rc_t write_statistic_into_db( KDirectory *dir, statistic * data,
const KNamelist *schema_list, const char *src_path,
uint64_t * written, bool show_progress )
{
VDBManager *my_manager;
rc_t rc;
if ( written != NULL ) *written = 0;
rc = VDBManagerMakeUpdate ( &my_manager, dir );
if ( rc != 0 )
LogErr( klogInt, rc, "VDBManagerMakeUpdate() failed\n" );
else
{
VSchema * my_schema;
rc = make_schema( schema_list, my_manager, &my_schema );
if ( rc == 0 )
{
VDatabase *my_database;
rc = VDBManagerOpenDBUpdate( my_manager, &my_database,
my_schema, src_path );
if ( rc != 0 )
LogErr( klogInt, rc, "VDBManagerOpenDBUpdate() failed\n" );
else
{
VTable * my_table;
rc = VDatabaseCreateTable( my_database, &my_table,
"QUAL_STAT",
kcmOpen | kcmParents,
"QUAL_STAT" );
if ( rc !=0 )
LogErr( klogInt, rc, "VDatabaseCreateTable() failed\n" );
else
{
rc = write_statistic_cmn( my_table, data, written, show_progress );
VTableRelease( my_table );
}
VDatabaseRelease( my_database );
}
VSchemaRelease( my_schema );
}
VDBManagerRelease( my_manager );
}
return rc;
}
rc_t correct( const char * obj )
{
KDirectory * dir;
rc_t rc = KDirectoryNativeDir( &dir );
if ( rc != 0 )
{
LOGERR( klogErr, rc, "creation of KDirectory failed" );
}
else
{
VDBManager * vdb_mgr;
rc = VDBManagerMakeUpdate ( &vdb_mgr, dir );
if ( rc != 0 )
{
LOGERR( klogErr, rc, "creation of VDBManager failed" );
}
else
{
VDatabase * vdb_db;
rc = VDBManagerOpenDBUpdate ( vdb_mgr, &vdb_db, NULL, "%s", obj );
if ( rc != 0 )
{
LOGERR( klogErr, rc, "vdb: open for update failed" );
}
else
{
KDatabase *kdb;
rc = VDatabaseOpenKDatabaseUpdate ( vdb_db, & kdb );
if ( rc != 0 )
{
LOGERR( klogErr, rc, "kdb: open for update failed" );
}
else
{
if ( KDatabaseExists ( kdb, kptTable, CONSENSUS ) )
{
if ( KDatabaseExists ( kdb, kptTable, PULSE ) )
{
OUTMSG(( "table >%s< does already exist in >%s<\n", PULSE, obj ));
}
else
{
if ( KDatabaseExists ( kdb, kptTable, SEQUENCE ) )
{
rc = KDatabaseRenameTable ( kdb, true, SEQUENCE, PULSE );
if ( rc != 0 )
{
LOGERR( klogErr, rc, "kdb: renaming table failed" );
}
else
{
OUTMSG(( "table >%s< renamed to >%s< in >%s<\n", SEQUENCE, PULSE, obj ));
}
if ( rc == 0 )
{
rc = KDatabaseAliasTable ( kdb, CONSENSUS, SEQUENCE );
if ( rc != 0 )
{
LOGERR( klogErr, rc, "kdb: creating table-alias failed" );
}
else
{
OUTMSG(( "alias >%s< created for >%s< in >%s<\n", SEQUENCE, CONSENSUS, obj ));
}
}
}
}
}
else
{
OUTMSG(( "table >%s< does not exist in >%s<\n", CONSENSUS, obj ));
}
KDatabaseRelease ( kdb );
}
VDatabaseRelease( vdb_db );
}
VDBManagerRelease( vdb_mgr );
}
KDirectoryRelease( dir );
}
return rc;
}
static rc_t DbInit(rc_t rc, const CmdLine* args, Db* db)
{
const char name[] = "READ_FILTER";
assert(args && db);
memset(db, 0, sizeof *db);
if (rc != 0)
{ return rc; }
db->table = args->table;
if (rc == 0) {
rc = VDBManagerMakeUpdate(&db->mgr, NULL);
DISP_RC(rc, "while calling VDBManagerMakeUpdate");
}
if (rc == 0) {
rc = VDBManagerWritable(db->mgr, args->table);
if (rc != 0) {
if (GetRCState(rc) == rcLocked)
{
rc = VDBManagerUnlock(db->mgr, args->table);
if (rc != 0) {
PLOGERR(klogErr, (klogErr, rc,
"while calling VDBManagerUnlock('$(table)')",
"table=%s", args->table));
}
db->locked = true;
}
else {
PLOGERR(klogErr, (klogErr, rc,
"while calling VDBManagerWritable('$(table)')",
"table=%s", args->table));
if (rc == RC(rcDB, rcPath, rcAccessing, rcPath, rcReadonly)) {
PLOGERR(klogErr, (klogErr, rc,
"N.B. It is possible '$(table)' was not locked properly"
, "table=%s", args->table));
}
}
}
}
if (rc == 0) {
db->locked = true; /* has to be locked in production mode */
rc = VDBManagerOpenTableUpdate (db->mgr, &db->tbl, NULL, args->table);
if (rc != 0) {
VDatabase *vdb;
rc_t rc2 = VDBManagerOpenDBUpdate ( db->mgr, &vdb, NULL , args->table );
if( rc2 == 0) {
rc2 = VDatabaseOpenTableUpdate ( vdb, &db->tbl, "SEQUENCE" );
if (rc2 == 0 ) rc = 0;
VDatabaseRelease ( vdb );
}
}
if(rc != 0){
PLOGERR(klogErr, (klogErr, rc,
"while opening VTable '$(table)'", "table=%s", args->table));
}
}
if( rc == 0) {
rc = VTableCreateCursorRead(db->tbl, &db->rCursor);
DISP_RC(rc, "while creating read cursor");
if (rc == 0) {
rc = VCursorAddColumn(db->rCursor, &db->rFilterIdx, "%s", name);
if (rc != 0) {
PLOGERR(klogErr, (klogErr, rc,
"while adding $(name) to read cursor", "name=%s", name));
}
}
if (rc == 0) {
rc = VCursorOpen(db->rCursor);
DISP_RC(rc, "while opening read cursor");
}
}
if (rc == 0) {
rc = VTableCreateCursorWrite(db->tbl, &db->wCursor, kcmInsert);
DISP_RC(rc, "while creating write cursor");
if (rc == 0) {
rc = VCursorAddColumn(db->wCursor, &db->wIdx, "%s", name);
if (rc != 0) {
PLOGERR(klogErr, (klogErr, rc,
"while adding $(name) to write cursor", "name=%s", name));
}
}
if (rc == 0) {
rc = VCursorOpen(db->wCursor);
DISP_RC(rc, "while opening write cursor");
}
}
return rc;
}
static rc_t process(const char* dbname)
{
rc_t rc;
KHashFile* hf = NULL;
rc = KHashFileMake(&hf, NULL);
if (rc) {
fprintf(stderr, "Couldn't create KHashFile\n");
return rc;
}
KDirectory* srcdir = NULL;
rc = KDirectoryNativeDir(&srcdir);
if (rc) {
fprintf(stderr, "Failed %d %d", __LINE__, rc);
return rc;
}
VDBManager* mgr = NULL;
rc = VDBManagerMakeUpdate(&mgr, NULL); // NULL=No working directory
if (rc) {
fprintf(stderr, "Failed %d %d", __LINE__, rc);
return rc;
}
VDatabase* db = NULL;
rc = VDBManagerOpenDBUpdate(mgr, &db, NULL, dbname);
if (rc) {
fprintf(stderr, "Failed %d %d", __LINE__, rc);
return rc;
}
const VTable* tbl = NULL;
rc = VDatabaseOpenTableRead(db, &tbl, "hdrs");
if (rc) {
