void sqlDeleterAddAcc(struct sqlDeleter* sd, char* acc)
/* Add an accession to list to to delete. */
{
if (sd->deletesDone)
errAbort("sqlDeleter: can't add accessions after a delete has been done");
#ifdef COPY_TO_DELETE_HACK
/* always use direct if no tmp dir */
if ((sd->accCount < sd->directMax) || (sd->tmpDir[0] == '\0'))
{
struct slName* accRec = lmAlloc(sd->lm, sizeof(struct slName)+strlen(acc));
strcpy(accRec->name, acc);
slAddHead(&sd->accs, accRec);
}
else
{
if (sd->accLoader == NULL)
initLoader(sd);
sqlUpdaterAddRow(sd->accLoader, "%s", acc);
}
#else
{
struct slName* accRec = lmAlloc(sd->lm, sizeof(struct slName)+strlen(acc));
strcpy(accRec->name, acc);
slAddHead(&sd->accs, accRec);
}
#endif
sd->accCount++;
}
static void refSeqSummaryUpdate(struct sqlConnection *conn, struct gbStatus* status)
/* Update the refSeqSummary table for the current entry */
{
/* only add to table if we actually have something */
if (((raRefSeqSummary->stringSize > 0) || (raRefSeqCompleteness != NULL))
&& (status->stateChg & (GB_NEW|GB_META_CHG)))
{
char query[256];
unsigned sumNew;
char* summary = sqlEscapeString2(alloca(2*raRefSeqSummary->stringSize+1),
raRefSeqSummary->string);
if (raRefSeqCompleteness == NULL)
raRefSeqCompleteness = "Unknown";
/* If sequence may not be new, but summary could be. This table is
* sparse, so must check it */
if (status->stateChg & GB_NEW)
sumNew = TRUE;
else
{
sqlSafef(query, sizeof(query), "SELECT count(*) from refSeqSummary "
"WHERE mrnaAcc = '%s'", raAcc);
sumNew = (sqlQuickNum(conn, query) == 0);
}
if (sumNew)
sqlUpdaterAddRow(refSeqSummaryUpd, "%s\t%s\t%s", raAcc, raRefSeqCompleteness,
summary);
else
sqlUpdaterModRow(refSeqSummaryUpd, 1, "completeness='%s', summary='%s'"
" WHERE mrnaAcc='%s'", raRefSeqCompleteness,
summary, raAcc);
}
}
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 refSeqStatusUpdate(struct gbStatus* status)
/* Update the refSeqStatus table for the current entry */
{
if (status->stateChg & GB_NEW)
{
if (haveRsMol)
sqlUpdaterAddRow(refSeqStatusUpd, "%s\t%s\t%s", raAcc, raRefSeqStatus, raMol);
else
sqlUpdaterAddRow(refSeqStatusUpd, "%s\t%s", raAcc, raRefSeqStatus);
}
else if (status->stateChg & GB_META_CHG)
{
if (haveRsMol)
sqlUpdaterModRow(refSeqStatusUpd, 1, "status='%s', mol='%s' WHERE mrnaAcc='%s'",
raRefSeqStatus, raMol, raAcc);
else
sqlUpdaterModRow(refSeqStatusUpd, 1, "status='%s' WHERE mrnaAcc='%s'",
raRefSeqStatus, raAcc);
}
}
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 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));
}
}
static void refLinkUpdate(struct sqlConnection *conn, struct gbStatus* status)
/* Update the refLink table for the current entry */
{
int geneId;
char *gen = emptyForNull(raFieldCurVal("gen"));
char *pro = emptyForNull(raFieldCurVal("pro"));
gen = sqlEscapeString2(alloca(2*strlen(gen)+1), gen);
pro = sqlEscapeString2(alloca(2*strlen(pro)+1), pro);
/* can either have locus id (old locus link db) or gene id, or both,
* in which case the geneId is used */
geneId = (raGeneId != 0) ? raGeneId : raLocusLinkId;
if (status->stateChg & GB_NEW)
sqlUpdaterAddRow(refLinkUpd, "%s\t%s\t%s\t%s\t%u\t%u\t%u\t%u",
gen, pro, raAcc, raProtAcc, raFieldCurId("gen"),
raFieldCurId("pro"), geneId, raOmimId);
else if (status->stateChg & GB_META_CHG)
sqlUpdaterModRow(refLinkUpd, 1, "name='%s', product='%s', protAcc='%s', "
"geneName=%u, prodName=%u, locusLinkId=%u, "
"omimId=%u where mrnaAcc='%s'",
gen, pro, raProtAcc, raFieldCurId("gen"),
raFieldCurId("pro"), geneId, raOmimId, raAcc);
}
static void gbCdnaInfoUpdate(struct gbStatus* status, struct sqlConnection *conn)
/* Update the mrna table for the current entry */
{
