DataLoader<MData>::
DataLoader(const char* filename, float th, const char* pf_scales,
const BPMatrix::Options& bp_opts, bool use_bp)
: th_(th),
bp_opts_(bp_opts),
use_bp_(use_bp),
filename_(filename),
type_(check_filetype(filename)),
fi_(),
pf_is_(NULL)
{
switch (type_) {
case TP_FA:
case TP_ALN:
case TP_MAF:
fi_ = BOOST_SPIRIT_CLASSIC_NS::file_iterator<>(filename_);
break;
default:
break;
}
if (!fi_) {
std::ostringstream os;
os << filename_ << ": no such file";
throw os.str().c_str();
//return false;
}
pf_is_ = new std::ifstream(pf_scales);
}
static int check_dir_block(ext2_filsys fs,
struct ext2_db_entry2 *db,
void *priv_data)
{
struct dx_dir_info *dx_dir;
#ifdef ENABLE_HTREE
struct dx_dirblock_info *dx_db = 0;
#endif /* ENABLE_HTREE */
struct ext2_dir_entry *dirent, *prev;
ext2_dirhash_t hash;
unsigned int offset = 0;
int dir_modified = 0;
int dot_state;
unsigned int rec_len;
blk64_t block_nr = db->blk;
ext2_ino_t ino = db->ino;
ext2_ino_t subdir_parent;
__u16 links;
struct check_dir_struct *cd;
char *buf;
e2fsck_t ctx;
int problem;
struct ext2_dx_root_info *root;
struct ext2_dx_countlimit *limit;
static dict_t de_dict;
struct problem_context pctx;
int dups_found = 0;
int ret;
int dx_csum_size = 0, de_csum_size = 0;
int failed_csum = 0;
int is_leaf = 1;
cd = (struct check_dir_struct *) priv_data;
buf = cd->buf;
ctx = cd->ctx;
if (ctx->flags & E2F_FLAG_SIGNAL_MASK || ctx->flags & E2F_FLAG_RESTART)
return DIRENT_ABORT;
if (ctx->progress && (ctx->progress)(ctx, 2, cd->count++, cd->max))
return DIRENT_ABORT;
if (EXT2_HAS_RO_COMPAT_FEATURE(fs->super,
EXT4_FEATURE_RO_COMPAT_METADATA_CSUM)) {
dx_csum_size = sizeof(struct ext2_dx_tail);
de_csum_size = sizeof(struct ext2_dir_entry_tail);
}
/*
* Make sure the inode is still in use (could have been
* deleted in the duplicate/bad blocks pass.
*/
if (!(ext2fs_test_inode_bitmap2(ctx->inode_used_map, ino)))
return 0;
cd->pctx.ino = ino;
cd->pctx.blk = block_nr;
cd->pctx.blkcount = db->blockcnt;
cd->pctx.ino2 = 0;
cd->pctx.dirent = 0;
cd->pctx.num = 0;
if (db->blk == 0) {
if (allocate_dir_block(ctx, db, buf, &cd->pctx))
return 0;
block_nr = db->blk;
}
if (db->blockcnt)
dot_state = 2;
else
dot_state = 0;
if (ctx->dirs_to_hash &&
ext2fs_u32_list_test(ctx->dirs_to_hash, ino))
dups_found++;
#if 0
printf("In process_dir_block block %lu, #%d, inode %lu\n", block_nr,
db->blockcnt, ino);
#endif
ehandler_operation(_("reading directory block"));
cd->pctx.errcode = ext2fs_read_dir_block4(fs, block_nr, buf, 0, ino);
ehandler_operation(0);
if (cd->pctx.errcode == EXT2_ET_DIR_CORRUPTED)
cd->pctx.errcode = 0; /* We'll handle this ourselves */
else if (cd->pctx.errcode == EXT2_ET_DIR_CSUM_INVALID) {
cd->pctx.errcode = 0; /* We'll handle this ourselves */
failed_csum = 1;
}
if (cd->pctx.errcode) {
char *buf2;
if (!fix_problem(ctx, PR_2_READ_DIRBLOCK, &cd->pctx)) {
ctx->flags |= E2F_FLAG_ABORT;
return DIRENT_ABORT;
}
ext2fs_new_dir_block(fs, db->blockcnt == 0 ? ino : 0,
EXT2_ROOT_INO, &buf2);
memcpy(buf, buf2, fs->blocksize);
ext2fs_free_mem(&buf2);
}
#ifdef ENABLE_HTREE
dx_dir = e2fsck_get_dx_dir_info(ctx, ino);
if (dx_dir && dx_dir->numblocks) {
if (db->blockcnt >= dx_dir->numblocks) {
if (fix_problem(ctx, PR_2_UNEXPECTED_HTREE_BLOCK,
&pctx)) {
clear_htree(ctx, ino);
dx_dir->numblocks = 0;
dx_db = 0;
goto out_htree;
}
fatal_error(ctx, _("Can not continue."));
}
dx_db = &dx_dir->dx_block[db->blockcnt];
dx_db->type = DX_DIRBLOCK_LEAF;
dx_db->phys = block_nr;
dx_db->min_hash = ~0;
dx_db->max_hash = 0;
dirent = (struct ext2_dir_entry *) buf;
(void) ext2fs_get_rec_len(fs, dirent, &rec_len);
limit = (struct ext2_dx_countlimit *) (buf+8);
if (db->blockcnt == 0) {
root = (struct ext2_dx_root_info *) (buf + 24);
dx_db->type = DX_DIRBLOCK_ROOT;
dx_db->flags |= DX_FLAG_FIRST | DX_FLAG_LAST;
if ((root->reserved_zero ||
root->info_length < 8 ||
root->indirect_levels > 1) &&
fix_problem(ctx, PR_2_HTREE_BAD_ROOT, &cd->pctx)) {
clear_htree(ctx, ino);
dx_dir->numblocks = 0;
dx_db = 0;
}
dx_dir->hashversion = root->hash_version;
if ((dx_dir->hashversion <= EXT2_HASH_TEA) &&
(fs->super->s_flags & EXT2_FLAGS_UNSIGNED_HASH))
dx_dir->hashversion += 3;
dx_dir->depth = root->indirect_levels + 1;
} else if ((dirent->inode == 0) &&
(rec_len == fs->blocksize) &&
(dirent->name_len == 0) &&
(ext2fs_le16_to_cpu(limit->limit) ==
((fs->blocksize - (8 + dx_csum_size)) /
sizeof(struct ext2_dx_entry))))
dx_db->type = DX_DIRBLOCK_NODE;
is_leaf = 0;
}
out_htree:
#endif /* ENABLE_HTREE */
/* Verify checksum. */
if (is_leaf && de_csum_size) {
/* No space for csum? Rebuild dirs in pass 3A. */
if (!ext2fs_dirent_has_tail(fs, (struct ext2_dir_entry *)buf)) {
de_csum_size = 0;
if (e2fsck_dir_will_be_rehashed(ctx, ino))
goto skip_checksum;
if (!fix_problem(cd->ctx, PR_2_LEAF_NODE_MISSING_CSUM,
&cd->pctx))
goto skip_checksum;
e2fsck_rehash_dir_later(ctx, ino);
goto skip_checksum;
}
if (failed_csum) {
char *buf2;
if (!fix_problem(cd->ctx, PR_2_LEAF_NODE_CSUM_INVALID,
&cd->pctx))
goto skip_checksum;
ext2fs_new_dir_block(fs,
db->blockcnt == 0 ? ino : 0,
EXT2_ROOT_INO, &buf2);
memcpy(buf, buf2, fs->blocksize);
ext2fs_free_mem(&buf2);
dir_modified++;
failed_csum = 0;
}
}
/* htree nodes don't use fake dirents to store checksums */
if (!is_leaf)
de_csum_size = 0;
skip_checksum:
dict_init(&de_dict, DICTCOUNT_T_MAX, dict_de_cmp);
prev = 0;
do {
int group;
ext2_ino_t first_unused_inode;
problem = 0;
dirent = (struct ext2_dir_entry *) (buf + offset);
(void) ext2fs_get_rec_len(fs, dirent, &rec_len);
cd->pctx.dirent = dirent;
cd->pctx.num = offset;
if (((offset + rec_len) > fs->blocksize) ||
(rec_len < 12) ||
((rec_len % 4) != 0) ||
(((dirent->name_len & (unsigned) 0xFF)+8) > rec_len)) {
if (fix_problem(ctx, PR_2_DIR_CORRUPTED, &cd->pctx)) {
salvage_directory(fs, dirent, prev, &offset);
dir_modified++;
continue;
} else
goto abort_free_dict;
}
if (dot_state == 0) {
if (check_dot(ctx, dirent, ino, &cd->pctx))
dir_modified++;
} else if (dot_state == 1) {
ret = check_dotdot(ctx, dirent, ino, &cd->pctx);
if (ret < 0)
goto abort_free_dict;
if (ret)
dir_modified++;
} else if (dirent->inode == ino) {
problem = PR_2_LINK_DOT;
if (fix_problem(ctx, PR_2_LINK_DOT, &cd->pctx)) {
dirent->inode = 0;
dir_modified++;
goto next;
}
}
if (!dirent->inode)
goto next;
/*
* Make sure the inode listed is a legal one.
*/
if (((dirent->inode != EXT2_ROOT_INO) &&
(dirent->inode < EXT2_FIRST_INODE(fs->super))) ||
(dirent->inode > fs->super->s_inodes_count)) {
problem = PR_2_BAD_INO;
} else if (ctx->inode_bb_map &&
(ext2fs_test_inode_bitmap2(ctx->inode_bb_map,
dirent->inode))) {
/*
* If the inode is in a bad block, offer to
* clear it.
*/
problem = PR_2_BB_INODE;
} else if ((dot_state > 1) &&
((dirent->name_len & 0xFF) == 1) &&
(dirent->name[0] == '.')) {
/*
* If there's a '.' entry in anything other
* than the first directory entry, it's a
* duplicate entry that should be removed.
*/
problem = PR_2_DUP_DOT;
} else if ((dot_state > 1) &&
((dirent->name_len & 0xFF) == 2) &&
(dirent->name[0] == '.') &&
(dirent->name[1] == '.')) {
/*
* If there's a '..' entry in anything other
* than the second directory entry, it's a
* duplicate entry that should be removed.
*/
problem = PR_2_DUP_DOT_DOT;
} else if ((dot_state > 1) &&
(dirent->inode == EXT2_ROOT_INO)) {
/*
* Don't allow links to the root directory.
* We check this specially to make sure we
* catch this error case even if the root
* directory hasn't been created yet.
*/
problem = PR_2_LINK_ROOT;
} else if ((dot_state > 1) &&
(dirent->name_len & 0xFF) == 0) {
/*
* Don't allow zero-length directory names.
*/
problem = PR_2_NULL_NAME;
}
if (problem) {
if (fix_problem(ctx, problem, &cd->pctx)) {
dirent->inode = 0;
dir_modified++;
goto next;
} else {
ext2fs_unmark_valid(fs);
if (problem == PR_2_BAD_INO)
goto next;
}
}
/*
* If the inode was marked as having bad fields in
* pass1, process it and offer to fix/clear it.
