char *userRegionsParse(char *db, char *regionsText, int maxRegions, int maxErrs,
int *retRegionCount, char **retWarnText)
/* Parse user regions entered as BED3, BED4 or chr:start-end optionally followed by name.
* Return name of trash file containing BED for parsed regions if regionsText contains
* valid regions; otherwise NULL.
* If maxRegions <= 0, it is ignored; likewise for maxErrs.
* If retRegionCount is non-NULL, it will be set to the number of valid parsed regions
* in the trash file.
* If retWarnText is non-NULL, it will be set to a string containing warning and error
* messages encountered while parsing input. */
{
char *trashFileName = NULL;
if (isNotEmpty(regionsText))
{
char *copy = cloneString(regionsText);
struct dyString *dyWarn = dyStringNew(0);
struct bed4 *bedList = parseRegionInput(db, copy, maxRegions, maxErrs, dyWarn);
if (retWarnText != NULL)
{
if (dyWarn->stringSize > 0)
*retWarnText = dyStringCannibalize(&dyWarn);
else
{
*retWarnText = NULL;
dyStringFree(&dyWarn);
}
}
int regionCount = slCount(bedList);
if (retRegionCount != NULL)
*retRegionCount = regionCount;
if (regionCount > 0)
{
struct tempName tn;
trashDirFile(&tn, "hgtData", "user", ".region");
trashFileName = cloneString(tn.forCgi);
FILE *f = mustOpen(trashFileName, "w");
struct bed4 *bed;
for (bed = bedList; bed; bed = bed->next )
{
char *name = bed->name ? bed->name : "";
fprintf(f, "%s\t%d\t%d\t%s\n",
bed->chrom, bed->chromStart, bed->chromEnd, name);
}
carefulClose(&f);
}
freeMem(copy);
}
else
{
if (retRegionCount != NULL)
*retRegionCount = 0;
if (retWarnText != NULL)
*retWarnText = NULL;
}
return trashFileName;
}
void doSubmitUserRegions(struct sqlConnection *conn)
/* Process submit in set regions page. */
{
char *idText = trimSpaces(cartString(cart, hgtaEnteredUserRegions));
char *userRegionFile = trimSpaces(cartString(cart, hgtaEnteredUserRegionFile));
boolean hasData = (idText != NULL && idText[0] != 0) ||
(userRegionFile != NULL && userRegionFile[0] != 0);
/* beware, the string pointers from cartString() point to strings in the
* cart hash. If they are manipulated and changed, they will get saved
* back to the cart in their changed form. You don't want to be
* altering them like that. Thus, the idText is duplicated below with
* the cloneString(idText)
*/
htmlOpen("Table Browser (Region definitions)");
/* presence of fileName text overrides previously existing text area
* contents
*/
if (userRegionFile != NULL && userRegionFile[0] != 0)
{
idText = cloneString(userRegionFile);
cartRemove(cart, hgtaEnteredUserRegions);
cartRemove(cart, hgtaUserRegionsFile);
cartSetString(cart, hgtaEnteredUserRegions, idText);
}
else
idText = cloneString(idText);
char *lineLimitText = limitText(idText);
if ( (strlen(lineLimitText) > 0) && (strlen(lineLimitText) != strlen(idText)) )
{
freeMem(idText);
idText = lineLimitText;
cartSetString(cart, hgtaEnteredUserRegions, lineLimitText);
}
else
freeMem(lineLimitText);
if (hasData)
{
struct tempName tn;
FILE *f;
struct bed *bedEl;
struct bed *bedList = parseRegionInput(idText);
if (NULL == bedList)
errAbort("no valid data points found in input");
trashDirFile(&tn, "hgtData", "user", ".region");
f = mustOpen(tn.forCgi, "w");
for (bedEl = bedList; bedEl; bedEl = bedEl->next )
{
if (bedEl->name)
fprintf(f, "%s\t%d\t%d\t%s\n",
bedEl->chrom, bedEl->chromStart, bedEl->chromEnd, bedEl->name);
else
fprintf(f, "%s\t%d\t%d\n",
bedEl->chrom, bedEl->chromStart, bedEl->chromEnd);
}
carefulClose(&f);
cartSetString(cart, hgtaUserRegionsDb, database);
cartSetString(cart, hgtaUserRegionsTable, curTable);
cartSetString(cart, hgtaUserRegionsFile, tn.forCgi);
cartSetString(cart, hgtaRegionType, hgtaRegionTypeUserRegions);
if (strlen(idText) > 64 * 1024)
cartRemove(cart, hgtaEnteredUserRegions);
}
else
{
cartRemove(cart, hgtaUserRegionsFile);
cartRemove(cart, hgtaEnteredUserRegionFile);
cartRemove(cart, hgtaRegionType);
}
mainPageAfterOpen(conn);
htmlClose();
}
