Feature 1716-mn-reindex

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

@@ -3514,7 +3514,7 @@ public boolean reindex(Session session, List<Identifier> identifiers, boolean al
         String notAuthorizedError ="The provided identity does not have permission to reindex "
                                     + "objects on the Node: ";
         if (session == null) {
-            throw new NotAuthorized(notAuthorizedCode,notAuthorizedError + "public");
+            throw new NotAuthorized(notAuthorizedCode, notAuthorizedError + "public");
         }
         try {
             Identifier identifier = null;
@@ -3523,10 +3523,10 @@ public boolean reindex(Session session, List<Identifier> identifiers, boolean al
             authDel.doAdminAuthorization(session);
         } catch (NotAuthorized na) {
             if (session.getSubject() != null) {
-                throw new NotAuthorized(notAuthorizedCode,notAuthorizedError
+                throw new NotAuthorized(notAuthorizedCode, notAuthorizedError
                         + session.getSubject().getValue());
             } else {
-                throw new NotAuthorized(notAuthorizedCode,notAuthorizedError + "public");
+                throw new NotAuthorized(notAuthorizedCode, notAuthorizedError + "public");
             }
         }
 
@@ -3547,8 +3547,7 @@ protected void handleReindexAction(List<Identifier> pids) {
         if (pids == null) {
             return;
         }
-        for (int i = 0; i < pids.size(); i++) {
-            Identifier identifier = pids.get(i);
+        for (Identifier identifier : pids) {
             if (identifier != null) {
                 logMetacat.debug("MNodeService.handleReindexAction: queueing doc index for pid "
                                                                     + identifier.getValue());
@@ -3564,7 +3563,6 @@ protected void handleReindexAction(List<Identifier> pids) {
                 } catch (Exception e) {
                     logMetacat.info("MNodeService.handleReindexAction: Error submitting to "
                             + "index for pid " + identifier.getValue());
-                    continue;
                 }
             }
         }
@@ -3577,7 +3575,7 @@ protected void handleReindexAction(List<Identifier> pids) {
     protected void handleReindexAllAction() {
         // Process all of the documents
         logMetacat.debug("MNodeService.handleReindexAllAction - "
-                                               + "reindexl all objects in this Metacat instance");
+                                               + "reindex all objects in this Metacat instance");
         Runnable indexAll = new Runnable() {
             public void run() {
                 List<String> resourceMapFormats = ResourceMapNamespaces.getNamespaces();
@@ -3595,23 +3593,24 @@ public void run() {
      */
     private void buildAllNonResourceMapIndex(List<String> resourceMapFormatList) {
         boolean firstTime = true;
-        String sql = "select guid from systemmetadata";
+        StringBuilder sql = new StringBuilder("select guid from systemmetadata");
         if (resourceMapFormatList != null && resourceMapFormatList.size() > 0) {
             for (String format : resourceMapFormatList) {
                 if (format != null && !format.trim().equals("")) {
                     if (firstTime) {
-                        sql = sql + " where object_format !='" + format + "'";
+                        sql.append(" where object_format !='" + format + "'");
                         firstTime = false;
                     } else {
-                        sql = sql + " and object_format !='" + format + "'";
+                        sql.append(" and object_format !='" + format + "'");
                     }
                 }
             }
-            sql = sql + " order by date_uploaded asc";
+            sql.append(" order by date_uploaded asc");
         }
-        logMetacat.debug("MNodeService.buildAllNonResourceMapIndex - the final query is " + sql);
+        logMetacat.debug("MNodeService.buildAllNonResourceMapIndex - the final query is "
+                                                                        + sql.toString());
         try {
-            long size = buildIndexFromQuery(sql);
+            long size = buildIndexFromQuery(sql.toString());
             logMetacat.info(
                 "MNodeService.buildAllNonResourceMapIndex - the number of non-resource map "
                     + "objects is "
@@ -3628,24 +3627,25 @@ private void buildAllNonResourceMapIndex(List<String> resourceMapFormatList) {
      * @param resourceMapFormatList
      */
     private void buildAllResourceMapIndex(List<String> resourceMapFormatList) {
-        String sql = "select guid from systemmetadata";
+        StringBuilder sql = new StringBuilder("select guid from systemmetadata");
         if (resourceMapFormatList != null && resourceMapFormatList.size() > 0) {
             boolean firstTime = true;
             for (String format : resourceMapFormatList) {
                 if (format != null && !format.trim().equals("")) {
                     if (firstTime) {
-                        sql = sql + " where object_format ='" + format + "'";
+                        sql.append(" where object_format ='" + format + "'");
                         firstTime = false;
                     } else {
-                        sql = sql + " or object_format ='" + format + "'";
+                        sql.append(" or object_format ='" + format + "'");
                     }
                 }
             }
-            sql = sql + " order by date_uploaded asc";
+            sql.append(" order by date_uploaded asc");
         }
-        logMetacat.info("MNodeService.buildAllResourceMapIndex - the final query is " + sql);
+        logMetacat.info("MNodeService.buildAllResourceMapIndex - the final query is "
+                                                                    + sql.toString());
         try {
-            long size = buildIndexFromQuery(sql);
+            long size = buildIndexFromQuery(sql.toString());
             logMetacat.info(
                 "MNodeService.buildAllResourceMapIndex - the number of resource map objects is "
                     + size + " being submitted to the index queue.");
@@ -3699,8 +3699,6 @@ private long buildIndexFromQuery(String sql) throws SQLException {
             }
             rs.close();
             stmt.close();
-        } catch (SQLException e) {
-            throw e;
         } finally {
             // Return database connection to the pool
             DBConnectionPool.returnDBConnection(dbConn, serialNumber);