* (We wait until now so that we can display the
* pathname to the user.)
*/
if (ctx->inode_bad_map &&
ext2fs_test_inode_bitmap2(ctx->inode_bad_map,
dirent->inode)) {
if (e2fsck_process_bad_inode(ctx, ino,
dirent->inode,
buf + fs->blocksize)) {
dirent->inode = 0;
dir_modified++;
goto next;
}
if (ctx->flags & E2F_FLAG_SIGNAL_MASK)
return DIRENT_ABORT;
}
group = ext2fs_group_of_ino(fs, dirent->inode);
first_unused_inode = group * fs->super->s_inodes_per_group +
1 + fs->super->s_inodes_per_group -
ext2fs_bg_itable_unused(fs, group);
cd->pctx.group = group;
/*
* Check if the inode was missed out because
* _INODE_UNINIT flag was set or bg_itable_unused was
* incorrect. If so, clear the _INODE_UNINIT flag and
* restart e2fsck. In the future it would be nice if
* we could call a function in pass1.c that checks the
* newly visible inodes.
*/
if (ext2fs_bg_flags_test(fs, group, EXT2_BG_INODE_UNINIT)) {
pctx.num = dirent->inode;
if (fix_problem(ctx, PR_2_INOREF_BG_INO_UNINIT,
&cd->pctx)){
ext2fs_bg_flags_clear(fs, group,
EXT2_BG_INODE_UNINIT);
ext2fs_mark_super_dirty(fs);
ctx->flags |= E2F_FLAG_RESTART_LATER;
} else {
ext2fs_unmark_valid(fs);
if (problem == PR_2_BAD_INO)
goto next;
}
} else if (dirent->inode >= first_unused_inode) {
pctx.num = dirent->inode;
if (fix_problem(ctx, PR_2_INOREF_IN_UNUSED, &cd->pctx)){
ext2fs_bg_itable_unused_set(fs, group, 0);
ext2fs_mark_super_dirty(fs);
ctx->flags |= E2F_FLAG_RESTART_LATER;
} else {
ext2fs_unmark_valid(fs);
if (problem == PR_2_BAD_INO)
goto next;
}
}
/*
* Offer to clear unused inodes; if we are going to be
* restarting the scan due to bg_itable_unused being
* wrong, then don't clear any inodes to avoid zapping
* inodes that were skipped during pass1 due to an
* incorrect bg_itable_unused; we'll get any real
* problems after we restart.
*/
if (!(ctx->flags & E2F_FLAG_RESTART_LATER) &&
!(ext2fs_test_inode_bitmap2(ctx->inode_used_map,
dirent->inode)))
problem = PR_2_UNUSED_INODE;
if (problem) {
if (fix_problem(ctx, problem, &cd->pctx)) {
dirent->inode = 0;
dir_modified++;
goto next;
} else {
ext2fs_unmark_valid(fs);
if (problem == PR_2_BAD_INO)
goto next;
}
}
if (check_name(ctx, dirent, ino, &cd->pctx))
dir_modified++;
if (check_filetype(ctx, dirent, ino, &cd->pctx))
dir_modified++;
#ifdef ENABLE_HTREE
if (dx_db) {
ext2fs_dirhash(dx_dir->hashversion, dirent->name,
(dirent->name_len & 0xFF),
fs->super->s_hash_seed, &hash, 0);
if (hash < dx_db->min_hash)
dx_db->min_hash = hash;
if (hash > dx_db->max_hash)
dx_db->max_hash = hash;
}
#endif
/*
* If this is a directory, then mark its parent in its
* dir_info structure. If the parent field is already
* filled in, then this directory has more than one
* hard link. We assume the first link is correct,
* and ask the user if he/she wants to clear this one.
*/
if ((dot_state > 1) &&
(ext2fs_test_inode_bitmap2(ctx->inode_dir_map,
dirent->inode))) {
if (e2fsck_dir_info_get_parent(ctx, dirent->inode,
&subdir_parent)) {
cd->pctx.ino = dirent->inode;
fix_problem(ctx, PR_2_NO_DIRINFO, &cd->pctx);
goto abort_free_dict;
}
if (subdir_parent) {
cd->pctx.ino2 = subdir_parent;
if (fix_problem(ctx, PR_2_LINK_DIR,
&cd->pctx)) {
dirent->inode = 0;
dir_modified++;
goto next;
}
cd->pctx.ino2 = 0;
} else {
(void) e2fsck_dir_info_set_parent(ctx,
dirent->inode, ino);
}
}
if (dups_found) {
;
} else if (dict_lookup(&de_dict, dirent)) {
clear_problem_context(&pctx);
pctx.ino = ino;
pctx.dirent = dirent;
fix_problem(ctx, PR_2_REPORT_DUP_DIRENT, &pctx);
e2fsck_rehash_dir_later(ctx, ino);
dups_found++;
} else
dict_alloc_insert(&de_dict, dirent, dirent);
ext2fs_icount_increment(ctx->inode_count, dirent->inode,
&links);
if (links > 1)
ctx->fs_links_count++;
ctx->fs_total_count++;
next:
prev = dirent;
if (dir_modified)
(void) ext2fs_get_rec_len(fs, dirent, &rec_len);
offset += rec_len;
dot_state++;
} while (offset < fs->blocksize - de_csum_size);
#if 0
printf("\n");
#endif
#ifdef ENABLE_HTREE
if (dx_db) {
#ifdef DX_DEBUG
printf("db_block %d, type %d, min_hash 0x%0x, max_hash 0x%0x\n",
db->blockcnt, dx_db->type,
dx_db->min_hash, dx_db->max_hash);
#endif
cd->pctx.dir = cd->pctx.ino;
if ((dx_db->type == DX_DIRBLOCK_ROOT) ||
(dx_db->type == DX_DIRBLOCK_NODE))
parse_int_node(fs, db, cd, dx_dir, buf, failed_csum);
}
#endif /* ENABLE_HTREE */
if (offset != fs->blocksize - de_csum_size) {
cd->pctx.num = rec_len - (fs->blocksize - de_csum_size) +
offset;
if (fix_problem(ctx, PR_2_FINAL_RECLEN, &cd->pctx)) {
dirent->rec_len = cd->pctx.num;
dir_modified++;
}
}
if (dir_modified) {
/* leaf block with no tail? Rehash dirs later. */
if (EXT2_HAS_RO_COMPAT_FEATURE(fs->super,
EXT4_FEATURE_RO_COMPAT_METADATA_CSUM) &&
is_leaf &&
!ext2fs_dirent_has_tail(fs, (struct ext2_dir_entry *)buf))
e2fsck_rehash_dir_later(ctx, ino);
write_and_fix:
if (e2fsck_dir_will_be_rehashed(ctx, ino))
ctx->fs->flags |= EXT2_FLAG_IGNORE_CSUM_ERRORS;
cd->pctx.errcode = ext2fs_write_dir_block4(fs, block_nr, buf,
0, ino);
if (e2fsck_dir_will_be_rehashed(ctx, ino))
ctx->fs->flags &= ~EXT2_FLAG_IGNORE_CSUM_ERRORS;
if (cd->pctx.errcode) {
if (!fix_problem(ctx, PR_2_WRITE_DIRBLOCK,
&cd->pctx))
goto abort_free_dict;
}
ext2fs_mark_changed(fs);
} else if (is_leaf && failed_csum && !dir_modified) {
/*
* If a leaf node that fails csum makes it this far without
* alteration, ask the user if the checksum should be fixed.
*/
if (fix_problem(ctx, PR_2_LEAF_NODE_ONLY_CSUM_INVALID,
&cd->pctx))
goto write_and_fix;
}
dict_free_nodes(&de_dict);
return 0;
abort_free_dict:
ctx->flags |= E2F_FLAG_ABORT;
dict_free_nodes(&de_dict);
return DIRENT_ABORT;
}
static int check_dir_block(ext2_filsys fs,
struct ext2_db_entry *db,
void *priv_data)
{
struct dx_dir_info *dx_dir;
#ifdef ENABLE_HTREE
struct dx_dirblock_info *dx_db = 0;
#endif
struct ext2_dir_entry *dirent, *prev;
ext2_dirhash_t hash;
unsigned int offset = 0;
const char * old_op;
int dir_modified = 0;
int dot_state;
unsigned int rec_len;
blk_t block_nr = db->blk;
ext2_ino_t ino = db->ino;
ext2_ino_t subdir_parent;
__u16 links;
struct check_dir_struct *cd;
char *buf;
e2fsck_t ctx;
int problem;
struct ext2_dx_root_info *root;
struct ext2_dx_countlimit *limit;
static dict_t de_dict;
struct problem_context pctx;
int dups_found = 0;
int ret;
cd = (struct check_dir_struct *) priv_data;
buf = cd->buf;
ctx = cd->ctx;
if (ctx->flags & E2F_FLAG_SIGNAL_MASK || ctx->flags & E2F_FLAG_RESTART)
return DIRENT_ABORT;
if (ctx->progress && (ctx->progress)(ctx, 2, cd->count++, cd->max))
return DIRENT_ABORT;
if (!(ext2fs_test_inode_bitmap(ctx->inode_used_map, ino)))
return 0;
cd->pctx.ino = ino;
cd->pctx.blk = block_nr;
cd->pctx.blkcount = db->blockcnt;
cd->pctx.ino2 = 0;
cd->pctx.dirent = 0;
cd->pctx.num = 0;
if (db->blk == 0) {
if (allocate_dir_block(ctx, db, buf, &cd->pctx))
return 0;
block_nr = db->blk;
}
if (db->blockcnt)
dot_state = 2;
else
dot_state = 0;
if (ctx->dirs_to_hash &&
ext2fs_u32_list_test(ctx->dirs_to_hash, ino))
dups_found++;
#if 0
printf("In process_dir_block block %lu, #%d, inode %lu\n", block_nr,
db->blockcnt, ino);
#endif
old_op = ehandler_operation(_("reading directory block"));
cd->pctx.errcode = ext2fs_read_dir_block(fs, block_nr, buf);
ehandler_operation(0);
if (cd->pctx.errcode == EXT2_ET_DIR_CORRUPTED)
cd->pctx.errcode = 0;
if (cd->pctx.errcode) {
if (!fix_problem(ctx, PR_2_READ_DIRBLOCK, &cd->pctx)) {
ctx->flags |= E2F_FLAG_ABORT;
return DIRENT_ABORT;
}
memset(buf, 0, fs->blocksize);
}
#ifdef ENABLE_HTREE
dx_dir = e2fsck_get_dx_dir_info(ctx, ino);
if (dx_dir && dx_dir->numblocks) {
if (db->blockcnt >= dx_dir->numblocks) {
if (fix_problem(ctx, PR_2_UNEXPECTED_HTREE_BLOCK,
&pctx)) {
clear_htree(ctx, ino);
dx_dir->numblocks = 0;
dx_db = 0;
goto out_htree;
}
fatal_error(ctx, _("Can not continue."));
}
dx_db = &dx_dir->dx_block[db->blockcnt];
dx_db->type = DX_DIRBLOCK_LEAF;
dx_db->phys = block_nr;
dx_db->min_hash = ~0;
dx_db->max_hash = 0;
