4d72ed9554069edb885ff2f793add75e422a5459
hiram
Thu Mar 21 15:58:39 2019 -0700
error catch aroung bbi file open and better sample getData links refs #18869
diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c
index e03035b..410a905 100644
--- src/hg/hubApi/hubApi.c
+++ src/hg/hubApi/hubApi.c
@@ -192,93 +192,101 @@
hashIncInt(countTracks, "superTrack child");
hashIncInt(countTracks, stripType);
hashIncInt(countTracks, "track count");
}
else if (isEmpty(tdb->type))
hashIncInt(countTracks, "no type specified");
else
{
hashIncInt(countTracks, stripType);
hashIncInt(countTracks, "track count");
}
freeMem(stripType);
// showCounts(countTracks);
}
-static void sampleUrl(struct trackHub *hub, char *db, struct trackDb *tdb, char *chrom, long long chromSize)
+static void sampleUrl(struct trackHub *hub, char *db, struct trackDb *tdb, char *chrom, long long chromSize, char *errorString)
/* print out a sample getData URL */
{
+char errorPrint[2048];
+errorPrint[0] = 0;
+
+if (isNotEmpty(errorString))
+ {
+ safef(errorPrint, sizeof(errorPrint), " ERROR: %s", errorString);
+ }
+
unsigned start = chromSize / 4;
unsigned end = start + 10000;
if (end > chromSize)
end = chromSize;
char *genome = NULL;
if (hub)
genome = hub->genomeList->name;
if (db)
{
if (hub)
{
if (tdb->parent)
- hPrintf("%s : %s subtrack of parent: %s (sample getData)\n", tdb->track, tdb->type, tdb->parent->track, urlPrefix, hub->url, genome, chrom, tdb->track, start, end );
+ hPrintf("%s : %s subtrack of parent: %s (sample getData)%s\n", tdb->track, tdb->type, tdb->parent->track, urlPrefix, hub->url, genome, chrom, tdb->track, start, end, errorPrint);
else
- hPrintf("%s : %s (sample getData)\n", tdb->track, tdb->type, urlPrefix, hub->url, genome, chrom, tdb->track, start, end );
+ hPrintf("%s : %s (sample getData)%s\n", tdb->track, tdb->type, urlPrefix, hub->url, genome, chrom, tdb->track, start, end, errorPrint);
}
else
{
if (tdb->parent)
- hPrintf("%s : %s subtrack of parent: %s (sample getData)\n", tdb->track, tdb->type, tdb->parent->track, urlPrefix, db, chrom, tdb->track, start, end );
+ hPrintf("%s : %s subtrack of parent: %s (sample getData)%s\n", tdb->track, tdb->type, tdb->parent->track, urlPrefix, db, chrom, tdb->track, start, end, errorPrint);
else
- hPrintf("%s : %s (sample getData)\n", tdb->track, tdb->type, urlPrefix, db, chrom, tdb->track, start, end );
+ hPrintf("%s : %s (sample getData)%s\n", tdb->track, tdb->type, urlPrefix, db, chrom, tdb->track, start, end, errorPrint);
}
}
else if (hub)
{
if (tdb->parent)
- hPrintf("%s : %s subtrack of parent: %s (sample getData)\n", tdb->track, tdb->type, tdb->parent->track, urlPrefix, hub->url, genome, chrom, tdb->track, start, end );
+ hPrintf("%s : %s subtrack of parent: %s (sample getData)%s\n", tdb->track, tdb->type, tdb->parent->track, urlPrefix, hub->url, genome, chrom, tdb->track, start, end, errorPrint);
else
- hPrintf("%s : %s (sample getData)\n", tdb->track, tdb->type, urlPrefix, hub->url, genome, chrom, tdb->track, start, end );
+ hPrintf("%s : %s (sample getData)%s\n", tdb->track, tdb->type, urlPrefix, hub->url, genome, chrom, tdb->track, start, end, errorPrint);
}
else
hPrintf("%s : %s not db hub track ?\n", tdb->track, tdb->type);
}
static void showSubTracks(struct trackHub *hub, char *db, struct trackDb *tdb, struct hash *countTracks,
- char *chromName, long long chromSize)
+ char *chromName, long long chromSize, char *errorString)
/* tdb has subtracks, show only subTracks, no details */
{
hPrintf(" \n");
if (debug)
hPrintf(" - subtracks for '%s' db: '%s'
\n", tdb->track, db);
if (tdb->subtracks)
{
struct trackDb *tdbEl = NULL;
for (tdbEl = tdb->subtracks; tdbEl; tdbEl = tdbEl->next)
{
if (tdbIsCompositeView(tdbEl))
hPrintf("- %s : %s : composite view of parent: %s
\n", tdbEl->track, tdbEl->type, tdbEl->parent->track);
else
{
if (isSupportedType(tdbEl->type))
- sampleUrl(hub, db, tdbEl, chromName, chromSize);
+ sampleUrl(hub, db, tdbEl, chromName, chromSize, errorString);
else
hPrintf("- %s : %s : subtrack of parent: %s
\n", tdbEl->track, tdbEl->type, tdbEl->parent->track);
}
hashCountTrack(tdbEl, countTracks);
if (tdbEl->subtracks)
- showSubTracks(hub, db, tdbEl, countTracks, chromName, chromSize);
+ showSubTracks(hub, db, tdbEl, countTracks, chromName, chromSize, errorString);
}
}
hPrintf("
\n");
}
static void trackSettings(struct trackDb *tdb, struct hash *countTracks)
/* process the settingsHash for a trackDb, recursive when subtracks */
{
hPrintf(" \n");
// if (tdb->children) haven't yet seen a track with children ?