src/edu/ucsb/nceas/metacat/restservice/v2/MNResourceHandler.java

@@ -1873,7 +1873,7 @@ protected void reindex() throws InvalidRequest, ServiceFailure, NotAuthorized, N
         String[] allValueArray = params.get("all");
         if (allValueArray != null) {
             if (allValueArray.length != 1) {
-                throw new InvalidRequest("5903", "The \"all\" should only have one vaule");
+                throw new InvalidRequest("5903", "The \"all\" should only have one value");
             } else {
                 String allValue = allValueArray[0];
                 if (allValue != null && allValue.equalsIgnoreCase("true")) {
@@ -1893,7 +1893,7 @@ protected void reindex() throws InvalidRequest, ServiceFailure, NotAuthorized, N
                     }
                 }
             } else {
-                throw new InvalidRequest("5903", "Users should specify the \"pid\" vaule "
+                throw new InvalidRequest("5903", "Users should specify the \"pid\" value "
                                                                             + "for reindexing");
             }
         }

test/edu/ucsb/nceas/metacat/dataone/MNodeServiceTest.java → test/edu/ucsb/nceas/metacat/dataone/MNodeServiceIT.java

@@ -4,7 +4,7 @@
 import edu.ucsb.nceas.metacat.database.DBConnection;
 import edu.ucsb.nceas.metacat.database.DBConnectionPool;
 import edu.ucsb.nceas.metacat.doi.DOIServiceFactory;
-import edu.ucsb.nceas.metacat.index.queue.FailedIndexResubmitTimerTaskTestIT;
+import edu.ucsb.nceas.metacat.index.queue.FailedIndexResubmitTimerTaskIT;
 import edu.ucsb.nceas.metacat.object.handler.JsonLDHandlerTest;
 import edu.ucsb.nceas.metacat.object.handler.NonXMLMetadataHandlers;
 import edu.ucsb.nceas.metacat.properties.PropertyService;
@@ -88,7 +88,7 @@
  *
  * @author cjones
  */
-public class MNodeServiceTest extends D1NodeServiceTest {
+public class MNodeServiceIT extends D1NodeServiceTest {
 
     private static String unmatchingEncodingFilePath = "test/incorrect-encoding-declaration.xml";
 
