6bbfd4220159b66826230dfaf577a67c4a2d7236
hiram
  Mon Mar 1 10:52:48 2021 -0800
add full table psl test and bring tests up to date no redmine

diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile
index 85cd452..784ebb2 100644
--- src/hg/hubApi/tests/makefile
+++ src/hg/hubApi/tests/makefile
@@ -1,28 +1,28 @@
 
 test:: all
 
 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 list16 list17 list18
 
 getFunctions: test8 test9 test10 test11 test12 test13 test14 \
 	test15 test16 test19 test21 test26 test27 test28 \
 	test29 test39 test40 test41 test42 test43 test44 test45 test46 test47 \
-	test48 test49 test50 test51 test52 test53 test54 test55 test56
+	test48 test49 test50 test51 test52 test53 test54 test55 test56 test57
 
 listSchema: schema01 schema02 schema03 schema04 schema05 schema06 schema07 \
 	schema08 schema09 schema10 schema11 schema12
 
 getSequence: getSeq01 getSeq02 getSeq03 getSeq04 getSeq05
 
 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 ctgPos expRatio \
 	interact netAlign peptideMapping pgSnp
 
 supportedTypes0: altGraphX barChart chain ctgPos expRatio factorSource gvf \
 	interact netAlign peptideMapping pgSnp
@@ -352,30 +352,38 @@
 	@./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=clonePos -maxItemsOutput=5 -jsonOutputArrays | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # get data from clonePos track with chrom specified
 test55: setOutput
 	@printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=clonePos;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5;chrom=chr22'\n"
 	@./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=clonePos -maxItemsOutput=5 -jsonOutputArrays -chrom=chr22 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # get data from clonePos track with chrom and start,end specified
 test56: setOutput
 	@printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=clonePos;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5;chrom=chr21;start=20000000;end=30000000'\n"
 	@./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=clonePos -maxItemsOutput=5 -jsonOutputArrays -chrom=chr21 -start=20000000 -end=30000000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
+# https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?genome=ce11;track=mrna;maxItemsOutput=5
+
+# PSL track, no chrom specified, exercise column name tName instead of chrom
+test57: setOutput
+	@printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=mrna;genome=ce11;jsonOutputArrays=1;maxItemsOutput=5'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome=ce11 -track=mrna -maxItemsOutput=5 -jsonOutputArrays | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
+
 ###############################################################################
 #  /getData/sequence testing
 ###############################################################################
 # testing /getData/sequence? hubUrl genome=hg19&chrom=chrCp&start=4321&end=5647
 getSeq01: setOutput
 	@printf "### $@ "
 	@./jsonConsumer.pl -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -chrom="chrCp" -start=4321 -end=5678 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/sequence? hubUrl Bejerano genome=hg19&chrom=chrM&start=4321&end=5647
 getSeq02: setOutput
 	@printf "### $@ "
 	@./jsonConsumer.pl -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -chrom="chrM" -start=4321 -end=5678 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
@@ -1035,50 +1043,50 @@
 	@./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
+	@printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=knownGene;genome=hg19;chrom=chr1;end=48000;start=47000'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=knownGene -chrom=chr1 -start=47000 -end=48000 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | grep -v "^#" | sort | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # end coordinate for get sequence past end of chromosome, database genome
 redmine24089a: setOutput
 	@printf "### $@ 'https://api-test.gi.ucsc.edu/getData/sequence?genome=hg19;chrom=chrM;start=16560;end=16572'\n"
 	@./jsonConsumer.pl -endpoint="/getData/sequence" -genome=hg19 -chrom=chrM -start=16560 -end=16572 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # end coordinate for get sequence past end of chromosome, asmHub genome
 redmine24089b: setOutput
 	@printf "### $@ 'https://api-test.gi.ucsc.edu/getData/sequence?genome=araTha1;chrom=chrCp;start=154470;end=154479;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n"
 	@./jsonConsumer.pl -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -chrom="chrCp" -start=154470 -end=154479 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # full chromosome fetch from a NIB based genom
 redmine24666: setOutput
 	@printf "### $@ 'https://api-test.gi.ucsc.edu/getData/sequence?genome=ci2;chrom=scaffold_8534'\n"
-	@./jsonConsumer.pl -endpoint="/getData/sequence" -genome=ci2 -chrom=scaffold_8534 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" |  gzip -c > testOutput/$@.gz
+	@./jsonConsumer.pl -endpoint="/getData/sequence" -genome=ci2 -chrom=scaffold_8534 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | grep -v "^#" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # full chromosome fetch from a NIB based genom
 redmine25840: setOutput
 	@printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?genome=hg18;track=cnpSebat2'\n"
 	@./jsonConsumer.pl -endpoint="/getData/track" -genome="hg18" -track="cnpSebat2" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 #	curl -L "https://api-test.gi.ucsc.edu/getData/sequence?genome=ci2;chrom=scaffold_8534" 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz
 # track types found in hg19 and hg38 trackDb 'type' column:
 #   4586 narrowPeak
 #   4472 bigWig
 #   3294 bed
 #   1745 broadPeak
 #    872 chain