org.cloudgraph.hbase.mapreduce.GraphMapReduceSetup Maven / Gradle / Ivy
/**
* CloudGraph Community Edition (CE) License
*
* This is a community release of CloudGraph, a dual-license suite of
* Service Data Object (SDO) 2.1 services designed for relational and
* big-table style "cloud" databases, such as HBase and others.
* This particular copy of the software is released under the
* version 2 of the GNU General Public License. CloudGraph was developed by
* TerraMeta Software, Inc.
*
* Copyright (c) 2013, TerraMeta Software, Inc. All rights reserved.
*
* General License information can be found below.
*
* This distribution may include materials developed by third
* parties. For license and attribution notices for these
* materials, please refer to the documentation that accompanies
* this distribution (see the "Licenses for Third-Party Components"
* appendix) or view the online documentation at
* scans = createScans(from, where, type, columnFilter, conf);
conf.set(GraphInputFormat.QUERY, marshal(query));
conf.set(GraphInputFormat.ROOT_TABLE, graphReader.getRootTableReader()
.getTableName());
List scanStrings = new ArrayList();
for (Scan scan : scans) {
scan.setAttribute(Scan.SCAN_ATTRIBUTES_TABLE_NAME,
Bytes.toBytes(graphReader.getRootTableReader().getTableName()));
scanStrings.add(convertScanToString(scan));
}
conf.setStrings(GraphInputFormat.SCANS,
scanStrings.toArray(new String[scanStrings.size()]));
if (addDependencyJars) {
addDependencyJars(job);
}
initCredentials(job);
}
private static List createScans(From from, Where where, PlasmaType type,
Filter columnFilter, Configuration conf) throws IOException {
List result = new ArrayList();
if (where == null) {
conf.setBoolean(GraphInputFormat.RECOGNIZER, false);
Scan scan = createDefaultScan(from, type, columnFilter);
result.add(scan);
return result;
}
ScanRecognizerSyntaxTreeAssembler recognizerAssembler =
new ScanRecognizerSyntaxTreeAssembler(where, type);
Expr scanRecognizerRootExpr = recognizerAssembler.getResult();
if (LOG.isDebugEnabled()) {
ExprPrinter printer = new ExprPrinter();
scanRecognizerRootExpr.accept(printer);
LOG.debug("Scan Recognizer: " + printer.toString());
}
ScanCollector scanCollector = new ScanCollector(type);
scanRecognizerRootExpr.accept(scanCollector);
List partialScans = scanCollector.getPartialRowKeyScans();
List fuzzyScans = scanCollector.getFuzzyRowKeyScans();
List completeKeys = scanCollector.getCompleteRowKeys();
if (!scanCollector.isQueryRequiresGraphRecognizer()) {
conf.setBoolean(GraphInputFormat.RECOGNIZER, false);
scanRecognizerRootExpr = null;
}
else {
conf.setBoolean(GraphInputFormat.RECOGNIZER, true);
}
if (completeKeys.size() > 0)
throw new GraphServiceException(
"expected no complete key values");
//FIXME: table split by region entirely based on partial key start stop bytes
for (FuzzyRowKey fuzzyKey : fuzzyScans) {
Scan scan = createScan(fuzzyKey, columnFilter);
result.add(scan);
}
for (PartialRowKey partialKey : partialScans) {
Scan scan = createScan(partialKey, columnFilter);
result.add(scan);
}
if (result.size() == 0)
{
Scan scan = createDefaultScan(from, type, columnFilter);
result.add(scan);
}
return result;
}
private static Scan createDefaultScan(From from, PlasmaType type, Filter columnFilter) {
Scan scan;
PartialRowKeyScanAssembler scanAssembler = new PartialRowKeyScanAssembler(type);
scanAssembler.assemble();
byte[] startKey = scanAssembler.getStartKey();
if (startKey != null && startKey.length > 0) {
LOG.warn("using default graph partial "
+ "key scan - could result in very large results set");
scan = createScan(scanAssembler, columnFilter);
}
else {
Float sample = from.getRandomSample();
if (sample == null) {
FilterList rootFilter = new FilterList(
FilterList.Operator.MUST_PASS_ALL);
scan = new Scan();
rootFilter.addFilter(columnFilter);
scan.setFilter(rootFilter);
LOG.warn("query resulted in no filters or scans - using full table scan - "
+ "could result in very large results set");
}
else {
FilterList rootFilter = new FilterList(
FilterList.Operator.MUST_PASS_ALL);
RandomRowFilter rowFilter = new RandomRowFilter(sample);
rootFilter.addFilter(rowFilter);
rootFilter.addFilter(columnFilter);
scan = new Scan();
scan.setFilter(rootFilter);
LOG.warn("using random-sample scan ("+sample+") - "
+ "could result in very large results set");
}
}
return scan;
}
/**
* Use this before submitting a graph map job. It will appropriately set up
* the job.
*
* @param query The query defining the {@link GraphMapper} input graphs.
* @param mapper
* The mapper class to use.
* @param outputKeyClass
* The class of the output key.
* @param outputValueClass
* The class of the output value.
* @param job
* The current job to adjust. Make sure the passed job is
* carrying all necessary HBase configuration.
* @param addDependencyJars
* upload HBase jars and jars for any of the configured job
* classes via the distributed cache (tmpjars).
* @throws IOException
* When setting up the details fails.
*/
public static void setupGraphMapperJob(Query query,
Class mapper,
Class outputKeyClass,
Class outputValueClass, Job job,
boolean addDependencyJars) throws IOException {
setupGraphMapperJob(query, mapper, outputKeyClass, outputValueClass,
job, addDependencyJars, GraphInputFormat.class);
}
public static void initCredentials(Job job) throws IOException {
UserProvider userProvider = UserProvider.instantiate(job.getConfiguration());
if (userProvider.isHadoopSecurityEnabled()) {
// propagate delegation related props from launcher job to MR job
if (System.getenv("HADOOP_TOKEN_FILE_LOCATION") != null) {
job.getConfiguration().set("mapreduce.job.credentials.binary",
System.getenv("HADOOP_TOKEN_FILE_LOCATION"));
}
}
if (userProvider.isHBaseSecurityEnabled()) {
try {
// init credentials for remote cluster
String quorumAddress = job.getConfiguration().get(TableOutputFormat.QUORUM_ADDRESS);
User user = userProvider.getCurrent();
if (quorumAddress != null) {
Configuration peerConf = HBaseConfiguration.createClusterConf(job.getConfiguration(),
quorumAddress, TableOutputFormat.OUTPUT_CONF_PREFIX);
Connection peerConn = ConnectionFactory.createConnection(peerConf);
try {
TokenUtil.addTokenForJob(peerConn, user, job);
} finally {
peerConn.close();
}
}
Connection conn = ConnectionFactory.createConnection(job.getConfiguration());
try {
TokenUtil.addTokenForJob(conn, user, job);
} finally {
conn.close();
}
} catch (InterruptedException ie) {
LOG.info("Interrupted obtaining user authentication token");
Thread.currentThread().interrupt();
}
}
}
/**
* Writes the given scan into a Base64 encoded string.
*
* @param scan The scan to write out.
* @return The scan saved in a Base64 encoded string.
* @throws IOException When writing the scan fails.
*/
static String convertScanToString(Scan scan) throws IOException {
ClientProtos.Scan proto = ProtobufUtil.toScan(scan);
return Base64.encodeBytes(proto.toByteArray());
}
/**
* Converts the given Base64 string back into a Scan instance.
*
* @param base64 The scan details.
* @return The newly created Scan instance.
* @throws IOException When reading the scan instance fails.
*/
static Scan convertStringToScan(String base64) throws IOException {
byte [] decoded = Base64.decode(base64);
ClientProtos.Scan scan;
try {
scan = ClientProtos.Scan.parseFrom(decoded);
} catch (InvalidProtocolBufferException ipbe) {
throw new IOException(ipbe);
}
return ProtobufUtil.toScan(scan);
}
/**
* Use this before submitting a graph reduce job. It will appropriately set
* up the JobConf.
*
* @param tableConfig
* The output table.
* @param reducer
* The reducer class to use.
* @param job
* The current job to adjust.
* @throws IOException
* When determining the region count fails.
*/
public static void setupGraphReducerJob(Query query,
Class reducer, Job job) throws IOException {
setupGraphReducerJob(query, reducer, job, null);
}
/**
* Use this before submitting a graph reduce job. It will appropriately set
* up the JobConf.
