add patch to use Debian paths for resources
Sascha Steinbiss
4 years ago
| 0 | --- a/src/gth/bssm_param.c | |
| 1 | +++ b/src/gth/bssm_param.c | |
| 2 | @@ -29,6 +29,7 @@ | |
| 3 | #include "gth/gthprobdef.h" | |
| 4 | #include "gth/gthspeciestab.h" | |
| 5 | #include "gth/showbool.h" | |
| 6 | +#include "libgenomethreader/findfile.h" | |
| 7 | ||
| 8 | /* | |
| 9 | This is a collection of functions associated with | |
| 10 | @@ -451,42 +452,7 @@ | |
| 11 | if (gt_file_exists(filename)) | |
| 12 | gt_str_append_cstr(path, filename); | |
| 13 | else { | |
| 14 | - if (strchr(filename, GT_PATH_SEPARATOR)) { | |
| 15 | - gt_error_set(err, "filename \"%s\" contains illegal symbol '%c': the " | |
| 16 | - "path list specified by environment variable \"%s\" " | |
| 17 | - "cannot be searched for it", filename, | |
| 18 | - GT_PATH_SEPARATOR, BSSMENVNAME); | |
| 19 | - had_err = -1; | |
| 20 | - } | |
| 21 | - /* check for file path in environment variable */ | |
| 22 | - if (!had_err) | |
| 23 | - had_err = gt_file_find_in_env(path, filename, BSSMENVNAME, err); | |
| 24 | - if (!had_err && !gt_str_length(path)) { | |
| 25 | - gt_error_set(err, "file \"%s\" not found in directory list specified " | |
| 26 | - "by environment variable %s", filename, BSSMENVNAME); | |
| 27 | - had_err = -1; | |
| 28 | - } | |
| 29 | - if (!had_err) { | |
| 30 | - /* path found -> append filename */ | |
| 31 | - gt_str_append_char(path, GT_PATH_SEPARATOR); | |
| 32 | - gt_str_append_cstr(path, filename); | |
| 33 | - } | |
| 34 | - else { | |
| 35 | - /* check for file path relative to binary */ | |
| 36 | - int new_err = gt_file_find_exec_in_path(path, gt_error_get_progname(err), | |
| 37 | - NULL); | |
| 38 | - if (!new_err) { | |
| 39 | - gt_assert(gt_str_length(path)); | |
| 40 | - gt_str_append_char(path, GT_PATH_SEPARATOR); | |
| 41 | - gt_str_append_cstr(path, "bssm"); | |
| 42 | - gt_str_append_char(path, GT_PATH_SEPARATOR); | |
| 43 | - gt_str_append_cstr(path, filename); | |
| 44 | - if (gt_file_exists(gt_str_get(path))) { | |
| 45 | - gt_error_unset(err); | |
| 46 | - had_err = 0; | |
| 47 | - } | |
| 48 | - } | |
| 49 | - } | |
| 50 | + had_err = gth_find_file(filename, BSSMENVNAME, "bssm", path, err); | |
| 51 | } | |
| 52 | ||
| 53 | if (!had_err) { | |
| 54 | --- a/src/gth/input.c | |
| 55 | +++ b/src/gth/input.c | |
| 56 | @@ -30,6 +30,7 @@ | |
| 57 | #include "gth/input.h" | |
| 58 | #include "gth/md5_cache.h" | |
| 59 | #include "gth/parse_options.h" | |
| 60 | +#include "libgenomethreader/findfile.h" | |
| 61 | ||
| 62 | #define GTHFORWARD 1 /* run program to match forward */ | |
| 63 | #define GTHREVERSE (1 << 1) /* run program to match reverse */ | |
| 64 | @@ -653,45 +654,14 @@ | |
| 65 | { | |
| 66 | GtStr *path = gt_str_new(); | |
| 67 | int had_err = 0; | |
| 68 | + | |
| 69 | if (gt_file_exists(scorematrixfile)) { | |
| 70 | gt_str_set(path, scorematrixfile); | |
| 71 | return path; | |
| 72 | } | |
| 73 | - if (strchr(scorematrixfile, GT_PATH_SEPARATOR)) { | |
| 74 | - gt_error_set(err, "filename \"%s\" contains illegal symbol '%c': the path " | |
| 75 | - "list specified by environment variable \"%s\" cannot be " | |
| 76 | - "searched for it", scorematrixfile, GT_PATH_SEPARATOR, | |
| 77 | - GTHDATAENVNAME); | |
| 78 | - had_err = -1; | |
| 79 | - } | |
| 80 | - if (!had_err) | |
| 81 | - had_err = gt_file_find_in_env(path, scorematrixfile, GTHDATAENVNAME, err); | |
| 82 | - if (!had_err && !gt_str_length(path)) { | |
| 83 | - gt_error_set(err, "file \"%s\" not found in directory list specified by " | |
| 84 | - "environment variable %s", scorematrixfile, GTHDATAENVNAME); | |
| 85 | - had_err = -1; | |
| 86 | - } | |
| 87 | - if (!had_err) { | |
| 88 | - gt_assert(gt_str_length(path)); | |
| 89 | - /* path found -> append score matrix file name */ | |
| 90 | - gt_str_append_char(path, GT_PATH_SEPARATOR); | |
| 91 | - gt_str_append_cstr(path, scorematrixfile); | |
| 92 | - } | |
| 93 | - else { | |
| 94 | - /* check for file relative to binary */ | |
| 95 | - int new_err = gt_file_find_exec_in_path(path, gt_error_get_progname(err), | |
| 96 | - NULL); | |
| 97 | - if (!new_err) { | |
| 98 | - gt_str_append_char(path, GT_PATH_SEPARATOR); | |
| 99 | - gt_str_append_cstr(path, GTHDATADIRNAME); | |
| 100 | - gt_str_append_char(path, GT_PATH_SEPARATOR); | |
| 101 | - gt_str_append_cstr(path, scorematrixfile); | |
| 102 | - if (gt_file_exists(gt_str_get(path))) { | |
| 103 | - gt_error_unset(err); | |
| 104 | - had_err = 0; | |
| 105 | - } | |
| 106 | - } | |
| 107 | - } | |
| 108 | + | |
| 109 | + had_err = gth_find_file(scorematrixfile, GTHDATAENVNAME, GTHDATADIRNAME, path, | |
| 110 | + err); | |
| 111 | if (had_err) { | |
| 112 | gt_str_delete(path); | |
| 113 | return NULL; | |
| 114 | --- /dev/null | |
| 115 | +++ b/src/libgenomethreader/findfile.c | |
| 116 | @@ -0,0 +1,74 @@ | |
| 117 | +/* | |
| 118 | + Copyright (c) 2020 Sascha Steinbiss <sascha@steinbiss.name> | |
| 119 | + | |
| 120 | + Permission to use, copy, modify, and distribute this software for any | |
| 121 | + purpose with or without fee is hereby granted, provided that the above | |
| 122 | + copyright notice and this permission notice appear in all copies. | |
| 123 | + | |
| 124 | + THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES | |
| 125 | + WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF | |
| 126 | + MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR | |
| 127 | + ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES | |
| 128 | + WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN | |
| 129 | + ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF | |
| 130 | + OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. | |
| 131 | +*/ | |
| 132 | + | |
| 133 | +#include "findfile.h" | |
| 134 | +#include "core/fileutils_api.h" | |
| 135 | +#include "core/compat_api.h" | |
| 136 | + | |
