コード例 #1
0
ファイル: blob-headers.c プロジェクト: ncbi/ncbi-vdb
rc_t VBlobHeaderReplace( VBlobHeader *targ, const VBlobHeader *src ) {
    BlobHeaders *parent;
    struct VBlobHeaderData *data;
    atomic32_t temp;
    
    if (src == NULL || targ == NULL)
        return RC(rcVDB, rcHeader, rcCopying, rcParam, rcNull);

    if (src->vt != &VBlobHeader_vt[1] || targ->vt != &VBlobHeader_vt[0])
        return RC(rcVDB, rcHeader, rcCopying, rcParam, rcInvalid);
    
    if (atomic32_read(&targ->refcount) != 1)
        return RC(rcVDB, rcHeader, rcCopying, rcParam, rcInvalid);
    
    data = calloc(1, sizeof(*data));
    if (data == NULL)
        return RC(rcVDB, rcHeader, rcCopying, rcMemory, rcExhausted);

    *data = *src->parent->data;
    atomic32_set(&data->refcount, 1);
    
    parent = (BlobHeaders *)targ->parent;
    VBlobHeaderDataRelease(parent->data);
    parent->data = data;
    
    atomic32_set(&temp, atomic32_read(&src->refcount));
    *targ = *src;
    atomic32_set(&targ->refcount, atomic32_read(&temp));
    targ->parent = parent;
    targ->vt = &VBlobHeader_vt[0];
    
    return 0;
}
コード例 #2
0
ファイル: cccopier.c プロジェクト: Bhumi28/sra-tools
rc_t CopierMake (Copier ** c, KDirectory * dir, const char * path, uint32_t timeout, uint32_t length)
{
    rc_t rc = 0, orc;
    Copier * self;

    self = malloc (sizeof *self);
    if (self == NULL)
    {
	rc = RC (rcExe, rcNoTarg, rcAllocating, rcMemory, rcExhausted);
    }
    else
    {
	atomic32_set (&self->refcount, 1);
	self->f = NULL;
	self->q = NULL;
	rc = CopierMakeF (self, dir, path);
	if (rc == 0)
	{
	    rc = BufferQMake (&self->q, timeout, length);
	    if (rc == 0)
	    {
		*c = self;
		atomic32_set (&self->refcount, 1);
		return rc;
	    }	    
	}
	orc = CopierRelease (self);
        if (orc)
            LOGERR (klogInt, orc, "Error releasing Copier");
    }
    return rc;
}
コード例 #3
0
ファイル: queue.c プロジェクト: ncbi/ncbi-vdb
/* Make
 * create an empty queue object
 *
 *  "capacity" [ IN ] - minimum queue length
 *  always expands to a power of 2, i.e. providing
 *  a length of 10 will result in a length of 16.
 */
LIB_EXPORT rc_t CC KQueueMake ( KQueue **qp, uint32_t capacity )
{
    rc_t rc;
    if ( qp == NULL )
        rc = RC ( rcCont, rcQueue, rcConstructing, rcParam, rcNull );
    else
    {
        KQueue *q;

        uint32_t cap = 1;
        while ( cap < capacity )
            cap += cap;

        q = malloc ( sizeof * q - sizeof q -> buffer + cap * sizeof q -> buffer [ 0 ] );
        if ( q == NULL )
            rc = RC ( rcCont, rcQueue, rcConstructing, rcMemory, rcExhausted );
        else
        {
            rc = KSemaphoreMake ( & q -> rc, 0 );
            if ( rc == 0 )
            {
                rc = KSemaphoreMake ( & q -> wc, cap );
                if ( rc == 0 )
                {
                    rc = KLockMake ( & q -> rl );
                    if ( rc == 0 )
                    {
                        rc = KLockMake ( & q -> wl );
                        if ( rc == 0 )
                        {
                            q -> capacity = cap;
                            q -> bmask = cap - 1;
                            q -> imask = ( cap + cap ) - 1;
                            q -> read = q -> write = 0;
                            atomic32_set ( & q -> refcount, 1 );
                            atomic32_set ( & q -> sealed, 0 );

