cdb81647deb6096ff29d18a21b4f9e83f45b4ac9 chmalee Tue Mar 7 14:38:53 2023 -0800 Fix bug where hubApi was allowing ranged requests for tracks with 'tableBrowser off' setting in trackDb. Fix cartTrackDbIsAccessDenied function to recognize correctly when 'tableBrowser off' setting is present on the same host as the CGI is running. Add tests to hubApi system to check more 'tableBrowser' settings and check getting data from more than one track at once diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile index 5d97940..86ec2b4 100644 --- src/hg/hubApi/tests/makefile +++ src/hg/hubApi/tests/makefile @@ -1,1131 +1,1151 @@ # If SERVERNAME is defined in the environment use it, else use api-test SERVERNAME ?= https://api-test.gi.ucsc.edu 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 list16 list17 list18 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 + test48 test49 test50 test51 test52 test53 test54 test55 test56 test57 \ + multiTrack1 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 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 err47 + err41 err42 err43 err44 err45 err46 err47 err48 err49 notSupported: notSup01 notSup02 notSup03 notSup07 notSup10 bugReports: redmine23733 redmine24089a redmine24089b redmine24666 redmine25840 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 -serverName="${SERVERNAME}" -test0 2>&1 | sed -e 's#https://.*/list#/list#;' | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz @echo '### test0: ./jsonConsumer.pl -serverName="${SERVERNAME}" -test0 - OK' ################################################### list functions ########### # testing /list/hubGenomes list01: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/list/hubGenomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -endpoint="/list/hubGenomes" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/tracks? hubUrl genome=araTha1 trackLeavesOnly list02: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/list/tracks?trackLeavesOnly=1;genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -endpoint="/list/tracks" -genome="araTha1" -trackLeavesOnly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/tracks?genome=ce11 trackLeavesOnly=1 # the grep " : {" will pick out just the track names to compare, so that # the changing genbank tables do not mess up the comparison, this will only # be comparing the track listing. The other egrep -v removes table names that # only exist on hgwdev so this test will work on public site list03: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/list/tracks?trackLeavesOnly=1;genome=ce11'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/tracks" -genome="ce11" -trackLeavesOnly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | grep " : {" | egrep -v "chainStrRat1|microsat|netStrRat1|tandemDups" | sort | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes?genome=ce11 list04: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/list/chromosomes?genome=ce11'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="ce11" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes?genome=ce11&track=gold list05: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/list/chromosomes?track=gold;genome=ce11'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="ce11" -track="gold" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes? hubUrl genome=araTha1 list06: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/list/chromosomes?genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes? hubUrl genome=araTha1 track=assembly list07: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/list/chromosomes?track=assembly;genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -track="assembly" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/tracks? hubUrl genome=araTha1 list08: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/list/tracks?genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -endpoint="/list/tracks" -genome="araTha1" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/tracks?genome=ce11 # the grep " : {" will pick out just the track names to compare, so that # the changing genbank tables do not mess up the comparison, this will only # be comparing the track listing list09: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/list/tracks?genome=ce11'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/tracks" -genome="ce11" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | grep " : {" | egrep -v "chainStrRat1|netStrRat1|tandemDups|microsat|tanDups" | sort | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes?genome=ce11&track=mrna SQL table name is all_mrna list10: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/list/chromosomes?track=mrna;genome=ce11'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="ce11" -track="mrna" 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=mrna SQL table name is all_mrna # and ce4 has split tables list11: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/list/chromosomes?track=mrna;genome=ce4'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="ce4" -track="mrna" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes?genome=ce11&track=rmsk different chrom name column list12: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/list/chromosomes?track=rmsk;genome=ce11'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="ce11" -track="rmsk" 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=rmsk different chrom name column # and ce4 has split tables list13: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/list/chromosomes?track=rmsk;genome=ce4'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="ce4" -track="rmsk" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes?genome=ce11&track=est different chrom name column list14: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/list/chromosomes?track=est;genome=ce11'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/list/chromosomes?track=est;genome=ce4'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 # list chromosomes for a track that only has a bigDataUrl specification, # no database table # testing /list/chromosomes?genome=equCab3&track=transMapEnsemblV5 list16: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/list/chromosomes?track=transMapEnsemblV5;genome=equCab3'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="equCab3" -track="transMapEnsemblV5" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # list chromosomes for a bigWig track=gc5BaseBw genome=rheMac10 list17: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/list/chromosomes?track=gc5BaseBw;genome=rheMac10'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="rheMac10" -track="gc5BaseBw" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # list chromosomes for a wigMaf table track=multiz7way genome=hg38 list18: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/list/chromosomes?track=multiz7way;genome=hg38'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg38" -track="multiz7way" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz ########################## getData functions ############################# # testing /getData/track?genome=ce11&track=gold test8: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -maxItemsOutput=123 -endpoint="/getData/track" -genome="ce11" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track?genome=ce11&track=gold&chrom=chrM test9: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="ce11" -track="gold" -chrom="chrI" -start=1 -end=1024 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl Plants &track=gold assembly hub test11: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -track="assembly" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl Plants &track=gold&chrom=chrM assembly hub test12: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -track="assembly" -chrom="chrCp" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl Plants &track=gold&chrom=chrI&start=1&end=1024 assembly hub test13: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -track="assembly" -chrom="chrCp" -start=1 -end=1024 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl Bejerano &track=ultraConserved track hub test14: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -track="ultraConserved" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl Bejerano &track=ultraConserved&chrom=chr1 track hub test15: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -track="ultraConserved" -chrom="chr1" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl Bejerano &track=ultraConserved&chrom=chr1&start=N&end=M track hub test16: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -track="ultraConserved" -chrom="chr1" -start=10600000 -end=10800000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # bigBed data from a database # /getData/track? genome=galGal6 &track=ncbiRefSeqOther&chrom=chr1&start=750000&end=5700000 test19: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="galGal6" -track="ncbiRefSeqOther" -chrom="chr1" -start=750000 -end=55700000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # wiggle data from a database where the SQL table name is different than the # track name # /getData/track? genome=hg19 &track=wgEncodeRegMarkH3k4me1H1hesc&chrom=chr1&start=62300000&end=62301000 test21: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg19" -track="wgEncodeRegMarkH3k4me1H1hesc" -chrom="chr1" -start=62300000 -end=62301000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing genePred track # /getData/track?genome=ce11&chrom=chrV&track=augustusGene&start=5231045&end=5241045 test26: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="ce11" -track="augustusGene" -chrom="chrV" -start=5231045 -end=5241045 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing PSL track # /getData/track?genome=ce11&chrom=chrV&track=ncbiRefSeqPsl&start=5231045&end=5241045 test27: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="ce11" -track="ncbiRefSeqPsl" -chrom="chrV" -start=5231045 -end=5241045 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing RMSK track # /getData/track?genome=ce11&debug=0&chrom=chrV&track=rmsk&start=5231045&end=5241045 test28: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="ce11" -track="rmsk" -chrom="chrV" -start=5231045 -end=5241045 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # test superTrack child getData # /getData/track?genome=ce11&chrom=chrV&track=cpgIslandExt&start=5001045&end=5241045 test29: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="ce11" -track="cpgIslandExt" -chrom="chrV" -start=5001045 -end=5241045 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track?genome=ce4&track=gold for split table operation test39: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 -serverName="${SERVERNAME}" -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -genome="ce4" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # bigDataUrl for bigGenePred track with no table, only trackDb test41: setOutput @printf "### $@ ### 'https://apibeta.soe.ucsc.edu/getData/track?track=mane;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg38 -track=mane -maxItemsOutput=5 -jsonOutputArrays | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from wigMaf database table test42: setOutput @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=multiz7way;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg38 -track=multiz7way -maxItemsOutput=5 -jsonOutputArrays | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from wigMaf database table with chrom specified test43: setOutput @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=multiz7way;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5;chrom=chr22'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg38 -track=multiz7way -maxItemsOutput=5 -jsonOutputArrays -chrom=chr22 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from wigMaf database table with chrom and start,end specified test44: setOutput @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=multiz7way;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5;chrom=chr21;start=20000000;end=30000000'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg38 -track=multiz7way -maxItemsOutput=5 -jsonOutputArrays -chrom=chr21 -start=20000000 -end=30000000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from bigLolly track test45: setOutput @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=BLCA;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg38 -track=BLCA -maxItemsOutput=5 -jsonOutputArrays | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from bigLolly track with chrom specified test46: setOutput @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=BLCA;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5;chrom=chr22'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg38 -track=BLCA -maxItemsOutput=5 -jsonOutputArrays -chrom=chr22 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from bigLolly track with chrom and start,end specified test47: setOutput @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=BLCA;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5;chrom=chr21;start=20000000;end=30000000'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg38 -track=BLCA -maxItemsOutput=5 -jsonOutputArrays -chrom=chr21 -start=20000000 -end=30000000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from bigBarChart track test48: setOutput @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=gtexTranscExpr;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=gtexTranscExpr -maxItemsOutput=5 -jsonOutputArrays | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from bigBarChart track with chrom specified test49: setOutput @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=gtexTranscExpr;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5;chrom=chr22'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=gtexTranscExpr -maxItemsOutput=5 -jsonOutputArrays -chrom=chr22 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from bigBarChart track with chrom and start,end specified test50: setOutput @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=gtexTranscExpr;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5;chrom=chr21;start=20000000;end=30000000'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=gtexTranscExpr -maxItemsOutput=5 -jsonOutputArrays -chrom=chr21 -start=20000000 -end=30000000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from bigInteract track test51: setOutput @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=geneHancerInteractions;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=geneHancerInteractions -maxItemsOutput=5 -jsonOutputArrays | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from bigInteract track with chrom specified test52: setOutput @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=geneHancerInteractions;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5;chrom=chr22'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=geneHancerInteractions -maxItemsOutput=5 -jsonOutputArrays -chrom=chr22 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from bigInteract track with chrom and start,end specified test53: setOutput @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=geneHancerInteractions;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5;chrom=chr21;start=20000000;end=30000000'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=geneHancerInteractions -maxItemsOutput=5 -jsonOutputArrays -chrom=chr21 -start=20000000 -end=30000000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from clonePos track test54: setOutput @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=clonePos;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=clonePos -maxItemsOutput=5 -jsonOutputArrays | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from clonePos track with chrom specified test55: setOutput @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=clonePos;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5;chrom=chr22'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=clonePos -maxItemsOutput=5 -jsonOutputArrays -chrom=chr22 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from clonePos track with chrom and start,end specified test56: setOutput @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=clonePos;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5;chrom=chr21;start=20000000;end=30000000'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=clonePos -maxItemsOutput=5 -jsonOutputArrays -chrom=chr21 -start=20000000 -end=30000000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?genome=ce11;track=mrna;maxItemsOutput=5 # PSL track, no chrom specified, exercise column name tName instead of chrom test57: setOutput @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=mrna;genome=ce11;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=ce11 -track=mrna -maxItemsOutput=5 -jsonOutputArrays | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz +# getData but with multiple tracks +multiTrack1: + @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?tracks=gold,gap;genome=hg38;jsonOutputArrays=1;chrom=chr2;start=16129261;end=16163278'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg38 -track=gold,gap -jsonOutputArrays -chrom=chr2 -start=16129261 -end=16163278 | 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 "### $@ " @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 "### $@ " @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 "### $@ " @./jsonConsumer.pl -serverName="${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 ############################################################################### # /list/schema testing ############################################################################### # testing /list/schema? genome=monDom5&track=gold schema01: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/schema?track=gold;genome=monDom5'\n" @./jsonConsumer.pl -serverName="${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 "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/schema?track=ctgPos;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/schema" -genome="hg19" -track=ctgPos | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz schema03: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/schema?track=gold;genome=ce2'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/schema" -genome="ce2" -track=gold | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz schema04: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/schema?track=assembly;genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/schema" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -track=assembly | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # can list schema for tables without trackDb schema05: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/schema?track=chromAlias;genome=hg38'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/schema" -genome="hg38" -track=chromAlias | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # list schema for bigBed file via table fileName reference schema06: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/schema?track=crispr10KTargets;genome=hg38'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/schema" -genome="hg38" -track=crispr10KTargets | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # list schema for bigWig file with table and bigWig file schema07: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/schema?track=gc5BaseBw;genome=ce11'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/schema" -genome="ce11" -track=gc5BaseBw | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # list schema for wigMaf table type schema08: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/list/schema?track=multiz7way;genome=hg38'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/schema" -genome="hg38" -track=multiz7way | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # list schema for bigLolly table type schema09: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/list/schema?track=BLCA;genome=hg38'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/schema" -genome="hg38" -track=BLCA | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # list schema for bigBarChart table type schema10: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/list/schema?track=gtexTranscExpr;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/schema" -genome="hg19" -track=gtexTranscExpr | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # list schema for bigInteract table type schema11: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/list/schema?track=geneHancerInteractions;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/schema" -genome="hg19" -track=geneHancerInteractions | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # list schema for clonePos table type schema12: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/list/schema?track=clonePos;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/schema" -genome="hg19" -track=clonePos | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz ############################################################################### # ERROR testing ############################################################################### # generate an error: ask for non-existent chrom in a track hub # /getData/track? hubUrl Plants &track=assembly&chrom=chrI&start=1&end=14309681 err01: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?track=assembly;chrom=chrI;genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;end=14309681;start=1\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -track="assembly" -chrom="chrI" -start=1 -end=14309681 2>&1 | sed -e 's#https://.*/getData#/getData#;' | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # error test, can not open bigWig file err02: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?track=gc5Base;chrom=chrA9;genome=braRap1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/bPlants/hub.txt\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/bPlants/hub.txt" -genome="braRap1" -track="gc5Base" -chrom=chrA9 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # error test, can not find hubUrl err03: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?track=gc5Base;chrom=chrA9;genome=braRap1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/xPlants/hub.txt\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/xPlants/hub.txt" -genome="braRap1" -track="gc5Base" -chrom=chrA9 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # error test, missing argument genome for /getData/track with hubUrl err04: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?track=gc5Base;chrom=chrA9;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -track="gc5Base" -chrom=chrA9 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # error test, missing argument genome for /getData/sequence with hubUrl err05: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/sequence?chrom=chrA9;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -chrom=chrA9 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # error test, missing argument genome for /list/tracks with hubUrl err06: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/list/tracks?trackLeavesOnly=1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -endpoint="/list/tracks" -trackLeavesOnly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # error test, missing argument hubUrl for /list/tracks err07: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/list/tracks?trackLeavesOnly=1;genome=araTha1\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -genome="araTha1" -endpoint="/list/tracks" -trackLeavesOnly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # error test, missing argument hubUrl and genome for /list/tracks err08: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/list/tracks?trackLeavesOnly=1\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/tracks" -trackLeavesOnly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/sequence?genome=cxe6 - error test illegal database name # plus jsonArrayOutput err09: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/sequence?genome=cxe6;jsonOutputArrays=1;maxItemsOutput=123\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/sequence" -genome="cxe6" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/tracks?genome=cxe6 - error test illegal database name # plus jsonArrayOutput err10: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/list/tracks?genome=cxe6;jsonOutputArrays=1;maxItemsOutput=123\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -jsonOutputArrays -maxItemsOutput=123 -endpoint="/list/tracks" -genome="cxe6" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track?genome=ce6 - error test illegal maxItemsOutput err11: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?genome=ce6;track=gold;maxItemsOutput=1x23\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -maxItemsOutput=1x23 -endpoint="/getData/track" -genome="ce6" -track=gold 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track?genome=ce6 - error test illegal maxItemsOutput err12: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?genome=ce6;track=gold;maxItemsOutput=-2\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -maxItemsOutput=-2 -endpoint="/getData/track" -genome="ce6" -track=gold 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track?genome=ce6 - error test illegal maxItemsOutput err13: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?genome=ce6;track=gold;maxItemsOutput=0\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -maxItemsOutput=0 -endpoint="/getData/track" -genome="ce6" -track=gold 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track?genome=ce6 - error test illegal maxItemsOutput err14: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/track?genome=ce6;track=gold;maxItemsOutput=0\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -maxItemsOutput=0 -endpoint="/getData/track" -genome="ce6" -track=gold 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/tracks?genome=ce6 - error test no such function on endpoint err15: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/getData/tracks?genome=ce6;track=gold\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/tracks" -genome="ce6" -track=gold 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/endpoints - error test no such function err16: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/list/endpoints\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/endpoints" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/hubGenomes with hubUrl but no genome specified err17: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/list/hubGenomes?genome=araTha1'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/tracks" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" 2>&1 | sed -e 's#https://.*/list#/list#;' | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes? hubUrl missing genome= err18: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes? hubUrl missing incorrect genome=araTha err19: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome=araTha 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes? hubUrl can not # find specified track for genome=braRap1 track=assembly (wrong name) err20: setOutput @printf "### $@ https://hgwdev-api.gi.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/bPlants/hub.txt;genome=braRap1;track=assemblx\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/bPlants/hub.txt" -genome=braRap1 -track=assemblx 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes? hubUrl can not # find specified database in track hub err21: setOutput @printf "### $@ 'https://apibeta.soe.ucsc.edu/list/chromosomes?genome=hg18;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome=hg18 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes? bad hubUrl err22: setOutput @printf "### $@ http://genome-test.gi.ucsc.edu/~hiram/hubs/xGillBejerano/hub.txt\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/xGillBejerano/hub.txt" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes? genome=ce11 track=gbLoaded - not a position track err23: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/list/chromosomes?genome=ce11;track=gbLoaded'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome=ce11 -track=gbLoaded 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/hubGenomes extraneous genome=araTha1 causes error err24: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/list/hubGenomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=araTha1'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -endpoint="/list/hubGenomes" -genome=araTha1 2>&1 | sed -e 's#https://.*/list#/list#;' | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes missing hubUrl or db err25: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/list/chromosomes'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl no track specified err26: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/getData/track?genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -genome=araTha1 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl incorrect genome specified err27: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/getData/track?track=assembly;genome=axaTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -genome=axaTha1 -track=assembly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl incorrect track specified err28: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/getData/track?track=asemblx;genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -genome=araTha1 -track=assemblx 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes hubUrl bad genome name err29: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/list/chromosomes?genome=arxTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -genome=arxTha1 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing extraneous parameters on functions err30: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/list/publicHubs?hubUrl=araTha1;genome=abc'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/publicHubs" -hubUrl=araTha1 -genome=abc 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing extraneous parameters on functions err31: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/list/ucscGenomes?hubUrl=araTha1;genome=abc'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/ucscGenomes" -hubUrl=araTha1 -genome=abc 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing extraneous parameters on functions err32: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/list/hubGenomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/hubGenomes" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -genome=araTha1 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing extraneous parameters on functions err33: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/list/tracks?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;trackLeavesOnly=1;chrom=chr1'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/tracks" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -genome=araTha1 -trackLeavesOnly -chrom=chr1 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing extraneous parameters on functions err34: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;trackLeavesOnly=1;chrom=chr1'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -genome=araTha1 -trackLeavesOnly -chrom=chr1 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing extraneous parameters on functions err35: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/getData/sequence?