Description: use Debian's resource paths GenomeThreader in the original form requires environment variables set to specific paths _or_ uses hardcoded subdirectories of the directory where the gth binary is. Since this is /usr/bin in Debian and the FHS disallows subdirs there. we patch the source to add new default search directories. Author: Sascha Steinbiss --- a/src/gth/bssm_param.c +++ b/src/gth/bssm_param.c @@ -29,6 +29,7 @@ #include "gth/gthprobdef.h" #include "gth/gthspeciestab.h" #include "gth/showbool.h" +#include "libgenomethreader/findfile.h" /* This is a collection of functions associated with @@ -451,42 +452,7 @@ if (gt_file_exists(filename)) gt_str_append_cstr(path, filename); else { - if (strchr(filename, GT_PATH_SEPARATOR)) { - gt_error_set(err, "filename \"%s\" contains illegal symbol '%c': the " - "path list specified by environment variable \"%s\" " - "cannot be searched for it", filename, - GT_PATH_SEPARATOR, BSSMENVNAME); - had_err = -1; - } - /* check for file path in environment variable */ - if (!had_err) - had_err = gt_file_find_in_env(path, filename, BSSMENVNAME, err); - if (!had_err && !gt_str_length(path)) { - gt_error_set(err, "file \"%s\" not found in directory list specified " - "by environment variable %s", filename, BSSMENVNAME); - had_err = -1; - } - if (!had_err) { - /* path found -> append filename */ - gt_str_append_char(path, GT_PATH_SEPARATOR); - gt_str_append_cstr(path, filename); - } - else { - /* check for file path relative to binary */ - int new_err = gt_file_find_exec_in_path(path, gt_error_get_progname(err), - NULL); - if (!new_err) { - gt_assert(gt_str_length(path)); - gt_str_append_char(path, GT_PATH_SEPARATOR); - gt_str_append_cstr(path, "bssm"); - gt_str_append_char(path, GT_PATH_SEPARATOR); - gt_str_append_cstr(path, filename); - if (gt_file_exists(gt_str_get(path))) { - gt_error_unset(err); - had_err = 0; - } - } - } + had_err = gth_find_file(filename, BSSMENVNAME, "bssm", path, err); } if (!had_err) { --- a/src/gth/input.c +++ b/src/gth/input.c @@ -30,6 +30,7 @@ #include "gth/input.h" #include "gth/md5_cache.h" #include "gth/parse_options.h" +#include "libgenomethreader/findfile.h" #define GTHFORWARD 1 /* run program to match forward */ #define GTHREVERSE (1 << 1) /* run program to match reverse */ @@ -653,45 +654,14 @@ { GtStr *path = gt_str_new(); int had_err = 0; + if (gt_file_exists(scorematrixfile)) { gt_str_set(path, scorematrixfile); return path; } - if (strchr(scorematrixfile, GT_PATH_SEPARATOR)) { - gt_error_set(err, "filename \"%s\" contains illegal symbol '%c': the path " - "list specified by environment variable \"%s\" cannot be " - "searched for it", scorematrixfile, GT_PATH_SEPARATOR, - GTHDATAENVNAME); - had_err = -1; - } - if (!had_err) - had_err = gt_file_find_in_env(path, scorematrixfile, GTHDATAENVNAME, err); - if (!had_err && !gt_str_length(path)) { - gt_error_set(err, "file \"%s\" not found in directory list specified by " - "environment variable %s", scorematrixfile, GTHDATAENVNAME); - had_err = -1; - } - if (!had_err) { - gt_assert(gt_str_length(path)); - /* path found -> append score matrix file name */ - gt_str_append_char(path, GT_PATH_SEPARATOR); - gt_str_append_cstr(path, scorematrixfile); - } - else { - /* check for file relative to binary */ - int new_err = gt_file_find_exec_in_path(path, gt_error_get_progname(err), - NULL); - if (!new_err) { - gt_str_append_char(path, GT_PATH_SEPARATOR); - gt_str_append_cstr(path, GTHDATADIRNAME); - gt_str_append_char(path, GT_PATH_SEPARATOR); - gt_str_append_cstr(path, scorematrixfile); - if (gt_file_exists(gt_str_get(path))) { - gt_error_unset(err); - had_err = 0; - } - } - } + + had_err = gth_find_file(scorematrixfile, GTHDATAENVNAME, GTHDATADIRNAME, path, + err); if (had_err) { gt_str_delete(path); return NULL; --- /dev/null +++ b/src/libgenomethreader/findfile.c @@ -0,0 +1,74 @@ +/* + Copyright (c) 2020 Sascha Steinbiss + + Permission to use, copy, modify, and distribute this software for any + purpose with or without fee is hereby granted, provided that the above + copyright notice and this permission notice appear in all copies. + + THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES + WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF + MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR + ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES + WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN + ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF + OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. +*/ + +#include "findfile.h" +#include "core/fileutils_api.h" +#include "core/compat_api.h" + +int gth_find_file(const char *filename, const char *envname, + const char *dirname, GtStr *out, GtError *err) +{ + int had_err = 0; + const char **defaultpath; + static const char *defaultpaths[] = { + "/usr/share/genomethreader", + "/usr/local/share/genomethreader", + "/usr/lib/genomethreader", + "/usr/local/lib/genomethreader", + NULL + }; + + gt_str_reset(out); + /* check in directory given by envname */ + if (getenv(envname)) { + gt_str_append_cstr(out, getenv(envname)); + gt_str_append_char(out, GT_PATH_SEPARATOR); + gt_str_append_cstr(out, filename); + if (gt_file_exists(gt_str_get(out))) { + return 0; + } + } + + /* check for file relative to binary */ + gt_str_reset(out); + had_err = gt_file_find_exec_in_path(out, gt_error_get_progname(err), NULL); + if (!had_err) { + gt_str_append_char(out, GT_PATH_SEPARATOR); + gt_str_append_cstr(out, dirname); + gt_str_append_char(out, GT_PATH_SEPARATOR); + gt_str_append_cstr(out, filename); + if (gt_file_exists(gt_str_get(out))) { + return 0; + } + } + + /* check for file in set of default paths */ + for (defaultpath = defaultpaths; *defaultpath; defaultpath++) { + gt_str_reset(out); + gt_str_append_cstr(out, *defaultpath); + gt_str_append_char(out, GT_PATH_SEPARATOR); + gt_str_append_cstr(out, dirname); + gt_str_append_char(out, GT_PATH_SEPARATOR); + gt_str_append_cstr(out, filename); + if (gt_file_exists(gt_str_get(out))) { + return 0; + } + } + + gt_error_set(err, "could not find file '%s' in any of the search paths", + filename); + return -1; +} --- /dev/null +++ b/src/libgenomethreader/findfile.h @@ -0,0 +1,26 @@ +/* + Copyright (c) 2020 Sascha Steinbiss + + Permission to use, copy, modify, and distribute this software for any + purpose with or without fee is hereby granted, provided that the above + copyright notice and this permission notice appear in all copies. + + THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES + WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF + MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR + ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES + WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN + ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF + OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. +*/ + +#ifndef GTH_FINDFILE_H +#define GTH_FINDFILE_H + +#include "core/str_api.h" +#include "core/error_api.h" + +int gth_find_file(const char *filename, const char *envname, + const char *dirname, GtStr *out, GtError *err); + +#endif --- a/src/libgenomethreader/gthmkvtree.c +++ b/src/libgenomethreader/gthmkvtree.c @@ -6,6 +6,7 @@ #include "core/ma_api.h" #include "gth/gthdef.h" #include "gth/gthoutput.h" +#include "libgenomethreader/findfile.h" #include "libgenomethreader/gthmkvtree.h" #include "types.h" #include "virtualdef.h" @@ -52,39 +53,14 @@ { int rval, had_err = 0; gt_error_check(err); - if (!getenv(GTHDATAENVNAME)) { - gt_error_set(err, "$%s not defined. Please set correctly", GTHDATAENVNAME); - had_err = -1; - } + + GtStr *path = gt_str_new(); + had_err = gth_find_file(mapping, GTHDATAENVNAME, GTHDATADIRNAME, path, err); if (!had_err) { - rval = snprintf(smapfile, PATH_MAX+1, "%s%c%s", getenv(GTHDATAENVNAME), - GT_PATH_SEPARATOR, mapping); - gt_assert(rval < PATH_MAX + 1); - if (!gt_file_exists(smapfile)) { - gt_error_set(err, "cannot open smap file '%s'", smapfile); - had_err = -1; - } - } - if (had_err) { - /* check for file relative to binary */ - GtStr *path; - int new_err; - path = gt_str_new(); - new_err = gt_file_find_exec_in_path(path, gt_error_get_progname(err), NULL); - if (!new_err) { - gt_str_append_char(path, GT_PATH_SEPARATOR); - gt_str_append_cstr(path, GTHDATADIRNAME); - gt_str_append_char(path, GT_PATH_SEPARATOR); - gt_str_append_cstr(path, mapping); - if (gt_file_exists(gt_str_get(path))) { - rval = snprintf(smapfile, PATH_MAX+1, "%s", gt_str_get(path)); - gt_assert(rval < PATH_MAX + 1); - gt_error_unset(err); - had_err = 0; - } - } - gt_str_delete(path); + rval = snprintf(smapfile, PATH_MAX+1, "%s", gt_str_get(path)); + gt_assert(rval < PATH_MAX + 1); } + gt_str_delete(path); return had_err; } --- a/src/libgenomethreader/gthpre.c +++ b/src/libgenomethreader/gthpre.c @@ -11,6 +11,7 @@ #include "gth/gthdef.h" #include "gth/gthoutput.h" #include "gth/input.h" +#include "libgenomethreader/findfile.h" #include "libgenomethreader/gthmkvtree.h" #include "libgenomethreader/gthpolyafunc.h" #include "libgenomethreader/gthpre.h" @@ -301,49 +302,22 @@ /* create masked file if necessary */ if (createmaskedfile) { - sprintf(dnafilename, "%s.%s", POLYA_FASTAFILENAME, DNASUFFIX); - /* check if polyatail.dna exists */ - fp = scanpathsforfile(GTHDATAENVNAME, dnafilename); /* XXX */ - if (!fp) { - gt_error_set(err, "file \"%s\" not found in $%s. Set correctly?", - dnafilename, GTHDATAENVNAME); - had_err = -1; - } - if (!had_err /* XXX */ && DELETEFILEHANDLE(fp)) { - fprintf(stderr,"%s\n", messagespace()); - exit(EXIT_FAILURE); - } - - /* call vmatch and save masked file */ - if (!had_err && !getenv(GTHDATAENVNAME)) { - gt_error_set(err, "$%s not defined. Please set correctly", - GTHDATAENVNAME); - had_err = -1; - } + int rval = 0; + GtStr *path = gt_str_new(); + sprintf(dnafilename, "%s.%s", POLYA_FASTAFILENAME, DNASUFFIX); + had_err = gth_find_file(dnafilename, GTHDATAENVNAME, GTHDATADIRNAME, path, + err); if (!had_err) { - sprintf(dnafilename, "%s%c%s", getenv(GTHDATAENVNAME), GT_PATH_SEPARATOR, - POLYA_FASTAFILENAME); - } - else { - /* check for file relative to binary */ - GtStr *path; - int new_err; - path = gt_str_new(); - new_err = gt_file_find_exec_in_path(path, gt_error_get_progname(err), - NULL); - if (!new_err) { - gt_str_append_char(path, GT_PATH_SEPARATOR); - gt_str_append_cstr(path, GTHDATADIRNAME); - if (gt_file_exists_and_is_dir(gt_str_get(path))) { - sprintf(dnafilename, "%s%c%s", gt_str_get(path), GT_PATH_SEPARATOR, - POLYA_FASTAFILENAME); - gt_error_unset(err); - had_err = 0; - } - } + rval = snprintf(dnafilename, PATH_MAX+1, "%s", gt_str_get(path)); + gt_assert(rval < PATH_MAX + 1); + /* clip off DNASUFFIX */ + gt_assert(strlen(dnafilename) > 5); + dnafilename[strlen(dnafilename)-4] = '\0'; } + gt_str_delete(path); + /* call vmatch and save masked file */ if (!had_err) { /* open file pointer for masked reference file */ fp = gt_fa_xfopen(maskedfilename, "w");