30f28e6c849cd0601459aa3f12b006233c9cc82a hiram Sun Apr 28 09:43:19 2019 -0700 eliminating the db= argument everywhere, only need genome= refs #18869 diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile index 515ac3c..8b68a92 100644 --- src/hg/hubApi/tests/makefile +++ src/hg/hubApi/tests/makefile @@ -1,412 +1,412 @@ test:: test0 test1 test2 test3 test4 test5 test6 test7 test8 test9 test10 \ test11 test12 test13 test14 test15 test16 test17 test18 test19 \ test21 test22 test23 test26 \ test27 test28 test29 test30 \ test31 test39 test40 \ test41 test42 test42 getSequence errorTests all:: listFunctions getFunctions getSequence errorTests listFunctions: test1 test2 test3 test4 test5 test22 test23 test30 test31 getFunctions: test6 test7 test8 test9 test10 test11 test12 test13 test14 \ test15 test16 test17 test18 test19 test21 test26 test27 test28 \ test29 test39 test40 test41 test42 getSequence: getSeq01 getSeq02 getSeq03 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 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 @echo '### test0: ./jsonConsumer.pl -test0 - OK' # testing /list/hubGenomes test1: setOutput @./jsonConsumer.pl -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -endpoint="/list/hubGenomes" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/tracks? hubUrl genome=_araTha1 trackLeavesOnly test2: setOutput @./jsonConsumer.pl -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -endpoint="/list/tracks" -genome="_araTha1" -trackLeavesOnly | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /list/tracks?db=ce11 trackLeavesOnly=1 +# testing /list/tracks?genome=ce11 trackLeavesOnly=1 test3: setOutput - @./jsonConsumer.pl -endpoint="/list/tracks" -db="ce11" -trackLeavesOnly | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -endpoint="/list/tracks" -genome="ce11" -trackLeavesOnly | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /list/chromosomes?db=ce11 +# testing /list/chromosomes?genome=ce11 test4: setOutput - @./jsonConsumer.pl -endpoint="/list/chromosomes" -db="ce11" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="ce11" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /list/chromosomes?db=ce11&track=gold +# testing /list/chromosomes?genome=ce11&track=gold test5: setOutput - @./jsonConsumer.pl -endpoint="/list/chromosomes" -db="ce11" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="ce11" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /getData/sequence?db=ce11&chrom=chrM +# testing /getData/sequence?genome=ce11&chrom=chrM test6: setOutput - @./jsonConsumer.pl -endpoint="/getData/sequence" -db="ce11" -chrom="chrM" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -endpoint="/getData/sequence" -genome="ce11" -chrom="chrM" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /getData/sequence?db=ce11&chrom=chrM&start=1&end=128 +# testing /getData/sequence?genome=ce11&chrom=chrM&start=1&end=128 test7: setOutput - @./jsonConsumer.pl -endpoint="/getData/sequence" -db="ce11" -chrom="chrM" -start=1 -end=128 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -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/track?db=ce11&track=gold +# testing /getData/track?genome=ce11&track=gold test8: setOutput - @./jsonConsumer.pl -maxItemsOutput=123 -endpoint="/getData/track" -db="ce11" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -maxItemsOutput=123 -endpoint="/getData/track" -genome="ce11" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /getData/track?db=ce11&track=gold&chrom=chrM +# testing /getData/track?genome=ce11&track=gold&chrom=chrM test9: setOutput - @./jsonConsumer.pl -endpoint="/getData/track" -db="ce11" -track="gold" -chrom="chrM" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -endpoint="/getData/track" -genome="ce11" -track="gold" -chrom="chrM" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /getData/track?db=ce11&track=gold&chrom=chrI&start=1&end=1024 +# testing /getData/track?genome=ce11&track=gold&chrom=chrI&start=1&end=1024 test10: setOutput - @./jsonConsumer.pl -endpoint="/getData/track" -db="ce11" -track="gold" -chrom="chrI" -start=1 -end=1024 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -endpoint="/getData/track" -genome="ce11" -track="gold" -chrom="chrI" -start=1 -end=1024 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl Plants &track=gold assembly hub test11: setOutput @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="assembly_" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl Plants &track=gold&chrom=chrM assembly hub test12: setOutput @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="assembly_" -chrom="chrCp" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl Plants &track=gold&chrom=chrI&start=1&end=1024 assembly hub test13: setOutput @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="assembly_" -chrom="chrCp" -start=1 -end=1024 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl Bejerano &track=ultraConserved track hub test14: setOutput @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -track="ultraConserved" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl Bejerano &track=ultraConserved&chrom=chr1 track hub test15: setOutput @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -track="ultraConserved" -chrom="chr1" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl Bejerano &track=ultraConserved&chrom=chr1&start=N&end=M track hub test16: setOutput @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -track="ultraConserved" -chrom="chr1" -start=10600000 -end=10800000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # wiggle data from a track hub # testing /getData/track? hubUrl Plants &track=gc5Base_&chrom=chrCp&start=1&end=1024 assembly hub test17: setOutput @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="gc5Base_" -chrom="chrCp" -start=1 -end=1024 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # bigWig data from a database -# /getData/track? db=galGal6 &track=gc5BaseBw&chrom=chr1&start=1&end=1024 +# /getData/track? genome=galGal6 &track=gc5BaseBw&chrom=chr1&start=1&end=1024 test18: setOutput - @./jsonConsumer.pl -endpoint="/getData/track" -db="galGal6" -track="gc5BaseBw" -chrom="chr1" -start=1 -end=1024 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -endpoint="/getData/track" -genome="galGal6" -track="gc5BaseBw" -chrom="chr1" -start=1 -end=1024 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # bigBed data from a database -# /getData/track? db=galGal6 &track=ncbiRefSeqOther&chrom=chr1&start=750000&end=5700000 +# /getData/track? genome=galGal6 &track=ncbiRefSeqOther&chrom=chr1&start=750000&end=5700000 test19: setOutput - @./jsonConsumer.pl -endpoint="/getData/track" -db="galGal6" -track="ncbiRefSeqOther" -chrom="chr1" -start=750000 -end=55700000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -endpoint="/getData/track" -genome="galGal6" -track="ncbiRefSeqOther" -chrom="chr1" -start=750000 -end=55700000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # wiggle data from a database where the SQL table name is different than the # track name -# /getData/track? db=hg19 &track=wgEncodeRegMarkH3k4me1H1hesc&chrom=chr1&start=62300000&end=62301000 +# /getData/track? genome=hg19 &track=wgEncodeRegMarkH3k4me1H1hesc&chrom=chr1&start=62300000&end=62301000 test21: setOutput - @./jsonConsumer.pl -endpoint="/getData/track" -db="hg19" -track="wgEncodeRegMarkH3k4me1H1hesc" -chrom="chr1" -start=62300000 -end=62301000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -endpoint="/getData/track" -genome="hg19" -track="wgEncodeRegMarkH3k4me1H1hesc" -chrom="chr1" -start=62300000 -end=62301000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes? hubUrl genome=_araTha1 test22: setOutput @./jsonConsumer.pl -endpoint="/list/chromosomes" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes? hubUrl genome=_araTha1 track=assembly_ test23: setOutput @./jsonConsumer.pl -endpoint="/list/chromosomes" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="assembly_" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing genePred track -# /getData/track?db=ce11&chrom=chrV&track=refGene&start=5231045&end=5241045 +# /getData/track?genome=ce11&chrom=chrV&track=refGene&start=5231045&end=5241045 test26: setOutput - @./jsonConsumer.pl -endpoint="/getData/track" -db="ce11" -track="refGene" -chrom="chrV" -start=5231045 -end=5241045 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -endpoint="/getData/track" -genome="ce11" -track="refGene" -chrom="chrV" -start=5231045 -end=5241045 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing PSL track -# /getData/track?db=ce11&chrom=chrV&track=ncbiRefSeqPsl&start=5231045&end=5241045 +# /getData/track?genome=ce11&chrom=chrV&track=ncbiRefSeqPsl&start=5231045&end=5241045 test27: setOutput - @./jsonConsumer.pl -endpoint="/getData/track" -db="ce11" -track="ncbiRefSeqPsl" -chrom="chrV" -start=5231045 -end=5241045 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -endpoint="/getData/track" -genome="ce11" -track="ncbiRefSeqPsl" -chrom="chrV" -start=5231045 -end=5241045 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing RMSK track -# /getData/track?db=ce11&debug=0&chrom=chrV&track=rmsk&start=5231045&end=5241045 +# /getData/track?genome=ce11&debug=0&chrom=chrV&track=rmsk&start=5231045&end=5241045 test28: setOutput - @./jsonConsumer.pl -endpoint="/getData/track" -db="ce11" -track="rmsk" -chrom="chrV" -start=5231045 -end=5241045 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -endpoint="/getData/track" -genome="ce11" -track="rmsk" -chrom="chrV" -start=5231045 -end=5241045 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # test superTrack child getData -# /getData/track?db=ce11&chrom=chrV&track=cpgIslandExt&start=5001045&end=5241045 +# /getData/track?genome=ce11&chrom=chrV&track=cpgIslandExt&start=5001045&end=5241045 test29: setOutput - @./jsonConsumer.pl -endpoint="/getData/track" -db="ce11" -track="cpgIslandExt" -chrom="chrV" -start=5001045 -end=5241045 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -endpoint="/getData/track" -genome="ce11" -track="cpgIslandExt" -chrom="chrV" -start=5001045 -end=5241045 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/tracks? hubUrl genome=_araTha1 test30: setOutput @./jsonConsumer.pl -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -endpoint="/list/tracks" -genome="_araTha1" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /list/tracks?db=ce11 +# testing /list/tracks?genome=ce11 test31: setOutput - @./jsonConsumer.pl -endpoint="/list/tracks" -db="ce11" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -endpoint="/list/tracks" -genome="ce11" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /getData/track?db=ce4&track=gold for split table operation +# testing /getData/track?genome=ce4&track=gold for split table operation test39: setOutput - @./jsonConsumer.pl -maxItemsOutput=123 -endpoint="/getData/track" -db="ce4" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -maxItemsOutput=123 -endpoint="/getData/track" -genome="ce4" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /getData/track?db=ce4&track=gold for split table operation +# testing /getData/track?genome=ce4&track=gold for split table operation # plus jsonArrayOutput test40: setOutput - @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -db="ce4" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -genome="ce4" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /getData/track?db=ce11&track=gc5BaseBw - bigWig data output +# testing /getData/track?genome=ce11&track=gc5BaseBw - bigWig data output # plus jsonArrayOutput test41: setOutput - @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -db="ce11" -track="gc5BaseBw" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -genome="ce11" -track="gc5BaseBw" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /getData/track?db=ce6&track=gc5Base - wiggle database table +# testing /getData/track?genome=ce6&track=gc5Base - wiggle database table # plus jsonArrayOutput test42: setOutput - @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -db="ce6" -track="gc5Base" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -genome="ce6" -track="gc5Base" | 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 -# testing /getData/sequence? db=monDom5&chrom=chr1&start=4321&end=5647 +# testing /getData/sequence? genome=monDom5&chrom=chr1&start=4321&end=5647 getSeq03: setOutput @printf "### $@ " - @./jsonConsumer.pl -endpoint="/getData/sequence" -db="monDom5" -chrom="chr1" -start=748055061 -end=748055161 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -endpoint="/getData/sequence" -genome="monDom5" -chrom="chr1" -start=748055061 -end=748055161 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz ############################################################################### # ERROR testing ############################################################################### # generate an error: ask for non-existent chrom in a track hub # /getData/track? hubUrl Plants &track=assembly_&chrom=chrI&start=1&end=14309681 err01: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?track=assembly_;chrom=chrI;genome=_araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;end=14309681;start=1\n" @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="assembly_" -chrom="chrI" -start=1 -end=14309681 2>&1 | sed -e 's#https://.*/getData#/getData#;' | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # error test, can not open bigWig file err02: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?track=gc5Base_;chrom=chrA9;genome=_braRap1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/bPlants/hub.txt\n" @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/bPlants/hub.txt" -genome="_braRap1" -track="gc5Base_" -chrom=chrA9 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # error test, can not find hubUrl err03: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?track=gc5Base_;chrom=chrA9;genome=_braRap1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/xPlants/hub.txt\n" @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/xPlants/hub.txt" -genome="_braRap1" -track="gc5Base_" -chrom=chrA9 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # error test, missing argument genome for /getData/track with hubUrl err04: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?track=gc5Base_;chrom=chrA9;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt\n" @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -track="gc5Base_" -chrom=chrA9 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # error test, missing argument genome for /getData/sequence with hubUrl err05: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/sequence?chrom=chrA9;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt\n" @./jsonConsumer.pl -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -chrom=chrA9 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # error test, missing argument genome for /list/tracks with hubUrl err06: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/list/tracks?trackLeavesOnly=1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt\n" @./jsonConsumer.pl -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -endpoint="/list/tracks" -trackLeavesOnly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # error test, missing argument hubUrl for /list/tracks err07: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/list/tracks?trackLeavesOnly=1;genome=_araTha1\n" @./jsonConsumer.pl -genome="_araTha1" -endpoint="/list/tracks" -trackLeavesOnly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # error test, missing argument hubUrl and genome for /list/tracks err08: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/list/tracks?trackLeavesOnly=1\n" @./jsonConsumer.pl -endpoint="/list/tracks" -trackLeavesOnly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /getData/sequence?db=cxe6 - error test illegal database name +# testing /getData/sequence?genome=cxe6 - error test illegal database name # plus jsonArrayOutput err09: setOutput - @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/sequence?db=cxe6;jsonOutputArrays=1;maxItemsOutput=123\n" - @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/sequence" -db="cxe6" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/sequence?genome=cxe6;jsonOutputArrays=1;maxItemsOutput=123\n" + @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/sequence" -genome="cxe6" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /list/tracks?db=cxe6 - error test illegal database name +# testing /list/tracks?genome=cxe6 - error test illegal database name # plus jsonArrayOutput err10: setOutput - @printf "### $@ https://hgwdev-api.gi.ucsc.edu/list/tracks?db=cxe6;jsonOutputArrays=1;maxItemsOutput=123\n" - @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/list/tracks" -db="cxe6" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz + @printf "### $@ https://hgwdev-api.gi.ucsc.edu/list/tracks?genome=cxe6;jsonOutputArrays=1;maxItemsOutput=123\n" + @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/list/tracks" -genome="cxe6" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /getData/track?db=ce6 - error test illegal maxItemsOutput +# testing /getData/track?genome=ce6 - error test illegal maxItemsOutput err11: setOutput - @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?db=ce6;track=gold;maxItemsOutput=1x23\n" - @./jsonConsumer.pl -maxItemsOutput=1x23 -endpoint="/getData/track" -db="ce6" -track=gold 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?genome=ce6;track=gold;maxItemsOutput=1x23\n" + @./jsonConsumer.pl -maxItemsOutput=1x23 -endpoint="/getData/track" -genome="ce6" -track=gold 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /getData/track?db=ce6 - error test illegal maxItemsOutput +# testing /getData/track?genome=ce6 - error test illegal maxItemsOutput err12: setOutput - @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?db=ce6;track=gold;maxItemsOutput=-2\n" - @./jsonConsumer.pl -maxItemsOutput=-2 -endpoint="/getData/track" -db="ce6" -track=gold 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?genome=ce6;track=gold;maxItemsOutput=-2\n" + @./jsonConsumer.pl -maxItemsOutput=-2 -endpoint="/getData/track" -genome="ce6" -track=gold 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /getData/track?db=ce6 - error test illegal maxItemsOutput +# testing /getData/track?genome=ce6 - error test illegal maxItemsOutput err13: setOutput - @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?db=ce6;track=gold;maxItemsOutput=0\n" - @./jsonConsumer.pl -maxItemsOutput=0 -endpoint="/getData/track" -db="ce6" -track=gold 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?genome=ce6;track=gold;maxItemsOutput=0\n" + @./jsonConsumer.pl -maxItemsOutput=0 -endpoint="/getData/track" -genome="ce6" -track=gold 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /getData/track?db=ce6 - error test illegal maxItemsOutput +# testing /getData/track?genome=ce6 - error test illegal maxItemsOutput err14: setOutput - @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?db=ce6;track=gold;maxItemsOutput=0\n" - @./jsonConsumer.pl -maxItemsOutput=0 -endpoint="/getData/track" -db="ce6" -track=gold 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?genome=ce6;track=gold;maxItemsOutput=0\n" + @./jsonConsumer.pl -maxItemsOutput=0 -endpoint="/getData/track" -genome="ce6" -track=gold 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /getData/tracks?db=ce6 - error test no such function on endpoint +# testing /getData/tracks?genome=ce6 - error test no such function on endpoint err15: setOutput - @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/tracks?db=ce6;track=gold\n" - @./jsonConsumer.pl -endpoint="/getData/tracks" -db="ce6" -track=gold 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/tracks?genome=ce6;track=gold\n" + @./jsonConsumer.pl -endpoint="/getData/tracks" -genome="ce6" -track=gold 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/endpoints - error test no such function err16: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/list/endpoints\n" @./jsonConsumer.pl -endpoint="/list/endpoints" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/hubGenomes with hubUrl but no genome specified err17: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/list/hubGenomes?genome=araTha1'\n" @./jsonConsumer.pl -endpoint="/list/tracks" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" 2>&1 | sed -e 's#https://.*/list#/list#;' | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes? hubUrl missing genome= err18: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt\n" @./jsonConsumer.pl -endpoint="/list/chromosomes" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes? hubUrl missing incorrect genome=araTha err19: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha\n" @./jsonConsumer.pl -endpoint="/list/chromosomes" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome=araTha 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes? hubUrl can not # find specified track for genome=_braRap1 track=_assembly (wrong name) err20: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/bPlants/hub.txt;genome=_braRap1;track=_assembly\n" @./jsonConsumer.pl -endpoint="/list/chromosomes" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/bPlants/hub.txt" -genome=_braRap1 -track=_assembly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes? hubUrl can not # find specified database in track hub err21: setOutput @printf "### $@ http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt?genome=hg19\n" @./jsonConsumer.pl -endpoint="/list/chromosomes" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome=hg19 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes? bad hubUrl err22: setOutput @printf "### $@ http://genome-test.gi.ucsc.edu/~hiram/hubs/xGillBejerano/hub.txt\n" @./jsonConsumer.pl -endpoint="/list/chromosomes" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/xGillBejerano/hub.txt" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /list/chromosomes? db=ce11 track=gbLoaded - not a position track +# testing /list/chromosomes? genome=ce11 track=gbLoaded - not a position track err23: setOutput - @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/list/chromosomes?db=ce11;track=gbLoaded'\n" - @./jsonConsumer.pl -endpoint="/list/chromosomes" -db=ce11 -track=gbLoaded 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz + @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/list/chromosomes?genome=ce11;track=gbLoaded'\n" + @./jsonConsumer.pl -endpoint="/list/chromosomes" -genome=ce11 -track=gbLoaded 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /list/hubGenomes illegal db=araTha1 +# testing /list/hubGenomes illegal genome=araTha1 err24: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/list/hubGenomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt'\n" - @./jsonConsumer.pl -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -endpoint="/list/hubGenomes" -db=araTha1 2>&1 | sed -e 's#https://.*/list#/list#;' | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -endpoint="/list/hubGenomes" -genome=araTha1 2>&1 | sed -e 's#https://.*/list#/list#;' | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes missing hubUrl or db err25: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/list/chromosomes'\n" @./jsonConsumer.pl -endpoint="/list/chromosomes" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl no track specified err26: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/getData/track?genome=_araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -genome=_araTha1 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl incorrect genome specified err27: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/getData/track?track=assembly_;genome=araTha1_;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -genome=araTha1_ -track=assembly_ 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl incorrect track specified err28: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/getData/track?track=_assembly;genome=_araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -genome=_araTha1 -track=_assembly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes hubUrl bad genome name err29: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/list/chromosomes?genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'" @./jsonConsumer.pl -endpoint="/list/chromosomes" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -genome=araTha1 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz