static void free_config() {
free_if_not_null((void**)&am_conf_app_title);
free_if_not_null((void**)&am_conf_app_id);
free_if_not_null((void**)&am_conf_app_version);
free_if_not_null((void**)&am_conf_app_shortname);
free_if_not_null((void**)&am_conf_app_org);
}
int parser_clear_data_buffers(parser_t *self) {
free_if_not_null(self->stream);
free_if_not_null(self->words);
free_if_not_null(self->word_starts);
free_if_not_null(self->line_start);
free_if_not_null(self->line_fields);
return 0;
}
static void free_config() {
free_if_not_null((void**)&am_conf_app_title);
free_if_not_null((void**)&am_conf_app_author);
free_if_not_null((void**)&am_conf_app_id);
free_if_not_null((void**)&am_conf_app_version);
free_if_not_null((void**)&am_conf_app_shortname);
free_if_not_null((void**)&am_conf_app_display_name);
free_if_not_null((void**)&am_conf_app_dev_region);
free_if_not_null((void**)&am_conf_app_supported_languages);
free_if_not_null((void**)&am_conf_app_icon);
free_if_not_null((void**)&am_conf_app_launch_image);
}
/* ---------------- sub_mat_destroy ---------------------------
*/
void
sub_mat_destroy (struct sub_mat *s)
{
free_if_not_null (s->comment);
free (s->fname);
free (s);
}
/* ---------------- kill_f_matrix -----------------------------
*/
void
kill_f_matrix ( float **matrix)
{
if ( ! matrix)
return;
free_if_not_null (matrix[0]);
free (matrix);
}
/* ---------------- kill_uc_matrix ----------------------------
*/
void
kill_uc_matrix ( unsigned char **matrix)
{
if ( ! matrix)
return;
free_if_not_null (matrix[0]);
free (matrix);
}
int parser_cleanup(parser_t *self) {
if (self->cb_cleanup(self->source) < 0) {
return -1;
}
if (parser_clear_data_buffers(self) < 0) {
return -1;
}
// XXX where to put this
free_if_not_null(self->error_msg);
free_if_not_null(self->warn_msg);
if (self->skipset != NULL)
kh_destroy_int64((kh_int64_t*) self->skipset);
return 0;
}
/* ---------------- kill_i_matrix -----------------------------
*/
void
kill_i_matrix ( int **matrix, size_t n_rows)
{
size_t i;
if ( ! matrix)
return;
for(i=0; i<n_rows; i++)
free_if_not_null (matrix[i]);
free (matrix);
}
/* ---------------- prob_vec_destroy --------------------------
*/
void
prob_vec_destroy ( struct prob_vec *p_vec)
{
const char *this_sub = "prob_vec_destroy";
extern const char *prog_bug;
extern const char *null_point;
if ( ! p_vec ) {
err_printf (this_sub, prog_bug, __FILE__, __LINE__);
err_printf (this_sub, null_point);
return;
}
free_if_not_null (p_vec->cmpct_n);
free_if_not_null (p_vec->cmpct_prob);
free_if_not_null (p_vec->cmpct_ndx);
if (p_vec->mship)
kill_f_matrix (p_vec->mship);
free (p_vec);
}
/* ---------------- dme_thresh --------------------------------
* We are given two sets of coordinates, probably coming from
* the same molecule. Unfortunately, one may be imcomplete. This
* is the model. We assume that all of its residues are present
* in the larger structure.
* Begin by building a mask which can be applied to the larger
* system. We will calculate a distance matrix only for the
* residues present in both molecules.
* Our return value is success/failure, but our numerical return
* is via a pointer to a float.
*/
int
dme_thresh (float *frac, struct coord *c1, struct coord *c2, float thresh)
{
struct coord *ref, *mdl;
char *ref_mask;
struct dme_res result;
struct dmat ref_dmat, mdl_dmat;
if (c1->size > c2->size)
ref = c1, mdl = c2;
else
ref = c2, mdl = c1;
if (mdl->size <= 1) { /* If given a tiny model, should we return */
*frac = 0.0; /* failure or success ? */
return EXIT_SUCCESS; /* There is no correct answer. Depends on what */
} /* caller expects */
ref_mask = dmat_make_mask(mdl, ref);
alloc_dmat (&ref_dmat, mdl->size); /*same as model size - not a bug ! */
alloc_dmat (&mdl_dmat, mdl->size);
fill_dmat (&ref_dmat, ref, mdl->size, ref_mask);
fill_dmat (&mdl_dmat, mdl, mdl->size, NULL);
result = get_dme (ref_dmat, mdl_dmat, thresh);
del_dmat (&ref_dmat);
del_dmat (&mdl_dmat);
free_if_not_null (ref_mask);
*frac = (float) result.n_left / result.sz;
return EXIT_SUCCESS;
}
int recursively_install(char* pkg_name, char* pkg_version, char* install_root_name, char* link_to_root, char* overlay_path, int is_upgrade, int overwrite_config, int overwrite_other_package_files, char* tmp_dir, opkg_conf* conf, string_map* package_data, string_map* install_called_pkgs)
{
int err=0;
/* variables not allocated in this function, do not need to be freed */
string_map* install_pkg_data = get_package_with_version(package_data, pkg_name, pkg_version);
char* src_file_path = get_string_map_element(install_pkg_data, "Install-File-Location");
char* src_id = get_string_map_element(install_pkg_data, "Source-ID");
char* pkg_filename = get_string_map_element(install_pkg_data, "Filename");
string_map* pkg_dependencies = get_string_map_element(install_pkg_data, "Required-Depends");
char* install_root_path = get_string_map_element(conf->dest_names, install_root_name);
char* link_root_path = link_to_root != NULL && safe_strcmp(link_to_root, install_root_name) != 0 ? get_string_map_element(conf->dest_names, link_to_root) : NULL;
char* base_url = NULL;
/* variables that may need to be freed */
char* pkg_dest = NULL;
string_map* files_to_link = NULL;
char* info_dir = NULL;
char* control_name_prefix = NULL;
char* list_file_name = NULL;
string_map* conf_files = NULL;
string_map* copied_conf_files = NULL;
int install_root_len = strlen(install_root_path);
char* fs_terminated_install_root = install_root_path[install_root_len-1] == '/' ? strdup(install_root_path) : dynamic_strcat(2, install_root_path, "/");
int overlay_root_len;
char* fs_terminated_overlay_root = NULL;
if(overlay_path != NULL)
{
overlay_root_len = strlen(overlay_path);
fs_terminated_overlay_root = overlay_path[overlay_root_len-1] == '/' ? strdup(overlay_path) : dynamic_strcat(2, overlay_path, "/");
}
else
{
fs_terminated_overlay_root = strdup(fs_terminated_install_root);
}
int link_root_len;
char* fs_terminated_link_root = NULL;
if(link_root_path != NULL)
{
link_root_len = strlen(link_root_path);
fs_terminated_link_root = link_root_path[link_root_len-1] == '/' ? strdup(link_root_path) : dynamic_strcat(2, link_root_path, "/");
}
set_string_map_element(install_called_pkgs, pkg_name, strdup("D"));
if(pkg_dependencies != NULL)
{
//recurse
unsigned long num_deps;
char** deps = get_string_map_keys(pkg_dependencies, &num_deps);
int dep_index;
for(dep_index=0; err == 0 && dep_index < num_deps ; dep_index++)
{
if(get_string_map_element(install_called_pkgs, deps[dep_index]) == NULL )
{
char** dep_def = get_string_map_element(pkg_dependencies, deps[dep_index]);
int is_current;
char* matching_version;
string_map* dep_pkg = get_package_current_or_latest_matching(package_data, deps[dep_index], dep_def, &is_current, &matching_version);
if(dep_pkg != NULL)
{
char* dep_status = get_string_map_element(dep_pkg, "Status");
if(strstr(dep_status, " half-installed") != NULL)
{
err = recursively_install(deps[dep_index], matching_version, install_root_name, link_to_root, overlay_path, is_upgrade, overwrite_config, overwrite_other_package_files, tmp_dir, conf, package_data, install_called_pkgs);
}
}
else
{
err = 1;
}
}
}
}
if(install_root_path == NULL || ( src_id == NULL && install_pkg_data == NULL) || (pkg_filename == NULL && install_pkg_data == NULL) )
{
//sanity check
err = 1;
}
if(err == 0)
{
printf("Preparing to install package %s...\n", pkg_name);
}
if(err == 0 && src_file_path == NULL)
{
//determine source url
string_map* src_lists[2] = { conf->gzip_sources, conf->plain_sources };
int src_list_index;
for(src_list_index=0; src_list_index < 2 && base_url == NULL; src_list_index++)
{
base_url = (char*)get_string_map_element(src_lists[src_list_index], src_id);
}
err = base_url == NULL ? 1 : err;
if(err == 1)
{
fprintf(stderr, "ERROR: Could determine download URL for package %s\n", pkg_name);
}
}
if(err == 0 && src_file_path == NULL)
{
//download package
printf("\tDownloading...\n");
char* src_url = dynamic_strcat(3, base_url, "/", pkg_filename);
pkg_dest = dynamic_strcat(3, tmp_dir, "/", pkg_name);
FILE* package_file = fopen(pkg_dest, "w");
if(package_file != NULL)
{
err = write_url_to_stream(src_url, "gpkg", NULL, package_file, NULL);
fclose(package_file);
}
else
{
err = 1;
}
if(err == 1)
{
fprintf(stderr, "ERROR: Could not download package %s\n", pkg_name);
}
free(src_url);
}
if(err == 0 && src_file_path != NULL)
{
pkg_dest = strdup(src_file_path);
}
if(err == 0 && src_file_path == NULL)
{
//check md5sum
char* md5sum = file_md5sum_alloc(pkg_dest);
char* expected_md5sum = (char*)get_string_map_element(install_pkg_data, "MD5Sum");
//printf("md5sum = %s\n", md5sum);
//printf("package md5sum = %s\n", (char*)get_string_map_element(install_pkg_data, "MD5Sum"));
if(md5sum == NULL || expected_md5sum == NULL)
{
fprintf(stderr, "ERROR: Expected MD5Sum for %s not specified, cannot verify package\n", pkg_name);
err = 1;
}
else if (safe_strcmp(md5sum, expected_md5sum) != 0)
{
fprintf(stderr, "ERROR: MD5Sum mismatch for %s package\n", pkg_name);
fprintf(stderr, " Expected: %s\n", expected_md5sum);
fprintf(stderr, " Downloaded: %s\n\n", md5sum);
err = 1;
}
else
{
printf("\tDownloaded %s successfully.\n\tInstalling %s...\n", pkg_name, pkg_name);
}
if(md5sum != NULL) { free(md5sum); }
}
if(err == 0)
{
// Extract list file contaiing list of files to install
info_dir = dynamic_strcat(2, fs_terminated_overlay_root, "usr/lib/opkg/info");
control_name_prefix = dynamic_strcat(4, info_dir, "/", pkg_name, ".");
list_file_name = dynamic_strcat(4, info_dir, "/", pkg_name, ".list");
mkdir_p(info_dir, S_IRWXU | S_IRGRP | S_IXGRP | S_IROTH | S_IXOTH );
FILE* list_file = fopen(list_file_name, "w");
deb_extract( pkg_dest,
list_file,
extract_quiet | extract_data_tar_gz | extract_list,
NULL,
NULL,
&err);
fclose(list_file);
if(err)
{
rm_r(list_file_name);
fprintf(stderr, "ERROR: could not extract file list from packge %s.\n", pkg_name);
fprintf(stderr, " package file may be corrupt\n\n");
}
}
if(err == 0)
{
//extract control files
deb_extract( pkg_dest,
stderr,
extract_control_tar_gz | extract_all_to_fs| extract_preserve_date | extract_unconditional,
control_name_prefix,
NULL,
&err);
if(err)
{
fprintf(stderr, "ERROR: could not extract control files from packge %s.\n", pkg_name);
fprintf(stderr, " package file may be corrupt\n\n");
}
}
if(err == 0)
{
//check for file conflicts & correct list file to contain real root name in file paths
unsigned long num_list_lines;
char** list_file_lines = get_file_lines(list_file_name, &num_list_lines);
char* conf_file_path = dynamic_strcat(4, info_dir, "/", pkg_name, ".conffiles");
if(path_exists(conf_file_path))
{
unsigned long num_conf_lines;
char** conf_file_lines = get_file_lines(conf_file_path, &num_conf_lines);
int conf_line_index;
conf_files = initialize_string_map(1);
for(conf_line_index=0; conf_line_index < num_conf_lines; conf_line_index++)
{
char* adjusted_conf_path = dynamic_strcat(2, fs_terminated_install_root, conf_file_lines[conf_line_index] + 1);
set_string_map_element(conf_files, adjusted_conf_path, strdup("D"));
free(adjusted_conf_path);
}
free_null_terminated_string_array(conf_file_lines);
}
free(conf_file_path);
FILE* list_file = fopen(list_file_name, "w");
int line_index;
for(line_index=0; line_index < num_list_lines && (!err) ; line_index++)
{
int line_len = strlen( list_file_lines[line_index] );
if(line_len > 2)
{
if(list_file_lines[line_index][0] == '.' && list_file_lines[line_index][1] == '/' && list_file_lines[line_index][line_len-1] != '/')
{
char* adjusted_file_path = dynamic_strcat(2, fs_terminated_install_root, list_file_lines[line_index] + 2);
int is_conf_file = conf_files != NULL ?
(get_string_map_element(conf_files, adjusted_file_path) != NULL ? 1 : 0) :
0;
if(strcmp(pkg_name, "opkg") == 0 && strcmp(list_file_lines[line_index], "./bin/opkg") == 0 && path_exists("/bin/opkg") == PATH_IS_SYMLINK)
{
//very special case: we're installing opkg, and here all the preliminary checks have already been passed
//remove symlink placeholder to gpkg from /bin/opkg if it exists
rm_r("/bin/opkg");
}
err = path_exists(adjusted_file_path) && is_conf_file == 0 && overwrite_other_package_files == 0 ? 1 : 0;
if(err)
{
fprintf(stderr, "ERROR: file '%s'\n", adjusted_file_path);
fprintf(stderr, " from package %s already exists.\n\n", pkg_name);
}
else
{
fprintf(list_file, "%s\n", adjusted_file_path);
if(link_root_path != NULL)
{
char* link_to_path = dynamic_strcat(2, fs_terminated_link_root, list_file_lines[line_index] + 2);
files_to_link = files_to_link == NULL ? initialize_string_map(1) : files_to_link;
set_string_map_element(files_to_link, adjusted_file_path, link_to_path);
//don't free link_to_path, should be freed with files_to_link map
}
if(is_conf_file && path_exists(adjusted_file_path) && overwrite_config == 0)
{
char* tmp_conf_path = dynamic_strcat(2, tmp_dir, adjusted_file_path);
cp(adjusted_file_path, tmp_conf_path);
copied_conf_files = copied_conf_files == NULL ? initialize_string_map(1) : copied_conf_files;
set_string_map_element(copied_conf_files, adjusted_file_path, tmp_conf_path);
//don't free tmp_conf_path, should be freed with copied_conf_files map
}
}
free(adjusted_file_path);
}
}
}
fclose(list_file);
if(list_file_lines != NULL) { free_null_terminated_string_array(list_file_lines); }
}
if(err == 0)
{
//run preinst
err = run_script_if_exists(install_root_path, link_root_path, pkg_name, "preinst", (is_upgrade ? "upgrade" : "install") );
}
if(err == 0)
{
//extract package files
deb_extract( pkg_dest,
stderr,
extract_data_tar_gz | extract_all_to_fs| extract_preserve_date| extract_unconditional,
fs_terminated_overlay_root,
NULL,
&err);
if(err)
{
fprintf(stderr, "ERROR: could not extract application files from packge %s.\n", pkg_name);
fprintf(stderr, " package file may be corrupt\n\n");
}
//move any conf files back
if(copied_conf_files != NULL)
{
unsigned long num_conf_paths;
char** conf_paths = get_string_map_keys(copied_conf_files, &num_conf_paths);
int conf_index;
for(conf_index=0; conf_index < num_conf_paths; conf_index++)
{
char* tmp_conf_path = get_string_map_element(copied_conf_files, conf_paths[conf_index]);
cp(tmp_conf_path, conf_paths[conf_index]);
}
destroy_string_map(copied_conf_files, DESTROY_MODE_FREE_VALUES, &num_conf_paths);
if(conf_paths != NULL ) { free_null_terminated_string_array(conf_paths); }
copied_conf_files = NULL;
}
}
if(err == 0 && files_to_link != NULL)
{
unsigned long num_files;
char** real_files = get_string_map_keys(files_to_link, &num_files);
int file_index;
if(num_files > 0)
{
char* link_file_name = dynamic_strcat(4, info_dir, "/", pkg_name, ".linked");
FILE* link_file = fopen(link_file_name, "w");
for(file_index=0; link_file != NULL && file_index < num_files; file_index++)
{
char* link_path = get_string_map_element(files_to_link, real_files[file_index]);
if(!path_exists(link_path))
{
int sym_success;
mkdir_p(link_path, S_IRWXU | S_IRGRP | S_IXGRP | S_IROTH | S_IXOTH );
rm_r(link_path);
sym_success = symlink(real_files[file_index], link_path);
fprintf(link_file, "%s\n", link_path);
}
}
if(link_file != NULL) { fclose(link_file); }
free(link_file_name);
}
destroy_string_map(files_to_link, DESTROY_MODE_FREE_VALUES, &num_files);
free_null_terminated_string_array(real_files);
files_to_link = NULL;
}
if(err == 0)
{
//run postinst
int warn = run_script_if_exists(install_root_path, link_root_path, pkg_name, "postinst", (is_upgrade ? "upgrade" : "install") );
if(warn != 0)
{
fprintf(stderr, "Warning: postinstall script failed for package %s.\n", pkg_name);
}
}
if(err == 0)
{
// remove downloaded package file in tmp dir & print success
if(src_file_path == NULL) { rm_r(pkg_dest); }
printf("\tSuccessfully installed %s.\n", pkg_name);
}
//cleanup
unsigned long num_destroyed;
free_if_not_null(pkg_dest);
free_if_not_null(info_dir);
free_if_not_null(control_name_prefix);
free_if_not_null(list_file_name);
free_if_not_null(fs_terminated_install_root);
free_if_not_null(fs_terminated_overlay_root);
free_if_not_null(fs_terminated_link_root);
if(files_to_link != NULL) { destroy_string_map(files_to_link, DESTROY_MODE_FREE_VALUES, &num_destroyed); }
if(conf_files != NULL) { destroy_string_map(conf_files, DESTROY_MODE_FREE_VALUES, &num_destroyed); }
if(copied_conf_files!= NULL){ destroy_string_map(copied_conf_files, DESTROY_MODE_FREE_VALUES, &num_destroyed); }
return err;
}
//void do_install(opkg_conf* conf, char* pkg_name, char* install_root_name, char* link_root_name, char** version_criteria)
void do_install(opkg_conf* conf, string_map* pkgs, char* install_root_name, char* link_root_name, int is_upgrade, int overwrite_config, int overwrite_other_package_files, int force_reinstall, char* tmp_root)
{
string_map* package_data = initialize_string_map(1);
string_map* matching_packages = initialize_string_map(1);
string_map* pkgs_from_file = initialize_string_map(1);
unsigned long num_destroyed;
char* install_root_path = (char*)get_string_map_element(conf->dest_names, install_root_name);
char* overlay_path = NULL; // no special treatment of overlay, can be reenabled by setting this variable here if we ever need it
char* test_dir = dynamic_strcat(2, (overlay_path != NULL ? overlay_path : install_root_path), "/usr/lib/opkg/info");
if(!create_dir_and_test_writable(test_dir))
{
fprintf(stderr, "ERROR: Specified install destination is not writable, exiting\n");
exit(1);
}
free(test_dir);
if(install_root_path == NULL)
{
printf("ERROR: No destination %s found, cannot install\n\n", install_root_name);
exit(1);
}
char* tmp_dir = (char*)malloc(1024);
if(create_tmp_dir(tmp_root == NULL ? "/tmp" : tmp_root, &tmp_dir) != 0)
{
fprintf(stderr, "ERROR: Could not create tmp dir, exiting\n");
exit(1);
}
/* Determine all packages to install by first loading all package names, status & dependencies (and no other variables) */
load_all_package_data(conf, package_data, matching_packages, NULL, LOAD_MINIMAL_PKG_VARIABLES_FOR_ALL, install_root_name, 1, NULL );
destroy_string_map(matching_packages, DESTROY_MODE_FREE_VALUES, &num_destroyed);
/* determine list of all packiages we are about to install, including dependencies */
string_map* install_pkgs_map = initialize_string_map(1);
char** install_pkg_list = NULL;
unsigned long install_pkg_list_len = 0;
char* unsatisfied_dep_err = NULL;
/* new string map var with all pkgs to install = pkgs, keys = version */
unsigned long num_pkg_names;
char** pkg_names = get_string_map_keys(pkgs, &num_pkg_names);
int pkg_name_index;
/*
* Load data for any packages being installed via ipk and
* determine if any packages we are about to install
* provide anything, and if so set package we are installing to preferred
*/
string_map* preferred_provides = initialize_string_map(1);
for(pkg_name_index=0;pkg_name_index < num_pkg_names; pkg_name_index++)
{
char* pkg_name = pkg_names[pkg_name_index];
char** version_criteria = get_string_map_element(pkgs, pkg_name);
char* install_pkg_version = NULL;
int install_pkg_is_current;
/* deal with case where we're installing from file */
if(path_exists(pkg_name))
{
//installing from file
char* pkg_file = pkg_name;
//extract control files
int err = 0;
char* tmp_control = dynamic_strcat(2, tmp_dir, "/tmp_ctrl");
char* tmp_control_prefix = dynamic_strcat(2, tmp_control, "/tmp.");
char* tmp_control_name = dynamic_strcat(2, tmp_control_prefix, "control");
mkdir_p(tmp_control, S_IRWXU | S_IRGRP | S_IXGRP | S_IROTH | S_IXOTH );
deb_extract( pkg_file,
stderr,
extract_control_tar_gz | extract_all_to_fs| extract_preserve_date | extract_unconditional,
tmp_control_prefix,
NULL,
&err);
if(err != 0)
{
fprintf(stderr, "ERROR: %s is not a valid package file, cannot install\n", pkg_file);
rm_r(tmp_dir);
exit(1);
}
string_map* tmp_control_pkg_data = initialize_string_map(1);
matching_packages = initialize_string_map(1);
load_package_data(tmp_control_name, 0, tmp_control_pkg_data, matching_packages, NULL, LOAD_ALL_PKG_VARIABLES, NULL, NULL);
unsigned long num_ctrl_names;
char** ctrl_name_list = get_string_map_keys(tmp_control_pkg_data, &num_ctrl_names);
destroy_string_map(matching_packages, DESTROY_MODE_FREE_VALUES, &num_destroyed);
err = 1; //set back to 0 when data successfully loaded
if(num_ctrl_names > 0)
{
int ctrl_name_index;
for(ctrl_name_index=0; ctrl_name_list[ctrl_name_index] != NULL; ctrl_name_index++)
{
if( strcmp(ctrl_name_list[ctrl_name_index], PROVIDES_STRING) != 0)
{
pkg_name = strdup(ctrl_name_list[ctrl_name_index]);
}
}
char* version = NULL;
int is_current;
string_map* pkg_info = get_package_current_or_latest(tmp_control_pkg_data, pkg_name, &is_current, &version);
if(pkg_info != NULL)
{
err = 0;
set_string_map_element(pkg_info, "Install-File-Location", strdup(pkg_file));