dirent = (struct ext2_dir_entry *) buf;
(void) ext2fs_get_rec_len(fs, dirent, &rec_len);
limit = (struct ext2_dx_countlimit *) (buf+8);
if (db->blockcnt == 0) {
root = (struct ext2_dx_root_info *) (buf + 24);
dx_db->type = DX_DIRBLOCK_ROOT;
dx_db->flags |= DX_FLAG_FIRST | DX_FLAG_LAST;
if ((root->reserved_zero ||
root->info_length < 8 ||
root->indirect_levels > 1) &&
fix_problem(ctx, PR_2_HTREE_BAD_ROOT, &cd->pctx)) {
clear_htree(ctx, ino);
dx_dir->numblocks = 0;
dx_db = 0;
}
dx_dir->hashversion = root->hash_version;
if ((dx_dir->hashversion <= EXT2_HASH_TEA) &&
(fs->super->s_flags & EXT2_FLAGS_UNSIGNED_HASH))
dx_dir->hashversion += 3;
dx_dir->depth = root->indirect_levels + 1;
} else if ((dirent->inode == 0) &&
(rec_len == fs->blocksize) &&
(dirent->name_len == 0) &&
(ext2fs_le16_to_cpu(limit->limit) ==
((fs->blocksize-8) /
sizeof(struct ext2_dx_entry))))
dx_db->type = DX_DIRBLOCK_NODE;
}
out_htree:
#endif
dict_init(&de_dict, DICTCOUNT_T_MAX, dict_de_cmp);
prev = 0;
do {
int group;
ext2_ino_t first_unused_inode;
problem = 0;
dirent = (struct ext2_dir_entry *) (buf + offset);
(void) ext2fs_get_rec_len(fs, dirent, &rec_len);
cd->pctx.dirent = dirent;
cd->pctx.num = offset;
if (((offset + rec_len) > fs->blocksize) ||
(rec_len < 12) ||
((rec_len % 4) != 0) ||
(((dirent->name_len & (unsigned) 0xFF)+8) > rec_len)) {
if (fix_problem(ctx, PR_2_DIR_CORRUPTED, &cd->pctx)) {
salvage_directory(fs, dirent, prev, &offset);
dir_modified++;
continue;
} else
goto abort_free_dict;
}
if ((dirent->name_len & 0xFF) > EXT2_NAME_LEN) {
if (fix_problem(ctx, PR_2_FILENAME_LONG, &cd->pctx)) {
dirent->name_len = EXT2_NAME_LEN;
dir_modified++;
}
}
if (dot_state == 0) {
if (check_dot(ctx, dirent, ino, &cd->pctx))
dir_modified++;
} else if (dot_state == 1) {
ret = check_dotdot(ctx, dirent, ino, &cd->pctx);
if (ret < 0)
goto abort_free_dict;
if (ret)
dir_modified++;
} else if (dirent->inode == ino) {
problem = PR_2_LINK_DOT;
if (fix_problem(ctx, PR_2_LINK_DOT, &cd->pctx)) {
dirent->inode = 0;
dir_modified++;
goto next;
}
}
if (!dirent->inode)
goto next;
if (((dirent->inode != EXT2_ROOT_INO) &&
(dirent->inode < EXT2_FIRST_INODE(fs->super))) ||
(dirent->inode > fs->super->s_inodes_count)) {
problem = PR_2_BAD_INO;
} else if (ctx->inode_bb_map &&
(ext2fs_test_inode_bitmap(ctx->inode_bb_map,
dirent->inode))) {
problem = PR_2_BB_INODE;
} else if ((dot_state > 1) &&
((dirent->name_len & 0xFF) == 1) &&
(dirent->name[0] == '.')) {
problem = PR_2_DUP_DOT;
} else if ((dot_state > 1) &&
((dirent->name_len & 0xFF) == 2) &&
(dirent->name[0] == '.') &&
(dirent->name[1] == '.')) {
problem = PR_2_DUP_DOT_DOT;
} else if ((dot_state > 1) &&
(dirent->inode == EXT2_ROOT_INO)) {
problem = PR_2_LINK_ROOT;
} else if ((dot_state > 1) &&
(dirent->name_len & 0xFF) == 0) {
problem = PR_2_NULL_NAME;
}
if (problem) {
if (fix_problem(ctx, problem, &cd->pctx)) {
dirent->inode = 0;
dir_modified++;
goto next;
} else {
ext2fs_unmark_valid(fs);
if (problem == PR_2_BAD_INO)
goto next;
}
}
if (ctx->inode_bad_map &&
ext2fs_test_inode_bitmap(ctx->inode_bad_map,
dirent->inode)) {
if (e2fsck_process_bad_inode(ctx, ino,
dirent->inode,
buf + fs->blocksize)) {
dirent->inode = 0;
dir_modified++;
goto next;
}
if (ctx->flags & E2F_FLAG_SIGNAL_MASK)
return DIRENT_ABORT;
}
group = ext2fs_group_of_ino(fs, dirent->inode);
first_unused_inode = group * fs->super->s_inodes_per_group +
1 + fs->super->s_inodes_per_group -
fs->group_desc[group].bg_itable_unused;
cd->pctx.group = group;
if (fs->group_desc[group].bg_flags & EXT2_BG_INODE_UNINIT) {
pctx.num = dirent->inode;
if (fix_problem(ctx, PR_2_INOREF_BG_INO_UNINIT,
&cd->pctx)){
fs->group_desc[group].bg_flags &=
~EXT2_BG_INODE_UNINIT;
ext2fs_mark_super_dirty(fs);
ctx->flags |= E2F_FLAG_RESTART_LATER;
} else {
ext2fs_unmark_valid(fs);
if (problem == PR_2_BAD_INO)
goto next;
}
} else if (dirent->inode >= first_unused_inode) {
pctx.num = dirent->inode;
if (fix_problem(ctx, PR_2_INOREF_IN_UNUSED, &cd->pctx)){
fs->group_desc[group].bg_itable_unused = 0;
ext2fs_mark_super_dirty(fs);
ctx->flags |= E2F_FLAG_RESTART_LATER;
} else {
ext2fs_unmark_valid(fs);
if (problem == PR_2_BAD_INO)
goto next;
}
}
if (!(ctx->flags & E2F_FLAG_RESTART_LATER) &&
!(ext2fs_test_inode_bitmap(ctx->inode_used_map,
dirent->inode)))
problem = PR_2_UNUSED_INODE;
if (problem) {
if (fix_problem(ctx, problem, &cd->pctx)) {
dirent->inode = 0;
dir_modified++;
goto next;
} else {
ext2fs_unmark_valid(fs);
if (problem == PR_2_BAD_INO)
goto next;
}
}
if (check_name(ctx, dirent, ino, &cd->pctx))
dir_modified++;
if (check_filetype(ctx, dirent, ino, &cd->pctx))
dir_modified++;
#ifdef ENABLE_HTREE
if (dx_db) {
ext2fs_dirhash(dx_dir->hashversion, dirent->name,
(dirent->name_len & 0xFF),
fs->super->s_hash_seed, &hash, 0);
if (hash < dx_db->min_hash)
dx_db->min_hash = hash;
if (hash > dx_db->max_hash)
dx_db->max_hash = hash;
}
#endif
if ((dot_state > 1) &&
(ext2fs_test_inode_bitmap(ctx->inode_dir_map,
dirent->inode))) {
if (e2fsck_dir_info_get_parent(ctx, dirent->inode,
&subdir_parent)) {
cd->pctx.ino = dirent->inode;
fix_problem(ctx, PR_2_NO_DIRINFO, &cd->pctx);
goto abort_free_dict;
}
if (subdir_parent) {
cd->pctx.ino2 = subdir_parent;
if (fix_problem(ctx, PR_2_LINK_DIR,
&cd->pctx)) {
dirent->inode = 0;
dir_modified++;
goto next;
}
cd->pctx.ino2 = 0;
} else {
(void) e2fsck_dir_info_set_parent(ctx,
dirent->inode, ino);
}
}
if (dups_found) {
;
} else if (dict_lookup(&de_dict, dirent)) {
clear_problem_context(&pctx);
pctx.ino = ino;
pctx.dirent = dirent;
fix_problem(ctx, PR_2_REPORT_DUP_DIRENT, &pctx);
if (!ctx->dirs_to_hash)
ext2fs_u32_list_create(&ctx->dirs_to_hash, 50);
if (ctx->dirs_to_hash)
ext2fs_u32_list_add(ctx->dirs_to_hash, ino);
dups_found++;
} else
dict_alloc_insert(&de_dict, dirent, dirent);
ext2fs_icount_increment(ctx->inode_count, dirent->inode,
&links);
if (links > 1)
ctx->fs_links_count++;
ctx->fs_total_count++;
next:
prev = dirent;
if (dir_modified)
(void) ext2fs_get_rec_len(fs, dirent, &rec_len);
offset += rec_len;
dot_state++;
} while (offset < fs->blocksize);
#if 0
printf("\n");
#endif
#ifdef ENABLE_HTREE
if (dx_db) {
#ifdef DX_DEBUG
printf("db_block %d, type %d, min_hash 0x%0x, max_hash 0x%0x\n",
db->blockcnt, dx_db->type,
dx_db->min_hash, dx_db->max_hash);
#endif
cd->pctx.dir = cd->pctx.ino;
if ((dx_db->type == DX_DIRBLOCK_ROOT) ||
(dx_db->type == DX_DIRBLOCK_NODE))
parse_int_node(fs, db, cd, dx_dir, buf);
}
#endif
if (offset != fs->blocksize) {
cd->pctx.num = rec_len - fs->blocksize + offset;
if (fix_problem(ctx, PR_2_FINAL_RECLEN, &cd->pctx)) {
dirent->rec_len = cd->pctx.num;
dir_modified++;
}
}
if (dir_modified) {
cd->pctx.errcode = ext2fs_write_dir_block(fs, block_nr, buf);
if (cd->pctx.errcode) {
if (!fix_problem(ctx, PR_2_WRITE_DIRBLOCK,
&cd->pctx))
goto abort_free_dict;
}
ext2fs_mark_changed(fs);
}
dict_free_nodes(&de_dict);
return 0;
abort_free_dict:
ctx->flags |= E2F_FLAG_ABORT;
dict_free_nodes(&de_dict);
return DIRENT_ABORT;
}
void unpack_extension( char *package )
{
int error;
int fd;
char tmp[2048];
int ftype;
fwrite( "Uncompressing files...", 1, 22, stdout );
memcpy( TMPDIR, "/tmp/grass.extension.XXXXXX", 28 );
mkstemp( TMPDIR );
fd = open( TMPDIR, 64, 511 );
if ( fd == -1 )
{
print_error( -7, "could not create temp directory name: %s", strerror( *(int*)(__errno_location( )) ) );
exit( -7 );
}
if ( VERBOSE )
fprintf( stdout, "\nUncompressing to: %s.\n", TMPDIR );
close( fd );
remove( TMPDIR );
mkdir_s( TMPDIR, "0700" );
atexit( &exit_tmp );
sprintf( tmp, "cp %s %s", package, TMPDIR );
error = system( tmp );
if ( error < 0 )
{
print_error( -7, "could not copy extension files to temp dir.\n" );
exit( -7 );
}
ftype = check_filetype( package );
if ( ftype == 0 )
{
print_warning( "file name not '.tar.gz', '.tgz', '.tar.bz2', '.tbz' or '.zip'. Assuming '.tgz'.\n" );
ftype = 1;
}
if ( ftype == 1 )
{
if ( VERBOSE )
