static void loadGbCdnaInfoRow(struct metaDataTbls* metaDataTbls,
struct sqlConnection* conn, char** row)
/* load one row from the gbCdnaInfo table */
{
struct metaData* md;
int len, numNonZero, iRow = 0;
char *acc, *dir;
boolean gotError, isOk;
/* columns: acc,id,moddate,version,moddate,type */
acc = row[iRow++];
md = metaDataTblsGet(metaDataTbls, acc);
if (md->inGbCdnaInfo)
{
gbError("%s: acc occurs multiple times in the mrna table", acc);
return;
}
md->inGbCdnaInfo = TRUE;
md->gbCdnaInfoId = strToUnsigned(row[iRow++], acc, "gbCdnaInfo.id", NULL);
len = strlen(acc);
md->gbCdnaInfoVersion = strToUnsigned(row[iRow++], "gbCdnaInfo.version", acc, &gotError);
if (!gotError && (md->gbCdnaInfoVersion <= 0))
gbError("%s: gbCdnaInfo.version invalid: \"%d\"", acc, md->gbCdnaInfoVersion);
isOk = TRUE;
md->gbCdnaInfoModdate = gbParseChkDate(row[iRow++], &isOk);
if (!isOk)
gbError("%s: invalid gbCdnaInfo.moddate value: \"%s\"", acc, row[iRow-1]);
md->gbCdnaInfoType = gbParseType(row[iRow++]);
md->typeFlags |= md->gbCdnaInfoType;
dir = row[iRow++];
if ((strlen(dir) > 1) || (strchr("053", *dir) == NULL))
gbError("%s: invalid gbCdnaInfo.direction value: \"%s\"", acc, dir);
/* Make sure that at least a few of the id fields have data */
numNonZero = 0;
while (iRow < 20)
{
int id = strToUnsigned(row[iRow++], md->acc, "gbCdnaInfo.?", NULL);
if (id > 0)
numNonZero++;
/* remember if we have a description */
if (iRow-1 == 16)
md->haveDesc = (id != 0);
}
if (numNonZero == 0)
gbError("%s: none of gbCdnaInfo string ids have non-zero values", dir);
else if (numNonZero < 4)
gbError("%s: only %d of gbCdnaInfo string ids have non-zero values",
dir, numNonZero);
}
time_t gbParseDate(struct lineFile* lf, char* dateStr)
/* parse a date, in YYYY-MM-DD format, converting it to a unix time (as
* returned by time()). If lf is not null, the file information will be
* included in error message. */
{
boolean isOk = TRUE;
time_t numTime = gbParseChkDate(dateStr, &isOk);
if (!isOk)
{
if (lf != NULL)
errAbort("invalid date \"%s\" in %s line %d, must be YYYY-MM-DD",
dateStr, lf->fileName, lf->lineIx);
else
errAbort("invalid date \"%s\", must be YYYY-MM-DD", dateStr);
}
return numTime;
}
static void loadGbStatusRow(struct metaDataTbls* metaDataTbls,
struct sqlConnection* conn, char** row,
unsigned descOrgCats)
/* load a row of the gbStatus table */
{
struct metaData* md;
int iRow = 0;
boolean isOk;
HGID seqId;
/* columns: acc,version,modDate,type,srcDb,gbSeq,numAligns */
md = metaDataTblsGet(metaDataTbls, row[iRow++]);
if (md->inGbStatus)
gbError("%s: occurs multiple times in the gbStatus table", md->acc);
md->inGbStatus = TRUE;
md->gbsVersion = strToUnsigned(row[iRow++], md->acc, "gbStatus.version", NULL);
isOk = TRUE;
md->gbsModDate = gbParseChkDate(row[iRow++], &isOk);
if (!isOk)
gbError("%s: invalid gbStatus.moddate value: \"%s\"", md->acc, row[iRow-1]);
md->gbsType = gbParseType(row[iRow++]);
md->gbsSrcDb = gbParseSrcDb(row[iRow++]);
md->gbsOrgCat = gbParseOrgCat(row[iRow++]);
seqId = strToUnsigned(row[iRow++], md->acc, "gbStatus.gbSeq", NULL);
md->gbsNumAligns = strToUnsigned(row[iRow++], md->acc, "gbStatus.numAligns",
NULL);
md->typeFlags |= md->gbsType;
if (md->inGbCdnaInfo)
{
if (seqId != md->gbCdnaInfoId)
gbError("%s: gbStatus.gbSeq (%d) not same gbCdnaInfo.id (%d)", md->acc, seqId,
md->gbCdnaInfoId);
if (md->gbsType != md->gbCdnaInfoType)
gbError("%s: gbStatus.type (%s) not same as gbCdnaInfo.type (%s)", md->acc,
gbFmtSelect(md->gbsType), gbFmtSelect(md->gbCdnaInfoType));
if (md->gbsSrcDb != (md->typeFlags & GB_SRC_DB_MASK))
gbError("%s: gbStatus.srcDb (%s) not same gbCdnaInfo.srcDb (%s)", md->acc,
gbFmtSelect(md->gbsSrcDb), gbFmtSelect(md->typeFlags));
if (md->gbsVersion != md->gbCdnaInfoVersion)
gbError("%s: gbStatus.version (%d) not same gbCdnaInfo.version (%d)", md->acc,
md->gbsVersion, md->gbCdnaInfoVersion);
if ((md->gbsModDate != md->gbCdnaInfoModdate))
gbError("%s: gbStatus.modDate (%s) not same gbCdnaInfo.moddate (%s)", md->acc,
gbFormatDate(md->gbsModDate), gbFormatDate(md->gbCdnaInfoModdate));
/* verify either have or don't have a description */
if (descOrgCats & md->gbsOrgCat)
{
if (!md->haveDesc)
gbError("%s: should have gbCdnaInfo.description: %s", md->acc,
gbFmtSelect(md->gbsType|md->gbsOrgCat|md->gbsSrcDb));
}
else
{
if (md->haveDesc)
gbError("%s: should not have gbCdnaInfo.description: %s", md->acc,
gbFmtSelect(md->gbsType|md->gbsOrgCat|md->gbsSrcDb));
}
}
}