*
* @param tableConfig
* The output table.
* @param reducer
* The reducer class to use.
* @param job
* The current job to adjust.
* @param partitioner
* Partitioner to use. Pass null to use default
* partitioner.
* @throws IOException
* When determining the region count fails.
*/
public static void setupGraphReducerJob(Query query,
Class reducer, Job job, Class partitioner)
throws IOException {
setupGraphReducerJob(query, reducer, job, partitioner, null, null, null);
}
/**
* Use this before submitting a graph reduce job. It will appropriately set
* up the JobConf.
*
* @param query
* The output query.
* @param reducer
* The reducer class to use.
* @param job
* The current job to adjust. Make sure the passed job is
* carrying all necessary HBase configuration.
* @param partitioner
* Partitioner to use. Pass null to use default
* partitioner.
* @param quorumAddress
* Distant cluster to write to; default is null for output to the
* cluster that is designated in hbase-site.xml. Set
* this String to the zookeeper ensemble of an alternate remote
* cluster when you would have the reduce write a cluster that is
* other than the default; e.g. copying tables between clusters,
* the source would be designated by hbase-site.xml
* and this param would have the ensemble address of the remote
* cluster. The format to pass is particular. Pass
* <hbase.zookeeper.quorum>:<hbase.zookeeper.client.port>:<zookeeper.znode.parent>
* such as server,server2,server3:2181:/hbase.
* @param serverClass
* redefined hbase.regionserver.class
* @param serverImpl
* redefined hbase.regionserver.impl
* @throws IOException
* When determining the region count fails.
*/
public static void setupGraphReducerJob(Query query,
Class reducer, Job job, Class partitioner,
String quorumAddress, String serverClass, String serverImpl)
throws IOException {
setupGraphReducerJob(query, reducer, job, partitioner, quorumAddress,
serverClass, serverImpl, true);
}
/**
* Use this before submitting a TableReduce job. It will appropriately set
* up the JobConf.
*
* @param query
* The output query.
* @param reducer
* The reducer class to use.
* @param job
* The current job to adjust. Make sure the passed job is
* carrying all necessary HBase configuration.
* @param partitioner
* Partitioner to use. Pass null to use default
* partitioner.
* @param quorumAddress
* Distant cluster to write to; default is null for output to the
* cluster that is designated in hbase-site.xml. Set
* this String to the zookeeper ensemble of an alternate remote
* cluster when you would have the reduce write a cluster that is
* other than the default; e.g. copying tables between clusters,
* the source would be designated by hbase-site.xml
* and this param would have the ensemble address of the remote
* cluster. The format to pass is particular. Pass
* <hbase.zookeeper.quorum>:<hbase.zookeeper.client.port>:<zookeeper.znode.parent>
* such as server,server2,server3:2181:/hbase.
* @param serverClass
* redefined hbase.regionserver.class
* @param serverImpl
* redefined hbase.regionserver.impl
* @param addDependencyJars
* upload HBase jars and jars for any of the configured job
* classes via the distributed cache (tmpjars).
* @throws IOException
* When determining the region count fails.
*/
public static void setupGraphReducerJob(Query query,
Class reducer, Job job, Class partitioner,
String quorumAddress, String serverClass, String serverImpl,
boolean addDependencyJars) throws IOException {
Configuration conf = job.getConfiguration();
HBaseConfiguration.merge(conf, HBaseConfiguration.create(conf));
PlasmaType type = getRootType(query);
Where where = query.getModel().findWhereClause();
SelectionCollector selectionCollector = null;
if (where != null)
selectionCollector = new SelectionCollector(query.getModel()
.getSelectClause(), where, type);
else
selectionCollector = new SelectionCollector(query.getModel()
.getSelectClause(), type);
selectionCollector.setOnlyDeclaredProperties(false);
// FIXME: generalize collectRowKeyProperties
for (Type t : selectionCollector.getTypes())
collectRowKeyProperties(selectionCollector, (PlasmaType) t);
StateMarshalingContext marshallingContext = null;
try {
marshallingContext = new SimpleStateMarshallingContext(
new StateNonValidatingDataBinding());
} catch (JAXBException e) {
throw new GraphServiceException(e);
} catch (SAXException e) {
throw new GraphServiceException(e);
}
DistributedGraphReader graphReader = new DistributedGraphReader(type,
selectionCollector.getTypes(), marshallingContext);
//job.setOutputFormatClass(GraphOutputFormat.class);
if (reducer != null)
job.setReducerClass(reducer);
/*
conf.set(TableOutputFormat.OUTPUT_TABLE, graphReader.getRootTableReader().getTableName());
// If passed a quorum/ensemble address, pass it on to TableOutputFormat.
