0969409c52a6e1f50cc34ede97ee87fcd897200e hiram Mon Jun 17 13:18:27 2024 -0700 allow the same trick for getData functions genArk genome name without URL will work no redmine diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile index 1be34f5..e70fee4 100644 --- src/hg/hubApi/tests/makefile +++ src/hg/hubApi/tests/makefile @@ -28,31 +28,31 @@ 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 list22 list23 list24 list25 list26 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 \ test48 test49 test50 test51 test52 test53 test54 test55 test56 test57 \ - multiTrack01 multiTrack02 multiTrack03 + test58 test59 multiTrack01 multiTrack02 multiTrack03 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 \ @@ -482,30 +482,44 @@ # get data from clonePos track with chrom and start,end specified test56: setOutput @printf "### $@ ### '${SERVERNAME}/getData/track?track=clonePos;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5;chrom=chr21;start=20000000;end=30000000'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=clonePos -maxItemsOutput=5 -jsonOutputArrays -chrom=chr21 -start=20000000 -end=30000000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # 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/$@.gz +# testing /getData/track?genome=GCF_000002985.6&track=assembly +# without the hubUrl +# https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/985/GCF_000002985.6/ +test58: setOutput + @./jsonConsumer.pl -serverName="${SERVERNAME}" -maxItemsOutput=123 -endpoint="/getData/track" -genome="GCF_000002985.6" -track="assembly" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# testing /getData/track?genome=GCF_000002985.6&track=assembly +# 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 multiTrack03: