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Posted to commits@rya.apache.org by mi...@apache.org on 2016/08/26 00:07:11 UTC
[50/52] [abbrv] incubator-rya git commit: Merging in a handful of PRs;
Fixing compile / license errors
Merging in a handful of PRs; Fixing compile / license errors
Project: http://git-wip-us.apache.org/repos/asf/incubator-rya/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-rya/commit/71ab4f3a
Tree: http://git-wip-us.apache.org/repos/asf/incubator-rya/tree/71ab4f3a
Diff: http://git-wip-us.apache.org/repos/asf/incubator-rya/diff/71ab4f3a
Branch: refs/heads/master
Commit: 71ab4f3a59877e4ddc3fcb7cc5daaae73f0408c0
Parents: 1490b5d
Author: Aaron Mihalik <mi...@alum.mit.edu>
Authored: Tue Aug 23 15:37:37 2016 -0400
Committer: Aaron Mihalik <mi...@alum.mit.edu>
Committed: Tue Aug 23 15:37:37 2016 -0400
----------------------------------------------------------------------
.github/PULL_REQUEST_TEMPLATE | 18 ++++++++++++++++++
.../mvm/rya/mongodb/MongoConnectorFactory.java | 7 +------
.../java/mvm/rya/mongodb/MongoDBRyaDAO.java | 1 -
.../mvm/rya/mongodb/MongoSecondaryIndex.java | 19 +++++++++++++++++++
extras/indexing/pom.xml | 20 ++++++++++++++++++++
.../mvm/rya/sail/config/RyaSailFactory.java | 2 --
.../indexing/accumulo/geo/GeoIndexerSfTest.java | 2 +-
.../src/main/java/MongoRyaDirectExample.java | 1 +
extras/rya.merger/pom.xml | 6 ++++--
.../AbstractDualInstanceAccumuloMRTool.java | 2 +-
.../mvm/rya/accumulo/mr/merge/CopyTool.java | 20 ++++++++++++--------
.../mvm/rya/accumulo/mr/merge/MergeTool.java | 10 +++++-----
.../mr/merge/mappers/BaseCopyToolMapper.java | 2 +-
.../mr/merge/mappers/BaseRuleMapper.java | 2 +-
.../mr/merge/mappers/MergeToolMapper.java | 2 +-
.../mr/merge/mappers/RowRuleMapper.java | 2 +-
.../mr/merge/util/AccumuloInstanceDriver.java | 4 +++-
.../mr/merge/util/AccumuloRyaUtils.java | 2 +-
.../mvm/rya/accumulo/mr/merge/CopyToolTest.java | 2 +-
.../rya/accumulo/mr/merge/MergeToolTest.java | 2 +-
.../rya/accumulo/mr/merge/RulesetCopyIT.java | 2 +-
.../accumulo/mr/merge/demo/CopyToolDemo.java | 2 +-
.../accumulo/mr/merge/demo/MergeToolDemo.java | 2 +-
23 files changed, 95 insertions(+), 37 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/.github/PULL_REQUEST_TEMPLATE
----------------------------------------------------------------------
diff --git a/.github/PULL_REQUEST_TEMPLATE b/.github/PULL_REQUEST_TEMPLATE
index ab29333..8269e05 100644
--- a/.github/PULL_REQUEST_TEMPLATE
+++ b/.github/PULL_REQUEST_TEMPLATE
@@ -1,3 +1,21 @@
+<!--
+Licensed to the Apache Software Foundation (ASF) under one
+or more contributor license agreements. See the NOTICE file
+distributed with this work for additional information
+regarding copyright ownership. The ASF licenses this file
+to you under the Apache License, Version 2.0 (the
+"License"); you may not use this file except in compliance
+with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing,
+software distributed under the License is distributed on an
+"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+KIND, either express or implied. See the License for the
+specific language governing permissions and limitations
+under the License.
+-->
## Description
>What Changed?
[Brief Description of what changed]
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/dao/mongodb.rya/src/main/java/mvm/rya/mongodb/MongoConnectorFactory.java
----------------------------------------------------------------------
diff --git a/dao/mongodb.rya/src/main/java/mvm/rya/mongodb/MongoConnectorFactory.java b/dao/mongodb.rya/src/main/java/mvm/rya/mongodb/MongoConnectorFactory.java
index b91c9df..77a9f16 100644
--- a/dao/mongodb.rya/src/main/java/mvm/rya/mongodb/MongoConnectorFactory.java
+++ b/dao/mongodb.rya/src/main/java/mvm/rya/mongodb/MongoConnectorFactory.java
@@ -91,12 +91,7 @@ public class MongoConnectorFactory {
// Connect to a running Mongo server
final String host = requireNonNull(conf.get(MongoDBRdfConfiguration.MONGO_INSTANCE), MSG_INTRO+"host name is required");
final int port = requireNonNullInt(conf.get(MongoDBRdfConfiguration.MONGO_INSTANCE_PORT), MSG_INTRO+"Port number is required.");
- ServerAddress server;
- try {
- server = new ServerAddress(host, port);
- } catch (UnknownHostException e) {
- throw new MongoException(MSG_INTRO + "cannot find host="+host,e);
- }
+ ServerAddress server = new ServerAddress(host, port);
// check for authentication credentials
if (conf.get(MongoDBRdfConfiguration.MONGO_USER) != null) {
final String username = conf.get(MongoDBRdfConfiguration.MONGO_USER);
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/dao/mongodb.rya/src/main/java/mvm/rya/mongodb/MongoDBRyaDAO.java
----------------------------------------------------------------------
diff --git a/dao/mongodb.rya/src/main/java/mvm/rya/mongodb/MongoDBRyaDAO.java b/dao/mongodb.rya/src/main/java/mvm/rya/mongodb/MongoDBRyaDAO.java
index b0fd1db..bb5d58e 100644
--- a/dao/mongodb.rya/src/main/java/mvm/rya/mongodb/MongoDBRyaDAO.java
+++ b/dao/mongodb.rya/src/main/java/mvm/rya/mongodb/MongoDBRyaDAO.java
@@ -35,7 +35,6 @@ import com.mongodb.DBObject;
import com.mongodb.DuplicateKeyException;
import com.mongodb.InsertOptions;
import com.mongodb.MongoClient;
-import com.mongodb.MongoException.DuplicateKey;
import de.flapdoodle.embed.mongo.tests.MongodForTestsFactory;
import mvm.rya.api.RdfCloudTripleStoreConfiguration;
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/dao/mongodb.rya/src/main/java/mvm/rya/mongodb/MongoSecondaryIndex.java
----------------------------------------------------------------------
diff --git a/dao/mongodb.rya/src/main/java/mvm/rya/mongodb/MongoSecondaryIndex.java b/dao/mongodb.rya/src/main/java/mvm/rya/mongodb/MongoSecondaryIndex.java
index 553a78f..e32216f 100644
--- a/dao/mongodb.rya/src/main/java/mvm/rya/mongodb/MongoSecondaryIndex.java
+++ b/dao/mongodb.rya/src/main/java/mvm/rya/mongodb/MongoSecondaryIndex.java
@@ -1,5 +1,24 @@
package mvm.rya.mongodb;
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
import com.mongodb.MongoClient;
import mvm.rya.api.persist.index.RyaSecondaryIndexer;
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/indexing/pom.xml
----------------------------------------------------------------------
diff --git a/extras/indexing/pom.xml b/extras/indexing/pom.xml
index d2d7e10..fb3042f 100644
--- a/extras/indexing/pom.xml
+++ b/extras/indexing/pom.xml
@@ -166,6 +166,16 @@
<transformer
implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
</transformers>
+ <filters>
+ <filter>
+ <artifact>*:*</artifact>
+ <excludes>
+ <exclude>META-INF/*.SF</exclude>
+ <exclude>META-INF/*.DSA</exclude>
+ <exclude>META-INF/*.RSA</exclude>
+ </excludes>
+ </filter>
+ </filters>
</configuration>
</execution>
<execution>
@@ -191,6 +201,16 @@
<transformer
implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
