87ec277a5cc1915db16b58a4107b7a39e7a5da70
hiram
  Fri Jun 14 13:34:16 2024 -0700
add new option to getSeq -revComp to reverse complement sequence output refs #26691

diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile
index 6a7ddf9..e06893c 100644
--- src/hg/hubApi/tests/makefile
+++ src/hg/hubApi/tests/makefile
@@ -34,31 +34,31 @@
 listFunctions: list01 list02 list03 list04 list05 list06 list07 list08 list09 \
 	list10 list11 list12 list13 list14 list15 list16 list17 list18 list19 \
 	list20 list21 list22 list23 list24 list25 list26
 
 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 test57 \
 	multiTrack01 multiTrack02 multiTrack03
 
 findGenome: findGenome01
 
 listSchema: schema01 schema02 schema03 schema04 schema05 schema06 schema07 \
 	schema08 schema09 schema10 schema11 schema12
 
-getSequence: getSeq01 getSeq02 getSeq03 getSeq04 getSeq05
+getSequence: getSeq01 getSeq02 getSeq03 getSeq04 getSeq05 getSeq06 getSeq07
 
 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
 
 search: search01
 
 chrAlias: chrAlias01 chrAlias02 chrAlias03 chrAlias04 chrAlias05 chrAlias06 \
 	chrAlias07 chrAlias08 chrAlias09 chrAlias10 chrAlias11
 
 supportedTypes: altGraphX barChart chain ctgPos expRatio \
 	interact netAlign peptideMapping pgSnp bigDbSnp bigMaf bigChain
 
 supportedTypes0: altGraphX barChart chain ctgPos expRatio factorSource gvf \
 	interact netAlign peptideMapping pgSnp
@@ -502,30 +502,41 @@
 getSeq03: setOutput
 	@printf "### $@ "
 	@./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/sequence" -genome="monDom5" -chrom="chr1" -start=748055061 -end=748055161 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/sequence?genome=ce11&chrom=chrM
 getSeq04: setOutput
 	@./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/sequence" -genome="ce11" -chrom="chrM" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 # testing /getData/sequence?genome=ce11&chrom=chrM&start=1&end=128
 getSeq05: setOutput
 	@./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/sequence" -genome="ce11" -chrom="chrM" -start=1 -end=128 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
+# testing /getData/sequence? hubUrl genome=hg19&chrom=chrCp&start=4321&end=5647
+getSeq06: setOutput
+	@printf "### $@ "
+	@./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -chrom="chrCp" -start=4321 -end=5678 -revComp=1 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
+
+# testing /getData/sequence? genome=monDom5;chrom=chr1;start=4321;end=5647;revComp=1
+getSeq07: setOutput
+	@printf "### $@ "
+	@./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/sequence" -genome="monDom5" -chrom="chr1" -start=748055061 -end=748055161 -revComp=1 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
+	@zdiff expected/$@.gz testOutput/$@.gz
 
 ###############################################################################
 #  /findGenome testing
 ###############################################################################
 # simple findGenome test
 findGenome01: setOutput
 	@printf "### $@ ### '${SERVERNAME}/cgi-bin/hubApi/findGenome?genomeSearch=hg38'\n"
 	@curl -L "${SERVERNAME}/cgi-bin/hubApi/findGenome?genomeSearch=hg38" 2> /dev/null | python -mjson.tool | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 	@zdiff expected/$@.gz testOutput/$@.gz
 
 #	@ curl -L "${SERVERNAME}/search?search=brca;genome=hg38" 2> /dev/null | python -mjson.tool | egrep -c -n "\[|\]" | awk -v t="$@" '{if (($$1 < 30) || ($$1 > 50)) {printf "test %s failed, count %d not in range 30-40\n", t, $$1; exit 255;}}'
 # | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz
 
 ###############################################################################
 #  /list/schema testing