a0eba0964baabf512bdace17b3df2b203a923df9
braney
  Wed Jan 14 12:36:56 2015 -0800
hubCheck should make sure that the number on "type bigBed #" lines has anumber that's less than equal to the number of fields in the table.

diff --git src/hg/lib/trackHubCheck.c src/hg/lib/trackHubCheck.c
index 740edcf..07a8110 100644
--- src/hg/lib/trackHubCheck.c
+++ src/hg/lib/trackHubCheck.c
@@ -1,207 +1,215 @@
 #include "common.h"
 #include "dystring.h"
 #include "trackDb.h"
 #include "bigWig.h"
 #include "bigBed.h"
 #include "errCatch.h"
 #include "vcf.h"
 #include "hgBam.h"
 #include "net.h"
 #include "htmshell.h"
 #include "trackHub.h"
 
 #ifdef USE_HAL
 #include "halBlockViz.h"
 #endif
 
 static int hubCheckTrack(struct trackHub *hub, struct trackHubGenome *genome, 
     struct trackDb *tdb, struct dyString *errors, FILE *searchFp)
 /* Make sure that track is ok. */
 {
 int retVal = 0;
 struct errCatch *errCatch = errCatchNew();
 
 if (errCatchStart(errCatch))
     {
 #ifdef NOTNOW   // at the moment we're not getting text from the HTML
     if (searchFp != NULL)
 	{
 	addOneDescription(genome->trackDbFile, tdb);
 	if (tdb->html != NULL)
 	    {
 	    char *stripHtml =htmlTextStripTags(tdb->html);
 	    strSwapChar(stripHtml, '\n', ' ');
 	    strSwapChar(stripHtml, '\t', ' ');
 	    strSwapChar(stripHtml, '\r', ' ');
 	    strSwapChar(stripHtml, ')', ' ');
 	    strSwapChar(stripHtml, '(', ' ');
 	    strSwapChar(stripHtml, '[', ' ');
 	    strSwapChar(stripHtml, ']', ' ');
 	    fprintf(searchFp, "%s.%s\t%s\t%s\t%s\n",hub->url, tdb->track, 
 		tdb->shortLabel, tdb->longLabel, stripHtml);
 	    }
 	else
 	    fprintf(searchFp, "%s.%s\t%s\t%s\n",hub->url, tdb->track, 
 		tdb->shortLabel, tdb->longLabel);
 	}
     else 
 #endif
 	{
 	char *relativeUrl = trackDbSetting(tdb, "bigDataUrl");
 
 	if (relativeUrl != NULL)
 	    {
 	    char *type = trackDbRequiredSetting(tdb, "type");
 	    char *bigDataUrl = trackHubRelativeUrl(genome->trackDbFile, relativeUrl);
 	    verbose(2, "checking %s.%s type %s at %s\n", genome->name, tdb->track, type, bigDataUrl);
 	    if (startsWithWord("bigWig", type))
 		{
 		/* Just open and close to verify file exists and is correct type. */
 		struct bbiFile *bbi = bigWigFileOpen(bigDataUrl);
 		bbiFileClose(&bbi);
 		}
 	    else if (startsWithWord("bigBed", type) || startsWithWord("bigGenePred", type))
 		{
 		/* Just open and close to verify file exists and is correct type. */
 		struct bbiFile *bbi = bigBedFileOpen(bigDataUrl);
+		char *typeString = cloneString(type);
+		nextWord(&typeString);
+		if (typeString != NULL)
+		    {
+		    unsigned numFields = sqlUnsigned(nextWord(&typeString));
+		    if (numFields > bbi->fieldCount)
+			errAbort("fewer fields in bigBed (%d) than in type statement (%d) for track %s with bigDataUrl %s\n", bbi->fieldCount, numFields, trackHubSkipHubName(tdb->track), bigDataUrl);
+		    }
 		bbiFileClose(&bbi);
 		}
 	    else if (startsWithWord("vcfTabix", type))
 		{
 		/* Just open and close to verify file exists and is correct type. */
 		struct vcfFile *vcf = vcfTabixFileMayOpen(bigDataUrl, NULL, 0, 0, 1, 1);
 		if (vcf == NULL)
 		    // Warnings already indicated whether the tabix file is missing etc.
 		    errAbort("Couldn't open %s and/or its tabix index (.tbi) file.  "
 			     "See http://genome.ucsc.edu/goldenPath/help/vcf.html",
 			     bigDataUrl);
 		vcfFileFree(&vcf);
 		}
 	    else if (startsWithWord("bam", type))
 		{
 		bamFileAndIndexMustExist(bigDataUrl);
 		}
 #ifdef USE_HAL
 	    else if (startsWithWord("halSnake", type))
 		{
 		char *errString;
 		int handle = halOpenLOD(bigDataUrl, &errString);
 		if (handle < 0)
 		    errAbort("HAL open error: %s\n", errString);
 		if (halClose(handle, &errString) < 0)
 		    errAbort("HAL close error: %s\n", errString);
 		}
 #endif
 	    else
 		errAbort("unrecognized type %s in genome %s track %s", type, genome->name, tdb->track);
 	    freez(&bigDataUrl);
 	    }
 	}
     }
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     {
     retVal = 1;
     dyStringPrintf(errors, "%s", errCatch->message->string);
     }
 errCatchFree(&errCatch);
 