@@ -119,68 +119,68 @@ public void tearDown() {
     public static Test suite() {
 
         TestSuite suite = new TestSuite();
-        suite.addTest(new MNodeServiceTest("initialize"));
+        suite.addTest(new MNodeServiceIT("initialize"));
         // MNStorage tests
-        suite.addTest(new MNodeServiceTest("testMissMatchMetadataCreate"));
-        suite.addTest(new MNodeServiceTest("testMissMatchChecksumInCreate"));
-        suite.addTest(new MNodeServiceTest("testCreate"));
-        suite.addTest(new MNodeServiceTest("testCreateInvalidIdentifier"));
-        suite.addTest(new MNodeServiceTest("testUpdate"));
-        suite.addTest(new MNodeServiceTest("testMissMatchedCheckSumUpdate"));
-        suite.addTest(new MNodeServiceTest("testMissMatchedChecksumUpdateSciMetadata"));
-        suite.addTest(new MNodeServiceTest("testUpdateSystemMetadata"));
-        suite.addTest(new MNodeServiceTest("testUpdateObsoletesAndObsoletedBy"));
-        suite.addTest(new MNodeServiceTest("testArchive"));
-        suite.addTest(new MNodeServiceTest("testUpdateSciMetadata"));
+        suite.addTest(new MNodeServiceIT("testMissMatchMetadataCreate"));
+        suite.addTest(new MNodeServiceIT("testMissMatchChecksumInCreate"));
+        suite.addTest(new MNodeServiceIT("testCreate"));
+        suite.addTest(new MNodeServiceIT("testCreateInvalidIdentifier"));
+        suite.addTest(new MNodeServiceIT("testUpdate"));
+        suite.addTest(new MNodeServiceIT("testMissMatchedCheckSumUpdate"));
+        suite.addTest(new MNodeServiceIT("testMissMatchedChecksumUpdateSciMetadata"));
+        suite.addTest(new MNodeServiceIT("testUpdateSystemMetadata"));
+        suite.addTest(new MNodeServiceIT("testUpdateObsoletesAndObsoletedBy"));
+        suite.addTest(new MNodeServiceIT("testArchive"));
+        suite.addTest(new MNodeServiceIT("testUpdateSciMetadata"));
         // this requires MN certificate
-        suite.addTest(new MNodeServiceTest("testDelete"));
+        suite.addTest(new MNodeServiceIT("testDelete"));
 
         // MNRead tests
-        suite.addTest(new MNodeServiceTest("testGet"));
-        suite.addTest(new MNodeServiceTest("testGetChecksum"));
-        suite.addTest(new MNodeServiceTest("testGetSystemMetadata"));
-        suite.addTest(new MNodeServiceTest("testDescribe"));
-        suite.addTest(new MNodeServiceTest("testListObjects"));
-        suite.addTest(new MNodeServiceTest("testGetSID"));
+        suite.addTest(new MNodeServiceIT("testGet"));
+        suite.addTest(new MNodeServiceIT("testGetChecksum"));
+        suite.addTest(new MNodeServiceIT("testGetSystemMetadata"));
+        suite.addTest(new MNodeServiceIT("testDescribe"));
+        suite.addTest(new MNodeServiceIT("testListObjects"));
+        suite.addTest(new MNodeServiceIT("testGetSID"));
         // this requires CN certificate
-        suite.addTest(new MNodeServiceTest("testSynchronizationFailed"));
+        suite.addTest(new MNodeServiceIT("testSynchronizationFailed"));
 
         // MNCore tests
-        suite.addTest(new MNodeServiceTest("testPing"));
-        suite.addTest(new MNodeServiceTest("testGetLogRecords"));
-        suite.addTest(new MNodeServiceTest("testGetCapabilities"));
+        suite.addTest(new MNodeServiceIT("testPing"));
+        suite.addTest(new MNodeServiceIT("testGetLogRecords"));
+        suite.addTest(new MNodeServiceIT("testGetCapabilities"));
 
