long long edwNeedFileIdForLicensePlate(struct sqlConnection *conn, char *licensePlate)
/* Return id in edwFile table that corresponds to licensePlate, or die with error message
* if it doesn't exist. */
{
long long result = edwFileIdForLicensePlate(conn, licensePlate);
if (result == 0)
errAbort("%s doesn't exist in warehouse.", licensePlate);
return result;
}
struct submitFileRow *submitFileRowFromFieldedTable(
struct sqlConnection *conn, struct fieldedTable *table,
int fileIx, int md5Ix, int sizeIx, int modifiedIx, int replacesIx, int replaceReasonIx)
/* Turn parsed out table (still all just strings) into list of edwFiles. */
{
struct submitFileRow *sfr, *sfrList = NULL;
struct edwFile *bf;
struct fieldedRow *fr;
struct dyString *tags = dyStringNew(0);
char *ucscDbTag = "ucsc_db";
int ucscDbField = stringArrayIx(ucscDbTag, table->fields, table->fieldCount);
for (fr = table->rowList; fr != NULL; fr = fr->next)
{
char **row = fr->row;
AllocVar(bf);
bf->submitFileName = cloneString(row[fileIx]);
safef(bf->md5, sizeof(bf->md5), "%s", row[md5Ix]);
bf->size = sqlLongLong(row[sizeIx]);
bf->updateTime = sqlLongLong(row[modifiedIx]);
/* Add as tags any fields not included in fixed fields. */
dyStringClear(tags);
int i;
for (i=0; i<table->fieldCount; ++i)
{
if (i != fileIx && i != md5Ix && i != sizeIx && i != modifiedIx)
{
cgiEncodeIntoDy(table->fields[i], row[i], tags);
}
}
if (ucscDbField < 0)
{
/* Try to make this field up from file name */
char *slash = strchr(bf->submitFileName, '/');
if (slash == NULL)
errAbort("Can't make up '%s' field from '%s'", ucscDbTag, bf->submitFileName);
int len = slash - bf->submitFileName;
char ucscDbVal[len+1];
memcpy(ucscDbVal, bf->submitFileName, len);
ucscDbVal[len] = 0;
/* Do a little check on it */
if (!sameString("mm9", ucscDbVal) && !sameString("mm10", ucscDbVal)
&& !sameString("dm3", ucscDbVal) && !sameString("ce10", ucscDbVal)
&& !sameString("hg19", ucscDbVal))
errAbort("Unrecognized ucsc_db %s - please arrange files so that the top "
"level directory in the fileName in the manifest is a UCSC database name "
"like 'hg19' or 'mm10.' Alternatively please include a ucsc_db column.",
ucscDbVal);
/* Add it to tags. */
cgiEncodeIntoDy(ucscDbTag, ucscDbVal, tags);
}
bf->tags = cloneString(tags->string);
/* Fake other fields. */
bf->edwFileName = cloneString("");
/* Allocate wrapper structure */
AllocVar(sfr);
sfr->file = bf;
/* fill in fields about replacement maybe */
if (replacesIx != -1)
{
char *replacesAcc = row[replacesIx];
char *reason = row[replaceReasonIx];
int fileId = edwFileIdForLicensePlate(conn, replacesAcc);
if (fileId == 0)
errAbort("%s in %s column doesn't exist in warehouse", replacesAcc, replacesTag);
sfr->replaces = cloneString(replacesAcc);
sfr->replaceReason = cloneString(reason);
sfr->replacesFile = fileId;
}
slAddHead(&sfrList, sfr);
}
slReverse(&sfrList);
dyStringFree(&tags);
return sfrList;
}
