56b3f3c3405aa741906781abc2a65062911f7c10 hiram Tue Apr 23 11:08:48 2019 -0700 naming tests per their category refs #18869 diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile index a686dbb..0a1f440 100644 --- src/hg/hubApi/tests/makefile +++ src/hg/hubApi/tests/makefile @@ -1,35 +1,35 @@ test:: test0 test1 test2 test3 test4 test5 test6 test7 test8 test9 test10 \ - test11 test12 test13 test14 test15 test16 test17 test18 test19 test20 \ - test21 test22 test23 test24 test25 test26 test27 test28 test29 test30 \ - test31 test32 test33 test34 test35 test36 test37 test38 test39 test40 \ - test41 test42 test42 test43 test45 + 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 +all:: listFunctions getFunctions getSequence errorTests -listFunctions: test1 test2 test3 test4 test5 test22 test23 test30 test31 \ - test36 test37 test38 test44 +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 test20 test21 test26 test27 test28 \ - test29 test32 test33 test34 test39 test40 test41 test42 test45 + test15 test16 test17 test18 test19 test21 test26 test27 test28 \ + test29 test39 test40 test41 test42 -getSequence: test24 test25 test35 test43 +getSequence: getSeq01 getSeq02 getSeq03 -errorTests: test20 test32 test33 test34 test35 test36 test37 test38 test43 \ - test44 test45 +errorTests: err01 err02 err03 err04 err05 err06 err07 err08 err09 \ + err10 err11 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 @@ -121,64 +121,47 @@ @./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 test18: setOutput @./jsonConsumer.pl -endpoint="/getData/track" -db="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 test19: setOutput @./jsonConsumer.pl -endpoint="/getData/track" -db="galGal6" -track="ncbiRefSeqOther" -chrom="chr1" -start=750000 -end=55700000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# generate an error: ask for non-existent chrom in a track hub -# /getData/track? hubUrl Plants &track=assembly_&chrom=chrI&start=1&end=14309681 -test20: setOutput - @./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 - @echo '### test20: ./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' - # 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 test21: setOutput @./jsonConsumer.pl -endpoint="/getData/track" -db="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 /getData/sequence? hubUrl genome=hg19&chrom=chrCp&start=4321&end=5647 -test24: setOutput - @./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 -test25: setOutput - @./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 genePred track # /getData/track?db=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 @zdiff expected/$@.gz testOutput/$@.gz # testing PSL track # /getData/track?db=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 @zdiff expected/$@.gz testOutput/$@.gz # testing RMSK track # /getData/track?db=ce11&debug=0&chrom=chrV&track=rmsk&start=5231045&end=5241045 test28: setOutput @@ -189,101 +172,131 @@ # /getData/track?db=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 @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 test31: setOutput @./jsonConsumer.pl -endpoint="/list/tracks" -db="ce11" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz +# testing /getData/track?db=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 + @zdiff expected/$@.gz testOutput/$@.gz + +# testing /getData/track?db=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 + @zdiff expected/$@.gz testOutput/$@.gz + +# testing /getData/track?db=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 + @zdiff expected/$@.gz testOutput/$@.gz + +# testing /getData/track?db=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 + @zdiff expected/$@.gz testOutput/$@.gz + +# testing /getData/track?db=cxe6&track=gc5Base - error test illegal database +# plus jsonArrayOutput +err11: setOutput + @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -db="cxe6" 2>&1 -track="gc5Base" | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + @echo '### err11 ./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -db="cxe6" 2>&1 -track="gc5Base"' + +############################################################################### +# /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 +getSeq03: setOutput + @printf "### $@ " + @./jsonConsumer.pl -endpoint="/getData/sequence" -db="monDom5" -chrom="chr1" -start=748055061 -end=748055161 | egrep -v "${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 -test32: setOutput +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 - @echo "### $@: can not open bigWig file OK" # error test, can not find hubUrl -test33: setOutput +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 - @echo "### $@: can not open hubUrl OK" # error test, missing argument genome for /getData/track with hubUrl -test34: setOutput +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 - @echo "### $@: missing genome argument OK" # error test, missing argument genome for /getData/sequence with hubUrl -test35: setOutput +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 - @echo "### $@: missing genome argument OK" # error test, missing argument genome for /list/tracks with hubUrl -test36: setOutput +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 - @echo "### $@: missing genome argument OK" # error test, missing argument hubUrl for /list/tracks -test37: setOutput +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 - @echo "### $@: missing hubUrl argument OK" # error test, missing argument hubUrl and genome for /list/tracks -test38: setOutput +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 - @echo "### $@: missing hubUrl and genome argument OK" - -# testing /getData/track?db=ce4&track=gold for split table operation -test39: setOutput - @./jsonConsumer.pl -maxItemsOutput=123 -endpoint="/getData/track" -db="ce4" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz - -# testing /getData/track?db=ce4&track=gold for split table operation -# plus jsonArrayOutput -test40: setOutput - @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -db="ce4" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz - -# testing /getData/track?db=ce11&track=gc5BaseBw - bigWig data output -# plus jsonArrayOutput -test41: setOutput - @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -db="ce11" -track="gc5BaseBw" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz - -# testing /getData/track?db=ce6&track=gc5Base - wiggle database table -# plus jsonArrayOutput -test42: setOutput - @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -db="ce6" -track="gc5Base" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/sequence?db=cxe6 - error test illegal database name # plus jsonArrayOutput -test43: setOutput +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/$@.gz @zdiff expected/$@.gz testOutput/$@.gz - @echo '### test43 ./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/sequence" -db="cxe6"' # testing /list/tracks?db=cxe6 - error test illegal database name # plus jsonArrayOutput -test44: setOutput +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/$@.gz @zdiff expected/$@.gz testOutput/$@.gz - @echo '### test44 ./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/list/tracks" -db="cxe6"' - -# testing /getData/track?db=cxe6&track=gc5Base - error test illegal database -# plus jsonArrayOutput -test45: setOutput - @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -db="cxe6" 2>&1 -track="gc5Base" | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz - @echo '### test45 ./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -db="cxe6" 2>&1 -track="gc5Base"' -