51db0a5d14bdc077c2092dc632b57c17d09d0404
hiram
  Wed Mar 27 14:49:28 2019 -0700
provide list chrom function for hubs refs #18869

diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile
index 234fa85..61fef78 100644
--- src/hg/hubApi/tests/makefile
+++ src/hg/hubApi/tests/makefile
@@ -1,136 +1,140 @@
 
 test::	test0 test1 test2 test3 test4 test5 test6 test7 test8 test9 test10 \
 	test11 test12 test13 test14 test15 test16 test17 test18 test19 test20 \
-	test21
+	test21 test22 test23
 
 setOutput:
-	if [ ! -d testOutput ]; then mkdir testOutput; fi
+	@if [ ! -d testOutput ]; then mkdir testOutput; fi
 
 clean::
 	rm -f testOutput/*.gz
 	rmdir testOutput
 
+# exclude these lines from the JSON output for comparison with expected
 excludeLines = downloadTime|dataTime
 
-# test::
-# 	@./jsonConsumer.pl 2> /dev/null | gzip -c > testOutput.json.gz
-# 	@zdiff testOutput.json.gz expected.json.gz
-
 # testing /list/noSubCommand, /list/publicHubs and /list/ucscGenomes
 test0: setOutput
 	@./jsonConsumer.pl 2> /dev/null | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /list/hubGenomes
 test1: setOutput
 	@./jsonConsumer.pl -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -endpoint="/list/hubGenomes" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
-# testing /list/tracks?genome=_araTha1
+# testing /list/tracks? hubUrl genome=_araTha1
 test2: setOutput
 	@./jsonConsumer.pl -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -endpoint="/list/tracks" -genome="_araTha1" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /list/tracks?db=ce11
 test3: setOutput
 	@./jsonConsumer.pl -endpoint="/list/tracks" -db="ce11" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
-# TBD XXX testing /list/chromosomes with a hub
 # testing /list/chromosomes?db=ce11
 test4: setOutput
 	@./jsonConsumer.pl -endpoint="/list/chromosomes" -db="ce11" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
-# TBD XXX testing /list/chromosomes with a hub and track
 # testing /list/chromosomes?db=ce11&track=gold
 test5: setOutput
 	@./jsonConsumer.pl -endpoint="/list/chromosomes" -db="ce11" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/sequence?db=ce11&chrom=chrM
 test6: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/sequence" -db="ce11" -chrom="chrM" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/sequence?db=ce11&chrom=chrM&start=1&end=128
 test7: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/sequence" -db="ce11" -chrom="chrM" -start=1 -end=128 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/track?db=ce11&track=gold
 test8: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -db="ce11" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/track?db=ce11&track=gold&chrom=chrM
 test9: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -db="ce11" -track="gold" -chrom="chrM" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/track?db=ce11&track=gold&chrom=chrI&start=1&end=1024
 test10: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -db="ce11" -track="gold" -chrom="chrI" -start=1 -end=1024 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/track? hubUrl Plants &track=gold assembly hub
 test11: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="assembly_" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/track? hubUrl Plants &track=gold&chrom=chrM assembly hub
 test12: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="assembly_" -chrom="chrCp" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/track? hubUrl Plants &track=gold&chrom=chrI&start=1&end=1024 assembly hub
 test13: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="assembly_" -chrom="chrCp" -start=1 -end=1024 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/track? hubUrl Bejerano &track=ultraConserved  track hub
 test14: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -track="ultraConserved" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/track? hubUrl Bejerano &track=ultraConserved&chrom=chr1  track hub
 test15: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -track="ultraConserved" -chrom="chr1" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/track? hubUrl Bejerano &track=ultraConserved&chrom=chr1&start=N&end=M  track hub
 test16: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -track="ultraConserved" -chrom="chr1" -start=10600000 -end=10800000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # wiggle data from a track hub
 # testing /getData/track? hubUrl Plants &track=gc5Base_&chrom=chrCp&start=1&end=1024 assembly hub
 test17: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="gc5Base_" -chrom="chrCp" -start=1 -end=1024 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # bigWig data from a database
 # /getData/track? db=galGal6 &track=gc5BaseBw&chrom=chr1&start=1&end=1024
 test18: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -db="galGal6" -track="gc5BaseBw" -chrom="chr1" -start=1 -end=1024 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # bigBed data from a database
 # /getData/track? db=galGal6 &track=gc5BaseBw&chrom=chr1&start=1&end=1024
 test19: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -db="galGal6" -track="ncbiRefSeqOther" -chrom="chr1" -start=750000 -end=55700000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # generate an error: ask for non-existent chrom in a track hub
 # /getData/track? hubUrl Plants &track=assembly_&chrom=chrI&start=1&end=14309681
 test20: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="assembly_" -chrom="chrI" -start=1 -end=14309681 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # wiggle data from a database where the SQL table name is different than the
 #    track name
 # /getData/track? db=hg19 &track=wgEncodeRegMarkH3k4me1H1hesc&chrom=chr1&start=62300000&end=62301000
 test21: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -db="hg19" -track="wgEncodeRegMarkH3k4me1H1hesc" -chrom="chr1" -start=62300000 -end=62301000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
+# testing /list/chromosomes? hubUrl genome=_araTha1
+test22: setOutput
+	@./jsonConsumer.pl -endpoint="/list/chromosomes" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
+
+# testing /list/chromosomes? hubUrl genome=_araTha1 track=assembly_
+test23: setOutput
+	@./jsonConsumer.pl -endpoint="/list/chromosomes" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="assembly_" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz