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