PageTable* LongModePaging::allocate_page_directory( unsigned pml4_entry_id , unsigned pdpt_entry_id )
{
PageTable* pdp_table = get_next_level_address<PageTable>( pml4 , pml4_entry_id);
if( pdp_table )
{
if(!is_present(pdp_table , pdpt_entry_id))
{
PageTable* table_tmp= gm_memalign<PageTable>( CACHE_LINE_BYTES, 1);
PageTable* pd_table = new (table_tmp) PageTable(ENTRY_512);
validate_entry(pdp_table , pdpt_entry_id , pd_table);
cur_pd_num++;
return pd_table;
}
else
{
PageTable* table = get_next_level_address<PageTable>( pdp_table, pdpt_entry_id);
return table;
}
}
else
{
if(allocate_page_directory_pointer(pml4_entry_id))
{
PageTable* pdpt_table = get_next_level_address<PageTable>(pml4,pml4_entry_id);
PageTable* table_tmp= gm_memalign<PageTable>( CACHE_LINE_BYTES, 1);
PageTable* pd_table=new (table_tmp)PageTable(ENTRY_512);
validate_entry(pdpt_table , pdpt_entry_id , pd_table);
cur_pd_num++;
return pd_table;
}
}
return NULL;
}
/****----basic call back of Legacy-Paging----****/
PageTable* PAEPaging::allocate_page_table( unsigned pdpt_entry_id , unsigned pd_entry_id)
{
//only on PAE-NORMAL mode,can allocate page table
assert( mode == PAE_Normal && cur_pt_num< ENTRY_512);
//page directory
PageTable* table = get_next_level_address<PageTable>( page_directory_pointer , pdpt_entry_id);
PageTable* page=NULL;
if( !table)
{
//page directory
table = new PageTable(ENTRY_512);
validate_entry( page_directory_pointer , pdpt_entry_id , table);
//page table
page = new PageTable(ENTRY_512);
validate_entry( table, pd_entry_id ,page);
cur_pt_num++;
cur_pdt_num++;
return page;
}
else
{
page = get_next_level_address<PageTable>(table,pd_entry_id);
if( !page)
{
//new page table
page = new PageTable(ENTRY_512);
validate_entry(table , pd_entry_id, page);
cur_pt_num++;
}
//page table already exist
}
return page;
}
PageTable* LongModePaging::allocate_page_table(unsigned pml4_entry_id , unsigned pdpt_entry_id , unsigned pdt_entry_id)
{
assert( mode == LongMode_Normal);
PageTable* pdp_table=get_next_level_address<PageTable>(pml4 , pml4_entry_id);
if( pdp_table )
{
PageTable* pd_table=get_next_level_address<PageTable>(pdp_table , pdpt_entry_id);
if(pd_table)
{
if(is_present(pd_table , pdt_entry_id))
{
PageTable* table = get_next_level_address<PageTable>(pd_table,pdt_entry_id);
return table;
}
else
{
PageTable* table_tmp= gm_memalign<PageTable>( CACHE_LINE_BYTES, 1);
PageTable* table = new (table_tmp)PageTable(ENTRY_512);
validate_entry(pd_table , pdt_entry_id ,table );
cur_pt_num++;
return table;
}
}
//page_direcory doesn't exist allocate
else
{
if( allocate_page_directory(pml4_entry_id,pdpt_entry_id))
{
//get page directory
PageTable* page_dir = get_next_level_address<PageTable>( pdp_table , pdpt_entry_id);
PageTable* table= gm_memalign<PageTable>( CACHE_LINE_BYTES, 1);
PageTable* pg_table=new (table)PageTable(ENTRY_512);
validate_entry(page_dir , pdt_entry_id , pg_table );
cur_pt_num++;
return pg_table;
}
}
}
else
{
PageTable* g_tables = gm_memalign<PageTable>(CACHE_LINE_BYTES,3);
PageTable* pdp_table=new (&g_tables[0])PageTable(ENTRY_512);
//std::cout<<"validate pg dir pointer in pml4"<<std::dec<<pml4_entry_id<<std::endl;
validate_entry(pml4,pml4_entry_id,pdp_table);
cur_pdp_num++;
PageTable* pd_table=new (&g_tables[1])PageTable(ENTRY_512);
//std::cout<<"validate page directory table in pg dir pointer"<<std::dec<<pdpt_entry_id<<std::endl;
validate_entry(pdp_table,pdpt_entry_id , pd_table);
cur_pd_num++;
PageTable* pg_table=new (&g_tables[2])PageTable(ENTRY_512);
//std::cout<<"new page table"<<std::endl;
validate_entry(pd_table , pdt_entry_id , pg_table);
//std::cout<<"validate: "<<std::dec<<pml4_entry_id<<","<<std::dec<<pdpt_entry_id<<","<<std::dec<<pdt_entry_id<<std::endl;
cur_pt_num++;
return pg_table;
}
return NULL;
}
/*****-----functional interface of LongMode-Paging----*****/
bool LongModePaging::map_page_table(Address addr , void* pg_ptr , bool pbuffer)
{
//std::cout<<"map:"<<std::hex<<addr<<std::endl;
unsigned pml4,pdp,pd,pt;
get_domains(addr , pml4 , pdp , pd , pt , mode);
unsigned buffer_entry_id = get_buffer_table_off(addr,buffer_table_shift,mode);
assert( (pml4!=(unsigned)(-1)) && (pdp!=(unsigned)(-1)));
PageTable* table;
if( mode == LongMode_Normal)
{
assert( (pd!=(unsigned)(-1)) &&(pt!=(unsigned)(-1)));
table = allocate_page_table(pml4,pdp,pd);
if( !table )
{
debug_printf("allocate page table for LongMode_Normal failed!");
return false;
}
if( pbuffer)
{
//std::cout<<"extend one buffer map"<<std::endl;
extend_one_buffer_map(addr,table,pg_ptr , pt, buffer_entry_id, buffer_table_entry_num);
}
else
{
validate_entry(table , pt , pg_ptr);
}
}
else if( mode == LongMode_Middle )
{
table = allocate_page_directory( pml4 , pdp);
if(!table)
{
debug_printf("allocate page directory for LongMode_Middle failed!");
return false;
}
if( pbuffer )
extend_one_buffer_map(addr , table , pg_ptr , pd , buffer_entry_id , buffer_table_entry_num);
else
validate_entry( table,pd, pg_ptr);
}
else if( mode == LongMode_Huge )
{
table = allocate_page_directory_pointer(pml4);
if(!table)
{
debug_printf("allocate page directory pointer for LongMode_Huge failed!");
return false;
}
if(pbuffer)
extend_one_buffer_map(addr , table ,pg_ptr, pdp,buffer_entry_id , buffer_table_entry_num);
else
validate_entry(table,pdp,pg_ptr);
}
return true;
}
int validate_interleaved(char *f) {
unsigned long cline=1;
unsigned long nreads1=0;
gzFile fd1=NULL;
fprintf(stderr,"Paired-end interleaved\n");
fd1=open_fastq(f);
gzFile fdf=open_fixed_fastq(f);
while(!gzeof(fd1)) {
long start_pos=gztell(fd1);
// Read 1
char *hdr1=READ_LINE_HDR(fd1);
if ( hdr1==NULL) break;
int len;
char *seq1=READ_LINE_SEQ(fd1);