                            QMSG ( "%s[%p]: created queue with capacity %u, "
                                   "bmask %#032b, imask %#032b.\n"
                                   , __func__, q, q -> capacity, q -> bmask, q -> imask
                                );

                            * qp = q;
                            return 0;
                        }

                        KLockRelease ( q -> rl );
                    }

                    KSemaphoreRelease ( q -> wc );
                }

                KSemaphoreRelease ( q -> rc );
            }
            free ( q );
        }
        * qp = NULL;
    }
    return rc;
}
コード例 #4
0
ファイル: blob-headers.c プロジェクト: ncbi/ncbi-vdb
static rc_t BlobHeadersCreateInternal ( BlobHeaders **lhs, unsigned ops, unsigned args ) {
    BlobHeaders *y = calloc(1, sizeof *y);

    *lhs = NULL;
    if (y) {
        atomic32_set(&y->refcount, 1);
        y->data = calloc(1, sizeof(*y->data) + args * sizeof(y->data->args[0]) + ops);
        if (y->data) {
            atomic32_set(&y->data->refcount, 1);
            if (args) {
                y->data->args = (void *)(&y->data[1]);
                if (ops) {
                    y->data->ops = (void *)(&y->data->args[args]);
                    y->data->op_count = ops;
                }
                y->data->arg_count = args;
            }
            else if (ops) {
                y->data->ops = (void *)(&y->data[1]);
                y->data->op_count = ops;
            }
            *lhs = y;
            
            return 0;
        }
        free(y);
    }
    return RC(rcVDB, rcHeader, rcConstructing, rcMemory, rcExhausted);
}
コード例 #5
0
ファイル: syscond.c プロジェクト: mariux/sratoolkit
/* Init
 */
rc_t KConditionInit ( KCondition *self )
{
    int status;

    assert ( self != NULL );
    status = pthread_cond_init ( & self -> cond, NULL );
    switch ( status )
    {
    case 0:
        break;
    case EAGAIN:
        return RC ( rcPS, rcCondition, rcConstructing, rcCondition, rcExhausted );
    case ENOMEM:
        return RC ( rcPS, rcCondition, rcConstructing, rcMemory, rcExhausted );
    case EBUSY:
        return RC ( rcPS, rcCondition, rcConstructing, rcCondition, rcBusy );
    case EINVAL:
        return RC ( rcPS, rcCondition, rcConstructing, rcCondition, rcInvalid );
    default:
        return RC ( rcPS, rcCondition, rcConstructing, rcNoObj, rcUnknown );
    }

    atomic32_set ( & self -> refcount, 1 );
    return 0;
}
コード例 #6
0
ファイル: syslock.c プロジェクト: mariux/sratoolkit
/* Make
 *  make a simple mutex
 */
LIB_EXPORT rc_t CC KLockMake ( KLock **lockp )
{
    rc_t rc;
    if ( lockp == NULL )
        rc = RC ( rcPS, rcLock, rcConstructing, rcParam, rcNull );
    else
    {
        KLock *lock = malloc ( sizeof * lock );
        if ( lock == NULL )
            rc = RC ( rcPS, rcLock, rcConstructing, rcMemory, rcExhausted );
        else
        {
            int status = pthread_mutex_init ( & lock -> mutex, NULL );
            if ( status == 0 )
            {
                atomic32_set ( & lock -> refcount, 1 );
                * lockp = lock;
                return 0;
            }

            /* pthread_mutex_init is documented as always returning 0 */
            rc = RC ( rcPS, rcLock, rcConstructing, rcNoObj, rcUnknown );

            free ( lock );
        }

        * lockp = NULL;
    }
    return rc;
}
コード例 #7
0
ファイル: align-access.c プロジェクト: gconcepcion/sratoolkit
LIB_EXPORT rc_t CC AlignAccessMgrMake(const AlignAccessMgr **mgr) {
    AlignAccessMgr *self = malloc(sizeof(*self));

