46671c77d37fb4c642e84a38c53c6494f56223c5 hiram Thu Mar 23 14:47:42 2023 -0700 using bigBedFileOpenAlias in place of bigBedFileOpen supplies alias functions for mixed and match tracks with different naming authorities refs #30544 diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile index 4357a2c..66e75cd 100644 --- src/hg/hubApi/tests/makefile +++ src/hg/hubApi/tests/makefile @@ -24,31 +24,31 @@ 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 \ list20 list21 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 + multiTrack01 multiTrack02 multiTrack03 listSchema: schema01 schema02 schema03 schema04 schema05 schema06 schema07 \ schema08 schema09 schema10 schema11 schema12 getSequence: getSeq01 getSeq02 getSeq03 getSeq04 getSeq05 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 @@ -415,39 +415,44 @@ # https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?genome=ce11;track=mrna;maxItemsOutput=5 # PSL track, no chrom specified, exercise column name tName instead of chrom test57: setOutput @printf "### $@ ### '${SERVERNAME}/getData/track?track=mrna;genome=ce11;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=ce11 -track=mrna -maxItemsOutput=5 -jsonOutputArrays | egrep -v "${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 -### XXX ### THIS DOES NOT WORK - the sequence name in the assembly is chr2 ### 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=gc5Base;genome=hs1;jsonOutputArrays=1;chrom=chr2;start=16129261;end=16163278'\n" - @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hs1 -track=gc5Base -jsonOutputArrays -chrom=chr2 -start=16129261 -end=16163278 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @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}" | 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}" | 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 @zdiff expected/$@.gz testOutput/$@.gz @@ -1049,30 +1054,42 @@ @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/sequence" -hubUrl="https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/735/GCF_000001735.4/hub.txt" -genome="GCF_000001735.4" -chrom="Pltd" -start=4321 -end=5678 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/sequence#/sequence#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/sequence? genome=hg19&chrom=MT&start=4321&end=5647 chrAlias08: setOutput @ printf "### $@ '${SERVERNAME}/getData/sequence?genome=hg19;chrom=MT;start=4321;end=5678'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/sequence" -genome="hg19" -chrom="MT" -start=4321 -end=5678 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/sequence#/sequence#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/sequence? genome=hs1&chrom=MT&start=4321&end=5647 chrAlias09: setOutput @ printf "### $@ '${SERVERNAME}/getData/sequence?genome=hs1;chrom=MT;start=4321;end=5678'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/sequence" -genome="hs1" -chrom="MT" -start=4321 -end=5678 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/sequence#/sequence#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz +# testing /getData/track? track=assembly&genome=hs1&chrom=chr1 +chrAlias10: setOutput + @ printf "### $@ '${SERVERNAME}/getData/track?genome=hs1;chrom=chr1;track=assembly'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hs1" -chrom="chr1" -track=assembly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# testing /getData/track? track=assembly&genome=hs1&chrom=CP068276.2 +chrAlias11: setOutput + @ printf "### $@ '${SERVERNAME}/getData/track?genome=hs1;chrom=CP068276.2;track=assembly'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hs1" -chrom="CP068276.2" -track=assembly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + ############################################################################## ### supportedTypes - test both /list/chromosomes and /getData/track ### - for each type ############################################################################## altGraphX: setOutput @printf "### $@ '${SERVERNAME}/list/chromosomes?track=sibTxGraph;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg19" -track="sibTxGraph" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=sibTxGraph;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg19" -track="sibTxGraph" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz barChart: setOutput @printf "### $@ '${SERVERNAME}/list/chromosomes?track=gtexBrain;genome=hg38'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg38" -track="gtexBrain" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz