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 <config.h>
65
66 #include <stdlib.h>
67 #include <stdio.h>
68 #include <string.h>
69 #include <unistd.h>
70 #include <limits.h>
71 #include <errno.h>
72 #include <sys/types.h>
73 #include <sys/stat.h>
74 #include "cram/os.h"
75 #ifndef PATH_MAX
76 # define PATH_MAX 1024
77 #endif
78
79 #include "cram/open_trace_file.h"
80 #include "cram/misc.h"
81 #include "htslib/hfile.h"
82 #include "htslib/hts_log.h"
83
84 /*
85 * Tokenises the search path splitting on colons (unix) or semicolons
86 * (windows).
87 * We also explicitly add a "./" to the end of the search path
88 *
89 * Returns: A new search path with items separated by nul chars. Two nul
90 * chars in a row represent the end of the tokenised path.
91 * Returns NULL for a failure.
92 *
93 * The returned data has been malloced. It is up to the caller to free this
94 * memory.
95 */
tokenise_search_path(char * searchpath)96 char *tokenise_search_path(char *searchpath) {
97 char *newsearch;
98 unsigned int i, j;
99 size_t len;
100 #ifdef _WIN32
101 char path_sep = ';';
102 #else
103 char path_sep = ':';
104 #endif
105
106 if (!searchpath)
107 searchpath="";
108
109 newsearch = (char *)malloc((len = strlen(searchpath))+5);
110 if (!newsearch)
111 return NULL;
112
113 for (i = 0, j = 0; i < len; i++) {
114 /* "::" => ":". Used for escaping colons in http://foo */
115 if (i < len-1 && searchpath[i] == ':' && searchpath[i+1] == ':') {
116 newsearch[j++] = ':';
117 i++;
118 continue;
119 }
120
121 /* Handle http:// and ftp:// too without :: */
122 if (path_sep == ':') {
123 if ((i == 0 || (i > 0 && searchpath[i-1] == ':')) &&
124 (!strncmp(&searchpath[i], "http:", 5) ||
125 !strncmp(&searchpath[i], "https:", 6) ||
126 !strncmp(&searchpath[i], "ftp:", 4) ||
127 !strncmp(&searchpath[i], "|http:", 6) ||
128 !strncmp(&searchpath[i], "|https:", 7) ||
129 !strncmp(&searchpath[i], "|ftp:", 5) ||
130 !strncmp(&searchpath[i], "URL=http:", 9) ||
131 !strncmp(&searchpath[i], "URL=https:",10)||
132 !strncmp(&searchpath[i], "URL=ftp:", 8))) {
133 do {
134 newsearch[j++] = searchpath[i];
135 } while (i<len && searchpath[i++] != ':');
136 if (searchpath[i] == ':')
137 i++;
138 if (searchpath[i]=='/')
139 newsearch[j++] = searchpath[i++];
140 if (searchpath[i]=='/')
141 newsearch[j++] = searchpath[i++];
142 // Look for host:port
143 do {
144 newsearch[j++] = searchpath[i++];
145 } while (i<len && searchpath[i] != ':' && searchpath[i] != '/');
146 newsearch[j++] = searchpath[i++];
147 if (searchpath[i] == ':')
148 i++;
149 }
150 }
151
152 if (searchpath[i] == path_sep) {
153 /* Skip blank path components */
154 if (j && newsearch[j-1] != 0)
155 newsearch[j++] = 0;
156 } else {
157 newsearch[j++] = searchpath[i];
158 }
159 }
160
161 if (j)
162 newsearch[j++] = 0;
163 newsearch[j++] = '.';
164 newsearch[j++] = '/';
165 newsearch[j++] = 0;
166 newsearch[j++] = 0;
167
168 return newsearch;
169 }
170
find_file_url(char * file,char * url)171 mFILE *find_file_url(char *file, char *url) {
172 char buf[8192], *cp;
173 mFILE *mf = NULL;
174 int maxlen = 8190 - strlen(file), len;
175 hFILE *hf;
176
177 /* Expand %s for the trace name */
178 for (cp = buf; *url && cp - buf < maxlen; url++) {
179 if (*url == '%' && *(url+1) == 's') {
180 url++;
181 cp += strlen(strcpy(cp, file));
182 } else {
183 *cp++ = *url;
184 }
185 }
186 *cp++ = 0;
187
188 if (!(hf = hopen(buf, "r"))) {
189 if (errno != ENOENT)
190 hts_log_warning("Failed to open reference \"%s\": %s", buf, strerror(errno));
191 return NULL;
192 }
193
194 if (NULL == (mf = mfcreate(NULL, 0)))
195 return NULL;
196 while ((len = hread(hf, buf, 8192)) > 0) {
197 if (mfwrite(buf, len, 1, mf) <= 0) {
198 hclose_abruptly(hf);
199 mfdestroy(mf);
200 return NULL;
201 }
202 }
203 if (hclose(hf) < 0 || len < 0) {
204 mfdestroy(mf);
205 return NULL;
206 }
207
208 mrewind(mf);
209 return mf;
210 }
211
212 /*
213 * Takes a dirname possibly including % rules and appends the filename
214 * to it.
215 *
216 * Returns expanded pathname or NULL for malloc failure.
217 */
expand_path(char * file,char * dirname)218 static char *expand_path(char *file, char *dirname) {
219 size_t len = strlen(dirname);
220 size_t lenf = strlen(file);
221 char *cp, *path;
222
223 path = malloc(len+lenf+2); // worst expansion DIR/FILE
224 if (!path)
225 return NULL;
226
227 if (dirname[len-1] == '/')
228 len--;
229
230 /* Special case for "./" or absolute filenames */
231 if (*file == '/' || (len==1 && *dirname == '.')) {
232 sprintf(path, "%s", file);
233 } else {
234 /* Handle %[0-9]*s expansions, if required */
235 char *path_end = path;
236 *path = 0;
237 while ((cp = strchr(dirname, '%'))) {
238 char *endp;
239 long l = strtol(cp+1, &endp, 10);
240 if (*endp != 's') {
241 strncpy(path_end, dirname, (endp+1)-dirname);
242 path_end += (endp+1)-dirname;
243 dirname = endp+1;
244 continue;
245 }
246
247 strncpy(path_end, dirname, cp-dirname);
248 path_end += cp-dirname;
249 if (l) {
250 strncpy(path_end, file, l);
251 path_end += MIN(strlen(file), l);
252 file += MIN(strlen(file), l);
253 } else {
254 strcpy(path_end, file);
255 path_end += strlen(file);
256 file += strlen(file);
257 }
258 len -= (endp+1) - dirname;
259 dirname = endp+1;
260 }
261 strncpy(path_end, dirname, len);
262 path_end += MIN(strlen(dirname), len);
263 *path_end = 0;
264 if (*file) {
265 *path_end++ = '/';
266 strcpy(path_end, file);
267 }
268 }
269
270 //fprintf(stderr, "*PATH=\"%s\"\n", path);
271 return path;
272 }
273
274 /*
275 * Searches for file in the directory 'dirname'. If it finds it, it opens
276 * it. This also searches for compressed versions of the file in dirname
277 * too.
278 *
279 * Returns mFILE pointer if found
280 * NULL if not
281 */
find_file_dir(char * file,char * dirname)282 static mFILE *find_file_dir(char *file, char *dirname) {
283 char *path;
284 mFILE *mf = NULL;
285
286 path = expand_path(file, dirname);
287
288 if (is_file(path))
289 mf = mfopen(path, "rbm");
290
291 free(path);
292 return mf;
293 }
294
295 /*
296 * ------------------------------------------------------------------------
297 * Public functions below.
