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comparison ezBAMQC/src/htslib/cram/open_trace_file.c @ 0:dfa3745e5fd8

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date Thu, 24 Mar 2016 17:12:52 -0400
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1 /*
2 Author: James Bonfield
3
4 Copyright (c) 2000-2001 MEDICAL RESEARCH COUNCIL
5 All rights reserved
6
7 Redistribution and use in source and binary forms, with or without
8 modification, are permitted provided that the following conditions are met:
9
10 1. Redistributions of source code must retain the above copyright notice,
11 this list of conditions and the following disclaimer.
12
13 2. Redistributions in binary form must reproduce the above copyright notice,
14 this list of conditions and the following disclaimer in the documentation
15 and/or other materials provided with the distribution.
16
17 3. Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF
18 MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or
19 promote products derived from this software without specific prior written
20 permission.
21
22 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
23 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
24 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
25 DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
26 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
27 (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
28 LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
29 ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
30 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
31 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
32 */
33
34 /*
35 Copyright (c) 2008, 2009, 2013, 2014 Genome Research Ltd.
36 Author: James Bonfield <jkb@sanger.ac.uk>
37
38 Redistribution and use in source and binary forms, with or without
39 modification, are permitted provided that the following conditions are met:
40
41 1. Redistributions of source code must retain the above copyright notice,
42 this list of conditions and the following disclaimer.
43
44 2. Redistributions in binary form must reproduce the above copyright notice,
45 this list of conditions and the following disclaimer in the documentation
46 and/or other materials provided with the distribution.
47
48 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
49 Institute nor the names of its contributors may be used to endorse or promote
50 products derived from this software without specific prior written permission.
51
52 THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
53 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
54 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
55 DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
56 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
57 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
58 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
59 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
60 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
61 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
62 */
63
64 #include <stdlib.h>
65 #include <stdio.h>
66 #include <string.h>
67 #include <unistd.h>
68 #include <ctype.h>
69 #include <limits.h>
70 #include <sys/types.h>
71 #include <sys/stat.h>
72 #include "cram/os.h"
73 #ifndef PATH_MAX
74 # define PATH_MAX 1024
75 #endif
76
77 #include "cram/open_trace_file.h"
78 #include "cram/misc.h"
79 #include "htslib/hfile.h"
80
81 /*
82 * Tokenises the search path splitting on colons (unix) or semicolons
83 * (windows).
84 * We also explicitly add a "./" to the end of the search path
85 *
86 * Returns: A new search path with items separated by nul chars. Two nul
87 * chars in a row represent the end of the tokenised path.
88 * Returns NULL for a failure.
89 *
90 * The returned data has been malloced. It is up to the caller to free this
91 * memory.
92 */
93 char *tokenise_search_path(char *searchpath) {
94 char *newsearch;
95 unsigned int i, j;
96 size_t len;
97 #ifdef _WIN32
98 char path_sep = ';';
99 #else
100 char path_sep = ':';
101 #endif
102
103 if (!searchpath)
104 searchpath="";
105
106 newsearch = (char *)malloc((len = strlen(searchpath))+5);
107 if (!newsearch)
108 return NULL;
109
110 for (i = 0, j = 0; i < len; i++) {
111 /* "::" => ":". Used for escaping colons in http://foo */
112 if (i < len-1 && searchpath[i] == ':' && searchpath[i+1] == ':') {
113 newsearch[j++] = ':';
114 i++;
115 continue;
116 }
117
118 /* Handle http:// and ftp:// too without :: */
119 if (path_sep == ':') {
120 if ((i == 0 || (i > 0 && searchpath[i-1] == ':')) &&
121 (!strncmp(&searchpath[i], "http:", 5) ||
122 !strncmp(&searchpath[i], "ftp:", 4) ||
123 !strncmp(&searchpath[i], "|http:", 6) ||
124 !strncmp(&searchpath[i], "|ftp:", 5) ||
125 !strncmp(&searchpath[i], "URL=http:", 9) ||
126 !strncmp(&searchpath[i], "URL=ftp:", 8))) {
127 do {
128 newsearch[j++] = searchpath[i];
129 } while (i<len && searchpath[i++] != ':');
130 if (searchpath[i] == ':')
131 i++;
132 if (searchpath[i]=='/')
133 newsearch[j++] = searchpath[i++];
134 if (searchpath[i]=='/')
135 newsearch[j++] = searchpath[i++];
136 // Look for host:port
137 do {
138 newsearch[j++] = searchpath[i++];
139 } while (i<len && searchpath[i] != ':' && searchpath[i] != '/');
140 newsearch[j++] = searchpath[i++];
141 if (searchpath[i] == ':')
142 i++;
143 }
144 }
145
146 if (searchpath[i] == path_sep) {
147 /* Skip blank path components */
148 if (j && newsearch[j-1] != 0)
149 newsearch[j++] = 0;
150 } else {
151 newsearch[j++] = searchpath[i];
152 }
153 }
154
155 if (j)
156 newsearch[j++] = 0;
157 newsearch[j++] = '.';
158 newsearch[j++] = '/';
159 newsearch[j++] = 0;
160 newsearch[j++] = 0;
161
162 return newsearch;
163 }
164
165 mFILE *find_file_url(char *file, char *url) {
166 char buf[8192], *cp;
167 mFILE *mf = NULL;
168 int maxlen = 8190 - strlen(file), len;
169 hFILE *hf;
170
171 /* Expand %s for the trace name */
172 for (cp = buf; *url && cp - buf < maxlen; url++) {
173 if (*url == '%' && *(url+1) == 's') {
174 url++;
175 cp += strlen(strcpy(cp, file));
176 } else {
177 *cp++ = *url;
178 }
179 }
180 *cp++ = 0;
181
182 if (!(hf = hopen(buf, "r")))
183 return NULL;
184
185 if (NULL == (mf = mfcreate(NULL, 0)))
186 return NULL;
187 while ((len = hread(hf, buf, 8192)) > 0) {
188 if (mfwrite(buf, len, 1, mf) <= 0) {
189 hclose_abruptly(hf);
190 mfdestroy(mf);
191 return NULL;
192 }
193 }
194 if (hclose(hf) < 0) {
195 mfdestroy(mf);
196 return NULL;
197 }
198
199 mrewind(mf);
200 return mf;
201 }
202
203 /*
204 * Searches for file in the directory 'dirname'. If it finds it, it opens
205 * it. This also searches for compressed versions of the file in dirname
206 * too.