char *hdr1_2=READ_LINE_HDR2(fd1);
char *qual1=READ_LINE_QUAL(fd1);
// Read 2
char *hdr2=READ_LINE_HDR2_1(fd1);
char *seq2=READ_LINE_SEQ2(fd1);
char *hdr2_2=READ_LINE_HDR2_2(fd1);
char *qual2=READ_LINE_QUAL2(fd1);
if ( seq1==NULL || hdr1_2==NULL || qual1==NULL ||
hdr2==NULL || seq2==NULL || hdr2_2==NULL || qual2==NULL ) {
fprintf(stderr,"\nError in file %s, line %lu: file truncated?\n",f,cline);
return(1);
}
if (validate_entry(hdr1,hdr1_2,seq1,qual1,cline,f)!=0) {
return(1);
}
if (validate_entry(hdr2,hdr2_2,seq2,qual2,cline+4,f)!=0) {
return(1);
}
char* readname1=get_readname(hdr1,&len,cline,f);
char* readname2=get_readname(hdr2,&len,cline+4,f);
if ( strcmp(readname1,readname2) ) {
fprintf(stderr,"\nError in file %s, line %lu: unpaired read - %s\n",f,cline,readname1);
return(1);
}
PRINT_READS_PROCESSED(cline/4);
replace_dots(start_pos,seq1,hdr1,hdr1_2,qual1,fdf);
replace_dots(start_pos,seq2,hdr2,hdr2_2,qual2,fdf);
//
cline+=8;
nreads1+=2;
}
printf("\n");
close_fixed_fastq(fdf);
gzclose(fd1);
return(nreads1);
}
int
main(int argc, char **argv)
{
char fbuf[PATH_MAX+1], *fb;
FILE *pwf;
int c;
struct passwd *pw;
struct disk *entry;
while ((c = getopt(argc, argv, "p:u:")) != EOF) {
switch (c) {
case 'u':
if ((nchrg = fopen(optarg, "w")) == NULL)
openerr(optarg);
(void) chmod(optarg, S_IRUSR|S_IWUSR|S_IRGRP|S_IROTH);
break;
case 'p':
pfile = optarg;
break;
default:
exit(1);
}
}
if (pfile) {
if ((pwf = fopen(pfile, "r")) == NULL) {
openerr(pfile);
}
/* fill usglist with the user's in the passwd file */
while ((pw = fgetpwent(pwf)) != NULL) {
if ((entry = hash_find(pw->pw_uid)) == NULL)
entry = hash_insert(pw->pw_uid);
validate_entry(entry, pw);
}
(void) fclose(pwf);
}
/* charge the files listed in names to users listed in the usglist */
while (fgets(fbuf, sizeof (fbuf), stdin) != NULL) {
if ((fb = strchr(fbuf, '\n')) != NULL) {
/*
* replace the newline char at the end of the
* filename with a null character
*/
*fb = '\0';
}
charge(fbuf);
}
output();
if (nchrg)
(void) fclose(nchrg);
#ifdef DEBUG
pdisk();
#endif
return (0);
}
/*****-----functional interface of Legacy-Paging----*****/
bool NormalPaging::map_page_table(Address addr ,void* pg_ptr , bool is_buffer)
{
if( is_buffer )
debug_printf("map address:(%x,%x)",addr);
//update page table
unsigned pd_entry_id = get_page_directory_off( addr , mode );
unsigned buffer_entry_id = get_buffer_table_off(addr,buffer_table_shift,mode);
//4KB small pages
if( mode == Legacy_Normal )
{
unsigned pt_entry_id = get_pagetable_off(addr , mode);
PageTable* table = allocate_one_pagetable( pd_entry_id );
if( !table )
{
return false;
}
if( is_buffer)
{
//main memory block size is equal to buffer block size
extend_one_buffer_map(addr,table,pg_ptr , pt_entry_id ,buffer_entry_id, buffer_table_entry_num);
}
else
{
//debug_printf("validate entry %d",pt_entry_id);
validate_entry(table , pt_entry_id , pg_ptr , false);
}
}
//4MB Huge pages
else if( mode == Legacy_Huge)
{
if( is_buffer)
{
extend_one_buffer_map(addr ,page_directory,pg_ptr,pd_entry_id ,buffer_entry_id, buffer_table_entry_num);
}
else
{
//std::cout<<"validate "<<pd_entry_id<<std::endl;
validate_entry(page_directory,pd_entry_id, pg_ptr, false);
//std::cout<<"validate "<<pd_entry_id<<" end"<<std::endl;
}
}
return true;
}
static void
charge(char *n)
{
struct stat statb;
struct disk *entry;
struct passwd *pw;
if (lstat(n, &statb) == -1)
return;
/*
* do not count the duplicate entries.
*/
if (statb.st_nlink > 1) {
switch (add_tnode(&tree, statb.st_dev, statb.st_ino)) {
case 0:
/* already exist */
return;
case 1:
/* added */
break;
default:
perror("acctdusg");
exit(1);
}
}
/*
* st_blocks is not defined for character/block special files.
*/
if (S_ISCHR(statb.st_mode) || S_ISBLK(statb.st_mode))
statb.st_blocks = 0;
/*
* If -p is given, we've all loaded the passwd entries.
* Files with unknown uid should go into nchrg. Otherwise
* (without -p), we try creating new entry for the uid.
*/
if ((entry = hash_find(statb.st_uid)) == NULL) {
if (pfile == NULL) {
pw = getpwuid(statb.st_uid);
entry = hash_insert(statb.st_uid);
if (pw != NULL) {
validate_entry(entry, pw);
}
}
}
if (entry != NULL && entry->validuser) {
entry->dsk_du += statb.st_blocks;
} else if (nchrg) {
(void) fprintf(nchrg, "%9ld\t%7llu\t%s\n",
statb.st_uid, statb.st_blocks, n);
}
}
PageTable* NormalPaging::allocate_one_pagetable(unsigned pd_entry_id )
{
PageTable* table = get_next_level_address<PageTable>(page_directory,pd_entry_id);
if(table == NULL)
{
assert( cur_page_table_num<= 1024 && mode==Legacy_Normal);
table = new PageTable(ENTRY_1024);
validate_entry(page_directory , pd_entry_id , table);
cur_page_table_num++;
}
return table;
}
void index_file(char *filename,hashtable sn_index,long start_offset,long length) {
gzFile fd1=open_fastq(filename);
gzFile fdf=open_fixed_fastq(filename);
if (fd1==NULL) {
fprintf(stderr,"\nError: Unable to open %s\n",filename);
exit(1);
}
// move to the right position
if(length>0) {
fprintf(stderr, "\nInternal error: Not implemented\n");
exit(2);
}
long cline=1;
// sn_index creation could be done in parallel
while(!gzeof(fd1)) {
long long start_pos=gztell(fd1);
char *hdr=READ_LINE_HDR(fd1);
if ( hdr==NULL) break;
int len;
//fprintf(stderr,"sn_index: =%s=\n",readname);
// get seq
//printf("cline=%ld\nLEN=%ld hdr=%s\n",cline,len,hdr);
char *seq=READ_LINE_SEQ(fd1);
char *hdr2=READ_LINE_HDR2(fd1);
char *qual=READ_LINE_QUAL(fd1);
char* readname=get_readname(hdr,&len,cline,filename);
if (seq==NULL || hdr2==NULL || qual==NULL ) {
fprintf(stderr,"\nError in file %s, line %lu: file truncated?\n",filename,cline);
exit(1);
}
if (validate_entry(hdr,hdr2,seq,qual,cline,filename)!=0) {
exit(1);
}
