05c7e605c01e595561c32690eb44a7512041e540
braney
  Wed Sep 23 09:34:08 2026 -0700
hubCheck: reject a bigBed type line that declares fewer than three fields, refs #36940

hgc already stops on "type bigBed 1" or "type bigBed 2", but hubCheck
passed both, so a hub author only found out when a user clicked an item.
Check the declared count against the minimum of three next to the
existing check against the file's field count.  A bare "type bigBed"
does not reach this code and is unchanged.

Adds a fieldCountTooFew test with bigBed 1 and bigBed 2 tracks.

diff --git src/hg/utils/hubCheck/tests/makefile src/hg/utils/hubCheck/tests/makefile
index 6e251d6b7a4..24ac7ce051b 100644
--- src/hg/utils/hubCheck/tests/makefile
+++ src/hg/utils/hubCheck/tests/makefile
@@ -1,21 +1,21 @@
 kentSrc = ../../../..
 include ../../../../inc/common.mk
 
 hubCheck = ${DESTBINDIR}/hubCheck
 
-test:: one two errors supertrackChild genomesErrors badType badSubgroups autoScale noLongLabel badGroups goodGroups noCompositeGroup allowWarnings seqNameCheck noSeqNameCheck selfParent dotInName fieldCountMismatch relPath missingFile
+test:: one two errors supertrackChild genomesErrors badType badSubgroups autoScale noLongLabel badGroups goodGroups noCompositeGroup allowWarnings seqNameCheck noSeqNameCheck selfParent dotInName fieldCountMismatch fieldCountTooFew relPath missingFile
 
 one:	mkout
 	-${hubCheck} input/hub1.txt > output/output1.txt
 	diff expected/output1.txt output/output1.txt
 
 two:	mkout
 	-${hubCheck} input/hub2.txt > output/output2.txt 2> /dev/null
 	diff expected/output2.txt output/output2.txt
 
 supertrackChild: mkout
 	-${hubCheck} input/supertrackChild.txt > output/supertrackChild.txt 2> /dev/null
 	diff expected/supertrackChild.txt output/supertrackChild.txt
 
 errors:	mkout
 	-${hubCheck} input/manyErrorsHub.txt > output/manyErrors.output.txt 2>/dev/null
@@ -65,30 +65,34 @@
 	-${hubCheck} -noSeqNameCheck input/seqNameHub.txt > output/noSeqNameCheck.output.txt 2>/dev/null
 	diff expected/noSeqNameCheck.output.txt output/noSeqNameCheck.output.txt
 
 selfParent: mkout
 	-${hubCheck} input/selfParent.txt > output/selfParent.output.txt 2>/dev/null
 	diff expected/selfParent.output.txt output/selfParent.output.txt
 
 dotInName: mkout
 	-${hubCheck} input/dotInName.txt > output/dotInName.output.txt 2>/dev/null
 	diff expected/dotInName.output.txt output/dotInName.output.txt
 
 fieldCountMismatch: mkout
 	-cd input && ${hubCheck} fieldCountMismatch.txt > ../output/fieldCountMismatch.output.txt 2>/dev/null
 	diff expected/fieldCountMismatch.output.txt output/fieldCountMismatch.output.txt
 
+fieldCountTooFew: mkout
+	-cd input && ${hubCheck} fieldCountTooFew.txt > ../output/fieldCountTooFew.output.txt 2>/dev/null
+	diff expected/fieldCountTooFew.output.txt output/fieldCountTooFew.output.txt
+
 # A hub reached by a relative path, with its data file in a subdirectory below
 # hub.txt. Deliberately NOT run from inside input/, because the point is to check
 # that the hub directory is prepended to bigDataUrl once and not twice. The
 # expected output is a field count mismatch, which hubCheck can only report if it
 # found and opened the file.
 relPath: mkout
 	-${hubCheck} input/relPath/hub.txt > output/relPath.output.txt 2>/dev/null
 	diff expected/relPath.output.txt output/relPath.output.txt
 
 # A bigDataUrl that does not exist has to be reported. hubCheck used to prune such a
 # track out of the list before it ever got checked, and then exited 0 saying nothing.
 missingFile: mkout
 	-${hubCheck} input/relPath/missingFile.txt > output/missingFile.output.txt 2>/dev/null
 	diff expected/missingFile.output.txt output/missingFile.output.txt