8c01fb3679ac642e37aaaea705a5365e41f6f013 mspeir Thu Nov 13 15:52:59 2025 -0800 updates to hubApi makefile and expected outputs, refs #36463 diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile index 7d318880c4c..7971a25abeb 100644 --- src/hg/hubApi/tests/makefile +++ src/hg/hubApi/tests/makefile @@ -21,31 +21,31 @@ 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 \ - list20 list21 list22 list23 list24 list25 list26 list27 list28 list29 \ + 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 \ test48 test49 test50 test51 test52 test53 test54 test55 test56 test57 \ 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 @@ -61,41 +61,41 @@ supportedTypes: altGraphX barChart chain ctgPos expRatio \ interact netAlign peptideMapping pgSnp bigDbSnp bigMaf bigChain 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 \ err51 err52 err53 notSupported: notSup01 notSup02 notSup03 notSup07 notSup10 -bugReports: redmine23733 redmine24089a redmine24089b redmine24666 redmine25840 +bugReports: redmine24089a redmine24089b redmine24666 redmine25840 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 +excludeLines = downloadTime|dataTime|priority # testing /list/noSubCommand, /list/publicHubs and /list/ucscGenomes test0: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -test0 2>&1 | sed -e 's#https://.*/list#/list#;' | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz @echo '### test0: ./jsonConsumer.pl -serverName="${SERVERNAME}" -test0 - OK' ################################################### list functions ########### # testing /list/hubGenomes list01: setOutput @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 @@ -206,34 +206,34 @@ @./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 -# testing /list/tracks? for a 'curated' assembly genome=hs1 trackLeavesOnly +# testing /list/tracks? for a 'curated' assembly genome=mpxvRivers 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#; s#/hubs/.*/hub#/hubs/hub#;' | gzip -c > testOutput/$@.gz + @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 @printf "### $@ '${SERVERNAME}/list/files?genome=ce2'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/files" -genome="ce2" 2>&1 | egrep -v "${excludeLines}" | egrep -v "dateTime" | sed -e 's#https://.*/list#/list#; s#/hubs/.*/hub#/hubs/hub#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/files?genome=GCA_021951015.1 @@ -243,34 +243,34 @@ @zdiff expected/$@.gz testOutput/$@.gz # testing /list/files?genome=ce2;maxItemsOutput=5 list24: setOutput @printf "### $@ '${SERVERNAME}/list/files?genome=ce2;maxItemsOutput=5'\n" @./jsonConsumer.pl -maxItemsOutput=5 -serverName="${SERVERNAME}" -endpoint="/list/files" -genome="ce2" 2>&1 | egrep -v "${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;maxItemsOutput=5;format=text list25: setOutput @printf "### $@ '${SERVERNAME}/list/files?genome=ce2;maxItemsOutput=5;format=text'\n" @ 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 +#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 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/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/tracks?genome=GCA_021951015.1 with hubUrl list29: setOutput @@ -317,41 +317,41 @@ @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -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/track? hubUrl Plants &track=gold&chrom=chrM assembly hub test12: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -track="assembly" -chrom="chrCp" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl Plants &track=gold&chrom=chrI&start=1&end=1024 assembly hub test13: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -track="assembly" -chrom="chrCp" -start=1 -end=1024 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl Bejerano &track=ultraConserved track hub test14: setOutput - @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -track="ultraConserved" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -track="hub_9604_ultraConserved" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl Bejerano &track=ultraConserved&chrom=chr1 track hub test15: setOutput - @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -track="ultraConserved" -chrom="chr1" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -track="hub_9604_ultraConserved" -chrom="chr1" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl Bejerano &track=ultraConserved&chrom=chr1&start=N&end=M track hub test16: setOutput - @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -track="ultraConserved" -chrom="chr1" -start=10600000 -end=10800000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -track="hub_9604_ultraConserved" -chrom="chr1" -start=10600000 -end=10800000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # bigBed data from a database # /getData/track? genome=galGal6 &track=ncbiRefSeqOther&chrom=chr1&start=750000&end=5700000 test19: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="galGal6" -track="ncbiRefSeqOther" -chrom="chr1" -start=750000 -end=55700000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # wiggle data from a database where the SQL table name is different than the # track name # /getData/track? genome=hg19 &track=wgEncodeRegMarkH3k4me1H1hesc&chrom=chr1&start=62300000&end=62301000 test21: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg19" -track="wgEncodeRegMarkH3k4me1H1hesc" -chrom="chr1" -start=62300000 -end=62301000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz @@ -1364,34 +1364,34 @@ @printf "### $@ '${SERVERNAME}/getData/track?track=hapmapLdPhCeu;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg19" -track="hapmapLdPhCeu" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # 34 bam - not supported</li> # 2 bigBarChart - not supported</li> # 3 bigInteract - not supported</li> # 18 bigMaf - not supported</li> # 152 composite container - not supported</li> # 93 composite view - not supported</li> # 37 halSnake - not supported</li> # 31 superTrack child - not supported</li> # 5 vcfTabix - not supported</li> -redmine23733: setOutput - @printf "### $@ '${SERVERNAME}/getData/track?track=knownGene;genome=hg19;chrom=chr1;end=48000;start=47000'\n" - @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=knownGene -chrom=chr1 -start=47000 -end=48000 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | grep -v "^#" | sort | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz +#redmine23733: setOutput +# @printf "### $@ '${SERVERNAME}/getData/track?track=knownGene;genome=hg19;chrom=chr1;end=48000;start=47000'\n" +# @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=knownGene -chrom=chr1 -start=47000 -end=48000 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | grep -v "^#" | sort | gzip -c > testOutput/$@.gz +# @zdiff expected/$@.gz testOutput/$@.gz # end coordinate for get sequence past end of chromosome, database genome redmine24089a: setOutput @printf "### $@ '${SERVERNAME}/getData/sequence?genome=hg19;chrom=chrM;start=16560;end=16572'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/sequence" -genome=hg19 -chrom=chrM -start=16560 -end=16572 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # end coordinate for get sequence past end of chromosome, asmHub genome redmine24089b: setOutput @printf "### $@ '${SERVERNAME}/getData/sequence?genome=araTha1;chrom=chrCp;start=154470;end=154479;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -chrom="chrCp" -start=154470 -end=154479 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # full chromosome fetch from a NIB based genom redmine24666: setOutput