fprintf(stderr, "Failed %d %d", __LINE__, rc);
return rc;
}
const VCursor* curs = NULL;
rc = VTableCreateCursorRead(tbl, &curs);
if (rc) {
fprintf(stderr, "Failed %d %d", __LINE__, rc);
return rc;
}
uint32_t group_idx = 0; // HDR, TAG, VALUE
uint32_t hdr_idx = 0;
uint32_t tag_idx = 0;
uint32_t value_idx = 0;
rc = VCursorAddColumn(curs, &group_idx, "GROUP");
if (rc) {
fprintf(stderr, "Failed %d %d", __LINE__, rc);
return rc;
}
rc = VCursorAddColumn(curs, &hdr_idx, "HDR");
if (rc) {
fprintf(stderr, "Failed %d %d", __LINE__, rc);
return rc;
}
rc = VCursorAddColumn(curs, &tag_idx, "TAG");
if (rc) {
fprintf(stderr, "Failed %d %d", __LINE__, rc);
return rc;
}
rc = VCursorAddColumn(curs, &value_idx, "VALUE");
if (rc) {
fprintf(stderr, "Failed %d %d", __LINE__, rc);
return rc;
}
rc = VCursorOpen(curs);
if (rc) {
fprintf(stderr, "Failed %d %d", __LINE__, rc);
return rc;
}
int64_t start = 0;
uint64_t count = 0;
rc = VCursorIdRange(curs, 0, &start, &count);
if (rc) {
fprintf(stderr, "Failed %d %d", __LINE__, rc);
return rc;
}
printf("start=%ld,count=%lu\n", start, count);
while (count--) {
uint64_t group;
uint32_t row_len = 0;
rc = VCursorReadDirect(curs, start, group_idx, 64, &group, 1,
&row_len);
if (rc) {
fprintf(stderr, "Failed %d %d", __LINE__, rc);
return rc;
}
printf("group=%lu, row_len=%d\n", group, row_len);
char hdr[8];
rc = VCursorReadDirect(curs, start, hdr_idx, 8, &hdr, sizeof(hdr),
&row_len);
if (rc) {
fprintf(stderr, "Failed %d %d", __LINE__, rc);
return rc;
}
hdr[row_len] = '\0';
printf("hdr=%s, row_len=%d\n", hdr, row_len);
char tag[8];
rc = VCursorReadDirect(curs, start, tag_idx, 8, &tag, sizeof(tag),
&row_len);
if (rc) {
fprintf(stderr, "Failed %d %d", __LINE__, rc);
return rc;
}
tag[row_len] = '\0';
printf("tag=%s, row_len=%d\n", tag, row_len);
char value[8192];
rc = VCursorReadDirect(curs, start, value_idx, 8, &value,
sizeof(value), &row_len);
if (rc) {
fprintf(stderr, "Failed %d %d", __LINE__, rc);
return rc;
}
value[row_len] = '\0';
printf("value=%s, row_len=%d\n", value, row_len);
if (!strcmp(hdr, "SQ") && !strcmp(tag, "SN")) {
if (check_dup(hf, "SQ:SN", value)) {
fprintf(stderr, "Duplicate SQ:SN value '%s'\n", value);
}
}
if (!strcmp(hdr, "RG") && !strcmp(tag, "ID")) {
if (check_dup(hf, "RG:ID", value)) {
fprintf(stderr, "Duplicate RG:ID value '%s'\n", value);
}
}
if (!strcmp(hdr, "PG") && !strcmp(tag, "ID")) {
if (check_dup(hf, "PG:ID", value)) {
fprintf(stderr, "Duplicate PG:ID value '%s'\n", value);
}
}
start++;
printf("\n");
}
printf("Set has %lu elements\n", KHashFileCount(hf));
fprintf(stderr, "Made verifier for %s\n", dbname);
KHashFileDispose(hf);
VCursorRelease(curs);
VTableRelease(tbl);
VDatabaseRelease(db);
VDBManagerRelease(mgr);
KDirectoryRelease(srcdir);
return 0;
}