298 */
299
300 /*
301 * Opens a trace file named 'file'. This is initially looked for as a
302 * pathname relative to a file named "relative_to". This may (for
303 * example) be the name of an experiment file referencing the trace
304 * file. In this case by passing relative_to as the experiment file
305 * filename the trace file will be picked up in the same directory as
306 * the experiment file. Relative_to may be supplied as NULL.
307 *
308 * 'file' is looked for at relative_to, then the current directory, and then
309 * all of the locations listed in 'path' (which is a colon separated list).
310 * If 'path' is NULL it uses the RAWDATA environment variable instead.
311 *
312 * Returns a mFILE pointer when found.
313 * NULL otherwise.
314 */
open_path_mfile(char * file,char * path,char * relative_to)315 mFILE *open_path_mfile(char *file, char *path, char *relative_to) {
316 char *newsearch;
317 char *ele;
318 mFILE *fp;
319
320 /* Use path first */
321 if (!path)
322 path = getenv("RAWDATA");
323 if (NULL == (newsearch = tokenise_search_path(path)))
324 return NULL;
325
326 /*
327 * Step through the search path testing out each component.
328 * We now look through each path element treating some prefixes as
329 * special, otherwise we treat the element as a directory.
330 */
331 for (ele = newsearch; *ele; ele += strlen(ele)+1) {
332 char *ele2;
333
334 /*
335 * '|' prefixing a path component indicates that we do not
336 * wish to perform the compression extension searching in that
337 * location.
338 *
339 * NB: this has been removed from the htslib implementation.
340 */
341 if (*ele == '|') {
342 ele2 = ele+1;
343 } else {
344 ele2 = ele;
345 }
346
347 if (0 == strncmp(ele2, "URL=", 4)) {
348 if ((fp = find_file_url(file, ele2+4))) {
349 free(newsearch);
350 return fp;
351 }
352 } else if (!strncmp(ele2, "http:", 5) ||
353 !strncmp(ele2, "https:", 6) ||
354 !strncmp(ele2, "ftp:", 4)) {
355 if ((fp = find_file_url(file, ele2))) {
356 free(newsearch);
357 return fp;
358 }
359 } else if ((fp = find_file_dir(file, ele2))) {
360 free(newsearch);
361 return fp;
362 }
363 }
364
365 free(newsearch);
366
367 /* Look in the same location as the incoming 'relative_to' filename */
368 if (relative_to) {
369 char *cp;
370 char relative_path[PATH_MAX+1];
371 strcpy(relative_path, relative_to);
372 if ((cp = strrchr(relative_path, '/')))
373 *cp = 0;
374 if ((fp = find_file_dir(file, relative_path)))
375 return fp;
376 }
377
378 return NULL;
379 }
380
381
382 /*
383 * As per open_path_mfile, but searching only for local filenames.
384 * This is useful as we may avoid doing a full mfopen and loading
385 * the entire file into memory.
386 *
387 * Returns the expanded pathname if found.
388 * NULL if not
389 */
find_path(char * file,char * path)390 char *find_path(char *file, char *path) {
391 char *newsearch;
392 char *ele;
393 char *outpath = NULL;
394
395 /* Use path first */
396 if (!path)
397 path = getenv("RAWDATA");
398 if (NULL == (newsearch = tokenise_search_path(path)))
399 return NULL;
400
401 for (ele = newsearch; *ele; ele += strlen(ele)+1) {
402 char *ele2 = (*ele == '|') ? ele+1 : ele;
403
404 if (!strncmp(ele2, "URL=", 4) ||
405 !strncmp(ele2, "http:", 5) ||
406 !strncmp(ele2, "https:", 6) ||
407 !strncmp(ele2, "ftp:", 4)) {
408 continue;
409 } else {
410 outpath = expand_path(file, ele2);
411 if (is_file(outpath)) {
412 free(newsearch);
413 return outpath;
414 } else {
415 free(outpath);
416 }
417 }
418 }
419
420 free(newsearch);
421
422 return NULL;
423 }
424