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source: trunk/grails-app/services/nl/tno/metagenomics/files/FileService.groovy @ 12

Last change on this file since 12 was 12, checked in by robert@…, 9 years ago
Implemented basic exporting functionality
File size: 15.1 KB

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1	/**
2	* FileService Service
3	*
4	* Contains methods for file uploads
5	*
6	* @author Robert Horlings
7	* @since 20100521
8	* @package dbnp.studycapturing
9	*
10	* Revision information:
11	* $Rev$
12	* $Author$
13	* $Date$
14	*/
15	package nl.tno.metagenomics.files
16
17	import org.codehaus.groovy.grails.commons.ApplicationHolder
18	import org.codehaus.groovy.grails.commons.ConfigurationHolder
19	import java.io.File;
20	import java.util.zip.*
21
22	/**
23	* Convenience methods for uploading and handling files
24	* @author robert@isdat.nl
25	*
26	*/
27	class FileService implements Serializable {
28	// ApplicationContext applicationContext
29
30	// Must be false, since the webflow can't use a transactional service. See
31	// http://www.grails.org/WebFlow for more information
32	static transactional = false
33
34	/**
35	* Handles the upload of a file using the ajax upload method
36	* @param value The value entered into the new filed. May be a File object of an uploaded file or a string containing a filename
37	* @param currentFile Filename of the current file in the database.
38	* @param directory Path to the directory where the file should move to. See absolutePath() method for more information.
39	* Defaults to the uploadDir from configuration
40	* @return Filename of the uploaded file
41	*/
42	def String handleUploadedFile( def value, String currentFile, File directory = null) {
43	if( directory == null )
44	directory = getUploadDir();
45
46	// If NULL is given or "deleted", the field value is emptied and the old file is removed
47	// If an empty string is given, the field value is kept as was
48	// If a file is given, it is moved to the right directory. Old files are deleted. If
49	// the file does not exist, the field is kept
50	// If a string is given, it is supposed to be a file in the upload directory. If
51	// it is different from the old one, the old one is deleted. If the file does not
52	// exist, the old one is kept.
53
54	if (value == null \|\| ( value.class == String && value == 'deleted' ) ) {
55	// If NULL is given, the field value is emptied and the old file is removed
56	value = "";
57	if (currentFile) {
58	delete(currentFile, directory)
59	}
60	} else if (value.class == File) {
61	// a file was given. Attempt to move it to the upload directory, and
62	// afterwards, store the filename. If the file doesn't exist
63	// or can't be moved, "" is returned
64	value = moveFileToUploadDir(value, directory);
65
66	if (value) {
67	if (currentFile) {
68	delete(currentFile, directory)
69	}
70	} else {
71	value = currentFile;
72	}
73	} else if (value == "") {
74	value = currentFile;
75	} else {
76	if (value != currentFile) {
77	if (fileExists(value, directory)) {
78	// When a FILE field is filled, and a new file is set
79	// the existing file should be deleted
80	if (currentFile) {
81	delete(currentFile, directory)
82	}
83	} else {
84	// If the file does not exist, the field is kept
85	value = currentFile;
86	}
87	}
88	}
89
90	return value as String;
91	}
92
93	/**
94	* Returns the directory for uploading files. Makes it easy to change the
95	* path to the directory, if needed
96	*/
97	def File getUploadDir() {
98	// Find the file upload directory name from the configuration
99	String uploadDir = ConfigurationHolder.config.metagenomics.fileUploadDir
100
101	if( !uploadDir )
102	uploadDir = "fileuploads"
103
104	return absolutePath( uploadDir );
105	}
106
107	/**
108	* Returns as File object to a given file
109	*/
110	def File get( String filename, File directory = null ) {
111	if( directory == null )
112	directory = getUploadDir()
113
114	return new File( directory, filename );
115	}
116
117	/**
118	* Check whether the given file exists in the upload directory
119	*/
120	def boolean fileExists( String filename, File directory = null ) {
121	if( directory == null )
122	directory = getUploadDir()
123
124	return new File( directory, filename ).exists();
125	}
126
127	/**
128	* Deletes a file in the upload dir, if it exists
129	*/
130	def boolean delete( String filename, File directory = null ) {
131	if( directory == null )
132	directory = getUploadDir()
133
134	def f = new File( directory, filename );
135	if( f.exists() ) {
136	f.delete();
137	}
138	}
139
140	/**
141	* Moves the given file to the upload directory.