         // MNAuthorization tests
-        suite.addTest(new MNodeServiceTest("testIsAuthorized"));
-        suite.addTest(new MNodeServiceTest("testIsEquivIdentityAuthorized"));
-        suite.addTest(new MNodeServiceTest("testSetAccessPolicy"));
+        suite.addTest(new MNodeServiceIT("testIsAuthorized"));
+        suite.addTest(new MNodeServiceIT("testIsEquivIdentityAuthorized"));
+        suite.addTest(new MNodeServiceIT("testSetAccessPolicy"));
         // MNreplication tests
-        suite.addTest(new MNodeServiceTest("testReplicate"));
+        suite.addTest(new MNodeServiceIT("testReplicate"));
         // MN packaging tests
-        suite.addTest(new MNodeServiceTest("testGetPackage"));
-        suite.addTest(new MNodeServiceTest("testGetOREPackage"));
-        suite.addTest(new MNodeServiceTest("testReadDeletedObject"));
-        suite.addTest(new MNodeServiceTest("testCreateAndUpdateXMLWithUnmatchingEncoding"));
-        suite.addTest(new MNodeServiceTest("testListViews"));
-        suite.addTest(new MNodeServiceTest("testCreateNOAAObject"));
-
-        suite.addTest(new MNodeServiceTest("testPermissionOfUpdateSystemmeta"));
-
-        suite.addTest(new MNodeServiceTest("testUpdateSystemMetadataWithCircularObsoletesChain"));
-
-        suite.addTest(new MNodeServiceTest("testUpdateSystemMetadataWithCircularObsoletedByChain"));
-        suite.addTest(new MNodeServiceTest("testUpdateSystemMetadataImmutableFields"));
-        suite.addTest(new MNodeServiceTest("testUpdateAuthoritativeMN"));
-        suite.addTest(new MNodeServiceTest("testInvalidIds"));
-        suite.addTest(new MNodeServiceTest("testPublishPackage"));
-        suite.addTest(new MNodeServiceTest("testPublishPrivatePackage"));
-        suite.addTest(new MNodeServiceTest("testAllowList"));
-        suite.addTest(new MNodeServiceTest("testInsertJson_LD"));
-        suite.addTest(new MNodeServiceTest("testCreateAndUpdateEventLog"));
-        suite.addTest(new MNodeServiceTest("testUpdateSystemMetadataPermission"));
-        suite.addTest(new MNodeServiceTest("testCreateAndUpdateWithDoiDisabled"));
-        suite.addTest(new MNodeServiceTest("testCreateAndUpdateFGDC"));
-        suite.addTest(new MNodeServiceTest("testReindex"));
+        suite.addTest(new MNodeServiceIT("testGetPackage"));
+        suite.addTest(new MNodeServiceIT("testGetOREPackage"));
+        suite.addTest(new MNodeServiceIT("testReadDeletedObject"));
+        suite.addTest(new MNodeServiceIT("testCreateAndUpdateXMLWithUnmatchingEncoding"));
+        suite.addTest(new MNodeServiceIT("testListViews"));
+        suite.addTest(new MNodeServiceIT("testCreateNOAAObject"));
+
+        suite.addTest(new MNodeServiceIT("testPermissionOfUpdateSystemmeta"));
+
+        suite.addTest(new MNodeServiceIT("testUpdateSystemMetadataWithCircularObsoletesChain"));
+
+        suite.addTest(new MNodeServiceIT("testUpdateSystemMetadataWithCircularObsoletedByChain"));
+        suite.addTest(new MNodeServiceIT("testUpdateSystemMetadataImmutableFields"));
+        suite.addTest(new MNodeServiceIT("testUpdateAuthoritativeMN"));
+        suite.addTest(new MNodeServiceIT("testInvalidIds"));
+        suite.addTest(new MNodeServiceIT("testPublishPackage"));
+        suite.addTest(new MNodeServiceIT("testPublishPrivatePackage"));
+        suite.addTest(new MNodeServiceIT("testAllowList"));
+        suite.addTest(new MNodeServiceIT("testInsertJson_LD"));
+        suite.addTest(new MNodeServiceIT("testCreateAndUpdateEventLog"));
+        suite.addTest(new MNodeServiceIT("testUpdateSystemMetadataPermission"));
+        suite.addTest(new MNodeServiceIT("testCreateAndUpdateWithDoiDisabled"));
+        suite.addTest(new MNodeServiceIT("testCreateAndUpdateFGDC"));
+        suite.addTest(new MNodeServiceIT("testReindex"));
         return suite;
 
