static rc_t Work(Db* db, SpotIterator* it)
{
rc_t rc = 0;
bool toRedact = false;
int64_t row_id = 0;
spotid_t nSpots = 0;
spotid_t redactedSpots = 0;
uint8_t filter[64];
memset(filter, SRA_READ_FILTER_REDACTED, sizeof filter);
assert(it);
while (rc == 0 && SpotIteratorNext(it, &rc, &row_id, &toRedact)) {
uint8_t nreads = 0;
char bufferIn[64];
void* buffer = NULL;
uint32_t row_len = 0;
rc = Quitting();
++nSpots;
if (rc == 0) {
uint32_t elem_bits = 8;
rc = VCursorReadDirect(db->rCursor, row_id, db->rFilterIdx,
elem_bits, bufferIn, sizeof bufferIn, &row_len);
DISP_RC(rc, "while reading READ_FILTER");
nreads = row_len;
}
if (toRedact) {
buffer = filter;
++redactedSpots;
DBGMSG(DBG_APP,DBG_COND_1,
("Redacting spot %d: %d reads\n",row_id,nreads));
}
else {
buffer = bufferIn;
}
if (rc == 0) {
rc = VCursorOpenRow(db->wCursor);
DISP_RC(rc, "while opening row to write");
if (rc == 0) {
rc = VCursorWrite
(db->wCursor, db->wIdx, 8 * nreads, buffer, 0, 1);
DISP_RC(rc, "while writing READ_FILTER");
}
if (rc == 0) {
rc = VCursorCommitRow(db->wCursor);
DISP_RC(rc, "while committing row");
}
if (rc == 0) {
rc = VCursorCloseRow(db->wCursor);
DISP_RC(rc, "while closing row");
}
}
}
db->nSpots = nSpots;
db->redactedSpots = redactedSpots;
if (rc == 0) {
rc = VCursorCommit(db->wCursor);
DISP_RC(rc, "while committing cursor");
}
return rc;
}
static rc_t SDataUpdate(struct SData* self,
const char* newColName, const char* redactFileName,
spotid_t* redactedSpots, spotid_t* all)
{
struct SBlob blob;
uint8_t filter[32];
rc_t rc = 0, rc2 = 0;
uint32_t colIdx = 0;
spotid_t spot = 0, last = 0;
bool toRedact = false;
struct SpotIterator it;
assert(self && redactedSpots && all);
memset(filter, SRA_READ_FILTER_REDACTED, sizeof filter);
if ((rc = SpotIteratorInit(&it, self->_rdTbl, redactFileName))
== 0)
{
rc = SRATableOpenColumnWrite
(self->_wrTbl, &colIdx, NULL, newColName, sra_read_filter_t);
if (rc != 0) {
plogerr(klogErr, rc,
"cannot open Column $(path) for Write", "path=%s", newColName);
return rc;
}
}
else {
return rc;
}
rc = SBlobInit(&blob, self, &it);
if (rc != 0) {
return rc;
}
while (rc == 0 && SpotIteratorNext(&it, &rc, &spot, &toRedact)) {
bitsz_t offset = 0, size = 0;
const void *base = NULL;
uint8_t nReads = 0;
if (rc != 0) {
break;
}
plogmsg(klogDebug2, "Spot $(spot): $(action)",
PLOG_U32(spot) ",action=%s",
spot, toRedact ? "redact" : "original");
/* GET NEXT BLOB RANGE */
if (spot == 1 || spot > last) {
rc = SBlobGetRange(&blob, spot, &last);
if (rc != 0) {
break;
}
}
assert(spot <= last);
/* GET NREADS */
if ((rc = SRAColumnRead
(self->_NReadsCol, spot, &base, &offset, &size)) != 0)
{
logerr(klogErr, rc, "cannot SRAColumnRead");
break;
}
else if (offset != 0 || size != sizeof nReads * 8) {
rc = RC(rcExe, rcColumn, rcReading, rcData, rcInvalid);
plogerr(klogErr, rc,
"Bad SRAColumnRead(\"NREADS\", $(spot)) result",
PLOG_U32(spot), spot);
}
else {
nReads = *((uint8_t*) base);
if (spot == 1) {
if (nReads == 1) {
plogmsg(klogInfo, "The first spot has $(nreads) read",
"nreads=%d", nReads);
}
else {
plogmsg(klogInfo, "The first spot has $(nreads) reads",
"nreads=%d", nReads);
}
}
}
/* GET READ_FILTER */
if (toRedact) {
base = filter;
++(*redactedSpots);
}
else {
if ((rc = SRAColumnRead(self->_origFilterCol,
spot, &base, &offset, &size)) != 0)
{
plogerr(klogErr, rc,
"while calling SRAColumnRead($(name))", "name=%s",
"READ_FILTER");
break;
}
else if (offset != 0
|| size != sizeof (uint8_t) * 8 * nReads)
{
rc = RC(rcExe, rcColumn, rcReading, rcData, rcInvalid);
plogerr(klogErr, rc, "Bad SRAColumnRead($(spot)) result",
PLOG_U32(spot), spot);
}
}
if ((rc = SRATableOpenSpot(self->_wrTbl, spot)) != 0) {
plogerr(klogErr, rc, "cannot open Spot $(id)", PLOG_U32(id), spot);
break;
}
if ((rc = SRATableWriteIdxColumn(self->_wrTbl,
colIdx, base, 0, sizeof (uint8_t) * 8 * nReads)) != 0)
{
logerr(klogErr, rc, "cannot SRATableWriteIdxColumn");
break;
}
if ((rc = SRATableCloseSpot(self->_wrTbl)) != 0) {
logerr(klogErr, rc, "cannot SRATableCloseSpot");
break;
}
/* CUT THE BLOB */
if (spot == last) {
rc = SRATableCloseCursor(self->_wrTbl);
if (rc != 0) {
plogerr(klogErr, rc, "cannot SRATableCloseCursor $(id)",
PLOG_U32(id), spot);
break;
}
}
}
rc2 = SpotIteratorDestroy(&it);
if (rc == 0)
{ rc = rc2; }
*all = spot;
return rc;
}
