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);
}
}
void gbMetaDataInit(struct sqlConnection *conn, unsigned srcDb,
struct dbLoadOptions* options, char *gbdbGenBank,
char *tmpDir)
/* initialize for parsing metadata */
{
gOptions = options;
gSrcDb = srcDb;
gGbdbGenBank[0] = '\0';
if (gbdbGenBank != NULL)
strcpy(gGbdbGenBank, gbdbGenBank);
strcpy(gTmpDir, tmpDir);
if (seqTbl == NULL)
seqTbl = seqTblNew(conn, gTmpDir, (gbVerbose >= 4));
if (imageCloneTbl == NULL)
imageCloneTbl = imageCloneTblNew(conn, gTmpDir, (gbVerbose >= 4));
if (!sqlTableExists(conn, "gbCdnaInfo"))
{
sqlUpdate(conn, gbCdnaInfoCreate);
haveGi = TRUE;
haveMol = TRUE;
}
else
{
haveGi = sqlFieldIndex(conn, "gbCdnaInfo", "gi") >= 0;
haveMol = sqlFieldIndex(conn, "gbCdnaInfo", "mol") >= 0;
if (haveMol && !haveGi)
errAbort("must have gi column to have mol");
}
setGeneTblFlags(conn, options);
if (!sqlTableExists(conn, "gbMiscDiff"))
sqlUpdate(conn, gbMiscDiffCreate);
if (!sqlTableExists(conn, "gbWarn"))
sqlUpdate(conn, gbWarnCreate);
if (gbCdnaInfoUpd == NULL)
gbCdnaInfoUpd = sqlUpdaterNew("gbCdnaInfo", gTmpDir, (gbVerbose >= 4), &allUpdaters);
if (gSrcDb == GB_REFSEQ)
{
if (!sqlTableExists(conn, "refSeqStatus"))
{
sqlUpdate(conn, refSeqStatusCreate);
haveRsMol = TRUE;
}
else
{
haveRsMol = sqlFieldIndex(conn, "refSeqStatus", "mol") >= 0;
}
if (refSeqStatusUpd == NULL)
refSeqStatusUpd = sqlUpdaterNew("refSeqStatus", gTmpDir, (gbVerbose >= 4),
&allUpdaters);
if (!sqlTableExists(conn, "refSeqSummary"))
sqlUpdate(conn, refSeqSummaryCreate);
if (refSeqSummaryUpd == NULL)
refSeqSummaryUpd = sqlUpdaterNew("refSeqSummary", gTmpDir, (gbVerbose >= 4),
&allUpdaters);
if (!sqlTableExists(conn, "refLink"))
sqlUpdate(conn, refLinkCreate);
if (refLinkUpd == NULL)
refLinkUpd = sqlUpdaterNew("refLink", gTmpDir, (gbVerbose >= 4),
&allUpdaters);
}
}