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;trackLeavesOnly=1;chrom=chr1;start=4567;end=8901;trackLeavesOnly'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/sequence" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -genome=araTha1 -trackLeavesOnly -chrom=chr1 -start=4567 -end=8901 -trackLeavesOnly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing extraneous parameters on functions err36: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;trackLeavesOnly=1;chrom=chr1;start=4567;end=8901;trackLeavesOnly;track=assembly;maxItemsOutput=5;jsonOutputArrays=1;trackLeavesOnly=1'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -genome=araTha1 -trackLeavesOnly -chrom=chr1 -start=4567 -end=8901 -trackLeavesOnly -track=assembly -maxItemsOutput=5 -jsonOutputArrays -trackLeavesOnly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing duplicated parameters on functions err37: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;chrom=chr1;start=4567;end=8901;track=assembly;maxItemsOutput=5;jsonOutputArrays=1;maxItemsOutput=0'\n" @htmlCheck getAll 'https://api-test.gi.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;chrom=chr1;start=4567;end=8901;track=assembly;maxItemsOutput=5;jsonOutputArrays=1;maxItemsOutput=0' 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${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 "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=cosmicRegions;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 # testing protected track data err40: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=decipherRaw;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=decipher;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=knownToDecipher;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=knownCanonToDecipher;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=decipherSnvsRaw;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=lovdShort;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=lovdShort -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 "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=hgmd;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 # testing protected track data err47: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=lovdLong;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=lovdLong -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 always protected tracks, even with a range +err48: setOutput + @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?tracks=gold,gap,decipher;genome=hg38;jsonOutputArrays=1;chrom=chr2;start=16129261;end=16163278'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg38 -track=gold,gap,decipher -jsonOutputArrays -chrom=chr2 -start=16129261 -end=16163278 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# testing protected tracks that are allowed if not whole genome +err49: setOutput + @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?tracks=gold,gap,omimGene2;genome=hg38;jsonOutputArrays=1;chrom=chr2;start=16129261;end=16163278'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg38 -track=gold,gap,omimGene2 -jsonOutputArrays -chrom=chr2 -start=16129261 -end=16163278 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + ##################### wiggle data ########################################### # classic wiggle with wig table and wib file wig01: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5Base;genome=ce4;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5Base;genome=ce4;chrom=chrIV;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 # classic wiggle with wig table and wib file with chrom start,end specified wig03: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5Base;genome=ce4;chrom=chrIII;start=12345;end=45678;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=ce4 -track=gc5Base -chrom=chrIII -start=12345 -end=45678 -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # classic bigWig with table and bigWig file wig04: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5BaseBw;genome=ce11;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=ce11 -track=gc5BaseBw -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 wig05: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5BaseBw;genome=ce11;chrom=chrIV;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=ce11 -track=gc5BaseBw -chrom=chrIV -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 start,end specified wig06: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5BaseBw;genome=ce11;chrom=chrIII;start=12345;end=45678;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=ce11 -track=gc5BaseBw -chrom=chrIII -start=12345 -end=45678 -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # a bigWig track without a database table, just a bigDataUrl wig07: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gnomadGenomesMeanCoverage;genome=hg19;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=gnomadGenomesMeanCoverage -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # a bigWig track without a database table, just a bigDataUrl with chrom wig08: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gnomadGenomesMeanCoverage;genome=hg19;chrom=chr19;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=gnomadGenomesMeanCoverage -chrom=chr19 -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # a bigWig track with no database table, just a bigDataUrl with chrom,start,end wig09: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gnomadGenomesMeanCoverage;genome=hg19;chrom=chrX;start=123456;end=456789;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=gnomadGenomesMeanCoverage -chrom=chrX -start=123456 -end=456789 -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # wiggle data from a track hub bigWig file wig10: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=gc5Base;genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -track="gc5Base" -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # wiggle data from a track hub bigWig file, with chrom wig11: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=gc5Base;chrom=chrCp;genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -track="gc5Base" -chrom="chrCp" -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # wiggle data from a track hub bigWig file, with chrom, start, end wig12: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=gc5Base;chrom=chrCp;genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;end=5647;start=1234;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -track="gc5Base" -chrom="chrCp" -start=1234 -end=5647 -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 jsonArrayOutput wig13: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5Base;genome=ce4;maxItemsOutput=5;jsonOutputArrays=1'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -jsonOutputArrays -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 wig14: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5Base;genome=ce4;chrom=chrIV;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=ce4 -track=gc5Base -chrom=chrIV -jsonOutputArrays -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 start,end specified wig15: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5Base;genome=ce4;chrom=chrIII;start=12345;end=45678;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=ce4 -track=gc5Base -chrom=chrIII -start=12345 -end=45678 -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # classic bigWig with table and bigWig file wig16: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5BaseBw;genome=ce11;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=ce11 -track=gc5BaseBw -jsonOutputArrays -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 wig17: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5BaseBw;genome=ce11;chrom=chrIV;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=ce11 -track=gc5BaseBw -chrom=chrIV -jsonOutputArrays -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 start,end specified wig18: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5BaseBw;genome=ce11;chrom=chrIII;start=12345;end=45678;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=ce11 -track=gc5BaseBw -chrom=chrIII -start=12345 -end=45678 -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # a bigWig track without a database table, just a bigDataUrl wig19: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gnomadGenomesMeanCoverage;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=gnomadGenomesMeanCoverage -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # a bigWig track without a database table, just a bigDataUrl with chrom wig20: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gnomadGenomesMeanCoverage;genome=hg19;chrom=chr19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=gnomadGenomesMeanCoverage -chrom=chr19 -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # a bigWig track with no database table, just a bigDataUrl with chrom,start,end wig21: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gnomadGenomesMeanCoverage;genome=hg19;chrom=chrX;start=123456;end=456789;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=gnomadGenomesMeanCoverage -chrom=chrX -start=123456 -end=456789 -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # wiggle data from a track hub bigWig file wig22: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=gc5Base;genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -track="gc5Base" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # wiggle data from a track hub bigWig file, with chrom wig23: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=gc5Base;chrom=chrCp;genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -track="gc5Base" -chrom="chrCp" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # wiggle data from a track hub bigWig file, with chrom, start, end wig24: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=gc5Base;chrom=chrCp;genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;end=5647;start=1234;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -track="gc5Base" -chrom="chrCp" -start=1234 -end=5647 -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz ############################################################################## ### supportedTypes - test both /list/chromosomes and /getData/track ### - for each type ############################################################################## altGraphX: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=sibTxGraph;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg19" -track="sibTxGraph" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=sibTxGraph;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg19" -track="sibTxGraph" -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 barChart: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=gtexBrain;genome=hg38'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg38" -track="gtexBrain" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=gtexBrain;chrom=chr1;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg38" -track="gtexBrain" -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 chain: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=chainMelGal1;genome=hg38'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg38" -track="chainMelGal1" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=chainMelGal1;chrom=chr1;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg38" -track="chainMelGal1" -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 # clonePos does not have an 'as' definiton in tableDescriptions clonePos: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=clonePos;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg19" -track="clonePos" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=clonePos;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg19" -track="clonePos" -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 ctgPos: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=ctgPos;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg19" -track="ctgPos" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=ctgPos;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg19" -track="ctgPos" -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 expRatio: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=gnfAtlas2;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg19" -track="gnfAtlas2" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=gnfAtlas2;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg19" -track="gnfAtlas2" -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 