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NCBI C++ ToolKit: src/objtools/data_loaders/genbank/gicache/gicache.c Source File

(

severity,

* fmt, ...)

__attribute__ ((

(printf, 2, 3)))

(

severity,

* fmt, ...)

(

>=

(

) - 1)

=

(

) - 1;

(data_index && data_index->

) {

(data_index->

)

(data_index->

) {

fstat_err =

(data_index, &fstat);

(fstat_err != 0 || fstat.st_size == 0) {

snprintf(logmsg,

(logmsg),

, data_index->

,

(rc));

snprintf(logmsg,

(logmsg),

,

(rc));

snprintf(logmsg,

(logmsg),

,

,

(rc));

snprintf(logmsg,

(logmsg),

,

,

(rc));

snprintf(logmsg,

(logmsg),

, mapsize,

(rc));

snprintf(logmsg,

(logmsg),

, data_index->

,

(rc));

snprintf(logmsg,

(logmsg),

,

(rc));

snprintf(logmsg,

(logmsg),

,

,

(rc));

snprintf(logmsg,

(logmsg),

,

,

(rc));

snprintf(logmsg,

(logmsg),

,

(rc));

snprintf(logmsg,

(logmsg),

,

(rc));

gi_len_bytes =

& 0x7;

gi_len_neg =

& 0x8;

* pacc = (

*)

->mv_data + gi_len_bytes + 2;

(acc_buf_len <= acclen) {

(

,

, acc_buf_len, acclen, gi);

memcpy(acc_buf, pacc, acclen);

(acc_buf && acc_buf_len > 0)

(!data_index || !data_index->

) {

snprintf(logmsg,

(logmsg),

);

snprintf(logmsg,

(logmsg),

,

(rc));

.mv_size =

(gi64);

.mv_data = &gi64;

snprintf(logmsg,

(logmsg),

, gi,

(rc));

snprintf(logmsg,

(logmsg),

,

(rc));

snprintf(logmsg,

(logmsg),

,

(rc));

snprintf(logmsg,

(logmsg),

,

(rc));

snprintf(logmsg,

(logmsg),

,

(rc));

(!

.mv_data ||

.mv_size !=

(gi64)) {

snprintf(logmsg,

(logmsg),

);

snprintf(logmsg,

(logmsg),

,

(rc));

gi_len_bytes = 0;

acclen = strlen(acc);

snprintf(logmsg,

(logmsg),

, acclen,

);

(is_incremental) {

rc =

(data_index, gi, lacc,

(lacc), &lgi_len);

changed_acc =

(lacc, acc) != 0;

changed_len = lgi_len != gi_len;

(!changed_acc && !changed_len)

snprintf(logmsg,

(logmsg),

, gi, lacc, acc);

snprintf(logmsg,

(logmsg),

, gi, lgi_len, gi_len);

(!data_index->

) {

snprintf(logmsg,

(logmsg),

,

(rc));

.mv_size =

(gi64);

.mv_data = &gi64;

gi_len_neg = gi_len < 0;

(gi_len != 0 && gi_len != -1) {

= (gi_len_bytes & 0x7) | ((gi_len_neg ? 1 : 0) << 3);

memcpy(gidata + 1, &gi_len, gi_len_bytes);

gidata[1 + gi_len_bytes] = acclen;

memcpy(gidata + 1 + gi_len_bytes + 1, acc, acclen);

.mv_size = datalen;

.mv_data = gidata;

snprintf(logmsg,

(logmsg),

,

(rc));

(data_index->

) {

(!cache_found && !prefix) {

(acc && buf_len > 0)

(

,

);

snprintf(accbuf,

(accbuf),

, acc,

);

snprintf(accbuf,

(accbuf),

, acc);

(

* cache_prefix,

* filename,

* quitting) {

= fopen(filename,

);

snprintf(logmsg,

(logmsg),

, filename, errno);

setvbuf(

,

, _IOFBF, 128 * 1024);

snprintf(logmsg,

(logmsg),

,

(rc));

snprintf(logmsg,

(logmsg),

,

(rc));

(!

