Java tutorial
/* GenReverseEdge.java 2012 CloudBrush, developed by Chien-Chih Chen (rocky@iis.sinica.edu.tw), released under Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) at: https://github.com/ice91/CloudBrush */ package Brush; import java.io.IOException; import java.util.Collections; import java.util.Comparator; import java.util.ArrayList; import java.util.HashMap; import java.util.HashSet; import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Set; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.conf.Configured; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.LongWritable; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapred.FileInputFormat; import org.apache.hadoop.mapred.FileOutputFormat; import org.apache.hadoop.mapred.JobClient; import org.apache.hadoop.mapred.JobConf; import org.apache.hadoop.mapred.MapReduceBase; import org.apache.hadoop.mapred.Mapper; import org.apache.hadoop.mapred.OutputCollector; import org.apache.hadoop.mapred.Reducer; import org.apache.hadoop.mapred.Reporter; import org.apache.hadoop.mapred.RunningJob; import org.apache.hadoop.mapred.TextInputFormat; import org.apache.hadoop.mapred.TextOutputFormat; import org.apache.hadoop.util.Tool; import org.apache.hadoop.util.ToolRunner; import org.apache.log4j.Logger; public class GenReverseEdge extends Configured implements Tool { private static final Logger sLogger = Logger.getLogger(GenReverseEdge.class); // GenReverseEdgeMapper /////////////////////////////////////////////////////////////////////////// public static class GenReverseEdgeMapper extends MapReduceBase implements Mapper<LongWritable, Text, Text, Text> { public void map(LongWritable lineid, Text nodetxt, OutputCollector<Text, Text> output, Reporter reporter) throws IOException { Node node = new Node(); node.fromNodeMsg(nodetxt.toString()); for (String key : Node.edgetypes) { List<String> edges = node.getEdges(key); if (edges != null) { for (int i = 0; i < edges.size(); i++) { String[] vals = edges.get(i).split("!"); String edge_id = vals[0]; String oval_size = vals[1]; //String con = Node.flip_dir(adj) + "f"; String con = Node.flip_link(key); output.collect(new Text(edge_id), new Text(Node.OVALMSG + "\t" + node.getNodeId() + "\t" + node.str_raw() + "\t" + con + "\t" + oval_size)); //\\// emit reverse edge //output.collect(new Text(edge_id), new Text(Node.OVALMSG + "\t" + node.getNodeId() + "\t" + node.str_raw() + "\t" + key + "\t" + oval_size)); } } } List<String> emit_node = new ArrayList<String>(); output.collect(new Text(node.getNodeId()), new Text(node.toNodeMsg())); reporter.incrCounter("Brush", "nodes", 1); } } // GenReverseEdgeReducer /////////////////////////////////////////////////////////////////////////// public static class GenReverseEdgeReducer extends MapReduceBase implements Reducer<Text, Text, Text, Text> { private static int K = 0; public void configure(JobConf job) { K = Integer.parseInt(job.get("K")); } public class OverlapInfo { public String id; public String str; public String edge_type; //node overlap?e.g. node [r,f]f overlap public int overlap_size; public OverlapInfo(String[] vals, int offset) throws IOException { //print "$major\t$BUBBLELINKMSG\t$majord\t$nodeid\t$minord\t$minor\t$str\t$cov\n"; if (!vals[offset].equals(Node.OVALMSG)) { throw new IOException("Unknown message type"); } id = vals[offset + 1]; str = vals[offset + 2]; edge_type = vals[offset + 3]; overlap_size = Integer.parseInt(vals[offset + 4]); } public String toString() { return edge_type + " " + id + " " + overlap_size + " " + str; } } class OvelapSizeComparator implements Comparator { public int compare(Object element1, Object element2) { OverlapInfo obj1 = (OverlapInfo) element1; OverlapInfo obj2 = (OverlapInfo) element2; if ((int) (obj1.overlap_size - obj2.overlap_size) >= 0) { return -1; } else { return 1; } } } public class Prefix { public String id; public String str; public String edge_type; public Prefix(String id1, String edge_type1, String str1) { id = id1; edge_type = edge_type1; str = str1; } } public void reduce(Text nodeid, Iterator<Text> iter, OutputCollector<Text, Text> output, Reporter reporter) throws IOException { Node node = new Node(nodeid.toString()); List<OverlapInfo> olist = new ArrayList<OverlapInfo>(); int sawnode = 0; while (iter.hasNext()) { String msg = iter.next().toString(); //System.err.println(key.toString() + "\t" + msg); String[] vals = msg.split("\t"); if (vals[0].equals(Node.NODEMSG)) { node.parseNodeMsg(vals, 0); sawnode++; } else if (vals[0].equals(Node.OVALMSG)) { OverlapInfo oi = new OverlapInfo(vals, 0); olist.add(oi); //output.collect(new Text(node.getNodeId()), new Text("X" + "\t" + oi.id )); } else { throw new IOException("Unknown msgtype: " + msg); } } //\\ one node if (sawnode != 1) { throw new IOException( "ERROR: Didn't see exactly 1 nodemsg (" + sawnode + ") for " + nodeid.toString()); } //\\ store confirmed edges Map<String, List<String>> edges_list = new HashMap<String, List<String>>(); Map<String, List<String>> IDs_list = new HashMap<String, List<String>>(); Map<String, List<Prefix>> PREFIXs_list = new HashMap<String, List<Prefix>>(); int choices = olist.size(); //output.collect(new Text(node.getNodeId()), new Text(choices + "")); if (choices > 0) { // Sort overlap strings in order of decreasing overlap size Collections.sort(olist, new OvelapSizeComparator()); //output.collect(new Text(node.getNodeId()), new Text(olist.size() + "!")); // See if there are any pairwise compatible strings for (int i = 0; i < choices; i++) { String oval_id = olist.get(i).id; String oval_type = olist.get(i).edge_type; String node_dir = oval_type.substring(0, 1); String oval_dir = oval_type.substring(1); int oval_size = olist.get(i).overlap_size; String edge_content = oval_id + "!" + oval_size; //\\\\\\\\\\\ filter by already existing edge List<String> exist_edge = node.getEdges(oval_type); if (exist_edge != null && exist_edge.contains(edge_content)) { continue; } //\\\\\\\\\\\\\ Store confirmed edge if (edges_list.containsKey(oval_type)) { edges_list.get(oval_type).add(edge_content); } else { List<String> tmp_edges = null; tmp_edges = new ArrayList<String>(); tmp_edges.add(edge_content); edges_list.put(oval_type, tmp_edges); } } } //\\\\\\\\\\\\\\\\\ set Edges for (String con : Node.edgetypes) { //node.clearEdges(con); List<String> edges = edges_list.get(con); if (edges != null) { //node.setEdges(con, edges); for (int i = 0; i < edges.size(); i++) { node.addEdge(con, edges.get(i)); } } } output.collect(new Text(node.getNodeId()), new Text(node.toNodeMsg())); } } public RunningJob run(String inputPath, String outputPath) throws Exception { sLogger.info("Tool name: GenReverseEdge"); sLogger.info(" - input: " + inputPath); sLogger.info(" - output: " + outputPath); //JobConf conf = new JobConf(Stats.class); JobConf conf = new JobConf(GenReverseEdge.class); conf.setJobName("GenReverseEdge " + inputPath); BrushConfig.initializeConfiguration(conf); FileInputFormat.addInputPath(conf, new Path(inputPath)); FileOutputFormat.setOutputPath(conf, new Path(outputPath)); conf.setInputFormat(TextInputFormat.class); conf.setOutputFormat(TextOutputFormat.class); conf.setMapOutputKeyClass(Text.class); conf.setMapOutputValueClass(Text.class); conf.setOutputKeyClass(Text.class); conf.setOutputValueClass(Text.class); //conf.setBoolean("mapred.output.compress", true); conf.setMapperClass(GenReverseEdgeMapper.class); conf.setReducerClass(GenReverseEdgeReducer.class); //delete the output directory if it exists already FileSystem.get(conf).delete(new Path(outputPath), true); return JobClient.runJob(conf); } public int run(String[] args) throws Exception { String inputPath = ""; String outputPath = ""; run(inputPath, outputPath); return 0; } public static void main(String[] args) throws Exception { int res = ToolRunner.run(new Configuration(), new GenReverseEdge(), args); System.exit(res); } }