static void gbWarnUpdate(struct gbStatus* status, struct sqlConnection *conn)
/* update gbWarn table */
{
if (status->stateChg & (GB_NEW|GB_META_CHG|GB_REBUILD_DERIVED))
{
if (gbWarnUpd == NULL)
gbWarnUpd = sqlUpdaterNew("gbWarn", gTmpDir, (gbVerbose >= 4), &allUpdaters);
sqlUpdaterAddRow(gbWarnUpd, "%s\t%s", raAcc, raWarn);
}
}
static void initLoader(struct sqlDeleter* sd)
/* setup loader and copy access to tab file */
{
struct slName* acc;
sd->accLoader = sqlUpdaterNew(GB_DELETE_TMP, sd->tmpDir, sd->verbose, NULL);
for (acc = sd->accs; acc != NULL; acc = acc->next)
sqlUpdaterAddRow(sd->accLoader, "%s", acc->name);
sd->useDeleteJoin = TRUE;
sd->accs = NULL; /* mark as not in use (list in localmem) */
}
static FILE *gbGeneTblGetFlatTabFh(struct gbGeneTbl *ggt,
struct sqlConnection* conn)
/* get tab file for genePred flat table, create updater and table if needed */
{
if (ggt->flatUpd == NULL)
{
if (!sqlTableExists(conn, ggt->flatTbl))
createFlatTbl(ggt, conn);
ggt->flatUpd = sqlUpdaterNew(ggt->flatTbl, ggt->tmpDir, (gbVerbose >= 4), NULL);
}
return sqlUpdaterGetFh(ggt->flatUpd, 1);
}
static void gbMiscDiffUpdate(struct gbStatus* status, struct sqlConnection *conn)
/* update gbMiscDiff table */
{
if (status->stateChg & (GB_NEW|GB_META_CHG|GB_REBUILD_DERIVED))
{
if (gbMiscDiffUpd == NULL)
gbMiscDiffUpd = sqlUpdaterNew("gbMiscDiff", gTmpDir, (gbVerbose >= 4), &allUpdaters);
struct gbMiscDiff *gmd;
for (gmd = raMiscDiffs; gmd != NULL; gmd = gmd->next)
sqlUpdaterAddRow(gbMiscDiffUpd, "%s\t%d\t%d\t%s\t%s\t%s",
gmd->acc, gmd->mrnaStart, gmd->mrnaEnd,
gbSqlStrOrNullTabVar(gmd->notes),
gbSqlStrOrNullTabVar(gmd->gene),
gbSqlStrOrNullTabVar(gmd->replacement));
}
}
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);
}
}