if (status->stateChg & GB_NEW)
{
if (haveMol)
sqlUpdaterAddRow(gbCdnaInfoUpd, "%u\t%s\t%u\t%s\t%s\t%c\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%s",
status->gbSeqId, raAcc, raVersion, gbFormatDate(raModDate),
((status->type == GB_MRNA) ? "mRNA" : "EST"), raDir,
raFieldCurId("src"), raFieldCurId("org"),
raFieldCurId("lib"), raFieldCurId("clo"),
raFieldCurId("sex"), raFieldCurId("tis"),
raFieldCurId("dev"), raFieldCurId("cel"),
raFieldCurId("cds"), raFieldCurId("key"),
raFieldCurId("def"), raFieldCurId("gen"),
raFieldCurId("pro"), raFieldCurId("aut"),
raGi, raMol);
else if (haveGi)
sqlUpdaterAddRow(gbCdnaInfoUpd, "%u\t%s\t%u\t%s\t%s\t%c\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u",
status->gbSeqId, raAcc, raVersion, gbFormatDate(raModDate),
((status->type == GB_MRNA) ? "mRNA" : "EST"), raDir,
raFieldCurId("src"), raFieldCurId("org"),
raFieldCurId("lib"), raFieldCurId("clo"),
raFieldCurId("sex"), raFieldCurId("tis"),
raFieldCurId("dev"), raFieldCurId("cel"),
raFieldCurId("cds"), raFieldCurId("key"),
raFieldCurId("def"), raFieldCurId("gen"),
raFieldCurId("pro"), raFieldCurId("aut"),
raGi);
else
sqlUpdaterAddRow(gbCdnaInfoUpd, "%u\t%s\t%u\t%s\t%s\t%c\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u",
status->gbSeqId, raAcc, raVersion, gbFormatDate(raModDate),
((status->type == GB_MRNA) ? "mRNA" : "EST"), raDir,
raFieldCurId("src"), raFieldCurId("org"),
raFieldCurId("lib"), raFieldCurId("clo"),
raFieldCurId("sex"), raFieldCurId("tis"),
raFieldCurId("dev"), raFieldCurId("cel"),
raFieldCurId("cds"), raFieldCurId("key"),
raFieldCurId("def"), raFieldCurId("gen"),
raFieldCurId("pro"), raFieldCurId("aut"));
}
else if (status->stateChg & GB_META_CHG)
{
if (haveMol)
sqlUpdaterModRow(gbCdnaInfoUpd, 1, "version='%u', moddate='%s', direction='%c', "
"source=%u, organism=%u, library=%u, mrnaClone=%u, sex=%u, "
"tissue=%u, development=%u, cell=%u, cds=%u, keyword=%u, "
"description=%u, geneName=%u, productName=%u, author=%u, gi=%u, mol='%s' "
"WHERE id=%u",
raVersion, gbFormatDate(raModDate), raDir,
raFieldCurId("src"), raFieldCurId("org"),
raFieldCurId("lib"), raFieldCurId("clo"),
raFieldCurId("sex"), raFieldCurId("tis"),
raFieldCurId("dev"), raFieldCurId("cel"),
raFieldCurId("cds"), raFieldCurId("key"),
raFieldCurId("def"), raFieldCurId("gen"),
raFieldCurId("pro"), raFieldCurId("aut"),
raGi, raMol, status->gbSeqId);
else if (haveGi)
sqlUpdaterModRow(gbCdnaInfoUpd, 1, "version='%u', moddate='%s', direction='%c', "
"source=%u, organism=%u, library=%u, mrnaClone=%u, sex=%u, "
"tissue=%u, development=%u, cell=%u, cds=%u, keyword=%u, "
"description=%u, geneName=%u, productName=%u, author=%u, gi=%u "
"WHERE id=%u",
raVersion, gbFormatDate(raModDate), raDir,
raFieldCurId("src"), raFieldCurId("org"),
raFieldCurId("lib"), raFieldCurId("clo"),
raFieldCurId("sex"), raFieldCurId("tis"),
raFieldCurId("dev"), raFieldCurId("cel"),
raFieldCurId("cds"), raFieldCurId("key"),
raFieldCurId("def"), raFieldCurId("gen"),
raFieldCurId("pro"), raFieldCurId("aut"),
raGi, status->gbSeqId);
else
sqlUpdaterModRow(gbCdnaInfoUpd, 1, "version='%u', moddate='%s', direction='%c', "
"source=%u, organism=%u, library=%u, mrnaClone=%u, sex=%u, "
"tissue=%u, development=%u, cell=%u, cds=%u, keyword=%u, "
"description=%u, geneName=%u, productName=%u, author=%u "
"WHERE id=%u",
raVersion, gbFormatDate(raModDate), raDir,
raFieldCurId("src"), raFieldCurId("org"),
raFieldCurId("lib"), raFieldCurId("clo"),
raFieldCurId("sex"), raFieldCurId("tis"),
raFieldCurId("dev"), raFieldCurId("cel"),
raFieldCurId("cds"), raFieldCurId("key"),
raFieldCurId("def"), raFieldCurId("gen"),
raFieldCurId("pro"), raFieldCurId("aut"),
status->gbSeqId);
}
}
