") String expand,
 
         try
         {
-            context = createContext(getUser(headers));
+            context = createContext(headers);
             org.dspace.content.Bitstream[] dspaceBitstreams = org.dspace.content.Bitstream.findAll(context);
 
             if (!((limit != null) && (limit >= 0) && (offset != null) && (offset >= 0)))
@@ -295,7 +294,7 @@ public javax.ws.rs.core.Response getBitstreamData(@PathParam("bitstream_id") Int
 
         try
         {
-            context = createContext(getUser(headers));
+            context = createContext(headers);
             org.dspace.content.Bitstream dspaceBitstream = findBitstream(context, bitstreamId, org.dspace.core.Constants.READ);
 
             writeStats(dspaceBitstream, UsageEvent.Action.VIEW, user_ip, user_agent, xforwardedfor, headers,
@@ -367,7 +366,7 @@ public javax.ws.rs.core.Response addBitstreamPolicy(@PathParam("bitstream_id") I
 
         try
         {
-            context = createContext(getUser(headers));
+            context = createContext(headers);
             org.dspace.content.Bitstream dspaceBitstream = findBitstream(context, bitstreamId, org.dspace.core.Constants.WRITE);
 
             writeStats(dspaceBitstream, UsageEvent.Action.UPDATE, user_ip, user_agent, xforwardedfor, headers,
@@ -437,7 +436,7 @@ public Response updateBitstream(@PathParam("bitstream_id") Integer bitstreamId,
 
         try
         {
-            context = createContext(getUser(headers));
+            context = createContext(headers);
             org.dspace.content.Bitstream dspaceBitstream = findBitstream(context, bitstreamId, org.dspace.core.Constants.WRITE);
 
             writeStats(dspaceBitstream, UsageEvent.Action.UPDATE, user_ip, user_agent, xforwardedfor,
@@ -539,7 +538,7 @@ public Response updateBitstreamData(@PathParam("bitstream_id") Integer bitstream
 
         try
         {
-            context = createContext(getUser(headers));
+            context = createContext(headers);
             org.dspace.content.Bitstream dspaceBitstream = findBitstream(context, bitstreamId, org.dspace.core.Constants.WRITE);
 
             writeStats(dspaceBitstream, UsageEvent.Action.UPDATE, user_ip, user_agent, xforwardedfor,
@@ -623,7 +622,7 @@ public Response deleteBitstream(@PathParam("bitstream_id") Integer bitstreamId,
 
         try
         {
-            context = createContext(getUser(headers));
+            context = createContext(headers);
             org.dspace.content.Bitstream dspaceBitstream = findBitstream(context, bitstreamId, org.dspace.core.Constants.DELETE);
 
             writeStats(dspaceBitstream, UsageEvent.Action.DELETE, user_ip, user_agent, xforwardedfor,
@@ -689,7 +688,7 @@ public javax.ws.rs.core.Response deleteBitstreamPolicy(@PathParam("bitstream_id"
 
         try
         {
-            context = createContext(getUser(headers));
+            context = createContext(headers);
             org.dspace.content.Bitstream dspaceBitstream = findBitstream(context, bitstreamId, org.dspace.core.Constants.WRITE);
 
             writeStats(dspaceBitstream, UsageEvent.Action.UPDATE, user_ip, user_agent, xforwardedfor, headers,

diff --git a/dspace-rest/src/main/java/org/dspace/rest/CollectionsResource.java b/dspace-rest/src/main/java/org/dspace/rest/CollectionsResource.java
@@ -34,11 +34,15 @@
 import org.dspace.authorize.AuthorizeManager;
 import org.dspace.browse.BrowseException;
 import org.dspace.content.service.ItemService;
+import org.dspace.core.Constants;
+import org.dspace.identifier.IdentifierException;
+import org.dspace.identifier.IdentifierService;
 import org.dspace.rest.common.Collection;
 import org.dspace.rest.common.Item;
 import org.dspace.rest.common.MetadataEntry;
 import org.dspace.rest.exceptions.ContextException;
 import org.dspace.usage.UsageEvent;
+import org.dspace.utils.DSpace;
 
 /**
  * This class provides all CRUD operation over collections.
@@ -96,7 +100,7 @@ public org.dspace.rest.common.Collection getCollection(@PathParam("collection_id
 
         try
         {
-            context = createContext(getUser(headers));
+            context = createContext(headers);
 
             org.dspace.content.Collection dspaceCollection = findCollection(context, collectionId, org.dspace.core.Constants.READ);
             writeStats(dspaceCollection, UsageEvent.Action.VIEW, user_ip, user_agent, xforwardedfor,
@@ -165,7 +169,7 @@ public org.dspace.rest.common.Collection[] getCollections(@QueryParam("expand")
 
         try
         {
-            context = createContext(getUser(headers));
+            context = createContext(headers);
 
             if (!((limit != null) && (limit >= 0) && (offset != null) && (offset >= 0)))
             {
@@ -251,7 +255,7 @@ public org.dspace.rest.common.Item[] getCollectionItems(@PathParam("collection_i
 
         try
         {
-            context = createContext(getUser(headers));
+            context = createContext(headers);
 
             org.dspace.content.Collection dspaceCollection = findCollection(context, collectionId, org.dspace.core.Constants.READ);
             writeStats(dspaceCollection, UsageEvent.Action.VIEW, user_ip, user_agent, xforwardedfor,
@@ -334,11 +338,11 @@ public Item addCollectionItem(@PathParam("collection_id") Integer collectionId,
 
         try
         {
-            context = createContext(getUser(headers));
+            context = createContext(headers);
             org.dspace.content.Collection dspaceCollection = findCollection(context, collectionId,
-                    org.dspace.core.Constants.WRITE);
+                    org.dspace.core.Constants.ADD);
 
-            writeStats(dspaceCollection, UsageEvent.Action.UPDATE, user_ip, user_agent, xforwardedfor,
+            writeStats(dspaceCollection, UsageEvent.Action.ADD, user_ip, user_agent, xforwardedfor,
                     headers, request, context);
 
             log.trace("Creating item in collection(id=" + collectionId + ").");
@@ -362,6 +366,11 @@ public Item addCollectionItem(@PathParam("collection_id") Integer collectionId,
             browse.indexItem(dspaceItem);
 
             log.trace("Installing item to collection(id=" + collectionId + ").");
+            IdentifierService identifierService = new DSpace().getSingletonService(IdentifierService.class);
+            context.turnOffAuthorisationSystem();
+            identifierService.reserve(context, dspaceItem);
+            dspaceItem.update();
+            context.restoreAuthSystemState();
             dspaceItem = org.dspace.content.InstallItem.installItem(context, workspaceItem);
 
             returnItem = new Item(dspaceItem, "", context);
@@ -391,8 +400,9 @@ public Item addCollectionItem(@PathParam("collection_id") Integer collectionId,
             processException(
                     "Could not add item into collection(id=" + collectionId + "), ContextException. Message: " + e.getMessage(),
                     context);
-        }
-        finally
+        } catch (IdentifierException e) {
+            processException("Could not reserve handle, IdentifierException. Message: " + e.getMessage(), context);
+        } finally
         {
             processFinally(context);
         }
@@ -434,7 +444,7 @@ public Response updateCollection(@PathParam("collection_id") Integer collectionI
 
         try
         {
-            context = createContext(getUser(headers));
+            context = createContext(headers);
             org.dspace.content.Collection dspaceCollection = findCollection(context, collectionId,
                     org.dspace.core.Constants.WRITE);
 
@@ -506,7 +516,7 @@ public Response deleteCollection(@PathParam("collection_id") Integer collectionI
 
         try
         {
-            context = createContext(getUser(headers));
+            context = createContext(headers);
             org.dspace.content.Collection dspaceCollection = findCollection(context, collectionId,
                     org.dspace.core.Constants.DELETE);
 
@@ -577,9 +587,9 @@ public Response deleteCollectionItem(@PathParam("collection_id") Integer collect
 
         try
         {
-            context = createContext(getUser(headers));
+            context = createContext(headers);
             org.dspace.content.Collection dspaceCollection = findCollection(context, collectionId,
-                    org.dspace.core.Constants.WRITE);
+                    Constants.REMOVE);
 
             org.dspace.content.Item item = null;
             org.dspace.content.ItemIterator dspaceItems = dspaceCollection.getItems();
@@ -598,19 +608,6 @@ public Response deleteCollectionItem(@PathParam("collection_id") Integer collect
                 log.warn("Item(id=" + itemId + ") was not found!");
                 throw new WebApplicationException(Response.Status.NOT_FOUND);
             }
-            else if (!AuthorizeManager.authorizeActionBoolean(context, item, org.dspace.core.Constants.REMOVE))
-            {
-                context.abort();
-                if (context.getCurrentUser() != null)
-                {
-                    log.error("User(" + context.getCurrentUser().getEmail() + ") has not permission to delete item!");
-                }
-                else
-                {
-                    log.error("User(anonymous) has not permission to delete item!");
-                }
-                throw new WebApplicationException(Response.Status.UNAUTHORIZED);
-            }
 
             writeStats(dspaceCollection, UsageEvent.Action.UPDATE, user_ip, user_agent, xforwardedfor,
                     headers, request, context);
@@ -674,7 +671,7 @@ public Collection findCollectionByName(String name, @Context HttpHeaders headers
 
         try
         {
-            context = createContext(getUser(headers));
+            context = createContext(headers);
             org.dspace.content.Collection[] dspaceCollections;
 
             dspaceCollections = org.dspace.content.Collection.findAll(context);