if (quorumAddress != null) {
// Calling this will validate the format
ZKUtil.transformClusterKey(quorumAddress);
conf.set(TableOutputFormat.QUORUM_ADDRESS, quorumAddress);
}
if (serverClass != null && serverImpl != null) {
conf.set(TableOutputFormat.REGION_SERVER_CLASS, serverClass);
conf.set(TableOutputFormat.REGION_SERVER_IMPL, serverImpl);
}
job.setOutputKeyClass(ImmutableBytesWritable.class);
job.setOutputValueClass(Writable.class);
if (partitioner == HRegionPartitioner.class) {
job.setPartitionerClass(HRegionPartitioner.class);
HTable outputTable = new HTable(conf, graphReader.getRootTableReader().getTableName());
int regions = outputTable.getRegionsInfo().size();
if (job.getNumReduceTasks() > regions) {
job.setNumReduceTasks(outputTable.getRegionsInfo().size());
}
} else if (partitioner != null) {
job.setPartitionerClass(partitioner);
}
*/
if (addDependencyJars) {
addDependencyJars(job);
}
initCredentials(job);
}
/**
* Ensures that the given number of reduce tasks for the given job
* configuration does not exceed the number of regions for the given table.
*
* @param table
* The table to get the region count for.
* @param job
* The current job to adjust.
* @throws IOException
* When retrieving the table details fails.
*/
public static void limitNumReduceTasks(String table, Job job)
throws IOException {
HTable outputTable = new HTable(job.getConfiguration(), table);
int regions = outputTable.getRegionLocations().size();
if (job.getNumReduceTasks() > regions)
job.setNumReduceTasks(regions);
}
/**
* Sets the number of reduce tasks for the given job configuration to the
* number of regions the given table has.
*
* @param table
* The table to get the region count for.
* @param job
* The current job to adjust.
* @throws IOException
* When retrieving the table details fails.
*/
public static void setNumReduceTasks(String table, Job job)
throws IOException {
HTable outputTable = new HTable(job.getConfiguration(), table);
int regions = outputTable.getRegionLocations().size();
job.setNumReduceTasks(regions);
}
/**
* Sets the number of rows to return and cache with each scanner iteration.
* Higher caching values will enable faster mapreduce jobs at the expense of
* requiring more heap to contain the cached rows.
*
* @param job
* The current job to adjust.
* @param batchSize
* The number of rows to return in batch with each scanner
* iteration.
*/
public static void setScannerCaching(Job job, int batchSize) {
job.getConfiguration()
.setInt("hbase.client.scanner.caching", batchSize);
}
/**
* Add the HBase dependency jars as well as jars for any of the configured
* job classes to the job configuration, so that JobClient will ship them to
* the cluster and add them to the DistributedCache.
*/
public static void addDependencyJars(Job job) throws IOException {
try {
addDependencyJars(
job.getConfiguration(),
org.apache.zookeeper.ZooKeeper.class,
com.google.protobuf.Message.class,
com.google.common.collect.ImmutableSet.class,
org.apache.hadoop.hbase.util.Bytes.class, // one class from
// hbase.jar
job.getMapOutputKeyClass(), job.getMapOutputValueClass(),
job.getInputFormatClass(), job.getOutputKeyClass(),
job.getOutputValueClass(), job.getOutputFormatClass(),
job.getPartitionerClass(), job.getCombinerClass());
} catch (ClassNotFoundException e) {
throw new IOException(e);
}
}
/**
* Add the jars containing the given classes to the job's configuration such
* that JobClient will ship them to the cluster and add them to the
* DistributedCache.
*/
public static void addDependencyJars(Configuration conf,
Class... classes) throws IOException {
FileSystem localFs = FileSystem.getLocal(conf);
Set jars = new HashSet();
// Add jars that are already in the tmpjars variable
jars.addAll(conf.getStringCollection("tmpjars"));
// add jars as we find them to a map of contents jar name so that we can
// avoid
// creating new jars for classes that have already been packaged.