set_string_map_element(pkg_info, "Version", version); //we need to save this, since we are going to set a special version to make sure data doesn't get over-written later, also no need to free version now
char* special_version = dynamic_strcat(2, version, "@@_FILE_INSTALL_VERSION_@@");
char** new_version_criteria = malloc(3*sizeof(char*));
new_version_criteria[0] = strdup("=");
new_version_criteria[1] = special_version;
new_version_criteria[2] = NULL;
version_criteria = new_version_criteria;
string_map* all_current_versions = get_string_map_element(package_data, pkg_name);
if(all_current_versions == NULL)
{
all_current_versions=initialize_string_map(1);
set_string_map_element(package_data, pkg_name, all_current_versions);
}
set_string_map_element(all_current_versions, special_version, pkg_info);
set_string_map_element(all_current_versions, LATEST_VERSION_STRING, special_version);
free(pkg_names[pkg_name_index]);
pkg_names[pkg_name_index] = strdup(pkg_name);
set_string_map_element(pkgs, pkg_name, copy_null_terminated_string_array(new_version_criteria));
set_string_map_element(pkgs_from_file, pkg_name, strdup("D"));
}
}
free_null_terminated_string_array(ctrl_name_list);
if(err != 0)
{
fprintf(stderr, "ERROR: %s is not a valid package file, cannot install\n", pkg_file);
rm_r(tmp_dir);
exit(1);
}
free_if_not_null(tmp_control);
free_if_not_null(tmp_control_prefix);
free_if_not_null(tmp_control_name);
rm_r(tmp_control);
}
/* determine if package provides anything, and set this package to preferred if so*/
string_map* install_pkg_data = get_package_current_or_latest_matching(package_data, pkg_name, version_criteria, &install_pkg_is_current, &install_pkg_version);
if(install_pkg_data != NULL)
{
char* provides_str = get_string_map_element(install_pkg_data, "Provides");
if(provides_str != NULL)
{
if(strlen(provides_str) > 0)
{
unsigned long num_provides;
char package_separators[] = {' ', ',', ':', ';', '\'', '\"', '\t', '\r', '\n'};
char** provides_list = split_on_separators(provides_str, package_separators, 9, -1, 0, &num_provides);
int provides_index;
char* provides_unique_key = dynamic_strcat(3, pkg_name, "@", install_pkg_version);
for(provides_index=0; provides_index < num_provides; provides_index++)
{
char* provides_name = strdup(provides_list[provides_index]);
char* eq = strchr(provides_name, '=');
if(eq != NULL) { *eq = '\0' ; }
if(strlen(provides_name) > 0)
{
set_string_map_element(preferred_provides, provides_name, strdup(provides_unique_key));
}
}
}
}
}
}
/* reload with new preferred_provides */
free_recursive_package_vars(package_data);
matching_packages = initialize_string_map(1);
load_all_package_data(conf, package_data, matching_packages, NULL, LOAD_MINIMAL_PKG_VARIABLES_FOR_ALL, install_root_name, 1, preferred_provides );
destroy_string_map(matching_packages, DESTROY_MODE_FREE_VALUES, &num_destroyed);
/* load data and do sanity checks for packages we are about to install */
for(pkg_name_index=0;pkg_name_index < num_pkg_names; pkg_name_index++)
{
char* pkg_name = pkg_names[pkg_name_index];
char** version_criteria = get_string_map_element(pkgs, pkg_name);
char* install_pkg_version = NULL;
int install_pkg_is_current;
load_recursive_package_data_variables(package_data, pkg_name, 1, 0, 0); // load required-depends for package of interest only
string_map* install_pkg_data = get_package_current_or_latest_matching(package_data, pkg_name, version_criteria, &install_pkg_is_current, &install_pkg_version);
char* install_status = install_pkg_data == NULL ? NULL : get_string_map_element(install_pkg_data, "Status");
if(install_status != NULL)
{
char** old_el = set_string_map_element(install_pkgs_map, pkg_name, copy_null_terminated_string_array(version_criteria) );
if(old_el != NULL){ free_null_terminated_string_array(old_el); }
string_map* install_pkg_depend_map = get_string_map_element(install_pkg_data, "Required-Depends");
if(install_pkg_depend_map != NULL)
{
unsigned long num_keys;
char** load_detail_pkgs = get_string_map_keys(install_pkg_depend_map, &num_keys);
int ldp_index;
for(ldp_index=0;ldp_index < num_keys && unsatisfied_dep_err == NULL; ldp_index++)
{
char* dep_name = load_detail_pkgs[ldp_index];
char** dep_def= get_string_map_element(install_pkg_depend_map, dep_name);
if(get_string_map_element(install_pkgs_map, dep_name) != NULL)
{
/*
* We really should check here whether old dependency def can be reconciled with the new one, and report an error if it can't
* Right now we just use the heuristic that top-level (user specified, not dependency) package defs get preference, followed
* by first dependency encountered.
*
* Since right now versioning features aren't really being used very much other than kernel dependencies in Gargoyle/OpenWrt
* I'm just leaving this comment here as a reminder that this should be addressed at some point rather than messing with it now
*
*/
dep_def = get_string_map_element(install_pkgs_map, dep_name);
}
else
{
set_string_map_element(install_pkgs_map, dep_name, copy_null_terminated_string_array(dep_def));
}
//error checking, check that dependency definition exists
char* latest_version = NULL;
int latest_is_current = 0;
string_map* dep_info = get_package_current_or_latest_matching(package_data, dep_name, dep_def, &latest_is_current, &latest_version);
//check if we have a version installed different than what is required
int have_current;
char* current_version = NULL;
string_map* cur_info = get_package_current_or_latest(package_data, dep_name, &have_current, ¤t_version);
if(have_current && (latest_is_current == 0 || dep_info == NULL))
{
//should only get here if dep_def[1] is not null (version mismatch doesn't make sense if no version is specified)
char* cur_status = get_string_map_element(cur_info, "Status");
if(strstr(cur_status, " hold ") != NULL)
{
unsatisfied_dep_err = dynamic_strcat(11, "ERROR: Dependency ", dep_name, " (", dep_def[0], " ", dep_def[1], ") of package ", pkg_name, " is installed,\n\t\tbut has incompatible version ", current_version, " and is marked as 'hold'");
}
else
{
unsatisfied_dep_err = dynamic_strcat(10, "ERROR: Dependency ", dep_name, " (", dep_def[0], " ", dep_def[1], ") of package ", pkg_name, " is installed,\n\t\tbut has incompatible version ", current_version);
}
}
free_if_not_null(current_version);
free_if_not_null(latest_version);
// check that dependency definition exists
if(unsatisfied_dep_err == NULL && dep_info == NULL)
{
if(dep_def[1] != NULL)
{
unsatisfied_dep_err = dynamic_strcat(9, "ERROR: Dependency ", dep_name, " (", dep_def[0], " ", dep_def[1], ") of package ", pkg_name, " cannot be found, try updating your package lists");
}
else
{
unsatisfied_dep_err = dynamic_strcat(5, "ERROR: Dependency ", dep_name, " of package ", pkg_name, " cannot be found, try updating your package lists");
}
}
}
free_null_terminated_string_array(load_detail_pkgs);
}
}
install_status = install_pkg_data == NULL ? NULL : get_string_map_element(install_pkg_data, "Status");
/* error checking before we start install */
if(install_pkg_data == NULL || install_status == NULL)
{
fprintf(stderr, "ERROR: No package named %s found, try updating your package lists\n\n", pkg_name);
rm_r(tmp_dir);
exit(1);
}
if(strstr(install_status, " installed") != NULL)
{
if(force_reinstall)
{
fprintf(stderr, "WARNING: Package %s is already installed, forcing removal and reinstallation\n\n", pkg_name);
free_package_data(package_data);
string_map* rm_pkg = initialize_string_map(1);
set_string_map_element(rm_pkg, pkg_name, alloc_depend_def(NULL));
do_remove(conf, rm_pkg, (overwrite_config ? 0 : 1), 0, 1, 0, tmp_root);
//restart install
return do_install(conf, pkgs, install_root_name, link_root_name, is_upgrade, overwrite_config, overwrite_other_package_files, force_reinstall, tmp_root);
}
else
{
fprintf(stderr, "WARNING: Package %s is already installed, ignoring\n", pkg_name);
fprintf(stderr, " Use --force-reinstall to force reinstallation\n\n");
char** old_el = remove_string_map_element(install_pkgs_map, pkg_name);
if(old_el != NULL){ free_null_terminated_string_array(old_el); };
}
}
if(unsatisfied_dep_err != NULL)
{
fprintf(stderr, "%s\n", unsatisfied_dep_err);
rm_r(tmp_dir);
exit(1);
}
}
/* load more detailed data on packages we are about to install */
free_recursive_package_vars(package_data); /* note: whacks install_pkg_depend_map */
string_map* parameters = initialize_string_map(1);
matching_packages = initialize_string_map(1);
set_string_map_element(parameters, "package-list", install_pkgs_map);
load_all_package_data(conf, package_data, matching_packages, parameters, LOAD_MINIMAL_FOR_ALL_PKGS_ALL_FOR_MATCHING, install_root_name, 0, preferred_provides);
unsigned long from_file_pkg_list_len;
char** from_file_pkg_list = get_string_map_keys(pkgs_from_file, &from_file_pkg_list_len);
int from_file_index;
for(from_file_index=0; from_file_index < from_file_pkg_list_len; from_file_index++)
{
char* old = set_string_map_element(matching_packages, from_file_pkg_list[from_file_index], strdup("D"));
free_if_not_null(old);
}
free_null_terminated_string_array(from_file_pkg_list);
install_pkg_list = get_string_map_keys(matching_packages, &install_pkg_list_len);
destroy_string_map(matching_packages, DESTROY_MODE_FREE_VALUES, &num_destroyed);
destroy_string_map(parameters, DESTROY_MODE_IGNORE_VALUES, &num_destroyed);
char* all_pkg_list_str = join_strs(", ", install_pkg_list, install_pkg_list_len, 0, 0);
uint64_t combined_size = 0;
int pkg_index;
for(pkg_index=0; pkg_index < install_pkg_list_len; pkg_index++)
{
char** match_criteria = get_string_map_element(install_pkgs_map, install_pkg_list[pkg_index]);
string_map* pkg = get_package_current_or_latest_matching(package_data, install_pkg_list[pkg_index], match_criteria, NULL, NULL);
char* next_size_str = get_string_map_element(pkg, "Installed-Size");
uint64_t next_size = 0;
if(sscanf(next_size_str, SCANFU64, &next_size) > 0)
{
combined_size = combined_size + next_size;
}
}
uint64_t root_size = destination_bytes_free(conf, install_root_name);
if(combined_size >= root_size )
{
fprintf(stderr, "ERROR: Not enough space in destination %s to install specified packages:\n\t%s\n\n", install_root_name, all_pkg_list_str);
rm_r(tmp_dir);
exit(1);
}
if(all_pkg_list_str != NULL)
{
printf("Preparing to install the following packages, which will require " SCANFU64 " bytes:\n\t%s\n\n", combined_size, all_pkg_list_str);
}
else
{
fprintf(stderr, "No packages to install.\n\n");
}
/* Set status of new required packages to half-installed, set user-installed on requested package, installed time on all */
char* install_root_status_path = dynamic_strcat(2, install_root_path, "/usr/lib/opkg/status");
string_map* install_root_status = initialize_string_map(1);
matching_packages = initialize_string_map(1);
if(path_exists(install_root_status_path))
{
load_package_data(install_root_status_path, 0, install_root_status, matching_packages, NULL, LOAD_ALL_PKG_VARIABLES, install_root_name, preferred_provides);
}
destroy_string_map(matching_packages, DESTROY_MODE_FREE_VALUES, &num_destroyed);
time_t now = time(NULL);
char install_time[20];
sprintf(install_time, "%lu", now);
for(pkg_index=0; pkg_index < install_pkg_list_len; pkg_index++)
{
int is_installed;
char* install_version = NULL;
char** match_criteria = get_string_map_element(install_pkgs_map, install_pkg_list[pkg_index]);