    *mgr = self;
    if (self != NULL) {
        atomic32_set(&self->refcount, 1);
        return 0;
    }
    return RC(rcAlign, rcMgr, rcConstructing, rcMemory, rcExhausted);
}
コード例 #8
0
ファイル: utils.c プロジェクト: Jingyu9/sra-tools
rc_t CC
XTaskerSetDone ( const struct XTasker * self )
{
    if ( self == NULL ) {
        return RC ( rcExe, rcNoTarg, rcProcessing, rcParam, rcNull );
    }

    atomic32_set ( ( atomic32_t * ) & ( self -> is_done ), 1 );

    return 0;
}   /* XTaskerSetDone () */
コード例 #9
0
ファイル: utils.c プロジェクト: Jingyu9/sra-tools
rc_t CC
XTaskerDispose ( const struct XTasker * self )
{
    struct XTasker * Tasker;
    size_t llp;

    Tasker = ( struct XTasker * ) self;
    llp = 0;

    if ( Tasker != NULL ) {
        if ( Tasker -> stat != NULL ) {
            XStatsDispose ( Tasker -> stat );
            Tasker -> stat = NULL;
        }

        if ( Tasker -> tasks != NULL ) {
            for ( llp = 0; llp < Tasker -> task_qty; llp ++ ) {
                if ( Tasker -> tasks [ llp ] != NULL ) {
                    _TaskDispose ( Tasker -> tasks [ llp ] );
                    Tasker -> tasks [ llp ] = NULL;
                }
            }
        }
        Tasker -> tasks = NULL;
        Tasker -> task_qty = 0;

        atomic32_set ( & ( Tasker -> iteration ), 0 );
        atomic32_set ( & ( Tasker -> is_run ), 0 );
        atomic32_set ( & ( Tasker -> is_done ), 0 );

        Tasker -> stop_at = 0;

        Tasker -> job_4_task_data = NULL;
        Tasker -> job_4_task = NULL;

        free ( Tasker );
    }

    return 0;
}   /* XTaskerDispose () */
コード例 #10
0
rc_t CCCopyMake (CCCopy ** p, const KDirectory * in,  KDirectory * out, 
		  KDirectory * xml, bool force, KMD5SumFmt * md5,
		  CCFileFormat * ff, CCTree * tree, const char * path)
{
    rc_t rc;
    size_t pathlen;
    CCCopy * self;
    char relpath [4096];

    assert (in != NULL);
    assert (out != NULL);
    assert (xml != NULL);
    assert (path != NULL);

    rc = KDirectoryVResolvePath (in, false, relpath, sizeof relpath, path, NULL);
    if (rc != 0)
    {
	pLOGERR (klogErr, rc, "unable to resolve path $(P)", PLOG_S(P), path);
	return rc;
    }
    if ((relpath[0] == '.') && (relpath[1] == '.') && (relpath[2] == '/'))
    {
	rc = RC (rcExe, rcDirectory, rcResolving, rcPath, rcOutOfKDirectory);
	pLOGERR (klogErr, rc, "Path must resolve to current directory or subdirectories $(P)",
		 PLOG_S(P), relpath);
	return rc;
    }