{
sprintf( tmp, "tar -xzvf %s/%s -C %s", TMPDIR, basename( package ), TMPDIR );
}
else
{
sprintf( tmp, "tar -xzf %s/%s -C %s", TMPDIR, basename( package ), TMPDIR );
}
}
if ( ftype == 2 )
{
if ( VERBOSE )
{
sprintf( tmp, "tar -xjvf %s/%s -C %s", TMPDIR, basename( package ), TMPDIR );
}
else
{
sprintf( tmp, "tar -xjvf %s/%s -C %s", TMPDIR, basename( package ), TMPDIR );
}
}
if ( ftype == 3 )
{
if ( VERBOSE )
{
sprintf( tmp, "unzip %s/%s -d %s", TMPDIR, basename( package ), TMPDIR );
}
else
{
sprintf( tmp, "unzip -qq %s/%s -d %s", TMPDIR, basename( package ), TMPDIR );
}
}
if ( ftype == 4 )
{
if ( VERBOSE )
{
sprintf( tmp, "tar -xvf %s/%s -C %s", TMPDIR, basename( package ), TMPDIR );
}
else
{
sprintf( tmp, "tar -xf %s/%s -C %s", TMPDIR, basename( package ), TMPDIR );
}
}
error = system( tmp );
if ( error < 0 )
{
if ( ftype == 1 )
print_error( -7, "could not extract files using 'tar' and 'gzip'. \n \t\t\t\t\tExtract manually using 'tar -xzvf %s'.\n", package );
if ( ftype == 2 )
print_error( -7, "could not extract files using 'tar' and 'bunzip2'.\n \t\t\t\tExtract manually using 'tar -xjvf %s'.\n", package );
if ( ftype == 3 )
print_error( -7, "could not extract files using 'unzip'.\n \t\t\t\tExtract manually using 'unzip %s'.\n", package );
exit( -7 );
}
else
{
print_done( );
return;
}
}
static int check_dir_block(ext2_filsys fs,
struct ext2_db_entry *db,
void *priv_data)
{
struct dir_info *subdir, *dir;
struct ext2_dir_entry *dirent;
int offset = 0;
int dir_modified = 0;
int dot_state;
blk_t block_nr = db->blk;
ext2_ino_t ino = db->ino;
__u16 links;
struct check_dir_struct *cd;
char *buf;
e2fsck_t ctx;
int problem;
cd = (struct check_dir_struct *) priv_data;
buf = cd->buf;
ctx = cd->ctx;
if (ctx->progress)
if ((ctx->progress)(ctx, 2, cd->count++, cd->max))
return DIRENT_ABORT;
/*
* Make sure the inode is still in use (could have been
* deleted in the duplicate/bad blocks pass.
*/
if (!(ext2fs_test_inode_bitmap(ctx->inode_used_map, ino)))
return 0;
cd->pctx.ino = ino;
cd->pctx.blk = block_nr;
cd->pctx.blkcount = db->blockcnt;
cd->pctx.ino2 = 0;
cd->pctx.dirent = 0;
cd->pctx.num = 0;
if (db->blk == 0) {
if (allocate_dir_block(ctx, db, buf, &cd->pctx))
return 0;
block_nr = db->blk;
}
if (db->blockcnt)
dot_state = 2;
else
dot_state = 0;
#if 0
printf("In process_dir_block block %lu, #%d, inode %lu\n", block_nr,
db->blockcnt, ino);
#endif
cd->pctx.errcode = ext2fs_read_dir_block(fs, block_nr, buf);
if (cd->pctx.errcode == EXT2_ET_DIR_CORRUPTED)
cd->pctx.errcode = 0; /* We'll handle this ourselves */
if (cd->pctx.errcode) {
if (!fix_problem(ctx, PR_2_READ_DIRBLOCK, &cd->pctx)) {
ctx->flags |= E2F_FLAG_ABORT;
return DIRENT_ABORT;
}
memset(buf, 0, fs->blocksize);
}
do {
dot_state++;
problem = 0;
dirent = (struct ext2_dir_entry *) (buf + offset);
cd->pctx.dirent = dirent;
cd->pctx.num = offset;
if (((offset + dirent->rec_len) > fs->blocksize) ||
(dirent->rec_len < 12) ||
((dirent->rec_len % 4) != 0) ||
(((dirent->name_len & 0xFF)+8) > dirent->rec_len)) {
if (fix_problem(ctx, PR_2_DIR_CORRUPTED, &cd->pctx)) {
dirent->rec_len = fs->blocksize - offset;
dirent->name_len = 0;
dirent->inode = 0;
dir_modified++;
} else
return DIRENT_ABORT;
}
if ((dirent->name_len & 0xFF) > EXT2_NAME_LEN) {
if (fix_problem(ctx, PR_2_FILENAME_LONG, &cd->pctx)) {
dirent->name_len = EXT2_NAME_LEN;
dir_modified++;
}
}
if (dot_state == 1) {
if (check_dot(ctx, dirent, ino, &cd->pctx))
dir_modified++;
} else if (dot_state == 2) {
dir = e2fsck_get_dir_info(ctx, ino);
if (!dir) {
fix_problem(ctx, PR_2_NO_DIRINFO, &cd->pctx);
ctx->flags |= E2F_FLAG_ABORT;
return DIRENT_ABORT;
}
if (check_dotdot(ctx, dirent, dir, &cd->pctx))
dir_modified++;
} else if (dirent->inode == ino) {
problem = PR_2_LINK_DOT;
if (fix_problem(ctx, PR_2_LINK_DOT, &cd->pctx)) {
dirent->inode = 0;
dir_modified++;
goto next;
}
}
if (!dirent->inode)
goto next;
/*
* Make sure the inode listed is a legal one.
