Clover coverage report -

Coverage timestamp: Mon May 5 2008 11:56:20 GMT-05:00

FRAMES NO FRAMES

file stats:	LOC:	104		Methods:	1
	NCLOC:	73		Classes:	1

Source file

Conditionals

Statements

Methods

TOTAL

MigrateOldData.java

1		package org.proteomecommons.tranche.util;
2
3		import java.io.BufferedOutputStream;
4		import java.io.File;
5		import java.io.FileOutputStream;
6		import org.apache.tools.tar.TarEntry;
7		import org.apache.tools.tar.TarOutputStream;
8		import org.proteomecommons.tranche.flatfile.DataBlockUtil;
9		import org.proteomecommons.tranche.flatfile.DataDirectoryConfiguration;
10
11		/**
12		* A class designed to help migrate data from the single-file data structure used by old Tranche servers to the new block data structure.
13		* @author Jayson Falkner - jfalkner@umich.edu
14		*/
15		public class MigrateOldData {
16
17	0	public static void main(String[] args) throws Exception {
18		// check args
19	0	if (args.length < 3) {
20	0	System.out.println("Usage: <zip dir> <old data dir> <new data dir> ");
21	0	return;
22		}
23		// take a starting directory
24	0	File zipDirectory = new File(args[0]);
25	0	File oldDataDirectory = new File(args[1]);
26	0	System.out.println("ZIP Dir: "+zipDirectory);
27	0	System.out.println("OLD Data Dir: "+oldDataDirectory);
28
29		// make a data block util for the new format
30	0	DataBlockUtil dbu = new DataBlockUtil();
31
32		// use a set of directories for the new
33	0	for (int i=2;i<args.length;i++) {
34	0	DataDirectoryConfiguration ddc = new DataDirectoryConfiguration(args[i], Long.MAX_VALUE);
35	0	dbu.add(ddc);
36	0	System.out.println("Loading DDC: "+args[i]);
37		}
38
39		// iterate over the directories
40	0	File[] firstLevel = oldDataDirectory.listFiles();
41	0	for (int i=0;i<firstLevel.length;i++) {
42		// for each top level directory, make a zip file
43	0	File zipFile = new File(zipDirectory, firstLevel[i].getName()+".tar");
44	0	FileOutputStream fos = new FileOutputStream(zipFile);
45	0	BufferedOutputStream bos = new BufferedOutputStream(fos);
46	0	TarOutputStream tos = new TarOutputStream(bos);
47		// set to allow long file names (GNU style!)
48	0	tos.setLongFileMode(2);
49
50	0	File[] secondLevel = firstLevel[i].listFiles();
51	0	for (int j=0;j<secondLevel.length;j++) {
52		// handle all of the actual files
53	0	File[] dirs = secondLevel[j].listFiles();
54	0	for (int k=0;k<dirs.length;k++) {
55		// make the big hash
56	0	BigHash hash = BigHash.createHashFromString(dirs[k].getName());
57		// handle all of the data/meta-data pairs
58	0	File data = new File(dirs[k], "data");
59	0	if (data.exists()) {
60		// get the bytes
61	0	byte[] bytes = IOUtil.getBytes(data);
62		// add to the dbu
63	0	dbu.addData(hash, bytes);
64
65		// add to the zip
66	0	String name = firstLevel[i].getName()+ "/" + secondLevel[j].getName() + "/" + dirs[k].getName()+"/data";
67	0	System.out.println("Adding: "+name);
68	0	TarEntry te = new TarEntry(name);
69	0	te.setSize(bytes.length);
70	0	tos.putNextEntry(te);
71	0	tos.write(bytes);
72	0	tos.closeEntry();
73		}
74		// handle all of the data/meta-data pairs
75	0	File metaData = new File(dirs[k], "metaData");
76	0	if (metaData.exists()) {
77		// get the bytes
78	0	byte[] bytes = IOUtil.getBytes(metaData);
79		// add to the dbu
80	0	dbu.addMetaData(hash, bytes);
81
82		// add to the zip
83	0	String name = firstLevel[i].getName()+ "/" + secondLevel[j].getName() + "/" + dirs[k].getName()+"/metaData";
84	0	System.out.println("Adding: "+name);
85	0	TarEntry ze = new TarEntry(name);
86	0	ze.setSize(bytes.length);
87	0	tos.putNextEntry(ze);
88	0	tos.write(bytes);
89	0	tos.closeEntry();
90		}
91		}
92		}
93
94	0	tos.flush();
95	0	tos.finish();
96	0	bos.flush();
97	0	fos.flush();
98	0	tos.close();
99	0	bos.close();
100	0	fos.close();
101	0	System.out.println("Finished "+i+" out of "+firstLevel.length+": "+zipFile);
102		}
103		}
104		}