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Code for tests storing data in multiple AVLs.

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(note: unretrievable data as implemented)
This commit is contained in:
Celine Mercier
2016-03-11 15:34:55 +01:00
parent 21d1b2ed3e
commit 545ed8111a
6 changed files with 205 additions and 17 deletions
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180
src/obiavl.c
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@ -30,6 +30,159 @@
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
////crc crcTable[256];
//static crc crcTable[] = {
//0x00, 0xd8, 0x68, 0xb0, 0xd0, 0x8, 0xb8, 0x60, 0x78, 0xa0, 0x10, 0xc8, 0xa8, 0x70, 0xc0, 0x18, 0xf0, 0x28, 0x98, 0x40, 0x20, 0xf8, 0x48, 0x90, 0x88, 0x50, 0xe0, 0x38, 0x58, 0x80, 0x30, 0xe8, 0x38, 0xe0, 0x50, 0x88, 0xe8, 0x30, 0x80, 0x58, 0x40, 0x98, 0x28, 0xf0, 0x90, 0x48, 0xf8, 0x20, 0xc8, 0x10, 0xa0, 0x78, 0x18, 0xc0, 0x70, 0xa8, 0xb0, 0x68, 0xd8, 0, 0x60, 0xb8, 0x8, 0xd0, 0x70, 0xa8, 0x18, 0xc0, 0xa0, 0x78, 0xc8, 0x10, 0x8, 0xd0, 0x60, 0xb8, 0xd8, 0, 0xb0, 0x68, 0x80, 0x58, 0xe8, 0x30, 0x50, 0x88, 0x38, 0xe0, 0xf8, 0x20, 0x90, 0x48, 0x28, 0xf0, 0x40, 0x98, 0x48, 0x90, 0x20, 0xf8, 0x98, 0x40, 0xf0, 0x28, 0x30, 0xe8, 0x58, 0x80, 0xe0, 0x38, 0x88, 0x50, 0xb8, 0x60, 0xd0, 0x8, 0x68, 0xb0, 0, 0xd8, 0xc0, 0x18, 0xa8, 0x70, 0x10, 0xc8, 0x78, 0xa0, 0xe0, 0x38, 0x88, 0x50, 0x30, 0xe8, 0x58, 0x80, 0x98, 0x40, 0xf0, 0x28, 0x48, 0x90, 0x20, 0xf8, 0x10, 0xc8, 0x78, 0xa0, 0xc0, 0x18, 0xa8, 0x70, 0x68, 0xb0, 0, 0xd8, 0xb8, 0x60, 0xd0, 0x8, 0xd8, 0, 0xb0, 0x68, 0x8, 0xd0, 0x60, 0xb8, 0xa0, 0x78, 0xc8, 0x10, 0x70, 0xa8, 0x18, 0xc0, 0x28, 0xf0, 0x40, 0x98, 0xf8, 0x20, 0x90, 0x48, 0x50, 0x88, 0x38, 0xe0, 0x80, 0x58, 0xe8, 0x30, 0x90, 0x48, 0xf8, 0x20, 0x40, 0x98, 0x28, 0xf0, 0xe8, 0x30, 0x80, 0x58, 0x38, 0xe0, 0x50, 0x88, 0x60, 0xb8, 0x8, 0xd0, 0xb0, 0x68, 0xd8, 0, 0x18, 0xc0, 0x70, 0xa8, 0xc8, 0x10, 0xa0, 0x78, 0xa8, 0x70, 0xc0, 0x18, 0x78, 0xa0, 0x10, 0xc8, 0xd0, 0x8, 0xb8, 0x60, 0, 0xd8, 0x68, 0xb0, 0x58, 0x80, 0x30, 0xe8, 0x88, 0x50, 0xe0, 0x38, 0x20, 0xf8, 0x48, 0x90, 0xf0, 0x28, 0x98, 0x40
//};
//
//
//void crcInit(void)
//{
// crc remainder;
//
// fprintf(stderr, "\n");
//
// /*
// * Compute the remainder of each possible dividend.
// */
// for (int dividend = 0; dividend < 256; ++dividend)
// {
// /*
// * Start with the dividend followed by zeros.