*/
if (((dirent->inode != EXT2_ROOT_INO) &&
(dirent->inode < EXT2_FIRST_INODE(fs->super))) ||
(dirent->inode > fs->super->s_inodes_count)) {
problem = PR_2_BAD_INO;
} else if (!(ext2fs_test_inode_bitmap(ctx->inode_used_map,
dirent->inode))) {
/*
* If the inode is unused, offer to clear it.
*/
problem = PR_2_UNUSED_INODE;
} else if (ctx->inode_bb_map &&
(ext2fs_test_inode_bitmap(ctx->inode_bb_map,
dirent->inode))) {
/*
* If the inode is in a bad block, offer to
* clear it.
*/
problem = PR_2_BB_INODE;
} else if ((dot_state > 2) &&
((dirent->name_len & 0xFF) == 1) &&
(dirent->name[0] == '.')) {
/*
* If there's a '.' entry in anything other
* than the first directory entry, it's a
* duplicate entry that should be removed.
*/
problem = PR_2_DUP_DOT;
} else if ((dot_state > 2) &&
((dirent->name_len & 0xFF) == 2) &&
(dirent->name[0] == '.') &&
(dirent->name[1] == '.')) {
/*
* If there's a '..' entry in anything other
* than the second directory entry, it's a
* duplicate entry that should be removed.
*/
problem = PR_2_DUP_DOT_DOT;
} else if ((dot_state > 2) &&
(dirent->inode == EXT2_ROOT_INO)) {
/*
* Don't allow links to the root directory.
* We check this specially to make sure we
* catch this error case even if the root
* directory hasn't been created yet.
*/
problem = PR_2_LINK_ROOT;
} else if ((dot_state > 2) &&
(dirent->name_len & 0xFF) == 0) {
/*
* Don't allow zero-length directory names.
*/
problem = PR_2_NULL_NAME;
}
if (problem) {
if (fix_problem(ctx, problem, &cd->pctx)) {
dirent->inode = 0;
dir_modified++;
goto next;
} else {
ext2fs_unmark_valid(fs);
if (problem == PR_2_BAD_INO)
goto next;
}
}
/*
* If the inode was marked as having bad fields in
* pass1, process it and offer to fix/clear it.
* (We wait until now so that we can display the
* pathname to the user.)
*/
if (ctx->inode_bad_map &&
ext2fs_test_inode_bitmap(ctx->inode_bad_map,
dirent->inode)) {
if (e2fsck_process_bad_inode(ctx, ino,
dirent->inode)) {
dirent->inode = 0;
dir_modified++;
goto next;
}
if (ctx->flags & E2F_FLAG_SIGNAL_MASK)
return DIRENT_ABORT;
}
if (check_name(ctx, dirent, ino, &cd->pctx))
dir_modified++;
if (check_filetype(ctx, dirent, ino, &cd->pctx))
dir_modified++;
/*
* If this is a directory, then mark its parent in its
* dir_info structure. If the parent field is already
* filled in, then this directory has more than one
* hard link. We assume the first link is correct,
* and ask the user if he/she wants to clear this one.
*/
if ((dot_state > 2) &&
(ext2fs_test_inode_bitmap(ctx->inode_dir_map,
dirent->inode))) {
subdir = e2fsck_get_dir_info(ctx, dirent->inode);
if (!subdir) {
cd->pctx.ino = dirent->inode;
fix_problem(ctx, PR_2_NO_DIRINFO, &cd->pctx);
ctx->flags |= E2F_FLAG_ABORT;
return DIRENT_ABORT;
}
if (subdir->parent) {
cd->pctx.ino2 = subdir->parent;
if (fix_problem(ctx, PR_2_LINK_DIR,
&cd->pctx)) {
dirent->inode = 0;
dir_modified++;
goto next;
}
cd->pctx.ino2 = 0;
} else
subdir->parent = ino;
}
ext2fs_icount_increment(ctx->inode_count, dirent->inode,
&links);
if (links > 1)
ctx->fs_links_count++;
ctx->fs_total_count++;
next:
offset += dirent->rec_len;
} while (offset < fs->blocksize);
#if 0
printf("\n");
#endif
if (offset != fs->blocksize) {
cd->pctx.num = dirent->rec_len - fs->blocksize + offset;
if (fix_problem(ctx, PR_2_FINAL_RECLEN, &cd->pctx)) {
dirent->rec_len = cd->pctx.num;
dir_modified++;
}
}
if (dir_modified) {
cd->pctx.errcode = ext2fs_write_dir_block(fs, block_nr, buf);
if (cd->pctx.errcode) {
if (!fix_problem(ctx, PR_2_WRITE_DIRBLOCK,
&cd->pctx)) {
ctx->flags |= E2F_FLAG_ABORT;
return DIRENT_ABORT;
}
}
ext2fs_mark_changed(fs);
}
return 0;
}