Merge pull request #1367 from NCEAS/dev-2.10

Dev 2.10 for 2.10.4 release

README.md

@@ -1,6 +1,6 @@
 # Metacat: Data Preservation and Discovery System
 
-Version: 2.10.3 Release
+Version: 2.10.4 Release
 
 Send feedback and bugs to: [email protected]
                            http://github.com/NCEAS/metacat
@@ -67,6 +67,11 @@ for the next release.
 
 ## Release Notes
 
+### Release Notes for 2.10.4:
+Bugs fixed in this release:
+* Publishing dataset with provenance loses all provenance relationships
+* Publish call fails after adding provenance information
+
 ### Release Notes for 2.10.3:
 New features and bugs fixed in this release:
 * Update DOI registrations for EML objects with complete metadata

build.properties

@@ -2,7 +2,7 @@
 
 #Version of this build.  This needs to be a dotted numeric version.  For
 #instance 1.9.1 is okay.  1.9.1_rc1 is not.
-metacat.version=2.10.3
+metacat.version=2.10.4
 
 #This is for packaging purposes.  leave it blank for final production release.
 metacat.releaseCandidate=

build.xml

@@ -32,7 +32,7 @@
 <project name="metacat" default="jar" basedir="."
          xmlns:artifact="antlib:org.apache.maven.artifact.ant">
 
-	<property name="metacatui-tag" value="2.6.2" />
+	<property name="metacatui-tag" value="2.6.4" />
     <property name="eml2-style-tag" value="RELEASE_EML_UTILS_1_1_2" />
     <property name="seek-tag" value="tags/ECOGRID_1_2_3" />
 

lib/admin/metacat-configuration.jsp

@@ -349,8 +349,6 @@
 	%> 	
 				<div class="alert alert-success"><i class="icon-thumbs-up"></i>Configuration of Metacat is complete. Please restart Tomcat so that the webapps are initialized with these settings.
 				Note that this may take some time while the system initializes with the new configuration values.</div>
-				<div class="alert alert-success">All objects on this server need to be re-indexed because this Metacat release modified the schema file of the Solr server.
-                The details of re-indexing can be found in the documentation.</div>
 	<%
 			}
 		}

lib/metacat.properties

@@ -25,7 +25,7 @@ server.internalPort=80
 ############### Application Values ############
 
 ## one of the few places where we use ANT tokens
-application.metacatVersion=2.10.3
+application.metacatVersion=2.10.4
 application.metacatReleaseInfo=-1
 application.readOnlyMode=false 
 
@@ -113,6 +113,7 @@ database.upgradeVersion.2.10.0=upgrade-db-to-2.10.0
 database.upgradeVersion.2.10.1=upgrade-db-to-2.10.1
 database.upgradeVersion.2.10.2=upgrade-db-to-2.10.2
 database.upgradeVersion.2.10.3=upgrade-db-to-2.10.3
+database.upgradeVersion.2.10.4=upgrade-db-to-2.10.4
 ## for running java-based utilities
 database.upgradeUtility.1.5.0=edu.ucsb.nceas.metacat.admin.upgrade.Upgrade1_5_0
 database.upgradeUtility.2.0.0=edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_0_0

metacat-common/pom.xml

@@ -4,7 +4,7 @@
 	<groupId>edu.ucsb.nceas.metacat.common</groupId>
 	<artifactId>metacat-common</artifactId>
 	<packaging>jar</packaging>
-	<version>2.10.3</version>
+	<version>2.10.4</version>
 	<name>metacat-common</name>
 	<url>http://maven.apache.org</url>
 	<properties>

metacat-index/pom.xml

@@ -4,13 +4,13 @@
 	<groupId>edu.ucsb.nceas.metacat.index</groupId>
 	<artifactId>metacat-index</artifactId>
 	<packaging>war</packaging>
-	<version>2.10.3</version>
+	<version>2.10.4</version>
 	<name>metacat-index</name>
 	<url>http://maven.apache.org</url>
 
 	<properties>
         <d1_cn_index_processor_version>2.3.8</d1_cn_index_processor_version>
-        <metacat_common_version>2.10.3</metacat_common_version>
+        <metacat_common_version>2.10.4</metacat_common_version>
     </properties>
 
 	<repositories>

pom.xml

@@ -4,15 +4,15 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.ecoinformatics</groupId>
     <artifactId>metacat</artifactId>
-    <version>2.10.3</version>
+    <version>2.10.4</version>
     <name>metacat</name>
     <packaging>war</packaging>
     <url>http://maven.apache.org</url>
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <d1_libclient_version>2.3.1</d1_libclient_version>
         <d1_portal_version>2.3.1</d1_portal_version>
-        <metacat_common_version>2.10.3</metacat_common_version>            
+        <metacat_common_version>2.10.4</metacat_common_version>            
     </properties>
     <repositories>
         <repository>