142	*
143	* @return Filename given to the file on our system or "" if the moving fails
144	*/
145	def String moveFileToUploadDir( File file, String originalFilename, File directory = null ) {
146	if( directory == null )
147	directory = getUploadDir()
148
149	try {
150	if( file.exists() ) {
151	def newFilename = getUniqueFilename( originalFilename, directory );
152	file.renameTo( new File( directory, newFilename ) )
153	return newFilename
154	} else {
155	return "";
156	}
157	} catch(Exception exception) {
158	throw exception; // return ""
159	}
160	}
161
162	/**
163	* Moves the given uploaded file to the upload directory
164	*
165	* MultipartFile is the class used for uploaded files
166	*
167	* @return Filename given to the file on our system or "" if the moving fails
168	*/
169	def String moveFileToUploadDir( org.springframework.web.multipart.MultipartFile file, String originalFilename, File directory = null ) {
170	if( directory == null )
171	directory = getUploadDir()
172
173	try {
174	def newFilename = getUniqueFilename( originalFilename, directory );
175	file.transferTo( new File( directory, newFilename ))
176	return newFilename
177	} catch(Exception exception) {
178	throw exception; // return ""
179	}
180	}
181
182	/**
183	* Moves the given file to the upload directory.
184	*
185	* @return Filename given to the file on our system or "" if the moving fails
186	*/
187	def String moveFileToUploadDir( File file, File dir = null ) {
188	moveFileToUploadDir( file, file.getName(), dir );
189	}
190
191	/**
192	* Moves the given uploaded file to the upload directory
193	*
194	* MultipartFile is the class used for uploaded files
195	*
196	* @return Filename given to the file on our system or "" if the moving fails
197	*/
198	def String moveFileToUploadDir( org.springframework.web.multipart.MultipartFile file, File dir = null ) {
199	moveFileToUploadDir( file, file.getOriginalFilename(), dir );
200	}
201
202	/**
203	* Returns a filename that looks like the originalFilename and does not yet
204	* exist in the upload directory.
205	*
206	* @return String filename that does not yet exist in the upload directory
207	*/
208	def String getUniqueFilename( String originalFilename, File directory = null ) {
209	if( directory == null )
210	directory = getUploadDir()
211
212	if( fileExists( originalFilename, directory ) ) {
213	def basename;
214	def extension;
215
216	// Split the filename into basename and extension
217	if( originalFilename.lastIndexOf('.') >= 0 ) {
218	basename = originalFilename[ 0 .. originalFilename.lastIndexOf('.') - 1 ];
219	extension = originalFilename[ originalFilename.lastIndexOf('.')..originalFilename.size() - 1];
220	} else {
221	basename = originalFilename;
222	extension = '';
223	}
224
225	// Find a filename that does not yet exist
226	def postfix = 0;
227	def newFilename = basename + '.copy' + postfix + extension;
228	while( fileExists( newFilename, directory ) ) {
229	postfix++;
230	newFilename = basename + '.copy' + postfix + extension;
231	}
232
233	return newFilename;
234	} else {
235	return originalFilename;
236	}
237	}
238
239	/**
240	* Returns the original filename for a file that has been uploaded, but renamed
241	* using the uniqueFilename method
242	*
243	* @return String Original filename
244	*/
245	def String originalFilename( String filename ) {
246	def basename;
247	def extension;
248
249	// Split the filename into basename and extension
250	if( filename.lastIndexOf('.') >= 0 ) {
251	basename = filename[ 0 .. filename.lastIndexOf('.') - 1 ];
252	extension = filename[ filename.lastIndexOf('.')..filename.size() - 1];
253	} else {
254	basename = originalFilename;
255	extension = '';
256	}
257
258	// Search whether this file has been renamed (containing copy#)
259	if( basename.lastIndexOf('.') >= 0 ) {
260	def copypart = basename[ basename.lastIndexOf('.')+1..basename.size() - 1];
261	def rest = basename[ 0 .. basename.lastIndexOf('.') - 1 ];
262	if( copypart ==~ /copy[0-9]+/ ) {
263	return rest + extension;
264	} else {
265	return filename;
266	}
267	} else {
268	return filename;
269	}
270	}
271
272	/**
273	* Returns the absolute path for the given pathname. If the pathname is relative, it is taken relative to the web-app directory
274	* @param pathname
275	* @return
276	*/
277	private File absolutePath( String pathname ) {
278	if( pathname == null)
279	return null
280
281	// Check if this is an absolute path
282	File f = new File( pathname );
283
284	if( f.isAbsolute() ) {
285	return f
286	} else {
287	// Find the absolute path relative to the web-app directory. This code is found on
288	// http://stackoverflow.com/questions/491067/how-to-find-the-physical-path-of-a-gsp-file-in-a-deployed-grails-application
289	return ApplicationHolder.application.parentContext.getResource(pathname).getFile()
290	}
291	}
292
293	/**
294	* Removes all files with modified date older than 'age' from the given directory. This method doesn't recurse into directories.
295	* @param directory File object of the directory to clean
296	* @param age Maximum age of the files that should be kept in seconds. If you want to delete all files older than 1 hour, enter 3600
297	*/
298	public void cleanDirectory( File directory = null, long age = 0 ) {
299	if( !directory ) {
300	directory = getUploadDir();
301	}
302
303	if( !age ) {
304	age = ConfigurationHolder.config.metagenomics.fileUploadMaxAge
305	}
306
307	// Compute the minimum timestamp a file should have not to be deleted
308	Date today = new Date();
309	long treshold = today.getTime() - age * 1000;
310
311	// Loop through all files in this directory
312	File[] files = directory.listFiles();
313	for (File file : files) {
314	// Check for the age of the file
315	if (file.lastModified() < treshold) {
316	file.delete();
317	}
318	}
319
320	}
321
322	/**
323	* Determines the file type of a given file, based on the extension.
324	* @param file File to assess
325	* @return
326	*/
327	public String determineFileType( File file ) {
328	if( !file )
329	return null
330
331	// Determine the extension of the file
332	String name = file.getName();
333	if( name.lastIndexOf( '.' ) == -1 ) {
334	// Without an extension the file type is unknown
335	return ""
336	}
337
338	String extension = name.substring( name.lastIndexOf( '.' ) + 1 ).toLowerCase();
339
340	switch( extension ) {
341	case "fasta":
342	case "fna":
343	return "fasta";
344	case "qual":
345	case "fqa":
346	return "qual";
347	case "xls":
348	return "excel";
349	case "zip":
350	return "zip";
351	case "gz":
352	return "gzip";
353	default:
354	return ""; // meaning 'unknown'
355	}
356	}
357
358	/**********************************************************************************
359	*
360	* Methods for handling zip files
361	*
362	**********************************************************************************/
363
364	/**
365	* Determines whether a given file is a parsable zip file
366	* @param filename Filename to assess
367	* @return
368	*/
369	public boolean isZipFile( String filename ) {
370	File f = this.get( filename ) ;
371	switch( this.determineFileType( f ) ) {
372	case "zip":
373	case "gzip":
374	return true;
375	}
376
377	return false;
378	}
379
380	/**
381	* Extracts a given zip file and returns a list of the filenames of the extracted files.
382	*
383	* Files will be extracted in the temp directory, as used by the file service
384	*
385	* @param filename Filename of the zip file to assess
386	* @return List of filenames
387	*/
388	public ArrayList extractZipFile( String filename, Closure onProgress ) {
389	File f = this.get( filename );
390
391	if( !f ) {
392	log.error "No files was given for extracting files."
393	return []
394	}
395
396	switch( this.determineFileType( f ) ) {
397	case "zip":
398	return extractZip( f, onProgress );
399	case "gzip":
400	return extractGzip( f, onProgress );
401	default:
402	log.error "File given for extracting files is not a valid zip file."
403
404	return [];
405	}
406	}
407
408	/**
409	* Extracts a ZIP file
410	* @param f Zipfile to extract
411	* @return A list of extracted filenames; files can be found in the fileService temporary directory
412	*/
413	protected ArrayList extractZip( File f, Closure onProgress ) {
414	return extractZip( f, getUploadDir(), onProgress );
415	}
416
417	/**
418	* Extracts a ZIP file
419	* @param f Zipfile to extract
420	* @param dir Directory to extract the files to
421	* @return A list of extracted filenames
422	*/
423	protected ArrayList extractZip( File f, File outdir, Closure onProgress ) {
424	// Create a list of filenames to return later
425	def filenames = [];
426
427	// create a buffer to improve copy performance later.
428	byte[] buffer = new byte[2048];
429
430	// open the zip file stream
431	ZipInputStream stream = new ZipInputStream(new FileInputStream( f ) );
432
433	try
434	{
435	// now iterate through each item in the stream. The get next
436	// entry call will return a ZipEntry for each file in the
437	// stream
438	ZipEntry entry;
439	while((entry = stream.getNextEntry()) != null)
440	{
441	String s = String.format("Entry: %s len %d added %TD",
442	entry.getName(), entry.getSize(),
443	new Date(entry.getTime()));
444	log.debug s;
445
446	// Determine a unique filename for this entry
447	def newfilename = this.getUniqueFilename( entry.getName(), outdir )
448
449	// Once we get the entry from the stream, the stream is
450	// positioned read to read the raw data, and we keep
451	// reading until read returns 0 or less.
452	File outpath = new File( outdir, newfilename );
453	FileOutputStream output = null;
454	try
455	{
456	output = new FileOutputStream(outpath);
457	int len = 0;
458	while ((len = stream.read(buffer)) > 0)
459	{
460	output.write(buffer, 0, len);
461	}
462
463	filenames << newfilename
464	} catch( Exception e ) {
465	// Delete the file if it exists
466	if( outpath?.exists() ) {
467	outpath.delete();
468	}
469	}
470	finally
471	{
472	// we must always close the output file
473	if(output!=null) output.close();
474	}
475
476	// Update progress
477	onProgress( 0, entry.getCompressedSize(), 1, outpath.length())
478	}
479	}
480	finally
481	{
482	// we must always close the zip file.
483	stream.close();
484	}
485
486	return filenames;
487	}
488
489	/**
490	* Extracts a GZip file
491	* @param f Zipfile to extract
492	* @return A list of extracted filenames; files can be found in the fileService temporary directory
493	*/
494	protected ArrayList extractGZip( File f, Closure onProgress ) {
495	return extractGZip( f, getUploadDir(), onProgress );
496	}
497
498	/**
499	* Extracts a GZip file
500	* @param f GZipfile to extract
501	* @param dir Directory to extract the files to
502	* @return A list of extracted filenames
503	*/
504	protected ArrayList extractGZip( File f, File outdir, Closure onProgress ) {
505	def filenames = [];
506
507	// open the input (compressed) file.
508	FileInputStream stream = new FileInputStream( f );
509	FileOutputStream output = null;
510	File outpath;
511
512	try
513	{
514	// open the gziped file to decompress.
515	GZIPInputStream gzipstream = new GZIPInputStream(stream);
516	byte[] buffer = new byte[2048];
517
518	// create the output file without the .gz extension.
519	String outname = f.getName()[0..f.getName().size()-3];
520	def newfilename = this.getUniqueFilename( outname, outdir )
521	outpath = new File( outdir, newfilename );
522	output = new FileOutputStream(outpath);
523
524	// and copy it to a new file
525	int len;
526	while((len = gzipstream.read(buffer))>0)
527	{
528	output.write(buffer, 0, len);
529	}
530
531	filenames << newfilename;
532
533	// Update progress
534	onProgress( 0, f.length(), 1, outpath.length())
535	} catch( Exception e ) {
536	// Delete the file if it exists
537	if( outpath?.exists() ) {
538	outpath.delete();
539	}
540	}
541	finally
542	{
543	// both streams must always be closed.
544	if(output != null) output.close();
545	stream.close();
546	}
547
548	return filenames;
549	}
550	}

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