207 *
208 * Returns mFILE pointer if found
209 * NULL if not
210 */
211 static mFILE *find_file_dir(char *file, char *dirname) {
212 char path[PATH_MAX+1];
213 size_t len = strlen(dirname);
214 char *cp;
215
216 if (dirname[len-1] == '/')
217 len--;
218
219 /* Special case for "./" or absolute filenames */
220 if (*file == '/' || (len==1 && *dirname == '.')) {
221 sprintf(path, "%s", file);
222 } else {
223 /* Handle %[0-9]*s expansions, if required */
224 char *path_end = path;
225 *path = 0;
226 while ((cp = strchr(dirname, '%'))) {
227 char *endp;
228 long l = strtol(cp+1, &endp, 10);
229 if (*endp != 's') {
230 strncpy(path_end, dirname, (endp+1)-dirname);
231 path_end += (endp+1)-dirname;
232 dirname = endp+1;
233 continue;
234 }
235
236 strncpy(path_end, dirname, cp-dirname);
237 path_end += cp-dirname;
238 if (l) {
239 strncpy(path_end, file, l);
240 path_end += MIN(strlen(file), l);
241 file += MIN(strlen(file), l);
242 } else {
243 strcpy(path_end, file);
244 path_end += strlen(file);
245 file += strlen(file);
246 }
247 len -= (endp+1) - dirname;
248 dirname = endp+1;
249 }
250 strncpy(path_end, dirname, len);
251 path_end += MIN(strlen(dirname), len);
252 *path_end = 0;
253 if (*file) {
254 *path_end++ = '/';
255 strcpy(path_end, file);
256 }
257
258 //fprintf(stderr, "*PATH=\"%s\"\n", path);
259 }
260
261 if (is_file(path)) {
262 return mfopen(path, "rb");
263 }
264
265 return NULL;
266 }
267
268 /*
269 * ------------------------------------------------------------------------
270 * Public functions below.
271 */
272
273 /*
274 * Opens a trace file named 'file'. This is initially looked for as a
275 * pathname relative to a file named "relative_to". This may (for
276 * example) be the name of an experiment file referencing the trace
277 * file. In this case by passing relative_to as the experiment file
278 * filename the trace file will be picked up in the same directory as
279 * the experiment file. Relative_to may be supplied as NULL.
280 *
281 * 'file' is looked for at relative_to, then the current directory, and then
282 * all of the locations listed in 'path' (which is a colon separated list).
283 * If 'path' is NULL it uses the RAWDATA environment variable instead.
284 *
285 * Returns a mFILE pointer when found.
286 * NULL otherwise.
287 */
288 mFILE *open_path_mfile(char *file, char *path, char *relative_to) {
289 char *newsearch;
290 char *ele;
291 mFILE *fp;
292
293 /* Use path first */
294 if (!path)
295 path = getenv("RAWDATA");
296 if (NULL == (newsearch = tokenise_search_path(path)))
297 return NULL;
298
299 /*
300 * Step through the search path testing out each component.
301 * We now look through each path element treating some prefixes as
302 * special, otherwise we treat the element as a directory.
303 */
304 for (ele = newsearch; *ele; ele += strlen(ele)+1) {
305 char *ele2;
306
307 /*
308 * '|' prefixing a path component indicates that we do not
309 * wish to perform the compression extension searching in that
310 * location.
311 *
312 * NB: this has been removed from the htslib implementation.
313 */
314 if (*ele == '|') {
315 ele2 = ele+1;
316 } else {
317 ele2 = ele;
318 }
319
320 if (0 == strncmp(ele2, "URL=", 4)) {
321 if ((fp = find_file_url(file, ele2+4))) {
322 free(newsearch);
323 return fp;
324 }
325 } else if (!strncmp(ele2, "http:", 5) ||
326 !strncmp(ele2, "ftp:", 4)) {
327 if ((fp = find_file_url(file, ele2))) {
328 free(newsearch);
329 return fp;
330 }
331 } else if ((fp = find_file_dir(file, ele2))) {
332 free(newsearch);
333 return fp;
334 }
335 }
336
337 free(newsearch);
338
339 /* Look in the same location as the incoming 'relative_to' filename */
340 if (relative_to) {
341 char *cp;
342 char relative_path[PATH_MAX+1];
343 strcpy(relative_path, relative_to);
344 if ((cp = strrchr(relative_path, '/')))
345 *cp = 0;
346 if ((fp = find_file_dir(file, relative_path)))
347 return fp;
348 }
349
350 return NULL;
351 }