aee63b855980c1124d156b36dfe7d0e93c7fe005 mspeir Tue Dec 9 18:59:22 2025 -0800 removing some tests that are likely to change frequently, refs #36463 diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile index 7971a25abeb..1e13d6e9346 100644 --- src/hg/hubApi/tests/makefile +++ src/hg/hubApi/tests/makefile @@ -19,40 +19,40 @@ Note: Your sandbox trackDb needs to be up to date to allow the tests\n\ to function correctly. If one fails, update that trackDb.\n" hgwdev:: SERVERNAME="https://api-test.gi.ucsc.edu" make test alpha:: SERVERNAME="https://genome-test.gi.ucsc.edu" make test beta:: SERVERNAME="https://apibeta.soe.ucsc.edu" make test all:: test0 listFunctions getFunctions listSchema getSequence wigData \ search supportedTypes errorTests notSupported bugReports -listFunctions: list01 list02 list03 list04 list05 list06 list07 list08 list09 \ - list10 list11 list12 list13 list14 list15 list16 list17 list18 list19 \ +listFunctions: list01 list02 list04 list05 list06 list07 list08 \ + list10 list11 list12 list13 list14 list15 list16 list17 list18 \ list20 list21 list22 list23 list24 list25 list27 list28 list29 \ list30 list31 list32 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 \ + test29 test39 test40 test42 test43 test44 test45 test46 test47 \ test48 test49 test50 test51 test52 test53 test54 test55 test56 test57 \ - test58 test59 multiTrack01 multiTrack02 multiTrack03 + test58 test59 multiTrack01 findGenome: findGenome01 listSchema: schema01 schema02 schema03 schema04 schema05 schema06 schema07 \ schema08 schema09 schema10 schema11 schema12 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 \ @@ -97,34 +97,34 @@ @printf "### $@ '${SERVERNAME}/cgi-bin/hubApi/list/hubGenomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" "${SERVERNAME}" @./jsonConsumer.pl -serverName="${SERVERNAME}" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -endpoint="/list/hubGenomes" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/tracks? hubUrl genome=araTha1 trackLeavesOnly list02: setOutput @printf "### $@ '${SERVERNAME}/cgi-bin/hubApi/list/tracks?trackLeavesOnly=1;genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -endpoint="/list/tracks" -genome="araTha1" -trackLeavesOnly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/tracks?genome=ce11 trackLeavesOnly=1 # the grep " : {" will pick out just the track names to compare, so that # the changing genbank tables do not mess up the comparison, this will only # be comparing the track listing. The other egrep -v removes table names that # only exist on hgwdev so this test will work on public site -list03: setOutput - @printf "### $@ '${SERVERNAME}/cgi-bin/hubApi/list/tracks?trackLeavesOnly=1;genome=ce11'\n" - @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/tracks" -genome="ce11" -trackLeavesOnly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | grep " : {" | egrep -v "chainStrRat1|microsat|netStrRat1|tandemDups" | sort | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz +#list03: setOutput +# @printf "### $@ '${SERVERNAME}/cgi-bin/hubApi/list/tracks?trackLeavesOnly=1;genome=ce11'\n" +# @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/tracks" -genome="ce11" -trackLeavesOnly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | grep " : {" | egrep -v "chainStrRat1|microsat|netStrRat1|tandemDups" | sort | gzip -c > testOutput/$@.gz +# @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes?genome=ce11 list04: setOutput @printf "### $@ '${SERVERNAME}/cgi-bin/hubApi/list/chromosomes?genome=ce11'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="ce11" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes?genome=ce11&track=gold list05: setOutput @printf "### $@ '${SERVERNAME}/cgi-bin/hubApi/list/chromosomes?track=gold;genome=ce11'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="ce11" -track="gold" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes? hubUrl genome=araTha1 list06: setOutput @@ -136,34 +136,34 @@ list07: setOutput @printf "### $@ '${SERVERNAME}/cgi-bin/hubApi/list/chromosomes?track=assembly;genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -track="assembly" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/tracks? hubUrl genome=araTha1 list08: setOutput @printf "### $@ '${SERVERNAME}/cgi-bin/hubApi/list/tracks?genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -endpoint="/list/tracks" -genome="araTha1" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/tracks?genome=ce11 # the grep " : {" will pick out just the track names to compare, so that # the changing genbank tables do not mess up the comparison, this will only # be comparing the track listing -list09: setOutput - @printf "### $@ '${SERVERNAME}/cgi-bin/hubApi/list/tracks?genome=ce11'\n" - @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/tracks" -genome="ce11" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | grep " : {" | egrep -v "chainStrRat1|netStrRat1|tandemDups|microsat|tanDups" | sort | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz +#list09: setOutput +# @printf "### $@ '${SERVERNAME}/cgi-bin/hubApi/list/tracks?genome=ce11'\n" +# @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/tracks" -genome="ce11" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | grep " : {" | egrep -v "chainStrRat1|netStrRat1|tandemDups|microsat|tanDups" | sort | gzip -c > testOutput/$@.gz +# @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes?genome=ce11&track=mrna SQL table name is all_mrna list10: setOutput @printf "### $@ '${SERVERNAME}/cgi-bin/hubApi/list/chromosomes?track=mrna;genome=ce11'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="ce11" -track="mrna" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes?genome=ce4&track=mrna SQL table name is all_mrna # and ce4 has split tables list11: setOutput @printf "### $@ '${SERVERNAME}/cgi-bin/hubApi/list/chromosomes?track=mrna;genome=ce4'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="ce4" -track="mrna" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes?genome=ce11&track=rmsk different chrom name column @@ -201,34 +201,34 @@ @zdiff expected/$@.gz testOutput/$@.gz # list chromosomes for a bigWig track=gc5BaseBw genome=rheMac10 list17: setOutput @printf "### $@ '${SERVERNAME}/list/chromosomes?track=gc5BaseBw;genome=rheMac10'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="rheMac10" -track="gc5BaseBw" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # list chromosomes for a wigMaf table track=multiz7way genome=hg38 list18: setOutput @printf "### $@ '${SERVERNAME}/list/chromosomes?track=multiz7way;genome=hg38'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg38" -track="multiz7way" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # list chromosomes for a 'curated' assembly track=assembly genome=hs1 -list19: setOutput - @printf "### $@ '${SERVERNAME}/list/chromosomes?track=assembly;genome=hs1'\n" - @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hs1" -track="assembly" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#; s#/hubs/.*/hub#/hubs/hub#;' | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz +#list19: setOutput +# @printf "### $@ '${SERVERNAME}/list/chromosomes?track=assembly;genome=hs1'\n" +# @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hs1" -track="assembly" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#; s#/hubs/.*/hub#/hubs/hub#;' | gzip -c > testOutput/$@.gz +# @zdiff expected/$@.gz testOutput/$@.gz # testing /list/tracks? for a 'curated' assembly genome=mpxvRivers trackLeavesOnly list20: setOutput @printf "### $@ '${SERVERNAME}/list/tracks?trackLeavesOnly=1;genome=mpxvRivers'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/tracks" -genome="mpxvRivers" -trackLeavesOnly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#; s#/hubs/.*/hub#/hubs/hub#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes?genome=hs1 - a 'curated' assembly list21: setOutput @printf "### $@ '${SERVERNAME}/list/chromosomes?genome=hs1'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hs1" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#; s#/hubs/.*/hub#/hubs/hub#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/files?genome=ce2 list22: setOutput @@ -254,40 +254,40 @@ @ curl -L "${SERVERNAME}/list/files?genome=ce2;maxItemsOutput=5;format=text" 2> /dev/null | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#; s#/hubs/.*/hub#/hubs/hub#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/genarkGenomes #list26: setOutput # @printf "### $@ '${SERVERNAME}/list/genarkGenomes?maxItemsOutput=5'\n" # @./jsonConsumer.pl -maxItemsOutput=5 -serverName="${SERVERNAME}" -endpoint="/list/genarkGenomes" 2>&1 | egrep -v "${excludeLines}|totalAssemblies" | sed -e 's#https://.*/list#/list#; s#/hubs/.*/hub#/hubs/hub#;' | gzip -c > testOutput/$@.gz #@zdiff expected/$@.gz testOutput/$@.gz # testing /list/genarkGenomes verify existence of genome GCA_000002765.3 list27: setOutput @printf "### $@ '${SERVERNAME}/list/genarkGenomes?genome=GCA_000002765.3;maxItemsOutput=5'\n" @./jsonConsumer.pl -genome=GCA_000002765.3 -maxItemsOutput=5 -serverName="${SERVERNAME}" -endpoint="/list/genarkGenomes" 2>&1 | egrep -v "${excludeLines}|totalAssemblies" | sed -e 's#https://.*/list#/list#; s#/hubs/.*/hub#/hubs/hub#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /list/tracks?genome=GCA_021951015.1 without hubUrl +# testing /list/tracks?genome=GCA_001698545.1 without hubUrl list28: setOutput - @printf "### $@ '${SERVERNAME}/list/tracks?genome=GCA_021951015.1'\n" - @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/tracks" -genome="GCA_021951015.1" 2>&1 | egrep -v "${excludeLines}" | egrep -v "dateTime" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz + @printf "### $@ '${SERVERNAME}/list/tracks?genome=GCA_001698545.1'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/tracks" -genome="GCA_001698545.1" 2>&1 | egrep -v "${excludeLines}" | egrep -v "dateTime" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /list/tracks?genome=GCA_021951015.1 with hubUrl +# testing /list/tracks?genome=GCA_001698545.1 with hubUrl list29: setOutput - @printf "### $@ '${SERVERNAME}/list/tracks?genome=GCA_021951015.1;hubUrl=https://hgdownload.soe.ucsc.edu/hubs/GCA/021/951/015/GCA_021951015.1/hub.txt'\n" - @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/tracks" -genome="GCA_021951015.1" -hubUrl="https://hgdownload.soe.ucsc.edu/hubs/GCA/021/951/015/GCA_021951015.1/hub.txt" 2>&1 | egrep -v "${excludeLines}" | egrep -v "dateTime" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz + @printf "### $@ '${SERVERNAME}/list/tracks?genome=GCA_001698545.1;hubUrl=https://hgdownload.soe.ucsc.edu/hubs/GCA/001/698/545/GCA_001698545.1/hub.txt'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/tracks" -genome="GCA_001698545.1" -hubUrl="https://hgdownload.soe.ucsc.edu/hubs/GCA/001/698/545/GCA_001698545.1/hub.txt" 2>&1 | egrep -v "${excludeLines}" | egrep -v "dateTime" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes?genome=GCA_021951015.1 without hubUrl list30: setOutput @printf "### $@ '${SERVERNAME}/list/chromosomes?genome=GCA_021951015.1'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="GCA_021951015.1" 2>&1 | egrep -v "${excludeLines}" | egrep -v "dateTime" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes?genome=GCA_021951015.1 with hubUrl list31: setOutput @printf "### $@ '${SERVERNAME}/list/chromosomes?genome=GCA_021951015.1;hubUrl=https://hgdownload.soe.ucsc.edu/hubs/GCA/021/951/015/GCA_021951015.1/hub.txt'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="GCA_021951015.1" -hubUrl="https://hgdownload.soe.ucsc.edu/hubs/GCA/021/951/015/GCA_021951015.1/hub.txt" 2>&1 | egrep -v "${excludeLines}" | egrep -v "dateTime" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/schema?genome=GCA_021951015.1;track=cpgIslandExt without hubUrl @@ -379,34 +379,34 @@ @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 /getData/track?genome=ce4&track=gold for split table operation test39: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -maxItemsOutput=123 -endpoint="/getData/track" -genome="ce4" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track?genome=ce4&track=gold for split table operation # plus jsonArrayOutput test40: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -genome="ce4" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # bigDataUrl for bigGenePred track with no table, only trackDb -test41: setOutput - @printf "### $@ ### '${SERVERNAME}/track?track=mane;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n" - @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg38 -track=mane -maxItemsOutput=5 -jsonOutputArrays | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz +#test41: setOutput +# @printf "### $@ ### '${SERVERNAME}/track?track=mane;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n" +# @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg38 -track=mane -maxItemsOutput=5 -jsonOutputArrays | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz +# @zdiff expected/$@.gz testOutput/$@.gz # get data from wigMaf database table test42: setOutput @printf "### $@ ### '${SERVERNAME}/getData/track?track=multiz7way;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg38 -track=multiz7way -maxItemsOutput=5 -jsonOutputArrays | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from wigMaf database table with chrom specified test43: setOutput @printf "### $@ ### '${SERVERNAME}/getData/track?track=multiz7way;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5;chrom=chr22'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg38 -track=multiz7way -maxItemsOutput=5 -jsonOutputArrays -chrom=chr22 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from wigMaf database table with chrom and start,end specified test44: setOutput @@ -505,39 +505,39 @@ # with the hubUrl # https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/985/GCF_000002985.6/ test59: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -maxItemsOutput=123 -endpoint="/getData/track" -genome="GCF_000002985.6" -track="assembly" -hubUrl="https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/985/GCF_000002985.6//hub.txt" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # getData but with multiple tracks multiTrack01: @printf "### $@ ### '${SERVERNAME}/getData/track?tracks=gold,gap;genome=hg38;jsonOutputArrays=1;chrom=chr2;start=16129261;end=16163278'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg38 -track=gold,gap -jsonOutputArrays -chrom=chr2 -start=16129261 -end=16163278 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz ### but the name in the track is CP068276.2 ### can not decide what name to use to fetch data # getData but with multiple tracks from a 'curated' hub -multiTrack02: - @printf "### $@ ### '${SERVERNAME}/getData/track?tracks=assembly,cpgIslandExtUnmasked,simpleRepeat;genome=hs1;jsonOutputArrays=1;chrom=chr2;start=16129261;end=16163278'\n" - @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hs1 -track=assembly,cpgIslandExtUnmasked,simpleRepeat -jsonOutputArrays -chrom=chr2 -start=16129261 -end=16163278 | egrep -v "${excludeLines}" | sed -e 's#hubs/.*/hub.txt#hubs/hub.txt#;' | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz +#multiTrack02: +# @printf "### $@ ### '${SERVERNAME}/getData/track?tracks=assembly,cpgIslandExtUnmasked,simpleRepeat;genome=hs1;jsonOutputArrays=1;chrom=chr2;start=16129261;end=16163278'\n" +# @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hs1 -track=assembly,cpgIslandExtUnmasked,simpleRepeat -jsonOutputArrays -chrom=chr2 -start=16129261 -end=16163278 | egrep -v "${excludeLines}" | sed -e 's#hubs/.*/hub.txt#hubs/hub.txt#;' | gzip -c > testOutput/$@.gz +# @zdiff expected/$@.gz testOutput/$@.gz -multiTrack03: - @printf "### $@ ### '${SERVERNAME}/getData/track?tracks=assembly,cpgIslandExtUnmasked,simpleRepeat;genome=hs1;jsonOutputArrays=1;chrom=CP068276.2;start=16129261;end=16163278'\n" - @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hs1 -track=assembly,cpgIslandExtUnmasked,simpleRepeat -jsonOutputArrays -chrom=CP068276.2 -start=16129261 -end=16163278 | egrep -v "${excludeLines}" | sed -e 's#hubs/.*/hub.txt#hubs/hub.txt#;' | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz +#multiTrack03: +# @printf "### $@ ### '${SERVERNAME}/getData/track?tracks=assembly,cpgIslandExtUnmasked,simpleRepeat;genome=hs1;jsonOutputArrays=1;chrom=CP068276.2;start=16129261;end=16163278'\n" +# @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hs1 -track=assembly,cpgIslandExtUnmasked,simpleRepeat -jsonOutputArrays -chrom=CP068276.2 -start=16129261 -end=16163278 | egrep -v "${excludeLines}" | sed -e 's#hubs/.*/hub.txt#hubs/hub.txt#;' | 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 "### $@ " @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -chrom="chrCp" -start=4321 -end=5678 | 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 "### $@ " @./jsonConsumer.pl -serverName="${SERVERNAME}" -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