src/edu/ucsb/nceas/metacat/dataone/MNodeService.java

@@ -158,6 +158,7 @@
 import edu.ucsb.nceas.metacat.common.query.EnabledQueryEngines;
 import edu.ucsb.nceas.metacat.common.query.stream.ContentTypeByteArrayInputStream;
 import edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService;
+import edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier;
 import edu.ucsb.nceas.metacat.index.MetacatSolrEngineDescriptionHandler;
 import edu.ucsb.nceas.metacat.index.MetacatSolrIndex;
 import edu.ucsb.nceas.metacat.properties.PropertyService;
@@ -2158,8 +2159,20 @@ public Identifier publish(Session session, Identifier originalIdentifier) throws
 				logMetacat.warn("No potential ORE map found for: " + potentialOreIdentifier.getValue()+" by the name convention.");
 				// try the SOLR index
 				List<Identifier> potentialOreIdentifiers = this.lookupOreFor(session, originalIdentifier);
-				if (potentialOreIdentifiers != null) {
-					potentialOreIdentifier = potentialOreIdentifiers.get(0);
+				if (potentialOreIdentifiers != null && potentialOreIdentifiers.size() >0) {
+				    int size = potentialOreIdentifiers.size();
+				    for (int i = size-1; i>=0; i--) {
+				        Identifier id = potentialOreIdentifiers.get(i);
+				        if (id != null && id.getValue() != null && !id.getValue().trim().equals("")) {
+				            SystemMetadata sys = this.getSystemMetadata(session, id);
+				            if(sys != null && sys.getObsoletedBy() == null) {
+				                //found the non-obsoletedBy ore document.
+				                logMetacat.debug("MNodeService.publish - found the ore map from the list when the index is " + i);
+				                potentialOreIdentifier = id;
+				                break;
+				            }
+				        }
+				    }
 					try {
 						oreInputStream = this.get(session, potentialOreIdentifier);
 					} catch (NotFound nf2) {
@@ -2173,22 +2186,10 @@ public Identifier publish(Session session, Identifier originalIdentifier) throws
 			if (oreInputStream != null) {
 			    logMetacat.info("MNodeService.publish - we find the old ore document "+potentialOreIdentifier+" for the metacat object "+originalIdentifier);
 				Identifier newOreIdentifier = MNodeService.getInstance(request).generateIdentifier(session, MNodeService.UUID_SCHEME, null);
-
-				Map<Identifier, Map<Identifier, List<Identifier>>> resourceMapStructure = ResourceMapFactory.getInstance().parseResourceMap(oreInputStream);
-				Map<Identifier, List<Identifier>> sciMetaMap = resourceMapStructure.get(potentialOreIdentifier);
-				List<Identifier> dataIdentifiers = sciMetaMap.get(originalIdentifier);
-
-				// reconstruct the ORE with the new identifiers
-				//the original identifier can be in the data object list, we should replace it if does exist.
-                if(dataIdentifiers.contains(originalIdentifier)) {
-                    dataIdentifiers.remove(originalIdentifier);
-                    dataIdentifiers.add(newIdentifier);
-                }
-				sciMetaMap.remove(originalIdentifier);
-				sciMetaMap.put(newIdentifier, dataIdentifiers);
-
-				ResourceMap resourceMap = ResourceMapFactory.getInstance().createResourceMap(newOreIdentifier, sciMetaMap);
-				String resourceMapString = ResourceMapFactory.getInstance().serializeResourceMap(resourceMap);
+				ResourceMapModifier modifier = new ResourceMapModifier(potentialOreIdentifier, oreInputStream, newOreIdentifier);
+				ByteArrayOutputStream out = new ByteArrayOutputStream();
+		        modifier.replaceObsoletedId(originalIdentifier, newIdentifier, out, session.getSubject());
+				String resourceMapString = out.toString("UTF-8");
 
 				// get the original ORE SM and update the values
 				SystemMetadata originalOreSysMeta = this.getSystemMetadata(session, potentialOreIdentifier);
@@ -2209,17 +2210,19 @@ public Identifier publish(Session session, Identifier originalIdentifier) throws
 				oreSysMeta.setObsoletedBy(null);
 				oreSysMeta.setSize(BigInteger.valueOf(resourceMapString.getBytes("UTF-8").length));
 				oreSysMeta.setChecksum(ChecksumUtil.checksum(resourceMapString.getBytes("UTF-8"), oreSysMeta.getChecksum().getAlgorithm()));
+				oreSysMeta.setFileName("resourceMap_" + newOreIdentifier.getValue() + ".rdf.xml");
 
 				// ensure ORE is publicly readable
-				oreSysMeta = makePublicIfNot(oreSysMeta, potentialOreIdentifier);
-				
+                oreSysMeta = makePublicIfNot(oreSysMeta, potentialOreIdentifier);
+                List<Identifier> dataIdentifiers = modifier.getSubjectsOfDocumentedBy(newIdentifier);
 				// ensure all data objects allow public read
 				List<String> pidsToSync = new ArrayList<String>();
 				for (Identifier dataId: dataIdentifiers) {
-					SystemMetadata dataSysMeta = this.getSystemMetadata(session, dataId);
-					dataSysMeta = makePublicIfNot(dataSysMeta, dataId);
-					this.updateSystemMetadata(dataSysMeta);
-					pidsToSync.add(dataId.getValue());
+			            SystemMetadata dataSysMeta = this.getSystemMetadata(session, dataId);
+			            dataSysMeta = makePublicIfNot(dataSysMeta, dataId);
+			            this.updateSystemMetadata(dataSysMeta);
+			            pidsToSync.add(dataId.getValue());
+
 				}
 				SyncAccessPolicy sap = new SyncAccessPolicy();
 				try {
@@ -2264,26 +2267,6 @@ public Identifier publish(Session session, Identifier originalIdentifier) throws
 			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
 			sf.initCause(e);
 			throw sf;
-		} catch (OREException e) {
-			// report as service failure
-			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
-			sf.initCause(e);
-			throw sf;
-		} catch (URISyntaxException e) {
-			// report as service failure
-			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
-			sf.initCause(e);
-			throw sf;
-		} catch (OREParserException e) {
-			// report as service failure
-			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
-			sf.initCause(e);
-			throw sf;
-		} catch (ORESerialiserException e) {
-			// report as service failure
-			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
-			sf.initCause(e);
-			throw sf;
 		} catch (NoSuchAlgorithmException e) {
 			// report as service failure
 			ServiceFailure sf = new ServiceFailure("1030", e.getMessage());