360e462570bd06a078eaea70efdc84d5498db76a hiram Fri Oct 11 15:24:42 2019 -0700 eliminate tests for not supported as they are now supported refs #23589 diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile index 656dc24..ae42994 100644 --- src/hg/hubApi/tests/makefile +++ src/hg/hubApi/tests/makefile @@ -21,32 +21,31 @@ wig11 wig12 wig13 wig14 wig15 wig16 wig17 wig18 wig19 wig20 \ wig21 wig22 wig23 wig24 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 -notSupported: notSup01 notSup02 notSup03 notSup04 notSup05 notSup06 \ - notSup07 notSup08 notSup09 notSup10 +notSupported: notSup01 notSup02 notSup03 notSup07 notSup10 bugReports: redmine23733 redmine24089a redmine24089b 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 # testing /list/noSubCommand, /list/publicHubs and /list/ucscGenomes test0: setOutput @@ -1005,66 +1004,36 @@ @./jsonConsumer.pl -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 "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=variants;chrom=chr1;genome=danRer11;hubUrl=http://research.nhgri.nih.gov/manuscripts/Burgess/zebrafish/downloads/NHGRI-1/hub.txt;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://research.nhgri.nih.gov/manuscripts/Burgess/zebrafish/downloads/NHGRI-1/hub.txt" -genome="danRer11" -track="variants" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${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: ld2 notSup03: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=hapmapLdPhCeu;genome=hg19'\n" @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track="hapmapLdPhCeu" 2>&1 | egrep -v "${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: bigBarChart -notSup04: setOutput - @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=gtexTranscExpr;genome=hg38'\n" - @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg38 -track="gtexTranscExpr" 2>&1 | egrep -v "${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: bigLolly -notSup05: setOutput - @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=allCancer;genome=hg38'\n" - @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg38 -track="allCancer" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz - -# request a track type that is a container, not a data track -notSup06: setOutput - @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=gdcCancer;genome=hg38'\n" - @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg38 -track="gdcCancer" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz - # request chromosome list from a track that is a container, not a data track notSup07: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=gdcCancer;genome=hg38'\n" @./jsonConsumer.pl -endpoint="/list/chromosomes" -genome=hg38 -track="gdcCancer" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# request chromosome list from a track that is a container, not a data track -notSup08: setOutput - @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=allCancer;genome=hg38'\n" - @./jsonConsumer.pl -endpoint="/list/chromosomes" -genome=hg38 -track="allCancer" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz - -# clonePos does not have an 'as' definiton in tableDescriptions -notSup09: setOutput - @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=clonePos;genome=hg19'\n" - @./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="hg19" -track="clonePos" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz - # hapmapLdPhCeu does not have an 'as' definiton in tableDescriptions notSup10: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=hapmapLdPhCeu;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -endpoint="/getData/track" -genome="hg19" -track="hapmapLdPhCeu" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${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>