    pathlen = strlen(relpath);
    self = malloc (sizeof (*self) - sizeof (*self->path) + pathlen + 1);
    if (self == NULL)
	rc = RC (rcExe, rcNoTarg, rcAllocating, rcMemory, rcExhausted);
    else
    {
	atomic32_set (&self->refcount, 1);
	KDirectoryAddRef (in);
	KDirectoryAddRef (out);
	KDirectoryAddRef (xml);
	KMD5SumFmtAddRef (md5);
	CCFileFormatAddRef (ff);
	self->in = in;
	self->out = out;
	self->xml = xml;
	self->force = force;
	self->md5 = md5;
	self->ff = ff;
	self->tree = tree;
	memcpy (self->path, relpath, pathlen+1);
	*p = self;
    }
    return rc;
}
コード例 #11
0
ファイル: syslock.c プロジェクト: mariux/sratoolkit
LIB_EXPORT rc_t CC KRWLockRelease ( const KRWLock *cself )
{
    KRWLock *self = ( KRWLock* ) cself;
    if ( cself != NULL )
    {
        if ( atomic32_dec_and_test ( & self -> refcount ) )
        {
            atomic32_set ( & self -> refcount, 1 );
            return KRWLockWhack ( self );
        }
    }
    return 0;
}
コード例 #12
0
ファイル: srapath.c プロジェクト: gconcepcion/sratoolkit
/* Make
 *  create path manager
 *
 *  the path manager should already be configured with
 *  standard search paths, but can be augmented by using
 *  the Add*Path messages.
 *
 *  "dir" [ IN, NULL OKAY ] - optional root directory to use
 *  attaches a new reference
 */
MOD_EXPORT
rc_t CC SRAPathMakeImpl ( SRAPath **pm, const KDirectory *dir )
{
    rc_t rc;

    if ( pm == NULL )
        rc = RC ( rcSRA, rcMgr, rcConstructing, rcParam, rcNull );
    else
    {
        NCBISRAPath *p = (NCBISRAPath *) malloc ( sizeof * p );
        if ( p == NULL )
            rc = RC ( rcSRA, rcMgr, rcConstructing, rcMemory, rcExhausted );
        else
        {
            p -> dad . vt = ( SRAPath_vt* ) & vtSRAPath;
            p -> dir = dir;
            if ( dir != NULL )
                rc = KDirectoryAddRef ( dir );
            else
            {
                KDirectory *wd;
                rc = KDirectoryNativeDir ( & wd );
                p -> dir = wd;
            }

            if ( rc != 0 )
                free ( p );
            else
            {
                DLListInit ( & p -> repos );
                p -> dflt_repo = NULL;
                atomic32_set ( & p -> refcount, 1 );

                /* the object is now complete */
                rc = SRAPathConfig ( p );
                if ( rc == 0 )
                {
                    * pm = & p -> dad;
                    return 0;
                }

                SRAPathWhack ( p );
            }
        }

        * pm = NULL;
    }

    return rc;
}
コード例 #13
0
ファイル: column.c プロジェクト: binlu1981/ncbi-vdb
/* Make
 */
static
rc_t KColumnBlobMake ( KColumnBlob **blobp, bool bswap )
{
    KColumnBlob *blob = malloc ( sizeof * blob );
    if ( blob == NULL )
        return RC ( rcDB, rcBlob, rcConstructing, rcMemory, rcExhausted );

    memset ( blob, 0, sizeof * blob );
    atomic32_set ( & blob -> refcount, 1 );
    blob -> bswap = bswap;

    * blobp = blob;
    return 0;
}
コード例 #14
0
ファイル: blob-headers.c プロジェクト: ncbi/ncbi-vdb
VBlobHeader *BlobHeadersCreateDummyHeader ( uint8_t version, uint32_t fmt, uint8_t flags, uint64_t size )
{
    struct BlobHeaderDummy *y;
    
    y = calloc(1, sizeof(*y));
    if (y) {
        y->data.fmt = fmt;
        y->data.version = version;
        y->data.osize = size;
        y->data.flags = flags;
        atomic32_set(&y->data.refcount, 1);

        y->dummy.data = &y->data;
        atomic32_set(&y->dummy.refcount, 1);
        
        y->hdr.vt = &VBlobHeader_vt[1];
        y->hdr.parent = &y->dummy;
        atomic32_set(&y->hdr.refcount, 1);
        
        return &y->hdr;
    }
    return 0;
}
コード例 #15
0
ファイル: bam-reader.c プロジェクト: Bhumi28/sra-tools
rc_t BAMReaderMake( const BAMReader **result,
                    char const headerText[],
                    char const path[] )
{
    rc_t rc;
    BAMReader *self = malloc(sizeof(BAMReader));
    if ( self == NULL )
    {
        *result = NULL;
        return RC(rcAlign, rcFile, rcConstructing, rcMemory, rcExhausted);
    }
    else
    {
        atomic32_set( & self->refcount, 1 );
        rc = BAMFileMakeWithHeader( & self->file, headerText, "%s", path);
        if ( rc != 0 )
        {
            free(self);
            *result = 0;
        }
        else
            *result = self;
    }
    
    self->nque = 0;
    self->rc = 0;
    self->eof = false;
    
    rc = KLockMake(&self->lock);
    if (rc == 0) 
    {
        rc = KConditionMake(&self->have_data);
        if (rc == 0) 
        {
            rc = KConditionMake(&self->need_data);
            if (rc == 0) 
            {
                rc = KThreadMake(&self->th, BAMReaderThreadMain, self);
                if (rc == 0) 
                    return 0;
                KConditionRelease(self->need_data);
            }
            KConditionRelease(self->have_data);
        }
        KLockRelease(self->lock);
    }
    
    return rc;
}           
コード例 #16
0
ファイル: arrayfile.c プロジェクト: ImAWolf/ncbi-vdb
/* Release
 *  discard reference to file
 *  ignores NULL references
 */
LIB_EXPORT rc_t CC KArrayFileRelease ( const KArrayFile *cself )
{
    KArrayFile *self = ( KArrayFile* ) cself;
    if ( cself != NULL )
    {
        if ( atomic32_dec_and_test ( & self -> refcount ) )
        {
            rc_t rc = KArrayFileDestroy ( self );
            if ( rc != 0 )
                atomic32_set ( & self -> refcount, 1 );
            return rc;
        }
    }
    return 0;
}
コード例 #17
0
ファイル: align-access.c プロジェクト: gconcepcion/sratoolkit
LIB_EXPORT rc_t CC AlignAccessMgrRelease(const AlignAccessMgr *cself) {
    rc_t rc = 0;
    AlignAccessMgr *self = (AlignAccessMgr *)cself;
    
    if (cself != NULL) {
        if (atomic32_dec_and_test(&self->refcount)) {
            rc = AlignAccessMgrWhack(self);
            if (rc)
                atomic32_set(&self->refcount, 1);
            else
                free(self);
        }
    }
    return rc;
}
コード例 #18
0
/* Wait
 *  waits for a thread to exit
 *
 *  "status" [ OUT ] - return parameter for thread's exit code
 */
LIB_EXPORT rc_t CC KThreadWait ( KThread *self, rc_t *out )
{
    DWORD wait_res;

    if ( self == NULL )
        return RC ( rcPS, rcThread, rcWaiting, rcSelf, rcNull );

    /* prevent multiple waiters */
    if ( atomic32_test_and_set ( & self -> waiting, 0, 1 ) != 0 )
        return RC ( rcPS, rcThread, rcWaiting, rcThread, rcBusy );

    wait_res = WaitForSingleObject( self->thread_handle, INFINITE );

    /* release waiter lock */
    atomic32_set ( & self -> waiting, 0 );

    switch( wait_res )
    {
    case WAIT_FAILED :
        return RC ( rcPS, rcThread, rcWaiting, rcNoObj, rcUnknown );
    }
    /*
        switch ( status )
        {
        case 0:
            break;
        case ESRCH:
            return RC ( rcPS, rcThread, rcWaiting, rcThread, rcDestroyed );
        case EINVAL:
            return RC ( rcPS, rcThread, rcWaiting, rcThread, rcDetached );
        case EDEADLK:
            return RC ( rcPS, rcThread, rcWaiting, rcThread, rcDeadlock );
        default:
            return RC ( rcPS, rcThread, rcWaiting, rcNoObj, rcUnknown );
        }
    */

    self -> join = false;

    /*
        if ( td == PTHREAD_CANCELED )
            self -> rc = RC ( rcPS, rcThread, rcWaiting, rcThread, rcCanceled );
    */
    if ( out != NULL )
        * out = self -> rc;

    return 0;
}
コード例 #19
0
ファイル: blob-headers.c プロジェクト: ncbi/ncbi-vdb
VBlobHeader *BlobHeadersGetHeader ( const BlobHeaders *self )
{
    VBlobHeader *y = calloc(1, sizeof(*y));
    
    if (y) {
        y->vt = &VBlobHeader_vt[0];
        atomic32_set(&y->refcount, 1);
        y->parent = self;
        BlobHeadersAddRef(y->parent);
        if (self->data) {
            y->op_tail = self->data->op_count;
            y->arg_tail = self->data->arg_count;
        }
    }
    return y;
}
コード例 #20
0
ファイル: syslock.c プロジェクト: mariux/sratoolkit
/* Make
 *  make a simple read/write lock
 */
LIB_EXPORT rc_t CC KRWLockMake ( KRWLock **lockp )
{
    rc_t rc;

    if ( lockp == NULL )
        rc = RC ( rcPS, rcRWLock, rcConstructing, rcParam, rcNull );
    else
    {
        KRWLock *lock = malloc ( sizeof * lock );
        if ( lock == NULL )
            rc = RC ( rcPS, rcRWLock, rcConstructing, rcMemory, rcExhausted );
        else
        {
            int status = pthread_rwlock_init ( & lock -> lock, NULL );
            if ( status == 0 )
            {
                atomic32_set ( & lock -> refcount, 1 );
                * lockp = lock;
                return 0;
            }

            switch ( status )
            {
            case EAGAIN:
                rc = RC ( rcPS, rcRWLock, rcConstructing, rcRWLock, rcExhausted );
                break;
            case ENOMEM:
                rc = RC ( rcPS, rcRWLock, rcConstructing, rcMemory, rcExhausted );
                break;
            case EPERM:
                rc = RC ( rcPS, rcRWLock, rcConstructing, rcProcess, rcUnauthorized );
                break;
            case EBUSY:
                rc = RC ( rcPS, rcRWLock, rcConstructing, rcRWLock, rcBusy );
                break;
            default:
                rc = RC ( rcPS, rcRWLock, rcConstructing, rcNoObj, rcUnknown );
            }

            free ( lock );
        }

        * lockp = NULL;
    }

    return rc;
}
コード例 #21
0
ファイル: align-access.c プロジェクト: gconcepcion/sratoolkit
static rc_t CC AlignAccessDBMakeEnumerator(const AlignAccessDB *self, AlignAccessAlignmentEnumerator **align_enum) {
    AlignAccessAlignmentEnumerator *lhs = malloc(sizeof(*lhs));
    
    *align_enum = lhs;
    if (lhs == NULL)
        return RC(rcAlign, rcTable, rcConstructing, rcMemory, rcExhausted);
    
    lhs->innerSelf = NULL;
    lhs->parent = self;
    AlignAccessDBAddRef(lhs->parent);
    atomic32_set(&lhs->refcount, 1);
    lhs->atend = 0;
    lhs->refSeqID = -1;
    lhs->endpos = 0;
    lhs->startpos = 0;
    
    return 0;
}
コード例 #22
0
ファイル: align-access.c プロジェクト: gconcepcion/sratoolkit
LIB_EXPORT rc_t CC AlignAccessMgrMakeBAMDB(const AlignAccessMgr *self, const AlignAccessDB **db, const VPath *bam) {
    AlignAccessDB *lhs = malloc(sizeof(*lhs));
    rc_t rc;

    if (lhs == NULL)
        return RC(rcAlign, rcMgr, rcConstructing, rcMemory, rcExhausted);
    
    rc = BAMFileMakeWithVPath(&lhs->innerSelf, bam);
    if (rc) {
        free(lhs);
        return rc;
    }
    lhs->mgr = self;
    AlignAccessMgrAddRef(lhs->mgr);
    atomic32_set(&lhs->refcount, 1);
    
    *db = lhs;
    return 0;
}
コード例 #23
0
rc_t ProcessOneMake (ProcessOne ** ppo, const KDirectory * dir, KDirectory * xml,
		     const KFile * file, KMD5SumFmt *md5, CCFileFormat * ff,
		     const char * path)
{
    ProcessOne * self;
    rc_t rc = 0;
    size_t pathlen;

    PLOGMSG (klogDebug10, "ProcessOneMake $(f)", PLOG_S(f), path);
    /* legit seeming inputs? these could be replaced with RC returns */
    assert (ppo != NULL);
    assert (file != NULL);
    assert (path != NULL);

    /* allocate the object */
    pathlen = strlen (path);
    self = malloc (sizeof (*self) - sizeof(self->path) + pathlen + 1);
    if (self == NULL)
    {
	rc = RC (rcExe, rcNoTarg, rcAllocating, rcMemory, rcExhausted);
    }
    else
    {
	atomic32_set (&self->refcount, 1);
	KDirectoryAddRef (dir);
	KDirectoryAddRef (xml);
	KMD5SumFmtAddRef (md5);
	CCFileFormatAddRef (ff);
	KFileAddRef (file);
	self->dir = dir;
	self->xml = xml;
	self->md5 = md5;
	self->file = file;
	self->ff = ff;
	memcpy (self->path, path, pathlen);
	self->path[pathlen] = '\0';
	rc = 0;
    }
    *ppo = self;
    return rc;
}
コード例 #24
0
ファイル: ccbufferq.c プロジェクト: Bhumi28/sra-tools
rc_t BufferQMake (BufferQ ** q, uint32_t timeout, uint32_t length)
{
    rc_t rc = 0;
    BufferQ * self;

    assert (q != NULL);

    self = malloc (sizeof * self);
    if (self == NULL)
	rc = RC (rcExe, rcQueue, rcAllocating, rcMemory, rcExhausted);
    else
    {
	rc = KQueueMake (&self->q, length);
	if (rc == 0)
	{
	    self->timeout = timeout;
	    atomic32_set (&self->refcount, 1);
	    *q = self;
	}
    }

    return rc;
}
コード例 #25
0
ファイル: align-access.c プロジェクト: gconcepcion/sratoolkit
LIB_EXPORT rc_t CC AlignAccessDBEnumerateRefSequences(const AlignAccessDB *self, AlignAccessRefSeqEnumerator **refseq_enum) {
    AlignAccessRefSeqEnumerator *lhs;
    unsigned cur = 0;
    unsigned end;
    
    BAMFileGetRefSeqCount(self->innerSelf, &end);
    if (BAMFileIsIndexed(self->innerSelf)) {
        while (cur != end && BAMFileIndexHasRefSeqId(self->innerSelf, cur) == 0)
            ++cur;
        if (cur == end)
            return AlignAccessRefSeqEnumeratorEOFCode;
    }
    lhs = malloc(sizeof(*lhs));
    *refseq_enum = lhs;
    if (lhs != NULL) {
        lhs->parent = self;
        AlignAccessDBAddRef(lhs->parent);
        lhs->cur = cur;
        lhs->end = end;
        atomic32_set(&lhs->refcount, 1);
        return 0;
    }
    return RC(rcAlign, rcDatabase, rcConstructing, rcMemory, rcExhausted);
}
コード例 #26
0
/* Make
 *  create and run a thread
 *
 *  "run_thread" [ IN ] - thread entrypoint
 *
 *  "data" [ IN, OPAQUE ] - user-supplied thread data
 */
LIB_EXPORT rc_t CC KThreadMake ( KThread **tp,
                                 rc_t ( CC * run_thread ) ( const KThread*, void* ), void *data )
{
    rc_t rc;
    if ( tp == NULL )
        rc = RC ( rcPS, rcThread, rcCreating, rcParam, rcNull );
    else
    {
        if ( run_thread == NULL )
            rc = RC ( rcPS, rcThread, rcCreating, rcFunction, rcNull );
        else
        {
            KThread *t = malloc ( sizeof * t );
            if ( t == NULL )
                rc = RC ( rcPS, rcThread, rcCreating, rcMemory, rcExhausted );
            else
            {
                /* finish constructing thread */
                t -> run = run_thread;
                t -> data = data;
                atomic32_set ( & t -> waiting, 0 );
                atomic32_set ( & t -> refcount, 2 );
                t -> rc = 0;
                t -> join = true;

