e1a1fb5375a5511bd57e4fb67182e7fa8627b37b hiram Wed Mar 22 11:11:50 2023 -0700 add some tests on hs1 refs #30544 diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile index 9658baa..4eed613 100644 --- src/hg/hubApi/tests/makefile +++ src/hg/hubApi/tests/makefile @@ -17,50 +17,52 @@ SERVERNAME=\"https://genome-test.gi.ucsc.edu\" make test8\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 + 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 \ - multiTrack1 + multiTrack01 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 +chrAlias: chrAlias01 chrAlias02 chrAlias03 chrAlias04 chrAlias05 chrAlias06 \ + chrAlias07 chrAlias08 chrAlias09 supportedTypes: altGraphX barChart chain ctgPos expRatio \ interact netAlign peptideMapping pgSnp supportedTypes0: altGraphX barChart chain ctgPos expRatio factorSource gvf \ interact netAlign peptideMapping pgSnp 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 err30 \ err31 err32 err33 err34 err35 err36 err37 err38 err39 err40 \ err41 err42 err43 err44 err45 err46 err47 err48 err49 err50 notSupported: notSup01 notSup02 notSup03 notSup07 notSup10 @@ -191,30 +193,48 @@ @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="equCab3" -track="transMapEnsemblV5" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.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#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# testing /list/tracks? for a 'curated' assembly genome=hs1 trackLeavesOnly +list20: setOutput + @printf "### $@ '${SERVERNAME}/list/tracks?trackLeavesOnly=1;genome=hs1'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/tracks" -genome="hs1" -trackLeavesOnly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | 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#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + ########################## getData functions ############################# # testing /getData/track?genome=ce11&track=gold test8: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -maxItemsOutput=123 -endpoint="/getData/track" -genome="ce11" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track?genome=ce11&track=gold&chrom=chrM test9: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="ce11" -track="gold" -chrom="chrM" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track?genome=ce11&track=gold&chrom=chrI&start=1&end=1024 test10: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 @@ -390,35 +410,43 @@ # 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 # getData but with multiple tracks -multiTrack1: +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/$@.gz + @zdiff expected/$@.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 @@ -1004,43 +1032,47 @@ @zdiff expected/$@.gz testOutput/$@.gz # chrom alias on an assembly hub chrAlias05: setOutput @ printf "### $@ '${SERVERNAME}/getData/track?genome=GCF_000001735.4;track=assembly;chrom=chrPltd;hubUrl=https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/735/GCF_000001735.4/hub.txt'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/735/GCF_000001735.4/hub.txt" -genome="GCF_000001735.4" -track="assembly" -chrom="chrPltd" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # chrom alias on an assembly hub chrAlias06: setOutput @ printf "### $@ '${SERVERNAME}/getData/track?genome=GCF_000001735.4;track=assembly;chrom=Pltd;hubUrl=https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/735/GCF_000001735.4/hub.txt'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/735/GCF_000001735.4/hub.txt" -genome="GCF_000001735.4" -track="assembly" -chrom="Pltd" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/sequence? hubUrl genome=GCF_000001735.4&chrom=Pltd&start=4321&end=5647 -# Pltd chrAlias07: setOutput @ printf "### $@ '${SERVERNAME}/getData/sequence?genome=GCF_000001735.4;chrom=Pltd;start=4321;end=5678;hubUrl=https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/735/GCF_000001735.4/hub.txt'\n" @./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 -# Pltd 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 + ############################################################################## ### 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