// hPrintf(" - %s: has children
\n", tdb->track);
// else
// hPrintf(" - %s: NO children
\n", tdb->track);
struct hashEl *hel;
struct hashCookie hc = hashFirst(tdb->settingsHash);
@@ -419,171 +427,189 @@
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
retVal = 1;
dyStringPrintf(errors, "%s", errCatch->message->string);
}
errCatchFree(&errCatch);
return retVal;
} /* static int bbiBriefMeasure() */
static void hubSampleUrl(struct trackHub *hub, struct trackDb *tdb,
long chromCount, long itemCount, char *chromName, unsigned chromSize,
- char *genome)
+ char *genome, char *errorString)
{
unsigned start = chromSize / 4;
unsigned end = start + 10000;
if (end > chromSize)
end = chromSize;
+char errorPrint[2048];
+errorPrint[0] = 0;
+
+if (isNotEmpty(errorString))
+ {
+ safef(errorPrint, sizeof(errorPrint), " : ERROR: %s", errorString);
+ }
+
if (isSupportedType(tdb->type))
{
if (startsWithWord("bigBed", tdb->type))
- hPrintf(" - %s : %s : %ld chroms : %ld item count (Xsample getData)
\n", tdb->track, tdb->type, chromCount, itemCount, urlPrefix, hub->url, genome, tdb->track, chromName, start, end);
+ hPrintf(" - %s : %s : %ld chroms : %ld item count (sample getData)%s
\n", tdb->track, tdb->type, chromCount, itemCount, urlPrefix, hub->url, genome, tdb->track, chromName, start, end, errorPrint);
else if (startsWithWord("bigWig", tdb->type))
- hPrintf(" - %s : %s : %ld chroms : %ld bases covered (Xsample getData)
\n", tdb->track, tdb->type, chromCount, itemCount, urlPrefix, hub->url, genome, tdb->track, chromName, start, end);
+ hPrintf(" - %s : %s : %ld chroms : %ld bases covered (sample getData)%s
\n", tdb->track, tdb->type, chromCount, itemCount, urlPrefix, hub->url, genome, tdb->track, chromName, start, end, errorPrint);
else
- hPrintf(" - %s : %s : %ld chroms : %ld count <(Xsample getData)
\n", tdb->track, tdb->type, chromCount, itemCount, urlPrefix, hub->url, genome, tdb->track, chromName, start, end);
+ hPrintf(" - %s : %s : %ld chroms : %ld count <(sample getData)%s
\n", tdb->track, tdb->type, chromCount, itemCount, urlPrefix, hub->url, genome, tdb->track, chromName, start, end, errorPrint);
}
else
{
if (startsWithWord("bigBed", tdb->type))
hPrintf(" - %s : %s : %ld chroms : %ld item count
\n", tdb->track, tdb->type, chromCount, itemCount);
else if (startsWithWord("bigWig", tdb->type))
hPrintf(" - %s : %s : %ld chroms : %ld bases covered
\n", tdb->track, tdb->type, chromCount, itemCount);
else
hPrintf(" - %s : %s : %ld chroms : %ld count
\n", tdb->track, tdb->type, chromCount, itemCount);
}
-}
+} /* static void hubSampleUrl(struct trackHub *hub, struct trackDb *tdb,
+ * long chromCount, long itemCount, char *chromName, unsigned chromSize,
+ * char *genome)
+ */
static void hubCountOneTdb(struct trackHub *hub, char *db, struct trackDb *tdb,
char *bigDataIndex, struct hash *countTracks, char *chromName,
unsigned chromSize, char *genome)
{
char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl");
// char *compositeTrack = trackDbSetting(tdb, "compositeTrack");
boolean compositeContainer = tdbIsComposite(tdb);
boolean compositeView = tdbIsCompositeView(tdb);
// char *superTrack = trackDbSetting(tdb, "superTrack");
boolean superChild = tdbIsSuperTrackChild(tdb);
boolean depthSearch = cartUsualBoolean(cart, "depthSearch", FALSE);
hashCountTrack(tdb, countTracks);
char *longName = NULL;
unsigned longSize = 0;
long chromCount = 0;
long itemCount = 0;
-if (! (compositeContainer || compositeView) )
- {
struct dyString *errors = newDyString(1024);
- int retVal = bbiBriefMeasure(tdb->type, bigDataUrl, bigDataIndex, &chromCount, &itemCount, errors, &longName, &longSize);
- if (retVal)
- hPrintf(" - %s : %s : ERROR: %s
\n", tdb->track, tdb->type, errors->string);
