Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FileUtils	44	110	53	0.00%	Show methods

Class FileUtils

Class FileUtils	Line # 44	Total Statements 110	Complexity 53	TOTAL Coverage 0.00%
getFilesFromGlob(String) : List<File>   getFilesFromGlob(String) : List<File>	5252	1.01	1.01	0.0 0.00%
visitFile(Path,BasicFileAttributes) : FileVisitResult   visitFile(Path,BasicFileAttributes) : FileVisitResult	108108	3.03	2.02	0.0 0.00%
visitFileFailed(Path,IOException) : FileVisitResult   visitFileFailed(Path,IOException) : FileVisitResult	119119	1.01	1.01	0.0 0.00%
getFilesFromGlob(String,boolean) : List<File>   getFilesFromGlob(String,boolean) : List<File>	5757	28.028	12.012	0.0 0.00%
getFilenamesFromGlob(String) : List<String>   getFilenamesFromGlob(String) : List<String>	146146	1.01	1.01	0.0 0.00%
substituteHomeDir(String) : String   substituteHomeDir(String) : String	153153	1.01	2.02	0.0 0.00%
getBasename(File) : String   getBasename(File) : String	163163	1.01	1.01	0.0 0.00%
getExtension(File) : String   getExtension(File) : String	171171	1.01	1.01	0.0 0.00%
getBasenameOrExtension(File,boolean) : String   getBasenameOrExtension(File,boolean) : String	176176	9.09	5.05	0.0 0.00%
getDirname(File) : String   getDirname(File) : String	200200	9.09	3.03	0.0 0.00%
convertWildcardsToPath(String,String,String,String) : String   convertWildcardsToPath(String,String,String,String) : String	216216	17.017	5.05	0.0 0.00%
getParentDir(File) : File   getParentDir(File) : File	254254	4.04	2.02	0.0 0.00%
checkParentDir(File,boolean) : boolean   checkParentDir(File,boolean) : boolean	264264	14.014	6.06	0.0 0.00%
getExtension(String) : String   getExtension(String) : String	304304	1.01	1.01	0.0 0.00%
getBase(String) : String   getBase(String) : String	319319	1.01	1.01	0.0 0.00%
getBaseOrExtension(String,boolean) : String   getBaseOrExtension(String,boolean) : String	324324	18.018	9.09	0.0 0.00%

 

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1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.util;
22
23		import java.io.File;
24		import java.io.IOException;
25		import java.net.MalformedURLException;
26		import java.net.URL;
27		import java.nio.file.FileSystems;
28		import java.nio.file.FileVisitOption;
29		import java.nio.file.FileVisitResult;
30		import java.nio.file.Files;
31		import java.nio.file.Path;
32		import java.nio.file.PathMatcher;
33		import java.nio.file.Paths;
34		import java.nio.file.SimpleFileVisitor;
35		import java.nio.file.attribute.BasicFileAttributes;
36		import java.util.ArrayList;
37		import java.util.Collections;
38		import java.util.EnumSet;
39		import java.util.List;
40		import java.util.stream.Collectors;
41
42		import jalview.bin.Console;
43
		0% Uncovered Elements: 186 (186) Complexity: 53 Complexity Density: 0.48
44		public class FileUtils
45		{
46		/*
47		* Given string glob pattern (see
48		* https://docs.oracle.com/javase/7/docs/api/java/nio/file/FileSystem.html#getPathMatcher(java.lang.String)
49		* ) return a List of Files that match the pattern.
50		* Note this is a java style glob, not necessarily a bash-style glob, though there are sufficient similarities.
51		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
52	0	public static List<File> getFilesFromGlob(String pattern)...
53		{
54	0	return getFilesFromGlob(pattern, true);
55		}
56
		0% Uncovered Elements: 42 (42) Complexity: 12 Complexity Density: 0.43
57	0	public static List<File> getFilesFromGlob(String pattern,...
58		boolean allowSingleFilenameThatDoesNotExist)
59		{
60	0	pattern = substituteHomeDir(pattern);
61	0	String relativePattern = pattern.startsWith(File.separator) ? null
62		: pattern;
63	0	List<File> files = new ArrayList<>();
64		/*
65		* For efficiency of the Files.walkFileTree(), let's find the longest path that doesn't need globbing.
66		* We look for the first glob character * { ? and then look for the last File.separator before that.
67		* Then we can reset the path to look at and shorten the globbing pattern.
68		* Relative paths can be used in pattern, which work from the pwd (though these are converted into
69		* full paths in the match).
70		*/
71	0	int firstGlobChar = -1;
72	0	boolean foundGlobChar = false;
73	0	for (char c : new char[] { '*', '{', '?' })
74		{
75	0	if (pattern.indexOf(c) > -1
76		&& (pattern.indexOf(c) < firstGlobChar || !foundGlobChar))
77		{
78	0	firstGlobChar = pattern.indexOf(c);
79	0	foundGlobChar = true;
80		}
81		}
82	0	int lastFS = pattern.lastIndexOf(File.separatorChar, firstGlobChar);
83	0	if (foundGlobChar)
84		{
85	0	String pS = pattern.substring(0, lastFS + 1);
86	0	String rest = pattern.substring(lastFS + 1);
87	0	if ("".equals(pS))
88		{
89	0	pS = ".";
90		}
91	0	Path parentDir = Paths.get(pS);
92	0	if (parentDir.toFile().exists())
93		{
94	0	try
95		{
96	0	String glob = "glob:" + parentDir.toString() + File.separator
97		+ rest;
98	0	PathMatcher pm = FileSystems.getDefault().getPathMatcher(glob);
99	0	int maxDepth = rest.contains("**") ? 1028
100		: (int) (rest.chars()
101		.filter(ch -> ch == File.separatorChar).count())
102		+ 1;
103
104	0	Files.walkFileTree(parentDir,
105		EnumSet.of(FileVisitOption.FOLLOW_LINKS), maxDepth,
106		new SimpleFileVisitor<Path>()
107		{
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
108	0	@Override...
109		public FileVisitResult visitFile(Path path,
110		BasicFileAttributes attrs) throws IOException
111		{
112	0	if (pm.matches(path))
113		{
114	0	files.add(path.toFile());
115		}
116	0	return FileVisitResult.CONTINUE;
117		}
118
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
119	0	@Override...
120		public FileVisitResult visitFileFailed(Path file,
121		IOException exc) throws IOException
122		{
123	0	return FileVisitResult.CONTINUE;
124		}
125		});
126		} catch (IOException e)
127		{
128	0	e.printStackTrace();
129		}
130		}
131		}
132		else
133		{
134		// no wildcards
135	0	File f = new File(pattern);
136	0	if (allowSingleFilenameThatDoesNotExist || f.exists())
137		{
138	0	files.add(f);
139		}
140		}
141	0	Collections.sort(files);
142
143	0	return files;
144		}
145
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
146	0	public static List<String> getFilenamesFromGlob(String pattern)...
147		{
148		// convert list of Files to list of File.getPath() Strings
149	0	return getFilesFromGlob(pattern).stream().map(f -> f.getPath())
150		.collect(Collectors.toList());
151		}
152
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
153	0	public static String substituteHomeDir(String path)...
154		{
155	0	return path.startsWith("~" + File.separator)
156		? System.getProperty("user.home") + path.substring(1)
157		: path;
158		}
159
160		/*
161		* This method returns the basename of File file
162		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
163	0	public static String getBasename(File file)...
164		{
165	0	return getBasenameOrExtension(file, false);
166		}
167
168		/*
169		* This method returns the extension of File file.
170		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
171	0	public static String getExtension(File file)...
172		{
173	0	return getBasenameOrExtension(file, true);
174		}
175
		0% Uncovered Elements: 17 (17) Complexity: 5 Complexity Density: 0.56
176	0	public static String getBasenameOrExtension(File file, boolean extension)...
177		{
178	0	if (file == null)
179	0	return null;
180
181	0	String value = null;
182	0	String filename = file.getName();
183	0	int lastDot = filename.lastIndexOf('.');
184	0	if (lastDot > 0) // don't truncate if starts with '.'
185		{
186	0	value = extension ? filename.substring(lastDot + 1)
187		: filename.substring(0, lastDot);
188		}
189		else
190		{
191	0	value = extension ? "" : filename;
192		}
193	0	return value;
194		}
195
196		/*
197		* This method returns the dirname of the first --append or --open value.
198		* Used primarily for substitutions in output filenames.
199		*/
		0% Uncovered Elements: 13 (13) Complexity: 3 Complexity Density: 0.33
200	0	public static String getDirname(File file)...
201		{
202	0	if (file == null)
203	0	return null;
204
205	0	String dirname = null;
206	0	File p = file.getParentFile();
207	0	if (p == null)
208		{
209	0	p = new File(".");
210		}
211	0	File d = new File(substituteHomeDir(p.getPath()));
212	0	dirname = d.getPath();
213	0	return dirname;
214		}
215
		0% Uncovered Elements: 23 (23) Complexity: 5 Complexity Density: 0.29
216	0	public static String convertWildcardsToPath(String value, String wildcard,...