</transformers>
+ <filters>
+ <filter>
+ <artifact>*:*</artifact>
+ <excludes>
+ <exclude>META-INF/*.SF</exclude>
+ <exclude>META-INF/*.DSA</exclude>
+ <exclude>META-INF/*.RSA</exclude>
+ </excludes>
+ </filter>
+ </filters>
</configuration>
</execution>
</executions>
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/indexing/src/main/java/mvm/rya/sail/config/RyaSailFactory.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/main/java/mvm/rya/sail/config/RyaSailFactory.java b/extras/indexing/src/main/java/mvm/rya/sail/config/RyaSailFactory.java
index 44c5ee7..4c4a0fb 100644
--- a/extras/indexing/src/main/java/mvm/rya/sail/config/RyaSailFactory.java
+++ b/extras/indexing/src/main/java/mvm/rya/sail/config/RyaSailFactory.java
@@ -157,8 +157,6 @@ public class RyaSailFactory {
RyaDetailsToConfiguration.addRyaDetailsToConfiguration(ryaDetailsRepo.getRyaInstanceDetails(), config);
} catch(final RyaDetailsRepositoryException e) {
LOG.info("Instance does not have a rya details collection, skipping.");
- } catch (final UnknownHostException ue) {
- throw new RyaDAOException("Unable to connect to mongo at the configured location.", ue);
}
return client;
}
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/indexing/src/test/java/mvm/rya/indexing/accumulo/geo/GeoIndexerSfTest.java
----------------------------------------------------------------------
diff --git a/extras/indexing/src/test/java/mvm/rya/indexing/accumulo/geo/GeoIndexerSfTest.java b/extras/indexing/src/test/java/mvm/rya/indexing/accumulo/geo/GeoIndexerSfTest.java
index 0f7d018..5395267 100644
--- a/extras/indexing/src/test/java/mvm/rya/indexing/accumulo/geo/GeoIndexerSfTest.java
+++ b/extras/indexing/src/test/java/mvm/rya/indexing/accumulo/geo/GeoIndexerSfTest.java
@@ -28,7 +28,6 @@ import java.util.Map;
import java.util.Set;
import org.apache.accumulo.core.client.admin.TableOperations;
-import org.apache.hadoop.conf.Configuration;
import org.geotools.geometry.jts.Geometries;
import org.junit.Assert;
import org.junit.Before;
@@ -61,6 +60,7 @@ import com.vividsolutions.jts.io.ParseException;
import com.vividsolutions.jts.io.gml2.GMLWriter;
import info.aduna.iteration.CloseableIteration;
+import mvm.rya.accumulo.AccumuloRdfConfiguration;
import mvm.rya.api.domain.RyaStatement;
import mvm.rya.api.resolver.RdfToRyaConversions;
import mvm.rya.api.resolver.RyaToRdfConversions;
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/indexingExample/src/main/java/MongoRyaDirectExample.java
----------------------------------------------------------------------
diff --git a/extras/indexingExample/src/main/java/MongoRyaDirectExample.java b/extras/indexingExample/src/main/java/MongoRyaDirectExample.java
index 5dbd260..60b437e 100644
--- a/extras/indexingExample/src/main/java/MongoRyaDirectExample.java
+++ b/extras/indexingExample/src/main/java/MongoRyaDirectExample.java
@@ -43,6 +43,7 @@ import org.openrdf.repository.sail.SailRepository;
import org.openrdf.repository.sail.SailRepositoryConnection;
import org.openrdf.sail.Sail;
+import mvm.rya.api.RdfCloudTripleStoreConfiguration;
import mvm.rya.indexing.accumulo.ConfigUtils;
import mvm.rya.indexing.accumulo.geo.GeoConstants;
import mvm.rya.mongodb.MongoDBRdfConfiguration;
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/rya.merger/pom.xml
----------------------------------------------------------------------
diff --git a/extras/rya.merger/pom.xml b/extras/rya.merger/pom.xml
index 57470bf..2886afd 100644
--- a/extras/rya.merger/pom.xml
+++ b/extras/rya.merger/pom.xml
@@ -63,13 +63,15 @@ under the License.
<dependency>
<groupId>org.apache.rya</groupId>
+ <artifactId>rya.mapreduce</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.rya</groupId>
<artifactId>mongodb.rya</artifactId>
- <version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.rya</groupId>
<artifactId>rya.indexing</artifactId>
- <version>${project.version}</version>
</dependency>
<dependency>
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/AbstractDualInstanceAccumuloMRTool.java
----------------------------------------------------------------------
diff --git a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/AbstractDualInstanceAccumuloMRTool.java b/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/AbstractDualInstanceAccumuloMRTool.java
index edc6ea4..7e863c0 100644
--- a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/AbstractDualInstanceAccumuloMRTool.java
+++ b/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/AbstractDualInstanceAccumuloMRTool.java
@@ -25,7 +25,7 @@ import org.apache.hadoop.util.Tool;
import mvm.rya.accumulo.AccumuloRdfConstants;
import mvm.rya.accumulo.mr.AbstractAccumuloMRTool;
-import mvm.rya.accumulo.mr.utils.MRUtils;
+import mvm.rya.accumulo.mr.MRUtils;
import mvm.rya.api.RdfCloudTripleStoreConstants;
/**
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/CopyTool.java
----------------------------------------------------------------------
diff --git a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/CopyTool.java b/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/CopyTool.java
index 067ff49..196863b 100644
--- a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/CopyTool.java
+++ b/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/CopyTool.java
@@ -83,13 +83,15 @@ import org.apache.log4j.xml.DOMConfigurator;
import com.google.common.base.Joiner;
import mvm.rya.accumulo.AccumuloRdfConfiguration;
+import mvm.rya.accumulo.mr.AccumuloHDFSFileInputFormat;
+import mvm.rya.accumulo.mr.MRUtils;
import mvm.rya.accumulo.mr.merge.common.InstanceType;
import mvm.rya.accumulo.mr.merge.gui.DateTimePickerDialog;
import mvm.rya.accumulo.mr.merge.mappers.AccumuloCopyToolMapper;
import mvm.rya.accumulo.mr.merge.mappers.AccumuloRyaRuleMapper;
import mvm.rya.accumulo.mr.merge.mappers.FileCopyToolMapper;
-import mvm.rya.accumulo.mr.merge.mappers.RowRuleMapper;
import mvm.rya.accumulo.mr.merge.mappers.MergeToolMapper;
+import mvm.rya.accumulo.mr.merge.mappers.RowRuleMapper;
import mvm.rya.accumulo.mr.merge.reducers.MultipleFileReducer;
import mvm.rya.accumulo.mr.merge.util.AccumuloInstanceDriver;
import mvm.rya.accumulo.mr.merge.util.AccumuloQueryRuleset;
@@ -97,8 +99,6 @@ import mvm.rya.accumulo.mr.merge.util.AccumuloRyaUtils;
import mvm.rya.accumulo.mr.merge.util.GroupedRow;
import mvm.rya.accumulo.mr.merge.util.TimeUtils;
import mvm.rya.accumulo.mr.merge.util.ToolConfigUtils;
-import mvm.rya.accumulo.mr.utils.AccumuloHDFSFileInputFormat;
-import mvm.rya.accumulo.mr.utils.MRUtils;
import mvm.rya.api.RdfCloudTripleStoreConstants;
import mvm.rya.api.RdfCloudTripleStoreUtils;
import mvm.rya.api.layout.TablePrefixLayoutStrategy;
@@ -314,11 +314,13 @@ public class CopyTool extends AbstractDualInstanceAccumuloMRTool {
tables.add(tablePrefix + RdfCloudTripleStoreConstants.TBL_EVAL_SUFFIX);
tables.add(tablePrefix + RdfCloudTripleStoreConstants.TBL_STATS_SUFFIX);
tables.add(tablePrefix + RdfCloudTripleStoreConstants.TBL_SEL_SUFFIX);
+ /* TODO: SEE RYA-160
tables.add(ConfigUtils.getFreeTextDocTablename(conf));
tables.add(ConfigUtils.getFreeTextTermTablename(conf));
tables.add(ConfigUtils.getGeoTablename(conf));
tables.add(ConfigUtils.getTemporalTableName(conf));
tables.add(ConfigUtils.getEntityTableName(conf));
+ */
}
if (tables.isEmpty()) {
log.warn("No list of tables to copy was provided.");
@@ -368,7 +370,7 @@ public class CopyTool extends AbstractDualInstanceAccumuloMRTool {
Job job = Job.getInstance(conf);
job.setJarByClass(CopyTool.class);
- setupInputFormat(job);
+ setupAccumuloInput(job);
AccumuloInputFormat.setInputTableName(job, table);
@@ -385,7 +387,7 @@ public class CopyTool extends AbstractDualInstanceAccumuloMRTool {
job.setOutputValueClass(Mutation.class);
}
- setupOutputFormat(job, childTable);
+ setupAccumuloOutput(job, childTable);
// Set mapper and reducer classes
if (useCopyFileOutput) {
@@ -478,6 +480,7 @@ public class CopyTool extends AbstractDualInstanceAccumuloMRTool {
// Copy namespaces if they exist
tables.add(prefixStrategy.getNs());
// Add tables associated with any configured indexers
+ /* TODO: SEE RYA-160
if (aconf.getBoolean(ConfigUtils.USE_FREETEXT, false)) {
tables.add(ConfigUtils.getFreeTextDocTablename(conf));
tables.add(ConfigUtils.getFreeTextTermTablename(conf));
@@ -491,6 +494,7 @@ public class CopyTool extends AbstractDualInstanceAccumuloMRTool {
if (aconf.getBoolean(ConfigUtils.USE_ENTITY, false)) {
tables.add(ConfigUtils.getEntityTableName(conf));
}
+ */
// Ignore anything else, e.g. statistics -- must be recalculated for the child if desired
// Extract the ruleset, and copy the namespace table directly
@@ -504,7 +508,7 @@ public class CopyTool extends AbstractDualInstanceAccumuloMRTool {
Job job = Job.getInstance(aconf);
job.setJarByClass(this.getClass());
setupMultiTableInputFormat(job, ruleset);
- setupOutputFormat(job, "");
+ setupAccumuloOutput(job, "");
if (useCopyFileOutput) {
// Configure job for file output
@@ -703,7 +707,7 @@ public class CopyTool extends AbstractDualInstanceAccumuloMRTool {
}
@Override
- protected void setupInputFormat(Job job) throws AccumuloSecurityException {
+ protected void setupAccumuloInput(Job job) throws AccumuloSecurityException {
if (useCopyFileImport) {
try {
AccumuloHDFSFileInputFormat.setInputPaths(job, localCopyFileImportDir);
@@ -776,7 +780,7 @@ public class CopyTool extends AbstractDualInstanceAccumuloMRTool {
}
@Override
- protected void setupOutputFormat(Job job, String outputTable) throws AccumuloSecurityException {
+ protected void setupAccumuloOutput(Job job, String outputTable) throws AccumuloSecurityException {
AccumuloOutputFormat.setConnectorInfo(job, childUserName, new PasswordToken(childPwd));
AccumuloOutputFormat.setCreateTables(job, true);
AccumuloOutputFormat.setDefaultTableName(job, outputTable);
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/MergeTool.java
----------------------------------------------------------------------
diff --git a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/MergeTool.java b/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/MergeTool.java
index 89fb787..8780599 100644
--- a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/MergeTool.java
+++ b/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/MergeTool.java
@@ -63,13 +63,13 @@ import com.google.common.collect.ImmutableList;
import com.google.common.collect.ImmutableMap;
import mvm.rya.accumulo.AccumuloRdfConfiguration;
+import mvm.rya.accumulo.mr.AccumuloHDFSFileInputFormat;
+import mvm.rya.accumulo.mr.MRUtils;
import mvm.rya.accumulo.mr.merge.gui.DateTimePickerDialog;
import mvm.rya.accumulo.mr.merge.mappers.MergeToolMapper;
import mvm.rya.accumulo.mr.merge.util.AccumuloRyaUtils;
import mvm.rya.accumulo.mr.merge.util.TimeUtils;
import mvm.rya.accumulo.mr.merge.util.ToolConfigUtils;
-import mvm.rya.accumulo.mr.utils.AccumuloHDFSFileInputFormat;
-import mvm.rya.accumulo.mr.utils.MRUtils;
import mvm.rya.api.RdfCloudTripleStoreConfiguration;
import mvm.rya.api.RdfCloudTripleStoreConstants;
import mvm.rya.api.RdfCloudTripleStoreUtils;
@@ -277,7 +277,7 @@ public class MergeTool extends AbstractDualInstanceAccumuloMRTool {
importChildFilesToTempParentTable(childTable);
}
- setupInputFormat(job);
+ setupAccumuloInput(job);
AccumuloInputFormat.setInputTableName(job, table);
@@ -287,7 +287,7 @@ public class MergeTool extends AbstractDualInstanceAccumuloMRTool {
job.setOutputKeyClass(Text.class);
job.setOutputValueClass(Mutation.class);
- setupOutputFormat(job, table);
+ setupAccumuloOutput(job, table);
// Set mapper and reducer classes
job.setMapperClass(MergeToolMapper.class);
@@ -435,7 +435,7 @@ public class MergeTool extends AbstractDualInstanceAccumuloMRTool {
}
@Override
- protected void setupInputFormat(Job job) throws AccumuloSecurityException {
+ protected void setupAccumuloInput(Job job) throws AccumuloSecurityException {
// set up accumulo input
if (!hdfsInput) {
job.setInputFormatClass(AccumuloInputFormat.class);
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/BaseCopyToolMapper.java
----------------------------------------------------------------------
diff --git a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/BaseCopyToolMapper.java b/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/BaseCopyToolMapper.java
index ca4d0c2..0af3e03 100644
--- a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/BaseCopyToolMapper.java
+++ b/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/BaseCopyToolMapper.java
@@ -46,10 +46,10 @@ import com.google.common.collect.Lists;
import mvm.rya.accumulo.AccumuloRdfConfiguration;
import mvm.rya.accumulo.AccumuloRyaDAO;
+import mvm.rya.accumulo.mr.MRUtils;
import mvm.rya.accumulo.mr.merge.CopyTool;
import mvm.rya.accumulo.mr.merge.MergeTool;
import mvm.rya.accumulo.mr.merge.util.AccumuloRyaUtils;
-import mvm.rya.accumulo.mr.utils.MRUtils;
import mvm.rya.api.persist.RyaDAOException;
import mvm.rya.api.resolver.RyaTripleContext;
import twitter4j.Logger;
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/BaseRuleMapper.java
----------------------------------------------------------------------
diff --git a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/BaseRuleMapper.java b/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/BaseRuleMapper.java
index a0abe0d..9bbf4fe 100644
--- a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/BaseRuleMapper.java
+++ b/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/BaseRuleMapper.java
@@ -34,11 +34,11 @@ import org.openrdf.query.algebra.Or;
import org.openrdf.query.algebra.ValueExpr;
import mvm.rya.accumulo.AccumuloRdfConfiguration;
+import mvm.rya.accumulo.mr.MRUtils;
import mvm.rya.accumulo.mr.merge.MergeTool;
import mvm.rya.accumulo.mr.merge.util.AccumuloQueryRuleset;
import mvm.rya.accumulo.mr.merge.util.CopyRule;
import mvm.rya.accumulo.mr.merge.util.QueryRuleset.QueryRulesetException;
-import mvm.rya.accumulo.mr.utils.MRUtils;
import mvm.rya.api.RdfCloudTripleStoreConstants.TABLE_LAYOUT;
import mvm.rya.api.RdfCloudTripleStoreUtils;
import mvm.rya.api.domain.RyaStatement;
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/MergeToolMapper.java
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diff --git a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/MergeToolMapper.java b/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/MergeToolMapper.java
index 0b5dddd..a662ee6 100644
--- a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/MergeToolMapper.java
+++ b/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/MergeToolMapper.java
@@ -49,11 +49,11 @@ import mvm.rya.accumulo.AccumuloRdfConfiguration;
import mvm.rya.accumulo.AccumuloRdfConstants;
import mvm.rya.accumulo.AccumuloRyaDAO;
import mvm.rya.accumulo.RyaTableMutationsFactory;
+import mvm.rya.accumulo.mr.MRUtils;
import mvm.rya.accumulo.mr.merge.CopyTool;
import mvm.rya.accumulo.mr.merge.MergeTool;
import mvm.rya.accumulo.mr.merge.util.AccumuloRyaUtils;
import mvm.rya.accumulo.mr.merge.util.TimeUtils;
-import mvm.rya.accumulo.mr.utils.MRUtils;
import mvm.rya.api.RdfCloudTripleStoreConfiguration;
import mvm.rya.api.RdfCloudTripleStoreConstants;
import mvm.rya.api.RdfCloudTripleStoreConstants.TABLE_LAYOUT;
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/RowRuleMapper.java
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diff --git a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/RowRuleMapper.java b/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/RowRuleMapper.java
index 76b24be..5960ab1 100644
--- a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/RowRuleMapper.java
+++ b/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/mappers/RowRuleMapper.java
@@ -34,10 +34,10 @@ import org.apache.accumulo.core.data.Value;
import org.apache.accumulo.core.security.Authorizations;
import org.apache.log4j.Logger;
+import mvm.rya.accumulo.mr.MRUtils;
import mvm.rya.accumulo.mr.merge.MergeTool;
import mvm.rya.accumulo.mr.merge.util.AccumuloRyaUtils;
import mvm.rya.accumulo.mr.merge.util.GroupedRow;
-import mvm.rya.accumulo.mr.utils.MRUtils;
import mvm.rya.api.domain.RyaStatement;
import mvm.rya.api.persist.RyaDAOException;
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/util/AccumuloInstanceDriver.java
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diff --git a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/util/AccumuloInstanceDriver.java b/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/util/AccumuloInstanceDriver.java
index bc7abdc..896bdb4 100644
--- a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/util/AccumuloInstanceDriver.java
+++ b/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/util/AccumuloInstanceDriver.java
@@ -51,8 +51,8 @@ import com.google.common.io.Files;
import mvm.rya.accumulo.AccumuloRdfConfiguration;
import mvm.rya.accumulo.AccumuloRyaDAO;
+import mvm.rya.accumulo.mr.MRUtils;
import mvm.rya.accumulo.mr.merge.MergeTool;
-import mvm.rya.accumulo.mr.utils.MRUtils;
import mvm.rya.api.RdfCloudTripleStoreConstants;
import mvm.rya.api.persist.RyaDAOException;
import mvm.rya.indexing.accumulo.ConfigUtils;
@@ -236,11 +236,13 @@ public class AccumuloInstanceDriver {
if (shouldCreateIndices) {
indices = Arrays.asList(
+ /* TODO: SEE RYA-160
ConfigUtils.getFreeTextDocTablename(config),
ConfigUtils.getFreeTextTermTablename(config),
ConfigUtils.getGeoTablename(config),
ConfigUtils.getTemporalTableName(config),
ConfigUtils.getEntityTableName(config)
+ */
);
tableList.addAll(indices);
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/util/AccumuloRyaUtils.java
----------------------------------------------------------------------
diff --git a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/util/AccumuloRyaUtils.java b/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/util/AccumuloRyaUtils.java
index daead31..a3d5961 100644
--- a/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/util/AccumuloRyaUtils.java
+++ b/extras/rya.merger/src/main/java/mvm/rya/accumulo/mr/merge/util/AccumuloRyaUtils.java
@@ -59,7 +59,7 @@ import com.google.common.collect.ImmutableSet;
import info.aduna.iteration.CloseableIteration;
import mvm.rya.accumulo.AccumuloRdfConfiguration;
import mvm.rya.accumulo.AccumuloRyaDAO;
-import mvm.rya.accumulo.mr.utils.MRUtils;
+import mvm.rya.accumulo.mr.MRUtils;
import mvm.rya.api.RdfCloudTripleStoreConstants;
import mvm.rya.api.domain.RyaStatement;
import mvm.rya.api.domain.RyaType;
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/CopyToolTest.java
----------------------------------------------------------------------
diff --git a/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/CopyToolTest.java b/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/CopyToolTest.java
index 475d647..d8b505b 100644
--- a/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/CopyToolTest.java
+++ b/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/CopyToolTest.java
@@ -54,12 +54,12 @@ import org.junit.Test;
import info.aduna.iteration.CloseableIteration;
import mvm.rya.accumulo.AccumuloRdfConfiguration;
import mvm.rya.accumulo.AccumuloRyaDAO;
+import mvm.rya.accumulo.mr.MRUtils;
import mvm.rya.accumulo.mr.merge.common.InstanceType;
import mvm.rya.accumulo.mr.merge.driver.AccumuloDualInstanceDriver;
import mvm.rya.accumulo.mr.merge.util.AccumuloRyaUtils;
import mvm.rya.accumulo.mr.merge.util.TestUtils;
import mvm.rya.accumulo.mr.merge.util.TimeUtils;
-import mvm.rya.accumulo.mr.utils.MRUtils;
import mvm.rya.api.RdfCloudTripleStoreConfiguration;
import mvm.rya.api.RdfCloudTripleStoreConstants;
import mvm.rya.api.domain.RyaStatement;
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/MergeToolTest.java
----------------------------------------------------------------------
diff --git a/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/MergeToolTest.java b/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/MergeToolTest.java
index ad6cad9..f27146e 100644
--- a/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/MergeToolTest.java
+++ b/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/MergeToolTest.java
@@ -51,12 +51,12 @@ import org.junit.Test;
import info.aduna.iteration.CloseableIteration;
import mvm.rya.accumulo.AccumuloRdfConfiguration;
import mvm.rya.accumulo.AccumuloRyaDAO;
+import mvm.rya.accumulo.mr.MRUtils;
import mvm.rya.accumulo.mr.merge.driver.AccumuloDualInstanceDriver;
import mvm.rya.accumulo.mr.merge.util.AccumuloInstanceDriver;
import mvm.rya.accumulo.mr.merge.util.AccumuloRyaUtils;
import mvm.rya.accumulo.mr.merge.util.TestUtils;
import mvm.rya.accumulo.mr.merge.util.TimeUtils;
-import mvm.rya.accumulo.mr.utils.MRUtils;
import mvm.rya.api.RdfCloudTripleStoreConfiguration;
import mvm.rya.api.RdfCloudTripleStoreConstants;
import mvm.rya.api.domain.RyaStatement;
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/RulesetCopyIT.java
----------------------------------------------------------------------
diff --git a/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/RulesetCopyIT.java b/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/RulesetCopyIT.java
index f34b798..b131591 100644
--- a/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/RulesetCopyIT.java
+++ b/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/RulesetCopyIT.java
@@ -60,11 +60,11 @@ import info.aduna.iteration.CloseableIteration;
import junit.framework.Assert;
import mvm.rya.accumulo.AccumuloRdfConfiguration;
import mvm.rya.accumulo.AccumuloRyaDAO;
+import mvm.rya.accumulo.mr.MRUtils;
import mvm.rya.accumulo.mr.merge.common.InstanceType;
import mvm.rya.accumulo.mr.merge.driver.AccumuloDualInstanceDriver;
import mvm.rya.accumulo.mr.merge.util.AccumuloRyaUtils;
import mvm.rya.accumulo.mr.merge.util.TestUtils;
-import mvm.rya.accumulo.mr.utils.MRUtils;
import mvm.rya.api.RdfCloudTripleStoreConfiguration;
import mvm.rya.api.domain.RyaStatement;
import mvm.rya.api.domain.RyaType;
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/demo/CopyToolDemo.java
----------------------------------------------------------------------
diff --git a/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/demo/CopyToolDemo.java b/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/demo/CopyToolDemo.java
index a6e640a..a160d3c 100644
--- a/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/demo/CopyToolDemo.java
+++ b/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/demo/CopyToolDemo.java
@@ -49,6 +49,7 @@ import org.apache.log4j.Logger;
import mvm.rya.accumulo.AccumuloRdfConfiguration;
import mvm.rya.accumulo.AccumuloRyaDAO;
+import mvm.rya.accumulo.mr.MRUtils;
import mvm.rya.accumulo.mr.merge.CopyTool;
import mvm.rya.accumulo.mr.merge.MergeTool;
import mvm.rya.accumulo.mr.merge.common.InstanceType;
@@ -57,7 +58,6 @@ import mvm.rya.accumulo.mr.merge.demo.util.DemoUtilities.LoggingDetail;
import mvm.rya.accumulo.mr.merge.driver.AccumuloDualInstanceDriver;
import mvm.rya.accumulo.mr.merge.util.AccumuloRyaUtils;
import mvm.rya.accumulo.mr.merge.util.TimeUtils;
-import mvm.rya.accumulo.mr.utils.MRUtils;
import mvm.rya.api.RdfCloudTripleStoreConstants;
import mvm.rya.api.domain.RyaStatement;
import mvm.rya.indexing.accumulo.ConfigUtils;
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/71ab4f3a/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/demo/MergeToolDemo.java
----------------------------------------------------------------------
diff --git a/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/demo/MergeToolDemo.java b/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/demo/MergeToolDemo.java
index cebeb13..d017504 100644
--- a/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/demo/MergeToolDemo.java
+++ b/extras/rya.merger/src/test/java/mvm/rya/accumulo/mr/merge/demo/MergeToolDemo.java
@@ -36,6 +36,7 @@ import org.apache.log4j.Logger;
import mvm.rya.accumulo.AccumuloRdfConfiguration;
import mvm.rya.accumulo.AccumuloRyaDAO;
+import mvm.rya.accumulo.mr.MRUtils;
import mvm.rya.accumulo.mr.merge.CopyTool;
import mvm.rya.accumulo.mr.merge.MergeTool;
import mvm.rya.accumulo.mr.merge.demo.util.DemoUtilities;
@@ -44,7 +45,6 @@ import mvm.rya.accumulo.mr.merge.driver.AccumuloDualInstanceDriver;
import mvm.rya.accumulo.mr.merge.util.AccumuloRyaUtils;
import mvm.rya.accumulo.mr.merge.util.TestUtils;
import mvm.rya.accumulo.mr.merge.util.TimeUtils;
-import mvm.rya.accumulo.mr.utils.MRUtils;
import mvm.rya.api.RdfCloudTripleStoreConstants;
import mvm.rya.api.domain.RyaStatement;