                /* attempt to create thread */
                t -> thread_handle = CreateThread(
                                         NULL,               /* default security attributes */
                                         0,                  /* use default stack size */
                                         int_ThreadProc,     /* thread function */
                                         t,                  /* argument to thread function */
                                         0,                  /* run immediately */
                                         &t->thread_id );    /* returns the thread identifier */

                /* status = pthread_create ( & t -> thread, 0, KThreadRun, t ); */
                if ( t->thread_handle != NULL )
                {
                    * tp = t;
                    return 0;
                }

                rc = RC ( rcPS, rcThread, rcCreating, rcNoObj, rcUnknown );
                /* see why we failed */
                /*
                switch ( status )
                {
                case EAGAIN:
                    rc = RC ( rcPS, rcThread, rcCreating, rcThread, rcExhausted );
                    break;
                default:
                    rc = RC ( rcPS, rcThread, rcCreating, rcNoObj, rcUnknown );
                }
                */

                free ( t );
            }
        }

        * tp = NULL;
    }
    return rc;
}
コード例 #27
0
ファイル: utils.c プロジェクト: Jingyu9/sra-tools
/* JOJOBA here will be variable part */
rc_t CC
XTaskerMake (
            const struct XTasker ** Tasker,
            size_t NumThreads,
            void * Data,
            Job4Task Jobber
)
{
    rc_t RCt;
    struct XTasker * Ret;
    size_t llp;

    RCt = 0;
    Ret = NULL;
    llp = 0;

    if ( Tasker != NULL ) {
        * Tasker = NULL;
    }

    if ( Tasker == NULL ) {
        return RC ( rcExe, rcNoTarg, rcProcessing, rcParam, rcNull );
    }

    if ( Jobber == NULL ) {
        return RC ( rcExe, rcNoTarg, rcProcessing, rcParam, rcNull );
    }

    if ( NumThreads == 0 ) {
        return RC ( rcExe, rcNoTarg, rcProcessing, rcParam, rcInvalid );
    }

    Ret = calloc ( 1, sizeof ( struct XTasker ) );
    if ( Ret == NULL ) {
        return RC ( rcExe, rcNoTarg, rcProcessing, rcParam, rcExhausted );
    }
    else {
        Ret -> tasks = calloc ( NumThreads, sizeof ( struct XTask * ) );
        if ( Ret -> tasks == NULL ) {
            RCt = RC ( rcExe, rcNoTarg, rcProcessing, rcParam, rcExhausted );
        }
        else {
            if ( RCt == 0 ) {
                Ret -> task_qty = NumThreads;
                for ( llp = 0; llp < NumThreads; llp ++ ) {
                    RCt = _TaskMake ( Ret -> tasks + llp, Ret, llp );
                    if ( RCt != 0 ) {
                        break;
                    }
                }
                if ( RCt == 0 ) {
                    RCt = XStatsMake ( & ( Ret -> stat ) );
                    if ( RCt == 0 ) { 
                        atomic32_set ( & ( Ret -> iteration ), 0 );
                        atomic32_set ( & ( Ret -> is_run ), 0 );
                        atomic32_set ( & ( Ret -> is_done ), 0 );
                        Ret -> stop_at = 0;
                        Ret -> job_4_task_data = Data;
                        Ret -> job_4_task = Jobber;

                        * Tasker = Ret;
                    }
                }
            }
        }
    }

    if ( RCt != 0 ) {
        * Tasker = NULL;

        if ( Ret != NULL ) {
            XTaskerDispose ( Ret );
        }
    }

    return RCt;
}   /* XTaskerMake () */