| 137 | +int gth_find_file(const char *filename, const char *envname, | |
| 138 | + const char *dirname, GtStr *out, GtError *err) | |
| 139 | +{ | |
| 140 | + int had_err = 0; | |
| 141 | + const char **defaultpath; | |
| 142 | + static const char *defaultpaths[] = { | |
| 143 | + "/usr/share/genomethreader", | |
| 144 | + "/usr/local/share/genomethreader", | |
| 145 | + "/usr/lib/genomethreader", | |
| 146 | + "/usr/local/lib/genomethreader", | |
| 147 | + NULL | |
| 148 | + }; | |
| 149 | + | |
| 150 | + gt_str_reset(out); | |
| 151 | + /* check in directory given by envname */ | |
| 152 | + if (getenv(envname)) { | |
| 153 | + gt_str_append_cstr(out, getenv(envname)); | |
| 154 | + gt_str_append_char(out, GT_PATH_SEPARATOR); | |
| 155 | + gt_str_append_cstr(out, filename); | |
| 156 | + if (gt_file_exists(gt_str_get(out))) { | |
| 157 | + return 0; | |
| 158 | + } | |
| 159 | + } | |
| 160 | + | |
| 161 | + /* check for file relative to binary */ | |
| 162 | + gt_str_reset(out); | |
| 163 | + had_err = gt_file_find_exec_in_path(out, gt_error_get_progname(err), NULL); | |
| 164 | + if (!had_err) { | |
| 165 | + gt_str_append_char(out, GT_PATH_SEPARATOR); | |
| 166 | + gt_str_append_cstr(out, dirname); | |
| 167 | + gt_str_append_char(out, GT_PATH_SEPARATOR); | |
| 168 | + gt_str_append_cstr(out, filename); | |
| 169 | + if (gt_file_exists(gt_str_get(out))) { | |
| 170 | + return 0; | |
| 171 | + } | |
| 172 | + } | |
| 173 | + | |
| 174 | + /* check for file in set of default paths */ | |
| 175 | + for (defaultpath = defaultpaths; *defaultpath; defaultpath++) { | |
| 176 | + gt_str_reset(out); | |
| 177 | + gt_str_append_cstr(out, *defaultpath); | |
| 178 | + gt_str_append_char(out, GT_PATH_SEPARATOR); | |
| 179 | + gt_str_append_cstr(out, dirname); | |
| 180 | + gt_str_append_char(out, GT_PATH_SEPARATOR); | |
| 181 | + gt_str_append_cstr(out, filename); | |
| 182 | + if (gt_file_exists(gt_str_get(out))) { | |
| 183 | + return 0; | |
| 184 | + } | |
| 185 | + } | |
| 186 | + | |
| 187 | + gt_error_set(err, "could not find file '%s' in any of the search paths", | |
| 188 | + filename); | |
| 189 | + return -1; | |
| 190 | +} | |
| 191 | --- /dev/null | |
| 192 | +++ b/src/libgenomethreader/findfile.h | |
| 193 | @@ -0,0 +1,26 @@ | |
| 194 | +/* | |
| 195 | + Copyright (c) 2020 Sascha Steinbiss <sascha@steinbiss.name> | |
| 196 | + | |
| 197 | + Permission to use, copy, modify, and distribute this software for any | |
| 198 | + purpose with or without fee is hereby granted, provided that the above | |
| 199 | + copyright notice and this permission notice appear in all copies. | |
| 200 | + | |
| 201 | + THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES | |
| 202 | + WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF | |
| 203 | + MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR | |
| 204 | + ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES | |
| 205 | + WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN | |
| 206 | + ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF | |
| 207 | + OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. | |
| 208 | +*/ | |
| 209 | + | |
| 210 | +#ifndef GTH_FINDFILE_H | |
| 211 | +#define GTH_FINDFILE_H | |
| 212 | + | |
| 213 | +#include "core/str_api.h" | |
| 214 | +#include "core/error_api.h" | |
| 215 | + | |
| 216 | +int gth_find_file(const char *filename, const char *envname, | |
| 217 | + const char *dirname, GtStr *out, GtError *err); | |
| 218 | + | |
| 219 | +#endif | |
| 220 | --- a/src/libgenomethreader/gthmkvtree.c | |
| 221 | +++ b/src/libgenomethreader/gthmkvtree.c | |
| 222 | @@ -6,6 +6,7 @@ | |
| 223 | #include "core/ma_api.h" | |
| 224 | #include "gth/gthdef.h" | |
| 225 | #include "gth/gthoutput.h" | |
| 226 | +#include "libgenomethreader/findfile.h" | |
| 227 | #include "libgenomethreader/gthmkvtree.h" | |
| 228 | #include "types.h" | |
| 229 | #include "virtualdef.h" | |
| 230 | @@ -52,39 +53,14 @@ | |
| 231 | { | |
| 232 | int rval, had_err = 0; | |
| 233 | gt_error_check(err); | |
| 234 | - if (!getenv(GTHDATAENVNAME)) { | |
| 235 | - gt_error_set(err, "$%s not defined. Please set correctly", GTHDATAENVNAME); | |
| 236 | - had_err = -1; | |
| 237 | - } | |
| 238 | + | |
| 239 | + GtStr *path = gt_str_new(); | |
| 240 | + had_err = gth_find_file(mapping, GTHDATAENVNAME, GTHDATADIRNAME, path, err); | |
| 241 | if (!had_err) { | |
| 242 | - rval = snprintf(smapfile, PATH_MAX+1, "%s%c%s", getenv(GTHDATAENVNAME), | |
| 243 | - GT_PATH_SEPARATOR, mapping); | |
| 244 | - gt_assert(rval < PATH_MAX + 1); | |
| 245 | - if (!gt_file_exists(smapfile)) { | |
| 246 | - gt_error_set(err, "cannot open smap file '%s'", smapfile); | |
| 247 | - had_err = -1; | |
| 248 | - } | |
| 249 | - } | |
| 250 | - if (had_err) { | |
| 251 | - /* check for file relative to binary */ | |
| 252 | - GtStr *path; | |
| 253 | - int new_err; | |
| 254 | - path = gt_str_new(); | |
| 255 | - new_err = gt_file_find_exec_in_path(path, gt_error_get_progname(err), NULL); | |
| 256 | - if (!new_err) { | |
| 257 | - gt_str_append_char(path, GT_PATH_SEPARATOR); | |
| 258 | - gt_str_append_cstr(path, GTHDATADIRNAME); | |
| 259 | - gt_str_append_char(path, GT_PATH_SEPARATOR); | |
| 260 | - gt_str_append_cstr(path, mapping); | |
| 261 | - if (gt_file_exists(gt_str_get(path))) { | |
| 262 | - rval = snprintf(smapfile, PATH_MAX+1, "%s", gt_str_get(path)); | |
| 263 | - gt_assert(rval < PATH_MAX + 1); | |
| 264 | - gt_error_unset(err); | |
| 265 | - had_err = 0; | |
| 266 | - } | |
| 267 | - } | |
| 268 | - gt_str_delete(path); | |
| 269 | + rval = snprintf(smapfile, PATH_MAX+1, "%s", gt_str_get(path)); | |
| 270 | + gt_assert(rval < PATH_MAX + 1); | |
| 271 | } | |
| 272 | + gt_str_delete(path); | |
| 273 | return had_err; | |
| 274 | } | |
| 275 | ||
| 276 | --- a/src/libgenomethreader/gthpre.c | |
| 277 | +++ b/src/libgenomethreader/gthpre.c | |
| 278 | @@ -11,6 +11,7 @@ | |
