static void loadGbCdnaInfoData(struct metaDataTbls* metaDataTbls,
struct gbSelect* select, struct sqlConnection* conn)
/* load the gbCdnaInfo table */
{
char accWhere[64];
char query[512];
struct sqlResult* result;
char** row;
gbVerbMsg(2, "load gbCdnaInfo table data");
accWhere[0] = '\0';
if (select->accPrefix != NULL)
safef(accWhere, sizeof(accWhere), " AND (acc LIKE '%s%%')",
select->accPrefix);
safef(query, sizeof(query),
"SELECT acc,id,version,moddate,type,direction,"
/* 0 1 2 3 4 5 */
"source,organism,library,mrnaClone,sex,tissue,development,cell,cds,"
/* 6 7 8 9 10 11 12 13 14 */
"keyword,description,geneName,productName,author "
/* 15 16 17 18 19 */
"FROM gbCdnaInfo WHERE (type='%s')%s",
((select->type == GB_MRNA) ? "mRNA" : "EST"), accWhere);
/* mrna doesn't have a srcDb, so we guess from acc */
result = sqlGetResult(conn, query);
while ((row = sqlNextRow(result)) != NULL)
{
if (gbGuessSrcDb(row[0]) == select->release->srcDb)
loadGbCdnaInfoRow(metaDataTbls, conn, row);
}
sqlFreeResult(&result);
}
static boolean keepGbEntry(boolean isEst)
/* should the current entry in the kvt be kept? */
{
char *acc = gbAccessionField->val->string;
char *cat = kvtGet(kvt, "cat")->val;
char *org = kvtGet(kvt, "org")->val;
if (genbankBlackListFail(acc, blackListRanges))
return FALSE;
else if (gbOrg && (differentString(org, gbOrg)))
return FALSE;
else if (gbGuessSrcDb(acc) == GB_REFSEQ)
{
return (startsWith("NM_", acc) || startsWith("NR_", acc)
|| ((startsWith("XM_", acc) && inclXMs)));
}
else if ((sameString(cat, "GSS") ||
sameString(cat, "HTG") ||
sameString(cat, "STS") ||
sameString(cat, "CON")) && !(gbType & GB_DNA))
return FALSE; // division to ignore
else
{
if (sameString(cat, "EST")) {
return (gbType & GB_EST) != 0;
}
else if (gbType & GB_MRNA)
{
// not an EST, keep any type of RNA
return containsStringNoCase(kvtGet(kvt, "mol")->val, "RNA") != NULL;
}
else if (gbType & GB_DNA)
{
// keep any type of DNA if DNA filter set
return containsStringNoCase(kvtGet(kvt, "mol")->val, "DNA") != NULL;
}
else
return FALSE;
}
}
static struct sqlDeleter* buildReloadDeleter(char *reloadList, unsigned srcDb, char *tmpDir)
/* read reload list, building a deleter for the specified source DB */
{
struct sqlDeleter* deleter = NULL;
struct lineFile *lf = gzLineFileOpen(reloadList);
int cnt = 0;
char *row[1];
while (lineFileChopNext(lf, row, ArraySize(row)))
{
char *acc = trimSpaces(row[0]);
if (gbGuessSrcDb(acc) == srcDb)
{
if (deleter == NULL)
deleter = sqlDeleterNew(tmpDir, (gbVerbose >= 4));
sqlDeleterAddAcc(deleter, acc);
cnt++;
gbVerbMsg(5, "%s delete for reloading", acc);
}
}
gzLineFileClose(&lf);
gbVerbMsg(1, "delete %d entries for reloading", cnt);
return deleter;
}