.mv_data ||

.mv_size !=

(gi64)) {

(

,

);

snprintf(line,

(line),

, gi64, acc_buf, gi_len);

(quitting && *quitting)

snprintf(logmsg,

(logmsg),

,

(rc));

snprintf(logmsg,

(logmsg),

);

snprintf(logmsg,

(logmsg),

);

snprintf(logmsg,

(logmsg),

);

snprintf(logmsg,

(logmsg),

,

(rc));

snprintf(logmsg,

(logmsg),

,

(rc));

snprintf(logmsg,

(logmsg),

,

(rc));

snprintf(logmsg,

(logmsg),

,

(rc));

.mv_data = (

*)Name;

.mv_size = strlen(Name);

meta[512], stime[128];

snprintf(logmsg,

(logmsg),

);

snprintf(logmsg,

(logmsg),

);

snprintf(logmsg,

(logmsg),

);

snprintf(logmsg,

(logmsg),

,

(rc));

snprintf(logmsg,

(logmsg),

,

(rc));

meta[512], stime[128];

(gethostname(meta,

(meta)) != 0)

snprintf(stime,

(stime),

, (

)starttime);

snprintf(logmsg,

(logmsg),

);

snprintf(logmsg,

(logmsg),

,

(rc));

.mv_size = strlen(Name);

.mv_data = (

*)Name;

snprintf(logmsg,

(logmsg),

,

(rc));

snprintf(

, ValueSz,

, (

)

.mv_size, (

*)

.mv_data);

snprintf(logmsg,

(logmsg),

,

(rc));

totlen = 0, totcomprlen = 0;

memset(tab, 0,

(*tab));

snprintf(logmsg,

(logmsg),

);

snprintf(logmsg,

(logmsg),

,

(rc));

snprintf(logmsg,

(logmsg),

,

(rc));

(!

.mv_data ||

.mv_size !=

(gi64)) {

(

,

);

tab->

[(

)(*p)]++;

bits = tablen->

[(

)(*p)];

totcomprlen +=

;

totcomprlen += (compr + 7) / 8;

snprintf(logmsg,

(logmsg),

,

(rc));

(totcomprlen * 100L) / totlen;

int64_t GICache_GetLength(int64_t gi)

static int64_t x_GetMaxGi(SGiDataIndex *data_index)

static void(* __LogFuncEx)(int severity, char *msg)

static void LOG(int severity, char *fmt,...)

#define MAX_ACCESSION_LENGTH

static int x_PutData(SGiDataIndex *data_index, int64_t gi, int64_t gi_len, const char *acc, int overwrite, int is_incremental)

static void(* __LogFunc)(char *)

static int x_GetGiData(SGiDataIndex *data_index, int64_t gi, char *acc_buf, int acc_buf_len, int64_t *gi_len)

int x_Commit(SGiDataIndex *data_index, int force_sync)

static int x_DataToGiData(int64_t gi, MDB_val *data, char *acc_buf, int acc_buf_len, int64_t *gi_len)

void GICache_Dump(const char *cache_prefix, const char *filename, volatile int *quitting)

static int xFindFile(SGiDataIndex *data_index, struct stat *fstat)

static void GiDataIndex_Free(SGiDataIndex *data_index)

int GICache_ReadData(const char *prefix)

void GICache_SetLogEx(void(*logfunc)(int severity, char *msg))

static SGiDataIndex * gi_cache

int GICache_GetAccessionLen(int64_t gi, char *acc, int buf_len, int64_t *gi_len)

static SGiDataIndex * GiDataIndex_New(const char *prefix, Uint1 readonly)

static int x_mdb_txn_begin(MDB_env *env, MDB_txn *parent, unsigned int flags, MDB_txn **txn)

int GICache_SetMeta(const char *Name, const char *Value)

static int x_GICacheInit(const char *prefix, Uint1 readonly)

static int x_PutMeta(const char *Name, const char *Value)

int GICache_GetAccession(int64_t gi, char *acc, int buf_len)

int GICache_GetAccFreqTab(FreqTab *tab, const FreqTab *tablen)

int GICache_UpdateMeta(int is_incremental, const char *DB, time_t starttime)

int GiDataIndex_Commit(int force_sync)

int GICache_GetMeta(const char *Name, char *Value, size_t ValueSz)

int GICache_LoadStart(const char *cache_prefix)

int GICache_LoadAdd(int64_t gi, int64_t gi_len, const char *acc, int version, int is_incremental)

#define MAX_ROWS_PER_TRANSACTION

static Nlm_Boolean data_index_notfound

void GICache_SetLog(void(*logfunc)(char *))

int64_t GICache_GetMaxGi(void)

#define META_INCREMENTAL_HOST

#define RC_ALREADY_EXISTS

#define META_INCREMENTAL_TIME

#define DEFAULT_GI_CACHE_PATH

#define META_INCREMENTAL_DB

#define DEFAULT_GI_CACHE_PREFIX

uint8_t Uint1

1-byte (8-bit) unsigned integer

#define MDB_NOTFOUND

key/data pair not found (EOF)

#define MDB_SUCCESS

Successful result.

#define MDB_READERS_FULL

Environment maxreaders reached.

unsigned int

A callback function used to compare two keys in a database.

int mdb_env_open(MDB_env *env, const char *path, unsigned int flags, mdb_mode_t mode)

Open an environment handle.

int mdb_reader_check(MDB_env *env, int *dead)

Check for stale entries in the reader lock table.

void mdb_env_close(MDB_env *env)

Close the environment and release the memory map.

int mdb_cursor_get(MDB_cursor *cursor, MDB_val *key, MDB_val *data, MDB_cursor_op op)

Retrieve by cursor.

int mdb_put(MDB_txn *txn, MDB_dbi dbi, MDB_val *key, MDB_val *data, unsigned int flags)

Store items into a database.

void mdb_dbi_close(MDB_env *env, MDB_dbi dbi)

Close a database handle.

void mdb_txn_abort(MDB_txn *txn)

Abandon all the operations of the transaction instead of saving them.

int mdb_txn_commit(MDB_txn *txn)

Commit all the operations of a transaction into the database.

int mdb_env_sync(MDB_env *env, int force)

Flush the data buffers to disk.

int mdb_get(MDB_txn *txn, MDB_dbi dbi, MDB_val *key, MDB_val *data)

Get items from a database.

char * mdb_strerror(int err)

Return a string describing a given error code.

int mdb_cursor_open(MDB_txn *txn, MDB_dbi dbi, MDB_cursor **cursor)

Create a cursor handle.

int mdb_env_set_mapsize(MDB_env *env, size_t size)

Set the size of the memory map to use for this environment.

int mdb_env_set_maxdbs(MDB_env *env, MDB_dbi dbs)

Set the maximum number of named databases for the environment.

int mdb_env_create(MDB_env **env)

Create an LMDB environment handle.

int mdb_del(MDB_txn *txn, MDB_dbi dbi, MDB_val *key, MDB_val *data)

Delete items from a database.

int mdb_drop(MDB_txn *txn, MDB_dbi dbi, int del)

Empty or delete+close a database.

int mdb_dbi_open(MDB_txn *txn, const char *name, unsigned int flags, MDB_dbi *dbi)

Open a database in the environment.

void mdb_cursor_close(MDB_cursor *cursor)

Close a cursor handle.

int mdb_txn_begin(MDB_env *env, MDB_txn *parent, unsigned int flags, MDB_txn **txn)

Create a transaction for use with the environment.

int mdb_env_set_maxreaders(MDB_env *env, unsigned int readers)

Set the maximum number of threads/reader slots for the environment.

@ MDB_LAST

Position at last key/data item.

@ MDB_NEXT

Position at next data item.

#define MDB_INTEGERKEY

numeric keys in native byte order: either unsigned int or size_t.

#define MDB_CREATE

create DB if not already existing

#define MDB_NOMETASYNC

don't fsync metapage after commit

#define MDB_NOSYNC

don't fsync after commit

#define MDB_NOSUBDIR

no environment directory

#define MDB_RDONLY

read only

#define MDB_NOOVERWRITE

For put: Don't write if the key already exists.

unsigned int MDB_dbi

A handle for an individual database in the DB environment.

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

if(yy_accept[yy_current_state])

const string version

version string

const struct ncbi::grid::netcache::search::fields::KEY key

GenericValue< UTF8<> > Value

GenericValue with UTF8 encoding.

int strcmp(const char *str1, const char *str2)

Uint1 Boolean

bool replacment for C

#define TRUE

bool replacment for C indicating true.

#define FALSE

bool replacment for C indicating false.

#define NULLB

terminating byte of a char* string.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Cursors are used for all DB operations.

The database environment.

Generic structure used for passing keys and data in and out of the database.

char m_FileName[PATH_MAX]

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