cd9835e35a7381da350289f1eb287005bfac1826 hiram Fri Mar 17 13:22:45 2023 -0700 fixup makefile to show server and allow other targets for convenient server setting refs #30457 diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile index 86ec2b4..6c025bc 100644 --- src/hg/hubApi/tests/makefile +++ src/hg/hubApi/tests/makefile @@ -1,20 +1,37 @@ # If SERVERNAME is defined in the environment use it, else use api-test -SERVERNAME ?= https://api-test.gi.ucsc.edu + +SERVERNAME ?= https://hgwdev-${USER}.gi.ucsc.edu test:: all +help:: + printf "makefile targets:\n\ +default - your sandbox hgwdev-${USER}.gi.ucsc.edu\n\ +hgwdev - a unique vhost on hgwdev: api-test.gi.ucsc.edu\n\ +alpha - genome-test.gi.ucsc.edu\n\ +beta - apibeta-soe.ucsc.edu\n" + +hgwdev:: + SERVERNAME" https://api-test.gi.ucsc.edu" make test + +alpha:: + SERVERNAME="https://genome-test.gi.ucsc.edu" make test + +beta:: + SERVERNAME="https://apibeta.soe.ucsc.edu" make test + 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 \ multiTrack1 listSchema: schema01 schema02 schema03 schema04 schema05 schema06 schema07 \ schema08 schema09 schema10 schema11 schema12 @@ -47,145 +64,145 @@ 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" + @printf "### $@ '${SERVERNAME}/cgi-bin/hubApi/list/hubGenomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" "${SERVERNAME}" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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/$@.gz # testing /getData/track?genome=ce11&track=gold&chrom=chrI&start=1&end=1024 @@ -261,135 +278,135 @@ @zdiff expected/$@.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" + @printf "### $@ ### '${SERVERNAME}/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" + @printf "### $@ ### '${SERVERNAME}/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" + @printf "### $@ ### '${SERVERNAME}/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" + @printf "### $@ ### '${SERVERNAME}/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" + @printf "### $@ ### '${SERVERNAME}/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" + @printf "### $@ ### '${SERVERNAME}/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" + @printf "### $@ ### '${SERVERNAME}/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" + @printf "### $@ ### '${SERVERNAME}/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" + @printf "### $@ ### '${SERVERNAME}/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" + @printf "### $@ ### '${SERVERNAME}/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" + @printf "### $@ ### '${SERVERNAME}/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" + @printf "### $@ ### '${SERVERNAME}/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" + @printf "### $@ ### '${SERVERNAME}/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" + @printf "### $@ ### '${SERVERNAME}/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" + @printf "### $@ ### '${SERVERNAME}/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" + @printf "### $@ ### '${SERVERNAME}/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" + @printf "### $@ ### '${SERVERNAME}/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" + @printf "### $@ ### '${SERVERNAME}/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 @@ -406,714 +423,714 @@ # 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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ ${SERVERNAME}/getData/track?track=assembly;chrom=chrI;genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;end=14309681;start=1\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ ${SERVERNAME}/getData/track?track=gc5Base;chrom=chrA9;genome=braRap1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/bPlants/hub.txt\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ ${SERVERNAME}/getData/track?track=gc5Base;chrom=chrA9;genome=braRap1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/xPlants/hub.txt\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ ${SERVERNAME}/getData/track?track=gc5Base;chrom=chrA9;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ ${SERVERNAME}/getData/sequence?chrom=chrA9;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ ${SERVERNAME}/list/tracks?trackLeavesOnly=1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ ${SERVERNAME}/list/tracks?trackLeavesOnly=1;genome=araTha1\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ ${SERVERNAME}/list/tracks?trackLeavesOnly=1\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ ${SERVERNAME}/getData/sequence?genome=cxe6;jsonOutputArrays=1;maxItemsOutput=123\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ ${SERVERNAME}/list/tracks?genome=cxe6;jsonOutputArrays=1;maxItemsOutput=123\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ ${SERVERNAME}/getData/track?genome=ce6;track=gold;maxItemsOutput=1x23\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ ${SERVERNAME}/getData/track?genome=ce6;track=gold;maxItemsOutput=-2\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ ${SERVERNAME}/getData/track?genome=ce6;track=gold;maxItemsOutput=0\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ ${SERVERNAME}/getData/track?genome=ce6;track=gold;maxItemsOutput=0\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ ${SERVERNAME}/getData/tracks?genome=ce6;track=gold\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ ${SERVERNAME}/list/endpoints\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ ${SERVERNAME}/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ ${SERVERNAME}/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ ${SERVERNAME}/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/bPlants/hub.txt;genome=braRap1;track=assemblx\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/xGillBejerano/hub.txt\n" @./jsonConsumer.pl -serverName="${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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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'" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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 + @printf "### $@ '${SERVERNAME}/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 "${SERVERNAME}/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;chrom=chr1;start=4567;end=8901;track=assembly;maxItemsOutput=5;jsonOutputArrays=1;maxItemsOutput=0" 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${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 + @printf "### $@ '${SERVERNAME}/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 "${SERVERNAME}/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;chrom=chr1;start=4567;end=8901;track=assembly;maxItemsOutput=5;jsonOutputArrays=xyz" 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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 + @printf "### $@ ### '${SERVERNAME}.edu/getData/track?tracks=gold,gap,decipher;genome=hg38;jsonOutputArrays=1;chrom=chr2;start=16129261;end=16163278'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg38 -track=gold,gap,decipher -jsonOutputArrays -chrom=chr2 -start=16129261 -end=16163278 2>&1 | sed -e 's/, /,\n/g; s#http.*/getData#/getData#;' | egrep -v "${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 + @printf "### $@ ### '${SERVERNAME}.edu/getData/track?tracks=gold,gap,omimGene2;genome=hg38;jsonOutputArrays=1;chrom=chr2;start=16129261;end=16163278'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome=hg38 -track=gold,gap,omimGene2 -jsonOutputArrays -chrom=chr2 -start=16129261 -end=16163278 2>&1 | sed -e 's/, /,\n/g; s#http.*/getData#/getData#;' | egrep -v "${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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/cgi-bin/hubApi/getData/track?track=shMethylSubtrack;chrom=chr1;genome=hg19;hubUrl=http://lasallelab.genomecenter.ucdavis.edu/UCSChub/hub.txt;jsonOutputArrays=1;maxItemsOutput=5'\n" @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -hubUrl="http://lasallelab.genomecenter.ucdavis.edu/UCSChub/hub.txt" -genome="hg19" -track="shMethylSubtrack" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # request a track type that is not yet supported: vcfTabix notSup02: setOutput - @printf "### $@ '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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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</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=hg19;chrom=chr1;end=48000;start=47000'\n" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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" + @printf "### $@ '${SERVERNAME}/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