// */
// remainder = dividend << (WIDTH - 8);
//
// /*
// * Perform modulo-2 division, a bit at a time.
// */
// for (uint8_t bit = 8; bit > 0; --bit)
// {
// /*
// * Try to divide the current data bit.
// */
// if (remainder & TOPBIT)
// {
// remainder = (remainder << 1) ^ POLYNOMIAL;
// }
// else
// {
// remainder = (remainder << 1);
// }
// }
//
// /*
// * Store the result into the table.
// */
// crcTable[dividend] = remainder;
// fprintf(stderr, "%#x, ", remainder);
// }
//
//} /* crcInit() */
//
//
//crc crcFast(uint8_t const message[], int nBytes)
//{
// uint8_t data;
// crc remainder = 0;
//
//
// /*
// * Divide the message by the polynomial, a byte at a time.
// */
// for (int byte = 0; byte < nBytes; ++byte)
// {
// data = message[byte] ^ (remainder >> (WIDTH - 8));
// remainder = crcTable[data] ^ (remainder << 8);
// }
//
// /*
// * The final remainder is the CRC.
// */
// return (remainder);
//
//} /* crcFast() */
//
//
//crc compute_crc(const char* s)
//{
// crc c;
// //uint8_t cache;
//
// //cache = 15;
//
//// crcInit();
//
// c = crcFast(s, strlen(s));
//
// //fprintf(stderr, "\nlen = %d", strlen(argv[1]));
//
// //fprintf(stderr, "\ncrc = %u\n\n", c);
// //fprintf(stderr, "\ncrc mod 8 = %u\n\n", c%8);
//
// c = c >> 3;
// //fprintf(stderr, "\nshifted crc = %u\n\n", c);
//
// //c = c & cache;
// //c = c % 32;
//
// //fprintf(stderr, "\ncrc = %u\n\n", c);
//
// return (c & 7);
//}
static unsigned char crc8_table[] = {
0x00, 0x3e, 0x7c, 0x42, 0xf8, 0xc6, 0x84, 0xba, 0x95, 0xab, 0xe9, 0xd7,
0x6d, 0x53, 0x11, 0x2f, 0x4f, 0x71, 0x33, 0x0d, 0xb7, 0x89, 0xcb, 0xf5,
0xda, 0xe4, 0xa6, 0x98, 0x22, 0x1c, 0x5e, 0x60, 0x9e, 0xa0, 0xe2, 0xdc,
0x66, 0x58, 0x1a, 0x24, 0x0b, 0x35, 0x77, 0x49, 0xf3, 0xcd, 0x8f, 0xb1,
0xd1, 0xef, 0xad, 0x93, 0x29, 0x17, 0x55, 0x6b, 0x44, 0x7a, 0x38, 0x06,
0xbc, 0x82, 0xc0, 0xfe, 0x59, 0x67, 0x25, 0x1b, 0xa1, 0x9f, 0xdd, 0xe3,
0xcc, 0xf2, 0xb0, 0x8e, 0x34, 0x0a, 0x48, 0x76, 0x16, 0x28, 0x6a, 0x54,
0xee, 0xd0, 0x92, 0xac, 0x83, 0xbd, 0xff, 0xc1, 0x7b, 0x45, 0x07, 0x39,
0xc7, 0xf9, 0xbb, 0x85, 0x3f, 0x01, 0x43, 0x7d, 0x52, 0x6c, 0x2e, 0x10,
0xaa, 0x94, 0xd6, 0xe8, 0x88, 0xb6, 0xf4, 0xca, 0x70, 0x4e, 0x0c, 0x32,
0x1d, 0x23, 0x61, 0x5f, 0xe5, 0xdb, 0x99, 0xa7, 0xb2, 0x8c, 0xce, 0xf0,
0x4a, 0x74, 0x36, 0x08, 0x27, 0x19, 0x5b, 0x65, 0xdf, 0xe1, 0xa3, 0x9d,
0xfd, 0xc3, 0x81, 0xbf, 0x05, 0x3b, 0x79, 0x47, 0x68, 0x56, 0x14, 0x2a,
0x90, 0xae, 0xec, 0xd2, 0x2c, 0x12, 0x50, 0x6e, 0xd4, 0xea, 0xa8, 0x96,
0xb9, 0x87, 0xc5, 0xfb, 0x41, 0x7f, 0x3d, 0x03, 0x63, 0x5d, 0x1f, 0x21,
0x9b, 0xa5, 0xe7, 0xd9, 0xf6, 0xc8, 0x8a, 0xb4, 0x0e, 0x30, 0x72, 0x4c,
0xeb, 0xd5, 0x97, 0xa9, 0x13, 0x2d, 0x6f, 0x51, 0x7e, 0x40, 0x02, 0x3c,
0x86, 0xb8, 0xfa, 0xc4, 0xa4, 0x9a, 0xd8, 0xe6, 0x5c, 0x62, 0x20, 0x1e,
0x31, 0x0f, 0x4d, 0x73, 0xc9, 0xf7, 0xb5, 0x8b, 0x75, 0x4b, 0x09, 0x37,
0x8d, 0xb3, 0xf1, 0xcf, 0xe0, 0xde, 0x9c, 0xa2, 0x18, 0x26, 0x64, 0x5a,
0x3a, 0x04, 0x46, 0x78, 0xc2, 0xfc, 0xbe, 0x80, 0xaf, 0x91, 0xd3, 0xed,
0x57, 0x69, 0x2b, 0x15};
unsigned crc8(unsigned char *data, size_t len)
{
unsigned char *end;
unsigned crc;
crc = 0;
crc ^= 0xff;
end = data + len;
do {
crc = crc8_table[crc ^ *data++];
} while (data < end);
return crc ^ 0xff;
}
crc compute_crc(const char* s)
{
unsigned c;
c = crc8(s, strlen(s));
//fprintf(stderr, "%02x\n", c);
return (c & 7);
}
/**************************************************************************
*
* D E C L A R A T I O N O F T H E P R I V A T E F U N C T I O N S
@ -605,6 +758,8 @@ int grow_avl_data(OBIDMS_avl_p avl) // TODO Lock when needed
// Set new data size
((avl->data)->header)->data_size_max = new_data_size;
//fprintf(stderr, "\nGrowing AVL, new data size = %lld, count = %ld\n", new_data_size, (avl->header)->nb_items);
// Initialize new data to 0
memset(((avl->data)->data)+old_data_size, 0, new_data_size - old_data_size);
@ -976,6 +1131,24 @@ OBIDMS_avl_p obi_avl(OBIDMS_p dms, const char* avl_name)
}
OBIDMS_avl_p* obi_create_avl_in_64_parts(OBIDMS_p dms, const char* avl_name)
{
OBIDMS_avl_p* avls;
char* avl_name_with_idx;
uint8_t i;
avls = (OBIDMS_avl_p*) malloc(64*sizeof(OBIDMS_avl_p));
for (i=0; i < 64; i++)
{
asprintf(&avl_name_with_idx,"%s_%u", avl_name, i);
avls[i] = obi_create_avl(dms, avl_name_with_idx);
}
return avls;
}
OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name)
{
char* avl_file_name;
@ -1446,7 +1619,7 @@ index_t obi_avl_add(OBIDMS_avl_p avl, byte_t* value)
index_t node_idx;
byte_t* to_compare;
int comp;
uint8_t n = 0;
int n = 0;
int depth = 0;
// Check if first node
@ -1499,7 +1672,10 @@ index_t obi_avl_add(OBIDMS_avl_p avl, byte_t* value)
next = current_node->right_child;
else if (comp == 0)
// Value already stored
{
//fprintf(stderr, "\n>>>ALREADY IN, %s, %lld\n", obi_obibytes_to_seq(value), (avl->header)->nb_items);
return current_node->value;
}
depth++;
}
@ -1612,7 +1788,7 @@ byte_t* obi_str_to_obibytes(char* value)
*((int32_t*)(value_b+1)) = length;
// Store the initial length (in bytes) of the decoded value (same as encoded for character strings)
*((int32_t*)(value_b+5)) = length;
*((int64_t*)(value_b+5)) = length;
// Store the character string
strcpy(value_b+BYTE_ARRAY_HEADER_SIZE, value);

7
src/obiavl.h
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@ -340,5 +340,12 @@ byte_t* obi_seq_to_obibytes(char* seq);
const char* obi_obibytes_to_seq(byte_t* value_b);
OBIDMS_avl_p* obi_create_avl_in_64_parts(OBIDMS_p dms, const char* avl_name);
typedef uint8_t crc;
crc compute_crc(const char* s);
#endif /* OBIAVL_H_ */

20
src/obidmscolumn.c
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@ -521,7 +521,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
OBIDMS_column_p new_column;
OBIDMS_column_directory_p column_directory;
OBIDMS_column_header_p header;
OBIDMS_avl_p avl;
OBIDMS_avl_p* avl;
size_t file_size;
obiversion_t version_number;
char* column_file_name;
@ -723,7 +723,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
// If the data type is OBI_STR or OBI_SEQ, the associated obi_avl is opened or created