 return retVal;
 }
 
 static int hubCheckGenome(struct trackHub *hub, struct trackHubGenome *genome,
     struct dyString *errors, boolean checkTracks, FILE *searchFp)
 /* Check out genome within hub. */
 {
 struct errCatch *errCatch = errCatchNew();
 struct trackDb *tdbList = NULL;
 int retVal = 0;
 
 if (errCatchStart(errCatch))
     {
     tdbList = trackHubTracksForGenome(hub, genome);
     trackHubPolishTrackNames(hub, tdbList);
     }
 errCatchEnd(errCatch);
 
 if (errCatch->gotError)
     {
     retVal = 1;
     dyStringPrintf(errors, "%s", errCatch->message->string);
     }
 errCatchFree(&errCatch);
 
 if (!checkTracks)
     return retVal;
 
 struct trackDb *tdb;
 for (tdb = tdbList; tdb != NULL; tdb = tdb->next)
     retVal |= hubCheckTrack(hub, genome, tdb, errors, searchFp);
 verbose(2, "%d tracks in %s\n", slCount(tdbList), genome->name);
 
 return retVal;
 }
 
 int trackHubCheck(char *hubUrl, struct dyString *errors, 
     boolean checkTracks, FILE *searchFp)
 /* hubCheck - Check a track data hub for integrity. Put errors in dyString.
  *      return 0 if hub has no errors, 1 otherwise 
  *      if checkTracks is TRUE, individual tracks are checked
  */
 
 {
 struct errCatch *errCatch = errCatchNew();
 struct trackHub *hub = NULL;
 int retVal = 0;
 
 if (errCatchStart(errCatch))
     hub = trackHubOpen(hubUrl, "hub_0");
 errCatchEnd(errCatch);
 
 if (errCatch->gotError)
     {
     retVal = 1;
     dyStringPrintf(errors, "%s", errCatch->message->string);
     }
 errCatchFree(&errCatch);
 
 if (hub == NULL)
     return 1;
 
 verbose(2, "hub %s\nshortLabel %s\nlongLabel %s\n", hubUrl, hub->shortLabel, hub->longLabel);
 verbose(2, "%s has %d elements\n", hub->genomesFile, slCount(hub->genomeList));
 
 if (searchFp != NULL)
     {
     struct trackHubGenome *genomeList = hub->genomeList;
 
     for(; genomeList ; genomeList = genomeList->next)
 	fprintf(searchFp, "%s\t%s\n",hub->url,  trackHubSkipHubName(genomeList->name));
     fprintf(searchFp, "%s\t%s\t%s\n",hub->url, hub->shortLabel, hub->longLabel);
 
     if (hub->descriptionUrl != NULL)
 	{
 	char *html = netReadTextFileIfExists(hub->descriptionUrl);
 	char *stripHtml =htmlTextStripTags(html);
 	strSwapChar(stripHtml, '\n', ' ');
 	strSwapChar(stripHtml, '\t', ' ');
 	strSwapChar(stripHtml, '\015', ' ');
 	strSwapChar(stripHtml, ')', ' ');
 	strSwapChar(stripHtml, '(', ' ');
 	strSwapChar(stripHtml, '[', ' ');
 	strSwapChar(stripHtml, ']', ' ');
 	fprintf(searchFp, "%s\t%s\n",hub->url,  stripHtml);
 	}
 
     return 0;
     }
 
 struct trackHubGenome *genome;
 for (genome = hub->genomeList; genome != NULL; genome = genome->next)
     {
     retVal |= hubCheckGenome(hub, genome, errors, checkTracks, NULL);
     }
 trackHubClose(&hub);
 
 return retVal;
 }