static void gbGeneTblFree(struct gbGeneTbl **ggtPtr)
/* free a gbGeneTbl object */
{
struct gbGeneTbl *ggt = *ggtPtr;
if (ggt != NULL)
{
freeMem(ggt->tbl);
freeMem(ggt->flatTbl);
sqlUpdaterFree(&ggt->upd);
sqlUpdaterFree(&ggt->flatUpd);
*ggtPtr = NULL;
}
}
void gbMetaDataDbLoad(struct sqlConnection *conn)
/* load the metadata changes into the database */
{
struct sqlUpdater *nextUpd;
/* this should never have been called if these tables not set up */
assert(imageCloneTbl != NULL);
assert(seqTbl != NULL);
/* seq must be first */
seqTblCommit(seqTbl, conn);
seqTblFree(&seqTbl);
/* unique string tables next, before mrna */
gbMDParseCommit(conn);
/* image ids are loaded next */
imageCloneTblCommit(imageCloneTbl, conn);
/* other metadata */
while ((nextUpd = slPopHead(&allUpdaters)) != NULL)
{
sqlUpdaterCommit(nextUpd, conn);
sqlUpdaterFree(&nextUpd);
}
gbCdnaInfoUpd = NULL;
refSeqStatusUpd = NULL;
refSeqSummaryUpd = NULL;
refLinkUpd = NULL;
gbMiscDiffUpd = NULL;
gbWarnUpd = NULL;
/* cache unique string tables in goFaster mode */
if ((gOptions->flags & DBLOAD_GO_FASTER) == 0)
gbMDParseFree();
}
void sqlDeleterFree(struct sqlDeleter** sdPtr)
/* Free an object */
{
struct sqlDeleter* sd = *sdPtr;
if (sd != NULL)
{
sqlUpdaterFree(&sd->accLoader);
lmCleanup(&sd->lm);
freez(sdPtr);
}
}
void loadDelayedTables()
/* If we are delaying table load, now is the time */
{
struct sqlConnection* conn = hAllocConn(gDatabase);
if (gPendingStatusUpdates == NULL)
errAbort("no data update were found to loaded with -initialLoad");
loadMetaData(conn);
loadAligns(conn);
while (gPendingStatusUpdates != NULL)
{
struct sqlUpdater* statUpd = gPendingStatusUpdates;
gPendingStatusUpdates = gPendingStatusUpdates->next;
sqlUpdaterCommit(statUpd, conn);
sqlUpdaterFree(&statUpd);
}
gbLoadedTblCommit(gLoadedTbl);
hFreeConn(&conn);
}
static void deleteJoin(struct sqlDeleter* sd, struct sqlConnection *conn,
char* table, char* column)
/* delete by creating a new table with a join */
{
char query[512], newTmpTable[64], oldTmpTable[64];
if (sd->accLoader != NULL)
{
/* build table, free to indicate it's completed */
assert(!sd->deletesDone);
sqlRemakeTable(conn, GB_DELETE_TMP, createGbDeleteTmp);
sqlUpdaterCommit(sd->accLoader, conn);
sqlUpdaterFree(&sd->accLoader);
}
sd->deletesDone = TRUE;
/* remove existing tmp tables */
safef(newTmpTable, sizeof(newTmpTable), "%s_new_tmp", table);
safef(oldTmpTable, sizeof(oldTmpTable), "%s_old_tmp", table);
sqlDropTable(conn, newTmpTable);
sqlDropTable(conn, oldTmpTable);
gbSqlDupTableDef(conn, table, newTmpTable);
/* do join into new table of entries not in accession table */
safef(query, sizeof(query),
"INSERT INTO %s SELECT %s.* FROM %s LEFT JOIN %s "
"ON (%s.%s = %s.acc) WHERE %s.acc IS NULL",
newTmpTable, table, table, GB_DELETE_TMP, table, column,
GB_DELETE_TMP, GB_DELETE_TMP);
sqlUpdate(conn, query);
/* Now swap the table into place */
safef(query, sizeof(query), "RENAME TABLE %s TO %s, %s TO %s",
table, oldTmpTable, newTmpTable, table);
sqlUpdate(conn, query);
sqlDropTable(conn, oldTmpTable);
}
