1fa309a4080795a05783d3255631e8991eb18e04 hiram Wed Jun 12 15:14:52 2024 -0700 correct bigChain example refs #24430 diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile index fedba6f..7fda9fe 100644 --- src/hg/hubApi/tests/makefile +++ src/hg/hubApi/tests/makefile @@ -1243,37 +1243,39 @@ @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 +# https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?genome=hg38;track=chainSynGCA_011100615.1;maxItemsOutput=5 + 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 + @printf "### $@ '${SERVERNAME}/list/chromosomes?track=chainSynGCA_011100615.1;genome=hg38'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg38" -track="chainSynGCA_011100615.1" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz + @printf "### $@ '${SERVERNAME}/getData/track?track=chainSynGCA_011100615.1;chrom=chr1;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg38" -track="chainSynGCA_011100615.1" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c >> testOutput/$@.gz + @printf "### $@ '${SERVERNAME}/list/schema?track=chainSynGCA_011100615.1;genome=hg38'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/schema" -genome="hg38" -track="chainSynGCA_011100615.1" 2>&1 | egrep -v "${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"