b419b8deda078f3e9aa2c245622f20b3bb2d2cb5
hiram
  Fri Jul 5 16:17:44 2019 -0700
adding support for track types ctgPos, expRatio, factorSource, gvf, interact, netAlign, peptideMapping, pgSnp refs #23589

diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile
index c681fba..1f310b7 100644
--- src/hg/hubApi/tests/makefile
+++ src/hg/hubApi/tests/makefile
@@ -7,39 +7,40 @@
 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
+supportedTypes: altGraphX barChart chain ctgPos expRatio factorSource gvf \
+	interact netAlign peptideMapping pgSnp
 
 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 notSup09
+	notSup07 notSup08 notSup09 notSup10
 
 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
@@ -706,49 +707,113 @@
 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
 
+ctgPos: setOutput
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=ctgPos;genome=hg19'\n"
+	@./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="hg19" -track="ctgPos" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=ctgPos;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome="hg19" -track="ctgPos" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
+
+expRatio: setOutput
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=gnfAtlas2;genome=hg19'\n"
+	@./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="hg19" -track="gnfAtlas2" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=gnfAtlas2;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome="hg19" -track="gnfAtlas2" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
+
+factorSource: setOutput
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=encRegTfbsClustered;genome=hg19'\n"
+	@./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="hg19" -track="encRegTfbsClustered" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=encRegTfbsClustered;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome="hg19" -track="encRegTfbsClustered" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
+
+gvf: setOutput
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=iscaCuratedBenign;genome=hg19'\n"
+	@./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="hg19" -track="iscaCuratedBenign" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=iscaCuratedBenign;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome="hg19" -track="iscaCuratedBenign" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
+
+interact: setOutput
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=gtexTransEqtl;genome=hg19'\n"
+	@./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="hg19" -track="gtexTransEqtl" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=gtexTransEqtl;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome="hg19" -track="gtexTransEqtl" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
+
+# hapmapLdPhCeu does not have an 'as' definiton in tableDescriptions
+ld2: setOutput
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=hapmapLdPhCeu;genome=hg19'\n"
+	@./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="hg19" -track="hapmapLdPhCeu" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=hapmapLdPhCeu;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome="hg19" -track="hapmapLdPhCeu" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
+
+netAlign: setOutput
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=netMelGal1;genome=hg38'\n"
+	@./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="hg38" -track="netMelGal1" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=netMelGal1;chrom=chr1;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome="hg38" -track="netMelGal1" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
+
+peptideMapping: setOutput
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=wgEncodeUncBsuProtGm12878MembranefractionSig;genome=hg19'\n"
+	@./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="hg19" -track="wgEncodeUncBsuProtGm12878MembranefractionSig" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=wgEncodeUncBsuProtGm12878MembranefractionSig;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome="hg19" -track="wgEncodeUncBsuProtGm12878MembranefractionSig" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
+
+pgSnp: setOutput
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=pgKb1454;genome=hg19'\n"
+	@./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="hg19" -track="pgKb1454" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=pgKb1454;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome="hg19" -track="pgKb1454" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${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
+# request a track type that is not yet supported: ld2
 notSup03: setOutput
-	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=cnvDevDelayCase;genome=hg38'\n"
-	@./jsonConsumer.pl -endpoint="/getData/track" -genome=hg38 -track="cnvDevDelayCase" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=hapmapLdPhCeu;genome=hg19'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track="hapmapLdPhCeu" 2>&1 | egrep -v "${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: bigBarChart
 notSup04: setOutput
 	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=gtexTranscExpr;genome=hg38'\n"
 	@./jsonConsumer.pl -endpoint="/getData/track" -genome=hg38 -track="gtexTranscExpr" 2>&1 | egrep -v "${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: bigLolly
 notSup05: setOutput
 	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=allCancer;genome=hg38'\n"
 	@./jsonConsumer.pl -endpoint="/getData/track" -genome=hg38 -track="allCancer" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # request a track type that is a container, not a data track
@@ -763,30 +828,36 @@
 	@./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
 
+# hapmapLdPhCeu does not have an 'as' definiton in tableDescriptions
+notSup10: setOutput
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=hapmapLdPhCeu;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome="hg19" -track="hapmapLdPhCeu" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
+
 
 #     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