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();
}
static void makeRepairs(struct brokenRefPepTbl *brpTbl,
struct sqlConnection *conn,
struct extFileTbl* extFileTbl,
boolean dryRun)
/* make repairs once data is collected */
{
static char *tmpDir = "/var/tmp";
struct hashCookie cookie;
struct hashEl *hel;
int repairCnt = 0;
int dropCnt = 0;
struct seqTbl* seqTbl = seqTblNew(conn, tmpDir, (gbVerbose > 3));
struct sqlDeleter* seqTblDeleter = sqlDeleterNew(tmpDir, (gbVerbose > 3));
cookie = hashFirst(brpTbl->protAccHash);
while ((hel = hashNext(&cookie)) != NULL)
{
struct brokenRefPep *brp = hel->val;
if ((brp->mrnaAcc != NULL) && (brp->newFaOff >= 0))
{
refPepRepairOne(conn, brp, seqTbl, extFileTbl, dryRun);
repairCnt++;
}
else
{
refPepDropOne(conn, brp, seqTblDeleter, dryRun);
dropCnt++;
}
}
if (dryRun)
{
gbVerbMsg(1, "%s: would have repaired %d refseq protein gbExtFile entries",
sqlGetDatabase(conn), repairCnt);
gbVerbMsg(1, "%s: would have dropped %d refseq protein gbExtFile entries",
sqlGetDatabase(conn), dropCnt);
}
else
{
seqTblCommit(seqTbl, conn);
gbVerbMsg(1, "%s: repaired %d refseq protein gbExtFile entries",
sqlGetDatabase(conn), repairCnt);
sqlDeleterDel(seqTblDeleter, conn, SEQ_TBL, "acc");
gbVerbMsg(1, "%s: dropped %d refseq protein gbExtFile entries",
sqlGetDatabase(conn), dropCnt);
}
}