// check for duplicates
if ( lookup_header(sn_index,readname)!=NULL ) {
fprintf(stderr,"\nError in file %s, line %lu: duplicated sequence %s\n",filename,cline,readname);
exit(1);
}
if ( new_indexentry(sn_index,readname,len,start_pos)==NULL) {
fprintf(stderr,"\nError in file %s, line %lu: malloc failed?",filename,cline);
exit(1);
}
replace_dots(start_pos,seq,hdr,hdr2,qual,fdf);
PRINT_READS_PROCESSED(cline/4);
//
cline+=4;
}
close_fixed_fastq(fdf);
gzclose(fd1);
return;
}
//allocate
PageTable* LongModePaging::allocate_page_directory_pointer( unsigned pml4_entry_id)
{
assert( pml4_entry_id<512 && cur_pdp_num<ENTRY_512);
if( !is_present(pml4, pml4_entry_id))
{
PageTable* table_tmp= gm_memalign<PageTable>( CACHE_LINE_BYTES, 1);
PageTable* table = new (table_tmp) PageTable(ENTRY_512);
validate_entry(pml4 , pml4_entry_id , table);
cur_pdp_num++;
return table;
}
PageTable* pg_dir_p = get_next_level_address<PageTable>( pml4,pml4_entry_id);
return pg_dir_p;
}
/*****-----functional interface of paging----*****/
bool PAEPaging::map_page_table(Address addr, void* pg_ptr , bool pbuffer)
{
unsigned pdp_id = get_page_directory_pointer_off( addr , mode);
unsigned pd_id = get_page_directory_off(addr,mode);
unsigned buffer_entry_id = get_buffer_table_off(addr,buffer_table_shift,mode);
PageTable* table;
if( mode == PAE_Normal)
{
unsigned pt_id = get_pagetable_off(addr , mode);
if( (table = allocate_page_table(pdp_id , pd_id))==NULL )
{
debug_printf("allocate page table failed");
return false;
}
if( pbuffer )
{
extend_one_buffer_map(addr , table , pg_ptr , pt_id , buffer_entry_id , buffer_table_entry_num);
}
else
{
validate_entry(table , pt_id ,pg_ptr);
}
}
else if( mode == PAE_Huge)
{
if( (table=allocate_pdt(pdp_id))==NULL)
{
debug_printf("allocate page directory failed !");
return false;
}
if( pbuffer)
extend_one_buffer_map(addr,table, pg_ptr , pd_id, buffer_entry_id , buffer_table_entry_num);
else
validate_entry( table , pd_id , pg_ptr);
}
return true;
}
PageTable* PAEPaging::allocate_pdt( unsigned pdpt_entry )
{
assert( cur_pdt_num < 4 && pdpt_entry < 4 );
PageTable* page_dir = NULL;
//pdpt_entry of page_direcotry_pointer has already pointed to page directory
if( (page_dir = get_next_level_address<PageTable>(page_directory_pointer, pdpt_entry))!=NULL )
return page_dir;
else
{
//page directory
page_dir=new PageTable(ENTRY_512);
validate_entry( page_directory_pointer , pdpt_entry ,page_dir);
cur_pt_num++;
}
return page_dir;
}
static void
custom_entry_changed_cb (GtkEditable *entry, gpointer user_data)
{
NemoMimeApplicationChooser *chooser = user_data;
const gchar *entry_text = gtk_entry_get_text (GTK_ENTRY (entry));
gboolean empty = g_strcmp0 (entry_text, "") == 0;
if (!empty && validate_entry (GTK_ENTRY (entry), entry_text)) {
GAppInfo *default_app;
gchar *cl = g_strdup_printf ("%s", entry_text);
GAppInfo *info = g_app_info_create_from_commandline (cl, get_nice_name (cl),
G_APP_INFO_CREATE_NONE, NULL);
default_app = g_app_info_get_default_for_type (chooser->details->content_type, FALSE);
gtk_widget_set_sensitive (chooser->details->set_as_default_button,
!g_app_info_equal (info, default_app));
gtk_widget_set_sensitive (chooser->details->add_button,
app_info_can_add (info, chooser->details->content_type));
g_object_unref (default_app);
if (chooser->details->custom_info != NULL) {
g_object_unref (chooser->details->custom_info);
chooser->details->custom_info = NULL;
}
chooser->details->custom_info = info;
} else {
if (chooser->details->custom_info != NULL) {
g_object_unref (chooser->details->custom_info);
chooser->details->custom_info = NULL;
}
if (empty) {
gtk_entry_set_icon_from_icon_name (GTK_ENTRY (entry),
GTK_ENTRY_ICON_SECONDARY,
NULL);
gtk_entry_set_icon_tooltip_text (GTK_ENTRY (entry),
GTK_ENTRY_ICON_SECONDARY,
NULL);
}
gtk_widget_set_sensitive (chooser->details->set_as_default_button, FALSE);
gtk_widget_set_sensitive (chooser->details->add_button, FALSE);
}
}
int main(int argc, char **argv ) {
//long paired=0;
unsigned long num_reads1=0,
num_reads2=0;
is_paired_data=FALSE;
is_interleaved=FALSE;
fix_dot=FALSE;
int nopt=0;
int c;
opterr = 0;
fprintf(stderr,"Version iRAP %s\n",VERSION);
while ((c = getopt (argc, argv, "f")) != -1)
switch (c)
{
case 'f':
fix_dot = TRUE;
fprintf(stderr,"Fixing (-f) enabled: Replacing . by N (creating .fix.gz files)\n");
++nopt;
break;
default:
++nopt;
fprintf(stderr,"ERROR: Option -%c invalid\n",optopt);
exit(1);
}
if (argc-nopt<2 || argc-nopt>3) {
fprintf(stderr,"Usage: fastq_info [-f] fastq1 [fastq2 file|pe]\n");
//fprintf(stderr,"%d",argc);
exit(1);
}
//gzFile fd1=NULL;
gzFile fd2=NULL;
if (argc-nopt ==3) {
is_paired_data=TRUE;
//fprintf(stderr,"%d %d %d %s\n",argc,nopt,argc-nopt,argv[2+nopt]);
if ( !strncmp(argv[2+nopt],"pe",2) ) {
is_interleaved=FALSE;
}
//else {
// fd2=open_fastq(argv[2+nopt]);
// gzclose(fd2);
//
}
// ************************************************************
if ( is_interleaved ) {
// interleaved
num_reads1=validate_interleaved(argv[1+nopt]);
} else {
// single or pair of fastq file(s)
unsigned long cline=1;
fprintf(stderr,"HASHSIZE=%lu\n",(long unsigned int)HASHSIZE);
//memset(&collisions[0],0,HASHSIZE+1);
hashtable sn_index=new_hashtable(HASHSIZE);
index_mem+=sizeof(hashtable);
index_file(argv[1+nopt],sn_index,0,-1);
num_reads1=sn_index->n_entries;
fprintf(stderr,"\n");
// print some info
fprintf(stderr,"Reads processed: %ld\n",sn_index->n_entries);
fprintf(stderr,"Memory used in indexing: ~%ld MB\n",index_mem/1024/1024);
// pair-end
if (argc-nopt ==3 ) {
fprintf(stderr,"File %s processed\n",argv[1+nopt]);
fprintf(stderr,"Next file %s\n",argv[2+nopt]);
// validate the second file and check if all reads are paired
fd2=open_fastq(argv[2+nopt]);
gzFile fdf=open_fixed_fastq(argv[2+nopt]);
INDEX_ENTRY* e;
// read the entry using another fd
cline=1;
// TODO: improve code - mostly duplicated:(
while(!gzeof(fd2)) {
long long start_pos=gztell(fd2);
char *hdr=READ_LINE_HDR(fd2);
if ( hdr==NULL) break;
int len;
char *seq=READ_LINE_SEQ(fd2);
char *hdr2=READ_LINE_HDR2(fd2);
char *qual=READ_LINE_QUAL(fd2);
char* readname=get_readname(hdr,&len,cline,argv[2+nopt]);
if (seq==NULL || hdr2==NULL || qual==NULL ) {
fprintf(stderr,"\nError in file %s, line %lu: file truncated?\n",argv[2+nopt],cline);
exit(1);
}
if (validate_entry(hdr,hdr2,seq,qual,cline,argv[2+nopt])!=0) {
exit(1);
}
//fprintf(stderr,"Reads processed: %ld\n",sn_index->n_entries);
// check for duplicates
if ( (e=lookup_header(sn_index,readname))==NULL ) {
fprintf(stderr,"\nError in file %s, line %lu: unpaired read - %s\n",argv[2+nopt],cline,readname);
exit(1);
} else {
ulong key=hashit(readname);
// remove entry from sn_index
if (delete(sn_index,key,e)!=e) {
fprintf(stderr,"\nError in file %s, line %lu: unable to delete entry from sn_index - %s\n",argv[2+nopt],cline,readname);
exit(1);
}
free_indexentry(e);
}
PRINT_READS_PROCESSED(cline/4);
++num_reads2;
//
replace_dots(start_pos,seq,hdr,hdr2,qual,fdf);
cline+=4;
}
printf("\n");
close_fixed_fastq(fdf);
if (sn_index->n_entries>0 ) {
fprintf(stderr,"\nError in file %s: found %lu unpaired reads\n",argv[1+nopt],sn_index->n_entries);
exit(1);
}
}
}
FILE* out;
if (fix_dot) {
out=stderr;
} else {
out=stdout;
}
fprintf(out,"------------------------------------\n");
if ( num_reads2>0 ) {
fprintf(out,"Number of reads: %lu %lu\n",num_reads1,num_reads2);
} else {
fprintf(out,"Number of reads: %lu\n",num_reads1);
}
fprintf(out,"Quality encoding range: %lu %lu\n",min_qual,max_qual);
char *enc=qualRange2enc(min_qual,max_qual);
if ( enc == NULL ) {
fprintf(stderr,"\nERROR: Unable to determine quality encoding - unknown range [%lu,%lu]\n",min_qual,max_qual);
exit(1);
}
fprintf(out,"Quality encoding: %s\n",qualRange2enc(min_qual,max_qual));
fprintf(out,"Read length: %lu %lu\n",min_rl,max_rl);
fprintf(out,"OK\n");
exit(0);
}
/************************************************************************
* BASIC TEST ROUTINES TO CHECK UNIQUE DATA STRUCTURES LIKE SUPERBLOCK AND
* ROOT DIRECTORY AND GET MEMORY FOR THE CHECKER
*
* - Make sure, that the superblock and all copies are valid.
*
* THIS TEST HAS BEEN REMOVED FROM THE BASIC VERSION, BECAUSE THE SUPERBLOCK
* DATA IS ACTUALLY NOT USED BY THE FILE-SERVER. ALL DATA, DESCRIBING A FILE
* SYSTEM IS DERIVED FROM 'devinfo'. ON THE OTHER SIDE, IT IS A NON-TRIVIAL
* TASK TO FIND OTHER, EVENTUALLY PARTLY DAMAGED SUPERBLOCKS ON THE MEDIA TO
* BE CHECKED. TO HAVE A BASIC IDEA, WHETHER THE RELEVANT DATA (number of
* cyl.groups, cyl.group size and cyl.group offset) KEPT IN THE 'devinfo'-
* FILE AND ON DISK DESCRIBE THE SAME PHYSICAL DISK, THEY ARE COMPARED FOR
* ALL CYLINDER-GROUPS.
*
* - Compare the # number of free blocks in the bit-maps with the
* values, referenced in the cylinder group info structs.
* - Allocate all needed memory for the checker.
* - Check the root-directory inode and look for the /lost+found - directory
*
* Parameter : - nothing -
* Return : TRUE = no error at all
* FALSE = occurrence of a fatal error
*
*************************************************************************/
word
check_unique ( void )
{
struct fs tmp; /* For intermediate operation */
struct buf *bp, *bp_2;
word cgnr, i, j, c, free_cnt, ecnt, try, off;
/*--------- Make a basic comparison of file-system parameters ---------*/
IOdebug ("%s*** Step 1.1 : Plausibility test of file-system parameters", S_INFO);
/* cgnr and ncg are the values */
/* taken from devinfo. If no */
/* valid superblock is found */
/* there or the disk parameters */
/* are different, the checking */
/* process is aborted. */
/* Make incore copies of the */
/* superblock data into i_fs and*/
/* incore_fs. */
/*------------------ Tests on the super-block -------------------------*/
/* We have to copy the first */
/* superblock from the cg 0 info-block. */
bp = bread ( 0, 2, 1, SAVEA );
memcpy ( &tmp, &bp->b_un.b_info->fs, sizeof (struct fs) );
brelse ( bp->b_tbp, TAIL );
/* Run until we have a valid copy and */
/* scan the cylinder groups */
for ( cgnr = 0 , try = -1 ;; cgnr++ )
{
corrupt_cnt = 0; /* At the beginning: no errors at all */
try++; /* Count the tries which are needed to */
/* get a valid super-block. */
#if DEBUG
IOdebug (" check_unique : Try to validate a sample superblock.");
#endif
/*------- I.Definitely errors ----------*/
/* Block-no 1-3 are always the same ! */
if ( tmp.fs_sblknr != 1 || tmp.fs_iblknr != 2 || tmp.fs_rblknr != 3 )
corrupt_cnt++;
/* The magic number is fixed. */
if ( tmp.fs_magic != MAGIC_NUMBER )
corrupt_cnt++;
if ( tmp.fs_szfs != sizeof (struct fs) )
corrupt_cnt++;
if ( tmp.fs_szcg != sizeof (struct cg) )
corrupt_cnt++;
/*------ II.Plausibility errors --------*/
if ( tmp.fs_size != tmp.fs_cgsize * tmp.fs_ncg )
corrupt_cnt++;
if ( tmp.fs_dsize != tmp.fs_size - tmp.fs_ncg - 3 )
corrupt_cnt++;
if ( tmp.fs_fsize != tmp.fs_bsize / tmp.fs_frag )
corrupt_cnt++;
if ( tmp.fs_maxdpb != tmp.fs_bsize / sizeof (struct dir_elem) )
corrupt_cnt++;
if ( tmp.fs_maxcontig != tmp.fs_bsize / sizeof (daddr_t) )
corrupt_cnt++;
if ( tmp.fs_ncgcgoff != tmp.fs_ncg * tmp.fs_cgoffset )
corrupt_cnt++;
if ( tmp.fs_minfree < 0 || tmp.fs_minfree > 99 )
corrupt_cnt++;
if ( tmp.fs_psmal > tmp.fs_maxpsz || tmp.fs_pmedi > tmp.fs_maxpsz ||
tmp.fs_phuge > tmp.fs_maxpsz )
corrupt_cnt++;
/* Were there errors detected ? */
if ( corrupt_cnt )
{
unique_err++;
if ( cgnr == 0 )
cgnr++;
IOdebug ("The Superblock is damaged (%d errors counted) !",
corrupt_cnt);
/* Is it possible to select */
/* automatically a new one ? */
if ( tmp.fs_size == tmp.fs_cgsize * tmp.fs_ncg &&
tmp.fs_ncgcgoff == tmp.fs_cgoffset * tmp.fs_ncg &&
tmp.fs_size != 0 &&
tmp.fs_ncgcgoff != 0 )
{
IOdebug ("Try to interpret block no: %d as an info-block.",
map_cgtoib (cgnr,tmp.fs_cgoffset,tmp.fs_cgsize));
/* Read in info-blk from next cg */
bp = bread ( 0, map_cgtoib (cgnr,tmp.fs_cgoffset,tmp.fs_cgsize),
1, SAVEA );
/* There are possibly two reasons why we cannot */
/* read the block. If we have used a block-num */
/* which is invalid, we need help from the user */
/* to find a correct number for an info-block */
/* Copy in temporary struct */
memcpy ( &tmp, &bp->b_un.b_info->fs,
sizeof (struct fs) );
/* Release unused packet */
brelse ( bp->b_tbp, TAIL );
/* Try to validate the new copy */
/* of the Superblock. */
continue;
}
else /* No automatically selection: */
/* Give the user the choice to */
{ /* select manually a new one */
IOdebug ("Unable to select a new info block automatically!");
/* Assisted search or manual */
/* 'rebuild' of a superblock! */
return FALSE;
}
}
else /* No errors were detected */
{
if ( try > 0 )
IOdebug ("Valid superblock in use now !");
/* Keep the valid data incore */
/* in a separated storage area. */
memcpy ( &incore_fs, &tmp, sizeof (struct fs) );
/* Make a copy in i_fs, which is*/
/* for exclusive checker's use */
memcpy ( &i_fs, &tmp, sizeof (struct fs) );
break; /* We can finish the search for */
/* a valid superblock ! */
} /* end of <if (corrupt_cnt)> */
} /* end of <for(cgnr)> */
/* At this point we are sure, that the incore- */
/* copy of the super-block is valid. So we can */
/* use it further on, if we need file system */
/* parameters! */
{
/* Update each cylinder-group */
/* if necessary. */
for ( cgnr = 0 ; cgnr < i_fs.fs_ncg ; cgnr++ )
{ /* Read appropriate info block */
bp = bread ( 0, map_cgtoib (cgnr,i_fs.fs_cgoffset,i_fs.fs_cgsize),
1, SAVEA );
#if DEBUG
IOdebug (" check_unique : Compare it with the copy in cylinder-group %d.", cgnr);
#endif
/* Updating is only recommended, */
/* if changes were made. */
if ( my_memcmp ( &i_fs, &bp->b_un.b_info->fs, tmp.fs_szfs ) )
{
#if DEBUG
IOdebug (" check_unique : Copy superblock to cylinder-group %d.", cgnr);
#endif
unique_err++;
/* Update it's superblock copy */
memcpy ( &bp->b_un.b_info->fs, &i_fs, sizeof (struct fs) );
/* ... and write it back to disk */
fst.corrected_sb++;
test_bwrite ( bp );
}
else /* They are the same: don't copy */
brelse ( bp->b_tbp, TAIL );
} /* end <for (cgnr)> */
}
/* Report differences between data kept */
/* in the superblock and in the 'devinfo'*/
/* structures */
#if DEBUG
IOdebug (" check_unique : Compare 'devinfo' data with the superblock");
#endif
if ( i_fs.fs_ncg != vvi->CgCount )
IOdebug ("Number of cylinder groups Sb : %4d / devinfo : %d",
i_fs.fs_ncg, vvi->CgCount);
if ( i_fs.fs_cgsize != vvi->CgSize )
IOdebug ("Size of a cylinder group Sb : %4d / devinfo : %d",
i_fs.fs_cgsize, vvi->CgSize);
if ( i_fs.fs_cgoffset != vvi->CgOffset )
IOdebug ("Relative offset into a cylinder group Sb : %4d / devinfo : %d",
i_fs.fs_cgoffset, vvi->CgOffset);
if ( i_fs.fs_psmal != fsi->SmallPkt )
IOdebug ("Size of a of small packet Sb : %d / devinfo : %d",
i_fs.fs_psmal, fsi->SmallPkt);
if ( i_fs.fs_pmedi != fsi->MediumPkt )
IOdebug ("Size of a of medium packet Sb : %d / devinfo : %d",
i_fs.fs_pmedi, fsi->MediumPkt);
if ( i_fs.fs_phuge != fsi->HugePkt )
IOdebug ("Size of a huge packet Sb : %d / devinfo : %d",
i_fs.fs_phuge, fsi->HugePkt);
if ( i_fs.fs_pscnt != fsi->SmallCount )
IOdebug ("Number of samll packets Sb : %d / devinfo : %d",
i_fs.fs_pscnt, fsi->SmallCount);
if ( i_fs.fs_pmcnt != fsi->MediumCount )
IOdebug ("Number of medium packtes Sb : %d / devinfo : %d",
i_fs.fs_pmcnt, fsi->MediumCount);
if ( i_fs.fs_phcnt != fsi->HugeCount )
IOdebug ("Number of huge packets Sb : %d / devinfo : %d",
i_fs.fs_phcnt, fsi->HugeCount);
if ( i_fs.fs_maxnii != fsi->MaxInodes )
IOdebug ("Maximal number of incore inodes Sb : %d / devinfo : %d",
i_fs.fs_maxnii, fsi->MaxInodes);
if ( i_fs.fs_minfree != vvi->MinFree )
IOdebug ("Percentage of space to be kept free Sb : %d / devinfo : %d",
i_fs.fs_minfree, vvi->MinFree);
/*---- To ease addressing of info-blocks: create an info-bnr table ----*/
#if DEBUG
IOdebug (" check_unique : Create an info-block number table.");
#endif
/* Calculate all block numbers */
for ( cgnr = 0 ; cgnr < i_fs.fs_ncg ; cgnr++ )
/* ... and fill the table */
info_blocks[cgnr] = map_cgtoib (cgnr, i_fs.fs_cgoffset, i_fs.fs_cgsize);
/*--------- Discrepancy between bit-maps and cg-info ? ----------------*/
/* This part is only used to detect differences */
/* in the bit-maps and summary-structures and */
/* to report them. No attempts to correct them */
/* are made. This is done later by check_blocks.*/
IOdebug ("%s*** Step 1.2 : First inspection of bitmap-data", S_INFO);
/* Scan all cylinder groups */
for ( corrupt_cnt = 0 , cgnr = 0 ; cgnr < i_fs.fs_ncg ; cgnr++ )
{ /* Read the cg info-block */
bp = bread ( 0, info_blocks[cgnr], 1, SAVEA );
/* Read error */
if ( bp == (struct buf *) NULL )
{
IOdebug ("%sUnexpected read error for block no: %d.",
S_SERIOUS, info_blocks[cgnr]);
return FALSE;
}
if ( bp->b_un.b_info->cgx.cg_cgx != cgnr ) {
IOdebug ("%sInvalid cgnr (%d) found in info block %d!", S_WARNING, bp->b_un.b_info->cgx.cg_cgx ,cgnr);
}
/* Scan through the bit-map ! */
for ( i = 0 , free_cnt = 0 , ecnt = 0 ; i < i_fs.fs_cgsize ; i++ )
{
switch ( bp->b_un.b_info->cgx.cg_free[i] )
{ /* Test for errors */
case 0x00 : free_cnt++;
break;
