2561e20e2d24e53c562c67c64adc01e19a44f7cb hiram Wed Jun 12 15:00:00 2024 -0700 adding tests for bigDbSnp bigMaf and bigChain refs #24430 diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile index 2e9c3f8..fedba6f 100644 --- src/hg/hubApi/tests/makefile +++ src/hg/hubApi/tests/makefile @@ -29,46 +29,48 @@ 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 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 +findGenome: findGenome01 + 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 chrAlias10 chrAlias11 supportedTypes: altGraphX barChart chain ctgPos expRatio \ - interact netAlign peptideMapping pgSnp + 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 @@ -488,30 +490,43 @@ getSeq03: setOutput @printf "### $@ " @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/sequence" -genome="monDom5" -chrom="chr1" -start=748055061 -end=748055161 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/sequence?genome=ce11&chrom=chrM getSeq04: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/sequence" -genome="ce11" -chrom="chrM" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/sequence?genome=ce11&chrom=chrM&start=1&end=128 getSeq05: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/sequence" -genome="ce11" -chrom="chrM" -start=1 -end=128 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz + +############################################################################### +# /findGenome testing +############################################################################### +# simple findGenome test +findGenome01: setOutput + @printf "### $@ ### '${SERVERNAME}/cgi-bin/hubApi/findGenome?genomeSearch=hg38'\n" + @curl -L "${SERVERNAME}/cgi-bin/hubApi/findGenome?genomeSearch=hg38" 2> /dev/null | python -mjson.tool | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# @ curl -L "${SERVERNAME}/search?search=brca;genome=hg38" 2> /dev/null | python -mjson.tool | egrep -c -n "\[|\]" | awk -v t="$@" '{if (($$1 < 30) || ($$1 > 50)) {printf "test %s failed, count %d not in range 30-40\n", t, $$1; exit 255;}}' +# | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + ############################################################################### # /list/schema testing ############################################################################### # testing /list/schema? genome=monDom5&track=gold schema01: setOutput @printf "### $@ '${SERVERNAME}/list/schema?track=gold;genome=monDom5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/schema" -genome="monDom5" -track=gold | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/schema? genome=hg19&track=ctgPos schema02: setOutput @printf "### $@ '${SERVERNAME}/list/schema?track=ctgPos;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/schema" -genome="hg19" -track=ctgPos | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz @@ -1210,30 +1225,58 @@ peptideMapping: setOutput @printf "### $@ '${SERVERNAME}/list/chromosomes?track=wgEncodeUncBsuProtGm12878MembranefractionSig;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg19" -track="wgEncodeUncBsuProtGm12878MembranefractionSig" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @printf "### $@ '${SERVERNAME}/getData/track?track=wgEncodeUncBsuProtGm12878MembranefractionSig;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg19" -track="wgEncodeUncBsuProtGm12878MembranefractionSig" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz pgSnp: setOutput @printf "### $@ '${SERVERNAME}/list/chromosomes?track=pgKb1454;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg19" -track="pgKb1454" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @printf "### $@ '${SERVERNAME}/getData/track?track=pgKb1454;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg19" -track="pgKb1454" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz +bigDbSnp: setOutput + @printf "### $@ '${SERVERNAME}/list/chromosomes?track=dbSnp153Mult;genome=hg38'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg38" -track="dbSnp153Mult" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz + @printf "### $@ '${SERVERNAME}/getData/track?track=dbSnp153Mult;chrom=chr1;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg38" -track="dbSnp153Mult" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz + @printf "### $@ '${SERVERNAME}/list/schema?track=dbSnp153Mult;genome=hg38'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/schema" -genome="hg38" -track="dbSnp153Mult" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +bigMaf: setOutput + @printf "### $@ '${SERVERNAME}/list/chromosomes?track=rbestNetHs1;genome=hg38'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg38" -track="rbestNetHs1" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz + @printf "### $@ '${SERVERNAME}/getData/track?track=rbestNetHs1;chrom=chr1;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg38" -track="rbestNetHs1" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz + @printf "### $@ '${SERVERNAME}/list/schema?track=rbestNetHs1;genome=hg38'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/schema" -genome="hg38" -track="rbestNetHs1" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +bigChain: setOutput + @printf "### $@ '${SERVERNAME}/list/chromosomes?track=netHprcGCA_018503285v1;genome=hg38'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg38" -track="netHprcGCA_018503285v1" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz + @printf "### $@ '${SERVERNAME}/getData/track?track=netHprcGCA_018503285v1;chrom=chr1;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg38" -track="netHprcGCA_018503285v1" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz + @printf "### $@ '${SERVERNAME}/list/schema?track=netHprcGCA_018503285v1;genome=hg38'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/schema" -genome="hg38" -track="netHprcGCA_018503285v1" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + + ############################################################################## ### notSupported ############################################################################## # request a track type that is not yet supported: bam notSup01: setOutput @printf "### $@ '${SERVERNAME}/cgi-bin/hubApi/getData/track?track=shMethylSubtrack;chrom=chr1;genome=hg19;hubUrl=http://lasallelab.genomecenter.ucdavis.edu/UCSChub/hub.txt;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://lasallelab.genomecenter.ucdavis.edu/UCSChub/hub.txt" -genome="hg19" -track="shMethylSubtrack" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # request a track type that is not yet supported: vcfTabix notSup02: setOutput @printf "### $@ '${SERVERNAME}/cgi-bin/hubApi/getData/track?track=gnomadGenomesVariantsV3;chrom=chr21;start=5033429;end=5033498;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg38" -track="gnomadGenomesVariantsV3" -chrom="chr21" -start="5033429" -end="5033498" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz