@Test
public void testOptions() {
final Set<Option> options = new HashSet<Option>();
jjJobRunner.fillOptions(options);
assertTrue(
PropertyManagement.hasOption(options, CommonParameters.Common.DISTANCE_FUNCTION_CLASS));
assertTrue(PropertyManagement.hasOption(options, Partition.MAX_MEMBER_SELECTION));
assertTrue(PropertyManagement.hasOption(options, Partition.PARTITION_DISTANCE));
assertTrue(PropertyManagement.hasOption(options, Partition.PARTITIONER_CLASS));
/*
*
* Should this be part of the test? When options are requested, the
* runner does not know the selected partition algorithm.
*
* assertTrue(PropertyManagement.hasOption( options,
* GlobalParameters.Global.CRS_ID));
*
* assertTrue(PropertyManagement.hasOption( options,
* ExtractParameters.Extract.DIMENSION_EXTRACT_CLASS));
*
* assertTrue(PropertyManagement.hasOption( options,
* ClusteringParameters.Clustering.GEOMETRIC_DISTANCE_UNIT));
*
* assertTrue(PropertyManagement.hasOption( options,
* CommonParameters.Common.INDEX_MODEL_BUILDER_CLASS));
*
* assertTrue(PropertyManagement.hasOption( options,
* ClusteringParameters.Clustering.DISTANCE_THRESHOLDS));
*/
}
@Override
public int run(final Configuration config, final PropertyManagement runTimeProperties)
throws Exception {
final int k = runTimeProperties.getPropertyAsInt(SampleParameters.Sample.SAMPLE_SIZE, 1);
final int minkplusplus =
runTimeProperties.getPropertyAsInt(JumpParameters.Jump.KPLUSPLUS_MIN, 3);
if (k >= minkplusplus) {
return parallelJobRunner.run(config, runTimeProperties);
} else {
return singleSamplekmeansJobRunner.run(config, runTimeProperties);
}
}
@Override
public Object getValue(final PropertyManagement propertyManagement) {
try {
return propertyManagement.getProperty(parent);
} catch (final Exception e) {
LOGGER.error("Unable to deserialize property '" + parent.toString() + "'", e);
return null;
}
}
public static final void fillOptions(Set<Option> options, Common[] params) {
if (contains(params, Common.DIMENSION_EXTRACT_CLASS)) {
options.add(
PropertyManagement.newOption(
Common.DIMENSION_EXTRACT_CLASS,
"dde",
"Dimension Extractor Class implements mil.nga.giat.geowave.analytics.extract.DimensionExtractor",
true));
}
if (contains(params, Common.ADAPTER_STORE_FACTORY)) {
options.add(
PropertyManagement.newOption(
Common.ADAPTER_STORE_FACTORY,
"caf",
"Adapter Store factory implements mil.nga.giat.geowave.analytics.tools.dbops.AdapterStoreFactory",
true));
}
if (contains(params, Common.INDEX_STORE_FACTORY)) {
options.add(
PropertyManagement.newOption(
Common.INDEX_STORE_FACTORY,
"cif",
"Index Store factory implements mil.nga.giat.geowave.analytics.tools.dbops.IndexStoreFactory",
true));
}
if (contains(params, Common.DISTANCE_FUNCTION_CLASS)) {
options.add(
PropertyManagement.newOption(
Common.DISTANCE_FUNCTION_CLASS,
"cdf",
"Distance Function Class implements mil.nga.giat.geowave.analytics.distance.DistanceFn",
true));
}
if (contains(params, Common.INDEX_MODEL_BUILDER_CLASS)) {
options.add(
PropertyManagement.newOption(
Common.INDEX_MODEL_BUILDER_CLASS,
"cim",
"Class implements mil.nga.giat.geowave.analytics.tools.model.IndexModelBuilder",
true));
}
}
@Override
public void setValue(final PropertyManagement propertyManagement, final Object value) {
Object storeValue = value;
if (this.isClass && value instanceof String) {
try {
storeValue = Class.forName(value.toString());
} catch (ClassNotFoundException e) {
LOGGER.error("Class " + value.toString() + " for property " + parent + " is not found", e);
}
}
propertyManagement.store(parent, storeValue);
}
@Override
@SuppressWarnings("unchecked")
public int run(final Configuration configuration, final PropertyManagement propertyManagement)
throws Exception {
propertyManagement.store(CentroidParameters.Centroid.ZOOM_LEVEL, currentZoomLevel);
propertyManagement.storeIfEmpty(GlobalParameters.Global.BATCH_ID, UUID.randomUUID().toString());
propertyManagement.storeIfEmpty(
CentroidParameters.Centroid.WRAPPER_FACTORY_CLASS, SimpleFeatureItemWrapperFactory.class);
propertyManagement.storeIfEmpty(
CommonParameters.Common.DISTANCE_FUNCTION_CLASS, FeatureCentroidDistanceFn.class);
propertyManagement.storeIfEmpty(
CentroidParameters.Centroid.EXTRACTOR_CLASS, SimpleFeatureCentroidExtractor.class);
propertyManagement.storeIfEmpty(
CommonParameters.Common.DIMENSION_EXTRACT_CLASS, SimpleFeatureGeometryExtractor.class);
propertyManagement.copy(
CentroidParameters.Centroid.DATA_TYPE_ID, SampleParameters.Sample.DATA_TYPE_ID);
propertyManagement.copy(CentroidParameters.Centroid.INDEX_ID, SampleParameters.Sample.INDEX_ID);
ClusteringUtils.createAdapter(propertyManagement);
ClusteringUtils.createIndex(propertyManagement);
final String currentBatchId =
propertyManagement.getPropertyAsString(
GlobalParameters.Global.BATCH_ID, UUID.randomUUID().toString());
try {
final NumericRange rangeOfIterations =
propertyManagement.getPropertyAsRange(
JumpParameters.Jump.RANGE_OF_CENTROIDS, new NumericRange(2, 200));
propertyManagement.store(GlobalParameters.Global.PARENT_BATCH_ID, currentBatchId);
final GenericStoreCommandLineOptions<DataStore> dataStoreOptions =
((PersistableDataStore) propertyManagement.getProperty(StoreParam.DATA_STORE))
.getCliOptions();
final GenericStoreCommandLineOptions<IndexStore> indexStoreOptions =
((PersistableIndexStore) propertyManagement.getProperty(StoreParam.INDEX_STORE))
.getCliOptions();
final GenericStoreCommandLineOptions<AdapterStore> adapterStoreOptions =
((PersistableAdapterStore) propertyManagement.getProperty(StoreParam.ADAPTER_STORE))
.getCliOptions();
final DistortionGroupManagement distortionGroupManagement =
new DistortionGroupManagement(
dataStoreOptions.createStore(),
indexStoreOptions.createStore(),
adapterStoreOptions.createStore());
for (int k = (int) Math.max(2, Math.round(rangeOfIterations.getMin()));
k < Math.round(rangeOfIterations.getMax());
k++) {
// regardless of the algorithm, the sample set is fixed in size
propertyManagement.store(SampleParameters.Sample.MIN_SAMPLE_SIZE, k);
propertyManagement.store(SampleParameters.Sample.MAX_SAMPLE_SIZE, k);
propertyManagement.store(SampleParameters.Sample.SAMPLE_SIZE, k);
jumpRunner.setCentroidsCount(k);
jumpRunner.setDataStoreOptions(dataStoreOptions);
final String iterationBatchId = currentBatchId + "_" + k;
propertyManagement.store(GlobalParameters.Global.BATCH_ID, iterationBatchId);
jumpRunner.setReducerCount(k);
LOGGER.info("KMeans for k: " + k + " and batch " + currentBatchId);
final int status = super.run(configuration, propertyManagement);
if (status != 0) {
return status;
}
}
propertyManagement.store(GlobalParameters.Global.BATCH_ID, currentBatchId);
@SuppressWarnings("rawtypes")
final Class<AnalyticItemWrapperFactory> analyticItemWrapperFC =
propertyManagement.getPropertyAsClass(
CentroidParameters.Centroid.WRAPPER_FACTORY_CLASS, AnalyticItemWrapperFactory.class);
/**
* Associate the batch id with the best set of groups so the caller can find the clusters for
* the given batch
*/
final int result =
distortionGroupManagement.retainBestGroups(
(AnalyticItemWrapperFactory<SimpleFeature>) analyticItemWrapperFC.newInstance(),
propertyManagement.getPropertyAsString(CentroidParameters.Centroid.DATA_TYPE_ID),
propertyManagement.getPropertyAsString(CentroidParameters.Centroid.INDEX_ID),
currentBatchId,
currentZoomLevel);
// distortionGroupManagement.cleanUp();
return result;
} catch (final Exception ex) {
LOGGER.error("Cannot create distortions", ex);
return 1;
}
}
@Override
public int run(final Configuration config, final PropertyManagement runTimeProperties)
throws Exception {
runTimeProperties.storeIfEmpty(GlobalParameters.Global.BATCH_ID, UUID.randomUUID().toString());
final FileSystem fs = FileSystem.get(config);
final String outputBaseDir =
runTimeProperties.getPropertyAsString(MapReduceParameters.MRConfig.HDFS_BASE_DIR, "/tmp");
Path startPath =
new Path(
outputBaseDir
+ "/"
+ runTimeProperties.getPropertyAsString(GlobalParameters.Global.ACCUMULO_NAMESPACE)
+ "_level_0");
if (fs.exists(startPath)) {
fs.delete(startPath, true);
}
AbstractPartitioner.putDistances(
runTimeProperties,
new double[] {runTimeProperties.getPropertyAsDouble(Partition.PARTITION_DISTANCE, 10)});
jobRunner.setInputFormatConfiguration(inputFormatConfiguration);
jobRunner.setOutputFormatConfiguration(new SequenceFileOutputFormatConfiguration(startPath));
LOGGER.info(
"Running with partition distance {}",
runTimeProperties.getPropertyAsDouble(Partition.PARTITION_DISTANCE, 10.0));
final int initialStatus = jobRunner.run(config, runTimeProperties);
if (initialStatus != 0) {
return initialStatus;
}
int maxIterationCount =
runTimeProperties.getPropertyAsInt(ClusteringParameters.Clustering.MAX_ITERATIONS, 15);
int iteration = 2;
long lastRecordCount = 0;
double precisionFactor = 0.9;
while (maxIterationCount > 0) {
// context does not mater in this case
try {
final Partitioner<?> partitioner =
runTimeProperties.getClassInstance(
PartitionParameters.Partition.PARTITIONER_CLASS,
Partitioner.class,
OrthodromicDistancePartitioner.class);
partitioner.initialize(runTimeProperties);
} catch (final IllegalArgumentException argEx) {
// this occurs if the partitioner decides that the distance is
// invalid (e.g. bigger than the map space).
// In this case, we just exist out of the loop.
// startPath has the final data
break;
} catch (final Exception e1) {
throw new IOException(e1);
}
final PropertyManagement localScopeProperties = new PropertyManagement(runTimeProperties);
localScopeProperties.store(Partition.PARTITION_PRECISION, precisionFactor);
jobRunner.setInputFormatConfiguration(new SequenceFileInputFormatConfiguration(startPath));
jobRunner.setFirstIteration(false);
localScopeProperties.store(HullParameters.Hull.ZOOM_LEVEL, zoomLevel);
localScopeProperties.store(HullParameters.Hull.ITERATION, iteration);
localScopeProperties.storeIfEmpty(
OutputParameters.Output.DATA_TYPE_ID,
localScopeProperties.getPropertyAsString(
HullParameters.Hull.DATA_TYPE_ID, "concave_hull"));
// Set to zero to force each cluster to be moved into the next
// iteration
// even if no merge occurs
localScopeProperties.store(ClusteringParameters.Clustering.MINIMUM_SIZE, 0);
final Path nextPath =
new Path(
outputBaseDir
+ "/"
+ runTimeProperties.getPropertyAsString(
GlobalParameters.Global.ACCUMULO_NAMESPACE)
+ "_level_"
+ iteration);
if (fs.exists(nextPath)) {
fs.delete(nextPath, true);
}
jobRunner.setOutputFormatConfiguration(new SequenceFileOutputFormatConfiguration(nextPath));
final int status = jobRunner.run(config, localScopeProperties);
if (status != 0) {
return status;
}
final long currentOutputCount = jobRunner.getCounterValue(TaskCounter.REDUCE_OUTPUT_RECORDS);
if (currentOutputCount == lastRecordCount) {
maxIterationCount = 0;
}
lastRecordCount = currentOutputCount;
startPath = nextPath;
maxIterationCount--;
precisionFactor -= 0.1;
iteration++;
}
final PropertyManagement localScopeProperties = new PropertyManagement(runTimeProperties);
localScopeProperties.storeIfEmpty(
OutputParameters.Output.DATA_TYPE_ID,
localScopeProperties.getPropertyAsString(HullParameters.Hull.DATA_TYPE_ID, "concave_hull"));
localScopeProperties.storeIfEmpty(
OutputParameters.Output.DATA_NAMESPACE_URI,
localScopeProperties.getPropertyAsString(
HullParameters.Hull.DATA_NAMESPACE_URI, BasicFeatureTypes.DEFAULT_NAMESPACE));
localScopeProperties.storeIfEmpty(
OutputParameters.Output.INDEX_ID, localScopeProperties.get(HullParameters.Hull.INDEX_ID));
inputLoadRunner.setInputFormatConfiguration(
new SequenceFileInputFormatConfiguration(startPath));
inputLoadRunner.run(config, runTimeProperties);
return 0;
}
@Before
public void init() {
jjJobRunner.setMapReduceIntegrater(
new MapReduceIntegration() {
@Override
public int submit(
final Configuration configuration,
final PropertyManagement runTimeProperties,
final GeoWaveAnalyticJobRunner tool)
throws Exception {
tool.setConf(configuration);
FeatureDataAdapterStoreFactory.transferState(configuration, runTimeProperties);
return tool.run(runTimeProperties.toGeoWaveRunnerArguments());
}
@Override
public Counters waitForCompletion(final Job job)
throws ClassNotFoundException, IOException, InterruptedException {
Assert.assertEquals(SequenceFileInputFormat.class, job.getInputFormatClass());
Assert.assertEquals(10, job.getNumReduceTasks());
final JobContextConfigurationWrapper configWrapper =
new JobContextConfigurationWrapper(job);
Assert.assertEquals("file://foo/bin", job.getConfiguration().get("mapred.input.dir"));
Assert.assertEquals(
0.4,
configWrapper.getDouble(Partition.PARTITION_DISTANCE, NNMapReduce.class, 0.0),
0.001);
Assert.assertEquals(
100, configWrapper.getInt(Partition.MAX_MEMBER_SELECTION, NNMapReduce.class, 1));
try {
final Partitioner<?> wrapper =
configWrapper.getInstance(
Partition.PARTITIONER_CLASS, NNMapReduce.class, Partitioner.class, null);
Assert.assertEquals(OrthodromicDistancePartitioner.class, wrapper.getClass());
final Partitioner<?> secondary =
configWrapper.getInstance(
Partition.SECONDARY_PARTITIONER_CLASS,
NNMapReduce.class,
Partitioner.class,
null);
Assert.assertEquals(OrthodromicDistancePartitioner.class, secondary.getClass());
final DistanceFn<?> distancFn =
configWrapper.getInstance(
CommonParameters.Common.DISTANCE_FUNCTION_CLASS,
NNMapReduce.class,
DistanceFn.class,
GeometryCentroidDistanceFn.class);
Assert.assertEquals(FeatureCentroidDistanceFn.class, distancFn.getClass());
} catch (final InstantiationException e) {
throw new IOException("Unable to configure system", e);
} catch (final IllegalAccessException e) {
throw new IOException("Unable to configure system", e);
}
Assert.assertEquals(10, job.getNumReduceTasks());
return new Counters();
}
@Override
public Job getJob(final Tool tool) throws IOException {
return new Job(tool.getConf());
}
});
jjJobRunner.setInputFormatConfiguration(
new SequenceFileInputFormatConfiguration(new Path("file://foo/bin")));
jjJobRunner.setReducerCount(10);
runTimeProperties.store(MRConfig.HDFS_BASE_DIR, "/");
runTimeProperties.store(GlobalParameters.Global.ZOOKEEKER, "localhost:3000");
runTimeProperties.store(GlobalParameters.Global.ACCUMULO_INSTANCE, "accumulo");
runTimeProperties.store(GlobalParameters.Global.ACCUMULO_USER, "root");
runTimeProperties.store(GlobalParameters.Global.ACCUMULO_PASSWORD, "pwd");
runTimeProperties.store(GlobalParameters.Global.ACCUMULO_NAMESPACE, "test");
runTimeProperties.store(
CommonParameters.Common.DISTANCE_FUNCTION_CLASS, FeatureCentroidDistanceFn.class);
runTimeProperties.store(Partition.PARTITIONER_CLASS, OrthodromicDistancePartitioner.class);
runTimeProperties.store(
Partition.SECONDARY_PARTITIONER_CLASS, OrthodromicDistancePartitioner.class);
runTimeProperties.store(Partition.PARTITION_DISTANCE, Double.valueOf(0.4));
runTimeProperties.store(Partition.MAX_MEMBER_SELECTION, Integer.valueOf(100));
}