| 279 | #include "gth/gthdef.h" | |
| 280 | #include "gth/gthoutput.h" | |
| 281 | #include "gth/input.h" | |
| 282 | +#include "libgenomethreader/findfile.h" | |
| 283 | #include "libgenomethreader/gthmkvtree.h" | |
| 284 | #include "libgenomethreader/gthpolyafunc.h" | |
| 285 | #include "libgenomethreader/gthpre.h" | |
| 286 | @@ -301,49 +302,22 @@ | |
| 287 | ||
| 288 | /* create masked file if necessary */ | |
| 289 | if (createmaskedfile) { | |
| 290 | - sprintf(dnafilename, "%s.%s", POLYA_FASTAFILENAME, DNASUFFIX); | |
| 291 | - /* check if polyatail.dna exists */ | |
| 292 | - fp = scanpathsforfile(GTHDATAENVNAME, dnafilename); /* XXX */ | |
| 293 | - if (!fp) { | |
| 294 | - gt_error_set(err, "file \"%s\" not found in $%s. Set correctly?", | |
| 295 | - dnafilename, GTHDATAENVNAME); | |
| 296 | - had_err = -1; | |
| 297 | - } | |
| 298 | - if (!had_err /* XXX */ && DELETEFILEHANDLE(fp)) { | |
| 299 | - fprintf(stderr,"%s\n", messagespace()); | |
| 300 | - exit(EXIT_FAILURE); | |
| 301 | - } | |
| 302 | - | |
| 303 | - /* call vmatch and save masked file */ | |
| 304 | - if (!had_err && !getenv(GTHDATAENVNAME)) { | |
| 305 | - gt_error_set(err, "$%s not defined. Please set correctly", | |
| 306 | - GTHDATAENVNAME); | |
| 307 | - had_err = -1; | |
| 308 | - } | |
| 309 | + int rval = 0; | |
| 310 | + GtStr *path = gt_str_new(); | |
| 311 | ||
| 312 | + sprintf(dnafilename, "%s.%s", POLYA_FASTAFILENAME, DNASUFFIX); | |
| 313 | + had_err = gth_find_file(dnafilename, GTHDATAENVNAME, GTHDATADIRNAME, path, | |
| 314 | + err); | |
| 315 | if (!had_err) { | |
| 316 | - sprintf(dnafilename, "%s%c%s", getenv(GTHDATAENVNAME), GT_PATH_SEPARATOR, | |
| 317 | - POLYA_FASTAFILENAME); | |
| 318 | - } | |
| 319 | - else { | |
| 320 | - /* check for file relative to binary */ | |
| 321 | - GtStr *path; | |
| 322 | - int new_err; | |
| 323 | - path = gt_str_new(); | |
| 324 | - new_err = gt_file_find_exec_in_path(path, gt_error_get_progname(err), | |
| 325 | - NULL); | |
| 326 | - if (!new_err) { | |
| 327 | - gt_str_append_char(path, GT_PATH_SEPARATOR); | |
| 328 | - gt_str_append_cstr(path, GTHDATADIRNAME); | |
| 329 | - if (gt_file_exists_and_is_dir(gt_str_get(path))) { | |
| 330 | - sprintf(dnafilename, "%s%c%s", gt_str_get(path), GT_PATH_SEPARATOR, | |
| 331 | - POLYA_FASTAFILENAME); | |
| 332 | - gt_error_unset(err); | |
| 333 | - had_err = 0; | |
| 334 | - } | |
| 335 | - } | |
| 336 | + rval = snprintf(dnafilename, PATH_MAX+1, "%s", gt_str_get(path)); | |
| 337 | + gt_assert(rval < PATH_MAX + 1); | |
| 338 | + /* clip off DNASUFFIX */ | |
| 339 | + gt_assert(strlen(dnafilename) > 5); | |
| 340 | + dnafilename[strlen(dnafilename)-4] = '\0'; | |
| 341 | } | |
| 342 | + gt_str_delete(path); | |
| 343 | ||
| 344 | + /* call vmatch and save masked file */ | |
| 345 | if (!had_err) { | |
| 346 | /* open file pointer for masked reference file */ | |
| 347 | fp = gt_fa_xfopen(maskedfilename, "w"); |