1340926c015448621f1896176dbb3107f5468b28
hiram
  Fri Jul 5 15:33:42 2019 -0700
adding supported types altGraphX, barChart, chain refs #23589

diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile
index 5410325..c681fba 100644
--- src/hg/hubApi/tests/makefile
+++ src/hg/hubApi/tests/makefile
@@ -1,44 +1,45 @@
 
-test:: test0 listFunctions getFunctions listSchema getSequence wigData \
-	errorTests notSupported bugReports
+test:: all
 
-all:: listFunctions getFunctions getSequence wigData errorTests \
-	notSupported
+all:: test0 listFunctions getFunctions listSchema getSequence wigData \
+	supportedTypes errorTests notSupported bugReports
 
 listFunctions: list01 list02 list03 list04 list05 list06 list07 list08 list09 \
 	list10 list11 list12 list13 list14 list15
 
 getFunctions: test6 test7 test8 test9 test10 test11 test12 test13 test14 \
 	test15 test16 test19 test21 test26 test27 test28 \
 	test29 test39 test40
 
 listSchema: schema01 schema02 schema03 schema04 schema05
 
 getSequence: getSeq01 getSeq02 getSeq03
 
 wigData: wig01 wig02 wig03 wig04 wig05 wig06 wig07 wig08 wig09 wig10 \
 	wig11 wig12 wig13 wig14 wig15 wig16 wig17 wig18 wig19 wig20 \
 	wig21 wig22 wig23 wig24
 
+supportedTypes: altGraphX barChart chain
+
 errorTests: err01 err02 err03 err04 err05 err06 err07 err08 err09 err10 \
 	err11 err12 err13 err14 err15 err16 err17 err18 err19 err20 \
 	err21 err22 err23 err24 err25 err26 err27 err28 err29 err30 \
 	err31 err32 err33 err34 err35 err36 err37 err38 err39
 
 notSupported: notSup01 notSup02 notSup03 notSup04 notSup05 notSup06 \
-	notSup07 notSup08
+	notSup07 notSup08 notSup09
 
 bugReports: redmine23733
 
 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
@@ -671,30 +672,67 @@
 	@./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -track="gc5Base" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # wiggle data from a track hub bigWig file, with chrom
 wig23: setOutput
 	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=gc5Base;chrom=chrCp;genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;jsonOutputArrays=1;maxItemsOutput=5'\n"
 	@./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -track="gc5Base" -chrom="chrCp" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # wiggle data from a track hub bigWig file, with chrom, start, end
 wig24: setOutput
 	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=gc5Base;chrom=chrCp;genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;end=5647;start=1234;jsonOutputArrays=1;maxItemsOutput=5'\n"
 	@./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -track="gc5Base" -chrom="chrCp" -start=1234 -end=5647 -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
+##############################################################################
+### supportedTypes - test both /list/chromosomes and /getData/track
+###                - for each type
+##############################################################################
+
+altGraphX: setOutput
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=sibTxGraph;genome=hg19'\n"
+	@./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="hg19" -track="sibTxGraph" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=sibTxGraph;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome="hg19" -track="sibTxGraph" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
+
+barChart: setOutput
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=gtexBrain;genome=hg38'\n"
+	@./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="hg38" -track="gtexBrain" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=gtexBrain;chrom=chr1;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome="hg38" -track="gtexBrain" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
+
+chain: setOutput
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=chainMelGal1;genome=hg38'\n"
+	@./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="hg38" -track="chainMelGal1" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=chainMelGal1;chrom=chr1;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome="hg38" -track="chainMelGal1" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
+
+# clonePos does not have an 'as' definiton in tableDescriptions
+clonePos: setOutput
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=clonePos;genome=hg19'\n"
+	@./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="hg19" -track="clonePos" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=clonePos;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome="hg19" -track="clonePos" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
+
+##############################################################################
+### notSupported
+##############################################################################
 # request a track type that is not yet supported: bam
 notSup01: setOutput
 	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=shMethylSubtrack;chrom=chr1;genome=hg19;hubUrl=http://lasallelab.genomecenter.ucdavis.edu/UCSChub/hub.txt;jsonOutputArrays=1;maxItemsOutput=5'\n"
 	@./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://lasallelab.genomecenter.ucdavis.edu/UCSChub/hub.txt" -genome="hg19" -track="shMethylSubtrack" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # request a track type that is not yet supported: vcfTabix
 notSup02: setOutput
 	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=variants;chrom=chr1;genome=danRer11;hubUrl=http://research.nhgri.nih.gov/manuscripts/Burgess/zebrafish/downloads/NHGRI-1/hub.txt;jsonOutputArrays=1;maxItemsOutput=5'\n"
 	@./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://research.nhgri.nih.gov/manuscripts/Burgess/zebrafish/downloads/NHGRI-1/hub.txt" -genome="danRer11" -track="variants" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # request a track type that is not yet supported: gvf
 notSup03: setOutput
 	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=cnvDevDelayCase;genome=hg38'\n"
@@ -719,30 +757,36 @@
 	@./jsonConsumer.pl -endpoint="/getData/track" -genome=hg38 -track="gdcCancer" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # request chromosome list from a track that is a container, not a data track
 notSup07: setOutput
 	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=gdcCancer;genome=hg38'\n"
 	@./jsonConsumer.pl -endpoint="/list/chromosomes" -genome=hg38 -track="gdcCancer" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # request chromosome list from a track that is a container, not a data track
 notSup08: setOutput
 	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=allCancer;genome=hg38'\n"
 	@./jsonConsumer.pl -endpoint="/list/chromosomes" -genome=hg38 -track="allCancer" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
+# clonePos does not have an 'as' definiton in tableDescriptions
+notSup09: setOutput
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=clonePos;genome=hg19'\n"
+	@./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="hg19" -track="clonePos" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
+
 
 #     34 bam - not supported</li>
 #      2 bigBarChart - not supported</li>
 #      3 bigInteract - not supported</li>
 #     18 bigMaf - not supported</li>
 #    152 composite container - not supported</li>
 #     93 composite view - not supported</li>
 #     37 halSnake - not supported</li>
 #     31 superTrack child - not supported</li>
 #      5 vcfTabix - not supported</li>
 
 redmine23733: setOutput
 	@printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=knownGene;genome=hg38;chrom=chr1;end=48000;start=47000'\n"
 	@./jsonConsumer.pl -endpoint="/getData/track" -genome=hg38 -track=knownGene -chrom=chr1 -start=47000 -end=48000 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz