7c28bed1b8d3dd630b67d92a4a784eab1d56c0ea hiram Thu Sep 5 16:34:12 2019 -0700 also check end coordinate vs chromSize for hub genome 2bit sequence getData refs #24089 diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile index 0a2dcc4..5727567 100644 --- src/hg/hubApi/tests/makefile +++ src/hg/hubApi/tests/makefile @@ -1,48 +1,48 @@ test:: all all:: test0 listFunctions getFunctions listSchema getSequence wigData \ supportedTypes errorTests notSupported bugReports listFunctions: list01 list02 list03 list04 list05 list06 list07 list08 list09 \ list10 list11 list12 list13 list14 list15 -getFunctions: test6 test7 test8 test9 test10 test11 test12 test13 test14 \ +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 +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 \ 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 notSupported: notSup01 notSup02 notSup03 notSup04 notSup05 notSup06 \ notSup07 notSup08 notSup09 notSup10 -bugReports: redmine23733 +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 @./jsonConsumer.pl -test0 2>&1 | sed -e 's#https://.*/list#/list#;' | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz @@ -131,40 +131,30 @@ # testing /list/chromosomes?genome=ce11&track=est different chrom name column list14: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/list/chromosomes?track=est;genome=ce11'\n" @./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="ce11" -track="est" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes?genome=ce4&track=est different chrom name column # and ce4 has split tables list15: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/list/chromosomes?track=est;genome=ce4'\n" @./jsonConsumer.pl -endpoint="/list/chromosomes" -genome="ce4" -track="est" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz ########################## getData functions ############################# -# testing /getData/sequence?genome=ce11&chrom=chrM -test6: setOutput - @./jsonConsumer.pl -endpoint="/getData/sequence" -genome="ce11" -chrom="chrM" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz - -# testing /getData/sequence?genome=ce11&chrom=chrM&start=1&end=128 -test7: setOutput - @./jsonConsumer.pl -endpoint="/getData/sequence" -genome="ce11" -chrom="chrM" -start=1 -end=128 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz - # testing /getData/track?genome=ce11&track=gold test8: setOutput @./jsonConsumer.pl -maxItemsOutput=123 -endpoint="/getData/track" -genome="ce11" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track?genome=ce11&track=gold&chrom=chrM test9: setOutput @./jsonConsumer.pl -endpoint="/getData/track" -genome="ce11" -track="gold" -chrom="chrM" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track?genome=ce11&track=gold&chrom=chrI&start=1&end=1024 test10: setOutput @./jsonConsumer.pl -endpoint="/getData/track" -genome="ce11" -track="gold" -chrom="chrI" -start=1 -end=1024 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz @@ -255,30 +245,40 @@ @./jsonConsumer.pl -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -chrom="chrCp" -start=4321 -end=5678 | egrep -v "${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 # testing /getData/sequence? genome=monDom5&chrom=chr1&start=4321&end=5647 getSeq03: setOutput @printf "### $@ " @./jsonConsumer.pl -endpoint="/getData/sequence" -genome="monDom5" -chrom="chr1" -start=748055061 -end=748055161 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz +# testing /getData/sequence?genome=ce11&chrom=chrM +getSeq04: setOutput + @./jsonConsumer.pl -endpoint="/getData/sequence" -genome="ce11" -chrom="chrM" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# testing /getData/sequence?genome=ce11&chrom=chrM&start=1&end=128 +getSeq05: setOutput + @./jsonConsumer.pl -endpoint="/getData/sequence" -genome="ce11" -chrom="chrM" -start=1 -end=128 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + ############################################################################### # /list/schema testing ############################################################################### # testing /list/schema? genome=monDom5&track=gold schema01: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/schema?track=gold;genome=monDom5'\n" @./jsonConsumer.pl -endpoint="/list/schema" -genome="monDom5" -track=gold | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/schema? genome=hg19&track=ctgPos schema02: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/schema?track=ctgPos;genome=hg19'\n" @./jsonConsumer.pl -endpoint="/list/schema" -genome="hg19" -track=ctgPos | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz @@ -868,30 +868,42 @@ # 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 "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=knownGene;genome=hg38;chrom=chr1;end=48000;start=47000'\n" @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg38 -track=knownGene -chrom=chr1 -start=47000 -end=48000 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz +# end coordinate for get sequence past end of chromosome, database genome +redmine24089a: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/sequence?genome=hg19;chrom=chrM;start=16560;end=16572'\n" + @./jsonConsumer.pl -endpoint="/getData/sequence" -genome=hg19 -chrom=chrM -start=16560 -end=16572 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${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 "### $@ 'https://api-test.gi.ucsc.edu/getData/sequence?genome=araTha1;chrom=chrCp;start=154470;end=154479;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" + @./jsonConsumer.pl -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -chrom="chrCp" -start=154470 -end=154479 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + # track types found in hg19 and hg38 trackDb 'type' column: # 4586 narrowPeak # 4472 bigWig # 3294 bed # 1745 broadPeak # 872 chain # 871 netAlign # 596 bam # 512 genePred # 438 bigBed # 368 pgSnp # 348 bedGraph # 286 wig # 106 psl # 46