Map packagedClasses = new HashMap();
// Add jars containing the specified classes
for (Class clazz : classes) {
if (clazz == null)
continue;
Path path = findOrCreateJar(clazz, localFs, packagedClasses);
if (path == null) {
LOG.warn("Could not find jar for class " + clazz
+ " in order to ship it to the cluster.");
continue;
}
if (!localFs.exists(path)) {
LOG.warn("Could not validate jar file " + path + " for class "
+ clazz);
continue;
}
jars.add(path.toString());
}
if (jars.isEmpty())
return;
conf.set("tmpjars",
StringUtils.arrayToString(jars.toArray(new String[0])));
}
/**
* If org.apache.hadoop.util.JarFinder is available (0.23+ hadoop), finds
* the Jar for a class or creates it if it doesn't exist. If the class is in
* a directory in the classpath, it creates a Jar on the fly with the
* contents of the directory and returns the path to that Jar. If a Jar is
* created, it is created in the system temporary directory. Otherwise,
* returns an existing jar that contains a class of the same name. Maintains
* a mapping from jar contents to the tmp jar created.
*
* @param my_class
* the class to find.
* @param fs
* the FileSystem with which to qualify the returned path.
* @param packagedClasses
* a map of class name to path.
* @return a jar file that contains the class.
* @throws IOException
*/
private static Path findOrCreateJar(Class my_class, FileSystem fs,
Map packagedClasses) throws IOException {
// attempt to locate an existing jar for the class.
String jar = findContainingJar(my_class, packagedClasses);
if (null == jar || jar.isEmpty()) {
jar = getJar(my_class);
updateMap(jar, packagedClasses);
}
if (null == jar || jar.isEmpty()) {
throw new IOException("Cannot locate resource for class "
+ my_class.getName());
}
LOG.debug(String.format("For class %s, using jar %s",
my_class.getName(), jar));
return new Path(jar).makeQualified(fs);
}
/**
* Add entries to packagedClasses corresponding to class files
* contained in jar.
*
* @param jar
* The jar who's content to list.
* @param packagedClasses
* map[class -> jar]
*/
private static void updateMap(String jar,
Map packagedClasses) throws IOException {
ZipFile zip = null;
try {
zip = new ZipFile(jar);
for (Enumeration iter = zip.entries(); iter
.hasMoreElements();) {
ZipEntry entry = iter.nextElement();
if (entry.getName().endsWith("class")) {
packagedClasses.put(entry.getName(), jar);
}
}
} finally {
if (null != zip)
zip.close();
}
}
/**
* Find a jar that contains a class of the same name, if any. It will return
* a jar file, even if that is not the first thing on the class path that
* has a class with the same name. Looks first on the classpath and then in
* the packagedClasses map.
*
* @param my_class
* the class to find.
* @return a jar file that contains the class, or null.
* @throws IOException
*/
private static String findContainingJar(Class my_class,
Map packagedClasses) throws IOException {
ClassLoader loader = my_class.getClassLoader();
String class_file = my_class.getName().replaceAll("\\.", "/")
+ ".class";
// first search the classpath
for (Enumeration itr = loader.getResources(class_file); itr
.hasMoreElements();) {
URL url = itr.nextElement();
if ("jar".equals(url.getProtocol())) {
String toReturn = url.getPath();
if (toReturn.startsWith("file:")) {
toReturn = toReturn.substring("file:".length());
}
// URLDecoder is a misnamed class, since it actually decodes
// x-www-form-urlencoded MIME type rather than actual
// URL encoding (which the file path has). Therefore it would
// decode +s to ' 's which is incorrect (spaces are actually
// either unencoded or encoded as "%20"). Replace +s first, so
// that they are kept sacred during the decoding process.
toReturn = toReturn.replaceAll("\\+", "%2B");
toReturn = URLDecoder.decode(toReturn, "UTF-8");
return toReturn.replaceAll("!.*$", "");
}
}
// now look in any jars we've packaged using JarFinder. Returns null
// when
// no jar is found.
return packagedClasses.get(class_file);
}
/**
* Invoke 'getJar' on a JarFinder implementation. Useful for some job
* configuration contexts (HBASE-8140) and also for testing on MRv2. First
* check if we have HADOOP-9426. Lacking that, fall back to the backport.
