7e0eae4d90be1d4575c00d24592b969d97df14a9
hiram
  Sat Apr 20 21:20:15 2019 -0700
group tests into functions refs #18669

diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile
index 46d7c6c..a686dbb 100644
--- src/hg/hubApi/tests/makefile
+++ src/hg/hubApi/tests/makefile
@@ -1,275 +1,289 @@
 
 test::	test0 test1 test2 test3 test4 test5 test6 test7 test8 test9 test10 \
 	test11 test12 test13 test14 test15 test16 test17 test18 test19 test20 \
 	test21 test22 test23 test24 test25 test26 test27 test28 test29 test30 \
 	test31 test32 test33 test34 test35 test36 test37 test38 test39 test40 \
 	test41 test42 test42 test43 test45
 
+all:: listFunctions getFunctions getSequence
+
+listFunctions:	test1 test2 test3 test4 test5 test22 test23 test30 test31 \
+	test36 test37 test38 test44
+
+getFunctions: test6 test7 test8 test9 test10 test11 test12 test13 test14 \
+	test15 test16 test17 test18 test19 test20 test21 test26 test27 test28 \
+	test29 test32 test33 test34 test39 test40 test41 test42 test45
+
+getSequence: test24 test25 test35 test43
+
+errorTests: test20 test32 test33 test34 test35 test36 test37 test38 test43 \
+	test44 test45
+
 setOutput:
 	@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
 
 # testing /list/noSubCommand, /list/publicHubs and /list/ucscGenomes
 test0: setOutput
 	@./jsonConsumer.pl -test0 2>&1 | sed -e 's#https://.*/list#/list#;' | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 	@echo '### test0: ./jsonConsumer.pl -test0 - OK'
 
 # 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? hubUrl genome=_araTha1 trackLeavesOnly
 test2: setOutput
 	@./jsonConsumer.pl -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -endpoint="/list/tracks" -genome="_araTha1" -trackLeavesOnly | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /list/tracks?db=ce11 trackLeavesOnly=1
 test3: setOutput
 	@./jsonConsumer.pl -endpoint="/list/tracks" -db="ce11" -trackLeavesOnly | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # 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
 
 # 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 -maxItemsOutput=123 -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=ncbiRefSeqOther&chrom=chr1&start=750000&end=5700000
 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 2>&1 | sed -e 's#https://.*/getData#/getData#;' | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 	@echo '### test20: ./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'
 
 # 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
 
 # testing /getData/sequence? hubUrl genome=hg19&chrom=chrCp&start=4321&end=5647
 test24: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -chrom="chrCp" -start=4321 -end=5678 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/sequence? hubUrl Bejerano genome=hg19&chrom=chrM&start=4321&end=5647
 test25: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -chrom="chrM" -start=4321 -end=5678 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing genePred track
 #    /getData/track?db=ce11&chrom=chrV&track=refGene&start=5231045&end=5241045
 test26: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -db="ce11" -track="refGene"  -chrom="chrV" -start=5231045 -end=5241045 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing PSL track
 #    /getData/track?db=ce11&chrom=chrV&track=ncbiRefSeqPsl&start=5231045&end=5241045
 test27: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -db="ce11" -track="ncbiRefSeqPsl"  -chrom="chrV" -start=5231045 -end=5241045 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing RMSK track
 #    /getData/track?db=ce11&debug=0&chrom=chrV&track=rmsk&start=5231045&end=5241045
 test28: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -db="ce11" -track="rmsk"  -chrom="chrV" -start=5231045 -end=5241045 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # test superTrack child getData
 #    /getData/track?db=ce11&chrom=chrV&track=cpgIslandExt&start=5001045&end=5241045
 test29: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -db="ce11" -track="cpgIslandExt"  -chrom="chrV" -start=5001045 -end=5241045 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /list/tracks? hubUrl genome=_araTha1
 test30: 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
 test31: setOutput
 	@./jsonConsumer.pl -endpoint="/list/tracks" -db="ce11" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # error test, can not open bigWig file
 test32: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/bPlants/hub.txt" -genome="_braRap1" -track="gc5Base_" -chrom=chrA9 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 	@echo "### $@: can not open bigWig file OK"
 
 # error test, can not find hubUrl
 test33: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/xPlants/hub.txt" -genome="_braRap1" -track="gc5Base_" -chrom=chrA9 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 	@echo "### $@: can not open hubUrl OK"
 
 # error test, missing argument genome for /getData/track  with hubUrl
 test34: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -track="gc5Base_" -chrom=chrA9 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 	@echo "### $@: missing genome argument OK"
 
 # error test, missing argument genome for /getData/sequence  with hubUrl
 test35: setOutput
 	@./jsonConsumer.pl -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -chrom=chrA9 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 	@echo "### $@: missing genome argument OK"
 
 # error test, missing argument genome for /list/tracks  with hubUrl
 test36: setOutput
 	@./jsonConsumer.pl -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -endpoint="/list/tracks" -trackLeavesOnly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 	@echo "### $@: missing genome argument OK"
 
 # error test, missing argument hubUrl for /list/tracks
 test37: setOutput
 	@./jsonConsumer.pl -genome="_araTha1" -endpoint="/list/tracks" -trackLeavesOnly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 	@echo "### $@: missing hubUrl argument OK"
 
 # error test, missing argument hubUrl and genome for /list/tracks
 test38: setOutput
 	@./jsonConsumer.pl -endpoint="/list/tracks" -trackLeavesOnly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 	@echo "### $@: missing hubUrl and genome argument OK"
 
 # testing /getData/track?db=ce4&track=gold for split table operation
 test39: setOutput
 	@./jsonConsumer.pl -maxItemsOutput=123 -endpoint="/getData/track" -db="ce4" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/track?db=ce4&track=gold for split table operation
 # plus jsonArrayOutput
 test40: setOutput
 	@./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -db="ce4" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/track?db=ce11&track=gc5BaseBw - bigWig data output
 # plus jsonArrayOutput
 test41: setOutput
 	@./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -db="ce11" -track="gc5BaseBw" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/track?db=ce6&track=gc5Base - wiggle database table
 # plus jsonArrayOutput
 test42: setOutput
 	@./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -db="ce6" -track="gc5Base" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/sequence?db=cxe6 - error test illegal database name
 # plus jsonArrayOutput
 test43: setOutput
-	@./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/sequence" -db="cxe6" 2>&1 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
+	@./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/sequence" -db="cxe6" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 	@echo '### test43 ./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/sequence" -db="cxe6"'
 
 # testing /list/tracks?db=cxe6 - error test illegal database name
 # plus jsonArrayOutput
 test44: setOutput
-	@./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/list/tracks" -db="cxe6" 2>&1 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
+	@./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/list/tracks" -db="cxe6" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 	@echo '### test44 ./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/list/tracks" -db="cxe6"'
 
 # testing /getData/track?db=cxe6&track=gc5Base - error test illegal database
 # plus jsonArrayOutput
 test45: setOutput
-	@./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -db="cxe6" 2>&1 -track="gc5Base" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
+	@./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -db="cxe6" 2>&1 -track="gc5Base" | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 	@echo '### test45 ./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -db="cxe6" 2>&1 -track="gc5Base"'