int hubCheckTrack(struct trackHub *hub, struct trackHubGenome *genome, struct trackDb *tdb,
struct trackHubCheckOptions *options, struct dyString *errors)
/* Check track settings and optionally, files */
{
int retVal = 0;
if (options->checkSettings && options->settings)
{
//verbose(3, "Found %d settings to check to spec\n", slCount(settings));
verbose(3, "Checking track: %s\n", tdb->shortLabel);
verbose(3, "Found %d settings to check to spec\n", hashNumEntries(tdb->settingsHash));
struct hashEl *hel;
struct hashCookie cookie = hashFirst(tdb->settingsHash);
while ((hel = hashNext(&cookie)) != NULL)
retVal |= hubCheckTrackSetting(hub, tdb, hel->name, options, errors);
/* TODO: ? also need to check settings not in this list (other tdb fields) */
}
if (options->printMeta)
{
struct slPair *metaPairs = trackDbMetaPairs(tdb);
if (metaPairs != NULL)
{
printf("%s\n", trackHubSkipHubName(tdb->track));
struct slPair *pair;
for(pair = metaPairs; pair; pair = pair->next)
{
printf("\t%s : %s\n", pair->name, (char *)pair->val);
}
printf("\n");
}
slPairFreeValsAndList(&metaPairs);
}
if (!options->checkFiles)
return retVal;
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
hubCheckBigDataUrl(hub, genome, tdb);
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
retVal = 1;
dyStringPrintf(errors, "%s", errCatch->message->string);
}
errCatchFree(&errCatch);
return retVal;
}
void findToFixBedGraphLimits(char *input, char *output)
/* findToFixBedGraphLimits - Scan through ra file of bedGraphs and calculate limits.. */
{
struct lineFile *lf = lineFileOpen(input, TRUE);
FILE *f = mustOpen(output, "w");
struct slPair *el, *list;
while ((list = raNextRecordAsSlPairList(lf)) != NULL)
{
/* Find required fields for calcs. */
char *db = mustFindVal(list, "db", lf);
char *track = mustFindVal(list, "track", lf);
char *type = cloneString(mustFindVal(list, "type", lf));
/* Parse out type value, which should be "bedGraph 4" and put the 4 or whatever other number
* in dataFieldIndex. */
char *typeWords[3];
int typeWordCount = chopLine(type, typeWords);
if (typeWordCount != 2 || !sameString(typeWords[0], "bedGraph"))
errAbort("Not well formed bedGraph type line %d of %s", lf->lineIx, lf->fileName);
int dataFieldIndex = sqlUnsigned(typeWords[1]);
/* Figure out field corresponding to dataFieldIndex. */
struct sqlConnection *conn = sqlConnect(db);
struct slName *fieldList = sqlFieldNames(conn, track);
struct slName *pastBin = fieldList;
if (sameString(pastBin->name, "bin"))
pastBin = pastBin->next;
struct slName *fieldName = slElementFromIx(pastBin, dataFieldIndex - 1);
if (fieldName == NULL)
errAbort("%s doesn't have enough fields", track);
char *field = fieldName->name;
assert(sqlFieldIndex(conn, track, field) >= 0);
/* Print reassuring status message */
verbose(1, "%s.%s has %d elements. Data field is %s\n", db, track, sqlTableSize(conn, track), field);
/* Get min/max dataValues in fields. Do it ourselves rather than using SQL min/max because sometimes
* the data field is a name column.... */
char query[512];
safef(query, sizeof(query), "select %s from %s", field, track);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
row = sqlNextRow(sr);
assert(row != NULL);
double val = sqlDouble(row[0]);
double minLimit = val, maxLimit = val;
while ((row = sqlNextRow(sr)) != 0)
{
double val = sqlDouble(row[0]);
if (val < minLimit) minLimit = val;
if (val > maxLimit) maxLimit = val;
}
sqlFreeResult(&sr);
verbose(1, " %g %g\n", minLimit, maxLimit);
/* Output original table plus new minLimit/maxLimit. */
for (el = list; el != NULL; el = el->next)
fprintf(f, "%s %s\n", el->name, (char *)el->val);
fprintf(f, "minLimit %g\n", minLimit);
fprintf(f, "maxLimit %g\n", maxLimit);
fprintf(f, "\n");
sqlDisconnect(&conn);
slFreeList(&fieldList);
slPairFreeValsAndList(&list);
}
lineFileClose(&lf);
carefulClose(&f);
}