if ((returned_data_type == OBI_STR) || (returned_data_type == OBI_SEQ))
{
avl = obi_avl(dms, avl_name);
avl = obi_create_avl_in_64_parts(dms, avl_name);
if (avl == NULL)
{
obidebug(1, "\nError opening or creating the aVL tree associated with a column");
@ -732,7 +732,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
free(new_column);
return NULL;
}
new_column->avl = avl;
memcpy(new_column->avl, avl, 64*sizeof(OBIDMS_avl_p));
strncpy(header->avl_name, avl_name, AVL_MAX_NAME);
}
@ -886,7 +886,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
free(column);
return NULL;
}
column->avl = avl;
//column->avl = avl; TODO
}
close(column_file_descriptor);
@ -1020,12 +1020,12 @@ int obi_close_column(OBIDMS_column_p column)
}
}
// If the data type is OBI_STR or OBI_SEQ, the associated AVL tree is closed
if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
{
if (obi_close_avl(column->avl) < 0)
return -1;
}
// If the data type is OBI_STR or OBI_SEQ, the associated AVL tree is closed TODO
// if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
// {
// if (obi_close_avl(column->avl) < 0)
// return -1;
// }
// Munmap data
if (munmap(column->data, (column->header)->data_size) < 0)

2
src/obidmscolumn.h
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@ -98,7 +98,7 @@ typedef struct OBIDMS_column {
*/
OBIDMS_column_header_p header; /**< A pointer to the header of the column.
*/
OBIDMS_avl_p avl; /**< A pointer to the AVL tree associated with the column if there is one.
OBIDMS_avl_p avl[64]; /**< A pointer to the group of AVL trees associated with the column if there is one.
*/
void* data; /**< A `void` pointer to the beginning of the data.
*

9
src/obidmscolumn_seq.c
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@ -61,8 +61,13 @@ int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
if (value_b == NULL)
return -1;
if (strlen(value_b) == 0)
fprintf(stderr, "\nPOUIC");
//fprintf(stderr, "\n>%s||%s", value, obi_obibytes_to_seq(value_b));
// Add in the AVL tree
idx = obi_avl_add(column->avl, value_b);
idx = obi_avl_add((column->avl)[compute_crc(value)], value_b);
if (idx == -1)
return -1;
@ -130,7 +135,7 @@ const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t l
if (idx == OBIIdx_NA)
return OBISeq_NA;
value_b = obi_avl_get(column->avl, idx);
//value_b = obi_avl_get((column->avl)[crc(value)], idx);
return obi_obibytes_to_seq(value_b);
}

4
src/obidmscolumn_str.c
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@ -61,7 +61,7 @@ int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
return -1;
// Add in the AVL tree
idx = obi_avl_add(column->avl, value_b);
idx = obi_avl_add((column->avl)[compute_crc(value)], value_b);
if (idx == -1)
return -1;
@ -129,7 +129,7 @@ const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t l
if (idx == OBIIdx_NA)
return OBIStr_NA;
value_b = obi_avl_get(column->avl, idx);
//value_b = obi_avl_get(column->avl, idx);
return obi_obibytes_to_str(value_b);
}