string_map* pkg = get_package_current_or_latest_matching(package_data, install_pkg_list[pkg_index], match_criteria, &is_installed, &install_version);
if(is_installed == 0) /* should never be true, but check anyway */
{
char* old_status = remove_string_map_element(pkg, "Status");
free(old_status);
char* status_parts[3] = { "install", "ok", "half-installed" };
status_parts[1] = get_string_map_element(pkgs, install_pkg_list[pkg_index]) != NULL ? "user" : status_parts[1];
char* new_status = dynamic_strcat(5, status_parts[0], " ", status_parts[1], " ", status_parts[2]);
set_string_map_element(pkg, "Status", new_status);
set_string_map_element(pkg, "Installed-Time", strdup(install_time));
set_string_map_element(pkg, "Install-Destination", strdup(install_root_name));
if(link_root_name != NULL)
{
set_string_map_element(pkg, "Link-Destination", strdup(link_root_name));
}
add_package_data(install_root_status, &pkg, install_pkg_list[pkg_index], install_version, NULL);
/* Note: we just added pkg data structure from package_data to install_root_status, Be careful on cleanup! */
}
}
save_package_data_as_status_file(install_root_status, install_root_status_path);
string_map* install_called_pkgs = initialize_string_map(1);
int err = 0;
for(pkg_name_index=0;pkg_name_index < num_pkg_names; pkg_name_index++)
{
char* pkg_name = pkg_names[pkg_name_index];
if(get_string_map_element(install_pkgs_map, pkg_name) != NULL && get_string_map_element(install_called_pkgs, pkg_name) == NULL)
{
int install_pkg_is_current;
char* install_pkg_version = NULL;
char** version_criteria = get_string_map_element(pkgs, pkg_name);
get_package_current_or_latest_matching(package_data, pkg_name, version_criteria, &install_pkg_is_current, &install_pkg_version);
err = recursively_install(pkg_name, install_pkg_version, install_root_name, link_root_name, overlay_path, is_upgrade, overwrite_config, overwrite_other_package_files, tmp_dir, conf, package_data, install_called_pkgs);
free_if_not_null(install_pkg_version);
}
}
if(err)
{
fprintf(stderr, "An error occurred during Installation, removing partially installed packages.\n");
unsigned long num_install_called_pkgs;
char** install_called_pkg_list = get_string_map_keys(install_called_pkgs, &num_install_called_pkgs);
int pkg_index;
for(pkg_index=0; pkg_index < num_install_called_pkgs; pkg_index++)
{
remove_individual_package(install_called_pkg_list[pkg_index], conf, package_data, tmp_dir, 0, 0);
}
free_null_terminated_string_array(install_called_pkg_list);
//call remove function to do cleanup of partial install
//DO NOT EXIT HERE, fixup status file below
}
//remove tmp dir -- need to do this whether or not there is an error
rm_r(tmp_dir);
free(tmp_dir);
//set status of new packages to installed on success, and remove on failure
for(pkg_index=0; pkg_index < install_pkg_list_len; pkg_index++)
{
/* no need to check version, should only be one installed version at a time... */
string_map* pkg = get_package_current_or_latest(install_root_status, install_pkg_list[pkg_index], NULL, NULL);
if(pkg != NULL)
{
if(!err)
{
char* status = get_string_map_element(pkg, "Status");
if(strstr(status, " half-installed") != NULL)
{
char* status_parts[3] = { "install", "ok", "installed" };
status_parts[1] = get_string_map_element(pkgs, install_pkg_list[pkg_index]) != NULL ? "user" : status_parts[1];
char* new_status = dynamic_strcat(5, status_parts[0], " ", status_parts[1], " ", status_parts[2]);
char* old_status = set_string_map_element(pkg, "Status", new_status);
free_if_not_null(old_status);
}
}
else
{
string_map* all_pkg_versions = remove_string_map_element(install_root_status, install_pkg_list[pkg_index]);
free_all_package_versions(all_pkg_versions);
}
}
}
save_package_data_as_status_file(install_root_status, install_root_status_path);
if(!err)
{
if(all_pkg_list_str != NULL)
{
printf("Installation of packages successful.\n\n");
}
}
else
{
printf("Finished removing partially installed packages.\n\n");
}
}
/* ---------------- seq_strct_2_duplicated_prob_vec -----------------------
* Duplikate the pvec while structure estimation and also duplicate the sequence,
* each n-times.
* return:
* struct prob_vec *pvec
* Notice: not used, but who knows if it will became useful one day !
* (Martin May, 2007)
*/
struct prob_vec *
strct_2_duplicated_prob_vec (struct coord *structure, const struct seq *seq,
const struct seqprof *sp, const size_t size,
const struct aa_strct_clssfcn *cmodel, const size_t n_duplications)
{
size_t i, j;
float *fragment;
struct prob_vec *pvec;
float **aa_prob;
struct aa_clssfcn *aa_class;
const size_t n_pvec = size - cmodel->n_att + 1;
if ((pvec = new_pvec (cmodel->n_att, n_duplications * size , n_duplications * n_pvec,
cmodel->strct->n_class))!= NULL) {
for (i = 0; i < (n_duplications * n_pvec); i++) /* Initialize mship */
for (j = 0; j < cmodel->strct->n_class; j++)
pvec->mship[i][j] = cmodel->strct->class_weight[j];
if (structure) { /* Structure membership */
for (i = 0; i < n_pvec; i++){ /* for every fragment...*/
/* twice for every fragment on position i as on i + size */
fragment = getFragment (i , cmodel->n_att, structure);
for (j = 0; j < n_duplications; j++){
if (computeMembershipStrct(pvec->mship[ i + j * n_pvec], fragment,
cmodel->strct) == NULL) {
prob_vec_destroy (pvec);
return NULL;
}
}
}
free_if_not_null (fragment);
}
if (sp || seq) { /* Sequence or profile membership */
aa_prob = f_matrix (n_duplications * n_pvec, cmodel->strct->n_class);
aa_class = E_MALLOC (sizeof (struct aa_clssfcn));
aa_class->n_class = cmodel->strct->n_class;
aa_class->n_att = cmodel->n_att;
aa_class->log_pp = cmodel->log_pp;
aa_class->class_wt = cmodel->strct->class_weight;
if (seq){
struct seq *s = seq_duplicate ( seq , n_duplications );
if (computeMembershipAA (aa_prob, s, aa_class)
== EXIT_FAILURE) {
prob_vec_destroy (pvec);
return NULL;
}
seq_destroy (s);
} else if (sp) {
if (computeMembershipAAProf (aa_prob, sp, aa_class)
== EXIT_FAILURE) {
prob_vec_destroy (pvec);
return NULL;
}
}
free (aa_class);
for (i = 0; i < n_duplications * n_pvec; i++)
for (j = 0; j < cmodel->strct->n_class; j++)
pvec->mship[i][j] *= aa_prob[i][j];
kill_f_matrix (aa_prob);
}
for (i = 0; i < (n_duplications * n_pvec); i++){
double sum = 0.0;
for (j = 0; j < cmodel->strct->n_class; j++)
sum += pvec->mship[i][j];
for (j = 0; j < cmodel->strct->n_class; j++)
pvec->mship[i][j] /= sum;
}
pvec->norm_type = PVEC_TRUE_PROB;
}
return pvec;
}
/* ---------------- seq_strct_2_prob_vec -----------------------
* This calculates probabilities for using combinations of
* sequence and structure, sequence profile and structure,
* sequence only, sequence profile only, and structure only.