- }
+
+if (! (compositeContainer || compositeView) )
+ (void) bbiBriefMeasure(tdb->type, bigDataUrl, bigDataIndex, &chromCount, &itemCount, errors, &longName, &longSize);
if (depthSearch && bigDataUrl)
{
if (isSupportedType(tdb->type))
{
if (chromSize > 0)
- hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome);
+ hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome, errors->string);
else
- hubSampleUrl(hub, tdb, chromCount, itemCount, longName, longSize, genome);
+ hubSampleUrl(hub, tdb, chromCount, itemCount, longName, longSize, genome, errors->string);
}
}
else
{
if (compositeContainer)
hPrintf(" - %s : %s : composite track container has %d subtracks
\n", tdb->track, tdb->type, slCount(tdb->subtracks));
else if (compositeView)
hPrintf(" - %s : %s : composite view of parent: %s
\n", tdb->track, tdb->type, tdb->parent->track);
else if (superChild)
hPrintf(" - %s : %s : superTrack child of parent: %s (sample getData)
\n", tdb->track, tdb->type, tdb->parent->track);
else if (! depthSearch && bigDataUrl)
- hPrintf(" - %s : %s : %s
\n", tdb->track, tdb->type, bigDataUrl);
+ {
+ if (isSupportedType(tdb->type))
+ {
+ if (chromSize > 0)
+ hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome, errors->string);
+ else
+ hubSampleUrl(hub, tdb, chromCount, itemCount, longName, longSize, genome, errors->string);
+ }
+ // hPrintf(" - %s : %s : %s (maybe sample ?)
\n", tdb->track, tdb->type, bigDataUrl);
+ }
else
{
if (isSupportedType(tdb->type))
{
if (chromSize > 0)
- hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome);
+ hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome, errors->string);
else
- hubSampleUrl(hub, tdb, chromCount, itemCount, longName, longSize, genome);
+ hubSampleUrl(hub, tdb, chromCount, itemCount, longName, longSize, genome, errors->string);
}
else
- hPrintf(" - %s : %s
\n", tdb->track, tdb->type);
+ hPrintf(" - %s : %s (what is this)
\n", tdb->track, tdb->type);
}
}
if (allTrackSettings)
{
hPrintf(" \n");
trackSettings(tdb, countTracks); /* show all settings */
hPrintf("
- %s : %s : composite track container has %d subtracks
\n", tdb->track, tdb->type, slCount(tdb->subtracks));
else if (compositeView)
hPrintf(" - %s : %s : composite view of parent: %s
\n", tdb->track, tdb->type, tdb->parent->track);
else if (superChild)
hPrintf(" - %s : %s : superTrack child of parent: %s
\n", tdb->track, tdb->type, tdb->parent->track);
else if (! depthSearch && bigDataUrl)
hPrintf(" - %s : %s : %s
\n", tdb->track, tdb->type, bigDataUrl);
else
{
if (isSupportedType(tdb->type))
- sampleUrl(NULL, db, tdb, chromName, chromSize);
+ sampleUrl(NULL, db, tdb, chromName, chromSize, errorString);
else
hPrintf(" - %s : %s
\n", tdb->track, tdb->type);
}
if (allTrackSettings)
{
hPrintf(" \n");
trackSettings(tdb, countTracks); /* show all settings */
hPrintf("
Tracks in UCSC genome: '%s', longest chrom: %s:%u
\n", db, chromName, chromSize);
struct trackDb *tdbList = obtainTdb(NULL, db);
struct trackDb *tdb;
hPrintf("\n");
hPrintf("- %s:%u
\n", chromName, chromSize);
for (tdb = tdbList; tdb != NULL; tdb = tdb->next )
{
- countOneTdb(db, tdb, countTracks, chromName, chromSize);
+ countOneTdb(db, tdb, countTracks, chromName, chromSize, NULL);
if (timeOutReached())
break;
}
int trackCount = ptToInt(hashFindVal(countTracks, "track count"));
/* elCount - 1 since the 'track count' element isn't a track */
hPrintf(" - %d total tracks counted, %d different track types
\n", trackCount, countTracks->elCount - 1);
if (countTracks->elCount)
{
hPrintf(" \n");
struct hashEl *hel, *helList = hashElListHash(countTracks);
slSort(&helList, hashElCmpIntValDesc);
for (hel = helList; hel; hel = hel->next)
{
if (sameOk("track count", hel->name))
continue;