case 0xff : continue;
break;
default : ecnt++;
fst.bitmap_errors++;
corrupt_cnt++;
}
}
if ( free_cnt != bp->b_un.b_info->cgx.cg_s.s_nbfree )
{ /* By comparing with cg-sum */
corrupt_cnt++;
unique_err++;
fst.summary_errors++;
IOdebug ("%sDifferent number of free blocks found.", S_WARNING);
IOdebug ("%s> Cyl. Group : %d FREE counted= %d cg-summary= %u",
S_INFO, cgnr, free_cnt,
bp->b_un.b_info->cgx.cg_s.s_nbfree);
}
/* Definitely errors in maps ? */
if ( ecnt ) /* ( != 0 && != 0xff ) */
{
unique_err++;
IOdebug ("%sCorrupted bits in bit-map found.", S_WARNING);
IOdebug ("%s> Cyl. Group : %d ERRORS =%d blocks",
S_INFO, cgnr, ecnt);
/* We have reached the limit ? */
if ( ecnt > i_fs.fs_cgsize * maxbmerr / 100 )
{ /* Note cg-bitmap as unusable */
cg_bitmap_usable[cgnr] = FALSE;
IOdebug ("%sThe bit-map is not usable!", S_SERIOUS);
}
else
cg_bitmap_usable[cgnr] = TRUE;
} /* We have found a bitmap in an */
else /* usable state ! */
cg_bitmap_usable[cgnr] = TRUE;
/* Release unused block */
brelse ( bp->b_tbp, TAIL );
} /* end < for (cgnr) > */
/*--------- Allocate enough memory for a reference bit-map array ------*/
IOdebug ("%s*** Step 1.3 : Allocate memory for reference bit-map array.", S_INFO);
bit_maps_allocated = alloc_ref_maps ();
if ( ! bit_maps_allocated ) /* No success again, that's bad! */
{
IOdebug ("%sUnable to allocate memory for reference bit-maps.", S_FATAL);
return FALSE;
}
/* Blocks 0-2 always allocated ! */
bit_maps[0][0] = 1; /* Boot-block */
found_blocks++;
bitmap_incr (1); /* Summary block */
found_blocks++;
/* Mark all info-blocks as being */
/* allocated. */
for ( cgnr = 0 ; cgnr < i_fs.fs_ncg ; cgnr++ )
{
found_blocks++;
bitmap_incr (info_blocks[cgnr]);
}
/*----------- Prepare the hash-table for directory entries ------------*/
#if DEBUG
IOdebug (" check_unique : Prepare directory-entry hash table.");
#endif
/* We have to initialize all */
for ( i = 0 ; i < DEHASHSZ ; i++ ) /* hash-pointers ! */
de_hash_tab[i].denxt = (struct de_name *) NULL;
/*------ Prepare the hash-table for duplicate block numbers ---------*/
#if DEBUG
IOdebug (" check_unique : Prepare duplicate block-number hash table.");
#endif
/* We have to initialize all */
for ( i = 0 ; i < DUPHASHSZ ; i++ ) /* hash-pointers ! */
dup_hash_tab[i].dupnxt = (struct dup_bnr *) NULL;
/*-------- Prepare the hash-table for symbolic link references ------*/
#if DEBUG
IOdebug (" check_unique : Prepare symbolic-link hash-table.");
#endif
/* We have to initialize all */
for ( i = 0 ; i < LINKHASHSZ ; i++ ) /* hash-pointers */
link_hash_tab[i].lnnxt = (struct de_link *) NULL;
/*--------------- Valid root directory data ? -------------------------*/
IOdebug ("%s*** Step 1.4 : Check the root directory inode.", S_INFO);
/* Read summary block with the */
bp = bread ( 0, 1, 1, SAVEA ); /* root-dir inode in it. */
/* if read fails, longjmp */
/* term_jmp */
changes_de = 0; /* Nothing done so far ... */
/* Check the root-dir entry */
if ( ! validate_entry ( &bp->b_un.b_sum->root_dir , "/", Type_Directory, TRUE ) )
{ /* Is it totally damaged ! */
/* It is a very dangerous situation, if we have no root-*/
/* directory available. The user can create an */
/* empty one and hope, that lost subdiretory-information*/
/* is picked up during the "lost+found" pass over the */
/* cylinder-group bit-maps. */
unique_err++;
IOdebug ("%sThe root-directory is not usable !", S_SERIOUS);
/* Pioneer's work: we create a */
/* new inode from scratch ! */
IOdebug ("%sA new root-directory is created from scratch.", S_INFO);
/* Pioneer's work: we create a */
/* new root-inode from scratch */
create_new_root_dir ( &bp->b_un.b_sum->root_dir );
/* Write the root-inode back on */
/* disk. */
test_bwrite ( bp );
}
else /* After finding a usable root- */
{ /* directory entry ... */
if (!bp->b_un.b_sum->sum_same)
unique_err++;
if ( changes_de ) /* Any changes made ? */
{
#if DEBUG
IOdebug (" check_unique : Update root-directory inode on disk.");
#endif
unique_err++;
/* Write corrected summary-block */
test_bwrite ( bp ); /* directly to disk */
}
else
brelse ( bp->b_tbp, TAIL );
}
/*---------------- Look for the "lost+found" directory --------------*/
IOdebug ("%s*** Step 1.5 : Look for the '/lost+found'- directory.", S_INFO);
bp = bread ( 0, 1, 1, SAVEA ); /* Get root-directory */
/* if read fails, longjmp */
/* term_jmp */
/* Look for the "lost+found"-dir */
bp_2 = search_entry ( &bp->b_un.b_sum->root_dir.de_inode, "lost+found", &off );
/* We have found it ? */
if ( bp_2 != (struct buf *) NULL )
{ /* We have found a usable */
lost_found = TRUE; /* /lost+found - directory. */
brelse ( bp_2->b_tbp, TAIL );
brelse ( bp->b_tbp, TAIL );
}
/* If we have not found the */
else /* /lost+found-inode, we have to */
{ /* create a new one. */
IOdebug ("%sUnable to find a '/lost+found' entry in the root-directory.", S_WARNING);
IOdebug ("%sA new '/lost+found' entry is created.", S_INFO);
unique_err++;
if ( create_lostfound_inode ( &bp->b_un.b_sum->root_dir.de_inode ) )
{
IOdebug ("%sHave created a new /lost+found directory!", S_INFO);
lost_found = TRUE;
test_bwrite ( bp ); /* Write modified root back. */
}
else /* We cannot create a /lost+found*/
{ /* inode, because we have no */
/* slot available. */
IOdebug ("%sCannot create a new '/lost+found' directory !", S_WARNING);
lost_found = FALSE;
brelse ( bp->b_tbp, TAIL );
}
}
return TRUE;
}
/*-- Procedures dealing with the creation of a new basic structures ---*/
/************************************************************************
* CREATE A TOTALLY EMPTY ROOT-DIRECTORY ENTRY FROM SCRATCH
*
* - This procedure is called, if the checker was not able to find a
* valid root-directory.