factorSource: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=encRegTfbsClustered;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg19" -track="encRegTfbsClustered" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=encRegTfbsClustered;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg19" -track="encRegTfbsClustered" -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 gvf: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=iscaCuratedBenign;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg19" -track="iscaCuratedBenign" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=iscaCuratedBenign;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg19" -track="iscaCuratedBenign" -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 interact: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=gtexTransEqtl;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg19" -track="gtexTransEqtl" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=gtexTransEqtl;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg19" -track="gtexTransEqtl" -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 # hapmapLdPhCeu does not have an 'as' definiton in tableDescriptions ld2: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=hapmapLdPhCeu;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg19" -track="hapmapLdPhCeu" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=hapmapLdPhCeu;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 netAlign: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=netMelGal1;genome=hg38'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg38" -track="netMelGal1" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=netMelGal1;chrom=chr1;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg38" -track="netMelGal1" -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 peptideMapping: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=wgEncodeUncBsuProtGm12878MembranefractionSig;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg19" -track="wgEncodeUncBsuProtGm12878MembranefractionSig" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=wgEncodeUncBsuProtGm12878MembranefractionSig;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${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 "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=pgKb1454;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="hg19" -track="pgKb1454" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=pgKb1454;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${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 ############################################################################## ### notSupported ############################################################################## # request a track type that is not yet supported: bam notSup01: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=shMethylSubtrack;chrom=chr1;genome=hg19;hubUrl=http://lasallelab.genomecenter.ucdavis.edu/UCSChub/hub.txt;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${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 "### $@ 'https://hgwdev-api.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=gnomadGenomesVariantsV3;chrom=chr21;start=5033429;end=5033498;genome=hg38;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${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 # request a track type that is not yet supported: ld2 notSup03: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=hapmapLdPhCeu;genome=hg19'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 chromosome list from a track that is a container, not a data track notSup07: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/list/chromosomes?track=gdcCancer;genome=hg38'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 # hapmapLdPhCeu does not have an 'as' definiton in tableDescriptions notSup10: setOutput @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/getData/track?track=hapmapLdPhCeu;chrom=chr1;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 # 2 bigBarChart - not supported # 3 bigInteract - not supported # 18 bigMaf - not supported # 152 composite container - not supported # 93 composite view - not supported # 37 halSnake - not supported # 31 superTrack child - not supported # 5 vcfTabix - not supported redmine23733: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=knownGene;genome=hg19;chrom=chr1;end=48000;start=47000'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg19 -track=knownGene -chrom=chr1 -start=47000 -end=48000 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | grep -v "^#" | sort | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # end coordinate for get sequence past end of chromosome, database genome redmine24089a: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/sequence?genome=hg19;chrom=chrM;start=16560;end=16572'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 "### $@ 'https://api-test.gi.ucsc.edu/getData/sequence?genome=araTha1;chrom=chrCp;start=154470;end=154479;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -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 # full chromosome fetch from a NIB based genom redmine24666: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/sequence?genome=ci2;chrom=scaffold_8534'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/sequence" -genome=ci2 -chrom=scaffold_8534 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | grep -v "^#" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # full chromosome fetch from a NIB based genom redmine25840: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?genome=hg18;track=cnpSebat2'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="hg18" -track="cnpSebat2" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # curl -L "https://api-test.gi.ucsc.edu/getData/sequence?genome=ci2;chrom=scaffold_8534" 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.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 # 35 bigLolly # 26 wigMaf # 22 gvf # 22 chromGraph # 22 bigPsl # 21 vcfTabix # 17 expRatio # 13 bigBarChart # 12 rmsk # 12 bigInteract # 8 ld2 # 8 bedDetail # 7 peptideMapping # 6 sample # 6 altGraphX # 5 factorSource # 5 bed5FloatScore # 4 ctgPos # 2 type # 2 downloadsOnly # 2 coloredExon # 2 clonePos # 1 maf # 1 interact # 1 bigGenePred # 1 bed6FloatScore # 1 barChart # 1 bamWig