*/
static struct prob_vec *
seq_strct_2_prob_vec (struct coord *structure, const struct seq *seq,
const struct seqprof *sp, const size_t size,
const struct aa_strct_clssfcn *cmodel,
const enum yes_no norm)
{
size_t i, j, compnd_len;
float *fragment;
struct prob_vec *pvec;
float **aa_prob;
struct aa_clssfcn *aa_class;
const size_t n_pvec = size - cmodel->n_att + 1;
if ((pvec = new_pvec (cmodel->n_att, size,n_pvec,
cmodel->strct->n_class))!= NULL) {
for (i = 0; i < n_pvec; i++) /* Initialize mship */
for (j = 0; j < cmodel->strct->n_class; j++)
pvec->mship[i][j] = cmodel->strct->class_weight[j];
if (structure) { /* Structure membership */
for (i = 0; i < n_pvec; i++) { /* for every fragment...*/
fragment = getFragment (i, cmodel->n_att, structure);
if (computeMembershipStrct(pvec->mship[i], fragment,
cmodel->strct) == NULL) {
prob_vec_destroy (pvec);
return NULL;
}
}
free_if_not_null (fragment);
}
if (sp || seq) { /* Sequence or profile membership */
aa_prob = f_matrix (n_pvec, cmodel->strct->n_class);
aa_class = E_MALLOC (sizeof (struct aa_clssfcn));
aa_class->n_class = cmodel->strct->n_class;
aa_class->n_att = cmodel->n_att;
aa_class->log_pp = cmodel->log_pp;
aa_class->class_wt = cmodel->strct->class_weight;
if (seq){
struct seq *s = seq_copy (seq);
if (computeMembershipAA (aa_prob, s, aa_class)
== EXIT_FAILURE) {
prob_vec_destroy (pvec);
return NULL;
}
seq_destroy (s);
} else if (sp) {
if (computeMembershipAAProf (aa_prob, sp, aa_class)
== EXIT_FAILURE) {
prob_vec_destroy (pvec);
return NULL;
}
}
free (aa_class);
for (i = 0; i < n_pvec; i++)
for (j = 0; j < cmodel->strct->n_class; j++)
pvec->mship[i][j] *= aa_prob[i][j];
kill_f_matrix (aa_prob);
}
if (norm == YES) {
for (i = 0; i < n_pvec; i++){
double sum = 0.0;
for (j = 0; j < cmodel->strct->n_class; j++)
sum += pvec->mship[i][j];
for (j = 0; j < cmodel->strct->n_class; j++)
pvec->mship[i][j] /= sum;
}
pvec->norm_type = PVEC_TRUE_PROB;
}
}
/*shoffmann*/
compnd_len = structure->compnd_len;
/*finally read compound*/
if(compnd_len > 0){
pvec->compnd = E_MALLOC(compnd_len*sizeof(char));
pvec->compnd = memmove(pvec->compnd, structure->compnd, compnd_len);
}
pvec->compnd_len = compnd_len;
return pvec;
}
/* ---------------- sub_mat_read ------------------------------
*/
struct sub_mat *
sub_mat_read (const char *fname)
{
# ifndef BUFSIZ
# error please define BUFSIZ to around 1024
# endif
fpos_t pos;
struct sub_mat *smat = NULL;
FILE *fp;
char buf [BUFSIZ];
char aanames [ MAX_AA + 3];
const char *this_sub = "read_mat";
const char comment = '#';
if ((fp = mfopen (fname, "r", this_sub)) == NULL)
return NULL;
/* Portably initialise the fpos_t structure
* because =0 is insufficient
*/
if (fgetpos(fp, &pos)) {
mperror (this_sub);
goto broken;
}
smat = E_MALLOC ( sizeof (*smat));
smat -> fname = NULL;
smat -> comment = NULL;
smat->fname = save_str (fname);
while (fgets (buf, BUFSIZ, fp) != NULL) {
if ( buf[0] != comment) {
if (fsetpos (fp, &pos)) {
mperror (this_sub);
goto broken;
}
break;
}
smat->comment = save_str_append (smat->comment, buf);
if (fgetpos(fp, &pos)) {
mperror (this_sub);
goto broken;
}
}
if (fgets (buf, BUFSIZ, fp) == NULL)
goto broken;
memset (aanames, BAD_AA, MAX_AA);
if (get_aa_names (aanames, buf, BAD_AA) == EXIT_FAILURE)
goto broken;
{
int n, m;
for (n = 0; n < MAX_AA; n++)
for ( m = 0; m < MAX_AA; m++)
smat->data[n][m] = (mat_t) INVALID;
}
{
int n = 0;
for ( ;fgets(buf, BUFSIZ, fp) != NULL; n++) {
if (aanames [n] == BAD_AA)
continue;
if (add_to_mat (smat, aanames, buf, n) == EXIT_FAILURE)
err_printf (this_sub, "Ignoring matrix line\n");
}
}
fclose (fp);
return smat;
broken:
fclose (fp);
free_if_not_null (smat->comment);
free_if_not_null (smat->fname);
free_if_not_null (smat);
return NULL;
}