     }
@@ -190,7 +190,7 @@ public static Test suite() {
      *
      * @param name - the name of the test
      */
-    public MNodeServiceTest(String name) {
+    public MNodeServiceIT(String name) {
         super(name);
 
     }
@@ -4518,7 +4518,7 @@ public void testReindex() throws Exception {
             stream = MNodeService.getInstance(request).query(session, "solr", query);
             resultStr = IOUtils.toString(stream, "UTF-8");
         }
-        String version = FailedIndexResubmitTimerTaskTestIT.getSolrDocVersion(resultStr);
+        String version = FailedIndexResubmitTimerTaskIT.getSolrDocVersion(resultStr);
         //second object
         Identifier guid1 = new Identifier();
         guid1.setValue("testCreateFailure." + System.currentTimeMillis());
@@ -4540,7 +4540,7 @@ public void testReindex() throws Exception {
             stream = MNodeService.getInstance(request).query(session, "solr", query1);
             resultStr = IOUtils.toString(stream, "UTF-8");
         }
-        String version1 = FailedIndexResubmitTimerTaskTestIT.getSolrDocVersion(resultStr);
+        String version1 = FailedIndexResubmitTimerTaskIT.getSolrDocVersion(resultStr);
 
         List<Identifier> identifiers = new ArrayList<Identifier>();
         identifiers.add(guid);
@@ -4575,7 +4575,7 @@ public void testReindex() throws Exception {
             count++;
             stream = MNodeService.getInstance(request).query(session, "solr", query);
             resultStr = IOUtils.toString(stream, "UTF-8");
-            newVersion = FailedIndexResubmitTimerTaskTestIT.getSolrDocVersion(resultStr);
+            newVersion = FailedIndexResubmitTimerTaskIT.getSolrDocVersion(resultStr);
             versionChanged = !newVersion.equals(version);
         }
         assertTrue(versionChanged);
@@ -4590,7 +4590,7 @@ public void testReindex() throws Exception {
             count++;
             stream = MNodeService.getInstance(request).query(session, "solr", query1);
             resultStr = IOUtils.toString(stream, "UTF-8");
-            newVersion1 = FailedIndexResubmitTimerTaskTestIT.getSolrDocVersion(resultStr);
+            newVersion1 = FailedIndexResubmitTimerTaskIT.getSolrDocVersion(resultStr);
             versionChanged = !newVersion1.equals(version1);
         }
         assertTrue(versionChanged);

test/edu/ucsb/nceas/metacat/index/queue/FailedIndexResubmitTimerTaskTestIT.java → test/edu/ucsb/nceas/metacat/index/queue/FailedIndexResubmitTimerTaskIT.java

@@ -48,7 +48,7 @@
  * @author tao
  *
  */
-public class FailedIndexResubmitTimerTaskTestIT {
+public class FailedIndexResubmitTimerTaskIT {
     private Session session = null;
     private Identifier guid = null;
     private String query = null;

test/edu/ucsb/nceas/metacat/util/AuthUtilIT.java

@@ -41,7 +41,7 @@
 import org.dataone.service.util.TypeMarshaller;
 
 import edu.ucsb.nceas.metacat.dataone.MNodeService;
-import edu.ucsb.nceas.metacat.dataone.MNodeServiceTest;
+import edu.ucsb.nceas.metacat.dataone.MNodeServiceIT;
 import edu.ucsb.nceas.metacat.properties.PropertyService;
 import junit.framework.Test;
 import junit.framework.TestSuite;
@@ -57,7 +57,7 @@
  * @author tao
  *
  */
-public class AuthUtilIT extends MNodeServiceTest {
+public class AuthUtilIT extends MNodeServiceIT {
 
     private File tmpPasswordFile = null;
     private String thirdUser = null;