e40ef673e43640059fa00f7ee103f12367152f3d
hiram
  Thu Jan 2 10:32:53 2020 -0800
update restricted list for lovd tables Short Long and add redmine24666 test refs #24666

diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile
index ae42994..e475f46 100644
--- src/hg/hubApi/tests/makefile
+++ src/hg/hubApi/tests/makefile
@@ -19,35 +19,35 @@
 
 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
 
 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 err40 \
-	err41 err42 err43 err44 err45 err46
+	err41 err42 err43 err44 err45 err46 err47
 
 notSupported: notSup01 notSup02 notSup03 notSup07 notSup10
 
-bugReports: redmine23733 redmine24089a redmine24089b
+bugReports: redmine23733 redmine24089a redmine24089b redmine24666
 
 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
@@ -730,40 +730,46 @@
 
 # testing protected track data
 err43: setOutput
 	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=knownCanonToDecipher;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n"
 	@./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=knownCanonToDecipher -maxItemsOutput=5 -jsonOutputArrays 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing protected track data
 err44: setOutput
 	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=decipherSnvsRaw;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n"
 	@./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=decipherSnvsRaw -maxItemsOutput=5 -jsonOutputArrays 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing protected track data
 err45: setOutput
-	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=lovd;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n"
-	@./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=lovd -maxItemsOutput=5 -jsonOutputArrays 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=lovdShort;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=lovdShort -maxItemsOutput=5 -jsonOutputArrays 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing protected track data
 err46: setOutput
 	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=hgmd;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n"
 	@./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=hgmd -maxItemsOutput=5 -jsonOutputArrays 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
+# testing protected track data
+err47: setOutput
+	@printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=lovdLong;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n"
+	@./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=lovdLong -maxItemsOutput=5 -jsonOutputArrays 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
+
 #####################  wiggle data ###########################################
 # classic wiggle with wig table and wib file
 wig01: setOutput
 	@printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5Base;genome=ce4;maxItemsOutput=5'\n"
 	@./jsonConsumer.pl -endpoint="/getData/track" -genome=ce4 -track=gc5Base -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # classic wiggle with wig table and wib file with chrom specified
 wig02: setOutput
 	@printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5Base;genome=ce4;chrom=chrIV;maxItemsOutput=5'\n"
 	@./jsonConsumer.pl -endpoint="/getData/track" -genome=ce4 -track=gc5Base -chrom=chrIV -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # classic wiggle with wig table and wib file with chrom start,end specified
 wig03: setOutput
@@ -1044,30 +1050,37 @@
 	@./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
 
 # 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/$@.gz
+	@zdiff expected/$@.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
 #    871 netAlign
 #    596 bam
 #    512 genePred
 #    438 bigBed
 #    368 pgSnp
 #    348 bedGraph
 #    286 wig
 #    106 psl
 #     46