*
* Parameter : dp = Pointer to the root directory-element
* Return : - nothing -
*
***********************************************************************/
static void
create_new_root_dir ( struct dir_elem *dp )
{
Date date;
#if DEBUG
IOdebug (" create_new_root_dir : Create the new entry");
#endif
/* Clear the directory-entry */
memset ( dp, 0, sizeof (struct dir_elem) );
/* .. and fill in with the data */
/* for the root-directory */
strcpy ( dp->de_name, i_fs.fs_name );
dp->de_inode.i_mode = Type_Directory;
dp->de_inode.i_matrix = DefDirMatrix;
date = GetDate ();
dp->de_inode.i_ctime = date;
dp->de_inode.i_mtime = date;
dp->de_inode.i_atime = date;
}
int main(int argc, char **argv ) {
//long paired=0;
is_paired_data=0;
is_interleaved=0;
printf("Version iRAP %s\n",VERSION);
if (argc<2 || argc>3) {
fprintf(stderr,"Usage: fastq_validator fastq1 [fastq2 file|pe]\n");
//fprintf(stderr,"%d",argc);
exit(1);
}
FILE *fd1=NULL;
FILE *fd2=NULL;
// open & close
fd1=open_fastq(argv[1]);
fclose(fd1);
//fprintf(stderr,"%d\n",argc);
//bin/fprintf(stderr,"%s\n",argv[0]);
if (argc ==3) {
is_paired_data=1;
if ( !strncmp(argv[2],"pe",2) ) {
is_interleaved=1;
} else {
fd2=open_fastq(argv[2]);
fclose(fd2);
}
}
// ************************************************************
// casava 1.8?
is_casava_18=is_casava_1_8(argv[1]);
if (is_casava_18) fprintf(stderr,"CASAVA=1.8\n");
// ************************************************************
//off_t cur_offset=1;
// interleaved
if ( is_interleaved ) {
exit(validate_interleaved(argv[1]));
}
unsigned long cline=1;
fprintf(stderr,"HASHSIZE=%lu\n",(long unsigned int)HASHSIZE);
//memset(&collisions[0],0,HASHSIZE+1);
hashtable sn_index=new_hashtable(HASHSIZE);
index_mem+=sizeof(hashtable);
index_file(argv[1],sn_index,0,-1);
fprintf(stderr,"\n");
// print some info
fprintf(stderr,"Reads processed: %ld\n",sn_index->n_entries);
fprintf(stderr,"Memory used in indexing: ~%ld MB\n",index_mem/1024/1024);
// pair-end
if (argc ==3 ) {
fprintf(stderr,"File %s processed\n",argv[1]);
fprintf(stderr,"Next file %s\n",argv[2]);
// validate the second file and check if all reads are paired
fd2=open_fastq(argv[2]);
INDEX_ENTRY* e;
// read the entry using another fd
cline=1;
// TODO: improve code - mostly duplicated:(
while(!feof(fd2)) {
//long start_pos=ftell(fd2);
char *hdr=READ_LINE_HDR(fd2);
if ( hdr==NULL) break;
int len;
char *seq=READ_LINE_SEQ(fd2);
char *hdr2=READ_LINE_HDR2(fd2);
char *qual=READ_LINE_QUAL(fd2);
char* readname=get_readname(hdr,&len,cline,argv[2]);
if (seq==NULL || hdr2==NULL || qual==NULL ) {
fprintf(stderr,"Error in file %s, line %lu: file truncated?\n",argv[2],cline);
exit(1);
}
if (validate_entry(hdr,hdr2,seq,qual,cline,argv[2])!=0) {
exit(1);
}
//fprintf(stderr,"Reads processed: %ld\n",sn_index->n_entries);
// check for duplicates
if ( (e=lookup_header(sn_index,readname))==NULL ) {
fprintf(stderr,"Error in file %s, line %lu: unpaired read - %s\n",argv[2],cline,readname);
exit(1);
} else {
ulong key=hashit(readname);
// remove entry from sn_index
if (delete(sn_index,key,e)!=e) {
fprintf(stderr,"Error in file %s, line %lu: unable to delete entry from sn_index - %s\n",argv[2],cline,readname);
exit(1);
}
free_indexentry(e);
}
PRINT_READS_PROCESSED(cline/4);
//
cline+=4;
}
printf("\n");
if (sn_index->n_entries>0 ) {
fprintf(stderr,"Error in file %s: found %lu unpaired reads\n",argv[1],sn_index->n_entries);
exit(1);
}
}
printf("OK\n");
exit(0);
}
/*************************************************************************
* TESTS ON SINGLE DATA STRUCTURES LIKE INODES
*
* - This procedure is the central routine for working on the directory
* tree. A backtracking mechanism with no recursive procedure-overhead
* is used to avoid memory allocation and stack overflow problems.
* - It is called as "step 2" during the checking process after working
* on unique data-structures and allocation all needed buffers for
* tables etc.
* - The root-inode was validated during a separate step in check_unique().
*
* Parameter : root_de = The directory-entry of the local root which
* has to be examined
* root_bnr = The number of the directory block which keeps
* the root entry
* root_offs = The offset in this directory block
* Return : TRUE : under all normal checking conditions
* FALSE : if a fatal error occurs
*
*************************************************************************/
word
check_inodes ( struct dir_elem *root_de, daddr_t root_bnr, word root_offs )
{
word spare; /* # of entries in the direct. */
daddr_t bnr; /* For temporary storage */
word offset;
word depth; /* To keep track about the dis- */
/* tance from the root-direct. */
struct buf *bpar; /* Points to the current parent */
/* directory - block */
struct buf *blpt; /* For symbolic-link reference- */
/* path block */
tree_e head;
word first_time; /* Used to signal, if an entry */
/* is scanned the first time */
tree_e *parent; /* Pointer to the actual parent */
/* tree-element */
tree_e *tpt; /* Pointer to the actual wor- */
/* king element. */
struct dir_elem *de_pt; /* Used for temporary storage */
/*---------------------- Init operations ----------------------------*/
head.bnr = root_bnr; /* Init the head element */
head.offset = root_offs;
head.parent_used = TRUE;
/* Copy the root entry */
memcpy ( (void *) &head.de, (void *) root_de, sizeof (struct dir_elem) );
head.enxt = (tree_e *) NULL; /* Zero the head-pointers */
head.eprv = (tree_e *) NULL;
head.lnxt = (tree_e *) NULL;
head.lprv = (tree_e *) NULL;
/* Clear the comparison struct */
memset ( &dir_cmp, 0, sizeof (struct dir_elem) );
strcpy ( path, "/" ); /* Set the name of the root */
strcat ( path, head.de.de_name ); /* of the filesystem */
spare = 0; /* No entry at the beginning */
first_time = TRUE; /* Start up value */
parent = &head; /* At the beginning the head */
tpt = &head; /* element is the only one. */
remove_de_hash (); /* Free previously used hash- */
/* table elements */
changes_de = 0; /* Nothing changed so far... */
depth = 0; /* We start on root-position */
/*--------------- Traverse the whole directory tree -----------------*/
for ( ;; )
{
/* Get the next entry to check */
de_pt = get_next_entry ( &parent->de.de_inode, first_time,
&bnr, &offset );
first_time = FALSE; /* We want to get all other en- */
/* tries from this directory */
/* We have got an entry ? */
if ( de_pt != (struct dir_elem *) NULL )
{
strncpy (actual_path, path, 512);
#if 0
IOdebug ("%sChecking %s / [%s]",
S_INFO, path, de_pt->de_name);
#endif
/* An entry was extracted. Now */
/* check it's validity */
if ( validate_entry ( de_pt, path, UNKNOWN, TRUE ) )
{
/* Put the entry name into the */
/* appropriate hash-queue */
append_de_hash ( de_pt->de_name );
/* We have to increment the */
spare++; /* total count of entries */
/*-------------- Storage of symbolic-link information ----------------*/
/* Was it a symbolic link ? */
if ( de_pt->de_inode.i_mode == Type_Link )
{ /* Read the block with the re- */
/* ference path in buffer-cache */
blpt = bread ( 0, de_pt->de_inode.i_db[0],
1, SAVEA );
/* Append the link to the hash- */
/* table for symbolic links */
append_link_hash ( bnr, offset,
parent->bnr, parent->offset,
blpt->b_un.b_link->name);
/* One more symbolic link found */
found_links++;
/* The ref-block is not used */
/* anymore */
brelse ( blpt->b_tbp, TAIL );
}
/*----- Appending new elements to the hierarchical directory-tree ----*/
if ( de_pt->de_inode.i_mode == Type_Directory )
{
/* Increment the counter for */
/* the number of valid directo- */
/* ries in a cylinder group. */
add_dir ( bnr );
found_dirs++;
if ( tpt == parent )
/* Add a new directory level */
tpt = append_level ( tpt );
else
/* .. or a new entry */
tpt = append_entry ( tpt );
/* Save the entry's location */
tpt->bnr = bnr;
tpt->offset = offset;
/* Save the entry's content */
memcpy ( &tpt->de, de_pt, sizeof (struct dir_elem) );
/* At this time NOT used as a */
/* parent-dir */
tpt->parent_used = FALSE;
#if DEBUG
IOdebug (" check_inodes : New element created for %s (bnr= %d, off= %d)",
tpt->de.de_name, tpt->bnr, tpt->offset );
#endif
}
/* Update the actual number of */
/* file checked. */
if ( de_pt->de_inode.i_mode == Type_File )
found_files++;
}
else /* If the validation does not */
{ /* succeeds: */
/* We have to make a note, if */
/* /lost+found will be deleted ! */
if ( depth == 0 &&
! strcmp ( de_pt->de_name, "lost+found" ) )
{
IOdebug ("%sUnusable /lost+found-dir !", S_WARNING);
lost_found = FALSE;
}
IOdebug ("%sThe entry is invalid and will be deleted!",
S_SERIOUS);
if ( ! no_corrections )
{
/* We cannot make use anymore */
/* of the corrupted entry and */
/* delete it. */
memset ( (void *) de_pt, 0, sizeof (struct dir_elem) );
/* Note the deletion */
fst.deleted_inodes++;
changes_de++;
}
}
}
/*------ After checking a complete directory with all entries: --------*/
else /* One directory fully scanned: */
{
#if DEBUG
IOdebug (" check_inodes : Have examined all entries. Change the directory");
IOdebug (" Current parent = %s 'used' = %d",
parent->de.de_name, parent->parent_used);
IOdebug (" Current entry = %s 'used' = %d",
tpt->de.de_name, tpt->parent_used);
#endif
/*------- Go on with the last directory of the current sub-dir ------*/
if ( tpt->enxt == (tree_e *) NULL &&
tpt->lnxt == (tree_e *) NULL &&
tpt != parent &&
! tpt->parent_used )
{
#if DEBUG
IOdebug (" check_inodes : Take the last sub-dir as parent directory");
#endif
#if DEBUG
IOdebug (" check_inodes : Spare value found = %d , counted = %d",
parent->de.de_inode.i_spare, spare );
#endif
/* Different # of entries ? */
if ( spare != parent->de.de_inode.i_spare )
{ /* Save the new spare value */
/* Read the parent-directory */
#if DEBUG
IOdebug (" check_inodes : Correct number of entries (spare value)");
#endif
bpar = bread ( 0, parent->bnr, 1, SAVEA );
/* Change the entry */
if ( parent->bnr == 1 )
{ /* Special handling for root */
bpar->b_un.b_sum->root_dir.de_inode.i_spare =
spare;
bpar->b_un.b_sum->root_dir.de_inode.i_size =
spare * sizeof(struct dir_elem);
}
else
{
bpar->b_un.b_dir[parent->offset].de_inode.i_spare =
spare;
bpar->b_un.b_dir[parent->offset].de_inode.i_size =
spare * sizeof(struct dir_elem);
}
/* ... and write it back. */
test_bwrite ( bpar );
}
/* Prepare the tree-element */
/* for a new pass as "parent": */
parent = tpt;
parent->parent_used = TRUE;
first_time = TRUE;
spare = 0;
/* Append to the pathname-string*/
strcat ( path , "/" );
/* ... a new sub-dir branch */
strcat ( path , parent->de.de_name );
/* One level lower than the */
depth++; /* root-directory */
/* Clear the name-hash-table */
remove_de_hash ();
/* Begin with the first entry.. */
continue; /* and scan again all entries. */
}
/*-------------------- Backtracking conditions ----------------------*/
if ( tpt->enxt == (tree_e *) NULL &&
tpt->lnxt == (tree_e *) NULL &&
tpt == parent &&
tpt->parent_used )
{
#if DEBUG
IOdebug (" check_inodes : Use backtracking to get a new parent-dir");
#endif
#if DEBUG
IOdebug (" check_inodes : Spare value found = %d , counted = %d",
parent->de.de_inode.i_spare, spare );
#endif
/* Different # of entries ? */
if ( spare != parent->de.de_inode.i_spare )
{
#if DEBUG
IOdebug (" check_inodes : Correct number of entries (spare value)");
#endif
/* Save the new spare value */
/* Read the directory block */
bpar = bread ( 0, parent->bnr, 1, SAVEA );
/* Change the entry */
if ( parent->bnr == 1 )
{ /* Special handling for root */
bpar->b_un.b_sum->root_dir.de_inode.i_spare =
spare;
bpar->b_un.b_sum->root_dir.de_inode.i_size =
spare * sizeof(struct dir_elem);
}
else
{
bpar->b_un.b_dir[parent->offset].de_inode.i_spare =
spare;
bpar->b_un.b_dir[parent->offset].de_inode.i_size =
spare * sizeof(struct dir_elem);
}
/* ... and write it back. */
test_bwrite ( bpar );
}
/* Look for a directory, which */
/* wasn't used as a "parent" */
do
{ /* THE MAIN EXIT-POINT ! */
if ( tpt->eprv == (tree_e *) NULL &&
tpt->lprv == (tree_e *) NULL )
return TRUE;
/* The "move-back" operation */
if ( tpt->lprv != (tree_e *) NULL )
{
/* Remove the lowest level */
parent = remove_level ( tpt );
depth--;
}
else /* Remove the last entry from */
/* the directory */
parent = remove_entry ( tpt );
/* Adjust the work-pointer */
tpt = parent;
/* Cut the pathname string and */
*( strrchr ( path , '/' ) ) = '\0';
#if DEBUG
IOdebug (" check_inodes : Backtracking to path = %s (depth: %d)",
path, depth );
#endif
} /* try it again until an unused */
/* dir-entry is found */
while ( tpt->parent_used );
/* Append the new sub-dir */
if ( tpt->de.de_name )
{
strcat ( path, "/" );
strcat ( path, tpt->de.de_name );
}
/* Prepare the tree-element as */
/* the new parent-directory */
tpt->parent_used = TRUE;
first_time = TRUE;
spare = 0;
/* Clear the hash-table */
remove_de_hash ();
/* ... and go to the beginning */
continue; /* Now we will examine the en- */
/* tries of the "new" directory.*/
}
}
} /* end of <for (;;)> */
}