*
* @param my_class
* the class to find.
* @return a jar file that contains the class, or null.
*/
private static String getJar(Class my_class) {
String ret = null;
String hadoopJarFinder = "org.apache.hadoop.util.JarFinder";
Class jarFinder = null;
try {
LOG.debug("Looking for " + hadoopJarFinder + ".");
jarFinder = Class.forName(hadoopJarFinder);
LOG.debug(hadoopJarFinder + " found.");
Method getJar = jarFinder.getMethod("getJar", Class.class);
ret = (String) getJar.invoke(null, my_class);
} catch (ClassNotFoundException e) {
LOG.debug("Using backported JarFinder.");
ret = JarFinder.getJar(my_class);
} catch (InvocationTargetException e) {
// function was properly called, but threw it's own exception.
// Unwrap it
// and pass it on.
throw new RuntimeException(e.getCause());
} catch (Exception e) {
// toss all other exceptions, related to reflection failure
throw new RuntimeException("getJar invocation failed.", e);
}
return ret;
}
// FIXME: generalize
private static Scan createScan(PartialRowKey partialRowKey,
Filter columnFilter) {
FilterList rootFilter = new FilterList(
FilterList.Operator.MUST_PASS_ALL);
rootFilter.addFilter(columnFilter);
Scan scan = new Scan();
scan.setFilter(rootFilter);
scan.setStartRow(partialRowKey.getStartKey()); // inclusive
scan.setStopRow(partialRowKey.getStopKey()); // exclusive
LOG.info("using partial row key scan: (" + "start: '"
+ Bytes.toString(scan.getStartRow()) + "' stop: '"
+ Bytes.toString(scan.getStopRow()) + "')");
return scan;
}
// FIXME: generalize
private static Scan createScan(FuzzyRowKey fuzzyScan, Filter columnFilter)
throws IOException {
FilterList rootFilter = new FilterList(
FilterList.Operator.MUST_PASS_ALL);
rootFilter.addFilter(columnFilter);
Scan scan = new Scan();
scan.setFilter(rootFilter);
Filter fuzzyFilter = fuzzyScan.getFilter();
rootFilter.addFilter(fuzzyFilter);
LOG.info("using fuzzy scan: " + FilterUtil.printFilterTree(fuzzyFilter));
return scan;
}
private static void collectRowKeyProperties(SelectionCollector collector,
PlasmaType type) {
Config config = CloudGraphConfig.getInstance();
DataGraphConfig graph = config.findDataGraph(type.getQualifiedName());
if (graph != null) {
UserDefinedRowKeyFieldConfig[] fields = new UserDefinedRowKeyFieldConfig[graph
.getUserDefinedRowKeyFields().size()];
graph.getUserDefinedRowKeyFields().toArray(fields);
for (UserDefinedRowKeyFieldConfig field : fields) {
List types = collector.addProperty(graph.getRootType(),
field.getPropertyPath());
for (Type nextType : types)
collectRowKeyProperties(collector, (PlasmaType) nextType);
}
}
}
private static Query unmarshal(File queryFile) {
try {
PlasmaQueryDataBinding binding = new PlasmaQueryDataBinding(
new DefaultValidationEventHandler());
FileInputStream fis = new FileInputStream(queryFile);
return (Query) binding.unmarshal(fis);
} catch (JAXBException e1) {
throw new GraphServiceException(e1);
} catch (SAXException e1) {
throw new GraphServiceException(e1);
} catch (FileNotFoundException e) {
throw new GraphServiceException(e);
}
}
private static Query unmarshal(String xmlQuery) {
try {
PlasmaQueryDataBinding binding = new PlasmaQueryDataBinding(
new DefaultValidationEventHandler());
return (Query) binding.unmarshal(xmlQuery);
} catch (JAXBException e1) {
throw new GraphServiceException(e1);
} catch (SAXException e1) {
throw new GraphServiceException(e1);
}
}
private static String marshal(Query query) {
try {
PlasmaQueryDataBinding binding = new PlasmaQueryDataBinding(
new DefaultValidationEventHandler());
return binding.marshal(query);
} catch (JAXBException e1) {
throw new GraphServiceException(e1);
} catch (SAXException e1) {
throw new GraphServiceException(e1);
}
}
}
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