217		String dirname, String basename)
218		{
219	0	if (value == null)
220		{
221	0	return null;
222		}
223	0	StringBuilder path = new StringBuilder();
224	0	int lastFileSeparatorIndex = value.lastIndexOf(File.separatorChar);
225	0	int wildcardBeforeIndex = value.indexOf(wildcard);
226	0	if (lastFileSeparatorIndex > wildcard.length() - 1
227		&& wildcardBeforeIndex < lastFileSeparatorIndex)
228		{
229	0	path.append(value.substring(0, wildcardBeforeIndex));
230	0	path.append(dirname);
231	0	path.append(value.substring(wildcardBeforeIndex + wildcard.length(),
232		lastFileSeparatorIndex + 1));
233		}
234		else
235		{
236	0	path.append(value.substring(0, lastFileSeparatorIndex + 1));
237		}
238	0	int wildcardAfterIndex = value.indexOf(wildcard,
239		lastFileSeparatorIndex);
240	0	if (wildcardAfterIndex > lastFileSeparatorIndex)
241		{
242	0	path.append(value.substring(lastFileSeparatorIndex + 1,
243		wildcardAfterIndex));
244	0	path.append(basename);
245	0	path.append(value.substring(wildcardAfterIndex + wildcard.length()));
246		}
247		else
248		{
249	0	path.append(value.substring(lastFileSeparatorIndex + 1));
250		}
251	0	return path.toString();
252		}
253
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
254	0	public static File getParentDir(File file)...
255		{
256	0	if (file == null)
257		{
258	0	return null;
259		}
260	0	File parentDir = file.getAbsoluteFile().getParentFile();
261	0	return parentDir;
262		}
263
		0% Uncovered Elements: 24 (24) Complexity: 6 Complexity Density: 0.43
264	0	public static boolean checkParentDir(File file, boolean mkdirs)...
265		{
266	0	if (file == null)
267		{
268	0	return false;
269		}
270	0	File parentDir = getParentDir(file);
271	0	if (parentDir.exists())
272		{
273		// already exists, nothing to do so nothing to worry about!
274	0	return true;
275		}
276
277	0	if (!mkdirs)
278		{
279	0	return false;
280		}
281
282	0	Path path = file.toPath();
283	0	for (int i = 0; i < path.getNameCount(); i++)
284		{
285	0	Path p = path.getName(i);
286	0	if ("..".equals(p.toString()))
287		{
288	0	Console.warn("Cautiously not running mkdirs on " + file.toString()
289		+ " because the path to be made contains '..'");
290	0	return false;
291		}
292		}
293
294	0	return parentDir.mkdirs();
295		}
296
297		/**
298		* get a guessed file extension from a String only
299		*
300		* @param String
301		* filename
302		* @return String extension
303		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
304	0	public static String getExtension(String filename)...
305		{
306	0	return getBaseOrExtension(filename, true);
307		}
308
309		/**
310		* getBase returns everything in a path/URI up to (and including) an extension
311		* dot. Note this is not the same as getBasename() since getBasename() only
312		* gives the filename base, not the path too. If no extension dot is found
313		* (i.e. a dot in character position 2 or more of the filename (after the last
314		* slash) then the whole path is considered the base.
315		*
316		* @param filename
317		* @return String base
318		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
319	0	public static String getBase(String filename)...
320		{
321	0	return getBaseOrExtension(filename, false);
322		}
323
		0% Uncovered Elements: 30 (30) Complexity: 9 Complexity Density: 0.5
324	0	public static String getBaseOrExtension(String filename0,...
325		boolean extension)
326		{
327	0	if (filename0 == null)
328		{
329	0	return null;
330		}
331	0	String filename = filename0;
332	0	boolean isUrl = false;
333	0	if (HttpUtils.startsWithHttpOrHttps(filename))
334		{
335	0	try
336		{
337	0	URL url = new URL(filename);
338	0	filename = url.getPath();
339	0	isUrl = true;
340		} catch (MalformedURLException e)
341		{
342		// continue to treat as a filename
343		}
344		}
345	0	int dot = filename.lastIndexOf('.');
346	0	int slash = filename.lastIndexOf('/');
347	0	if (!File.separator.equals("/") && !isUrl)
348		{
349	0	slash = filename.lastIndexOf(File.separator);
350		}
351		// only the dot of the filename (not dots in path) and not if it's a .hidden
352		// file
353	0	boolean hasExtension = dot > slash + 1;
354	0	if (extension)
355		{
356	0	return hasExtension ? filename.substring(dot + 1) : null;
357		}
358		else
359		{
360	0	dot = filename0.lastIndexOf('.');
361	0	return hasExtension ? filename0.substring(0, dot + 1) : filename0;
362		}
363		}
364		}