9c835eff071e0d0439042a30012634119712bc27 hiram Thu Oct 10 11:34:10 2019 -0700 updated error testing refs #23589 diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile index 3fe6c99..06543d3 100644 --- src/hg/hubApi/tests/makefile +++ src/hg/hubApi/tests/makefile @@ -7,37 +7,41 @@ listFunctions: list01 list02 list03 list04 list05 list06 list07 list08 list09 \ list10 list11 list12 list13 list14 list15 list16 getFunctions: test8 test9 test10 test11 test12 test13 test14 \ test15 test16 test19 test21 test26 test27 test28 \ test29 test39 test40 listSchema: schema01 schema02 schema03 schema04 schema05 schema06 schema07 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 -supportedTypes: altGraphX barChart chain ctgPos expRatio factorSource gvf \ +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 + 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 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 @@ -239,30 +243,36 @@ test29: setOutput @./jsonConsumer.pl -endpoint="/getData/track" -genome="ce11" -track="cpgIslandExt" -chrom="chrV" -start=5001045 -end=5241045 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track?genome=ce4&track=gold for split table operation test39: setOutput @./jsonConsumer.pl -maxItemsOutput=123 -endpoint="/getData/track" -genome="ce4" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track?genome=ce4&track=gold for split table operation # plus jsonArrayOutput test40: setOutput @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -genome="ce4" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz +# bigDataUrl for bigGenePred track with no table, only trackDb +test41: setOutput + @printf "### $@ ### 'https://apibeta.soe.ucsc.edu/getData/track?track=mane;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg38 -track=mane -maxItemsOutput=5 -jsonOutputArrays | egrep -v "${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 "### $@ " @./jsonConsumer.pl -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -chrom="chrCp" -start=4321 -end=5678 | egrep -v "${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 "### $@ " @./jsonConsumer.pl -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -chrom="chrM" -start=4321 -end=5678 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz @@ -555,34 +565,71 @@ @htmlCheck getAll 'https://api-test.gi.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;chrom=chr1;start=4567;end=8901;track=assembly;maxItemsOutput=5;jsonOutputArrays=1;maxItemsOutput=0' 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing illegal values on parameters err38: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;chrom=chr1;start=4567;end=8901;track=assembly;maxItemsOutput=5;jsonOutputArrays=xyz'\n" @htmlCheck getAll 'https://api-test.gi.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;chrom=chr1;start=4567;end=8901;track=assembly;maxItemsOutput=5;jsonOutputArrays=xyz' 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing protected track data err39: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=cosmicRegions;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=cosmicRegions -maxItemsOutput=5 -jsonOutputArrays 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# bigDataUrl for bigGenePred track with no table, only trackDb +# testing protected track data err40: setOutput - @printf "### $@ ### 'https://apibeta.soe.ucsc.edu/getData/track?track=mane;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n" - @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg38 -track=mane -maxItemsOutput=5 -jsonOutputArrays 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz + @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=decipherRaw;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=decipherRaw -maxItemsOutput=5 -jsonOutputArrays 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + + +# testing protected track data +err41: setOutput + @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=decipher;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=decipher -maxItemsOutput=5 -jsonOutputArrays 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# testing protected track data +err42: setOutput + @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=knownToDecipher;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=knownToDecipher -maxItemsOutput=5 -jsonOutputArrays 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# testing protected track data +err43: setOutput + @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=knownCanonToDecipher;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=knownCanonToDecipher -maxItemsOutput=5 -jsonOutputArrays 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# testing protected track data +err44: setOutput + @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=decipherSnvsRaw;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=decipherSnvsRaw -maxItemsOutput=5 -jsonOutputArrays 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# testing protected track data +err45: setOutput + @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=lovd;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=lovd -maxItemsOutput=5 -jsonOutputArrays 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# testing protected track data +err46: setOutput + @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=hgmd;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=hgmd -maxItemsOutput=5 -jsonOutputArrays 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz ##################### wiggle data ########################################### # classic wiggle with wig table and wib file wig01: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5Base;genome=ce4;maxItemsOutput=5'\n" @./jsonConsumer.pl -endpoint="/getData/track" -genome=ce4 -track=gc5Base -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # classic wiggle with wig table and wib file with chrom specified wig02: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5Base;genome=ce4;chrom=chrIV;maxItemsOutput=5'\n" @./jsonConsumer.pl -endpoint="/getData/track" -genome=ce4 -track=gc5Base -chrom=chrIV -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz